Describe the bug
hello, I performed the CNMF plugin on a tiff image. Everything went well until it raised an error on saving files in the end
To Reproduce
Steps to reproduce the behavior, for example:
Go to 'batch manager'
Click on 'start'
Scroll down to 'output'
See error
Expected behavior
I wished it could successfully finish CNMF algorithm and when I double click the batch name, I could see the final segmentation result
Copy paste message from the error window (if any)
status: 0
output_info: Traceback (most recent call last):
File "/home/donglab/mesmerize/lib/python3.6/site-packages/mesmerize/viewer/modules/batch_run_modules/CNMF.py", line 60, in run
run_single(batch_dir, UUID, output)
File "/home/donglab/mesmerize/lib/python3.6/site-packages/mesmerize/viewer/modules/batch_run_modules/CNMF.py", line 158, in run_single
cnm.save(out_filename)
File "/home/donglab/mesmerize/CaImAn/caiman/source_extraction/cnmf/cnmf.py", line 667, in save
save_dict_to_hdf5(self.dict, filename)
File "/home/donglab/mesmerize/CaImAn/caiman/utils/utils.py", line 429, in save_dict_to_hdf5
recursively_save_dict_contents_to_group(h5file, subdir, dic)
File "/home/donglab/mesmerize/CaImAn/caiman/utils/utils.py", line 524, in recursively_save_dict_contents_to_group
recursively_save_dict_contents_to_group(h5file, path + key + '/', item.dict)
File "/home/donglab/mesmerize/CaImAn/caiman/utils/utils.py", line 509, in recursively_save_dict_contents_to_group
recursively_save_dict_contents_to_group(h5file, path + key + '/', item)
File "/home/donglab/mesmerize/CaImAn/caiman/utils/utils.py", line 496, in recursively_save_dict_contents_to_group
raise ValueError('Error while saving {}.'.format(key))
ValueError: Error while saving var_name_hdf5.
Copy-paste or take a screenshot of the terminal that Mesmerize is running in
Describe the bug hello, I performed the CNMF plugin on a tiff image. Everything went well until it raised an error on saving files in the end
To Reproduce Steps to reproduce the behavior, for example:
Expected behavior I wished it could successfully finish CNMF algorithm and when I double click the batch name, I could see the final segmentation result
Copy paste message from the error window (if any) status: 0 output_info: Traceback (most recent call last): File "/home/donglab/mesmerize/lib/python3.6/site-packages/mesmerize/viewer/modules/batch_run_modules/CNMF.py", line 60, in run run_single(batch_dir, UUID, output) File "/home/donglab/mesmerize/lib/python3.6/site-packages/mesmerize/viewer/modules/batch_run_modules/CNMF.py", line 158, in run_single cnm.save(out_filename) File "/home/donglab/mesmerize/CaImAn/caiman/source_extraction/cnmf/cnmf.py", line 667, in save save_dict_to_hdf5(self.dict, filename) File "/home/donglab/mesmerize/CaImAn/caiman/utils/utils.py", line 429, in save_dict_to_hdf5 recursively_save_dict_contents_to_group(h5file, subdir, dic) File "/home/donglab/mesmerize/CaImAn/caiman/utils/utils.py", line 524, in recursively_save_dict_contents_to_group recursively_save_dict_contents_to_group(h5file, path + key + '/', item.dict) File "/home/donglab/mesmerize/CaImAn/caiman/utils/utils.py", line 509, in recursively_save_dict_contents_to_group recursively_save_dict_contents_to_group(h5file, path + key + '/', item) File "/home/donglab/mesmerize/CaImAn/caiman/utils/utils.py", line 496, in recursively_save_dict_contents_to_group raise ValueError('Error while saving {}.'.format(key)) ValueError: Error while saving var_name_hdf5. Copy-paste or take a screenshot of the terminal that Mesmerize is running in
Make sure the entire stack trace is visible, and all messages relevant to the issue are visible.
If relevant, messages from the batch manager terminal
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