From 27d02ab3b98b04ee112c8fa5e734415e946efd20 Mon Sep 17 00:00:00 2001
From: "Gilbert, Andrew" <andrew.gilbert@ge.com>
Date: Mon, 23 Nov 2020 20:09:58 +0100
Subject: [PATCH] Restructuring (initialized one directory up)

---
 public-segmentation/.gitignore => .gitignore  |   1 -
 public-segmentation/LICENSE => LICENSE        |   0
 README.md                                     |  48 +++++++++++++++++-
 .../datasets => datasets}/__init__.py         |   0
 .../adversarial_dataset.py                    |   0
 .../datasets => datasets}/base_dataset.py     |   0
 .../datasets => datasets}/image_folder.py     |   0
 .../datasets => datasets}/infer_dataset.py    |   0
 .../segmentation_dataset.py                   |   0
 .../segmentation_transforms.py                |   0
 .../docs => docs}/seg_task.png                | Bin
 .../evaluate.py => evaluate.py                |   0
 .../Curvature/LV_mask_analysis.py             |   0
 .../Curvature/__init__.py                     |   0
 .../Curvature/_io_data_generation.py          |   0
 .../Curvature/alternative.py                  |   0
 .../Curvature/curvature.py                    |   0
 .../Curvature/graph_sorting.py                |   0
 .../Curvature/read_frames_from_avi.py         |   0
 .../Curvature/single_mask_processing.py       |   0
 .../evaluators => evaluators}/__init__.py     |   0
 .../evaluators => evaluators}/confidence.py   |   0
 .../evaluators => evaluators}/loss.py         |   0
 .../evaluators => evaluators}/metrics.py      |   0
 .../weighted_cross_entropy.py                 |   0
 .../inference.py => inference.py              |   0
 .../models => models}/__init__.py             |   0
 .../models => models}/coordconv.py            |   0
 {public-segmentation/models => models}/net.py |   0
 .../models => models}/resnet.py               |   0
 .../models => models}/unet.py                 |   0
 .../options => options}/__init__.py           |   0
 .../options => options}/base_options.py       |   0
 .../options => options}/test_options.py       |   0
 .../options => options}/train_options.py      |   0
 public-segmentation/README.md                 |  47 -----------------
 .../requirements.txt => requirements.txt      |   0
 .../calc_dataset_mean_std.py                  |   0
 .../scripts => scripts}/network_stats.py      |   0
 .../seg_utils => seg_utils}/__init__.py       |   0
 .../post_process_masks.py                     |   0
 .../seg_utils => seg_utils}/utils.py          |   0
 .../seg_utils => seg_utils}/visualizer.py     |   0
 public-segmentation/train.py => train.py      |   0
 44 files changed, 47 insertions(+), 49 deletions(-)
 rename public-segmentation/.gitignore => .gitignore (73%)
 rename public-segmentation/LICENSE => LICENSE (100%)
 rename {public-segmentation/datasets => datasets}/__init__.py (100%)
 rename {public-segmentation/datasets => datasets}/adversarial_dataset.py (100%)
 rename {public-segmentation/datasets => datasets}/base_dataset.py (100%)
 rename {public-segmentation/datasets => datasets}/image_folder.py (100%)
 rename {public-segmentation/datasets => datasets}/infer_dataset.py (100%)
 rename {public-segmentation/datasets => datasets}/segmentation_dataset.py (100%)
 rename {public-segmentation/datasets => datasets}/segmentation_transforms.py (100%)
 rename {public-segmentation/docs => docs}/seg_task.png (100%)
 rename public-segmentation/evaluate.py => evaluate.py (100%)
 rename {public-segmentation/evaluators => evaluators}/Curvature/LV_mask_analysis.py (100%)
 rename {public-segmentation/evaluators => evaluators}/Curvature/__init__.py (100%)
 rename {public-segmentation/evaluators => evaluators}/Curvature/_io_data_generation.py (100%)
 rename {public-segmentation/evaluators => evaluators}/Curvature/alternative.py (100%)
 rename {public-segmentation/evaluators => evaluators}/Curvature/curvature.py (100%)
 rename {public-segmentation/evaluators => evaluators}/Curvature/graph_sorting.py (100%)
 rename {public-segmentation/evaluators => evaluators}/Curvature/read_frames_from_avi.py (100%)
 rename {public-segmentation/evaluators => evaluators}/Curvature/single_mask_processing.py (100%)
 rename {public-segmentation/evaluators => evaluators}/__init__.py (100%)
 rename {public-segmentation/evaluators => evaluators}/confidence.py (100%)
 rename {public-segmentation/evaluators => evaluators}/loss.py (100%)
 rename {public-segmentation/evaluators => evaluators}/metrics.py (100%)
 rename {public-segmentation/evaluators => evaluators}/weighted_cross_entropy.py (100%)
 rename public-segmentation/inference.py => inference.py (100%)
 rename {public-segmentation/models => models}/__init__.py (100%)
 rename {public-segmentation/models => models}/coordconv.py (100%)
 rename {public-segmentation/models => models}/net.py (100%)
 rename {public-segmentation/models => models}/resnet.py (100%)
 rename {public-segmentation/models => models}/unet.py (100%)
 rename {public-segmentation/options => options}/__init__.py (100%)
 rename {public-segmentation/options => options}/base_options.py (100%)
 rename {public-segmentation/options => options}/test_options.py (100%)
 rename {public-segmentation/options => options}/train_options.py (100%)
 delete mode 100644 public-segmentation/README.md
 rename public-segmentation/requirements.txt => requirements.txt (100%)
 rename {public-segmentation/scripts => scripts}/calc_dataset_mean_std.py (100%)
 rename {public-segmentation/scripts => scripts}/network_stats.py (100%)
 rename {public-segmentation/seg_utils => seg_utils}/__init__.py (100%)
 rename {public-segmentation/seg_utils => seg_utils}/post_process_masks.py (100%)
 rename {public-segmentation/seg_utils => seg_utils}/utils.py (100%)
 rename {public-segmentation/seg_utils => seg_utils}/visualizer.py (100%)
 rename public-segmentation/train.py => train.py (100%)

diff --git a/public-segmentation/.gitignore b/.gitignore
similarity index 73%
rename from public-segmentation/.gitignore
rename to .gitignore
index 0a5f7de..b32d8aa 100644
--- a/public-segmentation/.gitignore
+++ b/.gitignore
@@ -1,3 +1,2 @@
 *.pyc
-../
 .idea
\ No newline at end of file
diff --git a/public-segmentation/LICENSE b/LICENSE
similarity index 100%
rename from public-segmentation/LICENSE
rename to LICENSE
diff --git a/README.md b/README.md
index 20e89c5..bb8c34e 100644
--- a/README.md
+++ b/README.md
@@ -1 +1,47 @@
-# 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).
\ No newline at end of file
diff --git a/public-segmentation/datasets/__init__.py b/datasets/__init__.py
similarity index 100%
rename from public-segmentation/datasets/__init__.py
rename to datasets/__init__.py
diff --git a/public-segmentation/datasets/adversarial_dataset.py b/datasets/adversarial_dataset.py
similarity index 100%
rename from public-segmentation/datasets/adversarial_dataset.py
rename to datasets/adversarial_dataset.py
diff --git a/public-segmentation/datasets/base_dataset.py b/datasets/base_dataset.py
similarity index 100%
rename from public-segmentation/datasets/base_dataset.py
rename to datasets/base_dataset.py
diff --git a/public-segmentation/datasets/image_folder.py b/datasets/image_folder.py
similarity index 100%
rename from public-segmentation/datasets/image_folder.py
rename to datasets/image_folder.py
diff --git a/public-segmentation/datasets/infer_dataset.py b/datasets/infer_dataset.py
similarity index 100%
rename from public-segmentation/datasets/infer_dataset.py
rename to datasets/infer_dataset.py
diff --git a/public-segmentation/datasets/segmentation_dataset.py b/datasets/segmentation_dataset.py
similarity index 100%
rename from public-segmentation/datasets/segmentation_dataset.py
rename to datasets/segmentation_dataset.py
diff --git a/public-segmentation/datasets/segmentation_transforms.py b/datasets/segmentation_transforms.py
similarity index 100%
rename from public-segmentation/datasets/segmentation_transforms.py
rename to datasets/segmentation_transforms.py
diff --git a/public-segmentation/docs/seg_task.png b/docs/seg_task.png
similarity index 100%
rename from public-segmentation/docs/seg_task.png
rename to docs/seg_task.png
diff --git a/public-segmentation/evaluate.py b/evaluate.py
similarity index 100%
rename from public-segmentation/evaluate.py
rename to evaluate.py
diff --git a/public-segmentation/evaluators/Curvature/LV_mask_analysis.py b/evaluators/Curvature/LV_mask_analysis.py
similarity index 100%
rename from public-segmentation/evaluators/Curvature/LV_mask_analysis.py
rename to evaluators/Curvature/LV_mask_analysis.py
diff --git a/public-segmentation/evaluators/Curvature/__init__.py b/evaluators/Curvature/__init__.py
similarity index 100%
rename from public-segmentation/evaluators/Curvature/__init__.py
rename to evaluators/Curvature/__init__.py
diff --git a/public-segmentation/evaluators/Curvature/_io_data_generation.py b/evaluators/Curvature/_io_data_generation.py
similarity index 100%
rename from public-segmentation/evaluators/Curvature/_io_data_generation.py
rename to evaluators/Curvature/_io_data_generation.py
diff --git a/public-segmentation/evaluators/Curvature/alternative.py b/evaluators/Curvature/alternative.py
similarity index 100%
rename from public-segmentation/evaluators/Curvature/alternative.py
rename to evaluators/Curvature/alternative.py
diff --git a/public-segmentation/evaluators/Curvature/curvature.py b/evaluators/Curvature/curvature.py
similarity index 100%
rename from public-segmentation/evaluators/Curvature/curvature.py
rename to evaluators/Curvature/curvature.py
diff --git a/public-segmentation/evaluators/Curvature/graph_sorting.py b/evaluators/Curvature/graph_sorting.py
similarity index 100%
rename from public-segmentation/evaluators/Curvature/graph_sorting.py
rename to evaluators/Curvature/graph_sorting.py
diff --git a/public-segmentation/evaluators/Curvature/read_frames_from_avi.py b/evaluators/Curvature/read_frames_from_avi.py
similarity index 100%
rename from public-segmentation/evaluators/Curvature/read_frames_from_avi.py
rename to evaluators/Curvature/read_frames_from_avi.py
diff --git a/public-segmentation/evaluators/Curvature/single_mask_processing.py b/evaluators/Curvature/single_mask_processing.py
similarity index 100%
rename from public-segmentation/evaluators/Curvature/single_mask_processing.py
rename to evaluators/Curvature/single_mask_processing.py
diff --git a/public-segmentation/evaluators/__init__.py b/evaluators/__init__.py
similarity index 100%
rename from public-segmentation/evaluators/__init__.py
rename to evaluators/__init__.py
diff --git a/public-segmentation/evaluators/confidence.py b/evaluators/confidence.py
similarity index 100%
rename from public-segmentation/evaluators/confidence.py
rename to evaluators/confidence.py
diff --git a/public-segmentation/evaluators/loss.py b/evaluators/loss.py
similarity index 100%
rename from public-segmentation/evaluators/loss.py
rename to evaluators/loss.py
diff --git a/public-segmentation/evaluators/metrics.py b/evaluators/metrics.py
similarity index 100%
rename from public-segmentation/evaluators/metrics.py
rename to evaluators/metrics.py
diff --git a/public-segmentation/evaluators/weighted_cross_entropy.py b/evaluators/weighted_cross_entropy.py
similarity index 100%
rename from public-segmentation/evaluators/weighted_cross_entropy.py
rename to evaluators/weighted_cross_entropy.py
diff --git a/public-segmentation/inference.py b/inference.py
similarity index 100%
rename from public-segmentation/inference.py
rename to inference.py
diff --git a/public-segmentation/models/__init__.py b/models/__init__.py
similarity index 100%
rename from public-segmentation/models/__init__.py
rename to models/__init__.py
diff --git a/public-segmentation/models/coordconv.py b/models/coordconv.py
similarity index 100%
rename from public-segmentation/models/coordconv.py
rename to models/coordconv.py
diff --git a/public-segmentation/models/net.py b/models/net.py
similarity index 100%
rename from public-segmentation/models/net.py
rename to models/net.py
diff --git a/public-segmentation/models/resnet.py b/models/resnet.py
similarity index 100%
rename from public-segmentation/models/resnet.py
rename to models/resnet.py
diff --git a/public-segmentation/models/unet.py b/models/unet.py
similarity index 100%
rename from public-segmentation/models/unet.py
rename to models/unet.py
diff --git a/public-segmentation/options/__init__.py b/options/__init__.py
similarity index 100%
rename from public-segmentation/options/__init__.py
rename to options/__init__.py
diff --git a/public-segmentation/options/base_options.py b/options/base_options.py
similarity index 100%
rename from public-segmentation/options/base_options.py
rename to options/base_options.py
diff --git a/public-segmentation/options/test_options.py b/options/test_options.py
similarity index 100%
rename from public-segmentation/options/test_options.py
rename to options/test_options.py
diff --git a/public-segmentation/options/train_options.py b/options/train_options.py
similarity index 100%
rename from public-segmentation/options/train_options.py
rename to options/train_options.py
diff --git a/public-segmentation/README.md b/public-segmentation/README.md
deleted file mode 100644
index bb8c34e..0000000
--- a/public-segmentation/README.md
+++ /dev/null
@@ -1,47 +0,0 @@
-# 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).
\ No newline at end of file
diff --git a/public-segmentation/requirements.txt b/requirements.txt
similarity index 100%
rename from public-segmentation/requirements.txt
rename to requirements.txt
diff --git a/public-segmentation/scripts/calc_dataset_mean_std.py b/scripts/calc_dataset_mean_std.py
similarity index 100%
rename from public-segmentation/scripts/calc_dataset_mean_std.py
rename to scripts/calc_dataset_mean_std.py
diff --git a/public-segmentation/scripts/network_stats.py b/scripts/network_stats.py
similarity index 100%
rename from public-segmentation/scripts/network_stats.py
rename to scripts/network_stats.py
diff --git a/public-segmentation/seg_utils/__init__.py b/seg_utils/__init__.py
similarity index 100%
rename from public-segmentation/seg_utils/__init__.py
rename to seg_utils/__init__.py
diff --git a/public-segmentation/seg_utils/post_process_masks.py b/seg_utils/post_process_masks.py
similarity index 100%
rename from public-segmentation/seg_utils/post_process_masks.py
rename to seg_utils/post_process_masks.py
diff --git a/public-segmentation/seg_utils/utils.py b/seg_utils/utils.py
similarity index 100%
rename from public-segmentation/seg_utils/utils.py
rename to seg_utils/utils.py
diff --git a/public-segmentation/seg_utils/visualizer.py b/seg_utils/visualizer.py
similarity index 100%
rename from public-segmentation/seg_utils/visualizer.py
rename to seg_utils/visualizer.py
diff --git a/public-segmentation/train.py b/train.py
similarity index 100%
rename from public-segmentation/train.py
rename to train.py