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
    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)
diff --git a/nibabel/imageclasses.py b/nibabel/imageclasses.py
 from .nifti1 import Nifti1Pair, Nifti1Image
 from .nifti2 import Nifti2Pair, Nifti2Image
 from .parrec import PARRECImage
 from .xmlrec import XMLRECImage
 from .spm99analyze import Spm99AnalyzeImage
 from .spm2analyze import Spm2AnalyzeImage
 from .volumeutils import Recoder
                     Cifti2Image, Nifti2Image,  # Cifti2 before Nifti2
                     Spm2AnalyzeImage, Spm99AnalyzeImage, AnalyzeImage,
                     Minc1Image, Minc2Image, MGHImage,
                     PARRECImage, GiftiImage, AFNIImage]
                     PARRECImage,XMLRECImage,GiftiImage, AFNIImage]


 # DEPRECATED: mapping of names to classes and class functionality
         'has_affine': True,
         'makeable': False,
         'rw': False},
    xml={'class': XMLRECImage,
         'ext': '.xml',
         'has_affine': True,
         'makeable': False,
         'rw': False},
    afni={'class': AFNIImage,
          'ext': '.brik',
          'has_affine': True,
    ('mgh', '.mgh'),
    ('mgz', '.mgz'),
    ('par', '.par'),
    ('xml', '.xml'),
    ('brik', '.brik')
 ))

 # here.
 KNOWN_SPATIAL_FIRST = (Nifti1Pair, Nifti1Image, Nifti2Pair, Nifti2Image,
                       Spm2AnalyzeImage, Spm99AnalyzeImage, AnalyzeImage,
                       MGHImage, PARRECImage, AFNIImage)
                       MGHImage, PARRECImage,XMLRECImage,AFNIImage)


 def spatial_axes_first(img):
diff --git a/nibabel/loadsave.py b/nibabel/loadsave.py
 from .arrayproxy import is_proxy
 from .py3k import FileNotFoundError
 from .deprecated import deprecate_with_version
 from .parrec import PARRECImage


 def load(filename, **kwargs):
    for image_klass in all_image_classes:
        is_valid, sniff = image_klass.path_maybe_image(filename, sniff)
        if is_valid:
            if image_klass is PARRECImage and '.REC' in filename:
                # a .REC file can have either a .PAR of .xml header.
                # This skip case assumes PARRECImage is beforeXMLRECImage in
                # all_image_classes.
                par_exists = os.path.exists(filename.replace('.REC', '.PAR'))
                xml_exists = os.path.exists(filename.replace('.REC', '.xml'))
                if not par_exists and xml_exists:
                    continue  # skip trying .PAR and proceed to .xml
            print(image_klass)
            img = image_klass.from_filename(filename, **kwargs)
            return img

diff --git a/nibabel/parrec.py b/nibabel/parrec.py
    def set_data_offset(self, offset):
        """ PAR header always has 0 data offset (into REC file) """
        if offset != 0:
            raise PARRECError("PARheader assumes offset 0")
            raise PARRECError("header assumes offset 0")

    def _calc_zooms(self):
        """Compute image zooms from header data.
        # If 4D dynamic scan, convert time from milliseconds to seconds
        if len(zooms) > 3 and self.general_info['dyn_scan']:
            if len(self.general_info['repetition_time']) > 1:
                warnings.warn("multiple TRs found in.PAR file")
                warnings.warn("multiple TRs found inheader file")
            zooms[3] = self.general_info['repetition_time'][0] / 1000.
        return zooms
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 +148,15 @@ 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
		else:
		pr_module = pr

		if opts.outdir is not None:
		# set output path
		basefilename = os.path.join(opts.outdir, basefilename)
Expand All		@@ -165,10 +174,10 @@ 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
Original file line number	Diff line number	Diff line change
Expand Up		@@ -18,6 +18,7 @@
		from .nifti1 import Nifti1Pair, Nifti1Image
		from .nifti2 import Nifti2Pair, Nifti2Image
		from .parrec import PARRECImage
		from .xmlrec import XMLRECImage
		from .spm99analyze import Spm99AnalyzeImage
		from .spm2analyze import Spm2AnalyzeImage
		from .volumeutils import Recoder
Expand All		@@ -32,7 +33,7 @@
		Cifti2Image, Nifti2Image, # Cifti2 before Nifti2
		Spm2AnalyzeImage, Spm99AnalyzeImage, AnalyzeImage,
		Minc1Image, Minc2Image, MGHImage,
		PARRECImage, GiftiImage, AFNIImage]
		PARRECImage,XMLRECImage,GiftiImage, AFNIImage]


		# DEPRECATED: mapping of names to classes and class functionality
Expand DownExpand Up		@@ -90,6 +91,11 @@ def __getitem__(self, args, *kwargs):
		'has_affine': True,
		'makeable': False,
		'rw': False},
		xml={'class': XMLRECImage,
		'ext': '.xml',
		'has_affine': True,
		'makeable': False,
		'rw': False},
		afni={'class': AFNIImage,
		'ext': '.brik',
		'has_affine': True,
Expand All		@@ -113,6 +119,7 @@ def __getitem__(self, args, *kwargs):
		('mgh', '.mgh'),
		('mgz', '.mgz'),
		('par', '.par'),
		('xml', '.xml'),
		('brik', '.brik')
		))

Expand All		@@ -121,7 +128,7 @@ def __getitem__(self, args, *kwargs):
		# here.
		KNOWN_SPATIAL_FIRST = (Nifti1Pair, Nifti1Image, Nifti2Pair, Nifti2Image,
		Spm2AnalyzeImage, Spm99AnalyzeImage, AnalyzeImage,
		MGHImage, PARRECImage, AFNIImage)
		MGHImage, PARRECImage,XMLRECImage,AFNIImage)


		def spatial_axes_first(img):
Expand Down
Original file line number	Diff line number	Diff line change
Expand Up		@@ -865,7 +865,7 @@ def get_data_offset(self):
		def set_data_offset(self, offset):
		""" PAR header always has 0 data offset (into REC file) """
		if offset != 0:
		raise PARRECError("PARheader assumes offset 0")
		raise PARRECError("header assumes offset 0")

		def _calc_zooms(self):
		"""Compute image zooms from header data.
Expand DownExpand Up		@@ -894,7 +894,7 @@ def _calc_zooms(self):
		# If 4D dynamic scan, convert time from milliseconds to seconds
		if len(zooms) > 3 and self.general_info['dyn_scan']:
		if len(self.general_info['repetition_time']) > 1:
		warnings.warn("multiple TRs found in.PAR file")
		warnings.warn("multiple TRs found inheader file")
		zooms[3] = self.general_info['repetition_time'][0] / 1000.
		return zooms

Expand Down