renamed dunder routines in indexing

src/agora/utils/indexing.py

@@ -73,7 +73,7 @@ def validate_lineage(
     """
     if lineage.ndim == 2:
         # [trap, mother, daughter] becomes [[trap, mother], [trap, daughter]]
-        lineage = _assoc_indices_to_3d(lineage)
+        lineage = assoc_indices_to_3d(lineage)
     if how == "mothers":
         c_index = 0
     elif how == "daughters":
@@ -123,7 +123,7 @@ def index_isin(x: np.ndarray, y: np.ndarray) -> np.ndarray:
     return x_bool
 
 
-def _assoc_indices_to_3d(ndarray: np.ndarray):
+def assoc_indices_to_3d(ndarray: np.ndarray):
     """
     Convert the last column to a new row and repeat first column's values.
 
@@ -153,6 +153,16 @@ def _assoc_indices_to_3d(ndarray: np.ndarray):
     return result
 
 
+def assoc_indices_to_2d(array: np.ndarray):
+    """Convert indices to 2d."""
+    result = array
+    if len(array):
+        result = np.concatenate(
+            (array[:, 0, :], array[:, 1, 1, np.newaxis]), axis=1
+        )
+    return result
+
+
 ###################################################################
 
 
@@ -250,16 +260,6 @@ def validate_association(
     return valid_association, valid_indices
 
 
-def _3d_index_to_2d(array: np.ndarray):
-    """Revert _assoc_indices_to_3d."""
-    result = array
-    if len(array):
-        result = np.concatenate(
-            (array[:, 0, :], array[:, 1, 1, np.newaxis]), axis=1
-        )
-    return result
-
-
 def compare_indices(x: np.ndarray, y: np.ndarray) -> np.ndarray:
     """
     Fetch two 2-D indices and return a binary 2-D matrix

src/postprocessor/core/postprocessing.py

@@ -10,8 +10,8 @@ from agora.io.cells import Cells
 from agora.io.signal import Signal
 from agora.io.writer import Writer
 from agora.utils.indexing import (
-    _3d_index_to_2d,
-    _assoc_indices_to_3d,
+    assoc_indices_to_2d,
+    assoc_indices_to_3d,
 )
 from agora.utils.merge import merge_lineage
 from postprocessor.core.abc import get_parameters, get_process
@@ -133,19 +133,19 @@ class PostProcessor(ProcessABC):
         record = self.signal.get_raw(self.targets["merging_picking"]["merger"])
         merges = self.merger.run(record)
         # get lineages from cells object attached to picker
-        lineage = _assoc_indices_to_3d(self.picker.cells.mothers_daughters)
+        lineage = assoc_indices_to_3d(self.picker.cells.mothers_daughters)
         if merges.any():
             # update lineages and merges after merging
             new_lineage, new_merges = merge_lineage(lineage, merges)
         else:
             new_lineage = lineage
             new_merges = merges
-        self.lineage = _3d_index_to_2d(new_lineage)
+        self.lineage = assoc_indices_to_2d(new_lineage)
         self.writer.write(
             "modifiers/merges", data=[np.array(x) for x in new_merges]
         )
         self.writer.write(
-            "modifiers/lineage_merged", _3d_index_to_2d(new_lineage)
+            "modifiers/lineage_merged", assoc_indices_to_2d(new_lineage)
         )
         # run picker
         picked_indices = self.picker.run(