Merge pull request #1399 from girder/harden-readers

Improve checks for formats we shouldn't read
girder · Dec 6, 2023 · 018fef8 · 018fef8
2 parents 2c33d35 + 83d5b09
commit 018fef8
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Showing 5 changed files with 17 additions and 14 deletions.
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -5,6 +5,7 @@
 ### Improvements
 - Reduce stderr noise in PIL and rasterio sources ([#1397](../../pull/1397))
 - Harden OME tiff reader ([#1398](../../pull/1398))
+- Improve checks for formats we shouldn't read ([#1399](../../pull/1399))
 
 ### Changes
 - Use an enum for priority constants ([#1400](../../pull/1400))

diff --git a/docs/config_options.rst b/docs/config_options.rst
@@ -1,7 +1,7 @@
 Configuration Options
 =====================
 
-Some functionality of large_image is controlled through configuration parameters.  These can be read or set via python using functions in the ``large_image.config`` module, `getConfig <./large_image/large_image.html#large_image.config.getConfig>`_ and `setConfig <./large_image/large_image.html#large_image.config.setConfig>`_.
+Some functionality of large_image is controlled through configuration parameters.  These can be read or set via python using functions in the ``large_image.config`` module, `getConfig <./_build/large_image/large_image.html#large_image.config.getConfig>`_ and `setConfig <./_build/large_image/large_image.html#large_image.config.setConfig>`_.
 
 Configuration parameters:
 

diff --git a/sources/pil/large_image_source_pil/__init__.py b/sources/pil/large_image_source_pil/__init__.py
@@ -14,6 +14,7 @@
 #  limitations under the License.
 #############################################################################
 
+import contextlib
 import json
 import math
 import os
@@ -202,18 +203,17 @@ def _fromRawpy(self, largeImagePath):
         try:
             import rawpy
 
-            rgb = rawpy._rawpy.RawPy(1)
-            rgb.open_file(largeImagePath)
-            rgb = rgb.postprocess()
-            rgb = large_image.tilesource.utilities._imageToNumpy(rgb)[0]
-            if rgb.shape[2] == 2:
-                rgb = rgb[:, :, :1]
-            elif rgb.shape[2] > 3:
-                rgb = rgb[:, :, :3]
-            self._pilImage = PIL.Image.fromarray(
-                rgb.astype(np.uint8) if rgb.dtype != np.uint16 else rgb,
-                ('RGB' if rgb.dtype != np.uint16 else 'RGB;16') if rgb.shape[2] == 3 else
-                ('L' if rgb.dtype != np.uint16 else 'L;16'))
+            with contextlib.redirect_stderr(open(os.devnull, 'w')):
+                rgb = rawpy.imread(largeImagePath).postprocess()
+                rgb = large_image.tilesource.utilities._imageToNumpy(rgb)[0]
+                if rgb.shape[2] == 2:
+                    rgb = rgb[:, :, :1]
+                elif rgb.shape[2] > 3:
+                    rgb = rgb[:, :, :3]
+                self._pilImage = PIL.Image.fromarray(
+                    rgb.astype(np.uint8) if rgb.dtype != np.uint16 else rgb,
+                    ('RGB' if rgb.dtype != np.uint16 else 'RGB;16') if rgb.shape[2] == 3 else
+                    ('L' if rgb.dtype != np.uint16 else 'L;16'))
         except Exception:
             pass
 

diff --git a/sources/tifffile/large_image_source_tifffile/__init__.py b/sources/tifffile/large_image_source_tifffile/__init__.py
@@ -498,6 +498,8 @@ def getTile(self, x, y, z, pilImageAllowed=False, numpyAllowed=False, **kwargs):
             if sidx not in self._zarrcache:
                 if len(self._zarrcache) > 10:
                     self._zarrcache = {}
+                if self.frames > 1:
+                    series.keyframe.nodata = None
                 za = zarr.open(series.aszarr(), mode='r')
                 hasgbs = hasattr(za[0], 'get_basic_selection')
                 self._zarrcache[sidx] = (za, hasgbs)

diff --git a/test/test_source_base.py b/test/test_source_base.py
@@ -84,7 +84,7 @@
         'skipTiles': r'(sample_image\.ptif|one_layer_missing_tiles)'},
     'tifffile': {
         'read': r'',
-        'noread': r'((\.(nc|nd2|yml|yaml|json|czi|png|jpg|jpeg|jp2|dcm|zarr\.db|zarr\.zip)$)' +
+        'noread': r'((\.(nc|nd2|yml|yaml|json|czi|png|jpg|jpeg|jp2|dcm|zarr\.db|zarr\.zip)|(nokeyframe\.ome\.tiff|XY01\.ome\.tif)$)' +  # noqa
                   (r'|bad_axes' if sys.version_info < (3, 9) else '') +
                   r')',
     },