GGiecold-zz
commented
8 years ago Thank you for reporting this issue.
It seems that on Windows the name of a temporary file cannot be used to access that file a second time while the file is still open. In DBSCN_multiplex, I believe this explains the error you get: On line 652, the file is created and left open until the end of the block of context management starting at "with". But then, within the call to procedure 'load', an attempt is made on line 354 to read this file.
I do not have access to a machine running on Windows. I therefore intend to remove support of this module for this particular type of operating system. However, it should still be possible for you to run DBSCN_multiplex by creating any file and calling 'load' and 'shoot' with the name of this file as an argument.
Please let me know if this solves the problem you've encountered.
Kind regards,
Gregory
On Dec 7, 2015, at 5:30 AM, Michael Jendryke notifications@github.com wrote:
I have the following code to run, but HDF5 tells me in the error back trace that i have no permission to create the temporary file.
The code I run is a script to run DBSCAN_multiplex.py:
import numpy as np import DBSCAN_multiplex as DB print("hey ;-)") data = np.random.randn(15000, 7) N_iterations = 50 N_sub = 9 * data.shape[0] / 10 subsamples_matrix = np.zeros((N_iterations, N_sub), dtype = int) for i in xrange(N_iterations): subsamples_matrix[i] = np.random.choice(data.shape[0], N_sub, replace = False) eps, labels_matrix = DB.DBSCAN(data, minPts = 3, subsamples_matrix = subsamples_matrix, verbose = True) The error message in PyCharm is:
C:\Anaconda2\python.exe E:/Dropbox/DATA/research/GhostTowns/WB/untitled/dbscan.py hey ;-) INFO: DBSCAN_multiplex @ load: starting the determination of an appropriate value of 'eps' for this data-set and for the other parameter of the DBSCAN algorithm set to 3. This might take a while.
INFO: DBSCAN_multiplex @ load: done with evaluating parameter 'eps' from the data-set provided. This took 1.737 seconds. Value of epsilon: 0.921.
INFO: DBSCAN_multiplex @ load: identifying the neighbors within an hypersphere of radius 0.921 around each sample, while at the same time evaluating the number of epsilon-neighbors for each sample. This might take a fair amount of time. Traceback (most recent call last): File "E:/Dropbox/DATA/research/GhostTowns/WB/untitled/dbscan.py", line 9, in
eps, labels_matrix = DB.DBSCAN(data, minPts = 3, subsamples_matrix = subsamples_matrix, verbose = True) File "C:\Anaconda2\lib\site-packages\DBSCAN_multiplex.py", line 656, in DBSCAN eps = load(f.name, data, minPts, eps, quantile, subsamples_matrix, samples_weights, metric, p, verbose) File "C:\Anaconda2\lib\site-packages\DBSCAN_multiplex.py", line 354, in load fileh = tables.open_file(hdf5_file_name, mode = 'r+') File "C:\Anaconda2\lib\site-packages\tables\file.py", line 318, in open_file return File(filename, mode, title, root_uep, filters, _kwargs) File "C:\Anaconda2\lib\site-packages\tables\file.py", line 784, in init self._g_new(filename, mode, _params) File "tables\hdf5extension.pyx", line 488, in tables.hdf5extension.File._g_new (tables\hdf5extension.c:5458) tables.exceptions.HDF5ExtError: HDF5 error back trace File "C:\Python27\conda-bld\work\hdf5-1.8.15-patch1\src\H5F.c", line 604, in H5Fopen unable to open file File "C:\Python27\conda-bld\work\hdf5-1.8.15-patch1\src\H5Fint.c", line 990, in H5F_open unable to open file: time = Mon Dec 07 18:12:12 2015 , name = 'F:\temp\tmpthbz3d.h5', tent_flags = 1 File "C:\Python27\conda-bld\work\hdf5-1.8.15-patch1\src\H5FD.c", line 993, in H5FD_open open failed File "C:\Python27\conda-bld\work\hdf5-1.8.15-patch1\src\H5FDsec2.c", line 343, in H5FD_sec2_open unable to open file: name = 'F:\temp\tmpthbz3d.h5', errno = 13, error message = 'Permission denied', flags = 1, o_flags = 2
End of HDF5 error back trace
Unable to open/create file 'F:\temp\tmpthbz3d.h5'
Process finished with exit code 1 What it boils down to is the last line which says that permissions are not set. However, I have allowed full read and write permissions for the folder and I tried to run python with administrator rights. I also guess, that the issue is somehow connected to HDF5, or HDF5 is trying to create this temporary file but fails. At this point I am clueless on how to solve this issue and I would be happy about any input.
This question might be connected to http://stackoverflow.com/questions/23212435/permission-denied-to-write-to-my-temporary-file but since the mode is set to 'w' I had no luck with it.
Thanks
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MichaelJendryke
StatguyUser
I have the following code to run, but HDF5 tells me in the error back trace that i have no permission to create the temporary file.
The code I run is a script to run DBSCAN_multiplex.py:
The error message in PyCharm is:
What it boils down to is the last line which says that permissions are not set. However, I have allowed full read and write permissions for the folder and I tried to run python with administrator rights. I also guess, that the issue is somehow connected to HDF5, or HDF5 is trying to create this temporary file but fails. At this point I am clueless on how to solve this issue and I would be happy about any input.
This question might be connected to http://stackoverflow.com/questions/23212435/permission-denied-to-write-to-my-temporary-file but since the mode is set to 'w' I had no luck with it.
Thanks