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PEP8: test file
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‎nibabel/cifti2/tests/test_new_cifti2.py

Lines changed: 44 additions & 23 deletions
Original file line numberDiff line numberDiff line change
@@ -1,9 +1,10 @@
11
"""Tests the generation of new CIFTI2 files from scratch
22
3-
Contains a series of functions to create and check each of the 5 CIFTI index types
4-
(i.e. BRAIN_MODELS, PARCELS, SCALARS, LABELS, and SERIES).
3+
Contains a series of functions to create and check each of the 5 CIFTI index
4+
types (i.e. BRAIN_MODELS, PARCELS, SCALARS, LABELS, and SERIES).
55
6-
These functions are used in the tests to generate most CIFTI file types from scratch.
6+
These functions are used in the tests to generate most CIFTI file types from
7+
scratch.
78
"""
89
import numpy as np
910

@@ -29,19 +30,27 @@
2930

3031
def create_geometry_map(applies_to_matrix_dimension):
3132
voxels = ci.Cifti2VoxelIndicesIJK(brain_models[0][1])
32-
left_thalamus= ci.Cifti2BrainModel(index_offset=0, index_count=4, model_type='CIFTI_MODEL_TYPE_VOXELS',
33-
brain_structure=brain_models[0][0], voxel_indices_ijk=voxels)
33+
left_thalamus = ci.Cifti2BrainModel(index_offset=0, index_count=4,
34+
model_type='CIFTI_MODEL_TYPE_VOXELS',
35+
brain_structure=brain_models[0][0],
36+
voxel_indices_ijk=voxels)
3437
vertices = ci.Cifti2VertexIndices(np.array(brain_models[1][1]))
35-
left_cortex = ci.Cifti2BrainModel(index_offset=4, index_count=5, model_type='CIFTI_MODEL_TYPE_SURFACE',
36-
brain_structure=brain_models[1][0], vertex_indices=vertices)
38+
left_cortex = ci.Cifti2BrainModel(index_offset=4, index_count=5,
39+
model_type='CIFTI_MODEL_TYPE_SURFACE',
40+
brain_structure=brain_models[1][0],
41+
vertex_indices=vertices)
3742
left_cortex.surface_number_of_vertices = number_of_vertices
38-
volume = ci.Cifti2Volume(dimensions, ci.Cifti2TransformationMatrixVoxelIndicesIJKtoXYZ(-3, affine))
39-
return ci.Cifti2MatrixIndicesMap(applies_to_matrix_dimension, 'CIFTI_INDEX_TYPE_BRAIN_MODELS',
43+
volume = ci.Cifti2Volume(dimensions,
44+
ci.Cifti2TransformationMatrixVoxelIndicesIJKtoXYZ(-3,
45+
affine))
46+
return ci.Cifti2MatrixIndicesMap(applies_to_matrix_dimension,
47+
'CIFTI_INDEX_TYPE_BRAIN_MODELS',
4048
maps=[left_thalamus, left_cortex, volume])
4149

4250

4351
def check_geometry_map(mapping):
44-
assert_equal(mapping.indices_map_to_data_type, 'CIFTI_INDEX_TYPE_BRAIN_MODELS')
52+
assert_equal(mapping.indices_map_to_data_type,
53+
'CIFTI_INDEX_TYPE_BRAIN_MODELS')
4554
assert_equal(len(list(mapping.brain_models)), 2)
4655
left_thalamus, left_cortex = mapping.brain_models
4756

@@ -68,15 +77,18 @@ def check_geometry_map(mapping):
6877
[61, 59, 60],
6978
[61, 60, 59],
7079
[80, 90, 92]], )),
71-
('surface_parcel', (('CIFTI_STRUCTURE_CORTEX_LEFT', [0, 1000, 1301, 19972, 27312]),
72-
('CIFTI_STRUCTURE_CORTEX_RIGHT', [0, 100, 381]))),
80+
('surface_parcel', (('CIFTI_STRUCTURE_CORTEX_LEFT',
81+
[0, 1000, 1301, 19972, 27312]),
82+
('CIFTI_STRUCTURE_CORTEX_RIGHT',
83+
[0, 100, 381]))),
7384
('mixed_parcel', ([[71, 81, 39],
7485
[53, 21, 91]],
7586
('CIFTI_STRUCTURE_CORTEX_LEFT', [71, 88, 999])))]
7687

7788

7889
def create_parcel_map(applies_to_matrix_dimension):
79-
mapping = ci.Cifti2MatrixIndicesMap(applies_to_matrix_dimension, 'CIFTI_INDEX_TYPE_PARCELS')
90+
mapping = ci.Cifti2MatrixIndicesMap(applies_to_matrix_dimension,
91+
'CIFTI_INDEX_TYPE_PARCELS')
8092
for name, elements in parcels:
8193
surfaces = []
8294
volume = None
@@ -89,7 +101,8 @@ def create_parcel_map(applies_to_matrix_dimension):
89101

90102
mapping.extend([ci.Cifti2Surface('CIFTI_STRUCTURE_CORTEX_%s' % orientation,
91103
number_of_vertices) for orientation in ['LEFT', 'RIGHT']])
92-
mapping.volume = ci.Cifti2Volume(dimensions, ci.Cifti2TransformationMatrixVoxelIndicesIJKtoXYZ(-3, affine))
104+
mapping.volume = ci.Cifti2Volume(dimensions,
105+
ci.Cifti2TransformationMatrixVoxelIndicesIJKtoXYZ(-3, affine))
93106
return mapping
94107

95108

@@ -109,7 +122,8 @@ def check_parcel_map(mapping):
109122
assert_equal(parcel.voxel_indices_ijk._indices, element)
110123

111124
for surface, orientation in zip(mapping.surfaces, ('LEFT', 'RIGHT')):
112-
assert_equal(surface.brain_structure, 'CIFTI_STRUCTURE_CORTEX_%s' % orientation)
125+
assert_equal(surface.brain_structure,
126+
'CIFTI_STRUCTURE_CORTEX_%s' % orientation)
113127
assert_equal(surface.surface_number_of_vertices, number_of_vertices)
114128

115129
assert_equal(mapping.volume.volume_dimensions, dimensions)
@@ -121,8 +135,10 @@ def check_parcel_map(mapping):
121135

122136

123137
def create_scalar_map(applies_to_matrix_dimension):
124-
maps = [ci.Cifti2NamedMap(name, ci.Cifti2MetaData(meta)) for name, meta in scalars]
125-
return ci.Cifti2MatrixIndicesMap(applies_to_matrix_dimension, 'CIFTI_INDEX_TYPE_SCALARS',
138+
maps = [ci.Cifti2NamedMap(name, ci.Cifti2MetaData(meta))
139+
for name, meta in scalars]
140+
return ci.Cifti2MatrixIndicesMap(applies_to_matrix_dimension,
141+
'CIFTI_INDEX_TYPE_SCALARS',
126142
maps=maps)
127143

128144

@@ -138,8 +154,9 @@ def check_scalar_map(mapping):
138154
assert_equal(named_map.metadata, expected[1])
139155

140156

141-
labels = [('first_name', {'meta_key': 'some_metadata'}, {0: ('label0', (0.1, 0.3, 0.2, 0.5)),
142-
1: ('new_label', (0.5, 0.3, 0.1, 0.4))}),
157+
labels = [('first_name', {'meta_key': 'some_metadata'},
158+
{0: ('label0', (0.1, 0.3, 0.2, 0.5)),
159+
1: ('new_label', (0.5, 0.3, 0.1, 0.4))}),
143160
('another name', {}, {0: ('???', (0, 0, 0, 0)),
144161
1: ('great region', (0.4, 0.1, 0.23, 0.15))})]
145162

@@ -150,8 +167,10 @@ def create_label_map(applies_to_matrix_dimension):
150167
label_table = ci.Cifti2LabelTable()
151168
for key, (tag, rgba) in label.items():
152169
label_table[key] = ci.Cifti2Label(key, tag, *rgba)
153-
maps.append(ci.Cifti2NamedMap(name, ci.Cifti2MetaData(meta), label_table))
154-
return ci.Cifti2MatrixIndicesMap(applies_to_matrix_dimension, 'CIFTI_INDEX_TYPE_LABELS',
170+
maps.append(ci.Cifti2NamedMap(name, ci.Cifti2MetaData(meta),
171+
label_table))
172+
return ci.Cifti2MatrixIndicesMap(applies_to_matrix_dimension,
173+
'CIFTI_INDEX_TYPE_LABELS',
155174
maps=maps)
156175

157176

@@ -168,8 +187,10 @@ def check_label_map(mapping):
168187

169188

170189
def create_series_map(applies_to_matrix_dimension):
171-
return ci.Cifti2MatrixIndicesMap(applies_to_matrix_dimension, 'CIFTI_INDEX_TYPE_SERIES',
172-
number_of_series_points=13, series_exponent=-3, series_start=18.2,
190+
return ci.Cifti2MatrixIndicesMap(applies_to_matrix_dimension,
191+
'CIFTI_INDEX_TYPE_SERIES',
192+
number_of_series_points=13,
193+
series_exponent=-3, series_start=18.2,
173194
series_step=10.5, series_unit='SECOND')
174195

175196

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