Replace jupyter notebooks with example scripts.

fmi-faim · Dec 13, 2023 · a0d5f8e · a0d5f8e
1 parent 3dfe0e4
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diff --git a/examples/CellVoyagerPlateExample.py → ...les/CellVoyagerStackAcquisitionExample.py b/examples/CellVoyagerPlateExample.py → ...les/CellVoyagerStackAcquisitionExample.py
@@ -1,30 +1,43 @@
 import shutil
+from pathlib import Path
 
 from faim_hcs.hcs.acquisition import TileAlignmentOptions
 from faim_hcs.hcs.cellvoyager import StackAcquisition
 from faim_hcs.hcs.converter import ConvertToNGFFPlate, NGFFPlate
 from faim_hcs.hcs.plate import PlateLayout
+from faim_hcs.stitching import stitching_utils
 
 
 def main():
+    # Remove existing zarr.
+    shutil.rmtree("cv-stack.zarr", ignore_errors=True)
+
+    # Parse CV plate acquisition.
     plate = StackAcquisition(
-        acquisition_dir="/home/tibuch/Gitrepos/faim-hcs/resources/CV8000"
-        "/CV8000-Minimal-DataSet-2C-3W-4S-FP2-stack_20230918_135839/CV8000-Minimal-DataSet-2C-3W-4S-FP2-stack",
+        acquisition_dir=Path(__file__).parent.parent
+        / "resources"
+        / "CV8000"
+        / "CV8000-Minimal-DataSet-2C-3W-4S-FP2-stack_20230918_135839"
+        / "CV8000-Minimal-DataSet-2C-3W-4S-FP2-stack",
         alignment=TileAlignmentOptions.GRID,
     )
-    shutil.rmtree("cv-test-plate.zarr", ignore_errors=True)
+
+    # Create converter.
     converter = ConvertToNGFFPlate(
         ngff_plate=NGFFPlate(
             root_dir=".",
-            name="cv-test-plate",
+            name="cv-stack",
             layout=PlateLayout.I384,
             order_name="order",
             barcode="barcode",
         ),
         yx_binning=2,
         dask_chunk_size_factor=2,
+        warp_func=stitching_utils.translate_tiles_2d,
+        fuse_func=stitching_utils.fuse_mean,
     )
 
+    # Run conversion.
     converter.run(
         plate_acquisition=plate,
         well_sub_group="0",