So I have code that completes an analysis for me on imaging data. This code is working fine except that the data is not being outputted into the correct folder. Instead, it is being outputted one folder too high. This is something I obviously want to fix in the long run, but as I am under certain time constraints I want to input code into my script that will simply move the files to the correct folder/directory that I have created. I have tried the mv and shutil commands but they don't seem to be working. I would be grateful if someone had a suggestion for how to fix/improve my method of moving these files to the correct location. If someone has a suggestion for why the files are being outputted to the wrong directory as well that would be awesome. I am relatively new to coding and no expert so please forgive any obvious mistakes. Thank you.
This is where I set up my directories
subject_dir = os.getcwd()
dti_dir = os.path.abspath( os.path.join(subject_dir, 'dti'))
dti_input_dir = os.path.abspath( os.path.join(dti_dir, 'input'))
This is where I entered a few shortcuts
eddy_prefix = 'eddy'
input_path = dti_input_dir
output_prefix = 'dtifit'
output_path = '../dti/dtifit'
output_basename = os.path.abspath(os.path.join(dti_dir, output_path))
infinite_path = os.path.join(os.getenv('INFINITE_PATH'), 'infinite')
dti30 = 'dti30.nii.gz'
dti30_brain = 'bet.b0.dti30.nii.gz'
dti30_mask = 'bet.b0.dti30_mask.nii.gz'
This is where I ran my test.
The test is being run, but my data is being outpputed in dti_dir and not output_basename (this is my second question)
dti = fsl.DTIFit()
dti.inputs.dwi = os.path.join(input_path, eddy_prefix + '.nii.gz')
dti.inputs.bvecs = os.path.join(input_path, eddy_prefix + '.eddy_rotated_bvecs')
dti.inputs.bvals = os.path.abspath(os.path.join(infinite_path, 'dti30.bval'))
dti.inputs.base_name = output_basename
dti.inputs.mask = os.path.join(input_path, dti30_mask)
dti.cmdline
Creating output directory if doesn't exist.
This is working fine and the directory is created in the proper location.
if not os.path.exists(output_basename):
os.makedirs(output_basename)
print('DTI Command line')
print(dti.cmdline)
res = dti.run()
exit()
print('DTIFIT Complete!')
Here I try to move the files and I get the error: IOError: [Errno 2] No such file or directory: even though I know the files exist
src = dti_dir
dst = output_basename
files = os.listdir(src)
for f in files:
if (f.startswith("dtifit_")):
shutil.move(f, dst)
Your problem is most likely in the very first line. You may want to change that to be more exact, pointing to an exact directory rather than os.getcwd(). os.getcwd() will point to wherever the process is executing from, wherever you kicked off your python run, so it could change. You probably want to hard-code it somehow.
For example, you could use something like this, to point to the directory that the file lives in: Find current directory and file's directory
Another thing you could consider doing is printing out dst in your last few lines and seeing if it's what you expect. You could also use PDB to inspect that value live:
https://pymotw.com/2/pdb/
Edit:
Your problem is using a relative path with shutil.move(). You should make sure that the path is absolute, please see this answer for more info:
stackoverflow.com/a/22230227/7299836