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Benjamin Morris
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,370 @@ | ||
| experiment_name: YOUR_EXP_NAME | ||
| run_name: YOUR_RUN_NAME | ||
| task_name: train | ||
| tags: | ||
| - dev | ||
| train: true | ||
| test: true | ||
| ckpt_path: null | ||
| seed: 12345 | ||
| data: | ||
| _target_: cyto_dl.datamodules.dataframe.DataframeDatamodule | ||
| path: //allen/aics/assay-dev/users/Benji/CurrentProjects/im2im_dev/cyto-dl/data/golgi_seg/plugin | ||
| cache_dir: /storage/benji.the.kid/cache/plugin_test | ||
| num_workers: 4 | ||
| batch_size: 1 | ||
| pin_memory: true | ||
| split_column: null | ||
| columns: | ||
| - ${source_col} | ||
| - ${target_col1} | ||
| - ${target_col2} | ||
| - ${merge_mask_col} | ||
| - ${exclude_mask_col} | ||
| - ${base_image_col} | ||
| transforms: | ||
| train: | ||
| _target_: monai.transforms.Compose | ||
| transforms: | ||
| - _target_: cyto_dl.datamodules.dataframe.utils.RemoveNaNKeysd | ||
| - _target_: monai.transforms.LoadImaged | ||
| keys: ${source_col} | ||
| reader: | ||
| - _target_: cyto_dl.image.io.MonaiBioReader | ||
| dimension_order_out: ${eval:'"CZYX" if ${spatial_dims}==3 else "CYX"'} | ||
| C: ${input_channel} | ||
| - _target_: monai.transforms.LoadImaged | ||
| keys: ${target_col1} | ||
| reader: | ||
| - _target_: cyto_dl.image.io.MonaiBioReader | ||
| dimension_order_out: ${eval:'"CZYX" if ${spatial_dims}==3 else "CYX"'} | ||
| C: 0 | ||
| - _target_: monai.transforms.LoadImaged | ||
| keys: ${target_col2} | ||
| allow_missing_keys: true | ||
| reader: | ||
| - _target_: cyto_dl.image.io.MonaiBioReader | ||
| dimension_order_out: ${eval:'"CZYX" if ${spatial_dims}==3 else "CYX"'} | ||
| C: 1 | ||
|
|
||
| - _target_: monai.transforms.ThresholdIntensityd | ||
| allow_missing_keys: true | ||
| keys: | ||
| - ${target_col1} | ||
| - ${target_col2} | ||
| threshold: 0.1 | ||
| above: false | ||
| cval: 1 | ||
| - _target_: cyto_dl.image.io.PolygonLoaderd | ||
| keys: | ||
| - ${merge_mask_col} | ||
| shape_reference_key: ${target_col1} | ||
| missing_key_mode: ignore | ||
| - _target_: cyto_dl.image.io.PolygonLoaderd | ||
| keys: | ||
| - ${exclude_mask_col} | ||
| shape_reference_key: ${target_col1} | ||
| missing_key_mode: create | ||
| - _target_: monai.transforms.NormalizeIntensityd | ||
| keys: ${source_col} | ||
| channel_wise: true | ||
| - _target_: cyto_dl.image.transforms.merge.Merged | ||
| mask_key: ${merge_mask_col} | ||
| image_keys: | ||
| - ${target_col1} | ||
| - ${target_col2} | ||
| base_image_key: ${base_image_col} | ||
| output_name: target | ||
| - _target_: monai.transforms.ToTensord | ||
| keys: | ||
| - ${source_col} | ||
| - target | ||
| - ${exclude_mask_col} | ||
| dtype: float16 | ||
| - _target_: cyto_dl.image.transforms.RandomMultiScaleCropd | ||
| keys: | ||
| - ${source_col} | ||
| - target | ||
| - ${exclude_mask_col} | ||
| patch_shape: ${data._aux.patch_shape} | ||
| patch_per_image: 8 | ||
| scales_dict: ${kv_to_dict:${data._aux._scales_dict}} | ||
|
|
||
| test: | ||
| _target_: monai.transforms.Compose | ||
| transforms: | ||
| - _target_: cyto_dl.datamodules.dataframe.utils.RemoveNaNKeysd | ||
| - _target_: monai.transforms.LoadImaged | ||
| keys: ${source_col} | ||
| reader: | ||
| - _target_: cyto_dl.image.io.MonaiBioReader | ||
| dimension_order_out: ${eval:'"CZYX" if ${spatial_dims}==3 else "CYX"'} | ||
| C: ${input_channel} | ||
| - _target_: monai.transforms.LoadImaged | ||
| keys: ${target_col1} | ||
| reader: | ||
| - _target_: cyto_dl.image.io.MonaiBioReader | ||
| dimension_order_out: ${eval:'"CZYX" if ${spatial_dims}==3 else "CYX"'} | ||
| C: 0 | ||
| - _target_: monai.transforms.LoadImaged | ||
| keys: ${target_col2} | ||
| allow_missing_keys: true | ||
| reader: | ||
| - _target_: cyto_dl.image.io.MonaiBioReader | ||
| dimension_order_out: ${eval:'"CZYX" if ${spatial_dims}==3 else "CYX"'} | ||
| C: 0 | ||
| - _target_: cyto_dl.image.io.PolygonLoaderd | ||
| keys: | ||
| - ${merge_mask_col} | ||
| shape_reference_key: ${target_col1} | ||
| missing_key_mode: ignore | ||
| - _target_: cyto_dl.image.io.PolygonLoaderd | ||
| keys: | ||
| - ${exclude_mask_col} | ||
| shape_reference_key: ${target_col1} | ||
| missing_key_mode: create | ||
| - _target_: monai.transforms.NormalizeIntensityd | ||
| keys: ${source_col} | ||
| channel_wise: true | ||
| - _target_: cyto_dl.image.transforms.merge.Merged | ||
| mask_key: ${merge_mask_col} | ||
| image_keys: | ||
| - ${target_col1} | ||
| - ${target_col2} | ||
| base_image_key: ${base_image_col} | ||
| output_name: target | ||
| - _target_: monai.transforms.ToTensord | ||
| keys: | ||
| - ${source_col} | ||
| - target | ||
| - ${exclude_mask_col} | ||
| dtype: float16 | ||
| predict: | ||
| _target_: monai.transforms.Compose | ||
| transforms: | ||
| - _target_: monai.transforms.LoadImaged | ||
| keys: ${source_col} | ||
| reader: | ||
| - _target_: cyto_dl.image.io.MonaiBioReader | ||
| dimension_order_out: ${eval:'"CZYX" if ${spatial_dims}==3 else "CYX"'} | ||
| C: ${input_channel} | ||
| - _target_: monai.transforms.NormalizeIntensityd | ||
| keys: ${source_col} | ||
| channel_wise: true | ||
| - _target_: monai.transforms.ToTensord | ||
| keys: | ||
| - ${source_col} | ||
| valid: | ||
| _target_: monai.transforms.Compose | ||
| transforms: | ||
| - _target_: cyto_dl.datamodules.dataframe.utils.RemoveNaNKeysd | ||
| - _target_: monai.transforms.LoadImaged | ||
| keys: ${source_col} | ||
| reader: | ||
| - _target_: cyto_dl.image.io.MonaiBioReader | ||
| dimension_order_out: ${eval:'"CZYX" if ${spatial_dims}==3 else "CYX"'} | ||
| C: ${input_channel} | ||
| - _target_: monai.transforms.LoadImaged | ||
| keys: ${target_col1} | ||
| reader: | ||
| - _target_: cyto_dl.image.io.MonaiBioReader | ||
| dimension_order_out: ${eval:'"CZYX" if ${spatial_dims}==3 else "CYX"'} | ||
| C: 0 | ||
| - _target_: monai.transforms.LoadImaged | ||
| keys: ${target_col2} | ||
| allow_missing_keys: true | ||
| reader: | ||
| - _target_: cyto_dl.image.io.MonaiBioReader | ||
| dimension_order_out: ${eval:'"CZYX" if ${spatial_dims}==3 else "CYX"'} | ||
| C: 1 | ||
| - _target_: monai.transforms.ThresholdIntensityd | ||
| allow_missing_keys: true | ||
| keys: | ||
| - ${target_col1} | ||
| - ${target_col2} | ||
| threshold: 0.1 | ||
| above: false | ||
| cval: 1 | ||
| - _target_: cyto_dl.image.io.PolygonLoaderd | ||
| keys: | ||
| - ${merge_mask_col} | ||
| shape_reference_key: ${target_col1} | ||
| missing_key_mode: ignore | ||
| - _target_: cyto_dl.image.io.PolygonLoaderd | ||
| keys: | ||
| - ${exclude_mask_col} | ||
| shape_reference_key: ${target_col1} | ||
| missing_key_mode: create | ||
| - _target_: monai.transforms.NormalizeIntensityd | ||
| keys: ${source_col} | ||
| channel_wise: true | ||
| - _target_: cyto_dl.image.transforms.merge.Merged | ||
| mask_key: ${merge_mask_col} | ||
| image_keys: | ||
| - ${target_col1} | ||
| - ${target_col2} | ||
| base_image_key: ${base_image_col} | ||
| output_name: target | ||
| - _target_: monai.transforms.ToTensord | ||
| keys: | ||
| - ${source_col} | ||
| - target | ||
| - ${exclude_mask_col} | ||
| dtype: float16 | ||
| - _target_: cyto_dl.image.transforms.RandomMultiScaleCropd | ||
| keys: | ||
| - ${source_col} | ||
| - target | ||
| - ${exclude_mask_col} | ||
| patch_shape: ${data._aux.patch_shape} | ||
| patch_per_image: 1 | ||
| scales_dict: ${kv_to_dict:${data._aux._scales_dict}} | ||
| _aux: | ||
| _scales_dict: | ||
| - - target | ||
| - - 1 | ||
| - - ${source_col} | ||
| - - 1 | ||
| - - ${exclude_mask_col} | ||
| - - 1 | ||
| patch_shape: | ||
| - 16 | ||
| - 128 | ||
| - 128 | ||
| model: | ||
| _target_: cyto_dl.models.im2im.MultiTaskIm2Im | ||
| save_images_every_n_epochs: 1 | ||
| save_dir: ${paths.output_dir} | ||
| x_key: ${source_col} | ||
| backbone: | ||
| _target_: monai.networks.nets.DynUNet | ||
| spatial_dims: ${spatial_dims} | ||
| in_channels: ${raw_im_channels} | ||
| out_channels: 1 | ||
| strides: ${model._aux.strides} | ||
| kernel_size: ${model._aux.kernel_size} | ||
| upsample_kernel_size: ${model._aux.upsample_kernel_size} | ||
| dropout: 0.0 | ||
| res_block: true | ||
| task_heads: | ||
| target: | ||
| _target_: cyto_dl.nn.head.MaskHead | ||
| mask_key: ${exclude_mask_col} | ||
| loss: | ||
| _target_: monai.losses.MaskedDiceLoss | ||
| sigmoid: true | ||
| postprocess: | ||
| input: | ||
| _target_: cyto_dl.models.im2im.utils.postprocessing.ActThreshLabel | ||
| rescale_dtype: numpy.uint8 | ||
| prediction: | ||
| _target_: cyto_dl.models.im2im.utils.postprocessing.AutoThreshold | ||
| method: threshold_otsu | ||
|
|
||
| save_input: true | ||
| optimizer: | ||
| generator: | ||
| _partial_: true | ||
| _target_: torch.optim.Adam | ||
| lr: 0.0001 | ||
| weight_decay: 0.0001 | ||
| lr_scheduler: | ||
| generator: | ||
| _partial_: true | ||
| _target_: torch.optim.lr_scheduler.ExponentialLR | ||
| gamma: 0.995 | ||
| inference_args: | ||
| sw_batch_size: 1 | ||
| roi_size: ${data._aux.patch_shape} | ||
| overlap: 0.0 | ||
| mode: gaussian | ||
| _aux: | ||
| strides: | ||
| - 1 | ||
| - 2 | ||
| - 2 | ||
| kernel_size: | ||
| - 3 | ||
| - 3 | ||
| - 3 | ||
| upsample_kernel_size: | ||
| - 2 | ||
| - 2 | ||
| filters: | ||
| - 16 | ||
| - 32 | ||
| - 64 | ||
| callbacks: | ||
| model_checkpoint: | ||
| _target_: lightning.pytorch.callbacks.ModelCheckpoint | ||
| dirpath: ${paths.output_dir}/checkpoints | ||
| filename: epoch_{epoch:03d} | ||
| monitor: val/loss | ||
| verbose: false | ||
| save_last: true | ||
| save_top_k: 1 | ||
| mode: min | ||
| auto_insert_metric_name: false | ||
| save_weights_only: false | ||
| every_n_train_steps: null | ||
| train_time_interval: null | ||
| every_n_epochs: 1 | ||
| save_on_train_epoch_end: null | ||
| early_stopping: | ||
| _target_: lightning.pytorch.callbacks.EarlyStopping | ||
| monitor: val/loss | ||
| min_delta: 0.0 | ||
| patience: 100 | ||
| verbose: false | ||
| mode: min | ||
| strict: true | ||
| check_finite: true | ||
| stopping_threshold: null | ||
| divergence_threshold: null | ||
| check_on_train_epoch_end: null | ||
| model_summary: | ||
| _target_: lightning.pytorch.callbacks.RichModelSummary | ||
| max_depth: -1 | ||
| rich_progress_bar: | ||
| _target_: lightning.pytorch.callbacks.RichProgressBar | ||
| logger: | ||
| csv: | ||
| _target_: lightning.pytorch.loggers.csv_logs.CSVLogger | ||
| save_dir: ${paths.output_dir} | ||
| name: csv/ | ||
| prefix: '' | ||
| trainer: | ||
| _target_: lightning.Trainer | ||
| default_root_dir: ${paths.output_dir} | ||
| min_epochs: 1 | ||
| max_epochs: 100 | ||
| accelerator: gpu | ||
| devices: 1 | ||
| precision: 16 | ||
| check_val_every_n_epoch: 1 | ||
| deterministic: false | ||
| detect_anomaly: false | ||
| max_time: null | ||
| paths: | ||
| root_dir: ${oc.env:PROJECT_ROOT, './'} | ||
| data_dir: ${paths.root_dir}/data/ | ||
| log_dir: ${paths.root_dir}/logs/ | ||
| output_dir: //allen/aics/assay-dev/users/Benji/office_hours/cyto-dl/logs | ||
| work_dir: //allen/aics/assay-dev/users/Benji/office_hours/cyto-dl/logs | ||
| extras: | ||
| ignore_warnings: true | ||
| enforce_tags: false | ||
| print_config: false | ||
| precision: | ||
| _target_: torch.set_float32_matmul_precision | ||
| precision: medium | ||
| persist_cache: True | ||
| source_col: raw | ||
| target_col1: seg1 | ||
| target_col2: seg2 | ||
| merge_mask_col: merge_mask | ||
| exclude_mask_col: exclude_mask | ||
| base_image_col: base_image | ||
| spatial_dims: 3 | ||
| input_channel: 3 | ||
| raw_im_channels: 1 |
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