Upload 3 files
Browse files- dataset.json +11 -0
- plans.json +169 -0
- predict_from_raw_data_args.json +11 -0
dataset.json
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{
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"channel_names": {
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"0": "GelIntensity"
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},
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"labels": {
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"background": 0,
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"band": 1
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},
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"numTraining": 470,
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"file_ending": ".tif"
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}
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plans.json
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{
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"dataset_name": "Dataset088_GELSEG",
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"plans_name": "nnUNetPlans",
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"original_median_spacing_after_transp": [
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999.0,
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1.0,
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1.0
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],
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"original_median_shape_after_transp": [
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1,
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1024,
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1360
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],
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"image_reader_writer": "NaturalImage2DIO",
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"transpose_forward": [
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0,
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1,
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2
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],
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"transpose_backward": [
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0,
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1,
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2
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],
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"configurations": {
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"2d": {
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"data_identifier": "nnUNetPlans_2d",
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"preprocessor_name": "DefaultPreprocessor",
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"batch_size": 13,
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"patch_size": [
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448,
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576
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],
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"median_image_size_in_voxels": [
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1024.0,
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1360.0
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],
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"spacing": [
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1.0,
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1.0
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],
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"normalization_schemes": [
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"ZScoreNormalization"
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],
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"use_mask_for_norm": [
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false
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],
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"UNet_class_name": "PlainConvUNet",
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"UNet_base_num_features": 32,
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"n_conv_per_stage_encoder": [
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2,
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2,
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],
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"n_conv_per_stage_decoder": [
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2,
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2,
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],
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"num_pool_per_axis": [
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6,
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6
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],
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"pool_op_kernel_sizes": [
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[
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1,
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],
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[
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],
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[
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],
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[
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],
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[
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],
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[
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],
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[
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2,
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]
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],
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"conv_kernel_sizes": [
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[
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3,
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],
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[
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3,
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],
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[
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3,
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],
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[
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3,
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],
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[
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3,
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],
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[
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],
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[
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3,
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]
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],
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"unet_max_num_features": 512,
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"resampling_fn_data": "resample_data_or_seg_to_shape",
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"resampling_fn_seg": "resample_data_or_seg_to_shape",
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"resampling_fn_data_kwargs": {
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"is_seg": false,
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"order": 3,
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"order_z": 0,
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"force_separate_z": null
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},
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"resampling_fn_seg_kwargs": {
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"is_seg": true,
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"order": 1,
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"order_z": 0,
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"force_separate_z": null
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},
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"resampling_fn_probabilities": "resample_data_or_seg_to_shape",
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"resampling_fn_probabilities_kwargs": {
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"is_seg": false,
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"order": 1,
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"order_z": 0,
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"force_separate_z": null
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},
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"batch_dice": true
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}
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},
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"experiment_planner_used": "ExperimentPlanner",
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"label_manager": "LabelManager",
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"foreground_intensity_properties_per_channel": {
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"0": {
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"max": 61398.0,
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"mean": 15909.5625,
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"median": 982.0,
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"min": 0.0,
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"percentile_00_5": 21.0,
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"percentile_99_5": 55435.0,
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"std": 19753.626953125
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}
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}
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}
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predict_from_raw_data_args.json
ADDED
@@ -0,0 +1,11 @@
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{
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"folder_with_segs_from_prev_stage": null,
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"list_of_lists_or_source_folder": "/exports/csce/eddie/eng/groups/DunnGroup/matthew/nnunet_training/full_set_with_val_dec_23/raw_data/test_set",
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"num_parts": 1,
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"num_processes_preprocessing": 3,
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"num_processes_segmentation_export": 3,
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"output_folder_or_list_of_truncated_output_files": "/exports/csce/eddie/eng/groups/DunnGroup/matthew/nnunet_training/full_set_with_val_dec_23/test_inference/epoch_best_fold_0",
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"overwrite": true,
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"part_id": 0,
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"save_probabilities": false
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}
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