From 77836e623112c8efdbfee1c1e3281efda73485f9 Mon Sep 17 00:00:00 2001 From: Sizheng Guo <745134809@qq.com> Date: Sat, 6 May 2023 17:39:12 +0800 Subject: [PATCH] [Project] add Vampire dataset project (#2633) --- .../fluorescein_angriogram/vampire/README.md | 158 ++++++++++++++++++ ...6_unet_1xb16-0.0001-20k_vampire-512x512.py | 19 +++ ...16_unet_1xb16-0.001-20k_vampire-512x512.py | 19 +++ ...d16_unet_1xb16-0.01-20k_vampire-512x512.py | 22 +++ .../vampire/configs/vampire_512x512.py | 42 +++++ .../vampire/datasets/__init__.py | 3 + .../vampire/datasets/vampire_dataset.py | 28 ++++ .../vampire/tools/prepare_dataset.py | 44 +++++ 8 files changed, 335 insertions(+) create mode 100644 projects/medical/2d_image/fluorescein_angriogram/vampire/README.md create mode 100755 projects/medical/2d_image/fluorescein_angriogram/vampire/configs/fcn-unet-s5-d16_unet_1xb16-0.0001-20k_vampire-512x512.py create mode 100755 projects/medical/2d_image/fluorescein_angriogram/vampire/configs/fcn-unet-s5-d16_unet_1xb16-0.001-20k_vampire-512x512.py create mode 100755 projects/medical/2d_image/fluorescein_angriogram/vampire/configs/fcn-unet-s5-d16_unet_1xb16-0.01-20k_vampire-512x512.py create mode 100755 projects/medical/2d_image/fluorescein_angriogram/vampire/configs/vampire_512x512.py create mode 100755 projects/medical/2d_image/fluorescein_angriogram/vampire/datasets/__init__.py create mode 100755 projects/medical/2d_image/fluorescein_angriogram/vampire/datasets/vampire_dataset.py create mode 100644 projects/medical/2d_image/fluorescein_angriogram/vampire/tools/prepare_dataset.py diff --git a/projects/medical/2d_image/fluorescein_angriogram/vampire/README.md b/projects/medical/2d_image/fluorescein_angriogram/vampire/README.md new file mode 100644 index 000000000..c2c61c46a --- /dev/null +++ b/projects/medical/2d_image/fluorescein_angriogram/vampire/README.md @@ -0,0 +1,158 @@ +# Vessel Assessment and Measurement Platform for Images of the REtina + +## Description + +This project support **`Vessel Assessment and Measurement Platform for Images of the REtina`**, and the dataset used in this project can be downloaded from [here](https://vampire.computing.dundee.ac.uk/vesselseg.html). + +### Dataset Overview + +In order to promote evaluation of vessel segmentation on ultra-wide field-of-view (UWFV) fluorescein angriogram (FA) frames, we make public 8 frames from two different sequences, the manually annotated images and the result of our automatic vessel segmentation algorithm. + +### Original Statistic Information + +| Dataset name | Anatomical region | Task type | Modality | Num. Classes | Train/Val/Test Images | Train/Val/Test Labeled | Release Date | License | +| ---------------------------------------------------------------- | ----------------- | ------------ | ---------------------- | ------------ | --------------------- | ---------------------- | ------------ | --------------------------------------------------------------- | +| [Vampire](https://vampire.computing.dundee.ac.uk/vesselseg.html) | vessel | segmentation | fluorescein angriogram | 2 | 8/-/- | yes/-/- | 2017 | [CC-BY-NC 4.0](https://creativecommons.org/licenses/by-sa/4.0/) | + +| Class Name | Num. Train | Pct. Train | Num. Val | Pct. Val | Num. Test | Pct. Test | +| :--------: | :--------: | :--------: | :------: | :------: | :-------: | :-------: | +| background | 8 | 96.75 | - | - | - | - | +| vessel | 8 | 3.25 | - | - | - | - | + +Note: + +- `Pct` means percentage of pixels in this category in all pixels. + +### Visualization + +![bac](https://raw.githubusercontent.com/uni-medical/medical-datasets-visualization/main/2d/semantic_seg/fluorescein_angriogram/vampire/vampire_dataset.png) + +## Dataset Citation + +```bibtex + +@inproceedings{perez2011improving, + title={Improving vessel segmentation in ultra-wide field-of-view retinal fluorescein angiograms}, + author={Perez-Rovira, Adria and Zutis, K and Hubschman, Jean Pierre and Trucco, Emanuele}, + booktitle={2011 Annual International Conference of the IEEE Engineering in Medicine and Biology Society}, + pages={2614--2617}, + year={2011}, + organization={IEEE} +} + +@article{perez2011rerbee, + title={RERBEE: robust efficient registration via bifurcations and elongated elements applied to retinal fluorescein angiogram sequences}, + author={Perez-Rovira, Adria and Cabido, Raul and Trucco, Emanuele and McKenna, Stephen J and Hubschman, Jean Pierre}, + journal={IEEE Transactions on Medical Imaging}, + volume={31}, + number={1}, + pages={140--150}, + year={2011}, + publisher={IEEE} +} + +``` + +### Prerequisites + +- Python v3.8 +- PyTorch v1.10.0 +- pillow(PIL) v9.3.0 +- scikit-learn(sklearn) v1.2.0 +- [MIM](https://github.com/open-mmlab/mim) v0.3.4 +- [MMCV](https://github.com/open-mmlab/mmcv) v2.0.0rc4 +- [MMEngine](https://github.com/open-mmlab/mmengine) v0.2.0 or higher +- [MMSegmentation](https://github.com/open-mmlab/mmsegmentation) v1.0.0rc5 + +All the commands below rely on the correct configuration of `PYTHONPATH`, which should point to the project's directory so that Python can locate the module files. In `vampire/` root directory, run the following line to add the current directory to `PYTHONPATH`: + +```shell +export PYTHONPATH=`pwd`:$PYTHONPATH +``` + +### Dataset preparing + +- download dataset from [here](https://vampire.computing.dundee.ac.uk/vesselseg.html) and decompression data to path `'data/'`. +- run script `"python tools/prepare_dataset.py"` to split dataset and change folder structure as below. +- run script `python ../../tools/split_seg_dataset.py` to split dataset. For the Bacteria_detection dataset, as there is no test or validation dataset, we sample 20% samples from the whole dataset as the validation dataset and 80% samples for training data and make two filename lists `train.txt` and `val.txt`. As we set the random seed as the hard code, we eliminated the randomness, the dataset split actually can be reproducible. + +```none + mmsegmentation + ├── mmseg + ├── projects + │ ├── medical + │ │ ├── 2d_image + │ │ │ ├── fluorescein_angriogram + │ │ │ │ ├── vampire + │ │ │ │ │ ├── configs + │ │ │ │ │ ├── datasets + │ │ │ │ │ ├── tools + │ │ │ │ │ ├── data + │ │ │ │ │ │ ├── train.txt + │ │ │ │ │ │ ├── val.txt + │ │ │ │ │ │ ├── images + │ │ │ │ │ │ │ ├── train + │ │ │ │ | │ │ │ ├── xxx.png + │ │ │ │ | │ │ │ ├── ... + │ │ │ │ | │ │ │ └── xxx.png + │ │ │ │ │ │ ├── masks + │ │ │ │ │ │ │ ├── train + │ │ │ │ | │ │ │ ├── xxx.png + │ │ │ │ | │ │ │ ├── ... + │ │ │ │ | │ │ │ └── xxx.png +``` + +### Divided Dataset Information + +***Note: The table information below is divided by ourselves.*** + +| Class Name | Num. Train | Pct. Train | Num. Val | Pct. Val | Num. Test | Pct. Test | +| :--------: | :--------: | :--------: | :------: | :------: | :-------: | :-------: | +| background | 6 | 97.48 | 2 | 94.54 | - | - | +| vessel | 6 | 2.52 | 2 | 5.46 | - | - | + +### Training commands + +To train models on a single server with one GPU. (default） + +```shell +mim train mmseg ./configs/${CONFIG_PATH} +``` + +### Testing commands + +To test models on a single server with one GPU. (default) + +```shell +mim test mmseg ./configs/${CONFIG_PATH} --checkpoint ${CHECKPOINT_PATH} +``` + +## Checklist + +- [x] Milestone 1: PR-ready, and acceptable to be one of the `projects/`. + + - [x] Finish the code + + - [x] Basic docstrings & proper citation + + - [ ] Test-time correctness + + - [x] A full README + +- [ ] Milestone 2: Indicates a successful model implementation. + + - [ ] Training-time correctness + +- [ ] Milestone 3: Good to be a part of our core package! + + - [ ] Type hints and docstrings + + - [ ] Unit tests + + - [ ] Code polishing + + - [ ] Metafile.yml + +- [ ] Move your modules into the core package following the codebase's file hierarchy structure. + +- [ ] Refactor your modules into the core package following the codebase's file hierarchy structure. diff --git a/projects/medical/2d_image/fluorescein_angriogram/vampire/configs/fcn-unet-s5-d16_unet_1xb16-0.0001-20k_vampire-512x512.py b/projects/medical/2d_image/fluorescein_angriogram/vampire/configs/fcn-unet-s5-d16_unet_1xb16-0.0001-20k_vampire-512x512.py new file mode 100755 index 000000000..7f5273aaf --- /dev/null +++ b/projects/medical/2d_image/fluorescein_angriogram/vampire/configs/fcn-unet-s5-d16_unet_1xb16-0.0001-20k_vampire-512x512.py @@ -0,0 +1,19 @@ +_base_ = [ + 'mmseg::_base_/models/fcn_unet_s5-d16.py', './vampire_512x512.py', + 'mmseg::_base_/default_runtime.py', + 'mmseg::_base_/schedules/schedule_20k.py' +] +custom_imports = dict(imports='datasets.vampire_dataset') +img_scale = (512, 512) +data_preprocessor = dict(size=img_scale) +optimizer = dict(lr=0.0001) +optim_wrapper = dict(optimizer=optimizer) +model = dict( + type='EncoderDecoder', + data_preprocessor=data_preprocessor, + pretrained=None, + decode_head=dict(num_classes=2), + auxiliary_head=None, + test_cfg=dict(mode='whole', _delete_=True)) +vis_backends = None +visualizer = dict(vis_backends=vis_backends) diff --git a/projects/medical/2d_image/fluorescein_angriogram/vampire/configs/fcn-unet-s5-d16_unet_1xb16-0.001-20k_vampire-512x512.py b/projects/medical/2d_image/fluorescein_angriogram/vampire/configs/fcn-unet-s5-d16_unet_1xb16-0.001-20k_vampire-512x512.py new file mode 100755 index 000000000..438222998 --- /dev/null +++ b/projects/medical/2d_image/fluorescein_angriogram/vampire/configs/fcn-unet-s5-d16_unet_1xb16-0.001-20k_vampire-512x512.py @@ -0,0 +1,19 @@ +_base_ = [ + 'mmseg::_base_/models/fcn_unet_s5-d16.py', './vampire_512x512.py', + 'mmseg::_base_/default_runtime.py', + 'mmseg::_base_/schedules/schedule_20k.py' +] +custom_imports = dict(imports='datasets.vampire_dataset') +img_scale = (512, 512) +data_preprocessor = dict(size=img_scale) +optimizer = dict(lr=0.001) +optim_wrapper = dict(optimizer=optimizer) +model = dict( + type='EncoderDecoder', + data_preprocessor=dict(size=img_scale), + pretrained=None, + decode_head=dict(num_classes=2), + auxiliary_head=None, + test_cfg=dict(mode='whole', _delete_=True)) +vis_backends = None +visualizer = dict(vis_backends=vis_backends) diff --git a/projects/medical/2d_image/fluorescein_angriogram/vampire/configs/fcn-unet-s5-d16_unet_1xb16-0.01-20k_vampire-512x512.py b/projects/medical/2d_image/fluorescein_angriogram/vampire/configs/fcn-unet-s5-d16_unet_1xb16-0.01-20k_vampire-512x512.py new file mode 100755 index 000000000..8d93e1762 --- /dev/null +++ b/projects/medical/2d_image/fluorescein_angriogram/vampire/configs/fcn-unet-s5-d16_unet_1xb16-0.01-20k_vampire-512x512.py @@ -0,0 +1,22 @@ +_base_ = [ + 'mmseg::_base_/models/fcn_unet_s5-d16.py', './vampire_512x512.py', + 'mmseg::_base_/default_runtime.py', + 'mmseg::_base_/schedules/schedule_20k.py' +] +custom_imports = dict(imports='datasets.vampire_dataset') +img_scale = (512, 512) +data_preprocessor = dict(size=img_scale) +optimizer = dict(lr=0.01) +optim_wrapper = dict(optimizer=optimizer) +model = dict( + type='EncoderDecoder', + data_preprocessor=data_preprocessor, + pretrained=None, + decode_head=dict( + num_classes=2, + loss_decode=dict(type='CrossEntropyLoss', use_sigmoid=True), + out_channels=1), + auxiliary_head=None, + test_cfg=dict(mode='whole', _delete_=True)) +vis_backends = None +visualizer = dict(vis_backends=vis_backends) diff --git a/projects/medical/2d_image/fluorescein_angriogram/vampire/configs/vampire_512x512.py b/projects/medical/2d_image/fluorescein_angriogram/vampire/configs/vampire_512x512.py new file mode 100755 index 000000000..4eda92f9f --- /dev/null +++ b/projects/medical/2d_image/fluorescein_angriogram/vampire/configs/vampire_512x512.py @@ -0,0 +1,42 @@ +dataset_type = 'VampireDataset' +data_root = 'data' +img_scale = (512, 512) +train_pipeline = [ + dict(type='LoadImageFromFile'), + dict(type='LoadAnnotations'), + dict(type='Resize', scale=img_scale, keep_ratio=False), + dict(type='RandomFlip', prob=0.5), + dict(type='PhotoMetricDistortion'), + dict(type='PackSegInputs') +] +test_pipeline = [ + dict(type='LoadImageFromFile'), + dict(type='Resize', scale=img_scale, keep_ratio=False), + dict(type='LoadAnnotations'), + dict(type='PackSegInputs') +] +train_dataloader = dict( + batch_size=16, + num_workers=4, + persistent_workers=True, + sampler=dict(type='InfiniteSampler', shuffle=True), + dataset=dict( + type=dataset_type, + data_root=data_root, + ann_file='train.txt', + data_prefix=dict(img_path='images/', seg_map_path='masks/'), + pipeline=train_pipeline)) +val_dataloader = dict( + batch_size=1, + num_workers=4, + persistent_workers=True, + sampler=dict(type='DefaultSampler', shuffle=False), + dataset=dict( + type=dataset_type, + data_root=data_root, + ann_file='val.txt', + data_prefix=dict(img_path='images/', seg_map_path='masks/'), + pipeline=test_pipeline)) +test_dataloader = val_dataloader +val_evaluator = dict(type='IoUMetric', iou_metrics=['mIoU', 'mDice']) +test_evaluator = dict(type='IoUMetric', iou_metrics=['mIoU', 'mDice']) diff --git a/projects/medical/2d_image/fluorescein_angriogram/vampire/datasets/__init__.py b/projects/medical/2d_image/fluorescein_angriogram/vampire/datasets/__init__.py new file mode 100755 index 000000000..93f9cbf05 --- /dev/null +++ b/projects/medical/2d_image/fluorescein_angriogram/vampire/datasets/__init__.py @@ -0,0 +1,3 @@ +from .vampire_dataset import VampireDataset + +__all__ = ['VampireDataset'] diff --git a/projects/medical/2d_image/fluorescein_angriogram/vampire/datasets/vampire_dataset.py b/projects/medical/2d_image/fluorescein_angriogram/vampire/datasets/vampire_dataset.py new file mode 100755 index 000000000..4d38040f7 --- /dev/null +++ b/projects/medical/2d_image/fluorescein_angriogram/vampire/datasets/vampire_dataset.py @@ -0,0 +1,28 @@ +from mmseg.datasets import BaseSegDataset +from mmseg.registry import DATASETS + + +@DATASETS.register_module() +class VampireDataset(BaseSegDataset): + """VampireDataset dataset. + + In segmentation map annotation for VampireDataset, 0 stands for background, + which is included in 2 categories. ``reduce_zero_label`` is fixed to + False. The ``img_suffix`` is fixed to '.png' and ``seg_map_suffix`` is + fixed to '.png'. + Args: + img_suffix (str): Suffix of images. Default: '.png' + seg_map_suffix (str): Suffix of segmentation maps. Default: '.png' + """ + METAINFO = dict(classes=('background', 'vessel')) + + def __init__(self, + img_suffix='.png', + seg_map_suffix='.png', + reduce_zero_label=False, + **kwargs) -> None: + super().__init__( + img_suffix=img_suffix, + seg_map_suffix=seg_map_suffix, + reduce_zero_label=reduce_zero_label, + **kwargs) diff --git a/projects/medical/2d_image/fluorescein_angriogram/vampire/tools/prepare_dataset.py b/projects/medical/2d_image/fluorescein_angriogram/vampire/tools/prepare_dataset.py new file mode 100644 index 000000000..2755b5d28 --- /dev/null +++ b/projects/medical/2d_image/fluorescein_angriogram/vampire/tools/prepare_dataset.py @@ -0,0 +1,44 @@ +import os +import shutil + +from PIL import Image + +path = 'data' + +if not os.path.exists(os.path.join(path, 'images', 'train')): + os.system(f'mkdir -p {os.path.join(path, "images", "train")}') + +if not os.path.exists(os.path.join(path, 'masks', 'train')): + os.system(f'mkdir -p {os.path.join(path, "masks", "train")}') + +origin_data_path = os.path.join(path, 'vesselSegmentation') + +imgs_amd14 = os.listdir(os.path.join(origin_data_path, 'AMD14')) +imgs_ger7 = os.listdir(os.path.join(origin_data_path, 'GER7')) + +for img in imgs_amd14: + shutil.copy( + os.path.join(origin_data_path, 'AMD14', img), + os.path.join(path, 'images', 'train', img)) + # copy GT + img_gt = img.replace('.png', '-GT.png') + shutil.copy( + os.path.join(origin_data_path, 'AMD14-GT', f'{img_gt}'), + os.path.join(path, 'masks', 'train', img)) + +for img in imgs_ger7: + shutil.copy( + os.path.join(origin_data_path, 'GER7', img), + os.path.join(path, 'images', 'train', img)) + # copy GT + img_gt = img.replace('.bmp', '-GT.png') + img = img.replace('bmp', 'png') + shutil.copy( + os.path.join(origin_data_path, 'GER7-GT', img_gt), + os.path.join(path, 'masks', 'train', img)) + +imgs = os.listdir(os.path.join(path, 'images', 'train')) +for img in imgs: + if not img.endswith('.png'): + im = Image.open(os.path.join(path, 'images', 'train', img)) + im.save(os.path.join(path, 'images', 'train', img[:-4] + '.png'))