class AllenBrainReference:
def __init__(self, graph: str = "adult") -> None:
self._onto = OntologiesApi()
if graph == "adult":
self._struct_dicts_list = self._onto.get_structures(
structure_graph_ids=1, num_rows='all')
elif graph == "development":
self._struct_dicts_list = self._onto.get_structures(
structure_graph_ids=17, num_rows='all')
self._structures = {
i["id"]: AllenBrainStructure(i, self)
for i in self._struct_dicts_list
}
self._link()
def __getitem__(self, key: int) -> Any:
return self._structures[key]
def __iter__(self) -> Any:
for k, v in self._structures.items():
yield v
def _link(self) -> None:
for name, structure in self._structures.items():
structure.connect()
def oapi():
oa = OntologiesApi()
oa.get_structures = mock.MagicMock(return_value=[{'id': 1, 'structure_id_path': '1'}])
oa.get_structure_set_map = mock.MagicMock(return_value={1: [2, 3]})
return oa
def oapi():
oa = OntologiesApi()
oa.get_structures = mock.MagicMock(return_value=[{'id': 1, 'structure_id_path': '1'}])
oa.get_structure_set_map = mock.MagicMock(return_value={1: [2, 3]})
return oa
class OntologiesApiTests(unittest.TestCase):
def __init__(self, *args, **kwargs):
super(OntologiesApiTests, self).__init__(*args, **kwargs)
def setUp(self):
self.oa = OntologiesApi()
def tearDown(self):
self.oa = None
def test_get_structure_graph(self):
expected = "http://api.brain-map.org/api/v2/data/query.json?q=model::Structure,rma::criteria,[graph_id$in1],rma::options[num_rows$eq'all'][order$eqstructures.graph_order][count$eqfalse]"
structure_graph_id = 1
self.oa.json_msg_query = \
MagicMock(name='json_msg_query')
self.oa.get_structures(structure_graph_id)
self.oa.json_msg_query.assert_called_once_with(expected)
def test_list_structure_graphs(self):
expected = "http://api.brain-map.org/api/v2/data/query.json?q=model::StructureGraph,rma::options[num_rows$eq'all'][count$eqfalse]"
self.oa.json_msg_query = \
MagicMock(name='json_msg_query')
self.oa.get_structure_graphs()
self.oa.json_msg_query.assert_called_once_with(expected)
def test_list_structure_sets(self):
expected = "http://api.brain-map.org/api/v2/data/query.json?q=model::StructureSet,rma::options[num_rows$eq'all'][count$eqfalse]"
self.oa.json_msg_query = \
MagicMock(name='json_msg_query')
self.oa.get_structure_sets()
self.oa.json_msg_query.assert_called_once_with(expected)
def test_list_atlases(self):
expected = "http://api.brain-map.org/api/v2/data/query.json?q=model::Atlas,rma::options[num_rows$eq'all'][count$eqfalse]"
self.oa.json_msg_query = \
MagicMock(name='json_msg_query')
self.oa.get_atlases()
self.oa.json_msg_query.assert_called_once_with(expected)
def test_structure_graph_by_name(self):
expected = u"http://api.brain-map.org/api/v2/data/query.json?q=model::Structure,rma::criteria,graph[structure_graphs.name$in'Mouse Brain Atlas'],rma::options[num_rows$eq'all'][order$eqstructures.graph_order][count$eqfalse]"
self.oa.json_msg_query = \
MagicMock(name='json_msg_query')
self.oa.get_structures(structure_graph_names="'Mouse Brain Atlas'")
self.oa.json_msg_query.assert_called_once_with(expected)
def test_structure_graphs_by_names(self):
expected = "http://api.brain-map.org/api/v2/data/query.json?q=model::Structure,rma::criteria,graph[structure_graphs.name$in'Mouse Brain Atlas','Human Brain Atlas'],rma::options[num_rows$eq'all'][order$eqstructures.graph_order][count$eqfalse]"
self.oa.json_msg_query = \
MagicMock(name='json_msg_query')
self.oa.get_structures(structure_graph_names=["'Mouse Brain Atlas'",
"'Human Brain Atlas'"])
self.oa.json_msg_query.assert_called_once_with(expected)
def test_structure_set_by_id(self):
expected = "http://api.brain-map.org/api/v2/data/query.json?q=model::Structure,rma::criteria,[structure_set_id$in8],rma::options[num_rows$eq'all'][order$eqstructures.graph_order][count$eqfalse]"
self.oa.json_msg_query = \
MagicMock(name='json_msg_query')
self.oa.get_structures(structure_set_ids=8)
self.oa.json_msg_query.assert_called_once_with(expected)
def test_structure_sets_by_ids(self):
expected = "http://api.brain-map.org/api/v2/data/query.json?q=model::Structure,rma::criteria,[structure_set_id$in7,8],rma::options[num_rows$eq'all'][order$eqstructures.graph_order][count$eqfalse]"
self.oa.json_msg_query = \
MagicMock(name='json_msg_query')
self.oa.get_structures(structure_set_ids=[7,8])
self.oa.json_msg_query.assert_called_once_with(expected)
def test_structure_set_by_name(self):
expected = "http://api.brain-map.org/api/v2/data/query.json?q=model::Structure,rma::criteria,structure_sets[name$in'Mouse Connectivity - Summary'],rma::options[num_rows$eq'all'][order$eqstructures.graph_order][count$eqfalse]"
self.oa.json_msg_query = \
MagicMock(name='json_msg_query')
self.oa.get_structures(structure_set_names="'Mouse Connectivity - Summary'")
self.oa.json_msg_query.assert_called_once_with(expected)
def test_structure_set_by_names(self):
expected = "http://api.brain-map.org/api/v2/data/query.json?q=model::Structure,rma::criteria,structure_sets[name$in'NHP - Coarse','Mouse Connectivity - Summary'],rma::options[num_rows$eq'all'][order$eqstructures.graph_order][count$eqfalse]"
self.oa.json_msg_query = \
MagicMock(name='json_msg_query')
self.oa.get_structures(structure_set_names=["'NHP - Coarse'",
"'Mouse Connectivity - Summary'"])
self.oa.json_msg_query.assert_called_once_with(expected)
def test_structure_set_no_order(self):
expected = "http://api.brain-map.org/api/v2/data/query.json?q=model::Structure,rma::criteria,[graph_id$in1],rma::options[num_rows$eq'all'][count$eqfalse]"
self.oa.json_msg_query = \
MagicMock(name='json_msg_query')
self.oa.get_structures(1, order=None)
self.oa.json_msg_query.assert_called_once_with(expected)
def test_atlas_1(self):
expected = "http://api.brain-map.org/api/v2/data/query.json?q=model::Atlas,rma::criteria,[id$in1],structure_graph(ontology),graphic_group_labels,rma::include,structure_graph(ontology),graphic_group_labels,rma::options[only$eq'atlases.id,atlases.name,atlases.image_type,ontologies.id,ontologies.name,structure_graphs.id,structure_graphs.name,graphic_group_labels.id,graphic_group_labels.name'][num_rows$eq'all'][count$eqfalse]"
atlas_id = 1
self.oa.json_msg_query = \
MagicMock(name='json_msg_query')
self.oa.get_atlases_table(atlas_id)
self.oa.json_msg_query.assert_called_once_with(expected)
def test_atlas_verbose(self):
expected = "http://api.brain-map.org/api/v2/data/query.json?q=model::Atlas,rma::criteria,structure_graph(ontology),graphic_group_labels,rma::include,structure_graph(ontology),graphic_group_labels,rma::options[num_rows$eq'all'][count$eqfalse]"
self.oa.json_msg_query = \
MagicMock(name='json_msg_query')
self.oa.get_atlases_table(brief=False)
self.oa.json_msg_query.assert_called_once_with(expected)
qform = np.array([[0, 0, allen_resolution*pow(10, -3), 0], [-allen_resolution*pow(10, -3), 0, 0, 0], [0, -allen_resolution*pow(10, -3), 0, 0], [0, 0, 0, 1]]) img_annotation = nib.Nifti1Image(annot, np.eye(4)) img_average_template = nib.Nifti1Image(template, np.eye(4)) img_annotation.set_qform(qform, code=1) img_average_template.set_qform(qform, code=1) img_annotation.set_sform(np.eye(4), code=0) img_average_template.set_sform(np.eye(4), code=0) # img_average_template.set_qform(img_average_template_wrongread.get_qform()) nib.save(img_annotation, allen_annotation_path) nib.save(img_average_template, allen_average_template_path) # Get structure graph oapi = OntologiesApi() allen_structure_graph_dict = oapi.get_structures([1]) # Get structure graph with structure graph id = 1, which is the Mouse Brain Atlas structure graph # This removes some unused fields returned by the query allen_structure_graph_dict = StructureTree.clean_structures(allen_structure_graph_dict) # Get tree allen_structure_graph_tree = StructureTree(allen_structure_graph_dict) # now let's take a look at a structure allen_structure_graph_tree.get_structures_by_name(['Dorsal auditory area']) # Look at children or parent of structure, important for later (volume calculations) # Define path of structure graph table allen_average_template_csv_path=os.path.join(allen_dir, 'structure_graph.csv') allen_average_template_csv_remapped_path = os.path.join(allen_dir, 'structure_graph_remapped.csv')
