def test_section_types():
morphology = vasculature.Vasculature(os.path.join(_path, "h5/vasculature1.h5"))
assert morphology.section(0).type == VasculatureSectionType.vein
assert morphology.section(1).type == VasculatureSectionType.artery
assert morphology.section(2).type == VasculatureSectionType.venule
assert morphology.section(3).type == VasculatureSectionType.arteriole
assert morphology.section(4).type == VasculatureSectionType.venous_capillary
assert morphology.section(5).type == VasculatureSectionType.arterial_capillary
with pytest.raises(RawDataError):
vasculature.Vasculature(os.path.join(_path, "h5/vasculature-broken-section-type.h5"))
def test_components_vasculature():
morphology = vasculature.Vasculature(os.path.join(_path, "h5/vasculature1.h5"))
assert_array_almost_equal(morphology.section(0).points,
np.array([[1265.47399902, 335.42364502, 1869.19274902],
[1266.26647949, 335.57000732, 1869.74914551],
[1267.09082031, 335.68869019, 1870.31469727],
[1267.89404297, 335.78134155, 1870.91418457],
[1268.67077637, 335.85733032, 1871.54992676],
[1269.42773438, 335.92602539, 1872.21008301],
[1270.17431641, 335.99368286, 1872.88195801],
[1270.92016602, 336.06558228, 1873.55395508],
[1271.6739502 , 336.14227295, 1874.21740723],
[1272.44091797, 336.23706055, 1874.86047363],
[1273.22216797, 336.31613159, 1875.49523926],
[1274. , 336.70001221, 1876. ]]))
assert_array_almost_equal(morphology.section(0).diameters,
np.array([1.96932483, 1.96932483, 1.96932483, 1.96932483, 1.96932483,
1.96932483, 1.96932483, 1.96932483, 1.96932483, 1.96932483,
1.96932483, 2.15068388]))
assert len(morphology.sections) == 3080
assert len(morphology.points) == 55807
assert len(morphology.diameters) == 55807
assert_array_almost_equal(morphology.diameters[-5:],
np.array([0.78039801, 0.78039801, 0.78039801, 2.11725187, 2.11725187]))
assert len(morphology.section_types) == 3080
assert len(morphology.section(0).predecessors) == 0
assert len(morphology.section(0).successors) == 2
assert morphology.section(0).successors[0].id == 1
assert morphology.section(0).successors[1].id == 2
def test_iterators_vasculature():
morphology = vasculature.Vasculature(os.path.join(_path, "h5/vasculature1.h5"))
assert_array_equal([sec.id for sec in morphology.sections], range(3080))
assert len([section.id for section in morphology.iter()]) == 3080
all_sections = set([sec.id for sec in morphology.sections])
for sec in morphology.iter():
all_sections.remove(sec.id)
assert len(all_sections) == 0
def test_section_types():
morphology = vasculature.Vasculature(os.path.join(_path, "h5/vasculature1.h5"))
assert_equal(morphology.section(0).type, VasculatureSectionType.vein)
assert_equal(morphology.section(1).type, VasculatureSectionType.artery)
assert_equal(morphology.section(2).type, VasculatureSectionType.venule)
assert_equal(morphology.section(3).type, VasculatureSectionType.arteriole)
assert_equal(morphology.section(4).type, VasculatureSectionType.venous_capillary)
assert_equal(morphology.section(5).type, VasculatureSectionType.arterial_capillary)
assert_raises(RawDataError, vasculature.Vasculature, os.path.join(_path, "h5/vasculature-broken-section-type.h5"))
def test_from_pathlib():
vasc = vasculature.Vasculature(Path(_path, "h5/vasculature1.h5"))
assert len(vasc.sections) == 3080
def test_empty_vasculature():
with pytest.raises(RawDataError):
vasculature.Vasculature(os.path.join(_path, "h5/empty_vasculature.h5"))
def read_data_from_file(self, center_at_origin=False):
"""Loads the data from the given file in the constructor.
:param: center_at_origin:
Centers the morphology at the origin.
"""
try:
# Import the required module
import numpy
import vmv.utilities
import vmv.skeleton
import morphio.vasculature as vasculature
from morphio import RawDataError, VasculatureSectionType
# Ignore the console warning and output
vmv.utilities.disable_std_output()
# Load the morphology data using MorphIO
morphology_data = vasculature.Vasculature(self.morphology_file)
# Get a list of points using the iterator
points = numpy.vstack(
[section.points for section in morphology_data.iter()])
# Get a list of all the points to compute the bounding box quickly
points_list = [
Vector((point[0], point[1], point[2])) for point in points
]
# Compute the bounding box of the morphology
self.bounding_box = vmv.bbox.compute_bounding_box_for_list_of_points(
points_list)
# Update the number of samples
self.number_loaded_vertices = copy.deepcopy(len(points_list))
# Delete the points list
points_list.clear()
# Transform the data of the morphology into a normal structure
sections_morphio = numpy.vstack([
self.SectionMorphIO(section.id, section.points,
0.5 * section.diameters,
section.predecessors, section.successors)
for section in morphology_data.iter()
])
# A dictionary to keep track on the indices of the parents in the array
index_parent_dictionary = {}
for i_section, sec in enumerate(sections_morphio):
index_parent_dictionary[sec[0].id] = i_section
# Construct a list of sections to be given to the Morphology constructor
sections_list = list()
# On-a-per-section basis
for section_morphio in sections_morphio:
# Just construct the section
section = vmv.skeleton.Section(index=section_morphio[0].id)
# Build the Samples list
samples = list()
for i in range(len(section_morphio[0].points)):
# A reference to the point
point = Vector((section_morphio[0].points[i][0],
section_morphio[0].points[i][1],
section_morphio[0].points[i][2]))
# Center the morphology at the origin if required by the user
if center_at_origin:
point[0] -= self.bounding_box.center[0]
point[1] -= self.bounding_box.center[1]
point[2] -= self.bounding_box.center[2]
# Build the sample
sample = vmv.skeleton.Sample(
point=point, radius=section_morphio[0].radii[i])
# Add it to the samples list
samples.append(sample)
# Link the samples list to the section
section.samples = samples
# Append the section to the sections list
sections_list.append(section)
# Updating parents and children
# This is only needed in case we use the ConnectedSectionsBuilder
for i in range(len(sections_list)):
# Update the parents IDs
parents_ids = [
j.id for j in sections_morphio[i][0].predecessors
]
# Update the children IDs
children_ids = [
k.id for k in sections_morphio[i][0].successors
]
# Update the parents list
sections_list[i].parents = [
sections_list[index_parent_dictionary[parent_id]]
for parent_id in parents_ids
]
# Update the children list
sections_list[i].children = [
sections_list[index_parent_dictionary[children_id]]
for children_id in children_ids
]
# Data
self.sections_list = sections_list
# Number of strands
self.number_loaded_strands = len(sections_list)
# Detect the root sections and update the list
for section in self.sections_list:
if section.is_root():
self.roots.append(section)
# Enable std output again
vmv.utilities.enable_std_output()
# Raise an exception if we cannot import the h5py module
except ImportError:
print('ERROR: Cannot *import h5py* to read the file [%s]' %
self.morphology_file)
exit(0)
