Merge pull request #161 from henrypinkard/main

fix 8 bit bug

python/ndstorage/_version.py

@@ -1,2 +1,2 @@
-version_info = (0, 1, 5)
+version_info = (0, 1, 6)
 __version__ = ".".join(map(str, version_info))

python/ndstorage/ndtiff_file.py

@@ -276,6 +276,8 @@ def _bytes_per_image_pixels(self, pixels, rgb):
                 return len(pixels)
             elif isinstance(pixels, np.ndarray) and pixels.dtype == np.uint16:
                 return pixels.size * 2
+            elif isinstance(pixels, np.ndarray) and pixels.dtype == np.uint8:
+                return pixels.size
             else:
                 raise RuntimeError("unknown pixel type")
 

python/ndstorage/test/writing_test.py

@@ -63,6 +63,34 @@ def test_write_full_dataset(test_data_path):
         assert np.all(read_image == pixels)
         assert dataset.read_metadata(**axes) == {'time_metadata': time}
 
+def test_write_full_dataset_8_bit(test_data_path):
+    """
+    Write an NDTiff dataset and read it back in, testing pixels and metadata
+    """
+    full_path = os.path.join(test_data_path, 'test_write_full_dataset')
+    dataset = NDTiffDataset(full_path, summary_metadata={}, writable=True)
+
+    image_height = 256
+    image_width = 256
+    images = []
+    for time in range(10):
+        pixels = np.ones(image_height * image_width, dtype=np.uint16).reshape((image_height, image_width)) * time
+        images.append(pixels)
+    for time in range(10):
+        axes = {'time': time}
+        dataset.put_image(axes, images[time], {'time_metadata': time})
+
+    dataset.finish()
+
+    # read the file back in
+    dataset = NDTiffDataset(full_path)
+    for time in range(10):
+        pixels = np.ones(image_height * image_width, dtype=np.uint8).reshape((image_height, image_width)) * time
+        axes = {'time': time}
+        read_image = dataset.read_image(**axes)
+        assert np.all(read_image == pixels)
+        assert dataset.read_metadata(**axes) == {'time_metadata': time}
+
 def test_write_full_dataset_RAM():
     dataset = NDRAMDataset()