feat: tile masks #6
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@@ -180,3 +180,4 @@ lightning_logs/ | |
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| # Project | ||
| /data | ||
| playground.ipynb | ||
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| defaults: | ||
| - hydra: default | ||
| - logger: mlflow | ||
| - _self_ | ||
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| metadata: | ||
| experiment_name: Ulcerative Colitis |
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| defaults: | ||
| - /dataset/raw/ftn@_here_ | ||
| - _self_ | ||
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| uri: mlflow-artifacts:/86/142642fc780f4a96800c691168b5c2c3/artifacts/dataset.csv # TODO update URI |
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| defaults: | ||
| - /dataset/raw/ikem@_here_ | ||
| - _self_ | ||
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| uri: mlflow-artifacts:/86/52d0081d60ba4585a16a3bd341d5ab09/artifacts/dataset.csv # TODO update URI |
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| @@ -0,0 +1,5 @@ | ||
| defaults: | ||
| - /dataset/raw/knl_patos@_here_ | ||
| - _self_ | ||
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| uri: mlflow-artifacts:/86/afbcfd43cb3c4fd0b1e9b5dbe7327d91/artifacts/dataset.csv # TODO update URI |
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| @@ -0,0 +1,6 @@ | ||
| defaults: | ||
| - /dataset/processed/ftn@_here_ | ||
| - _self_ | ||
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| tissue_mask_uri: mlflow-artifacts:/86/04778b10de254572b69ce0a101c1eee4/artifacts/tissue_masks # TODO update URI | ||
| qc_mask_uri: mlflow-artifacts:/86/c8edfb2541e84b44b1a28be3540c1a35/artifacts # TODO update URI |
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,6 @@ | ||
| defaults: | ||
| - /dataset/processed/ikem@_here_ | ||
| - _self_ | ||
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| tissue_mask_uri: mlflow-artifacts:/86/13359cdd5d1a47ddabc352b9aa0d7635/artifacts/tissue_masks # TODO update URI | ||
| qc_mask_uri: mlflow-artifacts:/86/98443fe2b67445d5a56598bff15b7f27/artifacts # TODO update URI |
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,6 @@ | ||
| defaults: | ||
| - /dataset/processed/knl_patos@_here_ | ||
| - _self_ | ||
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| tissue_mask_uri: mlflow-artifacts:/86/8ef6d6f0c9af4f35a087596960f675aa/artifacts/tissue_masks # TODO update URI | ||
| qc_mask_uri: mlflow-artifacts:/86/75fc3e53112f4634ae5238777d87e88c/artifacts # TODO update URI |
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| @@ -0,0 +1,5 @@ | ||
| institution: ftn | ||
| folder: /mnt/data/FTN/colon/IBD_AI | ||
| labels: | ||
| - IBD_AI_FTN.xlsx | ||
| - IBD_AI_FTN_doplnek.xlsx |
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| institution: ikem | ||
| folder: /mnt/data/IKEM/colon/IBD_AI/20x | ||
| labels: | ||
| - Fab_IBD_AI_12_2024.csv | ||
| - IBD_AI_2.xlsx | ||
| - missing.xlsx |
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,7 @@ | ||
| institution: knl_patos | ||
| folder: /mnt/data/KNL_PATOS/colon/IBD_AI | ||
| labels: | ||
| - IBD_AI_Liberec.xlsx | ||
| - IBD_AI_Liberec_02.xlsx | ||
| - IBD_AI_Liberec_10_2025.xlsx | ||
| - IBD_AI_Liberec_28_10_2025.xlsx |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,11 @@ | ||
| defaults: | ||
| - /dataset/processed_w_masks/ftn@_here_ | ||
| - _self_ | ||
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| mpp: 0.17 | ||
| tile_extent: 320 | ||
| level: 0 | ||
| tiling_uris: | ||
| train: "mlflow-artifacts:/86/bbbe4603bc30495d85ac99093fc9269a/artifacts/train - ftn" # TODO update URI | ||
| test_preliminary: "mlflow-artifacts:/86/bbbe4603bc30495d85ac99093fc9269a/artifacts/test preliminary - ftn" # TODO update URI | ||
| test_final: "mlflow-artifacts:/86/bbbe4603bc30495d85ac99093fc9269a/artifacts/test final - ftn" # TODO update URI | ||
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,11 @@ | ||
| defaults: | ||
| - /dataset/processed_w_masks/ftn@_here_ | ||
| - _self_ | ||
|
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| mpp: 0.17 | ||
| tile_extent: 430 | ||
| level: 0 | ||
| tiling_uris: | ||
| train: "mlflow-artifacts:/86/de450f835f0d4462a91b35f4a79a500f/artifacts/train - ftn" # TODO update URI | ||
| test_preliminary: "mlflow-artifacts:/86/de450f835f0d4462a91b35f4a79a500f/artifacts/test preliminary - ftn" # TODO update URI | ||
| test_final: "mlflow-artifacts:/86/de450f835f0d4462a91b35f4a79a500f/artifacts/test final - ftn" # TODO update URI | ||
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,11 @@ | ||
| defaults: | ||
| - /dataset/processed_w_masks/ftn@_here_ | ||
| - _self_ | ||
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| mpp: 0.52 | ||
| tile_extent: 224 | ||
| level: 1 | ||
| tiling_uris: | ||
| train: "mlflow-artifacts:/86/f85b64a7f96c41e38f86d84956e2dbe9/artifacts/train - ftn" # TODO update URI | ||
| test_preliminary: "mlflow-artifacts:/86/f85b64a7f96c41e38f86d84956e2dbe9/artifacts/test preliminary - ftn" # TODO update URI | ||
| test_final: "mlflow-artifacts:/86/f85b64a7f96c41e38f86d84956e2dbe9/artifacts/test final - ftn" # TODO update URI | ||
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,11 @@ | ||
| defaults: | ||
| - /dataset/processed_w_masks/ftn@_here_ | ||
| - _self_ | ||
|
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| mpp: 1.55 | ||
| tile_extent: 224 | ||
| level: 2 | ||
| tiling_uris: | ||
| train: "mlflow-artifacts:/86/5814484b6cd7467e9d712889655479af/artifacts/train - ftn" # TODO update URI | ||
| test_preliminary: "mlflow-artifacts:/86/5814484b6cd7467e9d712889655479af/artifacts/test preliminary - ftn" # TODO update URI | ||
| test_final: "mlflow-artifacts:/86/5814484b6cd7467e9d712889655479af/artifacts/test final - ftn" # TODO update URI | ||
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,11 @@ | ||
| defaults: | ||
| - /dataset/processed_w_masks/ikem@_here_ | ||
| - _self_ | ||
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| mpp: 0.17 | ||
| tile_extent: 320 | ||
| level: 0 | ||
| tiling_uris: | ||
| train: "mlflow-artifacts:/86/4486e598446d412d926ac66dadb35e51/artifacts/train - ikem" # TODO update URI | ||
| test_preliminary: "mlflow-artifacts:/86/4486e598446d412d926ac66dadb35e51/artifacts/test preliminary - ikem" # TODO update URI | ||
| test_final: "mlflow-artifacts:/86/4486e598446d412d926ac66dadb35e51/artifacts/test final - ikem" # TODO update URI | ||
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,11 @@ | ||
| defaults: | ||
| - /dataset/processed_w_masks/ikem@_here_ | ||
| - _self_ | ||
|
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| mpp: 0.17 | ||
| tile_extent: 430 | ||
| level: 0 | ||
| tiling_uris: | ||
| train: "mlflow-artifacts:/86/fd112e63819c49d999502542b35bfce1/artifacts/train - ikem" # TODO update URI | ||
| test_preliminary: "mlflow-artifacts:/86/fd112e63819c49d999502542b35bfce1/artifacts/test preliminary - ikem" # TODO update URI | ||
| test_final: "mlflow-artifacts:/86/fd112e63819c49d999502542b35bfce1/artifacts/test final - ikem" # TODO update URI | ||
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,11 @@ | ||
| defaults: | ||
| - /dataset/processed_w_masks/ikem@_here_ | ||
| - _self_ | ||
|
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| mpp: 0.52 | ||
| tile_extent: 224 | ||
| level: 1 | ||
| tiling_uris: | ||
| train: "mlflow-artifacts:/86/ece822e7c0e3416f97212267c773c8ac/artifacts/train - ikem" # TODO update URI | ||
| test_preliminary: "mlflow-artifacts:/86/ece822e7c0e3416f97212267c773c8ac/artifacts/test preliminary - ikem" # TODO update URI | ||
| test_final: "mlflow-artifacts:/86/ece822e7c0e3416f97212267c773c8ac/artifacts/test final - ikem" # TODO update URI | ||
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,11 @@ | ||
| defaults: | ||
| - /dataset/processed_w_masks/ikem@_here_ | ||
| - _self_ | ||
|
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||
| mpp: 1.55 | ||
| tile_extent: 224 | ||
| level: 2 | ||
| tiling_uris: | ||
| train: "mlflow-artifacts:/86/0c09e1c61d294fa3877b6b21703bab2f/artifacts/train - ikem" # TODO update URI | ||
| test_preliminary: "mlflow-artifacts:/86/0c09e1c61d294fa3877b6b21703bab2f/artifacts/test preliminary - ikem" # TODO update URI | ||
| test_final: "mlflow-artifacts:/86/0c09e1c61d294fa3877b6b21703bab2f/artifacts/test final - ikem" # TODO update URI | ||
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,10 @@ | ||
| defaults: | ||
| - /dataset/processed_w_masks/knl_patos@_here_ | ||
| - _self_ | ||
|
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| mpp: 0.17 | ||
| tile_extent: 320 | ||
| level: 0 | ||
| tiling_uris: | ||
| test_preliminary: "mlflow-artifacts:/86/7b9a446145b14965981bbac88e8e2c8b/artifacts/test preliminary - knl_patos" # TODO update URI | ||
| test_final: "mlflow-artifacts:/86/7b9a446145b14965981bbac88e8e2c8b/artifacts/test final - knl_patos" # TODO update URI | ||
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,10 @@ | ||
| defaults: | ||
| - /dataset/processed_w_masks/knl_patos@_here_ | ||
| - _self_ | ||
|
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| mpp: 0.17 | ||
| tile_extent: 430 | ||
| level: 0 | ||
| tiling_uris: | ||
| test_preliminary: "mlflow-artifacts:/86/eb29255c944d4dad926160a7cb102ad9/artifacts/test preliminary - knl_patos" # TODO update URI | ||
| test_final: "mlflow-artifacts:/86/eb29255c944d4dad926160a7cb102ad9/artifacts/test final - knl_patos" # TODO update URI | ||
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,10 @@ | ||
| defaults: | ||
| - /dataset/processed_w_masks/knl_patos@_here_ | ||
| - _self_ | ||
|
|
||
| mpp: 0.52 | ||
| tile_extent: 224 | ||
| level: 1 | ||
| tiling_uris: | ||
| test_preliminary: "mlflow-artifacts:/86/6782155362d54ecc9f1beccb4362d359/artifacts/test preliminary - knl_patos" # TODO update URI | ||
| test_final: "mlflow-artifacts:/86/6782155362d54ecc9f1beccb4362d359/artifacts/test final - knl_patos" # TODO update URI | ||
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,10 @@ | ||
| defaults: | ||
| - /dataset/processed_w_masks/knl_patos@_here_ | ||
| - _self_ | ||
|
|
||
| mpp: 1.55 | ||
| tile_extent: 224 | ||
| level: 2 | ||
| tiling_uris: | ||
| test_preliminary: "mlflow-artifacts:/86/d7486bb6b667433989c3ce1c8ce31d60/artifacts/test preliminary - knl_patos" # TODO update URI | ||
| test_final: "mlflow-artifacts:/86/d7486bb6b667433989c3ce1c8ce31d60/artifacts/test final - knl_patos" # TODO update URI | ||
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,14 @@ | ||
| # @package _global_ | ||
|
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| defaults: | ||
| - /dataset/processed_w_masks/ftn@dataset | ||
| - _self_ | ||
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| mpp: 0.17 # level 0 | ||
| tile_extent: 320 | ||
| stride: 320 | ||
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| splits: | ||
| train: 0.7 | ||
| test_preliminary: 0.15 | ||
| test_final: 0.15 |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,14 @@ | ||
| # @package _global_ | ||
|
|
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| defaults: | ||
| - /dataset/processed_w_masks/ftn@dataset | ||
| - _self_ | ||
|
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| mpp: 0.17 # level 0 | ||
| tile_extent: 430 # 75 / 0.17 ≈ 430 | ||
| stride: 430 | ||
|
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||
| splits: | ||
| train: 0.7 | ||
| test_preliminary: 0.15 | ||
| test_final: 0.15 |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,14 @@ | ||
| # @package _global_ | ||
|
|
||
| defaults: | ||
| - /dataset/processed_w_masks/ftn@dataset | ||
| - _self_ | ||
|
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| mpp: 0.52 # level 1 | ||
| tile_extent: 224 | ||
| stride: 112 | ||
|
|
||
| splits: | ||
| train: 0.7 | ||
| test_preliminary: 0.15 | ||
| test_final: 0.15 |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,14 @@ | ||
| # @package _global_ | ||
|
|
||
| defaults: | ||
| - /dataset/processed_w_masks/ftn@dataset | ||
| - _self_ | ||
|
|
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| mpp: 1.55 # level 2 | ||
| tile_extent: 224 | ||
| stride: 112 | ||
|
|
||
| splits: | ||
| train: 0.7 | ||
| test_preliminary: 0.15 | ||
| test_final: 0.15 |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,14 @@ | ||
| # @package _global_ | ||
|
|
||
| defaults: | ||
| - /dataset/processed_w_masks/ikem@dataset | ||
| - _self_ | ||
|
|
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| mpp: 0.17 # level 0 | ||
| tile_extent: 320 | ||
| stride: 320 | ||
|
|
||
| splits: | ||
| train: 0.7 | ||
| test_preliminary: 0.15 | ||
| test_final: 0.15 |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,14 @@ | ||
| # @package _global_ | ||
|
|
||
| defaults: | ||
| - /dataset/processed_w_masks/ikem@dataset | ||
| - _self_ | ||
|
|
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| mpp: 0.17 # level 0 | ||
| tile_extent: 430 # 75 / 0.17 ≈ 430 | ||
| stride: 430 | ||
|
|
||
| splits: | ||
| train: 0.7 | ||
| test_preliminary: 0.15 | ||
| test_final: 0.15 |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,14 @@ | ||
| # @package _global_ | ||
|
|
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| defaults: | ||
| - /dataset/processed_w_masks/ikem@dataset | ||
| - _self_ | ||
|
|
||
| mpp: 0.52 # level 1 | ||
| tile_extent: 224 | ||
| stride: 112 | ||
|
|
||
| splits: | ||
| train: 0.7 | ||
| test_preliminary: 0.15 | ||
| test_final: 0.15 |
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The URIs in this configuration file contain
TODO update URIcomments, indicating they are placeholders. These should be updated with the correct values before merging to ensure the configuration is complete and functional. Additionally, the file is missing a final newline character, which is a standard convention for text files and can prevent issues with some tools.