Merge pull request #827 from girder/write-with-mask

Fix adding tiles with a mask

sources/vips/large_image_source_vips/__init__.py

@@ -323,9 +323,11 @@ def addTile(self, tile, x=0, y=0, mask=None, interpretation=None):
             newarr[:, :, :tile.shape[2]] = tile
             newarr[:, :, -1] = 255
             tile = newarr
-        if mask:
+        if mask is not None:
+            if len(mask.shape) == 3:
+                mask = numpy.logical_or.reduce(mask, axis=2)
             if tile.shape[2] in {2, 4}:
-                tile[:, :, -1] *= mask.astype(numpy.dtype.bool)
+                tile[:, :, -1] *= mask.astype(bool)
             else:
                 raise TileSourceError('Cannot apply a mask if the source is not 1 or 3 channels.')
         if tile.dtype.char not in dtypeToGValue:

test/test_source_vips.py

@@ -184,3 +184,29 @@ def testNewAndWriteJPEG():
         assert image[:len(utilities.JPEGHeader)] == utilities.JPEGHeader
     finally:
         shutil.rmtree(tmpdir)
+
+
+def testNewAndWriteWithMask():
+    imagePath = datastore.fetch('sample_image.ptif')
+    source = large_image.open(imagePath)
+    out = large_image_source_vips.new()
+    for tile in source.tileIterator(
+        format=large_image.constants.TILE_FORMAT_NUMPY,
+        region=dict(right=4000, bottom=2000),
+    ):
+        if tile['tile_position']['position']:
+            mask = tile['tile'] > 128
+        else:
+            mask = None
+        out.addTile(tile['tile'], x=tile['x'], y=tile['y'], mask=mask)
+
+    tmpdir = tempfile.mkdtemp()
+    outputPath = os.path.join(tmpdir, 'temp.tiff')
+    try:
+        out.write(outputPath, lossy=False)
+        assert os.path.getsize(outputPath) > 50000
+        result = large_image.open(outputPath)
+        resultMetadata = result.getMetadata()
+        assert resultMetadata['sizeX'] == 4000
+    finally:
+        shutil.rmtree(tmpdir)