lyroi 0.1.0__tar.gz

lyroi-0.1.0/LICENSE

@@ -0,0 +1,201 @@
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lyroi-0.1.0/PKG-INFO

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+Metadata-Version: 2.4
+Name: lyroi
+Version: 0.1.0
+Summary: LyROI - nnU-Net-based Lymphoma Total Metabolic Tumor Volume Segmentation
+Author-email: Pavel Nikulin <p.nikulin@hzdr.de>, Jens Maus <j.maus@hzdr.de>
+License-Expression: Apache-2.0
+Project-URL: Homepage, https://github.com/hzdr-MedImaging/LyROI
+Project-URL: Documentation, https://github.com/hzdr-MedImaging/LyROI/blob/main/README.md
+Project-URL: Source, https://github.com/hzdr-MedImaging/LyROI
+Keywords: deep learning,ai,lymphoma,pet,petct,tmtv,mtv,nnunet,lyroi,delineations,segmentation,cancer
+Classifier: Development Status :: 3 - Alpha
+Classifier: Intended Audience :: Developers
+Classifier: Intended Audience :: Science/Research
+Classifier: Intended Audience :: Healthcare Industry
+Classifier: Programming Language :: Python :: 3
+Classifier: Operating System :: Unix
+Classifier: Topic :: Scientific/Engineering :: Artificial Intelligence
+Classifier: Topic :: Scientific/Engineering :: Image Recognition
+Classifier: Topic :: Scientific/Engineering :: Medical Science Apps.
+Requires-Python: >=3.9
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: torch>=2.1.2
+Requires-Dist: numpy
+Requires-Dist: acvl-utils==0.2
+Requires-Dist: nnunetv2>=2.5.2
+Requires-Dist: requests
+Requires-Dist: nibabel
+Requires-Dist: packaging
+Requires-Dist: psutil
+Dynamic: license-file
+
+# LyROI – nnU-Net-based Lymphoma Total Metabolic Tumor Volume Delineation
+
+> [!IMPORTANT]
+> **Regulatory status:** This software and the bundled model are intended **solely for research and development (R&D)**.
+> They are **not** intended for primary diagnosis, therapy, or any other clinical decision-making and must **not** be used
+> as a medical device.
+
+## Overview
+
+**Ly**mphoma **ROI** prediction framework (**LyROI**) is a collection of neural network models and support tools for
+metabolic tumor volume delineation in (Non-Hodgkin) lymphoma patients in FDG-PET/CT images.
+
+A comprehensive description of development and evaluation of the models is given in the respective [paper](DOI:XXX).
+Briefly, the models were trained with the [nnU-Net](https://github.com/MIC-DKFZ/nnUNet) software package. A total of
+1192 FDG-PET/CT scans from 716 patients with Non-Hodgkin
+lymphoma participating in the [PETAL](https://doi.org/10.1200/jco.2017.76.8093) trial comprised the training dataset.
+The ground truth delineation included all lesions (irrespective of size or uptake) that were clinically considered as
+lymphoma manifestations by an experienced observer. It was developed iteratively with the assistance of intermediate CNN
+models. Accurate contouring of each lesion was achieved by selecting the most appropriate semi-automated delineation
+algorithm, manually adjusting its settings, and performing manual corrections when necessary.
+
+Training and testing were performed following a 5-fold cross-validation scheme. Three configurations of the nnU-Net were
+used for training: regular U-Net, residual encoder U-Net (8 GB GPU memory target), and large residual encoder U-Net
+(24 GB GPU memory target).
+They can be installed as described below and used separately, however, their use in an ensemble (merging individual
+outputs via union operation) is recommended to maximize lesion detection sensitivity.
+
+The collection of the trained models can be found here:
+
+[![DOI: 10.14278/rodare.4160](https://zenodo.org/badge/DOI/10.14278/rodare.4160.svg)](https://doi.org/10.14278/rodare.4160)
+
+List of available models:
+- `LyROI_Orig.zip`: regular U-Net
+- `LyROI_ResM.zip`: residual encoder U-Net (medium)
+- `LyROI_ResL.zip`: residual encoder U-Net (large)
+
+
+
+[Scripts](scripts/) subfolder
+provides example code snippets to execute the prediction with each model and merge the resulting delineations when using
+directly within existing nnU-Net installation. See [manual installation](#manual-installation-and-use) section for more
+details.
+For simplified workflow, LyROI is also available as a stand-alone tool, see [quick start](#quick-start) section for
+usage and installation instructions.
+
+Please cite [nnU-Net](https://www.nature.com/articles/s41592-020-01008-z) and the [following paper](DOI:XXX) when using
+LyROI:
+
+```
+XXX
+```
+
+Special thanks to the PETAL study group for the access to the [PETAL](https://doi.org/10.1200/jco.2017.76.8093) trial dataset
+for the network training and agreeing to share the resulting models.
+
+## Quick Start
+
+> [!IMPORTANT]
+> Working within a dedicated virtual environment (`venv` or `conda`) is highly recommended.
+
+> **Requirements**
+> - `python` (>= 3.9)
+> - [`pytorch`](https://pytorch.org/get-started/locally/) (>= 2.1.2)
+
+1. Install `python` and `pytorch` (see requirements list above).
+
+   **Note: As of now, torch >=2.9.0 leads to severe performance
+   reduction. Earlier versions are recommended.**
+2. Install `lyroi` as a package (recommended):
+   ```
+   pip install lyroi
+   ```
+   or as modifiable copy (for experienced users):
+   ```
+   git clone https://github.com/hzdr-MedImaging/LyROI.git
+   cd LyROI
+   pip install -e .
+   ```
+3. (OPTIONAL) To change the default model installation directory (default: `$HOME/.lyroi`), set the environment variable
+   `LYROI_DIR` to the desired location. See, e.g.
+   [here](https://www.freecodecamp.org/news/how-to-set-an-environment-variable-in-linux/) for guidance.
+4. Download and install the model files:
+    ```
+    lyroi_install
+    ```
+5. Run LyROI for
+    - all images in the `input_folder` (see [below](#data-format) for input data format) and output delineation in
+      `output_folder`:
+       ```
+       lyroi -i input_folder -o output_folder
+       ```
+    - a single patient with CT image `ct.nii.gz` and PET image `pet.nii.gz` (must be coregistered and have the same
+      matrix and voxel sizes) and output delineation to `roi.nii.gz`:
+      ```
+      lyroi -i ct.nii.gz pet.nii.gz -o roi.nii.gz
+      ```
+   Execution on a GPU-equipped workstation is highly recommended. In case if no GPU is available, use a flag `-d cpu` to force
+   run on CPU (can be **VERY** slow). Flag `-d cpu-max` can help with cpu performance by using all available
+   computational resources (may slow down other programs). `nnUNet_def_n_proc` environment variable can be set to limit
+   the number of utilized cpu cores in `cpu-max` mode.
+
+## Manual Installation and Use
+
+> **Requirements**
+> - `python` (>= 3.9)
+> - [`pytorch`](https://pytorch.org/get-started/locally/) (>= 2.1.2)
+> - [`nnU-Net`](https://github.com/MIC-DKFZ/nnUNet/blob/dev/documentation/installation_instructions.md) (>= 2.5.2)
+
+1. To download and install the models for each used nnU-Net configuration, execute:
+    ```
+    nnUNetv2_install_pretrained_model_from_zip https://rodare.hzdr.de/record/4177/files/LyROI_Orig.zip
+    nnUNetv2_install_pretrained_model_from_zip https://rodare.hzdr.de/record/4177/files/LyROI_ResM.zip
+    nnUNetv2_install_pretrained_model_from_zip https://rodare.hzdr.de/record/4177/files/LyROI_ResL.zip
+    ``` 
+2. By default, the models will be installed in the folder ``$nnUNet_results/Dataset001_LyROI/``. This might create
+   conflicts if you already have a project with the number 001 in your ``$nnUNet_results`` folder. In this case, please
+   choose an unoccupied index ``XXX`` for the dataset and rename the LyROI folder to ``DatasetXXX_LyROI``.
+3. Download all files in [scripts](scripts/) folder and put them in the same folder. If you changed the dataset index of
+   LyROI, edit the [predict.sh](scripts/predict.sh) file and change the ``dataset_id="001"`` line to
+   ``dataset_id="XXX"``, where XXX is the new dataset index you selected.
+4. Prepare the input data according to the instructions [below](#data-format).
+5. Execute ``./predict.sh /path/to/your/folder/input_folder`` and wait for the process to complete. The resulting
+   delineations can be found in ``input_folder/pred/`` subfolder. If you want to keep the outputs of the intermediate
+   networks, comment out the last line in [predict.sh](scripts/predict.sh). Execution on a GPU-equipped workstation is
+   highly recommended. In case if no GPU is available, add a flag `-device cpu` to `nnUNetv2_predict` calls within the
+   script (can be **VERY** slow). Set `nnUNet_def_n_proc` environment variable to specify the number of cpu cores to use
+   for inference (set to the number of physical cpu cores for max performance).
+
+## Data Format
+
+The input data for batch processing should be presented in the nnU-Net compatible format
+(see [here](https://github.com/MIC-DKFZ/nnUNet/blob/master/documentation/dataset_format_inference.md) for details).
+Only compressed NIfTI (`.nii.gz`) images are currently supported. Corresponding CT and PET volumes must be coregistered
+and have the same matrix and voxel sizes.
+
+Input channels:
+- `0000` is CT
+- `0001` is PET
+
+Here is an example of how the input folder can look like:
+
+```
+input_folder
+      ├── lymph_20250101_0000.nii.gz
+      ├── lymph_20250101_0001.nii.gz
+      ├── pat01_0000.nii.gz
+      ├── pat01_0001.nii.gz
+      ├── rchop001_0000.nii.gz
+      ├── rchop001_0001.nii.gz
+      ├── ...
+```
+
+## Intended Purpose (Non-Medical)
+
+- The software is intended for **algorithmic research, benchmarking, and method exploration** in lymphoma delineation.
+- It is **not intended** to provide information for diagnostic or therapeutic purposes and **must not** be used in
+  clinical workflows.
+- Do **not** deploy or advertise this software as a medical product or service.
+
+## Disclaimer (Research Use Only – Not a Medical Device)
+
+This software and any bundled or referenced model weights are provided **exclusively for research and development
+purposes**. They are **not intended** for use in the diagnosis, cure, mitigation, treatment, or prevention of disease,
+or for any other clinical decision-making.
+
+- The software is **not** a medical device and is **not** CE-marked.
+- No clinical performance, safety, or effectiveness is claimed or implied.
+- Any results must not be used to guide patient management.
+- Users are responsible for compliance with all applicable laws, regulations, and data protection requirements when
+  processing data.
+
+THE SOFTWARE AND MODELS ARE PROVIDED “AS IS”, WITHOUT ANY WARRANTY, EXPRESS OR IMPLIED.
+
+## Licenses
+
+The **code** in this repository is licensed under **Apache-2.0** (see [`LICENSE`](LICENSE)).  
+The **model weights** are licensed under **CC-BY-SA-4.0** (see [`MODEL_LICENSE.md`](MODEL_LICENSE.md)).
+
+## Third-Party Licenses
+
+This project uses or interoperates with the following third-party components:
+
+- **nnU-Net v2** – Copyright © respective authors.
+    - License: **Apache-2.0**
+- **PyTorch**, **NumPy**, **Nibabel**, etc.
+    - Licensed under their respective open-source licenses.
+
+Each third-party component is the property of its respective owners and is provided under its own license terms. Copies
+of these licenses are available from the upstream projects.

lyroi-0.1.0/README.md

@@ -0,0 +1,189 @@
+# LyROI – nnU-Net-based Lymphoma Total Metabolic Tumor Volume Delineation
+
+> [!IMPORTANT]
+> **Regulatory status:** This software and the bundled model are intended **solely for research and development (R&D)**.
+> They are **not** intended for primary diagnosis, therapy, or any other clinical decision-making and must **not** be used
+> as a medical device.
+
+## Overview
+
+**Ly**mphoma **ROI** prediction framework (**LyROI**) is a collection of neural network models and support tools for
+metabolic tumor volume delineation in (Non-Hodgkin) lymphoma patients in FDG-PET/CT images.
+
+A comprehensive description of development and evaluation of the models is given in the respective [paper](DOI:XXX).
+Briefly, the models were trained with the [nnU-Net](https://github.com/MIC-DKFZ/nnUNet) software package. A total of
+1192 FDG-PET/CT scans from 716 patients with Non-Hodgkin
+lymphoma participating in the [PETAL](https://doi.org/10.1200/jco.2017.76.8093) trial comprised the training dataset.
+The ground truth delineation included all lesions (irrespective of size or uptake) that were clinically considered as
+lymphoma manifestations by an experienced observer. It was developed iteratively with the assistance of intermediate CNN
+models. Accurate contouring of each lesion was achieved by selecting the most appropriate semi-automated delineation
+algorithm, manually adjusting its settings, and performing manual corrections when necessary.
+
+Training and testing were performed following a 5-fold cross-validation scheme. Three configurations of the nnU-Net were
+used for training: regular U-Net, residual encoder U-Net (8 GB GPU memory target), and large residual encoder U-Net
+(24 GB GPU memory target).
+They can be installed as described below and used separately, however, their use in an ensemble (merging individual
+outputs via union operation) is recommended to maximize lesion detection sensitivity.
+
+The collection of the trained models can be found here:
+
+[![DOI: 10.14278/rodare.4160](https://zenodo.org/badge/DOI/10.14278/rodare.4160.svg)](https://doi.org/10.14278/rodare.4160)
+
+List of available models:
+- `LyROI_Orig.zip`: regular U-Net
+- `LyROI_ResM.zip`: residual encoder U-Net (medium)
+- `LyROI_ResL.zip`: residual encoder U-Net (large)
+
+
+
+[Scripts](scripts/) subfolder
+provides example code snippets to execute the prediction with each model and merge the resulting delineations when using
+directly within existing nnU-Net installation. See [manual installation](#manual-installation-and-use) section for more
+details.
+For simplified workflow, LyROI is also available as a stand-alone tool, see [quick start](#quick-start) section for
+usage and installation instructions.
+
+Please cite [nnU-Net](https://www.nature.com/articles/s41592-020-01008-z) and the [following paper](DOI:XXX) when using
+LyROI:
+
+```
+XXX
+```
+
+Special thanks to the PETAL study group for the access to the [PETAL](https://doi.org/10.1200/jco.2017.76.8093) trial dataset
+for the network training and agreeing to share the resulting models.
+
+## Quick Start
+
+> [!IMPORTANT]
+> Working within a dedicated virtual environment (`venv` or `conda`) is highly recommended.
+
+> **Requirements**
+> - `python` (>= 3.9)
+> - [`pytorch`](https://pytorch.org/get-started/locally/) (>= 2.1.2)
+
+1. Install `python` and `pytorch` (see requirements list above).
+
+   **Note: As of now, torch >=2.9.0 leads to severe performance
+   reduction. Earlier versions are recommended.**
+2. Install `lyroi` as a package (recommended):
+   ```
+   pip install lyroi
+   ```
+   or as modifiable copy (for experienced users):
+   ```
+   git clone https://github.com/hzdr-MedImaging/LyROI.git
+   cd LyROI
+   pip install -e .
+   ```
+3. (OPTIONAL) To change the default model installation directory (default: `$HOME/.lyroi`), set the environment variable
+   `LYROI_DIR` to the desired location. See, e.g.
+   [here](https://www.freecodecamp.org/news/how-to-set-an-environment-variable-in-linux/) for guidance.
+4. Download and install the model files:
+    ```
+    lyroi_install
+    ```
+5. Run LyROI for
+    - all images in the `input_folder` (see [below](#data-format) for input data format) and output delineation in
+      `output_folder`:
+       ```
+       lyroi -i input_folder -o output_folder
+       ```
+    - a single patient with CT image `ct.nii.gz` and PET image `pet.nii.gz` (must be coregistered and have the same
+      matrix and voxel sizes) and output delineation to `roi.nii.gz`:
+      ```
+      lyroi -i ct.nii.gz pet.nii.gz -o roi.nii.gz
+      ```
+   Execution on a GPU-equipped workstation is highly recommended. In case if no GPU is available, use a flag `-d cpu` to force
+   run on CPU (can be **VERY** slow). Flag `-d cpu-max` can help with cpu performance by using all available
+   computational resources (may slow down other programs). `nnUNet_def_n_proc` environment variable can be set to limit
+   the number of utilized cpu cores in `cpu-max` mode.
+
+## Manual Installation and Use
+
+> **Requirements**
+> - `python` (>= 3.9)
+> - [`pytorch`](https://pytorch.org/get-started/locally/) (>= 2.1.2)
+> - [`nnU-Net`](https://github.com/MIC-DKFZ/nnUNet/blob/dev/documentation/installation_instructions.md) (>= 2.5.2)
+
+1. To download and install the models for each used nnU-Net configuration, execute:
+    ```
+    nnUNetv2_install_pretrained_model_from_zip https://rodare.hzdr.de/record/4177/files/LyROI_Orig.zip
+    nnUNetv2_install_pretrained_model_from_zip https://rodare.hzdr.de/record/4177/files/LyROI_ResM.zip
+    nnUNetv2_install_pretrained_model_from_zip https://rodare.hzdr.de/record/4177/files/LyROI_ResL.zip
+    ``` 
+2. By default, the models will be installed in the folder ``$nnUNet_results/Dataset001_LyROI/``. This might create
+   conflicts if you already have a project with the number 001 in your ``$nnUNet_results`` folder. In this case, please
+   choose an unoccupied index ``XXX`` for the dataset and rename the LyROI folder to ``DatasetXXX_LyROI``.
+3. Download all files in [scripts](scripts/) folder and put them in the same folder. If you changed the dataset index of
+   LyROI, edit the [predict.sh](scripts/predict.sh) file and change the ``dataset_id="001"`` line to
+   ``dataset_id="XXX"``, where XXX is the new dataset index you selected.
+4. Prepare the input data according to the instructions [below](#data-format).
+5. Execute ``./predict.sh /path/to/your/folder/input_folder`` and wait for the process to complete. The resulting
+   delineations can be found in ``input_folder/pred/`` subfolder. If you want to keep the outputs of the intermediate
+   networks, comment out the last line in [predict.sh](scripts/predict.sh). Execution on a GPU-equipped workstation is
+   highly recommended. In case if no GPU is available, add a flag `-device cpu` to `nnUNetv2_predict` calls within the
+   script (can be **VERY** slow). Set `nnUNet_def_n_proc` environment variable to specify the number of cpu cores to use
+   for inference (set to the number of physical cpu cores for max performance).
+
+## Data Format
+
+The input data for batch processing should be presented in the nnU-Net compatible format
+(see [here](https://github.com/MIC-DKFZ/nnUNet/blob/master/documentation/dataset_format_inference.md) for details).
+Only compressed NIfTI (`.nii.gz`) images are currently supported. Corresponding CT and PET volumes must be coregistered
+and have the same matrix and voxel sizes.
+
+Input channels:
+- `0000` is CT
+- `0001` is PET
+
+Here is an example of how the input folder can look like:
+
+```
+input_folder
+      ├── lymph_20250101_0000.nii.gz
+      ├── lymph_20250101_0001.nii.gz
+      ├── pat01_0000.nii.gz
+      ├── pat01_0001.nii.gz
+      ├── rchop001_0000.nii.gz
+      ├── rchop001_0001.nii.gz
+      ├── ...
+```
+
+## Intended Purpose (Non-Medical)
+
+- The software is intended for **algorithmic research, benchmarking, and method exploration** in lymphoma delineation.
+- It is **not intended** to provide information for diagnostic or therapeutic purposes and **must not** be used in
+  clinical workflows.
+- Do **not** deploy or advertise this software as a medical product or service.
+
+## Disclaimer (Research Use Only – Not a Medical Device)
+
+This software and any bundled or referenced model weights are provided **exclusively for research and development
+purposes**. They are **not intended** for use in the diagnosis, cure, mitigation, treatment, or prevention of disease,
+or for any other clinical decision-making.
+
+- The software is **not** a medical device and is **not** CE-marked.
+- No clinical performance, safety, or effectiveness is claimed or implied.
+- Any results must not be used to guide patient management.
+- Users are responsible for compliance with all applicable laws, regulations, and data protection requirements when
+  processing data.
+
+THE SOFTWARE AND MODELS ARE PROVIDED “AS IS”, WITHOUT ANY WARRANTY, EXPRESS OR IMPLIED.
+
+## Licenses
+
+The **code** in this repository is licensed under **Apache-2.0** (see [`LICENSE`](LICENSE)).  
+The **model weights** are licensed under **CC-BY-SA-4.0** (see [`MODEL_LICENSE.md`](MODEL_LICENSE.md)).
+
+## Third-Party Licenses
+
+This project uses or interoperates with the following third-party components:
+
+- **nnU-Net v2** – Copyright © respective authors.
+    - License: **Apache-2.0**
+- **PyTorch**, **NumPy**, **Nibabel**, etc.
+    - Licensed under their respective open-source licenses.
+
+Each third-party component is the property of its respective owners and is provided under its own license terms. Copies
+of these licenses are available from the upstream projects.

lyroi-0.1.0/lyroi/__init__.py

@@ -0,0 +1,41 @@
+from datetime import datetime
+from importlib.metadata import version, PackageNotFoundError, metadata
+import re
+import sys
+import signal
+
+__package__ = "lyroi"
+creation_date = datetime(2025, 11, 26)
+
+try:
+    __version__ = version(__package__)
+except PackageNotFoundError:
+    __version__ = "0.0.0"
+
+meta = metadata(__package__)
+email_list = meta.get("Author-email", "")
+author_str = re.sub(r"<[^>]*>", "", email_list).strip()
+now_date = datetime.now()
+date_str = now_date.strftime("%Y") if creation_date.year == now_date.year else creation_date.strftime("%Y") + "-" + now_date.strftime("%Y")
+__copyright__ = "Copyright (c) " + date_str + " " + author_str + ", www.hzdr.de"
+__license__ = meta.get("License-Expression")
+
+__legal__ = ("Disclaimer:\n"
+            "This software is intended for research use only.\n"
+            "It is not a medical device and must not be used for clinical decisions.\n\n"
+            f"{__package__} {__version__}\n"
+            f"{__copyright__}\n"
+            f"License: {__license__}; models are licensed separately")
+
+def error_handler(exctype, value, traceback):
+  print()
+  print("Error:", value, file=sys.stderr)
+  sys.exit(1)
+
+def exit_handler(signal, frame):
+  print()
+  print("User abort (CTRL-C) received.")
+  sys.exit(0)
+
+signal.signal(signal.SIGINT, exit_handler)
+sys.excepthook = error_handler