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Handle an exceptional case when the loaded morphology does not have a…
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…ny basal dendrites.
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@marwan-abdellah
marwan-abdellah committed Oct 8, 2018
1 parent 5dc855b commit a99c6de
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Showing 4 changed files with 177 additions and 131 deletions.
60 changes: 33 additions & 27 deletions neuromorphovis/builders/mesh/piecewise_builder.py
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Original file line number Diff line number Diff line change
Expand Up @@ -286,33 +286,36 @@ def build_arbors(self,
# Draw the basal dendrites
if not self.options.morphology.ignore_basal_dendrites:

# Do it dendrite by dendrite
for i, basal_dendrite in enumerate(self.morphology.dendrites):
nmv.logger.info('Dendrite [%d]' % i)
# Ensure tha existence of basal dendrites
if self.morphology.dendrites is not None:

basal_dendrite_objects = []
# Do it dendrite by dendrite
for i, basal_dendrite in enumerate(self.morphology.dendrites):
nmv.logger.info('Dendrite [%d]' % i)

# Draw the basal dendrites as a set connected sections
basal_dendrite_prefix = '%s_%d' % (nmv.consts.Arbors.BASAL_DENDRITES_PREFIX, i)
nmv.skeleton.ops.draw_connected_sections(
section=copy.deepcopy(basal_dendrite),
max_branching_level=self.options.morphology.basal_dendrites_branch_order,
name=basal_dendrite_prefix,
material_list=self.basal_dendrites_materials,
bevel_object=bevel_object,
repair_morphology=True,
caps=caps,
sections_objects=basal_dendrite_objects,
roots_connection=roots_connection)
basal_dendrite_objects = []

# Ensure that basal dendrite objects were reconstructed
if len(basal_dendrite_objects) > 0:
# Draw the basal dendrites as a set connected sections
basal_dendrite_prefix = '%s_%d' % (nmv.consts.Arbors.BASAL_DENDRITES_PREFIX, i)
nmv.skeleton.ops.draw_connected_sections(
section=copy.deepcopy(basal_dendrite),
max_branching_level=self.options.morphology.basal_dendrites_branch_order,
name=basal_dendrite_prefix,
material_list=self.basal_dendrites_materials,
bevel_object=bevel_object,
repair_morphology=True,
caps=caps,
sections_objects=basal_dendrite_objects,
roots_connection=roots_connection)

# Add a reference to the mesh object
self.morphology.dendrites[i].mesh = basal_dendrite_objects[0]
# Ensure that basal dendrite objects were reconstructed
if len(basal_dendrite_objects) > 0:

# Add a reference to the mesh object
self.morphology.dendrites[i].mesh = basal_dendrite_objects[0]

# Add the sections (tubes) of the basal dendrite to the list
arbors_objects.extend(basal_dendrite_objects)
# Add the sections (tubes) of the basal dendrite to the list
arbors_objects.extend(basal_dendrite_objects)

# Draw the axon as a set connected sections
if not self.options.morphology.ignore_axon:
Expand Down Expand Up @@ -377,11 +380,14 @@ def connect_arbors_to_soma(self):
# Connecting basal dendrites
if not self.options.morphology.ignore_basal_dendrites:

# Do it dendrite by dendrite
for i, basal_dendrite in enumerate(self.morphology.dendrites):
nmv.logger.detail('Dendrite [%d]' % i)
nmv.skeleton.ops.connect_arbor_to_soma(
self.soma_mesh, basal_dendrite)
# Ensure tha existence of basal dendrites
if self.morphology.dendrites is not None:

# Do it dendrite by dendrite
for i, basal_dendrite in enumerate(self.morphology.dendrites):
nmv.logger.detail('Dendrite [%d]' % i)
nmv.skeleton.ops.connect_arbor_to_soma(
self.soma_mesh, basal_dendrite)

# Connecting axon
if not self.options.morphology.ignore_axon:
Expand Down
174 changes: 98 additions & 76 deletions neuromorphovis/builders/skeleton/skeleton_builder.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -477,18 +477,23 @@ def draw_morphology_as_disconnected_segments(self,

# Draw the basal dendrites
if not self.options.morphology.ignore_basal_dendrites:
basal_dendrites_segments_objects = []
for i, basal_dendrite in enumerate(self.morphology.dendrites):
dendrite_name = '%s_%d' % (nmv.consts.Arbors.BASAL_DENDRITES_PREFIX, i)
self.draw_section_as_disconnected_segments(
basal_dendrite, name=dendrite_name,
max_branching_level=self.options.morphology.basal_dendrites_branch_order,
material_list=self.basal_dendrites_materials,
bevel_object=bevel_object,
segments_objects=basal_dendrites_segments_objects)

# Extend the morphology objects list
morphology_objects.extend(basal_dendrites_segments_objects)
# Ensure tha existence of basal dendrites
if self.morphology.dendrites is not None:

basal_dendrites_segments_objects = []

for i, basal_dendrite in enumerate(self.morphology.dendrites):
dendrite_name = '%s_%d' % (nmv.consts.Arbors.BASAL_DENDRITES_PREFIX, i)
self.draw_section_as_disconnected_segments(
basal_dendrite, name=dendrite_name,
max_branching_level=self.options.morphology.basal_dendrites_branch_order,
material_list=self.basal_dendrites_materials,
bevel_object=bevel_object,
segments_objects=basal_dendrites_segments_objects)

# Extend the morphology objects list
morphology_objects.extend(basal_dendrites_segments_objects)

# Draw the apical dendrite
if not self.options.morphology.ignore_apical_dendrite:
Expand Down Expand Up @@ -553,19 +558,24 @@ def draw_morphology_as_disconnected_sections(self,

# Draw the basal dendrites
if not self.options.morphology.ignore_basal_dendrites:
basal_dendrites_sections_objects = []
for i, basal_dendrite in enumerate(self.morphology.dendrites):
dendrite_prefix = '%s_%d' % (nmv.consts.Arbors.BASAL_DENDRITES_PREFIX, i)
self.draw_root_as_disconnected_sections(
basal_dendrite,
name=dendrite_prefix,
material_list=self.basal_dendrites_materials,
bevel_object=bevel_object,
max_branching_level=self.options.morphology.basal_dendrites_branch_order,
sections_objects=basal_dendrites_sections_objects)

# Extend the morphology objects list
morphology_objects.extend(basal_dendrites_sections_objects)
# Ensure tha existence of basal dendrites
if self.morphology.dendrites is not None:

basal_dendrites_sections_objects = []

for i, basal_dendrite in enumerate(self.morphology.dendrites):
dendrite_prefix = '%s_%d' % (nmv.consts.Arbors.BASAL_DENDRITES_PREFIX, i)
self.draw_root_as_disconnected_sections(
basal_dendrite,
name=dendrite_prefix,
material_list=self.basal_dendrites_materials,
bevel_object=bevel_object,
max_branching_level=self.options.morphology.basal_dendrites_branch_order,
sections_objects=basal_dendrites_sections_objects)

# Extend the morphology objects list
morphology_objects.extend(basal_dendrites_sections_objects)

# Return a reference to the list of drawn objects
return morphology_objects
Expand Down Expand Up @@ -609,18 +619,22 @@ def draw_morphology_as_articulated_sections(self,

# Draw the basal dendrites joints
if not self.options.morphology.ignore_basal_dendrites:
basal_dendrites_spheres_objects = []
for i, basal_dendrite in enumerate(self.morphology.dendrites):

# Draw the basal dendrites as a set connected sections
self.draw_section_terminals_as_spheres(
root=basal_dendrite,
sphere_objects=basal_dendrites_spheres_objects,
max_branching_level=self.options.morphology.basal_dendrites_branch_order,
material_list=self.articulation_materials)
# Ensure tha existence of basal dendrites
if self.morphology.dendrites is not None:

# Extend the morphology objects list
morphology_objects.extend(basal_dendrites_spheres_objects)
basal_dendrites_spheres_objects = []
for i, basal_dendrite in enumerate(self.morphology.dendrites):

# Draw the basal dendrites as a set connected sections
self.draw_section_terminals_as_spheres(
root=basal_dendrite,
sphere_objects=basal_dendrites_spheres_objects,
max_branching_level=self.options.morphology.basal_dendrites_branch_order,
material_list=self.articulation_materials)

# Extend the morphology objects list
morphology_objects.extend(basal_dendrites_spheres_objects)

# Draw the apical dendrite joints
if not self.options.morphology.ignore_apical_dendrite:
Expand Down Expand Up @@ -696,29 +710,33 @@ def draw_morphology_as_connected_sections(self,
# Draw the basal dendrites
if not self.options.morphology.ignore_basal_dendrites:

# A list to keep all the drawn objects of the basal dendrites
basal_dendrites_sections_objects = []
# Ensure tha existence of basal dendrites
if self.morphology.dendrites is not None:

# A list to keep all the drawn objects of the basal dendrites
basal_dendrites_sections_objects = []

# Draw each basal dendrites as a set connected sections
for i, basal_dendrite in enumerate(self.morphology.dendrites):

dendrite_prefix = '%s_%d' % (nmv.consts.Arbors.BASAL_DENDRITES_PREFIX, i)
nmv.skeleton.ops.draw_connected_sections(
section=copy.deepcopy(basal_dendrite),
max_branching_level=self.options.morphology.basal_dendrites_branch_order,
name=dendrite_prefix,
material_list=self.basal_dendrites_materials,
bevel_object=bevel_object,
repair_morphology=repair_morphology,
caps=True,
sections_objects=basal_dendrites_sections_objects,
render_frame=self.options.morphology.render_progressive,
frame_destination=self.progressive_frames_directory,
camera=self.progressive_rendering_camera,
roots_connection=self.options.morphology.arbors_to_soma_connection,
ignore_branching_samples=disconnect_skelecton)

# Draw each basal dendrites as a set connected sections
for i, basal_dendrite in enumerate(self.morphology.dendrites):
dendrite_prefix = '%s_%d' % (nmv.consts.Arbors.BASAL_DENDRITES_PREFIX, i)
nmv.skeleton.ops.draw_connected_sections(
section=copy.deepcopy(basal_dendrite),
max_branching_level=self.options.morphology.basal_dendrites_branch_order,
name=dendrite_prefix,
material_list=self.basal_dendrites_materials,
bevel_object=bevel_object,
repair_morphology=repair_morphology,
caps=True,
sections_objects=basal_dendrites_sections_objects,
render_frame=self.options.morphology.render_progressive,
frame_destination=self.progressive_frames_directory,
camera=self.progressive_rendering_camera,
roots_connection=self.options.morphology.arbors_to_soma_connection,
ignore_branching_samples=disconnect_skelecton)

# Extend the morphology objects list
morphology_objects.extend(basal_dendrites_sections_objects)
# Extend the morphology objects list
morphology_objects.extend(basal_dendrites_sections_objects)

# Draw the apical dendrite
if not self.options.morphology.ignore_apical_dendrite:
Expand Down Expand Up @@ -849,28 +867,32 @@ def draw_morphology_as_disconnected_skeleton(self,
# Draw the basal dendrites
if not self.options.morphology.ignore_basal_dendrites:

basal_dendrites_sections_objects = []
for i, basal_dendrite in enumerate(self.morphology.dendrites):

# Draw the basal dendrites as a set connected sections
dendrite_prefix = '%s_%d' % (nmv.consts.Arbors.BASAL_DENDRITES_PREFIX, i)
nmv.skeleton.ops.draw_connected_sections(
section=copy.deepcopy(basal_dendrite),
max_branching_level=self.options.morphology.basal_dendrites_branch_order,
name=dendrite_prefix,
material_list=self.basal_dendrites_materials,
bevel_object=bevel_object,
repair_morphology=repair_morphology,
caps=True,
sections_objects=basal_dendrites_sections_objects,
render_frame=self.options.morphology.render_progressive,
frame_destination=self.progressive_frames_directory,
camera=self.progressive_rendering_camera,
roots_connection=self.options.morphology.arbors_to_soma_connection,
ignore_branching_samples=True)
# Ensure tha existence of basal dendrites
if self.morphology.dendrites is not None:

basal_dendrites_sections_objects = []

for i, basal_dendrite in enumerate(self.morphology.dendrites):

# Draw the basal dendrites as a set connected sections
dendrite_prefix = '%s_%d' % (nmv.consts.Arbors.BASAL_DENDRITES_PREFIX, i)
nmv.skeleton.ops.draw_connected_sections(
section=copy.deepcopy(basal_dendrite),
max_branching_level=self.options.morphology.basal_dendrites_branch_order,
name=dendrite_prefix,
material_list=self.basal_dendrites_materials,
bevel_object=bevel_object,
repair_morphology=repair_morphology,
caps=True,
sections_objects=basal_dendrites_sections_objects,
render_frame=self.options.morphology.render_progressive,
frame_destination=self.progressive_frames_directory,
camera=self.progressive_rendering_camera,
roots_connection=self.options.morphology.arbors_to_soma_connection,
ignore_branching_samples=True)

# Extend the morphology objects list
morphology_objects.extend(basal_dendrites_sections_objects)
# Extend the morphology objects list
morphology_objects.extend(basal_dendrites_sections_objects)

# Draw the apical dendrite
if not self.options.morphology.ignore_apical_dendrite:
Expand Down
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