retinotopic-maps/code/RetMap_phaseshift

#!/usr/bin/env python

# Shift the phase of the input nifti.
# It is useful to correct for different wedge or ring starting points,
# ie. if the polar angle wedge doesn't start from the upper vertical
# meridian and your further processing expects it to start at the upper
# vertical meridian.

def make_phaseshift(niftipath, shift):
    import nibabel as nib
    import numpy as np
    import os


    cond = os.path.basename(niftipath).split("_")[0]
    print "condition: ", cond
    
    ## get condition
    #dsback2niftisave = os.path.dirname(os.path.dirname(niftipath))+'/post_processing/'+cond+"_phShift.nii.gz"
    dsback2niftisave = 'post_processing/'+cond+"_phShift.nii.gz"

    ## set shift depending on condition
    #~ if cond == 'ccw':
        #~ shift = -281.25
    #~ elif cond == 'clw':
        #~ shift = 101.25
    #~ elif cond == "con":
        #~ shift = -337.5
    #~ elif cond == "exp":
        #~ shift = 0
    shift=float(shift)
    print "shifting by degree: ", shift
    ## get nifti 
    nifti= nib.load(niftipath)

    data = nifti.get_data()

    # do phase shift depending on condition
    tmp0 = (data[:,:,:,0] + shift)%360
    #tmp0[tmp0 >= 360] = tmp0[tmp0 >= 360] - 360
    #tmp0[tmp0 < 0] = tmp0[tmp0 < 0] + 360
    
    #~ if cond == 'ccw' or cond == "con":
        #~ tmp0 = 360-tmp0           
    
    data[:,:,:,0]=tmp0


    dsback2nifti = nib.Nifti1Image(data, nifti.get_affine())
    nib.save(dsback2nifti, dsback2niftisave)
    

if __name__ == "__main__":
    import sys
    niftipath = sys.argv[1]
    shift = sys.argv[2]
    print "processing file: \n", niftipath
    make_phaseshift(niftipath, shift)