Merge branch 'main' into protect_import_in_sima

catalystneuro · Aug 13, 2024 · be0fa79 · be0fa79
2 parents fea18ec + 28b843f
commit be0fa79
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Showing 3 changed files with 20 additions and 9 deletions.
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -27,6 +27,7 @@
 * Added `_image_mask` initialization in `BaseSegmentationExtractor`; combined `abstractmethod`s into top of file: [#327](https://github.com/catalystneuro/roiextractors/pull/327)
 * Optimize parsing of xml with `lxml` library for Burker extractors: [#346](https://github.com/catalystneuro/roiextractors/pull/346)
 * Protect sima and dill export [#351](https://github.com/catalystneuro/roiextractors/pull/351)
+* Improve error message when `TiffImagingExtractor` is not able to form memmap [#353](https://github.com/catalystneuro/roiextractors/pull/353)
 
 ### Testing
 

diff --git a/src/roiextractors/extractors/tiffimagingextractors/tiffimagingextractor.py b/src/roiextractors/extractors/tiffimagingextractors/tiffimagingextractor.py
@@ -56,13 +56,23 @@ def __init__(self, file_path: PathType, sampling_frequency: FloatType):
 
         try:
             self._video = tifffile.memmap(self.file_path, mode="r")
-        except ValueError:
-            warn(
-                "memmap of TIFF file could not be established. Reading entire matrix into memory. "
-                "Consider using the ScanImageTiffExtractor for lazy data access."
-            )
-            with tifffile.TiffFile(self.file_path) as tif:
-                self._video = tif.asarray()
+        except Exception as e:
+
+            try:
+                with tifffile.TiffFile(self.file_path) as tif:
+                    self._video = tif.asarray()
+                warn(
+                    f"memmap of TIFF file could not be established due to the following error: {e}. "
+                    "Reading entire matrix into memory. Consider using the ScanImageTiffSinglePlaneImagingExtractor or ScanImageTiffMultiPlaneImagingExtractor for lazy data access.",
+                    stacklevel=2,
+                )
+            except Exception as e2:
+                raise RuntimeError(
+                    f"Memory mapping failed: {e}. \n"
+                    f"Attempt to read the TIFF file directly also failed: {e2}. \n"
+                    f"Consider using ScanImageTiffSinglePlaneImagingExtractor or ScanImageTiffMultiPlaneImagingExtractor for lazy data access, check the file integrity. \n"
+                    f"If problems persist, please report an issue at roiextractors/issues."
+                )
 
         shape = self._video.shape
         if len(shape) == 3:

diff --git a/tests/test_scan_image_tiff.py b/tests/test_scan_image_tiff.py
@@ -37,8 +37,8 @@ def test_tiff_non_memmap_warning(self):
         with self.assertWarnsWith(
             warn_type=UserWarning,
             exc_msg=(
-                "memmap of TIFF file could not be established. Reading entire matrix into memory. "
-                "Consider using the ScanImageTiffExtractor for lazy data access."
+                "memmap of TIFF file could not be established due to the following error: image data are not memory-mappable. "
+                "Reading entire matrix into memory. Consider using the ScanImageTiffSinglePlaneImagingExtractor or ScanImageTiffMultiPlaneImagingExtractor for lazy data access."
             ),
         ):
             TiffImagingExtractor(file_path=self.file_path, sampling_frequency=30.0)