Minor: default dimension_order for render

OmeSliCC/OmeSource.py

@@ -257,7 +257,9 @@ def get_channel_window(self, channeli):
             min, max = start, end
         return {'start': start, 'end': end, 'min': min, 'max': max}
 
-    def render(self, image: np.ndarray, source_dimension_order: str, t: int = 0, z: int = 0, channels: list = []) -> np.ndarray:
+    def render(self, image: np.ndarray, source_dimension_order: str = None, t: int = 0, z: int = 0, channels: list = []) -> np.ndarray:
+        if source_dimension_order is None:
+            source_dimension_order = self.get_dimension_order()
         image = redimension_data(image, source_dimension_order, 'yxc', t=t, z=z)
         new_image = np.zeros(list(image.shape[:2]) + [3], dtype=np.float32)
         tot_alpha = 0

tests/conversion_test.py

@@ -17,7 +17,7 @@ def load_as_zarr_um(path, x0_um, x1_um, y0_um, y1_um):
     source = TiffSource(path)
     data = source.asarray_um(x0=x0_um, x1=x1_um, y0=y0_um, y1=y1_um)
     image = np.asarray(data)
-    image = source.render(image, source.get_dimension_order())
+    image = source.render(image)
     show_image(image)
 
 
@@ -58,43 +58,41 @@ def generated_conversion_test():
 
 def check_large_tiff_arrays(input):
     source = TiffSource(input, target_pixel_size=[(10, 'um')])
-    dimension_order = source.get_dimension_order()
-    image = source.render(source.asarray(), dimension_order)
+    image = source.render(source.asarray())
     x, y = source.get_size()
     show_image(image)
-    tile = source.render(source.asarray(x0=x//2, x1=x//2+1000, y0=y//2, y1=y//2+1000), dimension_order)
+    tile = source.render(source.asarray(x0=x//2, x1=x//2+1000, y0=y//2, y1=y//2+1000))
     show_image(tile)
-    tile = source.render(source.asarray(x0=x//2, x1=x//2+1000, y0=y//2, y1=y//2+1000, pixel_size=[10]), dimension_order)
+    tile = source.render(source.asarray(x0=x//2, x1=x//2+1000, y0=y//2, y1=y//2+1000, pixel_size=[10]))
     show_image(tile)
 
 
 def check_cached_loading(path):
     source = TiffSource(path)
-    dimension_order = source.get_dimension_order()
     pixel_size = [1]
     x, y = np.array(source.get_size()) * source.get_pixel_size_micrometer() / pixel_size / 2
 
     print('Read as dask')
     start = time.process_time()
     source._load_as_dask()
     print(f'Load process time:', time.process_time() - start)
-    data = source.render(source.asarray(x0=x, x1=x+100, y0=y, y1=y+100, pixel_size=pixel_size), dimension_order)
+    data = source.render(source.asarray(x0=x, x1=x+100, y0=y, y1=y+100, pixel_size=pixel_size))
     show_image(data)
     random_access_test(source, n=100)
 
     print('Read compressed')
     start = time.process_time()
     source.load()
     print(f'Load process time:', time.process_time() - start)
-    data = source.render(source.asarray(x0=x, x1=x+100, y0=y, y1=y+100, pixel_size=pixel_size), dimension_order)
+    data = source.render(source.asarray(x0=x, x1=x+100, y0=y, y1=y+100, pixel_size=pixel_size))
     show_image(data)
     random_access_test(source, n=100)
 
     print('Read decompressed')
     start = time.process_time()
     source.load(decompress=True)
     print(f'Load process time:', time.process_time() - start)
-    data = source.render(source.asarray(x0=x, x1=x+100, y0=y, y1=y+100, pixel_size=pixel_size), dimension_order)
+    data = source.render(source.asarray(x0=x, x1=x+100, y0=y, y1=y+100, pixel_size=pixel_size))
     show_image(data)
     random_access_test(source, n=100)