Make Gifti extend FileBasedImage, implement from_file_obj, to_file_obj.

Author: Ben Cipollini

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)
@@ -384,7 +385,9 @@ def metadata(self):
         return self.meta.metadata
 
 
-class GiftiImage(xml.XmlSerializable):
+class GiftiImage(FileBasedImage, xml.XmlSerializable):
+    files_types = (('image', '.gii'),)
+    valid_exts = ('.gii',)
 
     def __init__(self, meta=None, labeltable=None, darrays=None,
                  version="1.0"):
@@ -529,3 +532,66 @@ 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/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()
 
 

nibabel/gifti/tests/test_giftiio.py renamed to nibabel/gifti/tests/test_parse_gifti_fast.py

@@ -15,6 +15,8 @@
 import numpy as np
 
 from ... import gifti as gi
+from ...loadsave import load, save
+
 from ..util import gifti_endian_codes
 from ...nifti1 import xform_codes
 
@@ -102,23 +104,23 @@ def test_read_ordering():
     # DATA_FILE1 has an expected darray[0].data shape of (3,3).  However if we
     # read another image first (DATA_FILE2) then the shape is wrong
     # Read an image
-    img2 = gi.read(DATA_FILE2)
+    img2 = load(DATA_FILE2)
     assert_equal(img2.darrays[0].data.shape, (143479, 1))
     # Read image for which we know output shape
-    img = gi.read(DATA_FILE1)
+    img = load(DATA_FILE1)
     assert_equal(img.darrays[0].data.shape, (3,3))
 
 
 def test_load_metadata():
     for i, dat in enumerate(datafiles):
-        img = gi.read(dat)
+        img = load(dat)
         me = img.meta
         assert_equal(numDA[i], img.numDA)
         assert_equal(img.version,'1.0')
 
 
 def test_metadata_deprecations():
-    img = gi.read(datafiles[0])
+    img = load(datafiles[0])
     me = img.meta
 
     # Test deprecation
@@ -133,12 +135,11 @@ def test_metadata_deprecations():
 
 
 def test_load_dataarray1():
-    img1 = gi.read(DATA_FILE1)
-
+    img1 = load(DATA_FILE1)
     # Round trip
     with InTemporaryDirectory():
-        gi.write(img1, 'test.gii')
-        bimg = gi.read('test.gii')
+        save(img1, 'test.gii')
+        bimg = load('test.gii')
     for img in (img1, bimg):
         assert_array_almost_equal(img.darrays[0].data, DATA_FILE1_darr1)
         assert_array_almost_equal(img.darrays[1].data, DATA_FILE1_darr2)
@@ -152,40 +153,36 @@ def test_load_dataarray1():
 
 
 def test_load_dataarray2():
-    img2 = gi.read(DATA_FILE2)
-
+    img2 = load(DATA_FILE2)
     # Round trip
     with InTemporaryDirectory():
-        gi.write(img2, 'test.gii')
-        bimg = gi.read('test.gii')
+        save(img2, 'test.gii')
+        bimg = load('test.gii')
     for img in (img2, bimg):
         assert_array_almost_equal(img.darrays[0].data[:10], DATA_FILE2_darr1)
 
 
 def test_load_dataarray3():
-    img3 = gi.read(DATA_FILE3)
-
+    img3 = load(DATA_FILE3)
     with InTemporaryDirectory():
-        gi.write(img3, 'test.gii')
-        bimg = gi.read('test.gii')
+        save(img3, 'test.gii')
+        bimg = load('test.gii')
     for img in (img3, bimg):
         assert_array_almost_equal(img.darrays[0].data[30:50], DATA_FILE3_darr1)
 
 
 def test_load_dataarray4():
-    img4 = gi.read(DATA_FILE4)
-
+    img4 = load(DATA_FILE4)
     # Round trip
     with InTemporaryDirectory():
-        gi.write(img4, 'test.gii')
-        bimg = gi.read('test.gii')
+        save(img4, 'test.gii')
+        bimg = load('test.gii')
     for img in (img4, bimg):
         assert_array_almost_equal(img.darrays[0].data[:10], DATA_FILE4_darr1)
 
 
 def test_dataarray5():
-    img5 = gi.read(DATA_FILE5)
-
+    img5 = load(DATA_FILE5)
     for da in img5.darrays:
         assert_equal(gifti_endian_codes.byteorder[da.endian], 'little')
     assert_array_almost_equal(img5.darrays[0].data, DATA_FILE5_darr1)
@@ -204,8 +201,8 @@ def test_base64_written():
         assert_false(b'Base64Binary' in contents)
         assert_false(b'LittleEndian' in contents)
         # Round trip
-        img5 = gi.read(DATA_FILE5)
-        gi.write(img5, 'fixed.gii')
+        img5 = load(DATA_FILE5)
+        save(img5, 'fixed.gii')
         with open('fixed.gii', 'rb') as fobj:
             contents = fobj.read()
         # The bad codes have gone, replaced by the good ones
@@ -216,17 +213,17 @@ def test_base64_written():
             assert_true(b'LittleEndian' in contents)
         else:
             assert_true(b'BigEndian' in contents)
-        img5_fixed = gi.read('fixed.gii')
+        img5_fixed = load('fixed.gii')
         darrays = img5_fixed.darrays
         assert_array_almost_equal(darrays[0].data, DATA_FILE5_darr1)
         assert_array_almost_equal(darrays[1].data, DATA_FILE5_darr2)
 
 
 def test_readwritedata():
-    img = gi.read(DATA_FILE2)
+    img = load(DATA_FILE2)
     with InTemporaryDirectory():
-        gi.write(img, 'test.gii')
-        img2 = gi.read('test.gii')
+        save(img, 'test.gii')
+        img2 = load('test.gii')
         assert_equal(img.numDA,img2.numDA)
         assert_array_almost_equal(img.darrays[0].data,
                                   img2.darrays[0].data)
@@ -247,8 +244,7 @@ def test_write_newmetadata():
 
 
 def test_load_getbyintent():
-    img = gi.read(DATA_FILE1)
-
+    img = load(DATA_FILE1)
     da = img.get_arrays_from_intent("NIFTI_INTENT_POINTSET")
     assert_equal(len(da), 1)
 
@@ -268,12 +264,11 @@ def test_load_getbyintent():
 
 
 def test_load_labeltable():
-    img6 = gi.read(DATA_FILE6)
-
+    img6 = load(DATA_FILE6)
     # Round trip
     with InTemporaryDirectory():
-        gi.write(img6, 'test.gii')
-        bimg = gi.read('test.gii')
+        save(img6, 'test.gii')
+        bimg = load('test.gii')
     for img in (img6, bimg):
         assert_array_almost_equal(img.darrays[0].data[:3], DATA_FILE6_darr1)
         assert_equal(len(img.labeltable.labels), 36)
@@ -288,7 +283,7 @@ def test_load_labeltable():
 
 
 def test_labeltable_deprecations():
-    img = gi.read(DATA_FILE6)
+    img = load(DATA_FILE6)
     lt = img.labeltable
 
     # Test deprecation
@@ -307,7 +302,7 @@ def test_parse_dataarrays():
     img = gi.GiftiImage()
 
     with InTemporaryDirectory():
-        gi.write(img, fn)
+        save(img, fn)
         with open(fn, 'r') as fp:
             txt = fp.read()
         # Make a bad gifti.
@@ -317,6 +312,6 @@ def test_parse_dataarrays():
 
         with clear_and_catch_warnings() as w:
             warnings.filterwarnings('once', category=UserWarning)
-            gi.read(fn)
+            load(fn)
             assert_equal(len(w), 1)
             assert_equal(img.numDA, 0)