diff --git a/monai/deploy/operators/dicom_data_loader_operator.py b/monai/deploy/operators/dicom_data_loader_operator.py index f07a45ef..c31e1ef2 100644 --- a/monai/deploy/operators/dicom_data_loader_operator.py +++ b/monai/deploy/operators/dicom_data_loader_operator.py @@ -42,6 +42,9 @@ class DICOMDataLoaderOperator(Operator): DEFAULT_INPUT_FOLDER = Path.cwd() / "input" DEFAULT_OUTPUT_NAME = "dicom_study_list" + SOP_CLASSES_TO_IGNORE = [ + "1.2.840.10008.1.3.10", # Media Storage Directory Storage, aka DICOMDIR + ] # For now, need to have the input folder as an instance attribute, set on init, because even there is the optional # named input to receive data containing the path, there might not be upstream operator to emit the data. @@ -170,6 +173,18 @@ def _load_data(self, files: List[str]): for sop_instance in sop_instances: study_instance_uid = sop_instance[0x0020, 0x000D].value.name # name is the UID as str + # First need to eliminate the SOP instances whose SOP Class is to be ignored. + if "SOPInstanceUID" not in sop_instance: + self._logger.warn("Instance ignored due to missing SOP instance UID tag") + continue + sop_instance_uid = sop_instance["SOPInstanceUID"].value + if "SOPClassUID" not in sop_instance: + self._logger.warn(f"Instance ignored due to missing SOP Class UID tag, {sop_instance_uid}") + continue + if sop_instance["SOPClassUID"].value in DICOMDataLoaderOperator.SOP_CLASSES_TO_IGNORE: + self._logger.warn(f"Instance ignored for being in the ignored class, {sop_instance_uid}") + continue + if study_instance_uid not in study_dict: study = DICOMStudy(study_instance_uid) self.populate_study_attributes(study, sop_instance) diff --git a/notebooks/tutorials/01_simple_app.ipynb b/notebooks/tutorials/01_simple_app.ipynb index a1f10f59..11874ae0 100644 --- a/notebooks/tutorials/01_simple_app.ipynb +++ b/notebooks/tutorials/01_simple_app.ipynb @@ -54,7 +54,7 @@ }, { "cell_type": "code", - "execution_count": 1, + "execution_count": 28, "metadata": {}, "outputs": [], "source": [ @@ -82,7 +82,7 @@ }, { "cell_type": "code", - "execution_count": 2, + "execution_count": 29, "metadata": {}, "outputs": [ { @@ -95,10 +95,10 @@ { "data": { "text/plain": [ - "" + "" ] }, - "execution_count": 2, + "execution_count": 29, "metadata": {}, "output_type": "execute_result" }, @@ -145,7 +145,7 @@ }, { "cell_type": "code", - "execution_count": 3, + "execution_count": 30, "metadata": {}, "outputs": [ { @@ -179,7 +179,7 @@ }, { "cell_type": "code", - "execution_count": 4, + "execution_count": 31, "metadata": {}, "outputs": [], "source": [ @@ -212,7 +212,7 @@ }, { "cell_type": "code", - "execution_count": 5, + "execution_count": 32, "metadata": {}, "outputs": [], "source": [ @@ -283,7 +283,7 @@ }, { "cell_type": "code", - "execution_count": 6, + "execution_count": 33, "metadata": {}, "outputs": [], "source": [ @@ -335,7 +335,7 @@ }, { "cell_type": "code", - "execution_count": 7, + "execution_count": 34, "metadata": {}, "outputs": [], "source": [ @@ -428,7 +428,7 @@ }, { "cell_type": "code", - "execution_count": 8, + "execution_count": 35, "metadata": {}, "outputs": [ { @@ -507,15 +507,15 @@ }, { "cell_type": "code", - "execution_count": 9, + "execution_count": 36, "metadata": {}, "outputs": [ { "name": "stderr", "output_type": "stream", "text": [ - "[2024-04-10 16:18:44,711] [INFO] (root) - Parsed args: Namespace(log_level=None, input=None, output=None, model=None, workdir=None, argv=[])\n", - "[2024-04-10 16:18:44,717] [INFO] (root) - AppContext object: AppContext(input_path=/tmp/simple_app/normal-brain-mri-4.png, output_path=output, model_path=models, workdir=)\n" + "[2024-04-23 15:26:29,737] [INFO] (root) - Parsed args: Namespace(log_level=None, input=None, output=None, model=None, workdir=None, argv=[])\n", + "[2024-04-23 15:26:29,745] [INFO] (root) - AppContext object: AppContext(input_path=/tmp/simple_app/normal-brain-mri-4.png, output_path=output, model_path=models, workdir=)\n" ] }, { @@ -523,6 +523,7 @@ "output_type": "stream", "text": [ "sample_data_path: /tmp/simple_app/normal-brain-mri-4.png\n", + "\u001b[0m2024-04-23 15:26:29.768 INFO gxf/std/greedy_scheduler.cpp@191: Scheduling 3 entities\u001b[0m\n", "Number of times operator sobel_op whose class is defined in __main__ called: 1\n", "Input from: /tmp/simple_app/normal-brain-mri-4.png, whose absolute path: /tmp/simple_app/normal-brain-mri-4.png\n" ] @@ -531,13 +532,11 @@ "name": "stderr", "output_type": "stream", "text": [ - "[info] [gxf_executor.cpp:211] Creating context\n", - "[info] [gxf_executor.cpp:1674] Loading extensions from configs...\n", - "[info] [gxf_executor.cpp:1864] Activating Graph...\n", - "[info] [gxf_executor.cpp:1894] Running Graph...\n", - "[info] [gxf_executor.cpp:1896] Waiting for completion...\n", - "[info] [gxf_executor.cpp:1897] Graph execution waiting. Fragment: \n", - "[info] [greedy_scheduler.cpp:190] Scheduling 3 entities\n" + "[info] [gxf_executor.cpp:247] Creating context\n", + "[info] [gxf_executor.cpp:1672] Loading extensions from configs...\n", + "[info] [gxf_executor.cpp:1842] Activating Graph...\n", + "[info] [gxf_executor.cpp:1874] Running Graph...\n", + "[info] [gxf_executor.cpp:1876] Waiting for completion...\n" ] }, { @@ -547,19 +546,18 @@ "Number of times operator median_op whose class is defined in __main__ called: 1\n", "Number of times operator gaussian_op whose class is defined in __main__ called: 1\n", "Data type of output: , max = 0.35821119421406195\n", - "Data type of output post conversion: , max = 91\n" + "Data type of output post conversion: , max = 91\n", + "\u001b[0m2024-04-23 15:26:30.023 INFO gxf/std/greedy_scheduler.cpp@372: Scheduler stopped: Some entities are waiting for execution, but there are no periodic or async entities to get out of the deadlock.\u001b[0m\n", + "\u001b[0m2024-04-23 15:26:30.023 INFO gxf/std/greedy_scheduler.cpp@401: Scheduler finished.\u001b[0m\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ - "[info] [greedy_scheduler.cpp:369] Scheduler stopped: Some entities are waiting for execution, but there are no periodic or async entities to get out of the deadlock.\n", - "[info] [greedy_scheduler.cpp:398] Scheduler finished.\n", - "[info] [gxf_executor.cpp:1906] Graph execution deactivating. Fragment: \n", - "[info] [gxf_executor.cpp:1907] Deactivating Graph...\n", - "[info] [gxf_executor.cpp:1910] Graph execution finished. Fragment: \n", - "[info] [gxf_executor.cpp:230] Destroying context\n" + "[info] [gxf_executor.cpp:1879] Deactivating Graph...\n", + "[info] [gxf_executor.cpp:1887] Graph execution finished.\n", + "[info] [gxf_executor.cpp:275] Destroying context\n" ] } ], @@ -570,7 +568,7 @@ }, { "cell_type": "code", - "execution_count": 10, + "execution_count": 37, "metadata": {}, "outputs": [ { @@ -587,16 +585,16 @@ }, { "cell_type": "code", - "execution_count": 11, + "execution_count": 38, "metadata": {}, "outputs": [ { "data": { "text/plain": [ - "" + "" ] }, - "execution_count": 11, + "execution_count": 38, "metadata": {}, "output_type": "execute_result" }, @@ -643,7 +641,7 @@ }, { "cell_type": "code", - "execution_count": 12, + "execution_count": 39, "metadata": {}, "outputs": [], "source": [ @@ -661,7 +659,7 @@ }, { "cell_type": "code", - "execution_count": 13, + "execution_count": 40, "metadata": {}, "outputs": [ { @@ -741,7 +739,7 @@ }, { "cell_type": "code", - "execution_count": 14, + "execution_count": 41, "metadata": {}, "outputs": [ { @@ -803,7 +801,7 @@ }, { "cell_type": "code", - "execution_count": 15, + "execution_count": 42, "metadata": {}, "outputs": [ { @@ -899,7 +897,7 @@ }, { "cell_type": "code", - "execution_count": 16, + "execution_count": 43, "metadata": {}, "outputs": [ { @@ -1001,7 +999,7 @@ }, { "cell_type": "code", - "execution_count": 17, + "execution_count": 44, "metadata": {}, "outputs": [ { @@ -1022,7 +1020,7 @@ }, { "cell_type": "code", - "execution_count": 18, + "execution_count": 45, "metadata": {}, "outputs": [ { @@ -1052,94 +1050,92 @@ }, { "cell_type": "code", - "execution_count": 19, + "execution_count": 46, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ - "[2024-04-10 16:18:49,954] [INFO] (root) - Parsed args: Namespace(log_level='DEBUG', input=PosixPath('/tmp/simple_app'), output=PosixPath('/home/mqin/src/monai-deploy-app-sdk/notebooks/tutorials/output'), model=None, workdir=None, argv=['simple_imaging_app', '-i', '/tmp/simple_app', '-o', 'output', '-l', 'DEBUG'])\n", - "[2024-04-10 16:18:50,126] [INFO] (root) - AppContext object: AppContext(input_path=/tmp/simple_app, output_path=/home/mqin/src/monai-deploy-app-sdk/notebooks/tutorials/output, model_path=models, workdir=)\n", - "[2024-04-10 16:18:50,127] [INFO] (root) - sample_data_path: /tmp/simple_app\n", - "[\u001b[32minfo\u001b[m] [gxf_executor.cpp:211] Creating context\n", - "[\u001b[32minfo\u001b[m] [gxf_executor.cpp:1674] Loading extensions from configs...\n", - "[\u001b[32minfo\u001b[m] [gxf_executor.cpp:1864] Activating Graph...\n", - "[\u001b[32minfo\u001b[m] [gxf_executor.cpp:1894] Running Graph...\n", - "[\u001b[32minfo\u001b[m] [gxf_executor.cpp:1896] Waiting for completion...\n", - "[\u001b[32minfo\u001b[m] [gxf_executor.cpp:1897] Graph execution waiting. Fragment: \n", - "[\u001b[32minfo\u001b[m] [greedy_scheduler.cpp:190] Scheduling 3 entities\n", + "[2024-04-23 15:26:34,943] [INFO] (root) - Parsed args: Namespace(log_level='DEBUG', input=PosixPath('/tmp/simple_app'), output=PosixPath('/home/mqin/src/monai-deploy-app-sdk/notebooks/tutorials/output'), model=None, workdir=None, argv=['simple_imaging_app', '-i', '/tmp/simple_app', '-o', 'output', '-l', 'DEBUG'])\n", + "[2024-04-23 15:26:34,945] [INFO] (root) - AppContext object: AppContext(input_path=/tmp/simple_app, output_path=/home/mqin/src/monai-deploy-app-sdk/notebooks/tutorials/output, model_path=models, workdir=)\n", + "[2024-04-23 15:26:34,945] [INFO] (root) - sample_data_path: /tmp/simple_app\n", + "[\u001b[32minfo\u001b[m] [gxf_executor.cpp:247] Creating context\n", + "[\u001b[32minfo\u001b[m] [gxf_executor.cpp:1672] Loading extensions from configs...\n", + "[\u001b[32minfo\u001b[m] [gxf_executor.cpp:1842] Activating Graph...\n", + "[\u001b[32minfo\u001b[m] [gxf_executor.cpp:1874] Running Graph...\n", + "[\u001b[32minfo\u001b[m] [gxf_executor.cpp:1876] Waiting for completion...\n", + "\u001b[0m2024-04-23 15:26:34.968 INFO gxf/std/greedy_scheduler.cpp@191: Scheduling 3 entities\u001b[0m\n", "Number of times operator sobel_op whose class is defined in sobel_operator called: 1\n", "Input from: /tmp/simple_app, whose absolute path: /tmp/simple_app\n", - "[2024-04-10 16:18:50,179] [DEBUG] (PIL.PngImagePlugin) - STREAM b'IHDR' 16 13\n", - "[2024-04-10 16:18:50,179] [DEBUG] (PIL.PngImagePlugin) - STREAM b'sRGB' 41 1\n", - "[2024-04-10 16:18:50,179] [DEBUG] (PIL.PngImagePlugin) - STREAM b'gAMA' 54 4\n", - "[2024-04-10 16:18:50,179] [DEBUG] (PIL.PngImagePlugin) - STREAM b'pHYs' 70 9\n", - "[2024-04-10 16:18:50,179] [DEBUG] (PIL.PngImagePlugin) - STREAM b'IDAT' 91 65445\n", - "[2024-04-10 16:18:50,179] [DEBUG] (PIL.PngImagePlugin) - STREAM b'IHDR' 16 13\n", - "[2024-04-10 16:18:50,179] [DEBUG] (PIL.PngImagePlugin) - STREAM b'sRGB' 41 1\n", - "[2024-04-10 16:18:50,179] [DEBUG] (PIL.PngImagePlugin) - STREAM b'gAMA' 54 4\n", - "[2024-04-10 16:18:50,180] [DEBUG] (PIL.PngImagePlugin) - STREAM b'pHYs' 70 9\n", - "[2024-04-10 16:18:50,180] [DEBUG] (PIL.PngImagePlugin) - STREAM b'IDAT' 91 65445\n", - "[2024-04-10 16:18:50,185] [DEBUG] (PIL.Image) - Error closing: Operation on closed image\n", + "[2024-04-23 15:26:34,996] [DEBUG] (PIL.PngImagePlugin) - STREAM b'IHDR' 16 13\n", + "[2024-04-23 15:26:34,996] [DEBUG] (PIL.PngImagePlugin) - STREAM b'sRGB' 41 1\n", + "[2024-04-23 15:26:34,996] [DEBUG] (PIL.PngImagePlugin) - STREAM b'gAMA' 54 4\n", + "[2024-04-23 15:26:34,996] [DEBUG] (PIL.PngImagePlugin) - STREAM b'pHYs' 70 9\n", + "[2024-04-23 15:26:34,996] [DEBUG] (PIL.PngImagePlugin) - STREAM b'IDAT' 91 65445\n", + "[2024-04-23 15:26:34,996] [DEBUG] (PIL.PngImagePlugin) - STREAM b'IHDR' 16 13\n", + "[2024-04-23 15:26:34,996] [DEBUG] (PIL.PngImagePlugin) - STREAM b'sRGB' 41 1\n", + "[2024-04-23 15:26:34,996] [DEBUG] (PIL.PngImagePlugin) - STREAM b'gAMA' 54 4\n", + "[2024-04-23 15:26:34,996] [DEBUG] (PIL.PngImagePlugin) - STREAM b'pHYs' 70 9\n", + "[2024-04-23 15:26:34,996] [DEBUG] (PIL.PngImagePlugin) - STREAM b'IDAT' 91 65445\n", + "[2024-04-23 15:26:35,002] [DEBUG] (PIL.Image) - Error closing: Operation on closed image\n", "Number of times operator median_op whose class is defined in median_operator called: 1\n", "Number of times operator gaussian_op whose class is defined in gaussian_operator called: 1\n", "Data type of output: , max = 0.35821119421406195\n", "Data type of output post conversion: , max = 91\n", - 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Fragment: \n", - "[\u001b[32minfo\u001b[m] [gxf_executor.cpp:230] Destroying context\n" + "[2024-04-23 15:26:35,225] [DEBUG] (PIL.Image) - Importing BlpImagePlugin\n", + "[2024-04-23 15:26:35,226] [DEBUG] (PIL.Image) - Importing BmpImagePlugin\n", + "[2024-04-23 15:26:35,226] [DEBUG] (PIL.Image) - Importing BufrStubImagePlugin\n", + "[2024-04-23 15:26:35,227] [DEBUG] (PIL.Image) - Importing CurImagePlugin\n", + "[2024-04-23 15:26:35,227] [DEBUG] (PIL.Image) - Importing DcxImagePlugin\n", + "[2024-04-23 15:26:35,227] [DEBUG] (PIL.Image) - Importing DdsImagePlugin\n", + "[2024-04-23 15:26:35,230] [DEBUG] (PIL.Image) - Importing EpsImagePlugin\n", + "[2024-04-23 15:26:35,231] [DEBUG] (PIL.Image) - Importing FitsImagePlugin\n", + "[2024-04-23 15:26:35,231] [DEBUG] (PIL.Image) - Importing FliImagePlugin\n", + "[2024-04-23 15:26:35,231] [DEBUG] (PIL.Image) - Importing FpxImagePlugin\n", + "[2024-04-23 15:26:35,231] [DEBUG] (PIL.Image) - Image: failed to import FpxImagePlugin: No module named 'olefile'\n", + "[2024-04-23 15:26:35,231] [DEBUG] (PIL.Image) - Importing FtexImagePlugin\n", + "[2024-04-23 15:26:35,232] [DEBUG] (PIL.Image) - Importing GbrImagePlugin\n", + "[2024-04-23 15:26:35,232] [DEBUG] (PIL.Image) - Importing GifImagePlugin\n", + "[2024-04-23 15:26:35,232] [DEBUG] (PIL.Image) - Importing GribStubImagePlugin\n", + "[2024-04-23 15:26:35,232] [DEBUG] (PIL.Image) - Importing Hdf5StubImagePlugin\n", + "[2024-04-23 15:26:35,232] [DEBUG] (PIL.Image) - Importing IcnsImagePlugin\n", + "[2024-04-23 15:26:35,233] [DEBUG] (PIL.Image) - Importing IcoImagePlugin\n", + "[2024-04-23 15:26:35,233] [DEBUG] (PIL.Image) - Importing ImImagePlugin\n", + "[2024-04-23 15:26:35,234] [DEBUG] (PIL.Image) - Importing ImtImagePlugin\n", + "[2024-04-23 15:26:35,234] [DEBUG] (PIL.Image) - Importing IptcImagePlugin\n", + "[2024-04-23 15:26:35,235] [DEBUG] (PIL.Image) - Importing JpegImagePlugin\n", + "[2024-04-23 15:26:35,235] [DEBUG] (PIL.Image) - Importing Jpeg2KImagePlugin\n", + "[2024-04-23 15:26:35,235] [DEBUG] (PIL.Image) - Importing McIdasImagePlugin\n", + "[2024-04-23 15:26:35,235] [DEBUG] (PIL.Image) - Importing MicImagePlugin\n", + "[2024-04-23 15:26:35,235] [DEBUG] (PIL.Image) - Image: failed to import MicImagePlugin: No module named 'olefile'\n", + "[2024-04-23 15:26:35,235] [DEBUG] (PIL.Image) - Importing MpegImagePlugin\n", + "[2024-04-23 15:26:35,235] [DEBUG] (PIL.Image) - Importing MpoImagePlugin\n", + "[2024-04-23 15:26:35,236] [DEBUG] (PIL.Image) - Importing MspImagePlugin\n", + "[2024-04-23 15:26:35,237] [DEBUG] (PIL.Image) - Importing PalmImagePlugin\n", + "[2024-04-23 15:26:35,237] [DEBUG] (PIL.Image) - Importing PcdImagePlugin\n", + "[2024-04-23 15:26:35,237] [DEBUG] (PIL.Image) - Importing PcxImagePlugin\n", + "[2024-04-23 15:26:35,237] [DEBUG] (PIL.Image) - Importing PdfImagePlugin\n", + "[2024-04-23 15:26:35,242] [DEBUG] (PIL.Image) - Importing PixarImagePlugin\n", + "[2024-04-23 15:26:35,242] [DEBUG] (PIL.Image) - Importing PngImagePlugin\n", + "[2024-04-23 15:26:35,242] [DEBUG] (PIL.Image) - Importing PpmImagePlugin\n", + "[2024-04-23 15:26:35,242] [DEBUG] (PIL.Image) - Importing PsdImagePlugin\n", + "[2024-04-23 15:26:35,242] [DEBUG] (PIL.Image) - Importing QoiImagePlugin\n", + "[2024-04-23 15:26:35,242] [DEBUG] (PIL.Image) - Importing SgiImagePlugin\n", + "[2024-04-23 15:26:35,242] [DEBUG] (PIL.Image) - Importing SpiderImagePlugin\n", + "[2024-04-23 15:26:35,243] [DEBUG] (PIL.Image) - Importing SunImagePlugin\n", + "[2024-04-23 15:26:35,243] [DEBUG] (PIL.Image) - Importing TgaImagePlugin\n", + "[2024-04-23 15:26:35,243] [DEBUG] (PIL.Image) - Importing TiffImagePlugin\n", + "[2024-04-23 15:26:35,243] [DEBUG] (PIL.Image) - Importing WebPImagePlugin\n", + "[2024-04-23 15:26:35,244] [DEBUG] (PIL.Image) - Importing WmfImagePlugin\n", + "[2024-04-23 15:26:35,245] [DEBUG] (PIL.Image) - Importing XbmImagePlugin\n", + "[2024-04-23 15:26:35,245] [DEBUG] (PIL.Image) - Importing XpmImagePlugin\n", + "[2024-04-23 15:26:35,245] [DEBUG] (PIL.Image) - Importing XVThumbImagePlugin\n", + "\u001b[0m2024-04-23 15:26:35.273 INFO gxf/std/greedy_scheduler.cpp@372: Scheduler stopped: Some entities are waiting for execution, but there are no periodic or async entities to get out of the deadlock.\u001b[0m\n", + "\u001b[0m2024-04-23 15:26:35.273 INFO gxf/std/greedy_scheduler.cpp@401: Scheduler finished.\u001b[0m\n", + "[\u001b[32minfo\u001b[m] [gxf_executor.cpp:1879] Deactivating Graph...\n", + "[\u001b[32minfo\u001b[m] [gxf_executor.cpp:1887] Graph execution finished.\n", + "[\u001b[32minfo\u001b[m] [gxf_executor.cpp:275] Destroying context\n" ] } ], @@ -1150,16 +1146,16 @@ }, { "cell_type": "code", - "execution_count": 20, + "execution_count": 47, "metadata": {}, "outputs": [ { "data": { "text/plain": [ - "" + "" ] }, - "execution_count": 20, + "execution_count": 47, "metadata": {}, "output_type": "execute_result" }, @@ -1200,7 +1196,7 @@ }, { "cell_type": "code", - "execution_count": 21, + "execution_count": 48, "metadata": {}, "outputs": [ { @@ -1230,7 +1226,7 @@ }, { "cell_type": "code", - "execution_count": 22, + "execution_count": 49, "metadata": {}, "outputs": [ { @@ -1256,19 +1252,21 @@ }, { "cell_type": "code", - "execution_count": 23, + "execution_count": 50, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ - "[2024-04-10 16:18:52,341] [INFO] (packager.parameters) - Application: /home/mqin/src/monai-deploy-app-sdk/notebooks/tutorials/simple_imaging_app\n", - "[2024-04-10 16:18:52,341] [INFO] (packager.parameters) - Detected application type: Python Module\n", - "[2024-04-10 16:18:52,341] [INFO] (packager) - Reading application configuration from /home/mqin/src/monai-deploy-app-sdk/notebooks/tutorials/simple_imaging_app/app.yaml...\n", - "[2024-04-10 16:18:52,343] [INFO] (packager) - Generating app.json...\n", - "[2024-04-10 16:18:52,343] [INFO] (packager) - Generating pkg.json...\n", - "[2024-04-10 16:18:52,348] [DEBUG] (common) - \n", + "[2024-04-23 15:26:37,078] [INFO] (common) - Downloading CLI manifest file...\n", + "[2024-04-23 15:26:37,629] [DEBUG] (common) - Validating CLI manifest file...\n", + "[2024-04-23 15:26:37,631] [INFO] (packager.parameters) - Application: /home/mqin/src/monai-deploy-app-sdk/notebooks/tutorials/simple_imaging_app\n", + "[2024-04-23 15:26:37,632] [INFO] (packager.parameters) - Detected application type: Python Module\n", + "[2024-04-23 15:26:37,632] [INFO] (packager) - Reading application configuration from /home/mqin/src/monai-deploy-app-sdk/notebooks/tutorials/simple_imaging_app/app.yaml...\n", + "[2024-04-23 15:26:37,636] [INFO] (packager) - Generating app.json...\n", + "[2024-04-23 15:26:37,636] [INFO] (packager) - Generating pkg.json...\n", + "[2024-04-23 15:26:37,649] [DEBUG] (common) - \n", "=============== Begin app.json ===============\n", "{\n", " \"apiVersion\": \"1.0.0\",\n", @@ -1303,7 +1301,7 @@ "}\n", "================ End app.json ================\n", " \n", - "[2024-04-10 16:18:52,348] [DEBUG] (common) - \n", + "[2024-04-23 15:26:37,650] [DEBUG] (common) - \n", "=============== Begin pkg.json ===============\n", "{\n", " \"apiVersion\": \"1.0.0\",\n", @@ -1321,11 +1319,11 @@ "}\n", "================ End pkg.json ================\n", " \n", - "[2024-04-10 16:18:52,364] [DEBUG] (packager.builder) - \n", + "[2024-04-23 15:26:37,673] [DEBUG] (packager.builder) - \n", "========== Begin Dockerfile ==========\n", "\n", "\n", - "FROM nvcr.io/nvidia/clara-holoscan/holoscan:v1.0.3-dgpu\n", + "FROM nvcr.io/nvidia/clara-holoscan/holoscan:v2.0.0-dgpu\n", "\n", "ENV DEBIAN_FRONTEND=noninteractive\n", "ENV TERM=xterm-256color\n", @@ -1341,11 +1339,11 @@ " && mkdir -p /var/holoscan/input \\\n", " && mkdir -p /var/holoscan/output\n", "\n", - "LABEL base=\"nvcr.io/nvidia/clara-holoscan/holoscan:v1.0.3-dgpu\"\n", + "LABEL base=\"nvcr.io/nvidia/clara-holoscan/holoscan:v2.0.0-dgpu\"\n", "LABEL tag=\"simple_imaging_app:1.0\"\n", "LABEL org.opencontainers.image.title=\"MONAI Deploy App Package - Simple Imaging App\"\n", "LABEL org.opencontainers.image.version=\"1.0\"\n", - "LABEL org.nvidia.holoscan=\"1.0.3\"\n", + "LABEL org.nvidia.holoscan=\"2.0.0\"\n", "LABEL org.monai.deploy.app-sdk=\"0.5.1\"\n", "\n", "\n", @@ -1371,7 +1369,6 @@ "ENV PYTHONPATH=\"/opt/holoscan/app:$PYTHONPATH\"\n", "\n", "\n", - "\n", "RUN groupadd -f -g $GID $UNAME\n", "RUN useradd -rm -d /home/$UNAME -s /bin/bash -g $GID -G sudo -u $UID $UNAME\n", "RUN chown -R holoscan /var/holoscan \n", @@ -1397,14 +1394,12 @@ "RUN pip install --upgrade pip\n", "RUN pip install --no-cache-dir --user -r /tmp/requirements.txt\n", "\n", - "# Install Holoscan from PyPI only when sdk_type is Holoscan. \n", - "# For MONAI Deploy, the APP SDK will install it unless user specifies the Holoscan SDK file.\n", + " \n", + "# MONAI Deploy\n", "\n", "# Copy user-specified MONAI Deploy SDK file\n", - "COPY ./monai_deploy_app_sdk-0.5.1+25.g31e4165.dirty-py3-none-any.whl /tmp/monai_deploy_app_sdk-0.5.1+25.g31e4165.dirty-py3-none-any.whl\n", - "RUN pip install /tmp/monai_deploy_app_sdk-0.5.1+25.g31e4165.dirty-py3-none-any.whl\n", - "\n", - "\n", + "COPY ./monai_deploy_app_sdk-0.5.1+20.gb869749.dirty-py3-none-any.whl /tmp/monai_deploy_app_sdk-0.5.1+20.gb869749.dirty-py3-none-any.whl\n", + "RUN pip install /tmp/monai_deploy_app_sdk-0.5.1+20.gb869749.dirty-py3-none-any.whl\n", "\n", "\n", "\n", @@ -1417,31 +1412,31 @@ "ENTRYPOINT [\"/var/holoscan/tools\"]\n", "=========== End Dockerfile ===========\n", "\n", - "[2024-04-10 16:18:52,365] [INFO] (packager.builder) - \n", + "[2024-04-23 15:26:37,673] [INFO] (packager.builder) - \n", "===============================================================================\n", "Building image for: x64-workstation\n", " Architecture: linux/amd64\n", - " Base Image: nvcr.io/nvidia/clara-holoscan/holoscan:v1.0.3-dgpu\n", + " Base Image: nvcr.io/nvidia/clara-holoscan/holoscan:v2.0.0-dgpu\n", " Build Image: N/A\n", " Cache: Enabled\n", " Configuration: dgpu\n", " Holoscan SDK Package: pypi.org\n", - " MONAI Deploy App SDK Package: /home/mqin/src/monai-deploy-app-sdk/dist/monai_deploy_app_sdk-0.5.1+25.g31e4165.dirty-py3-none-any.whl\n", + " MONAI Deploy App SDK Package: /home/mqin/src/monai-deploy-app-sdk/dist/monai_deploy_app_sdk-0.5.1+20.gb869749.dirty-py3-none-any.whl\n", " gRPC Health Probe: N/A\n", - " SDK Version: 1.0.3\n", + " SDK Version: 2.0.0\n", " SDK: monai-deploy\n", " Tag: simple_imaging_app-x64-workstation-dgpu-linux-amd64:1.0\n", " \n", - "[2024-04-10 16:18:52,650] [INFO] (common) - Using existing Docker BuildKit builder `holoscan_app_builder`\n", - "[2024-04-10 16:18:52,650] [DEBUG] (packager.builder) - Building Holoscan Application Package: tag=simple_imaging_app-x64-workstation-dgpu-linux-amd64:1.0\n", + "[2024-04-23 15:26:38,231] [INFO] (common) - Using existing Docker BuildKit builder `holoscan_app_builder`\n", + "[2024-04-23 15:26:38,231] [DEBUG] (packager.builder) - Building Holoscan Application Package: tag=simple_imaging_app-x64-workstation-dgpu-linux-amd64:1.0\n", "#0 building with \"holoscan_app_builder\" instance using docker-container driver\n", "\n", "#1 [internal] load build definition from Dockerfile\n", - "#1 transferring dockerfile: 2.77kB done\n", + "#1 transferring dockerfile: 2.63kB done\n", "#1 DONE 0.0s\n", "\n", - "#2 [internal] load metadata for nvcr.io/nvidia/clara-holoscan/holoscan:v1.0.3-dgpu\n", - "#2 DONE 0.4s\n", + "#2 [internal] load metadata for nvcr.io/nvidia/clara-holoscan/holoscan:v2.0.0-dgpu\n", + "#2 DONE 0.5s\n", "\n", "#3 [internal] load .dockerignore\n", "#3 transferring context: 1.79kB done\n", @@ -1450,117 +1445,115 @@ "#4 [internal] load build context\n", "#4 DONE 0.0s\n", "\n", - "#5 importing cache manifest from local:14270000836931083776\n", + "#5 importing cache manifest from local:10678196058931023490\n", "#5 inferred cache manifest type: application/vnd.oci.image.index.v1+json done\n", "#5 DONE 0.0s\n", "\n", - "#6 [ 1/20] FROM nvcr.io/nvidia/clara-holoscan/holoscan:v1.0.3-dgpu@sha256:50343c616bf910e2a7651abb59db7833933e82cce64c3c4885f938d7e4af6155\n", - "#6 resolve nvcr.io/nvidia/clara-holoscan/holoscan:v1.0.3-dgpu@sha256:50343c616bf910e2a7651abb59db7833933e82cce64c3c4885f938d7e4af6155 0.0s done\n", + "#6 [ 1/20] FROM nvcr.io/nvidia/clara-holoscan/holoscan:v2.0.0-dgpu@sha256:20adbccd2c7b12dfb1798f6953f071631c3b85cd337858a7506f8e420add6d4a\n", + "#6 resolve nvcr.io/nvidia/clara-holoscan/holoscan:v2.0.0-dgpu@sha256:20adbccd2c7b12dfb1798f6953f071631c3b85cd337858a7506f8e420add6d4a 0.0s done\n", "#6 DONE 0.0s\n", "\n", - "#7 importing cache manifest from nvcr.io/nvidia/clara-holoscan/holoscan:v1.0.3-dgpu\n", + "#7 importing cache manifest from nvcr.io/nvidia/clara-holoscan/holoscan:v2.0.0-dgpu\n", "#7 inferred cache manifest type: application/vnd.docker.distribution.manifest.list.v2+json done\n", - "#7 DONE 0.4s\n", + "#7 DONE 0.9s\n", "\n", "#4 [internal] load build context\n", - "#4 transferring context: 157.50kB 0.0s done\n", + "#4 transferring context: 157.77kB 0.0s done\n", "#4 DONE 0.0s\n", "\n", "#8 [ 5/20] RUN useradd -rm -d /home/holoscan -s /bin/bash -g 1000 -G sudo -u 1000 holoscan\n", "#8 CACHED\n", "\n", - "#9 [11/20] RUN chmod +x /var/holoscan/tools\n", + "#9 [ 3/20] RUN apt-get update && apt-get install -y curl jq && rm -rf /var/lib/apt/lists/*\n", "#9 CACHED\n", "\n", - "#10 [ 2/20] RUN mkdir -p /etc/holoscan/ && mkdir -p /opt/holoscan/ && mkdir -p /var/holoscan && mkdir -p /opt/holoscan/app && mkdir -p /var/holoscan/input && mkdir -p /var/holoscan/output\n", + "#10 [ 6/20] RUN chown -R holoscan /var/holoscan\n", "#10 CACHED\n", "\n", - "#11 [ 4/20] RUN groupadd -f -g 1000 holoscan\n", + "#11 [13/20] RUN pip install --upgrade pip\n", "#11 CACHED\n", "\n", - "#12 [ 7/20] RUN chown -R holoscan /var/holoscan/input\n", + "#12 [ 8/20] RUN chown -R holoscan /var/holoscan/output\n", "#12 CACHED\n", "\n", - "#13 [ 8/20] RUN chown -R holoscan /var/holoscan/output\n", + "#13 [ 7/20] RUN chown -R holoscan /var/holoscan/input\n", "#13 CACHED\n", "\n", - "#14 [ 6/20] RUN chown -R holoscan /var/holoscan\n", + "#14 [ 2/20] RUN mkdir -p /etc/holoscan/ && mkdir -p /opt/holoscan/ && mkdir -p /var/holoscan && mkdir -p /opt/holoscan/app && mkdir -p /var/holoscan/input && mkdir -p /var/holoscan/output\n", "#14 CACHED\n", "\n", - "#15 [ 9/20] WORKDIR /var/holoscan\n", + "#15 [12/20] COPY ./pip/requirements.txt /tmp/requirements.txt\n", "#15 CACHED\n", "\n", - "#16 [ 3/20] RUN apt-get update && apt-get install -y curl jq && rm -rf /var/lib/apt/lists/*\n", + "#16 [11/20] RUN chmod +x /var/holoscan/tools\n", "#16 CACHED\n", "\n", - "#17 [12/20] COPY ./pip/requirements.txt /tmp/requirements.txt\n", + "#17 [ 9/20] WORKDIR /var/holoscan\n", "#17 CACHED\n", "\n", - "#18 [10/20] COPY ./tools /var/holoscan/tools\n", + "#18 [ 4/20] RUN groupadd -f -g 1000 holoscan\n", "#18 CACHED\n", "\n", - "#19 [13/20] RUN pip install --upgrade pip\n", + "#19 [10/20] COPY ./tools /var/holoscan/tools\n", "#19 CACHED\n", "\n", "#20 [14/20] RUN pip install --no-cache-dir --user -r /tmp/requirements.txt\n", "#20 CACHED\n", "\n", - "#21 [15/20] COPY ./monai_deploy_app_sdk-0.5.1+25.g31e4165.dirty-py3-none-any.whl /tmp/monai_deploy_app_sdk-0.5.1+25.g31e4165.dirty-py3-none-any.whl\n", - "#21 DONE 0.0s\n", - "\n", - "#22 [16/20] RUN pip install /tmp/monai_deploy_app_sdk-0.5.1+25.g31e4165.dirty-py3-none-any.whl\n", - "#22 0.662 Defaulting to user installation because normal site-packages is not writeable\n", - "#22 0.757 Processing /tmp/monai_deploy_app_sdk-0.5.1+25.g31e4165.dirty-py3-none-any.whl\n", - "#22 0.770 Requirement already satisfied: numpy>=1.21.6 in /usr/local/lib/python3.10/dist-packages (from monai-deploy-app-sdk==0.5.1+25.g31e4165.dirty) (1.23.5)\n", - "#22 0.949 Collecting holoscan~=1.0 (from monai-deploy-app-sdk==0.5.1+25.g31e4165.dirty)\n", - "#22 1.097 Downloading holoscan-1.0.3-cp310-cp310-manylinux_2_35_x86_64.whl.metadata (4.1 kB)\n", - "#22 1.154 Collecting colorama>=0.4.1 (from monai-deploy-app-sdk==0.5.1+25.g31e4165.dirty)\n", - "#22 1.158 Downloading colorama-0.4.6-py2.py3-none-any.whl.metadata (17 kB)\n", - "#22 1.227 Collecting typeguard>=3.0.0 (from monai-deploy-app-sdk==0.5.1+25.g31e4165.dirty)\n", - "#22 1.231 Downloading typeguard-4.2.1-py3-none-any.whl.metadata (3.7 kB)\n", - "#22 1.296 Collecting pip==23.3.2 (from holoscan~=1.0->monai-deploy-app-sdk==0.5.1+25.g31e4165.dirty)\n", - "#22 1.301 Downloading pip-23.3.2-py3-none-any.whl.metadata (3.5 kB)\n", - "#22 1.308 Requirement already satisfied: cupy-cuda12x==12.2 in /usr/local/lib/python3.10/dist-packages (from holoscan~=1.0->monai-deploy-app-sdk==0.5.1+25.g31e4165.dirty) (12.2.0)\n", - "#22 1.309 Requirement already satisfied: cloudpickle==2.2.1 in /usr/local/lib/python3.10/dist-packages (from holoscan~=1.0->monai-deploy-app-sdk==0.5.1+25.g31e4165.dirty) (2.2.1)\n", - "#22 1.310 Requirement already satisfied: python-on-whales==0.60.1 in /usr/local/lib/python3.10/dist-packages (from holoscan~=1.0->monai-deploy-app-sdk==0.5.1+25.g31e4165.dirty) (0.60.1)\n", - "#22 1.311 Requirement already satisfied: Jinja2==3.1.2 in /usr/local/lib/python3.10/dist-packages (from holoscan~=1.0->monai-deploy-app-sdk==0.5.1+25.g31e4165.dirty) (3.1.2)\n", - "#22 1.311 Requirement already satisfied: packaging==23.1 in /usr/local/lib/python3.10/dist-packages (from holoscan~=1.0->monai-deploy-app-sdk==0.5.1+25.g31e4165.dirty) (23.1)\n", - "#22 1.312 Requirement already satisfied: pyyaml==6.0 in /usr/local/lib/python3.10/dist-packages (from holoscan~=1.0->monai-deploy-app-sdk==0.5.1+25.g31e4165.dirty) (6.0)\n", - "#22 1.313 Requirement already satisfied: requests==2.28.2 in /usr/local/lib/python3.10/dist-packages (from holoscan~=1.0->monai-deploy-app-sdk==0.5.1+25.g31e4165.dirty) (2.28.2)\n", - "#22 1.314 Requirement already satisfied: psutil==5.9.6 in /usr/local/lib/python3.10/dist-packages (from 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Attempting uninstall: pip\n", - "#22 6.644 Found existing installation: pip 24.0\n", - "#22 6.709 Uninstalling pip-24.0:\n", - "#22 7.165 Successfully uninstalled pip-24.0\n", - "#22 8.769 Successfully installed colorama-0.4.6 filelock-3.13.4 holoscan-1.0.3 monai-deploy-app-sdk-0.5.1+25.g31e4165.dirty pip-23.3.2 typeguard-4.2.1 typing-extensions-4.11.0 wheel-axle-runtime-0.0.5\n", - "#22 DONE 9.3s\n", + "#21 [15/20] COPY ./monai_deploy_app_sdk-0.5.1+20.gb869749.dirty-py3-none-any.whl /tmp/monai_deploy_app_sdk-0.5.1+20.gb869749.dirty-py3-none-any.whl\n", + "#21 DONE 0.1s\n", + "\n", + "#22 [16/20] RUN pip install /tmp/monai_deploy_app_sdk-0.5.1+20.gb869749.dirty-py3-none-any.whl\n", + "#22 0.725 Defaulting to user installation because normal site-packages is not writeable\n", + "#22 0.802 Processing /tmp/monai_deploy_app_sdk-0.5.1+20.gb869749.dirty-py3-none-any.whl\n", + "#22 0.815 Requirement already satisfied: numpy>=1.21.6 in /usr/local/lib/python3.10/dist-packages (from 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done\n", + "#27 exporting config sha256:6485f181da93a3c0fc12abe1cf367c89306b7e8f7b110993be48f38b56164b89 0.0s done\n", "#27 sending tarball\n", "#27 ...\n", "\n", "#28 importing to docker\n", - "#28 loading layer 1a101d9210ae 32.77kB / 125.57kB\n", - "#28 loading layer c4b083b26ab0 557.06kB / 74.13MB\n", - "#28 loading layer c4b083b26ab0 71.30MB / 74.13MB 2.0s\n", - "#28 loading layer 77455b6ee5d5 492B / 492B\n", - "#28 loading layer 4583ff017de7 313B / 313B\n", - "#28 loading layer 90825b467166 293B / 293B\n", - "#28 loading layer e972a134a523 3.18kB / 3.18kB\n", - "#28 loading layer c4b083b26ab0 71.30MB / 74.13MB 3.1s done\n", - "#28 loading layer 1a101d9210ae 32.77kB / 125.57kB 3.2s done\n", - "#28 loading layer 77455b6ee5d5 492B / 492B 0.6s done\n", - "#28 loading layer 4583ff017de7 313B / 313B 0.6s done\n", - "#28 loading layer 90825b467166 293B / 293B 0.5s done\n", - "#28 loading layer e972a134a523 3.18kB / 3.18kB 0.5s done\n", - "#28 DONE 3.2s\n", + "#28 loading layer 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sha256:f06b2d19cffd90387b7ccd4e80ace09ab21995cf85c940091e6c80907532bda8\n", - "#29 preparing build cache for export 1.9s done\n", - "#29 writing layer sha256:f06b2d19cffd90387b7ccd4e80ace09ab21995cf85c940091e6c80907532bda8 0.0s done\n", - "#29 writing layer sha256:f33546e75bf1a7d9dc9e21b9a2c54c9d09b24790ad7a4192a8509002ceb14688 done\n", + "#29 writing layer sha256:f249faf9663a96b0911a903f8803b11a553c59b698013fb8343492fefdaaea90 done\n", "#29 writing layer sha256:f608e2fbff86e98627b7e462057e7d2416522096d73fe4664b82fe6ce8a4047d done\n", - "#29 writing layer sha256:f7702077ced42a1ee35e7f5e45f72634328ff3bcfe3f57735ba80baa5ec45daf done\n", - "#29 writing layer sha256:fa66a49172c6e821a1bace57c007c01da10cbc61507c44f8cdfeed8c4e5febab done\n", - "#29 writing config sha256:488336ab32415713da34c305ad87c5f983293c64534687f5fb685eb5b957c49c 0.0s done\n", - "#29 writing cache manifest sha256:69fe5811c303d48c634f794997602fd274d7922354e7aedf0dcd70b373a7a6a8 0.0s done\n", - "#29 DONE 1.9s\n", - "[2024-04-10 16:19:53,891] [INFO] (packager) - Build Summary:\n", + "#29 writing layer sha256:f65d191416580d6c38e3d95eee12377b75a4df548be1492618ce2a8c3c41b99e done\n", + "#29 writing config sha256:339862140e56654739f221a003e85d34c38ecd35b385c81ec1172b98fc0def66 0.0s done\n", + "#29 writing cache manifest sha256:5120653f7a3d293475e31a259659d8eb2d8883ab243f43924a2d526e754e676c 0.0s done\n", + "#29 DONE 1.7s\n", + "[2024-04-23 15:27:32,621] [INFO] (packager) - Build Summary:\n", "\n", "Platform: x64-workstation/dgpu\n", " Status: Succeeded\n", @@ -1710,14 +1705,14 @@ }, { "cell_type": "code", - "execution_count": 24, + "execution_count": 51, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ - "simple_imaging_app-x64-workstation-dgpu-linux-amd64 1.0 00503bdec781 51 seconds ago 12.3GB\n" + "simple_imaging_app-x64-workstation-dgpu-linux-amd64 1.0 6485f181da93 46 seconds ago 12.5GB\n" ] } ], @@ -1739,7 +1734,7 @@ }, { "cell_type": "code", - "execution_count": 25, + "execution_count": 52, "metadata": {}, "outputs": [ { @@ -1797,17 +1792,17 @@ " \"platformConfig\": \"dgpu\"\n", "}\n", "\n", - "2024-04-10 23:19:57 [INFO] Copying application from /opt/holoscan/app to /var/run/holoscan/export/app\n", + "2024-04-23 22:27:35 [INFO] Copying application from /opt/holoscan/app to /var/run/holoscan/export/app\n", "\n", - "2024-04-10 23:19:57 [INFO] Copying application manifest file from /etc/holoscan/app.json to /var/run/holoscan/export/config/app.json\n", - "2024-04-10 23:19:57 [INFO] Copying pkg manifest file from /etc/holoscan/pkg.json to /var/run/holoscan/export/config/pkg.json\n", - "2024-04-10 23:19:57 [INFO] Copying application configuration from /var/holoscan/app.yaml to /var/run/holoscan/export/config/app.yaml\n", + "2024-04-23 22:27:35 [INFO] Copying application manifest file from /etc/holoscan/app.json to /var/run/holoscan/export/config/app.json\n", + "2024-04-23 22:27:35 [INFO] Copying pkg manifest file from /etc/holoscan/pkg.json to /var/run/holoscan/export/config/pkg.json\n", + "2024-04-23 22:27:35 [INFO] Copying application configuration from /var/holoscan/app.yaml to /var/run/holoscan/export/config/app.yaml\n", "\n", - "2024-04-10 23:19:57 [INFO] Copying models from /opt/holoscan/models to /var/run/holoscan/export/models\n", - "2024-04-10 23:19:57 [INFO] '/opt/holoscan/models' cannot be found.\n", + "2024-04-23 22:27:35 [INFO] Copying models from /opt/holoscan/models to /var/run/holoscan/export/models\n", + "2024-04-23 22:27:35 [INFO] '/opt/holoscan/models' cannot be found.\n", "\n", - "2024-04-10 23:19:57 [INFO] Copying documentation from /opt/holoscan/docs/ to /var/run/holoscan/export/docs\n", - "2024-04-10 23:19:57 [INFO] '/opt/holoscan/docs/' cannot be found.\n", + "2024-04-23 22:27:35 [INFO] Copying documentation from /opt/holoscan/docs/ to /var/run/holoscan/export/docs\n", + "2024-04-23 22:27:35 [INFO] '/opt/holoscan/docs/' cannot be found.\n", "\n", "app config\n" ] @@ -1834,29 +1829,29 @@ }, { "cell_type": "code", - "execution_count": 26, + "execution_count": 53, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ - "[2024-04-10 16:19:58,260] [INFO] (runner) - Checking dependencies...\n", - "[2024-04-10 16:19:58,260] [INFO] (runner) - --> Verifying if \"docker\" is installed...\n", + "[2024-04-23 15:27:36,245] [INFO] (runner) - Checking dependencies...\n", + "[2024-04-23 15:27:36,245] [INFO] (runner) - --> Verifying if \"docker\" is installed...\n", "\n", - "[2024-04-10 16:19:58,260] [INFO] (runner) - --> Verifying if \"docker-buildx\" is installed...\n", + "[2024-04-23 15:27:36,245] [INFO] (runner) - --> Verifying if \"docker-buildx\" is installed...\n", "\n", - "[2024-04-10 16:19:58,260] [INFO] (runner) - --> Verifying if \"simple_imaging_app-x64-workstation-dgpu-linux-amd64:1.0\" is available...\n", + "[2024-04-23 15:27:36,245] [INFO] (runner) - --> Verifying if \"simple_imaging_app-x64-workstation-dgpu-linux-amd64:1.0\" is available...\n", "\n", - "[2024-04-10 16:19:58,323] [INFO] (runner) - Reading HAP/MAP manifest...\n", - "\u001b[sPreparing to copy...\u001b[?25l\u001b[u\u001b[2KCopying from container - 0B\u001b[?25h\u001b[u\u001b[2KSuccessfully copied 2.56kB to /tmp/tmpkogym2cj/app.json\n", - "\u001b[sPreparing to copy...\u001b[?25l\u001b[u\u001b[2KCopying from container - 0B\u001b[?25h\u001b[u\u001b[2KSuccessfully copied 2.05kB to /tmp/tmpkogym2cj/pkg.json\n", - "[2024-04-10 16:19:58,545] [INFO] (runner) - --> Verifying if \"nvidia-ctk\" is installed...\n", + "[2024-04-23 15:27:36,326] [INFO] (runner) - Reading HAP/MAP manifest...\n", + "\u001b[sPreparing to copy...\u001b[?25l\u001b[u\u001b[2KCopying from container - 0B\u001b[?25h\u001b[u\u001b[2KSuccessfully copied 2.56kB to /tmp/tmpv5e8cb_i/app.json\n", + "\u001b[sPreparing to copy...\u001b[?25l\u001b[u\u001b[2KCopying from container - 0B\u001b[?25h\u001b[u\u001b[2KSuccessfully copied 2.05kB to /tmp/tmpv5e8cb_i/pkg.json\n", + "[2024-04-23 15:27:36,492] [INFO] (runner) - --> Verifying if \"nvidia-ctk\" is installed...\n", "\n", - "[2024-04-10 16:19:58,545] [INFO] (runner) - --> Verifying \"nvidia-ctk\" version...\n", + "[2024-04-23 15:27:36,492] [INFO] (runner) - --> Verifying \"nvidia-ctk\" version...\n", "\n", - "[2024-04-10 16:19:58,814] [INFO] (common) - Launching container (8e18e862585f) using image 'simple_imaging_app-x64-workstation-dgpu-linux-amd64:1.0'...\n", - " container name: unruffled_kalam\n", + "[2024-04-23 15:27:36,761] [INFO] (common) - Launching container (94febd6eabce) using image 'simple_imaging_app-x64-workstation-dgpu-linux-amd64:1.0'...\n", + " container name: dazzling_kowalevski\n", " host name: mingq-dt\n", " network: host\n", " user: 1000:1000\n", @@ -1866,43 +1861,39 @@ " shared memory size: 67108864\n", " devices: \n", " group_add: 44\n", - "2024-04-10 23:19:59 [INFO] Launching application python3 /opt/holoscan/app ...\n", + "2024-04-23 22:27:37 [INFO] Launching application python3 /opt/holoscan/app ...\n", "\n", - "[2024-04-10 23:20:00,177] [INFO] (root) - Parsed args: Namespace(log_level=None, input=None, output=None, model=None, workdir=None, argv=['/opt/holoscan/app'])\n", + "[2024-04-23 22:27:37,772] [INFO] (root) - Parsed args: Namespace(log_level=None, input=None, output=None, model=None, workdir=None, argv=['/opt/holoscan/app'])\n", "\n", - "[2024-04-10 23:20:00,178] [INFO] (root) - AppContext object: AppContext(input_path=/var/holoscan/input, output_path=/var/holoscan/output, model_path=/opt/holoscan/models, workdir=/var/holoscan)\n", + "[2024-04-23 22:27:37,772] [INFO] (root) - AppContext object: AppContext(input_path=/var/holoscan/input, output_path=/var/holoscan/output, model_path=/opt/holoscan/models, workdir=/var/holoscan)\n", "\n", - "[2024-04-10 23:20:00,178] [INFO] (root) - sample_data_path: /var/holoscan/input\n", + "[2024-04-23 22:27:37,772] [INFO] (root) - sample_data_path: /var/holoscan/input\n", "\n", "[info] [app_driver.cpp:1161] Launching the driver/health checking service\n", "\n", - "[info] [gxf_executor.cpp:211] Creating context\n", + "[info] [gxf_executor.cpp:247] Creating context\n", "\n", "[info] [server.cpp:87] Health checking server listening on 0.0.0.0:8777\n", "\n", - "[info] [gxf_executor.cpp:1674] Loading extensions from configs...\n", - "\n", - "[info] [gxf_executor.cpp:1864] Activating Graph...\n", - "\n", - "[info] [gxf_executor.cpp:1894] Running Graph...\n", + "[info] [gxf_executor.cpp:1672] Loading extensions from configs...\n", "\n", - "[info] [gxf_executor.cpp:1896] Waiting for completion...\n", + "[info] [gxf_executor.cpp:1842] Activating Graph...\n", "\n", - "[info] [gxf_executor.cpp:1897] Graph execution waiting. Fragment: \n", + "[info] [gxf_executor.cpp:1874] Running Graph...\n", "\n", - "[info] [greedy_scheduler.cpp:190] Scheduling 3 entities\n", + "[info] [gxf_executor.cpp:1876] Waiting for completion...\n", "\n", - "[info] [greedy_scheduler.cpp:369] Scheduler stopped: Some entities are waiting for execution, but there are no periodic or async entities to get out of the deadlock.\n", + "\u001b[0m2024-04-23 22:27:37.797 INFO gxf/std/greedy_scheduler.cpp@191: Scheduling 3 entities\u001b[0m\n", "\n", - "[info] [greedy_scheduler.cpp:398] Scheduler finished.\n", + "\u001b[0m2024-04-23 22:27:38.257 INFO gxf/std/greedy_scheduler.cpp@372: Scheduler stopped: Some entities are waiting for execution, but there are no periodic or async entities to get out of the deadlock.\u001b[0m\n", "\n", - "[info] [gxf_executor.cpp:1906] Graph execution deactivating. Fragment: \n", + "\u001b[0m2024-04-23 22:27:38.257 INFO gxf/std/greedy_scheduler.cpp@401: Scheduler finished.\u001b[0m\n", "\n", - "[info] [gxf_executor.cpp:1907] Deactivating Graph...\n", + "[info] [gxf_executor.cpp:1879] Deactivating Graph...\n", "\n", - "[info] [gxf_executor.cpp:1910] Graph execution finished. Fragment: \n", + "[info] [gxf_executor.cpp:1887] Graph execution finished.\n", "\n", - "[info] [gxf_executor.cpp:230] Destroying context\n", + "[info] [gxf_executor.cpp:275] Destroying context\n", "\n", "Number of times operator sobel_op whose class is defined in sobel_operator called: 1\n", "\n", @@ -1916,7 +1907,7 @@ "\n", "Data type of output post conversion: , max = 91\n", "\n", - "[2024-04-10 16:20:01,327] [INFO] (common) - Container 'unruffled_kalam'(8e18e862585f) exited.\n" + "[2024-04-23 15:27:38,526] [INFO] (common) - Container 'dazzling_kowalevski'(94febd6eabce) exited.\n" ] } ], @@ -1928,16 +1919,16 @@ }, { "cell_type": "code", - "execution_count": 27, + "execution_count": 54, "metadata": {}, "outputs": [ { "data": { "text/plain": [ - "" + "" ] }, - "execution_count": 27, + "execution_count": 54, "metadata": {}, "output_type": "execute_result" }, diff --git a/notebooks/tutorials/02_mednist_app-prebuilt.ipynb b/notebooks/tutorials/02_mednist_app-prebuilt.ipynb index 97757a6e..60e6a2d5 100644 --- a/notebooks/tutorials/02_mednist_app-prebuilt.ipynb +++ b/notebooks/tutorials/02_mednist_app-prebuilt.ipynb @@ -28,11 +28,11 @@ "output_type": "stream", "text": [ "Cloning into 'source'...\n", - "remote: Enumerating objects: 276, done.\u001b[K\n", - "remote: Counting objects: 100% (276/276), done.\u001b[K\n", + "remote: Enumerating objects: 277, done.\u001b[K\n", + "remote: Counting objects: 100% (277/277), done.\u001b[K\n", "remote: Compressing objects: 100% (222/222), done.\u001b[K\n", - "remote: Total 276 (delta 55), reused 150 (delta 32), pack-reused 0\u001b[K\n", - "Receiving objects: 100% (276/276), 1.43 MiB | 3.51 MiB/s, done.\n", + "remote: Total 277 (delta 55), reused 159 (delta 33), pack-reused 0\u001b[K\n", + "Receiving objects: 100% (277/277), 1.44 MiB | 10.45 MiB/s, done.\n", "Resolving deltas: 100% (55/55), done.\n" ] } @@ -77,41 +77,38 @@ "name": "stdout", "output_type": "stream", "text": [ - "Requirement already satisfied: monai-deploy-app-sdk in /home/mqin/src/monai-deploy-app-sdk/.venv/lib/python3.10/site-packages (0.5.1+12.gb2f5a07.dirty)\n", + "Requirement already satisfied: monai-deploy-app-sdk in /home/mqin/src/monai-deploy-app-sdk/.venv/lib/python3.10/site-packages (0.5.1+18.gea0c032.dirty)\n", "Requirement already satisfied: numpy>=1.21.6 in /home/mqin/src/monai-deploy-app-sdk/.venv/lib/python3.10/site-packages (from monai-deploy-app-sdk) (1.26.4)\n", - "Requirement already satisfied: holoscan~=1.0 in /home/mqin/src/monai-deploy-app-sdk/.venv/lib/python3.10/site-packages (from monai-deploy-app-sdk) (1.0.3)\n", + "Requirement already satisfied: holoscan~=2.0 in /home/mqin/src/monai-deploy-app-sdk/.venv/lib/python3.10/site-packages (from monai-deploy-app-sdk) (2.0.0)\n", "Requirement already satisfied: colorama>=0.4.1 in /home/mqin/src/monai-deploy-app-sdk/.venv/lib/python3.10/site-packages (from monai-deploy-app-sdk) (0.4.6)\n", "Requirement already satisfied: typeguard>=3.0.0 in 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rich>=10.11.0->typer>=0.4.1->python-on-whales==0.60.1->holoscan~=1.0->monai-deploy-app-sdk) (3.0.0)\n", - "Requirement already satisfied: pygments<3.0.0,>=2.13.0 in /home/mqin/src/monai-deploy-app-sdk/.venv/lib/python3.10/site-packages (from rich>=10.11.0->typer>=0.4.1->python-on-whales==0.60.1->holoscan~=1.0->monai-deploy-app-sdk) (2.17.2)\n", - "Requirement already satisfied: mdurl~=0.1 in /home/mqin/src/monai-deploy-app-sdk/.venv/lib/python3.10/site-packages (from markdown-it-py>=2.2.0->rich>=10.11.0->typer>=0.4.1->python-on-whales==0.60.1->holoscan~=1.0->monai-deploy-app-sdk) (0.1.2)\n", - "\n", - "\u001b[1m[\u001b[0m\u001b[34;49mnotice\u001b[0m\u001b[1;39;49m]\u001b[0m\u001b[39;49m A new release of pip is available: \u001b[0m\u001b[31;49m23.3.2\u001b[0m\u001b[39;49m -> \u001b[0m\u001b[32;49m24.0\u001b[0m\n", - "\u001b[1m[\u001b[0m\u001b[34;49mnotice\u001b[0m\u001b[1;39;49m]\u001b[0m\u001b[39;49m To update, run: \u001b[0m\u001b[32;49mpip install --upgrade pip\u001b[0m\n" + 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wheel-axle-runtime<1.0->holoscan~=2.0->monai-deploy-app-sdk) (3.13.4)\n", + "Requirement already satisfied: click>=8.0.0 in /home/mqin/src/monai-deploy-app-sdk/.venv/lib/python3.10/site-packages (from typer>=0.4.1->python-on-whales==0.60.1->holoscan~=2.0->monai-deploy-app-sdk) (8.1.7)\n", + "Requirement already satisfied: shellingham>=1.3.0 in /home/mqin/src/monai-deploy-app-sdk/.venv/lib/python3.10/site-packages (from typer>=0.4.1->python-on-whales==0.60.1->holoscan~=2.0->monai-deploy-app-sdk) (1.5.4)\n", + "Requirement already satisfied: rich>=10.11.0 in /home/mqin/src/monai-deploy-app-sdk/.venv/lib/python3.10/site-packages (from typer>=0.4.1->python-on-whales==0.60.1->holoscan~=2.0->monai-deploy-app-sdk) (13.7.1)\n", + "Requirement already satisfied: markdown-it-py>=2.2.0 in /home/mqin/src/monai-deploy-app-sdk/.venv/lib/python3.10/site-packages (from rich>=10.11.0->typer>=0.4.1->python-on-whales==0.60.1->holoscan~=2.0->monai-deploy-app-sdk) (3.0.0)\n", + "Requirement already satisfied: pygments<3.0.0,>=2.13.0 in /home/mqin/src/monai-deploy-app-sdk/.venv/lib/python3.10/site-packages (from rich>=10.11.0->typer>=0.4.1->python-on-whales==0.60.1->holoscan~=2.0->monai-deploy-app-sdk) (2.17.2)\n", + "Requirement already satisfied: mdurl~=0.1 in /home/mqin/src/monai-deploy-app-sdk/.venv/lib/python3.10/site-packages (from markdown-it-py>=2.2.0->rich>=10.11.0->typer>=0.4.1->python-on-whales==0.60.1->holoscan~=2.0->monai-deploy-app-sdk) (0.1.2)\n" ] } ], @@ -140,11 +137,11 @@ "Requirement already satisfied: Pillow in /home/mqin/src/monai-deploy-app-sdk/.venv/lib/python3.10/site-packages (10.3.0)\n", "Requirement already satisfied: numpy>=1.20 in /home/mqin/src/monai-deploy-app-sdk/.venv/lib/python3.10/site-packages (from monai) (1.26.4)\n", "Requirement already satisfied: torch>=1.9 in /home/mqin/src/monai-deploy-app-sdk/.venv/lib/python3.10/site-packages (from monai) (2.0.1)\n", - "Requirement already satisfied: filelock in /home/mqin/src/monai-deploy-app-sdk/.venv/lib/python3.10/site-packages (from torch>=1.9->monai) (3.13.3)\n", + "Requirement already satisfied: filelock in /home/mqin/src/monai-deploy-app-sdk/.venv/lib/python3.10/site-packages (from torch>=1.9->monai) (3.13.4)\n", "Requirement already satisfied: typing-extensions in /home/mqin/src/monai-deploy-app-sdk/.venv/lib/python3.10/site-packages (from torch>=1.9->monai) (4.11.0)\n", "Requirement already satisfied: sympy in /home/mqin/src/monai-deploy-app-sdk/.venv/lib/python3.10/site-packages (from torch>=1.9->monai) (1.12)\n", "Requirement already satisfied: networkx in /home/mqin/src/monai-deploy-app-sdk/.venv/lib/python3.10/site-packages (from torch>=1.9->monai) (3.1)\n", - "Requirement already satisfied: jinja2 in /home/mqin/src/monai-deploy-app-sdk/.venv/lib/python3.10/site-packages (from torch>=1.9->monai) (3.1.2)\n", + "Requirement already satisfied: jinja2 in /home/mqin/src/monai-deploy-app-sdk/.venv/lib/python3.10/site-packages (from torch>=1.9->monai) (3.1.3)\n", "Requirement already satisfied: nvidia-cuda-nvrtc-cu11==11.7.99 in /home/mqin/src/monai-deploy-app-sdk/.venv/lib/python3.10/site-packages (from torch>=1.9->monai) (11.7.99)\n", "Requirement already satisfied: nvidia-cuda-runtime-cu11==11.7.99 in /home/mqin/src/monai-deploy-app-sdk/.venv/lib/python3.10/site-packages (from torch>=1.9->monai) (11.7.99)\n", "Requirement already satisfied: nvidia-cuda-cupti-cu11==11.7.101 in /home/mqin/src/monai-deploy-app-sdk/.venv/lib/python3.10/site-packages (from torch>=1.9->monai) (11.7.101)\n", @@ -157,15 +154,12 @@ "Requirement already satisfied: nvidia-nccl-cu11==2.14.3 in /home/mqin/src/monai-deploy-app-sdk/.venv/lib/python3.10/site-packages (from torch>=1.9->monai) (2.14.3)\n", "Requirement already satisfied: nvidia-nvtx-cu11==11.7.91 in /home/mqin/src/monai-deploy-app-sdk/.venv/lib/python3.10/site-packages (from torch>=1.9->monai) (11.7.91)\n", "Requirement already satisfied: triton==2.0.0 in /home/mqin/src/monai-deploy-app-sdk/.venv/lib/python3.10/site-packages (from torch>=1.9->monai) (2.0.0)\n", - "Requirement already satisfied: setuptools in /home/mqin/src/monai-deploy-app-sdk/.venv/lib/python3.10/site-packages (from nvidia-cublas-cu11==11.10.3.66->torch>=1.9->monai) (69.2.0)\n", + "Requirement already satisfied: setuptools in /home/mqin/src/monai-deploy-app-sdk/.venv/lib/python3.10/site-packages (from nvidia-cublas-cu11==11.10.3.66->torch>=1.9->monai) (69.5.1)\n", "Requirement already satisfied: wheel in /home/mqin/src/monai-deploy-app-sdk/.venv/lib/python3.10/site-packages (from nvidia-cublas-cu11==11.10.3.66->torch>=1.9->monai) (0.43.0)\n", - "Requirement already satisfied: cmake in /home/mqin/src/monai-deploy-app-sdk/.venv/lib/python3.10/site-packages (from triton==2.0.0->torch>=1.9->monai) (3.29.0.1)\n", - "Requirement already satisfied: lit in /home/mqin/src/monai-deploy-app-sdk/.venv/lib/python3.10/site-packages (from triton==2.0.0->torch>=1.9->monai) (18.1.2)\n", + "Requirement already satisfied: cmake in /home/mqin/src/monai-deploy-app-sdk/.venv/lib/python3.10/site-packages (from triton==2.0.0->torch>=1.9->monai) (3.29.2)\n", + "Requirement already satisfied: lit in /home/mqin/src/monai-deploy-app-sdk/.venv/lib/python3.10/site-packages (from triton==2.0.0->torch>=1.9->monai) (18.1.3)\n", "Requirement already satisfied: MarkupSafe>=2.0 in /home/mqin/src/monai-deploy-app-sdk/.venv/lib/python3.10/site-packages (from jinja2->torch>=1.9->monai) (2.1.5)\n", - "Requirement already satisfied: mpmath>=0.19 in /home/mqin/src/monai-deploy-app-sdk/.venv/lib/python3.10/site-packages (from sympy->torch>=1.9->monai) (1.3.0)\n", - "\n", - "\u001b[1m[\u001b[0m\u001b[34;49mnotice\u001b[0m\u001b[1;39;49m]\u001b[0m\u001b[39;49m A new release of pip is available: \u001b[0m\u001b[31;49m23.3.2\u001b[0m\u001b[39;49m -> \u001b[0m\u001b[32;49m24.0\u001b[0m\n", - "\u001b[1m[\u001b[0m\u001b[34;49mnotice\u001b[0m\u001b[1;39;49m]\u001b[0m\u001b[39;49m To update, run: \u001b[0m\u001b[32;49mpip install --upgrade pip\u001b[0m\n" + "Requirement already satisfied: mpmath>=0.19 in /home/mqin/src/monai-deploy-app-sdk/.venv/lib/python3.10/site-packages (from sympy->torch>=1.9->monai) (1.3.0)\n" ] } ], @@ -194,23 +188,20 @@ "text": [ "Requirement already satisfied: gdown in /home/mqin/src/monai-deploy-app-sdk/.venv/lib/python3.10/site-packages (5.1.0)\n", "Requirement already satisfied: beautifulsoup4 in /home/mqin/src/monai-deploy-app-sdk/.venv/lib/python3.10/site-packages (from gdown) (4.12.3)\n", - "Requirement already satisfied: filelock in /home/mqin/src/monai-deploy-app-sdk/.venv/lib/python3.10/site-packages (from gdown) (3.13.3)\n", - "Requirement already satisfied: requests[socks] in /home/mqin/src/monai-deploy-app-sdk/.venv/lib/python3.10/site-packages (from gdown) (2.28.2)\n", + "Requirement already satisfied: filelock in /home/mqin/src/monai-deploy-app-sdk/.venv/lib/python3.10/site-packages (from gdown) (3.13.4)\n", + "Requirement already satisfied: requests[socks] in /home/mqin/src/monai-deploy-app-sdk/.venv/lib/python3.10/site-packages (from gdown) (2.31.0)\n", "Requirement already satisfied: tqdm in /home/mqin/src/monai-deploy-app-sdk/.venv/lib/python3.10/site-packages (from gdown) (4.66.2)\n", "Requirement already satisfied: soupsieve>1.2 in /home/mqin/src/monai-deploy-app-sdk/.venv/lib/python3.10/site-packages (from beautifulsoup4->gdown) (2.5)\n", "Requirement already satisfied: charset-normalizer<4,>=2 in /home/mqin/src/monai-deploy-app-sdk/.venv/lib/python3.10/site-packages (from requests[socks]->gdown) (3.3.2)\n", - "Requirement already satisfied: idna<4,>=2.5 in /home/mqin/src/monai-deploy-app-sdk/.venv/lib/python3.10/site-packages (from requests[socks]->gdown) (3.6)\n", - "Requirement already satisfied: urllib3<1.27,>=1.21.1 in /home/mqin/src/monai-deploy-app-sdk/.venv/lib/python3.10/site-packages (from requests[socks]->gdown) (1.26.18)\n", + "Requirement already satisfied: idna<4,>=2.5 in /home/mqin/src/monai-deploy-app-sdk/.venv/lib/python3.10/site-packages (from requests[socks]->gdown) (3.7)\n", + "Requirement already satisfied: urllib3<3,>=1.21.1 in /home/mqin/src/monai-deploy-app-sdk/.venv/lib/python3.10/site-packages (from requests[socks]->gdown) (2.2.1)\n", "Requirement already satisfied: certifi>=2017.4.17 in /home/mqin/src/monai-deploy-app-sdk/.venv/lib/python3.10/site-packages (from requests[socks]->gdown) (2024.2.2)\n", "Requirement already satisfied: PySocks!=1.5.7,>=1.5.6 in /home/mqin/src/monai-deploy-app-sdk/.venv/lib/python3.10/site-packages (from requests[socks]->gdown) (1.7.1)\n", - "\n", - "\u001b[1m[\u001b[0m\u001b[34;49mnotice\u001b[0m\u001b[1;39;49m]\u001b[0m\u001b[39;49m A new release of pip is available: \u001b[0m\u001b[31;49m23.3.2\u001b[0m\u001b[39;49m -> \u001b[0m\u001b[32;49m24.0\u001b[0m\n", - "\u001b[1m[\u001b[0m\u001b[34;49mnotice\u001b[0m\u001b[1;39;49m]\u001b[0m\u001b[39;49m To update, run: \u001b[0m\u001b[32;49mpip install --upgrade pip\u001b[0m\n", "Downloading...\n", "From (original): https://drive.google.com/uc?id=1yJ4P-xMNEfN6lIOq_u6x1eMAq1_MJu-E\n", - "From (redirected): https://drive.google.com/uc?id=1yJ4P-xMNEfN6lIOq_u6x1eMAq1_MJu-E&confirm=t&uuid=8dfa9939-2267-4d12-ba17-3e35b1626357\n", + "From (redirected): https://drive.google.com/uc?id=1yJ4P-xMNEfN6lIOq_u6x1eMAq1_MJu-E&confirm=t&uuid=72f2b083-c6ce-44ba-aafd-19c9bd097d63\n", "To: /home/mqin/src/monai-deploy-app-sdk/notebooks/tutorials/mednist_classifier_data.zip\n", - "100%|██████████████████████████████████████| 28.6M/28.6M [00:00<00:00, 62.3MB/s]\n" + "100%|██████████████████████████████████████| 28.6M/28.6M [00:00<00:00, 34.3MB/s]\n" ] } ], @@ -305,14 +296,16 @@ "name": "stdout", "output_type": "stream", "text": [ - "[2024-04-10 16:23:51,962] [INFO] (packager.parameters) - Application: /home/mqin/src/monai-deploy-app-sdk/notebooks/tutorials/source/examples/apps/mednist_classifier_monaideploy/mednist_classifier_monaideploy.py\n", - "[2024-04-10 16:23:51,962] [INFO] (packager.parameters) - Detected application type: Python File\n", - "[2024-04-10 16:23:51,962] [INFO] (packager) - Scanning for models in /home/mqin/src/monai-deploy-app-sdk/notebooks/tutorials/models...\n", - "[2024-04-10 16:23:51,962] [DEBUG] (packager) - Model model=/home/mqin/src/monai-deploy-app-sdk/notebooks/tutorials/models/model added.\n", - "[2024-04-10 16:23:51,962] [INFO] (packager) - Reading application configuration from /home/mqin/src/monai-deploy-app-sdk/notebooks/tutorials/source/examples/apps/mednist_classifier_monaideploy/app.yaml...\n", - "[2024-04-10 16:23:51,964] [INFO] (packager) - Generating app.json...\n", - "[2024-04-10 16:23:51,964] [INFO] (packager) - Generating pkg.json...\n", - "[2024-04-10 16:23:51,969] [DEBUG] (common) - \n", + "[2024-04-23 15:33:53,163] [INFO] (common) - Downloading CLI manifest file...\n", + "[2024-04-23 15:33:53,444] [DEBUG] (common) - Validating CLI manifest file...\n", + "[2024-04-23 15:33:53,446] [INFO] (packager.parameters) - Application: /home/mqin/src/monai-deploy-app-sdk/notebooks/tutorials/source/examples/apps/mednist_classifier_monaideploy/mednist_classifier_monaideploy.py\n", + "[2024-04-23 15:33:53,446] [INFO] (packager.parameters) - Detected application type: Python File\n", + "[2024-04-23 15:33:53,447] [INFO] (packager) - Scanning for models in /home/mqin/src/monai-deploy-app-sdk/notebooks/tutorials/models...\n", + "[2024-04-23 15:33:53,447] [DEBUG] (packager) - Model model=/home/mqin/src/monai-deploy-app-sdk/notebooks/tutorials/models/model added.\n", + "[2024-04-23 15:33:53,447] [INFO] (packager) - Reading application configuration from /home/mqin/src/monai-deploy-app-sdk/notebooks/tutorials/source/examples/apps/mednist_classifier_monaideploy/app.yaml...\n", + "[2024-04-23 15:33:53,453] [INFO] (packager) - Generating app.json...\n", + "[2024-04-23 15:33:53,453] [INFO] (packager) - Generating pkg.json...\n", + "[2024-04-23 15:33:53,464] [DEBUG] (common) - \n", "=============== Begin app.json ===============\n", "{\n", " \"apiVersion\": \"1.0.0\",\n", @@ -347,7 +340,7 @@ "}\n", "================ End app.json ================\n", " \n", - "[2024-04-10 16:23:51,969] [DEBUG] (common) - \n", + "[2024-04-23 15:33:53,465] [DEBUG] (common) - \n", "=============== Begin pkg.json ===============\n", "{\n", " \"apiVersion\": \"1.0.0\",\n", @@ -367,11 +360,11 @@ "}\n", "================ End pkg.json ================\n", " \n", - "[2024-04-10 16:23:52,003] [DEBUG] (packager.builder) - \n", + "[2024-04-23 15:33:53,510] [DEBUG] (packager.builder) - \n", "========== Begin Dockerfile ==========\n", "\n", "\n", - "FROM nvcr.io/nvidia/clara-holoscan/holoscan:v1.0.3-dgpu\n", + "FROM nvcr.io/nvidia/clara-holoscan/holoscan:v2.0.0-dgpu\n", "\n", "ENV DEBIAN_FRONTEND=noninteractive\n", "ENV TERM=xterm-256color\n", @@ -387,11 +380,11 @@ " && mkdir -p /var/holoscan/input \\\n", " && mkdir -p /var/holoscan/output\n", "\n", - "LABEL base=\"nvcr.io/nvidia/clara-holoscan/holoscan:v1.0.3-dgpu\"\n", + "LABEL base=\"nvcr.io/nvidia/clara-holoscan/holoscan:v2.0.0-dgpu\"\n", "LABEL tag=\"mednist_app:1.0\"\n", "LABEL org.opencontainers.image.title=\"MONAI Deploy App Package - MedNIST Classifier App\"\n", "LABEL org.opencontainers.image.version=\"1.0\"\n", - "LABEL org.nvidia.holoscan=\"1.0.3\"\n", + "LABEL org.nvidia.holoscan=\"2.0.0\"\n", "LABEL org.monai.deploy.app-sdk=\"0.5.1\"\n", "\n", "\n", @@ -417,7 +410,6 @@ "ENV PYTHONPATH=\"/opt/holoscan/app:$PYTHONPATH\"\n", "\n", "\n", - "\n", "RUN groupadd -f -g $GID $UNAME\n", "RUN useradd -rm -d /home/$UNAME -s /bin/bash -g $GID -G sudo -u $UID $UNAME\n", "RUN chown -R holoscan /var/holoscan \n", @@ -443,14 +435,12 @@ "RUN pip install --upgrade pip\n", "RUN pip install --no-cache-dir --user -r /tmp/requirements.txt\n", "\n", - "# Install Holoscan from PyPI only when sdk_type is Holoscan. \n", - "# For MONAI Deploy, the APP SDK will install it unless user specifies the Holoscan SDK file.\n", + " \n", + "# MONAI Deploy\n", "\n", "# Copy user-specified MONAI Deploy SDK file\n", - "COPY ./monai_deploy_app_sdk-0.5.1+25.g31e4165.dirty-py3-none-any.whl /tmp/monai_deploy_app_sdk-0.5.1+25.g31e4165.dirty-py3-none-any.whl\n", - "RUN pip install /tmp/monai_deploy_app_sdk-0.5.1+25.g31e4165.dirty-py3-none-any.whl\n", - "\n", - "\n", + "COPY ./monai_deploy_app_sdk-0.5.1+20.gb869749.dirty-py3-none-any.whl /tmp/monai_deploy_app_sdk-0.5.1+20.gb869749.dirty-py3-none-any.whl\n", + "RUN pip install /tmp/monai_deploy_app_sdk-0.5.1+20.gb869749.dirty-py3-none-any.whl\n", "\n", "\n", "COPY ./models /opt/holoscan/models\n", @@ -464,151 +454,254 @@ "ENTRYPOINT [\"/var/holoscan/tools\"]\n", "=========== End Dockerfile ===========\n", "\n", - "[2024-04-10 16:23:52,003] [INFO] (packager.builder) - \n", + "[2024-04-23 15:33:53,510] [INFO] (packager.builder) - \n", "===============================================================================\n", "Building image for: x64-workstation\n", " Architecture: linux/amd64\n", - " Base Image: nvcr.io/nvidia/clara-holoscan/holoscan:v1.0.3-dgpu\n", + " Base Image: nvcr.io/nvidia/clara-holoscan/holoscan:v2.0.0-dgpu\n", " Build Image: N/A\n", " Cache: Enabled\n", " Configuration: dgpu\n", " Holoscan SDK Package: pypi.org\n", - " MONAI Deploy App SDK Package: /home/mqin/src/monai-deploy-app-sdk/dist/monai_deploy_app_sdk-0.5.1+25.g31e4165.dirty-py3-none-any.whl\n", + " MONAI Deploy App SDK Package: /home/mqin/src/monai-deploy-app-sdk/dist/monai_deploy_app_sdk-0.5.1+20.gb869749.dirty-py3-none-any.whl\n", " gRPC Health Probe: N/A\n", - " SDK Version: 1.0.3\n", + " SDK Version: 2.0.0\n", " SDK: monai-deploy\n", " Tag: mednist_app-x64-workstation-dgpu-linux-amd64:1.0\n", " \n", - "[2024-04-10 16:23:52,265] [INFO] (common) - Using existing Docker BuildKit builder `holoscan_app_builder`\n", - "[2024-04-10 16:23:52,265] [DEBUG] (packager.builder) - Building Holoscan Application Package: tag=mednist_app-x64-workstation-dgpu-linux-amd64:1.0\n", + "[2024-04-23 15:33:53,781] [INFO] (common) - Using existing Docker BuildKit builder `holoscan_app_builder`\n", + "[2024-04-23 15:33:53,782] [DEBUG] (packager.builder) - Building Holoscan Application Package: tag=mednist_app-x64-workstation-dgpu-linux-amd64:1.0\n", "#0 building with \"holoscan_app_builder\" instance using docker-container driver\n", "\n", "#1 [internal] load build definition from Dockerfile\n", - "#1 transferring dockerfile: 2.81kB done\n", - "#1 DONE 0.1s\n", + "#1 transferring dockerfile: 2.67kB done\n", + "#1 DONE 0.0s\n", "\n", - "#2 [internal] load metadata for nvcr.io/nvidia/clara-holoscan/holoscan:v1.0.3-dgpu\n", + "#2 [internal] load metadata for nvcr.io/nvidia/clara-holoscan/holoscan:v2.0.0-dgpu\n", "#2 DONE 0.1s\n", "\n", "#3 [internal] load .dockerignore\n", "#3 transferring context: 1.79kB done\n", - "#3 DONE 0.1s\n", + "#3 DONE 0.0s\n", "\n", - "#4 importing cache manifest from nvcr.io/nvidia/clara-holoscan/holoscan:v1.0.3-dgpu\n", - "#4 ...\n", + "#4 [internal] load build context\n", + "#4 DONE 0.0s\n", "\n", - "#5 [internal] load build context\n", + "#5 importing cache manifest from local:3840576277762201667\n", + "#5 inferred cache manifest type: application/vnd.oci.image.index.v1+json done\n", "#5 DONE 0.0s\n", "\n", - "#6 importing cache manifest from local:3023656059275295125\n", - "#6 inferred cache manifest type: application/vnd.oci.image.index.v1+json done\n", + "#6 [ 1/21] FROM nvcr.io/nvidia/clara-holoscan/holoscan:v2.0.0-dgpu@sha256:20adbccd2c7b12dfb1798f6953f071631c3b85cd337858a7506f8e420add6d4a\n", + "#6 resolve nvcr.io/nvidia/clara-holoscan/holoscan:v2.0.0-dgpu@sha256:20adbccd2c7b12dfb1798f6953f071631c3b85cd337858a7506f8e420add6d4a 0.0s done\n", "#6 DONE 0.0s\n", "\n", - "#7 [ 1/21] FROM nvcr.io/nvidia/clara-holoscan/holoscan:v1.0.3-dgpu@sha256:50343c616bf910e2a7651abb59db7833933e82cce64c3c4885f938d7e4af6155\n", - "#7 resolve nvcr.io/nvidia/clara-holoscan/holoscan:v1.0.3-dgpu@sha256:50343c616bf910e2a7651abb59db7833933e82cce64c3c4885f938d7e4af6155 0.1s done\n", - "#7 DONE 0.1s\n", - "\n", - "#4 importing cache manifest from nvcr.io/nvidia/clara-holoscan/holoscan:v1.0.3-dgpu\n", - "#4 inferred cache manifest type: application/vnd.docker.distribution.manifest.list.v2+json done\n", - "#4 DONE 0.7s\n", + "#7 importing cache manifest from nvcr.io/nvidia/clara-holoscan/holoscan:v2.0.0-dgpu\n", + "#7 inferred cache manifest type: application/vnd.docker.distribution.manifest.list.v2+json done\n", + "#7 DONE 0.4s\n", "\n", - "#5 [internal] load build context\n", - "#5 transferring context: 28.73MB 0.2s done\n", - "#5 DONE 0.2s\n", + "#4 [internal] load build context\n", + "#4 transferring context: 28.73MB 0.2s done\n", + "#4 DONE 0.2s\n", "\n", - "#8 [ 9/21] WORKDIR /var/holoscan\n", + "#8 [10/21] COPY ./tools /var/holoscan/tools\n", "#8 CACHED\n", "\n", - "#9 [ 2/21] RUN mkdir -p /etc/holoscan/ && mkdir -p /opt/holoscan/ && mkdir -p /var/holoscan && mkdir -p /opt/holoscan/app && mkdir -p /var/holoscan/input && mkdir -p /var/holoscan/output\n", + "#9 [11/21] RUN chmod +x /var/holoscan/tools\n", "#9 CACHED\n", "\n", "#10 [ 5/21] RUN useradd -rm -d /home/holoscan -s /bin/bash -g 1000 -G sudo -u 1000 holoscan\n", "#10 CACHED\n", "\n", - "#11 [12/21] COPY ./pip/requirements.txt /tmp/requirements.txt\n", + "#11 [ 4/21] RUN groupadd -f -g 1000 holoscan\n", "#11 CACHED\n", "\n", "#12 [ 6/21] RUN chown -R holoscan /var/holoscan\n", "#12 CACHED\n", "\n", - "#13 [11/21] RUN chmod +x /var/holoscan/tools\n", + "#13 [ 2/21] RUN mkdir -p /etc/holoscan/ && mkdir -p /opt/holoscan/ && mkdir -p /var/holoscan && mkdir -p /opt/holoscan/app && mkdir -p /var/holoscan/input && mkdir -p /var/holoscan/output\n", "#13 CACHED\n", "\n", - "#14 [13/21] RUN pip install --upgrade pip\n", + "#14 [ 9/21] WORKDIR /var/holoscan\n", "#14 CACHED\n", "\n", - "#15 [10/21] COPY ./tools /var/holoscan/tools\n", + "#15 [ 3/21] RUN apt-get update && apt-get install -y curl jq && rm -rf /var/lib/apt/lists/*\n", "#15 CACHED\n", "\n", "#16 [ 8/21] RUN chown -R holoscan /var/holoscan/output\n", "#16 CACHED\n", "\n", - "#17 [ 4/21] RUN groupadd -f -g 1000 holoscan\n", + "#17 [ 7/21] RUN chown -R holoscan /var/holoscan/input\n", "#17 CACHED\n", "\n", - "#18 [ 3/21] RUN apt-get update && apt-get install -y curl jq && rm -rf /var/lib/apt/lists/*\n", + "#18 [12/21] COPY ./pip/requirements.txt /tmp/requirements.txt\n", "#18 CACHED\n", "\n", - "#19 [ 7/21] RUN chown -R holoscan /var/holoscan/input\n", + "#19 [13/21] RUN pip install --upgrade pip\n", "#19 CACHED\n", "\n", "#20 [14/21] RUN pip install --no-cache-dir --user -r /tmp/requirements.txt\n", - "#20 CACHED\n", - "\n", - "#21 [15/21] COPY ./monai_deploy_app_sdk-0.5.1+25.g31e4165.dirty-py3-none-any.whl /tmp/monai_deploy_app_sdk-0.5.1+25.g31e4165.dirty-py3-none-any.whl\n", + "#20 0.770 Collecting monai>=1.2.0 (from -r /tmp/requirements.txt (line 1))\n", + "#20 0.845 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numpy>=1.20 in /usr/local/lib/python3.10/dist-packages (from monai>=1.2.0->-r /tmp/requirements.txt (line 1)) (1.23.5)\n", + "#20 1.536 Collecting torch>=1.9 (from monai>=1.2.0->-r /tmp/requirements.txt (line 1))\n", + "#20 1.541 Downloading torch-2.2.2-cp310-cp310-manylinux1_x86_64.whl.metadata (26 kB)\n", + "#20 1.728 Collecting pillow-jpls>=1.0 (from highdicom>=0.18.2->-r /tmp/requirements.txt (line 4))\n", + "#20 1.808 Downloading pillow_jpls-1.3.2-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (3.1 kB)\n", + "#20 1.882 Collecting filelock (from torch>=1.9->monai>=1.2.0->-r /tmp/requirements.txt (line 1))\n", + "#20 1.886 Downloading filelock-3.13.4-py3-none-any.whl.metadata (2.8 kB)\n", + "#20 1.912 Collecting typing-extensions>=4.8.0 (from torch>=1.9->monai>=1.2.0->-r /tmp/requirements.txt (line 1))\n", + "#20 1.915 Downloading typing_extensions-4.11.0-py3-none-any.whl.metadata (3.0 kB)\n", + "#20 1.942 Collecting sympy (from torch>=1.9->monai>=1.2.0->-r 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(line 1))\n", + "#20 2.077 Downloading nvidia_cuda_runtime_cu12-12.1.105-py3-none-manylinux1_x86_64.whl.metadata (1.5 kB)\n", + "#20 2.095 Collecting nvidia-cuda-cupti-cu12==12.1.105 (from torch>=1.9->monai>=1.2.0->-r /tmp/requirements.txt (line 1))\n", + "#20 2.099 Downloading nvidia_cuda_cupti_cu12-12.1.105-py3-none-manylinux1_x86_64.whl.metadata (1.6 kB)\n", + "#20 2.117 Collecting nvidia-cudnn-cu12==8.9.2.26 (from torch>=1.9->monai>=1.2.0->-r /tmp/requirements.txt (line 1))\n", + "#20 2.120 Downloading nvidia_cudnn_cu12-8.9.2.26-py3-none-manylinux1_x86_64.whl.metadata (1.6 kB)\n", + "#20 2.136 Collecting nvidia-cublas-cu12==12.1.3.1 (from torch>=1.9->monai>=1.2.0->-r /tmp/requirements.txt (line 1))\n", + "#20 2.139 Downloading nvidia_cublas_cu12-12.1.3.1-py3-none-manylinux1_x86_64.whl.metadata (1.5 kB)\n", + "#20 2.155 Collecting nvidia-cufft-cu12==11.0.2.54 (from torch>=1.9->monai>=1.2.0->-r /tmp/requirements.txt (line 1))\n", + "#20 2.158 Downloading 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nvidia-cuda-nvrtc-cu12, nvidia-cuda-cupti-cu12, nvidia-cublas-cu12, networkx, fsspec, filelock, triton, pillow-jpls, nvidia-cusparse-cu12, nvidia-cudnn-cu12, nvidia-cusolver-cu12, highdicom, torch, monai\n", + "#20 82.08 Successfully installed Pillow-10.3.0 SimpleITK-2.3.1 filelock-3.13.4 fsspec-2024.3.1 highdicom-0.22.0 monai-1.3.0 mpmath-1.3.0 networkx-3.3 nvidia-cublas-cu12-12.1.3.1 nvidia-cuda-cupti-cu12-12.1.105 nvidia-cuda-nvrtc-cu12-12.1.105 nvidia-cuda-runtime-cu12-12.1.105 nvidia-cudnn-cu12-8.9.2.26 nvidia-cufft-cu12-11.0.2.54 nvidia-curand-cu12-10.3.2.106 nvidia-cusolver-cu12-11.4.5.107 nvidia-cusparse-cu12-12.1.0.106 nvidia-nccl-cu12-2.19.3 nvidia-nvjitlink-cu12-12.4.127 nvidia-nvtx-cu12-12.1.105 pillow-jpls-1.3.2 pydicom-2.4.4 sympy-1.12 torch-2.2.2 triton-2.2.0 typing-extensions-4.11.0\n", + "#20 DONE 84.1s\n", + "\n", + "#21 [15/21] COPY ./monai_deploy_app_sdk-0.5.1+20.gb869749.dirty-py3-none-any.whl /tmp/monai_deploy_app_sdk-0.5.1+20.gb869749.dirty-py3-none-any.whl\n", "#21 DONE 0.3s\n", "\n", - "#22 [16/21] RUN pip install /tmp/monai_deploy_app_sdk-0.5.1+25.g31e4165.dirty-py3-none-any.whl\n", - "#22 0.682 Defaulting to user installation because normal site-packages is not writeable\n", - "#22 0.793 Processing /tmp/monai_deploy_app_sdk-0.5.1+25.g31e4165.dirty-py3-none-any.whl\n", - "#22 0.803 Requirement already satisfied: numpy>=1.21.6 in /usr/local/lib/python3.10/dist-packages (from monai-deploy-app-sdk==0.5.1+25.g31e4165.dirty) (1.23.5)\n", - "#22 0.906 Collecting holoscan~=1.0 (from monai-deploy-app-sdk==0.5.1+25.g31e4165.dirty)\n", - "#22 0.971 Downloading holoscan-1.0.3-cp310-cp310-manylinux_2_35_x86_64.whl.metadata (4.1 kB)\n", - "#22 1.044 Collecting colorama>=0.4.1 (from monai-deploy-app-sdk==0.5.1+25.g31e4165.dirty)\n", - "#22 1.050 Downloading colorama-0.4.6-py2.py3-none-any.whl.metadata (17 kB)\n", - "#22 1.135 Collecting typeguard>=3.0.0 (from monai-deploy-app-sdk==0.5.1+25.g31e4165.dirty)\n", - "#22 1.139 Downloading 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(2023.11.17)\n", - "#22 1.401 Requirement already satisfied: filelock in /home/holoscan/.local/lib/python3.10/site-packages (from wheel-axle-runtime<1.0->holoscan~=1.0->monai-deploy-app-sdk==0.5.1+25.g31e4165.dirty) (3.13.3)\n", - "#22 1.443 Requirement already satisfied: click<9.0.0,>=7.1.1 in /usr/local/lib/python3.10/dist-packages (from typer>=0.4.1->python-on-whales==0.60.1->holoscan~=1.0->monai-deploy-app-sdk==0.5.1+25.g31e4165.dirty) (8.1.7)\n", - "#22 1.490 Downloading colorama-0.4.6-py2.py3-none-any.whl (25 kB)\n", - "#22 1.516 Downloading holoscan-1.0.3-cp310-cp310-manylinux_2_35_x86_64.whl (33.6 MB)\n", - "#22 1.982 ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 33.6/33.6 MB 43.1 MB/s eta 0:00:00\n", - "#22 1.989 Downloading pip-23.3.2-py3-none-any.whl (2.1 MB)\n", - "#22 2.032 ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 2.1/2.1 MB 53.0 MB/s eta 0:00:00\n", - "#22 2.039 Downloading typeguard-4.2.1-py3-none-any.whl (34 kB)\n", - "#22 2.064 Downloading 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monai-deploy-app-sdk==0.5.1+20.gb869749.dirty) (1.23.5)\n", + "#22 0.676 Collecting holoscan~=2.0 (from monai-deploy-app-sdk==0.5.1+20.gb869749.dirty)\n", + "#22 0.744 Downloading holoscan-2.0.0-cp310-cp310-manylinux_2_35_x86_64.whl.metadata (6.7 kB)\n", + "#22 0.816 Collecting colorama>=0.4.1 (from monai-deploy-app-sdk==0.5.1+20.gb869749.dirty)\n", + "#22 0.820 Downloading colorama-0.4.6-py2.py3-none-any.whl.metadata (17 kB)\n", + "#22 0.892 Collecting typeguard>=3.0.0 (from monai-deploy-app-sdk==0.5.1+20.gb869749.dirty)\n", + "#22 0.896 Downloading typeguard-4.2.1-py3-none-any.whl.metadata (3.7 kB)\n", + "#22 0.935 Requirement already satisfied: pip>=20.3 in /home/holoscan/.local/lib/python3.10/site-packages (from holoscan~=2.0->monai-deploy-app-sdk==0.5.1+20.gb869749.dirty) (24.0)\n", + "#22 0.936 Requirement already satisfied: cupy-cuda12x==12.2 in /usr/local/lib/python3.10/dist-packages (from holoscan~=2.0->monai-deploy-app-sdk==0.5.1+20.gb869749.dirty) (12.2.0)\n", + "#22 0.937 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typer>=0.4.1->python-on-whales==0.60.1->holoscan~=2.0->monai-deploy-app-sdk==0.5.1+20.gb869749.dirty) (8.1.7)\n", + "#22 1.082 Requirement already satisfied: shellingham>=1.3.0 in /usr/local/lib/python3.10/dist-packages (from typer>=0.4.1->python-on-whales==0.60.1->holoscan~=2.0->monai-deploy-app-sdk==0.5.1+20.gb869749.dirty) (1.5.4)\n", + "#22 1.083 Requirement already satisfied: rich>=10.11.0 in /usr/local/lib/python3.10/dist-packages (from typer>=0.4.1->python-on-whales==0.60.1->holoscan~=2.0->monai-deploy-app-sdk==0.5.1+20.gb869749.dirty) (13.7.1)\n", + "#22 1.120 Requirement already satisfied: markdown-it-py>=2.2.0 in /usr/local/lib/python3.10/dist-packages (from rich>=10.11.0->typer>=0.4.1->python-on-whales==0.60.1->holoscan~=2.0->monai-deploy-app-sdk==0.5.1+20.gb869749.dirty) (3.0.0)\n", + "#22 1.121 Requirement already satisfied: pygments<3.0.0,>=2.13.0 in /usr/local/lib/python3.10/dist-packages (from rich>=10.11.0->typer>=0.4.1->python-on-whales==0.60.1->holoscan~=2.0->monai-deploy-app-sdk==0.5.1+20.gb869749.dirty) (2.17.2)\n", + "#22 1.143 Requirement already satisfied: mdurl~=0.1 in /usr/local/lib/python3.10/dist-packages (from markdown-it-py>=2.2.0->rich>=10.11.0->typer>=0.4.1->python-on-whales==0.60.1->holoscan~=2.0->monai-deploy-app-sdk==0.5.1+20.gb869749.dirty) (0.1.2)\n", + "#22 1.157 Downloading colorama-0.4.6-py2.py3-none-any.whl (25 kB)\n", + "#22 1.181 Downloading holoscan-2.0.0-cp310-cp310-manylinux_2_35_x86_64.whl (33.2 MB)\n", + "#22 1.668 ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 33.2/33.2 MB 36.8 MB/s eta 0:00:00\n", + "#22 1.673 Downloading typeguard-4.2.1-py3-none-any.whl (34 kB)\n", + "#22 1.696 Downloading wheel_axle_runtime-0.0.5-py3-none-any.whl (12 kB)\n", + "#22 2.029 Installing collected packages: wheel-axle-runtime, typeguard, colorama, holoscan, monai-deploy-app-sdk\n", + "#22 2.773 Successfully installed colorama-0.4.6 holoscan-2.0.0 monai-deploy-app-sdk-0.5.1+20.gb869749.dirty typeguard-4.2.1 wheel-axle-runtime-0.0.5\n", + "#22 DONE 3.3s\n", "\n", "#23 [17/21] COPY ./models /opt/holoscan/models\n", - "#23 DONE 0.2s\n", + "#23 DONE 0.3s\n", "\n", "#24 [18/21] COPY ./map/app.json /etc/holoscan/app.json\n", "#24 DONE 0.1s\n", @@ -624,116 +717,137 @@ "\n", "#28 exporting to docker image format\n", "#28 exporting layers\n", - "#28 exporting layers 6.0s done\n", - "#28 exporting manifest sha256:02c9015ef90dc072d10044946ce69d29e7dbd7e748cd98b56713e2a32f1823bc 0.0s done\n", - "#28 exporting config sha256:26b7cd41adaba5d7700f104387d1c2d4b66829292de9fe656dff6f30ba20e56d 0.0s done\n", + "#28 exporting layers 152.5s done\n", + "#28 exporting manifest sha256:c70218a06b33b272ca2399e48c3804a3632c64ad2026e95b55d9ddae0cae7e74 0.0s done\n", + "#28 exporting config sha256:553a0ca99a2e26fc278babfe7ad247254fbaeadbc8cbad3e0053f4aede0c3aae 0.0s done\n", "#28 sending tarball\n", "#28 ...\n", "\n", "#29 importing to docker\n", - "#29 loading layer 3c784a11874c 32.77kB / 125.57kB\n", - "#29 loading layer 71abc17edeb9 557.06kB / 73.96MB\n", - "#29 loading layer 71abc17edeb9 73.53MB / 73.96MB 2.0s\n", - "#29 loading layer 8eee96e0be35 262.14kB / 25.59MB\n", - "#29 loading layer 81dfa72eaf50 512B / 512B\n", - "#29 loading layer c726a53666d2 697B / 697B\n", - "#29 loading layer 0266dfb048c0 297B / 297B\n", - "#29 loading layer d4a6edcf43fc 4.17kB / 4.17kB\n", - "#29 loading layer 3c784a11874c 32.77kB / 125.57kB 5.0s done\n", - "#29 loading layer 71abc17edeb9 73.53MB / 73.96MB 4.9s done\n", - "#29 loading layer 8eee96e0be35 262.14kB / 25.59MB 2.8s done\n", - "#29 loading layer 81dfa72eaf50 512B / 512B 2.2s done\n", - "#29 loading layer c726a53666d2 697B / 697B 1.9s done\n", - "#29 loading layer 0266dfb048c0 297B / 297B 1.5s done\n", - "#29 loading layer d4a6edcf43fc 4.17kB / 4.17kB 1.1s done\n", - "#29 DONE 5.0s\n", + "#29 loading layer 072c1594ab9f 557.06kB / 2.90GB\n", + "#29 loading layer 072c1594ab9f 108.63MB / 2.90GB 6.2s\n", + "#29 loading layer 072c1594ab9f 317.52MB / 2.90GB 10.3s\n", + "#29 loading layer 072c1594ab9f 514.72MB / 2.90GB 14.5s\n", + "#29 loading layer 072c1594ab9f 706.90MB / 2.90GB 18.6s\n", + "#29 loading layer 072c1594ab9f 889.06MB / 2.90GB 22.7s\n", + "#29 loading layer 072c1594ab9f 1.09GB / 2.90GB 26.8s\n", + "#29 loading layer 072c1594ab9f 1.32GB / 2.90GB 31.0s\n", + "#29 loading layer 072c1594ab9f 1.52GB / 2.90GB 35.1s\n", + "#29 loading layer 072c1594ab9f 1.76GB / 2.90GB 39.2s\n", + "#29 loading layer 072c1594ab9f 1.95GB / 2.90GB 43.3s\n", + "#29 loading layer 072c1594ab9f 1.98GB / 2.90GB 50.1s\n", + "#29 loading layer 072c1594ab9f 2.13GB / 2.90GB 56.3s\n", + "#29 loading layer 072c1594ab9f 2.32GB / 2.90GB 60.5s\n", + "#29 loading layer 072c1594ab9f 2.54GB / 2.90GB 64.6s\n", + "#29 loading layer 072c1594ab9f 2.73GB / 2.90GB 68.8s\n", + "#29 loading layer 072c1594ab9f 2.90GB / 2.90GB 75.0s\n", + "#29 loading layer f11aaa8e87ac 32.77kB / 125.83kB\n", + "#29 loading layer fa504599989c 557.06kB / 67.36MB\n", + "#29 loading layer 671fce7ea0e7 262.14kB / 25.59MB\n", + "#29 loading layer 1c0f42dfa575 514B / 514B\n", + "#29 loading layer 6fb8bbe7fb20 698B / 698B\n", + "#29 loading layer 2903a6d1ea2e 300B / 300B\n", + "#29 loading layer 1602070f430e 4.17kB / 4.17kB\n", + "#29 loading layer fa504599989c 557.06kB / 67.36MB 3.3s done\n", + "#29 loading layer 072c1594ab9f 2.90GB / 2.90GB 78.6s done\n", + "#29 loading layer f11aaa8e87ac 32.77kB / 125.83kB 3.4s done\n", + "#29 loading layer 671fce7ea0e7 262.14kB / 25.59MB 1.4s done\n", + "#29 loading layer 1c0f42dfa575 514B / 514B 1.0s done\n", + "#29 loading layer 6fb8bbe7fb20 698B / 698B 0.9s done\n", + "#29 loading layer 2903a6d1ea2e 300B / 300B 0.9s done\n", + "#29 loading layer 1602070f430e 4.17kB / 4.17kB 0.8s done\n", + "#29 DONE 78.6s\n", "\n", "#28 exporting to docker image format\n", - "#28 sending tarball 65.8s done\n", - "#28 DONE 72.0s\n", + "#28 sending tarball 119.9s done\n", + "#28 DONE 272.5s\n", "\n", "#30 exporting cache to client directory\n", "#30 preparing build cache for export\n", - "#30 writing layer sha256:00bb4c1319ba1a33ac3edcb3aa1240d8abcb8d0383c6267ed8028d3b6228a8a4\n", - "#30 writing layer sha256:00bb4c1319ba1a33ac3edcb3aa1240d8abcb8d0383c6267ed8028d3b6228a8a4 done\n", + "#30 writing layer sha256:014cff740c9ec6e9a30d0b859219a700ae880eb385d62095d348f5ea136d6015\n", "#30 writing layer sha256:014cff740c9ec6e9a30d0b859219a700ae880eb385d62095d348f5ea136d6015 done\n", - "#30 writing layer sha256:03a29f2f0e10f79ee63a9017483d2f5c668ef6c02e479f306e7ec76203d450a9 0.0s done\n", + "#30 writing layer sha256:0487800842442c7a031a39e1e1857bc6dae4b4f7e5daf3d625f7a8a4833fb364 done\n", + "#30 writing layer sha256:06c6aee94862daf0603783db4e1de6f8524b30ac9fbe0374ab3f1d85b2f76f7f done\n", "#30 writing layer sha256:0a1756432df4a4350712d8ae5c003f1526bd2180800b3ae6301cfc9ccf370254 done\n", "#30 writing layer 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writing layer sha256:f65d191416580d6c38e3d95eee12377b75a4df548be1492618ce2a8c3c41b99e done\n", + "#30 writing config sha256:c5d7ca2ff9b60cb7174369608d683a7735902b5a315ccbd3661cdb01d19b7db3 0.0s done\n", + "#30 preparing build cache for export 48.8s done\n", + "#30 writing cache manifest sha256:43a5a705376a7f516f02e6223e10f78f54002aca9882c7de45970b0d70baa3e8 0.0s done\n", + "#30 DONE 48.8s\n", + "[2024-04-23 15:40:45,771] [INFO] (packager) - Build Summary:\n", "\n", "Platform: x64-workstation/dgpu\n", " Status: Succeeded\n", @@ -764,7 +878,7 @@ "name": "stdout", "output_type": "stream", "text": [ - "mednist_app-x64-workstation-dgpu-linux-amd64 1.0 26b7cd41adab About a minute ago 17.5GB\n" + "mednist_app-x64-workstation-dgpu-linux-amd64 1.0 553a0ca99a2e 5 minutes ago 17.7GB\n" ] } ], @@ -846,16 +960,16 @@ " \"platformConfig\": \"dgpu\"\n", "}\n", "\n", - "2024-04-10 23:25:19 [INFO] Copying application from /opt/holoscan/app to /var/run/holoscan/export/app\n", + "2024-04-23 22:40:48 [INFO] Copying application from /opt/holoscan/app to /var/run/holoscan/export/app\n", "\n", - "2024-04-10 23:25:19 [INFO] Copying application manifest file from /etc/holoscan/app.json to /var/run/holoscan/export/config/app.json\n", - "2024-04-10 23:25:19 [INFO] Copying pkg manifest file from /etc/holoscan/pkg.json to /var/run/holoscan/export/config/pkg.json\n", - "2024-04-10 23:25:19 [INFO] Copying application configuration from /var/holoscan/app.yaml to /var/run/holoscan/export/config/app.yaml\n", + "2024-04-23 22:40:48 [INFO] Copying application manifest file from /etc/holoscan/app.json to /var/run/holoscan/export/config/app.json\n", + "2024-04-23 22:40:48 [INFO] Copying pkg manifest file from /etc/holoscan/pkg.json to /var/run/holoscan/export/config/pkg.json\n", + "2024-04-23 22:40:48 [INFO] Copying application configuration from /var/holoscan/app.yaml to /var/run/holoscan/export/config/app.yaml\n", "\n", - "2024-04-10 23:25:19 [INFO] Copying models from /opt/holoscan/models to /var/run/holoscan/export/models\n", + "2024-04-23 22:40:48 [INFO] Copying models from /opt/holoscan/models to /var/run/holoscan/export/models\n", "\n", - "2024-04-10 23:25:19 [INFO] Copying documentation from /opt/holoscan/docs/ to /var/run/holoscan/export/docs\n", - "2024-04-10 23:25:19 [INFO] '/opt/holoscan/docs/' cannot be found.\n", + "2024-04-23 22:40:48 [INFO] Copying documentation from /opt/holoscan/docs/ to /var/run/holoscan/export/docs\n", + "2024-04-23 22:40:48 [INFO] '/opt/holoscan/docs/' cannot be found.\n", "\n", "app config models\n" ] @@ -887,22 +1001,22 @@ "name": "stdout", "output_type": "stream", "text": [ - "[2024-04-10 16:25:20,790] [INFO] (runner) - Checking dependencies...\n", - "[2024-04-10 16:25:20,790] [INFO] (runner) - --> Verifying if \"docker\" is installed...\n", + "[2024-04-23 15:40:49,986] [INFO] (runner) - Checking dependencies...\n", + "[2024-04-23 15:40:49,986] [INFO] (runner) - --> Verifying if \"docker\" is installed...\n", "\n", - "[2024-04-10 16:25:20,791] [INFO] (runner) - --> Verifying if \"docker-buildx\" is installed...\n", + "[2024-04-23 15:40:49,986] [INFO] (runner) - --> Verifying if \"docker-buildx\" is installed...\n", "\n", - "[2024-04-10 16:25:20,791] [INFO] (runner) - --> Verifying if \"mednist_app-x64-workstation-dgpu-linux-amd64:1.0\" is available...\n", + "[2024-04-23 15:40:49,986] [INFO] (runner) - --> Verifying if \"mednist_app-x64-workstation-dgpu-linux-amd64:1.0\" is available...\n", "\n", - "[2024-04-10 16:25:20,871] [INFO] (runner) - Reading HAP/MAP manifest...\n", - "\u001b[sPreparing to copy...\u001b[?25l\u001b[u\u001b[2KCopying from container - 0B\u001b[?25h\u001b[u\u001b[2KSuccessfully copied 2.56kB to /tmp/tmpryp430i1/app.json\n", - "\u001b[sPreparing to copy...\u001b[?25l\u001b[u\u001b[2KCopying from container - 0B\u001b[?25h\u001b[u\u001b[2KSuccessfully copied 2.05kB to /tmp/tmpryp430i1/pkg.json\n", - "[2024-04-10 16:25:21,124] [INFO] (runner) - --> Verifying if \"nvidia-ctk\" is installed...\n", + "[2024-04-23 15:40:50,062] [INFO] (runner) - Reading HAP/MAP manifest...\n", + "\u001b[sPreparing to copy...\u001b[?25l\u001b[u\u001b[2KCopying from container - 0B\u001b[?25h\u001b[u\u001b[2KSuccessfully copied 2.56kB to /tmp/tmp9_4t5v97/app.json\n", + "\u001b[sPreparing to copy...\u001b[?25l\u001b[u\u001b[2KCopying from container - 0B\u001b[?25h\u001b[u\u001b[2KSuccessfully copied 2.05kB to /tmp/tmp9_4t5v97/pkg.json\n", + "[2024-04-23 15:40:50,322] [INFO] (runner) - --> Verifying if \"nvidia-ctk\" is installed...\n", "\n", - "[2024-04-10 16:25:21,124] [INFO] (runner) - --> Verifying \"nvidia-ctk\" version...\n", + "[2024-04-23 15:40:50,322] [INFO] (runner) - --> Verifying \"nvidia-ctk\" version...\n", "\n", - "[2024-04-10 16:25:21,410] [INFO] (common) - Launching container (7cf522bd06c4) using image 'mednist_app-x64-workstation-dgpu-linux-amd64:1.0'...\n", - " container name: dazzling_hugle\n", + "[2024-04-23 15:40:50,636] [INFO] (common) - Launching container (f9af17c16239) using image 'mednist_app-x64-workstation-dgpu-linux-amd64:1.0'...\n", + " container name: objective_merkle\n", " host name: mingq-dt\n", " network: host\n", " user: 1000:1000\n", @@ -912,53 +1026,49 @@ " shared memory size: 67108864\n", " devices: \n", " group_add: 44\n", - "2024-04-10 23:25:22 [INFO] Launching application python3 /opt/holoscan/app/mednist_classifier_monaideploy.py ...\n", + "2024-04-23 22:40:51 [INFO] Launching application python3 /opt/holoscan/app/mednist_classifier_monaideploy.py ...\n", "\n", - "[2024-04-10 23:25:31,408] [INFO] (root) - Parsed args: Namespace(log_level=None, input=None, output=None, model=None, workdir=None, argv=['/opt/holoscan/app/mednist_classifier_monaideploy.py'])\n", + "[2024-04-23 22:40:54,170] [INFO] (root) - Parsed args: Namespace(log_level=None, input=None, output=None, model=None, workdir=None, argv=['/opt/holoscan/app/mednist_classifier_monaideploy.py'])\n", "\n", - "[2024-04-10 23:25:31,419] [INFO] (root) - AppContext object: AppContext(input_path=/var/holoscan/input, output_path=/var/holoscan/output, model_path=/opt/holoscan/models, workdir=/var/holoscan)\n", + "[2024-04-23 22:40:54,175] [INFO] (root) - AppContext object: AppContext(input_path=/var/holoscan/input, output_path=/var/holoscan/output, model_path=/opt/holoscan/models, workdir=/var/holoscan)\n", "\n", "[info] [app_driver.cpp:1161] Launching the driver/health checking service\n", "\n", - "[info] [gxf_executor.cpp:211] Creating context\n", + "[info] [gxf_executor.cpp:247] Creating context\n", "\n", "[info] [server.cpp:87] Health checking server listening on 0.0.0.0:8777\n", "\n", - "[info] [gxf_executor.cpp:1674] Loading extensions from configs...\n", - "\n", - "[info] [gxf_executor.cpp:1864] Activating Graph...\n", + "[info] [gxf_executor.cpp:1672] Loading extensions from configs...\n", "\n", - "[info] [gxf_executor.cpp:1894] Running Graph...\n", + "[info] [gxf_executor.cpp:1842] Activating Graph...\n", "\n", - "[info] [gxf_executor.cpp:1896] Waiting for completion...\n", + "[info] [gxf_executor.cpp:1874] Running Graph...\n", "\n", - "[info] [gxf_executor.cpp:1897] Graph execution waiting. Fragment: \n", + "[info] [gxf_executor.cpp:1876] Waiting for completion...\n", "\n", - "[info] [greedy_scheduler.cpp:190] Scheduling 3 entities\n", + "\u001b[0m2024-04-23 22:40:54.201 INFO gxf/std/greedy_scheduler.cpp@191: Scheduling 3 entities\u001b[0m\n", "\n", "/home/holoscan/.local/lib/python3.10/site-packages/monai/data/meta_tensor.py:116: UserWarning: The given NumPy array is not writable, and PyTorch does not support non-writable tensors. This means writing to this tensor will result in undefined behavior. You may want to copy the array to protect its data or make it writable before converting it to a tensor. This type of warning will be suppressed for the rest of this program. (Triggered internally at ../torch/csrc/utils/tensor_numpy.cpp:206.)\n", "\n", " return torch.as_tensor(x, *args, **_kwargs).as_subclass(cls)\n", "\n", - "[2024-04-10 23:25:34,063] [INFO] (root) - Finished writing DICOM instance to file /var/holoscan/output/1.2.826.0.1.3680043.8.498.23303108191806495091599558367348667557.dcm\n", - "\n", - "[2024-04-10 23:25:34,064] [INFO] (monai.deploy.operators.dicom_text_sr_writer_operator.DICOMTextSRWriterOperator) - DICOM SOP instance saved in /var/holoscan/output/1.2.826.0.1.3680043.8.498.23303108191806495091599558367348667557.dcm\n", + "[2024-04-23 22:40:55,396] [INFO] (root) - Finished writing DICOM instance to file /var/holoscan/output/1.2.826.0.1.3680043.8.498.27996829466530719648374470054709482881.dcm\n", "\n", - "[info] [greedy_scheduler.cpp:369] Scheduler stopped: Some entities are waiting for execution, but there are no periodic or async entities to get out of the deadlock.\n", + "[2024-04-23 22:40:55,396] [INFO] (monai.deploy.operators.dicom_text_sr_writer_operator.DICOMTextSRWriterOperator) - DICOM SOP instance saved in /var/holoscan/output/1.2.826.0.1.3680043.8.498.27996829466530719648374470054709482881.dcm\n", "\n", - "[info] [greedy_scheduler.cpp:398] Scheduler finished.\n", + "\u001b[0m2024-04-23 22:40:55.396 INFO gxf/std/greedy_scheduler.cpp@372: Scheduler stopped: Some entities are waiting for execution, but there are no periodic or async entities to get out of the deadlock.\u001b[0m\n", "\n", - "[info] [gxf_executor.cpp:1906] Graph execution deactivating. Fragment: \n", + "[info] [gxf_executor.cpp:1879] Deactivating Graph...\n", "\n", - "[info] [gxf_executor.cpp:1907] Deactivating Graph...\n", + "\u001b[0m2024-04-23 22:40:55.397 INFO gxf/std/greedy_scheduler.cpp@401: Scheduler finished.\u001b[0m\n", "\n", - "[info] [gxf_executor.cpp:1910] Graph execution finished. Fragment: \n", + "[info] [gxf_executor.cpp:1887] Graph execution finished.\n", "\n", - "[info] [gxf_executor.cpp:230] Destroying context\n", + "[info] [gxf_executor.cpp:275] Destroying context\n", "\n", "AbdomenCT\n", "\n", - "[2024-04-10 16:25:35,771] [INFO] (common) - Container 'dazzling_hugle'(7cf522bd06c4) exited.\n" + "[2024-04-23 15:40:56,349] [INFO] (common) - Container 'objective_merkle'(f9af17c16239) exited.\n" ] } ], @@ -1322,40 +1432,50 @@ "name": "stderr", "output_type": "stream", "text": [ - "[2024-04-10 16:25:39,884] [INFO] (root) - Parsed args: Namespace(log_level=None, input=None, output=None, model=None, workdir=None, argv=[])\n", - "[2024-04-10 16:25:39,898] [INFO] (root) - AppContext object: AppContext(input_path=input, output_path=output, model_path=models, workdir=)\n", - "[info] [gxf_executor.cpp:211] Creating context\n", - "[info] [gxf_executor.cpp:1674] Loading extensions from configs...\n", - "[info] [gxf_executor.cpp:1864] Activating Graph...\n", - "[info] [gxf_executor.cpp:1894] Running Graph...\n", - "[info] [gxf_executor.cpp:1896] Waiting for completion...\n", - "[info] [gxf_executor.cpp:1897] Graph execution waiting. Fragment: \n", - "[info] [greedy_scheduler.cpp:190] Scheduling 3 entities\n", + "[2024-04-23 15:41:01,799] [INFO] (root) - Parsed args: Namespace(log_level=None, input=None, output=None, model=None, workdir=None, argv=[])\n", + "[2024-04-23 15:41:01,818] [INFO] (root) - AppContext object: AppContext(input_path=input, output_path=output, model_path=models, workdir=)\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "\u001b[0m2024-04-23 15:41:01.850 INFO gxf/std/greedy_scheduler.cpp@191: Scheduling 3 entities\u001b[0m\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "[info] [gxf_executor.cpp:247] Creating context\n", + "[info] [gxf_executor.cpp:1672] Loading extensions from configs...\n", + "[info] [gxf_executor.cpp:1842] Activating Graph...\n", + "[info] [gxf_executor.cpp:1874] Running Graph...\n", + "[info] [gxf_executor.cpp:1876] Waiting for completion...\n", "/home/mqin/src/monai-deploy-app-sdk/.venv/lib/python3.10/site-packages/monai/data/meta_tensor.py:116: UserWarning: The given NumPy array is not writable, and PyTorch does not support non-writable tensors. This means writing to this tensor will result in undefined behavior. You may want to copy the array to protect its data or make it writable before converting it to a tensor. This type of warning will be suppressed for the rest of this program. (Triggered internally at ../torch/csrc/utils/tensor_numpy.cpp:206.)\n", " return torch.as_tensor(x, *args, **_kwargs).as_subclass(cls)\n", "/home/mqin/src/monai-deploy-app-sdk/.venv/lib/python3.10/site-packages/pydicom/valuerep.py:443: UserWarning: Invalid value for VR UI: 'xyz'. Please see for allowed values for each VR.\n", " warnings.warn(msg)\n", - "[2024-04-10 16:25:42,470] [INFO] (root) - Finished writing DICOM instance to file output/1.2.826.0.1.3680043.8.498.71636533308287156684391922232397043508.dcm\n", - "[2024-04-10 16:25:42,472] [INFO] (monai.deploy.operators.dicom_text_sr_writer_operator.DICOMTextSRWriterOperator) - DICOM SOP instance saved in output/1.2.826.0.1.3680043.8.498.71636533308287156684391922232397043508.dcm\n" + "[2024-04-23 15:41:04,196] [INFO] (root) - Finished writing DICOM instance to file output/1.2.826.0.1.3680043.8.498.35898050102915969373889764509894247367.dcm\n", + "[2024-04-23 15:41:04,198] [INFO] (monai.deploy.operators.dicom_text_sr_writer_operator.DICOMTextSRWriterOperator) - DICOM SOP instance saved in output/1.2.826.0.1.3680043.8.498.35898050102915969373889764509894247367.dcm\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ - "AbdomenCT\n" + "AbdomenCT\n", + "\u001b[0m2024-04-23 15:41:04.199 INFO gxf/std/greedy_scheduler.cpp@372: Scheduler stopped: Some entities are waiting for execution, but there are no periodic or async entities to get out of the deadlock.\u001b[0m\n", + "\u001b[0m2024-04-23 15:41:04.200 INFO gxf/std/greedy_scheduler.cpp@401: Scheduler finished.\u001b[0m\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ - "[info] [greedy_scheduler.cpp:369] Scheduler stopped: Some entities are waiting for execution, but there are no periodic or async entities to get out of the deadlock.\n", - "[info] [greedy_scheduler.cpp:398] Scheduler finished.\n", - "[info] [gxf_executor.cpp:1906] Graph execution deactivating. Fragment: \n", - "[info] [gxf_executor.cpp:1907] Deactivating Graph...\n", - "[info] [gxf_executor.cpp:1910] Graph execution finished. Fragment: \n", - "[info] [gxf_executor.cpp:230] Destroying context\n" + "[info] [gxf_executor.cpp:1879] Deactivating Graph...\n", + "[info] [gxf_executor.cpp:1887] Graph execution finished.\n", + "[info] [gxf_executor.cpp:275] Destroying context\n" ] } ], @@ -1682,45 +1802,44 @@ "name": "stdout", "output_type": "stream", "text": [ - "[2024-04-10 16:25:46,989] [INFO] (root) - Parsed args: Namespace(log_level='DEBUG', input=PosixPath('/home/mqin/src/monai-deploy-app-sdk/notebooks/tutorials/input'), output=PosixPath('/home/mqin/src/monai-deploy-app-sdk/notebooks/tutorials/output'), model=PosixPath('/home/mqin/src/monai-deploy-app-sdk/notebooks/tutorials/models'), workdir=None, argv=['mednist_app/mednist_classifier_monaideploy.py', '-i', 'input', '-o', 'output', '-m', 'models', '-l', 'DEBUG'])\n", - "[2024-04-10 16:25:46,993] [INFO] (root) - AppContext object: AppContext(input_path=/home/mqin/src/monai-deploy-app-sdk/notebooks/tutorials/input, output_path=/home/mqin/src/monai-deploy-app-sdk/notebooks/tutorials/output, model_path=/home/mqin/src/monai-deploy-app-sdk/notebooks/tutorials/models, workdir=)\n", - "[\u001b[32minfo\u001b[m] [gxf_executor.cpp:211] Creating context\n", - "[\u001b[32minfo\u001b[m] [gxf_executor.cpp:1674] Loading extensions from configs...\n", - "[\u001b[32minfo\u001b[m] [gxf_executor.cpp:1864] Activating Graph...\n", - "[\u001b[32minfo\u001b[m] [gxf_executor.cpp:1894] Running Graph...\n", - "[\u001b[32minfo\u001b[m] [gxf_executor.cpp:1896] Waiting for completion...\n", - "[\u001b[32minfo\u001b[m] [gxf_executor.cpp:1897] Graph execution waiting. Fragment: \n", - "[\u001b[32minfo\u001b[m] [greedy_scheduler.cpp:190] Scheduling 3 entities\n", + "[2024-04-23 15:41:08,736] [INFO] (root) - Parsed args: Namespace(log_level='DEBUG', input=PosixPath('/home/mqin/src/monai-deploy-app-sdk/notebooks/tutorials/input'), output=PosixPath('/home/mqin/src/monai-deploy-app-sdk/notebooks/tutorials/output'), model=PosixPath('/home/mqin/src/monai-deploy-app-sdk/notebooks/tutorials/models'), workdir=None, argv=['mednist_app/mednist_classifier_monaideploy.py', '-i', 'input', '-o', 'output', '-m', 'models', '-l', 'DEBUG'])\n", + "[2024-04-23 15:41:08,740] [INFO] (root) - AppContext object: AppContext(input_path=/home/mqin/src/monai-deploy-app-sdk/notebooks/tutorials/input, output_path=/home/mqin/src/monai-deploy-app-sdk/notebooks/tutorials/output, model_path=/home/mqin/src/monai-deploy-app-sdk/notebooks/tutorials/models, workdir=)\n", + "[\u001b[32minfo\u001b[m] [gxf_executor.cpp:247] Creating context\n", + "[\u001b[32minfo\u001b[m] [gxf_executor.cpp:1672] Loading extensions from configs...\n", + "[\u001b[32minfo\u001b[m] [gxf_executor.cpp:1842] Activating Graph...\n", + "[\u001b[32minfo\u001b[m] [gxf_executor.cpp:1874] Running Graph...\n", + "[\u001b[32minfo\u001b[m] [gxf_executor.cpp:1876] Waiting for completion...\n", + "\u001b[0m2024-04-23 15:41:08.763 INFO gxf/std/greedy_scheduler.cpp@191: Scheduling 3 entities\u001b[0m\n", "/home/mqin/src/monai-deploy-app-sdk/.venv/lib/python3.10/site-packages/monai/data/meta_tensor.py:116: UserWarning: The given NumPy array is not writable, and PyTorch does not support non-writable tensors. This means writing to this tensor will result in undefined behavior. You may want to copy the array to protect its data or make it writable before converting it to a tensor. This type of warning will be suppressed for the rest of this program. (Triggered internally at ../torch/csrc/utils/tensor_numpy.cpp:206.)\n", " return torch.as_tensor(x, *args, **_kwargs).as_subclass(cls)\n", "AbdomenCT\n", - "[2024-04-10 16:25:49,239] [DEBUG] (monai.deploy.operators.dicom_text_sr_writer_operator.DICOMTextSRWriterOperator) - Writing DICOM object...\n", + "[2024-04-23 15:41:10,980] [DEBUG] (monai.deploy.operators.dicom_text_sr_writer_operator.DICOMTextSRWriterOperator) - Writing DICOM object...\n", "\n", - "[2024-04-10 16:25:49,239] [DEBUG] (root) - Writing DICOM common modules...\n", + "[2024-04-23 15:41:10,980] [DEBUG] (root) - Writing DICOM common modules...\n", "/home/mqin/src/monai-deploy-app-sdk/.venv/lib/python3.10/site-packages/pydicom/valuerep.py:443: UserWarning: Invalid value for VR UI: 'xyz'. Please see for allowed values for each VR.\n", " warnings.warn(msg)\n", - "[2024-04-10 16:25:49,242] [DEBUG] (root) - DICOM common modules written:\n", + "[2024-04-23 15:41:10,983] [DEBUG] (root) - DICOM common modules written:\n", "Dataset.file_meta -------------------------------\n", "(0002, 0000) File Meta Information Group Length UL: 198\n", "(0002, 0001) File Meta Information Version OB: b'01'\n", "(0002, 0002) Media Storage SOP Class UID UI: Basic Text SR Storage\n", - "(0002, 0003) Media Storage SOP Instance UID UI: 1.2.826.0.1.3680043.8.498.10219575881227434107206425977009168141\n", + "(0002, 0003) Media Storage SOP Instance UID UI: 1.2.826.0.1.3680043.8.498.10612655328316632493342405878828496728\n", "(0002, 0010) Transfer Syntax UID UI: Implicit VR Little Endian\n", "(0002, 0012) Implementation Class UID UI: 1.2.40.0.13.1.1.1\n", - "(0002, 0013) Implementation Version Name SH: '0.5.1+25.g31e41'\n", + "(0002, 0013) Implementation Version Name SH: '0.5.1+20.gb8697'\n", "-------------------------------------------------\n", "(0008, 0005) Specific Character Set CS: 'ISO_IR 100'\n", - "(0008, 0012) Instance Creation Date DA: '20240410'\n", - "(0008, 0013) Instance Creation Time TM: '162549'\n", + "(0008, 0012) Instance Creation Date DA: '20240423'\n", + "(0008, 0013) Instance Creation Time TM: '154110'\n", "(0008, 0016) SOP Class UID UI: Basic Text SR Storage\n", - "(0008, 0018) SOP Instance UID UI: 1.2.826.0.1.3680043.8.498.10219575881227434107206425977009168141\n", - "(0008, 0020) Study Date DA: '20240410'\n", - "(0008, 0021) Series Date DA: '20240410'\n", - "(0008, 0023) Content Date DA: '20240410'\n", - "(0008, 002a) Acquisition DateTime DT: '20240410162549'\n", - "(0008, 0030) Study Time TM: '162549'\n", - "(0008, 0031) Series Time TM: '162549'\n", - "(0008, 0033) Content Time TM: '162549'\n", + "(0008, 0018) SOP Instance UID UI: 1.2.826.0.1.3680043.8.498.10612655328316632493342405878828496728\n", + "(0008, 0020) Study Date DA: '20240423'\n", + "(0008, 0021) Series Date DA: '20240423'\n", + "(0008, 0023) Content Date DA: '20240423'\n", + "(0008, 002a) Acquisition DateTime DT: '20240423154110'\n", + "(0008, 0030) Study Time TM: '154110'\n", + "(0008, 0031) Series Time TM: '154110'\n", + "(0008, 0033) Content Time TM: '154110'\n", "(0008, 0050) Accession Number SH: ''\n", "(0008, 0060) Modality CS: 'SR'\n", "(0008, 0070) Manufacturer LO: 'MOANI Deploy App SDK'\n", @@ -1735,7 +1854,7 @@ "(0010, 0030) Patient's Birth Date DA: ''\n", "(0010, 0040) Patient's Sex CS: ''\n", "(0018, 0015) Body Part Examined CS: ''\n", - "(0018, 1020) Software Versions LO: '0.5.1+25.g31e41'\n", + "(0018, 1020) Software Versions LO: '0.5.1+20.gb8697'\n", "(0018, a001) Contributing Equipment Sequence 1 item(s) ---- \n", " (0008, 0070) Manufacturer LO: 'MONAI WG Trainer'\n", " (0008, 1090) Manufacturer's Model Name LO: 'MEDNIST Classifier'\n", @@ -1747,33 +1866,33 @@ " (0008, 0104) Code Meaning LO: '\"Processing Algorithm'\n", " ---------\n", " ---------\n", - "(0020, 000d) Study Instance UID UI: 1.2.826.0.1.3680043.8.498.99895869772559254532078552857455521250\n", - "(0020, 000e) Series Instance UID UI: 1.2.826.0.1.3680043.8.498.11097411469528473023282906105369639673\n", + "(0020, 000d) Study Instance UID UI: 1.2.826.0.1.3680043.8.498.12077853224410842102200362099184100728\n", + "(0020, 000e) Series Instance UID UI: 1.2.826.0.1.3680043.8.498.11250566385163932995456431918851640579\n", "(0020, 0010) Study ID SH: '1'\n", - "(0020, 0011) Series Number IS: '7823'\n", + "(0020, 0011) Series Number IS: '2474'\n", "(0020, 0013) Instance Number IS: '1'\n", "(0040, 1001) Requested Procedure ID SH: ''\n", - "[2024-04-10 16:25:49,242] [DEBUG] (root) - DICOM dataset to be written:Dataset.file_meta -------------------------------\n", + "[2024-04-23 15:41:10,984] [DEBUG] (root) - DICOM dataset to be written:Dataset.file_meta -------------------------------\n", "(0002, 0000) File Meta Information Group Length UL: 198\n", "(0002, 0001) File Meta Information Version OB: b'01'\n", "(0002, 0002) Media Storage SOP Class UID UI: Basic Text SR Storage\n", - "(0002, 0003) Media Storage SOP Instance UID UI: 1.2.826.0.1.3680043.8.498.10219575881227434107206425977009168141\n", + "(0002, 0003) Media Storage SOP Instance UID UI: 1.2.826.0.1.3680043.8.498.10612655328316632493342405878828496728\n", "(0002, 0010) Transfer Syntax UID UI: Implicit VR Little Endian\n", "(0002, 0012) Implementation Class UID UI: 1.2.40.0.13.1.1.1\n", - "(0002, 0013) Implementation Version Name SH: '0.5.1+25.g31e41'\n", + "(0002, 0013) Implementation Version Name SH: '0.5.1+20.gb8697'\n", "-------------------------------------------------\n", "(0008, 0005) Specific Character Set CS: 'ISO_IR 100'\n", - "(0008, 0012) Instance Creation Date DA: '20240410'\n", - "(0008, 0013) Instance Creation Time TM: '162549'\n", + "(0008, 0012) Instance Creation Date DA: '20240423'\n", + "(0008, 0013) Instance Creation Time TM: '154110'\n", "(0008, 0016) SOP Class UID UI: Basic Text SR Storage\n", - "(0008, 0018) SOP Instance UID UI: 1.2.826.0.1.3680043.8.498.10219575881227434107206425977009168141\n", - "(0008, 0020) Study Date DA: '20240410'\n", - "(0008, 0021) Series Date DA: '20240410'\n", - "(0008, 0023) Content Date DA: '20240410'\n", - "(0008, 002a) Acquisition DateTime DT: '20240410162549'\n", - "(0008, 0030) Study Time TM: '162549'\n", - "(0008, 0031) Series Time TM: '162549'\n", - "(0008, 0033) Content Time TM: '162549'\n", + "(0008, 0018) SOP Instance UID UI: 1.2.826.0.1.3680043.8.498.10612655328316632493342405878828496728\n", + "(0008, 0020) Study Date DA: '20240423'\n", + "(0008, 0021) Series Date DA: '20240423'\n", + "(0008, 0023) Content Date DA: '20240423'\n", + "(0008, 002a) Acquisition DateTime DT: '20240423154110'\n", + "(0008, 0030) Study Time TM: '154110'\n", + "(0008, 0031) Series Time TM: '154110'\n", + "(0008, 0033) Content Time TM: '154110'\n", "(0008, 0050) Accession Number SH: ''\n", "(0008, 0060) Modality CS: 'SR'\n", "(0008, 0070) Manufacturer LO: 'MOANI Deploy App SDK'\n", @@ -1788,7 +1907,7 @@ "(0010, 0030) Patient's Birth Date DA: ''\n", "(0010, 0040) Patient's Sex CS: ''\n", "(0018, 0015) Body Part Examined CS: ''\n", - "(0018, 1020) Software Versions LO: '0.5.1+25.g31e41'\n", + "(0018, 1020) Software Versions LO: '0.5.1+20.gb8697'\n", "(0018, a001) Contributing Equipment Sequence 1 item(s) ---- \n", " (0008, 0070) Manufacturer LO: 'MONAI WG Trainer'\n", " (0008, 1090) Manufacturer's Model Name LO: 'MEDNIST Classifier'\n", @@ -1800,10 +1919,10 @@ " (0008, 0104) Code Meaning LO: '\"Processing Algorithm'\n", " ---------\n", " ---------\n", - "(0020, 000d) Study Instance UID UI: 1.2.826.0.1.3680043.8.498.99895869772559254532078552857455521250\n", - "(0020, 000e) Series Instance UID UI: 1.2.826.0.1.3680043.8.498.11097411469528473023282906105369639673\n", + "(0020, 000d) Study Instance UID UI: 1.2.826.0.1.3680043.8.498.12077853224410842102200362099184100728\n", + "(0020, 000e) Series Instance UID UI: 1.2.826.0.1.3680043.8.498.11250566385163932995456431918851640579\n", "(0020, 0010) Study ID SH: '1'\n", - "(0020, 0011) Series Number IS: '7823'\n", + "(0020, 0011) Series Number IS: '2474'\n", "(0020, 0013) Instance Number IS: '1'\n", "(0040, 1001) Requested Procedure ID SH: ''\n", "(0040, a040) Value Type CS: 'CONTAINER'\n", @@ -1824,14 +1943,13 @@ " ---------\n", " (0040, a160) Text Value UT: 'AbdomenCT'\n", " ---------\n", - "[2024-04-10 16:25:49,245] [INFO] (root) - Finished writing DICOM instance to file /home/mqin/src/monai-deploy-app-sdk/notebooks/tutorials/output/1.2.826.0.1.3680043.8.498.10219575881227434107206425977009168141.dcm\n", - "[2024-04-10 16:25:49,246] [INFO] (monai.deploy.operators.dicom_text_sr_writer_operator.DICOMTextSRWriterOperator) - DICOM SOP instance saved in /home/mqin/src/monai-deploy-app-sdk/notebooks/tutorials/output/1.2.826.0.1.3680043.8.498.10219575881227434107206425977009168141.dcm\n", - "[\u001b[32minfo\u001b[m] [greedy_scheduler.cpp:369] Scheduler stopped: Some entities are waiting for execution, but there are no periodic or async entities to get out of the deadlock.\n", - "[\u001b[32minfo\u001b[m] [greedy_scheduler.cpp:398] Scheduler finished.\n", - "[\u001b[32minfo\u001b[m] [gxf_executor.cpp:1906] Graph execution deactivating. Fragment: \n", - "[\u001b[32minfo\u001b[m] [gxf_executor.cpp:1907] Deactivating Graph...\n", - "[\u001b[32minfo\u001b[m] [gxf_executor.cpp:1910] Graph execution finished. Fragment: \n", - "[\u001b[32minfo\u001b[m] [gxf_executor.cpp:230] Destroying context\n" + "[2024-04-23 15:41:10,987] [INFO] (root) - Finished writing DICOM instance to file /home/mqin/src/monai-deploy-app-sdk/notebooks/tutorials/output/1.2.826.0.1.3680043.8.498.10612655328316632493342405878828496728.dcm\n", + "[2024-04-23 15:41:10,988] [INFO] (monai.deploy.operators.dicom_text_sr_writer_operator.DICOMTextSRWriterOperator) - DICOM SOP instance saved in /home/mqin/src/monai-deploy-app-sdk/notebooks/tutorials/output/1.2.826.0.1.3680043.8.498.10612655328316632493342405878828496728.dcm\n", + "\u001b[0m2024-04-23 15:41:10.988 INFO gxf/std/greedy_scheduler.cpp@372: Scheduler stopped: Some entities are waiting for execution, but there are no periodic or async entities to get out of the deadlock.\u001b[0m\n", + "\u001b[0m2024-04-23 15:41:10.988 INFO gxf/std/greedy_scheduler.cpp@401: Scheduler finished.\u001b[0m\n", + "[\u001b[32minfo\u001b[m] [gxf_executor.cpp:1879] Deactivating Graph...\n", + "[\u001b[32minfo\u001b[m] [gxf_executor.cpp:1887] Graph execution finished.\n", + "[\u001b[32minfo\u001b[m] [gxf_executor.cpp:275] Destroying context\n" ] } ], diff --git a/notebooks/tutorials/02_mednist_app.ipynb b/notebooks/tutorials/02_mednist_app.ipynb index 595cb471..57212003 100644 --- a/notebooks/tutorials/02_mednist_app.ipynb +++ b/notebooks/tutorials/02_mednist_app.ipynb @@ -71,7 +71,7 @@ "Pytorch Ignite version: 0.4.11\n", "ITK version: NOT INSTALLED or UNKNOWN VERSION.\n", "Nibabel version: 5.2.1\n", - "scikit-image version: 0.22.0\n", + "scikit-image version: 0.23.2\n", "scipy version: 1.13.0\n", "Pillow version: 10.3.0\n", "Tensorboard version: NOT INSTALLED or UNKNOWN VERSION.\n", @@ -163,7 +163,7 @@ "name": "stdout", "output_type": "stream", "text": [ - "/tmp/tmpz1q9ch5_\n" + "/tmp/tmp0iht_c0l\n" ] }, { @@ -172,16 +172,16 @@ "text": [ "Downloading...\n", "From (original): https://drive.google.com/uc?id=1QsnnkvZyJPcbRoV_ArW8SnE1OTuoVbKE\n", - "From (redirected): https://drive.google.com/uc?id=1QsnnkvZyJPcbRoV_ArW8SnE1OTuoVbKE&confirm=t&uuid=6052caf3-cb8c-4cb3-b8b8-804d8dc90e06\n", - "To: /tmp/tmpq9pcg2c8/MedNIST.tar.gz\n", - "100%|██████████| 61.8M/61.8M [00:00<00:00, 81.1MB/s]" + "From (redirected): https://drive.google.com/uc?id=1QsnnkvZyJPcbRoV_ArW8SnE1OTuoVbKE&confirm=t&uuid=af0469cc-fefc-4bd4-9ba2-60e15ffc2168\n", + "To: /tmp/tmpquityog6/MedNIST.tar.gz\n", + "100%|██████████| 61.8M/61.8M [00:00<00:00, 66.5MB/s]" ] }, { "name": "stdout", "output_type": "stream", "text": [ - "2024-04-10 16:28:05,802 - INFO - Downloaded: /tmp/tmpz1q9ch5_/MedNIST.tar.gz\n" + "2024-04-23 17:01:37,537 - INFO - Downloaded: /tmp/tmp0iht_c0l/MedNIST.tar.gz\n" ] }, { @@ -195,8 +195,8 @@ "name": "stdout", "output_type": "stream", "text": [ - "2024-04-10 16:28:05,912 - INFO - Verified 'MedNIST.tar.gz', md5: 0bc7306e7427e00ad1c5526a6677552d.\n", - "2024-04-10 16:28:05,914 - INFO - Writing into directory: /tmp/tmpz1q9ch5_.\n" + "2024-04-23 17:01:37,643 - INFO - Verified 'MedNIST.tar.gz', md5: 0bc7306e7427e00ad1c5526a6677552d.\n", + "2024-04-23 17:01:37,644 - INFO - Writing into directory: /tmp/tmp0iht_c0l.\n" ] } ], @@ -769,40 +769,50 @@ "name": "stderr", "output_type": "stream", "text": [ - "[2024-04-10 16:35:53,768] [INFO] (root) - Parsed args: Namespace(log_level=None, input=None, output=None, model=None, workdir=None, argv=[])\n", - "[2024-04-10 16:35:53,778] [INFO] (root) - AppContext object: AppContext(input_path=input, output_path=output, model_path=models, workdir=)\n", - "[info] [gxf_executor.cpp:211] Creating context\n", - "[info] [gxf_executor.cpp:1674] Loading extensions from configs...\n", - "[info] [gxf_executor.cpp:1864] Activating Graph...\n", - "[info] [gxf_executor.cpp:1894] Running Graph...\n", - "[info] [gxf_executor.cpp:1896] Waiting for completion...\n", - "[info] [gxf_executor.cpp:1897] Graph execution waiting. Fragment: \n", - "[info] [greedy_scheduler.cpp:190] Scheduling 3 entities\n", + "[2024-04-23 17:08:56,466] [INFO] (root) - Parsed args: Namespace(log_level=None, input=None, output=None, model=None, workdir=None, argv=[])\n", + "[2024-04-23 17:08:56,478] [INFO] (root) - AppContext object: AppContext(input_path=input, output_path=output, model_path=models, workdir=)\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "\u001b[0m2024-04-23 17:08:56.514 INFO gxf/std/greedy_scheduler.cpp@191: Scheduling 3 entities\u001b[0m\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "[info] [gxf_executor.cpp:247] Creating context\n", + "[info] [gxf_executor.cpp:1672] Loading extensions from configs...\n", + "[info] [gxf_executor.cpp:1842] Activating Graph...\n", + "[info] [gxf_executor.cpp:1874] Running Graph...\n", + "[info] [gxf_executor.cpp:1876] Waiting for completion...\n", "/home/mqin/src/monai-deploy-app-sdk/.venv/lib/python3.10/site-packages/monai/data/meta_tensor.py:116: UserWarning: The given NumPy array is not writable, and PyTorch does not support non-writable tensors. This means writing to this tensor will result in undefined behavior. You may want to copy the array to protect its data or make it writable before converting it to a tensor. This type of warning will be suppressed for the rest of this program. (Triggered internally at ../torch/csrc/utils/tensor_numpy.cpp:206.)\n", " return torch.as_tensor(x, *args, **_kwargs).as_subclass(cls)\n", "/home/mqin/src/monai-deploy-app-sdk/.venv/lib/python3.10/site-packages/pydicom/valuerep.py:443: UserWarning: Invalid value for VR UI: 'xyz'. Please see for allowed values for each VR.\n", " warnings.warn(msg)\n", - "[2024-04-10 16:35:54,545] [INFO] (root) - Finished writing DICOM instance to file output/1.2.826.0.1.3680043.8.498.91196297255331853052707757292596626343.dcm\n", - "[2024-04-10 16:35:54,548] [INFO] (monai.deploy.operators.dicom_text_sr_writer_operator.DICOMTextSRWriterOperator) - DICOM SOP instance saved in output/1.2.826.0.1.3680043.8.498.91196297255331853052707757292596626343.dcm\n" + "[2024-04-23 17:08:57,259] [INFO] (root) - Finished writing DICOM instance to file output/1.2.826.0.1.3680043.8.498.77299510031662020162686125612902317163.dcm\n", + "[2024-04-23 17:08:57,261] [INFO] (monai.deploy.operators.dicom_text_sr_writer_operator.DICOMTextSRWriterOperator) - DICOM SOP instance saved in output/1.2.826.0.1.3680043.8.498.77299510031662020162686125612902317163.dcm\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ - "AbdomenCT\n" + "AbdomenCT\n", + "\u001b[0m2024-04-23 17:08:57.263 INFO gxf/std/greedy_scheduler.cpp@372: Scheduler stopped: Some entities are waiting for execution, but there are no periodic or async entities to get out of the deadlock.\u001b[0m\n", + "\u001b[0m2024-04-23 17:08:57.263 INFO gxf/std/greedy_scheduler.cpp@401: Scheduler finished.\u001b[0m\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ - "[info] [greedy_scheduler.cpp:369] Scheduler stopped: Some entities are waiting for execution, but there are no periodic or async entities to get out of the deadlock.\n", - "[info] [greedy_scheduler.cpp:398] Scheduler finished.\n", - "[info] [gxf_executor.cpp:1906] Graph execution deactivating. Fragment: \n", - "[info] [gxf_executor.cpp:1907] Deactivating Graph...\n", - "[info] [gxf_executor.cpp:1910] Graph execution finished. Fragment: \n", - "[info] [gxf_executor.cpp:230] Destroying context\n" + "[info] [gxf_executor.cpp:1879] Deactivating Graph...\n", + "[info] [gxf_executor.cpp:1887] Graph execution finished.\n", + "[info] [gxf_executor.cpp:275] Destroying context\n" ] } ], @@ -1121,24 +1131,22 @@ "name": "stdout", "output_type": "stream", "text": [ - "[\u001b[32minfo\u001b[m] [gxf_executor.cpp:211] Creating context\n", - "[\u001b[32minfo\u001b[m] [gxf_executor.cpp:1674] Loading extensions from configs...\n", - "[\u001b[32minfo\u001b[m] [gxf_executor.cpp:1864] Activating Graph...\n", - "[\u001b[32minfo\u001b[m] [gxf_executor.cpp:1894] Running Graph...\n", - "[\u001b[32minfo\u001b[m] [gxf_executor.cpp:1896] Waiting for completion...\n", - "[\u001b[32minfo\u001b[m] [gxf_executor.cpp:1897] Graph execution waiting. Fragment: \n", - "[\u001b[32minfo\u001b[m] [greedy_scheduler.cpp:190] Scheduling 3 entities\n", + "[\u001b[32minfo\u001b[m] [gxf_executor.cpp:247] Creating context\n", + "[\u001b[32minfo\u001b[m] [gxf_executor.cpp:1672] Loading extensions from configs...\n", + "[\u001b[32minfo\u001b[m] [gxf_executor.cpp:1842] Activating Graph...\n", + "[\u001b[32minfo\u001b[m] [gxf_executor.cpp:1874] Running Graph...\n", + "[\u001b[32minfo\u001b[m] [gxf_executor.cpp:1876] Waiting for completion...\n", + "\u001b[0m2024-04-23 17:09:01.847 INFO gxf/std/greedy_scheduler.cpp@191: Scheduling 3 entities\u001b[0m\n", "/home/mqin/src/monai-deploy-app-sdk/.venv/lib/python3.10/site-packages/monai/data/meta_tensor.py:116: UserWarning: The given NumPy array is not writable, and PyTorch does not support non-writable tensors. This means writing to this tensor will result in undefined behavior. You may want to copy the array to protect its data or make it writable before converting it to a tensor. This type of warning will be suppressed for the rest of this program. (Triggered internally at ../torch/csrc/utils/tensor_numpy.cpp:206.)\n", " return torch.as_tensor(x, *args, **_kwargs).as_subclass(cls)\n", "AbdomenCT\n", "/home/mqin/src/monai-deploy-app-sdk/.venv/lib/python3.10/site-packages/pydicom/valuerep.py:443: UserWarning: Invalid value for VR UI: 'xyz'. Please see for allowed values for each VR.\n", " warnings.warn(msg)\n", - "[\u001b[32minfo\u001b[m] [greedy_scheduler.cpp:369] Scheduler stopped: Some entities are waiting for execution, but there are no periodic or async entities to get out of the deadlock.\n", - "[\u001b[32minfo\u001b[m] [greedy_scheduler.cpp:398] Scheduler finished.\n", - "[\u001b[32minfo\u001b[m] [gxf_executor.cpp:1906] Graph execution deactivating. Fragment: \n", - "[\u001b[32minfo\u001b[m] [gxf_executor.cpp:1907] Deactivating Graph...\n", - "[\u001b[32minfo\u001b[m] [gxf_executor.cpp:1910] Graph execution finished. Fragment: \n", - "[\u001b[32minfo\u001b[m] [gxf_executor.cpp:230] Destroying context\n" + "\u001b[0m2024-04-23 17:09:03.971 INFO gxf/std/greedy_scheduler.cpp@372: Scheduler stopped: Some entities are waiting for execution, but there are no periodic or async entities to get out of the deadlock.\u001b[0m\n", + "\u001b[0m2024-04-23 17:09:03.971 INFO gxf/std/greedy_scheduler.cpp@401: Scheduler finished.\u001b[0m\n", + "[\u001b[32minfo\u001b[m] [gxf_executor.cpp:1879] Deactivating Graph...\n", + "[\u001b[32minfo\u001b[m] [gxf_executor.cpp:1887] Graph execution finished.\n", + "[\u001b[32minfo\u001b[m] [gxf_executor.cpp:275] Destroying context\n" ] } ], @@ -1241,14 +1249,16 @@ "name": "stdout", "output_type": "stream", "text": [ - "[2024-04-10 16:36:05,007] [INFO] (packager.parameters) - Application: /home/mqin/src/monai-deploy-app-sdk/notebooks/tutorials/mednist_app/mednist_classifier_monaideploy.py\n", - "[2024-04-10 16:36:05,007] [INFO] (packager.parameters) - Detected application type: Python File\n", - "[2024-04-10 16:36:05,007] [INFO] (packager) - Scanning for models in /home/mqin/src/monai-deploy-app-sdk/notebooks/tutorials/models...\n", - "[2024-04-10 16:36:05,007] [DEBUG] (packager) - Model model=/home/mqin/src/monai-deploy-app-sdk/notebooks/tutorials/models/model added.\n", - "[2024-04-10 16:36:05,007] [INFO] (packager) - Reading application configuration from /home/mqin/src/monai-deploy-app-sdk/notebooks/tutorials/mednist_app/app.yaml...\n", - "[2024-04-10 16:36:05,009] [INFO] (packager) - Generating app.json...\n", - "[2024-04-10 16:36:05,009] [INFO] (packager) - Generating pkg.json...\n", - "[2024-04-10 16:36:05,015] [DEBUG] (common) - \n", + "[2024-04-23 17:09:06,108] [INFO] (common) - Downloading CLI manifest file...\n", + "[2024-04-23 17:09:06,368] [DEBUG] (common) - Validating CLI manifest file...\n", + "[2024-04-23 17:09:06,371] [INFO] (packager.parameters) - Application: /home/mqin/src/monai-deploy-app-sdk/notebooks/tutorials/mednist_app/mednist_classifier_monaideploy.py\n", + "[2024-04-23 17:09:06,372] [INFO] (packager.parameters) - Detected application type: Python File\n", + "[2024-04-23 17:09:06,372] [INFO] (packager) - Scanning for models in /home/mqin/src/monai-deploy-app-sdk/notebooks/tutorials/models...\n", + "[2024-04-23 17:09:06,373] [DEBUG] (packager) - Model model=/home/mqin/src/monai-deploy-app-sdk/notebooks/tutorials/models/model added.\n", + "[2024-04-23 17:09:06,373] [INFO] (packager) - Reading application configuration from /home/mqin/src/monai-deploy-app-sdk/notebooks/tutorials/mednist_app/app.yaml...\n", + "[2024-04-23 17:09:06,378] [INFO] (packager) - Generating app.json...\n", + "[2024-04-23 17:09:06,379] [INFO] (packager) - Generating pkg.json...\n", + "[2024-04-23 17:09:06,393] [DEBUG] (common) - \n", "=============== Begin app.json ===============\n", "{\n", " \"apiVersion\": \"1.0.0\",\n", @@ -1283,7 +1293,7 @@ "}\n", "================ End app.json ================\n", " \n", - "[2024-04-10 16:36:05,015] [DEBUG] (common) - \n", + "[2024-04-23 17:09:06,393] [DEBUG] (common) - \n", "=============== Begin pkg.json ===============\n", "{\n", " \"apiVersion\": \"1.0.0\",\n", @@ -1303,11 +1313,11 @@ "}\n", "================ End pkg.json ================\n", " \n", - "[2024-04-10 16:36:05,050] [DEBUG] (packager.builder) - \n", + "[2024-04-23 17:09:06,435] [DEBUG] (packager.builder) - \n", "========== Begin Dockerfile ==========\n", "\n", "\n", - "FROM nvcr.io/nvidia/clara-holoscan/holoscan:v1.0.3-dgpu\n", + "FROM nvcr.io/nvidia/clara-holoscan/holoscan:v2.0.0-dgpu\n", "\n", "ENV DEBIAN_FRONTEND=noninteractive\n", "ENV TERM=xterm-256color\n", @@ -1323,11 +1333,11 @@ " && mkdir -p /var/holoscan/input \\\n", " && mkdir -p /var/holoscan/output\n", "\n", - "LABEL base=\"nvcr.io/nvidia/clara-holoscan/holoscan:v1.0.3-dgpu\"\n", + "LABEL base=\"nvcr.io/nvidia/clara-holoscan/holoscan:v2.0.0-dgpu\"\n", "LABEL tag=\"mednist_app:1.0\"\n", "LABEL org.opencontainers.image.title=\"MONAI Deploy App Package - MedNIST Classifier App\"\n", "LABEL org.opencontainers.image.version=\"1.0\"\n", - "LABEL org.nvidia.holoscan=\"1.0.3\"\n", + "LABEL org.nvidia.holoscan=\"2.0.0\"\n", "LABEL org.monai.deploy.app-sdk=\"0.5.1\"\n", "\n", "\n", @@ -1353,7 +1363,6 @@ "ENV PYTHONPATH=\"/opt/holoscan/app:$PYTHONPATH\"\n", "\n", "\n", - "\n", "RUN groupadd -f -g $GID $UNAME\n", "RUN useradd -rm -d /home/$UNAME -s /bin/bash -g $GID -G sudo -u $UID $UNAME\n", "RUN chown -R holoscan /var/holoscan \n", @@ -1379,14 +1388,12 @@ "RUN pip install --upgrade pip\n", "RUN pip install --no-cache-dir --user -r /tmp/requirements.txt\n", "\n", - "# Install Holoscan from PyPI only when sdk_type is Holoscan. \n", - "# For MONAI Deploy, the APP SDK will install it unless user specifies the Holoscan SDK file.\n", + " \n", + "# MONAI Deploy\n", "\n", "# Copy user-specified MONAI Deploy SDK file\n", - "COPY ./monai_deploy_app_sdk-0.5.1+25.g31e4165.dirty-py3-none-any.whl /tmp/monai_deploy_app_sdk-0.5.1+25.g31e4165.dirty-py3-none-any.whl\n", - "RUN pip install /tmp/monai_deploy_app_sdk-0.5.1+25.g31e4165.dirty-py3-none-any.whl\n", - "\n", - "\n", + "COPY ./monai_deploy_app_sdk-0.5.1+20.gb869749.dirty-py3-none-any.whl /tmp/monai_deploy_app_sdk-0.5.1+20.gb869749.dirty-py3-none-any.whl\n", + "RUN pip install /tmp/monai_deploy_app_sdk-0.5.1+20.gb869749.dirty-py3-none-any.whl\n", "\n", "\n", "COPY ./models /opt/holoscan/models\n", @@ -1400,275 +1407,294 @@ "ENTRYPOINT [\"/var/holoscan/tools\"]\n", "=========== End Dockerfile ===========\n", "\n", - "[2024-04-10 16:36:05,050] [INFO] (packager.builder) - \n", + "[2024-04-23 17:09:06,435] [INFO] (packager.builder) - \n", "===============================================================================\n", "Building image for: x64-workstation\n", " Architecture: linux/amd64\n", - " Base Image: nvcr.io/nvidia/clara-holoscan/holoscan:v1.0.3-dgpu\n", + " Base Image: nvcr.io/nvidia/clara-holoscan/holoscan:v2.0.0-dgpu\n", " Build Image: N/A\n", " Cache: Enabled\n", " Configuration: dgpu\n", " Holoscan SDK Package: pypi.org\n", - " MONAI Deploy App SDK Package: /home/mqin/src/monai-deploy-app-sdk/dist/monai_deploy_app_sdk-0.5.1+25.g31e4165.dirty-py3-none-any.whl\n", + " MONAI Deploy App SDK Package: /home/mqin/src/monai-deploy-app-sdk/dist/monai_deploy_app_sdk-0.5.1+20.gb869749.dirty-py3-none-any.whl\n", " gRPC Health Probe: N/A\n", - " SDK Version: 1.0.3\n", + " SDK Version: 2.0.0\n", " SDK: monai-deploy\n", " Tag: mednist_app-x64-workstation-dgpu-linux-amd64:1.0\n", " \n", - "[2024-04-10 16:36:05,416] [INFO] (common) - Using existing Docker BuildKit builder `holoscan_app_builder`\n", - "[2024-04-10 16:36:05,416] [DEBUG] (packager.builder) - Building Holoscan Application Package: tag=mednist_app-x64-workstation-dgpu-linux-amd64:1.0\n", + "[2024-04-23 17:09:06,753] [INFO] (common) - Using existing Docker BuildKit builder `holoscan_app_builder`\n", + "[2024-04-23 17:09:06,753] [DEBUG] (packager.builder) - Building Holoscan Application Package: tag=mednist_app-x64-workstation-dgpu-linux-amd64:1.0\n", "#0 building with \"holoscan_app_builder\" instance using docker-container driver\n", "\n", "#1 [internal] load build definition from Dockerfile\n", - "#1 transferring dockerfile: 2.81kB done\n", - "#1 DONE 0.1s\n", + "#1 transferring dockerfile: 2.67kB done\n", + "#1 DONE 0.0s\n", "\n", - "#2 [internal] load metadata for nvcr.io/nvidia/clara-holoscan/holoscan:v1.0.3-dgpu\n", - "#2 DONE 0.5s\n", + "#2 [internal] load metadata for nvcr.io/nvidia/clara-holoscan/holoscan:v2.0.0-dgpu\n", + "#2 DONE 0.4s\n", "\n", "#3 [internal] load .dockerignore\n", "#3 transferring context: 1.79kB done\n", - "#3 DONE 0.1s\n", + "#3 DONE 0.0s\n", "\n", - "#4 importing cache manifest from nvcr.io/nvidia/clara-holoscan/holoscan:v1.0.3-dgpu\n", - "#4 ...\n", + "#4 [internal] load build context\n", + "#4 DONE 0.0s\n", "\n", - "#5 [internal] load build context\n", + "#5 importing cache manifest from local:14814255791215325379\n", + "#5 inferred cache manifest type: application/vnd.oci.image.index.v1+json done\n", "#5 DONE 0.0s\n", "\n", - "#6 importing cache manifest from local:12491137658764693548\n", - "#6 inferred cache manifest type: application/vnd.oci.image.index.v1+json done\n", + "#6 [ 1/21] FROM nvcr.io/nvidia/clara-holoscan/holoscan:v2.0.0-dgpu@sha256:20adbccd2c7b12dfb1798f6953f071631c3b85cd337858a7506f8e420add6d4a\n", + "#6 resolve nvcr.io/nvidia/clara-holoscan/holoscan:v2.0.0-dgpu@sha256:20adbccd2c7b12dfb1798f6953f071631c3b85cd337858a7506f8e420add6d4a 0.0s done\n", "#6 DONE 0.0s\n", "\n", - "#7 [ 1/21] FROM nvcr.io/nvidia/clara-holoscan/holoscan:v1.0.3-dgpu@sha256:50343c616bf910e2a7651abb59db7833933e82cce64c3c4885f938d7e4af6155\n", - "#7 resolve nvcr.io/nvidia/clara-holoscan/holoscan:v1.0.3-dgpu@sha256:50343c616bf910e2a7651abb59db7833933e82cce64c3c4885f938d7e4af6155 0.0s done\n", - "#7 DONE 0.0s\n", - "\n", - "#4 importing cache manifest from nvcr.io/nvidia/clara-holoscan/holoscan:v1.0.3-dgpu\n", - "#4 inferred cache manifest type: application/vnd.docker.distribution.manifest.list.v2+json done\n", - "#4 DONE 0.5s\n", + "#7 importing cache manifest from nvcr.io/nvidia/clara-holoscan/holoscan:v2.0.0-dgpu\n", + "#7 inferred cache manifest type: application/vnd.docker.distribution.manifest.list.v2+json done\n", + "#7 DONE 0.6s\n", "\n", - "#5 [internal] load build context\n", - "#5 transferring context: 28.75MB 0.2s done\n", - "#5 DONE 0.2s\n", + "#4 [internal] load build context\n", + "#4 transferring context: 28.76MB 0.2s done\n", + "#4 DONE 0.2s\n", "\n", - "#8 [13/21] RUN pip install --upgrade pip\n", + "#8 [ 6/21] RUN chown -R holoscan /var/holoscan\n", "#8 CACHED\n", "\n", - "#9 [10/21] COPY ./tools /var/holoscan/tools\n", + "#9 [ 3/21] RUN apt-get update && apt-get install -y curl jq && rm -rf /var/lib/apt/lists/*\n", "#9 CACHED\n", "\n", - "#10 [ 9/21] WORKDIR /var/holoscan\n", + "#10 [ 5/21] RUN useradd -rm -d /home/holoscan -s /bin/bash -g 1000 -G sudo -u 1000 holoscan\n", "#10 CACHED\n", "\n", - "#11 [ 7/21] RUN chown -R holoscan /var/holoscan/input\n", + "#11 [10/21] COPY ./tools /var/holoscan/tools\n", "#11 CACHED\n", "\n", - "#12 [ 5/21] RUN useradd -rm -d /home/holoscan -s /bin/bash -g 1000 -G sudo -u 1000 holoscan\n", + "#12 [ 4/21] RUN groupadd -f -g 1000 holoscan\n", "#12 CACHED\n", "\n", - "#13 [ 8/21] RUN chown -R holoscan /var/holoscan/output\n", + "#13 [12/21] COPY ./pip/requirements.txt /tmp/requirements.txt\n", "#13 CACHED\n", "\n", - "#14 [ 3/21] RUN apt-get update && apt-get install -y curl jq && rm -rf /var/lib/apt/lists/*\n", + "#14 [ 7/21] RUN chown -R holoscan /var/holoscan/input\n", "#14 CACHED\n", "\n", - "#15 [12/21] COPY ./pip/requirements.txt /tmp/requirements.txt\n", + "#15 [ 8/21] RUN chown -R holoscan /var/holoscan/output\n", "#15 CACHED\n", "\n", - "#16 [11/21] RUN chmod +x /var/holoscan/tools\n", + "#16 [13/21] RUN pip install --upgrade pip\n", "#16 CACHED\n", "\n", - "#17 [ 2/21] RUN mkdir -p /etc/holoscan/ && mkdir -p /opt/holoscan/ && mkdir -p /var/holoscan && mkdir -p /opt/holoscan/app && mkdir -p /var/holoscan/input && mkdir -p /var/holoscan/output\n", + "#17 [ 9/21] WORKDIR /var/holoscan\n", "#17 CACHED\n", "\n", - "#18 [ 4/21] RUN groupadd -f -g 1000 holoscan\n", + "#18 [ 2/21] RUN mkdir -p /etc/holoscan/ && mkdir -p /opt/holoscan/ && mkdir -p /var/holoscan && mkdir -p /opt/holoscan/app && mkdir -p /var/holoscan/input && mkdir -p /var/holoscan/output\n", "#18 CACHED\n", "\n", - "#19 [ 6/21] RUN chown -R holoscan /var/holoscan\n", + "#19 [11/21] RUN chmod +x /var/holoscan/tools\n", "#19 CACHED\n", "\n", "#20 [14/21] RUN pip install --no-cache-dir --user -r /tmp/requirements.txt\n", "#20 CACHED\n", "\n", - "#21 [15/21] COPY ./monai_deploy_app_sdk-0.5.1+25.g31e4165.dirty-py3-none-any.whl /tmp/monai_deploy_app_sdk-0.5.1+25.g31e4165.dirty-py3-none-any.whl\n", - "#21 DONE 0.3s\n", - "\n", - "#22 [16/21] RUN pip install /tmp/monai_deploy_app_sdk-0.5.1+25.g31e4165.dirty-py3-none-any.whl\n", - "#22 0.701 Defaulting to user installation because normal site-packages is not writeable\n", - "#22 0.799 Processing /tmp/monai_deploy_app_sdk-0.5.1+25.g31e4165.dirty-py3-none-any.whl\n", - "#22 0.810 Requirement already satisfied: numpy>=1.21.6 in /usr/local/lib/python3.10/dist-packages (from monai-deploy-app-sdk==0.5.1+25.g31e4165.dirty) (1.23.5)\n", - "#22 0.996 Collecting holoscan~=1.0 (from monai-deploy-app-sdk==0.5.1+25.g31e4165.dirty)\n", - "#22 1.066 Downloading holoscan-1.0.3-cp310-cp310-manylinux_2_35_x86_64.whl.metadata (4.1 kB)\n", - "#22 1.137 Collecting colorama>=0.4.1 (from monai-deploy-app-sdk==0.5.1+25.g31e4165.dirty)\n", - "#22 1.141 Downloading colorama-0.4.6-py2.py3-none-any.whl.metadata (17 kB)\n", - "#22 1.222 Collecting typeguard>=3.0.0 (from monai-deploy-app-sdk==0.5.1+25.g31e4165.dirty)\n", - "#22 1.227 Downloading typeguard-4.2.1-py3-none-any.whl.metadata (3.7 kB)\n", - "#22 1.322 Collecting pip==23.3.2 (from holoscan~=1.0->monai-deploy-app-sdk==0.5.1+25.g31e4165.dirty)\n", - "#22 1.327 Downloading pip-23.3.2-py3-none-any.whl.metadata (3.5 kB)\n", - "#22 1.343 Requirement already satisfied: cupy-cuda12x==12.2 in /usr/local/lib/python3.10/dist-packages (from holoscan~=1.0->monai-deploy-app-sdk==0.5.1+25.g31e4165.dirty) (12.2.0)\n", - "#22 1.343 Requirement already satisfied: cloudpickle==2.2.1 in /usr/local/lib/python3.10/dist-packages (from holoscan~=1.0->monai-deploy-app-sdk==0.5.1+25.g31e4165.dirty) (2.2.1)\n", - "#22 1.344 Requirement already satisfied: python-on-whales==0.60.1 in /usr/local/lib/python3.10/dist-packages (from holoscan~=1.0->monai-deploy-app-sdk==0.5.1+25.g31e4165.dirty) (0.60.1)\n", - "#22 1.346 Requirement already satisfied: Jinja2==3.1.2 in /usr/local/lib/python3.10/dist-packages (from holoscan~=1.0->monai-deploy-app-sdk==0.5.1+25.g31e4165.dirty) (3.1.2)\n", - "#22 1.346 Requirement already satisfied: packaging==23.1 in /usr/local/lib/python3.10/dist-packages (from holoscan~=1.0->monai-deploy-app-sdk==0.5.1+25.g31e4165.dirty) (23.1)\n", - "#22 1.347 Requirement already satisfied: pyyaml==6.0 in /usr/local/lib/python3.10/dist-packages (from holoscan~=1.0->monai-deploy-app-sdk==0.5.1+25.g31e4165.dirty) (6.0)\n", - "#22 1.348 Requirement already satisfied: requests==2.28.2 in /usr/local/lib/python3.10/dist-packages (from holoscan~=1.0->monai-deploy-app-sdk==0.5.1+25.g31e4165.dirty) (2.28.2)\n", - "#22 1.350 Requirement already satisfied: psutil==5.9.6 in /usr/local/lib/python3.10/dist-packages (from holoscan~=1.0->monai-deploy-app-sdk==0.5.1+25.g31e4165.dirty) (5.9.6)\n", - "#22 1.461 Collecting wheel-axle-runtime<1.0 (from holoscan~=1.0->monai-deploy-app-sdk==0.5.1+25.g31e4165.dirty)\n", - "#22 1.467 Downloading wheel_axle_runtime-0.0.5-py3-none-any.whl.metadata (7.7 kB)\n", - "#22 1.504 Requirement already satisfied: fastrlock>=0.5 in /usr/local/lib/python3.10/dist-packages (from cupy-cuda12x==12.2->holoscan~=1.0->monai-deploy-app-sdk==0.5.1+25.g31e4165.dirty) (0.8.2)\n", - "#22 1.508 Requirement already satisfied: MarkupSafe>=2.0 in /usr/local/lib/python3.10/dist-packages (from Jinja2==3.1.2->holoscan~=1.0->monai-deploy-app-sdk==0.5.1+25.g31e4165.dirty) (2.1.3)\n", - "#22 1.523 Requirement already satisfied: pydantic<2,>=1.5 in /usr/local/lib/python3.10/dist-packages (from python-on-whales==0.60.1->holoscan~=1.0->monai-deploy-app-sdk==0.5.1+25.g31e4165.dirty) (1.10.14)\n", - "#22 1.524 Requirement already satisfied: tqdm in /usr/local/lib/python3.10/dist-packages (from python-on-whales==0.60.1->holoscan~=1.0->monai-deploy-app-sdk==0.5.1+25.g31e4165.dirty) (4.66.1)\n", - "#22 1.525 Requirement already satisfied: typer>=0.4.1 in /usr/local/lib/python3.10/dist-packages (from python-on-whales==0.60.1->holoscan~=1.0->monai-deploy-app-sdk==0.5.1+25.g31e4165.dirty) (0.9.0)\n", - "#22 1.526 Requirement already satisfied: typing-extensions in /home/holoscan/.local/lib/python3.10/site-packages (from python-on-whales==0.60.1->holoscan~=1.0->monai-deploy-app-sdk==0.5.1+25.g31e4165.dirty) (4.10.0)\n", - "#22 1.533 Requirement already satisfied: charset-normalizer<4,>=2 in /usr/local/lib/python3.10/dist-packages (from requests==2.28.2->holoscan~=1.0->monai-deploy-app-sdk==0.5.1+25.g31e4165.dirty) (3.3.2)\n", - "#22 1.534 Requirement already satisfied: idna<4,>=2.5 in /usr/local/lib/python3.10/dist-packages (from requests==2.28.2->holoscan~=1.0->monai-deploy-app-sdk==0.5.1+25.g31e4165.dirty) (3.6)\n", - "#22 1.535 Requirement already satisfied: urllib3<1.27,>=1.21.1 in /usr/local/lib/python3.10/dist-packages (from requests==2.28.2->holoscan~=1.0->monai-deploy-app-sdk==0.5.1+25.g31e4165.dirty) (1.26.18)\n", - "#22 1.536 Requirement already satisfied: certifi>=2017.4.17 in /usr/local/lib/python3.10/dist-packages (from requests==2.28.2->holoscan~=1.0->monai-deploy-app-sdk==0.5.1+25.g31e4165.dirty) (2023.11.17)\n", - "#22 1.551 Requirement already satisfied: filelock in /home/holoscan/.local/lib/python3.10/site-packages (from wheel-axle-runtime<1.0->holoscan~=1.0->monai-deploy-app-sdk==0.5.1+25.g31e4165.dirty) (3.13.3)\n", - "#22 1.587 Requirement already satisfied: click<9.0.0,>=7.1.1 in /usr/local/lib/python3.10/dist-packages (from typer>=0.4.1->python-on-whales==0.60.1->holoscan~=1.0->monai-deploy-app-sdk==0.5.1+25.g31e4165.dirty) (8.1.7)\n", - "#22 1.630 Downloading colorama-0.4.6-py2.py3-none-any.whl (25 kB)\n", - "#22 1.653 Downloading holoscan-1.0.3-cp310-cp310-manylinux_2_35_x86_64.whl (33.6 MB)\n", - "#22 2.391 ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 33.6/33.6 MB 36.3 MB/s eta 0:00:00\n", - "#22 2.399 Downloading pip-23.3.2-py3-none-any.whl (2.1 MB)\n", - "#22 2.452 ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 2.1/2.1 MB 45.3 MB/s eta 0:00:00\n", - "#22 2.459 Downloading typeguard-4.2.1-py3-none-any.whl (34 kB)\n", - "#22 2.484 Downloading wheel_axle_runtime-0.0.5-py3-none-any.whl (12 kB)\n", - "#22 2.841 Installing collected packages: wheel-axle-runtime, typeguard, pip, colorama, holoscan, monai-deploy-app-sdk\n", - "#22 2.915 Attempting uninstall: pip\n", - "#22 2.916 Found existing installation: pip 24.0\n", - "#22 2.967 Uninstalling pip-24.0:\n", - "#22 3.365 Successfully uninstalled pip-24.0\n", - "#22 5.013 Successfully installed colorama-0.4.6 holoscan-1.0.3 monai-deploy-app-sdk-0.5.1+25.g31e4165.dirty pip-23.3.2 typeguard-4.2.1 wheel-axle-runtime-0.0.5\n", - "#22 DONE 5.6s\n", + "#21 [15/21] COPY ./monai_deploy_app_sdk-0.5.1+20.gb869749.dirty-py3-none-any.whl /tmp/monai_deploy_app_sdk-0.5.1+20.gb869749.dirty-py3-none-any.whl\n", + "#21 DONE 0.2s\n", + "\n", + "#22 [16/21] RUN pip install /tmp/monai_deploy_app_sdk-0.5.1+20.gb869749.dirty-py3-none-any.whl\n", + "#22 0.646 Defaulting to user installation because normal site-packages is not writeable\n", + "#22 0.740 Processing /tmp/monai_deploy_app_sdk-0.5.1+20.gb869749.dirty-py3-none-any.whl\n", + "#22 0.751 Requirement already satisfied: numpy>=1.21.6 in /usr/local/lib/python3.10/dist-packages (from monai-deploy-app-sdk==0.5.1+20.gb869749.dirty) (1.23.5)\n", + "#22 0.850 Collecting holoscan~=2.0 (from monai-deploy-app-sdk==0.5.1+20.gb869749.dirty)\n", + "#22 0.921 Downloading holoscan-2.0.0-cp310-cp310-manylinux_2_35_x86_64.whl.metadata (6.7 kB)\n", + "#22 0.978 Collecting colorama>=0.4.1 (from monai-deploy-app-sdk==0.5.1+20.gb869749.dirty)\n", + "#22 0.982 Downloading colorama-0.4.6-py2.py3-none-any.whl.metadata (17 kB)\n", + "#22 1.026 Collecting typeguard>=3.0.0 (from monai-deploy-app-sdk==0.5.1+20.gb869749.dirty)\n", + "#22 1.030 Downloading typeguard-4.2.1-py3-none-any.whl.metadata (3.7 kB)\n", + "#22 1.044 Requirement already satisfied: pip>=20.3 in /home/holoscan/.local/lib/python3.10/site-packages (from holoscan~=2.0->monai-deploy-app-sdk==0.5.1+20.gb869749.dirty) (24.0)\n", + "#22 1.045 Requirement already satisfied: cupy-cuda12x==12.2 in /usr/local/lib/python3.10/dist-packages (from holoscan~=2.0->monai-deploy-app-sdk==0.5.1+20.gb869749.dirty) (12.2.0)\n", + "#22 1.045 Requirement already satisfied: cloudpickle==2.2.1 in /usr/local/lib/python3.10/dist-packages (from holoscan~=2.0->monai-deploy-app-sdk==0.5.1+20.gb869749.dirty) (2.2.1)\n", + "#22 1.046 Requirement already satisfied: python-on-whales==0.60.1 in /usr/local/lib/python3.10/dist-packages (from holoscan~=2.0->monai-deploy-app-sdk==0.5.1+20.gb869749.dirty) (0.60.1)\n", + "#22 1.047 Requirement already satisfied: Jinja2==3.1.3 in /usr/local/lib/python3.10/dist-packages (from holoscan~=2.0->monai-deploy-app-sdk==0.5.1+20.gb869749.dirty) (3.1.3)\n", + "#22 1.048 Requirement already satisfied: packaging==23.1 in /usr/local/lib/python3.10/dist-packages (from holoscan~=2.0->monai-deploy-app-sdk==0.5.1+20.gb869749.dirty) (23.1)\n", + "#22 1.048 Requirement already satisfied: pyyaml==6.0 in /usr/local/lib/python3.10/dist-packages (from holoscan~=2.0->monai-deploy-app-sdk==0.5.1+20.gb869749.dirty) (6.0)\n", + "#22 1.049 Requirement already satisfied: requests==2.31.0 in /usr/local/lib/python3.10/dist-packages (from holoscan~=2.0->monai-deploy-app-sdk==0.5.1+20.gb869749.dirty) (2.31.0)\n", + "#22 1.050 Requirement already satisfied: psutil==5.9.6 in /usr/local/lib/python3.10/dist-packages (from holoscan~=2.0->monai-deploy-app-sdk==0.5.1+20.gb869749.dirty) (5.9.6)\n", + "#22 1.070 Collecting wheel-axle-runtime<1.0 (from holoscan~=2.0->monai-deploy-app-sdk==0.5.1+20.gb869749.dirty)\n", + "#22 1.075 Downloading wheel_axle_runtime-0.0.5-py3-none-any.whl.metadata (7.7 kB)\n", + "#22 1.107 Requirement already satisfied: fastrlock>=0.5 in /usr/local/lib/python3.10/dist-packages (from cupy-cuda12x==12.2->holoscan~=2.0->monai-deploy-app-sdk==0.5.1+20.gb869749.dirty) (0.8.2)\n", + "#22 1.112 Requirement already satisfied: MarkupSafe>=2.0 in /usr/local/lib/python3.10/dist-packages (from Jinja2==3.1.3->holoscan~=2.0->monai-deploy-app-sdk==0.5.1+20.gb869749.dirty) (2.1.3)\n", + "#22 1.126 Requirement already satisfied: pydantic<2,>=1.5 in /usr/local/lib/python3.10/dist-packages (from python-on-whales==0.60.1->holoscan~=2.0->monai-deploy-app-sdk==0.5.1+20.gb869749.dirty) (1.10.15)\n", + "#22 1.126 Requirement already satisfied: tqdm in /usr/local/lib/python3.10/dist-packages (from python-on-whales==0.60.1->holoscan~=2.0->monai-deploy-app-sdk==0.5.1+20.gb869749.dirty) (4.66.2)\n", + "#22 1.127 Requirement already satisfied: typer>=0.4.1 in /usr/local/lib/python3.10/dist-packages (from python-on-whales==0.60.1->holoscan~=2.0->monai-deploy-app-sdk==0.5.1+20.gb869749.dirty) (0.12.3)\n", + "#22 1.128 Requirement already satisfied: typing-extensions in /home/holoscan/.local/lib/python3.10/site-packages (from python-on-whales==0.60.1->holoscan~=2.0->monai-deploy-app-sdk==0.5.1+20.gb869749.dirty) (4.11.0)\n", + "#22 1.135 Requirement already satisfied: charset-normalizer<4,>=2 in /usr/local/lib/python3.10/dist-packages (from requests==2.31.0->holoscan~=2.0->monai-deploy-app-sdk==0.5.1+20.gb869749.dirty) (3.3.2)\n", + "#22 1.136 Requirement already satisfied: idna<4,>=2.5 in /usr/local/lib/python3.10/dist-packages (from requests==2.31.0->holoscan~=2.0->monai-deploy-app-sdk==0.5.1+20.gb869749.dirty) (3.7)\n", + "#22 1.137 Requirement already satisfied: urllib3<3,>=1.21.1 in /usr/local/lib/python3.10/dist-packages (from requests==2.31.0->holoscan~=2.0->monai-deploy-app-sdk==0.5.1+20.gb869749.dirty) (2.2.1)\n", + "#22 1.137 Requirement already satisfied: certifi>=2017.4.17 in /usr/local/lib/python3.10/dist-packages (from requests==2.31.0->holoscan~=2.0->monai-deploy-app-sdk==0.5.1+20.gb869749.dirty) (2024.2.2)\n", + "#22 1.155 Requirement already satisfied: filelock in /home/holoscan/.local/lib/python3.10/site-packages (from wheel-axle-runtime<1.0->holoscan~=2.0->monai-deploy-app-sdk==0.5.1+20.gb869749.dirty) (3.13.4)\n", + "#22 1.176 Requirement already satisfied: click>=8.0.0 in /usr/local/lib/python3.10/dist-packages (from typer>=0.4.1->python-on-whales==0.60.1->holoscan~=2.0->monai-deploy-app-sdk==0.5.1+20.gb869749.dirty) (8.1.7)\n", + "#22 1.177 Requirement already satisfied: shellingham>=1.3.0 in /usr/local/lib/python3.10/dist-packages (from typer>=0.4.1->python-on-whales==0.60.1->holoscan~=2.0->monai-deploy-app-sdk==0.5.1+20.gb869749.dirty) (1.5.4)\n", + "#22 1.178 Requirement already satisfied: rich>=10.11.0 in /usr/local/lib/python3.10/dist-packages (from typer>=0.4.1->python-on-whales==0.60.1->holoscan~=2.0->monai-deploy-app-sdk==0.5.1+20.gb869749.dirty) (13.7.1)\n", + "#22 1.212 Requirement already satisfied: markdown-it-py>=2.2.0 in /usr/local/lib/python3.10/dist-packages (from rich>=10.11.0->typer>=0.4.1->python-on-whales==0.60.1->holoscan~=2.0->monai-deploy-app-sdk==0.5.1+20.gb869749.dirty) (3.0.0)\n", + "#22 1.213 Requirement already satisfied: pygments<3.0.0,>=2.13.0 in /usr/local/lib/python3.10/dist-packages (from rich>=10.11.0->typer>=0.4.1->python-on-whales==0.60.1->holoscan~=2.0->monai-deploy-app-sdk==0.5.1+20.gb869749.dirty) (2.17.2)\n", + "#22 1.233 Requirement already satisfied: mdurl~=0.1 in /usr/local/lib/python3.10/dist-packages (from markdown-it-py>=2.2.0->rich>=10.11.0->typer>=0.4.1->python-on-whales==0.60.1->holoscan~=2.0->monai-deploy-app-sdk==0.5.1+20.gb869749.dirty) (0.1.2)\n", + "#22 1.245 Downloading colorama-0.4.6-py2.py3-none-any.whl (25 kB)\n", + "#22 1.260 Downloading holoscan-2.0.0-cp310-cp310-manylinux_2_35_x86_64.whl (33.2 MB)\n", + "#22 1.691 ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 33.2/33.2 MB 46.8 MB/s eta 0:00:00\n", + "#22 1.696 Downloading typeguard-4.2.1-py3-none-any.whl (34 kB)\n", + "#22 1.709 Downloading wheel_axle_runtime-0.0.5-py3-none-any.whl (12 kB)\n", + "#22 2.033 Installing collected packages: wheel-axle-runtime, typeguard, colorama, holoscan, monai-deploy-app-sdk\n", + "#22 2.711 Successfully installed colorama-0.4.6 holoscan-2.0.0 monai-deploy-app-sdk-0.5.1+20.gb869749.dirty typeguard-4.2.1 wheel-axle-runtime-0.0.5\n", + "#22 DONE 3.0s\n", "\n", "#23 [17/21] COPY ./models /opt/holoscan/models\n", - "#23 DONE 0.3s\n", + "#23 DONE 0.2s\n", "\n", "#24 [18/21] COPY ./map/app.json /etc/holoscan/app.json\n", - "#24 DONE 0.1s\n", + "#24 DONE 0.0s\n", "\n", "#25 [19/21] COPY ./app.config /var/holoscan/app.yaml\n", - "#25 DONE 0.1s\n", + "#25 DONE 0.0s\n", "\n", "#26 [20/21] COPY ./map/pkg.json /etc/holoscan/pkg.json\n", "#26 DONE 0.1s\n", "\n", "#27 [21/21] COPY ./app /opt/holoscan/app\n", - "#27 DONE 0.1s\n", + "#27 DONE 0.0s\n", "\n", "#28 exporting to docker image format\n", "#28 exporting layers\n", - "#28 exporting layers 5.9s done\n", - "#28 exporting manifest sha256:261bfd883479734974f9f01500b63a394537a84df186d0552794645b0152f0f5 0.0s done\n", - "#28 exporting config sha256:47a95542f89e8e3174bba11729dc605a923542cf7c48c180ae2eb42290619826 0.0s done\n", + "#28 exporting layers 4.4s done\n", + "#28 exporting manifest sha256:457dd7263681b35a427e304797922e6c9c1a453deadebb6e234e5d3f63947b18 0.0s done\n", + "#28 exporting config sha256:63c2bd27a2230b0ee99597a2475f434ae68969da3a8328b78d7d5bc277409172 0.0s done\n", "#28 sending tarball\n", "#28 ...\n", "\n", "#29 importing to docker\n", - "#29 loading layer 2c6ff491304f 32.77kB / 125.57kB\n", - "#29 loading layer 04072fb0fc22 557.06kB / 73.96MB\n", - "#29 loading layer 04072fb0fc22 71.86MB / 73.96MB 2.1s\n", - "#29 loading layer 1982c4813c35 262.14kB / 26.20MB\n", - "#29 loading layer dc0acf48e445 513B / 513B\n", - "#29 loading layer a50eb25f7721 320B / 320B\n", - "#29 loading layer 838ef774fdf1 298B / 298B\n", - "#29 loading layer 3401c98a4ff8 4.00kB / 4.00kB\n", - "#29 loading layer 838ef774fdf1 298B / 298B 0.8s done\n", - "#29 loading layer 2c6ff491304f 32.77kB / 125.57kB 4.0s done\n", - "#29 loading layer 04072fb0fc22 71.86MB / 73.96MB 3.8s done\n", - "#29 loading layer 1982c4813c35 262.14kB / 26.20MB 1.3s done\n", 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f50931954a7a 1.98GB / 2.90GB 50.1s\n", + "#29 loading layer f50931954a7a 2.10GB / 2.90GB 56.4s\n", + "#29 loading layer f50931954a7a 2.30GB / 2.90GB 62.4s\n", + "#29 loading layer f50931954a7a 2.47GB / 2.90GB 66.5s\n", + "#29 loading layer f50931954a7a 2.67GB / 2.90GB 70.6s\n", + "#29 loading layer f50931954a7a 2.84GB / 2.90GB 76.8s\n", + "#29 loading layer 6e852bd260ad 32.77kB / 125.82kB\n", + "#29 loading layer d8a5c55be301 557.06kB / 67.35MB\n", + "#29 loading layer 82e6702b8274 262.14kB / 26.20MB\n", + "#29 loading layer d1b690ac41a7 513B / 513B\n", + "#29 loading layer a85ba680dedd 318B / 318B\n", + "#29 loading layer 7e4618ac3cb0 297B / 297B\n", + "#29 loading layer 43922422e132 4.00kB / 4.00kB\n", + "#29 loading layer 5828d73ee0ce 65.54kB / 5.86MB 82.3s done\n", + "#29 loading layer 36f9dbeb2e4f 238B / 238B 82.4s done\n", + "#29 loading layer f50931954a7a 2.84GB / 2.90GB 81.6s done\n", + "#29 loading layer 6e852bd260ad 32.77kB / 125.82kB 3.0s done\n", + "#29 loading layer d8a5c55be301 557.06kB / 67.35MB 2.9s done\n", + "#29 loading layer 82e6702b8274 262.14kB / 26.20MB 1.1s done\n", + "#29 loading layer d1b690ac41a7 513B / 513B 0.7s done\n", + "#29 loading layer a85ba680dedd 318B / 318B 0.6s done\n", + "#29 loading layer 7e4618ac3cb0 297B / 297B 0.5s done\n", + "#29 loading layer 43922422e132 4.00kB / 4.00kB 0.5s done\n", + "#29 DONE 82.4s\n", "\n", "#28 exporting to docker image format\n", - "#28 sending tarball 68.3s done\n", - "#28 DONE 74.3s\n", + "#28 sending tarball 147.4s done\n", + "#28 DONE 151.9s\n", "\n", "#30 exporting cache to client directory\n", "#30 preparing build cache for export\n", - "#30 writing layer sha256:00bb4c1319ba1a33ac3edcb3aa1240d8abcb8d0383c6267ed8028d3b6228a8a4\n", - "#30 writing layer sha256:00bb4c1319ba1a33ac3edcb3aa1240d8abcb8d0383c6267ed8028d3b6228a8a4 done\n", + "#30 writing layer sha256:0023eecf78ab7134b1dd4aba34e20134fe1a5e0827f3a2a65dead15239c056dd\n", + "#30 writing layer 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minutes ago 17.7GB\n" ] } ], @@ -1730,22 +1756,22 @@ "name": "stdout", "output_type": "stream", "text": [ - "[2024-04-10 16:37:33,094] [INFO] (runner) - Checking dependencies...\n", - "[2024-04-10 16:37:33,094] [INFO] (runner) - --> Verifying if \"docker\" is installed...\n", + "[2024-04-23 17:11:48,890] [INFO] (runner) - Checking dependencies...\n", + "[2024-04-23 17:11:48,890] [INFO] (runner) - --> Verifying if \"docker\" is installed...\n", "\n", - "[2024-04-10 16:37:33,094] [INFO] (runner) - --> Verifying if \"docker-buildx\" is installed...\n", + "[2024-04-23 17:11:48,891] [INFO] (runner) - --> Verifying if \"docker-buildx\" is installed...\n", "\n", - "[2024-04-10 16:37:33,094] [INFO] (runner) - --> Verifying if \"mednist_app-x64-workstation-dgpu-linux-amd64:1.0\" is available...\n", + "[2024-04-23 17:11:48,891] [INFO] (runner) - --> Verifying if \"mednist_app-x64-workstation-dgpu-linux-amd64:1.0\" is available...\n", "\n", - "[2024-04-10 16:37:33,168] [INFO] (runner) - Reading HAP/MAP manifest...\n", - "\u001b[sPreparing to copy...\u001b[?25l\u001b[u\u001b[2KCopying from container - 0B\u001b[?25h\u001b[u\u001b[2KSuccessfully copied 2.56kB to /tmp/tmp96catisy/app.json\n", - "\u001b[sPreparing to copy...\u001b[?25l\u001b[u\u001b[2KCopying from container - 0B\u001b[?25h\u001b[u\u001b[2KSuccessfully copied 2.05kB to /tmp/tmp96catisy/pkg.json\n", - "[2024-04-10 16:37:33,777] [INFO] (runner) - --> Verifying if \"nvidia-ctk\" is installed...\n", + "[2024-04-23 17:11:48,968] [INFO] (runner) - Reading HAP/MAP manifest...\n", + "\u001b[sPreparing to copy...\u001b[?25l\u001b[u\u001b[2KCopying from container - 0B\u001b[?25h\u001b[u\u001b[2KSuccessfully copied 2.56kB to /tmp/tmpgkozmakd/app.json\n", + "\u001b[sPreparing to copy...\u001b[?25l\u001b[u\u001b[2KCopying from container - 0B\u001b[?25h\u001b[u\u001b[2KSuccessfully copied 2.05kB to /tmp/tmpgkozmakd/pkg.json\n", + "[2024-04-23 17:11:51,690] [INFO] (runner) - --> Verifying if \"nvidia-ctk\" is installed...\n", "\n", - "[2024-04-10 16:37:33,778] [INFO] (runner) - --> Verifying \"nvidia-ctk\" version...\n", + "[2024-04-23 17:11:51,690] [INFO] (runner) - --> Verifying \"nvidia-ctk\" version...\n", "\n", - "[2024-04-10 16:37:33,934] [INFO] (common) - Launching container (4b3bba81606f) using image 'mednist_app-x64-workstation-dgpu-linux-amd64:1.0'...\n", - " container name: flamboyant_jepsen\n", + "[2024-04-23 17:11:52,019] [INFO] (common) - Launching container (29c362c90847) using image 'mednist_app-x64-workstation-dgpu-linux-amd64:1.0'...\n", + " container name: competent_aryabhata\n", " host name: mingq-dt\n", " network: host\n", " user: 1000:1000\n", @@ -1755,25 +1781,23 @@ " shared memory size: 67108864\n", " devices: \n", " group_add: 44\n", - "2024-04-10 23:37:34 [INFO] Launching application python3 /opt/holoscan/app/mednist_classifier_monaideploy.py ...\n", + "2024-04-24 00:11:52 [INFO] Launching application python3 /opt/holoscan/app/mednist_classifier_monaideploy.py ...\n", "\n", "[info] [app_driver.cpp:1161] Launching the driver/health checking service\n", "\n", - "[info] [gxf_executor.cpp:211] Creating context\n", + "[info] [gxf_executor.cpp:247] Creating context\n", "\n", "[info] [server.cpp:87] Health checking server listening on 0.0.0.0:8777\n", "\n", - "[info] [gxf_executor.cpp:1674] Loading extensions from configs...\n", + "[info] [gxf_executor.cpp:1672] Loading extensions from configs...\n", "\n", - "[info] [gxf_executor.cpp:1864] Activating Graph...\n", + "[info] [gxf_executor.cpp:1842] Activating Graph...\n", "\n", - "[info] [gxf_executor.cpp:1894] Running Graph...\n", + "[info] [gxf_executor.cpp:1874] Running Graph...\n", "\n", - "[info] [gxf_executor.cpp:1896] Waiting for completion...\n", + "[info] [gxf_executor.cpp:1876] Waiting for completion...\n", "\n", - "[info] [gxf_executor.cpp:1897] Graph execution waiting. Fragment: \n", - "\n", - "[info] [greedy_scheduler.cpp:190] Scheduling 3 entities\n", + "\u001b[0m2024-04-24 00:11:55.786 INFO gxf/std/greedy_scheduler.cpp@191: Scheduling 3 entities\u001b[0m\n", "\n", "/home/holoscan/.local/lib/python3.10/site-packages/monai/data/meta_tensor.py:116: UserWarning: The given NumPy array is not writable, and PyTorch does not support non-writable tensors. This means writing to this tensor will result in undefined behavior. You may want to copy the array to protect its data or make it writable before converting it to a tensor. This type of warning will be suppressed for the rest of this program. (Triggered internally at ../torch/csrc/utils/tensor_numpy.cpp:206.)\n", "\n", @@ -1783,21 +1807,19 @@ "\n", " warnings.warn(msg)\n", "\n", - "[info] [greedy_scheduler.cpp:369] Scheduler stopped: Some entities are waiting for execution, but there are no periodic or async entities to get out of the deadlock.\n", - "\n", - "[info] [greedy_scheduler.cpp:398] Scheduler finished.\n", + "\u001b[0m2024-04-24 00:11:57.183 INFO gxf/std/greedy_scheduler.cpp@372: Scheduler stopped: Some entities are waiting for execution, but there are no periodic or async entities to get out of the deadlock.\u001b[0m\n", "\n", - "[info] [gxf_executor.cpp:1906] Graph execution deactivating. Fragment: \n", + "\u001b[0m2024-04-24 00:11:57.184 INFO gxf/std/greedy_scheduler.cpp@401: Scheduler finished.\u001b[0m\n", "\n", - "[info] [gxf_executor.cpp:1907] Deactivating Graph...\n", + "[info] [gxf_executor.cpp:1879] Deactivating Graph...\n", "\n", - "[info] [gxf_executor.cpp:1910] Graph execution finished. Fragment: \n", + "[info] [gxf_executor.cpp:1887] Graph execution finished.\n", "\n", - "[info] [gxf_executor.cpp:230] Destroying context\n", + "[info] [gxf_executor.cpp:275] Destroying context\n", "\n", "AbdomenCT\n", "\n", - "[2024-04-10 16:37:42,228] [INFO] (common) - Container 'flamboyant_jepsen'(4b3bba81606f) exited.\n" + "[2024-04-23 17:11:58,233] [INFO] (common) - Container 'competent_aryabhata'(29c362c90847) exited.\n" ] } ], diff --git a/notebooks/tutorials/03_segmentation_app.ipynb b/notebooks/tutorials/03_segmentation_app.ipynb index 946e2420..13c8e7ff 100644 --- a/notebooks/tutorials/03_segmentation_app.ipynb +++ b/notebooks/tutorials/03_segmentation_app.ipynb @@ -134,23 +134,20 @@ "text": [ "Requirement already satisfied: gdown in /home/mqin/src/monai-deploy-app-sdk/.venv/lib/python3.10/site-packages (5.1.0)\n", "Requirement already satisfied: beautifulsoup4 in /home/mqin/src/monai-deploy-app-sdk/.venv/lib/python3.10/site-packages (from gdown) (4.12.3)\n", - "Requirement already satisfied: filelock in /home/mqin/src/monai-deploy-app-sdk/.venv/lib/python3.10/site-packages (from gdown) (3.13.3)\n", - "Requirement already satisfied: requests[socks] in /home/mqin/src/monai-deploy-app-sdk/.venv/lib/python3.10/site-packages (from gdown) (2.28.2)\n", + "Requirement already satisfied: filelock in /home/mqin/src/monai-deploy-app-sdk/.venv/lib/python3.10/site-packages (from gdown) (3.13.4)\n", + "Requirement already satisfied: requests[socks] in /home/mqin/src/monai-deploy-app-sdk/.venv/lib/python3.10/site-packages (from gdown) (2.31.0)\n", "Requirement already satisfied: tqdm in /home/mqin/src/monai-deploy-app-sdk/.venv/lib/python3.10/site-packages (from gdown) (4.66.2)\n", "Requirement already satisfied: soupsieve>1.2 in /home/mqin/src/monai-deploy-app-sdk/.venv/lib/python3.10/site-packages (from beautifulsoup4->gdown) (2.5)\n", "Requirement already satisfied: charset-normalizer<4,>=2 in /home/mqin/src/monai-deploy-app-sdk/.venv/lib/python3.10/site-packages (from requests[socks]->gdown) (3.3.2)\n", - "Requirement already satisfied: idna<4,>=2.5 in /home/mqin/src/monai-deploy-app-sdk/.venv/lib/python3.10/site-packages (from requests[socks]->gdown) (3.6)\n", - "Requirement already satisfied: urllib3<1.27,>=1.21.1 in /home/mqin/src/monai-deploy-app-sdk/.venv/lib/python3.10/site-packages (from requests[socks]->gdown) (1.26.18)\n", + "Requirement already satisfied: idna<4,>=2.5 in /home/mqin/src/monai-deploy-app-sdk/.venv/lib/python3.10/site-packages (from requests[socks]->gdown) (3.7)\n", + "Requirement already satisfied: urllib3<3,>=1.21.1 in /home/mqin/src/monai-deploy-app-sdk/.venv/lib/python3.10/site-packages (from requests[socks]->gdown) (2.2.1)\n", "Requirement already satisfied: certifi>=2017.4.17 in /home/mqin/src/monai-deploy-app-sdk/.venv/lib/python3.10/site-packages (from requests[socks]->gdown) (2024.2.2)\n", "Requirement already satisfied: PySocks!=1.5.7,>=1.5.6 in /home/mqin/src/monai-deploy-app-sdk/.venv/lib/python3.10/site-packages (from requests[socks]->gdown) (1.7.1)\n", - "\n", - "\u001b[1m[\u001b[0m\u001b[34;49mnotice\u001b[0m\u001b[1;39;49m]\u001b[0m\u001b[39;49m A new release of pip is available: \u001b[0m\u001b[31;49m23.3.2\u001b[0m\u001b[39;49m -> \u001b[0m\u001b[32;49m24.0\u001b[0m\n", - "\u001b[1m[\u001b[0m\u001b[34;49mnotice\u001b[0m\u001b[1;39;49m]\u001b[0m\u001b[39;49m To update, run: \u001b[0m\u001b[32;49mpip install --upgrade pip\u001b[0m\n", "Downloading...\n", "From (original): https://drive.google.com/uc?id=1Uds8mEvdGNYUuvFpTtCQ8gNU97bAPCaQ\n", - "From (redirected): https://drive.google.com/uc?id=1Uds8mEvdGNYUuvFpTtCQ8gNU97bAPCaQ&confirm=t&uuid=03efbee4-6b67-4413-8b8e-522d9c7cc472\n", + "From (redirected): https://drive.google.com/uc?id=1Uds8mEvdGNYUuvFpTtCQ8gNU97bAPCaQ&confirm=t&uuid=cec9025c-9d57-4269-b01f-503cd7daf812\n", "To: /home/mqin/src/monai-deploy-app-sdk/notebooks/tutorials/ai_spleen_seg_bundle_data.zip\n", - "100%|███████████████████████████████████████| 79.4M/79.4M [00:00<00:00, 101MB/s]\n", + "100%|███████████████████████████████████████| 79.4M/79.4M [00:00<00:00, 105MB/s]\n", "Archive: ai_spleen_seg_bundle_data.zip\n", " inflating: dcm/1-001.dcm \n", " inflating: dcm/1-002.dcm \n", @@ -747,95 +744,111 @@ "name": "stderr", "output_type": "stream", "text": [ - "[2024-04-10 16:41:09,106] [INFO] (root) - Parsed args: Namespace(log_level=None, input=None, output=None, model=None, workdir=None, argv=[])\n", - "[2024-04-10 16:41:09,114] [INFO] (root) - AppContext object: AppContext(input_path=dcm, output_path=output, model_path=models, workdir=)\n", - "[2024-04-10 16:41:09,116] [INFO] (__main__.AISpleenSegApp) - App input and output path: dcm, output\n", - "[info] [gxf_executor.cpp:211] Creating context\n", - "[info] [gxf_executor.cpp:1674] Loading extensions from configs...\n", - "[info] [gxf_executor.cpp:1864] Activating Graph...\n", - "[info] [gxf_executor.cpp:1894] Running Graph...\n", - "[info] [gxf_executor.cpp:1896] Waiting for completion...\n", - "[info] [gxf_executor.cpp:1897] Graph execution waiting. Fragment: \n", - "[info] [greedy_scheduler.cpp:190] Scheduling 6 entities\n", - "[2024-04-10 16:41:09,164] [INFO] (monai.deploy.operators.dicom_data_loader_operator.DICOMDataLoaderOperator) - No or invalid input path from the optional input port: None\n", - "[2024-04-10 16:41:09,742] [INFO] (root) - Finding series for Selection named: CT Series\n", - "[2024-04-10 16:41:09,743] [INFO] (root) - Searching study, : 1.3.6.1.4.1.14519.5.2.1.7085.2626.822645453932810382886582736291\n", + "[2024-04-23 15:42:43,990] [INFO] (root) - Parsed args: Namespace(log_level=None, input=None, output=None, model=None, workdir=None, argv=[])\n", + "[2024-04-23 15:42:43,998] [INFO] (root) - AppContext object: AppContext(input_path=dcm, output_path=output, model_path=models, workdir=)\n", + "[2024-04-23 15:42:44,000] [INFO] (__main__.AISpleenSegApp) - App input and output path: dcm, output\n", + "[info] [gxf_executor.cpp:247] Creating context\n", + "[info] [gxf_executor.cpp:1672] Loading extensions from configs...\n", + "[info] [gxf_executor.cpp:1842] Activating Graph...\n", + "[info] [gxf_executor.cpp:1874] Running Graph...\n", + "[info] [gxf_executor.cpp:1876] Waiting for completion...\n", + "[2024-04-23 15:42:44,046] [INFO] (monai.deploy.operators.dicom_data_loader_operator.DICOMDataLoaderOperator) - No or invalid input path from the optional input port: None\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "\u001b[0m2024-04-23 15:42:44.043 INFO gxf/std/greedy_scheduler.cpp@191: Scheduling 6 entities\u001b[0m\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "[2024-04-23 15:42:44,615] [INFO] (root) - Finding series for Selection named: CT Series\n", + "[2024-04-23 15:42:44,616] [INFO] (root) - Searching study, : 1.3.6.1.4.1.14519.5.2.1.7085.2626.822645453932810382886582736291\n", " # of series: 1\n", - "[2024-04-10 16:41:09,744] [INFO] (root) - Working on series, instance UID: 1.3.6.1.4.1.14519.5.2.1.7085.2626.119403521930927333027265674239\n", - "[2024-04-10 16:41:09,745] [INFO] (root) - On attribute: 'StudyDescription' to match value: '(.*?)'\n", - "[2024-04-10 16:41:09,746] [INFO] (root) - Series attribute StudyDescription value: CT ABDOMEN W IV CONTRAST\n", - "[2024-04-10 16:41:09,747] [INFO] (root) - Series attribute string value did not match. Try regEx.\n", - "[2024-04-10 16:41:09,748] [INFO] (root) - On attribute: 'Modality' to match value: '(?i)CT'\n", - "[2024-04-10 16:41:09,749] [INFO] (root) - Series attribute Modality value: CT\n", - "[2024-04-10 16:41:09,750] [INFO] (root) - Series attribute string value did not match. Try regEx.\n", - "[2024-04-10 16:41:09,751] [INFO] (root) - On attribute: 'SeriesDescription' to match value: '(.*?)'\n", - "[2024-04-10 16:41:09,753] [INFO] (root) - Series attribute SeriesDescription value: ABD/PANC 3.0 B31f\n", - "[2024-04-10 16:41:09,754] [INFO] (root) - Series attribute string value did not match. Try regEx.\n", - "[2024-04-10 16:41:09,755] [INFO] (root) - On attribute: 'ImageType' to match value: ['PRIMARY', 'ORIGINAL']\n", - "[2024-04-10 16:41:09,756] [INFO] (root) - Series attribute ImageType value: None\n", - "[2024-04-10 16:41:09,757] [INFO] (root) - Selected Series, UID: 1.3.6.1.4.1.14519.5.2.1.7085.2626.119403521930927333027265674239\n", - "[2024-04-10 16:41:10,007] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - Converted Image object metadata:\n", - "[2024-04-10 16:41:10,009] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - SeriesInstanceUID: 1.3.6.1.4.1.14519.5.2.1.7085.2626.119403521930927333027265674239, type \n", - "[2024-04-10 16:41:10,009] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - SeriesDate: 20090831, type \n", - "[2024-04-10 16:41:10,010] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - SeriesTime: 101721.452, type \n", - "[2024-04-10 16:41:10,011] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - Modality: CT, type \n", - "[2024-04-10 16:41:10,012] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - SeriesDescription: ABD/PANC 3.0 B31f, type \n", - "[2024-04-10 16:41:10,012] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - PatientPosition: HFS, type \n", - "[2024-04-10 16:41:10,013] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - SeriesNumber: 8, type \n", - "[2024-04-10 16:41:10,014] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - row_pixel_spacing: 0.7890625, type \n", - "[2024-04-10 16:41:10,015] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - col_pixel_spacing: 0.7890625, type \n", - "[2024-04-10 16:41:10,015] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - depth_pixel_spacing: 1.5, type \n", - "[2024-04-10 16:41:10,016] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - row_direction_cosine: [1.0, 0.0, 0.0], type \n", - "[2024-04-10 16:41:10,017] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - col_direction_cosine: [0.0, 1.0, 0.0], type \n", - "[2024-04-10 16:41:10,018] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - depth_direction_cosine: [0.0, 0.0, 1.0], type \n", - "[2024-04-10 16:41:10,019] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - dicom_affine_transform: [[ 0.7890625 0. 0. -197.60547 ]\n", + "[2024-04-23 15:42:44,617] [INFO] (root) - Working on series, instance UID: 1.3.6.1.4.1.14519.5.2.1.7085.2626.119403521930927333027265674239\n", + "[2024-04-23 15:42:44,618] [INFO] (root) - On attribute: 'StudyDescription' to match value: '(.*?)'\n", + "[2024-04-23 15:42:44,618] [INFO] (root) - Series attribute StudyDescription value: CT ABDOMEN W IV CONTRAST\n", + "[2024-04-23 15:42:44,618] [INFO] (root) - Series attribute string value did not match. Try regEx.\n", + "[2024-04-23 15:42:44,619] [INFO] (root) - On attribute: 'Modality' to match value: '(?i)CT'\n", + "[2024-04-23 15:42:44,619] [INFO] (root) - Series attribute Modality value: CT\n", + "[2024-04-23 15:42:44,620] [INFO] (root) - Series attribute string value did not match. Try regEx.\n", + "[2024-04-23 15:42:44,620] [INFO] (root) - On attribute: 'SeriesDescription' to match value: '(.*?)'\n", + "[2024-04-23 15:42:44,621] [INFO] (root) - Series attribute SeriesDescription value: ABD/PANC 3.0 B31f\n", + "[2024-04-23 15:42:44,621] [INFO] (root) - Series attribute string value did not match. Try regEx.\n", + "[2024-04-23 15:42:44,622] [INFO] (root) - On attribute: 'ImageType' to match value: ['PRIMARY', 'ORIGINAL']\n", + "[2024-04-23 15:42:44,622] [INFO] (root) - Series attribute ImageType value: None\n", + "[2024-04-23 15:42:44,623] [INFO] (root) - Selected Series, UID: 1.3.6.1.4.1.14519.5.2.1.7085.2626.119403521930927333027265674239\n", + "[2024-04-23 15:42:44,860] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - Converted Image object metadata:\n", + "[2024-04-23 15:42:44,862] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - SeriesInstanceUID: 1.3.6.1.4.1.14519.5.2.1.7085.2626.119403521930927333027265674239, type \n", + "[2024-04-23 15:42:44,862] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - SeriesDate: 20090831, type \n", + "[2024-04-23 15:42:44,863] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - SeriesTime: 101721.452, type \n", + "[2024-04-23 15:42:44,864] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - Modality: CT, type \n", + "[2024-04-23 15:42:44,864] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - SeriesDescription: ABD/PANC 3.0 B31f, type \n", + "[2024-04-23 15:42:44,865] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - PatientPosition: HFS, type \n", + "[2024-04-23 15:42:44,866] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - SeriesNumber: 8, type \n", + "[2024-04-23 15:42:44,866] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - row_pixel_spacing: 0.7890625, type \n", + "[2024-04-23 15:42:44,867] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - col_pixel_spacing: 0.7890625, type \n", + "[2024-04-23 15:42:44,867] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - depth_pixel_spacing: 1.5, type \n", + "[2024-04-23 15:42:44,868] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - row_direction_cosine: [1.0, 0.0, 0.0], type \n", + "[2024-04-23 15:42:44,869] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - col_direction_cosine: [0.0, 1.0, 0.0], type \n", + "[2024-04-23 15:42:44,869] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - depth_direction_cosine: [0.0, 0.0, 1.0], type \n", + "[2024-04-23 15:42:44,870] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - dicom_affine_transform: [[ 0.7890625 0. 0. -197.60547 ]\n", " [ 0. 0.7890625 0. -398.60547 ]\n", " [ 0. 0. 1.5 -383. ]\n", " [ 0. 0. 0. 1. ]], type \n", - "[2024-04-10 16:41:10,020] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - nifti_affine_transform: [[ -0.7890625 -0. -0. 197.60547 ]\n", + "[2024-04-23 15:42:44,871] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - nifti_affine_transform: [[ -0.7890625 -0. -0. 197.60547 ]\n", " [ -0. -0.7890625 -0. 398.60547 ]\n", " [ 0. 0. 1.5 -383. ]\n", " [ 0. 0. 0. 1. ]], type \n", - "[2024-04-10 16:41:10,021] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - StudyInstanceUID: 1.3.6.1.4.1.14519.5.2.1.7085.2626.822645453932810382886582736291, type \n", - "[2024-04-10 16:41:10,022] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - StudyID: , type \n", - "[2024-04-10 16:41:10,023] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - StudyDate: 20090831, type \n", - "[2024-04-10 16:41:10,025] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - StudyTime: 095948.599, type \n", - "[2024-04-10 16:41:10,026] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - StudyDescription: CT ABDOMEN W IV CONTRAST, type \n", - "[2024-04-10 16:41:10,027] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - AccessionNumber: 5471978513296937, type \n", - "[2024-04-10 16:41:10,029] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - selection_name: CT Series, type \n" + "[2024-04-23 15:42:44,872] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - StudyInstanceUID: 1.3.6.1.4.1.14519.5.2.1.7085.2626.822645453932810382886582736291, type \n", + "[2024-04-23 15:42:44,873] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - StudyID: , type \n", + "[2024-04-23 15:42:44,875] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - StudyDate: 20090831, type \n", + "[2024-04-23 15:42:44,876] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - StudyTime: 095948.599, type \n", + "[2024-04-23 15:42:44,877] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - StudyDescription: CT ABDOMEN W IV CONTRAST, type \n", + "[2024-04-23 15:42:44,878] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - AccessionNumber: 5471978513296937, type \n", + "[2024-04-23 15:42:44,879] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - selection_name: CT Series, type \n" ] }, { "name": "stdout", "output_type": "stream", "text": [ - "2024-04-10 16:41:10,797 INFO image_writer.py:197 - writing: /home/mqin/src/monai-deploy-app-sdk/notebooks/tutorials/output/saved_images_folder/1.3.6.1.4.1.14519.5.2.1.7085.2626/1.3.6.1.4.1.14519.5.2.1.7085.2626.nii\n", - "2024-04-10 16:41:17,104 INFO image_writer.py:197 - writing: /home/mqin/src/monai-deploy-app-sdk/notebooks/tutorials/output/saved_images_folder/1.3.6.1.4.1.14519.5.2.1.7085.2626/1.3.6.1.4.1.14519.5.2.1.7085.2626_seg.nii\n" + "2024-04-23 15:42:45,610 INFO image_writer.py:197 - writing: /home/mqin/src/monai-deploy-app-sdk/notebooks/tutorials/output/saved_images_folder/1.3.6.1.4.1.14519.5.2.1.7085.2626/1.3.6.1.4.1.14519.5.2.1.7085.2626.nii\n", + "2024-04-23 15:42:51,791 INFO image_writer.py:197 - writing: /home/mqin/src/monai-deploy-app-sdk/notebooks/tutorials/output/saved_images_folder/1.3.6.1.4.1.14519.5.2.1.7085.2626/1.3.6.1.4.1.14519.5.2.1.7085.2626_seg.nii\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ - "[2024-04-10 16:41:19,060] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - Output Seg image numpy array shaped: (204, 512, 512)\n", - "[2024-04-10 16:41:19,067] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - Output Seg image pixel max value: 1\n", + "[2024-04-23 15:42:53,711] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - Output Seg image numpy array shaped: (204, 512, 512)\n", + "[2024-04-23 15:42:53,718] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - Output Seg image pixel max value: 1\n", "/home/mqin/src/monai-deploy-app-sdk/.venv/lib/python3.10/site-packages/highdicom/valuerep.py:54: UserWarning: The string \"C3N-00198\" is unlikely to represent the intended person name since it contains only a single component. Construct a person name according to the format in described in https://dicom.nema.org/dicom/2013/output/chtml/part05/sect_6.2.html#sect_6.2.1.2, or, in pydicom 2.2.0 or later, use the pydicom.valuerep.PersonName.from_named_components() method to construct the person name correctly. If a single-component name is really intended, add a trailing caret character to disambiguate the name.\n", " warnings.warn(\n", - "[2024-04-10 16:41:20,496] [INFO] (highdicom.base) - copy Image-related attributes from dataset \"1.3.6.1.4.1.14519.5.2.1.7085.2626.936983343951485811186213470191\"\n", - "[2024-04-10 16:41:20,497] [INFO] (highdicom.base) - copy attributes of module \"Specimen\"\n", - "[2024-04-10 16:41:20,498] [INFO] (highdicom.base) - copy Patient-related attributes from dataset \"1.3.6.1.4.1.14519.5.2.1.7085.2626.936983343951485811186213470191\"\n", - "[2024-04-10 16:41:20,499] [INFO] (highdicom.base) - copy attributes of module \"Patient\"\n", - "[2024-04-10 16:41:20,500] [INFO] (highdicom.base) - copy attributes of module \"Clinical Trial Subject\"\n", - "[2024-04-10 16:41:20,501] [INFO] (highdicom.base) - copy Study-related attributes from dataset \"1.3.6.1.4.1.14519.5.2.1.7085.2626.936983343951485811186213470191\"\n", - "[2024-04-10 16:41:20,502] [INFO] (highdicom.base) - copy attributes of module \"General Study\"\n", - "[2024-04-10 16:41:20,503] [INFO] (highdicom.base) - copy attributes of module \"Patient Study\"\n", - "[2024-04-10 16:41:20,503] [INFO] (highdicom.base) - copy attributes of module \"Clinical Trial Study\"\n", - "[info] [greedy_scheduler.cpp:369] Scheduler stopped: Some entities are waiting for execution, but there are no periodic or async entities to get out of the deadlock.\n", - "[info] [greedy_scheduler.cpp:398] Scheduler finished.\n", - "[info] [gxf_executor.cpp:1906] Graph execution deactivating. Fragment: \n", - "[info] [gxf_executor.cpp:1907] Deactivating Graph...\n", - "[info] [gxf_executor.cpp:1910] Graph execution finished. Fragment: \n", - "[2024-04-10 16:41:20,610] [INFO] (__main__.AISpleenSegApp) - End run\n" + "[2024-04-23 15:42:55,113] [INFO] (highdicom.base) - copy Image-related attributes from dataset \"1.3.6.1.4.1.14519.5.2.1.7085.2626.936983343951485811186213470191\"\n", + "[2024-04-23 15:42:55,114] [INFO] (highdicom.base) - copy attributes of module \"Specimen\"\n", + "[2024-04-23 15:42:55,115] [INFO] (highdicom.base) - copy Patient-related attributes from dataset \"1.3.6.1.4.1.14519.5.2.1.7085.2626.936983343951485811186213470191\"\n", + "[2024-04-23 15:42:55,116] [INFO] (highdicom.base) - copy attributes of module \"Patient\"\n", + "[2024-04-23 15:42:55,118] [INFO] (highdicom.base) - copy attributes of module \"Clinical Trial Subject\"\n", + "[2024-04-23 15:42:55,119] [INFO] (highdicom.base) - copy Study-related attributes from dataset \"1.3.6.1.4.1.14519.5.2.1.7085.2626.936983343951485811186213470191\"\n", + "[2024-04-23 15:42:55,120] [INFO] (highdicom.base) - copy attributes of module \"General Study\"\n", + "[2024-04-23 15:42:55,121] [INFO] (highdicom.base) - copy attributes of module \"Patient Study\"\n", + "[2024-04-23 15:42:55,122] [INFO] (highdicom.base) - copy attributes of module \"Clinical Trial Study\"\n", + "[info] [gxf_executor.cpp:1879] Deactivating Graph...\n", + "[info] [gxf_executor.cpp:1887] Graph execution finished.\n", + "[2024-04-23 15:42:55,233] [INFO] (__main__.AISpleenSegApp) - End run\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "\u001b[0m2024-04-23 15:42:55.231 INFO gxf/std/greedy_scheduler.cpp@372: Scheduler stopped: Some entities are waiting for execution, but there are no periodic or async entities to get out of the deadlock.\u001b[0m\n", + "\u001b[0m2024-04-23 15:42:55.231 INFO gxf/std/greedy_scheduler.cpp@401: Scheduler finished.\u001b[0m\n" ] } ], @@ -1274,84 +1287,82 @@ "name": "stdout", "output_type": "stream", "text": [ - "[2024-04-10 16:41:25,305] [INFO] (root) - Parsed args: Namespace(log_level=None, input=None, output=None, model=None, workdir=None, argv=['my_app'])\n", - "[2024-04-10 16:41:25,472] [INFO] (root) - AppContext object: AppContext(input_path=dcm, output_path=output, model_path=models, workdir=)\n", - "[2024-04-10 16:41:25,472] [INFO] (app.AISpleenSegApp) - App input and output path: dcm, output\n", - "[\u001b[32minfo\u001b[m] [gxf_executor.cpp:211] Creating context\n", - "[\u001b[32minfo\u001b[m] [gxf_executor.cpp:1674] Loading extensions from configs...\n", - "[\u001b[32minfo\u001b[m] [gxf_executor.cpp:1864] Activating Graph...\n", - "[\u001b[32minfo\u001b[m] [gxf_executor.cpp:1894] Running Graph...\n", - "[\u001b[32minfo\u001b[m] [gxf_executor.cpp:1896] Waiting for completion...\n", - "[\u001b[32minfo\u001b[m] [gxf_executor.cpp:1897] Graph execution waiting. Fragment: \n", - "[\u001b[32minfo\u001b[m] [greedy_scheduler.cpp:190] Scheduling 6 entities\n", - "[2024-04-10 16:41:25,505] [INFO] (monai.deploy.operators.dicom_data_loader_operator.DICOMDataLoaderOperator) - No or invalid input path from the optional input port: None\n", - "[2024-04-10 16:41:25,850] [INFO] (root) - Finding series for Selection named: CT Series\n", - "[2024-04-10 16:41:25,850] [INFO] (root) - Searching study, : 1.3.6.1.4.1.14519.5.2.1.7085.2626.822645453932810382886582736291\n", + "[2024-04-23 15:42:59,956] [INFO] (root) - Parsed args: Namespace(log_level=None, input=None, output=None, model=None, workdir=None, argv=['my_app'])\n", + "[2024-04-23 15:42:59,957] [INFO] (root) - AppContext object: AppContext(input_path=dcm, output_path=output, model_path=models, workdir=)\n", + "[2024-04-23 15:42:59,957] [INFO] (app.AISpleenSegApp) - App input and output path: dcm, output\n", + "[\u001b[32minfo\u001b[m] [gxf_executor.cpp:247] Creating context\n", + "[\u001b[32minfo\u001b[m] [gxf_executor.cpp:1672] Loading extensions from configs...\n", + "[\u001b[32minfo\u001b[m] [gxf_executor.cpp:1842] Activating Graph...\n", + "[\u001b[32minfo\u001b[m] [gxf_executor.cpp:1874] Running Graph...\n", + "[\u001b[32minfo\u001b[m] [gxf_executor.cpp:1876] Waiting for completion...\n", + "\u001b[0m2024-04-23 15:42:59.985 INFO gxf/std/greedy_scheduler.cpp@191: Scheduling 6 entities\u001b[0m\n", + "[2024-04-23 15:42:59,987] [INFO] (monai.deploy.operators.dicom_data_loader_operator.DICOMDataLoaderOperator) - No or invalid input path from the optional input port: None\n", + "[2024-04-23 15:43:00,516] [INFO] (root) - Finding series for Selection named: CT Series\n", + "[2024-04-23 15:43:00,517] [INFO] (root) - Searching study, : 1.3.6.1.4.1.14519.5.2.1.7085.2626.822645453932810382886582736291\n", " # of series: 1\n", - "[2024-04-10 16:41:25,850] [INFO] (root) - Working on series, instance UID: 1.3.6.1.4.1.14519.5.2.1.7085.2626.119403521930927333027265674239\n", - "[2024-04-10 16:41:25,850] [INFO] (root) - On attribute: 'StudyDescription' to match value: '(.*?)'\n", - "[2024-04-10 16:41:25,850] [INFO] (root) - Series attribute StudyDescription value: CT ABDOMEN W IV CONTRAST\n", - "[2024-04-10 16:41:25,850] [INFO] (root) - Series attribute string value did not match. Try regEx.\n", - "[2024-04-10 16:41:25,851] [INFO] (root) - On attribute: 'Modality' to match value: '(?i)CT'\n", - "[2024-04-10 16:41:25,851] [INFO] (root) - Series attribute Modality value: CT\n", - "[2024-04-10 16:41:25,851] [INFO] (root) - Series attribute string value did not match. Try regEx.\n", - "[2024-04-10 16:41:25,851] [INFO] (root) - On attribute: 'SeriesDescription' to match value: '(.*?)'\n", - "[2024-04-10 16:41:25,851] [INFO] (root) - Series attribute SeriesDescription value: ABD/PANC 3.0 B31f\n", - "[2024-04-10 16:41:25,851] [INFO] (root) - Series attribute string value did not match. Try regEx.\n", - "[2024-04-10 16:41:25,851] [INFO] (root) - On attribute: 'ImageType' to match value: ['PRIMARY', 'ORIGINAL']\n", - "[2024-04-10 16:41:25,851] [INFO] (root) - Series attribute ImageType value: None\n", - "[2024-04-10 16:41:25,851] [INFO] (root) - Selected Series, UID: 1.3.6.1.4.1.14519.5.2.1.7085.2626.119403521930927333027265674239\n", - "[2024-04-10 16:41:26,402] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - Converted Image object metadata:\n", - "[2024-04-10 16:41:26,402] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - SeriesInstanceUID: 1.3.6.1.4.1.14519.5.2.1.7085.2626.119403521930927333027265674239, type \n", - "[2024-04-10 16:41:26,402] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - SeriesDate: 20090831, type \n", - "[2024-04-10 16:41:26,402] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - SeriesTime: 101721.452, type \n", - "[2024-04-10 16:41:26,402] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - Modality: CT, type \n", - "[2024-04-10 16:41:26,402] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - SeriesDescription: ABD/PANC 3.0 B31f, type \n", - "[2024-04-10 16:41:26,402] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - PatientPosition: HFS, type \n", - "[2024-04-10 16:41:26,402] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - SeriesNumber: 8, type \n", - "[2024-04-10 16:41:26,402] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - row_pixel_spacing: 0.7890625, type \n", - "[2024-04-10 16:41:26,402] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - col_pixel_spacing: 0.7890625, type \n", - "[2024-04-10 16:41:26,402] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - depth_pixel_spacing: 1.5, type \n", - "[2024-04-10 16:41:26,402] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - row_direction_cosine: [1.0, 0.0, 0.0], type \n", - "[2024-04-10 16:41:26,402] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - col_direction_cosine: [0.0, 1.0, 0.0], type \n", - "[2024-04-10 16:41:26,402] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - depth_direction_cosine: [0.0, 0.0, 1.0], type \n", - "[2024-04-10 16:41:26,402] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - dicom_affine_transform: [[ 0.7890625 0. 0. -197.60547 ]\n", + "[2024-04-23 15:43:00,517] [INFO] (root) - Working on series, instance UID: 1.3.6.1.4.1.14519.5.2.1.7085.2626.119403521930927333027265674239\n", + "[2024-04-23 15:43:00,517] [INFO] (root) - On attribute: 'StudyDescription' to match value: '(.*?)'\n", + "[2024-04-23 15:43:00,517] [INFO] (root) - Series attribute StudyDescription value: CT ABDOMEN W IV CONTRAST\n", + "[2024-04-23 15:43:00,517] [INFO] (root) - Series attribute string value did not match. Try regEx.\n", + "[2024-04-23 15:43:00,517] [INFO] (root) - On attribute: 'Modality' to match value: '(?i)CT'\n", + "[2024-04-23 15:43:00,517] [INFO] (root) - Series attribute Modality value: CT\n", + "[2024-04-23 15:43:00,517] [INFO] (root) - Series attribute string value did not match. Try regEx.\n", + "[2024-04-23 15:43:00,517] [INFO] (root) - On attribute: 'SeriesDescription' to match value: '(.*?)'\n", + "[2024-04-23 15:43:00,517] [INFO] (root) - Series attribute SeriesDescription value: ABD/PANC 3.0 B31f\n", + "[2024-04-23 15:43:00,517] [INFO] (root) - Series attribute string value did not match. Try regEx.\n", + "[2024-04-23 15:43:00,517] [INFO] (root) - On attribute: 'ImageType' to match value: ['PRIMARY', 'ORIGINAL']\n", + "[2024-04-23 15:43:00,517] [INFO] (root) - Series attribute ImageType value: None\n", + "[2024-04-23 15:43:00,517] [INFO] (root) - Selected Series, UID: 1.3.6.1.4.1.14519.5.2.1.7085.2626.119403521930927333027265674239\n", + "[2024-04-23 15:43:00,884] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - Converted Image object metadata:\n", + "[2024-04-23 15:43:00,884] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - SeriesInstanceUID: 1.3.6.1.4.1.14519.5.2.1.7085.2626.119403521930927333027265674239, type \n", + "[2024-04-23 15:43:00,884] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - SeriesDate: 20090831, type \n", + "[2024-04-23 15:43:00,884] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - SeriesTime: 101721.452, type \n", + "[2024-04-23 15:43:00,884] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - Modality: CT, type \n", + "[2024-04-23 15:43:00,884] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - SeriesDescription: ABD/PANC 3.0 B31f, type \n", + "[2024-04-23 15:43:00,884] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - PatientPosition: HFS, type \n", + "[2024-04-23 15:43:00,884] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - SeriesNumber: 8, type \n", + "[2024-04-23 15:43:00,884] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - row_pixel_spacing: 0.7890625, type \n", + "[2024-04-23 15:43:00,884] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - col_pixel_spacing: 0.7890625, type \n", + "[2024-04-23 15:43:00,884] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - depth_pixel_spacing: 1.5, type \n", + "[2024-04-23 15:43:00,885] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - row_direction_cosine: [1.0, 0.0, 0.0], type \n", + "[2024-04-23 15:43:00,885] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - col_direction_cosine: [0.0, 1.0, 0.0], type \n", + "[2024-04-23 15:43:00,885] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - depth_direction_cosine: [0.0, 0.0, 1.0], type \n", + "[2024-04-23 15:43:00,885] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - dicom_affine_transform: [[ 0.7890625 0. 0. -197.60547 ]\n", " [ 0. 0.7890625 0. -398.60547 ]\n", " [ 0. 0. 1.5 -383. ]\n", " [ 0. 0. 0. 1. ]], type \n", - "[2024-04-10 16:41:26,403] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - nifti_affine_transform: [[ -0.7890625 -0. -0. 197.60547 ]\n", + "[2024-04-23 15:43:00,885] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - nifti_affine_transform: [[ -0.7890625 -0. -0. 197.60547 ]\n", " [ -0. -0.7890625 -0. 398.60547 ]\n", " [ 0. 0. 1.5 -383. ]\n", " [ 0. 0. 0. 1. ]], type \n", - "[2024-04-10 16:41:26,403] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - StudyInstanceUID: 1.3.6.1.4.1.14519.5.2.1.7085.2626.822645453932810382886582736291, type \n", - "[2024-04-10 16:41:26,403] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - StudyID: , type \n", - "[2024-04-10 16:41:26,403] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - StudyDate: 20090831, type \n", - "[2024-04-10 16:41:26,403] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - StudyTime: 095948.599, type \n", - "[2024-04-10 16:41:26,403] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - StudyDescription: CT ABDOMEN W IV CONTRAST, type \n", - "[2024-04-10 16:41:26,403] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - AccessionNumber: 5471978513296937, type \n", - "[2024-04-10 16:41:26,403] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - selection_name: CT Series, type \n", - "2024-04-10 16:41:27,452 INFO image_writer.py:197 - writing: /home/mqin/src/monai-deploy-app-sdk/notebooks/tutorials/output/saved_images_folder/1.3.6.1.4.1.14519.5.2.1.7085.2626/1.3.6.1.4.1.14519.5.2.1.7085.2626.nii\n", - "2024-04-10 16:41:34,092 INFO image_writer.py:197 - writing: /home/mqin/src/monai-deploy-app-sdk/notebooks/tutorials/output/saved_images_folder/1.3.6.1.4.1.14519.5.2.1.7085.2626/1.3.6.1.4.1.14519.5.2.1.7085.2626_seg.nii\n", - "[2024-04-10 16:41:35,714] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - Output Seg image numpy array shaped: (204, 512, 512)\n", - "[2024-04-10 16:41:35,720] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - Output Seg image pixel max value: 1\n", + "[2024-04-23 15:43:00,885] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - StudyInstanceUID: 1.3.6.1.4.1.14519.5.2.1.7085.2626.822645453932810382886582736291, type \n", + "[2024-04-23 15:43:00,885] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - StudyID: , type \n", + "[2024-04-23 15:43:00,885] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - StudyDate: 20090831, type \n", + "[2024-04-23 15:43:00,885] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - StudyTime: 095948.599, type \n", + "[2024-04-23 15:43:00,885] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - StudyDescription: CT ABDOMEN W IV CONTRAST, type \n", + "[2024-04-23 15:43:00,885] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - AccessionNumber: 5471978513296937, type \n", + "[2024-04-23 15:43:00,886] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - selection_name: CT Series, type \n", + "2024-04-23 15:43:01,872 INFO image_writer.py:197 - writing: /home/mqin/src/monai-deploy-app-sdk/notebooks/tutorials/output/saved_images_folder/1.3.6.1.4.1.14519.5.2.1.7085.2626/1.3.6.1.4.1.14519.5.2.1.7085.2626.nii\n", + "2024-04-23 15:43:08,194 INFO image_writer.py:197 - writing: /home/mqin/src/monai-deploy-app-sdk/notebooks/tutorials/output/saved_images_folder/1.3.6.1.4.1.14519.5.2.1.7085.2626/1.3.6.1.4.1.14519.5.2.1.7085.2626_seg.nii\n", + "[2024-04-23 15:43:09,761] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - Output Seg image numpy array shaped: (204, 512, 512)\n", + "[2024-04-23 15:43:09,767] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - Output Seg image pixel max value: 1\n", "/home/mqin/src/monai-deploy-app-sdk/.venv/lib/python3.10/site-packages/highdicom/valuerep.py:54: UserWarning: The string \"C3N-00198\" is unlikely to represent the intended person name since it contains only a single component. Construct a person name according to the format in described in https://dicom.nema.org/dicom/2013/output/chtml/part05/sect_6.2.html#sect_6.2.1.2, or, in pydicom 2.2.0 or later, use the pydicom.valuerep.PersonName.from_named_components() method to construct the person name correctly. If a single-component name is really intended, add a trailing caret character to disambiguate the name.\n", " warnings.warn(\n", - "[2024-04-10 16:41:37,387] [INFO] (highdicom.base) - copy Image-related attributes from dataset \"1.3.6.1.4.1.14519.5.2.1.7085.2626.936983343951485811186213470191\"\n", - "[2024-04-10 16:41:37,387] [INFO] (highdicom.base) - copy attributes of module \"Specimen\"\n", - "[2024-04-10 16:41:37,387] [INFO] (highdicom.base) - copy Patient-related attributes from dataset \"1.3.6.1.4.1.14519.5.2.1.7085.2626.936983343951485811186213470191\"\n", - "[2024-04-10 16:41:37,387] [INFO] (highdicom.base) - copy attributes of module \"Patient\"\n", - "[2024-04-10 16:41:37,387] [INFO] (highdicom.base) - copy attributes of module \"Clinical Trial Subject\"\n", - "[2024-04-10 16:41:37,388] [INFO] (highdicom.base) - copy Study-related attributes from dataset \"1.3.6.1.4.1.14519.5.2.1.7085.2626.936983343951485811186213470191\"\n", - "[2024-04-10 16:41:37,388] [INFO] (highdicom.base) - copy attributes of module \"General Study\"\n", - "[2024-04-10 16:41:37,388] [INFO] (highdicom.base) - copy attributes of module \"Patient Study\"\n", - "[2024-04-10 16:41:37,388] [INFO] (highdicom.base) - copy attributes of module \"Clinical Trial Study\"\n", - "[\u001b[32minfo\u001b[m] [greedy_scheduler.cpp:369] Scheduler stopped: Some entities are waiting for execution, but there are no periodic or async entities to get out of the deadlock.\n", - "[\u001b[32minfo\u001b[m] [greedy_scheduler.cpp:398] Scheduler finished.\n", - "[\u001b[32minfo\u001b[m] [gxf_executor.cpp:1906] Graph execution deactivating. Fragment: \n", - "[\u001b[32minfo\u001b[m] [gxf_executor.cpp:1907] Deactivating Graph...\n", - "[\u001b[32minfo\u001b[m] [gxf_executor.cpp:1910] Graph execution finished. Fragment: \n", - "[2024-04-10 16:41:37,477] [INFO] (app.AISpleenSegApp) - End run\n", - "[\u001b[32minfo\u001b[m] [gxf_executor.cpp:230] Destroying context\n" + "[2024-04-23 15:43:11,092] [INFO] (highdicom.base) - copy Image-related attributes from dataset \"1.3.6.1.4.1.14519.5.2.1.7085.2626.936983343951485811186213470191\"\n", + "[2024-04-23 15:43:11,093] [INFO] (highdicom.base) - copy attributes of module \"Specimen\"\n", + "[2024-04-23 15:43:11,093] [INFO] (highdicom.base) - copy Patient-related attributes from dataset \"1.3.6.1.4.1.14519.5.2.1.7085.2626.936983343951485811186213470191\"\n", + "[2024-04-23 15:43:11,093] [INFO] (highdicom.base) - copy attributes of module \"Patient\"\n", + "[2024-04-23 15:43:11,093] [INFO] (highdicom.base) - copy attributes of module \"Clinical Trial Subject\"\n", + "[2024-04-23 15:43:11,093] [INFO] (highdicom.base) - copy Study-related attributes from dataset \"1.3.6.1.4.1.14519.5.2.1.7085.2626.936983343951485811186213470191\"\n", + "[2024-04-23 15:43:11,093] [INFO] (highdicom.base) - copy attributes of module \"General Study\"\n", + "[2024-04-23 15:43:11,093] [INFO] (highdicom.base) - copy attributes of module \"Patient Study\"\n", + "[2024-04-23 15:43:11,093] [INFO] (highdicom.base) - copy attributes of module \"Clinical Trial Study\"\n", + "\u001b[0m2024-04-23 15:43:11.181 INFO gxf/std/greedy_scheduler.cpp@372: Scheduler stopped: Some entities are waiting for execution, but there are no periodic or async entities to get out of the deadlock.\u001b[0m\n", + "\u001b[0m2024-04-23 15:43:11.181 INFO gxf/std/greedy_scheduler.cpp@401: Scheduler finished.\u001b[0m\n", + "[\u001b[32minfo\u001b[m] [gxf_executor.cpp:1879] Deactivating Graph...\n", + "[\u001b[32minfo\u001b[m] [gxf_executor.cpp:1887] Graph execution finished.\n", + "[2024-04-23 15:43:11,183] [INFO] (app.AISpleenSegApp) - End run\n", + "[\u001b[32minfo\u001b[m] [gxf_executor.cpp:275] Destroying context\n" ] } ], @@ -1370,7 +1381,7 @@ "output_type": "stream", "text": [ "output:\n", - "1.2.826.0.1.3680043.10.511.3.12733408477402210746640758069824301.dcm\n", + "1.2.826.0.1.3680043.10.511.3.57940295875624111168999103278306755.dcm\n", "saved_images_folder\n", "\n", "output/saved_images_folder:\n", @@ -1477,14 +1488,16 @@ "name": "stdout", "output_type": "stream", "text": [ - "[2024-04-10 16:41:40,386] [INFO] (packager.parameters) - Application: /home/mqin/src/monai-deploy-app-sdk/notebooks/tutorials/my_app\n", - "[2024-04-10 16:41:40,386] [INFO] (packager.parameters) - Detected application type: Python Module\n", - "[2024-04-10 16:41:40,386] [INFO] (packager) - Scanning for models in /home/mqin/src/monai-deploy-app-sdk/notebooks/tutorials/models...\n", - "[2024-04-10 16:41:40,386] [DEBUG] (packager) - Model model=/home/mqin/src/monai-deploy-app-sdk/notebooks/tutorials/models/model added.\n", - "[2024-04-10 16:41:40,386] [INFO] (packager) - Reading application configuration from /home/mqin/src/monai-deploy-app-sdk/notebooks/tutorials/my_app/app.yaml...\n", - "[2024-04-10 16:41:40,387] [INFO] (packager) - Generating app.json...\n", - "[2024-04-10 16:41:40,387] [INFO] (packager) - Generating pkg.json...\n", - "[2024-04-10 16:41:40,394] [DEBUG] (common) - \n", + "[2024-04-23 15:43:13,349] [INFO] (common) - Downloading CLI manifest file...\n", + "[2024-04-23 15:43:13,718] [DEBUG] (common) - Validating CLI manifest file...\n", + "[2024-04-23 15:43:13,720] [INFO] (packager.parameters) - Application: /home/mqin/src/monai-deploy-app-sdk/notebooks/tutorials/my_app\n", + "[2024-04-23 15:43:13,721] [INFO] (packager.parameters) - Detected application type: Python Module\n", + "[2024-04-23 15:43:13,721] [INFO] (packager) - Scanning for models in /home/mqin/src/monai-deploy-app-sdk/notebooks/tutorials/models...\n", + "[2024-04-23 15:43:13,722] [DEBUG] (packager) - Model model=/home/mqin/src/monai-deploy-app-sdk/notebooks/tutorials/models/model added.\n", + "[2024-04-23 15:43:13,722] [INFO] (packager) - Reading application configuration from /home/mqin/src/monai-deploy-app-sdk/notebooks/tutorials/my_app/app.yaml...\n", + "[2024-04-23 15:43:13,725] [INFO] (packager) - Generating app.json...\n", + "[2024-04-23 15:43:13,726] [INFO] (packager) - Generating pkg.json...\n", + "[2024-04-23 15:43:13,738] [DEBUG] (common) - \n", "=============== Begin app.json ===============\n", "{\n", " \"apiVersion\": \"1.0.0\",\n", @@ -1519,7 +1532,7 @@ "}\n", "================ End app.json ================\n", " \n", - "[2024-04-10 16:41:40,394] [DEBUG] (common) - \n", + "[2024-04-23 15:43:13,739] [DEBUG] (common) - \n", "=============== Begin pkg.json ===============\n", "{\n", " \"apiVersion\": \"1.0.0\",\n", @@ -1539,11 +1552,11 @@ "}\n", "================ End pkg.json ================\n", " \n", - "[2024-04-10 16:41:40,461] [DEBUG] (packager.builder) - \n", + "[2024-04-23 15:43:13,775] [DEBUG] (packager.builder) - \n", "========== Begin Dockerfile ==========\n", "\n", "\n", - "FROM nvcr.io/nvidia/clara-holoscan/holoscan:v1.0.3-dgpu\n", + "FROM nvcr.io/nvidia/clara-holoscan/holoscan:v2.0.0-dgpu\n", "\n", "ENV DEBIAN_FRONTEND=noninteractive\n", "ENV TERM=xterm-256color\n", @@ -1559,11 +1572,11 @@ " && mkdir -p /var/holoscan/input \\\n", " && mkdir -p /var/holoscan/output\n", "\n", - "LABEL base=\"nvcr.io/nvidia/clara-holoscan/holoscan:v1.0.3-dgpu\"\n", + "LABEL base=\"nvcr.io/nvidia/clara-holoscan/holoscan:v2.0.0-dgpu\"\n", "LABEL tag=\"my_app:1.0\"\n", "LABEL org.opencontainers.image.title=\"MONAI Deploy App Package - MONAI Bundle AI App\"\n", "LABEL org.opencontainers.image.version=\"1.0\"\n", - "LABEL org.nvidia.holoscan=\"1.0.3\"\n", + "LABEL org.nvidia.holoscan=\"2.0.0\"\n", "LABEL org.monai.deploy.app-sdk=\"0.5.1\"\n", "\n", "\n", @@ -1589,7 +1602,6 @@ "ENV PYTHONPATH=\"/opt/holoscan/app:$PYTHONPATH\"\n", "\n", "\n", - "\n", "RUN groupadd -f -g $GID $UNAME\n", "RUN useradd -rm -d /home/$UNAME -s /bin/bash -g $GID -G sudo -u $UID $UNAME\n", "RUN chown -R holoscan /var/holoscan \n", @@ -1615,14 +1627,12 @@ "RUN pip install --upgrade pip\n", "RUN pip install --no-cache-dir --user -r /tmp/requirements.txt\n", "\n", - "# Install Holoscan from PyPI only when sdk_type is Holoscan. \n", - "# For MONAI Deploy, the APP SDK will install it unless user specifies the Holoscan SDK file.\n", + " \n", + "# MONAI Deploy\n", "\n", "# Copy user-specified MONAI Deploy SDK file\n", - "COPY ./monai_deploy_app_sdk-0.5.1+25.g31e4165.dirty-py3-none-any.whl /tmp/monai_deploy_app_sdk-0.5.1+25.g31e4165.dirty-py3-none-any.whl\n", - "RUN pip install /tmp/monai_deploy_app_sdk-0.5.1+25.g31e4165.dirty-py3-none-any.whl\n", - "\n", - "\n", + "COPY ./monai_deploy_app_sdk-0.5.1+20.gb869749.dirty-py3-none-any.whl /tmp/monai_deploy_app_sdk-0.5.1+20.gb869749.dirty-py3-none-any.whl\n", + "RUN pip install /tmp/monai_deploy_app_sdk-0.5.1+20.gb869749.dirty-py3-none-any.whl\n", "\n", "\n", "COPY ./models /opt/holoscan/models\n", @@ -1636,31 +1646,31 @@ "ENTRYPOINT [\"/var/holoscan/tools\"]\n", "=========== End Dockerfile ===========\n", "\n", - "[2024-04-10 16:41:40,461] [INFO] (packager.builder) - \n", + "[2024-04-23 15:43:13,775] [INFO] (packager.builder) - \n", "===============================================================================\n", "Building image for: x64-workstation\n", " Architecture: linux/amd64\n", - " Base Image: nvcr.io/nvidia/clara-holoscan/holoscan:v1.0.3-dgpu\n", + " Base Image: nvcr.io/nvidia/clara-holoscan/holoscan:v2.0.0-dgpu\n", " Build Image: N/A\n", " Cache: Enabled\n", " Configuration: dgpu\n", " Holoscan SDK Package: pypi.org\n", - " MONAI Deploy App SDK Package: /home/mqin/src/monai-deploy-app-sdk/dist/monai_deploy_app_sdk-0.5.1+25.g31e4165.dirty-py3-none-any.whl\n", + " MONAI Deploy App SDK Package: /home/mqin/src/monai-deploy-app-sdk/dist/monai_deploy_app_sdk-0.5.1+20.gb869749.dirty-py3-none-any.whl\n", " gRPC Health Probe: N/A\n", - " SDK Version: 1.0.3\n", + " SDK Version: 2.0.0\n", " SDK: monai-deploy\n", " Tag: my_app-x64-workstation-dgpu-linux-amd64:1.0\n", " \n", - "[2024-04-10 16:41:41,020] [INFO] (common) - Using existing Docker BuildKit builder `holoscan_app_builder`\n", - "[2024-04-10 16:41:41,021] [DEBUG] (packager.builder) - Building Holoscan Application Package: tag=my_app-x64-workstation-dgpu-linux-amd64:1.0\n", + "[2024-04-23 15:43:14,073] [INFO] (common) - Using existing Docker BuildKit builder `holoscan_app_builder`\n", + "[2024-04-23 15:43:14,073] [DEBUG] (packager.builder) - Building Holoscan Application Package: tag=my_app-x64-workstation-dgpu-linux-amd64:1.0\n", "#0 building with \"holoscan_app_builder\" instance using docker-container driver\n", "\n", "#1 [internal] load build definition from Dockerfile\n", - "#1 transferring dockerfile: 2.80kB done\n", + "#1 transferring dockerfile: 2.66kB done\n", "#1 DONE 0.1s\n", "\n", - "#2 [internal] load metadata for nvcr.io/nvidia/clara-holoscan/holoscan:v1.0.3-dgpu\n", - "#2 DONE 0.1s\n", + "#2 [internal] load metadata for nvcr.io/nvidia/clara-holoscan/holoscan:v2.0.0-dgpu\n", + "#2 DONE 0.4s\n", "\n", "#3 [internal] load .dockerignore\n", "#3 transferring context: 1.79kB done\n", @@ -1669,177 +1679,239 @@ "#4 [internal] load build context\n", "#4 DONE 0.0s\n", "\n", - "#5 importing cache manifest from local:6394528277147153176\n", + "#5 importing cache manifest from local:12311818318063394630\n", "#5 inferred cache manifest type: application/vnd.oci.image.index.v1+json done\n", "#5 DONE 0.0s\n", "\n", - "#6 [ 1/21] FROM nvcr.io/nvidia/clara-holoscan/holoscan:v1.0.3-dgpu@sha256:50343c616bf910e2a7651abb59db7833933e82cce64c3c4885f938d7e4af6155\n", - "#6 resolve nvcr.io/nvidia/clara-holoscan/holoscan:v1.0.3-dgpu@sha256:50343c616bf910e2a7651abb59db7833933e82cce64c3c4885f938d7e4af6155 0.0s done\n", + "#6 [ 1/21] FROM nvcr.io/nvidia/clara-holoscan/holoscan:v2.0.0-dgpu@sha256:20adbccd2c7b12dfb1798f6953f071631c3b85cd337858a7506f8e420add6d4a\n", + "#6 resolve nvcr.io/nvidia/clara-holoscan/holoscan:v2.0.0-dgpu@sha256:20adbccd2c7b12dfb1798f6953f071631c3b85cd337858a7506f8e420add6d4a 0.1s done\n", "#6 DONE 0.1s\n", "\n", - "#7 importing cache manifest from nvcr.io/nvidia/clara-holoscan/holoscan:v1.0.3-dgpu\n", + "#7 importing cache manifest from nvcr.io/nvidia/clara-holoscan/holoscan:v2.0.0-dgpu\n", "#7 inferred cache manifest type: application/vnd.docker.distribution.manifest.list.v2+json done\n", - "#7 DONE 0.9s\n", + "#7 DONE 0.7s\n", "\n", "#4 [internal] load build context\n", "#4 transferring context: 19.56MB 0.1s done\n", "#4 DONE 0.2s\n", "\n", - "#8 [ 3/21] RUN apt-get update && apt-get install -y curl jq && rm -rf /var/lib/apt/lists/*\n", + "#8 [ 8/21] RUN chown -R holoscan /var/holoscan/output\n", "#8 CACHED\n", "\n", - "#9 [14/21] RUN pip install --no-cache-dir --user -r /tmp/requirements.txt\n", + "#9 [ 9/21] WORKDIR /var/holoscan\n", "#9 CACHED\n", "\n", - "#10 [ 4/21] RUN groupadd -f -g 1000 holoscan\n", + "#10 [ 7/21] RUN chown -R holoscan /var/holoscan/input\n", "#10 CACHED\n", "\n", - "#11 [11/21] RUN chmod +x /var/holoscan/tools\n", + "#11 [ 4/21] RUN groupadd -f -g 1000 holoscan\n", "#11 CACHED\n", "\n", - "#12 [ 2/21] RUN mkdir -p /etc/holoscan/ && mkdir -p /opt/holoscan/ && mkdir -p /var/holoscan && mkdir -p /opt/holoscan/app && mkdir -p /var/holoscan/input && mkdir -p /var/holoscan/output\n", + "#12 [13/21] RUN pip install --upgrade pip\n", "#12 CACHED\n", "\n", - "#13 [ 9/21] WORKDIR /var/holoscan\n", + "#13 [10/21] COPY ./tools /var/holoscan/tools\n", "#13 CACHED\n", "\n", - "#14 [ 6/21] RUN chown -R holoscan /var/holoscan\n", + "#14 [12/21] COPY ./pip/requirements.txt /tmp/requirements.txt\n", "#14 CACHED\n", "\n", - "#15 [16/21] RUN pip install /tmp/monai_deploy_app_sdk-0.5.1+25.g31e4165.dirty-py3-none-any.whl\n", + "#15 [ 6/21] RUN chown -R holoscan /var/holoscan\n", "#15 CACHED\n", "\n", - "#16 [ 8/21] RUN chown -R holoscan /var/holoscan/output\n", + "#16 [ 2/21] RUN mkdir -p /etc/holoscan/ && mkdir -p /opt/holoscan/ && mkdir -p /var/holoscan && mkdir -p /opt/holoscan/app && mkdir -p /var/holoscan/input && mkdir -p /var/holoscan/output\n", "#16 CACHED\n", "\n", - "#17 [18/21] COPY ./map/app.json /etc/holoscan/app.json\n", + "#17 [ 3/21] RUN apt-get update && apt-get install -y curl jq && rm -rf /var/lib/apt/lists/*\n", "#17 CACHED\n", "\n", "#18 [ 5/21] RUN useradd -rm -d /home/holoscan -s /bin/bash -g 1000 -G sudo -u 1000 holoscan\n", "#18 CACHED\n", "\n", - "#19 [ 7/21] RUN chown -R holoscan /var/holoscan/input\n", + "#19 [11/21] RUN chmod +x /var/holoscan/tools\n", "#19 CACHED\n", "\n", - "#20 [12/21] COPY ./pip/requirements.txt /tmp/requirements.txt\n", + "#20 [14/21] RUN pip install --no-cache-dir --user -r /tmp/requirements.txt\n", "#20 CACHED\n", "\n", - "#21 [17/21] COPY ./models /opt/holoscan/models\n", - "#21 CACHED\n", - "\n", - "#22 [10/21] COPY ./tools /var/holoscan/tools\n", - "#22 CACHED\n", - "\n", - "#23 [15/21] COPY ./monai_deploy_app_sdk-0.5.1+25.g31e4165.dirty-py3-none-any.whl /tmp/monai_deploy_app_sdk-0.5.1+25.g31e4165.dirty-py3-none-any.whl\n", - "#23 CACHED\n", - "\n", - "#24 [19/21] COPY ./app.config /var/holoscan/app.yaml\n", - "#24 CACHED\n", - "\n", - "#25 [13/21] RUN pip install --upgrade pip\n", - "#25 CACHED\n", + "#21 [15/21] COPY ./monai_deploy_app_sdk-0.5.1+20.gb869749.dirty-py3-none-any.whl /tmp/monai_deploy_app_sdk-0.5.1+20.gb869749.dirty-py3-none-any.whl\n", + "#21 DONE 0.8s\n", + "\n", + "#22 [16/21] RUN pip install /tmp/monai_deploy_app_sdk-0.5.1+20.gb869749.dirty-py3-none-any.whl\n", + "#22 0.711 Defaulting to user installation because normal site-packages is not writeable\n", + "#22 0.833 Processing /tmp/monai_deploy_app_sdk-0.5.1+20.gb869749.dirty-py3-none-any.whl\n", + "#22 0.843 Requirement already satisfied: numpy>=1.21.6 in /usr/local/lib/python3.10/dist-packages (from monai-deploy-app-sdk==0.5.1+20.gb869749.dirty) (1.23.5)\n", + "#22 1.040 Collecting holoscan~=2.0 (from monai-deploy-app-sdk==0.5.1+20.gb869749.dirty)\n", + "#22 1.139 Downloading holoscan-2.0.0-cp310-cp310-manylinux_2_35_x86_64.whl.metadata (6.7 kB)\n", + "#22 1.213 Collecting colorama>=0.4.1 (from monai-deploy-app-sdk==0.5.1+20.gb869749.dirty)\n", + "#22 1.216 Downloading colorama-0.4.6-py2.py3-none-any.whl.metadata (17 kB)\n", + "#22 1.308 Collecting typeguard>=3.0.0 (from monai-deploy-app-sdk==0.5.1+20.gb869749.dirty)\n", + "#22 1.312 Downloading typeguard-4.2.1-py3-none-any.whl.metadata (3.7 kB)\n", + "#22 1.349 Requirement already satisfied: pip>=20.3 in /home/holoscan/.local/lib/python3.10/site-packages (from holoscan~=2.0->monai-deploy-app-sdk==0.5.1+20.gb869749.dirty) (24.0)\n", + "#22 1.350 Requirement already satisfied: cupy-cuda12x==12.2 in /usr/local/lib/python3.10/dist-packages (from holoscan~=2.0->monai-deploy-app-sdk==0.5.1+20.gb869749.dirty) (12.2.0)\n", + "#22 1.351 Requirement already satisfied: cloudpickle==2.2.1 in /usr/local/lib/python3.10/dist-packages (from holoscan~=2.0->monai-deploy-app-sdk==0.5.1+20.gb869749.dirty) (2.2.1)\n", + "#22 1.353 Requirement already satisfied: python-on-whales==0.60.1 in /usr/local/lib/python3.10/dist-packages (from holoscan~=2.0->monai-deploy-app-sdk==0.5.1+20.gb869749.dirty) (0.60.1)\n", + "#22 1.353 Requirement already satisfied: Jinja2==3.1.3 in /usr/local/lib/python3.10/dist-packages (from holoscan~=2.0->monai-deploy-app-sdk==0.5.1+20.gb869749.dirty) (3.1.3)\n", + "#22 1.354 Requirement already satisfied: packaging==23.1 in /usr/local/lib/python3.10/dist-packages (from holoscan~=2.0->monai-deploy-app-sdk==0.5.1+20.gb869749.dirty) (23.1)\n", + "#22 1.355 Requirement already satisfied: pyyaml==6.0 in /usr/local/lib/python3.10/dist-packages (from holoscan~=2.0->monai-deploy-app-sdk==0.5.1+20.gb869749.dirty) (6.0)\n", + "#22 1.356 Requirement already satisfied: requests==2.31.0 in /usr/local/lib/python3.10/dist-packages (from holoscan~=2.0->monai-deploy-app-sdk==0.5.1+20.gb869749.dirty) (2.31.0)\n", + "#22 1.357 Requirement already satisfied: psutil==5.9.6 in /usr/local/lib/python3.10/dist-packages (from holoscan~=2.0->monai-deploy-app-sdk==0.5.1+20.gb869749.dirty) (5.9.6)\n", + "#22 1.468 Collecting wheel-axle-runtime<1.0 (from holoscan~=2.0->monai-deploy-app-sdk==0.5.1+20.gb869749.dirty)\n", + "#22 1.474 Downloading wheel_axle_runtime-0.0.5-py3-none-any.whl.metadata (7.7 kB)\n", + "#22 1.512 Requirement already satisfied: fastrlock>=0.5 in /usr/local/lib/python3.10/dist-packages (from cupy-cuda12x==12.2->holoscan~=2.0->monai-deploy-app-sdk==0.5.1+20.gb869749.dirty) (0.8.2)\n", + "#22 1.515 Requirement already satisfied: MarkupSafe>=2.0 in /usr/local/lib/python3.10/dist-packages (from Jinja2==3.1.3->holoscan~=2.0->monai-deploy-app-sdk==0.5.1+20.gb869749.dirty) (2.1.3)\n", + "#22 1.529 Requirement already satisfied: pydantic<2,>=1.5 in /usr/local/lib/python3.10/dist-packages (from python-on-whales==0.60.1->holoscan~=2.0->monai-deploy-app-sdk==0.5.1+20.gb869749.dirty) (1.10.15)\n", + "#22 1.529 Requirement already satisfied: tqdm in /usr/local/lib/python3.10/dist-packages (from python-on-whales==0.60.1->holoscan~=2.0->monai-deploy-app-sdk==0.5.1+20.gb869749.dirty) (4.66.2)\n", + "#22 1.530 Requirement already satisfied: typer>=0.4.1 in /usr/local/lib/python3.10/dist-packages (from python-on-whales==0.60.1->holoscan~=2.0->monai-deploy-app-sdk==0.5.1+20.gb869749.dirty) (0.12.3)\n", + "#22 1.531 Requirement already satisfied: typing-extensions in /home/holoscan/.local/lib/python3.10/site-packages (from python-on-whales==0.60.1->holoscan~=2.0->monai-deploy-app-sdk==0.5.1+20.gb869749.dirty) (4.11.0)\n", + "#22 1.540 Requirement already satisfied: charset-normalizer<4,>=2 in /usr/local/lib/python3.10/dist-packages (from requests==2.31.0->holoscan~=2.0->monai-deploy-app-sdk==0.5.1+20.gb869749.dirty) (3.3.2)\n", + "#22 1.541 Requirement already satisfied: idna<4,>=2.5 in /usr/local/lib/python3.10/dist-packages (from 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/usr/local/lib/python3.10/dist-packages (from typer>=0.4.1->python-on-whales==0.60.1->holoscan~=2.0->monai-deploy-app-sdk==0.5.1+20.gb869749.dirty) (1.5.4)\n", + "#22 1.588 Requirement already satisfied: rich>=10.11.0 in /usr/local/lib/python3.10/dist-packages (from typer>=0.4.1->python-on-whales==0.60.1->holoscan~=2.0->monai-deploy-app-sdk==0.5.1+20.gb869749.dirty) (13.7.1)\n", + "#22 1.623 Requirement already satisfied: markdown-it-py>=2.2.0 in /usr/local/lib/python3.10/dist-packages (from rich>=10.11.0->typer>=0.4.1->python-on-whales==0.60.1->holoscan~=2.0->monai-deploy-app-sdk==0.5.1+20.gb869749.dirty) (3.0.0)\n", + "#22 1.624 Requirement already satisfied: pygments<3.0.0,>=2.13.0 in /usr/local/lib/python3.10/dist-packages (from rich>=10.11.0->typer>=0.4.1->python-on-whales==0.60.1->holoscan~=2.0->monai-deploy-app-sdk==0.5.1+20.gb869749.dirty) (2.17.2)\n", + "#22 1.645 Requirement already satisfied: mdurl~=0.1 in /usr/local/lib/python3.10/dist-packages (from markdown-it-py>=2.2.0->rich>=10.11.0->typer>=0.4.1->python-on-whales==0.60.1->holoscan~=2.0->monai-deploy-app-sdk==0.5.1+20.gb869749.dirty) (0.1.2)\n", + "#22 1.662 Downloading colorama-0.4.6-py2.py3-none-any.whl (25 kB)\n", + "#22 1.686 Downloading holoscan-2.0.0-cp310-cp310-manylinux_2_35_x86_64.whl (33.2 MB)\n", + "#22 2.182 ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 33.2/33.2 MB 44.5 MB/s eta 0:00:00\n", + "#22 2.187 Downloading typeguard-4.2.1-py3-none-any.whl (34 kB)\n", + "#22 2.210 Downloading wheel_axle_runtime-0.0.5-py3-none-any.whl (12 kB)\n", + "#22 2.567 Installing collected packages: wheel-axle-runtime, typeguard, colorama, holoscan, monai-deploy-app-sdk\n", + "#22 3.333 Successfully installed colorama-0.4.6 holoscan-2.0.0 monai-deploy-app-sdk-0.5.1+20.gb869749.dirty typeguard-4.2.1 wheel-axle-runtime-0.0.5\n", + "#22 DONE 3.7s\n", + "\n", + "#23 [17/21] COPY ./models /opt/holoscan/models\n", + "#23 DONE 0.2s\n", + "\n", + "#24 [18/21] COPY ./map/app.json /etc/holoscan/app.json\n", + "#24 DONE 0.1s\n", + "\n", + "#25 [19/21] COPY ./app.config /var/holoscan/app.yaml\n", + "#25 DONE 0.1s\n", "\n", "#26 [20/21] COPY ./map/pkg.json /etc/holoscan/pkg.json\n", - "#26 CACHED\n", + "#26 DONE 0.1s\n", "\n", "#27 [21/21] COPY ./app /opt/holoscan/app\n", - "#27 DONE 0.3s\n", + "#27 DONE 0.1s\n", "\n", "#28 exporting to docker image format\n", "#28 exporting layers\n", - "#28 exporting layers 0.2s done\n", - "#28 exporting manifest sha256:814514f05787bbad414758721a0e6e6c3bc4c8e15be135868bd5d22125ba1323 0.0s done\n", - "#28 exporting config sha256:5effa5125f3b256ed2e1063cc763040b2eac0f3a49c281b3fecbe3ebbddedce9 0.0s done\n", + "#28 exporting layers 4.7s done\n", + "#28 exporting manifest sha256:272f9320d555ec164d2cdbdf3af72c2508a3768b3438478dfebc976ab20bdef5 0.0s done\n", + "#28 exporting config sha256:af6b96cbe7081e40c1393d1adcbb0d90e60f1eee0f770de931c17ec7e661922f 0.0s done\n", "#28 sending tarball\n", "#28 ...\n", "\n", "#29 importing to 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"#30 writing layer sha256:f7702077ced42a1ee35e7f5e45f72634328ff3bcfe3f57735ba80baa5ec45daf done\n", - "#30 writing layer sha256:fa66a49172c6e821a1bace57c007c01da10cbc61507c44f8cdfeed8c4e5febab done\n", - "#30 writing config sha256:374c8d5f4f72f0b0a709492f153a59ebd070e903971483f2cefb3e9e45bda48a 0.0s done\n", - "#30 writing cache manifest sha256:00a618573e1678dbe93ffce1675eee120201710fa121207b43875632f6799a58 0.0s done\n", - "#30 DONE 0.7s\n", - "[2024-04-10 16:43:00,358] [INFO] (packager) - Build Summary:\n", + "#30 writing layer sha256:f65d191416580d6c38e3d95eee12377b75a4df548be1492618ce2a8c3c41b99e done\n", + "#30 writing config sha256:d8b1ede40893d3af61eaf7d4d58ae3afaa55e9e0fc7722d020635c545f81df0c 0.0s done\n", + "#30 preparing build cache for export 2.6s done\n", + "#30 writing cache manifest sha256:00058bfc69cbf02a85b5242dfe17b06ca30b9c7312be3f7b2cf3aa215c57747f 0.0s done\n", + "#30 DONE 2.6s\n", + "[2024-04-23 15:44:38,817] [INFO] (packager) - Build Summary:\n", "\n", "Platform: x64-workstation/dgpu\n", " Status: Succeeded\n", @@ -1872,7 +1944,7 @@ "name": "stdout", "output_type": "stream", "text": [ - "my_app-x64-workstation-dgpu-linux-amd64 1.0 5effa5125f3b About a minute ago 17.5GB\n" + "my_app-x64-workstation-dgpu-linux-amd64 1.0 af6b96cbe708 About a minute ago 17.7GB\n" ] } ], @@ -1900,22 +1972,22 @@ "text": [ "output\n", "dcm\n", - "[2024-04-10 16:43:03,135] [INFO] (runner) - Checking dependencies...\n", - "[2024-04-10 16:43:03,135] [INFO] (runner) - --> Verifying if \"docker\" is installed...\n", + "[2024-04-23 15:44:40,497] [INFO] (runner) - Checking dependencies...\n", + "[2024-04-23 15:44:40,497] [INFO] (runner) - --> Verifying if \"docker\" is installed...\n", "\n", - "[2024-04-10 16:43:03,135] [INFO] (runner) - --> Verifying if \"docker-buildx\" is installed...\n", + "[2024-04-23 15:44:40,497] [INFO] (runner) - --> Verifying if \"docker-buildx\" is installed...\n", "\n", - "[2024-04-10 16:43:03,135] [INFO] (runner) - --> Verifying if \"my_app-x64-workstation-dgpu-linux-amd64:1.0\" is available...\n", + "[2024-04-23 15:44:40,497] [INFO] (runner) - --> Verifying if \"my_app-x64-workstation-dgpu-linux-amd64:1.0\" is available...\n", "\n", - "[2024-04-10 16:43:03,211] [INFO] (runner) - Reading HAP/MAP manifest...\n", - "\u001b[sPreparing to copy...\u001b[?25l\u001b[u\u001b[2KCopying from container - 0B\u001b[?25h\u001b[u\u001b[2KSuccessfully copied 2.56kB to /tmp/tmpbbeybrjp/app.json\n", - "\u001b[sPreparing to copy...\u001b[?25l\u001b[u\u001b[2KCopying from container - 0B\u001b[?25h\u001b[u\u001b[2KSuccessfully copied 2.05kB to /tmp/tmpbbeybrjp/pkg.json\n", - "[2024-04-10 16:43:03,567] [INFO] (runner) - --> Verifying if \"nvidia-ctk\" is installed...\n", + "[2024-04-23 15:44:40,571] [INFO] (runner) - Reading HAP/MAP manifest...\n", + "\u001b[sPreparing to copy...\u001b[?25l\u001b[u\u001b[2KCopying from container - 0B\u001b[?25h\u001b[u\u001b[2KSuccessfully copied 2.56kB to /tmp/tmpojmzf387/app.json\n", + "\u001b[sPreparing to copy...\u001b[?25l\u001b[u\u001b[2KCopying from container - 0B\u001b[?25h\u001b[u\u001b[2KSuccessfully copied 2.05kB to /tmp/tmpojmzf387/pkg.json\n", + "[2024-04-23 15:44:41,518] [INFO] (runner) - --> Verifying if \"nvidia-ctk\" is installed...\n", "\n", - "[2024-04-10 16:43:03,568] [INFO] (runner) - --> Verifying \"nvidia-ctk\" version...\n", + "[2024-04-23 15:44:41,518] [INFO] (runner) - --> Verifying \"nvidia-ctk\" version...\n", "\n", - "[2024-04-10 16:43:03,864] [INFO] (common) - Launching container (5135fc45ca94) using image 'my_app-x64-workstation-dgpu-linux-amd64:1.0'...\n", - " container name: optimistic_jang\n", + "[2024-04-23 15:44:41,869] [INFO] (common) - Launching container (a6bc36c774bd) using image 'my_app-x64-workstation-dgpu-linux-amd64:1.0'...\n", + " container name: dreamy_goldberg\n", " host name: mingq-dt\n", " network: host\n", " user: 1000:1000\n", @@ -1925,95 +1997,93 @@ " shared memory size: 67108864\n", " devices: \n", " group_add: 44\n", - "2024-04-10 23:43:05 [INFO] Launching application python3 /opt/holoscan/app ...\n", + "2024-04-23 22:44:42 [INFO] Launching application python3 /opt/holoscan/app ...\n", "\n", - "[2024-04-10 23:43:09,781] [INFO] (root) - Parsed args: Namespace(log_level=None, input=None, output=None, model=None, workdir=None, argv=['/opt/holoscan/app'])\n", + "[2024-04-23 22:44:46,465] [INFO] (root) - Parsed args: Namespace(log_level=None, input=None, output=None, model=None, workdir=None, argv=['/opt/holoscan/app'])\n", "\n", - "[2024-04-10 23:43:09,784] [INFO] (root) - AppContext object: AppContext(input_path=/var/holoscan/input, output_path=/var/holoscan/output, model_path=/opt/holoscan/models, workdir=/var/holoscan)\n", + "[2024-04-23 22:44:46,467] [INFO] (root) - AppContext object: AppContext(input_path=/var/holoscan/input, output_path=/var/holoscan/output, model_path=/opt/holoscan/models, workdir=/var/holoscan)\n", "\n", - "[2024-04-10 23:43:09,784] [INFO] (app.AISpleenSegApp) - App input and output path: /var/holoscan/input, /var/holoscan/output\n", + "[2024-04-23 22:44:46,467] [INFO] (app.AISpleenSegApp) - App input and output path: /var/holoscan/input, /var/holoscan/output\n", "\n", "[info] [app_driver.cpp:1161] Launching the driver/health checking service\n", "\n", - "[info] [gxf_executor.cpp:211] Creating context\n", + "[info] [gxf_executor.cpp:247] Creating context\n", "\n", "[info] [server.cpp:87] Health checking server listening on 0.0.0.0:8777\n", "\n", - "[info] [gxf_executor.cpp:1674] Loading extensions from configs...\n", - "\n", - "[info] [gxf_executor.cpp:1864] Activating Graph...\n", + "[info] [gxf_executor.cpp:1672] Loading extensions from configs...\n", "\n", - "[info] [gxf_executor.cpp:1894] Running Graph...\n", + "[info] [gxf_executor.cpp:1842] Activating Graph...\n", "\n", - "[info] [gxf_executor.cpp:1896] Waiting for completion...\n", + "\u001b[0m2024-04-23 22:44:46.511 INFO gxf/std/greedy_scheduler.cpp@191: Scheduling 6 entities\u001b[0m\n", "\n", - "[info] [gxf_executor.cpp:1897] Graph execution waiting. Fragment: \n", + "[info] [gxf_executor.cpp:1874] Running Graph...\n", "\n", - "[info] [greedy_scheduler.cpp:190] Scheduling 6 entities\n", + "[info] [gxf_executor.cpp:1876] Waiting for completion...\n", "\n", - "[2024-04-10 23:43:09,895] [INFO] (monai.deploy.operators.dicom_data_loader_operator.DICOMDataLoaderOperator) - No or invalid input path from the optional input port: None\n", + "[2024-04-23 22:44:46,513] [INFO] (monai.deploy.operators.dicom_data_loader_operator.DICOMDataLoaderOperator) - No or invalid input path from the optional input port: None\n", "\n", - "[2024-04-10 23:43:10,851] [INFO] (root) - Finding series for Selection named: CT Series\n", + "[2024-04-23 22:44:46,974] [INFO] (root) - Finding series for Selection named: CT Series\n", "\n", - "[2024-04-10 23:43:10,851] [INFO] (root) - Searching study, : 1.3.6.1.4.1.14519.5.2.1.7085.2626.822645453932810382886582736291\n", + "[2024-04-23 22:44:46,974] [INFO] (root) - Searching study, : 1.3.6.1.4.1.14519.5.2.1.7085.2626.822645453932810382886582736291\n", "\n", " # of series: 1\n", "\n", - "[2024-04-10 23:43:10,851] [INFO] (root) - Working on series, instance UID: 1.3.6.1.4.1.14519.5.2.1.7085.2626.119403521930927333027265674239\n", + "[2024-04-23 22:44:46,974] [INFO] (root) - Working on series, instance UID: 1.3.6.1.4.1.14519.5.2.1.7085.2626.119403521930927333027265674239\n", "\n", - "[2024-04-10 23:43:10,851] [INFO] (root) - On attribute: 'StudyDescription' to match value: '(.*?)'\n", + "[2024-04-23 22:44:46,974] [INFO] (root) - On attribute: 'StudyDescription' to match value: '(.*?)'\n", "\n", - "[2024-04-10 23:43:10,852] [INFO] (root) - Series attribute StudyDescription value: CT ABDOMEN W IV CONTRAST\n", + "[2024-04-23 22:44:46,974] [INFO] (root) - Series attribute StudyDescription value: CT ABDOMEN W IV CONTRAST\n", "\n", - "[2024-04-10 23:43:10,852] [INFO] (root) - Series attribute string value did not match. Try regEx.\n", + "[2024-04-23 22:44:46,974] [INFO] (root) - Series attribute string value did not match. Try regEx.\n", "\n", - "[2024-04-10 23:43:10,852] [INFO] (root) - On attribute: 'Modality' to match value: '(?i)CT'\n", + "[2024-04-23 22:44:46,974] [INFO] (root) - On attribute: 'Modality' to match value: '(?i)CT'\n", "\n", - "[2024-04-10 23:43:10,852] [INFO] (root) - Series attribute Modality value: CT\n", + "[2024-04-23 22:44:46,974] [INFO] (root) - Series attribute Modality value: CT\n", "\n", - "[2024-04-10 23:43:10,852] [INFO] (root) - Series attribute string value did not match. Try regEx.\n", + "[2024-04-23 22:44:46,974] [INFO] (root) - Series attribute string value did not match. Try regEx.\n", "\n", - "[2024-04-10 23:43:10,852] [INFO] (root) - On attribute: 'SeriesDescription' to match value: '(.*?)'\n", + "[2024-04-23 22:44:46,974] [INFO] (root) - On attribute: 'SeriesDescription' to match value: '(.*?)'\n", "\n", - "[2024-04-10 23:43:10,852] [INFO] (root) - Series attribute SeriesDescription value: ABD/PANC 3.0 B31f\n", + "[2024-04-23 22:44:46,974] [INFO] (root) - Series attribute SeriesDescription value: ABD/PANC 3.0 B31f\n", "\n", - "[2024-04-10 23:43:10,852] [INFO] (root) - Series attribute string value did not match. Try regEx.\n", + "[2024-04-23 22:44:46,974] [INFO] (root) - Series attribute string value did not match. Try regEx.\n", "\n", - "[2024-04-10 23:43:10,852] [INFO] (root) - On attribute: 'ImageType' to match value: ['PRIMARY', 'ORIGINAL']\n", + "[2024-04-23 22:44:46,974] [INFO] (root) - On attribute: 'ImageType' to match value: ['PRIMARY', 'ORIGINAL']\n", "\n", - "[2024-04-10 23:43:10,852] [INFO] (root) - Series attribute ImageType value: None\n", + "[2024-04-23 22:44:46,974] [INFO] (root) - Series attribute ImageType value: None\n", "\n", - "[2024-04-10 23:43:10,852] [INFO] (root) - Selected Series, UID: 1.3.6.1.4.1.14519.5.2.1.7085.2626.119403521930927333027265674239\n", + "[2024-04-23 22:44:46,974] [INFO] (root) - Selected Series, UID: 1.3.6.1.4.1.14519.5.2.1.7085.2626.119403521930927333027265674239\n", "\n", - "[2024-04-10 23:43:11,263] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - Converted Image object metadata:\n", + "[2024-04-23 22:44:47,194] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - Converted Image object metadata:\n", "\n", - "[2024-04-10 23:43:11,263] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - SeriesInstanceUID: 1.3.6.1.4.1.14519.5.2.1.7085.2626.119403521930927333027265674239, type \n", + "[2024-04-23 22:44:47,194] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - SeriesInstanceUID: 1.3.6.1.4.1.14519.5.2.1.7085.2626.119403521930927333027265674239, type \n", "\n", - "[2024-04-10 23:43:11,263] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - SeriesDate: 20090831, type \n", + "[2024-04-23 22:44:47,194] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - SeriesDate: 20090831, type \n", "\n", - "[2024-04-10 23:43:11,263] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - SeriesTime: 101721.452, type \n", + "[2024-04-23 22:44:47,194] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - SeriesTime: 101721.452, type \n", "\n", - "[2024-04-10 23:43:11,263] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - Modality: CT, type \n", + "[2024-04-23 22:44:47,194] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - Modality: CT, type \n", "\n", - "[2024-04-10 23:43:11,263] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - SeriesDescription: ABD/PANC 3.0 B31f, type \n", + "[2024-04-23 22:44:47,194] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - SeriesDescription: ABD/PANC 3.0 B31f, type \n", "\n", - "[2024-04-10 23:43:11,263] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - PatientPosition: HFS, type \n", + "[2024-04-23 22:44:47,194] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - PatientPosition: HFS, type \n", "\n", - "[2024-04-10 23:43:11,263] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - SeriesNumber: 8, type \n", + "[2024-04-23 22:44:47,194] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - SeriesNumber: 8, type \n", "\n", - "[2024-04-10 23:43:11,263] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - row_pixel_spacing: 0.7890625, type \n", + "[2024-04-23 22:44:47,195] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - row_pixel_spacing: 0.7890625, type \n", "\n", - "[2024-04-10 23:43:11,264] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - col_pixel_spacing: 0.7890625, type \n", + "[2024-04-23 22:44:47,195] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - col_pixel_spacing: 0.7890625, type \n", "\n", - "[2024-04-10 23:43:11,264] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - depth_pixel_spacing: 1.5, type \n", + "[2024-04-23 22:44:47,195] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - depth_pixel_spacing: 1.5, type \n", "\n", - "[2024-04-10 23:43:11,264] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - row_direction_cosine: [1.0, 0.0, 0.0], type \n", + "[2024-04-23 22:44:47,195] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - row_direction_cosine: [1.0, 0.0, 0.0], type \n", "\n", - "[2024-04-10 23:43:11,264] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - col_direction_cosine: [0.0, 1.0, 0.0], type \n", + "[2024-04-23 22:44:47,195] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - col_direction_cosine: [0.0, 1.0, 0.0], type \n", "\n", - "[2024-04-10 23:43:11,264] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - depth_direction_cosine: [0.0, 0.0, 1.0], type \n", + "[2024-04-23 22:44:47,195] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - depth_direction_cosine: [0.0, 0.0, 1.0], type \n", "\n", - "[2024-04-10 23:43:11,264] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - dicom_affine_transform: [[ 0.7890625 0. 0. -197.60547 ]\n", + "[2024-04-23 22:44:47,195] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - dicom_affine_transform: [[ 0.7890625 0. 0. -197.60547 ]\n", "\n", " [ 0. 0.7890625 0. -398.60547 ]\n", "\n", @@ -2021,7 +2091,7 @@ "\n", " [ 0. 0. 0. 1. ]], type \n", "\n", - "[2024-04-10 23:43:11,264] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - nifti_affine_transform: [[ -0.7890625 -0. -0. 197.60547 ]\n", + "[2024-04-23 22:44:47,195] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - nifti_affine_transform: [[ -0.7890625 -0. -0. 197.60547 ]\n", "\n", " [ -0. -0.7890625 -0. 398.60547 ]\n", "\n", @@ -2029,65 +2099,63 @@ "\n", " [ 0. 0. 0. 1. ]], type \n", "\n", - "[2024-04-10 23:43:11,264] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - StudyInstanceUID: 1.3.6.1.4.1.14519.5.2.1.7085.2626.822645453932810382886582736291, type \n", + "[2024-04-23 22:44:47,196] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - StudyInstanceUID: 1.3.6.1.4.1.14519.5.2.1.7085.2626.822645453932810382886582736291, type \n", "\n", - "[2024-04-10 23:43:11,264] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - StudyID: , type \n", + "[2024-04-23 22:44:47,196] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - StudyID: , type \n", "\n", - "[2024-04-10 23:43:11,264] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - StudyDate: 20090831, type \n", + "[2024-04-23 22:44:47,196] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - StudyDate: 20090831, type \n", "\n", - "[2024-04-10 23:43:11,264] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - StudyTime: 095948.599, type \n", + "[2024-04-23 22:44:47,196] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - StudyTime: 095948.599, type \n", "\n", - "[2024-04-10 23:43:11,264] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - StudyDescription: CT ABDOMEN W IV CONTRAST, type \n", + "[2024-04-23 22:44:47,196] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - StudyDescription: CT ABDOMEN W IV CONTRAST, type \n", "\n", - "[2024-04-10 23:43:11,264] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - AccessionNumber: 5471978513296937, type \n", + "[2024-04-23 22:44:47,196] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - AccessionNumber: 5471978513296937, type \n", "\n", - "[2024-04-10 23:43:11,264] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - selection_name: CT Series, type \n", + "[2024-04-23 22:44:47,196] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - selection_name: CT Series, type \n", "\n", - "2024-04-10 23:43:12,277 INFO image_writer.py:197 - writing: /var/holoscan/output/saved_images_folder/1.3.6.1.4.1.14519.5.2.1.7085.2626/1.3.6.1.4.1.14519.5.2.1.7085.2626.nii\n", + "2024-04-23 22:44:47,986 INFO image_writer.py:197 - writing: /var/holoscan/output/saved_images_folder/1.3.6.1.4.1.14519.5.2.1.7085.2626/1.3.6.1.4.1.14519.5.2.1.7085.2626.nii\n", "\n", - "2024-04-10 23:43:16,177 INFO image_writer.py:197 - writing: /var/holoscan/output/saved_images_folder/1.3.6.1.4.1.14519.5.2.1.7085.2626/1.3.6.1.4.1.14519.5.2.1.7085.2626_seg.nii\n", + "2024-04-23 22:44:51,638 INFO image_writer.py:197 - writing: /var/holoscan/output/saved_images_folder/1.3.6.1.4.1.14519.5.2.1.7085.2626/1.3.6.1.4.1.14519.5.2.1.7085.2626_seg.nii\n", "\n", - "[2024-04-10 23:43:17,870] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - Output Seg image numpy array shaped: (204, 512, 512)\n", + "[2024-04-23 22:44:53,491] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - Output Seg image numpy array shaped: (204, 512, 512)\n", "\n", - "[2024-04-10 23:43:17,876] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - Output Seg image pixel max value: 1\n", + "[2024-04-23 22:44:53,497] [INFO] (monai.deploy.operators.monai_seg_inference_operator.MonaiSegInferenceOperator) - Output Seg image pixel max value: 1\n", "\n", "/home/holoscan/.local/lib/python3.10/site-packages/highdicom/valuerep.py:54: UserWarning: The string \"C3N-00198\" is unlikely to represent the intended person name since it contains only a single component. Construct a person name according to the format in described in https://dicom.nema.org/dicom/2013/output/chtml/part05/sect_6.2.html#sect_6.2.1.2, or, in pydicom 2.2.0 or later, use the pydicom.valuerep.PersonName.from_named_components() method to construct the person name correctly. If a single-component name is really intended, add a trailing caret character to disambiguate the name.\n", "\n", " warnings.warn(\n", "\n", - "[2024-04-10 23:43:19,386] [INFO] (highdicom.base) - copy Image-related attributes from dataset \"1.3.6.1.4.1.14519.5.2.1.7085.2626.936983343951485811186213470191\"\n", - "\n", - "[2024-04-10 23:43:19,386] [INFO] (highdicom.base) - copy attributes of module \"Specimen\"\n", + "[2024-04-23 22:44:54,694] [INFO] (highdicom.base) - copy Image-related attributes from dataset \"1.3.6.1.4.1.14519.5.2.1.7085.2626.936983343951485811186213470191\"\n", "\n", - "[2024-04-10 23:43:19,386] [INFO] (highdicom.base) - copy Patient-related attributes from dataset \"1.3.6.1.4.1.14519.5.2.1.7085.2626.936983343951485811186213470191\"\n", + "[2024-04-23 22:44:54,694] [INFO] (highdicom.base) - copy attributes of module \"Specimen\"\n", "\n", - "[2024-04-10 23:43:19,386] [INFO] (highdicom.base) - copy attributes of module \"Patient\"\n", + "[2024-04-23 22:44:54,694] [INFO] (highdicom.base) - copy Patient-related attributes from dataset \"1.3.6.1.4.1.14519.5.2.1.7085.2626.936983343951485811186213470191\"\n", "\n", - "[2024-04-10 23:43:19,387] [INFO] (highdicom.base) - copy attributes of module \"Clinical Trial Subject\"\n", + "[2024-04-23 22:44:54,694] [INFO] (highdicom.base) - copy attributes of module \"Patient\"\n", "\n", - "[2024-04-10 23:43:19,387] [INFO] (highdicom.base) - copy Study-related attributes from dataset \"1.3.6.1.4.1.14519.5.2.1.7085.2626.936983343951485811186213470191\"\n", + "[2024-04-23 22:44:54,694] [INFO] (highdicom.base) - copy attributes of module \"Clinical Trial Subject\"\n", "\n", - "[2024-04-10 23:43:19,387] [INFO] (highdicom.base) - copy attributes of module \"General Study\"\n", + "[2024-04-23 22:44:54,694] [INFO] (highdicom.base) - copy Study-related attributes from dataset \"1.3.6.1.4.1.14519.5.2.1.7085.2626.936983343951485811186213470191\"\n", "\n", - "[2024-04-10 23:43:19,387] [INFO] (highdicom.base) - copy attributes of module \"Patient Study\"\n", + "[2024-04-23 22:44:54,694] [INFO] (highdicom.base) - copy attributes of module \"General Study\"\n", "\n", - "[2024-04-10 23:43:19,388] [INFO] (highdicom.base) - copy attributes of module \"Clinical Trial Study\"\n", + "[2024-04-23 22:44:54,695] [INFO] (highdicom.base) - copy attributes of module \"Patient Study\"\n", "\n", - "[info] [greedy_scheduler.cpp:369] Scheduler stopped: Some entities are waiting for execution, but there are no periodic or async entities to get out of the deadlock.\n", + "[2024-04-23 22:44:54,695] [INFO] (highdicom.base) - copy attributes of module \"Clinical Trial Study\"\n", "\n", - "[info] [greedy_scheduler.cpp:398] Scheduler finished.\n", + "\u001b[0m2024-04-23 22:44:54.787 INFO gxf/std/greedy_scheduler.cpp@372: Scheduler stopped: Some entities are waiting for execution, but there are no periodic or async entities to get out of the deadlock.\u001b[0m\n", "\n", - "[info] [gxf_executor.cpp:1906] Graph execution deactivating. Fragment: \n", + "\u001b[0m2024-04-23 22:44:54.788 INFO gxf/std/greedy_scheduler.cpp@401: Scheduler finished.\u001b[0m\n", "\n", - "[info] [gxf_executor.cpp:1907] Deactivating Graph...\n", + "[info] [gxf_executor.cpp:1879] Deactivating Graph...\n", "\n", - "[info] [gxf_executor.cpp:1910] Graph execution finished. Fragment: \n", + "[info] [gxf_executor.cpp:1887] Graph execution finished.\n", "\n", - "[2024-04-10 23:43:19,487] [INFO] (app.AISpleenSegApp) - End run\n", + "[2024-04-23 22:44:54,793] [INFO] (app.AISpleenSegApp) - End run\n", "\n", - "[info] [gxf_executor.cpp:230] Destroying context\n", + "[info] [gxf_executor.cpp:275] Destroying context\n", "\n", - "[2024-04-10 16:43:21,271] [INFO] (common) - Container 'optimistic_jang'(5135fc45ca94) exited.\n" + "[2024-04-23 15:44:56,376] [INFO] (common) - Container 'dreamy_goldberg'(a6bc36c774bd) exited.\n" ] } ], @@ -2109,7 +2177,7 @@ "output_type": "stream", "text": [ "output:\n", - "1.2.826.0.1.3680043.10.511.3.10550615266418892085330010762562517.dcm\n", + "1.2.826.0.1.3680043.10.511.3.57272145768055517649062567242794544.dcm\n", "saved_images_folder\n", "\n", "output/saved_images_folder:\n", diff --git a/notebooks/tutorials/03_segmentation_viz_app.ipynb b/notebooks/tutorials/03_segmentation_viz_app.ipynb index fbaab63e..a2c29a98 100644 --- a/notebooks/tutorials/03_segmentation_viz_app.ipynb +++ b/notebooks/tutorials/03_segmentation_viz_app.ipynb @@ -85,7 +85,7 @@ }, { "cell_type": "code", - "execution_count": 1, + "execution_count": 3, "metadata": {}, "outputs": [], "source": [ @@ -123,7 +123,7 @@ }, { "cell_type": "code", - "execution_count": 2, + "execution_count": 4, "metadata": {}, "outputs": [ { @@ -132,23 +132,20 @@ "text": [ "Requirement already satisfied: gdown in /home/mqin/src/monai-deploy-app-sdk/.venv/lib/python3.10/site-packages (5.1.0)\n", "Requirement already satisfied: beautifulsoup4 in /home/mqin/src/monai-deploy-app-sdk/.venv/lib/python3.10/site-packages (from gdown) (4.12.3)\n", - "Requirement already satisfied: filelock in /home/mqin/src/monai-deploy-app-sdk/.venv/lib/python3.10/site-packages (from gdown) (3.13.3)\n", + "Requirement already satisfied: filelock in /home/mqin/src/monai-deploy-app-sdk/.venv/lib/python3.10/site-packages (from gdown) (3.13.4)\n", "Requirement already satisfied: requests[socks] in /home/mqin/src/monai-deploy-app-sdk/.venv/lib/python3.10/site-packages (from gdown) (2.31.0)\n", "Requirement already satisfied: tqdm in /home/mqin/src/monai-deploy-app-sdk/.venv/lib/python3.10/site-packages (from gdown) (4.66.2)\n", "Requirement already satisfied: soupsieve>1.2 in /home/mqin/src/monai-deploy-app-sdk/.venv/lib/python3.10/site-packages (from beautifulsoup4->gdown) (2.5)\n", "Requirement already satisfied: charset-normalizer<4,>=2 in /home/mqin/src/monai-deploy-app-sdk/.venv/lib/python3.10/site-packages (from requests[socks]->gdown) (3.3.2)\n", - "Requirement already satisfied: idna<4,>=2.5 in /home/mqin/src/monai-deploy-app-sdk/.venv/lib/python3.10/site-packages (from requests[socks]->gdown) (3.6)\n", - "Requirement already satisfied: urllib3<3,>=1.21.1 in /home/mqin/src/monai-deploy-app-sdk/.venv/lib/python3.10/site-packages (from requests[socks]->gdown) (1.26.18)\n", + "Requirement already satisfied: idna<4,>=2.5 in /home/mqin/src/monai-deploy-app-sdk/.venv/lib/python3.10/site-packages (from requests[socks]->gdown) (3.7)\n", + "Requirement already satisfied: urllib3<3,>=1.21.1 in /home/mqin/src/monai-deploy-app-sdk/.venv/lib/python3.10/site-packages (from requests[socks]->gdown) (2.2.1)\n", "Requirement already satisfied: certifi>=2017.4.17 in /home/mqin/src/monai-deploy-app-sdk/.venv/lib/python3.10/site-packages (from requests[socks]->gdown) (2024.2.2)\n", "Requirement already satisfied: PySocks!=1.5.7,>=1.5.6 in /home/mqin/src/monai-deploy-app-sdk/.venv/lib/python3.10/site-packages (from requests[socks]->gdown) (1.7.1)\n", - "\n", - "\u001b[1m[\u001b[0m\u001b[34;49mnotice\u001b[0m\u001b[1;39;49m]\u001b[0m\u001b[39;49m A new release of pip is available: \u001b[0m\u001b[31;49m23.3.2\u001b[0m\u001b[39;49m -> \u001b[0m\u001b[32;49m24.0\u001b[0m\n", - "\u001b[1m[\u001b[0m\u001b[34;49mnotice\u001b[0m\u001b[1;39;49m]\u001b[0m\u001b[39;49m To update, run: \u001b[0m\u001b[32;49mpip install --upgrade pip\u001b[0m\n", "Downloading...\n", "From (original): https://drive.google.com/uc?id=1Uds8mEvdGNYUuvFpTtCQ8gNU97bAPCaQ\n", - "From (redirected): https://drive.google.com/uc?id=1Uds8mEvdGNYUuvFpTtCQ8gNU97bAPCaQ&confirm=t&uuid=dcd169d3-fd74-406b-84df-e849918958a1\n", + "From (redirected): https://drive.google.com/uc?id=1Uds8mEvdGNYUuvFpTtCQ8gNU97bAPCaQ&confirm=t&uuid=c8244ec0-ca91-472f-8701-075a197bb44e\n", "To: /home/mqin/src/monai-deploy-app-sdk/notebooks/tutorials/ai_spleen_seg_bundle_data.zip\n", - "100%|██████████████████████████████████████| 79.4M/79.4M [00:00<00:00, 81.5MB/s]\n", + "100%|██████████████████████████████████████| 79.4M/79.4M [00:00<00:00, 99.7MB/s]\n", "Archive: ai_spleen_seg_bundle_data.zip\n", " inflating: dcm/1-001.dcm \n", " inflating: dcm/1-002.dcm \n", @@ -385,7 +382,7 @@ }, { "cell_type": "code", - "execution_count": 3, + "execution_count": 5, "metadata": {}, "outputs": [ { @@ -418,7 +415,7 @@ }, { "cell_type": "code", - "execution_count": 4, + "execution_count": 6, "metadata": {}, "outputs": [], "source": [ @@ -478,7 +475,7 @@ }, { "cell_type": "code", - "execution_count": 5, + "execution_count": 7, "metadata": {}, "outputs": [], "source": [ @@ -628,45 +625,56 @@ }, { "cell_type": "code", - "execution_count": 6, + "execution_count": 8, "metadata": {}, "outputs": [ { "name": "stderr", "output_type": "stream", "text": [ - "[2024-04-10 10:46:21,853] [INFO] (root) - Parsed args: Namespace(log_level=None, input=None, output=None, model=None, workdir=None, argv=[])\n", - "[2024-04-10 10:46:21,859] [INFO] (root) - AppContext object: AppContext(input_path=dcm, output_path=output, model_path=models, workdir=)\n", - "[2024-04-10 10:46:21,866] [INFO] (root) - End compose\n", - "[info] [gxf_executor.cpp:211] Creating context\n", - "[info] [gxf_executor.cpp:1674] Loading extensions from configs...\n", - "[info] [gxf_executor.cpp:1864] Activating Graph...\n", - "[info] [gxf_executor.cpp:1894] Running Graph...\n", - "[info] [gxf_executor.cpp:1896] Waiting for completion...\n", - "[info] [gxf_executor.cpp:1897] Graph execution waiting. Fragment: \n", - "[info] [greedy_scheduler.cpp:190] Scheduling 10 entities\n", - "[2024-04-10 10:46:21,911] [INFO] (monai.deploy.operators.dicom_data_loader_operator.DICOMDataLoaderOperator) - No or invalid input path from the optional input port: None\n", - "[2024-04-10 10:46:22,254] [INFO] (root) - Finding series for Selection named: CT Series\n", - "[2024-04-10 10:46:22,256] [INFO] (root) - Searching study, : 1.3.6.1.4.1.14519.5.2.1.7085.2626.822645453932810382886582736291\n", + "[2024-04-23 17:21:11,103] [INFO] (root) - Parsed args: Namespace(log_level=None, input=None, output=None, model=None, workdir=None, argv=[])\n", + "[2024-04-23 17:21:11,110] [INFO] (root) - AppContext object: AppContext(input_path=dcm, output_path=output, model_path=models, workdir=)\n", + "[2024-04-23 17:21:11,119] [INFO] (root) - End compose\n", + "[info] [gxf_executor.cpp:247] Creating context\n", + "[info] [gxf_executor.cpp:1672] Loading extensions from configs...\n", + "[info] [gxf_executor.cpp:1842] Activating Graph...\n", + "[info] [gxf_executor.cpp:1874] Running Graph...\n", + "[info] [gxf_executor.cpp:1876] Waiting for completion...\n", + "[2024-04-23 17:21:11,172] [INFO] (monai.deploy.operators.dicom_data_loader_operator.DICOMDataLoaderOperator) - No or invalid input path from the optional input port: None\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "\u001b[0m2024-04-23 17:21:11.171 INFO gxf/std/greedy_scheduler.cpp@191: Scheduling 10 entities\u001b[0m\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "[2024-04-23 17:21:11,733] [INFO] (root) - Finding series for Selection named: CT Series\n", + "[2024-04-23 17:21:11,734] [INFO] (root) - Searching study, : 1.3.6.1.4.1.14519.5.2.1.7085.2626.822645453932810382886582736291\n", " # of series: 1\n", - "[2024-04-10 10:46:22,257] [INFO] (root) - Working on series, instance UID: 1.3.6.1.4.1.14519.5.2.1.7085.2626.119403521930927333027265674239\n", - "[2024-04-10 10:46:22,257] [INFO] (root) - On attribute: 'StudyDescription' to match value: '(.*?)'\n", - "[2024-04-10 10:46:22,258] [INFO] (root) - Series attribute StudyDescription value: CT ABDOMEN W IV CONTRAST\n", - "[2024-04-10 10:46:22,259] [INFO] (root) - Series attribute string value did not match. Try regEx.\n", - "[2024-04-10 10:46:22,261] [INFO] (root) - On attribute: 'Modality' to match value: '(?i)CT'\n", - "[2024-04-10 10:46:22,262] [INFO] (root) - Series attribute Modality value: CT\n", - "[2024-04-10 10:46:22,262] [INFO] (root) - Series attribute string value did not match. Try regEx.\n", - "[2024-04-10 10:46:22,263] [INFO] (root) - On attribute: 'SeriesDescription' to match value: '(.*?)'\n", - "[2024-04-10 10:46:22,264] [INFO] (root) - Series attribute SeriesDescription value: ABD/PANC 3.0 B31f\n", - "[2024-04-10 10:46:22,265] [INFO] (root) - Series attribute string value did not match. Try regEx.\n", - "[2024-04-10 10:46:22,265] [INFO] (root) - Selected Series, UID: 1.3.6.1.4.1.14519.5.2.1.7085.2626.119403521930927333027265674239\n", - "[2024-04-10 10:46:22,497] [INFO] (root) - Parsing from bundle_path: /home/mqin/src/monai-deploy-app-sdk/notebooks/tutorials/models/model/model.ts\n" + "[2024-04-23 17:21:11,735] [INFO] (root) - Working on series, instance UID: 1.3.6.1.4.1.14519.5.2.1.7085.2626.119403521930927333027265674239\n", + "[2024-04-23 17:21:11,736] [INFO] (root) - On attribute: 'StudyDescription' to match value: '(.*?)'\n", + "[2024-04-23 17:21:11,736] [INFO] (root) - Series attribute StudyDescription value: CT ABDOMEN W IV CONTRAST\n", + "[2024-04-23 17:21:11,737] [INFO] (root) - Series attribute string value did not match. Try regEx.\n", + "[2024-04-23 17:21:11,737] [INFO] (root) - On attribute: 'Modality' to match value: '(?i)CT'\n", + "[2024-04-23 17:21:11,738] [INFO] (root) - Series attribute Modality value: CT\n", + "[2024-04-23 17:21:11,738] [INFO] (root) - Series attribute string value did not match. Try regEx.\n", + "[2024-04-23 17:21:11,739] [INFO] (root) - On attribute: 'SeriesDescription' to match value: '(.*?)'\n", + "[2024-04-23 17:21:11,739] [INFO] (root) - Series attribute SeriesDescription value: ABD/PANC 3.0 B31f\n", + "[2024-04-23 17:21:11,740] [INFO] (root) - Series attribute string value did not match. Try regEx.\n", + "[2024-04-23 17:21:11,740] [INFO] (root) - Selected Series, UID: 1.3.6.1.4.1.14519.5.2.1.7085.2626.119403521930927333027265674239\n", + "[2024-04-23 17:21:11,964] [INFO] (root) - Parsing from bundle_path: /home/mqin/src/monai-deploy-app-sdk/notebooks/tutorials/models/model/model.ts\n" ] }, { "data": { "application/vnd.jupyter.widget-view+json": { - "model_id": "76b80cc0d2af48c58237d1f8d5d1ec88", + "model_id": "211ff45336804adab6957c462290a405", "version_major": 2, "version_minor": 0 }, @@ -681,26 +689,31 @@ "name": "stderr", "output_type": "stream", "text": [ - "[2024-04-10 10:46:35,947] [INFO] (monai.deploy.operators.stl_conversion_operator.STLConversionOperator) - Output will be saved in file output/stl/spleen.stl.\n", - "[2024-04-10 10:46:37,415] [INFO] (monai.deploy.operators.stl_conversion_operator.SpatialImage) - 3D image\n", - "[2024-04-10 10:46:37,416] [INFO] (monai.deploy.operators.stl_conversion_operator.STLConverter) - Image ndarray shape:(204, 512, 512)\n", + "[2024-04-23 17:21:24,861] [INFO] (monai.deploy.operators.stl_conversion_operator.STLConversionOperator) - Output will be saved in file output/stl/spleen.stl.\n", + "[2024-04-23 17:21:26,556] [INFO] (monai.deploy.operators.stl_conversion_operator.SpatialImage) - 3D image\n", + "[2024-04-23 17:21:26,557] [INFO] (monai.deploy.operators.stl_conversion_operator.STLConverter) - Image ndarray shape:(204, 512, 512)\n", "/home/mqin/src/monai-deploy-app-sdk/.venv/lib/python3.10/site-packages/highdicom/valuerep.py:54: UserWarning: The string \"C3N-00198\" is unlikely to represent the intended person name since it contains only a single component. Construct a person name according to the format in described in https://dicom.nema.org/dicom/2013/output/chtml/part05/sect_6.2.html#sect_6.2.1.2, or, in pydicom 2.2.0 or later, use the pydicom.valuerep.PersonName.from_named_components() method to construct the person name correctly. If a single-component name is really intended, add a trailing caret character to disambiguate the name.\n", " warnings.warn(\n", - "[2024-04-10 10:46:47,813] [INFO] (highdicom.base) - copy Image-related attributes from dataset \"1.3.6.1.4.1.14519.5.2.1.7085.2626.936983343951485811186213470191\"\n", - "[2024-04-10 10:46:47,814] [INFO] (highdicom.base) - copy attributes of module \"Specimen\"\n", - "[2024-04-10 10:46:47,815] [INFO] (highdicom.base) - copy Patient-related attributes from dataset \"1.3.6.1.4.1.14519.5.2.1.7085.2626.936983343951485811186213470191\"\n", - "[2024-04-10 10:46:47,816] [INFO] (highdicom.base) - copy attributes of module \"Patient\"\n", - "[2024-04-10 10:46:47,817] [INFO] (highdicom.base) - copy attributes of module \"Clinical Trial Subject\"\n", - "[2024-04-10 10:46:47,818] [INFO] (highdicom.base) - copy Study-related attributes from dataset \"1.3.6.1.4.1.14519.5.2.1.7085.2626.936983343951485811186213470191\"\n", - "[2024-04-10 10:46:47,819] [INFO] (highdicom.base) - copy attributes of module \"General Study\"\n", - "[2024-04-10 10:46:47,821] [INFO] (highdicom.base) - copy attributes of module \"Patient Study\"\n", - "[2024-04-10 10:46:47,822] [INFO] (highdicom.base) - copy attributes of module \"Clinical Trial Study\"\n", - "[info] [greedy_scheduler.cpp:369] Scheduler stopped: Some entities are waiting for execution, but there are no periodic or async entities to get out of the deadlock.\n", - "[info] [greedy_scheduler.cpp:398] Scheduler finished.\n", - "[info] [gxf_executor.cpp:1906] Graph execution deactivating. Fragment: \n", - "[info] [gxf_executor.cpp:1907] Deactivating Graph...\n", - "[info] [gxf_executor.cpp:1910] Graph execution finished. Fragment: \n", - "[2024-04-10 10:46:47,929] [INFO] (__main__.AISpleenSegApp) - End run\n" + "[2024-04-23 17:21:38,046] [INFO] (highdicom.base) - copy Image-related attributes from dataset \"1.3.6.1.4.1.14519.5.2.1.7085.2626.936983343951485811186213470191\"\n", + "[2024-04-23 17:21:38,047] [INFO] (highdicom.base) - copy attributes of module \"Specimen\"\n", + "[2024-04-23 17:21:38,048] [INFO] (highdicom.base) - copy Patient-related attributes from dataset \"1.3.6.1.4.1.14519.5.2.1.7085.2626.936983343951485811186213470191\"\n", + "[2024-04-23 17:21:38,049] [INFO] (highdicom.base) - copy attributes of module \"Patient\"\n", + "[2024-04-23 17:21:38,051] [INFO] (highdicom.base) - copy attributes of module \"Clinical Trial Subject\"\n", + "[2024-04-23 17:21:38,052] [INFO] (highdicom.base) - copy Study-related attributes from dataset \"1.3.6.1.4.1.14519.5.2.1.7085.2626.936983343951485811186213470191\"\n", + "[2024-04-23 17:21:38,053] [INFO] (highdicom.base) - copy attributes of module \"General Study\"\n", + "[2024-04-23 17:21:38,054] [INFO] (highdicom.base) - copy attributes of module \"Patient Study\"\n", + "[2024-04-23 17:21:38,055] [INFO] (highdicom.base) - copy attributes of module \"Clinical Trial Study\"\n", + "[info] [gxf_executor.cpp:1879] Deactivating Graph...\n", + "[info] [gxf_executor.cpp:1887] Graph execution finished.\n", + "[2024-04-23 17:21:38,152] [INFO] (__main__.AISpleenSegApp) - End run\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "\u001b[0m2024-04-23 17:21:38.150 INFO gxf/std/greedy_scheduler.cpp@372: Scheduler stopped: Some entities are waiting for execution, but there are no periodic or async entities to get out of the deadlock.\u001b[0m\n", + "\u001b[0m2024-04-23 17:21:38.150 INFO gxf/std/greedy_scheduler.cpp@401: Scheduler finished.\u001b[0m\n" ] } ], @@ -727,7 +740,7 @@ }, { "cell_type": "code", - "execution_count": 7, + "execution_count": 9, "metadata": {}, "outputs": [], "source": [ @@ -745,7 +758,7 @@ }, { "cell_type": "code", - "execution_count": 8, + "execution_count": 10, "metadata": {}, "outputs": [ { @@ -948,7 +961,7 @@ }, { "cell_type": "code", - "execution_count": 9, + "execution_count": 11, "metadata": {}, "outputs": [ { @@ -969,7 +982,7 @@ }, { "cell_type": "code", - "execution_count": 10, + "execution_count": 12, "metadata": {}, "outputs": [ { @@ -998,60 +1011,58 @@ }, { "cell_type": "code", - "execution_count": 11, + "execution_count": 13, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ - "[2024-04-10 10:46:52,705] [INFO] (root) - Parsed args: Namespace(log_level=None, input=None, output=None, model=None, workdir=None, argv=['my_app'])\n", - "[2024-04-10 10:46:52,707] [INFO] (root) - AppContext object: AppContext(input_path=dcm, output_path=output, model_path=models, workdir=)\n", - "[2024-04-10 10:46:52,709] [INFO] (root) - End compose\n", - "[\u001b[32minfo\u001b[m] [gxf_executor.cpp:211] Creating context\n", - "[\u001b[32minfo\u001b[m] [gxf_executor.cpp:1674] Loading extensions from configs...\n", - "[\u001b[32minfo\u001b[m] [gxf_executor.cpp:1864] Activating Graph...\n", - "[\u001b[32minfo\u001b[m] [gxf_executor.cpp:1894] Running Graph...\n", - "[\u001b[32minfo\u001b[m] [gxf_executor.cpp:1896] Waiting for completion...\n", - "[\u001b[32minfo\u001b[m] [gxf_executor.cpp:1897] Graph execution waiting. Fragment: \n", - "[\u001b[32minfo\u001b[m] [greedy_scheduler.cpp:190] Scheduling 10 entities\n", - "[2024-04-10 10:46:52,747] [INFO] (monai.deploy.operators.dicom_data_loader_operator.DICOMDataLoaderOperator) - No or invalid input path from the optional input port: None\n", - "[2024-04-10 10:46:53,083] [INFO] (root) - Finding series for Selection named: CT Series\n", - "[2024-04-10 10:46:53,083] [INFO] (root) - Searching study, : 1.3.6.1.4.1.14519.5.2.1.7085.2626.822645453932810382886582736291\n", + "[2024-04-23 17:21:43,227] [INFO] (root) - Parsed args: Namespace(log_level=None, input=None, output=None, model=None, workdir=None, argv=['my_app'])\n", + "[2024-04-23 17:21:43,229] [INFO] (root) - AppContext object: AppContext(input_path=dcm, output_path=output, model_path=models, workdir=)\n", + "[2024-04-23 17:21:43,230] [INFO] (root) - End compose\n", + "[\u001b[32minfo\u001b[m] [gxf_executor.cpp:247] Creating context\n", + "[\u001b[32minfo\u001b[m] [gxf_executor.cpp:1672] Loading extensions from configs...\n", + "[\u001b[32minfo\u001b[m] [gxf_executor.cpp:1842] Activating Graph...\n", + "[\u001b[32minfo\u001b[m] [gxf_executor.cpp:1874] Running Graph...\n", + "[\u001b[32minfo\u001b[m] [gxf_executor.cpp:1876] Waiting for completion...\n", + "\u001b[0m2024-04-23 17:21:43.261 INFO gxf/std/greedy_scheduler.cpp@191: Scheduling 10 entities\u001b[0m\n", + "[2024-04-23 17:21:43,263] [INFO] (monai.deploy.operators.dicom_data_loader_operator.DICOMDataLoaderOperator) - No or invalid input path from the optional input port: None\n", + "[2024-04-23 17:21:43,601] [INFO] (root) - Finding series for Selection named: CT Series\n", + "[2024-04-23 17:21:43,601] [INFO] (root) - Searching study, : 1.3.6.1.4.1.14519.5.2.1.7085.2626.822645453932810382886582736291\n", " # of series: 1\n", - "[2024-04-10 10:46:53,083] [INFO] (root) - Working on series, instance UID: 1.3.6.1.4.1.14519.5.2.1.7085.2626.119403521930927333027265674239\n", - "[2024-04-10 10:46:53,083] [INFO] (root) - On attribute: 'StudyDescription' to match value: '(.*?)'\n", - "[2024-04-10 10:46:53,083] [INFO] (root) - Series attribute StudyDescription value: CT ABDOMEN W IV CONTRAST\n", - "[2024-04-10 10:46:53,083] [INFO] (root) - Series attribute string value did not match. Try regEx.\n", - "[2024-04-10 10:46:53,083] [INFO] (root) - On attribute: 'Modality' to match value: '(?i)CT'\n", - "[2024-04-10 10:46:53,083] [INFO] (root) - Series attribute Modality value: CT\n", - "[2024-04-10 10:46:53,083] [INFO] (root) - Series attribute string value did not match. Try regEx.\n", - "[2024-04-10 10:46:53,083] [INFO] (root) - On attribute: 'SeriesDescription' to match value: '(.*?)'\n", - "[2024-04-10 10:46:53,083] [INFO] (root) - Series attribute SeriesDescription value: ABD/PANC 3.0 B31f\n", - "[2024-04-10 10:46:53,083] [INFO] (root) - Series attribute string value did not match. Try regEx.\n", - "[2024-04-10 10:46:53,083] [INFO] (root) - Selected Series, UID: 1.3.6.1.4.1.14519.5.2.1.7085.2626.119403521930927333027265674239\n", - "[2024-04-10 10:46:53,297] [INFO] (root) - Parsing from bundle_path: /home/mqin/src/monai-deploy-app-sdk/notebooks/tutorials/models/model/model.ts\n", + "[2024-04-23 17:21:43,601] [INFO] (root) - Working on series, instance UID: 1.3.6.1.4.1.14519.5.2.1.7085.2626.119403521930927333027265674239\n", + "[2024-04-23 17:21:43,601] [INFO] (root) - On attribute: 'StudyDescription' to match value: '(.*?)'\n", + "[2024-04-23 17:21:43,601] [INFO] (root) - Series attribute StudyDescription value: CT ABDOMEN W IV CONTRAST\n", + "[2024-04-23 17:21:43,601] [INFO] (root) - Series attribute string value did not match. Try regEx.\n", + "[2024-04-23 17:21:43,601] [INFO] (root) - On attribute: 'Modality' to match value: '(?i)CT'\n", + "[2024-04-23 17:21:43,601] [INFO] (root) - Series attribute Modality value: CT\n", + "[2024-04-23 17:21:43,601] [INFO] (root) - Series attribute string value did not match. Try regEx.\n", + "[2024-04-23 17:21:43,601] [INFO] (root) - On attribute: 'SeriesDescription' to match value: '(.*?)'\n", + "[2024-04-23 17:21:43,601] [INFO] (root) - Series attribute SeriesDescription value: ABD/PANC 3.0 B31f\n", + "[2024-04-23 17:21:43,601] [INFO] (root) - Series attribute string value did not match. Try regEx.\n", + "[2024-04-23 17:21:43,601] [INFO] (root) - Selected Series, UID: 1.3.6.1.4.1.14519.5.2.1.7085.2626.119403521930927333027265674239\n", + "[2024-04-23 17:21:43,818] [INFO] (root) - Parsing from bundle_path: /home/mqin/src/monai-deploy-app-sdk/notebooks/tutorials/models/model/model.ts\n", "Box(children=(Widget(), VBox(children=(interactive(children=(Dropdown(description='View mode', index=2, options=(('Cinematic', 'CINEMATIC'), ('Slice', 'SLICE'), ('Slice Segmentation', 'SLICE_SEGMENTATION')), value='SLICE_SEGMENTATION'), Output()), _dom_classes=('widget-interact',)), interactive(children=(Dropdown(description='Camera', options=('Top', 'Right', 'Front'), value='Top'), Output()), _dom_classes=('widget-interact',))))))\n", - "[2024-04-10 10:47:05,685] [INFO] (monai.deploy.operators.stl_conversion_operator.STLConversionOperator) - Output will be saved in file output/stl/spleen.stl.\n", - "[2024-04-10 10:47:07,271] [INFO] (monai.deploy.operators.stl_conversion_operator.SpatialImage) - 3D image\n", - "[2024-04-10 10:47:07,271] [INFO] (monai.deploy.operators.stl_conversion_operator.STLConverter) - Image ndarray shape:(204, 512, 512)\n", + "[2024-04-23 17:21:56,304] [INFO] (monai.deploy.operators.stl_conversion_operator.STLConversionOperator) - Output will be saved in file output/stl/spleen.stl.\n", + "[2024-04-23 17:21:57,924] [INFO] (monai.deploy.operators.stl_conversion_operator.SpatialImage) - 3D image\n", + "[2024-04-23 17:21:57,924] [INFO] (monai.deploy.operators.stl_conversion_operator.STLConverter) - Image ndarray shape:(204, 512, 512)\n", "/home/mqin/src/monai-deploy-app-sdk/.venv/lib/python3.10/site-packages/highdicom/valuerep.py:54: UserWarning: The string \"C3N-00198\" is unlikely to represent the intended person name since it contains only a single component. Construct a person name according to the format in described in https://dicom.nema.org/dicom/2013/output/chtml/part05/sect_6.2.html#sect_6.2.1.2, or, in pydicom 2.2.0 or later, use the pydicom.valuerep.PersonName.from_named_components() method to construct the person name correctly. If a single-component name is really intended, add a trailing caret character to disambiguate the name.\n", " warnings.warn(\n", - "[2024-04-10 10:47:18,769] [INFO] (highdicom.base) - copy Image-related attributes from dataset \"1.3.6.1.4.1.14519.5.2.1.7085.2626.936983343951485811186213470191\"\n", - "[2024-04-10 10:47:18,769] [INFO] (highdicom.base) - copy attributes of module \"Specimen\"\n", - "[2024-04-10 10:47:18,769] [INFO] (highdicom.base) - copy Patient-related attributes from dataset \"1.3.6.1.4.1.14519.5.2.1.7085.2626.936983343951485811186213470191\"\n", - "[2024-04-10 10:47:18,769] [INFO] (highdicom.base) - copy attributes of module \"Patient\"\n", - "[2024-04-10 10:47:18,769] [INFO] (highdicom.base) - copy attributes of module \"Clinical Trial Subject\"\n", - "[2024-04-10 10:47:18,769] [INFO] (highdicom.base) - copy Study-related attributes from dataset \"1.3.6.1.4.1.14519.5.2.1.7085.2626.936983343951485811186213470191\"\n", - "[2024-04-10 10:47:18,769] [INFO] (highdicom.base) - copy attributes of module \"General Study\"\n", - "[2024-04-10 10:47:18,769] [INFO] (highdicom.base) - copy attributes of module \"Patient Study\"\n", - "[2024-04-10 10:47:18,769] [INFO] (highdicom.base) - copy attributes of module \"Clinical Trial Study\"\n", - "[\u001b[32minfo\u001b[m] [greedy_scheduler.cpp:369] Scheduler stopped: Some entities are waiting for execution, but there are no periodic or async entities to get out of the deadlock.\n", - "[\u001b[32minfo\u001b[m] [greedy_scheduler.cpp:398] Scheduler finished.\n", - "[\u001b[32minfo\u001b[m] [gxf_executor.cpp:1906] Graph execution deactivating. Fragment: \n", - "[\u001b[32minfo\u001b[m] [gxf_executor.cpp:1907] Deactivating Graph...\n", - "[\u001b[32minfo\u001b[m] [gxf_executor.cpp:1910] Graph execution finished. Fragment: \n", - "[2024-04-10 10:47:18,856] [INFO] (app.AISpleenSegApp) - End run\n" + "[2024-04-23 17:22:10,502] [INFO] (highdicom.base) - copy Image-related attributes from dataset \"1.3.6.1.4.1.14519.5.2.1.7085.2626.936983343951485811186213470191\"\n", + "[2024-04-23 17:22:10,502] [INFO] (highdicom.base) - copy attributes of module \"Specimen\"\n", + "[2024-04-23 17:22:10,502] [INFO] (highdicom.base) - copy Patient-related attributes from dataset \"1.3.6.1.4.1.14519.5.2.1.7085.2626.936983343951485811186213470191\"\n", + "[2024-04-23 17:22:10,502] [INFO] (highdicom.base) - copy attributes of module \"Patient\"\n", + "[2024-04-23 17:22:10,503] [INFO] (highdicom.base) - copy attributes of module \"Clinical Trial Subject\"\n", + "[2024-04-23 17:22:10,503] [INFO] (highdicom.base) - copy Study-related attributes from dataset \"1.3.6.1.4.1.14519.5.2.1.7085.2626.936983343951485811186213470191\"\n", + "[2024-04-23 17:22:10,503] [INFO] (highdicom.base) - copy attributes of module \"General Study\"\n", + "[2024-04-23 17:22:10,503] [INFO] (highdicom.base) - copy attributes of module \"Patient Study\"\n", + "[2024-04-23 17:22:10,503] [INFO] (highdicom.base) - copy attributes of module \"Clinical Trial Study\"\n", + "\u001b[0m2024-04-23 17:22:10.588 INFO gxf/std/greedy_scheduler.cpp@372: Scheduler stopped: Some entities are waiting for execution, but there are no periodic or async entities to get out of the deadlock.\u001b[0m\n", + "\u001b[0m2024-04-23 17:22:10.588 INFO gxf/std/greedy_scheduler.cpp@401: Scheduler finished.\u001b[0m\n", + "[\u001b[32minfo\u001b[m] [gxf_executor.cpp:1879] Deactivating Graph...\n", + "[\u001b[32minfo\u001b[m] [gxf_executor.cpp:1887] Graph execution finished.\n", + "[2024-04-23 17:22:10,590] [INFO] (app.AISpleenSegApp) - End run\n" ] } ], @@ -1062,14 +1073,14 @@ }, { "cell_type": "code", - "execution_count": 12, + "execution_count": 14, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ - "1.2.826.0.1.3680043.10.511.3.65335369220270763710273609202620247.dcm stl\n" + "1.2.826.0.1.3680043.10.511.3.28732173401945631043953175363609741.dcm stl\n" ] } ], diff --git a/notebooks/tutorials/04_monai_bundle_app.ipynb b/notebooks/tutorials/04_monai_bundle_app.ipynb index b546487b..174bc8e5 100644 --- a/notebooks/tutorials/04_monai_bundle_app.ipynb +++ b/notebooks/tutorials/04_monai_bundle_app.ipynb @@ -94,7 +94,7 @@ }, { "cell_type": "code", - "execution_count": 1, + "execution_count": 51, "metadata": {}, "outputs": [], "source": [ @@ -106,6 +106,9 @@ "!python -c \"import pydicom\" || pip install -q \"pydicom>=2.3.0\"\n", "!python -c \"import highdicom\" || pip install -q \"highdicom>=0.18.2\"\n", "!python -c \"import SimpleITK\" || pip install -q \"SimpleITK>=2.0.0\"\n", + "!python -c \"import skimage\" || pip install -q \"scikit-image>=0.17.2\"\n", + "!python -c \"import stl\" || pip install -q \"numpy-stl>=2.12.0\"\n", + "!python -c \"import trimesh\" || pip install -q \"trimesh>=3.8.11\"\n", "\n", "# Install MONAI Deploy App SDK package\n", "!python -c \"import holoscan\" || pip install --upgrade -q \"holoscan>=0.6.0\"\n", @@ -128,7 +131,7 @@ }, { "cell_type": "code", - "execution_count": 2, + "execution_count": 52, "metadata": {}, "outputs": [ { @@ -137,23 +140,20 @@ "text": [ "Requirement already satisfied: gdown in /home/mqin/src/monai-deploy-app-sdk/.venv/lib/python3.10/site-packages (5.1.0)\n", "Requirement already satisfied: beautifulsoup4 in /home/mqin/src/monai-deploy-app-sdk/.venv/lib/python3.10/site-packages (from gdown) (4.12.3)\n", - "Requirement already satisfied: filelock in /home/mqin/src/monai-deploy-app-sdk/.venv/lib/python3.10/site-packages (from gdown) (3.13.3)\n", - "Requirement already satisfied: requests[socks] in /home/mqin/src/monai-deploy-app-sdk/.venv/lib/python3.10/site-packages (from gdown) (2.28.2)\n", + "Requirement already satisfied: filelock in /home/mqin/src/monai-deploy-app-sdk/.venv/lib/python3.10/site-packages (from gdown) (3.13.4)\n", + "Requirement already satisfied: requests[socks] in /home/mqin/src/monai-deploy-app-sdk/.venv/lib/python3.10/site-packages (from gdown) (2.31.0)\n", "Requirement already satisfied: tqdm in /home/mqin/src/monai-deploy-app-sdk/.venv/lib/python3.10/site-packages (from gdown) (4.66.2)\n", "Requirement already satisfied: soupsieve>1.2 in /home/mqin/src/monai-deploy-app-sdk/.venv/lib/python3.10/site-packages (from beautifulsoup4->gdown) (2.5)\n", "Requirement already satisfied: charset-normalizer<4,>=2 in /home/mqin/src/monai-deploy-app-sdk/.venv/lib/python3.10/site-packages (from requests[socks]->gdown) (3.3.2)\n", - "Requirement already satisfied: idna<4,>=2.5 in /home/mqin/src/monai-deploy-app-sdk/.venv/lib/python3.10/site-packages (from requests[socks]->gdown) (3.6)\n", - "Requirement already satisfied: urllib3<1.27,>=1.21.1 in /home/mqin/src/monai-deploy-app-sdk/.venv/lib/python3.10/site-packages (from requests[socks]->gdown) (1.26.18)\n", + "Requirement already satisfied: idna<4,>=2.5 in /home/mqin/src/monai-deploy-app-sdk/.venv/lib/python3.10/site-packages (from requests[socks]->gdown) (3.7)\n", + "Requirement already satisfied: urllib3<3,>=1.21.1 in /home/mqin/src/monai-deploy-app-sdk/.venv/lib/python3.10/site-packages (from requests[socks]->gdown) (2.2.1)\n", "Requirement already satisfied: certifi>=2017.4.17 in /home/mqin/src/monai-deploy-app-sdk/.venv/lib/python3.10/site-packages (from requests[socks]->gdown) (2024.2.2)\n", "Requirement already satisfied: PySocks!=1.5.7,>=1.5.6 in /home/mqin/src/monai-deploy-app-sdk/.venv/lib/python3.10/site-packages (from requests[socks]->gdown) (1.7.1)\n", - "\n", - "\u001b[1m[\u001b[0m\u001b[34;49mnotice\u001b[0m\u001b[1;39;49m]\u001b[0m\u001b[39;49m A new release of pip is available: \u001b[0m\u001b[31;49m23.3.2\u001b[0m\u001b[39;49m -> \u001b[0m\u001b[32;49m24.0\u001b[0m\n", - "\u001b[1m[\u001b[0m\u001b[34;49mnotice\u001b[0m\u001b[1;39;49m]\u001b[0m\u001b[39;49m To update, run: \u001b[0m\u001b[32;49mpip install --upgrade pip\u001b[0m\n", "Downloading...\n", "From (original): https://drive.google.com/uc?id=1Uds8mEvdGNYUuvFpTtCQ8gNU97bAPCaQ\n", - "From (redirected): https://drive.google.com/uc?id=1Uds8mEvdGNYUuvFpTtCQ8gNU97bAPCaQ&confirm=t&uuid=e406b570-c957-4c12-9dc1-df625c4fb575\n", + "From (redirected): https://drive.google.com/uc?id=1Uds8mEvdGNYUuvFpTtCQ8gNU97bAPCaQ&confirm=t&uuid=acdd1e9c-2382-4003-8390-b86e2e103d74\n", "To: /home/mqin/src/monai-deploy-app-sdk/notebooks/tutorials/ai_spleen_seg_bundle_data.zip\n", - "100%|███████████████████████████████████████| 79.4M/79.4M [00:00<00:00, 115MB/s]\n", + "100%|██████████████████████████████████████| 79.4M/79.4M [00:00<00:00, 96.9MB/s]\n", "Archive: ai_spleen_seg_bundle_data.zip\n", " inflating: dcm/1-001.dcm \n", " inflating: dcm/1-002.dcm \n", @@ -387,7 +387,7 @@ }, { "cell_type": "code", - "execution_count": 3, + "execution_count": 53, "metadata": {}, "outputs": [ { @@ -418,7 +418,7 @@ }, { "cell_type": "code", - "execution_count": 4, + "execution_count": 54, "metadata": {}, "outputs": [], "source": [ @@ -475,7 +475,7 @@ }, { "cell_type": "code", - "execution_count": 5, + "execution_count": 55, "metadata": {}, "outputs": [], "source": [ @@ -619,60 +619,77 @@ }, { "cell_type": "code", - "execution_count": 6, + "execution_count": 56, "metadata": {}, "outputs": [ { "name": "stderr", "output_type": "stream", "text": [ - "[2024-04-10 15:03:17,151] [INFO] (root) - Parsed args: Namespace(log_level=None, input=None, output=None, model=None, workdir=None, argv=[])\n", - "[2024-04-10 15:03:17,160] [INFO] (root) - AppContext object: AppContext(input_path=dcm, output_path=output, model_path=models, workdir=)\n", - "[2024-04-10 15:03:17,167] [INFO] (root) - End compose\n", - "[info] [gxf_executor.cpp:211] Creating context\n", - "[info] [gxf_executor.cpp:1674] Loading extensions from configs...\n", - "[info] [gxf_executor.cpp:1864] Activating Graph...\n", - "[info] [gxf_executor.cpp:1894] Running Graph...\n", - "[info] [gxf_executor.cpp:1896] Waiting for completion...\n", - "[info] [gxf_executor.cpp:1897] Graph execution waiting. Fragment: \n", - "[info] [greedy_scheduler.cpp:190] Scheduling 8 entities\n", - "[2024-04-10 15:03:17,216] [INFO] (monai.deploy.operators.dicom_data_loader_operator.DICOMDataLoaderOperator) - No or invalid input path from the optional input port: None\n", - "[2024-04-10 15:03:17,807] [INFO] (root) - Finding series for Selection named: CT Series\n", - "[2024-04-10 15:03:17,809] [INFO] (root) - Searching study, : 1.3.6.1.4.1.14519.5.2.1.7085.2626.822645453932810382886582736291\n", + "[2024-04-23 16:51:59,898] [INFO] (root) - Begin __main__\n", + "[2024-04-23 16:51:59,901] [INFO] (__main__.AISpleenSegApp) - Begin run\n", + "[2024-04-23 16:51:59,902] [INFO] (root) - Begin compose\n", + "[2024-04-23 16:51:59,909] [INFO] (root) - Parsed args: Namespace(log_level=None, input=None, output=None, model=None, workdir=None, argv=[])\n", + "[2024-04-23 16:51:59,915] [INFO] (root) - AppContext object: AppContext(input_path=dcm, output_path=output, model_path=models, workdir=)\n", + "[2024-04-23 16:51:59,920] [INFO] (root) - End compose\n", + "[info] [gxf_executor.cpp:247] Creating context\n", + "[info] [gxf_executor.cpp:1672] Loading extensions from configs...\n", + "[info] [gxf_executor.cpp:1842] Activating Graph...\n", + "[info] [gxf_executor.cpp:1874] Running Graph...\n", + "[info] [gxf_executor.cpp:1876] Waiting for completion...\n", + "[2024-04-23 16:51:59,943] [INFO] (monai.deploy.operators.dicom_data_loader_operator.DICOMDataLoaderOperator) - No or invalid input path from the optional input port: None\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "\u001b[0m2024-04-23 16:51:59.940 INFO gxf/std/greedy_scheduler.cpp@191: Scheduling 8 entities\u001b[0m\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "[2024-04-23 16:52:00,393] [INFO] (root) - Finding series for Selection named: CT Series\n", + "[2024-04-23 16:52:00,394] [INFO] (root) - Searching study, : 1.3.6.1.4.1.14519.5.2.1.7085.2626.822645453932810382886582736291\n", " # of series: 1\n", - "[2024-04-10 15:03:17,809] [INFO] (root) - Working on series, instance UID: 1.3.6.1.4.1.14519.5.2.1.7085.2626.119403521930927333027265674239\n", - "[2024-04-10 15:03:17,810] [INFO] (root) - On attribute: 'StudyDescription' to match value: '(.*?)'\n", - "[2024-04-10 15:03:17,811] [INFO] (root) - Series attribute StudyDescription value: CT ABDOMEN W IV CONTRAST\n", - "[2024-04-10 15:03:17,812] [INFO] (root) - Series attribute string value did not match. Try regEx.\n", - "[2024-04-10 15:03:17,813] [INFO] (root) - On attribute: 'Modality' to match value: '(?i)CT'\n", - "[2024-04-10 15:03:17,813] [INFO] (root) - Series attribute Modality value: CT\n", - "[2024-04-10 15:03:17,814] [INFO] (root) - Series attribute string value did not match. Try regEx.\n", - "[2024-04-10 15:03:17,815] [INFO] (root) - On attribute: 'SeriesDescription' to match value: '(.*?)'\n", - "[2024-04-10 15:03:17,815] [INFO] (root) - Series attribute SeriesDescription value: ABD/PANC 3.0 B31f\n", - "[2024-04-10 15:03:17,816] [INFO] (root) - Series attribute string value did not match. Try regEx.\n", - "[2024-04-10 15:03:17,817] [INFO] (root) - Selected Series, UID: 1.3.6.1.4.1.14519.5.2.1.7085.2626.119403521930927333027265674239\n", - "[2024-04-10 15:03:18,040] [INFO] (root) - Parsing from bundle_path: /home/mqin/src/monai-deploy-app-sdk/notebooks/tutorials/models/model/model.ts\n", - "[2024-04-10 15:03:24,142] [INFO] (monai.deploy.operators.stl_conversion_operator.STLConversionOperator) - Output will be saved in file output/stl/spleen.stl.\n", - "[2024-04-10 15:03:25,752] [INFO] (monai.deploy.operators.stl_conversion_operator.SpatialImage) - 3D image\n", - "[2024-04-10 15:03:25,753] [INFO] (monai.deploy.operators.stl_conversion_operator.STLConverter) - Image ndarray shape:(204, 512, 512)\n", - "/home/mqin/src/monai-deploy-app-sdk/.venv/lib/python3.10/site-packages/highdicom/valuerep.py:54: UserWarning: The string \"C3N-00198\" is unlikely to represent the intended person name since it contains only a single component. Construct a person name according to the format in described in https://dicom.nema.org/dicom/2013/output/chtml/part05/sect_6.2.html#sect_6.2.1.2, or, in pydicom 2.2.0 or later, use the pydicom.valuerep.PersonName.from_named_components() method to construct the person name correctly. If a single-component name is really intended, add a trailing caret character to disambiguate the name.\n", - " warnings.warn(\n", - "[2024-04-10 15:03:36,659] [INFO] (highdicom.base) - copy Image-related attributes from dataset \"1.3.6.1.4.1.14519.5.2.1.7085.2626.936983343951485811186213470191\"\n", - "[2024-04-10 15:03:36,660] [INFO] (highdicom.base) - copy attributes of module \"Specimen\"\n", - "[2024-04-10 15:03:36,661] [INFO] (highdicom.base) - copy Patient-related attributes from dataset \"1.3.6.1.4.1.14519.5.2.1.7085.2626.936983343951485811186213470191\"\n", - "[2024-04-10 15:03:36,663] [INFO] (highdicom.base) - copy attributes of module \"Patient\"\n", - "[2024-04-10 15:03:36,664] [INFO] (highdicom.base) - copy attributes of module \"Clinical Trial Subject\"\n", - "[2024-04-10 15:03:36,665] [INFO] (highdicom.base) - copy Study-related attributes from dataset \"1.3.6.1.4.1.14519.5.2.1.7085.2626.936983343951485811186213470191\"\n", - "[2024-04-10 15:03:36,666] [INFO] (highdicom.base) - copy attributes of module \"General Study\"\n", - "[2024-04-10 15:03:36,667] [INFO] (highdicom.base) - copy attributes of module \"Patient Study\"\n", - "[2024-04-10 15:03:36,668] [INFO] (highdicom.base) - copy attributes of module \"Clinical Trial Study\"\n", - "[info] [greedy_scheduler.cpp:369] Scheduler stopped: Some entities are waiting for execution, but there are no periodic or async entities to get out of the deadlock.\n", - "[info] [greedy_scheduler.cpp:398] Scheduler finished.\n", - "[info] [gxf_executor.cpp:1906] Graph execution deactivating. Fragment: \n", - "[info] [gxf_executor.cpp:1907] Deactivating Graph...\n", - "[info] [gxf_executor.cpp:1910] Graph execution finished. Fragment: \n", - "[2024-04-10 15:03:36,762] [INFO] (__main__.AISpleenSegApp) - End run\n", - "[2024-04-10 15:03:36,763] [INFO] (root) - End __main__\n" + "[2024-04-23 16:52:00,395] [INFO] (root) - Working on series, instance UID: 1.3.6.1.4.1.14519.5.2.1.7085.2626.119403521930927333027265674239\n", + "[2024-04-23 16:52:00,396] [INFO] (root) - On attribute: 'StudyDescription' to match value: '(.*?)'\n", + "[2024-04-23 16:52:00,397] [INFO] (root) - Series attribute StudyDescription value: CT ABDOMEN W IV CONTRAST\n", + "[2024-04-23 16:52:00,397] [INFO] (root) - Series attribute string value did not match. Try regEx.\n", + "[2024-04-23 16:52:00,398] [INFO] (root) - On attribute: 'Modality' to match value: '(?i)CT'\n", + "[2024-04-23 16:52:00,399] [INFO] (root) - Series attribute Modality value: CT\n", + "[2024-04-23 16:52:00,399] [INFO] (root) - Series attribute string value did not match. Try regEx.\n", + "[2024-04-23 16:52:00,400] [INFO] (root) - On attribute: 'SeriesDescription' to match value: '(.*?)'\n", + "[2024-04-23 16:52:00,400] [INFO] (root) - Series attribute SeriesDescription value: ABD/PANC 3.0 B31f\n", + "[2024-04-23 16:52:00,401] [INFO] (root) - Series attribute string value did not match. Try regEx.\n", + "[2024-04-23 16:52:00,402] [INFO] (root) - Selected Series, UID: 1.3.6.1.4.1.14519.5.2.1.7085.2626.119403521930927333027265674239\n", + "[2024-04-23 16:52:00,641] [INFO] (root) - Parsing from bundle_path: /home/mqin/src/monai-deploy-app-sdk/notebooks/tutorials/models/model/model.ts\n", + "[2024-04-23 16:52:03,610] [INFO] (monai.deploy.operators.stl_conversion_operator.STLConversionOperator) - Output will be saved in file output/stl/spleen.stl.\n", + "[2024-04-23 16:52:05,137] [INFO] (monai.deploy.operators.stl_conversion_operator.SpatialImage) - 3D image\n", + "[2024-04-23 16:52:05,138] [INFO] (monai.deploy.operators.stl_conversion_operator.STLConverter) - Image ndarray shape:(204, 512, 512)\n", + "[2024-04-23 16:52:14,942] [INFO] (highdicom.base) - copy Image-related attributes from dataset \"1.3.6.1.4.1.14519.5.2.1.7085.2626.936983343951485811186213470191\"\n", + "[2024-04-23 16:52:14,943] [INFO] (highdicom.base) - copy attributes of module \"Specimen\"\n", + "[2024-04-23 16:52:14,944] [INFO] (highdicom.base) - copy Patient-related attributes from dataset \"1.3.6.1.4.1.14519.5.2.1.7085.2626.936983343951485811186213470191\"\n", + "[2024-04-23 16:52:14,945] [INFO] (highdicom.base) - copy attributes of module \"Patient\"\n", + "[2024-04-23 16:52:14,946] [INFO] (highdicom.base) - copy attributes of module \"Clinical Trial Subject\"\n", + "[2024-04-23 16:52:14,947] [INFO] (highdicom.base) - copy Study-related attributes from dataset \"1.3.6.1.4.1.14519.5.2.1.7085.2626.936983343951485811186213470191\"\n", + "[2024-04-23 16:52:14,948] [INFO] (highdicom.base) - copy attributes of module \"General Study\"\n", + "[2024-04-23 16:52:14,949] [INFO] (highdicom.base) - copy attributes of module \"Patient Study\"\n", + "[2024-04-23 16:52:14,951] [INFO] (highdicom.base) - copy attributes of module \"Clinical Trial Study\"\n", + "[info] [gxf_executor.cpp:1879] Deactivating Graph...\n", + "[info] [gxf_executor.cpp:1887] Graph execution finished.\n", + "[2024-04-23 16:52:15,056] [INFO] (__main__.AISpleenSegApp) - End run\n", + "[2024-04-23 16:52:15,057] [INFO] (root) - End __main__\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "\u001b[0m2024-04-23 16:52:15.054 INFO gxf/std/greedy_scheduler.cpp@372: Scheduler stopped: Some entities are waiting for execution, but there are no periodic or async entities to get out of the deadlock.\u001b[0m\n", + "\u001b[0m2024-04-23 16:52:15.055 INFO gxf/std/greedy_scheduler.cpp@401: Scheduler finished.\u001b[0m\n" ] } ], @@ -700,7 +717,7 @@ }, { "cell_type": "code", - "execution_count": 7, + "execution_count": 57, "metadata": {}, "outputs": [], "source": [ @@ -717,7 +734,7 @@ }, { "cell_type": "code", - "execution_count": 8, + "execution_count": 58, "metadata": {}, "outputs": [ { @@ -916,7 +933,7 @@ }, { "cell_type": "code", - "execution_count": 9, + "execution_count": 59, "metadata": {}, "outputs": [ { @@ -937,7 +954,7 @@ }, { "cell_type": "code", - "execution_count": 10, + "execution_count": 60, "metadata": {}, "outputs": [ { @@ -966,59 +983,57 @@ }, { "cell_type": "code", - "execution_count": 11, + "execution_count": 61, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ - "[2024-04-10 15:03:41,411] [INFO] (root) - Parsed args: Namespace(log_level=None, input=PosixPath('/home/mqin/src/monai-deploy-app-sdk/notebooks/tutorials/dcm'), output=PosixPath('/home/mqin/src/monai-deploy-app-sdk/notebooks/tutorials/output'), model=PosixPath('/home/mqin/src/monai-deploy-app-sdk/notebooks/tutorials/models'), workdir=None, argv=['my_app', '-i', 'dcm', '-o', 'output', '-m', 'models'])\n", - "[2024-04-10 15:03:41,413] [INFO] (root) - AppContext object: AppContext(input_path=/home/mqin/src/monai-deploy-app-sdk/notebooks/tutorials/dcm, output_path=/home/mqin/src/monai-deploy-app-sdk/notebooks/tutorials/output, model_path=/home/mqin/src/monai-deploy-app-sdk/notebooks/tutorials/models, workdir=)\n", - "[2024-04-10 15:03:41,414] [INFO] (root) - End compose\n", - "[\u001b[32minfo\u001b[m] [gxf_executor.cpp:211] Creating context\n", - "[\u001b[32minfo\u001b[m] [gxf_executor.cpp:1674] Loading extensions from configs...\n", - "[\u001b[32minfo\u001b[m] [gxf_executor.cpp:1864] Activating Graph...\n", - "[\u001b[32minfo\u001b[m] [gxf_executor.cpp:1894] Running Graph...\n", - "[\u001b[32minfo\u001b[m] [gxf_executor.cpp:1896] Waiting for completion...\n", - "[\u001b[32minfo\u001b[m] [gxf_executor.cpp:1897] Graph execution waiting. Fragment: \n", - "[\u001b[32minfo\u001b[m] [greedy_scheduler.cpp:190] Scheduling 8 entities\n", - "[2024-04-10 15:03:41,449] [INFO] (monai.deploy.operators.dicom_data_loader_operator.DICOMDataLoaderOperator) - No or invalid input path from the optional input port: None\n", - "[2024-04-10 15:03:41,784] [INFO] (root) - Finding series for Selection named: CT Series\n", - "[2024-04-10 15:03:41,784] [INFO] (root) - Searching study, : 1.3.6.1.4.1.14519.5.2.1.7085.2626.822645453932810382886582736291\n", + "[2024-04-23 16:52:19,843] [INFO] (root) - Parsed args: Namespace(log_level=None, input=PosixPath('/home/mqin/src/monai-deploy-app-sdk/notebooks/tutorials/dcm'), output=PosixPath('/home/mqin/src/monai-deploy-app-sdk/notebooks/tutorials/output'), model=PosixPath('/home/mqin/src/monai-deploy-app-sdk/notebooks/tutorials/models'), workdir=None, argv=['my_app', '-i', 'dcm', '-o', 'output', '-m', 'models'])\n", + "[2024-04-23 16:52:19,845] [INFO] (root) - AppContext object: AppContext(input_path=/home/mqin/src/monai-deploy-app-sdk/notebooks/tutorials/dcm, output_path=/home/mqin/src/monai-deploy-app-sdk/notebooks/tutorials/output, model_path=/home/mqin/src/monai-deploy-app-sdk/notebooks/tutorials/models, workdir=)\n", + "[2024-04-23 16:52:19,847] [INFO] (root) - End compose\n", + "[\u001b[32minfo\u001b[m] [gxf_executor.cpp:247] Creating context\n", + "[\u001b[32minfo\u001b[m] [gxf_executor.cpp:1672] Loading extensions from configs...\n", + "[\u001b[32minfo\u001b[m] [gxf_executor.cpp:1842] Activating Graph...\n", + "[\u001b[32minfo\u001b[m] [gxf_executor.cpp:1874] Running Graph...\n", + "[\u001b[32minfo\u001b[m] [gxf_executor.cpp:1876] Waiting for completion...\n", + "\u001b[0m2024-04-23 16:52:19.876 INFO gxf/std/greedy_scheduler.cpp@191: Scheduling 8 entities\u001b[0m\n", + "[2024-04-23 16:52:19,877] [INFO] (monai.deploy.operators.dicom_data_loader_operator.DICOMDataLoaderOperator) - No or invalid input path from the optional input port: None\n", + "[2024-04-23 16:52:20,224] [INFO] (root) - Finding series for Selection named: CT Series\n", + "[2024-04-23 16:52:20,224] [INFO] (root) - Searching study, : 1.3.6.1.4.1.14519.5.2.1.7085.2626.822645453932810382886582736291\n", " # of series: 1\n", - "[2024-04-10 15:03:41,784] [INFO] (root) - Working on series, instance UID: 1.3.6.1.4.1.14519.5.2.1.7085.2626.119403521930927333027265674239\n", - "[2024-04-10 15:03:41,784] [INFO] (root) - On attribute: 'StudyDescription' to match value: '(.*?)'\n", - "[2024-04-10 15:03:41,784] [INFO] (root) - Series attribute StudyDescription value: CT ABDOMEN W IV CONTRAST\n", - "[2024-04-10 15:03:41,784] [INFO] (root) - Series attribute string value did not match. Try regEx.\n", - "[2024-04-10 15:03:41,785] [INFO] (root) - On attribute: 'Modality' to match value: '(?i)CT'\n", - "[2024-04-10 15:03:41,785] [INFO] (root) - Series attribute Modality value: CT\n", - "[2024-04-10 15:03:41,785] [INFO] (root) - Series attribute string value did not match. Try regEx.\n", - "[2024-04-10 15:03:41,785] [INFO] (root) - On attribute: 'SeriesDescription' to match value: '(.*?)'\n", - "[2024-04-10 15:03:41,785] [INFO] (root) - Series attribute SeriesDescription value: ABD/PANC 3.0 B31f\n", - "[2024-04-10 15:03:41,785] [INFO] (root) - Series attribute string value did not match. Try regEx.\n", - "[2024-04-10 15:03:41,785] [INFO] (root) - Selected Series, UID: 1.3.6.1.4.1.14519.5.2.1.7085.2626.119403521930927333027265674239\n", - "[2024-04-10 15:03:42,204] [INFO] (root) - Parsing from bundle_path: /home/mqin/src/monai-deploy-app-sdk/notebooks/tutorials/models/model/model.ts\n", - "[2024-04-10 15:03:48,123] [INFO] (monai.deploy.operators.stl_conversion_operator.STLConversionOperator) - Output will be saved in file /home/mqin/src/monai-deploy-app-sdk/notebooks/tutorials/output/stl/spleen.stl.\n", - "[2024-04-10 15:03:49,607] [INFO] (monai.deploy.operators.stl_conversion_operator.SpatialImage) - 3D image\n", - "[2024-04-10 15:03:49,607] [INFO] (monai.deploy.operators.stl_conversion_operator.STLConverter) - Image ndarray shape:(204, 512, 512)\n", + "[2024-04-23 16:52:20,224] [INFO] (root) - Working on series, instance UID: 1.3.6.1.4.1.14519.5.2.1.7085.2626.119403521930927333027265674239\n", + "[2024-04-23 16:52:20,224] [INFO] (root) - On attribute: 'StudyDescription' to match value: '(.*?)'\n", + "[2024-04-23 16:52:20,224] [INFO] (root) - Series attribute StudyDescription value: CT ABDOMEN W IV CONTRAST\n", + "[2024-04-23 16:52:20,224] [INFO] (root) - Series attribute string value did not match. Try regEx.\n", + "[2024-04-23 16:52:20,225] [INFO] (root) - On attribute: 'Modality' to match value: '(?i)CT'\n", + "[2024-04-23 16:52:20,225] [INFO] (root) - Series attribute Modality value: CT\n", + "[2024-04-23 16:52:20,225] [INFO] (root) - Series attribute string value did not match. Try regEx.\n", + "[2024-04-23 16:52:20,225] [INFO] (root) - On attribute: 'SeriesDescription' to match value: '(.*?)'\n", + "[2024-04-23 16:52:20,225] [INFO] (root) - Series attribute SeriesDescription value: ABD/PANC 3.0 B31f\n", + "[2024-04-23 16:52:20,225] [INFO] (root) - Series attribute string value did not match. Try regEx.\n", + "[2024-04-23 16:52:20,225] [INFO] (root) - Selected Series, UID: 1.3.6.1.4.1.14519.5.2.1.7085.2626.119403521930927333027265674239\n", + "[2024-04-23 16:52:20,449] [INFO] (root) - Parsing from bundle_path: /home/mqin/src/monai-deploy-app-sdk/notebooks/tutorials/models/model/model.ts\n", + "[2024-04-23 16:52:26,711] [INFO] (monai.deploy.operators.stl_conversion_operator.STLConversionOperator) - Output will be saved in file /home/mqin/src/monai-deploy-app-sdk/notebooks/tutorials/output/stl/spleen.stl.\n", + "[2024-04-23 16:52:28,387] [INFO] (monai.deploy.operators.stl_conversion_operator.SpatialImage) - 3D image\n", + "[2024-04-23 16:52:28,388] [INFO] (monai.deploy.operators.stl_conversion_operator.STLConverter) - Image ndarray shape:(204, 512, 512)\n", "/home/mqin/src/monai-deploy-app-sdk/.venv/lib/python3.10/site-packages/highdicom/valuerep.py:54: UserWarning: The string \"C3N-00198\" is unlikely to represent the intended person name since it contains only a single component. Construct a person name according to the format in described in https://dicom.nema.org/dicom/2013/output/chtml/part05/sect_6.2.html#sect_6.2.1.2, or, in pydicom 2.2.0 or later, use the pydicom.valuerep.PersonName.from_named_components() method to construct the person name correctly. If a single-component name is really intended, add a trailing caret character to disambiguate the name.\n", " warnings.warn(\n", - "[2024-04-10 15:03:59,411] [INFO] (highdicom.base) - copy Image-related attributes from dataset \"1.3.6.1.4.1.14519.5.2.1.7085.2626.936983343951485811186213470191\"\n", - "[2024-04-10 15:03:59,412] [INFO] (highdicom.base) - copy attributes of module \"Specimen\"\n", - "[2024-04-10 15:03:59,412] [INFO] (highdicom.base) - copy Patient-related attributes from dataset \"1.3.6.1.4.1.14519.5.2.1.7085.2626.936983343951485811186213470191\"\n", - "[2024-04-10 15:03:59,412] [INFO] (highdicom.base) - copy attributes of module \"Patient\"\n", - "[2024-04-10 15:03:59,412] [INFO] (highdicom.base) - copy attributes of module \"Clinical Trial Subject\"\n", - "[2024-04-10 15:03:59,412] [INFO] (highdicom.base) - copy Study-related attributes from dataset \"1.3.6.1.4.1.14519.5.2.1.7085.2626.936983343951485811186213470191\"\n", - "[2024-04-10 15:03:59,412] [INFO] (highdicom.base) - copy attributes of module \"General Study\"\n", - "[2024-04-10 15:03:59,412] [INFO] (highdicom.base) - copy attributes of module \"Patient Study\"\n", - "[2024-04-10 15:03:59,412] [INFO] (highdicom.base) - copy attributes of module \"Clinical Trial Study\"\n", - "[\u001b[32minfo\u001b[m] [greedy_scheduler.cpp:369] Scheduler stopped: Some entities are waiting for execution, but there are no periodic or async entities to get out of the deadlock.\n", - "[\u001b[32minfo\u001b[m] [greedy_scheduler.cpp:398] Scheduler finished.\n", - "[\u001b[32minfo\u001b[m] [gxf_executor.cpp:1906] Graph execution deactivating. Fragment: \n", - "[\u001b[32minfo\u001b[m] [gxf_executor.cpp:1907] Deactivating Graph...\n", - "[\u001b[32minfo\u001b[m] [gxf_executor.cpp:1910] Graph execution finished. Fragment: \n", - "[2024-04-10 15:03:59,498] [INFO] (app.AISpleenSegApp) - End run\n" + "[2024-04-23 16:52:39,441] [INFO] (highdicom.base) - copy Image-related attributes from dataset \"1.3.6.1.4.1.14519.5.2.1.7085.2626.936983343951485811186213470191\"\n", + "[2024-04-23 16:52:39,441] [INFO] (highdicom.base) - copy attributes of module \"Specimen\"\n", + "[2024-04-23 16:52:39,441] [INFO] (highdicom.base) - copy Patient-related attributes from dataset \"1.3.6.1.4.1.14519.5.2.1.7085.2626.936983343951485811186213470191\"\n", + "[2024-04-23 16:52:39,441] [INFO] (highdicom.base) - copy attributes of module \"Patient\"\n", + "[2024-04-23 16:52:39,441] [INFO] (highdicom.base) - copy attributes of module \"Clinical Trial Subject\"\n", + "[2024-04-23 16:52:39,441] [INFO] (highdicom.base) - copy Study-related attributes from dataset \"1.3.6.1.4.1.14519.5.2.1.7085.2626.936983343951485811186213470191\"\n", + "[2024-04-23 16:52:39,441] [INFO] (highdicom.base) - copy attributes of module \"General Study\"\n", + "[2024-04-23 16:52:39,442] [INFO] (highdicom.base) - copy attributes of module \"Patient Study\"\n", + "[2024-04-23 16:52:39,442] [INFO] (highdicom.base) - copy attributes of module \"Clinical Trial Study\"\n", + "\u001b[0m2024-04-23 16:52:39.552 INFO gxf/std/greedy_scheduler.cpp@372: Scheduler stopped: Some entities are waiting for execution, but there are no periodic or async entities to get out of the deadlock.\u001b[0m\n", + "\u001b[0m2024-04-23 16:52:39.552 INFO gxf/std/greedy_scheduler.cpp@401: Scheduler finished.\u001b[0m\n", + "[\u001b[32minfo\u001b[m] [gxf_executor.cpp:1879] Deactivating Graph...\n", + "[\u001b[32minfo\u001b[m] [gxf_executor.cpp:1887] Graph execution finished.\n", + "[2024-04-23 16:52:39,552] [INFO] (app.AISpleenSegApp) - End run\n" ] } ], @@ -1029,14 +1044,14 @@ }, { "cell_type": "code", - "execution_count": 12, + "execution_count": 62, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ - "1.2.826.0.1.3680043.10.511.3.39077956786032602526223766812104927.dcm stl\n" + "1.2.826.0.1.3680043.10.511.3.31677856801140848641305221346725457.dcm stl\n" ] } ], @@ -1057,7 +1072,7 @@ }, { "cell_type": "code", - "execution_count": 13, + "execution_count": 63, "metadata": {}, "outputs": [ { @@ -1087,7 +1102,7 @@ }, { "cell_type": "code", - "execution_count": 14, + "execution_count": 64, "metadata": {}, "outputs": [ { @@ -1107,6 +1122,9 @@ "pydicom>=2.3.0\n", "setuptools>=59.5.0 # for pkg_resources\n", "SimpleITK>=2.0.0\n", + "scikit-image>=0.17.2\n", + "numpy-stl>=2.12.0\n", + "trimesh>=3.8.11\n", "torch>=1.12.0" ] }, @@ -1123,21 +1141,23 @@ }, { "cell_type": "code", - "execution_count": 15, + "execution_count": 65, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ - "[2024-04-10 15:04:01,696] [INFO] (packager.parameters) - Application: /home/mqin/src/monai-deploy-app-sdk/notebooks/tutorials/my_app\n", - "[2024-04-10 15:04:01,697] [INFO] (packager.parameters) - Detected application type: Python Module\n", - "[2024-04-10 15:04:01,697] [INFO] (packager) - Scanning for models in /home/mqin/src/monai-deploy-app-sdk/notebooks/tutorials/models...\n", - "[2024-04-10 15:04:01,697] [DEBUG] (packager) - Model model=/home/mqin/src/monai-deploy-app-sdk/notebooks/tutorials/models/model added.\n", - "[2024-04-10 15:04:01,697] [INFO] (packager) - Reading application configuration from /home/mqin/src/monai-deploy-app-sdk/notebooks/tutorials/my_app/app.yaml...\n", - "[2024-04-10 15:04:01,701] [INFO] (packager) - Generating app.json...\n", - "[2024-04-10 15:04:01,701] [INFO] (packager) - Generating pkg.json...\n", - "[2024-04-10 15:04:01,714] [DEBUG] (common) - \n", + "[2024-04-23 16:52:41,994] [INFO] (common) - Downloading CLI manifest file...\n", + "[2024-04-23 16:52:42,236] [DEBUG] (common) - Validating CLI manifest file...\n", + "[2024-04-23 16:52:42,237] [INFO] (packager.parameters) - Application: /home/mqin/src/monai-deploy-app-sdk/notebooks/tutorials/my_app\n", + "[2024-04-23 16:52:42,238] [INFO] (packager.parameters) - Detected application type: Python Module\n", + "[2024-04-23 16:52:42,238] [INFO] (packager) - Scanning for models in /home/mqin/src/monai-deploy-app-sdk/notebooks/tutorials/models...\n", + "[2024-04-23 16:52:42,238] [DEBUG] (packager) - Model model=/home/mqin/src/monai-deploy-app-sdk/notebooks/tutorials/models/model added.\n", + "[2024-04-23 16:52:42,238] [INFO] (packager) - Reading application configuration from /home/mqin/src/monai-deploy-app-sdk/notebooks/tutorials/my_app/app.yaml...\n", + "[2024-04-23 16:52:42,240] [INFO] (packager) - Generating app.json...\n", + "[2024-04-23 16:52:42,240] [INFO] (packager) - Generating pkg.json...\n", + "[2024-04-23 16:52:42,246] [DEBUG] (common) - \n", "=============== Begin app.json ===============\n", "{\n", " \"apiVersion\": \"1.0.0\",\n", @@ -1172,7 +1192,7 @@ "}\n", "================ End app.json ================\n", " \n", - "[2024-04-10 15:04:01,715] [DEBUG] (common) - \n", + "[2024-04-23 16:52:42,246] [DEBUG] (common) - \n", "=============== Begin pkg.json ===============\n", "{\n", " \"apiVersion\": \"1.0.0\",\n", @@ -1192,11 +1212,11 @@ "}\n", "================ End pkg.json ================\n", " \n", - "[2024-04-10 15:04:01,749] [DEBUG] (packager.builder) - \n", + "[2024-04-23 16:52:42,273] [DEBUG] (packager.builder) - \n", "========== Begin Dockerfile ==========\n", "\n", "\n", - "FROM nvcr.io/nvidia/clara-holoscan/holoscan:v1.0.3-dgpu\n", + "FROM nvcr.io/nvidia/clara-holoscan/holoscan:v2.0.0-dgpu\n", "\n", "ENV DEBIAN_FRONTEND=noninteractive\n", "ENV TERM=xterm-256color\n", @@ -1212,11 +1232,11 @@ " && mkdir -p /var/holoscan/input \\\n", " && mkdir -p /var/holoscan/output\n", "\n", - "LABEL base=\"nvcr.io/nvidia/clara-holoscan/holoscan:v1.0.3-dgpu\"\n", + "LABEL base=\"nvcr.io/nvidia/clara-holoscan/holoscan:v2.0.0-dgpu\"\n", "LABEL tag=\"my_app:1.0\"\n", "LABEL org.opencontainers.image.title=\"MONAI Deploy App Package - MONAI Bundle AI App\"\n", "LABEL org.opencontainers.image.version=\"1.0\"\n", - "LABEL org.nvidia.holoscan=\"1.0.3\"\n", + "LABEL org.nvidia.holoscan=\"2.0.0\"\n", "LABEL org.monai.deploy.app-sdk=\"0.5.1\"\n", "\n", "\n", @@ -1242,7 +1262,6 @@ "ENV PYTHONPATH=\"/opt/holoscan/app:$PYTHONPATH\"\n", "\n", "\n", - "\n", "RUN groupadd -f -g $GID $UNAME\n", "RUN useradd -rm -d /home/$UNAME -s /bin/bash -g $GID -G sudo -u $UID $UNAME\n", "RUN chown -R holoscan /var/holoscan \n", @@ -1268,14 +1287,12 @@ "RUN pip install --upgrade pip\n", "RUN pip install --no-cache-dir --user -r /tmp/requirements.txt\n", "\n", - "# Install Holoscan from PyPI only when sdk_type is Holoscan. \n", - "# For MONAI Deploy, the APP SDK will install it unless user specifies the Holoscan SDK file.\n", + " \n", + "# MONAI Deploy\n", "\n", "# Copy user-specified MONAI Deploy SDK file\n", - "COPY ./monai_deploy_app_sdk-0.5.1+25.g31e4165.dirty-py3-none-any.whl /tmp/monai_deploy_app_sdk-0.5.1+25.g31e4165.dirty-py3-none-any.whl\n", - "RUN pip install /tmp/monai_deploy_app_sdk-0.5.1+25.g31e4165.dirty-py3-none-any.whl\n", - "\n", - "\n", + "COPY ./monai_deploy_app_sdk-0.5.1+20.gb869749.dirty-py3-none-any.whl /tmp/monai_deploy_app_sdk-0.5.1+20.gb869749.dirty-py3-none-any.whl\n", + "RUN pip install /tmp/monai_deploy_app_sdk-0.5.1+20.gb869749.dirty-py3-none-any.whl\n", "\n", "\n", "COPY ./models /opt/holoscan/models\n", @@ -1289,31 +1306,31 @@ "ENTRYPOINT [\"/var/holoscan/tools\"]\n", "=========== End Dockerfile ===========\n", "\n", - "[2024-04-10 15:04:01,749] [INFO] (packager.builder) - \n", + "[2024-04-23 16:52:42,273] [INFO] (packager.builder) - \n", "===============================================================================\n", "Building image for: x64-workstation\n", " Architecture: linux/amd64\n", - " Base Image: nvcr.io/nvidia/clara-holoscan/holoscan:v1.0.3-dgpu\n", + " Base Image: nvcr.io/nvidia/clara-holoscan/holoscan:v2.0.0-dgpu\n", " Build Image: N/A\n", " Cache: Enabled\n", " Configuration: dgpu\n", " Holoscan SDK Package: pypi.org\n", - " MONAI Deploy App SDK Package: /home/mqin/src/monai-deploy-app-sdk/dist/monai_deploy_app_sdk-0.5.1+25.g31e4165.dirty-py3-none-any.whl\n", + " MONAI Deploy App SDK Package: /home/mqin/src/monai-deploy-app-sdk/dist/monai_deploy_app_sdk-0.5.1+20.gb869749.dirty-py3-none-any.whl\n", " gRPC Health Probe: N/A\n", - " SDK Version: 1.0.3\n", + " SDK Version: 2.0.0\n", " SDK: monai-deploy\n", " Tag: my_app-x64-workstation-dgpu-linux-amd64:1.0\n", " \n", - "[2024-04-10 15:04:02,349] [INFO] (common) - Using existing Docker BuildKit builder `holoscan_app_builder`\n", - "[2024-04-10 15:04:02,349] [DEBUG] (packager.builder) - Building Holoscan Application Package: tag=my_app-x64-workstation-dgpu-linux-amd64:1.0\n", + "[2024-04-23 16:52:42,564] [INFO] (common) - Using existing Docker BuildKit builder `holoscan_app_builder`\n", + "[2024-04-23 16:52:42,564] [DEBUG] (packager.builder) - Building Holoscan Application Package: tag=my_app-x64-workstation-dgpu-linux-amd64:1.0\n", "#0 building with \"holoscan_app_builder\" instance using docker-container driver\n", "\n", "#1 [internal] load build definition from Dockerfile\n", - "#1 transferring dockerfile: 2.80kB done\n", + "#1 transferring dockerfile: 2.66kB done\n", "#1 DONE 0.1s\n", "\n", - "#2 [internal] load metadata for nvcr.io/nvidia/clara-holoscan/holoscan:v1.0.3-dgpu\n", - "#2 DONE 0.4s\n", + "#2 [internal] load metadata for nvcr.io/nvidia/clara-holoscan/holoscan:v2.0.0-dgpu\n", + "#2 DONE 0.5s\n", "\n", "#3 [internal] load .dockerignore\n", "#3 transferring context: 1.79kB done\n", @@ -1322,15 +1339,15 @@ "#4 [internal] load build context\n", "#4 DONE 0.0s\n", "\n", - "#5 importing cache manifest from local:18341943591062161743\n", + "#5 importing cache manifest from local:13600691502778489948\n", "#5 inferred cache manifest type: application/vnd.oci.image.index.v1+json done\n", "#5 DONE 0.0s\n", "\n", - "#6 [ 1/21] FROM nvcr.io/nvidia/clara-holoscan/holoscan:v1.0.3-dgpu@sha256:50343c616bf910e2a7651abb59db7833933e82cce64c3c4885f938d7e4af6155\n", - "#6 resolve nvcr.io/nvidia/clara-holoscan/holoscan:v1.0.3-dgpu@sha256:50343c616bf910e2a7651abb59db7833933e82cce64c3c4885f938d7e4af6155 0.0s done\n", + "#6 [ 1/21] FROM nvcr.io/nvidia/clara-holoscan/holoscan:v2.0.0-dgpu@sha256:20adbccd2c7b12dfb1798f6953f071631c3b85cd337858a7506f8e420add6d4a\n", + "#6 resolve nvcr.io/nvidia/clara-holoscan/holoscan:v2.0.0-dgpu@sha256:20adbccd2c7b12dfb1798f6953f071631c3b85cd337858a7506f8e420add6d4a 0.0s done\n", "#6 DONE 0.1s\n", "\n", - "#7 importing cache manifest from nvcr.io/nvidia/clara-holoscan/holoscan:v1.0.3-dgpu\n", + "#7 importing cache manifest from nvcr.io/nvidia/clara-holoscan/holoscan:v2.0.0-dgpu\n", "#7 inferred cache manifest type: application/vnd.docker.distribution.manifest.list.v2+json done\n", "#7 DONE 0.7s\n", "\n", @@ -1338,99 +1355,240 @@ "#4 transferring context: 19.56MB 0.1s done\n", "#4 DONE 0.2s\n", "\n", - "#8 [ 8/21] RUN chown -R holoscan /var/holoscan/output\n", + "#8 [ 3/21] RUN apt-get update && apt-get install -y curl jq && rm -rf /var/lib/apt/lists/*\n", "#8 CACHED\n", "\n", - "#9 [13/21] RUN pip install --upgrade pip\n", + "#9 [ 7/21] RUN chown -R holoscan /var/holoscan/input\n", "#9 CACHED\n", "\n", - "#10 [ 4/21] RUN groupadd -f -g 1000 holoscan\n", + "#10 [ 8/21] RUN chown -R holoscan /var/holoscan/output\n", "#10 CACHED\n", "\n", - "#11 [ 5/21] RUN useradd -rm -d /home/holoscan -s /bin/bash -g 1000 -G sudo -u 1000 holoscan\n", + "#11 [11/21] RUN chmod +x /var/holoscan/tools\n", "#11 CACHED\n", "\n", - "#12 [10/21] COPY ./tools /var/holoscan/tools\n", + "#12 [ 4/21] RUN groupadd -f -g 1000 holoscan\n", "#12 CACHED\n", "\n", - "#13 [ 6/21] RUN chown -R holoscan /var/holoscan\n", + "#13 [ 9/21] WORKDIR /var/holoscan\n", "#13 CACHED\n", "\n", "#14 [ 2/21] RUN mkdir -p /etc/holoscan/ && mkdir -p /opt/holoscan/ && mkdir -p /var/holoscan && mkdir -p /opt/holoscan/app && mkdir -p /var/holoscan/input && mkdir -p /var/holoscan/output\n", "#14 CACHED\n", "\n", - "#15 [12/21] COPY ./pip/requirements.txt /tmp/requirements.txt\n", + "#15 [ 6/21] RUN chown -R holoscan /var/holoscan\n", "#15 CACHED\n", "\n", - "#16 [ 9/21] WORKDIR /var/holoscan\n", + "#16 [ 5/21] RUN useradd -rm -d /home/holoscan -s /bin/bash -g 1000 -G sudo -u 1000 holoscan\n", "#16 CACHED\n", "\n", - "#17 [ 7/21] RUN chown -R holoscan /var/holoscan/input\n", + "#17 [12/21] COPY ./pip/requirements.txt /tmp/requirements.txt\n", "#17 CACHED\n", "\n", - "#18 [11/21] RUN chmod +x /var/holoscan/tools\n", + "#18 [10/21] COPY ./tools /var/holoscan/tools\n", "#18 CACHED\n", "\n", - "#19 [ 3/21] RUN apt-get update && apt-get install -y curl jq && rm -rf /var/lib/apt/lists/*\n", + "#19 [13/21] RUN pip install --upgrade pip\n", "#19 CACHED\n", "\n", "#20 [14/21] RUN pip install --no-cache-dir --user -r /tmp/requirements.txt\n", - "#20 CACHED\n", - "\n", - "#21 [15/21] COPY ./monai_deploy_app_sdk-0.5.1+25.g31e4165.dirty-py3-none-any.whl /tmp/monai_deploy_app_sdk-0.5.1+25.g31e4165.dirty-py3-none-any.whl\n", - "#21 DONE 0.2s\n", - "\n", - "#22 [16/21] RUN pip install /tmp/monai_deploy_app_sdk-0.5.1+25.g31e4165.dirty-py3-none-any.whl\n", - "#22 0.845 Defaulting to user installation because normal site-packages is not writeable\n", - "#22 0.979 Processing /tmp/monai_deploy_app_sdk-0.5.1+25.g31e4165.dirty-py3-none-any.whl\n", - "#22 0.993 Requirement already satisfied: numpy>=1.21.6 in /usr/local/lib/python3.10/dist-packages (from monai-deploy-app-sdk==0.5.1+25.g31e4165.dirty) (1.23.5)\n", - "#22 1.183 Collecting holoscan~=1.0 (from monai-deploy-app-sdk==0.5.1+25.g31e4165.dirty)\n", - "#22 1.336 Downloading holoscan-1.0.3-cp310-cp310-manylinux_2_35_x86_64.whl.metadata (4.1 kB)\n", - "#22 1.412 Collecting colorama>=0.4.1 (from monai-deploy-app-sdk==0.5.1+25.g31e4165.dirty)\n", - "#22 1.416 Downloading colorama-0.4.6-py2.py3-none-any.whl.metadata (17 kB)\n", - "#22 1.507 Collecting typeguard>=3.0.0 (from monai-deploy-app-sdk==0.5.1+25.g31e4165.dirty)\n", - "#22 1.512 Downloading typeguard-4.2.1-py3-none-any.whl.metadata (3.7 kB)\n", - "#22 1.611 Collecting pip==23.3.2 (from holoscan~=1.0->monai-deploy-app-sdk==0.5.1+25.g31e4165.dirty)\n", - "#22 1.615 Downloading pip-23.3.2-py3-none-any.whl.metadata (3.5 kB)\n", - "#22 1.632 Requirement already satisfied: cupy-cuda12x==12.2 in /usr/local/lib/python3.10/dist-packages (from holoscan~=1.0->monai-deploy-app-sdk==0.5.1+25.g31e4165.dirty) (12.2.0)\n", - "#22 1.635 Requirement already satisfied: cloudpickle==2.2.1 in /usr/local/lib/python3.10/dist-packages (from holoscan~=1.0->monai-deploy-app-sdk==0.5.1+25.g31e4165.dirty) (2.2.1)\n", - "#22 1.638 Requirement already satisfied: python-on-whales==0.60.1 in /usr/local/lib/python3.10/dist-packages (from holoscan~=1.0->monai-deploy-app-sdk==0.5.1+25.g31e4165.dirty) (0.60.1)\n", - "#22 1.641 Requirement already satisfied: Jinja2==3.1.2 in /usr/local/lib/python3.10/dist-packages (from holoscan~=1.0->monai-deploy-app-sdk==0.5.1+25.g31e4165.dirty) (3.1.2)\n", - "#22 1.643 Requirement already satisfied: packaging==23.1 in /usr/local/lib/python3.10/dist-packages (from holoscan~=1.0->monai-deploy-app-sdk==0.5.1+25.g31e4165.dirty) (23.1)\n", - "#22 1.644 Requirement already satisfied: pyyaml==6.0 in /usr/local/lib/python3.10/dist-packages (from holoscan~=1.0->monai-deploy-app-sdk==0.5.1+25.g31e4165.dirty) (6.0)\n", - "#22 1.645 Requirement already satisfied: requests==2.28.2 in /usr/local/lib/python3.10/dist-packages (from holoscan~=1.0->monai-deploy-app-sdk==0.5.1+25.g31e4165.dirty) (2.28.2)\n", - "#22 1.646 Requirement already satisfied: psutil==5.9.6 in /usr/local/lib/python3.10/dist-packages (from holoscan~=1.0->monai-deploy-app-sdk==0.5.1+25.g31e4165.dirty) (5.9.6)\n", - "#22 1.757 Collecting wheel-axle-runtime<1.0 (from holoscan~=1.0->monai-deploy-app-sdk==0.5.1+25.g31e4165.dirty)\n", - "#22 1.763 Downloading wheel_axle_runtime-0.0.5-py3-none-any.whl.metadata (7.7 kB)\n", - "#22 1.806 Requirement already satisfied: fastrlock>=0.5 in /usr/local/lib/python3.10/dist-packages (from cupy-cuda12x==12.2->holoscan~=1.0->monai-deploy-app-sdk==0.5.1+25.g31e4165.dirty) (0.8.2)\n", - "#22 1.813 Requirement already satisfied: MarkupSafe>=2.0 in /usr/local/lib/python3.10/dist-packages (from Jinja2==3.1.2->holoscan~=1.0->monai-deploy-app-sdk==0.5.1+25.g31e4165.dirty) (2.1.3)\n", - "#22 1.829 Requirement already satisfied: pydantic<2,>=1.5 in /usr/local/lib/python3.10/dist-packages (from python-on-whales==0.60.1->holoscan~=1.0->monai-deploy-app-sdk==0.5.1+25.g31e4165.dirty) (1.10.14)\n", - "#22 1.829 Requirement already satisfied: tqdm in /usr/local/lib/python3.10/dist-packages (from python-on-whales==0.60.1->holoscan~=1.0->monai-deploy-app-sdk==0.5.1+25.g31e4165.dirty) (4.66.1)\n", - "#22 1.830 Requirement already satisfied: typer>=0.4.1 in /usr/local/lib/python3.10/dist-packages (from python-on-whales==0.60.1->holoscan~=1.0->monai-deploy-app-sdk==0.5.1+25.g31e4165.dirty) (0.9.0)\n", - "#22 1.831 Requirement already satisfied: typing-extensions in /home/holoscan/.local/lib/python3.10/site-packages (from python-on-whales==0.60.1->holoscan~=1.0->monai-deploy-app-sdk==0.5.1+25.g31e4165.dirty) (4.10.0)\n", - "#22 1.839 Requirement already satisfied: charset-normalizer<4,>=2 in /usr/local/lib/python3.10/dist-packages (from requests==2.28.2->holoscan~=1.0->monai-deploy-app-sdk==0.5.1+25.g31e4165.dirty) (3.3.2)\n", - "#22 1.840 Requirement already satisfied: idna<4,>=2.5 in /usr/local/lib/python3.10/dist-packages (from requests==2.28.2->holoscan~=1.0->monai-deploy-app-sdk==0.5.1+25.g31e4165.dirty) (3.6)\n", - "#22 1.841 Requirement already satisfied: urllib3<1.27,>=1.21.1 in /usr/local/lib/python3.10/dist-packages (from requests==2.28.2->holoscan~=1.0->monai-deploy-app-sdk==0.5.1+25.g31e4165.dirty) 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━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 2.1/2.1 MB 52.2 MB/s eta 0:00:00\n", - "#22 7.745 Downloading typeguard-4.2.1-py3-none-any.whl (34 kB)\n", - "#22 7.771 Downloading wheel_axle_runtime-0.0.5-py3-none-any.whl (12 kB)\n", - "#22 8.166 Installing collected packages: wheel-axle-runtime, typeguard, pip, colorama, holoscan, monai-deploy-app-sdk\n", - "#22 8.245 Attempting uninstall: pip\n", - "#22 8.248 Found existing installation: pip 24.0\n", - "#22 8.310 Uninstalling pip-24.0:\n", - "#22 8.744 Successfully uninstalled pip-24.0\n", - "#22 10.41 Successfully installed colorama-0.4.6 holoscan-1.0.3 monai-deploy-app-sdk-0.5.1+25.g31e4165.dirty pip-23.3.2 typeguard-4.2.1 wheel-axle-runtime-0.0.5\n", - "#22 DONE 11.1s\n", + "#20 0.822 Collecting highdicom>=0.18.2 (from -r /tmp/requirements.txt (line 1))\n", + "#20 0.909 Downloading highdicom-0.22.0-py3-none-any.whl.metadata (3.8 kB)\n", + "#20 0.940 Collecting monai>=1.0 (from -r /tmp/requirements.txt (line 2))\n", + "#20 0.944 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+ "#20 33.04 Downloading filelock-3.13.4-py3-none-any.whl (11 kB)\n", + "#20 33.05 Downloading fsspec-2024.3.1-py3-none-any.whl (171 kB)\n", + "#20 33.06 ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 172.0/172.0 kB 77.4 MB/s eta 0:00:00\n", + "#20 33.07 Downloading sympy-1.12-py3-none-any.whl (5.7 MB)\n", + "#20 33.12 ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 5.7/5.7 MB 117.1 MB/s eta 0:00:00\n", + "#20 33.13 Downloading mpmath-1.3.0-py3-none-any.whl (536 kB)\n", + "#20 33.14 ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 536.2/536.2 kB 146.2 MB/s eta 0:00:00\n", + "#20 33.14 Downloading nvidia_nvjitlink_cu12-12.4.127-py3-none-manylinux2014_x86_64.whl (21.1 MB)\n", + "#20 33.34 ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 21.1/21.1 MB 117.6 MB/s eta 0:00:00\n", + "#20 40.94 Installing collected packages: SimpleITK, mpmath, typing-extensions, trimesh, tifffile, sympy, scipy, pydicom, pillow, nvidia-nvtx-cu12, nvidia-nvjitlink-cu12, nvidia-nccl-cu12, nvidia-curand-cu12, nvidia-cufft-cu12, nvidia-cuda-runtime-cu12, nvidia-cuda-nvrtc-cu12, nvidia-cuda-cupti-cu12, nvidia-cublas-cu12, nibabel, networkx, lazy-loader, fsspec, filelock, triton, python-utils, pillow-jpls, nvidia-cusparse-cu12, nvidia-cudnn-cu12, imageio, scikit-image, nvidia-cusolver-cu12, numpy-stl, highdicom, torch, monai\n", + "#20 94.76 Successfully installed SimpleITK-2.3.1 filelock-3.13.4 fsspec-2024.3.1 highdicom-0.22.0 imageio-2.34.1 lazy-loader-0.4 monai-1.3.0 mpmath-1.3.0 networkx-3.3 nibabel-5.2.1 numpy-stl-3.1.1 nvidia-cublas-cu12-12.1.3.1 nvidia-cuda-cupti-cu12-12.1.105 nvidia-cuda-nvrtc-cu12-12.1.105 nvidia-cuda-runtime-cu12-12.1.105 nvidia-cudnn-cu12-8.9.2.26 nvidia-cufft-cu12-11.0.2.54 nvidia-curand-cu12-10.3.2.106 nvidia-cusolver-cu12-11.4.5.107 nvidia-cusparse-cu12-12.1.0.106 nvidia-nccl-cu12-2.19.3 nvidia-nvjitlink-cu12-12.4.127 nvidia-nvtx-cu12-12.1.105 pillow-10.3.0 pillow-jpls-1.3.2 pydicom-2.4.4 python-utils-3.8.2 scikit-image-0.23.2 scipy-1.13.0 sympy-1.12 tifffile-2024.4.18 torch-2.2.2 trimesh-4.3.1 triton-2.2.0 typing-extensions-4.11.0\n", + "#20 DONE 98.0s\n", + "\n", + "#21 [15/21] COPY ./monai_deploy_app_sdk-0.5.1+20.gb869749.dirty-py3-none-any.whl /tmp/monai_deploy_app_sdk-0.5.1+20.gb869749.dirty-py3-none-any.whl\n", + "#21 DONE 0.5s\n", + "\n", + "#22 [16/21] RUN pip install /tmp/monai_deploy_app_sdk-0.5.1+20.gb869749.dirty-py3-none-any.whl\n", + "#22 0.651 Defaulting to user installation because normal site-packages is not writeable\n", + "#22 0.747 Processing /tmp/monai_deploy_app_sdk-0.5.1+20.gb869749.dirty-py3-none-any.whl\n", + "#22 0.758 Requirement already satisfied: numpy>=1.21.6 in /usr/local/lib/python3.10/dist-packages (from monai-deploy-app-sdk==0.5.1+20.gb869749.dirty) (1.23.5)\n", + "#22 0.873 Collecting holoscan~=2.0 (from monai-deploy-app-sdk==0.5.1+20.gb869749.dirty)\n", + "#22 0.964 Downloading holoscan-2.0.0-cp310-cp310-manylinux_2_35_x86_64.whl.metadata (6.7 kB)\n", + "#22 1.036 Collecting colorama>=0.4.1 (from 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sha256:3b3b2102892c64900945ca4d84a328af1fb7350c84cb4d85ecee3b94f48ed85c 0.0s done\n", - "#28 exporting config sha256:d6463325d6640490c117da76b90d02687331b2ee1e486047f7c4c968023c3d89 0.0s done\n", + "#28 exporting layers 161.2s done\n", + "#28 exporting manifest sha256:db72052410ed3875bd2689b115d7ea706f74caa44be88c9b455c9761c991f225 0.0s done\n", + "#28 exporting config sha256:4fe495cf55e1086e3b466f4799218faa2b377e58348ae9b51253b56b560295b3 0.0s done\n", "#28 sending tarball\n", "#28 ...\n", "\n", "#29 importing to docker\n", - "#29 loading layer a292666cef7b 32.77kB / 125.57kB\n", - "#29 loading layer 23d575e38e71 557.06kB / 73.97MB\n", - "#29 loading layer 23d575e38e71 71.86MB / 73.97MB 2.2s\n", - "#29 loading layer 601aae96dba4 196.61kB / 17.81MB\n", - "#29 loading layer 8973e59624ba 492B / 492B\n", - "#29 loading layer 2c4cefc4de42 313B / 313B\n", - "#29 loading layer 450f1c5db7b9 301B / 301B\n", - "#29 loading layer e08583daa6d7 3.30kB / 3.30kB\n", - "#29 loading layer 2c4cefc4de42 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414c50de1c1c 1.81GB / 2.97GB 38.9s\n", + "#29 loading layer 414c50de1c1c 1.97GB / 2.97GB 43.1s\n", + "#29 loading layer 414c50de1c1c 2.04GB / 2.97GB 50.1s\n", + "#29 loading layer 414c50de1c1c 2.17GB / 2.97GB 56.4s\n", + "#29 loading layer 414c50de1c1c 2.42GB / 2.97GB 62.5s\n", + "#29 loading layer 414c50de1c1c 2.63GB / 2.97GB 66.6s\n", + "#29 loading layer 414c50de1c1c 2.79GB / 2.97GB 70.7s\n", + "#29 loading layer 2d2337d002b1 32.77kB / 125.83kB\n", + "#29 loading layer 05a9e332a339 557.06kB / 67.35MB\n", + "#29 loading layer 05a9e332a339 59.60MB / 67.35MB 2.1s\n", + "#29 loading layer b466f5b35107 196.61kB / 17.81MB\n", + "#29 loading layer 66a2f54a1b71 493B / 493B\n", + "#29 loading layer 9b5da571c07c 316B / 316B\n", + "#29 loading layer 69c6b6426338 301B / 301B\n", + "#29 loading layer bfe49db5ef06 3.33kB / 3.33kB\n", + "#29 loading layer b466f5b35107 196.61kB / 17.81MB 5.1s done\n", + "#29 loading layer 414c50de1c1c 2.90GB / 2.97GB 85.2s done\n", + "#29 loading layer 2d2337d002b1 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"#30 writing layer sha256:183aa7032b52e859f5de3dac98da7c8398ed5f8a984d74865561f126c0eecef2 0.0s done\n", + "#30 writing layer sha256:121c2168995bf46d9888919d105fe5a0d03a3640ee73ed00c9081e10794e7c58 0.0s done\n", + "#30 writing layer sha256:1c5c3aa9c2c8bfd1b9eb36248f5b6d67b3db73ef43440f9dd897615771974b39 done\n", + "#30 writing layer sha256:1f73278b7f17492ce1a8b28b139d54596961596d6790dc20046fa6d5909f3e9c done\n", "#30 writing layer sha256:20d331454f5fb557f2692dfbdbe092c718fd2cb55d5db9d661b62228dacca5c2 done\n", - "#30 writing layer sha256:2232aeb26b5b7ea57227e9a5b84da4fb229624d7bc976a5f7ce86d9c8653d277 done\n", + "#30 writing layer sha256:229f01f9a7c2d258af634b5b41c5f5b2998c54c7557b3e3cfec465152ebb0c8b\n", + "#30 writing layer sha256:229f01f9a7c2d258af634b5b41c5f5b2998c54c7557b3e3cfec465152ebb0c8b 0.4s done\n", + "#30 writing layer sha256:238f69a43816e481f0295995fcf5fe74d59facf0f9f99734c8d0a2fb140630e0\n", "#30 writing layer 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writing layer sha256:49bdc9abf8a437ccff67cc11490ba52c976577992909856a86be872a34d3b950\n", "#30 writing layer sha256:49bdc9abf8a437ccff67cc11490ba52c976577992909856a86be872a34d3b950 done\n", "#30 writing layer sha256:4b691ba9f48b41eaa0c754feba8366f1c030464fcbc55eeffa6c86675990933a done\n", "#30 writing layer sha256:4d04a8db404f16c2704fa10739cb6745a0187713a21a6ef0deb34b48629b54c1 done\n", + "#30 writing layer sha256:4d6542f3a7f5dc637e92c4ce4f54ad7edbfc4fcf629380921a76a1eaaa042085 0.0s done\n", "#30 writing layer sha256:4f4fb700ef54461cfa02571ae0db9a0dc1e0cdb5577484a6d75e68dc38e8acc1 done\n", - "#30 writing layer sha256:5275a41be8f6691a490c0a15589e0910c73bf971169ad33a850ef570d37f63dd done\n", - "#30 writing layer sha256:52fbfeaf78318d843054ce2bfb5bfc9f71278939a815f6035ab5b14573ad017b done\n", - "#30 writing layer sha256:5792b18b6f162bae61ff5840cdb9e8567e6847a56ac886f940b47e7271c529a7 done\n", + "#30 writing layer sha256:542bc8c8d18fbc95e6794122c3593a4a693f8ab6dda4460406f4d7b1ae64a2bc done\n", "#30 writing layer sha256:57f244836ad318f9bbb3b29856ae1a5b31038bfbb9b43d2466d51c199eb55041 done\n", "#30 writing layer sha256:5b5b131e0f20db4cb8e568b623a95f8fc16ed1c6b322a9366df70b59a881f24f done\n", - "#30 writing layer sha256:5ccb787d371fd3697122101438ddd0f55b537832e9756d2c51ab1d8158710ac5 done\n", - "#30 writing layer sha256:5ea668ffc2fc267d241dbf17ca283bc879643a189be4f7e3d9034a82fc64a1ea done\n", + "#30 writing layer sha256:5b90d17b5048adcadefd0b1e4dba9a99247a8827a887e1ca042df375c85b518d done\n", "#30 writing layer sha256:62452179df7c18e292f141d4aec29e6aba9ff8270c893731169fc6f41dc07631 done\n", + "#30 writing layer sha256:6545b2e110c927b4bf5b0cfdb2ae791686a503dd32470362873ccb4375dcc13c\n", + "#30 writing layer sha256:6545b2e110c927b4bf5b0cfdb2ae791686a503dd32470362873ccb4375dcc13c 1.5s done\n", + "#30 writing layer sha256:6630c387f5f2115bca2e646fd0c2f64e1f3d5431c2e050abe607633883eda230\n", "#30 writing layer 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done\n", + "#30 writing layer sha256:85713f9b166b5add777c524ee807f6265d88b967cbeb9f961d6b09bf220c9a65 done\n", + "#30 writing layer sha256:8ca81d63d0fea573e7b16da41370b55162415a5c07feac92012b101b79f8d5ae done\n", + "#30 writing layer sha256:8fe00505006a09966e763918147ef6ed55bb6695b26e4940c780ee430dc5da8e done\n", "#30 writing layer sha256:90eae6faa5cc5ba62f12c25915cdfb1a7a51abfba0d05cb5818c3f908f4e345f done\n", + "#30 writing layer sha256:9205d97d9d3e906698bcc6c42d45727c2fa6ec2622abf953d46778c3b8c78edc done\n", + "#30 writing layer sha256:993369dbcc13162a6654d2a3e990b8d8b5f37963564d25710e12764337261ae3 done\n", + "#30 writing layer sha256:99e42a4adebadb39bf55bf94bbd9fb8034230ee19b6b0a42e6ff96f2e7794f30 done\n", "#30 writing layer sha256:9ac855545fa90ed2bf3b388fdff9ef06ac9427b0c0fca07c9e59161983d8827e done\n", "#30 writing layer sha256:9d19ee268e0d7bcf6716e6658ee1b0384a71d6f2f9aa1ae2085610cf7c7b316f done\n", - "#30 writing layer 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sha256:e291ddecfbe16b95ee9e90b5e90b1a3d0cfd53dc5e720d6b0f3d28e4a47cf5ac done\n", "#30 writing layer sha256:e8acb678f16bc0c369d5cf9c184f2d3a1c773986816526e5e3e9c0354f7e757f done\n", "#30 writing layer sha256:e9225f7ab6606813ec9acba98a064826ebfd6713a9645a58cd068538af1ecddb done\n", - "#30 writing layer sha256:f33546e75bf1a7d9dc9e21b9a2c54c9d09b24790ad7a4192a8509002ceb14688 done\n", + "#30 writing layer sha256:f249faf9663a96b0911a903f8803b11a553c59b698013fb8343492fefdaaea90 done\n", "#30 writing layer sha256:f608e2fbff86e98627b7e462057e7d2416522096d73fe4664b82fe6ce8a4047d done\n", - "#30 writing layer sha256:f7702077ced42a1ee35e7f5e45f72634328ff3bcfe3f57735ba80baa5ec45daf done\n", - "#30 writing layer sha256:fa66a49172c6e821a1bace57c007c01da10cbc61507c44f8cdfeed8c4e5febab done\n", - "#30 writing config sha256:386c66fca187580548b7c0d95c25fecfb72f326f30df509c9860b977d7e32763 0.0s done\n", - "#30 writing cache manifest sha256:ebd62b21fd87e8654814f8093dffbbf555dced752810b2798c59b2b1a08ce0fd 0.0s done\n", - "#30 DONE 2.5s\n", - "[2024-04-10 15:05:33,378] [INFO] (packager) - Build Summary:\n", + "#30 writing layer sha256:f65d191416580d6c38e3d95eee12377b75a4df548be1492618ce2a8c3c41b99e done\n", + "#30 writing layer sha256:fbfd4de480c7037f0604cf64cef29e59cfb27193b257d66d110ff82ec6fc6715\n", + "#30 writing layer sha256:fbfd4de480c7037f0604cf64cef29e59cfb27193b257d66d110ff82ec6fc6715 47.3s done\n", + "#30 writing layer sha256:fcb10e9f191b92679f1cac7623b152400f374a3e3d90f3d2248bfced02b6bdca\n", + "#30 preparing build cache for export 50.0s done\n", + "#30 writing layer sha256:fcb10e9f191b92679f1cac7623b152400f374a3e3d90f3d2248bfced02b6bdca 0.0s done\n", + "#30 writing config sha256:1af23d9bb67b68807f26cc256ea0ba50bba21a62a52cdfab0bc82567fef2a35e 0.0s done\n", + "#30 writing cache manifest sha256:3e6252fe3fb73d49377342ccff9ce009489fdd34a8709b3c2e0e2c2cd1a54372 0.0s done\n", + "#30 DONE 50.0s\n", + "[2024-04-23 17:00:27,074] [INFO] (packager) - Build Summary:\n", "\n", "Platform: x64-workstation/dgpu\n", " Status: Succeeded\n", @@ -1579,14 +1758,14 @@ }, { "cell_type": "code", - "execution_count": 16, + "execution_count": 66, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ - "my_app-x64-workstation-dgpu-linux-amd64 1.0 d6463325d664 About a minute ago 17.5GB\n" + "my_app-x64-workstation-dgpu-linux-amd64 1.0 4fe495cf55e1 5 minutes ago 17.9GB\n" ] } ], @@ -1608,7 +1787,7 @@ }, { "cell_type": "code", - "execution_count": 17, + "execution_count": 67, "metadata": {}, "outputs": [ { @@ -1668,16 +1847,16 @@ " \"platformConfig\": \"dgpu\"\n", "}\n", "\n", - "2024-04-10 22:05:37 [INFO] Copying application from /opt/holoscan/app to /var/run/holoscan/export/app\n", + "2024-04-24 00:00:30 [INFO] Copying application from /opt/holoscan/app to /var/run/holoscan/export/app\n", "\n", - "2024-04-10 22:05:37 [INFO] Copying application manifest file from /etc/holoscan/app.json to /var/run/holoscan/export/config/app.json\n", - "2024-04-10 22:05:37 [INFO] Copying pkg manifest file from /etc/holoscan/pkg.json to /var/run/holoscan/export/config/pkg.json\n", - "2024-04-10 22:05:37 [INFO] Copying application configuration from /var/holoscan/app.yaml to /var/run/holoscan/export/config/app.yaml\n", + "2024-04-24 00:00:30 [INFO] Copying application manifest file from /etc/holoscan/app.json to /var/run/holoscan/export/config/app.json\n", + "2024-04-24 00:00:30 [INFO] Copying pkg manifest file from /etc/holoscan/pkg.json to /var/run/holoscan/export/config/pkg.json\n", + "2024-04-24 00:00:30 [INFO] Copying application configuration from /var/holoscan/app.yaml to /var/run/holoscan/export/config/app.yaml\n", "\n", - "2024-04-10 22:05:37 [INFO] Copying models from /opt/holoscan/models to /var/run/holoscan/export/models\n", + "2024-04-24 00:00:30 [INFO] Copying models from /opt/holoscan/models to /var/run/holoscan/export/models\n", "\n", - "2024-04-10 22:05:37 [INFO] Copying documentation from /opt/holoscan/docs/ to /var/run/holoscan/export/docs\n", - "2024-04-10 22:05:37 [INFO] '/opt/holoscan/docs/' cannot be found.\n", + "2024-04-24 00:00:30 [INFO] Copying documentation from /opt/holoscan/docs/ to /var/run/holoscan/export/docs\n", + "2024-04-24 00:00:30 [INFO] '/opt/holoscan/docs/' cannot be found.\n", "\n", "app config models\n" ] @@ -1702,29 +1881,29 @@ }, { "cell_type": "code", - "execution_count": 18, + "execution_count": 68, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ - "[2024-04-10 15:05:39,448] [INFO] (runner) - Checking dependencies...\n", - "[2024-04-10 15:05:39,448] [INFO] (runner) - --> Verifying if \"docker\" is installed...\n", + "[2024-04-23 17:00:31,900] [INFO] (runner) - Checking dependencies...\n", + "[2024-04-23 17:00:31,900] [INFO] (runner) - --> Verifying if \"docker\" is installed...\n", "\n", - "[2024-04-10 15:05:39,449] [INFO] (runner) - --> Verifying if \"docker-buildx\" is installed...\n", + "[2024-04-23 17:00:31,901] [INFO] (runner) - --> Verifying if \"docker-buildx\" is installed...\n", "\n", - "[2024-04-10 15:05:39,449] [INFO] (runner) - --> Verifying if \"my_app-x64-workstation-dgpu-linux-amd64:1.0\" is available...\n", + "[2024-04-23 17:00:31,901] [INFO] (runner) - --> Verifying if \"my_app-x64-workstation-dgpu-linux-amd64:1.0\" is available...\n", "\n", - "[2024-04-10 15:05:39,511] [INFO] (runner) - Reading HAP/MAP manifest...\n", - "\u001b[sPreparing to copy...\u001b[?25l\u001b[u\u001b[2KCopying from container - 0B\u001b[?25h\u001b[u\u001b[2KSuccessfully copied 2.56kB to /tmp/tmpba1clh6t/app.json\n", - "\u001b[sPreparing to copy...\u001b[?25l\u001b[u\u001b[2KCopying from container - 0B\u001b[?25h\u001b[u\u001b[2KSuccessfully copied 2.05kB to /tmp/tmpba1clh6t/pkg.json\n", - "[2024-04-10 15:05:39,743] [INFO] (runner) - --> Verifying if \"nvidia-ctk\" is installed...\n", + "[2024-04-23 17:00:31,971] [INFO] (runner) - Reading HAP/MAP manifest...\n", + "\u001b[sPreparing to copy...\u001b[?25l\u001b[u\u001b[2KCopying from container - 0B\u001b[?25h\u001b[u\u001b[2KSuccessfully copied 2.56kB to /tmp/tmpxev2hpxc/app.json\n", + "\u001b[sPreparing to copy...\u001b[?25l\u001b[u\u001b[2KCopying from container - 0B\u001b[?25h\u001b[u\u001b[2KSuccessfully copied 2.05kB to /tmp/tmpxev2hpxc/pkg.json\n", + "[2024-04-23 17:00:32,215] [INFO] (runner) - --> Verifying if \"nvidia-ctk\" is installed...\n", "\n", - "[2024-04-10 15:05:39,744] [INFO] (runner) - --> Verifying \"nvidia-ctk\" version...\n", + "[2024-04-23 17:00:32,216] [INFO] (runner) - --> Verifying \"nvidia-ctk\" version...\n", "\n", - "[2024-04-10 15:05:40,086] [INFO] (common) - Launching container (1d77a7676232) using image 'my_app-x64-workstation-dgpu-linux-amd64:1.0'...\n", - " container name: festive_hermann\n", + "[2024-04-23 17:00:32,528] [INFO] (common) - Launching container (6ffaea9917bd) using image 'my_app-x64-workstation-dgpu-linux-amd64:1.0'...\n", + " container name: fervent_bell\n", " host name: mingq-dt\n", " network: host\n", " user: 1000:1000\n", @@ -1734,141 +1913,101 @@ " shared memory size: 67108864\n", " devices: \n", " group_add: 44\n", - "2024-04-10 22:05:40 [INFO] Launching application python3 /opt/holoscan/app ...\n", + "2024-04-24 00:00:33 [INFO] Launching application python3 /opt/holoscan/app ...\n", "\n", - "[2024-04-10 22:05:45,192] [INFO] (root) - Parsed args: Namespace(log_level=None, input=None, output=None, model=None, workdir=None, argv=['/opt/holoscan/app'])\n", + "[2024-04-24 00:00:36,780] [INFO] (root) - Parsed args: Namespace(log_level=None, input=None, output=None, model=None, workdir=None, argv=['/opt/holoscan/app'])\n", "\n", - "[2024-04-10 22:05:45,195] [INFO] (root) - AppContext object: AppContext(input_path=/var/holoscan/input, output_path=/var/holoscan/output, model_path=/opt/holoscan/models, workdir=/var/holoscan)\n", + "[2024-04-24 00:00:36,783] [INFO] (root) - AppContext object: AppContext(input_path=/var/holoscan/input, output_path=/var/holoscan/output, model_path=/opt/holoscan/models, workdir=/var/holoscan)\n", "\n", - "[2024-04-10 22:05:45,197] [INFO] (root) - End compose\n", + "[2024-04-24 00:00:36,784] [INFO] (root) - End compose\n", "\n", "[info] [app_driver.cpp:1161] Launching the driver/health checking service\n", "\n", - "[info] [gxf_executor.cpp:211] Creating context\n", + "[info] [gxf_executor.cpp:247] Creating context\n", "\n", "[info] [server.cpp:87] Health checking server listening on 0.0.0.0:8777\n", "\n", - "[info] [gxf_executor.cpp:1674] Loading extensions from configs...\n", + "[info] [gxf_executor.cpp:1672] Loading extensions from configs...\n", "\n", - "[info] [gxf_executor.cpp:1864] Activating Graph...\n", + "[info] [gxf_executor.cpp:1842] Activating Graph...\n", "\n", - "[info] [gxf_executor.cpp:1894] Running Graph...\n", + "\u001b[0m2024-04-24 00:00:36.818 INFO gxf/std/greedy_scheduler.cpp@191: Scheduling 8 entities\u001b[0m\n", "\n", - "[info] [gxf_executor.cpp:1896] Waiting for completion...\n", + "[info] [gxf_executor.cpp:1874] Running Graph...\n", "\n", - "[info] [gxf_executor.cpp:1897] Graph execution waiting. Fragment: \n", + "[info] [gxf_executor.cpp:1876] Waiting for completion...\n", "\n", - "[info] [greedy_scheduler.cpp:190] Scheduling 8 entities\n", + "[2024-04-24 00:00:36,819] [INFO] (monai.deploy.operators.dicom_data_loader_operator.DICOMDataLoaderOperator) - No or invalid input path from the optional input port: None\n", "\n", - "[2024-04-10 22:05:45,297] [INFO] (monai.deploy.operators.dicom_data_loader_operator.DICOMDataLoaderOperator) - No or invalid input path from the optional input port: None\n", + "[2024-04-24 00:00:37,735] [INFO] (root) - Finding series for Selection named: CT Series\n", "\n", - "[2024-04-10 22:05:46,131] [INFO] (root) - Finding series for Selection named: CT Series\n", - "\n", - "[2024-04-10 22:05:46,131] [INFO] (root) - Searching study, : 1.3.6.1.4.1.14519.5.2.1.7085.2626.822645453932810382886582736291\n", + "[2024-04-24 00:00:37,735] [INFO] (root) - Searching study, : 1.3.6.1.4.1.14519.5.2.1.7085.2626.822645453932810382886582736291\n", "\n", " # of series: 1\n", "\n", - "[2024-04-10 22:05:46,131] [INFO] (root) - Working on series, instance UID: 1.3.6.1.4.1.14519.5.2.1.7085.2626.119403521930927333027265674239\n", - "\n", - "[2024-04-10 22:05:46,131] [INFO] (root) - On attribute: 'StudyDescription' to match value: '(.*?)'\n", - "\n", - "[2024-04-10 22:05:46,131] [INFO] (root) - Series attribute StudyDescription value: CT ABDOMEN W IV CONTRAST\n", - "\n", - "[2024-04-10 22:05:46,131] [INFO] (root) - Series attribute string value did not match. Try regEx.\n", - "\n", - "[2024-04-10 22:05:46,131] [INFO] (root) - On attribute: 'Modality' to match value: '(?i)CT'\n", - "\n", - "[2024-04-10 22:05:46,131] [INFO] (root) - Series attribute Modality value: CT\n", - "\n", - "[2024-04-10 22:05:46,132] [INFO] (root) - Series attribute string value did not match. Try regEx.\n", - "\n", - "[2024-04-10 22:05:46,132] [INFO] (root) - On attribute: 'SeriesDescription' to match value: '(.*?)'\n", - "\n", - "[2024-04-10 22:05:46,132] [INFO] (root) - Series attribute SeriesDescription value: ABD/PANC 3.0 B31f\n", - "\n", - "[2024-04-10 22:05:46,132] [INFO] (root) - Series attribute string value did not match. Try regEx.\n", - "\n", - "[2024-04-10 22:05:46,132] [INFO] (root) - Selected Series, UID: 1.3.6.1.4.1.14519.5.2.1.7085.2626.119403521930927333027265674239\n", + "[2024-04-24 00:00:37,735] [INFO] (root) - Working on series, instance UID: 1.3.6.1.4.1.14519.5.2.1.7085.2626.119403521930927333027265674239\n", "\n", - "[2024-04-10 22:05:46,349] [INFO] (root) - Parsing from bundle_path: /opt/holoscan/models/model/model.ts\n", + "[2024-04-24 00:00:37,735] [INFO] (root) - On attribute: 'StudyDescription' to match value: '(.*?)'\n", "\n", - "[2024-04-10 22:05:49,959] [INFO] (monai.deploy.operators.stl_conversion_operator.STLConversionOperator) - Output will be saved in file /var/holoscan/output/stl/spleen.stl.\n", + "[2024-04-24 00:00:37,735] [INFO] (root) - Series attribute StudyDescription value: CT ABDOMEN W IV CONTRAST\n", "\n", - "[2024-04-10 22:05:51,433] [INFO] (monai.deploy.operators.stl_conversion_operator.SpatialImage) - 3D image\n", + "[2024-04-24 00:00:37,735] [INFO] (root) - Series attribute string value did not match. Try regEx.\n", "\n", - "[2024-04-10 22:05:51,433] [INFO] (monai.deploy.operators.stl_conversion_operator.STLConverter) - Image ndarray shape:(204, 512, 512)\n", + "[2024-04-24 00:00:37,735] [INFO] (root) - On attribute: 'Modality' to match value: '(?i)CT'\n", "\n", - "Exception occurred in compute method of operator: 'stl_conversion_op'\n", + "[2024-04-24 00:00:37,735] [INFO] (root) - Series attribute Modality value: CT\n", "\n", - "Traceback (most recent call last):\n", + "[2024-04-24 00:00:37,735] [INFO] (root) - Series attribute string value did not match. Try regEx.\n", "\n", - " File \"/home/holoscan/.local/lib/python3.10/site-packages/monai/deploy/operators/stl_conversion_operator.py\", line 118, in compute\n", + "[2024-04-24 00:00:37,735] [INFO] (root) - On attribute: 'SeriesDescription' to match value: '(.*?)'\n", "\n", - " stl_bytes = self._convert(input_image, _output_file)\n", + "[2024-04-24 00:00:37,735] [INFO] (root) - Series attribute SeriesDescription value: ABD/PANC 3.0 B31f\n", "\n", - " File \"/home/holoscan/.local/lib/python3.10/site-packages/monai/deploy/operators/stl_conversion_operator.py\", line 135, in _convert\n", + "[2024-04-24 00:00:37,735] [INFO] (root) - Series attribute string value did not match. Try regEx.\n", "\n", - " return self._converter.convert(\n", + "[2024-04-24 00:00:37,735] [INFO] (root) - Selected Series, UID: 1.3.6.1.4.1.14519.5.2.1.7085.2626.119403521930927333027265674239\n", "\n", - " File \"/home/holoscan/.local/lib/python3.10/site-packages/monai/deploy/operators/stl_conversion_operator.py\", line 182, in convert\n", + "[2024-04-24 00:00:38,147] [INFO] (root) - Parsing from bundle_path: /opt/holoscan/models/model/model.ts\n", "\n", - " nda = STLConverter.get_largest_cc(nda)\n", + "[2024-04-24 00:00:41,393] [INFO] (monai.deploy.operators.stl_conversion_operator.STLConversionOperator) - Output will be saved in file /var/holoscan/output/stl/spleen.stl.\n", "\n", - " File \"/home/holoscan/.local/lib/python3.10/site-packages/monai/deploy/operators/stl_conversion_operator.py\", line 255, in get_largest_cc\n", + "[2024-04-24 00:00:43,045] [INFO] (monai.deploy.operators.stl_conversion_operator.SpatialImage) - 3D image\n", "\n", - " labels = label(nda)\n", - "\n", - " File \"/home/holoscan/.local/lib/python3.10/site-packages/monai/deploy/utils/importutil.py\", line 274, in __call__\n", - "\n", - " raise self._exception\n", - "\n", - " File \"/home/holoscan/.local/lib/python3.10/site-packages/monai/deploy/utils/importutil.py\", line 226, in optional_import\n", - "\n", - " pkg = __import__(module) # top level module\n", - "\n", - "monai.deploy.utils.importutil.OptionalImportError: from skimage.measure import label (No module named 'skimage').\n", - "\n", - "\n", - "\n", - "For details about installing the optional dependencies, please visit:\n", - "\n", - " https://docs.monai.io/en/latest/installation.html#installing-the-recommended-dependencies\n", + "[2024-04-24 00:00:43,045] [INFO] (monai.deploy.operators.stl_conversion_operator.STLConverter) - Image ndarray shape:(204, 512, 512)\n", "\n", "/home/holoscan/.local/lib/python3.10/site-packages/highdicom/valuerep.py:54: UserWarning: The string \"C3N-00198\" is unlikely to represent the intended person name since it contains only a single component. Construct a person name according to the format in described in https://dicom.nema.org/dicom/2013/output/chtml/part05/sect_6.2.html#sect_6.2.1.2, or, in pydicom 2.2.0 or later, use the pydicom.valuerep.PersonName.from_named_components() method to construct the person name correctly. If a single-component name is really intended, add a trailing caret character to disambiguate the name.\n", "\n", " warnings.warn(\n", "\n", - "[2024-04-10 22:05:52,708] [INFO] (highdicom.base) - copy Image-related attributes from dataset \"1.3.6.1.4.1.14519.5.2.1.7085.2626.936983343951485811186213470191\"\n", - "\n", - "[2024-04-10 22:05:52,708] [INFO] (highdicom.base) - copy attributes of module \"Specimen\"\n", + "[2024-04-24 00:00:53,817] [INFO] (highdicom.base) - copy Image-related attributes from dataset \"1.3.6.1.4.1.14519.5.2.1.7085.2626.936983343951485811186213470191\"\n", "\n", - "[2024-04-10 22:05:52,708] [INFO] (highdicom.base) - copy Patient-related attributes from dataset \"1.3.6.1.4.1.14519.5.2.1.7085.2626.936983343951485811186213470191\"\n", + "[2024-04-24 00:00:53,817] [INFO] (highdicom.base) - copy attributes of module \"Specimen\"\n", "\n", - "[2024-04-10 22:05:52,708] [INFO] (highdicom.base) - copy attributes of module \"Patient\"\n", + "[2024-04-24 00:00:53,817] [INFO] (highdicom.base) - copy Patient-related attributes from dataset \"1.3.6.1.4.1.14519.5.2.1.7085.2626.936983343951485811186213470191\"\n", "\n", - "[2024-04-10 22:05:52,709] [INFO] (highdicom.base) - copy attributes of module \"Clinical Trial Subject\"\n", + "[2024-04-24 00:00:53,817] [INFO] (highdicom.base) - copy attributes of module \"Patient\"\n", "\n", - "[2024-04-10 22:05:52,709] [INFO] (highdicom.base) - copy Study-related attributes from dataset \"1.3.6.1.4.1.14519.5.2.1.7085.2626.936983343951485811186213470191\"\n", + "[2024-04-24 00:00:53,817] [INFO] (highdicom.base) - copy attributes of module \"Clinical Trial Subject\"\n", "\n", - "[2024-04-10 22:05:52,709] [INFO] (highdicom.base) - copy attributes of module \"General Study\"\n", + "[2024-04-24 00:00:53,817] [INFO] (highdicom.base) - copy Study-related attributes from dataset \"1.3.6.1.4.1.14519.5.2.1.7085.2626.936983343951485811186213470191\"\n", "\n", - "[2024-04-10 22:05:52,709] [INFO] (highdicom.base) - copy attributes of module \"Patient Study\"\n", + "[2024-04-24 00:00:53,817] [INFO] (highdicom.base) - copy attributes of module \"General Study\"\n", "\n", - "[2024-04-10 22:05:52,709] [INFO] (highdicom.base) - copy attributes of module \"Clinical Trial Study\"\n", + "[2024-04-24 00:00:53,818] [INFO] (highdicom.base) - copy attributes of module \"Patient Study\"\n", "\n", - "[info] [greedy_scheduler.cpp:369] Scheduler stopped: Some entities are waiting for execution, but there are no periodic or async entities to get out of the deadlock.\n", + "[2024-04-24 00:00:53,818] [INFO] (highdicom.base) - copy attributes of module \"Clinical Trial Study\"\n", "\n", - "[info] [greedy_scheduler.cpp:398] Scheduler finished.\n", + "\u001b[0m2024-04-24 00:00:53.906 INFO gxf/std/greedy_scheduler.cpp@372: Scheduler stopped: Some entities are waiting for execution, but there are no periodic or async entities to get out of the deadlock.\u001b[0m\n", "\n", - "[info] [gxf_executor.cpp:1906] Graph execution deactivating. Fragment: \n", + "[info] [gxf_executor.cpp:1879] Deactivating Graph...\n", "\n", - "[info] [gxf_executor.cpp:1907] Deactivating Graph...\n", + "\u001b[0m2024-04-24 00:00:53.908 INFO gxf/std/greedy_scheduler.cpp@401: Scheduler finished.\u001b[0m\n", "\n", - "[info] [gxf_executor.cpp:1910] Graph execution finished. Fragment: \n", + "[info] [gxf_executor.cpp:1887] Graph execution finished.\n", "\n", - "[2024-04-10 22:05:52,805] [INFO] (app.AISpleenSegApp) - End run\n", + "[2024-04-24 00:00:53,915] [INFO] (app.AISpleenSegApp) - End run\n", "\n", - "[2024-04-10 15:05:54,069] [INFO] (common) - Container 'festive_hermann'(1d77a7676232) exited.\n" + "[2024-04-23 17:00:55,176] [INFO] (common) - Container 'fervent_bell'(6ffaea9917bd) exited.\n" ] } ], @@ -1880,14 +2019,14 @@ }, { "cell_type": "code", - "execution_count": 19, + "execution_count": 69, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ - "1.2.826.0.1.3680043.10.511.3.33232544284800485207819891596585914.dcm stl\n" + "1.2.826.0.1.3680043.10.511.3.91573472497917482579554686696126426.dcm stl\n" ] } ], diff --git a/notebooks/tutorials/05_multi_model_app.ipynb b/notebooks/tutorials/05_multi_model_app.ipynb index 2b505888..4052ff8e 100644 --- a/notebooks/tutorials/05_multi_model_app.ipynb +++ b/notebooks/tutorials/05_multi_model_app.ipynb @@ -177,21 +177,18 @@ "text": [ "Requirement already satisfied: gdown in /home/mqin/src/monai-deploy-app-sdk/.venv/lib/python3.10/site-packages (5.1.0)\n", "Requirement already satisfied: beautifulsoup4 in /home/mqin/src/monai-deploy-app-sdk/.venv/lib/python3.10/site-packages (from gdown) (4.12.3)\n", - "Requirement already satisfied: filelock in /home/mqin/src/monai-deploy-app-sdk/.venv/lib/python3.10/site-packages (from gdown) (3.13.3)\n", - "Requirement already satisfied: requests[socks] in /home/mqin/src/monai-deploy-app-sdk/.venv/lib/python3.10/site-packages (from gdown) (2.28.2)\n", + "Requirement already satisfied: filelock in /home/mqin/src/monai-deploy-app-sdk/.venv/lib/python3.10/site-packages (from gdown) (3.13.4)\n", + "Requirement already satisfied: requests[socks] in /home/mqin/src/monai-deploy-app-sdk/.venv/lib/python3.10/site-packages (from gdown) (2.31.0)\n", "Requirement already satisfied: tqdm in /home/mqin/src/monai-deploy-app-sdk/.venv/lib/python3.10/site-packages (from gdown) (4.66.2)\n", "Requirement already satisfied: soupsieve>1.2 in /home/mqin/src/monai-deploy-app-sdk/.venv/lib/python3.10/site-packages (from beautifulsoup4->gdown) (2.5)\n", "Requirement already satisfied: charset-normalizer<4,>=2 in /home/mqin/src/monai-deploy-app-sdk/.venv/lib/python3.10/site-packages (from requests[socks]->gdown) (3.3.2)\n", - "Requirement already satisfied: idna<4,>=2.5 in /home/mqin/src/monai-deploy-app-sdk/.venv/lib/python3.10/site-packages (from requests[socks]->gdown) (3.6)\n", - "Requirement already satisfied: urllib3<1.27,>=1.21.1 in /home/mqin/src/monai-deploy-app-sdk/.venv/lib/python3.10/site-packages (from requests[socks]->gdown) (1.26.18)\n", + "Requirement already satisfied: idna<4,>=2.5 in /home/mqin/src/monai-deploy-app-sdk/.venv/lib/python3.10/site-packages (from requests[socks]->gdown) (3.7)\n", + "Requirement already satisfied: urllib3<3,>=1.21.1 in /home/mqin/src/monai-deploy-app-sdk/.venv/lib/python3.10/site-packages (from requests[socks]->gdown) (2.2.1)\n", "Requirement already satisfied: certifi>=2017.4.17 in /home/mqin/src/monai-deploy-app-sdk/.venv/lib/python3.10/site-packages (from requests[socks]->gdown) (2024.2.2)\n", "Requirement already satisfied: PySocks!=1.5.7,>=1.5.6 in /home/mqin/src/monai-deploy-app-sdk/.venv/lib/python3.10/site-packages (from requests[socks]->gdown) (1.7.1)\n", - "\n", - "\u001b[1m[\u001b[0m\u001b[34;49mnotice\u001b[0m\u001b[1;39;49m]\u001b[0m\u001b[39;49m A new release of pip is available: \u001b[0m\u001b[31;49m23.3.2\u001b[0m\u001b[39;49m -> \u001b[0m\u001b[32;49m24.0\u001b[0m\n", - "\u001b[1m[\u001b[0m\u001b[34;49mnotice\u001b[0m\u001b[1;39;49m]\u001b[0m\u001b[39;49m To update, run: \u001b[0m\u001b[32;49mpip install --upgrade pip\u001b[0m\n", "Downloading...\n", "From (original): https://drive.google.com/uc?id=1llJ4NGNTjY187RLX4MtlmHYhfGxBNWmd\n", - "From (redirected): https://drive.google.com/uc?id=1llJ4NGNTjY187RLX4MtlmHYhfGxBNWmd&confirm=t&uuid=63a55326-90b2-463a-9bdc-a115a7336f1c\n", + "From (redirected): https://drive.google.com/uc?id=1llJ4NGNTjY187RLX4MtlmHYhfGxBNWmd&confirm=t&uuid=7d1b1592-17f3-4232-9d3b-02bf8cd726be\n", "To: /home/mqin/src/monai-deploy-app-sdk/notebooks/tutorials/ai_multi_model_bundle_data.zip\n", "100%|█████████████████████████████████████████| 647M/647M [00:06<00:00, 105MB/s]\n", "Archive: ai_multi_model_bundle_data.zip\n", @@ -747,59 +744,75 @@ "name": "stderr", "output_type": "stream", "text": [ - "[2024-04-10 15:07:47,589] [INFO] (root) - Parsed args: Namespace(log_level=None, input=None, output=None, model=None, workdir=None, argv=[])\n", - "[2024-04-10 15:07:47,599] [INFO] (root) - AppContext object: AppContext(input_path=dcm, output_path=output, model_path=multi_models, workdir=)\n", - "[2024-04-10 15:07:47,604] [INFO] (root) - End compose\n", - "[info] [gxf_executor.cpp:211] Creating context\n", - "[info] [gxf_executor.cpp:1674] Loading extensions from configs...\n", - "[info] [gxf_executor.cpp:1864] Activating Graph...\n", - "[info] [gxf_executor.cpp:1894] Running Graph...\n", - "[info] [gxf_executor.cpp:1896] Waiting for completion...\n", - "[info] [gxf_executor.cpp:1897] Graph execution waiting. Fragment: \n", - "[info] [greedy_scheduler.cpp:190] Scheduling 9 entities\n", - "[2024-04-10 15:07:47,665] [INFO] (monai.deploy.operators.dicom_data_loader_operator.DICOMDataLoaderOperator) - No or invalid input path from the optional input port: None\n", - "[2024-04-10 15:07:48,220] [INFO] (root) - Finding series for Selection named: CT Series\n", - "[2024-04-10 15:07:48,221] [INFO] (root) - Searching study, : 1.3.6.1.4.1.14519.5.2.1.7085.2626.822645453932810382886582736291\n", + "[2024-04-23 16:11:04,518] [INFO] (root) - Parsed args: Namespace(log_level=None, input=None, output=None, model=None, workdir=None, argv=[])\n", + "[2024-04-23 16:11:04,535] [INFO] (root) - AppContext object: AppContext(input_path=dcm, output_path=output, model_path=multi_models, workdir=)\n", + "[2024-04-23 16:11:04,542] [INFO] (root) - End compose\n", + "[info] [gxf_executor.cpp:247] Creating context\n", + "[info] [gxf_executor.cpp:1672] Loading extensions from configs...\n", + "[info] [gxf_executor.cpp:1842] Activating Graph...\n", + "[info] [gxf_executor.cpp:1874] Running Graph...\n", + "[info] [gxf_executor.cpp:1876] Waiting for completion...\n", + "[2024-04-23 16:11:04,579] [INFO] (monai.deploy.operators.dicom_data_loader_operator.DICOMDataLoaderOperator) - No or invalid input path from the optional input port: None\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "\u001b[0m2024-04-23 16:11:04.577 INFO gxf/std/greedy_scheduler.cpp@191: Scheduling 9 entities\u001b[0m\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "[2024-04-23 16:11:05,124] [INFO] (root) - Finding series for Selection named: CT Series\n", + "[2024-04-23 16:11:05,125] [INFO] (root) - Searching study, : 1.3.6.1.4.1.14519.5.2.1.7085.2626.822645453932810382886582736291\n", " # of series: 1\n", - "[2024-04-10 15:07:48,222] [INFO] (root) - Working on series, instance UID: 1.3.6.1.4.1.14519.5.2.1.7085.2626.119403521930927333027265674239\n", - "[2024-04-10 15:07:48,223] [INFO] (root) - On attribute: 'StudyDescription' to match value: '(.*?)'\n", - "[2024-04-10 15:07:48,224] [INFO] (root) - Series attribute StudyDescription value: CT ABDOMEN W IV CONTRAST\n", - "[2024-04-10 15:07:48,227] [INFO] (root) - Series attribute string value did not match. Try regEx.\n", - "[2024-04-10 15:07:48,228] [INFO] (root) - On attribute: 'Modality' to match value: '(?i)CT'\n", - "[2024-04-10 15:07:48,228] [INFO] (root) - Series attribute Modality value: CT\n", - "[2024-04-10 15:07:48,229] [INFO] (root) - Series attribute string value did not match. Try regEx.\n", - "[2024-04-10 15:07:48,230] [INFO] (root) - On attribute: 'SeriesDescription' to match value: '(.*?)'\n", - "[2024-04-10 15:07:48,231] [INFO] (root) - Series attribute SeriesDescription value: ABD/PANC 3.0 B31f\n", - "[2024-04-10 15:07:48,232] [INFO] (root) - Series attribute string value did not match. Try regEx.\n", - "[2024-04-10 15:07:48,233] [INFO] (root) - Selected Series, UID: 1.3.6.1.4.1.14519.5.2.1.7085.2626.119403521930927333027265674239\n", - "[2024-04-10 15:07:48,452] [INFO] (root) - Parsing from bundle_path: /home/mqin/src/monai-deploy-app-sdk/notebooks/tutorials/multi_models/pancreas_ct_dints/model.ts\n", - "[2024-04-10 15:09:28,757] [INFO] (root) - Parsing from bundle_path: /home/mqin/src/monai-deploy-app-sdk/notebooks/tutorials/multi_models/spleen_ct/model.ts\n", + "[2024-04-23 16:11:05,126] [INFO] (root) - Working on series, instance UID: 1.3.6.1.4.1.14519.5.2.1.7085.2626.119403521930927333027265674239\n", + "[2024-04-23 16:11:05,128] [INFO] (root) - On attribute: 'StudyDescription' to match value: '(.*?)'\n", + "[2024-04-23 16:11:05,129] [INFO] (root) - Series attribute StudyDescription value: CT ABDOMEN W IV CONTRAST\n", + "[2024-04-23 16:11:05,130] [INFO] (root) - Series attribute string value did not match. Try regEx.\n", + "[2024-04-23 16:11:05,131] [INFO] (root) - On attribute: 'Modality' to match value: '(?i)CT'\n", + "[2024-04-23 16:11:05,132] [INFO] (root) - Series attribute Modality value: CT\n", + "[2024-04-23 16:11:05,134] [INFO] (root) - Series attribute string value did not match. Try regEx.\n", + "[2024-04-23 16:11:05,136] [INFO] (root) - On attribute: 'SeriesDescription' to match value: '(.*?)'\n", + "[2024-04-23 16:11:05,136] [INFO] (root) - Series attribute SeriesDescription value: ABD/PANC 3.0 B31f\n", + "[2024-04-23 16:11:05,137] [INFO] (root) - Series attribute string value did not match. Try regEx.\n", + "[2024-04-23 16:11:05,137] [INFO] (root) - Selected Series, UID: 1.3.6.1.4.1.14519.5.2.1.7085.2626.119403521930927333027265674239\n", + "[2024-04-23 16:11:05,373] [INFO] (root) - Parsing from bundle_path: /home/mqin/src/monai-deploy-app-sdk/notebooks/tutorials/multi_models/pancreas_ct_dints/model.ts\n", + "[2024-04-23 16:12:44,188] [INFO] (root) - Parsing from bundle_path: /home/mqin/src/monai-deploy-app-sdk/notebooks/tutorials/multi_models/spleen_ct/model.ts\n", "/home/mqin/src/monai-deploy-app-sdk/.venv/lib/python3.10/site-packages/highdicom/valuerep.py:54: UserWarning: The string \"C3N-00198\" is unlikely to represent the intended person name since it contains only a single component. Construct a person name according to the format in described in https://dicom.nema.org/dicom/2013/output/chtml/part05/sect_6.2.html#sect_6.2.1.2, or, in pydicom 2.2.0 or later, use the pydicom.valuerep.PersonName.from_named_components() method to construct the person name correctly. If a single-component name is really intended, add a trailing caret character to disambiguate the name.\n", " warnings.warn(\n", - "[2024-04-10 15:09:34,244] [INFO] (highdicom.base) - copy Image-related attributes from dataset \"1.3.6.1.4.1.14519.5.2.1.7085.2626.936983343951485811186213470191\"\n", - "[2024-04-10 15:09:34,246] [INFO] (highdicom.base) - copy attributes of module \"Specimen\"\n", - "[2024-04-10 15:09:34,247] [INFO] (highdicom.base) - copy Patient-related attributes from dataset \"1.3.6.1.4.1.14519.5.2.1.7085.2626.936983343951485811186213470191\"\n", - "[2024-04-10 15:09:34,248] [INFO] (highdicom.base) - copy attributes of module \"Patient\"\n", - "[2024-04-10 15:09:34,249] [INFO] (highdicom.base) - copy attributes of module \"Clinical Trial Subject\"\n", - "[2024-04-10 15:09:34,250] [INFO] (highdicom.base) - copy Study-related attributes from dataset \"1.3.6.1.4.1.14519.5.2.1.7085.2626.936983343951485811186213470191\"\n", - "[2024-04-10 15:09:34,251] [INFO] (highdicom.base) - copy attributes of module \"General Study\"\n", - "[2024-04-10 15:09:34,252] [INFO] (highdicom.base) - copy attributes of module \"Patient Study\"\n", - "[2024-04-10 15:09:34,253] [INFO] (highdicom.base) - copy attributes of module \"Clinical Trial Study\"\n", - "[2024-04-10 15:09:35,375] [INFO] (highdicom.base) - copy Image-related attributes from dataset \"1.3.6.1.4.1.14519.5.2.1.7085.2626.936983343951485811186213470191\"\n", - "[2024-04-10 15:09:35,377] [INFO] (highdicom.base) - copy attributes of module \"Specimen\"\n", - "[2024-04-10 15:09:35,377] [INFO] (highdicom.base) - copy Patient-related attributes from dataset \"1.3.6.1.4.1.14519.5.2.1.7085.2626.936983343951485811186213470191\"\n", - "[2024-04-10 15:09:35,378] [INFO] (highdicom.base) - copy attributes of module \"Patient\"\n", - "[2024-04-10 15:09:35,380] [INFO] (highdicom.base) - copy attributes of module \"Clinical Trial Subject\"\n", - "[2024-04-10 15:09:35,381] [INFO] (highdicom.base) - copy Study-related attributes from dataset \"1.3.6.1.4.1.14519.5.2.1.7085.2626.936983343951485811186213470191\"\n", - "[2024-04-10 15:09:35,382] [INFO] (highdicom.base) - copy attributes of module \"General Study\"\n", - "[2024-04-10 15:09:35,383] [INFO] (highdicom.base) - copy attributes of module \"Patient Study\"\n", - "[2024-04-10 15:09:35,384] [INFO] (highdicom.base) - copy attributes of module \"Clinical Trial Study\"\n", - "[info] [greedy_scheduler.cpp:369] Scheduler stopped: Some entities are waiting for execution, but there are no periodic or async entities to get out of the deadlock.\n", - "[info] [greedy_scheduler.cpp:398] Scheduler finished.\n", - "[info] [gxf_executor.cpp:1906] Graph execution deactivating. Fragment: \n", - "[info] [gxf_executor.cpp:1907] Deactivating Graph...\n", - "[2024-04-10 15:09:35,488] [INFO] (__main__.App) - End run\n", - "[info] [gxf_executor.cpp:1910] Graph execution finished. Fragment: \n" + "[2024-04-23 16:12:49,664] [INFO] (highdicom.base) - copy Image-related attributes from dataset \"1.3.6.1.4.1.14519.5.2.1.7085.2626.936983343951485811186213470191\"\n", + "[2024-04-23 16:12:49,665] [INFO] (highdicom.base) - copy attributes of module \"Specimen\"\n", + "[2024-04-23 16:12:49,666] [INFO] (highdicom.base) - copy Patient-related attributes from dataset \"1.3.6.1.4.1.14519.5.2.1.7085.2626.936983343951485811186213470191\"\n", + "[2024-04-23 16:12:49,667] [INFO] (highdicom.base) - copy attributes of module \"Patient\"\n", + "[2024-04-23 16:12:49,669] [INFO] (highdicom.base) - copy attributes of module \"Clinical Trial Subject\"\n", + "[2024-04-23 16:12:49,670] [INFO] (highdicom.base) - copy Study-related attributes from dataset \"1.3.6.1.4.1.14519.5.2.1.7085.2626.936983343951485811186213470191\"\n", + "[2024-04-23 16:12:49,672] [INFO] (highdicom.base) - copy attributes of module \"General Study\"\n", + "[2024-04-23 16:12:49,673] [INFO] (highdicom.base) - copy attributes of module \"Patient Study\"\n", + "[2024-04-23 16:12:49,675] [INFO] (highdicom.base) - copy attributes of module \"Clinical Trial Study\"\n", + "[2024-04-23 16:12:50,843] [INFO] (highdicom.base) - copy Image-related attributes from dataset \"1.3.6.1.4.1.14519.5.2.1.7085.2626.936983343951485811186213470191\"\n", + "[2024-04-23 16:12:50,844] [INFO] (highdicom.base) - copy attributes of module \"Specimen\"\n", + "[2024-04-23 16:12:50,845] [INFO] (highdicom.base) - copy Patient-related attributes from dataset \"1.3.6.1.4.1.14519.5.2.1.7085.2626.936983343951485811186213470191\"\n", + "[2024-04-23 16:12:50,846] [INFO] (highdicom.base) - copy attributes of module \"Patient\"\n", + "[2024-04-23 16:12:50,847] [INFO] (highdicom.base) - copy attributes of module \"Clinical Trial Subject\"\n", + "[2024-04-23 16:12:50,848] [INFO] (highdicom.base) - copy Study-related attributes from dataset \"1.3.6.1.4.1.14519.5.2.1.7085.2626.936983343951485811186213470191\"\n", + "[2024-04-23 16:12:50,849] [INFO] (highdicom.base) - copy attributes of module \"General Study\"\n", + "[2024-04-23 16:12:50,850] [INFO] (highdicom.base) - copy attributes of module \"Patient Study\"\n", + "[2024-04-23 16:12:50,852] [INFO] (highdicom.base) - copy attributes of module \"Clinical Trial Study\"\n", + "[info] [gxf_executor.cpp:1879] Deactivating Graph...\n", + "[info] [gxf_executor.cpp:1887] Graph execution finished.\n", + "[2024-04-23 16:12:50,954] [INFO] (__main__.App) - End run\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "\u001b[0m2024-04-23 16:12:50.952 INFO gxf/std/greedy_scheduler.cpp@372: Scheduler stopped: Some entities are waiting for execution, but there are no periodic or async entities to get out of the deadlock.\u001b[0m\n", + "\u001b[0m2024-04-23 16:12:50.952 INFO gxf/std/greedy_scheduler.cpp@401: Scheduler finished.\u001b[0m\n" ] } ], @@ -1171,59 +1184,57 @@ "name": "stdout", "output_type": "stream", "text": [ - "[2024-04-10 15:09:40,274] [INFO] (root) - Parsed args: Namespace(log_level=None, input=None, output=None, model=None, workdir=None, argv=['my_app'])\n", - "[2024-04-10 15:09:40,282] [INFO] (root) - AppContext object: AppContext(input_path=dcm, output_path=output, model_path=multi_models, workdir=)\n", - "[2024-04-10 15:09:40,284] [INFO] (root) - End compose\n", - "[\u001b[32minfo\u001b[m] [gxf_executor.cpp:211] Creating context\n", - "[\u001b[32minfo\u001b[m] [gxf_executor.cpp:1674] Loading extensions from configs...\n", - "[\u001b[32minfo\u001b[m] [gxf_executor.cpp:1864] Activating Graph...\n", - "[\u001b[32minfo\u001b[m] [gxf_executor.cpp:1894] Running Graph...\n", - "[\u001b[32minfo\u001b[m] [gxf_executor.cpp:1896] Waiting for completion...\n", - "[\u001b[32minfo\u001b[m] [gxf_executor.cpp:1897] Graph execution waiting. Fragment: \n", - "[\u001b[32minfo\u001b[m] [greedy_scheduler.cpp:190] Scheduling 9 entities\n", - "[2024-04-10 15:09:40,321] [INFO] (monai.deploy.operators.dicom_data_loader_operator.DICOMDataLoaderOperator) - No or invalid input path from the optional input port: None\n", - "[2024-04-10 15:09:40,657] [INFO] (root) - Finding series for Selection named: CT Series\n", - "[2024-04-10 15:09:40,657] [INFO] (root) - Searching study, : 1.3.6.1.4.1.14519.5.2.1.7085.2626.822645453932810382886582736291\n", + "[2024-04-23 16:12:55,648] [INFO] (root) - Parsed args: Namespace(log_level=None, input=None, output=None, model=None, workdir=None, argv=['my_app'])\n", + "[2024-04-23 16:12:55,653] [INFO] (root) - AppContext object: AppContext(input_path=dcm, output_path=output, model_path=multi_models, workdir=)\n", + "[2024-04-23 16:12:55,655] [INFO] (root) - End compose\n", + "[\u001b[32minfo\u001b[m] [gxf_executor.cpp:247] Creating context\n", + "[\u001b[32minfo\u001b[m] [gxf_executor.cpp:1672] Loading extensions from configs...\n", + "[\u001b[32minfo\u001b[m] [gxf_executor.cpp:1842] Activating Graph...\n", + "[\u001b[32minfo\u001b[m] [gxf_executor.cpp:1874] Running Graph...\n", + "[\u001b[32minfo\u001b[m] [gxf_executor.cpp:1876] Waiting for completion...\n", + "\u001b[0m2024-04-23 16:12:55.684 INFO gxf/std/greedy_scheduler.cpp@191: Scheduling 9 entities\u001b[0m\n", + "[2024-04-23 16:12:55,685] [INFO] (monai.deploy.operators.dicom_data_loader_operator.DICOMDataLoaderOperator) - No or invalid input path from the optional input port: None\n", + "[2024-04-23 16:12:56,030] [INFO] (root) - Finding series for Selection named: CT Series\n", + "[2024-04-23 16:12:56,030] [INFO] (root) - Searching study, : 1.3.6.1.4.1.14519.5.2.1.7085.2626.822645453932810382886582736291\n", " # of series: 1\n", - "[2024-04-10 15:09:40,657] [INFO] (root) - Working on series, instance UID: 1.3.6.1.4.1.14519.5.2.1.7085.2626.119403521930927333027265674239\n", - "[2024-04-10 15:09:40,657] [INFO] (root) - On attribute: 'StudyDescription' to match value: '(.*?)'\n", - "[2024-04-10 15:09:40,657] [INFO] (root) - Series attribute StudyDescription value: CT ABDOMEN W IV CONTRAST\n", - "[2024-04-10 15:09:40,657] [INFO] (root) - Series attribute string value did not match. Try regEx.\n", - "[2024-04-10 15:09:40,657] [INFO] (root) - On attribute: 'Modality' to match value: '(?i)CT'\n", - "[2024-04-10 15:09:40,657] [INFO] (root) - Series attribute Modality value: CT\n", - "[2024-04-10 15:09:40,657] [INFO] (root) - Series attribute string value did not match. Try regEx.\n", - "[2024-04-10 15:09:40,657] [INFO] (root) - On attribute: 'SeriesDescription' to match value: '(.*?)'\n", - "[2024-04-10 15:09:40,657] [INFO] (root) - Series attribute SeriesDescription value: ABD/PANC 3.0 B31f\n", - "[2024-04-10 15:09:40,657] [INFO] (root) - Series attribute string value did not match. Try regEx.\n", - "[2024-04-10 15:09:40,657] [INFO] (root) - Selected Series, UID: 1.3.6.1.4.1.14519.5.2.1.7085.2626.119403521930927333027265674239\n", - "[2024-04-10 15:09:41,061] [INFO] (root) - Parsing from bundle_path: /home/mqin/src/monai-deploy-app-sdk/notebooks/tutorials/multi_models/pancreas_ct_dints/model.ts\n", - "[2024-04-10 15:11:19,819] [INFO] (root) - Parsing from bundle_path: /home/mqin/src/monai-deploy-app-sdk/notebooks/tutorials/multi_models/spleen_ct/model.ts\n", + "[2024-04-23 16:12:56,030] [INFO] (root) - Working on series, instance UID: 1.3.6.1.4.1.14519.5.2.1.7085.2626.119403521930927333027265674239\n", + "[2024-04-23 16:12:56,030] [INFO] (root) - On attribute: 'StudyDescription' to match value: '(.*?)'\n", + "[2024-04-23 16:12:56,030] [INFO] (root) - Series attribute StudyDescription value: CT ABDOMEN W IV CONTRAST\n", + "[2024-04-23 16:12:56,030] [INFO] (root) - Series attribute string value did not match. Try regEx.\n", + "[2024-04-23 16:12:56,031] [INFO] (root) - On attribute: 'Modality' to match value: '(?i)CT'\n", + "[2024-04-23 16:12:56,031] [INFO] (root) - Series attribute Modality value: CT\n", + "[2024-04-23 16:12:56,031] [INFO] (root) - Series attribute string value did not match. Try regEx.\n", + "[2024-04-23 16:12:56,031] [INFO] (root) - On attribute: 'SeriesDescription' to match value: '(.*?)'\n", + "[2024-04-23 16:12:56,031] [INFO] (root) - Series attribute SeriesDescription value: ABD/PANC 3.0 B31f\n", + "[2024-04-23 16:12:56,031] [INFO] (root) - Series attribute string value did not match. Try regEx.\n", + "[2024-04-23 16:12:56,031] [INFO] (root) - Selected Series, UID: 1.3.6.1.4.1.14519.5.2.1.7085.2626.119403521930927333027265674239\n", + "[2024-04-23 16:12:56,243] [INFO] (root) - Parsing from bundle_path: /home/mqin/src/monai-deploy-app-sdk/notebooks/tutorials/multi_models/pancreas_ct_dints/model.ts\n", + "[2024-04-23 16:14:36,645] [INFO] (root) - Parsing from bundle_path: /home/mqin/src/monai-deploy-app-sdk/notebooks/tutorials/multi_models/spleen_ct/model.ts\n", "/home/mqin/src/monai-deploy-app-sdk/.venv/lib/python3.10/site-packages/highdicom/valuerep.py:54: UserWarning: The string \"C3N-00198\" is unlikely to represent the intended person name since it contains only a single component. Construct a person name according to the format in described in https://dicom.nema.org/dicom/2013/output/chtml/part05/sect_6.2.html#sect_6.2.1.2, or, in pydicom 2.2.0 or later, use the pydicom.valuerep.PersonName.from_named_components() method to construct the person name correctly. If a single-component name is really intended, add a trailing caret character to disambiguate the name.\n", " warnings.warn(\n", - "[2024-04-10 15:11:25,386] [INFO] (highdicom.base) - copy Image-related attributes from dataset \"1.3.6.1.4.1.14519.5.2.1.7085.2626.936983343951485811186213470191\"\n", - "[2024-04-10 15:11:25,386] [INFO] (highdicom.base) - copy attributes of module \"Specimen\"\n", - "[2024-04-10 15:11:25,386] [INFO] (highdicom.base) - copy Patient-related attributes from dataset \"1.3.6.1.4.1.14519.5.2.1.7085.2626.936983343951485811186213470191\"\n", - "[2024-04-10 15:11:25,386] [INFO] (highdicom.base) - copy attributes of module \"Patient\"\n", - "[2024-04-10 15:11:25,386] [INFO] (highdicom.base) - copy attributes of module \"Clinical Trial Subject\"\n", - "[2024-04-10 15:11:25,386] [INFO] (highdicom.base) - copy Study-related attributes from dataset \"1.3.6.1.4.1.14519.5.2.1.7085.2626.936983343951485811186213470191\"\n", - "[2024-04-10 15:11:25,386] [INFO] (highdicom.base) - copy attributes of module \"General Study\"\n", - "[2024-04-10 15:11:25,387] [INFO] (highdicom.base) - copy attributes of module \"Patient Study\"\n", - "[2024-04-10 15:11:25,387] [INFO] (highdicom.base) - copy attributes of module \"Clinical Trial Study\"\n", - "[2024-04-10 15:11:26,671] [INFO] (highdicom.base) - copy Image-related attributes from dataset \"1.3.6.1.4.1.14519.5.2.1.7085.2626.936983343951485811186213470191\"\n", - "[2024-04-10 15:11:26,671] [INFO] (highdicom.base) - copy attributes of module \"Specimen\"\n", - "[2024-04-10 15:11:26,671] [INFO] (highdicom.base) - copy Patient-related attributes from dataset \"1.3.6.1.4.1.14519.5.2.1.7085.2626.936983343951485811186213470191\"\n", - "[2024-04-10 15:11:26,671] [INFO] (highdicom.base) - copy attributes of module \"Patient\"\n", - "[2024-04-10 15:11:26,671] [INFO] (highdicom.base) - copy attributes of module \"Clinical Trial Subject\"\n", - "[2024-04-10 15:11:26,671] [INFO] (highdicom.base) - copy Study-related attributes from dataset \"1.3.6.1.4.1.14519.5.2.1.7085.2626.936983343951485811186213470191\"\n", - "[2024-04-10 15:11:26,672] [INFO] (highdicom.base) - copy attributes of module \"General Study\"\n", - "[2024-04-10 15:11:26,672] [INFO] (highdicom.base) - copy attributes of module \"Patient Study\"\n", - "[2024-04-10 15:11:26,672] [INFO] (highdicom.base) - copy attributes of module \"Clinical Trial Study\"\n", - "[\u001b[32minfo\u001b[m] [greedy_scheduler.cpp:369] Scheduler stopped: Some entities are waiting for execution, but there are no periodic or async entities to get out of the deadlock.\n", - "[\u001b[32minfo\u001b[m] [greedy_scheduler.cpp:398] Scheduler finished.\n", - "[\u001b[32minfo\u001b[m] [gxf_executor.cpp:1906] Graph execution deactivating. Fragment: \n", - "[\u001b[32minfo\u001b[m] [gxf_executor.cpp:1907] Deactivating Graph...\n", - "[\u001b[32minfo\u001b[m] [gxf_executor.cpp:1910] Graph execution finished. Fragment: \n", - "[2024-04-10 15:11:26,772] [INFO] (app.App) - End run\n" + "[2024-04-23 16:14:42,011] [INFO] (highdicom.base) - copy Image-related attributes from dataset \"1.3.6.1.4.1.14519.5.2.1.7085.2626.936983343951485811186213470191\"\n", + "[2024-04-23 16:14:42,011] [INFO] (highdicom.base) - copy attributes of module \"Specimen\"\n", + "[2024-04-23 16:14:42,011] [INFO] (highdicom.base) - copy Patient-related attributes from dataset \"1.3.6.1.4.1.14519.5.2.1.7085.2626.936983343951485811186213470191\"\n", + "[2024-04-23 16:14:42,011] [INFO] (highdicom.base) - copy attributes of module \"Patient\"\n", + "[2024-04-23 16:14:42,012] [INFO] (highdicom.base) - copy attributes of module \"Clinical Trial Subject\"\n", + "[2024-04-23 16:14:42,012] [INFO] (highdicom.base) - copy Study-related attributes from dataset \"1.3.6.1.4.1.14519.5.2.1.7085.2626.936983343951485811186213470191\"\n", + "[2024-04-23 16:14:42,012] [INFO] (highdicom.base) - copy attributes of module \"General Study\"\n", + "[2024-04-23 16:14:42,012] [INFO] (highdicom.base) - copy attributes of module \"Patient Study\"\n", + "[2024-04-23 16:14:42,012] [INFO] (highdicom.base) - copy attributes of module \"Clinical Trial Study\"\n", + "[2024-04-23 16:14:43,063] [INFO] (highdicom.base) - copy Image-related attributes from dataset \"1.3.6.1.4.1.14519.5.2.1.7085.2626.936983343951485811186213470191\"\n", + "[2024-04-23 16:14:43,063] [INFO] (highdicom.base) - copy attributes of module \"Specimen\"\n", + "[2024-04-23 16:14:43,064] [INFO] (highdicom.base) - copy Patient-related attributes from dataset \"1.3.6.1.4.1.14519.5.2.1.7085.2626.936983343951485811186213470191\"\n", + "[2024-04-23 16:14:43,064] [INFO] (highdicom.base) - copy attributes of module \"Patient\"\n", + "[2024-04-23 16:14:43,064] [INFO] (highdicom.base) - copy attributes of module \"Clinical Trial Subject\"\n", + "[2024-04-23 16:14:43,064] [INFO] (highdicom.base) - copy Study-related attributes from dataset \"1.3.6.1.4.1.14519.5.2.1.7085.2626.936983343951485811186213470191\"\n", + "[2024-04-23 16:14:43,064] [INFO] (highdicom.base) - copy attributes of module \"General Study\"\n", + "[2024-04-23 16:14:43,064] [INFO] (highdicom.base) - copy attributes of module \"Patient Study\"\n", + "[2024-04-23 16:14:43,065] [INFO] (highdicom.base) - copy attributes of module \"Clinical Trial Study\"\n", + "\u001b[0m2024-04-23 16:14:43.154 INFO gxf/std/greedy_scheduler.cpp@372: Scheduler stopped: Some entities are waiting for execution, but there are no periodic or async entities to get out of the deadlock.\u001b[0m\n", + "\u001b[0m2024-04-23 16:14:43.155 INFO gxf/std/greedy_scheduler.cpp@401: Scheduler finished.\u001b[0m\n", + "[\u001b[32minfo\u001b[m] [gxf_executor.cpp:1879] Deactivating Graph...\n", + "[\u001b[32minfo\u001b[m] [gxf_executor.cpp:1887] Graph execution finished.\n", + "[2024-04-23 16:14:43,155] [INFO] (app.App) - End run\n" ] } ], @@ -1241,8 +1252,8 @@ "name": "stdout", "output_type": "stream", "text": [ - "1.2.826.0.1.3680043.10.511.3.15046048574363662193759299900270199.dcm\n", - "1.2.826.0.1.3680043.10.511.3.98214024482046978965335342071467925.dcm\n" + "1.2.826.0.1.3680043.10.511.3.10288134553125230635901121822410318.dcm\n", + "1.2.826.0.1.3680043.10.511.3.96971936458025058184826371322949123.dcm\n" ] } ], @@ -1342,15 +1353,17 @@ "name": "stdout", "output_type": "stream", "text": [ - "[2024-04-10 15:11:29,127] [INFO] (packager.parameters) - Application: /home/mqin/src/monai-deploy-app-sdk/notebooks/tutorials/my_app\n", - "[2024-04-10 15:11:29,127] [INFO] (packager.parameters) - Detected application type: Python Module\n", - "[2024-04-10 15:11:29,127] [INFO] (packager) - Scanning for models in /home/mqin/src/monai-deploy-app-sdk/notebooks/tutorials/multi_models...\n", - "[2024-04-10 15:11:29,127] [DEBUG] (packager) - Model spleen_ct=/home/mqin/src/monai-deploy-app-sdk/notebooks/tutorials/multi_models/spleen_ct added.\n", - "[2024-04-10 15:11:29,127] [DEBUG] (packager) - Model pancreas_ct_dints=/home/mqin/src/monai-deploy-app-sdk/notebooks/tutorials/multi_models/pancreas_ct_dints added.\n", - "[2024-04-10 15:11:29,127] [INFO] (packager) - Reading application configuration from /home/mqin/src/monai-deploy-app-sdk/notebooks/tutorials/my_app/app.yaml...\n", - "[2024-04-10 15:11:29,128] [INFO] (packager) - Generating app.json...\n", - "[2024-04-10 15:11:29,129] [INFO] (packager) - Generating pkg.json...\n", - "[2024-04-10 15:11:29,133] [DEBUG] (common) - \n", + "[2024-04-23 16:14:45,501] [INFO] (common) - Downloading CLI manifest file...\n", + "[2024-04-23 16:14:45,792] [DEBUG] (common) - Validating CLI manifest file...\n", + "[2024-04-23 16:14:45,794] [INFO] (packager.parameters) - Application: /home/mqin/src/monai-deploy-app-sdk/notebooks/tutorials/my_app\n", + "[2024-04-23 16:14:45,795] [INFO] (packager.parameters) - Detected application type: Python Module\n", + "[2024-04-23 16:14:45,795] [INFO] (packager) - Scanning for models in /home/mqin/src/monai-deploy-app-sdk/notebooks/tutorials/multi_models...\n", + "[2024-04-23 16:14:45,795] [DEBUG] (packager) - Model spleen_ct=/home/mqin/src/monai-deploy-app-sdk/notebooks/tutorials/multi_models/spleen_ct added.\n", + "[2024-04-23 16:14:45,795] [DEBUG] (packager) - Model pancreas_ct_dints=/home/mqin/src/monai-deploy-app-sdk/notebooks/tutorials/multi_models/pancreas_ct_dints added.\n", + "[2024-04-23 16:14:45,796] [INFO] (packager) - Reading application configuration from /home/mqin/src/monai-deploy-app-sdk/notebooks/tutorials/my_app/app.yaml...\n", + "[2024-04-23 16:14:45,799] [INFO] (packager) - Generating app.json...\n", + "[2024-04-23 16:14:45,799] [INFO] (packager) - Generating pkg.json...\n", + "[2024-04-23 16:14:45,809] [DEBUG] (common) - \n", "=============== Begin app.json ===============\n", "{\n", " \"apiVersion\": \"1.0.0\",\n", @@ -1385,7 +1398,7 @@ "}\n", "================ End app.json ================\n", " \n", - "[2024-04-10 15:11:29,134] [DEBUG] (common) - \n", + "[2024-04-23 16:14:45,810] [DEBUG] (common) - \n", "=============== Begin pkg.json ===============\n", "{\n", " \"apiVersion\": \"1.0.0\",\n", @@ -1406,11 +1419,11 @@ "}\n", "================ End pkg.json ================\n", " \n", - "[2024-04-10 15:11:29,632] [DEBUG] (packager.builder) - \n", + "[2024-04-23 16:14:46,274] [DEBUG] (packager.builder) - \n", "========== Begin Dockerfile ==========\n", "\n", "\n", - "FROM nvcr.io/nvidia/clara-holoscan/holoscan:v1.0.3-dgpu\n", + "FROM nvcr.io/nvidia/clara-holoscan/holoscan:v2.0.0-dgpu\n", "\n", "ENV DEBIAN_FRONTEND=noninteractive\n", "ENV TERM=xterm-256color\n", @@ -1426,11 +1439,11 @@ " && mkdir -p /var/holoscan/input \\\n", " && mkdir -p /var/holoscan/output\n", "\n", - "LABEL base=\"nvcr.io/nvidia/clara-holoscan/holoscan:v1.0.3-dgpu\"\n", + "LABEL base=\"nvcr.io/nvidia/clara-holoscan/holoscan:v2.0.0-dgpu\"\n", "LABEL tag=\"my_app:1.0\"\n", "LABEL org.opencontainers.image.title=\"MONAI Deploy App Package - Multi Model App\"\n", "LABEL org.opencontainers.image.version=\"1.0\"\n", - "LABEL org.nvidia.holoscan=\"1.0.3\"\n", + "LABEL org.nvidia.holoscan=\"2.0.0\"\n", "LABEL org.monai.deploy.app-sdk=\"0.5.1\"\n", "\n", "\n", @@ -1456,7 +1469,6 @@ "ENV PYTHONPATH=\"/opt/holoscan/app:$PYTHONPATH\"\n", "\n", "\n", - "\n", "RUN groupadd -f -g $GID $UNAME\n", "RUN useradd -rm -d /home/$UNAME -s /bin/bash -g $GID -G sudo -u $UID $UNAME\n", "RUN chown -R holoscan /var/holoscan \n", @@ -1482,14 +1494,12 @@ "RUN pip install --upgrade pip\n", "RUN pip install --no-cache-dir --user -r /tmp/requirements.txt\n", "\n", - "# Install Holoscan from PyPI only when sdk_type is Holoscan. \n", - "# For MONAI Deploy, the APP SDK will install it unless user specifies the Holoscan SDK file.\n", + " \n", + "# MONAI Deploy\n", "\n", "# Copy user-specified MONAI Deploy SDK file\n", - "COPY ./monai_deploy_app_sdk-0.5.1+25.g31e4165.dirty-py3-none-any.whl /tmp/monai_deploy_app_sdk-0.5.1+25.g31e4165.dirty-py3-none-any.whl\n", - "RUN pip install /tmp/monai_deploy_app_sdk-0.5.1+25.g31e4165.dirty-py3-none-any.whl\n", - "\n", - "\n", + "COPY ./monai_deploy_app_sdk-0.5.1+20.gb869749.dirty-py3-none-any.whl /tmp/monai_deploy_app_sdk-0.5.1+20.gb869749.dirty-py3-none-any.whl\n", + "RUN pip install /tmp/monai_deploy_app_sdk-0.5.1+20.gb869749.dirty-py3-none-any.whl\n", "\n", "\n", "COPY ./models /opt/holoscan/models\n", @@ -1503,223 +1513,226 @@ "ENTRYPOINT [\"/var/holoscan/tools\"]\n", "=========== End Dockerfile ===========\n", "\n", - "[2024-04-10 15:11:29,632] [INFO] (packager.builder) - \n", + "[2024-04-23 16:14:46,274] [INFO] (packager.builder) - \n", "===============================================================================\n", "Building image for: x64-workstation\n", " Architecture: linux/amd64\n", - " Base Image: nvcr.io/nvidia/clara-holoscan/holoscan:v1.0.3-dgpu\n", + " Base Image: nvcr.io/nvidia/clara-holoscan/holoscan:v2.0.0-dgpu\n", " Build Image: N/A\n", " Cache: Enabled\n", " Configuration: dgpu\n", " Holoscan SDK Package: pypi.org\n", - " MONAI Deploy App SDK Package: /home/mqin/src/monai-deploy-app-sdk/dist/monai_deploy_app_sdk-0.5.1+25.g31e4165.dirty-py3-none-any.whl\n", + " MONAI Deploy App SDK Package: /home/mqin/src/monai-deploy-app-sdk/dist/monai_deploy_app_sdk-0.5.1+20.gb869749.dirty-py3-none-any.whl\n", " gRPC Health Probe: N/A\n", - " SDK Version: 1.0.3\n", + " SDK Version: 2.0.0\n", " SDK: monai-deploy\n", " Tag: my_app-x64-workstation-dgpu-linux-amd64:1.0\n", " \n", - "[2024-04-10 15:11:29,935] [INFO] (common) - Using existing Docker BuildKit builder `holoscan_app_builder`\n", - "[2024-04-10 15:11:29,936] [DEBUG] (packager.builder) - Building Holoscan Application Package: tag=my_app-x64-workstation-dgpu-linux-amd64:1.0\n", + "[2024-04-23 16:14:46,562] [INFO] (common) - Using existing Docker BuildKit builder `holoscan_app_builder`\n", + "[2024-04-23 16:14:46,562] [DEBUG] (packager.builder) - Building Holoscan Application Package: tag=my_app-x64-workstation-dgpu-linux-amd64:1.0\n", "#0 building with \"holoscan_app_builder\" instance using docker-container driver\n", "\n", "#1 [internal] load build definition from Dockerfile\n", - "#1 transferring dockerfile: 2.79kB done\n", - "#1 DONE 0.1s\n", + "#1 transferring dockerfile: 2.65kB done\n", + "#1 DONE 0.0s\n", "\n", - "#2 [internal] load metadata for nvcr.io/nvidia/clara-holoscan/holoscan:v1.0.3-dgpu\n", - "#2 DONE 0.1s\n", + "#2 [internal] load metadata for nvcr.io/nvidia/clara-holoscan/holoscan:v2.0.0-dgpu\n", + "#2 DONE 0.4s\n", "\n", "#3 [internal] load .dockerignore\n", "#3 transferring context: 1.79kB done\n", - "#3 DONE 0.1s\n", + "#3 DONE 0.0s\n", "\n", "#4 [internal] load build context\n", "#4 DONE 0.0s\n", "\n", - "#5 importing cache manifest from local:3229340695933661696\n", + "#5 importing cache manifest from local:13557986215550987099\n", "#5 inferred cache manifest type: application/vnd.oci.image.index.v1+json done\n", "#5 DONE 0.0s\n", "\n", - "#6 [ 1/21] FROM nvcr.io/nvidia/clara-holoscan/holoscan:v1.0.3-dgpu@sha256:50343c616bf910e2a7651abb59db7833933e82cce64c3c4885f938d7e4af6155\n", - "#6 resolve nvcr.io/nvidia/clara-holoscan/holoscan:v1.0.3-dgpu@sha256:50343c616bf910e2a7651abb59db7833933e82cce64c3c4885f938d7e4af6155 0.0s done\n", - "#6 DONE 0.1s\n", + "#6 [ 1/21] FROM nvcr.io/nvidia/clara-holoscan/holoscan:v2.0.0-dgpu@sha256:20adbccd2c7b12dfb1798f6953f071631c3b85cd337858a7506f8e420add6d4a\n", + "#6 resolve nvcr.io/nvidia/clara-holoscan/holoscan:v2.0.0-dgpu@sha256:20adbccd2c7b12dfb1798f6953f071631c3b85cd337858a7506f8e420add6d4a 0.0s done\n", + "#6 DONE 0.0s\n", "\n", - "#7 importing cache manifest from nvcr.io/nvidia/clara-holoscan/holoscan:v1.0.3-dgpu\n", + "#7 importing cache manifest from nvcr.io/nvidia/clara-holoscan/holoscan:v2.0.0-dgpu\n", "#7 inferred cache manifest type: application/vnd.docker.distribution.manifest.list.v2+json done\n", - "#7 DONE 0.6s\n", + "#7 DONE 0.4s\n", "\n", "#4 [internal] load build context\n", "#4 transferring context: 636.05MB 3.2s done\n", "#4 DONE 3.2s\n", "\n", - "#8 [ 2/21] RUN mkdir -p /etc/holoscan/ && mkdir -p /opt/holoscan/ && mkdir -p /var/holoscan && mkdir -p /opt/holoscan/app && mkdir -p /var/holoscan/input && mkdir -p /var/holoscan/output\n", + "#8 [15/21] COPY ./monai_deploy_app_sdk-0.5.1+20.gb869749.dirty-py3-none-any.whl /tmp/monai_deploy_app_sdk-0.5.1+20.gb869749.dirty-py3-none-any.whl\n", "#8 CACHED\n", "\n", "#9 [ 6/21] RUN chown -R holoscan /var/holoscan\n", "#9 CACHED\n", "\n", - "#10 [15/21] COPY ./monai_deploy_app_sdk-0.5.1+25.g31e4165.dirty-py3-none-any.whl /tmp/monai_deploy_app_sdk-0.5.1+25.g31e4165.dirty-py3-none-any.whl\n", + "#10 [ 5/21] RUN useradd -rm -d /home/holoscan -s /bin/bash -g 1000 -G sudo -u 1000 holoscan\n", "#10 CACHED\n", "\n", - "#11 [10/21] COPY ./tools /var/holoscan/tools\n", + "#11 [ 4/21] RUN groupadd -f -g 1000 holoscan\n", "#11 CACHED\n", "\n", - "#12 [12/21] COPY ./pip/requirements.txt /tmp/requirements.txt\n", + "#12 [ 3/21] RUN apt-get update && apt-get install -y curl jq && rm -rf /var/lib/apt/lists/*\n", "#12 CACHED\n", "\n", - "#13 [ 9/21] WORKDIR /var/holoscan\n", + "#13 [11/21] RUN chmod +x /var/holoscan/tools\n", "#13 CACHED\n", "\n", - "#14 [13/21] RUN pip install --upgrade pip\n", + "#14 [12/21] COPY ./pip/requirements.txt /tmp/requirements.txt\n", "#14 CACHED\n", "\n", - "#15 [ 3/21] RUN apt-get update && apt-get install -y curl jq && rm -rf /var/lib/apt/lists/*\n", + "#15 [ 7/21] RUN chown -R holoscan /var/holoscan/input\n", "#15 CACHED\n", "\n", - "#16 [ 4/21] RUN groupadd -f -g 1000 holoscan\n", + "#16 [14/21] RUN pip install --no-cache-dir --user -r /tmp/requirements.txt\n", "#16 CACHED\n", "\n", - "#17 [ 5/21] RUN useradd -rm -d /home/holoscan -s /bin/bash -g 1000 -G sudo -u 1000 holoscan\n", + "#17 [ 8/21] RUN chown -R holoscan /var/holoscan/output\n", "#17 CACHED\n", "\n", - "#18 [ 7/21] RUN chown -R holoscan /var/holoscan/input\n", + "#18 [ 9/21] WORKDIR /var/holoscan\n", "#18 CACHED\n", "\n", - "#19 [14/21] RUN pip install --no-cache-dir --user -r /tmp/requirements.txt\n", + "#19 [ 2/21] RUN mkdir -p /etc/holoscan/ && mkdir -p /opt/holoscan/ && mkdir -p /var/holoscan && mkdir -p /opt/holoscan/app && mkdir -p /var/holoscan/input && mkdir -p /var/holoscan/output\n", "#19 CACHED\n", "\n", - "#20 [11/21] RUN chmod +x /var/holoscan/tools\n", + "#20 [10/21] COPY ./tools /var/holoscan/tools\n", "#20 CACHED\n", "\n", - "#21 [ 8/21] RUN chown -R holoscan /var/holoscan/output\n", + "#21 [13/21] RUN pip install --upgrade pip\n", "#21 CACHED\n", "\n", - "#22 [16/21] RUN pip install /tmp/monai_deploy_app_sdk-0.5.1+25.g31e4165.dirty-py3-none-any.whl\n", + "#22 [16/21] RUN pip install /tmp/monai_deploy_app_sdk-0.5.1+20.gb869749.dirty-py3-none-any.whl\n", "#22 CACHED\n", "\n", "#23 [17/21] COPY ./models /opt/holoscan/models\n", - "#23 DONE 6.7s\n", + "#23 DONE 3.9s\n", "\n", "#24 [18/21] COPY ./map/app.json /etc/holoscan/app.json\n", - "#24 DONE 0.1s\n", + "#24 DONE 0.0s\n", "\n", "#25 [19/21] COPY ./app.config /var/holoscan/app.yaml\n", - "#25 DONE 0.1s\n", + "#25 DONE 0.0s\n", "\n", "#26 [20/21] COPY ./map/pkg.json /etc/holoscan/pkg.json\n", - "#26 DONE 0.1s\n", + "#26 DONE 0.0s\n", "\n", "#27 [21/21] COPY ./app /opt/holoscan/app\n", - "#27 DONE 0.2s\n", + "#27 DONE 0.0s\n", "\n", "#28 exporting to docker image format\n", "#28 exporting layers\n", - "#28 exporting layers 20.5s done\n", - "#28 exporting manifest sha256:e77308187dcf97394b99101aa895bea8c1e7dc92572bedddb310476c65f828ab 0.0s done\n", - "#28 exporting config sha256:f820210cdcfe0c41a2791dcced8072f2413aa1f6f2b1076134249d6abc400141 0.0s done\n", + "#28 exporting layers 17.8s done\n", + "#28 exporting manifest sha256:26808437a116257ae2799583b42bbf04923e1157f8f98341c3403ee35eb234bf 0.0s done\n", + "#28 exporting config sha256:95614919d60e7f30ab5d64a25a5fc25ad64d0b166046c60549b5abae2745be7c 0.0s done\n", "#28 sending tarball\n", "#28 ...\n", "\n", "#29 importing to docker\n", - "#29 loading layer 0b7c827957f8 557.06kB / 584.49MB\n", - "#29 loading layer 0b7c827957f8 150.96MB / 584.49MB 2.1s\n", - "#29 loading layer 0b7c827957f8 305.82MB / 584.49MB 4.2s\n", - "#29 loading layer 0b7c827957f8 492.99MB / 584.49MB 6.3s\n", - "#29 loading layer 0f7d49f89e9c 492B / 492B\n", - "#29 loading layer 98aed7487fb0 312B / 312B\n", - "#29 loading layer 972f8aa128ec 322B / 322B\n", - "#29 loading layer db9d1b5a3f36 4.00kB / 4.00kB\n", - "#29 loading layer db9d1b5a3f36 4.00kB / 4.00kB 1.2s done\n", - "#29 loading layer 0b7c827957f8 492.99MB / 584.49MB 9.4s done\n", - "#29 loading layer 0f7d49f89e9c 492B / 492B 1.4s done\n", - "#29 loading layer 98aed7487fb0 312B / 312B 1.3s done\n", - "#29 loading layer 972f8aa128ec 322B / 322B 1.3s done\n", - "#29 DONE 9.4s\n", + "#29 loading layer ecf27683cffd 557.06kB / 584.49MB\n", + "#29 loading layer ecf27683cffd 154.86MB / 584.49MB 2.1s\n", + "#29 loading layer ecf27683cffd 309.72MB / 584.49MB 4.1s\n", + "#29 loading layer ecf27683cffd 464.03MB / 584.49MB 6.2s\n", + "#29 loading layer 3202d6efcdaa 493B / 493B\n", + "#29 loading layer 84f909517c68 311B / 311B\n", + "#29 loading layer 1d1958b729ff 323B / 323B\n", + "#29 loading layer 8f69ecd226c9 4.00kB / 4.00kB\n", + "#29 loading layer 3202d6efcdaa 493B / 493B 2.6s done\n", + "#29 loading layer ecf27683cffd 464.03MB / 584.49MB 10.6s done\n", + "#29 loading layer 84f909517c68 311B / 311B 2.2s done\n", + "#29 loading layer 1d1958b729ff 323B / 323B 1.8s done\n", + "#29 loading layer 8f69ecd226c9 4.00kB / 4.00kB 1.5s done\n", + "#29 DONE 10.6s\n", "\n", "#28 exporting to docker image format\n", - "#28 sending tarball 79.2s done\n", - "#28 DONE 99.9s\n", + "#28 sending tarball 72.8s done\n", + "#28 DONE 90.7s\n", "\n", "#30 exporting cache to client directory\n", "#30 preparing build cache for export\n", - "#30 writing layer sha256:00bb4c1319ba1a33ac3edcb3aa1240d8abcb8d0383c6267ed8028d3b6228a8a4\n", - "#30 writing layer sha256:00bb4c1319ba1a33ac3edcb3aa1240d8abcb8d0383c6267ed8028d3b6228a8a4 done\n", + "#30 writing layer sha256:014cff740c9ec6e9a30d0b859219a700ae880eb385d62095d348f5ea136d6015\n", "#30 writing layer sha256:014cff740c9ec6e9a30d0b859219a700ae880eb385d62095d348f5ea136d6015 done\n", - "#30 writing layer sha256:021b9bc7b766e946a42d4bf0d3f88658998d36cf2fa5f182af98d925b3d44f4f 0.0s done\n", + "#30 writing layer sha256:0487800842442c7a031a39e1e1857bc6dae4b4f7e5daf3d625f7a8a4833fb364 done\n", + "#30 writing layer sha256:06c6aee94862daf0603783db4e1de6f8524b30ac9fbe0374ab3f1d85b2f76f7f done\n", "#30 writing layer sha256:0a1756432df4a4350712d8ae5c003f1526bd2180800b3ae6301cfc9ccf370254 done\n", "#30 writing layer sha256:0a77dcbd0e648ddc4f8e5230ade8fdb781d99e24fa4f13ca96a360c7f7e6751f done\n", - "#30 writing layer sha256:0bf3a16e4f3f9ec99796b99e331a5c62472bc9377925e1fdc05f64709ed09895 done\n", + "#30 writing layer sha256:0cbe3b20b9b7d01bcb9770de54ba9a54febb401dc371bbb1d8debf1f9850b356 0.0s done\n", "#30 writing layer sha256:0ec682bf99715a9f88631226f3749e2271b8b9f254528ef61f65ed829984821c done\n", - "#30 writing layer sha256:1133dfcee0e851b490d17b3567f50c4b25ba5750da02ba4b3f3630655d0b1a7b done\n", - "#30 writing layer sha256:1294b2835667d633f938174d9fecb18a60bbbebb6fb49788a1f939893a25d1af done\n", - "#30 writing layer sha256:16a03c6e0373b62f9713416da0229bb7ce2585183141081d3ea8427ad2e84408 done\n", + "#30 writing layer sha256:1c5c3aa9c2c8bfd1b9eb36248f5b6d67b3db73ef43440f9dd897615771974b39 done\n", + "#30 writing layer sha256:1f4a978bb76db2d138cfe7c7c9e76db4096247b06e34d349a2ed504bcd6a7ead done\n", + "#30 writing layer sha256:1f73278b7f17492ce1a8b28b139d54596961596d6790dc20046fa6d5909f3e9c done\n", "#30 writing layer sha256:20d331454f5fb557f2692dfbdbe092c718fd2cb55d5db9d661b62228dacca5c2 done\n", - "#30 writing layer sha256:2232aeb26b5b7ea57227e9a5b84da4fb229624d7bc976a5f7ce86d9c8653d277 done\n", + "#30 writing layer sha256:20e14f0a8ca68167afb8296c10d7a1b4c3b17b54681cbf3b9b45e1be96afa699 done\n", "#30 writing layer sha256:238f69a43816e481f0295995fcf5fe74d59facf0f9f99734c8d0a2fb140630e0 done\n", + "#30 writing layer sha256:255cc51d2e47738a5db3059cbe9f403785cf9496c7df8a28a3c9f0c46a0b3b58 done\n", + "#30 writing layer sha256:29eb21ed7ba7894cd28ee75b082877845b969c6e65d34a16b7dbd8630c38f5fe\n", + "#30 writing layer sha256:29eb21ed7ba7894cd28ee75b082877845b969c6e65d34a16b7dbd8630c38f5fe 10.2s done\n", + "#30 writing layer sha256:2ad84487f9d4d31cd1e0a92697a5447dd241935253d036b272ef16d31620c1e7\n", "#30 writing layer sha256:2ad84487f9d4d31cd1e0a92697a5447dd241935253d036b272ef16d31620c1e7 done\n", - "#30 writing layer sha256:2bb73464628bd4a136c4937f42d522c847bea86b2215ae734949e24c1caf450e done\n", - "#30 writing layer sha256:3a663fdf00962d807df49af4b54ad7382e7d0b0c65355a78d706ee221758e691\n", - "#30 writing layer sha256:3a663fdf00962d807df49af4b54ad7382e7d0b0c65355a78d706ee221758e691 11.2s done\n", - "#30 writing layer sha256:3e3e04011ebdba380ab129f0ee390626cb2a600623815ca756340c18bedb9517\n", + "#30 writing layer sha256:2f65750928993b5b31fe572d9e085b53853c5a344feeb0e8615898e285a8c256 done\n", + "#30 writing layer sha256:3777c6498f08c0400339c243e827d465075b7296eb2526e38d9b01c84f8764d8 done\n", "#30 writing layer sha256:3e3e04011ebdba380ab129f0ee390626cb2a600623815ca756340c18bedb9517 done\n", "#30 writing layer sha256:42619ce4a0c9e54cfd0ee41a8e5f27d58b3f51becabd1ac6de725fbe6c42b14a done\n", - "#30 writing layer sha256:43a21fb6c76bd2b3715cc09d9f8c3865dc61c51dd9e2327b429f5bec8fff85d1 done\n", "#30 writing layer sha256:49bdc9abf8a437ccff67cc11490ba52c976577992909856a86be872a34d3b950 done\n", "#30 writing layer sha256:4b691ba9f48b41eaa0c754feba8366f1c030464fcbc55eeffa6c86675990933a done\n", "#30 writing layer sha256:4d04a8db404f16c2704fa10739cb6745a0187713a21a6ef0deb34b48629b54c1 done\n", "#30 writing layer sha256:4f4fb700ef54461cfa02571ae0db9a0dc1e0cdb5577484a6d75e68dc38e8acc1 done\n", - "#30 writing layer sha256:5275a41be8f6691a490c0a15589e0910c73bf971169ad33a850ef570d37f63dd done\n", - "#30 writing layer sha256:52fbfeaf78318d843054ce2bfb5bfc9f71278939a815f6035ab5b14573ad017b done\n", - "#30 writing layer sha256:5792b18b6f162bae61ff5840cdb9e8567e6847a56ac886f940b47e7271c529a7 done\n", + "#30 writing layer sha256:542bc8c8d18fbc95e6794122c3593a4a693f8ab6dda4460406f4d7b1ae64a2bc done\n", "#30 writing layer sha256:57f244836ad318f9bbb3b29856ae1a5b31038bfbb9b43d2466d51c199eb55041 done\n", "#30 writing layer sha256:5b5b131e0f20db4cb8e568b623a95f8fc16ed1c6b322a9366df70b59a881f24f done\n", - "#30 writing layer sha256:5ccb787d371fd3697122101438ddd0f55b537832e9756d2c51ab1d8158710ac5 done\n", - "#30 writing layer sha256:5ea668ffc2fc267d241dbf17ca283bc879643a189be4f7e3d9034a82fc64a1ea done\n", + "#30 writing layer sha256:5b90d17b5048adcadefd0b1e4dba9a99247a8827a887e1ca042df375c85b518d done\n", "#30 writing layer sha256:62452179df7c18e292f141d4aec29e6aba9ff8270c893731169fc6f41dc07631 done\n", - "#30 writing layer sha256:6399aeba5e066098b3fac85e23e402cd10f0c5d0f06107595840b9f7259f9b40 0.0s done\n", "#30 writing layer sha256:6630c387f5f2115bca2e646fd0c2f64e1f3d5431c2e050abe607633883eda230 done\n", - "#30 writing layer sha256:69af4b756272a77f683a8d118fd5ca55c03ad5f1bacc673b463f54d16b833da5 done\n", - "#30 writing layer sha256:6ae1f1fb92c0cb2b6e219f687b08c8e511501a7af696c943ca20d119eba7cd02 done\n", - "#30 writing layer sha256:6deb3d550b15a5e099c0b3d0cbc242e351722ca16c058d3a6c28ba1a02824d0f done\n", - "#30 writing layer sha256:6e80a527af94a864094c4f9116c2d29d3d7548ec8388579d9cf3f8a39a4b8178 done\n", - "#30 writing layer sha256:7386814d57100e2c7389fbf4e16f140f5c549d31434c62c3884a85a3ee5cd2a7 done\n", + "#30 writing layer sha256:6661e0146e77a8bcb03edbfda95bf7780c8bb4c4f98bc03a398c88f4b2403d12 done\n", + "#30 writing layer sha256:717ebf8c9c66ae393ad01e50dbac4413d7b026b9c97d4d348b22ad17052a1a35 done\n", + "#30 writing layer sha256:773c6815e5e7d6855a62f8c5e2fabce3d939ded36c5420f15b54dd7908cdbcfa done\n", "#30 writing layer sha256:7852b73ea931e3a8d3287ee7ef3cf4bad068e44f046583bfc2b81336fb299284 done\n", - "#30 writing layer sha256:7e73869c74822e4539e104a3d2aff853f4622cd0bb873576db1db53c9e91f621 done\n", - "#30 writing layer sha256:7eae142b38745fe88962874372374deb672998600264a17e638c010b79e6b535 done\n", - "#30 writing layer sha256:7f2e5ab2c599fa36698918d3e73c991d8616fff9037077cd230529e7cd1c5e0e done\n", + "#30 writing layer sha256:7f8ec130348bcdac81c295e37fe82b4a6e5e9a3ca980a6343809c561020d82d7 done\n", + "#30 writing layer sha256:80885adcad6b5d021bb9f68b6c952018085bb4ce72011bdc0cf7fe8178b5960b done\n", "#30 writing layer sha256:82a3436133b2b17bb407c7fe488932aa0ca55411f23ab55c34a6134b287c6a27 done\n", + "#30 writing layer sha256:8371d15eb4d69b1d98174dd098b8ddd5c4f19ec6f8d8b67e72dfa9891dc454b4 done\n", + "#30 writing layer sha256:85713f9b166b5add777c524ee807f6265d88b967cbeb9f961d6b09bf220c9a65 done\n", + "#30 writing layer sha256:8fe00505006a09966e763918147ef6ed55bb6695b26e4940c780ee430dc5da8e done\n", "#30 writing layer sha256:90eae6faa5cc5ba62f12c25915cdfb1a7a51abfba0d05cb5818c3f908f4e345f done\n", + "#30 writing layer sha256:9205d97d9d3e906698bcc6c42d45727c2fa6ec2622abf953d46778c3b8c78edc done\n", + "#30 writing layer sha256:92301d1270c19cab329818fb215b41138720ab9b588a2070107860f0b6fb5e11 done\n", + "#30 writing layer sha256:993369dbcc13162a6654d2a3e990b8d8b5f37963564d25710e12764337261ae3 done\n", + "#30 writing layer sha256:99e42a4adebadb39bf55bf94bbd9fb8034230ee19b6b0a42e6ff96f2e7794f30 done\n", "#30 writing layer sha256:9ac855545fa90ed2bf3b388fdff9ef06ac9427b0c0fca07c9e59161983d8827e done\n", "#30 writing layer sha256:9d19ee268e0d7bcf6716e6658ee1b0384a71d6f2f9aa1ae2085610cf7c7b316f done\n", - "#30 writing layer sha256:a10c8d7d2714eabf661d1f43a1ccb87a51748cbb9094d5bc0b713e2481b5d329 done\n", + "#30 writing layer sha256:9fafbd4203c4fefe007a462e0d2cd4c1c7c41db2cfdc58d212279e1b9b4b230c done\n", "#30 writing layer sha256:a1748eee9d376f97bd19225ba61dfada9986f063f4fc429e435f157abb629fc6 done\n", + "#30 writing layer sha256:a251fe5ae6c6d2d5034e4ca88b5dfe5d4827ff90b18e9b143a073232a32bb18d done\n", "#30 writing layer sha256:a68f4e0ec09ec3b78cb4cf8e4511d658e34e7b6f676d7806ad9703194ff17604 done\n", "#30 writing layer sha256:a8e4decc8f7289623b8fd7b9ba1ca555b5a755ebdbf81328d68209f148d9e602 done\n", + "#30 writing layer sha256:ac69ec878bf5e3f9294e9726cd393e4133a5ea3934256636de00ddc558f25e55 0.0s done\n", "#30 writing layer sha256:afde1c269453ce68a0f2b54c1ba8c5ecddeb18a19e5618a4acdef1f0fe3921af done\n", + "#30 writing layer sha256:b12b2b11632995c7c56700227a9c2f2016dab20c083c140a835c551bb2aed460 0.0s done\n", + "#30 writing layer sha256:b406feb20a37b8c87ef4f5ef814039e3adc90473d50c366b7d9bb6ded4e94a2e\n", + "#30 preparing build cache for export 11.6s done\n", + "#30 writing layer sha256:b406feb20a37b8c87ef4f5ef814039e3adc90473d50c366b7d9bb6ded4e94a2e done\n", "#30 writing layer sha256:b48a5fafcaba74eb5d7e7665601509e2889285b50a04b5b639a23f8adc818157 done\n", - "#30 writing layer sha256:b49326ff73acef905ddca0e7c2734fb9fa6d21d55c9b25feb30dd3a4aa99a9d9 0.0s done\n", "#30 writing layer sha256:ba9f7c75e4dd7942b944679995365aab766d3677da2e69e1d74472f471a484dd done\n", - "#30 writing layer sha256:bc42865e1c27a9b1bee751f3c99ad2c12a906d32aca396ace7a07231c9cafbd1 done\n", - "#30 writing layer sha256:bdfc73b2a0fa11b4086677e117a2f9feb6b4ffeccb23a3d58a30543339607e31 done\n", - "#30 writing layer sha256:c175bb235295e50de2961fa1e1a2235c57e6eba723a914287dfc26d3be0eac11 done\n", + "#30 writing layer sha256:bdc13166216ae226fa6976f9ce91f4f259d43972f1e0a9b723e436919534b2f4 done\n", + "#30 writing layer sha256:c815f0be64eded102822d81e029bd23b0d8d9a0fbfeb492ec0b4b0bc4ee777bf done\n", + "#30 writing layer sha256:c97f7fb19e2e0b8ee3e1065f4dee369e35029cc620cafb7fe3dec2e9e06a3ae0 done\n", "#30 writing layer sha256:c98533d2908f36a5e9b52faae83809b3b6865b50e90e2817308acfc64cd3655f done\n", - "#30 writing layer sha256:cb6c95b33bc30dd285c5b3cf99a05281b8f12decae1c932ab64bd58f56354021 done\n", - "#30 writing layer sha256:d57848e1e8b61049c64df4a786ec67b44ae3ffc2554b13b92ea4ce57b8686ab9 0.0s done\n", - "#30 writing layer sha256:d6b5d6e098aacb316146a428c6b5aef9692011c6dce0932e3bbfbf27a514b7ed done\n", "#30 writing layer sha256:d7da5c5e9a40c476c4b3188a845e3276dedfd752e015ea5113df5af64d4d43f7 done\n", - "#30 writing layer sha256:e4aedc686433c0ec5e676e6cc54a164345f7016aa0eb714f00c07e11664a1168\n", - "#30 preparing build cache for export 11.8s done\n", - "#30 writing layer sha256:e4aedc686433c0ec5e676e6cc54a164345f7016aa0eb714f00c07e11664a1168 done\n", + "#30 writing layer sha256:db20521a869adda8244cb64b783c65e1a911efaae0e73ae00e4a34ea6213d6ce done\n", + "#30 writing layer sha256:df4fd0ac710d7af949afbc6d25b5b4daf3f0596dabf3dec36fa7ca8fa6e1d049 done\n", + "#30 writing layer sha256:e291ddecfbe16b95ee9e90b5e90b1a3d0cfd53dc5e720d6b0f3d28e4a47cf5ac done\n", "#30 writing layer sha256:e8acb678f16bc0c369d5cf9c184f2d3a1c773986816526e5e3e9c0354f7e757f done\n", "#30 writing layer sha256:e9225f7ab6606813ec9acba98a064826ebfd6713a9645a58cd068538af1ecddb done\n", - "#30 writing layer sha256:f33546e75bf1a7d9dc9e21b9a2c54c9d09b24790ad7a4192a8509002ceb14688 done\n", + "#30 writing layer sha256:e9808a628d8776e25114053fec83adbf9c6dd084ac0c275042fa8b89db830da5 0.0s done\n", + "#30 writing layer sha256:f249faf9663a96b0911a903f8803b11a553c59b698013fb8343492fefdaaea90 done\n", "#30 writing layer sha256:f608e2fbff86e98627b7e462057e7d2416522096d73fe4664b82fe6ce8a4047d done\n", - "#30 writing layer sha256:f7702077ced42a1ee35e7f5e45f72634328ff3bcfe3f57735ba80baa5ec45daf done\n", - "#30 writing layer sha256:fa66a49172c6e821a1bace57c007c01da10cbc61507c44f8cdfeed8c4e5febab done\n", - "#30 writing config sha256:7d69b41abed153db28e437a954cc449f6c78804af5fd43d91d5b0b2b7d7e2b64 0.0s done\n", - "#30 writing cache manifest sha256:bf627b702e1d3cfae1b53eb29f8b0367eca39a3a4e756a966b4b5ee9054360fe 0.0s done\n", - "#30 DONE 11.8s\n", - "[2024-04-10 15:13:34,407] [INFO] (packager) - Build Summary:\n", + "#30 writing layer sha256:f65d191416580d6c38e3d95eee12377b75a4df548be1492618ce2a8c3c41b99e done\n", + "#30 writing config sha256:bad5d754263c9813832b5d1594a04b9c78a10052ec0a59ade6ee42de1baadb19 0.0s done\n", + "#30 writing cache manifest sha256:62a85925ced740e444a8f19b3c59ade29144854a44168d8786e00e93dbad2f5f 0.0s done\n", + "#30 DONE 11.6s\n", + "[2024-04-23 16:16:38,598] [INFO] (packager) - Build Summary:\n", "\n", "Platform: x64-workstation/dgpu\n", " Status: Succeeded\n", @@ -1750,7 +1763,7 @@ "name": "stdout", "output_type": "stream", "text": [ - "my_app-x64-workstation-dgpu-linux-amd64 1.0 f820210cdcfe About a minute ago 18.1GB\n" + "my_app-x64-workstation-dgpu-linux-amd64 1.0 95614919d60e About a minute ago 18.3GB\n" ] } ], @@ -1833,16 +1846,16 @@ " \"platformConfig\": \"dgpu\"\n", "}\n", "\n", - "2024-04-10 22:13:38 [INFO] Copying application from /opt/holoscan/app to /var/run/holoscan/export/app\n", + "2024-04-23 23:16:41 [INFO] Copying application from /opt/holoscan/app to /var/run/holoscan/export/app\n", "\n", - "2024-04-10 22:13:38 [INFO] Copying application manifest file from /etc/holoscan/app.json to /var/run/holoscan/export/config/app.json\n", - "2024-04-10 22:13:38 [INFO] Copying pkg manifest file from /etc/holoscan/pkg.json to /var/run/holoscan/export/config/pkg.json\n", - "2024-04-10 22:13:38 [INFO] Copying application configuration from /var/holoscan/app.yaml to /var/run/holoscan/export/config/app.yaml\n", + "2024-04-23 23:16:41 [INFO] Copying application manifest file from /etc/holoscan/app.json to /var/run/holoscan/export/config/app.json\n", + "2024-04-23 23:16:41 [INFO] Copying pkg manifest file from /etc/holoscan/pkg.json to /var/run/holoscan/export/config/pkg.json\n", + "2024-04-23 23:16:41 [INFO] Copying application configuration from /var/holoscan/app.yaml to /var/run/holoscan/export/config/app.yaml\n", "\n", - "2024-04-10 22:13:38 [INFO] Copying models from /opt/holoscan/models to /var/run/holoscan/export/models\n", + "2024-04-23 23:16:41 [INFO] Copying models from /opt/holoscan/models to /var/run/holoscan/export/models\n", "\n", - "2024-04-10 22:13:39 [INFO] Copying documentation from /opt/holoscan/docs/ to /var/run/holoscan/export/docs\n", - "2024-04-10 22:13:39 [INFO] '/opt/holoscan/docs/' cannot be found.\n", + "2024-04-23 23:16:42 [INFO] Copying documentation from /opt/holoscan/docs/ to /var/run/holoscan/export/docs\n", + "2024-04-23 23:16:42 [INFO] '/opt/holoscan/docs/' cannot be found.\n", "\n", "app config models\n" ] @@ -1874,22 +1887,22 @@ "name": "stdout", "output_type": "stream", "text": [ - "[2024-04-10 15:13:42,036] [INFO] (runner) - Checking dependencies...\n", - "[2024-04-10 15:13:42,036] [INFO] (runner) - --> Verifying if \"docker\" is installed...\n", + "[2024-04-23 16:16:45,664] [INFO] (runner) - Checking dependencies...\n", + "[2024-04-23 16:16:45,664] [INFO] (runner) - --> Verifying if \"docker\" is installed...\n", "\n", - "[2024-04-10 15:13:42,036] [INFO] (runner) - --> Verifying if \"docker-buildx\" is installed...\n", + "[2024-04-23 16:16:45,664] [INFO] (runner) - --> Verifying if \"docker-buildx\" is installed...\n", "\n", - "[2024-04-10 15:13:42,036] [INFO] (runner) - --> Verifying if \"my_app-x64-workstation-dgpu-linux-amd64:1.0\" is available...\n", + "[2024-04-23 16:16:45,664] [INFO] (runner) - --> Verifying if \"my_app-x64-workstation-dgpu-linux-amd64:1.0\" is available...\n", "\n", - "[2024-04-10 15:13:42,107] [INFO] (runner) - Reading HAP/MAP manifest...\n", - "\u001b[sPreparing to copy...\u001b[?25l\u001b[u\u001b[2KCopying from container - 0B\u001b[?25h\u001b[u\u001b[2KSuccessfully copied 2.56kB to /tmp/tmpor1kfks8/app.json\n", - "\u001b[sPreparing to copy...\u001b[?25l\u001b[u\u001b[2KCopying from container - 0B\u001b[?25h\u001b[u\u001b[2KSuccessfully copied 2.05kB to /tmp/tmpor1kfks8/pkg.json\n", - "[2024-04-10 15:13:42,350] [INFO] (runner) - --> Verifying if \"nvidia-ctk\" is installed...\n", + "[2024-04-23 16:16:45,739] [INFO] (runner) - Reading HAP/MAP manifest...\n", + "\u001b[sPreparing to copy...\u001b[?25l\u001b[u\u001b[2KCopying from container - 0B\u001b[?25h\u001b[u\u001b[2KSuccessfully copied 2.56kB to /tmp/tmpymoiz9gd/app.json\n", + "\u001b[sPreparing to copy...\u001b[?25l\u001b[u\u001b[2KCopying from container - 0B\u001b[?25h\u001b[u\u001b[2KSuccessfully copied 2.05kB to /tmp/tmpymoiz9gd/pkg.json\n", + "[2024-04-23 16:16:46,001] [INFO] (runner) - --> Verifying if \"nvidia-ctk\" is installed...\n", "\n", - "[2024-04-10 15:13:42,351] [INFO] (runner) - --> Verifying \"nvidia-ctk\" version...\n", + "[2024-04-23 16:16:46,002] [INFO] (runner) - --> Verifying \"nvidia-ctk\" version...\n", "\n", - "[2024-04-10 15:13:42,710] [INFO] (common) - Launching container (60a9bd0111e6) using image 'my_app-x64-workstation-dgpu-linux-amd64:1.0'...\n", - " container name: hungry_bassi\n", + "[2024-04-23 16:16:46,316] [INFO] (common) - Launching container (42b411558fd7) using image 'my_app-x64-workstation-dgpu-linux-amd64:1.0'...\n", + " container name: silly_davinci\n", " host name: mingq-dt\n", " network: host\n", " user: 1000:1000\n", @@ -1899,119 +1912,115 @@ " shared memory size: 67108864\n", " devices: \n", " group_add: 44\n", - "2024-04-10 22:13:43 [INFO] Launching application python3 /opt/holoscan/app ...\n", + "2024-04-23 23:16:46 [INFO] Launching application python3 /opt/holoscan/app ...\n", "\n", - "[2024-04-10 22:13:46,276] [INFO] (root) - Parsed args: Namespace(log_level=None, input=None, output=None, model=None, workdir=None, argv=['/opt/holoscan/app'])\n", + "[2024-04-23 23:16:50,090] [INFO] (root) - Parsed args: Namespace(log_level=None, input=None, output=None, model=None, workdir=None, argv=['/opt/holoscan/app'])\n", "\n", - "[2024-04-10 22:13:46,382] [INFO] (root) - AppContext object: AppContext(input_path=/var/holoscan/input, output_path=/var/holoscan/output, model_path=/opt/holoscan/models, workdir=/var/holoscan)\n", + "[2024-04-23 23:16:50,095] [INFO] (root) - AppContext object: AppContext(input_path=/var/holoscan/input, output_path=/var/holoscan/output, model_path=/opt/holoscan/models, workdir=/var/holoscan)\n", "\n", - "[2024-04-10 22:13:46,384] [INFO] (root) - End compose\n", + "[2024-04-23 23:16:50,097] [INFO] (root) - End compose\n", "\n", "[info] [app_driver.cpp:1161] Launching the driver/health checking service\n", "\n", - "[info] [gxf_executor.cpp:211] Creating context\n", + "[info] [gxf_executor.cpp:247] Creating context\n", "\n", "[info] [server.cpp:87] Health checking server listening on 0.0.0.0:8777\n", "\n", - "[info] [gxf_executor.cpp:1674] Loading extensions from configs...\n", + "[info] [gxf_executor.cpp:1672] Loading extensions from configs...\n", "\n", - "[info] [gxf_executor.cpp:1864] Activating Graph...\n", + "[info] [gxf_executor.cpp:1842] Activating Graph...\n", "\n", - "[info] [gxf_executor.cpp:1894] Running Graph...\n", + "[info] [gxf_executor.cpp:1874] Running Graph...\n", "\n", - "[info] [gxf_executor.cpp:1896] Waiting for completion...\n", + "[info] [gxf_executor.cpp:1876] Waiting for completion...\n", "\n", - "[info] [gxf_executor.cpp:1897] Graph execution waiting. Fragment: \n", + "\u001b[0m2024-04-23 23:16:50.129 INFO gxf/std/greedy_scheduler.cpp@191: Scheduling 9 entities\u001b[0m\n", "\n", - "[info] [greedy_scheduler.cpp:190] Scheduling 9 entities\n", + "[2024-04-23 23:16:50,131] [INFO] (monai.deploy.operators.dicom_data_loader_operator.DICOMDataLoaderOperator) - No or invalid input path from the optional input port: None\n", "\n", - "[2024-04-10 22:13:46,439] [INFO] (monai.deploy.operators.dicom_data_loader_operator.DICOMDataLoaderOperator) - No or invalid input path from the optional input port: None\n", + "[2024-04-23 23:16:50,512] [INFO] (root) - Finding series for Selection named: CT Series\n", "\n", - "[2024-04-10 22:13:47,210] [INFO] (root) - Finding series for Selection named: CT Series\n", - "\n", - "[2024-04-10 22:13:47,211] [INFO] (root) - Searching study, : 1.3.6.1.4.1.14519.5.2.1.7085.2626.822645453932810382886582736291\n", + "[2024-04-23 23:16:50,512] [INFO] (root) - Searching study, : 1.3.6.1.4.1.14519.5.2.1.7085.2626.822645453932810382886582736291\n", "\n", " # of series: 1\n", "\n", - "[2024-04-10 22:13:47,211] [INFO] (root) - Working on series, instance UID: 1.3.6.1.4.1.14519.5.2.1.7085.2626.119403521930927333027265674239\n", + "[2024-04-23 23:16:50,512] [INFO] (root) - Working on series, instance UID: 1.3.6.1.4.1.14519.5.2.1.7085.2626.119403521930927333027265674239\n", "\n", - "[2024-04-10 22:13:47,211] [INFO] (root) - On attribute: 'StudyDescription' to match value: '(.*?)'\n", + "[2024-04-23 23:16:50,512] [INFO] (root) - On attribute: 'StudyDescription' to match value: '(.*?)'\n", "\n", - "[2024-04-10 22:13:47,211] [INFO] (root) - Series attribute StudyDescription value: CT ABDOMEN W IV CONTRAST\n", + "[2024-04-23 23:16:50,512] [INFO] (root) - Series attribute StudyDescription value: CT ABDOMEN W IV CONTRAST\n", "\n", - "[2024-04-10 22:13:47,211] [INFO] (root) - Series attribute string value did not match. Try regEx.\n", + "[2024-04-23 23:16:50,512] [INFO] (root) - Series attribute string value did not match. Try regEx.\n", "\n", - "[2024-04-10 22:13:47,211] [INFO] (root) - On attribute: 'Modality' to match value: '(?i)CT'\n", + "[2024-04-23 23:16:50,512] [INFO] (root) - On attribute: 'Modality' to match value: '(?i)CT'\n", "\n", - "[2024-04-10 22:13:47,211] [INFO] (root) - Series attribute Modality value: CT\n", + "[2024-04-23 23:16:50,512] [INFO] (root) - Series attribute Modality value: CT\n", "\n", - "[2024-04-10 22:13:47,211] [INFO] (root) - Series attribute string value did not match. Try regEx.\n", + "[2024-04-23 23:16:50,512] [INFO] (root) - Series attribute string value did not match. Try regEx.\n", "\n", - "[2024-04-10 22:13:47,211] [INFO] (root) - On attribute: 'SeriesDescription' to match value: '(.*?)'\n", + "[2024-04-23 23:16:50,513] [INFO] (root) - On attribute: 'SeriesDescription' to match value: '(.*?)'\n", "\n", - "[2024-04-10 22:13:47,211] [INFO] (root) - Series attribute SeriesDescription value: ABD/PANC 3.0 B31f\n", + "[2024-04-23 23:16:50,513] [INFO] (root) - Series attribute SeriesDescription value: ABD/PANC 3.0 B31f\n", "\n", - "[2024-04-10 22:13:47,211] [INFO] (root) - Series attribute string value did not match. Try regEx.\n", + "[2024-04-23 23:16:50,513] [INFO] (root) - Series attribute string value did not match. Try regEx.\n", "\n", - "[2024-04-10 22:13:47,211] [INFO] (root) - Selected Series, UID: 1.3.6.1.4.1.14519.5.2.1.7085.2626.119403521930927333027265674239\n", + "[2024-04-23 23:16:50,513] [INFO] (root) - Selected Series, UID: 1.3.6.1.4.1.14519.5.2.1.7085.2626.119403521930927333027265674239\n", "\n", - "[2024-04-10 22:13:47,444] [INFO] (root) - Parsing from bundle_path: /opt/holoscan/models/pancreas_ct_dints/model.ts\n", + "[2024-04-23 23:16:50,745] [INFO] (root) - Parsing from bundle_path: /opt/holoscan/models/pancreas_ct_dints/model.ts\n", "\n", - "[2024-04-10 22:15:33,613] [INFO] (root) - Parsing from bundle_path: /opt/holoscan/models/spleen_ct/model.ts\n", + "[2024-04-23 23:18:36,681] [INFO] (root) - Parsing from bundle_path: /opt/holoscan/models/spleen_ct/model.ts\n", "\n", "/home/holoscan/.local/lib/python3.10/site-packages/highdicom/valuerep.py:54: UserWarning: The string \"C3N-00198\" is unlikely to represent the intended person name since it contains only a single component. Construct a person name according to the format in described in https://dicom.nema.org/dicom/2013/output/chtml/part05/sect_6.2.html#sect_6.2.1.2, or, in pydicom 2.2.0 or later, use the pydicom.valuerep.PersonName.from_named_components() method to construct the person name correctly. If a single-component name is really intended, add a trailing caret character to disambiguate the name.\n", "\n", " warnings.warn(\n", "\n", - "[2024-04-10 22:15:37,078] [INFO] (highdicom.base) - copy Image-related attributes from dataset \"1.3.6.1.4.1.14519.5.2.1.7085.2626.936983343951485811186213470191\"\n", - "\n", - "[2024-04-10 22:15:37,078] [INFO] (highdicom.base) - copy attributes of module \"Specimen\"\n", + "[2024-04-23 23:18:40,078] [INFO] (highdicom.base) - copy Image-related attributes from dataset \"1.3.6.1.4.1.14519.5.2.1.7085.2626.936983343951485811186213470191\"\n", "\n", - "[2024-04-10 22:15:37,078] [INFO] (highdicom.base) - copy Patient-related attributes from dataset \"1.3.6.1.4.1.14519.5.2.1.7085.2626.936983343951485811186213470191\"\n", + "[2024-04-23 23:18:40,078] [INFO] (highdicom.base) - copy attributes of module \"Specimen\"\n", "\n", - "[2024-04-10 22:15:37,078] [INFO] (highdicom.base) - copy attributes of module \"Patient\"\n", + "[2024-04-23 23:18:40,078] [INFO] (highdicom.base) - copy Patient-related attributes from dataset \"1.3.6.1.4.1.14519.5.2.1.7085.2626.936983343951485811186213470191\"\n", "\n", - "[2024-04-10 22:15:37,079] [INFO] (highdicom.base) - copy attributes of module \"Clinical Trial Subject\"\n", + "[2024-04-23 23:18:40,078] [INFO] (highdicom.base) - copy attributes of module \"Patient\"\n", "\n", - "[2024-04-10 22:15:37,079] [INFO] (highdicom.base) - copy Study-related attributes from dataset \"1.3.6.1.4.1.14519.5.2.1.7085.2626.936983343951485811186213470191\"\n", + "[2024-04-23 23:18:40,078] [INFO] (highdicom.base) - copy attributes of module \"Clinical Trial Subject\"\n", "\n", - "[2024-04-10 22:15:37,079] [INFO] (highdicom.base) - copy attributes of module \"General Study\"\n", + "[2024-04-23 23:18:40,079] [INFO] (highdicom.base) - copy Study-related attributes from dataset \"1.3.6.1.4.1.14519.5.2.1.7085.2626.936983343951485811186213470191\"\n", "\n", - "[2024-04-10 22:15:37,079] [INFO] (highdicom.base) - copy attributes of module \"Patient Study\"\n", + "[2024-04-23 23:18:40,079] [INFO] (highdicom.base) - copy attributes of module \"General Study\"\n", "\n", - "[2024-04-10 22:15:37,079] [INFO] (highdicom.base) - copy attributes of module \"Clinical Trial Study\"\n", + "[2024-04-23 23:18:40,079] [INFO] (highdicom.base) - copy attributes of module \"Patient Study\"\n", "\n", - "[2024-04-10 22:15:38,307] [INFO] (highdicom.base) - copy Image-related attributes from dataset \"1.3.6.1.4.1.14519.5.2.1.7085.2626.936983343951485811186213470191\"\n", + "[2024-04-23 23:18:40,079] [INFO] (highdicom.base) - copy attributes of module \"Clinical Trial Study\"\n", "\n", - "[2024-04-10 22:15:38,307] [INFO] (highdicom.base) - copy attributes of module \"Specimen\"\n", + "[2024-04-23 23:18:41,286] [INFO] (highdicom.base) - copy Image-related attributes from dataset \"1.3.6.1.4.1.14519.5.2.1.7085.2626.936983343951485811186213470191\"\n", "\n", - "[2024-04-10 22:15:38,307] [INFO] (highdicom.base) - copy Patient-related attributes from dataset \"1.3.6.1.4.1.14519.5.2.1.7085.2626.936983343951485811186213470191\"\n", + "[2024-04-23 23:18:41,286] [INFO] (highdicom.base) - copy attributes of module \"Specimen\"\n", "\n", - "[2024-04-10 22:15:38,307] [INFO] (highdicom.base) - copy attributes of module \"Patient\"\n", + "[2024-04-23 23:18:41,286] [INFO] (highdicom.base) - copy Patient-related attributes from dataset \"1.3.6.1.4.1.14519.5.2.1.7085.2626.936983343951485811186213470191\"\n", "\n", - "[2024-04-10 22:15:38,308] [INFO] (highdicom.base) - copy attributes of module \"Clinical Trial Subject\"\n", + "[2024-04-23 23:18:41,286] [INFO] (highdicom.base) - copy attributes of module \"Patient\"\n", "\n", - "[2024-04-10 22:15:38,308] [INFO] (highdicom.base) - copy Study-related attributes from dataset \"1.3.6.1.4.1.14519.5.2.1.7085.2626.936983343951485811186213470191\"\n", + "[2024-04-23 23:18:41,286] [INFO] (highdicom.base) - copy attributes of module \"Clinical Trial Subject\"\n", "\n", - "[2024-04-10 22:15:38,308] [INFO] (highdicom.base) - copy attributes of module \"General Study\"\n", + "[2024-04-23 23:18:41,286] [INFO] (highdicom.base) - copy Study-related attributes from dataset \"1.3.6.1.4.1.14519.5.2.1.7085.2626.936983343951485811186213470191\"\n", "\n", - "[2024-04-10 22:15:38,308] [INFO] (highdicom.base) - copy attributes of module \"Patient Study\"\n", + "[2024-04-23 23:18:41,286] [INFO] (highdicom.base) - copy attributes of module \"General Study\"\n", "\n", - "[2024-04-10 22:15:38,308] [INFO] (highdicom.base) - copy attributes of module \"Clinical Trial Study\"\n", + "[2024-04-23 23:18:41,286] [INFO] (highdicom.base) - copy attributes of module \"Patient Study\"\n", "\n", - "[info] [greedy_scheduler.cpp:369] Scheduler stopped: Some entities are waiting for execution, but there are no periodic or async entities to get out of the deadlock.\n", + "[2024-04-23 23:18:41,287] [INFO] (highdicom.base) - copy attributes of module \"Clinical Trial Study\"\n", "\n", - "[info] [greedy_scheduler.cpp:398] Scheduler finished.\n", + "\u001b[0m2024-04-23 23:18:41.373 INFO gxf/std/greedy_scheduler.cpp@372: Scheduler stopped: Some entities are waiting for execution, but there are no periodic or async entities to get out of the deadlock.\u001b[0m\n", "\n", - "[info] [gxf_executor.cpp:1906] Graph execution deactivating. Fragment: \n", + "[info] [gxf_executor.cpp:1879] Deactivating Graph...\n", "\n", - "[info] [gxf_executor.cpp:1907] Deactivating Graph...\n", + "\u001b[0m2024-04-23 23:18:41.377 INFO gxf/std/greedy_scheduler.cpp@401: Scheduler finished.\u001b[0m\n", "\n", - "[info] [gxf_executor.cpp:1910] Graph execution finished. Fragment: \n", + "[info] [gxf_executor.cpp:1887] Graph execution finished.\n", "\n", - "[2024-04-10 22:15:38,401] [INFO] (app.App) - End run\n", + "[2024-04-23 23:18:41,385] [INFO] (app.App) - End run\n", "\n", - "[2024-04-10 15:15:39,461] [INFO] (common) - Container 'hungry_bassi'(60a9bd0111e6) exited.\n" + "[2024-04-23 16:18:42,406] [INFO] (common) - Container 'silly_davinci'(42b411558fd7) exited.\n" ] } ], @@ -2037,8 +2046,8 @@ "name": "stdout", "output_type": "stream", "text": [ - "1.2.826.0.1.3680043.10.511.3.77817234108119246236647417839296398.dcm\n", - "1.2.826.0.1.3680043.10.511.3.83680469536583357494244170492806366.dcm\n" + "1.2.826.0.1.3680043.10.511.3.11468162564679998832192298844993783.dcm\n", + "1.2.826.0.1.3680043.10.511.3.22886221740567104559887431846790837.dcm\n" ] } ], diff --git a/requirements-dev.txt b/requirements-dev.txt index 81ac93f5..86c1f983 100644 --- a/requirements-dev.txt +++ b/requirements-dev.txt @@ -35,4 +35,4 @@ scikit-image>=0.17.2 nibabel>=3.2.1 numpy-stl>=2.12.0 trimesh>=3.8.11 -torch~=2.0.1 +torch>=2.0.1 diff --git a/requirements-examples.txt b/requirements-examples.txt index 1490e6fa..14756af7 100644 --- a/requirements-examples.txt +++ b/requirements-examples.txt @@ -4,10 +4,8 @@ PyPDF2>=2.11.1 highdicom>=0.18.2 SimpleITK>=2.0.0 Pillow>=8.4.0 -numpy-stl>=2.12.0 -trimesh>=3.8.11 nibabel>=3.2.1 numpy-stl>=2.12.0 trimesh>=3.8.11 -torch~=2.0.1 +torch>=2.0.1 monai>=1.0.0 \ No newline at end of file diff --git a/requirements.txt b/requirements.txt index 9034567c..73a56030 100644 --- a/requirements.txt +++ b/requirements.txt @@ -1,4 +1,4 @@ -holoscan~=1.0 +holoscan~=2.0 numpy>=1.21.6 colorama>=0.4.1 typeguard>=3.0.0 diff --git a/setup.cfg b/setup.cfg index c7e5e227..80a51572 100644 --- a/setup.cfg +++ b/setup.cfg @@ -24,7 +24,7 @@ python_requires = >= 3.8 # cucim install_requires = numpy>=1.21.6 - holoscan~=1.0 + holoscan~=2.0 colorama>=0.4.1 typeguard>=3.0.0 @@ -51,6 +51,8 @@ ignore = B905, # B026 Star-arg unpacking after a keyword argument is strongly discouraged B026 + # B909 editing a loop's mutable iterable often leads to unexpected results/bugs + B909 per_file_ignores = # e.g. F403 'from holoscan.conditions import *' used; unable to detect undefined names