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Merge branch 'refactor-napari-widget' into refactor
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IgorTatarnikov committed Feb 2, 2024
2 parents a145382 + 84d94f4 commit 82f65a8
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Showing 2 changed files with 7 additions and 1 deletion.
7 changes: 6 additions & 1 deletion mesospim_stitcher/big_stitcher_bridge.py
Original file line number Diff line number Diff line change
@@ -1,5 +1,6 @@
import subprocess
from pathlib import Path
from sys import platform


def run_big_stitcher(
Expand All @@ -13,6 +14,10 @@ def run_big_stitcher(
downsample_z: int = 4,
):
stitch_macro_path = Path(__file__).resolve().parent / "stitch_macro.ijm"

if platform.startswith("darwin"):
imagej_path = imagej_path / "Contents/MacOS/ImageJ-macosx"

command = (
f"{imagej_path} --ij2"
f" --headless -macro {stitch_macro_path} "
Expand All @@ -21,7 +26,7 @@ def run_big_stitcher(
)

result = subprocess.run(
command, capture_output=True, text=True, check=True
command, capture_output=True, text=True, check=True, shell=True
)

return result
1 change: 1 addition & 0 deletions mesospim_stitcher/stitching_widget.py
Original file line number Diff line number Diff line change
Expand Up @@ -234,6 +234,7 @@ def _on_create_pyramid_button_clicked(self):
worker.start()

def _on_add_tiles_button_clicked(self):
# Need to run in a separate worker thread
self.image_mosaic = load(self.working_directory)

self.fuse_channel_dropdown.clear()
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