Merge pull request #1711 from girder/guard-dtypes

Ensure tile source _dtype is an actual numpy dtype
girder · Oct 31, 2024 · 6b70806 · 6b70806
2 parents 06e467f + 7f61bf8
commit 6b70806
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Showing 5 changed files with 9 additions and 7 deletions.
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -5,6 +5,7 @@
 ### Improvements
 
 - Format dates in item lists ([#1707](../../pull/1707))
+- Guard dtype types ([#1710](../../pull/1710))
 
 ### Changes
 

diff --git a/large_image/tilesource/base.py b/large_image/tilesource/base.py
@@ -290,7 +290,7 @@ def dtype(self) -> np.dtype:
                     self, '_unstyledInstance', self).getRegion(
                         region=dict(left=0, top=0, width=1, height=1),
                         format=TILE_FORMAT_NUMPY))
-                self._dtype = sample.dtype
+                self._dtype = np.dtype(sample.dtype)
                 self._bandCount = len(
                     getattr(getattr(self, '_unstyledInstance', self), '_bandInfo', []))
                 if not self._bandCount:
@@ -1190,14 +1190,14 @@ def _outputTile(
 
         if self._dtype is None or (isinstance(self._dtype, str) and self._dtype == 'check'):
             if isinstance(tile, np.ndarray):
-                self._dtype = tile.dtype
+                self._dtype = np.dtype(tile.dtype)
                 self._bandCount = tile.shape[-1] if len(tile.shape) == 3 else 1
             elif isinstance(tile, PIL.Image.Image):
                 self._dtype = np.uint8 if ';16' not in tile.mode else np.uint16
                 self._bandCount = len(tile.mode)
             else:
                 _img = _imageToNumpy(tile)[0]
-                self._dtype = _img.dtype
+                self._dtype = np.dtype(_img.dtype)
                 self._bandCount = _img.shape[-1] if len(_img.shape) == 3 else 1
 
         mode = None

diff --git a/sources/multi/large_image_source_multi/__init__.py b/sources/multi/large_image_source_multi/__init__.py
@@ -897,7 +897,8 @@ def _openSource(self, source, params=None):
         if params is None:
             params = source.get('params', {})
         ts = openFunc(source['path'], **params)
-        if (self._dtype and np.dtype(ts.dtype).kind == 'f' and self._dtype.kind != 'f' and
+        if (self._dtype and np.dtype(ts.dtype).kind == 'f' and
+                np.dtype(self._dtype.kind) != 'f' and
                 'sampleScale' not in source and 'sampleOffset' not in source):
             minval = maxval = 0
             for f in range(ts.frames):

diff --git a/sources/test/large_image_source_test/__init__.py b/sources/test/large_image_source_test/__init__.py
@@ -128,7 +128,7 @@ def __init__(self, ignored_path=None, minLevel=0, maxLevel=9,
                 }
                 for idx, band in enumerate(bands)}
             if low < 0 or high < 2 or low >= 65536 or high >= 65536:
-                self._dtype = float
+                self._dtype = np.dtype(float)
             elif low >= 256 or high >= 256:
                 self._dtype = np.uint16
         # Used for reporting tile information

diff --git a/sources/zarr/large_image_source_zarr/__init__.py b/sources/zarr/large_image_source_zarr/__init__.py
@@ -433,7 +433,7 @@ def _validateZarr(self):
         #     self.tileWidth = self.tileHeight = baseArray.chunks[self._axes['x']]
         self.levels = int(max(1, math.ceil(math.log(max(
             self.sizeX / self.tileWidth, self.sizeY / self.tileHeight)) / math.log(2)) + 1))
-        self._dtype = baseArray.dtype
+        self._dtype = np.dtype(baseArray.dtype)
         self._bandCount = 1
         if ('c' in self._axes and 's' not in self._axes and not self._channels and
                 baseArray.shape[self._axes.get('c')] in {1, 3, 4}):
@@ -754,7 +754,7 @@ def addTile(self, tile, x=0, y=0, mask=None, axes=None, **kwargs):
 
             # If base data changed, update large_image attributes
             if store_path == '0':
-                self._dtype = tile.dtype
+                self._dtype = np.dtype(tile.dtype)
                 self._bandCount = new_dims.get(axes[-1])  # last axis is assumed to be bands
                 self.sizeX = new_dims.get('x')
                 self.sizeY = new_dims.get('y')