For matching parent cells to foci in an image

match_to_parents.py

# c_foci = an array with numbers indicating where foci are (e.g. all voxels corresponding to focus #1 = 1, all vx corresp to foci #2 = 2, etc.)
# segmented_cells = an array with #s indicating where cells are, same format as c_foci
# x = focus ID that is being checked for parent cells


if verbose:
  print('current ID: ' + str(x))
parent_cell, cell_cts = np.unique(
  self.segmented_cells[i][c_foci == x],
  return_counts=True
  )
cell_cts = cell_cts[parent_cell != 0]  # rm bgrd
parent_cell = parent_cell[parent_cell != 0]  # rm bgrd
if verbose:
  print('  overlapping parent cell(s): ')
  print(parent_cell)
  print('  # of pixels overlapping with parent(s):')
  print(cell_cts)
if parent_cell.size > 1:  # if part of >1 cell
  # assign to cell containing more of the focus's px
  if verbose:
      print('  more than one overlapping cell.')
      print('  determining which cell overlaps more.')
  parent_cell = parent_cell[np.argmax(cell_cts)]
  if verbose:
      print('  parent cell: ' + str(parent_cell))
elif parent_cell.size == 1:
  if verbose:
      print('matched to one parent cell.')
  parent_cell = parent_cell[0]  # extract value from arr