Oct 18, 2018 · Oct 18, 2018 · Oct 19, 2018 · Oct 19, 2018 · Oct 19, 2018 · Oct 19, 2018
diff --git a/bin/xmlrec2nii b/bin/xmlrec2nii
 #!python
 """XML/REC to NIfTI converter
 """

 # parrec2nii reads XML/REC as well
 from nibabel.cmdline.parrec2nii import main


 if __name__ == '__main__':
    main()
diff --git a/nibabel/cmdline/parrec2nii.py b/nibabel/cmdline/parrec2nii.py
 import csv
 import nibabel
 import nibabel.parrec as pr
 import nibabel.xmlrec as xr
 from nibabel.parrec import one_line
 from nibabel.mriutils import calculate_dwell_time, MRIError
 import nibabel.nifti1 as nifti1

 def proc_file(infile, opts):
    # figure out the output filename, and see if it exists
    basefilename = splitext_addext(os.path.basename(infile))[0]
    basefilename, ext = splitext_addext(os.path.basename(infile))[:2]

    ext = ext.lower()
    if (ext == '.xml' or
            (ext == '.rec' and os.path.exists(basefilename + '.xml'))):
        pr_module = xr
        if opts.permit_truncated:
            raise ValueError("The permit_truncated option is not currently "
                             "supported for .xml/.REC data")
    else:
        pr_module = pr

    if opts.outdir is not None:
        # set output path
        basefilename = os.path.join(opts.outdir, basefilename)
    # load the PAR header and data
    scaling = 'dv' if opts.scaling == 'off' else opts.scaling
    infile = fname_ext_ul_case(infile)
    pr_img =pr.load(infile,
                     permit_truncated=opts.permit_truncated,
                     scaling=scaling,
                     strict_sort=opts.strict_sort)
    pr_img =pr_module.load(infile,
 permit_truncated=opts.permit_truncated,
 scaling=scaling,
 strict_sort=opts.strict_sort)
    pr_hdr = pr_img.header
    affine = pr_hdr.get_affine(origin=opts.origin)
    slope, intercept = pr_hdr.get_data_scaling(scaling)
Original file line number	Diff line number	Diff line change
		@@ -0,0 +1,10 @@
		#!python
		"""XML/REC to NIfTI converter
		"""

		# parrec2nii reads XML/REC as well
		from nibabel.cmdline.parrec2nii import main


		if __name__ == '__main__':
		main()
Original file line number	Diff line number	Diff line change
Expand Up		@@ -10,6 +10,7 @@
		import csv
		import nibabel
		import nibabel.parrec as pr
		import nibabel.xmlrec as xr
		from nibabel.parrec import one_line
		from nibabel.mriutils import calculate_dwell_time, MRIError
		import nibabel.nifti1 as nifti1
Expand DownExpand Up		@@ -147,7 +148,18 @@ def error(msg, exit_code):

		def proc_file(infile, opts):
		# figure out the output filename, and see if it exists
		basefilename = splitext_addext(os.path.basename(infile))[0]
		basefilename, ext = splitext_addext(os.path.basename(infile))[:2]

		ext = ext.lower()
		if (ext == '.xml' or
		(ext == '.rec' and os.path.exists(basefilename + '.xml'))):
		pr_module = xr
		if opts.permit_truncated:
		raise ValueError("The permit_truncated option is not currently "
		"supported for .xml/.REC data")
		else:
		pr_module = pr

		if opts.outdir is not None:
		# set output path
		basefilename = os.path.join(opts.outdir, basefilename)
Expand All		@@ -165,10 +177,10 @@ def proc_file(infile, opts):
		# load the PAR header and data
		scaling = 'dv' if opts.scaling == 'off' else opts.scaling
		infile = fname_ext_ul_case(infile)
		pr_img =pr.load(infile,
		permit_truncated=opts.permit_truncated,
		scaling=scaling,
		strict_sort=opts.strict_sort)
		pr_img =pr_module.load(infile,
		permit_truncated=opts.permit_truncated,
		scaling=scaling,
		strict_sort=opts.strict_sort)
		pr_hdr = pr_img.header
		affine = pr_hdr.get_affine(origin=opts.origin)
		slope, intercept = pr_hdr.get_data_scaling(scaling)
Expand Down