Merge pull request #1687 from girder/zarr-sink-subprocess

Zarr Sink Subprocess

sources/zarr/large_image_source_zarr/__init__.py

@@ -631,14 +631,16 @@ def addTile(self, tile, x=0, y=0, mask=None, axes=None, **kwargs):
                 ])
             else:
                 arr = current_arrays[store_path]
-                arr.resize(*tuple(new_dims.values()))
-                if arr.chunks[-1] != new_dims.get('s'):
-                    # rechunk if length of samples axis changes
-                    chunking = tuple([
-                        self._tileSize if a in ['x', 'y'] else
-                        new_dims.get('s') if a == 's' else 1
-                        for a in axes
-                    ])
+                new_shape = tuple(max(v, arr.shape[i]) for i, v in enumerate(new_dims.values()))
+                if new_shape != arr.shape:
+                    arr.resize(*new_shape)
+                    if arr.chunks[-1] != new_dims.get('s'):
+                        # rechunk if length of samples axis changes
+                        chunking = tuple([
+                            self._tileSize if a in ['x', 'y'] else
+                            new_dims.get('s') if a == 's' else 1
+                            for a in axes
+                        ])
 
             if mask is not None:
                 arr[placement_slices] = np.where(mask, tile, arr[placement_slices])

test/test_sink.py

@@ -1,5 +1,7 @@
 import math
+import subprocess
 from multiprocessing.pool import Pool, ThreadPool
+from os import sys
 
 import large_image_source_test
 import large_image_source_zarr
@@ -535,3 +537,27 @@ def testConcurrency(tmp_path):
         assert data is not None
         assert data.shape == seed_data.shape
         assert np.allclose(data, seed_data)
+
+
+def testSubprocess(tmp_path):
+    sink = large_image_source_zarr.new()
+    path = sink.largeImagePath
+    subprocess.run([sys.executable, '-c', """import large_image_source_zarr
+import numpy as np
+sink = large_image_source_zarr.open('%s')
+sink.addTile(np.ones((1, 1, 1)), x=2047, y=2047, t=5, z=2)
+""" % path], capture_output=True, text=True, check=True)
+    sink.addTile(np.ones((1, 1, 1)), x=5000, y=4095, t=0, z=4)
+
+    assert sink.metadata['IndexRange']['IndexZ'] == 5
+    assert sink.getRegion(
+        region=dict(left=2047, top=2047, width=1, height=1),
+        format='numpy',
+        frame=27,
+    )[0] == 1
+    assert sink.getRegion(
+        region=dict(left=5000, top=4095, width=1, height=1),
+        format='numpy',
+        frame=4,
+    )[0] == 1
+    assert sink.sizeX == 5001