Merge pull request #105 from sameeul/fix_interleaved_ch_data

bugfix: Reading multi-channel data in correct order

pyproject.toml

@@ -56,6 +56,7 @@ requires-python = ">=3.8"
 [project.optional-dependencies]
 dev = [
     "ome_zarr",
+    "pillow",
     "requests>=2.26.0"
 ]
 

src/bfio/backends.py

@@ -988,17 +988,7 @@ def read_metadata(self):
 
         def _read_image(self, X, Y, Z, C, T, output):
             out = self._image
-            pseudo_interleaved = any(
-                channel.samples_per_pixel > 1
-                for channel in self.frontend.metadata.images[0].pixels.channels
-            )
-
-            interleaved = False
-            if (
-                self.frontend.metadata.images[0].pixels.interleaved
-                or pseudo_interleaved
-            ):
-                interleaved = True
+            interleaved = self.frontend.metadata.images[0].pixels.interleaved
 
             self._prev_read_cached_loc = None
             self._cached_read_data = None

tests/test_read.py

@@ -5,6 +5,8 @@
 import numpy as np
 import pickle
 import random
+import tifffile
+from PIL import Image
 import zarr
 from ome_zarr.utils import download as zarr_download
 
@@ -457,3 +459,37 @@ def test_tensorstore_backend_pickle(self):
         assert unpickled_rdr.Y == img_height
         assert unpickled_rdr[:].sum() == data_sum
         unpickled_rdr.close()
+
+
+class TestMultiChannelBioformats(unittest.TestCase):
+
+    def test_multi_channel_bioformats(self):
+
+        # Set image dimensions
+        width, height = 256, 256
+
+        # Create random 3-channel image data
+        random_image_data = np.random.randint(
+            0, 256, (height, width, 3), dtype=np.uint8
+        )
+
+        # Save interleaved TIFF (RGBRGB...)
+        interleaved_image = Image.fromarray(random_image_data, mode="RGB")
+        interleaved_image.save(TEST_DIR.joinpath("interleaved.tiff"))
+
+        # Create non-interleaved data (separate planes for R, G, B)
+        non_interleaved_data = np.moveaxis(
+            random_image_data, 2, 0
+        )  # Shape: (3, height, width)
+
+        # Save non-interleaved TIFF
+        with tifffile.TiffWriter(TEST_DIR.joinpath("non_interleaved.tiff")) as tif:
+            tif.write(non_interleaved_data, photometric="rgb")
+
+        with bfio.BioReader(TEST_DIR.joinpath("non_interleaved.tiff")) as br:
+            for c in range(br.C):
+                assert (br[:, :, :, c] - random_image_data[:, :, c]).sum() == 0
+
+        with bfio.BioReader(TEST_DIR.joinpath("interleaved.tiff")) as br:
+            for c in range(br.C):
+                assert (br[:, :, :, c] - non_interleaved_data[c, :, :]).sum() == 0