cvnlab / nsdcode

Code related to analyzing the Natural Scenes Dataset
BSD 2-Clause "Simplified" License
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load_data needs to handle lists #8

Closed iancharest closed 3 years ago

iancharest commented 3 years ago
subjix = 1

sourcedata = np.r_[
    np.tile(
        f'{nsd_dir}/freesurfer/subj{subjix:02d}/label/lh.Kastner2015.mgz', 3),
    np.tile(
        f'{nsd_dir}/freesurfer/subj{subjix:02d}/label/rh.Kastner2015.mgz', 3)
        ].tolist()

sourcespace = [
    'lh.layerB1',
    'lh.layerB2',
    'lh.layerB3',
    'rh.layerB1',
    'rh.layerB2',
    'rh.layerB3'
    ]
targetspace = 'anat0pt8'
nsd_mapdata(
    subjix,
    sourcespace,
    targetspace,
    sourcedata,
    interptype='surfacewta',
    badval=-1,
    outputfile='testH.nii.gz')

## -- End pasted text --
---------------------------------------------------------------------------
FileNotFoundError                         Traceback (most recent call last)
~/env-EL7-skylake/lib/python3.7/site-packages/nibabel/loadsave.py in load(filename, **kwargs)
     41     try:
---> 42         stat_result = os.stat(filename)
     43     except OSError:

FileNotFoundError: [Errno 2] No such file or directory: "/rds/projects/c/charesti-start/data/NSD/nsddata/ppdata/subj01/transforms/['lh.layerB1', 'lh.layerB2', 'lh.layerB3', 'rh.layerB1', 'rh.layerB2', 'rh.layerB3']-to-anat0pt8.nii.gz"

During handling of the above exception, another exception occurred:

FileNotFoundError                         Traceback (most recent call last)
<ipython-input-19-ce7c18cadb74> in <module>
     24     interptype='surfacewta',
     25     badval=-1,
---> 26     outputfile='testH.nii.gz')

/rds/projects/c/charesti-start/software/nsdcode/python/mapdata/nsd_mapdata.py in nsd_mapdata(subjix, sourcespace, targetspace, sourcedata, interptype, badval, outputfile, outputclass, fsdir)
    177 
    178     # load transform
--> 179     a1_data = load_transform(casenum, tfile)
    180 
    181     # load sourcedata

/rds/projects/c/charesti-start/software/nsdcode/python/mapdata/load_data.py in load_transform(casenum, tfile)
     17     # load transform
     18     if casenum == 1:
---> 19         a1_img = nib.load(tfile)
     20         a1_data = a1_img.get_fdata()  # X x Y x Z x 3
     21     elif casenum in (2, 3):

~/env-EL7-skylake/lib/python3.7/site-packages/nibabel/loadsave.py in load(filename, **kwargs)
     42         stat_result = os.stat(filename)
     43     except OSError:
---> 44         raise FileNotFoundError("No such file or no access: '%s'" % filename)
     45     if stat_result.st_size <= 0:
     46         raise ImageFileError("Empty file: '%s'" % filename)

FileNotFoundError: No such file or no access: '/rds/projects/c/charesti-start/data/NSD/nsddata/ppdata/subj01/transforms/['lh.layerB1', 'lh.layerB2', 'lh.layerB3', 'rh.layerB1', 'rh.layerB2', 'rh.layerB3']-to-anat0pt8.nii.gz'
iancharest commented 3 years ago

fixed with 026b6ec