Error while computing feret's diameter with regionprops

[Biswanath Saha]

Description:

Hello all! I am having some problems calculating feret_diameter_max in regionprops.

def calculate_feret_dia(lbl_img):
    props = measure.regionprops(lbl_img,spacing=(0.215,0.0401,0.0401)) #z,y,x px size
    feret_dia = [x.feret_diameter_max for x in props]
    return feret_dia

Error trace:

ValueError                                Traceback (most recent call last)
Cell In[26], line 1
----> 1 pre_feret_dia = calculate_feret_dia(pre_syn_label)

Cell In[24], line 3
      1 def calculate_feret_dia(lbl_img):
      2     props = measure.regionprops(lbl_img)
----> 3     feret_dia = [x.feret_diameter_max for x in props]
      4     return feret_dia

Cell In[24], line 3
      1 def calculate_feret_dia(lbl_img):
      2     props = measure.regionprops(lbl_img)
----> 3     feret_dia = [x.feret_diameter_max for x in props]
      4     return feret_dia

File c:\Users\BiswanathSaha\miniconda3\envs\stable\lib\site-packages\skimage\measure\_regionprops.py:482, in RegionProperties.feret_diameter_max(self)
    479     coordinates = np.vstack(find_contours(identity_convex_hull, .5,
    480                                           fully_connected='high'))
    481 elif self._ndim == 3:
--> 482     coordinates, _, _, _ = marching_cubes(identity_convex_hull,
    483                                           level=.5)
    484 distances = pdist(coordinates * self._spacing, 'sqeuclidean')
    485 return sqrt(np.max(distances))

File c:\Users\BiswanathSaha\miniconda3\envs\stable\lib\site-packages\skimage\measure\_marching_cubes_lewiner.py:131, in marching_cubes(volume, level, spacing, gradient_direction, step_size, allow_degenerate, method, mask)
    129 elif method != 'lewiner':
    130     raise ValueError("method should be either 'lewiner' or 'lorensen'")
--> 131 return _marching_cubes_lewiner(volume, level, spacing,
    132                                gradient_direction, step_size,
    133                                allow_degenerate, use_classic=use_classic,
    134                                mask=mask)

File c:\Users\BiswanathSaha\miniconda3\envs\stable\lib\site-packages\skimage\measure\_marching_cubes_lewiner.py:160, in _marching_cubes_lewiner(volume, level, spacing, gradient_direction, step_size, allow_degenerate, use_classic, mask)
    158     level = float(level)
    159     if level < volume.min() or level > volume.max():
--> 160         raise ValueError("Surface level must be within volume data range.")
    161 # spacing
    162 if len(spacing) != 3:

ValueError: Surface level must be within volume data range.

Way to reproduce:

def calculate_feret_dia(lbl_img):
props = measure.regionprops(lbl_img,spacing=(0.215,0.0401,0.0401)) #z,y,x px size
feret_dia = [x.feret_diameter_max for x in props]
return feret_dia
pre_feret_dia = calculate_feret_dia(pre_syn_label)

Version information:

3.9.18 (main, Sep 11 2023, 14:09:26) [MSC v.1916 64 bit (AMD64)]
Windows-10-10.0.22621-SP0
scikit-image version: 0.22.0
numpy version: 1.24.1