Merge branch 'stephan-master' into main-master

* stephan-master:
  BF - Writing data array encoding header according to specs
  ENH - Supporting two types of data array specification strings
  BF - binary gifti write. Add test
  BF - Reading binary encoded Gifti without line break

Author: matthew-brett

nibabel/gifti/gifti.py

@@ -196,32 +196,33 @@ def data_tag(dataarray, encoding, datatype, ordering):
     else:
         ord = 'C'
 
-    if encoding == "GIFTI_ENCODING_ASCII":
+    if encoding == gifti_encoding_codes.giistring[1] or \
+        encoding == gifti_encoding_codes.specs[1]:
         c = BytesIO()
         # np.savetxt(c, dataarray, format, delimiter for columns)
         np.savetxt(c, dataarray, datatype, ' ')
         c.seek(0)
         da = c.read()
 
-    elif encoding == "GIFTI_ENCODING_B64BIN":
-        cout = StringIO()
-        base64.encode(dataarray.tostring(ord), cout)
-        cout.seek(0)
-        da = cout.read()
+    elif encoding == gifti_encoding_codes.giistring[2] or \
+        encoding == gifti_encoding_codes.specs[2]:
+        da = base64.encodestring(dataarray.tostring(ord))
 
-    elif encoding == "GIFTI_ENCODING_B64GZ":        
+    elif encoding == gifti_encoding_codes.giistring[3] or \
+        encoding == gifti_encoding_codes.specs[3]:
         # first compress
         comp = zlib.compress(dataarray.tostring(ord))
         da = base64.encodestring(comp)
         da = da.decode()
 
-    elif encoding == "GIFTI_ENCODING_EXTBIN":
+    elif encoding == gifti_encoding_codes.giistring[4] or \
+        encoding == gifti_encoding_codes.specs[4]:
         raise NotImplementedError("In what format are the external files?")
         da = ''
     else:
         da = ''
 
-    return "<Data>\n"+da+"</Data>\n"
+    return "<Data>"+da+"</Data>\n"
 
 class GiftiDataArray(object):
 
@@ -323,7 +324,7 @@ def to_xml(self):
 
         # write data array depending on the encoding
         result += data_tag(self.data, \
-                           gifti_encoding_codes.giistring[self.encoding],\
+                           gifti_encoding_codes.specs[self.encoding],\
                            data_type_codes.fmt[self.datatype],\
                            self.ind_ord)
 
@@ -348,7 +349,7 @@ def to_xml_open(self):
                       array_index_order_codes.label[self.ind_ord], \
                       str(self.num_dim), \
                       str(di), \
-                      gifti_encoding_codes.giistring[self.encoding], \
+                      gifti_encoding_codes.specs[self.encoding], \
                       gifti_endian_codes.giistring[self.endian], \
                       self.ext_fname,
                       self.ext_offset,
@@ -364,7 +365,7 @@ def print_summary(self):
         print 'ArrayIndexingOrder: ', array_index_order_codes.label[self.ind_ord]
         print 'Dimensionality: ', self.num_dim
         print 'Dimensions: ', self.dims
-        print 'Encoding: ', gifti_encoding_codes.giistring[self.encoding]
+        print 'Encoding: ', gifti_encoding_codes.specs[self.encoding]
         print 'Endian: ', gifti_endian_codes.giistring[self.endian]
         print 'ExternalFileName: ', self.ext_fname
         print 'ExternalFileOffset: ', self.ext_offset

nibabel/gifti/parse_gifti_fast.py

@@ -44,7 +44,7 @@ def read_data_block(encoding, endian, ordering, datatype, shape, data):
         dec = base64.decodestring(data.encode('ascii'))
         dt = data_type_codes.type[datatype]
         sh = tuple(shape)
-        newarr = np.fromstring(zdec, dtype = dt, sep = '\n', count = c)
+        newarr = np.fromstring(dec, dtype = dt)
         if len(newarr.shape) == len(sh):
             return newarr
         else:

nibabel/gifti/tests/data/base64bin.gii

@@ -0,0 +1,63 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE GIFTI SYSTEM "http://www.nitrc.org/frs/download.php/115/gifti.dtd">
+<GIFTI Version="1.0"  NumberOfDataArrays="2">
+<MetaData>
+<MD>
+	<Name><![CDATA[gifticlib-version]]></Name>
+	<Value><![CDATA[gifti library version 1.08, 8 March, 2010]]></Value>
+</MD>
+</MetaData>
+<LabelTable/>
+<DataArray Intent="NIFTI_INTENT_POINTSET"
+	DataType="NIFTI_TYPE_FLOAT32"
+	ArrayIndexingOrder="RowMajorOrder"
+	Dimensionality="2"
+	Dim0="10"
+	Dim1="3"
+	Encoding="GIFTI_ENCODING_B64BIN"
+	Endian="GIFTI_ENDIAN_LITTLE"
+	ExternalFileName=""
+	ExternalFileOffset="">
+<MetaData/>
+<CoordinateSystemTransformMatrix>
+	<DataSpace><![CDATA[NIFTI_XFORM_UNKNOWN]]></DataSpace>
+	<TransformedSpace><![CDATA[NIFTI_XFORM_UNKNOWN]]></TransformedSpace>
+<MatrixData>
+  1.000000   0.000000   0.000000   0.000000
+  0.000000   1.000000   0.000000   0.000000
+  0.000000   0.000000   1.000000   0.000000
+  0.000000   0.000000   0.000000   1.000000
+</MatrixData>
+</CoordinateSystemTransformMatrix>
+<Data>5ywbQ7+UB0NDncRC+VYMQ5QMPkPbfpJCIlwdQ836REPyUKdCNXYrQ8ZvCUMh8ZxCwosUQ5MiwkJv
+7YNC/un2QtTv3kLYtoRCFk8HQ4ZJSkOkhhFCFEgyQz6YIkNSARdCYhwyQ4+T5kIvuGRC2tAOQ26k
+pUIqLfhB
+</Data>
+</DataArray>
+<DataArray Intent="NIFTI_INTENT_TRIANGLE"
+	DataType="NIFTI_TYPE_INT32"
+	ArrayIndexingOrder="RowMajorOrder"
+	Dimensionality="2"
+	Dim0="10"
+	Dim1="3"
+	Encoding="GIFTI_ENCODING_B64BIN"
+	Endian="GIFTI_ENDIAN_LITTLE"
+	ExternalFileName=""
+	ExternalFileOffset="">
+<MetaData/>
+<CoordinateSystemTransformMatrix>
+	<DataSpace><![CDATA[NIFTI_XFORM_UNKNOWN]]></DataSpace>
+	<TransformedSpace><![CDATA[NIFTI_XFORM_UNKNOWN]]></TransformedSpace>
+<MatrixData>
+  1.000000   0.000000   0.000000   0.000000
+  0.000000   1.000000   0.000000   0.000000
+  0.000000   0.000000   1.000000   0.000000
+  0.000000   0.000000   0.000000   1.000000
+</MatrixData>
+</CoordinateSystemTransformMatrix>
+<Data>AhkAAANGAAACZAAABTcAAAJkAAADRgAAAmQAAAU3AACDEQAAA0YAAEIGAAAFNwAAgxEAAANkAAAC
+ZAAABGQAAAJkAAADZAAAAmQAAARkAAACGQAAA2QAAMUNAAAEZAAAYwQAAAJGAACILwAABGQAAIgv
+AAACRgAA
+</Data>
+</DataArray>
+</GIFTI>

nibabel/gifti/tests/test_giftiio.py

@@ -31,9 +31,10 @@
 DATA_FILE2 = pjoin(IO_DATA_PATH, 'gzipbase64.gii')
 DATA_FILE3 = pjoin(IO_DATA_PATH, 'label.gii')
 DATA_FILE4 = pjoin(IO_DATA_PATH, 'rh.shape.curv.gii')
+DATA_FILE5 = pjoin(IO_DATA_PATH, 'base64bin.gii')
 
-datafiles = [DATA_FILE1, DATA_FILE2, DATA_FILE3, DATA_FILE4]
-numda = [2, 1, 1, 1]
+datafiles = [DATA_FILE1, DATA_FILE2, DATA_FILE3, DATA_FILE4, DATA_FILE5]
+numda = [2, 1, 1, 1, 2]
 
 DATA_FILE1_darr1 = np.array(
        [[-16.07201 , -66.187515,  21.266994],
@@ -65,6 +66,28 @@
        [-0.45624232],
        [-0.31101292]], dtype=np.float32)
 
+DATA_FILE5_darr1 = np.array([[ 155.17539978,  135.58103943,   98.30715179],
+       [ 140.33973694,  190.0491333 ,   73.24776459],
+       [ 157.3598938 ,  196.97969055,   83.65809631],
+       [ 171.46174622,  137.43661499,   78.4709549 ],
+       [ 148.54592896,   97.06752777,   65.96373749],
+       [ 123.45701599,  111.46841431,   66.3571167 ],
+       [ 135.30892944,  202.28720093,   36.38148499],
+       [ 178.28155518,  162.59469604,   37.75128937],
+       [ 178.11087036,  115.28820038,   57.17986679],
+       [ 142.81582642,   82.82115173,   31.02205276]], dtype=np.float32)
+
+
+DATA_FILE5_darr2 = np.array([[ 6402, 17923, 25602],
+       [14085, 25602, 17923],
+       [25602, 14085,  4483],
+       [17923,  1602, 14085],
+       [ 4483, 25603, 25602],
+       [25604, 25602, 25603],
+       [25602, 25604,  6402],
+       [25603,  3525, 25604],
+       [ 1123, 17922, 12168],
+       [25604, 12168, 17922]], dtype=np.int32)
 
 def test_read_ordering():
     # DATA_FILE1 has an expected darray[0].data shape of (3,3).  However if we
@@ -116,6 +139,11 @@ def test_dataarray3():
 def test_dataarray4():
     img4 = gi.read(DATA_FILE4)
     assert_array_almost_equal(img4.darrays[0].data[:10], DATA_FILE4_darr1)
+
+def test_dataarray5():
+    img3 = gi.read(DATA_FILE5)
+    assert_array_almost_equal(img3.darrays[0].data, DATA_FILE5_darr1)
+    assert_array_almost_equal(img3.darrays[1].data, DATA_FILE5_darr2)
 
 def test_readwritedata():
     img = gi.read(DATA_FILE2)