def test_store_load_structuralMRI(tmph5factory):
volume = Volume(
origin=numpy.zeros((3, 3)),
voxel_size=numpy.zeros((3, 3))
)
structural_mri = StructuralMRI(
array_data=numpy.zeros((3, 3)),
weighting="T1",
volume=volume
)
tmp_file = tmph5factory("StructuralMRI_{}.h5".format(volume.gid))
with StructuralMRIH5(tmp_file) as f:
f.store(structural_mri)
structural_mri_stored = StructuralMRI()
with pytest.raises(TraitAttributeError):
structural_mri_stored.array_data
with pytest.raises(TraitAttributeError):
structural_mri_stored.volume
with StructuralMRIH5(tmp_file) as f:
f.load_into(structural_mri_stored)
assert structural_mri_stored.array_data.shape == (3, 3)
# referenced datatype is not loaded
with pytest.raises(TraitAttributeError):
structural_mri_stored.volume
def _create_mri(self, volume):
mri = StructuralMRI(storage_path=self.storage_path)
mri.volume = volume
mri.title = "NIFTI Import - " + os.path.split(self.data_file)[1]
mri.dimensions_labels = ["X", "Y", "Z"]
mri.weighting = "T1"
self.parser.parse(mri, False)
return mri
def _create_mri(self, volume, title):
mri = StructuralMRI()
mri.title = title
mri.dimensions_labels = ["X", "Y", "Z"]
mri.weighting = "T1"
mri.array_data = self.parser.parse()
mri.volume = volume
return h5.store_complete(mri, self.storage_path)
def _create_mri(self, volume):
mri = StructuralMRI(storage_path=self.storage_path)
mri.volume = volume
mri.title = "NIFTI Import - " + os.path.split(self.data_file)[1]
mri.dimensions_labels = ["X", "Y", "Z"]
mri.weighting = "T1"
self.parser.parse(mri, False)
return mri
def launch(self, view_model):
resolution = view_model.resolution
weighting = view_model.weighting
inj_f_thresh = view_model.inj_f_thresh / 100.
vol_thresh = view_model.vol_thresh
project = dao.get_project_by_id(self.current_project_id)
manifest_file = self.file_handler.get_allen_mouse_cache_folder(
project.name)
manifest_file = os.path.join(manifest_file,
'mouse_connectivity_manifest.json')
cache = MouseConnectivityCache(resolution=resolution,
manifest_file=manifest_file)
# the method creates a dictionary with information about which experiments need to be downloaded
ist2e = dictionary_builder(cache, False)
# the method downloads experiments necessary to build the connectivity
projmaps = download_an_construct_matrix(cache, weighting, ist2e, False)
# the method cleans the file projmaps in 4 steps
projmaps = pms_cleaner(projmaps)
# download from the AllenSDK the annotation volume, the template volume
vol, annot_info = cache.get_annotation_volume()
template, template_info = cache.get_template_volume()
# rotate template in the TVB 3D reference:
template = rotate_reference(template)
# grab the StructureTree instance
structure_tree = cache.get_structure_tree()
# the method includes in the parcellation only brain regions whose volume is greater than vol_thresh
projmaps = areas_volume_threshold(cache, projmaps, vol_thresh,
resolution)
# the method exclude from the experimental dataset
# those exps where the injected fraction of pixel in the injection site is lower than than the inj_f_thr
projmaps = infected_threshold(cache, projmaps, inj_f_thresh)
# the method creates file order and keyword that will be the link between the SC order and the
# id key in the Allen database
[order, key_ord] = create_file_order(projmaps, structure_tree)
# the method builds the Structural Connectivity (SC) matrix
structural_conn = construct_structural_conn(projmaps, order, key_ord)
# the method returns the coordinate of the centres and the name of the brain areas in the selected parcellation
[centres, names] = construct_centres(cache, order, key_ord)
# the method returns the tract lengths between the brain areas in the selected parcellation
tract_lengths = construct_tract_lengths(centres)
# the method associated the parent and the grandparents to the child in the selected parcellation with
# the biggest volume
[unique_parents, unique_grandparents
] = parents_and_grandparents_finder(cache, order, key_ord,
structure_tree)
# the method returns a volume indexed between 0 and N-1, with N=tot brain areas in the parcellation.
# -1=background and areas that are not in the parcellation
vol_parcel = mouse_brain_visualizer(vol, order, key_ord,
unique_parents,
unique_grandparents,
structure_tree, projmaps)
# results: Connectivity, Volume & RegionVolumeMapping
# Connectivity
result_connectivity = Connectivity()
result_connectivity.centres = centres
result_connectivity.region_labels = numpy.array(names)
result_connectivity.weights = structural_conn
result_connectivity.tract_lengths = tract_lengths
result_connectivity.configure()
# Volume
result_volume = Volume()
result_volume.origin = numpy.array([[0.0, 0.0, 0.0]])
result_volume.voxel_size = numpy.array(
[resolution, resolution, resolution])
# result_volume.voxel_unit= micron
# Region Volume Mapping
result_rvm = RegionVolumeMapping()
result_rvm.volume = result_volume
result_rvm.array_data = vol_parcel
result_rvm.connectivity = result_connectivity
result_rvm.title = "Volume mouse brain "
result_rvm.dimensions_labels = ["X", "Y", "Z"]
# Volume template
result_template = StructuralMRI()
result_template.array_data = template
result_template.weighting = 'T1'
result_template.volume = result_volume
connectivity_index = h5.store_complete(result_connectivity,
self.storage_path)
volume_index = h5.store_complete(result_volume, self.storage_path)
rvm_index = h5.store_complete(result_rvm, self.storage_path)
template_index = h5.store_complete(result_template, self.storage_path)
return [connectivity_index, volume_index, rvm_index, template_index]
def launch(self, resolution, weighting, inf_vox_thresh, vol_thresh):
resolution = int(resolution)
weighting = int(weighting)
inf_vox_thresh = float(inf_vox_thresh)
vol_thresh = float(vol_thresh)
project = dao.get_project_by_id(self.current_project_id)
manifest_file = self.file_handler.get_allen_mouse_cache_folder(
project.name)
manifest_file = os.path.join(manifest_file,
'mouse_connectivity_manifest.json')
cache = MouseConnectivityCache(resolution=resolution,
manifest_file=manifest_file)
# the method creates a dictionary with information about which experiments need to be downloaded
ist2e = DictionaireBuilder(cache, False)
# the method downloads experiments necessary to build the connectivity
projmaps = DownloadAndConstructMatrix(cache, weighting, ist2e, False)
# the method cleans the file projmaps in 4 steps
projmaps = pmsCleaner(projmaps)
#download from the AllenSDK the annotation volume, the ontology, the template volume
Vol, annot_info = cache.get_annotation_volume()
ontology = cache.get_ontology()
template, template_info = cache.get_template_volume()
#rotate template in the TVB 3D reference:
template = RotateReference(template)
# the method includes in the parcellation only brain regions whose volume is greater than vol_thresh
projmaps = AreasVolumeTreshold(cache, projmaps, vol_thresh, resolution,
Vol, ontology)
# the method includes in the parcellation only brain regions where at least one injection experiment had infected more than N voxel (where N is inf_vox_thresh)
projmaps = AreasVoxelTreshold(cache, projmaps, inf_vox_thresh, Vol,
ontology)
# the method creates file order and keyord that will be the link between the SC order and the id key in the Allen database
[order, key_ord] = CreateFileOrder(projmaps, ontology)
# the method builds the Structural Connectivity (SC) matrix
SC = ConstructingSC(projmaps, order, key_ord)
# the method returns the coordinate of the centres and the name of the brain areas in the selected parcellation
[centres, names] = Construct_centres(cache, ontology, order, key_ord)
# the method returns the tract lengths between the brain areas in the selected parcellation
tract_lengths = ConstructTractLengths(centres)
# the method associated the parent and the grandparents to the child in the selected parcellation with the biggest volume
[unique_parents, unique_grandparents
] = ParentsAndGrandParentsFinder(cache, order, key_ord, ontology)
# the method returns a volume indexed between 0 and N-1, with N=tot brain areas in the parcellation. -1=background and areas that are not in the parcellation
Vol_parcel = MouseBrainVisualizer(Vol, order, key_ord, unique_parents,
unique_grandparents, ontology,
projmaps)
# results: Connectivity, Volume & RegionVolumeMapping
# Connectivity
result_connectivity = Connectivity(storage_path=self.storage_path)
result_connectivity.centres = centres
result_connectivity.region_labels = names
result_connectivity.weights = SC
result_connectivity.tract_lengths = tract_lengths
# Volume
result_volume = Volume(storage_path=self.storage_path)
result_volume.origin = [[0.0, 0.0, 0.0]]
result_volume.voxel_size = [resolution, resolution, resolution]
# result_volume.voxel_unit= micron
# Region Volume Mapping
result_rvm = RegionVolumeMapping(storage_path=self.storage_path)
result_rvm.volume = result_volume
result_rvm.array_data = Vol_parcel
result_rvm.connectivity = result_connectivity
result_rvm.title = "Volume mouse brain "
result_rvm.dimensions_labels = ["X", "Y", "Z"]
# Volume template
result_template = StructuralMRI(storage_path=self.storage_path)
result_template.array_data = template
result_template.weighting = 'T1'
result_template.volume = result_volume
return [
result_connectivity, result_volume, result_rvm, result_template
]
def launch(self, resolution, weighting, inj_f_thresh, vol_thresh):
resolution = int(resolution)
weighting = int(weighting)
inj_f_thresh = float(inj_f_thresh)/100.
vol_thresh = float(vol_thresh)
project = dao.get_project_by_id(self.current_project_id)
manifest_file = self.file_handler.get_allen_mouse_cache_folder(project.name)
manifest_file = os.path.join(manifest_file, 'mouse_connectivity_manifest.json')
cache = MouseConnectivityCache(resolution=resolution, manifest_file=manifest_file)
# the method creates a dictionary with information about which experiments need to be downloaded
ist2e = dictionary_builder(cache, False)
# the method downloads experiments necessary to build the connectivity
projmaps = download_an_construct_matrix(cache, weighting, ist2e, False)
# the method cleans the file projmaps in 4 steps
projmaps = pms_cleaner(projmaps)
# download from the AllenSDK the annotation volume, the template volume
vol, annot_info = cache.get_annotation_volume()
template, template_info = cache.get_template_volume()
# rotate template in the TVB 3D reference:
template = rotate_reference(template)
# grab the StructureTree instance
structure_tree = cache.get_structure_tree()
# the method includes in the parcellation only brain regions whose volume is greater than vol_thresh
projmaps = areas_volume_threshold(cache, projmaps, vol_thresh, resolution)
# the method exclude from the experimental dataset
# those exps where the injected fraction of pixel in the injection site is lower than than the inj_f_thr
projmaps = infected_threshold(cache, projmaps, inj_f_thresh)
# the method creates file order and keyword that will be the link between the SC order and the
# id key in the Allen database
[order, key_ord] = create_file_order(projmaps, structure_tree)
# the method builds the Structural Connectivity (SC) matrix
structural_conn = construct_structural_conn(projmaps, order, key_ord)
# the method returns the coordinate of the centres and the name of the brain areas in the selected parcellation
[centres, names] = construct_centres(cache, order, key_ord)
# the method returns the tract lengths between the brain areas in the selected parcellation
tract_lengths = construct_tract_lengths(centres)
# the method associated the parent and the grandparents to the child in the selected parcellation with
# the biggest volume
[unique_parents, unique_grandparents] = parents_and_grandparents_finder(cache, order, key_ord, structure_tree)
# the method returns a volume indexed between 0 and N-1, with N=tot brain areas in the parcellation.
# -1=background and areas that are not in the parcellation
vol_parcel = mouse_brain_visualizer(vol, order, key_ord, unique_parents, unique_grandparents,
structure_tree, projmaps)
# results: Connectivity, Volume & RegionVolumeMapping
# Connectivity
result_connectivity = Connectivity(storage_path=self.storage_path)
result_connectivity.centres = centres
result_connectivity.region_labels = names
result_connectivity.weights = structural_conn
result_connectivity.tract_lengths = tract_lengths
# Volume
result_volume = Volume(storage_path=self.storage_path)
result_volume.origin = [[0.0, 0.0, 0.0]]
result_volume.voxel_size = [resolution, resolution, resolution]
# result_volume.voxel_unit= micron
# Region Volume Mapping
result_rvm = RegionVolumeMapping(storage_path=self.storage_path)
result_rvm.volume = result_volume
result_rvm.array_data = vol_parcel
result_rvm.connectivity = result_connectivity
result_rvm.title = "Volume mouse brain "
result_rvm.dimensions_labels = ["X", "Y", "Z"]
# Volume template
result_template = StructuralMRI(storage_path=self.storage_path)
result_template.array_data = template
result_template.weighting = 'T1'
result_template.volume = result_volume
return [result_connectivity, result_volume, result_rvm, result_template]