Failure of script leaves behind tmp folder, rerunning script requires manual deletion of folder.

[id-b3]

Maybe possible to change the timing of the tmp folder creation, or to allow the script to ignore dirs when running.

(emc3) ivand@ID-Magic-Crate:~/Desktop/AirSeg_Py3$ python ./Code/scripts_util/convert_images_to_nifti.py BaseData/Airways_Dicom BaseData/CoarseAirways Print input arguments... 'input_dir' = BaseData/Airways_Dicom 'output_dir' = BaseData/CoarseAirways 'input_refdir' = None In FILE '\./Code/scripts_util/convert_images_to_nifti.py'\ and LINE '\53'\: ERROR: Extension file '' not known...... EXIT https://github.com/AntonioGUJ/AirwaySegmentation/blob/01d0cb549cc13b8a35b09397a1af250b74ab8a9b/scripts_util/convert_images_to_nifti.py#L24-L25

Additional issue: When I manually delete the tmp folder and rerun the script, I get the following error after one successful conversion:

Convert 1 DICOM as BaseData/CoarseAirways/vol01_anon3_s4_airways.dcmb (512x512x491x1) Conversion required 1.002215 seconds (1.001789 for core code). Traceback (most recent call last): File "./Code/scripts_util/convert_images_to_nifti.py", line 128, in <module> main(args) File "./Code/scripts_util/convert_images_to_nifti.py", line 80, in main removefile(out_json_file) File "/home/ivand/Desktop/AirSeg_Py3/Code/common/functionutil.py", line 50, in removefile os.remove(filename) FileNotFoundError: [Errno 2] No such file or directory: 'BaseData/CoarseAirways/vol01_anon3_s4_airways.json'

The file it's trying to delete is actually called 'BaseData/CoarseAirways/vol01_anon3_s4_airways.dcm.json'

https://github.com/AntonioGUJ/AirwaySegmentation/blob/01d0cb549cc13b8a35b09397a1af250b74ab8a9b/scripts_util/convert_images_to_nifti.py#L77-L80