Zarr file axis order

Ensure reading non-editable zarr files the c axis, if present, has a
stride of 1.  PR #1625 changed this.

CHANGELOG.md

@@ -12,6 +12,10 @@
 - Better handle images with signed pixel data ([#1695](../../pull/1695))
 - Reduce loading geojs when switching views in Girder ([#1699](../../pull/1699))
 
+### Changes
+
+- Ensure reading non-editable zarr files the c axis, if present, has a stride of 1 ([#1703](../../pull/1703))
+
 ## 1.30.1
 
 ### Improvements

sources/zarr/large_image_source_zarr/__init__.py

@@ -446,10 +446,16 @@ def _validateZarr(self):
         stride = 1
         self._strides = {}
         self._axisCounts = {}
-        for _, k in sorted(
-            (-self._axes.get(k, 'tzc'.index(k) if k in 'tzc' else -1), k)
-            for k in self._axes if k not in 'xys'
-        ):
+        # If we aren't in editable mode, prefer the channel axis to have a
+        # stride of 1, then the z axis, then the t axis, then sorted by the
+        # axis name.
+        axisOrder = ((-'tzc'.index(k) if k in 'tzc' else 1, k)
+                     for k in self._axes if k not in 'xys')
+        # In editable mode, prefer the order that the axes are being written.
+        if self._editable:
+            axisOrder = ((-self._axes.get(k, 'tzc'.index(k) if k in 'tzc' else -1), k)
+                         for k in self._axes if k not in 'xys')
+        for _, k in sorted(axisOrder):
             self._strides[k] = stride
             self._axisCounts[k] = baseArray.shape[self._axes[k]]
             stride *= baseArray.shape[self._axes[k]]

test/test_source_zarr.py

@@ -0,0 +1,9 @@
+import large_image_source_zarr
+
+from .datastore import datastore
+
+
+def testZarrAxisOrder():
+    imagePath = datastore.fetch('synthetic_multiaxis.zarr.db')
+    source = large_image_source_zarr.open(imagePath)
+    assert source.metadata['IndexStride']['IndexC'] == 1