SpaGCN
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NotADirectoryError
Hello developer! I have tried configure an environment for SpaGCN on ubuntu server, however, three ways to installation in tutorial are not worked. And all of them report same errors, as follows: `1.2.5 Calculateing adj matrix using histology image... Var of c0,c1,c2 = 33.30687202862215 174.55510595352243 46.84205750749746 Var of x,y,z = 5606737.526317932 4468793.817921193 5606737.526317932 Run 1: l [0.01, 1000], p [0.0, 3629.740622904294] Run 2: l [0.01, 500.005], p [0.0, 3605.19131298059] Run 3: l [0.01, 250.0075], p [0.0, 3510.2840084795375] Run 4: l [0.01, 125.00874999999999], p [0.0, 3176.0043843625317] Run 5: l [0.01, 62.509375], p [0.0, 2292.207220295841] Run 6: l [0.01, 31.2596875], p [0.0, 1045.6601323127943] Run 7: l [0.01, 15.63484375], p [0.0, 292.86805881857936] Run 8: l [0.01, 7.822421875], p [0.0, 59.204869260873146] Run 9: l [0.01, 3.9162109375], p [0.0, 9.650458958139229] Run 10: l [0.01, 1.9631054687499998], p [0.0, 1.3308386992026033] Run 11: l [0.9865527343749999, 1.9631054687499998], p [0.1348709909344703, 1.3308386992026033] Run 12: l [0.9865527343749999, 1.4748291015625], p [0.1348709909344703, 0.5474268365922781] Run 13: l [1.23069091796875, 1.4748291015625], p [0.30070770989879625, 0.5474268365922781] Run 14: l [1.352760009765625, 1.4748291015625], p [0.41318173153943594, 0.5474268365922781] Run 15: l [1.4137945556640625, 1.4748291015625], p [0.477488424145156, 0.5474268365922781] Run 16: l [1.4137945556640625, 1.4443118286132812], p [0.477488424145156, 0.511742077238301] recommended l = 1.4290531921386718 Traceback (most recent call last): File "/home/yli/anaconda3/envs/Hu_spagcn_env/lib/python3.8/linecache.py", line 95, in updatecache stat = os.stat(fullname) NotADirectoryError: [Errno 20] Not a directory: '/home/yli/.local/lib/python3.8/site-packages/SpaGCN-1.2.5-py3.8.egg/SpaGCN/util.py'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/home/yli/HuQiFeng/SpaGCN-master/tutorial/test_in_DLPFC.py", line 72, in
Process finished with exit code 1`
where 'test_DLPFC.py' is a file that copys the python code from toturial without any changing.
Maybe torch's problem? I have tried two ways to install pytorch: pip directly, or conda install as pytorch.org recommends, both of them are in same result.
I didn't try the python3 setup.py install --user
method, because this ways reported timeout errors.
All I have done is :
conda create -n Hu_spagcn_env python=3.8.8
conda activate Hu_spagcn_env
pip install pip3 install --user SpaGCN -i https://pypi.mirrors.ustc.edu.cn/simple/
pip install opencv-python -i https://pypi.mirrors.ustc.edu.cn/simple/
and run the test_DLPFC.py file.
Hello, don't kown the reasons, after a dinner, the problem is disappear.