Merge pull request #403 from bcipolli/gifti-fix4

MRG: More GIFTI fixes

More commits to make GIFTI more pythonic and test the functionality a bit more thoroughly.

Author: matthew-brett

nibabel/gifti/gifti.py

@@ -68,10 +68,10 @@ def print_summary(self):
 
 
 class GiftiNVPairs(object):
-
+    """
     name = str
     value = str
-
+    """
     def __init__(self, name='', value=''):
         self.name = name
         self.value = value
@@ -104,6 +104,7 @@ def print_summary(self):
 
 
 class GiftiLabel(xml.XmlSerializable):
+    """
     key = int
     label = str
     # rgba
@@ -114,6 +115,7 @@ class GiftiLabel(xml.XmlSerializable):
     green = float
     blue = float
     alpha = float
+    """
 
     def __init__(self, key=0, label='', red=None, green=None, blue=None,
                  alpha=None):
@@ -157,9 +159,11 @@ def _arr2txt(arr, elem_fmt):
 
 
 class GiftiCoordSystem(xml.XmlSerializable):
+    """
     dataspace = int
     xformspace = int
     xform = np.ndarray  # 4x4 numpy array
+    """
 
     def __init__(self, dataspace=0, xformspace=0, xform=None):
         self.dataspace = dataspace
@@ -224,12 +228,11 @@ def _data_tag_element(dataarray, encoding, datatype, ordering):
 
 
 class GiftiDataArray(xml.XmlSerializable):
-
+    """
     # These are for documentation only; we don't use these class variables
     intent = int
     datatype = int
     ind_ord = int
-    num_dim = int
     dims = list
     encoding = int
     endian = int
@@ -238,19 +241,38 @@ class GiftiDataArray(xml.XmlSerializable):
     data = np.ndarray
     coordsys = GiftiCoordSystem
     meta = GiftiMetaData
+    """
 
-    def __init__(self, data=None):
+    def __init__(self, data=None,
+                 encoding="GIFTI_ENCODING_B64GZ",
+                 endian=sys.byteorder,
+                 coordsys=None,
+                 ordering="C",
+                 meta=None):
+        """
+        Returns a shell object that cannot be saved.
+        """
         self.data = data
         self.dims = []
-        self.meta = GiftiMetaData()
-        self.coordsys = GiftiCoordSystem()
+        self.meta = meta or GiftiMetaData()
+        self.coordsys = coordsys or GiftiCoordSystem()
         self.ext_fname = ''
         self.ext_offset = ''
+        self.intent = 0  # required attribute, NIFTI_INTENT_NONE
+        self.datatype = 0  # required attribute, void/none
+        # python/numpy default: column major order
+        self.ind_ord = array_index_order_codes.code[ordering]
+        self.encoding = encoding
+        self.endian = endian
+
+    @property
+    def num_dim(self):
+        return len(self.dims)
 
     @classmethod
     def from_array(klass,
                    darray,
-                   intent,
+                   intent="NIFTI_INTENT_NONE",
                    datatype=None,
                    encoding="GIFTI_ENCODING_B64GZ",
                    endian=sys.byteorder,
@@ -289,7 +311,6 @@ def from_array(klass,
         if meta is None:
             meta = {}
         cda = klass(darray)
-        cda.num_dim = len(darray.shape)
         cda.dims = list(darray.shape)
         if datatype is None:
             cda.datatype = data_type_codes.code[darray.dtype]

nibabel/gifti/parse_gifti_fast.py

@@ -167,14 +167,14 @@ def StartElementHandler(self, name, attrs):
             if "ArrayIndexingOrder" in attrs:
                 self.da.ind_ord = array_index_order_codes.code[
                     attrs["ArrayIndexingOrder"]]
-            if "Dimensionality" in attrs:
-                self.da.num_dim = int(attrs["Dimensionality"])
-            for i in range(self.da.num_dim):
+            num_dim = int(attrs.get("Dimensionality", 0))
+            for i in range(num_dim):
                 di = "Dim%s" % str(i)
                 if di in attrs:
                     self.da.dims.append(int(attrs[di]))
             # dimensionality has to correspond to the number of DimX given
-            assert len(self.da.dims) == self.da.num_dim
+            # TODO (bcipolli): don't assert; raise parse warning, and recover.
+            assert len(self.da.dims) == num_dim
             if "Encoding" in attrs:
                 self.da.encoding = gifti_encoding_codes.code[attrs["Encoding"]]
             if "Endian" in attrs:

nibabel/gifti/tests/test_gifti.py

@@ -7,7 +7,7 @@
 import nibabel as nib
 from nibabel.externals.six import string_types
 from nibabel.gifti import (GiftiImage, GiftiDataArray, GiftiLabel,
-                           GiftiLabelTable, GiftiMetaData)
+                           GiftiLabelTable, GiftiMetaData, GiftiNVPairs)
 from nibabel.gifti.gifti import data_tag
 from nibabel.nifti1 import data_type_codes
 
@@ -34,29 +34,38 @@ def test_gifti_image():
     gi = GiftiImage()
     assert_equal(gi.numDA, 0)
 
-    da = GiftiDataArray(data='data')
+    # Test from numpy numeric array
+    data = np.random.random((5,))
+    da = GiftiDataArray.from_array(data)
     gi.add_gifti_data_array(da)
     assert_equal(gi.numDA, 1)
-    assert_equal(gi.darrays[0].data, 'data')
+    assert_array_equal(gi.darrays[0].data, data)
 
+    # Test removing
     gi.remove_gifti_data_array(0)
     assert_equal(gi.numDA, 0)
 
+    # Test from string
+    da = GiftiDataArray.from_array('zzzzz')
+    gi.add_gifti_data_array(da)
+    assert_equal(gi.numDA, 1)
+    assert_array_equal(gi.darrays[0].data, data)
+
+
     # Remove from empty
     gi = GiftiImage()
     gi.remove_gifti_data_array_by_intent(0)
     assert_equal(gi.numDA, 0)
 
     # Remove one
     gi = GiftiImage()
-    da = GiftiDataArray(data='data')
+    da = GiftiDataArray.from_array(np.zeros((5,)), intent=0)
     gi.add_gifti_data_array(da)
 
-    gi.remove_gifti_data_array_by_intent(0)
-    assert_equal(gi.numDA, 1)
+    gi.remove_gifti_data_array_by_intent(3)
+    assert_equal(gi.numDA, 1, "data array should exist on 'missed' remove")
 
-    gi.darrays[0].intent = 0
-    gi.remove_gifti_data_array_by_intent(0)
+    gi.remove_gifti_data_array_by_intent(da.intent)
     assert_equal(gi.numDA, 0)
 
 
@@ -97,13 +106,22 @@ def test_labeltable():
 def test_metadata():
     # Test deprecation
     with clear_and_catch_warnings() as w:
-        warnings.filterwarnings('once', category=DeprecationWarning)
+        warnings.filterwarnings('always', category=DeprecationWarning)
         assert_equal(len(GiftiDataArray().get_metadata()), 0)
+        assert_equal(len(w), 1)
 
     # Test deprecation
     with clear_and_catch_warnings() as w:
         warnings.filterwarnings('once', category=DeprecationWarning)
         assert_equal(len(GiftiMetaData().get_metadata()), 0)
+        assert_equal(len(w), 1)
+
+
+def test_metadata():
+    nvpair = GiftiNVPairs('key', 'value')
+    da = GiftiMetaData(nvpair=nvpair)
+    assert_equal(da.data[0].name, 'key')
+    assert_equal(da.data[0].value, 'value')
 
 
 def test_gifti_label_rgba():
@@ -133,6 +151,7 @@ def assign_rgba(gl, val):
     with clear_and_catch_warnings() as w:
         warnings.filterwarnings('once', category=DeprecationWarning)
         assert_equal(kwargs['red'], gl3.get_rgba()[0])
+        assert_equal(len(w), 1)
 
     # Test default value
     gl4 = GiftiLabel()

tox.ini

@@ -20,6 +20,6 @@ deps =
 deps =
 [flake8]
 max-line-length=100
-ignore=D100,D101,D102,D103,D104,D105,D200,D201,D204,D205,D208,D210,D300,D301,D400,D401,D403,E266,E402,E731,F821,I100,I101,I201,N802,N803,N804,N806
+ignore=D100,D101,D102,D103,D104,D105,D200,D201,D202,D204,D205,D208,D209,D210,D300,D301,D400,D401,D403,E266,E402,E731,F821,I100,I101,I201,N802,N803,N804,N806
 exclude=*test*,*sphinx*,nibabel/externals/*,*/__init__.py