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feat: preprocessing report #7
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base: feature/tile-masks
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@@ -181,3 +181,4 @@ lightning_logs/ | |
| # Project | ||
| /data | ||
| playground.ipynb | ||
| /outputs | ||
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| @@ -0,0 +1,20 @@ | ||
| defaults: | ||
| - _self_ | ||
| - hydra: default | ||
| - mlflow: kubas_cluster | ||
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| user: ??? | ||
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| reporter: | ||
| save: ??? | ||
| background: ??? | ||
| title: ??? | ||
| mask_retrievers: [] | ||
| metrics_run_ids: [] | ||
| template_asset_path: report_template.html | ||
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| metadata: | ||
| user: ${user} | ||
| experiment_name: ??? | ||
| run_name: ??? | ||
| description: ??? |
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| @@ -0,0 +1,6 @@ | ||
| job: | ||
| name: report | ||
| chdir: true | ||
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| help: | ||
| app_name: Experiment Report |
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| @@ -0,0 +1 @@ | ||
| tracking_uri: ??? |
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| @@ -0,0 +1 @@ | ||
| tracking_uri: http://mlflow.rationai-mlflow:5000/ |
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| @@ -0,0 +1 @@ | ||
| tracking_uri: https://mlflow.rationai.cloud.trusted.e-infra.cz/ |
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| @@ -0,0 +1 @@ | ||
| tracking_uri: file:./mlflow_store |
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| @@ -0,0 +1,3 @@ | ||
| _target_: report.masks.DriveMasksRetriever | ||
| dir_name: ??? | ||
| layer_name: ??? |
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| @@ -0,0 +1,3 @@ | ||
| _target_: report.masks.ArtifactURIMasksRetriever | ||
| artifact_uri: ??? | ||
| layer_name: ??? |
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|---|---|---|
| @@ -0,0 +1,4 @@ | ||
| _target_: report.masks.RunIDMlflowMaskRetriever | ||
| dir_name: ??? | ||
| run_id: ??? | ||
| layer_name: ??? |
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|---|---|---|
| @@ -0,0 +1,6 @@ | ||
| _target_: report.masks.TylerMLFlowMaskRetriever | ||
| artifact_uris: ??? | ||
| item_name_col: ??? | ||
| background_masks_directory: ??? | ||
| ground_truth_col: ??? | ||
| layer_name: ??? |
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|---|---|---|---|---|---|---|
| @@ -0,0 +1,76 @@ | ||||||
| defaults: | ||||||
| - background: drive | ||||||
| - save: mlflow_standalone_run | ||||||
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| title: Ulcerative Colitis Preprocessing - ftn | ||||||
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| background: | ||||||
| dir_name: /mnt/data/FTN/colon/IBD_AI | ||||||
| layer_name: Ulcerative Colitis | ||||||
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| mask_retrievers: | ||||||
| - _target_: report.masks.RunIDMlflowMaskRetriever | ||||||
| run_id: TODO | ||||||
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| dir_name: tissue_masks | ||||||
| layer_name: Tissue mask | ||||||
| shader_conf: | ||||||
| type: heatmap | ||||||
| opacity: 0.5 | ||||||
| color: "#ffff00" | ||||||
| visible: False | ||||||
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| - _target_: report.masks.RunIDMlflowMaskRetriever | ||||||
| run_id: TODO | ||||||
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| dir_name: blur_per_pixel | ||||||
| layer_name: Blur | ||||||
| shader_conf: | ||||||
| type: heatmap | ||||||
| opacity: 0.5 | ||||||
| color: "#00ffff" | ||||||
| visible: False | ||||||
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| - _target_: report.masks.RunIDMlflowMaskRetriever | ||||||
| run_id: TODO | ||||||
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| dir_name: artifacts_per_pixel | ||||||
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| dir_name: artifacts_per_pixel | |
| dir_name: artifacts_per_pixel |
Copilot
AI
Feb 12, 2026
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The run_id is set to "TODO" which is a placeholder value. This configuration will fail at runtime if used without a valid MLflow run ID.
Copilot
AI
Feb 12, 2026
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Inconsistent directory path compared to knl_patos.yaml which uses "tile_masks/clean_tiles" for the same layer. This inconsistency may cause the report to fail if the actual artifact structure matches knl_patos.yaml.
| dir_name: clean_tiles | |
| dir_name: tile_masks/clean_tiles |
Copilot
AI
Feb 12, 2026
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The run_id is set to "TODO" which is a placeholder value. This configuration will fail at runtime if used without a valid MLflow run ID.
Copilot
AI
Feb 12, 2026
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Inconsistent directory path compared to knl_patos.yaml which uses "tile_masks/blur_tiles" for the same layer. This inconsistency may cause the report to fail if the actual artifact structure matches knl_patos.yaml.
| dir_name: blur_tiles | |
| dir_name: tile_masks/blur_tiles |
Copilot
AI
Feb 12, 2026
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Inconsistent directory path compared to knl_patos.yaml which uses "tile_masks/artifacts_tiles" for the same layer. This inconsistency may cause the report to fail if the actual artifact structure matches knl_patos.yaml.
| dir_name: artifacts_tiles | |
| dir_name: tile_masks/artifacts_tiles |
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Copilot
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Feb 12, 2026
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Inconsistent capitalization in run_name. "ftn" should be capitalized (e.g., "FTN") to match the pattern used in other configuration files where dataset sources are uppercase (e.g., "ikem", "knl patos").
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| Original file line number | Diff line number | Diff line change | ||||
|---|---|---|---|---|---|---|
| @@ -0,0 +1,76 @@ | ||||||
| defaults: | ||||||
| - background: drive | ||||||
| - save: mlflow_standalone_run | ||||||
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| title: Ulcerative Colitis Preprocessing - IKEM | ||||||
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| background: | ||||||
| dir_name: /mnt/data/IKEM/colon/IBD_AI/20x | ||||||
| layer_name: Ulcerative Colitis | ||||||
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| mask_retrievers: | ||||||
| - _target_: report.masks.RunIDMlflowMaskRetriever | ||||||
| run_id: TODO | ||||||
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| dir_name: tissue_masks | ||||||
| layer_name: Tissue mask | ||||||
| shader_conf: | ||||||
| type: heatmap | ||||||
| opacity: 0.5 | ||||||
| color: "#ffff00" | ||||||
| visible: False | ||||||
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| - _target_: report.masks.RunIDMlflowMaskRetriever | ||||||
| run_id: TODO | ||||||
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| dir_name: blur_per_pixel | ||||||
| layer_name: Blur | ||||||
| shader_conf: | ||||||
| type: heatmap | ||||||
| opacity: 0.5 | ||||||
| color: "#00ffff" | ||||||
| visible: False | ||||||
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| - _target_: report.masks.RunIDMlflowMaskRetriever | ||||||
| run_id: TODO | ||||||
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| dir_name: artifacts_per_pixel | ||||||
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| dir_name: artifacts_per_pixel | |
| dir_name: artifacts_per_pixel |
Copilot
AI
Feb 12, 2026
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The run_id is set to "TODO" which is a placeholder value. This configuration will fail at runtime if used without a valid MLflow run ID.
Copilot
AI
Feb 12, 2026
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Inconsistent directory path compared to knl_patos.yaml which uses "tile_masks/clean_tiles" for the same layer. This inconsistency may cause the report to fail if the actual artifact structure matches knl_patos.yaml.
| dir_name: clean_tiles | |
| dir_name: tile_masks/clean_tiles |
Copilot
AI
Feb 12, 2026
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The run_id is set to "TODO" which is a placeholder value. This configuration will fail at runtime if used without a valid MLflow run ID.
Copilot
AI
Feb 12, 2026
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Inconsistent directory path compared to knl_patos.yaml which uses "tile_masks/blur_tiles" for the same layer. This inconsistency may cause the report to fail if the actual artifact structure matches knl_patos.yaml.
| dir_name: blur_tiles | |
| dir_name: tile_masks/blur_tiles |
Copilot
AI
Feb 12, 2026
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The run_id is set to "TODO" which is a placeholder value. This configuration will fail at runtime if used without a valid MLflow run ID.
Copilot
AI
Feb 12, 2026
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Inconsistent directory path compared to knl_patos.yaml which uses "tile_masks/artifacts_tiles" for the same layer. This inconsistency may cause the report to fail if the actual artifact structure matches knl_patos.yaml.
| dir_name: artifacts_tiles | |
| dir_name: tile_masks/artifacts_tiles |
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| Original file line number | Diff line number | Diff line change | ||||
|---|---|---|---|---|---|---|
| @@ -0,0 +1,78 @@ | ||||||
| defaults: | ||||||
| - save: mlflow_standalone_run | ||||||
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| title: Ulcerative Colitis Preprocessing - KNL Patos | ||||||
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| background: | ||||||
| _target_: report.masks.BasicImageRetriever | ||||||
| source_dir: /mnt/data/KNL_PATOS/colon/IBD_AI | ||||||
| globs: | ||||||
| - "*.czi" | ||||||
| layer_name: Ulcerative Colitis | ||||||
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| mask_retrievers: | ||||||
| - _target_: report.masks.RunIDMlflowMaskRetriever | ||||||
| run_id: 8ef6d6f0c9af4f35a087596960f675aa | ||||||
| dir_name: tissue_masks | ||||||
| layer_name: Tissue mask | ||||||
| shader_conf: | ||||||
| type: heatmap | ||||||
| opacity: 0.5 | ||||||
| color: "#ffff00" | ||||||
| visible: False | ||||||
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| - _target_: report.masks.RunIDMlflowMaskRetriever | ||||||
| run_id: 75fc3e53112f4634ae5238777d87e88c | ||||||
| dir_name: blur_per_pixel | ||||||
| layer_name: Blur | ||||||
| shader_conf: | ||||||
| type: heatmap | ||||||
| opacity: 0.5 | ||||||
| color: "#00ffff" | ||||||
| visible: False | ||||||
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| - _target_: report.masks.RunIDMlflowMaskRetriever | ||||||
| run_id: 75fc3e53112f4634ae5238777d87e88c | ||||||
| dir_name: artifacts_per_pixel | ||||||
|
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| dir_name: artifacts_per_pixel | |
| dir_name: artifacts_per_pixel |
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,2 @@ | ||
| _target_: report.save.LocalReportStorer | ||
| output_path: report.html |
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| _target_: report.save.RunIDMLFlowReportAttacher | ||
| artifact_path: report.html | ||
| run_id: ??? |
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| @@ -0,0 +1,3 @@ | ||
| _target_: report.save.MLFlowReportStorer | ||
| artifact_path: report.html | ||
| metadata: ${metadata} |
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Inconsistent capitalization in title. "ftn" should be capitalized (e.g., "FTN") to match the pattern used in other configuration files where dataset sources are uppercase (e.g., "IKEM", "KNL Patos").