I am trying to use the library tvb-gdist in Pycharm to compute geodesic distances in several meshes. To install it just:
pip install tvb-gdist
However for some reason it works for only some of them. I work with lots of meshes but I will just show you an example with 2 of them to simplify (Here is the link to a folder with the files: https://drive.google.com/drive/folders/1dFKc8wdQuFaUNa3EIKdS7eTj6WVwwZFn?usp=sharing) . The function "gdist.local_gdist_matrix" takes as inputs the vertices and the faces of the mesh, and when executing it for the mesh formed by "vertices2" and "faces2" it works just fine. However when using the mesh formed by "vertices" and "faces" the error appears and the python console shuts down. The entire code is quite big but here is the code I developed to read the files and easily reproduce the error:
import csv
import gdist
file = open('faces.csv')
csvreader = csv.reader(file)
faces = []
for row in csvreader:
faces.append(row)
file.close()
file = open('vertices.csv')
csvreader = csv.reader(file)
vertices = []
for row in csvreader:
vertices.append(row)
file.close()
file = open('faces2.csv')
csvreader = csv.reader(file)
faces2 = []
for row in csvreader:
faces2.append(row)
file.close()
file = open('vertices2.csv')
csvreader = csv.reader(file)
vertices2 = []
for row in csvreader:
vertices2.append(row)
file.close()
vertices2 = np.array(vertices2).astype('float64')
faces2 = np.array(faces2).astype('int32')
aux_distances2 = gdist.local_gdist_matrix(vertices2, faces2, max_distance=12)
vertices = np.array(vertices).astype('float64')
faces = np.array(faces).astype('int32')
aux_distances = gdist.local_gdist_matrix(vertices, faces, max_distance=12)
If you run first until "aux_distances2" you will see that no problem arises and that it gives back the desired matrix. However when runing "aux_distances" the error "process finished with exit code -1073741819 (0xc0000005)" appears and the console crashes. I believe that since it works for some files, the problem cant be with the python version or with something related to the path of the files (they are under the same directory) but anything may be possible. I thought that it might be related with the amount of faces and/or vertices but I did a mesh decimation using the library "quad_mesh_simplify" and the same error appeared after the remesh had been done. I also tried to run it in a notebook in Google Colab to check if Pycharm was the problem but the result was the same: for the second mesh it worked just fine but for the first mesh it crashed. The error showed: "KernelRestarter: restarting kernel (1/5), keep random ports" and then "WARNING:root:kernel 0c24cfc6-3530-4211-a4d2-b147c3444581 restarted". I have tried every solution that I have found and none of them have worked so if anyone could help me I would very much appreciate it.
I suppose you are referring to tvb-gdist from here: https://github.com/the-virtual-brain/tvb-gdist
I tested it myself, and I can reproduce the problem.
I think you are right, it is not the installation, or the IDE's culprit. I suspect the surface has problems. A minor inspection with tvb software shows the warnings bellow.
Could you alter the surface and get rid of its problems (pinched faces and possible small holes)? I suspect the piches produce an infinite loop in tvb-gdist.
2022-04-26 05:34:01,630 - WARNING [proc:21055] - tvb.datatypes.surfaces - Surface is pinched off.
2022-04-26 05:34:01,630 - DEBUG [proc:21055] - tvb.datatypes.surfaces - These are edges with more than 2 triangles:
[ 11022 11023 11033 11035 11036 11273 11280 11488 11489 11494
11495 11508 11509 11516 11517 11753 11759 11770 11775 11782
11976 11994 12238 12240 12247 12253 12279 12283 12485 12486
12490 12491 12495 12498 12519 12746 12747 12752 12753 12778
12781 12991 13033 13037 13045 13249 13250 13256 13258 13266
13317 13549 13572 13577 13761 13803 14031 14034 14037 14084
14319 14541 14589 14780 14784 15036 15286 15287 15293 15553
15559 15801 15804 15814 15815 15822 15826 16121 16335 16336
16632 16633 16636 16857 16866 17167 17169 17423 17717 17720
17993 18292 18561 18853 18854 19155 19159 19170 19763 19765
20093 20364 20685 20689 20984 21317 21602 21604 21978 22283
22288 22637 22961 23330 23709 23711 23721 24110 24436 24444
24865 25228 25234 25235 25674 25677 26061 26534 26921 26926
27380 27764 27769 28620 29051 29440 29899 29907 30678 30683
31028 31034 31495 31818 32303 32310 33042 33416 33418 33430
34170 34567 34571 34932 35327 35679 36083 36453 36457 36857
37213 38011 38443 38812 38815 38824 39347 39350 39632 39639
40060 40131 40138 40140 40406 40492 40841 40843 40851 40923
40928 41598 41603 41675 41682 41955 42025 42323 42329 42397
42676 43056 43119 43126 43425 43432 43488 43872 44168 44171
44237 44570 44621 44940 44996 45002 45335 45689 45735 45741
46092 46099 46516 46522 46884 46887 46902 46904 46908 46910
47275 47289 47295 47296 47325 47726 47735 47736 47740 47744
47745 47758 47790 47796 48110 48118 48126 48132 48139 48152
48153 48158 48160 48167 48170 48179 48181 48185 48579 48583
48605 48610 48611 48612 48616 48622 48628 48632 48653 49030
49038 49050 49051 49080 49086 49089 49100 49101 49106 49108
49568 49588 49593 49610 49620 49627 49631 50042 50047 50060
50061 50076 50598 50602 50603 50607 50613 118407 118416 118571
118574 118578 118926 118932 119068 119276 119387 119496 119499 119503
119606 119695 119811 119987 120165 120336 120482 120488 120797 120928
121081 121174 121185 121325 121391 121588 121607 121716 121780 121859
122210 122224 122337 122516 122518 122636 122750 122826 122832 123024
123103 123136 123223 123378 123385 123435 123436 123449 123474 123589
123760 123766 123799 123833 123933 123953 123963 123966 123967 123975
123976 124142 124143 124152 124161 124168 124284 124297 124482 124484
124485 124493 124501 124642]
2022-04-26 05:34:01,631 - WARNING [proc:21055] - tvb.datatypes.surfaces - Has holes.
2022-04-26 05:34:01,631 - DEBUG [proc:21055] - tvb.datatypes.surfaces - Free boundaries:
[108104 108106 108391 108430 117047 117051 117057 117068]