Refine, FileNotFound error if there is '.' in the name of the tomogram

[rkjensen]

Dear IsoNet maintainers,

When having a '.' (except for the one right before the file-extension) in the name of the tomogram, refine will fail with a file not found error. Making a symbolic link to the tomogram (or as I did, renaming just the subtomograms), makes it work as expected.

Best,
Rasmus

[jhennies]

others having the same issue here: #49

[procyontao]

Hi, sorry for the inconvenience. I am trying to fix this.

[mpm896]

Hi, bringing this back up as I ran into the same issue because the naming convention from Warp has the pixel size info in the tomogram names. To overcome this I modified a few lines in prepare.py and refine.py:

prepare.py line 120:
change root_name = mrc.split('/')[-1].split('.')[0] --> root_name = ''.join(mrc.split('/')[-1].split('.')[0:-1])

line 213:
change root_name = mrc.split('/')[-1].split('.')[0] --> root_name = ''.join(mrc.split('/')[-1].split('.')[0:-1])

line 214:
change extension = mrc.split('/')[-1].split('.')[1] --> extension = mrc.split('/')[-1].split('.')[-1]

refine.py line 122:
change root_name = mrc.split('/')[-1].split('.')[0] --> root_name = ''.join(mrc.split('/')[-1].split('.')[0:-1])

I also see this same line predict.py line 53. I'm not at that point yet, but I imagine simarly changing:
root_name = m_name.split('/')[-1].split('.')[0] --> root_name = ''.join(mrc.split('/')[-1].split('.')[0:-1])

Hope this helps!