fix: started cleaning up classes - removing prints and adding tests

Author: satra

nibabel/cifti/__init__.py

@@ -19,7 +19,7 @@
 
 from .parse_cifti_fast import create_cifti_image
 from .cifti import (CiftiMetaData, CiftiHeader, CiftiImage, CiftiLabel,
-                    CiftiLabelTable, CiftiNVPair, CiftiVertexIndices,
+                    CiftiLabelTable, CiftiVertexIndices,
                     CiftiVoxelIndicesIJK, CiftiBrainModel, CiftiMatrix,
                     CiftiMatrixIndicesMap, CiftiNamedMap, CiftiParcel,
                     CiftiSurface, CiftiTransformationMatrixVoxelIndicesIJKtoXYZ,

nibabel/cifti/cifti.py

@@ -22,6 +22,7 @@
 import numpy as np
 
 DEBUG_PRINT = False
+
 CIFTI_MAP_TYPES = ('CIFTI_INDEX_TYPE_BRAIN_MODELS',
                    'CIFTI_INDEX_TYPE_PARCELS',
                    'CIFTI_INDEX_TYPE_SERIES',
@@ -71,58 +72,77 @@
 
 
 class CiftiMetaData(object):
-    """ A list of GiftiNVPairs in stored in
-    the list self.data """
-    def __init__(self, nvpair = None):
+    """ A list of CiftiNVPairs in stored in the list self.data """
+
+    def __init__(self, nvpair=None):
         self.data = []
-        if not nvpair is None:
-            if isinstance(nvpair, list):
-                self.data.extend(nvpair)
+        self.add_metadata(nvpair)
+
+    def _add_remove_metadata(self, metadata, func):
+        pairs = []
+        if isinstance(metadata, (list, tuple)):
+            if isinstance(metadata[0], basestring):
+                if len(metadata) != 2:
+                    raise ValueError('nvpair must be a 2-list or 2-tuple')
+                pairs = [tuple((metadata[0], metadata[1]))]
+            else:
+                for item in metadata:
+                    self._add_remove_metadata(item, func)
+                return
+        elif isinstance(metadata, dict):
+            pairs = metadata.items()
+        else:
+            raise ValueError('nvpair input must be a list, tuple or dict')
+        for pair in pairs:
+            if func == 'add':
+                if pair not in self.data:
+                    self.data.append(pair)
+            elif func == 'remove':
+                self.data.remove(pair)
             else:
-                self.data.append(nvpair)
+                raise ValueError('Unknown func %s' % func)
 
-    @classmethod
-    def from_dict(klass, data_dict):
-        meda = klass()
-        for k,v in data_dict.items():
-            nv = CiftiNVPair(k, v)
-            meda.data.append(nv)
-        return meda
+    def add_metadata(self, metadata):
+        """Add metadata key-value pairs
 
-    def get_metadata(self):
-        """ Returns metadata as dictionary """
-        self.data_as_dict = {}
-        for ele in self.data:
-            self.data_as_dict[ele.name] = ele.value
-        return self.data_as_dict
+        This allows storing multiple keys with the same name but different
+        values.
+
+
+        Parameters
+        ----------
+        metadata : 2-List, 2-Tuple, Dictionary, List[2-List or 2-Tuple]
+                     Tuple[2-List or 2-Tuple]
+
+        Returns
+        -------
+        None
+
+        """
+        if metadata is None:
+            return
+        self._add_remove_metadata(metadata, 'add')
+
+    def remove_metadata(self, metadata):
+        if metadata is None:
+            return
+        self._add_remove_metadata(metadata, 'remove')
 
     def to_xml(self, prefix='', indent='    '):
         if len(self.data) == 0:
             return ''
         res = "%s<MetaData>\n" % prefix
         preindent = prefix + indent
-        for ele in self.data:
+        for name, value in self.data:
             nvpair = """%s<MD>
 %s<Name>%s</Name>
 %s<Value>%s</Value>
-%s</MD>\n""" % (preindent, preindent + indent, ele.name, preindent + indent,
-                  ele.value, preindent)
+%s</MD>\n""" % (preindent, preindent + indent, name, preindent + indent,
+                value, preindent)
             res += nvpair
         res += "%s</MetaData>\n" % prefix
         return res
 
-    def print_summary(self):
-        print(self.get_metadata())
-
-
-class CiftiNVPair(object):
-
-    name = str
-    value = str
-
-    def __init__(self, name = '', value = ''):
-        self.name = name
-        self.value = value
 
 class CiftiLabelTable(object):
 
@@ -160,16 +180,6 @@ def print_summary(self):
 
 
 class CiftiLabel(object):
-    key = int
-    label = str
-    # rgba
-    # freesurfer examples seem not to conform
-    # to datatype "NIFTI_TYPE_RGBA32" because they
-    # are floats, not unsigned 32-bit integers
-    red = float
-    green = float
-    blue = float
-    alpha = float
 
     def __init__(self, key = 0, label = '', red = None,\
                   green = None, blue = None, alpha = None):
@@ -337,7 +347,7 @@ def add_cifti_vertices(self, vertices):
             self.vertices.append(vertices)
             self.numVA += 1
         else:
-            print("mim paramater must be of type CiftiMatrixIndicesMap")
+            raise TypeError("Not a valid CiftiVertices instance")
 
     def remove_cifti_vertices(self, ith):
         """ Removes the ith vertices element from the CiftiParcel """
@@ -543,7 +553,7 @@ def add_cifti_brain_model(self, brain_model):
             self.brainModels.append(brain_model)
             self.numBrainModels += 1
         else:
-            print("brain_model parameter must be of type CiftiBrainModel")
+            raise TypeError("Not a valid CiftiBrainModel instance")
 
     def remove_cifti_brain_model(self, ith):
         """ Removes the ith brain model element from the CiftiMatrixIndicesMap """
@@ -561,7 +571,7 @@ def add_cifti_named_map(self, named_map):
             self.namedMaps.append(named_map)
             self.numNamedMaps += 1
         else:
-            print("named_map parameter must be of type CiftiNamedMap")
+            raise TypeError("Not a valid CiftiNamedMap instance")
 
     def remove_cifti_named_map(self, ith):
         """ Removes the ith named_map element from the CiftiMatrixIndicesMap """
@@ -579,7 +589,7 @@ def add_cifti_parcel(self, parcel):
             self.parcels.append(parcel)
             self.numParcels += 1
         else:
-            print("parcel parameter must be of type CiftiParcel")
+            raise TypeError("Not a valid CiftiParcel instance")
 
     def remove_cifti_parcel(self, ith):
         """ Removes the ith parcel element from the CiftiMatrixIndicesMap """
@@ -597,7 +607,7 @@ def add_cifti_surface(self, surface):
             self.surfaces.append(surface)
             self.numSurfaces += 1
         else:
-            print("surface parameter must be of type CiftiSurface")
+            raise TypeError("Not a valid CiftiSurface instance")
 
     def remove_cifti_surface(self, ith):
         """ Removes the ith surface element from the CiftiMatrixIndicesMap """
@@ -614,7 +624,7 @@ def set_cifti_volume(self, volume):
         if isinstance(volume, CiftiVolume):
             self.volume = volume
         else:
-            print("volume parameter must be of type CiftiVolume")
+            raise TypeError("Not a valid CiftiVolume instance")
 
     def remove_cifti_volume(self):
         """ Removes the volume element from the CiftiMatrixIndicesMap """
@@ -691,7 +701,7 @@ def add_cifti_matrix_indices_map(self, mim):
             self.mims.append(mim)
             self.numMIM += 1
         else:
-            print("mim paramater must be of type CiftiMatrixIndicesMap")
+            raise TypeError("Not a valid CiftiMatrixIndicesMap instance")
 
     def remove_cifti_matrix_indices_map(self, ith):
         """ Removes the ith matrix indices map element from the CiftiMatrix """
@@ -788,7 +798,7 @@ def to_filename(self, filename):
         if not filename.endswith('nii'):
             ValueError('CIFTI files have to be stored as uncompressed NIFTI2')
         from ..nifti2 import Nifti2Image
-        from ..nifti1 import Nifti1Extensions, Nifti1Extension
+        from ..nifti1 import Nifti1Extension
         data = np.reshape(self.data, [1, 1, 1, 1] + list(self.data.shape))
         header = self.extra
         extension = Nifti1Extension(32, self.header.to_xml())
@@ -837,7 +847,7 @@ def load(filename):
     IOError : if `filename` does not exist
     """
     from ..nifti2 import load as Nifti2load
-    return Nifti2load(filename)
+    return Nifti2load(filename).as_cifti()
 
 
 def save(img, filename):

nibabel/cifti/parse_cifti_fast.py

@@ -16,7 +16,7 @@
 import numpy as np
 
 from .cifti import (CiftiMetaData, CiftiImage, CiftiHeader, CiftiLabel,
-                    CiftiLabelTable, CiftiNVPair, CiftiVertexIndices,
+                    CiftiLabelTable, CiftiVertexIndices,
                     CiftiVoxelIndicesIJK, CiftiBrainModel, CiftiMatrix,
                     CiftiMatrixIndicesMap, CiftiNamedMap, CiftiParcel,
                     CiftiSurface, CiftiTransformationMatrixVoxelIndicesIJKtoXYZ,
@@ -66,7 +66,7 @@ def StartElementHandler(self, name, attrs):
             assert isinstance(parent, (CiftiMatrix, CiftiNamedMap))
             self.struct_state.append(meta)
         elif name == 'MD':
-            pair = CiftiNVPair()
+            pair = ['', '']
             self.fsm_state.append('MD')
             self.struct_state.append(pair)
         elif name == 'Name':
@@ -223,7 +223,7 @@ def EndElementHandler(self, name):
             self.fsm_state.pop()
             pair = self.struct_state.pop()
             meta = self.struct_state[-1]
-            if pair.name is not None:
+            if pair[0]:
                 meta.data.append(pair)
         elif name == 'Name':
             self.write_to = None
@@ -299,13 +299,11 @@ def flush_chardata(self):
         if self.write_to == 'Name':
             data = data.strip()
             pair = self.struct_state[-1]
-            assert isinstance(pair, CiftiNVPair)
-            pair.name = data
+            pair[0] = data
         elif self.write_to == 'Value':
             data = data.strip()
             pair = self.struct_state[-1]
-            assert isinstance(pair, CiftiNVPair)
-            pair.value = data
+            pair[1] = data
         elif self.write_to == 'Vertices':
             # conversion to numpy array
             c = StringIO(data.strip().decode('utf-8'))
@@ -320,13 +318,13 @@ def flush_chardata(self):
             c.close()
         elif self.write_to == 'VertexIndices':
             # conversion to numpy array
-            c = StringIO(data.strip().decode('utf-8'))
+            c = StringIO(data.strip())
             index = self.struct_state[-1]
             index.indices = np.genfromtxt(c, dtype=np.int)
             c.close()
         elif self.write_to == 'TransformMatrix':
             # conversion to numpy array
-            c = StringIO(data.strip().decode('utf-8'))
+            c = StringIO(data.strip())
             transform = self.struct_state[-1]
             transform.matrix = np.genfromtxt(c, dtype=np.float)
             c.close()

nibabel/cifti/tests/test_cifti.py

@@ -0,0 +1,35 @@
+""" Testing gifti objects
+"""
+
+import numpy as np
+
+from ...nifti1 import data_type_codes, intent_codes
+
+from ... import cifti as ci
+
+from numpy.testing import (assert_array_almost_equal,
+                           assert_array_equal)
+
+from nose.tools import assert_true, assert_equal, assert_raises
+
+
+def test_cifti_metadata():
+    md = ci.CiftiMetaData()
+    assert_equal(md.data, [])
+    assert_raises(ValueError, md.add_metadata, ['a'])
+    md.add_metadata([('a', 'aval'), ('b', 'bval')])
+    assert_true(len(md.data) == 2)
+    md.add_metadata([['a', 'aval'], ['b', 'bval']])
+    assert_true(len(md.data) == 2)
+    md.add_metadata({'a': 'aval', 'b': 'bval'})
+    assert_true(len(md.data) == 2)
+    md.add_metadata({'a': 'aval', 'd': 'dval'})
+    assert_true(len(md.data) == 3)
+    md.remove_metadata({'a': 'aval', 'd': 'dval'})
+    assert_true(len(md.data) == 1)
+    assert_raises(ValueError, md.remove_metadata, {'a': 'aval', 'd': 'dval'})
+    assert_equal(md.to_xml(),
+                 '<MetaData>\n    <MD>\n        <Name>b</Name>\n        <Value>bval</Value>\n    </MD>\n</MetaData>\n')
+    md.remove_metadata(['b', 'bval'])
+    assert_true(len(md.data) == 0)
+    assert_true(md.to_xml() == '')

nibabel/cifti/tests/test_ciftiio.py

@@ -81,16 +81,3 @@ def test_readwritedata():
             assert_array_almost_equal(img.data,
                                       img2.data)
 
-
-def test_newmetadata():
-    img = ci.CiftiImage()
-    attr = ci.CiftiNVPair(name = 'mykey', value = 'val1')
-    newmeta = ci.CiftiMetaData(attr)
-    img.header.matrix.meta = newmeta
-    myme = img.header.matrix.meta.get_metadata()
-    assert_true('mykey' in myme)
-    newmeta = ci.CiftiMetaData.from_dict( {'mykey1' : 'val2'} )
-    img.header.matrix.meta = newmeta
-    myme = img.header.matrix.meta.get_metadata()
-    assert_true('mykey1' in myme)
-    assert_false('mykey' in myme)