-
Notifications
You must be signed in to change notification settings - Fork 2.6k
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
[Project] Medical semantic seg dataset: ISIC-2017 Task1 (#2709)
- Loading branch information
1 parent
b24f422
commit 3cc9d30
Showing
7 changed files
with
407 additions
and
0 deletions.
There are no files selected for viewing
158 changes: 158 additions & 0 deletions
158
projects/medical/2d_image/dermoscopy/isic2017_task1/README.md
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Original file line number | Diff line number | Diff line change |
---|---|---|
@@ -0,0 +1,158 @@ | ||
# ISIC-2017 Task1 | ||
|
||
## Description | ||
|
||
This project support **`ISIC-2017 Task1 `**, and the dataset used in this project can be downloaded from [here](https://challenge.isic-archive.com/data/#2017). | ||
|
||
### Dataset Overview | ||
|
||
The goal of the challenge is to help participants develop image analysis tools to enable the automated diagnosis of melanoma from dermoscopic images. | ||
|
||
This challenge provides training data (~2000 images) for participants to engage in all 3 components of lesion image analysis. A separate public validation dataset (~150 images) and blind held-out test dataset (~600 images) will be provided for participants to generate and submit automated results. | ||
|
||
### Original Statistic Information | ||
|
||
| Dataset name | Anatomical region | Task type | Modality | Num. Classes | Train/Val/Test Images | Train/Val/Test Labeled | Release Date | License | | ||
| ---------------------------------------------------------------- | ----------------- | ------------ | ---------- | ------------ | --------------------- | ---------------------- | ------------ | ---------------------------------------------------------------------- | | ||
| [ISIC-2017 Task1](https://challenge.isic-archive.com/data/#2017) | full body | segmentation | dermoscopy | 2 | 2000/150/600 | yes/yes/yes | 2017 | [CC-0](https://creativecommons.org/share-your-work/public-domain/cc0/) | | ||
|
||
| Class Name | Num. Train | Pct. Train | Num. Val | Pct. Val | Num. Test | Pct. Test | | ||
| :---------: | :--------: | :--------: | :------: | :------: | :-------: | :-------: | | ||
| normal | 2000 | 82.86 | 150 | 73.88 | 600 | 70.62 | | ||
| skin lesion | 2000 | 17.14 | 150 | 26.12 | 600 | 29.38 | | ||
|
||
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/dermoscopy/isic2017_task1/isic2017_task1.png) | ||
|
||
### Prerequisites | ||
|
||
- Python 3.8 | ||
- PyTorch 1.10.0 | ||
- pillow(PIL) 9.3.0 | ||
- scikit-learn(sklearn) 1.2.0 | ||
- [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 isic2017_task1/ root directory, run the following line to add the current directory to PYTHONPATH: | ||
|
||
```shell | ||
export PYTHONPATH=`pwd`:$PYTHONPATH | ||
``` | ||
|
||
### Dataset preparing | ||
|
||
- download dataset from [here](https://challenge.isic-archive.com/data/#2017) and decompression data to path 'data/'. | ||
- run script `"python tools/prepare_dataset.py"` to split dataset and change folder structure as below. | ||
- run script `"python ../../tools/split_seg_dataset.py"` to split dataset and generate `train.txt` and `test.txt`. If the label of official validation set and test set can't be obtained, we generate `train.txt` and `val.txt` from the training set randomly. | ||
|
||
```none | ||
mmsegmentation | ||
├── mmseg | ||
├── projects | ||
│ ├── medical | ||
│ │ ├── 2d_image | ||
│ │ │ ├── dermoscopy | ||
│ │ │ │ ├── isic2017_task1 | ||
│ │ │ │ │ ├── configs | ||
│ │ │ │ │ ├── datasets | ||
│ │ │ │ │ ├── tools | ||
│ │ │ │ │ ├── data | ||
│ │ │ │ │ │ ├── train.txt | ||
│ │ │ │ │ │ ├── val.txt | ||
│ │ │ │ │ │ ├── test.txt | ||
│ │ │ │ │ │ ├── images | ||
│ │ │ │ │ │ │ ├── train | ||
│ │ │ │ | │ │ │ ├── xxx.png | ||
│ │ │ │ | │ │ │ ├── ... | ||
│ │ │ │ | │ │ │ └── xxx.png | ||
│ │ │ │ │ │ │ ├── val | ||
│ │ │ │ | │ │ │ ├── yyy.png | ||
│ │ │ │ | │ │ │ ├── ... | ||
│ │ │ │ | │ │ │ └── yyy.png | ||
│ │ │ │ │ │ │ ├── test | ||
│ │ │ │ | │ │ │ ├── yyy.png | ||
│ │ │ │ | │ │ │ ├── ... | ||
│ │ │ │ | │ │ │ └── yyy.png | ||
│ │ │ │ │ │ ├── masks | ||
│ │ │ │ │ │ │ ├── train | ||
│ │ │ │ | │ │ │ ├── xxx.png | ||
│ │ │ │ | │ │ │ ├── ... | ||
│ │ │ │ | │ │ │ └── xxx.png | ||
│ │ │ │ │ │ │ ├── val | ||
│ │ │ │ | │ │ │ ├── yyy.png | ||
│ │ │ │ | │ │ │ ├── ... | ||
│ │ │ │ | │ │ │ └── yyy.png | ||
│ │ │ │ │ │ │ ├── test | ||
│ │ │ │ | │ │ │ ├── yyy.png | ||
│ │ │ │ | │ │ │ ├── ... | ||
│ │ │ │ | │ │ │ └── yyy.png | ||
``` | ||
|
||
### Training commands | ||
|
||
```shell | ||
mim train mmseg ./configs/${CONFIG_PATH} | ||
``` | ||
|
||
To train on multiple GPUs, e.g. 8 GPUs, run the following command: | ||
|
||
```shell | ||
mim train mmseg ./configs/${CONFIG_PATH} --launcher pytorch --gpus 8 | ||
``` | ||
|
||
### Testing commands | ||
|
||
```shell | ||
mim test mmseg ./configs/${CONFIG_PATH} --checkpoint ${CHECKPOINT_PATH} | ||
``` | ||
|
||
<!-- List the results as usually done in other model's README. [Example](https://github.com/open-mmlab/mmsegmentation/tree/dev-1.x/configs/fcn#results-and-models) | ||
You should claim whether this is based on the pre-trained weights, which are converted from the official release; or it's a reproduced result obtained from retraining the model in this project. --> | ||
|
||
## Results | ||
|
||
### ISIC-2017 Task1 | ||
|
||
| Method | Backbone | Crop Size | lr | mIoU | mDice | config | | ||
| :-------------: | :------: | :-------: | :----: | :--: | :---: | :---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------: | | ||
| fcn_unet_s5-d16 | unet | 512x512 | 0.01 | - | - | [config](https://github.com/open-mmlab/mmsegmentation/tree/dev-1.x/projects/medical/2d_image/dermoscopy/isic2017_task1/configs/fcn-unet-s5-d16_unet_1xb16-0.01-20k_isic2017-task1-512x512.py) | | ||
| fcn_unet_s5-d16 | unet | 512x512 | 0.001 | - | - | [config](https://github.com/open-mmlab/mmsegmentation/tree/dev-1.x/projects/medical/2d_image/dermoscopy/isic2017_task1/configs/fcn-unet-s5-d16_unet_1xb16-0.001-20k_isic2017-task1-512x512.py) | | ||
| fcn_unet_s5-d16 | unet | 512x512 | 0.0001 | - | - | [config](https://github.com/open-mmlab/mmsegmentation/tree/dev-1.x/projects/medical/2d_image/dermoscopy/isic2017_task1/configs/fcn-unet-s5-d16_unet_1xb16-0.0001-20k_isic2017-task1-512x512.py) | | ||
|
||
## 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. |
17 changes: 17 additions & 0 deletions
17
...py/isic2017_task1/configs/fcn-unet-s5-d16_unet_1xb16-0.0001-20k_isic2017-task1-512x512.py
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Original file line number | Diff line number | Diff line change |
---|---|---|
@@ -0,0 +1,17 @@ | ||
_base_ = [ | ||
'mmseg::_base_/models/fcn_unet_s5-d16.py', './isic2017-task1_512x512.py', | ||
'mmseg::_base_/default_runtime.py', | ||
'mmseg::_base_/schedules/schedule_20k.py' | ||
] | ||
custom_imports = dict(imports='datasets.isic2017-task1_dataset') | ||
img_scale = (512, 512) | ||
data_preprocessor = dict(size=img_scale) | ||
optimizer = dict(lr=0.0001) | ||
optim_wrapper = dict(optimizer=optimizer) | ||
model = dict( | ||
data_preprocessor=data_preprocessor, | ||
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) |
17 changes: 17 additions & 0 deletions
17
...opy/isic2017_task1/configs/fcn-unet-s5-d16_unet_1xb16-0.001-20k_isic2017-task1-512x512.py
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Original file line number | Diff line number | Diff line change |
---|---|---|
@@ -0,0 +1,17 @@ | ||
_base_ = [ | ||
'mmseg::_base_/models/fcn_unet_s5-d16.py', './isic2017-task1_512x512.py', | ||
'mmseg::_base_/default_runtime.py', | ||
'mmseg::_base_/schedules/schedule_20k.py' | ||
] | ||
custom_imports = dict(imports='datasets.isic2017-task1_dataset') | ||
img_scale = (512, 512) | ||
data_preprocessor = dict(size=img_scale) | ||
optimizer = dict(lr=0.001) | ||
optim_wrapper = dict(optimizer=optimizer) | ||
model = dict( | ||
data_preprocessor=data_preprocessor, | ||
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) |
17 changes: 17 additions & 0 deletions
17
...copy/isic2017_task1/configs/fcn-unet-s5-d16_unet_1xb16-0.01-20k_isic2017-task1-512x512.py
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Original file line number | Diff line number | Diff line change |
---|---|---|
@@ -0,0 +1,17 @@ | ||
_base_ = [ | ||
'mmseg::_base_/models/fcn_unet_s5-d16.py', './isic2017-task1_512x512.py', | ||
'mmseg::_base_/default_runtime.py', | ||
'mmseg::_base_/schedules/schedule_20k.py' | ||
] | ||
custom_imports = dict(imports='datasets.isic2017-task1_dataset') | ||
img_scale = (512, 512) | ||
data_preprocessor = dict(size=img_scale) | ||
optimizer = dict(lr=0.01) | ||
optim_wrapper = dict(optimizer=optimizer) | ||
model = dict( | ||
data_preprocessor=data_preprocessor, | ||
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) |
41 changes: 41 additions & 0 deletions
41
projects/medical/2d_image/dermoscopy/isic2017_task1/configs/isic2017-task1_512x512.py
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Original file line number | Diff line number | Diff line change |
---|---|---|
@@ -0,0 +1,41 @@ | ||
dataset_type = 'ISIC2017Task1' | ||
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, | ||
data_prefix=dict( | ||
img_path='images/train/', seg_map_path='masks/train/'), | ||
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, | ||
data_prefix=dict(img_path='images/val/', seg_map_path='masks/val/'), | ||
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']) |
30 changes: 30 additions & 0 deletions
30
projects/medical/2d_image/dermoscopy/isic2017_task1/datasets/isic2017-task1_dataset.py
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Original file line number | Diff line number | Diff line change |
---|---|---|
@@ -0,0 +1,30 @@ | ||
from mmseg.datasets import BaseSegDataset | ||
from mmseg.registry import DATASETS | ||
|
||
|
||
@DATASETS.register_module() | ||
class ISIC2017Task1(BaseSegDataset): | ||
"""ISIC2017Task1 dataset. | ||
In segmentation map annotation for ISIC2017Task1, | ||
``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' | ||
reduce_zero_label (bool): Whether to mark label zero as ignored. | ||
Default to False. | ||
""" | ||
METAINFO = dict(classes=('normal', 'skin lesion')) | ||
|
||
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) |
Oops, something went wrong.