Closed id-b3 closed 1 year ago
Dear user,
I'm sorry for this issue. This is due to a function 'get_regex_file_pattern' used to obtain automatically the 'regex (regular expression)' file pattern of your input files, which is needed later in the code. For some reason, it assigns the pattern '[[0-9]+-9]+_0', which is clearly wrong.
I will look into this. In the meantime, you can solve this issue by assigning to the variable 'pattern_search' up above in the same script the correct 'regex' pattern directly, which is in your case: pattern_search = '[0-9]+_0' (in string format).
If your input filenames can contain a 1_digit suffix other than '0', you need to assign: patternsearch = '[0-9]+[0-9]'.
You will also need to do the same modification in other scripts within the pipeline to compute the airway predictions, namely in 'process_airway_tree.py' and 'compute_result_metrics.py'.
Please let me know if this solves your issues. Thanks
Dear user,
I've looked at this issue. It's due to a sneaky bug in the way I implemented the function "get_regex_file_pattern", and I need to figure out an alternative implementation. In the meantime, you can easily overcome this issue by using min. 2 digits in each component of your filenames, i.e. '000000_01' and '115236_00' instead of '000000_1' and '115236_0'. With this solution, you can ignore the 'workaround' that I proposed above.
Please let me know if this a solution for you. Thanks
There is a crash in the script then the input nifti image has a filename like this: 000000_0 or 000000_1 or 115236_0 etc. Here is the error code:
Changing the file end to words avoids the issue, e.g. 000000_zero or 000000_one however this is not idear when the filenames are generated using indexing.