Fixed bugs in asdask() and GeneratorSource, pinned some versions in p…

…ip requirements

CHANGELOG.md

@@ -1,3 +1,7 @@
+#### Version 0.6.7
+- Fixed bugs in asdask() and GeneratorSource
+- Pinned some versions in pip requirements 
+
 #### Version 0.6.6
 - Rewritten TiffSource using dask/zarr functionality
 - Added high level Dask function

OmeSliCC/GeneratorSource.py

@@ -58,11 +58,11 @@ def calc_color(self, *args, **kwargs):
         return np.stack(channels, axis=-1)
 
     def get_tile(self, indices, tile_size=None):
-        # tile in (z,),y,x,c
+        # indices / tile size in x,y(,z,...)
         if not tile_size:
             tile_size = np.flip(self.tile_shape)
-        range0 = np.flip(indices)
-        range1 = np.min([range0 + tile_size, self.size], 0)
+        range0 = indices
+        range1 = np.min([np.array(indices) + np.array(tile_size), self.size], 0)
         shape = list(reversed(range1 - range0))
         tile = np.fromfunction(self.calc_color, shape, dtype=int, range0=range0)
         # apply noise to each channel separately
@@ -77,14 +77,14 @@ def get_tile(self, indices, tile_size=None):
     def _asarray_level(self, level: int, x0: float = 0, y0: float = 0, x1: float = -1, y1: float = -1,
                        c: int = None, z: int = None, t: int = None) -> np.ndarray:
         # ignore c
-        indices = [y0, x0]
-        tile_size = [y1 - y0, x1 - x0]
+        indices = [x0, y0]
+        tile_size = [x1 - x0, y1 - y0]
         if z:
-            indices = [0] + indices
-            tile_size = [1] + tile_size
+            indices += [0]
+            tile_size += [1]
         if t:
-            indices = [0] + indices
-            tile_size = [1] + tile_size
+            indices += [0]
+            tile_size += [1]
         data = self.get_tile(indices, tile_size)
         if not z:
             data = np.expand_dims(data, 0)
@@ -95,7 +95,7 @@ def _asarray_level(self, level: int, x0: float = 0, y0: float = 0, x1: float = -
 
 
 if __name__ == '__main__':
-    # (tile) size in x,y(,z)
+    # (tile) size in x,y(,z,...)
     size = 256, 256, 256
     tile_size = 256, 256, 1
     dtype = np.uint8

OmeSliCC/OmeSource.py

@@ -353,6 +353,7 @@ def asdask(self, chunk_size: tuple) -> da.Array:
         while len(chunk_shape) < 5:
             chunk_shape = [1] + chunk_shape
         chunks = np.ceil(np.flip(self.get_size_xyzct()) / chunk_shape).astype(int)
+        w, h = self.get_size()
 
         delayed_reader = dask.delayed(self.asarray)
         dtype = self.get_pixel_type()
@@ -365,18 +366,24 @@ def asdask(self, chunk_size: tuple) -> da.Array:
                 for yi in range(chunks[3]):
                     dask_tiles = []
                     for xi in range(chunks[4]):
-                        x0, x1 = xi * chunk_shape[4], (xi + 1) * chunk_shape[4]
-                        y0, y1 = yi * chunk_shape[3], (yi + 1) * chunk_shape[3]
-                        z = zi * chunk_shape[2]
-                        t = ti * chunk_shape[0]
-                        dask_tile = da.from_delayed(delayed_reader(x0, y0, x1, y1, z=z, t=t), shape=chunk_shape,
+                        shape = list(chunk_shape).copy()
+                        x0, x1 = xi * shape[4], (xi + 1) * shape[4]
+                        y0, y1 = yi * shape[3], (yi + 1) * shape[3]
+                        if x1 > w:
+                            x1 = w
+                            shape[4] = w - x0
+                        if y1 > h:
+                            y1 = h
+                            shape[3] = h - y0
+                        z = zi * shape[2]
+                        t = ti * shape[0]
+                        dask_tile = da.from_delayed(delayed_reader(x0, y0, x1, y1, z=z, t=t), shape=shape,
                                                     dtype=dtype)
                         dask_tiles.append(dask_tile)
                     dask_rows.append(da.concatenate(dask_tiles, axis=4))
                 dask_planes.append(da.concatenate(dask_rows, axis=3))
             dask_times.append(da.concatenate(dask_planes, axis=1))
         dask_data = da.concatenate(dask_times, axis=0)
-
         return dask_data
 
     def clone_empty(self) -> np.ndarray:

pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "OmeSliCC"
-version = "0.6.6"
+version = "0.6.7"
 description = "Ome(ro) Slide Image Conversion and Compression pipeline"
 readme = "README.md"
 license = {file = "LICENSE.md"}

requirements.txt

@@ -3,9 +3,9 @@ pandas
 scikit-image
 scikit-learn
 opencv-python
-imagecodecs
+imagecodecs>=2023.3.16
 numcodecs
-tifffile
+tifffile>=2023.9.26
 zarr
 aiohttp
 omero-py

tests/conversion_test.py

@@ -22,8 +22,8 @@ def load_as_zarr(path, x_um, y_um, w_um, h_um):
 
 
 def save_source_as_ome_tiff(output, source, output_params):
-    data = source.asarray()
-    #data = source.asdask(output_params['tile_size'])
+    #data = source.asarray()
+    data = source.asdask(output_params['tile_size'])
     save_image_as_tiff(source, data, output, output_params, ome=True)
 
 
@@ -50,9 +50,10 @@ def conversion_test():
     path2 = 'test1.ome.zarr'
     path3 = 'test2.ome.tiff'
     size = [1024, 1024]
-    output_params = {'tile_size': [256, 256], 'npyramid_add': 3, 'pyramid_downsample': 2}
+    tile_size = [256, 256]
+    output_params = {'tile_size': tile_size, 'npyramid_add': 3, 'pyramid_downsample': 2}
 
-    source = create_source(size, [256, 256], np.uint8, [(1, 'um')])
+    source = create_source(size, tile_size, np.uint8, [(1, 'um')])
     nchannels = source.get_nchannels()
     save_source_as_ome_tiff(path1, source, output_params)