dcmstack output file path

[TheChymera]

Hello, I am trying to specify an ouput file path for the nipype.interfaces.dcmstack.DcmStack interface, which should be in my data hierarchy and not in my script hierarchy.

I am doing this ~via:

from nipype.interfaces.dcmstack import DcmStack
stacker = DcmStack()
stacker.inputs.out_format = "/path/to/my/data"

stubbornly, dcmstack will export the resulting file to /path/to/my/script/_path_to_my_data

Can we fix this somehow? Right now I hav to export to my script directory and then move the file -.- which is a dodgy and slow way to fix this (different hard drives etc).

[oesteban]

Right now, I guess that's not possible:

nipype/nipype/interfaces/dcmstack.py

Line 76 in 44f7566

return path.join(os.getcwd(), out_fn)

A nice solution to the problem could be adding a bool switch to NiftiGeneratorBaseInputSpec indicating if the path is absolute or relative. Then, modify the line I've pointed out to choose between op.join or op.abspath.

[TheChymera]

and how would that switch get triggered?

[oesteban]

@TheChymera I have written a fast patch, let me know if it works out for you. I'm not 100% sure this will work, but you'll need to check it out from my branch:

git remote add oesteban [email protected]:oesteban/nipype.git
git remote update
git pull oesteban fix/DCMStackOutput-1087

PS. When you use the interface, make sure you set the input use_cwd=False

[TheChymera]

Do I need to test this before the pull gets accepted? I am running the live nipype version, but setting up a development installation that works nicely with my package manager might take a while :-/

[TheChymera]

@oesteban how do I use this feature?

I installed the live version of nipype, and still stuff gets exported to /path/to/my/script/_path_to_my_data.

I guess I have t speify the destination via somethign other than stacker.inputs.out_format - but what?

[satra]

try use_cwd = False for that interface

[TheChymera]

@satra so:

stacker.inputs.out_format = "/path/to/my/data"
stacker.inputs.use_cwd = False

?

[satra]

yes

[TheChymera]

@satra tried it - that still exports the file to /path/to/my/script/_path_to_my_data

[satra]

i looked at the code, and it looks like it's doing the correct thing. can you insert a debug breakpoint and step through.

[TheChymera]

uhm, how do I do that? Can you maybe test this at your end as well?

I am just running the interface as:

            stacker.inputs.dicom_files = my_files_list
            stacker.inputs.embed_meta = True
            file_name = "EPIwhatever"
            stacker.inputs.out_format = /path/to/my/file
            stacker.inputs.use_cwd = False
            result = stacker.run()
            print(result.outputs.out_file)

And that prints /path/to/my/script/path_to_my_file, and puts the file there, as opposed to under the /path/to/my/file directory. By the way, how would the interface deal with an inexistent output path (i.e. one where some directories would need to be created) ?

[oesteban]

ok, I see. There is also this function

nipype/nipype/interfaces/dcmstack.py

Line 36 in df63a28

def sanitize_path_comp(path_comp):

converting slashes to underscores. @satra, what do you think of adding an out_path input that is cwd by default?

[oesteban]

@TheChymera now you can do (provided you checkout my branch):

stacker.inputs.dicom_files = my_files_list
stacker.inputs.embed_meta = True
file_name = "EPIwhatever"
stacker.inputs.out_path = '/path/to/my'
stacker.inputs.out_format = 'file'
result = stacker.run()
print(result.outputs.out_file)

[satra]

[OT] @oesteban - i think it would be good to start building a set of regression tests with actual data using Testkraut. i know we have stayed away from regression tests because of data and software requirements, but i think it would be good to start adding these test specs.

[oesteban]

@satra I've taken a glimpse on the testkraut project and it looks awesome. Very appropriate for nipype :)

[TheChymera]

@oesteban sadly, I have still not set up any ebuilds for different live sources than the main branch on the main tree. I believe I will not do so soon, actually. I hope you can pull this here within the next few days.

[oesteban]

I'm to merge this then. I've done the following:

import glob
from nipype.interfaces.dcmstack import DcmStack
s = DcmStack()
s.inputs.out_path = '/home/oesteban/tmp/very/long/nonexistent/path'
s.inputs.out_format = 'file'
s.inputs.embed_meta = True
s.inputs.dicom_files = glob.glob('../T1_1/MR.0003.0*.IMA')
res = s.run()

Then, print res.outputs yields:

out_file = /home/oesteban/tmp/very/long/nonexistent/path/file.nii.gz

[TheChymera]

Looks great!