Restructuring (initialized one directory up)

adgilbert · Nov 23, 2020 · 27d02ab · 27d02ab
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diff --git a/public-segmentation/.gitignore → .gitignore b/public-segmentation/.gitignore → .gitignore
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 *.pyc
-../
 .idea
diff --git a/public-segmentation/LICENSE → LICENSE b/public-segmentation/LICENSE → LICENSE
diff --git a/README.md b/README.md
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-# med-seg
+# Medical Segmentation
+
+![SegTask](docs/seg_task.png)
+
+A repository for training segmentation algorithms for medical images. This repository is primarily developed for 
+segmentation of apical four and two chamber echocardiography images like those from the 
+[Camus](https://www.creatis.insa-lyon.fr/Challenge/camus/) and 
+[EchoNet](https://echonet.github.io/dynamic/) datasets as well as other data with similar structure. 
+
+
+## Install 
+
+Clone this repo, create a new environment and install requirements using `pip install -r requirements.txt`
+
+
+## Training
+
+Use [train.py](train.py) to train a new model.
+
+Run `python train.py -h` to see all available options (defined in [base_options](options/base_options.py) and 
+[train_options](options/train_options.py)).
+
+The main options that need to be defined are:
+- **dataroot**: the path to the data. This should be a directory with subfolders for each phase. At least "train" and 
+ "val" and optionally other phases (e.g. "test"). Within each phase folder should be a "images" folder and a "labels"
+ folder. Each of these should contain pngs which have each training sample. The filenames in each directory should 
+ match.
+- **name**: The name of this training run.
+- **experiment**: The experiment to group this run into.
+
+See the provided help string for information on other options.
+
+## Inference
+
+Use [inference.py](inference.py) to evaluate a trained model. 
+
+Run `python inference.py -h` to see available options. The main options match those above.
+
+
+## Notes
+
+Some parts of the code are specifically adapted for apical segmentation of the left ventricle
+ (e.g. the [metrics](evaluators/__init__.py)) which assume 
+specific regions are associated with specific classes. These will need to be updated for a new segmentation task. 
+
+Some of the structure/code from this repository is based on 
+[CycleGAN_and_pix2pix](https://github.com/junyanz/pytorch-CycleGAN-and-pix2pix).
diff --git a/public-segmentation/datasets/__init__.py → datasets/__init__.py b/public-segmentation/datasets/__init__.py → datasets/__init__.py
diff --git a/...mentation/datasets/adversarial_dataset.py → datasets/adversarial_dataset.py b/...mentation/datasets/adversarial_dataset.py → datasets/adversarial_dataset.py
diff --git a/public-segmentation/datasets/base_dataset.py → datasets/base_dataset.py b/public-segmentation/datasets/base_dataset.py → datasets/base_dataset.py
diff --git a/public-segmentation/datasets/image_folder.py → datasets/image_folder.py b/public-segmentation/datasets/image_folder.py → datasets/image_folder.py
diff --git a/...ic-segmentation/datasets/infer_dataset.py → datasets/infer_dataset.py b/...ic-segmentation/datasets/infer_dataset.py → datasets/infer_dataset.py
diff --git a/...entation/datasets/segmentation_dataset.py → datasets/segmentation_dataset.py b/...entation/datasets/segmentation_dataset.py → datasets/segmentation_dataset.py
diff --git a/...ation/datasets/segmentation_transforms.py → datasets/segmentation_transforms.py b/...ation/datasets/segmentation_transforms.py → datasets/segmentation_transforms.py
diff --git a/public-segmentation/docs/seg_task.png → docs/seg_task.png b/public-segmentation/docs/seg_task.png → docs/seg_task.png
diff --git a/public-segmentation/evaluate.py → evaluate.py b/public-segmentation/evaluate.py → evaluate.py
diff --git a/.../evaluators/Curvature/LV_mask_analysis.py → evaluators/Curvature/LV_mask_analysis.py b/.../evaluators/Curvature/LV_mask_analysis.py → evaluators/Curvature/LV_mask_analysis.py
diff --git a/...entation/evaluators/Curvature/__init__.py → evaluators/Curvature/__init__.py b/...entation/evaluators/Curvature/__init__.py → evaluators/Curvature/__init__.py
diff --git a/...aluators/Curvature/_io_data_generation.py → evaluators/Curvature/_io_data_generation.py b/...aluators/Curvature/_io_data_generation.py → evaluators/Curvature/_io_data_generation.py
diff --git a/...ation/evaluators/Curvature/alternative.py → evaluators/Curvature/alternative.py b/...ation/evaluators/Curvature/alternative.py → evaluators/Curvature/alternative.py
diff --git a/...ntation/evaluators/Curvature/curvature.py → evaluators/Curvature/curvature.py b/...ntation/evaluators/Curvature/curvature.py → evaluators/Curvature/curvature.py
diff --git a/...ion/evaluators/Curvature/graph_sorting.py → evaluators/Curvature/graph_sorting.py b/...ion/evaluators/Curvature/graph_sorting.py → evaluators/Curvature/graph_sorting.py
diff --git a/...luators/Curvature/read_frames_from_avi.py → evaluators/Curvature/read_frames_from_avi.py b/...luators/Curvature/read_frames_from_avi.py → evaluators/Curvature/read_frames_from_avi.py
diff --git a/...ators/Curvature/single_mask_processing.py → ...ators/Curvature/single_mask_processing.py b/...ators/Curvature/single_mask_processing.py → ...ators/Curvature/single_mask_processing.py
diff --git a/public-segmentation/evaluators/__init__.py → evaluators/__init__.py b/public-segmentation/evaluators/__init__.py → evaluators/__init__.py
diff --git a/public-segmentation/evaluators/confidence.py → evaluators/confidence.py b/public-segmentation/evaluators/confidence.py → evaluators/confidence.py
diff --git a/public-segmentation/evaluators/loss.py → evaluators/loss.py b/public-segmentation/evaluators/loss.py → evaluators/loss.py
diff --git a/public-segmentation/evaluators/metrics.py → evaluators/metrics.py b/public-segmentation/evaluators/metrics.py → evaluators/metrics.py
diff --git a/...tion/evaluators/weighted_cross_entropy.py → evaluators/weighted_cross_entropy.py b/...tion/evaluators/weighted_cross_entropy.py → evaluators/weighted_cross_entropy.py
diff --git a/public-segmentation/inference.py → inference.py b/public-segmentation/inference.py → inference.py
diff --git a/public-segmentation/models/__init__.py → models/__init__.py b/public-segmentation/models/__init__.py → models/__init__.py
diff --git a/public-segmentation/models/coordconv.py → models/coordconv.py b/public-segmentation/models/coordconv.py → models/coordconv.py
diff --git a/public-segmentation/models/net.py → models/net.py b/public-segmentation/models/net.py → models/net.py
diff --git a/public-segmentation/models/resnet.py → models/resnet.py b/public-segmentation/models/resnet.py → models/resnet.py
diff --git a/public-segmentation/models/unet.py → models/unet.py b/public-segmentation/models/unet.py → models/unet.py
diff --git a/public-segmentation/options/__init__.py → options/__init__.py b/public-segmentation/options/__init__.py → options/__init__.py
diff --git a/public-segmentation/options/base_options.py → options/base_options.py b/public-segmentation/options/base_options.py → options/base_options.py
diff --git a/public-segmentation/options/test_options.py → options/test_options.py b/public-segmentation/options/test_options.py → options/test_options.py
diff --git a/public-segmentation/options/train_options.py → options/train_options.py b/public-segmentation/options/train_options.py → options/train_options.py
diff --git a/public-segmentation/README.md b/public-segmentation/README.md
diff --git a/public-segmentation/requirements.txt → requirements.txt b/public-segmentation/requirements.txt → requirements.txt
diff --git a/...entation/scripts/calc_dataset_mean_std.py → scripts/calc_dataset_mean_std.py b/...entation/scripts/calc_dataset_mean_std.py → scripts/calc_dataset_mean_std.py
diff --git a/public-segmentation/scripts/network_stats.py → scripts/network_stats.py b/public-segmentation/scripts/network_stats.py → scripts/network_stats.py
diff --git a/public-segmentation/seg_utils/__init__.py → seg_utils/__init__.py b/public-segmentation/seg_utils/__init__.py → seg_utils/__init__.py
diff --git a/...mentation/seg_utils/post_process_masks.py → seg_utils/post_process_masks.py b/...mentation/seg_utils/post_process_masks.py → seg_utils/post_process_masks.py
diff --git a/public-segmentation/seg_utils/utils.py → seg_utils/utils.py b/public-segmentation/seg_utils/utils.py → seg_utils/utils.py
diff --git a/public-segmentation/seg_utils/visualizer.py → seg_utils/visualizer.py b/public-segmentation/seg_utils/visualizer.py → seg_utils/visualizer.py
diff --git a/public-segmentation/train.py → train.py b/public-segmentation/train.py → train.py
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