Merge pull request #10 from DavidStirling/zarr-reader

Patch zarr reader for ome-zarr v0.4 plates

cellprofiler_core/__init__.py

@@ -1 +1 @@
-__version__ = "4.2.8"
+__version__ = "4.2.80002"

cellprofiler_core/utilities/zarr.py

@@ -204,9 +204,16 @@ def map_wells(self):
         if 'plate' not in attrs or 'wells' not in attrs['plate']:
             return False
         well_data = attrs['plate']['wells']
+        if not well_data:
+            # Empty well data for some reason
+            return False
         mapper = {}
-        if 'column_index' in well_data[0]:
-            # Standard format
+        if "columnIndex" in well_data[0]:
+            # NGFF v0.4 format
+            for row in well_data:
+                mapper[(str(row['columnIndex']), str(row['rowIndex']))] = row['path']
+        elif 'column_index' in well_data[0]:
+            # Older bioformats2raw format
             for row in well_data:
                 mapper[(str(row['column_index']), str(row['row_index']))] = row['path']
         else:

setup.py

@@ -42,6 +42,6 @@
     packages=setuptools.find_packages(exclude=["tests"]),
     python_requires=">=3.8, <4",
     url="https://github.com/CellProfiler/core",
-    version="4.2.8",
+    version="4.2.80002",
     zip_safe=False,
 )