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BF: allow for BrainModels or Parcels to contain a single vertex #739

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Merged
merged 2 commits into from
Mar 13, 2019
Merged

BF: allow for BrainModels or Parcels to contain a single vertex #739

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33d061f
BF: allow for BrainModel or Parcel objects to only contain a single v…
MichielCottaar Mar 12, 2019
3a1a94b
Replaces `atleast_1d` with 'ndmin' keyword in `loadtxt`
MichielCottaar Mar 12, 2019
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4 changes: 2 additions & 2 deletions nibabel/cifti2/parse_cifti2.py
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Original file line number Diff line number Diff line change
Expand Up @@ -517,7 +517,7 @@ def flush_chardata(self):
# conversion to numpy array
c = BytesIO(data.strip().encode('utf-8'))
vertices = self.struct_state[-1]
vertices.extend(np.loadtxt(c, dtype=np.int))
vertices.extend(np.loadtxt(c, dtype=np.int, ndmin=1))
c.close()

elif self.write_to == 'VoxelIndices':
Expand All @@ -531,7 +531,7 @@ def flush_chardata(self):
# conversion to numpy array
c = BytesIO(data.strip().encode('utf-8'))
index = self.struct_state[-1]
index.extend(np.loadtxt(c, dtype=np.int))
index.extend(np.loadtxt(c, dtype=np.int, ndmin=1))
c.close()

elif self.write_to == 'TransformMatrix':
Expand Down
35 changes: 29 additions & 6 deletions nibabel/cifti2/tests/test_new_cifti2.py
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Original file line number Diff line number Diff line change
Expand Up @@ -26,7 +26,9 @@
[61, 59, 60],
[61, 60, 59],
[80, 90, 92]]),
('CIFTI_STRUCTURE_CORTEX_LEFT', [0, 1000, 1301, 19972, 27312])]
('CIFTI_STRUCTURE_CORTEX_LEFT', [0, 1000, 1301, 19972, 27312]),
('CIFTI_STRUCTURE_CORTEX_RIGHT', [207])
]


def create_geometry_map(applies_to_matrix_dimension):
Expand All @@ -35,25 +37,34 @@ def create_geometry_map(applies_to_matrix_dimension):
model_type='CIFTI_MODEL_TYPE_VOXELS',
brain_structure=brain_models[0][0],
voxel_indices_ijk=voxels)

vertices = ci.Cifti2VertexIndices(np.array(brain_models[1][1]))
left_cortex = ci.Cifti2BrainModel(index_offset=4, index_count=5,
model_type='CIFTI_MODEL_TYPE_SURFACE',
brain_structure=brain_models[1][0],
vertex_indices=vertices)
left_cortex.surface_number_of_vertices = number_of_vertices

vertices = ci.Cifti2VertexIndices(np.array(brain_models[2][1]))
right_cortex = ci.Cifti2BrainModel(index_offset=9, index_count=1,
model_type='CIFTI_MODEL_TYPE_SURFACE',
brain_structure=brain_models[2][0],
vertex_indices=vertices)
right_cortex.surface_number_of_vertices = number_of_vertices

volume = ci.Cifti2Volume(dimensions,
ci.Cifti2TransformationMatrixVoxelIndicesIJKtoXYZ(-3,
affine))
return ci.Cifti2MatrixIndicesMap(applies_to_matrix_dimension,
'CIFTI_INDEX_TYPE_BRAIN_MODELS',
maps=[left_thalamus, left_cortex, volume])
maps=[left_thalamus, left_cortex, right_cortex, volume])


def check_geometry_map(mapping):
assert_equal(mapping.indices_map_to_data_type,
'CIFTI_INDEX_TYPE_BRAIN_MODELS')
assert_equal(len(list(mapping.brain_models)), 2)
left_thalamus, left_cortex = mapping.brain_models
assert_equal(len(list(mapping.brain_models)), 3)
left_thalamus, left_cortex, right_cortex = mapping.brain_models

assert_equal(left_thalamus.index_offset, 0)
assert_equal(left_thalamus.index_count, 4)
Expand All @@ -71,9 +82,18 @@ def check_geometry_map(mapping):
assert_equal(left_cortex.vertex_indices._indices, brain_models[1][1])
assert_equal(left_cortex.surface_number_of_vertices, number_of_vertices)

assert_equal(right_cortex.index_offset, 9)
assert_equal(right_cortex.index_count, 1)
assert_equal(right_cortex.model_type, 'CIFTI_MODEL_TYPE_SURFACE')
assert_equal(right_cortex.brain_structure, brain_models[2][0])
assert_equal(right_cortex.voxel_indices_ijk, None)
assert_equal(right_cortex.vertex_indices._indices, brain_models[2][1])
assert_equal(right_cortex.surface_number_of_vertices, number_of_vertices)

assert_equal(mapping.volume.volume_dimensions, dimensions)
assert_true((mapping.volume.transformation_matrix_voxel_indices_ijk_to_xyz.matrix == affine).all())


parcels = [('volume_parcel', ([[60, 60, 60],
[61, 59, 60],
[61, 60, 59],
Expand All @@ -84,7 +104,10 @@ def check_geometry_map(mapping):
[0, 100, 381]))),
('mixed_parcel', ([[71, 81, 39],
[53, 21, 91]],
('CIFTI_STRUCTURE_CORTEX_LEFT', [71, 88, 999])))]
('CIFTI_STRUCTURE_CORTEX_LEFT', [71, 88, 999]))),
('single_element', ([[71, 81, 39]],
('CIFTI_STRUCTURE_CORTEX_LEFT', [40]))),
]


def create_parcel_map(applies_to_matrix_dimension):
Expand All @@ -109,7 +132,7 @@ def create_parcel_map(applies_to_matrix_dimension):

def check_parcel_map(mapping):
assert_equal(mapping.indices_map_to_data_type, 'CIFTI_INDEX_TYPE_PARCELS')
assert_equal(len(list(mapping.parcels)), 3)
assert_equal(len(list(mapping.parcels)), len(parcels))
for (name, elements), parcel in zip(parcels, mapping.parcels):
assert_equal(parcel.name, name)
idx_surface = 0
Expand Down