WIP: add GIFTI to nib.load/save (and enable non-SpatialImage classes in load/save)

.gitignore

@@ -62,6 +62,7 @@ dist/
 .tox/
 .coverage
 .ropeproject/
+htmlcov/
 
 # Logs and databases #
 ######################

nibabel/gifti/gifti.py

@@ -13,6 +13,7 @@
 import numpy as np
 
 from .. import xmlutils as xml
+from ..filebasedimages import FileBasedImage
 from ..nifti1 import data_type_codes, xform_codes, intent_codes
 from .util import (array_index_order_codes, gifti_encoding_codes,
                    gifti_endian_codes, KIND2FMT)
@@ -190,6 +191,7 @@ def data_tag(dataarray, encoding, datatype, ordering):
     class DataTag(xml.XmlSerializable):
         def __init__(self, *args):
             self.args = args
+
         def _to_xml_element(self):
             return _data_tag_element(*self.args)
 
@@ -384,10 +386,15 @@ def metadata(self):
         return self.meta.metadata
 
 
-class GiftiImage(xml.XmlSerializable):
+class GiftiImage(FileBasedImage, xml.XmlSerializable):
+    valid_exts = ('.gii',)
+    files_types = (('image', '.gii'),)
+
+    def __init__(self, header=None, extra=None, file_map=None, meta=None,
+                 labeltable=None, darrays=None, version="1.0"):
+        FileBasedImage.__init__(self, header=header, extra=extra,
+                                file_map=file_map)
 
-    def __init__(self, meta=None, labeltable=None, darrays=None,
-                 version="1.0"):
         if darrays is None:
             darrays = []
         if meta is None:
@@ -511,7 +518,6 @@ def print_summary(self):
             print(da.print_summary())
         print('----end----')
 
-
     def _to_xml_element(self):
         GIFTI = xml.Element('GIFTI', attrib={
             'Version': self.version,
@@ -529,3 +535,67 @@ def to_xml(self, enc='utf-8'):
         return b"""<?xml version="1.0" encoding="UTF-8"?>
 <!DOCTYPE GIFTI SYSTEM "http://www.nitrc.org/frs/download.php/115/gifti.dtd">
 """ + xml.XmlSerializable.to_xml(self, enc)
+
+    @classmethod
+    def from_file_map(klass, file_map):
+        """ Load a Gifti image from a file_map
+
+        Parameters
+        file_map : string
+
+        Returns
+        -------
+        img : GiftiImage
+            Returns a GiftiImage
+         """
+        from .parse_gifti_fast import parse_gifti_file
+        return parse_gifti_file(
+            fptr=file_map['image'].get_prepare_fileobj('rb'))
+
+    def to_file_map(self, file_map=None):
+        """ Save the current image to the specified file_map
+
+        Parameters
+        ----------
+        file_map : string
+
+        Returns
+        -------
+        None
+
+        Notes
+        -----
+        We write all files with utf-8 encoding, and specify this at the top of
+        the XML file with the ``encoding`` attribute.
+
+        The Gifti spec suggests using the following suffixes to your
+        filename when saving each specific type of data:
+
+        .gii
+            Generic GIFTI File
+        .coord.gii
+            Coordinates
+        .func.gii
+            Functional
+        .label.gii
+            Labels
+        .rgba.gii
+            RGB or RGBA
+        .shape.gii
+            Shape
+        .surf.gii
+            Surface
+        .tensor.gii
+            Tensors
+        .time.gii
+            Time Series
+        .topo.gii
+            Topology
+
+        The Gifti file is stored in endian convention of the current machine.
+        """
+        # Our giftis are always utf-8 encoded - see GiftiImage.to_xml
+        if file_map is None:
+            file_map = self.file_map
+        f = file_map['image'].get_prepare_fileobj('wb')
+        f.write(self.to_xml())

nibabel/gifti/giftiio.py

@@ -10,12 +10,10 @@
 # Stephan Gerhard, Oktober 2010
 ##############
 
-import os
-import codecs
-
-from .parse_gifti_fast import parse_gifti_file
+import numpy as np
 
 
+@np.deprecate_with_doc("Use nibabel.load() instead.")
 def read(filename):
     """ Load a Gifti image from a file
 
@@ -29,11 +27,11 @@ def read(filename):
     img : GiftiImage
         Returns a GiftiImage
      """
-    if not os.path.isfile(filename):
-        raise IOError("No such file or directory: '%s'" % filename)
-    return parse_gifti_file(filename)
+    from ..loadsave import load
+    return load(filename)
 
 
+@np.deprecate_with_doc("Use nibabel.save() instead.")
 def write(image, filename):
     """ Save the current image to a new file
 
@@ -79,6 +77,5 @@ def write(image, filename):
 
     The Gifti file is stored in endian convention of the current machine.
     """
-    # Our giftis are always utf-8 encoded - see GiftiImage.to_xml
-    with open(filename, 'wb') as f:
-        f.write(image.to_xml())
+    from ..loadsave import save
+    return save(image, filename)

nibabel/gifti/parse_gifti_fast.py

@@ -318,7 +318,7 @@ def pending_data(self):
         return not self._char_blocks is None
 
 
-def parse_gifti_file(fname, buffer_size=None):
+def parse_gifti_file(fname=None, fptr=None, buffer_size=None):
     """ Parse gifti file named `fname`, return image
 
     Parameters
@@ -334,28 +334,37 @@ def parse_gifti_file(fname, buffer_size=None):
     -------
     img : gifti image
     """
+    assert (fname is not None) + (fptr is not None) == 1, "Specify only fname or fptr, not both"
+
+    if fptr is None:
+        with open(fname, 'rb') as datasource:
+            return parse_gifti_file(fptr=datasource, buffer_size=buffer_size)
+    else:
+        datasource = fptr
+
     if buffer_size is None:
         buffer_sz_val = 35000000
     else:
         buffer_sz_val = buffer_size
-    with open(fname, 'rb') as datasource:
-        parser = ParserCreate()
-        parser.buffer_text = True
-        try:
-            parser.buffer_size = buffer_sz_val
-        except AttributeError:
-            if not buffer_size is None:
-                raise ValueError('Cannot set buffer size for parser')
-        HANDLER_NAMES = ['StartElementHandler',
-                         'EndElementHandler',
-                         'CharacterDataHandler']
-        out = Outputter()
-        for name in HANDLER_NAMES:
-            setattr(parser, name, getattr(out, name))
-        try:
-            parser.ParseFile(datasource)
-        except ExpatError:
-            print('An expat error occured while parsing the  Gifti file.')
+
+    parser = ParserCreate()
+    parser.buffer_text = True
+    try:
+        parser.buffer_size = buffer_sz_val
+    except AttributeError:
+        if not buffer_size is None:
+            raise ValueError('Cannot set buffer size for parser')
+    HANDLER_NAMES = ['StartElementHandler',
+                     'EndElementHandler',
+                     'CharacterDataHandler']
+    out = Outputter()
+    for name in HANDLER_NAMES:
+        setattr(parser, name, getattr(out, name))
+    try:
+        parser.ParseFile(datasource)
+    except ExpatError:
+        print('An expat error occured while parsing the  Gifti file.')
+
     # Reality check for pending data
     assert out.pending_data is False
     # update filename

nibabel/gifti/tests/test_gifti.py

@@ -4,18 +4,19 @@
 
 import numpy as np
 
+import nibabel as nib
 from nibabel.externals.six import string_types
 from nibabel.gifti import (GiftiImage, GiftiDataArray, GiftiLabel,
-                           GiftiLabelTable, GiftiMetaData, giftiio)
+                           GiftiLabelTable, GiftiMetaData)
 from nibabel.gifti.gifti import data_tag
 from nibabel.nifti1 import data_type_codes, intent_codes
 
 from numpy.testing import (assert_array_almost_equal,
                            assert_array_equal)
 from nose.tools import (assert_true, assert_false, assert_equal, assert_raises)
 from nibabel.testing import clear_and_catch_warnings
-from .test_giftiio import (DATA_FILE1, DATA_FILE2, DATA_FILE3, DATA_FILE4,
-                           DATA_FILE5, DATA_FILE6)
+from .test_parse_gifti_fast import (DATA_FILE1, DATA_FILE2, DATA_FILE3,
+                                    DATA_FILE4, DATA_FILE5, DATA_FILE6)
 
 
 def test_gifti_image():
@@ -142,7 +143,7 @@ def assign_rgba(gl, val):
 def test_print_summary():
     for fil in [DATA_FILE1, DATA_FILE2, DATA_FILE3, DATA_FILE4,
                             DATA_FILE5, DATA_FILE6]:
-        gimg = giftiio.read(fil)
+        gimg = nib.load(fil)
         gimg.print_summary()