Merge pull request #322 from matthew-brett/read-par-exts

MRG: reading PAR headers from NIfTI extensions

A small function to fetch PARHeader object from PAR headers recorded in NIfTI
comment extensions.

Author: matthew-brett

nibabel/parrec.py

@@ -95,6 +95,8 @@
 import numpy as np
 from copy import deepcopy
 import re
+from io import StringIO
+from locale import getpreferredencoding
 
 from .keywordonly import kw_only_meth
 from .spatialimages import SpatialImage, Header
@@ -280,8 +282,6 @@ def _split_header(fobj):
     return version, gen_dict, image_lines
 
 
-
-
 def _process_gen_dict(gen_dict):
     """ Process `gen_dict` key, values into `general_info`
     """
@@ -504,6 +504,36 @@ def _data_from_rec(rec_fileobj, in_shape, dtype, slice_indices, out_shape,
     return rec_data
 
 
+def exts2pars(exts_source):
+    """Parse, return any PAR headers from NIfTI extensions in `exts_source`
+
+    Parameters
+    ----------
+    exts_source : sequence or `Nifti1Image`, `Nifti1Header` instance
+        A sequence of extensions, or header containing NIfTI extensions, or an
+        image containing a header with NIfTI extensions.
+
+    Returns
+    -------
+    par_headers : list
+        A list of PARRECHeader objects, usually empty or with one element, each
+        element contains a PARRECHeader read from the contained extensions.
+    """
+    headers = []
+    exts_source = (exts_source.header if hasattr(exts_source, 'header')
+                   else exts_source)
+    exts_source = (exts_source.extensions if hasattr(exts_source, 'extensions')
+                   else exts_source)
+    for extension in exts_source:
+        content = extension.get_content()
+        content = content.decode(getpreferredencoding(False))
+        if not content.startswith('# === DATA DESCRIPTION FILE ==='):
+            continue
+        gen_info, image_info = parse_PAR_header(StringIO(content))
+        headers.append(PARRECHeader(gen_info, image_info))
+    return headers
+
+
 class PARRECArrayProxy(object):
     @kw_only_meth(2)
     def __init__(self, file_like, header, mmap=True, scaling='dv'):

nibabel/tests/test_parrec.py

@@ -4,15 +4,15 @@
 from os.path import join as pjoin, dirname, basename
 from glob import glob
 from warnings import simplefilter
-import shutil
 
 import numpy as np
 from numpy import array as npa
 
 from .. import load as top_load
+from ..nifti1 import Nifti1Image, Nifti1Extension
 from .. import parrec
 from ..parrec import (parse_PAR_header, PARRECHeader, PARRECError, vol_numbers,
-                      vol_is_full, PARRECImage, PARRECArrayProxy)
+                      vol_is_full, PARRECImage, PARRECArrayProxy, exts2pars)
 from ..openers import Opener
 from ..fileholders import FileHolder
 from ..volumeutils import array_from_file
@@ -21,7 +21,7 @@
                            assert_array_equal)
 
 from nose.tools import (assert_true, assert_false, assert_raises,
-                        assert_equal, assert_not_equal)
+                        assert_equal)
 
 from ..testing import catch_warn_reset, suppress_warnings
 
@@ -600,3 +600,37 @@ def test_anonymized():
     assert_almost_equal(img_defs['window center'][-1], 236.385836385836, 6)
     assert_almost_equal(img_defs['window width'][0], 767.277167277167, 6)
     assert_almost_equal(img_defs['window width'][-1], 236.385836385836, 6)
+
+
+def test_exts2par():
+    # Test we can load PAR headers from NIfTI extensions
+    par_img = PARRECImage.from_filename(EG_PAR)
+    nii_img = Nifti1Image.from_image(par_img)
+    assert_equal(exts2pars(nii_img), [])
+    assert_equal(exts2pars(nii_img.header), [])
+    assert_equal(exts2pars(nii_img.header.extensions), [])
+    assert_equal(exts2pars([]), [])
+    # Add a header extension
+    with open(EG_PAR, 'rb') as fobj:
+        hdr_dump = fobj.read()
+        dump_ext = Nifti1Extension('comment', hdr_dump)
+    nii_img.header.extensions.append(dump_ext)
+    hdrs = exts2pars(nii_img)
+    assert_equal(len(hdrs), 1)
+    # Test attribute from PARRECHeader
+    assert_equal(hdrs[0].get_slice_orientation(), 'transverse')
+    # Add another PAR extension
+    nii_img.header.extensions.append(Nifti1Extension('comment', hdr_dump))
+    hdrs = exts2pars(nii_img)
+    assert_equal(len(hdrs), 2)
+    # Test attribute from PARRECHeader
+    assert_equal(hdrs[1].get_slice_orientation(), 'transverse')
+    # Add null extension, ignored
+    nii_img.header.extensions.append(Nifti1Extension('comment', b''))
+    # Check all valid inputs
+    for source in (nii_img,
+                   nii_img.header,
+                   nii_img.header.extensions,
+                   list(nii_img.header.extensions)):
+        hdrs = exts2pars(source)
+        assert_equal(len(hdrs), 2)