Refactoring

mesospim_stitcher/big_stitcher_bridge.py

@@ -3,7 +3,7 @@
 
 
 def run_big_stitcher(
-    imageJ_path: Path,
+    imagej_path: Path,
     xml_path: Path,
     tile_config_path: Path,
     all_channels: bool = False,
@@ -14,7 +14,7 @@ def run_big_stitcher(
 ):
     stitch_macro_path = Path(__file__).resolve().parent / "stitch_macro.ijm"
     command = (
-        f"{imageJ_path} --ij2"
+        f"{imagej_path} --ij2"
         f" --headless -macro {stitch_macro_path} "
         f'"{xml_path} {tile_config_path} {int(all_channels)}'
         f' {selected_channel} {downsample_x} {downsample_y} {downsample_z}"'

mesospim_stitcher/fuse.py

@@ -15,36 +15,62 @@
 from mesospim_stitcher.file_utils import write_bdv_xml
 
 
-def fuse_image(
-    xml_path: Path, input_path: Path, output_path: Path, overwrite: bool = True
-):
-    tree = ET.parse(xml_path)
+def fuse_image(xml_path: Path, input_path: Path, output_path: Path):
+    input_file = h5py.File(input_path, "r")
+    group = input_file["t00000"]
+    tile_names = list(group.keys())
 
-    root = tree.getroot()
+    tile = group[f"{tile_names[0]}/0/cells"]
+    z_size, y_size, x_size = tile.shape
 
+    tile_positions = get_big_stitcher_transforms(
+        xml_path, x_size, y_size, z_size
+    )
+
+    fused_image_shape = (
+        max(tile_position[5] for tile_position in tile_positions),
+        max(tile_position[3] for tile_position in tile_positions),
+        max(tile_position[1] for tile_position in tile_positions),
+    )
+
+    if output_path.suffix == ".zarr":
+        fuse_to_zarr(
+            fused_image_shape, group, output_path, tile_names, tile_positions
+        )
+    elif output_path.suffix == ".h5":
+        fuse_to_bdv_h5(
+            fused_image_shape,
+            group,
+            output_path,
+            tile_names,
+            tile_positions,
+            xml_path,
+        )
+
+    input_file.close()
+
+
+def get_big_stitcher_transforms(xml_path, x_size, y_size, z_size):
+    tree = ET.parse(xml_path)
+    root = tree.getroot()
     stitch_transforms = root.findall(
         ".//ViewTransform/[Name='Stitching Transform']/affine"
     )
     assert (
         stitch_transforms is not None
     ), "No stitching transforms found in XML file"
-
     grid_transforms = root.findall(
         ".//ViewTransform/[Name='Translation from Tile Configuration']/affine"
     )
-
     if len(grid_transforms) == 0:
         grid_transforms = root.findall(
             ".//ViewTransform/[Name='Translation to Regular Grid']/affine"
         )
-
     assert grid_transforms is not None, "No grid transforms found in XML file"
-
     z_scale_str = root.find(".//ViewTransform/[Name='calibration']/affine")
     assert z_scale_str is not None, "No z scale found in XML file"
     assert z_scale_str.text is not None, "No z scale found in XML file"
     z_scale = float(z_scale_str.text.split()[-2])
-
     deltas = []
     grids = []
     for i in range(len(stitch_transforms)):
@@ -76,50 +102,24 @@ def fuse_image(
 
     min_grid = [min([grid[i] for grid in grids]) for i in range(3)]
     grids = [[grid[i] - min_grid[i] for i in range(3)] for grid in grids]
-
-    input_file = h5py.File(input_path, "r")
-    group = input_file["t00000"]
-    tile_names = list(group.keys())
     max_delta = [max([abs(delta[i]) for delta in deltas]) for i in range(3)]
 
-    tile = group[f"{tile_names[0]}/0/cells"]
-    z_size = tile.shape[0]
-    x_y_size = tile.shape[1]
-
     translations = []
 
     for i in range(len(deltas)):
         curr_delta = deltas[i]
         curr_grid = grids[i]
 
         x_start = curr_grid[0] + curr_delta[0] + max_delta[0]
-        x_end = x_start + x_y_size
+        x_end = x_start + x_size
         y_start = curr_grid[1] + curr_delta[1] + max_delta[1]
-        y_end = y_start + x_y_size
+        y_end = y_start + y_size
         z_start = curr_grid[2] + curr_delta[2] + max_delta[2]
         z_end = z_start + z_size
 
         translations.append([x_start, x_end, y_start, y_end, z_start, z_end])
 
-    fused_image_shape = (
-        max(translation[5] for translation in translations),
-        max(translation[3] for translation in translations),
-        max(translation[1] for translation in translations),
-    )
-
-    # fuse_to_bdv_h5(
-    #     fused_image_shape,
-    #     group,
-    #     output_path,
-    #     tile_names,
-    #     translations,
-    #     xml_path,
-    # )
-    fuse_to_zarr(
-        fused_image_shape, group, output_path, tile_names, translations
-    )
-
-    input_file.close()
+    return translations
 
 
 def fuse_to_zarr(

mesospim_stitcher/workflow.py

@@ -8,14 +8,18 @@
     "C:/Users/Igor/Documents/NIU-dev/stitching/One_Channel/"
     "2.5x_tile_igor_rightonly_Mag2.5x_ch488_ch561_ch647_bdv.xml"
 )
+
 H5_PATH = "C:/Users/Igor/Documents/NIU-dev/stitching/One_Channel/test.h5"
+
 OUT_PATH = (
     "C:/Users/Igor/Documents/NIU-dev/stitching/One_Channel/test_out.zarr"
 )
+
 META_PATH = (
     "C:/Users/Igor/Documents/NIU-dev/stitching/One_Channel/"
     "2.5x_tile_igor_rightonly_Mag2.5x_ch488_ch561_ch647_bdv.h5_meta.txt"
 )
+
 TILE_CONFIG_PATH = (
     "C:/Users/Igor/Documents/NIU-dev/stitching/One_Channel/"
     "2.5x_tile_igor_rightonly_Mag2.5x"
@@ -25,6 +29,7 @@
 DOWNSAMPLE_ARRAY = np.array(
     [[1, 1, 1], [2, 2, 2], [4, 4, 4], [8, 8, 8], [16, 16, 16]]
 )
+
 SUBDIVISION_ARRAY = np.array(
     [[32, 32, 16], [32, 32, 16], [32, 32, 16], [32, 32, 16], [32, 32, 16]]
 )