Merge branch 'cherry-pick-b7cfba9c' into 'main'

Merge branch 'fix_jp2k' into '2.1'

See merge request !256

tomoscan/esrf/volume/jp2kvolume.py

@@ -183,13 +183,16 @@ class JP2KVolume(VolumeSingleFrameBase):
         if not has_glymur:
             raise RuntimeError(_MISSING_GLYMUR_MSG)
 
+        expected_output_dtype = frame.dtype
         if self.clip_values is not None:
             frame = numpy.clip(frame, self.clip_values[0], self.clip_values[1])
+        if expected_output_dtype not in (numpy.uint8, numpy.uint16):
+            _logger.info(
+                f"{self.get_identifier().to_str()} get {frame.dtype}. Cast it as {numpy.uint16}"
+            )
+            expected_output_dtype = numpy.uint16
         if self.rescale_data:
-            if frame.dtype in (numpy.uint8, numpy.uint16):
-                max_uint = numpy.iinfo(frame.dtype).max
-            else:
-                max_uint = numpy.iinfo(numpy.uint16).max
+            max_uint = numpy.iinfo(expected_output_dtype).max
             frame = rescale_data(
                 data=frame,
                 new_min=0,
@@ -197,13 +200,7 @@ class JP2KVolume(VolumeSingleFrameBase):
                 data_min=self.clip_values[0] if self.clip_values is not None else None,
                 data_max=self.clip_values[1] if self.clip_values is not None else None,
             )
-        if not isinstance(frame.dtype, (numpy.uint8, numpy.uint16)):
-            if self._cast_already_logged:
-                self._cast_already_logged = True
-                _logger.info(
-                    f"{self.get_identifier().to_str()} get {frame.dtype}. Cast it as {numpy.uint16}"
-                )
-            frame = frame.astype(numpy.uint16)
+        frame = frame.astype(expected_output_dtype)
 
         if scheme == "glymur":
             glymur.Jp2k(file_name, data=frame, psnr=self.psnr, cratios=self.cratios)

tomoscan/esrf/volume/tests/test_jp2kvolume.py

@@ -2,19 +2,24 @@
 
 import os
 import numpy
+import pytest
 
 from tomoscan.esrf.volume.jp2kvolume import JP2KVolume
 from tomoscan.esrf.volume.mock import create_volume
 
-_data = create_volume(
-    frame_dims=(100, 100), z_size=11
-)  # z_size need to be at least 10 to check loading from file name works
-for i in range(len(_data)):
-    _data[i] += 1
-_data = _data.astype(numpy.uint16)
 
+@pytest.fixture
+def raw_data(dtype: numpy.dtype):
+    data = create_volume(
+        frame_dims=(100, 100), z_size=11
+    )  # z_size need to be at least 10 to check loading from file name works
+    for i in range(len(data)):
+        data[i] += 1
+    return data.astype(dtype)
 
-def test_jp2kvolume_rescale(tmp_path):
+
+@pytest.mark.parametrize("dtype", (numpy.uint8, numpy.uint16))
+def test_jp2kvolume_rescale(raw_data, dtype, tmp_path):
     """
     Test that rescale is correctly applied by default by the JP2KVolume
     """
@@ -22,10 +27,13 @@ def test_jp2kvolume_rescale(tmp_path):
     os.makedirs(acquisition_dir)
     volume_dir = str(acquisition_dir / "volume")
     os.makedirs(volume_dir)
-    volume = JP2KVolume(folder=volume_dir, data=_data, metadata={})
+    assert raw_data.dtype == dtype
+    volume = JP2KVolume(folder=volume_dir, data=raw_data, metadata={})
+    assert volume.data.dtype == dtype
     volume.save()
 
     volume.clear_cache()
     volume.load()
+    assert volume.data.dtype == dtype
     assert volume.data.min() == 0
-    assert volume.data.max() == numpy.iinfo(numpy.uint16).max
+    assert volume.data.max() in (numpy.iinfo(dtype).max, numpy.iinfo(dtype).max - 1)