Elastix plugin: Cannot load parameter files

[ablot]

When trying to load any parameter file, the elastix plugin crashes (traceback below). The error comes from QtGui.QFileDialog.getOpenFileNames which, for me, returns the file list AND the filter selected. @raacampbell does the plugin work for you as is?

Traceback (most recent call last): File "/home/blota/Code/Python/Anatomy/lasagna/lasagna/plugins/registration_plugins/elastix_plugin.py", line 323, in loadParamFile_slot shutil.copyfile(path_to_param_file, self.tmpParamFiles[param_file_name]) File "/home/blota/Software/anaconda3/envs/lasagna/lib/python3.7/shutil.py", line 103, in copyfile if _samefile(src, dst): File "/home/blota/Software/anaconda3/envs/lasagna/lib/python3.7/shutil.py", line 88, in _samefile return os.path.samefile(src, dst) File "/home/blota/Software/anaconda3/envs/lasagna/lib/python3.7/genericpath.py", line 96, in samefile s1 = os.stat(f1) TypeError: stat: path should be string, bytes, os.PathLike or integer, not list

[ablot]

Would PR #240 break your setup @raacampbell ? If so we might have to play with Qt versions...
I use
Qt version: 5.12.2
SIP version: 4.19.15
PyQt version: 5.12.1

[raacampbell]

I will try tomorrow if I get a chance. Ping me back if I don't do it.

[apdals]

I am using the master branch and have been receiving the same error as @ablot. I know that this issue was addressed and the code was changed in the development branch. I also see that the dev branch has been merged with the master branch not long ago. However, after looking through the code in the master branch, the change is no longer present. Was the change passed on? Was there a reason why the change was removed in the master? Thanks.

[nsteinme]

hey @raacampbell, @apdals is in my lab and we're stuck moving forward with lasagna because of this error. Any ideas of what we're doing wrong? Are other labs in IBL not having this problem, should we talk with Steven West about it, would he be able to help us?

[raacampbell]

Is it necessary to use the Elastix plugin in Lasagna? We aren't doing it, actually. We are running Elastix via a MATLAB script: https://github.com/SainsburyWellcomeCentre/ara_tools the command is ARAregister

I know that doesn't address the issue of this Lasagna plugin not working but at the moment I don't have plans to fix it.

[nsteinme]

Thanks Rob - we had missed that. We'll try the matlab script. Might be worth adding a note about this here? https://github.com/SainsburyWellcomeCentre/lasagna/wiki/Elastix-Image-Registation-Plugin

[raacampbell]

Good point. I've added the info.