From 445203d159d4052b356183e501da58309cffbc4c Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Michal=20Ki=C5=A1=C5=A1?= <550439@mail.muni.cz>
Date: Fri, 6 Mar 2026 12:35:30 +0100
Subject: [PATCH 1/5] fix: add shm + conditional epithelium mask

---
 preprocessing/tiling.py             | 25 +++++++++++++++++++++----
 scripts/preprocessing/run_tiling.py |  5 +++--
 2 files changed, 24 insertions(+), 6 deletions(-)

diff --git a/preprocessing/tiling.py b/preprocessing/tiling.py
index cf66793..01be2f9 100644
--- a/preprocessing/tiling.py
+++ b/preprocessing/tiling.py
@@ -23,10 +23,14 @@
 from shapely.geometry import box
 from shapely.geometry.polygon import Polygon
 
-
 BATCH_SIZE = 256
 
 
+def add_missing_epithelium_overlap(batch: DataBatch) -> DataBatch:
+    batch["epithelium_overlap"] = np.nan
+    return batch
+
+
 def add_tile_overlap(
     tiles: Dataset,
     roi: Polygon,
@@ -238,9 +242,22 @@ def main(config: DictConfig, logger: MLFlowLogger) -> None:
     tiles = add_tile_overlap(
         tiles, full_roi, "residual_mask_path", "residual_overlap", "0"
     )
-    tiles = add_tile_overlap(
-        tiles, full_roi, "epithelium_mask_path", "epithelium_overlap", "0"
-    )
+    if epithelium_masks_path:
+        print("[INFO] Computing overlap: epithelium_overlap from epithelium_mask_path")
+        tiles = add_tile_overlap(
+            tiles, full_roi, "epithelium_mask_path", "epithelium_overlap", "0"
+        )
+    else:
+        print(
+            "[INFO] Skipping epithelium overlap: dataset.mlflow_uris.epithelium_masks is not set"
+        )
+
+        tiles = tiles.map_batches(
+            add_missing_epithelium_overlap,
+            batch_format="pandas",
+            num_cpus=1,
+            memory=BATCH_SIZE * 8 * 512**2,
+        )
 
     # Drop unnecessary columns
     tiles = tiles.drop_columns(
diff --git a/scripts/preprocessing/run_tiling.py b/scripts/preprocessing/run_tiling.py
index 134a55d..0811fea 100644
--- a/scripts/preprocessing/run_tiling.py
+++ b/scripts/preprocessing/run_tiling.py
@@ -5,8 +5,9 @@
     job_name="mammaprint-tiling-...",
     username=...,
     image="cerit.io/rationai/base:2.0.6",
-    cpu=8,
-    memory="32Gi",
+    cpu=16,
+    memory="64Gi",
+    shm="32Gi",
     gpu=None,
     public=False,
     script=[

From 240c4bf8368421d8a9a0dcc0adfba516ab47e70a Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Michal=20Ki=C5=A1=C5=A1?= <550439@mail.muni.cz>
Date: Sat, 7 Mar 2026 20:28:56 +0100
Subject: [PATCH 2/5] fix: lower memory, bigger repartition

---
 preprocessing/tiling.py | 14 +++++++-------
 1 file changed, 7 insertions(+), 7 deletions(-)

diff --git a/preprocessing/tiling.py b/preprocessing/tiling.py
index 01be2f9..2c177cc 100644
--- a/preprocessing/tiling.py
+++ b/preprocessing/tiling.py
@@ -82,7 +82,7 @@ def add_tile_overlap(
         col("mpp_y"),
     )
     tiles = tiles.with_column(
-        overlap_struct_col, overlap_struct, num_cpus=1, memory=BATCH_SIZE * 8 * 512**2
+        overlap_struct_col, overlap_struct, num_cpus=0.2, memory=256 * 1024**2
     )
 
     def extract_value(batch: DataBatch) -> DataBatch:
@@ -97,8 +97,8 @@ def extract_value(batch: DataBatch) -> DataBatch:
     tiles = tiles.map_batches(
         extract_value,
         batch_format="pandas",
-        num_cpus=1,
-        memory=BATCH_SIZE * 8 * 512**2,
+        num_cpus=0.1,
+        memory=128 * 1024**2,
     )
 
     return tiles.drop_columns([overlap_struct_col])
@@ -219,8 +219,8 @@ def main(config: DictConfig, logger: MLFlowLogger) -> None:
             epithelium_masks_path=epithelium_masks_path,
         ),
         num_cpus=0.2,
-        memory=BATCH_SIZE * 1024**2,
-    ).repartition(target_num_rows_per_block=BATCH_SIZE)
+        memory=128 * 1024**2,
+    ).repartition(target_num_rows_per_block=4096)
 
     # Compute masks and filter tissue tiles
     # Tissue mask checks center 50%
@@ -255,8 +255,8 @@ def main(config: DictConfig, logger: MLFlowLogger) -> None:
         tiles = tiles.map_batches(
             add_missing_epithelium_overlap,
             batch_format="pandas",
-            num_cpus=1,
-            memory=BATCH_SIZE * 8 * 512**2,
+            num_cpus=0.1,
+            memory=128 * 1024**2,
         )
 
     # Drop unnecessary columns

From 05fda03cf536b2747ac598260449ff5826812f99 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Michal=20Ki=C5=A1=C5=A1?= <550439@mail.muni.cz>
Date: Mon, 9 Mar 2026 12:58:17 +0100
Subject: [PATCH 3/5] fix: increase memory constrains

---
 preprocessing/tiling.py | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/preprocessing/tiling.py b/preprocessing/tiling.py
index 2c177cc..627bad3 100644
--- a/preprocessing/tiling.py
+++ b/preprocessing/tiling.py
@@ -82,7 +82,7 @@ def add_tile_overlap(
         col("mpp_y"),
     )
     tiles = tiles.with_column(
-        overlap_struct_col, overlap_struct, num_cpus=0.2, memory=256 * 1024**2
+        overlap_struct_col, overlap_struct, num_cpus=0.2, memory=512 * 1024**2
     )
 
     def extract_value(batch: DataBatch) -> DataBatch:
@@ -98,7 +98,7 @@ def extract_value(batch: DataBatch) -> DataBatch:
         extract_value,
         batch_format="pandas",
         num_cpus=0.1,
-        memory=128 * 1024**2,
+        memory=256 * 1024**2,
     )
 
     return tiles.drop_columns([overlap_struct_col])
@@ -208,7 +208,7 @@ def main(config: DictConfig, logger: MLFlowLogger) -> None:
     )
 
     # Create unique slide IDs and save slide metadata
-    slides = slides.map(row_hash, num_cpus=0.1, memory=128 * 1024**2)
+    slides = slides.map(row_hash, num_cpus=0.1, memory=256 * 1024**2)
 
     # Expand slides into tile coordinates
     tiles = slides.flat_map(
@@ -219,7 +219,7 @@ def main(config: DictConfig, logger: MLFlowLogger) -> None:
             epithelium_masks_path=epithelium_masks_path,
         ),
         num_cpus=0.2,
-        memory=128 * 1024**2,
+        memory=256 * 1024**2,
     ).repartition(target_num_rows_per_block=4096)
 
     # Compute masks and filter tissue tiles
@@ -256,7 +256,7 @@ def main(config: DictConfig, logger: MLFlowLogger) -> None:
             add_missing_epithelium_overlap,
             batch_format="pandas",
             num_cpus=0.1,
-            memory=128 * 1024**2,
+            memory=256 * 1024**2,
         )
 
     # Drop unnecessary columns

From 8f8efd05f9a3a3f18d0e5bb0db3c9c54883e78cb Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Michal=20Ki=C5=A1=C5=A1?= <550439@mail.muni.cz>
Date: Sat, 14 Mar 2026 11:07:16 +0100
Subject: [PATCH 4/5] fix: change materialize order

---
 preprocessing/tiling.py | 14 ++++++++++++--
 1 file changed, 12 insertions(+), 2 deletions(-)

diff --git a/preprocessing/tiling.py b/preprocessing/tiling.py
index 627bad3..b744698 100644
--- a/preprocessing/tiling.py
+++ b/preprocessing/tiling.py
@@ -210,6 +210,11 @@ def main(config: DictConfig, logger: MLFlowLogger) -> None:
     # Create unique slide IDs and save slide metadata
     slides = slides.map(row_hash, num_cpus=0.1, memory=256 * 1024**2)
 
+    # Materialize slides so the source pipeline (read + join + hash) runs once
+    # and is reused for both slides_df and the tiles pipeline.
+    slides = slides.materialize()
+    slides_df = slides.to_pandas()
+
     # Expand slides into tile coordinates
     tiles = slides.flat_map(
         partial(
@@ -235,6 +240,12 @@ def main(config: DictConfig, logger: MLFlowLogger) -> None:
         tiles, tissue_roi, "tissue_mask_path", "tissue_overlap", "0"
     )
     tiles = tiles.filter(expr=col("tissue_overlap") > 0.0)
+
+    # Materialize after tissue filter to:
+    # 1. Lock in the reduction (discard background tiles before computing remaining overlaps)
+    # 2. Break the long operator chain to prevent streaming backpressure starvation
+    tiles = tiles.materialize()
+
     tiles = add_tile_overlap(tiles, full_roi, "blur_mask_path", "blur_overlap", "255")
     tiles = add_tile_overlap(
         tiles, full_roi, "folding_mask_path", "folding_overlap", "255"
@@ -272,8 +283,7 @@ def main(config: DictConfig, logger: MLFlowLogger) -> None:
         ]
     )
 
-    # Convert Ray Datasets to pandas DataFrames
-    slides_df = slides.to_pandas()
+    # Convert tiles Ray Dataset to pandas DataFrame
     tiles_df = tiles.to_pandas()
 
     save_mlflow_dataset(

From 0230d9715a7cae7353c5ae6e847a711293212cd8 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Michal=20Ki=C5=A1=C5=A1?= <550439@mail.muni.cz>
Date: Wed, 15 Apr 2026 09:36:12 +0200
Subject: [PATCH 5/5] fix: bump versions

---
 pyproject.toml |   4 +-
 uv.lock        | 326 +++++++++++++++++++++++++++++++++++++++++++++----
 2 files changed, 303 insertions(+), 27 deletions(-)

diff --git a/pyproject.toml b/pyproject.toml
index 3bc52fa..b79cda3 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -13,10 +13,10 @@ dependencies = [
     "hydra-core>=1.3.2",
     "lightning>=2.5.5",
     "omegaconf>=2.3.0",
-    "rationai-mlkit>=0.2.2",
+    "rationai-mlkit>=0.4.0",
     "rationai-masks>=1.1.1",
     "rationai-tiling>=1.1.1",
-    "ratiopath>=1.1.1",
+    "ratiopath>=1.3.1",
     "rationai-sdk"
 ]
 
diff --git a/uv.lock b/uv.lock
index 6c14139..7c81364 100644
--- a/uv.lock
+++ b/uv.lock
@@ -384,6 +384,40 @@ wheels = [
     { url = "https://files.pythonhosted.org/packages/92/38/3afd8da94fa076226c470f33632d6df726c469738c01224068f009357985/databricks_sdk-0.91.0-py3-none-any.whl", hash = "sha256:f4481780e66a4c7d24d9d2acdf6778efdb82031532852ccc42b8619b81d0f73f", size = 808425, upload-time = "2026-02-19T08:22:19.161Z" },
 ]
 
+[[package]]
+name = "datasets"
+version = "4.8.4"
+source = { registry = "https://pypi.org/simple" }
+dependencies = [
+    { name = "dill" },
+    { name = "filelock" },
+    { name = "fsspec", extra = ["http"] },
+    { name = "httpx" },
+    { name = "huggingface-hub" },
+    { name = "multiprocess" },
+    { name = "numpy" },
+    { name = "packaging" },
+    { name = "pandas" },
+    { name = "pyarrow" },
+    { name = "pyyaml" },
+    { name = "requests" },
+    { name = "tqdm" },
+    { name = "xxhash" },
+]
+sdist = { url = "https://files.pythonhosted.org/packages/22/22/73e46ac7a8c25e7ef0b3bd6f10da3465021d90219a32eb0b4d2afea4c56e/datasets-4.8.4.tar.gz", hash = "sha256:a1429ed853275ce7943a01c6d2e25475b4501eb758934362106a280470df3a52", size = 604382, upload-time = "2026-03-23T14:21:17.987Z" }
+wheels = [
+    { url = "https://files.pythonhosted.org/packages/b0/e5/247d094108e42ac26363ab8dc57f168840cf7c05774b40ffeb0d78868fcc/datasets-4.8.4-py3-none-any.whl", hash = "sha256:cdc8bee4698e549d78bf1fed6aea2eebc760b22b084f07e6fc020c6577a6ce6d", size = 526991, upload-time = "2026-03-23T14:21:15.89Z" },
+]
+
+[[package]]
+name = "dill"
+version = "0.4.1"
+source = { registry = "https://pypi.org/simple" }
+sdist = { url = "https://files.pythonhosted.org/packages/81/e1/56027a71e31b02ddc53c7d65b01e68edf64dea2932122fe7746a516f75d5/dill-0.4.1.tar.gz", hash = "sha256:423092df4182177d4d8ba8290c8a5b640c66ab35ec7da59ccfa00f6fa3eea5fa", size = 187315, upload-time = "2026-01-19T02:36:56.85Z" }
+wheels = [
+    { url = "https://files.pythonhosted.org/packages/1e/77/dc8c558f7593132cf8fefec57c4f60c83b16941c574ac5f619abb3ae7933/dill-0.4.1-py3-none-any.whl", hash = "sha256:1e1ce33e978ae97fcfcff5638477032b801c46c7c65cf717f95fbc2248f79a9d", size = 120019, upload-time = "2026-01-19T02:36:55.663Z" },
+]
+
 [[package]]
 name = "docker"
 version = "7.1.0"
@@ -452,6 +486,19 @@ wheels = [
     { url = "https://files.pythonhosted.org/packages/7f/9c/34f6962f9b9e9c71f6e5ed806e0d0ff03c9d1b0b2340088a0cf4bce09b18/flask-3.1.3-py3-none-any.whl", hash = "sha256:f4bcbefc124291925f1a26446da31a5178f9483862233b23c0c96a20701f670c", size = 103424, upload-time = "2026-02-19T05:00:56.027Z" },
 ]
 
+[[package]]
+name = "flask-cors"
+version = "6.0.2"
+source = { registry = "https://pypi.org/simple" }
+dependencies = [
+    { name = "flask" },
+    { name = "werkzeug" },
+]
+sdist = { url = "https://files.pythonhosted.org/packages/70/74/0fc0fa68d62f21daef41017dafab19ef4b36551521260987eb3a5394c7ba/flask_cors-6.0.2.tar.gz", hash = "sha256:6e118f3698249ae33e429760db98ce032a8bf9913638d085ca0f4c5534ad2423", size = 13472, upload-time = "2025-12-12T20:31:42.861Z" }
+wheels = [
+    { url = "https://files.pythonhosted.org/packages/4f/af/72ad54402e599152de6d067324c46fe6a4f531c7c65baf7e96c63db55eaf/flask_cors-6.0.2-py3-none-any.whl", hash = "sha256:e57544d415dfd7da89a9564e1e3a9e515042df76e12130641ca6f3f2f03b699a", size = 13257, upload-time = "2025-12-12T20:31:41.3Z" },
+]
+
 [[package]]
 name = "fonttools"
 version = "4.61.1"
@@ -650,6 +697,22 @@ wheels = [
     { url = "https://files.pythonhosted.org/packages/04/4b/29cac41a4d98d144bf5f6d33995617b185d14b22401f75ca86f384e87ff1/h11-0.16.0-py3-none-any.whl", hash = "sha256:63cf8bbe7522de3bf65932fda1d9c2772064ffb3dae62d55932da54b31cb6c86", size = 37515, upload-time = "2025-04-24T03:35:24.344Z" },
 ]
 
+[[package]]
+name = "hf-xet"
+version = "1.4.3"
+source = { registry = "https://pypi.org/simple" }
+sdist = { url = "https://files.pythonhosted.org/packages/53/92/ec9ad04d0b5728dca387a45af7bc98fbb0d73b2118759f5f6038b61a57e8/hf_xet-1.4.3.tar.gz", hash = "sha256:8ddedb73c8c08928c793df2f3401ec26f95be7f7e516a7bee2fbb546f6676113", size = 670477, upload-time = "2026-03-31T22:40:07.874Z" }
+wheels = [
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+    { url = "https://files.pythonhosted.org/packages/0b/f8/7aacb8e5f4a7899d39c787b5984e912e6c18b11be136ef13947d7a66d265/hf_xet-1.4.3-cp37-abi3-macosx_11_0_arm64.whl", hash = "sha256:e23717ce4186b265f69afa66e6f0069fe7efbf331546f5c313d00e123dc84583", size = 3562178, upload-time = "2026-03-31T22:39:51.295Z" },
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+    { url = "https://files.pythonhosted.org/packages/bc/f5/067363e1c96c6b17256910830d1b54099d06287e10f4ec6ec4e7e08371fc/hf_xet-1.4.3-cp37-abi3-musllinux_1_2_aarch64.whl", hash = "sha256:49ad8a8cead2b56051aa84d7fce3e1335efe68df3cf6c058f22a65513885baac", size = 4193200, upload-time = "2026-03-31T22:40:01.936Z" },
+    { url = "https://files.pythonhosted.org/packages/42/4b/53951592882d9c23080c7644542fda34a3813104e9e11fa1a7d82d419cb8/hf_xet-1.4.3-cp37-abi3-musllinux_1_2_x86_64.whl", hash = "sha256:7716d62015477a70ea272d2d68cd7cad140f61c52ee452e133e139abfe2c17ba", size = 4429392, upload-time = "2026-03-31T22:40:03.492Z" },
+    { url = "https://files.pythonhosted.org/packages/8a/21/75a6c175b4e79662ad8e62f46a40ce341d8d6b206b06b4320d07d55b188c/hf_xet-1.4.3-cp37-abi3-win_amd64.whl", hash = "sha256:6b591fcad34e272a5b02607485e4f2a1334aebf1bc6d16ce8eb1eb8978ac2021", size = 3677359, upload-time = "2026-03-31T22:40:13.619Z" },
+    { url = "https://files.pythonhosted.org/packages/8a/7c/44314ecd0e89f8b2b51c9d9e5e7a60a9c1c82024ac471d415860557d3cd8/hf_xet-1.4.3-cp37-abi3-win_arm64.whl", hash = "sha256:7c2c7e20bcfcc946dc67187c203463f5e932e395845d098cc2a93f5b67ca0b47", size = 3533664, upload-time = "2026-03-31T22:40:12.152Z" },
+]
+
 [[package]]
 name = "httpcore"
 version = "1.0.9"
@@ -678,6 +741,35 @@ wheels = [
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 ]
 
+[[package]]
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+version = "2.6.0"
+source = { registry = "https://pypi.org/simple" }
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+wheels = [
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+]
+
+[[package]]
+name = "huggingface-hub"
+version = "1.10.2"
+source = { registry = "https://pypi.org/simple" }
+dependencies = [
+    { name = "filelock" },
+    { name = "fsspec" },
+    { name = "hf-xet", marker = "platform_machine == 'AMD64' or platform_machine == 'aarch64' or platform_machine == 'amd64' or platform_machine == 'arm64' or platform_machine == 'x86_64'" },
+    { name = "httpx" },
+    { name = "packaging" },
+    { name = "pyyaml" },
+    { name = "tqdm" },
+    { name = "typer" },
+    { name = "typing-extensions" },
+]
+sdist = { url = "https://files.pythonhosted.org/packages/0c/4d/00734890c7fcfe2c7ff04f1c1a167186c42b19e370a2dd8cfd8c34fc92c4/huggingface_hub-1.10.2.tar.gz", hash = "sha256:4b276f820483b709dc86a53bcb8183ea496b8d8447c9f7f88a115a12b498a95f", size = 758428, upload-time = "2026-04-14T10:42:28.498Z" }
+wheels = [
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