Closed wlugmayr closed 1 year ago
Thanks for reporting a bug! I have fixed that in commit 3164620 which is currently under develop
branch.
You may get dev version from that branch or wait until the next version will be released at the end of the next week. Hope it helps!
Hi @wlugmayr ! I do apologize that it took much more than expected, but the newly published release v0.3.0 (w/o binary this time) should now solve this issue in the full MATLAB version of the TomoBEAR.
I assume that this issue was resolved and could be closed, otherwise you are welcome to re-open it.
Describe the bug
When using the interactive Matlab TomoBear version the file extension is duplicated. This worked in older TomoBEAR versions and works with the compiled MATLAb standalone executable.
Project JSON file ribosome_empiar_10064_dynamo.json
Error message Error using getOriginalMRCsorTIFs ERROR: No micrographs found at location /gpfs/cssb/software/tutorials/empiar_data/EMPIAR-10064-CTEM/10064/data/.mrc/.mrc
Error in getFileCountChanged (line 2) [file_list, ~] = getOriginalMRCsorTIFs(configuration);
Error in LocalPipeline/execute (line 465) file_count_changed = getFileCountChanged(configuration.general);
Error in runPipeline (line 131) pipeline.execute(starting_tomogram, ending_tomogram, step, gpu);
Error in runTomoBear (line 15) runPipeline(compute_environment, configuration_path, default_configuration_path, starting_tomogram, ending_tomogram, step, gpu);
Error in run_ribosome (line 1) runTomoBear("local", "./ribosome_empiar_10064_dynamo.json", "/gpfs/cssb/software/centos7/x86_64/tomobear/0.2.0/configurations/defaults.json")
To Reproduce Run the tutorial in the MATLAB GUI (matlab/R2022b).
Additional context When using no extensions it gets the error:
INFO:DATA_PATH: /gpfs/cssb/software/tutorials/empiar_data/EMPIAR-10064-CTEM/10064/data/ Error using getUnprocessedTomograms ERROR: Multiple unknown extensions found!
Error in LocalPipeline/execute (line 178) [dynamic_configuration, file_count_changed] = getUnprocessedTomograms(configuration.general, log_file_id);
Error in runPipeline (line 131) pipeline.execute(starting_tomogram, ending_tomogram, step, gpu);
Error in runTomoBear (line 15) runPipeline(compute_environment, configuration_path, default_configuration_path, starting_tomogram, ending_tomogram, step, gpu);
Error in run_ribosome (line 1) runTomoBear("local", "./ribosome_empiar_10064_dynamo.json", "/gpfs/cssb/software/centos7/x86_64/tomobear/0.2.0/configurations/defaults.json")