add option to change the fuse function for create mosaic

ditb/stitching/tiles.py

@@ -149,6 +149,7 @@ def fuse_func(
     load_tile_func=None,
     block_info=None,
     data_dtype=np.uint16,
+    fuse_math_fun=np.max 
 ) -> np.ndarray:
     """
     Fuses the tiles that intersect the current chunk of a dask array using maximum projection.
@@ -187,7 +188,7 @@ def fuse_func(
         # note that the dtype comversion here happens without scaling
         # may want to use one of the skimage.img_as_* functions instead
         stack = np.stack([fused, tile_shifted])
-        fused = np.max(stack, axis=0)
+        fused = fuse_math_fun(stack, axis=0)
         fused[fused == bad_value] = 0
 
     return fused
@@ -269,7 +270,7 @@ def tiles_as_shapely(metadata: dict, selected_tiles: [list, int] = -1,
 
 def create_mosaic(zarr_file: str, roi: int = -1, channels: [list, int] = -1, mosaic_chunk_size: [int, int] = (1024, 1024),
                   output_file: str = None, nz: int = -1, scale_z: bool = True, data_dtype=np.uint16, 
-                  return_dask_array=False):
+                  return_dask_array=False, fuse_math_fun=np.max):
     """
     Stitch tiles together to create a stiched large image saved with as pyramid ome-zarr
     
@@ -290,7 +291,8 @@ def create_mosaic(zarr_file: str, roi: int = -1, channels: [list, int] = -1, mos
     
     _fuse_func = partial(fuse_func, 
                          load_tile_func=mmzarr_load_one_tile,
-                         data_dtype=data_dtype)
+                         data_dtype=data_dtype,
+                         fuse_math_fun=fuse_math_fun)
     
     if roi == -1:
         roi = [int(r.replace('roi', '')) for r in roi_tiles]
@@ -410,9 +412,8 @@ def create_mosaic(zarr_file: str, roi: int = -1, channels: [list, int] = -1, mos
         
         # Compute and save the mosaic inside a Roi:XX parent group
         roi_group = root_group.create_group(f'Roi{r}')
-        dask_out = dask.array.stack(t_mosaic)
         with ProgressBar():
-            writer.write_image(dask_out, roi_group, 
+            writer.write_image(dask.array.stack(t_mosaic), roi_group, 
                                scaler=scaler, axes='tczyx', 
                                coordinate_transformations=scale_omezarr)
         
@@ -426,4 +427,7 @@ def create_mosaic(zarr_file: str, roi: int = -1, channels: [list, int] = -1, mos
         #    roi_group['0']
 
     if return_dask_array:
+        with ProgressBar():
+            dask_out = dask.array.stack(t_mosaic)
+            
         return dask_out
\ No newline at end of file

pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "DITB"
-version = "20240525rc4"
+version = "20240525rc5"
 readme = "README.md"
 requires-python = ">=3.11"
 authors = [{ name = "Hugo Chauvet", email = "hugo.chauvet@synchrotron-soleil.fr" }]