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--- |
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imports: |
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- "$from scipy import ndimage" |
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arch_ckpt_path: models |
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amp: true |
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data_file_base_dir: /workspace/data/msd/Task07_Pancreas |
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data_list_file_path: configs/dataset_0.json |
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determ: true |
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input_channels: 1 |
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learning_rate: 0.025 |
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learning_rate_arch: 0.001 |
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learning_rate_milestones: |
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- 0.4 |
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- 0.8 |
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num_images_per_batch: 1 |
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num_epochs: 1430 |
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num_epochs_per_validation: 100 |
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num_epochs_warmup: 715 |
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num_patches_per_image: 1 |
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num_sw_batch_size: 6 |
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output_classes: 3 |
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overlap_ratio: 0.625 |
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patch_size: |
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- 96 |
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- 96 |
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- 96 |
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patch_size_valid: |
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- 96 |
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- 96 |
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- 96 |
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ram_cost_factor: 0.8 |
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image_key: image |
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label_key: label |
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transform_train: |
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_target_: Compose |
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transforms: |
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- _target_: LoadImaged |
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keys: |
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- "@image_key" |
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- "@label_key" |
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- _target_: EnsureChannelFirstd |
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keys: |
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- "@image_key" |
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- "@label_key" |
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- _target_: Orientationd |
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keys: |
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- "@image_key" |
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- "@label_key" |
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axcodes: RAS |
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- _target_: Spacingd |
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keys: |
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- "@image_key" |
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- "@label_key" |
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pixdim: |
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- 1 |
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- 1 |
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- 1 |
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mode: |
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- bilinear |
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- nearest |
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align_corners: |
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- true |
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- true |
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- _target_: CastToTyped |
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keys: "@image_key" |
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dtype: "$torch.float32" |
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- _target_: ScaleIntensityRanged |
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keys: "@image_key" |
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a_min: -87 |
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a_max: 199 |
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b_min: 0 |
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b_max: 1 |
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clip: true |
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- _target_: CastToTyped |
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keys: |
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- "@image_key" |
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- "@label_key" |
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dtype: |
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- "$np.float16" |
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- "$np.uint8" |
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- _target_: CopyItemsd |
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keys: "@label_key" |
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times: 1 |
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names: |
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- label4crop |
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- _target_: Lambdad |
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keys: label4crop |
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func: "$lambda x, s=@output_classes: np.concatenate(tuple([ndimage.binary_dilation((x==_k).astype(x.dtype), iterations=48).astype(float) for _k in range(s)]), axis=0)" |
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overwrite: true |
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- _target_: EnsureTyped |
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keys: |
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- "@image_key" |
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- "@label_key" |
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- _target_: CastToTyped |
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keys: "@image_key" |
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dtype: "$torch.float32" |
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- _target_: SpatialPadd |
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keys: |
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- "@image_key" |
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- "@label_key" |
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- label4crop |
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spatial_size: "@patch_size" |
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mode: |
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- reflect |
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- constant |
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- constant |
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- _target_: RandCropByLabelClassesd |
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keys: |
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- "@image_key" |
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- "@label_key" |
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label_key: label4crop |
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num_classes: "@output_classes" |
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ratios: "$[1,] * @output_classes" |
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spatial_size: "@patch_size" |
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num_samples: "@num_patches_per_image" |
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- _target_: Lambdad |
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keys: label4crop |
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func: "$lambda x: 0" |
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- _target_: RandRotated |
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keys: |
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- "@image_key" |
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- "@label_key" |
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range_x: 0.3 |
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range_y: 0.3 |
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range_z: 0.3 |
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mode: |
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- bilinear |
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- nearest |
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prob: 0.2 |
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- _target_: RandZoomd |
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keys: |
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- "@image_key" |
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- "@label_key" |
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min_zoom: 0.8 |
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max_zoom: 1.2 |
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mode: |
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- trilinear |
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- nearest |
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align_corners: |
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- null |
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- null |
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prob: 0.16 |
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- _target_: RandGaussianSmoothd |
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keys: "@image_key" |
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sigma_x: |
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- 0.5 |
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- 1.15 |
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sigma_y: |
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- 0.5 |
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- 1.15 |
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sigma_z: |
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- 0.5 |
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- 1.15 |
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prob: 0.15 |
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- _target_: RandScaleIntensityd |
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keys: "@image_key" |
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factors: 0.3 |
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prob: 0.5 |
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- _target_: RandShiftIntensityd |
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keys: "@image_key" |
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offsets: 0.1 |
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prob: 0.5 |
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- _target_: RandGaussianNoised |
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keys: "@image_key" |
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std: 0.01 |
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prob: 0.15 |
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- _target_: RandFlipd |
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keys: |
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- "@image_key" |
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- "@label_key" |
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spatial_axis: 0 |
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prob: 0.5 |
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- _target_: RandFlipd |
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keys: |
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- "@image_key" |
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- "@label_key" |
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spatial_axis: 1 |
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prob: 0.5 |
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- _target_: RandFlipd |
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keys: |
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- "@image_key" |
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- "@label_key" |
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spatial_axis: 2 |
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prob: 0.5 |
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- _target_: CastToTyped |
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keys: |
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- "@image_key" |
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- "@label_key" |
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dtype: |
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- "$torch.float32" |
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- "$torch.uint8" |
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- _target_: ToTensord |
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keys: |
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- "@image_key" |
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- "@label_key" |
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transform_validation: |
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_target_: Compose |
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transforms: |
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- _target_: LoadImaged |
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keys: |
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- "@image_key" |
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- "@label_key" |
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- _target_: EnsureChannelFirstd |
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keys: |
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- "@image_key" |
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- "@label_key" |
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- _target_: Orientationd |
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keys: |
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- "@image_key" |
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- "@label_key" |
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axcodes: RAS |
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- _target_: Spacingd |
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keys: |
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- "@image_key" |
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- "@label_key" |
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pixdim: |
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- 1 |
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- 1 |
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- 1 |
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mode: |
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- bilinear |
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- nearest |
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align_corners: |
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- true |
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- true |
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- _target_: CastToTyped |
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keys: "@image_key" |
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dtype: "$torch.float32" |
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- _target_: ScaleIntensityRanged |
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keys: "@image_key" |
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a_min: -87 |
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a_max: 199 |
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b_min: 0 |
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b_max: 1 |
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clip: true |
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- _target_: CastToTyped |
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keys: |
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- "@image_key" |
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- "@label_key" |
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dtype: |
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- "$np.float16" |
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- "$np.uint8" |
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- _target_: CastToTyped |
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keys: |
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- "@image_key" |
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- "@label_key" |
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dtype: |
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- "$torch.float32" |
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- "$torch.uint8" |
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- _target_: ToTensord |
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keys: |
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- "@image_key" |
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- "@label_key" |
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loss: |
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_target_: DiceCELoss |
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include_background: false |
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to_onehot_y: true |
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softmax: true |
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squared_pred: true |
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batch: true |
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smooth_nr: 0.00001 |
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smooth_dr: 0.00001 |
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dints_space: |
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_target_: monai.networks.nets.TopologySearch |
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channel_mul: 0.5 |
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num_blocks: 12 |
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num_depths: 4 |
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use_downsample: true |
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device: "$torch.device('cuda')" |
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network: |
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_target_: monai.networks.nets.DiNTS |
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dints_space: "@dints_space" |
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in_channels: "@input_channels" |
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num_classes: "@output_classes" |
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use_downsample: true |
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