Call BigStitcher via command line

mesospim_stitcher/big_stitcher_bridge.py

@@ -1,2 +1,42 @@
-def run_big_stitcher():
-    return
+import subprocess
+from pathlib import Path
+
+XML_PATH = (
+    "D:/TiledDataset/2.5x_tile/"
+    "2.5x_tile_igor_rightonly_Mag2.5x_ch488_ch561_ch647_bdv3.xml"
+)
+TILE_CONFIG_PATH = (
+    "D:/TiledDataset/"
+    "2.5x_tile/"
+    "2.5x_tile_igor_rightonly_Mag2.5x"
+    "_ch488_ch561_ch647_bdv_tile_config.txt"
+)
+
+
+def run_big_stitcher(
+    imageJ_path: Path, xml_path: Path, tile_config_path: Path
+):
+    stitch_macro_path = Path(__file__).resolve().parent / "stitch_macro.ijm"
+    command = (
+        f"{imageJ_path} --ij2"
+        f" --headless -macro {stitch_macro_path} "
+        f'"{xml_path} {tile_config_path}"'
+    )
+
+    result = subprocess.run(
+        command, capture_output=True, text=True, check=True
+    )
+
+    return result
+
+
+if __name__ == "__main__":
+    result = run_big_stitcher(
+        Path("C:/Users/Igor/Documents/Fiji.app/ImageJ-win64.exe"),
+        Path(XML_PATH),
+        Path(TILE_CONFIG_PATH),
+    )
+
+    with open("big_stitcher_output.txt", "w") as f:
+        f.write(result.stdout)
+        f.write(result.stderr)

mesospim_stitcher/stitch_macro.ijm

@@ -1,24 +1,31 @@
-args = getArgument()
-args = split(args, " ")
-xmlPath = args[0]
+args = getArgument();
+args = split(args, " ");
+xmlPath = args[0];
 tilePath = args[1]
 
+print("Stitching " + xmlPath);
+print("Loading TileConfiguration from " + tilePath)
 run("Load TileConfiguration from File...",
     "browse=" + xmlPath +
     " select=" + xmlPath +
     " tileconfiguration=" + tilePath +
     " use_pixel_units keep_metadata_rotation");
 
+print("Calculating pairwise shifts");
 run("Calculate pairwise shifts ...",
     "select=" + xmlPath +
     " process_angle=[All angles] process_channel=[All channels] process_illumination=[All illuminations]" +
     " process_tile=[All tiles] process_timepoint=[All Timepoints]" +
     " method=[Phase Correlation] channels=[Average Channels]" +
     " downsample_in_x=4 downsample_in_y=4 downsample_in_z=4");
 
+print("Optimizing globally and applying shifts")
 run("Optimize globally and apply shifts ...",
     "select=" + xmlPath +
     " process_angle=[All angles] process_channel=[All channels] process_illumination=[All illuminations]" +
     " process_tile=[All tiles] process_timepoint=[All Timepoints] relative=2.500 absolute=3.500" +
     " global_optimization_strategy=[Two-Round using Metadata to align unconnected Tiles and iterative dropping of bad links]" +
     " fix_group_0-0,");
+
+print("Done");
+eval("script", "System.exit(0);");