Add script for gerbil block extraction

Author: constantinpape

scripts/more-annotations/extraxt_vglut3_gerbil.py

@@ -0,0 +1,43 @@
+import os
+import json
+from flamingo_tools.extract_block_util import extract_block
+
+
+blocks_to_annotate = [
+    "[1157.0001356895104,1758.4586038866773,994.1494008046312]",
+    "[1257.4854619519856,1712.418054399143,942.993234707371]",
+    "[1329.892068232878,1421.8487165158099,712.9291398862247]",
+    "[1035.3286672774282,1844.919679510697,826.5595378176982]"
+]
+
+empty_blocks = [
+    "[1066.8140315229548,1654.678601097876,994.1494008046308]",
+    "[1372.9314226188667,1698.1843589090392,805.5965454893357]",
+    "[1079.515087933512,1425.90033123735,1006.1353228190363]",
+    "[825.208612674945,565.9088211207202,1170.995860154057]",
+]
+
+
+input_path = "G_EK_000233_L/images/ome-zarr/Vglut3.ome.zarr"
+input_key = "s0"
+output_key = None
+resolution = 0.38
+
+output_folder = "./G_EK_000233_L_VGlut3"
+os.makedirs(output_folder, exist_ok=True)
+for coords in blocks_to_annotate:
+    halo = [196, 196, 48]
+    coords = json.loads(coords)
+    extract_block(
+        input_path, coords, output_folder, input_key, output_key, resolution, halo,
+        tif=True, s3=True,
+    )
+
+output_folder = "./G_EK_000233_L_VGlut3_empty"
+os.makedirs(output_folder, exist_ok=True)
+for coords in empty_blocks:
+    coords = json.loads(coords)
+    extract_block(
+        input_path, coords, output_folder, input_key, output_key, resolution, halo,
+        tif=True, s3=True,
+    )