make load quint json function more general

PyNutil/io/read_and_write.py

@@ -182,7 +182,7 @@ def load_segmentation(segmentation_path: str):
 
 # related to read and write
 # this function reads a VisuAlign JSON and returns the slices
-def load_visualign_json(filename, apply_damage_mask):
+def load_quint_json(filename, apply_damage_mask=True):
     """
     Reads a VisuAlign JSON file (.waln or .wwrp) and extracts slice information.
     Slices may include anchoring, grid spacing, and other image metadata.
@@ -215,12 +215,9 @@ def load_visualign_json(filename, apply_damage_mask):
         slices = vafile["slices"]
     if len(slices) > 1:
         slices = propagate(slices)
-    for slice in slices:
-        if not apply_damage_mask:
-            if "grid" in slice:
-                slice.pop("grid")
-    gridspacing = vafile["gridspacing"] if "gridspacing" in vafile else None
-    return slices, gridspacing
+    vafile["slices"] = slices
+    return vafile
+
 
 
 # related to read_and_write, used in write_points_to_meshview

PyNutil/processing/coordinate_extraction.py

 import numpy as np
 import pandas as pd
-from ..io.read_and_write import load_visualign_json
+from ..io.read_and_write import load_quint_json
 from .counting_and_load import flat_to_dataframe, rescale_image, load_image
 from .generate_target_slice import generate_target_slice
 from .visualign_deformations import triangulate
@@ -134,7 +134,16 @@ def folder_to_atlas_space(
     Returns:
         tuple: Various arrays and lists containing transformed coordinates and labels.
     """
-    slices, gridspacing = load_visualign_json(quint_alignment, apply_damage_mask)
+    quint_json = load_quint_json(quint_alignment, apply_damage_mask)
+    slices = quint_json['slices']
+    if apply_damage_mask and "gridspacing" in quint_json:
+        gridspacing = quint_json["gridspacing"]
+    else:
+        gridspacing = None
+    if not apply_damage_mask:
+        for slice in slices:
+            if "grid" in slice:
+                slice.pop("grid")
     segmentations = get_segmentations(folder)
     flat_files, flat_file_nrs = get_flat_files(folder, use_flat)
     region_areas_list = [