Add 2d diffusion model bundle

ci/bundle_custom_data.py

@@ -18,6 +18,7 @@
     "lung_nodule_ct_detection",
     "pathology_nuclei_segmentation_classification",
     "brats_mri_generative_diffusion",
+    "brats_mri_axial_slices_generative_diffusion",
 ]
 
 # This list is used for our CI tests to determine whether a bundle contains the preferred files.
@@ -34,13 +35,15 @@
     "breast_density_classification",
     "mednist_reg",
     "brats_mri_generative_diffusion",
+    "brats_mri_axial_slices_generative_diffusion",
 ]
 
 # This dict is used for our CI tests to install required dependencies that cannot be installed by `pip install` directly.
 # If a bundle has this kind of dependencies, please add the bundle name (key), and the path of the install script (value)
 # into the dict.
 install_dependency_dict = {
-    "brats_mri_generative_diffusion": "ci/install_scripts/install_brats_mri_generative_diffusion_dependency.sh"
+    "brats_mri_generative_diffusion": "ci/install_scripts/install_brats_mri_generative_diffusion_dependency.sh",
+    "brats_mri_axial_slices_generative_diffusion": "ci/install_scripts/install_brats_mri_axial_slices_generative_diffusion.sh",
 }
 
 # This list is used for our CI tests to determine whether a bundle supports TensorRT export. Related

ci/install_scripts/install_brats_mri_axial_slices_generative_diffusion.sh

@@ -0,0 +1,14 @@
+# Copyright (c) MONAI Consortium
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#     http://www.apache.org/licenses/LICENSE-2.0
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+# install cython to avoid error:
+# https://github.com/Project-MONAI/model-zoo/actions/runs/4980530305/jobs/8913560199#step:2:550
+pip install git+https://github.com/Project-MONAI/[email protected]

ci/install_scripts/install_brats_mri_generative_diffusion_dependency.sh

@@ -11,8 +11,4 @@
 
 # install cython to avoid error:
 # https://github.com/Project-MONAI/model-zoo/actions/runs/4980530305/jobs/8913560199#step:2:550
-git clone https://github.com/Project-MONAI/GenerativeModels.git
-cd GenerativeModels/
-git checkout f969c24f88d013dc0045fb7b2885a01fb219992b
-python setup.py install
-cd ..
+pip install git+https://github.com/Project-MONAI/[email protected]

ci/verify_bundle.py

@@ -51,13 +51,17 @@ def _get_weights_names(bundle: str):
     # TODO: this function is temporarily used. It should be replaced by detailed config tests.
     if bundle == "brats_mri_generative_diffusion":
         return "model_autoencoder.pt", "model_autoencoder.ts"
+    if bundle == "brats_mri_axial_slices_generative_diffusion":
+        return "model_autoencoder.pt", None
     return "model.pt", "model.ts"
 
 
 def _get_net_id(bundle: str):
     # TODO: this function is temporarily used. It should be replaced by detailed config tests.
     if bundle == "brats_mri_generative_diffusion":
         return "autoencoder_def"
+    if bundle == "brats_mri_axial_slices_generative_diffusion":
+        return "autoencoder_def"
     return "network_def"
 
 

models/brats_mri_axial_slices_generative_diffusion/LICENSE

@@ -0,0 +1,201 @@
+                                 Apache License
+                           Version 2.0, January 2004
+                        http://www.apache.org/licenses/
+
+   TERMS AND CONDITIONS FOR USE, REPRODUCTION, AND DISTRIBUTION
+
+   1. Definitions.
+
+      "License" shall mean the terms and conditions for use, reproduction,
+      and distribution as defined by Sections 1 through 9 of this document.
+
+      "Licensor" shall mean the copyright owner or entity authorized by
+      the copyright owner that is granting the License.
+
+      "Legal Entity" shall mean the union of the acting entity and all
+      other entities that control, are controlled by, or are under common
+      control with that entity. For the purposes of this definition,
+      "control" means (i) the power, direct or indirect, to cause the
+      direction or management of such entity, whether by contract or
+      otherwise, or (ii) ownership of fifty percent (50%) or more of the
+      outstanding shares, or (iii) beneficial ownership of such entity.
+
+      "You" (or "Your") shall mean an individual or Legal Entity
+      exercising permissions granted by this License.
+
+      "Source" form shall mean the preferred form for making modifications,
+      including but not limited to software source code, documentation
+      source, and configuration files.
+
+      "Object" form shall mean any form resulting from mechanical
+      transformation or translation of a Source form, including but
+      not limited to compiled object code, generated documentation,
+      and conversions to other media types.
+
+      "Work" shall mean the work of authorship, whether in Source or
+      Object form, made available under the License, as indicated by a
+      copyright notice that is included in or attached to the work
+      (an example is provided in the Appendix below).
+
+      "Derivative Works" shall mean any work, whether in Source or Object
+      form, that is based on (or derived from) the Work and for which the
+      editorial revisions, annotations, elaborations, or other modifications
+      represent, as a whole, an original work of authorship. For the purposes
+      of this License, Derivative Works shall not include works that remain
+      separable from, or merely link (or bind by name) to the interfaces of,
+      the Work and Derivative Works thereof.
+
+      "Contribution" shall mean any work of authorship, including
+      the original version of the Work and any modifications or additions
+      to that Work or Derivative Works thereof, that is intentionally
+      submitted to Licensor for inclusion in the Work by the copyright owner
+      or by an individual or Legal Entity authorized to submit on behalf of
+      the copyright owner. For the purposes of this definition, "submitted"
+      means any form of electronic, verbal, or written communication sent
+      to the Licensor or its representatives, including but not limited to
+      communication on electronic mailing lists, source code control systems,
+      and issue tracking systems that are managed by, or on behalf of, the
+      Licensor for the purpose of discussing and improving the Work, but
+      excluding communication that is conspicuously marked or otherwise
+      designated in writing by the copyright owner as "Not a Contribution."
+
+      "Contributor" shall mean Licensor and any individual or Legal Entity
+      on behalf of whom a Contribution has been received by Licensor and
+      subsequently incorporated within the Work.
+
+   2. Grant of Copyright License. Subject to the terms and conditions of
+      this License, each Contributor hereby grants to You a perpetual,
+      worldwide, non-exclusive, no-charge, royalty-free, irrevocable
+      copyright license to reproduce, prepare Derivative Works of,
+      publicly display, publicly perform, sublicense, and distribute the
+      Work and such Derivative Works in Source or Object form.
+
+   3. Grant of Patent License. Subject to the terms and conditions of
+      this License, each Contributor hereby grants to You a perpetual,
+      worldwide, non-exclusive, no-charge, royalty-free, irrevocable
+      (except as stated in this section) patent license to make, have made,
+      use, offer to sell, sell, import, and otherwise transfer the Work,
+      where such license applies only to those patent claims licensable
+      by such Contributor that are necessarily infringed by their
+      Contribution(s) alone or by combination of their Contribution(s)
+      with the Work to which such Contribution(s) was submitted. If You
+      institute patent litigation against any entity (including a
+      cross-claim or counterclaim in a lawsuit) alleging that the Work
+      or a Contribution incorporated within the Work constitutes direct
+      or contributory patent infringement, then any patent licenses
+      granted to You under this License for that Work shall terminate
+      as of the date such litigation is filed.
+
+   4. Redistribution. You may reproduce and distribute copies of the
+      Work or Derivative Works thereof in any medium, with or without
+      modifications, and in Source or Object form, provided that You
+      meet the following conditions:
+
+      (a) You must give any other recipients of the Work or
+          Derivative Works a copy of this License; and
+
+      (b) You must cause any modified files to carry prominent notices
+          stating that You changed the files; and
+
+      (c) You must retain, in the Source form of any Derivative Works
+          that You distribute, all copyright, patent, trademark, and
+          attribution notices from the Source form of the Work,
+          excluding those notices that do not pertain to any part of
+          the Derivative Works; and
+
+      (d) If the Work includes a "NOTICE" text file as part of its
+          distribution, then any Derivative Works that You distribute must
+          include a readable copy of the attribution notices contained
+          within such NOTICE file, excluding those notices that do not
+          pertain to any part of the Derivative Works, in at least one
+          of the following places: within a NOTICE text file distributed
+          as part of the Derivative Works; within the Source form or
+          documentation, if provided along with the Derivative Works; or,
+          within a display generated by the Derivative Works, if and
+          wherever such third-party notices normally appear. The contents
+          of the NOTICE file are for informational purposes only and
+          do not modify the License. You may add Your own attribution
+          notices within Derivative Works that You distribute, alongside
+          or as an addendum to the NOTICE text from the Work, provided
+          that such additional attribution notices cannot be construed
+          as modifying the License.
+
+      You may add Your own copyright statement to Your modifications and
+      may provide additional or different license terms and conditions
+      for use, reproduction, or distribution of Your modifications, or
+      for any such Derivative Works as a whole, provided Your use,
+      reproduction, and distribution of the Work otherwise complies with
+      the conditions stated in this License.
+
+   5. Submission of Contributions. Unless You explicitly state otherwise,
+      any Contribution intentionally submitted for inclusion in the Work
+      by You to the Licensor shall be under the terms and conditions of
+      this License, without any additional terms or conditions.
+      Notwithstanding the above, nothing herein shall supersede or modify
+      the terms of any separate license agreement you may have executed
+      with Licensor regarding such Contributions.
+
+   6. Trademarks. This License does not grant permission to use the trade
+      names, trademarks, service marks, or product names of the Licensor,
+      except as required for reasonable and customary use in describing the
+      origin of the Work and reproducing the content of the NOTICE file.
+
+   7. Disclaimer of Warranty. Unless required by applicable law or
+      agreed to in writing, Licensor provides the Work (and each
+      Contributor provides its Contributions) on an "AS IS" BASIS,
+      WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or
+      implied, including, without limitation, any warranties or conditions
+      of TITLE, NON-INFRINGEMENT, MERCHANTABILITY, or FITNESS FOR A
+      PARTICULAR PURPOSE. You are solely responsible for determining the
+      appropriateness of using or redistributing the Work and assume any
+      risks associated with Your exercise of permissions under this License.
+
+   8. Limitation of Liability. In no event and under no legal theory,
+      whether in tort (including negligence), contract, or otherwise,
+      unless required by applicable law (such as deliberate and grossly
+      negligent acts) or agreed to in writing, shall any Contributor be
+      liable to You for damages, including any direct, indirect, special,
+      incidental, or consequential damages of any character arising as a
+      result of this License or out of the use or inability to use the
+      Work (including but not limited to damages for loss of goodwill,
+      work stoppage, computer failure or malfunction, or any and all
+      other commercial damages or losses), even if such Contributor
+      has been advised of the possibility of such damages.
+
+   9. Accepting Warranty or Additional Liability. While redistributing
+      the Work or Derivative Works thereof, You may choose to offer,
+      and charge a fee for, acceptance of support, warranty, indemnity,
+      or other liability obligations and/or rights consistent with this
+      License. However, in accepting such obligations, You may act only
+      on Your own behalf and on Your sole responsibility, not on behalf
+      of any other Contributor, and only if You agree to indemnify,
+      defend, and hold each Contributor harmless for any liability
+      incurred by, or claims asserted against, such Contributor by reason
+      of your accepting any such warranty or additional liability.
+
+   END OF TERMS AND CONDITIONS
+
+   APPENDIX: How to apply the Apache License to your work.
+
+      To apply the Apache License to your work, attach the following
+      boilerplate notice, with the fields enclosed by brackets "[]"
+      replaced with your own identifying information. (Don't include
+      the brackets!)  The text should be enclosed in the appropriate
+      comment syntax for the file format. We also recommend that a
+      file or class name and description of purpose be included on the
+      same "printed page" as the copyright notice for easier
+      identification within third-party archives.
+
+   Copyright [yyyy] [name of copyright owner]
+
+   Licensed under the Apache License, Version 2.0 (the "License");
+   you may not use this file except in compliance with the License.
+   You may obtain a copy of the License at
+
+       http://www.apache.org/licenses/LICENSE-2.0
+
+   Unless required by applicable law or agreed to in writing, software
+   distributed under the License is distributed on an "AS IS" BASIS,
+   WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+   See the License for the specific language governing permissions and
+   limitations under the License.

models/brats_mri_axial_slices_generative_diffusion/configs/inference.json

@@ -0,0 +1,108 @@
+{
+    "imports": [
+        "$import torch",
+        "$from datetime import datetime",
+        "$from pathlib import Path",
+        "$from PIL import Image",
+        "$from scripts.utils import visualize_2d_image"
+    ],
+    "bundle_root": ".",
+    "model_dir": "$@bundle_root + '/models'",
+    "output_dir": "$@bundle_root + '/output'",
+    "create_output_dir": "$Path(@output_dir).mkdir(exist_ok=True)",
+    "device": "$torch.device('cuda:0' if torch.cuda.is_available() else 'cpu')",
+    "output_postfix": "$datetime.now().strftime('sample_%Y%m%d_%H%M%S')",
+    "channel": 0,
+    "spatial_dims": 2,
+    "image_channels": 1,
+    "latent_channels": 1,
+    "latent_shape": [
+        "@latent_channels",
+        64,
+        64
+    ],
+    "autoencoder_def": {
+        "_target_": "generative.networks.nets.AutoencoderKL",
+        "spatial_dims": "@spatial_dims",
+        "in_channels": "@image_channels",
+        "out_channels": "@image_channels",
+        "latent_channels": "@latent_channels",
+        "num_channels": [
+            64,
+            128,
+            256
+        ],
+        "num_res_blocks": 2,
+        "norm_num_groups": 32,
+        "norm_eps": 1e-06,
+        "attention_levels": [
+            false,
+            false,
+            false
+        ],
+        "with_encoder_nonlocal_attn": true,
+        "with_decoder_nonlocal_attn": true
+    },
+    "network_def": {
+        "_target_": "generative.networks.nets.DiffusionModelUNet",
+        "spatial_dims": "@spatial_dims",
+        "in_channels": "@latent_channels",
+        "out_channels": "@latent_channels",
+        "num_channels": [
+            32,
+            64,
+            128,
+            256
+        ],
+        "attention_levels": [
+            false,
+            true,
+            true,
+            true
+        ],
+        "num_head_channels": [
+            0,
+            32,
+            32,
+            32
+        ],
+        "num_res_blocks": 2
+    },
+    "load_autoencoder_path": "$@bundle_root + '/models/model_autoencoder.pt'",
+    "load_autoencoder": "$@autoencoder_def.load_state_dict(torch.load(@load_autoencoder_path))",
+    "autoencoder": "$@autoencoder_def.to(@device)",
+    "load_diffusion_path": "$@model_dir + '/model.pt'",
+    "load_diffusion": "$@network_def.load_state_dict(torch.load(@load_diffusion_path))",
+    "diffusion": "$@network_def.to(@device)",
+    "noise_scheduler": {
+        "_target_": "generative.networks.schedulers.DDIMScheduler",
+        "_requires_": [
+            "@load_diffusion",
+            "@load_autoencoder"
+        ],
+        "num_train_timesteps": 1000,
+        "beta_start": 0.0015,
+        "beta_end": 0.0195,
+        "beta_schedule": "scaled_linear",
+        "clip_sample": false
+    },
+    "noise": "$torch.randn([1]+@latent_shape).to(@device)",
+    "set_timesteps": "$@noise_scheduler.set_timesteps(num_inference_steps=50)",
+    "inferer": {
+        "_target_": "scripts.ldm_sampler.LDMSampler",
+        "_requires_": "@set_timesteps"
+    },
+    "sample": "[email protected]_fn(@noise, @autoencoder, @diffusion, @noise_scheduler)",
+    "saver": {
+        "_target_": "SaveImage",
+        "_requires_": "@create_output_dir",
+        "output_dir": "@output_dir",
+        "output_postfix": "@output_postfix"
+    },
+    "generated_image": "$@sample",
+    "generated_image_np": "$@generated_image[0,0].cpu().numpy().transpose(1, 0)[::-1, ::-1]",
+    "img_pil": "$Image.fromarray(visualize_2d_image(@generated_image_np), 'RGB')",
+    "run": [
+        "$@img_pil.save(@output_dir+'/synimg_'+@output_postfix+'.png')"
+    ]
+}