Merge branch 'fixing-parrec' into main-master

* fixing-parrec: (21 commits)
  RF: rewrite parrec affine routine after testing
  NF: dot_reduce utility function
  RF: remove unused inport in funcs
  RF: refactor parrec affine, possibly breaks stuff
  DOC: fix tiny typo in docstring
  DOC: fix errors in top-level docstring
  TST: add regression tests for affine
  RF: remove use of deprecated read_img_data
  RF: error if trying to set par data offset !=0
  RF: avoid setting data offset of 0 if already set
  DOC: pep8 + expand / format docstrings for parrec
  BF: parrec2nii ignored FH image offset
  TST: Verify PARREC affines differ in the right places
  RF: python 3 fixes for openers test
  RF: some python 3 fixes for par / rec stuff
  RF: change slice orientation names for par/rec
  TST: add test of parrec2nii script
  RF+BF: refactor parrec to use latest nibabel
  NF: add skeleton for tests for PAR/REC conversion
  NF: add PAR / REC data for testing
  ...

Conflicts:
	COPYING

Author: matthew-brett

COPYING

@@ -19,12 +19,12 @@ documentation is covered by the MIT license.
 
   The MIT License
 
-  Copyright (c) 2009-2011 Matthew Brett <[email protected]>
-  Copyright (c) 2010-2011 Stephan Gerhard <[email protected]>
+  Copyright (c) 2009-2014 Matthew Brett <[email protected]>
+  Copyright (c) 2010-2013 Stephan Gerhard <[email protected]>
   Copyright (c) 2006-2010 Michael Hanke <[email protected]>
   Copyright (c) 2011 Christian Haselgrove <[email protected]>
   Copyright (c) 2010-2011 Jarrod Millman <[email protected]>
-  Copyright (c) 2011-2012 Yaroslav Halchenko <[email protected]>
+  Copyright (c) 2011-2014 Yaroslav Halchenko <[email protected]>
 
   Permission is hereby granted, free of charge, to any person obtaining a copy
   of this software and associated documentation files (the "Software"), to deal
@@ -45,8 +45,8 @@ documentation is covered by the MIT license.
   THE SOFTWARE.
 
 
-3rd Party Code
-==============
+3rd party code and data
+=======================
 
 Some code distributed within the nibabel sources was developed by other
 projects. This code is distributed under its respective licenses that are
@@ -151,7 +151,6 @@ subject to the following conditions:
     FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
     OTHER DEALINGS IN THE SOFTWARE.
 
-
 mni_icbm152_t1_tal_nlin_asym_09a
 --------------------------------
 
@@ -171,3 +170,24 @@ following license (where 'softwware' refers to the image):
     implied warranty.  The authors are not responsible for any data loss,
     equipment damage, property loss, or injury to subjects or patients
     resulting from the use or misuse of this software package.
+
+Philips PAR/REC data
+--------------------
+
+The files::
+
+    nibabel/tests/data/phantom_EPI_asc_CLEAR_2_1.PAR
+    nibabel/tests/data/phantom_EPI_asc_CLEAR_2_1.REC
+    nibabel/tests/data/Phantom_EPI_3mm_cor_20APtrans_15RLrot_SENSE_15_1.PAR
+    nibabel/tests/data/Phantom_EPI_3mm_cor_SENSE_8_1.PAR
+    nibabel/tests/data/Phantom_EPI_3mm_sag_15AP_SENSE_13_1.PAR
+    nibabel/tests/data/Phantom_EPI_3mm_sag_15FH_SENSE_12_1.PAR
+    nibabel/tests/data/Phantom_EPI_3mm_sag_15RL_SENSE_11_1.PAR
+    nibabel/tests/data/Phantom_EPI_3mm_sag_SENSE_7_1.PAR
+    nibabel/tests/data/Phantom_EPI_3mm_tra_-30AP_10RL_20FH_SENSE_14_1.PAR
+    nibabel/tests/data/Phantom_EPI_3mm_tra_15FH_SENSE_9_1.PAR
+    nibabel/tests/data/Phantom_EPI_3mm_tra_15RL_SENSE_10_1.PAR
+    nibabel/tests/data/Phantom_EPI_3mm_tra_SENSE_6_1.PAR
+
+are from http://psydata.ovgu.de/philips_achieva_testfiles, and released under
+the PDDL version 1.0 available at http://opendatacommons.org/licenses/pddl/1.0/

bin/parrec2nii

@@ -10,7 +10,6 @@ import gzip
 import nibabel
 import nibabel.parrec as pr
 import nibabel.nifti1 as nifti1
-from nibabel.loadsave import read_img_data
 from nibabel.filename_parser import splitext_addext
 from nibabel.volumeutils import seek_tell
 
@@ -86,7 +85,7 @@ def proc_file(infile, opts):
     pr_img = pr.load(infile)
     pr_hdr = pr_img.header
     # get the raw unscaled data form the REC file
-    raw_data = read_img_data(pr_img, prefer='unscaled')
+    raw_data = pr_img.dataobj.get_unscaled()
 
     # compute affine with desired origin
     affine = pr_hdr.get_affine(origin=opts.origin)
@@ -165,10 +164,10 @@ def proc_file(infile, opts):
     if opts.compressed:
         verbose('Using gzip compression')
         outfilename += '.nii.gz'
-        outfile = gzip.open(outfilename, 'w')
+        outfile = gzip.open(outfilename, 'wb')
     else:
         outfilename += '.nii'
-        outfile = open(outfilename, 'w')
+        outfile = open(outfilename, 'wb')
 
     verbose('Writing %s' % outfilename)
     # first write the header

nibabel/affines.py

@@ -5,6 +5,8 @@
 
 import numpy as np
 
+from .externals.six.moves import reduce
+
 
 def apply_affine(aff, pts):
     """ Apply affine matrix `aff` to points `pts`
@@ -225,3 +227,23 @@ def append_diag(aff, steps, starts=()):
     # Add translations for new affine, plus last 1
     aff_plus[old_n_out:,-1] = list(starts) + [1]
     return aff_plus
+
+
+def dot_reduce(*args):
+    """ Apply numpy dot product function from right to left on arrays
+
+    For passed arrays :math:`A, B, C, ... Z` returns :math:`A \dot B \dot C ...
+    \dot Z` where "." is the numpy array dot product.
+
+    Parameters
+    ----------
+    \*\*args : arrays
+        Arrays that can be passed to numpy ``dot`` function
+
+    Returns
+    -------
+    dot_product : array
+        If there are N arguments, result of ``arg[0].dot(arg[1].dot(arg[2].dot
+        ...  arg[N-2].dot(arg[N-1])))...``
+    """
+    return reduce(lambda x, y: np.dot(y, x), args[::-1])

nibabel/funcs.py

@@ -10,7 +10,7 @@
 ''' Processor functions for images '''
 import numpy as np
 
-from .orientations import (io_orientation, inv_ornt_aff, flip_axis,
+from .orientations import (io_orientation, inv_ornt_aff,
                            apply_orientation, OrientationError)
 from .loadsave import load
 
@@ -204,4 +204,3 @@ def _aff_is_diag(aff):
     ''' Utility function returning True if affine is nearly diagonal '''
     rzs_aff = aff[:3, :3]
     return np.allclose(rzs_aff, np.diag(np.diag(rzs_aff)))
-

nibabel/loadsave.py

@@ -202,7 +202,7 @@ def read_img_data(img, prefer='scaled'):
     # the consumed values back from the proxy
     if is_proxy(dao) and (default_offset or default_scaling):
         hdr = hdr.copy()
-        if default_offset:
+        if default_offset and dao.offset != 0:
             hdr.set_data_offset(dao.offset)
         if default_scaling and (dao.slope, dao.inter) != (1, 0):
             hdr.set_slope_inter(dao.slope, dao.inter)

nibabel/openers.py

@@ -108,6 +108,9 @@ def tell(self, *args, **kwargs):
     def close(self, *args, **kwargs):
         return self.fobj.close(*args, **kwargs)
 
+    def __iter__(self):
+        return iter(self.fobj)
+
     def close_if_mine(self):
         """ Close ``self.fobj`` iff we opened it in the constructor
         """