def __init__(self, morph, PtSrc=None): PtSrc = SectionVistorFactory.array3_all_points() if PtSrc == None else PtSrc X = PtSrc(morph) # Refactored out 'map' in August 2012 offset = np.array([sum(col) for col in X.T]) / len(X) # _get_mean(PtSrc(morph)) * -1.0 super(MorphologyMeanCenterer, self).__init__(offset)
def cell_location_distance_from_soma(cell_location): morph = cell_location.cell.morphology sect_dist_dict = SectionVistorFactory.dict_section_proximal_dist_from_soma(morph, soma_centre=False)() section_dist = sect_dist_dict[cell_location.morphlocation.section] celllocdist = ( section_dist + cell_location.morphlocation.section.get_length() * cell_location.morphlocation.sectionpos ) return celllocdist
def cell_location_distance_from_soma(cell_location): morph = cell_location.cell.morphology sect_dist_dict = SectionVistorFactory.dict_section_proximal_dist_from_soma( morph, soma_centre=False)() section_dist = sect_dist_dict[cell_location.morphlocation.section] celllocdist = section_dist + cell_location.morphlocation.section.get_length( ) * cell_location.morphlocation.sectionpos return celllocdist
def __init__(self, morph): axes = _pca(SectionVistorFactory.array3_all_points(morph)()) eigenvec1 = axes[0][1] / norm(axes[0][1]) eigenvec2 = axes[1][1] / norm(axes[1][1]) eigenvec3 = axes[2][1] / norm(axes[2][1]) self.eigen_matrix = numpy.array((eigenvec1, eigenvec2, eigenvec3)).T self.inv_mat = linalg.inv(self.eigen_matrix)
def __init__(self, morph, PtSrc=None): PtSrc = SectionVistorFactory.array3_all_points( ) if PtSrc == None else PtSrc X = PtSrc(morph) # Refactored out 'map' in August 2012 # offset = array(map(numpy.sum, X.T)) / len(X) offset = array([sum(col) for col in X.T]) / len(X) # _get_mean(PtSrc(morph)) * -1.0 super(MorphologyMeanCenterer, self).__init__(offset)
def _showSimple(): morph_pts = [SectionVistorFactory.array4_all_points(morph)() for morph in self.morphs] pts = numpy.concatenate(morph_pts) return mlab.points3d( pts[:, 0], pts[:, 1], pts[:, 2], pts[:, 3], colormap=self.colormap, scale_factor=self.scale_factor, )
def _showSimple(): morph_pts = [ SectionVistorFactory.array4_all_points(morph)() for morph in self.morphs ] pts = numpy.concatenate(morph_pts) return mlab.points3d( pts[:, 0], pts[:, 1], pts[:, 2], pts[:, 3], colormap=self.colormap, scale_factor=self.scale_factor, )
def trim_axon_from_morphology(cls, morphology, max_dist_to_parent): dist_to_parent = SectionVistorFactory.dict_section_proximal_dist_from_soma( morph=morphology, soma_centre=False)() print sorted(dist_to_parent.values()) section_mapping_table = {} region_mapping_table = {} # Create New Regions: region_mapping_table[None] = None for rOld in morphology.get_regions(): r_new = Region(name=rOld.name) region_mapping_table[rOld] = r_new # Create New Sections: dummy_root_old = morphology.get_dummy_section() dummy_root_new = Section( region=region_mapping_table[dummy_root_old.region], x=dummy_root_old.d_x, y=dummy_root_old.d_y, z=dummy_root_old.d_z, r=dummy_root_old.d_r) section_mapping_table[dummy_root_old] = dummy_root_new for sectionOld in morphology: print 'DistToParent', dist_to_parent[sectionOld] if dist_to_parent[sectionOld] > max_dist_to_parent: continue print 'Extruding Section' old_parent = sectionOld.parent new_parent = section_mapping_table[old_parent] section_new = new_parent.create_distal_section( region=region_mapping_table[sectionOld.region], x=sectionOld.d_x, y=sectionOld.d_y, z=sectionOld.d_z, r=sectionOld.d_r, idtag=sectionOld.idtag, ) section_mapping_table[sectionOld] = section_new m = MorphologyTree('TrimmedNeuron', dummysection=dummy_root_new, metadata={}) return m
def trim_axon_from_morphology(cls, morphology, max_dist_to_parent): dist_to_parent = SectionVistorFactory.dict_section_proximal_dist_from_soma(morph=morphology, soma_centre=False)() print sorted(dist_to_parent.values()) section_mapping_table = {} region_mapping_table = {} # Create New Regions: region_mapping_table[None] = None for rOld in morphology.get_regions(): r_new = Region(name=rOld.name) region_mapping_table[rOld] = r_new # Create New Sections: dummy_root_old = morphology.get_dummy_section() dummy_root_new = Section( region=region_mapping_table[dummy_root_old.region], x=dummy_root_old.d_x, y=dummy_root_old.d_y, z=dummy_root_old.d_z, r=dummy_root_old.d_r) section_mapping_table[dummy_root_old] = dummy_root_new for sectionOld in morphology: print 'DistToParent', dist_to_parent[sectionOld] if dist_to_parent[sectionOld] > max_dist_to_parent: continue print 'Extruding Section' old_parent = sectionOld.parent new_parent = section_mapping_table[old_parent] section_new = new_parent.create_distal_section( region=region_mapping_table[sectionOld.region], x=sectionOld.d_x, y=sectionOld.d_y, z=sectionOld.d_z, r=sectionOld.d_r, idtag=sectionOld.idtag, ) section_mapping_table[sectionOld] = section_new m = MorphologyTree('TrimmedNeuron', dummysection=dummy_root_new, metadata={}) return m
def get_locations_at_distance_away_from_dummy(cls, morphology, distance, section_predicate=None): dist_to_section_distal = SectionVistorFactory.dict_section_distal_dist_from_soma(morph=morphology)() # Section predicates: allows us to generate only on a path, region, etc section_predicate = section_predicate if section_predicate else lambda s:True locations = [] for section in morphology: if not section_predicate(section): continue if section.is_a_root_section(): if distance < dist_to_section_distal[section]: #assert False, 'Not implemented' locations.append(MorphLocation(section=section, sectionpos=distance/dist_to_section_distal[section]) ) else: pass else: proximal_dist = dist_to_section_distal[section.parent] distal_dist = dist_to_section_distal[section] # Does a distance fall on this section: if proximal_dist < distance < distal_dist: prop = (distance - proximal_dist) / (distal_dist - proximal_dist) assert 0.0 <= prop <= 1.0 locations.append(MorphLocation(section=section, sectionpos=prop)) else: pass dummy = MorphLocation(morphology.get_dummy_section().children[0], 0.0) # Some sanity checking: for loc in locations: p = MorphPath(loc, dummy) assert np.fabs(p.get_length() - distance) < 0.01 return locations