Error in initial pipeline with example data

[veenstje]

Hi Vito, I hope you are well! I've been attempting to get your IMC segmentation pipeline established but have been running into an error early in the process. I'm currently using all the example files supplied without any changes and I'm encountering the below error. Any thoughts on how to resolve this issue? All prior aspects of the pipeline appear to be working properly without any errors. I can confirm the aquisition_metadata.csv file does get loaded into the cpinp folder. Thanks

Export a copy of the panel to the output folder

shutil.copy(file_path_csv_panel, file_path_cp_csv)

FileNotFoundError Traceback (most recent call last)

in ----> 1 shutil.copy(file_path_csv_panel, file_path_cp_csv) ~\anaconda3\envs\imctools\lib\shutil.py in copy(src, dst, follow_symlinks) 416 if os.path.isdir(dst): 417 dst = os.path.join(dst, os.path.basename(src)) --> 418 copyfile(src, dst, follow_symlinks=follow_symlinks) 419 copymode(src, dst, follow_symlinks=follow_symlinks) 420 return dst ~\anaconda3\envs\imctools\lib\shutil.py in copyfile(src, dst, follow_symlinks) 262 os.symlink(os.readlink(src), dst) 263 else: --> 264 with open(src, 'rb') as fsrc, open(dst, 'wb') as fdst: 265 # macOS 266 if _HAS_FCOPYFILE: FileNotFoundError: [Errno 2] No such file or directory: '../config/example_panel.csv'

[votti]

Hi, Sorry for taking so long. I tried to reproduce this on the weekend on Linux and now today again an Windows and cannot reproduce this error.

As these scripts are using relative filepaths, it is crucial to not move the files around (at least without changing file paths). So after downloading the repository from Github as Zip (or via Github Desktop) the files shall not be moved around relatively to each other.

Are you sure you did not accidentally move the files around?

Best, Vito

[veenstje]

Hi Vito, I didn't alter any of the files/folders so I'm unsure why it would be doing that. I will delete everything and try again when I have a chance. I will keep you posted.

Thanks

[veenstje]

Hi Vito,

The issue has unfortunately persisted even after deleting everything and restarting from scratch; no folders were moved or manipulated after creation. I've attached images below showing what files are created in what folders in the primary analysis folder. All subfolders in the analysis folder are empty with the exception of the ometiff and cpinp folders. Maybe this will provide you a little more insight into what the problem is? I appreciate any other thoughts you have. Thanks!

[veenstje]

Hi Vito, good news! I tried an install on a separate computer and was able to successfully run through the script. It appears that there was some kind of folder handling issue on my other computer that was causing the problems. Thank you for your assistance with this.

Jesse