Use temporary local Zarr for regionprops to prevent file errors

spimquant/workflow/Snakefile

@@ -314,6 +314,7 @@ if config.get("analysis_level") == "group":
 
 
 wildcard_constraints:
+    acq="[a-zA-Z0-9]+",
     stain="[a-zA-Z0-9]+",
     pairwise_contrast="[a-zA-Z0-9+_-]+",
     n4_spline="[0-9]+",

spimquant/workflow/rules/regionprops.smk

@@ -28,8 +28,8 @@ rule compute_filtered_regionprops:
         ),
     threads: 64 if config["dask_scheduler"] == "distributed" else 32
     resources:
-        mem_mb=256000,
-        runtime=180,
+        mem_mb=500000,
+        runtime=360,
     script:
         "../scripts/compute_filtered_regionprops.py"
 

spimquant/workflow/rules/segstats.smk

@@ -143,7 +143,7 @@ rule merge_into_segstats_tsv:
         ),
     threads: 1
     resources:
-        mem_mb=1500,
+        mem_mb=16000,
         runtime=15,
     script:
         "../scripts/merge_into_segstats_tsv.py"

spimquant/workflow/scripts/compute_filtered_regionprops.py

@@ -1,23 +1,41 @@
 """Compute region properties from filtered segmentation masks using ZarrNii.
-
 This script reads a segmentation mask from an OME-Zarr file, performs
 connected components on chunks with overlap, applys filters based on 
 region properties, and outputs region properties on these filtered objects
 """
 
+import os
+import shutil
+import tempfile
+import zipfile
 from dask_setup import get_dask_client
 from zarrnii import ZarrNii
 
 if __name__ == "__main__":
     with get_dask_client(snakemake.config["dask_scheduler"], snakemake.threads):
 
-        znimg = ZarrNii.from_file(
-            snakemake.input.mask,
-            level=0,  # input image is already downsampled to the wildcard level
-        )
+        # 1. Create a secure, temporary directory in the system default tempdir
+        with tempfile.TemporaryDirectory(suffix=".ome.zarr") as temp_dir:
+            print(f"Extracting zip archive to temporary directory: {temp_dir}")
+
+            # 2. Open and extract the entire input zip file safely
+            with zipfile.ZipFile(snakemake.input.mask, "r") as zip_ref:
+                zip_ref.extractall(temp_dir)
+
+            # 3. Locate the extracted directory/file path inside the temp folder
+            # OME-Zarr is usually a single top-level directory inside the zip.
+            extracted_contents = os.listdir(temp_dir)
+            if not extracted_contents:
+                raise ValueError("The input zip file is empty.")
+
+            # Direct path to the extracted .zarr directory structure
+            zarr_temp_path = os.path.join(temp_dir, extracted_contents[0])
+
+            # 4. Point ZarrNii to the unzipped DirectoryStore instead of the ZipStore
+            znimg = ZarrNii.from_file(temp_dir)
 
-        znimg.compute_region_properties(
-            output_path=snakemake.output.regionprops_parquet,
-            region_filters=snakemake.params.region_filters,
-            output_properties=snakemake.params.output_properties,
-        )
+            znimg.compute_region_properties(
+                output_path=snakemake.output.regionprops_parquet,
+                region_filters=snakemake.params.region_filters,
+                output_properties=snakemake.params.output_properties,
+            )