Merge pull request #148 from catalystneuro/swap_to_suffix_warnings

Swap suffix assertions to warnings (ImagingExtractors)
catalystneuro · Jun 20, 2022 · e8927dc · e8927dc
2 parents 4667c27 + d054919
commit e8927dc
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Showing 3 changed files with 15 additions and 8 deletions.
diff --git a/src/roiextractors/extractors/hdf5imagingextractor/hdf5imagingextractor.py b/src/roiextractors/extractors/hdf5imagingextractor/hdf5imagingextractor.py
@@ -1,4 +1,5 @@
 from pathlib import Path
+from warnings import warn
 
 import numpy as np
 
@@ -39,10 +40,8 @@ def __init__(
         self.filepath = Path(file_path)
         self._sampling_frequency = sampling_frequency
         self._mov_field = mov_field
-        assert self.filepath.suffix in [
-            ".h5",
-            ".hdf5",
-        ], "'file_path' file is not an .hdf5 or .h5 file"
+        if self.filepath.suffix not in [".h5", ".hdf5"]:
+            warn("'file_path' file is not an .hdf5 or .h5 file")
         self._channel_names = channel_names
 
         self._file = h5py.File(file_path, "r")

diff --git a/src/roiextractors/extractors/sbximagingextractor/sbximagingextractor.py b/src/roiextractors/extractors/sbximagingextractor/sbximagingextractor.py
@@ -1,5 +1,6 @@
 import os
 from pathlib import Path
+from warnings import warn
 
 import numpy as np
 
@@ -47,7 +48,10 @@ def _check_file_path(file_path):
         file_path = Path(file_path)
         assertion_msg = "for file_path arg, provide a path to one .sbx /  .mat file"
         file_type = file_path.suffix
-        assert file_type in [".mat", ".sbx"], assertion_msg
+        if file_type not in [".mat", ".sbx"]:
+            warn(
+                "File suffix ({file_type}) is not one of .mat or .sbx - the SbxImagingExtractor may not be appropriate!"
+            )
         if file_type == ".mat":
             mat_file_path = file_path
             sbx_file_path = file_path.with_suffix(".sbx")

diff --git a/src/roiextractors/extractors/tiffimagingextractors/tiffimagingextractor.py b/src/roiextractors/extractors/tiffimagingextractors/tiffimagingextractor.py
@@ -1,5 +1,5 @@
 from pathlib import Path
-import warnings
+from warnings import warn
 
 import numpy as np
 from tqdm import tqdm
@@ -36,15 +36,19 @@ def __init__(self, file_path: PathType, sampling_frequency: FloatType):
         ImagingExtractor.__init__(self)
         self.file_path = Path(file_path)
         self._sampling_frequency = sampling_frequency
-        assert self.file_path.suffix in [".tiff", ".tif", ".TIFF", ".TIF"]
+        if self.file_path.suffix not in [".tiff", ".tif", ".TIFF", ".TIF"]:
+            warn(
+                "File suffix ({self.file_path.suffix}) is not one of .tiff, .tif, .TIFF, or .TIF! "
+                "The TiffImagingExtracto may not be appropriate."
+            )
 
         with tifffile.TiffFile(self.file_path) as tif:
             self._num_channels = len(tif.series)
 
         try:
             self._video = tifffile.memmap(self.file_path, mode="r")
         except ValueError:
-            warnings.warn(
+            warn(
                 "memmap of TIFF file could not be established. Reading entire matrix into memory. "
                 "Consider using the ScanImageTiffExtractor for lazy data access."
             )