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https://github.com/open-mmlab/mmsegmentation.git
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Add 4 retinal vessel segmentation benchmark (#315)
* add 4 retinal vessel segmentation configs of UNet * fix flip augmentation * add unet benchmark on 4 medical datasets * fix hrf bug
This commit is contained in:
Junjun2016
GitHub
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59
configs/_base_/datasets/chase_db1.py
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59
configs/_base_/datasets/chase_db1.py
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# dataset settings
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dataset_type = 'ChaseDB1Dataset'
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data_root = 'data/CHASE_DB1'
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img_norm_cfg = dict(
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mean=[123.675, 116.28, 103.53], std=[58.395, 57.12, 57.375], to_rgb=True)
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img_scale = (960, 999)
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crop_size = (128, 128)
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train_pipeline = [
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dict(type='LoadImageFromFile'),
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dict(type='LoadAnnotations'),
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dict(type='Resize', img_scale=img_scale, ratio_range=(0.5, 2.0)),
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dict(type='RandomCrop', crop_size=crop_size, cat_max_ratio=0.75),
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dict(type='RandomFlip', prob=0.5),
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dict(type='PhotoMetricDistortion'),
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dict(type='Normalize', **img_norm_cfg),
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dict(type='Pad', size=crop_size, pad_val=0, seg_pad_val=255),
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dict(type='DefaultFormatBundle'),
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dict(type='Collect', keys=['img', 'gt_semantic_seg'])
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]
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test_pipeline = [
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dict(type='LoadImageFromFile'),
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dict(
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type='MultiScaleFlipAug',
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img_scale=img_scale,
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# img_ratios=[0.5, 0.75, 1.0, 1.25, 1.5, 1.75, 2.0],
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flip=False,
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transforms=[
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dict(type='Resize', keep_ratio=True),
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dict(type='RandomFlip'),
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dict(type='Normalize', **img_norm_cfg),
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dict(type='ImageToTensor', keys=['img']),
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dict(type='Collect', keys=['img'])
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])
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]
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data = dict(
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samples_per_gpu=4,
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workers_per_gpu=4,
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train=dict(
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type='RepeatDataset',
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times=40000,
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dataset=dict(
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type=dataset_type,
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data_root=data_root,
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img_dir='images/training',
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ann_dir='annotations/training',
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pipeline=train_pipeline)),
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val=dict(
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type=dataset_type,
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data_root=data_root,
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img_dir='images/validation',
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ann_dir='annotations/validation',
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pipeline=test_pipeline),
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test=dict(
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type=dataset_type,
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data_root=data_root,
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img_dir='images/validation',
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ann_dir='annotations/validation',
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pipeline=test_pipeline))
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59
configs/_base_/datasets/drive.py
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59
configs/_base_/datasets/drive.py
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# dataset settings
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dataset_type = 'DRIVEDataset'
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data_root = 'data/DRIVE'
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img_norm_cfg = dict(
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mean=[123.675, 116.28, 103.53], std=[58.395, 57.12, 57.375], to_rgb=True)
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img_scale = (584, 565)
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crop_size = (64, 64)
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train_pipeline = [
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dict(type='LoadImageFromFile'),
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dict(type='LoadAnnotations'),
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dict(type='Resize', img_scale=img_scale, ratio_range=(0.5, 2.0)),
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dict(type='RandomCrop', crop_size=crop_size, cat_max_ratio=0.75),
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dict(type='RandomFlip', prob=0.5),
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dict(type='PhotoMetricDistortion'),
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dict(type='Normalize', **img_norm_cfg),
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dict(type='Pad', size=crop_size, pad_val=0, seg_pad_val=255),
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dict(type='DefaultFormatBundle'),
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dict(type='Collect', keys=['img', 'gt_semantic_seg'])
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]
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test_pipeline = [
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dict(type='LoadImageFromFile'),
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dict(
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type='MultiScaleFlipAug',
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img_scale=img_scale,
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# img_ratios=[0.5, 0.75, 1.0, 1.25, 1.5, 1.75, 2.0],
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flip=False,
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transforms=[
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dict(type='Resize', keep_ratio=True),
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dict(type='RandomFlip'),
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dict(type='Normalize', **img_norm_cfg),
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dict(type='ImageToTensor', keys=['img']),
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dict(type='Collect', keys=['img'])
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])
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]
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data = dict(
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samples_per_gpu=4,
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workers_per_gpu=4,
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train=dict(
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type='RepeatDataset',
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times=40000,
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dataset=dict(
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type=dataset_type,
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data_root=data_root,
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img_dir='images/training',
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ann_dir='annotations/training',
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pipeline=train_pipeline)),
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val=dict(
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type=dataset_type,
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data_root=data_root,
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img_dir='images/validation',
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ann_dir='annotations/validation',
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pipeline=test_pipeline),
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test=dict(
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type=dataset_type,
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data_root=data_root,
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img_dir='images/validation',
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ann_dir='annotations/validation',
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pipeline=test_pipeline))
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59
configs/_base_/datasets/hrf.py
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59
configs/_base_/datasets/hrf.py
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# dataset settings
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dataset_type = 'HRFDataset'
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data_root = 'data/HRF'
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img_norm_cfg = dict(
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mean=[123.675, 116.28, 103.53], std=[58.395, 57.12, 57.375], to_rgb=True)
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img_scale = (2336, 3504)
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crop_size = (256, 256)
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train_pipeline = [
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dict(type='LoadImageFromFile'),
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dict(type='LoadAnnotations'),
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dict(type='Resize', img_scale=img_scale, ratio_range=(0.5, 2.0)),
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dict(type='RandomCrop', crop_size=crop_size, cat_max_ratio=0.75),
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dict(type='RandomFlip', prob=0.5),
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dict(type='PhotoMetricDistortion'),
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dict(type='Normalize', **img_norm_cfg),
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dict(type='Pad', size=crop_size, pad_val=0, seg_pad_val=255),
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dict(type='DefaultFormatBundle'),
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dict(type='Collect', keys=['img', 'gt_semantic_seg'])
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]
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test_pipeline = [
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dict(type='LoadImageFromFile'),
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dict(
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type='MultiScaleFlipAug',
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img_scale=img_scale,
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# img_ratios=[0.5, 0.75, 1.0, 1.25, 1.5, 1.75, 2.0],
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flip=False,
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transforms=[
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dict(type='Resize', keep_ratio=True),
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dict(type='RandomFlip'),
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dict(type='Normalize', **img_norm_cfg),
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dict(type='ImageToTensor', keys=['img']),
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dict(type='Collect', keys=['img'])
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])
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]
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data = dict(
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samples_per_gpu=4,
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workers_per_gpu=4,
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train=dict(
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type='RepeatDataset',
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times=40000,
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dataset=dict(
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type=dataset_type,
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data_root=data_root,
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img_dir='images/training',
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ann_dir='annotations/training',
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pipeline=train_pipeline)),
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val=dict(
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type=dataset_type,
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data_root=data_root,
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img_dir='images/validation',
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ann_dir='annotations/validation',
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pipeline=test_pipeline),
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test=dict(
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type=dataset_type,
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data_root=data_root,
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img_dir='images/validation',
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ann_dir='annotations/validation',
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pipeline=test_pipeline))
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59
configs/_base_/datasets/stare.py
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59
configs/_base_/datasets/stare.py
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# dataset settings
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dataset_type = 'STAREDataset'
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data_root = 'data/STARE'
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img_norm_cfg = dict(
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mean=[123.675, 116.28, 103.53], std=[58.395, 57.12, 57.375], to_rgb=True)
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img_scale = (605, 700)
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crop_size = (128, 128)
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train_pipeline = [
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dict(type='LoadImageFromFile'),
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dict(type='LoadAnnotations'),
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dict(type='Resize', img_scale=img_scale, ratio_range=(0.5, 2.0)),
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dict(type='RandomCrop', crop_size=crop_size, cat_max_ratio=0.75),
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dict(type='RandomFlip', prob=0.5),
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dict(type='PhotoMetricDistortion'),
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dict(type='Normalize', **img_norm_cfg),
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dict(type='Pad', size=crop_size, pad_val=0, seg_pad_val=255),
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dict(type='DefaultFormatBundle'),
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dict(type='Collect', keys=['img', 'gt_semantic_seg'])
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]
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test_pipeline = [
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dict(type='LoadImageFromFile'),
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dict(
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type='MultiScaleFlipAug',
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img_scale=img_scale,
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# img_ratios=[0.5, 0.75, 1.0, 1.25, 1.5, 1.75, 2.0],
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flip=False,
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transforms=[
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dict(type='Resize', keep_ratio=True),
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dict(type='RandomFlip'),
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dict(type='Normalize', **img_norm_cfg),
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dict(type='ImageToTensor', keys=['img']),
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dict(type='Collect', keys=['img'])
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])
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]
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data = dict(
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samples_per_gpu=4,
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workers_per_gpu=4,
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train=dict(
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type='RepeatDataset',
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times=40000,
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dataset=dict(
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type=dataset_type,
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data_root=data_root,
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img_dir='images/training',
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ann_dir='annotations/training',
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pipeline=train_pipeline)),
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val=dict(
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type=dataset_type,
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data_root=data_root,
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img_dir='images/validation',
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ann_dir='annotations/validation',
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pipeline=test_pipeline),
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test=dict(
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type=dataset_type,
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data_root=data_root,
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img_dir='images/validation',
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ann_dir='annotations/validation',
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pipeline=test_pipeline))
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51
configs/_base_/models/unet_s5-d16.py
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51
configs/_base_/models/unet_s5-d16.py
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# model settings
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norm_cfg = dict(type='SyncBN', requires_grad=True)
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model = dict(
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type='EncoderDecoder',
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pretrained=None,
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backbone=dict(
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type='UNet',
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in_channels=3,
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base_channels=64,
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num_stages=5,
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strides=(1, 1, 1, 1, 1),
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enc_num_convs=(2, 2, 2, 2, 2),
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dec_num_convs=(2, 2, 2, 2),
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downsamples=(True, True, True, True),
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enc_dilations=(1, 1, 1, 1, 1),
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dec_dilations=(1, 1, 1, 1),
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with_cp=False,
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conv_cfg=None,
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norm_cfg=norm_cfg,
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act_cfg=dict(type='ReLU'),
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upsample_cfg=dict(type='InterpConv'),
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norm_eval=False),
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decode_head=dict(
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type='FCNHead',
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in_channels=64,
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in_index=4,
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channels=64,
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num_convs=1,
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concat_input=False,
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dropout_ratio=0.1,
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num_classes=2,
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norm_cfg=norm_cfg,
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align_corners=False,
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loss_decode=dict(
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type='CrossEntropyLoss', use_sigmoid=False, loss_weight=1.0)),
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auxiliary_head=dict(
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type='FCNHead',
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in_channels=128,
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in_index=3,
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channels=64,
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num_convs=1,
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concat_input=False,
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dropout_ratio=0.1,
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num_classes=2,
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norm_cfg=norm_cfg,
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align_corners=False,
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loss_decode=dict(
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type='CrossEntropyLoss', use_sigmoid=False, loss_weight=0.4)))
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# model training and testing settings
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train_cfg = dict()
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test_cfg = dict(mode='slide', crop_size=256, stride=170)
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23
configs/unet/README.md
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23
configs/unet/README.md
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# U-Net: Convolutional Networks for Biomedical Image Segmentation
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## Introduction
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```latex
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@inproceedings{ronneberger2015u,
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title={U-net: Convolutional networks for biomedical image segmentation},
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author={Ronneberger, Olaf and Fischer, Philipp and Brox, Thomas},
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booktitle={International Conference on Medical image computing and computer-assisted intervention},
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pages={234--241},
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year={2015},
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organization={Springer}
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}
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```
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## Results and models
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| Backbone | Head | Dataset | Image Size | Crop Size | Stride | Lr schd | Mem (GB) | Inf time (fps) | Dice | download |
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|--------|----------|----------|----------|-----------|--------:|----------|----------------|------:|--------------:|------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
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| UNet-S5-D16 | FCN | DRIVE | 584x565 | 64x64 | 42x42 | 40000 | 0.680 | - | 78.67 | [model](https://download.openmmlab.com/mmsegmentation/v0.5/unet/unet_s5-d16_64x64_40k_drive/unet_s5-d16_64x64_40k_drive_20201223_191051-9cd163b8.pth) | [log](https://download.openmmlab.com/mmsegmentation/v0.5/unet/unet_s5-d16_64x64_40k_drive/unet_s5-d16_64x64_40k_drive-20201223_191051.log.json) |
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| UNet-S5-D16 | FCN | STARE | 605x700 | 128x128 | 85x85 | 40000 | 0.968 | - | 81.02 | [model](https://download.openmmlab.com/mmsegmentation/v0.5/unet/unet_s5-d16_128x128_40k_stare/unet_s5-d16_128x128_40k_stare_20201223_191051-e5439846.pth) | [log](https://download.openmmlab.com/mmsegmentation/v0.5/unet/unet_s5-d16_128x128_40k_stare/unet_s5-d16_128x128_40k_stare-20201223_191051.log.json) |
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| UNet-S5-D16 | FCN | CHASE_DB1 | 960x999 | 128x128 | 85x85 | 40000 | 0.968 | - | 80.24 | [model](https://download.openmmlab.com/mmsegmentation/v0.5/unet/unet_s5-d16_128x128_40k_chase_db1/unet_s5-d16_128x128_40k_chase_db1_20201223_191051-8b16ca0b.pth) | [log](https://download.openmmlab.com/mmsegmentation/v0.5/unet/unet_s5-d16_128x128_40k_chase_db1/unet_s5-d16_128x128_40k_chase_db1-20201223_191051.log.json) |
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| UNet-S5-D16 | FCN | HRF | 2336x3504 | 256x256 | 170x170 | 40000 | 2.525 | - | 79.45 | [model](https://download.openmmlab.com/mmsegmentation/v0.5/unet/unet_s5-d16_256x256_40k_hrf/unet_s5-d16_256x256_40k_hrf_20201223_173724-d89cf1ed.pth) | [log](https://download.openmmlab.com/mmsegmentation/v0.5/unet/unet_s5-d16_256x256_40k_hrf/unet_s5-d16_256x256_40k_hrf-20201223_173724.log.json) |
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6
configs/unet/unet_s5-d16_128x128_40k_chase_db1.py
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6
configs/unet/unet_s5-d16_128x128_40k_chase_db1.py
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_base_ = [
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'../_base_/models/unet_s5-d16.py', '../_base_/datasets/chase_db1.py',
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'../_base_/default_runtime.py', '../_base_/schedules/schedule_40k.py'
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]
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test_cfg = dict(crop_size=(128, 128), stride=(85, 85))
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evaluation = dict(metric='mDice')
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6
configs/unet/unet_s5-d16_128x128_40k_stare.py
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6
configs/unet/unet_s5-d16_128x128_40k_stare.py
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_base_ = [
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'../_base_/models/unet_s5-d16.py', '../_base_/datasets/stare.py',
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'../_base_/default_runtime.py', '../_base_/schedules/schedule_40k.py'
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]
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test_cfg = dict(crop_size=(128, 128), stride=(85, 85))
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evaluation = dict(metric='mDice')
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6
configs/unet/unet_s5-d16_256x256_40k_hrf.py
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6
configs/unet/unet_s5-d16_256x256_40k_hrf.py
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_base_ = [
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'../_base_/models/unet_s5-d16.py', '../_base_/datasets/hrf.py',
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'../_base_/default_runtime.py', '../_base_/schedules/schedule_40k.py'
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]
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test_cfg = dict(crop_size=(256, 256), stride=(170, 170))
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evaluation = dict(metric='mDice')
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6
configs/unet/unet_s5-d16_64x64_40k_drive.py
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6
configs/unet/unet_s5-d16_64x64_40k_drive.py
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_base_ = [
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'../_base_/models/unet_s5-d16.py', '../_base_/datasets/drive.py',
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'../_base_/default_runtime.py', '../_base_/schedules/schedule_40k.py'
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]
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test_cfg = dict(crop_size=(64, 64), stride=(42, 42))
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evaluation = dict(metric='mDice')
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