Closed WhereWolf72 closed 1 year ago
Mesmerize and caiman version?
I you can't get it working by late this afternoon just use the VM for the workshop.
On Tue, May 31, 2022, 23:06 WhereWolf72 @.***> wrote:
Assigned #103 https://github.com/kushalkolar/MESmerize/issues/103 to @kushalkolar https://github.com/kushalkolar.
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Mesmerize == 0.7.1 and caiman == 1.8.8
Thanks for your assistance, I'm not sure why this install is any different than what is running on my desktop (which runs perfectly).
Describe the bug I can import a .tif file using the tiff importer and json_minimal metadata importer. Further, I can run motion correction and inspect the correlation and PNR after running that preliminary analysis. However, when I go to run the full CNMFe analysis, I get an error and don't get an output .hdf5 file, but get the other output files that I have gotten previously upon successful CNMFe analysis. I had this problem previously on an older laptop, but it was fixed when I did a fresh install on a new desktop. Now, I'm attempting to get Mesmerize working on a newer laptop in preparation for the CCN Caiman Workshop in a couple days. Thanks in advance for the help!
To Reproduce
Expected behavior Upon running full CNMF-E, I expected to get an .hdf5 file along with other file outputs so that I could visualize the ROIs as I have before.
Copy paste message from the error window (if any) status: 0 output_info: Traceback (most recent call last): File "/home/trevor/Desktop/Calcium_Imaging/mez/lib/python3.6/site-packages/mesmerize/viewer/modules/batch_run_modules/CNMFE.py", line 173, in run cnm.fit(Y) File "/home/trevor/CaImAn/caiman/source_extraction/cnmf/cnmf.py", line 606, in fit indices=indices) File "/home/trevor/CaImAn/caiman/source_extraction/cnmf/map_reduce.py", line 249, in run_CNMF_patches file_res = dview.map_async(cnmf_patches, args_in).get(4294967) File "/usr/lib/python3.6/multiprocessing/pool.py", line 644, in get raise self._value multiprocessing.pool.MaybeEncodingError: Error sending result: '<multiprocessing.pool.ExceptionWithTraceback object at 0x7f989d7a6240>'. Reason: 'PicklingError("Can't pickle <class '_flapack.error'>: import of module '_flapack' failed",)'
Y.shape: [535, 512, 512] processing_time: 0.6470573385556538
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If relevant, messages from the batch manager terminal![image](https://user-images.githubusercontent.com/92590376/171317532-dd4ceac1-8b52-4365-80fd-94710a109e0b.png)
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in your environmentAdditional context Just in case it was a similar problem to my previous bug report (#82), I followed the suggested steps around liblapack and libopenblas, but it didn't fix the issue. I did get an error surrounding tensorflow-gpu's dependencies (see below), but I don't believe that I'm even utilizing that package for this step.
Tensorflow dependency error: