Merge pull request #478 from ilogue/qform-provided-then-qform-code-2

MRG: parrec2nii sets qform code to 2

Set qform code to 2 instead of 0 when writing out parrec2nii images.

Closes #463

Author: matthew-brett

.travis.yml

@@ -88,7 +88,7 @@ before_install:
     - source venv/bin/activate
     - python --version # just to check
     - pip install -U pip wheel  # upgrade to latest pip find 3.5 wheels; wheel to avoid errors
-    - retry pip install nose flake8  # always
+    - retry pip install nose flake8 mock  # always
     - wheelhouse_pip_install $EXTRA_PIP_FLAGS $DEPENDS
     # pydicom <= 0.9.8 doesn't install on python 3
     - if [ "${TRAVIS_PYTHON_VERSION:0:1}" == "2" ]; then

appveyor.yml

@@ -46,7 +46,7 @@ install:
   - "python -c \"import struct; print(struct.calcsize('P') * 8)\""
 
   # Install the dependencies of the project.
-  - "conda install --yes --quiet numpy scipy matplotlib nose h5py"
+  - "conda install --yes --quiet numpy scipy matplotlib nose h5py mock"
   - "pip install pydicom"
   - "python setup.py install"
   - "SET NIBABEL_DATA_DIR=%CD%\\nibabel-data"

bin/parrec2nii

@@ -1,333 +1,8 @@
 #!python
 """PAR/REC to NIfTI converter
 """
-from __future__ import division, print_function, absolute_import
 
-from optparse import OptionParser, Option
-import numpy as np
-import numpy.linalg as npl
-import sys
-import os
-import csv
-import nibabel
-import nibabel.parrec as pr
-from nibabel.parrec import one_line
-from nibabel.mriutils import calculate_dwell_time, MRIError
-import nibabel.nifti1 as nifti1
-from nibabel.filename_parser import splitext_addext
-from nibabel.volumeutils import fname_ext_ul_case
-from nibabel.orientations import (io_orientation, inv_ornt_aff,
-                                  apply_orientation)
-from nibabel.affines import apply_affine, from_matvec, to_matvec
-
-
-def get_opt_parser():
-    # use module docstring for help output
-    p = OptionParser(
-        usage="%s [OPTIONS] <PAR files>\n\n" % sys.argv[0] + __doc__,
-        version="%prog " + nibabel.__version__)
-    p.add_option(
-        Option("-v", "--verbose", action="store_true", dest="verbose",
-               default=False,
-               help="""Make some noise."""))
-    p.add_option(
-        Option("-o", "--output-dir", action="store", type="string",
-               dest="outdir", default=None,
-               help=one_line("""Destination directory for NIfTI files.
-                             Default: current directory.""")))
-    p.add_option(
-        Option("-c", "--compressed", action="store_true",
-               dest="compressed", default=False,
-               help="Whether to write compressed NIfTI files or not."))
-    p.add_option(
-        Option("-p", "--permit-truncated", action="store_true",
-               dest="permit_truncated", default=False,
-               help=one_line(
-                   """Permit conversion of truncated recordings. Support for
-                   this is experimental, and results *must* be checked
-                   afterward for validity.""")))
-    p.add_option(
-        Option("-b", "--bvs", action="store_true", dest="bvs", default=False,
-               help=one_line(
-                   """Output bvals/bvecs files in addition to NIFTI
-                   image.""")))
-    p.add_option(
-        Option("-d", "--dwell-time", action="store_true", default=False,
-               dest="dwell_time",
-               help=one_line(
-                   """Calculate the scan dwell time. If supplied, the magnetic
-                   field strength should also be supplied using
-                   --field-strength (default 3). The field strength must be
-                   supplied because it is not encoded in the PAR/REC
-                   format.""")))
-    p.add_option(
-        Option("--field-strength", action="store", type="float",
-               dest="field_strength",
-               help=one_line(
-                   """The magnetic field strength of the recording, only needed
-                   for --dwell-time. The field strength must be supplied
-                   because it is not encoded in the PAR/REC format.""")))
-    p.add_option(
-        Option("-i", "--volume-info", action="store_true", dest="vol_info",
-               default=False,
-               help=one_line(
-                   """Export .PAR volume labels corresponding to the fourth
-                   dimension of the data.  The dimension info will be stored in
-                   CSV format with the first row containing dimension labels
-                   and the subsequent rows (one per volume), the corresponding
-                   indices.  Only labels that vary along the 4th dimension are
-                   exported (e.g. for a single volume structural scan there
-                   are no dynamic labels and no output file will be created).
-                   """)))
-    p.add_option(
-        Option("--origin", action="store", dest="origin", default="scanner",
-               help=one_line(
-                   """Reference point of the q-form transformation of the NIfTI
-                   image. If 'scanner' the (0,0,0) coordinates will refer to
-                   the scanner's iso center. If 'fov', this coordinate will be
-                   the center of the recorded volume (field of view). Default:
-                   'scanner'.""")))
-    p.add_option(
-        Option("--minmax", action="store", nargs=2, dest="minmax",
-               help=one_line(
-                   """Mininum and maximum settings to be stored in the NIfTI
-                   header. If any of them is set to 'parse', the scaled data is
-                   scanned for the actual minimum and maximum.  To bypass this
-                   potentially slow and memory intensive step (the data has to
-                   be scaled and fully loaded into memory), fixed values can be
-                   provided as space-separated pair, e.g. '5.4 120.4'. It is
-                   possible to set a fixed minimum as scan for the actual
-                   maximum (and vice versa). Default: 'parse parse'.""")))
-    p.set_defaults(minmax=('parse', 'parse'))
-    p.add_option(
-        Option("--store-header", action="store_true", dest="store_header",
-               default=False,
-               help=one_line(
-                   """If set, all information from the PAR header is stored in
-                   an extension ofthe NIfTI file header.  Default: off""")))
-    p.add_option(
-        Option("--scaling", action="store", dest="scaling", default='dv',
-               help=one_line(
-                   """Choose data scaling setting. The PAR header defines two
-                   different data scaling settings: 'dv' (values displayed on
-                   console) and 'fp' (floating point values). Either one can be
-                   chosen, or scaling can be disabled completely ('off').  Note
-                   that neither method will actually scale the data, but just
-                   store the corresponding settings in the NIfTI header, unless
-                   non-uniform scaling is used, in which case the data is
-                   stored in the file in scaled form. Default: 'dv'""")))
-    p.add_option(
-        Option('--keep-trace', action="store_true", dest='keep_trace',
-               default=False,
-               help=one_line("""Do not discard the diagnostic Philips DTI
-                             trace volume, if it exists in the data.""")))
-    p.add_option(
-        Option("--overwrite", action="store_true", dest="overwrite",
-               default=False,
-               help=one_line("""Overwrite file if it exists. Default:
-                             False""")))
-    p.add_option(
-        Option("--strict-sort", action="store_true", dest="strict_sort",
-               default=False,
-               help=one_line("""Use additional keys in determining the order
-                to sort the slices within the .REC file.  This may be necessary
-                for more complicated scans with multiple echos,
-                cardiac phases, ASL label states, etc.""")))
-    return p
-
-
-def verbose(msg, indent=0):
-    if verbose.switch:
-        print("%s%s" % (' ' * indent, msg))
-
-
-def error(msg, exit_code):
-    sys.stderr.write(msg + '\n')
-    sys.exit(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]
-    if opts.outdir is not None:
-        # set output path
-        basefilename = os.path.join(opts.outdir, basefilename)
-
-    # prep a file
-    if opts.compressed:
-        verbose('Using gzip compression')
-        outfilename = basefilename + '.nii.gz'
-    else:
-        outfilename = basefilename + '.nii'
-    if os.path.isfile(outfilename) and not opts.overwrite:
-        raise IOError('Output file "%s" exists, use --overwrite to '
-                      'overwrite it' % outfilename)
-
-    # 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_hdr = pr_img.header
-    affine = pr_hdr.get_affine(origin=opts.origin)
-    slope, intercept = pr_hdr.get_data_scaling(scaling)
-    if opts.scaling != 'off':
-        verbose('Using data scaling "%s"' % opts.scaling)
-    # get original scaling, and decide if we scale in-place or not
-    if opts.scaling == 'off':
-        slope = np.array([1.])
-        intercept = np.array([0.])
-        in_data = pr_img.dataobj.get_unscaled()
-        out_dtype = pr_hdr.get_data_dtype()
-    elif not np.any(np.diff(slope)) and not np.any(np.diff(intercept)):
-        # Single scalefactor case
-        slope = slope.ravel()[0]
-        intercept = intercept.ravel()[0]
-        in_data = pr_img.dataobj.get_unscaled()
-        out_dtype = pr_hdr.get_data_dtype()
-    else:
-        # Multi scalefactor case
-        slope = np.array([1.])
-        intercept = np.array([0.])
-        in_data = np.array(pr_img.dataobj)
-        out_dtype = np.float64
-    # Reorient data block to LAS+ if necessary
-    ornt = io_orientation(np.diag([-1, 1, 1, 1]).dot(affine))
-    if np.all(ornt == [[0, 1],
-                       [1, 1],
-                       [2, 1]]):  # already in LAS+
-        t_aff = np.eye(4)
-    else:  # Not in LAS+
-        t_aff = inv_ornt_aff(ornt, pr_img.shape)
-        affine = np.dot(affine, t_aff)
-        in_data = apply_orientation(in_data, ornt)
-
-    bvals, bvecs = pr_hdr.get_bvals_bvecs()
-    if not opts.keep_trace:  # discard Philips DTI trace if present
-        if bvecs is not None:
-            bad_mask = np.logical_and(bvals != 0, (bvecs == 0).all(axis=1))
-            if bad_mask.sum() > 0:
-                pl = 's' if bad_mask.sum() != 1 else ''
-                verbose('Removing %s DTI trace volume%s'
-                        % (bad_mask.sum(), pl))
-                good_mask = ~bad_mask
-                in_data = in_data[..., good_mask]
-                bvals = bvals[good_mask]
-                bvecs = bvecs[good_mask]
-
-    # Make corresponding NIfTI image
-    nimg = nifti1.Nifti1Image(in_data, affine, pr_hdr)
-    nhdr = nimg.header
-    nhdr.set_data_dtype(out_dtype)
-    nhdr.set_slope_inter(slope, intercept)
-
-    if 'parse' in opts.minmax:
-        # need to get the scaled data
-        verbose('Loading (and scaling) the data to determine value range')
-    if opts.minmax[0] == 'parse':
-        nhdr['cal_min'] = in_data.min() * slope + intercept
-    else:
-        nhdr['cal_min'] = float(opts.minmax[0])
-    if opts.minmax[1] == 'parse':
-        nhdr['cal_max'] = in_data.max() * slope + intercept
-    else:
-        nhdr['cal_max'] = float(opts.minmax[1])
-
-    # container for potential NIfTI1 header extensions
-    if opts.store_header:
-        # dump the full PAR header content into an extension
-        with open(infile, 'rb') as fobj:  # contents must be bytes
-            hdr_dump = fobj.read()
-            dump_ext = nifti1.Nifti1Extension('comment', hdr_dump)
-        nhdr.extensions.append(dump_ext)
-
-    verbose('Writing %s' % outfilename)
-    nibabel.save(nimg, outfilename)
-
-    # write out bvals/bvecs if requested
-    if opts.bvs:
-        if bvals is None and bvecs is None:
-            verbose('No DTI volumes detected, bvals and bvecs not written')
-        elif bvecs is None:
-            verbose('DTI volumes detected, but no diffusion direction info was'
-                    'found.  Writing .bvals file only.')
-            with open(basefilename + '.bvals', 'w') as fid:
-                # np.savetxt could do this, but it's just a loop anyway
-                for val in bvals:
-                    fid.write('%s ' % val)
-                fid.write('\n')
-        else:
-            verbose('Writing .bvals and .bvecs files')
-            # Transform bvecs with reorientation affine
-            orig2new = npl.inv(t_aff)
-            bv_reorient = from_matvec(to_matvec(orig2new)[0], [0, 0, 0])
-            bvecs = apply_affine(bv_reorient, bvecs)
-            with open(basefilename + '.bvals', 'w') as fid:
-                # np.savetxt could do this, but it's just a loop anyway
-                for val in bvals:
-                    fid.write('%s ' % val)
-                fid.write('\n')
-            with open(basefilename + '.bvecs', 'w') as fid:
-                for row in bvecs.T:
-                    for val in row:
-                        fid.write('%s ' % val)
-                    fid.write('\n')
-
-    # export data labels varying along the 4th dimensions if requested
-    if opts.vol_info:
-        labels = pr_img.header.get_volume_labels()
-        if len(labels) > 0:
-            vol_keys = list(labels.keys())
-            with open(basefilename + '.ordering.csv', 'w') as csvfile:
-                csvwriter = csv.writer(csvfile, delimiter=',')
-                csvwriter.writerow(vol_keys)
-                for vals in zip(*[labels[k] for k in vol_keys]):
-                    csvwriter.writerow(vals)
-
-    # write out dwell time if requested
-    if opts.dwell_time:
-        try:
-            dwell_time = calculate_dwell_time(
-                pr_hdr.get_water_fat_shift(),
-                pr_hdr.get_echo_train_length(),
-                opts.field_strength)
-        except MRIError:
-            verbose('No EPI factors, dwell time not written')
-        else:
-            verbose('Writing dwell time (%r sec) calculated assuming %sT '
-                    'magnet' % (dwell_time, opts.field_strength))
-            with open(basefilename + '.dwell_time', 'w') as fid:
-                fid.write('%r\n' % dwell_time)
-    # done
-
-
-def main():
-    parser = get_opt_parser()
-    (opts, infiles) = parser.parse_args()
-
-    verbose.switch = opts.verbose
-
-    if opts.origin not in ['scanner', 'fov']:
-        error("Unrecognized value for --origin: '%s'." % opts.origin, 1)
-    if opts.dwell_time and opts.field_strength is None:
-        error('Need --field-strength for dwell time calculation', 1)
-
-    # store any exceptions
-    errs = []
-    for infile in infiles:
-        verbose('Processing %s' % infile)
-        try:
-            proc_file(infile, opts)
-        except Exception as e:
-            errs.append('%s: %s' % (infile, e))
-
-    if len(errs):
-        error('Caught %i exceptions. Dump follows:\n\n %s'
-              % (len(errs), '\n'.join(errs)), 1)
-    else:
-        verbose('Done')
+from nibabel.parrec2nii_cmd import main
 
 
 if __name__ == '__main__':

dev-requirements.txt

@@ -1,3 +1,4 @@
 # Requirements for running tests
 -r requirements.txt
 nose
+mock

doc/source/installation.rst

@@ -92,6 +92,7 @@ Requirements
 *  PyDICOM_ 0.9.7 or greater (optional, for DICOM support)
 *  `Python Imaging Library`_ (optional, for PNG conversion in DICOMFS)
 *  nose_ 0.11 or greater (optional, to run the tests)
+*  mock_ (optional, to run the tests)
 *  sphinx_ (optional, to build the documentation)
 
 Get the development sources

nibabel/__init__.py

@@ -67,16 +67,17 @@
 from . import streamlines
 from . import viewers
 
-# be friendly on systems with ancient numpy -- no tests, but at least
-# importable
+# Note test requirement for "mock".  Requirement for "nose" tested by numpy.
 try:
+    import mock
+except ImportError:
+    def test(*args, **kwargs):
+        raise RuntimeError('Need "mock" package for tests')
+else:
     from numpy.testing import Tester
     test = Tester().test
     bench = Tester().bench
-    del Tester
-except ImportError:
-    def test(*args, **kwargs):
-        raise RuntimeError('Need numpy >= 1.2 for tests')
+    del mock, Tester
 
 from .pkg_info import get_pkg_info as _get_pkg_info