diff --git a/biapy/__init__.py b/biapy/__init__.py index 093c17ed..c520d4ad 100644 --- a/biapy/__init__.py +++ b/biapy/__init__.py @@ -1,4 +1,4 @@ -__version__ = "3.5.3" +__version__ = "3.5.4" import argparse import os diff --git a/biapy/utils/env/Dockerfile b/biapy/utils/env/Dockerfile index 916d536c..92473215 100755 --- a/biapy/utils/env/Dockerfile +++ b/biapy/utils/env/Dockerfile @@ -31,14 +31,14 @@ RUN conda update -qy conda \ SHELL ["conda", "run", "-n", "BiaPy_env", "/bin/bash", "-c"] # Install BiaPy -RUN pip install biapy==3.5.3 +RUN pip install biapy==3.5.4 # Install Pytorch 2.2.0 + CUDA 11.8 RUN pip install torch==2.4.0 torchvision==0.19.0 torchaudio==2.4.0 --index-url https://download.pytorch.org/whl/cu118 RUN pip install timm pytorch-msssim torchmetrics[image] # Clone BiaPy, as running it with python -c "" stops the container with no error after a few seconds running - RUN git clone --depth 1 https://github.com/BiaPyX/BiaPy.git --branch v3.5.3 /installations/BiaPy + RUN git clone --depth 1 https://github.com/BiaPyX/BiaPy.git --branch v3.5.4 /installations/BiaPy # This time clone the last commit (25729c ; v3.5.2) as some minor bugs were solved but not created a new release yet #RUN git clone --depth 1 https://github.com/BiaPyX/BiaPy.git /installations/BiaPy diff --git a/biapy/utils/env/Dockerfile_CUDA10.2 b/biapy/utils/env/Dockerfile_CUDA10.2 index a4201c53..a061ea4f 100755 --- a/biapy/utils/env/Dockerfile_CUDA10.2 +++ b/biapy/utils/env/Dockerfile_CUDA10.2 @@ -32,14 +32,14 @@ RUN conda update -qy conda \ SHELL ["conda", "run", "-n", "BiaPy_env", "/bin/bash", "-c"] # Install BiaPy -RUN pip install biapy==3.5.3 +RUN pip install biapy==3.5.4 # Install Pytorch 1.12.1 + CUDA 10.2 RUN conda install pytorch==1.12.1 torchvision==0.13.1 torchaudio==0.12.1 cudatoolkit=10.2 -c pytorch RUN pip install timm pytorch-msssim torchmetrics[image] # Clone BiaPy, as running it with python -c "" stops the container with no error after a few seconds running -RUN git clone --depth 1 https://github.com/BiaPyX/BiaPy.git --branch v3.5.3 /installations/BiaPy +RUN git clone --depth 1 https://github.com/BiaPyX/BiaPy.git --branch v3.5.4 /installations/BiaPy # This time clone the last commit (25729c ; v3.5.2) as some minor bugs were solved but not created a new release yet # RUN git clone --depth 1 https://github.com/BiaPyX/BiaPy.git /installations/BiaPy diff --git a/biapy/utils/scripts/export_bmz_test.py b/biapy/utils/scripts/export_bmz_test.py index d89e7f9a..424cef1f 100644 --- a/biapy/utils/scripts/export_bmz_test.py +++ b/biapy/utils/scripts/export_bmz_test.py @@ -1,4 +1,3 @@ -import os import sys import argparse @@ -34,7 +33,7 @@ # import pdb; pdb.set_trace() if args["reuse_original_bmz_config"]: - biapy.export_model_to_bmz("/data/dfranco/bmz_check", reuse_original_bmz_config=True) + biapy.export_model_to_bmz(args["bmz_folder"], reuse_original_bmz_config=True) else: # Create a dict with all BMZ requirements bmz_cfg = {} diff --git a/biapy/utils/scripts/run_checks.py b/biapy/utils/scripts/run_checks.py index a1b93962..8abb9eaf 100644 --- a/biapy/utils/scripts/run_checks.py +++ b/biapy/utils/scripts/run_checks.py @@ -75,9 +75,9 @@ "yaml": "test_5.yaml", "internal_checks": [ {"type": "DatasetMatching", "pattern": "DatasetMatching(criterion='iou', thresh=0.3,", "nApparition": 1, "metric": "f1", - "gt": True, "value": 0.6}, + "gt": True, "value": 0.55}, {"type": "DatasetMatching", "pattern": "DatasetMatching(criterion='iou', thresh=0.3,", "nApparition": 2, "metric": "f1", - "gt": True, "value": 0.6}, # Post-processing + "gt": True, "value": 0.55}, # Post-processing ] } diff --git a/pyproject.toml b/pyproject.toml index ebcf383b..994cff2f 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta" [project] name = "biapy" -version = "3.5.3" +version = "3.5.4" description = "BiaPy: Bioimage analysis pipelines in Python" readme = "README.md" requires-python = ">=3.10" diff --git a/templates/classification/2d_classification.yaml b/templates/classification/2d_classification.yaml index 3ac2fd75..1656e650 100644 --- a/templates/classification/2d_classification.yaml +++ b/templates/classification/2d_classification.yaml @@ -1,4 +1,4 @@ -# BiaPy version: 3.5.3 +# BiaPy version: 3.5.4 SYSTEM: NUM_CPUS: -1 diff --git a/templates/classification/2d_classification_rgb.yaml b/templates/classification/2d_classification_rgb.yaml index 6e2a8bd3..7f7dbeef 100644 --- a/templates/classification/2d_classification_rgb.yaml +++ b/templates/classification/2d_classification_rgb.yaml @@ -1,4 +1,4 @@ -# BiaPy version: 3.5.3 +# BiaPy version: 3.5.4 SYSTEM: NUM_CPUS: -1 diff --git a/templates/classification/3d_classification.yaml b/templates/classification/3d_classification.yaml index 0b45b9ff..76f5bd48 100644 --- a/templates/classification/3d_classification.yaml +++ b/templates/classification/3d_classification.yaml @@ -1,4 +1,4 @@ -# BiaPy version: 3.5.3 +# BiaPy version: 3.5.4 SYSTEM: NUM_CPUS: -1 diff --git a/templates/denoising/2d_denoising.yaml b/templates/denoising/2d_denoising.yaml index a0c04c85..c75bf290 100644 --- a/templates/denoising/2d_denoising.yaml +++ b/templates/denoising/2d_denoising.yaml @@ -1,4 +1,4 @@ -# BiaPy version: 3.5.3 +# BiaPy version: 3.5.4 # We try to mimic here N2Void project parameters SYSTEM: NUM_CPUS: -1 diff --git a/templates/denoising/3d_denoising.yaml b/templates/denoising/3d_denoising.yaml index f1975c18..0c6000cf 100644 --- a/templates/denoising/3d_denoising.yaml +++ b/templates/denoising/3d_denoising.yaml @@ -1,4 +1,4 @@ -# BiaPy version: 3.5.3 +# BiaPy version: 3.5.4 # We try to mimic here N2Void project parameters SYSTEM: diff --git a/templates/detection/2d_detection.yaml b/templates/detection/2d_detection.yaml index 620da6ad..0496cacc 100644 --- a/templates/detection/2d_detection.yaml +++ b/templates/detection/2d_detection.yaml @@ -1,4 +1,4 @@ -# BiaPy version: 3.5.3 +# BiaPy version: 3.5.4 SYSTEM: NUM_CPUS: -1 diff --git a/templates/detection/3D_cell_detection_zarr_tutorial.yaml b/templates/detection/3D_cell_detection_zarr_tutorial.yaml index a8f43e2c..6a03da15 100644 --- a/templates/detection/3D_cell_detection_zarr_tutorial.yaml +++ b/templates/detection/3D_cell_detection_zarr_tutorial.yaml @@ -1,4 +1,4 @@ -# BiaPy version: 3.5.3 +# BiaPy version: 3.5.4 SYSTEM: NUM_CPUS: -1 diff --git a/templates/detection/3d_detection.yaml b/templates/detection/3d_detection.yaml index a0a534d6..2deb6a95 100644 --- a/templates/detection/3d_detection.yaml +++ b/templates/detection/3d_detection.yaml @@ -1,4 +1,4 @@ -# BiaPy version: 3.5.3 +# BiaPy version: 3.5.4 SYSTEM: NUM_CPUS: -1 diff --git a/templates/image-to-image/2d_image-to-image.yaml b/templates/image-to-image/2d_image-to-image.yaml index 76cd8a67..9620f747 100644 --- a/templates/image-to-image/2d_image-to-image.yaml +++ b/templates/image-to-image/2d_image-to-image.yaml @@ -1,4 +1,4 @@ -# BiaPy version: 3.5.3 +# BiaPy version: 3.5.4 SYSTEM: NUM_CPUS: -1 diff --git a/templates/image-to-image/3d_image-to-image.yaml b/templates/image-to-image/3d_image-to-image.yaml index e52e6fcf..7feede9e 100644 --- a/templates/image-to-image/3d_image-to-image.yaml +++ b/templates/image-to-image/3d_image-to-image.yaml @@ -1,4 +1,4 @@ -# BiaPy version: 3.5.3 +# BiaPy version: 3.5.4 SYSTEM: NUM_CPUS: -1 diff --git a/templates/instance_segmentation/2d_instance_segmentation.yaml b/templates/instance_segmentation/2d_instance_segmentation.yaml index 664dfd33..b60581d0 100644 --- a/templates/instance_segmentation/2d_instance_segmentation.yaml +++ b/templates/instance_segmentation/2d_instance_segmentation.yaml @@ -1,4 +1,4 @@ -# BiaPy version: 3.5.3 +# BiaPy version: 3.5.4 SYSTEM: NUM_CPUS: -1 diff --git a/templates/instance_segmentation/3d_instance_segmentation.yaml b/templates/instance_segmentation/3d_instance_segmentation.yaml index 34c3313a..614aa840 100644 --- a/templates/instance_segmentation/3d_instance_segmentation.yaml +++ b/templates/instance_segmentation/3d_instance_segmentation.yaml @@ -1,4 +1,4 @@ -# BiaPy version: 3.5.3 +# BiaPy version: 3.5.4 SYSTEM: NUM_CPUS: -1 diff --git a/templates/self-supervised/2d_self-supervised.yaml b/templates/self-supervised/2d_self-supervised.yaml index 8e7a1e05..5a16ef5b 100644 --- a/templates/self-supervised/2d_self-supervised.yaml +++ b/templates/self-supervised/2d_self-supervised.yaml @@ -1,4 +1,4 @@ -# BiaPy version: 3.5.3 +# BiaPy version: 3.5.4 SYSTEM: NUM_CPUS: -1 diff --git a/templates/self-supervised/3d_self-supervised.yaml b/templates/self-supervised/3d_self-supervised.yaml index d7d67b29..24199751 100644 --- a/templates/self-supervised/3d_self-supervised.yaml +++ b/templates/self-supervised/3d_self-supervised.yaml @@ -1,4 +1,4 @@ -# BiaPy version: 3.5.3 +# BiaPy version: 3.5.4 SYSTEM: NUM_CPUS: -1 diff --git a/templates/semantic_segmentation/2d_semantic_segmentation.yaml b/templates/semantic_segmentation/2d_semantic_segmentation.yaml index 49aece27..a9916f3a 100644 --- a/templates/semantic_segmentation/2d_semantic_segmentation.yaml +++ b/templates/semantic_segmentation/2d_semantic_segmentation.yaml @@ -1,4 +1,4 @@ -# BiaPy version: 3.5.3 +# BiaPy version: 3.5.4 SYSTEM: NUM_CPUS: -1 diff --git a/templates/semantic_segmentation/3d_semantic_segmentation.yaml b/templates/semantic_segmentation/3d_semantic_segmentation.yaml index 6462bdf3..1fb2b008 100644 --- a/templates/semantic_segmentation/3d_semantic_segmentation.yaml +++ b/templates/semantic_segmentation/3d_semantic_segmentation.yaml @@ -1,4 +1,4 @@ -# BiaPy version: 3.5.3 +# BiaPy version: 3.5.4 SYSTEM: NUM_CPUS: -1 diff --git a/templates/semantic_segmentation/wound_segmentation.yaml b/templates/semantic_segmentation/wound_segmentation.yaml index 659fbdc5..faec5850 100644 --- a/templates/semantic_segmentation/wound_segmentation.yaml +++ b/templates/semantic_segmentation/wound_segmentation.yaml @@ -1,4 +1,4 @@ -# BiaPy version: 3.5.3 +# BiaPy version: 3.5.4 SYSTEM: NUM_CPUS: -1 diff --git a/templates/super-resolution/2d_super-resolution.yaml b/templates/super-resolution/2d_super-resolution.yaml index 21143369..7f88ca11 100644 --- a/templates/super-resolution/2d_super-resolution.yaml +++ b/templates/super-resolution/2d_super-resolution.yaml @@ -1,4 +1,4 @@ -# BiaPy version: 3.5.3 +# BiaPy version: 3.5.4 SYSTEM: NUM_CPUS: -1 diff --git a/templates/super-resolution/2d_super-resolution_rgb.yaml b/templates/super-resolution/2d_super-resolution_rgb.yaml index 9ee7118a..90764945 100644 --- a/templates/super-resolution/2d_super-resolution_rgb.yaml +++ b/templates/super-resolution/2d_super-resolution_rgb.yaml @@ -1,4 +1,4 @@ -# BiaPy version: 3.5.3 +# BiaPy version: 3.5.4 SYSTEM: NUM_CPUS: -1 diff --git a/templates/super-resolution/3d_super-resolution.yaml b/templates/super-resolution/3d_super-resolution.yaml index 511c3ad4..18eb4c15 100644 --- a/templates/super-resolution/3d_super-resolution.yaml +++ b/templates/super-resolution/3d_super-resolution.yaml @@ -1,4 +1,4 @@ -# BiaPy version: 3.5.3 +# BiaPy version: 3.5.4 SYSTEM: NUM_CPUS: -1