def test_overlap_2_volumes(self):
background_path = get_data_file(
self.subject_modif, self.mri_path, self.T1)
overlay_path = get_data_file(
self.subject_modif, self.mri_path, self.brain)
self.processor.overlap_2_volumes(background_path, overlay_path, False)
resulted_file_name = self.processor.generate_file_name(AXIAL, SNAPSHOT_NAME)
self._assert_writer_path_exists(resulted_file_name)
def test_overlap_volume_surface(self):
volume_path = get_data_file(self.subject_modif, self.mri_path, self.T1)
surface_path = get_data_file(self.subject, self.surf_path, self.surf)
self.processor.overlap_volume_surfaces(
volume_path, [surface_path], False, False)
resulted_file_name = self.processor.generate_file_name(AXIAL,
SNAPSHOT_NAME)
self._assert_writer_path_exists(resulted_file_name)
def test_show_aparc_aseg_with_new_values(self):
volume_path = get_data_file(
self.subject_modif, self.mri_path, "aparc+aseg.nii.gz")
conn_measure_path = get_data_file("connectivity_measure.txt")
self.processor.show_aparc_aseg_with_new_values(
volume_path, conn_measure_path, '', False)
resulted_file_name = self.processor.generate_file_name(
AXIAL, SNAPSHOT_NAME)
self._assert_writer_path_exists(resulted_file_name)
def test_overlap_surface_annotation(self):
writer = ImageWriter(SNAPSHOTS_DIRECTORY)
surface_path = get_data_file(self.head2, "SurfaceCortical.h5")
surface = IOUtils.read_surface(surface_path, False)
annot_path = get_data_file(self.head2, "RegionMapping.h5")
annot = IOUtils.read_annotation(annot_path)
annot.region_names = ['reg1', 'reg2']
annot.regions_color_table = numpy.array(
[[200, 200, 200, 255, 30567], [100, 150, 200, 255, 30568]])
resulted_file_name = self.processor.generate_file_name(
'surface_annotation', SNAPSHOT_NAME)
writer.write_surface_with_annotation(surface, annot, resulted_file_name)
fname = '%s0' % (resulted_file_name, )
self._assert_writer_path_exists(fname)
def test_merge_surfaces(self,):
h5_surface_path = get_data_file("head2", "SurfaceCortical.h5")
h5_surface = IOUtils.read_surface(h5_surface_path, False)
vtx = h5_surface.vertices
tri = h5_surface.triangles
nv = vtx.size
nt = tri.size
nv2 = int(nv / 2)
nt2 = int(nt / 2)
lh_surface = Surface(vtx[:nv2], tri[:nt2])
rh_surface = Surface(vtx[nv2:], tri[nt2:])
# h5_region_mapping_path = get_data_file("head2", "RegionMapping.h5")
# annotation = IOUtils.read_annotation(h5_region_mapping_path)
#
# lh_region_mapping = annotation.region_mapping[:len(annotation.region_mapping) / 2]
# rh_region_mapping = annotation.region_mapping[len(annotation.region_mapping) / 2:]
out_surface = self.service.merge_surfaces([lh_surface, rh_surface])
self.assertEqual(len(out_surface.vertices),
len(lh_surface.vertices) + len(rh_surface.vertices))
self.assertEqual(len(out_surface.triangles),
len(lh_surface.triangles) + len(rh_surface.triangles))
def test_tri_area(self):
h5_path = get_data_file('head2', 'SurfaceCortical.h5')
h5_io = H5SurfaceIO()
surface = h5_io.read(h5_path)
rfi = numpy.array([0])
area = self.service.tri_area(surface.vertices[surface.triangles[rfi]])
self.assertEqual(5000, area[0])
def test_write_volume():
in_file_path = get_data_file(TEST_MODIF_SUBJECT, TEST_VOLUME_FOLDER,
"T1.nii.gz")
volume = IOUtils.read_volume(in_file_path)
out_file_path = get_temporary_files_path('T1-out.nii.gz')
IOUtils.write_volume(out_file_path, volume)
assert os.path.exists(out_file_path)
def test_write_volume():
in_file_path = get_data_file(
TEST_MODIF_SUBJECT, TEST_VOLUME_FOLDER, "T1.nii.gz")
volume = IOUtils.read_volume(in_file_path)
out_file_path = get_temporary_files_path('T1-out.nii.gz')
IOUtils.write_volume(out_file_path, volume)
assert os.path.exists(out_file_path)
def test_write_annotation(self):
file_path = get_data_file(
self.subject, self.annot_path, "lh.aparc.annot")
annotation = IOUtils.read_annotation(file_path)
out_annotation_path = self.temp_file_path("lh-test.aparc.annot")
IOUtils.write_annotation(out_annotation_path, annotation)
new_annotation = IOUtils.read_annotation(out_annotation_path)
self.assertEqual(annotation.region_names, new_annotation.region_names)
def test_read_transformation_matrix_from_gifti_metadata():
file_path = get_data_file(TEST_MODIF_SUBJECT, TEST_SURFACE_FOLDER,
"lh.pial.gii")
surface_io = IOUtils.surface_io_factory(file_path)
surf = surface_io.read(file_path, False)
matrix = surface_io.read_transformation_matrix_from_metadata(
surf.get_main_metadata())
assert matrix == [[-1, 0, 0, 0], [0, 0, 1, 0], [0, -1, 0, 0], [0, 0, 0, 1]]
def test_read_transformation_matrix_from_gifti_metadata():
file_path = get_data_file(
TEST_MODIF_SUBJECT, TEST_SURFACE_FOLDER, "lh.pial.gii")
surface_io = IOUtils.surface_io_factory(file_path)
surf = surface_io.read(file_path, False)
matrix = surface_io.read_transformation_matrix_from_metadata(
surf.get_main_metadata())
assert matrix == [[-1, 0, 0, 0], [0, 0, 1, 0], [0, -1, 0, 0], [0, 0, 0, 1]]
def test_vertex_connectivity(self,):
surf_path = get_data_file("head2", 'SurfaceCortical.h5')
surface_parser = H5SurfaceIO()
surface = surface_parser.read(surf_path)
conn = self.service.vertex_connectivity(surface)
self.assertEqual(conn.shape, (16, 16))
self.assertEqual(conn[0, 1], 1)
self.assertEqual(conn[0, 10], 0)
def test_write_transformation_matrix_fs_metadata():
file_path = get_data_file(TEST_FS_SUBJECT, TEST_SURFACE_FOLDER, "lh.pial")
surface_io = IOUtils.surface_io_factory(file_path)
surf = surface_io.read(file_path, False)
surface_io.write_transformation_matrix(surf.get_main_metadata())
matrix = surface_io.read_transformation_matrix_from_metadata(
surf.get_main_metadata())
assert matrix.tolist() == [[1.0, 0.0, 0.0, 0.0], [0.0, 1.0, 0.0, 0.0], [
0.0, 0.0, 1.0, 0.0], [0.0, 0.0, 0.0, 1.0]]
def test_annot_to_lut(self,):
service = self.annotation.AnnotationService()
lut_path = self.temp_file_path('colorLUT-temp.txt')
service.annot_to_lut(
get_data_file('freesurfer_fsaverage', 'label', 'lh.aparc.annot'),
lut_path=lut_path,
subject=self.subject
)
self.assertTrue(os.path.exists(lut_path))
def test_write_transformation_matrix_fs_metadata():
file_path = get_data_file(TEST_FS_SUBJECT, TEST_SURFACE_FOLDER, "lh.pial")
surface_io = IOUtils.surface_io_factory(file_path)
surf = surface_io.read(file_path, False)
surface_io.write_transformation_matrix(surf.get_main_metadata())
matrix = surface_io.read_transformation_matrix_from_metadata(
surf.get_main_metadata())
assert matrix.tolist() == [[1.0, 0.0, 0.0, 0.0], [0.0, 1.0, 0.0, 0.0],
[0.0, 0.0, 1.0, 0.0], [0.0, 0.0, 0.0, 1.0]]
def test_write_write_brain_visa_surf():
surface_path = get_data_file(
TEST_FS_SUBJECT, TEST_SURFACE_FOLDER, "lh.pial")
out_path = get_temporary_files_path("lh.pial.tri")
surface = IOUtils.read_surface(surface_path, False)
IOUtils.write_surface(out_path, surface)
assert os.path.exists(out_path)
def test_write_write_brain_visa_surf():
surface_path = get_data_file(TEST_FS_SUBJECT, TEST_SURFACE_FOLDER,
"lh.pial")
out_path = get_temporary_files_path("lh.pial.tri")
surface = IOUtils.read_surface(surface_path, False)
IOUtils.write_surface(out_path, surface)
assert os.path.exists(out_path)
def test_write_fs_surface():
file_path = get_data_file(TEST_FS_SUBJECT, TEST_SURFACE_FOLDER, "lh.pial")
original_surface = IOUtils.read_surface(file_path, False)
triangles_number = len(original_surface.triangles)
output_file_path = get_temporary_files_path("lh-test.pial")
IOUtils.write_surface(output_file_path, original_surface)
new_surface = IOUtils.read_surface(output_file_path, False)
assert triangles_number == len(new_surface.triangles) == 327680
def test_extract_subsurf(self,):
surface_parser = FreesurferIO()
annot_parser = AnnotationIO()
surface_file = get_data_file("freesurfer_fsaverage", "surf", "lh.pial")
annot_file = get_data_file(
"freesurfer_fsaverage", "label", "lh.aparc.annot")
surface = surface_parser.read(surface_file, False)
verts = surface.vertices
annot = annot_parser.read(annot_file)
labels = annot.region_mapping
verts_mask = labels == 7
subsurf_verts, subsurf_faces = self.service.extract_subsurf(
surface, verts_mask, output='verts_triangls')[:2]
self.assertEqual(subsurf_verts.all(),
verts[numpy.where(verts_mask)].all())
subsurf = self.service.extract_subsurf(
surface, verts_mask, output='surface')
self.assertEqual(subsurf.vertices.all(),
verts[numpy.where(verts_mask)].all())
def test_write_fs_surface():
file_path = get_data_file(TEST_FS_SUBJECT, TEST_SURFACE_FOLDER, "lh.pial")
original_surface = IOUtils.read_surface(file_path, False)
triangles_number = len(original_surface.triangles)
output_file_path = get_temporary_files_path("lh-test.pial")
IOUtils.write_surface(output_file_path, original_surface)
new_surface = IOUtils.read_surface(output_file_path, False)
assert triangles_number == len(new_surface.triangles) == 327680
def test_read_lut_by_label(self,):
lut_path = get_data_file(self.color_lut_name)
service = self.annotation.AnnotationService()
labels, names, colors = service.read_lut(
lut_path=lut_path, key_mode='label')
self.assertIsInstance(names, OrderedDict)
self.assertIsInstance(colors, OrderedDict)
self.assertEqual(labels, _expected_color_lut_labels)
self.assertEqual(list(names.keys()), _expected_color_lut_labels)
self.assertEqual(list(colors.keys()), _expected_color_lut_labels)
def test_annot_names_to_labels(self,):
service = self.annotation.AnnotationService()
lut_path = get_data_file(self.color_lut_name)
labels = service.annot_names_to_labels(['Unknown'], lut_path=lut_path)
self.assertEqual(0, labels[0])
labels = service.annot_names_to_labels(
['unknown'],
add_string='ctx-lh-',
lut_path=lut_path
)
self.assertEqual(1000, labels[0])
labels = service.annot_names_to_labels(
['bankssts'],
add_string='ctx-rh-',
lut_path=lut_path
)
self.assertEqual(2001, labels[0])
def test_aseg_surf_conc_annot(self,):
out_surf_path = get_temporary_files_path("out_aseg")
out_annot_path = get_temporary_files_path("out_annot")
labels = "10 11"
colorLUT = get_data_file("colorLUT.txt")
self.service.aseg_surf_conc_annot(
data_path, out_surf_path, out_annot_path, labels, colorLUT)
self.assertTrue(os.path.exists(out_surf_path))
self.assertTrue(os.path.exists(out_annot_path))
surface_parser = FreesurferIO()
surface = surface_parser.read(out_surf_path, False)
self.assertEqual(len(surface.vertices), 5714)
self.assertEqual(len(surface.triangles), 11420)
annotation = IOUtils.read_annotation(out_annot_path)
assert_array_equal(
annotation.regions_color_table,
[[0, 118, 14, 0, 947712], [122, 186, 220, 0, 14465658]])
def test_lut_to_annot_names_ctab(self,):
service = self.annotation.AnnotationService()
lut_path = get_data_file(self.color_lut_name)
names1, ctab1 = service.lut_to_annot_names_ctab(lut_path=lut_path)
names2, ctab2 = service.lut_to_annot_names_ctab(
lut_path=lut_path,
labels=[0, 1, 2]
)
names3, ctab3 = service.lut_to_annot_names_ctab(
lut_path=lut_path,
labels="0 1 2"
)
expected = 'Unknown'
self.assertEqual(expected, names1[0])
self.assertEqual(expected, names2[0])
self.assertEqual(expected, names3[0])
expected = all([0, 0, 0, 0, service.rgb_to_fs_magic_number([0, 0, 0])])
self.assertEqual(expected, all(ctab1[0]))
self.assertEqual(expected, all(ctab2[0]))
self.assertEqual(expected, all(ctab3[0]))
def test_parse_annotation(self):
file_path = get_data_file(
self.subject, self.annot_path, "lh.aparc.annot")
annot = IOUtils.read_annotation(file_path)
self.assertEqual(_expected_region_names, annot.region_names)
def test_parse_centered_fs_surface():
file_path = get_data_file(
TEST_MODIF_SUBJECT, TEST_SURFACE_FOLDER, "lh-centered.pial")
surf = IOUtils.read_surface(file_path, False)
assert surf.center_ras == [0, 0, 0]
def test_parse_not_surface():
file_path = get_data_file(TEST_FS_SUBJECT, "label", "lh.aparc.annot")
with pytest.raises(ValueError):
IOUtils.read_surface(file_path, False)
def test_parse_volume():
file_path = get_data_file(TEST_MODIF_SUBJECT, TEST_VOLUME_FOLDER,
"T1.nii.gz")
volume = IOUtils.read_volume(file_path)
assert volume.dimensions == (256, 256, 256)
def test_parse_gifti_centered_surface():
file_path = get_data_file(
TEST_MODIF_SUBJECT, TEST_SURFACE_FOLDER, "lh.pial.gii")
surf = IOUtils.read_surface(file_path, True)
assert len(surf.triangles) == 327680
def test_parse_not_volume():
file_path = get_data_file(TEST_FS_SUBJECT, "surf", "lh.pial")
volume_io = IOUtils.volume_io_factory(file_path)
with pytest.raises(ImageFileError):
volume_io.read(file_path)
def test_parse_h5_surface():
h5_path = get_data_file('head2', 'SurfaceCortical.h5')
surface = IOUtils.read_surface(h5_path, False)
assert len(surface.vertices) == 16
assert len(surface.triangles) == 24
def test_parse_not_surface():
file_path = get_data_file(TEST_FS_SUBJECT, "label", "lh.aparc.annot")
with pytest.raises(ValueError):
IOUtils.read_surface(file_path, False)
def test_parse_fs_surface():
file_path = get_data_file(TEST_FS_SUBJECT, TEST_SURFACE_FOLDER, "lh.pial")
surf = IOUtils.read_surface(file_path, False)
assert len(surf.triangles) == 327680
def test_parse_h5_surface():
h5_path = get_data_file('head2', 'SurfaceCortical.h5')
surface = IOUtils.read_surface(h5_path, False)
assert len(surface.vertices) == 16
assert len(surface.triangles) == 24
def test_parse_volume():
file_path = get_data_file(
TEST_MODIF_SUBJECT, TEST_VOLUME_FOLDER, "T1.nii.gz")
volume = IOUtils.read_volume(file_path)
assert volume.dimensions == (256, 256, 256)
def test_parse_h5_volume():
h5_path = get_data_file('head2', 'VolumeT1Background.h5')
volume = IOUtils.read_volume(h5_path)
assert volume.dimensions == (6, 5, 4)
def test_parse_not_volume():
file_path = get_data_file(TEST_FS_SUBJECT, "surf", "lh.pial")
volume_io = IOUtils.volume_io_factory(file_path)
with pytest.raises(ImageFileError):
volume_io.read(file_path)
def test_parse_centered_fs_surface():
file_path = get_data_file(TEST_MODIF_SUBJECT, TEST_SURFACE_FOLDER,
"lh-centered.pial")
surf = IOUtils.read_surface(file_path, False)
assert surf.center_ras == [0, 0, 0]
def test_parse_not_annotation(self):
file_path = get_data_file(self.subject, "surf", "lh.pial")
annotation_io = IOUtils.annotation_io_factory(file_path)
self.assertRaises(ValueError, annotation_io.read, file_path)
def test_parse_gifti_centered_surface():
file_path = get_data_file(TEST_MODIF_SUBJECT, TEST_SURFACE_FOLDER,
"lh.pial.gii")
surf = IOUtils.read_surface(file_path, True)
assert len(surf.triangles) == 327680
def test_parse_h5_annotation(self):
h5_path = get_data_file('head2', 'RegionMapping.h5')
annotation = IOUtils.read_annotation(h5_path)
self.assertEqual(annotation.region_mapping.size, 16)
def test_read_cc_point():
generic_io = GenericIO()
file_path = get_data_file("fsaverage_modified",
"scripts", "ponscc.cut.log")
cc_point = generic_io.read_cc_point(file_path, GenericIO.point_line_flag)
assert cc_point == [100.0, 100.0, 100.0, 1]
def test_parse_h5_volume():
h5_path = get_data_file('head2', 'VolumeT1Background.h5')
volume = IOUtils.read_volume(h5_path)
assert volume.dimensions == (6, 5, 4)
