Sorry, this might turn out to be a very basic problem but I'm stumped:
I'm trying to get the lengths of skeleton branches. I'm able to skeletonize my image and can see the skeleton with draw.overlay_skeleton_2d() but when I try to get any statistics on the skeleton back I get an error:
TypeError Traceback (most recent call last)
<ipython-input-3-5924e1b8ffc8> in <module>
4 # fig, ax = plt.subplots()
5 # draw.overlay_skeleton_2d(img, skeleton0, dilate=1, axes=ax)
----> 6 branch_data = summarize(Skeleton(skeleton0))
7 branch_data.head()
~\AppData\Roaming\Python\Python38\site-packages\skan\csr.py in __init__(self, skeleton_image, spacing, source_image, _buffer_size_offset, keep_images, junction_mode, unique_junctions)
383 self.nbgraph = csr_to_nbgraph(graph, pixel_values)
384 self.coordinates = coords
--> 385 self.paths = _build_skeleton_path_graph(
386 self.nbgraph, _buffer_size_offset=_buffer_size_offset
387 )
~\AppData\Roaming\Python\Python38\site-packages\skan\csr.py in _build_skeleton_path_graph(graph, _buffer_size_offset)
259 def _build_skeleton_path_graph(graph, *, _buffer_size_offset=None):
260 if _buffer_size_offset is None:
--> 261 max_num_cycles = graph.indices.size // 4
262 _buffer_size_offset = max_num_cycles
263 degrees = np.diff(graph.indptr)
TypeError: expected dtype object, got 'numpy.dtype[int32]'
Any tips would be great. I'm still a Python beginner so, like I said, the mistake might be a very basic one.
Rgds,
Olie
*Edits included
This is my code:
import cv2
from skan import draw, skeleton_to_csgraph, Skeleton, summarize
from skimage import morphology
# import numpy as np
from matplotlib import pyplot as plt
%matplotlib notebook
# load image and convert to bool
img = cv2.imread(save_p + "\\" + img_name + ".png")
img = cv2.cvtColor(img, cv2.COLOR_BGR2GRAY)
img = img.astype(bool)
# skeletonize
skeleton0 = morphology.skeletonize(img)
### check skeleton
# fig, ax = plt.subplots()
# draw.overlay_skeleton_2d(img, skeleton0, dilate=1, axes=ax)
### from Documentation (linked below)
branch_data = summarize(Skeleton(skeleton0)) # ignoring scaling for now
branch_data.head()
# Skel_obj = Skeleton(skeleton0) # testing this but same problem
# Skel_obj.path_lengths(0)
I have attempted to follow a couple of posts (e.g. this but for that particular case the module wont install and anyway... it seems like skan.summarize is exactly what I need - documentation
Name: numpy Version: 1.23.4
Name: scikit-image Version: 0.19.3
Name: pandas Version: 1.3.4
Name: skan Version: 0.10.0
Name: numba Version: 0.50.1
Windows 10 PC
