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improved volume import
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@schlegelp
schlegelp committed Apr 19, 2017
1 parent d7e1c8e commit b8e7e65
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219 changes: 125 additions & 94 deletions CATMAIDImport.py
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Original file line number Diff line number Diff line change
Expand Up @@ -18,6 +18,10 @@

### CATMAID to Blender Import Script - Version History:

### V5.71 19/04/2017:
- added import of volumes by name (enables import of multiple volumes at a time)
- imported volumes are now smoothed

### V5.7 30/03/2017:
- added import of gap junctions and abutting connectors

Expand Down Expand Up @@ -348,7 +352,7 @@
bl_info = {
"name": "CATMAIDImport",
"author": "Philipp Schlegel",
"version": (5, 6, 3),
"version": (5, 7, 1),
"for_catmaid_version": '2017.01.19-3-g1e99030',
"blender": (2, 7, 8),
"location": "Properties > Scene > CATMAID Import",
Expand Down Expand Up @@ -6715,7 +6719,30 @@ def create_barplot(self, f, neurons_to_plot , x_coord, y_coord, x_factor = 1, y_
f.write(line_to_write + '\n')

"""


def fibonacci_sphere(samples=1,randomize=True):
""" Calculates points on a sphere
"""
rnd = 1.
if randomize:
rnd = random.random() * samples

points = []
offset = 2./samples
increment = math.pi * (3. - math.sqrt(5.));

for i in range(samples):
y = ((i * offset) - 1) + (offset / 2);
r = math.sqrt(1 - pow(y,2))

phi = ((i + rnd) % samples) * increment

x = math.cos(phi) * r
z = math.sin(phi) * r

points.append([x,y,z])

return points

class Create_Mesh (Operator):
"""Class used to instance neurons"""
Expand All @@ -6732,9 +6759,7 @@ def make_connector_objects ( neuron_name, connectors_post, connectors_pre, node_
if create_as == 'Curves':
node_list = { n[0]:n[3:6] for n in node_data[0] }
elif create_as == 'Spheres':
pi = np.pi
cos = np.cos
sin = np.sin
points = fibonacci_sphere( 10 )

for i,connector in enumerate( connectors_post ):
if round(i/len(connectors_post)*100,2) % 10 == 0:
Expand All @@ -6750,25 +6775,9 @@ def make_connector_objects ( neuron_name, connectors_post, connectors_pre, node_
co_parent = connectors_post[connector]['parent_node']

if create_as == 'Spheres':
"""
#Generate coords
r = co_size
phi, theta = np.mgrid[0.0:pi:6j, 0.0:2.0*pi:5j]
x = r*sin(phi)*cos(theta)
y = r*sin(phi)*sin(theta)
z = r*cos(phi)
"""

connector_post_ob = bpy.ops.mesh.primitive_ico_sphere_add( subdivisions=1, view_align=False, enter_editmode=False, \
location=co_loc, size = co_size, \
layers=layers)


"""
connector_post_ob = bpy.ops.mesh.primitive_uv_sphere_add(segments=4, ring_count=4, size=co_size, view_align=False, \
enter_editmode=False, location=co_loc, rotation=(0, 0, 0), \
layers=layers)
"""
layers=layers)

bpy.context.active_object.name = 'Post_Connector %s of %s' % (connectors_post[connector]['id'], neuron_name)
bpy.ops.object.shade_smooth()
Expand All @@ -6777,7 +6786,7 @@ def make_connector_objects ( neuron_name, connectors_post, connectors_pre, node_
Create_Mesh.assign_material (bpy.context.active_object, 'PreSynapses_Mat of' + neuron_name, connector_color[0] , connector_color[1] , connector_color[2])
else:
Create_Mesh.assign_material (bpy.context.active_object, None , connector_color[0] , connector_color[1] , connector_color[2])
"""

elif create_as == 'Curves':
co_parent_coords = (
node_list[ co_parent ][0] / conversion_factor,
Expand Down Expand Up @@ -6809,9 +6818,7 @@ def make_connector_objects ( neuron_name, connectors_post, connectors_pre, node_
if unify_materials is False:
Create_Mesh.assign_material ( ob_post , 'PreSynapses_Mat of' + neuron_name, connector_color[0] , connector_color[1] , connector_color[2])
else:
Create_Mesh.assign_material ( ob_post , None , connector_color[0] , connector_color[1] , connector_color[2])
"""

Create_Mesh.assign_material ( ob_post , None , connector_color[0] , connector_color[1] , connector_color[2])

for i, connector in enumerate( connectors_pre ):
if round(i/len(connectors_pre)*100,2) % 10 == 0:
Expand All @@ -6826,12 +6833,7 @@ def make_connector_objects ( neuron_name, connectors_post, connectors_pre, node_
if create_as == 'Spheres':
connector_pre_ob = bpy.ops.mesh.primitive_ico_sphere_add( subdivisions=1, view_align=False, enter_editmode=False, \
location=co_loc, size = co_size, \
layers=layers)
"""
connector_pre_ob = bpy.ops.mesh.primitive_uv_sphere_add(segments=3, ring_count=3, size=co_size, view_align=False, \
enter_editmode=False, location=co_loc, rotation=(0, 0, 0), \
layers=layers)
"""
layers=layers)

bpy.context.active_object.name = 'Pre_Connector %s of %s' % (connectors_pre[connector]['id'], neuron_name)
bpy.ops.object.shade_smooth()
Expand Down Expand Up @@ -6875,7 +6877,7 @@ def make_connector_objects ( neuron_name, connectors_post, connectors_pre, node_
Create_Mesh.assign_material ( ob_pre , None , connector_color[0] , connector_color[1] , connector_color[2])

print('Done in ' + str(time.clock()-start_creation)+'s')
bpy.ops.wm.redraw_timer(type='DRAW_WIN_SWAP',iterations = 1)
bpy.ops.wm.redraw_timer(type='DRAW_WIN_SWAP',iterations = 1)

def make_curve_neuron (neuron_name, root_node, nodes_dic, child_list, soma, skid = '', name = '', resampling = 1, nodes_to_keep = [], radii = {}, strahler_indices = None):
### Creates Neuron from Curve data that was imported from CATMAID
Expand Down Expand Up @@ -11141,7 +11143,7 @@ def get_volume_list(project_id):

global available_volumes

available_volumes = [ ( str( e['id'] ) , e['name'], str( e['comment'] ) ) for e in response ]
available_volumes = [ ('None' , 'None', 'Do not import volume from this list') ] + [ ( str( e['id'] ) , e['name'], str( e['comment'] ) ) for e in response ]

return available_volumes

Expand All @@ -11159,89 +11161,114 @@ class ImportVolume(Operator):
bl_label = "Import volumes from CATMAID"
bl_options = {'UNDO'}

volume = EnumProperty( name='Volume to Import',
volume = EnumProperty( name='Import from List',
items=availableVolumes,
description = 'Select volume to be imported. Will refresh whenever this dialog is opened'
description = 'Select volume to be imported. Will refresh whenever this dialog is opened.'
)

by_name = StringProperty( name='Import by Name',
default = '',
description = 'Name of volume to import.'
)

allow_partial = BoolProperty( name = 'Allow partial match',
default = True,
description = 'If True, name can be a partial match.')

def execute(self,context):
volumes_to_retrieve = []

if self.volume != 'None':
volumes_to_retrieve.append(self.volume)

if self.by_name:
if self.allow_partial:
volumes_to_retrieve += [ v for v in available_volumes if self.by_name.lower() in v[1].lower() ]
else:
volumes_to_retrieve += [ v for v in available_volumes if self.by_name.lower() == v[1].lower() ]

conversion_factor = context.user_preferences.addons['CATMAIDImport'].preferences.conversion_factor

url = remote_instance.get_volume_details( project_id, self.volume )
for vol in volumes_to_retrieve:

response = remote_instance.fetch(url)
url = remote_instance.get_volume_details( project_id, vol[0] )

mesh_string = response['mesh']
mesh_name = response['name']
response = remote_instance.fetch(url)

mesh_type = re.search('<(.*?) ', mesh_string).group(1)
mesh_string = response['mesh']
mesh_name = response['name']

#Now reverse engineer the mesh
if mesh_type == 'IndexedTriangleSet':
t = re.search("index='(.*?)'", mesh_string).group(1).split(' ')
faces = [ ( int( t[i] ), int( t[i+1] ), int( t[i+2] ) ) for i in range( 0, len(t) - 2 , 3 ) ]
mesh_type = re.search('<(.*?) ', mesh_string).group(1)

v = re.search("point='(.*?)'", mesh_string).group(1).split(' ')
vertices = [ ( float( v[i] ), float( v[i+1] ), float( v[i+2] ) ) for i in range( 0, len(v) - 2 , 3 ) ]
#Now reverse engineer the mesh
if mesh_type == 'IndexedTriangleSet':
t = re.search("index='(.*?)'", mesh_string).group(1).split(' ')
faces = [ ( int( t[i] ), int( t[i+1] ), int( t[i+2] ) ) for i in range( 0, len(t) - 2 , 3 ) ]

elif mesh_type == 'IndexedFaceSet':
#For this type, each face is indexed and an index of -1 indicates the end of this face set
t = re.search("coordIndex='(.*?)'", mesh_string).group(1).split(' ')
faces = []
this_face = []
for f in t:
if int(f) != -1:
this_face.append( int(f) )
else:
faces.append( this_face )
this_face = []
v = re.search("point='(.*?)'", mesh_string).group(1).split(' ')
vertices = [ ( float( v[i] ), float( v[i+1] ), float( v[i+2] ) ) for i in range( 0, len(v) - 2 , 3 ) ]

#Make sure the last face is also appended
faces.append( this_face )
elif mesh_type == 'IndexedFaceSet':
#For this type, each face is indexed and an index of -1 indicates the end of this face set
t = re.search("coordIndex='(.*?)'", mesh_string).group(1).split(' ')
faces = []
this_face = []
for f in t:
if int(f) != -1:
this_face.append( int(f) )
else:
faces.append( this_face )
this_face = []

v = re.search("point='(.*?)'", mesh_string).group(1).split(' ')
vertices = [ ( float( v[i] ), float( v[i+1] ), float( v[i+2] ) ) for i in range( 0, len(v) - 2 , 3 ) ]
#Make sure the last face is also appended
faces.append( this_face )

else:
print("Unknown volume type:", mesh_type)
print(mesh_string)
osd.show("Export cancelled - unknown volume type" )
osd_timed = ClearOSDAfter(3)
osd_timed.start()
return{'FINISHED'}
v = re.search("point='(.*?)'", mesh_string).group(1).split(' ')
vertices = [ ( float( v[i] ), float( v[i+1] ), float( v[i+2] ) ) for i in range( 0, len(v) - 2 , 3 ) ]

else:
print("Unknown volume type:", mesh_type)
print(mesh_string)
osd.show("Export cancelled - unknown volume type" )
osd_timed = ClearOSDAfter(3)
osd_timed.start()
return{'FINISHED'}

#For some reason, in this format vertices occur multiple times - we have to collapse that to get a clean mesh
final_faces = []
final_vertices = []
#For some reason, in this format vertices occur multiple times - we have to collapse that to get a clean mesh
final_faces = []
final_vertices = []

for t in faces:
this_faces = []
for v in t:
if vertices[v] not in final_vertices:
final_vertices.append( vertices[v] )

this_faces.append( final_vertices.index( vertices[v] ) )
for t in faces:
this_faces = []
for v in t:
if vertices[v] not in final_vertices:
final_vertices.append( vertices[v] )
this_faces.append( final_vertices.index( vertices[v] ) )

final_faces.append( this_faces )
final_faces.append( this_faces )

print('Volume type:', mesh_type)
print('# of vertices after clean-up:' , len(final_vertices) )
print('# of faces after clean-up:' , len(final_faces) )
print('Volume name:', vol[1])
print('Volume type:', mesh_type)
print('# of vertices after clean-up:' , len(final_vertices) )
print('# of faces after clean-up:' , len(final_faces) )

#Now bring vertices in Blender space
blender_verts = [ ( v[0] / conversion_factor, v[2] / conversion_factor , v[1] / - conversion_factor ) for v in final_vertices ]
#Now bring vertices in Blender space
blender_verts = [ ( v[0] / conversion_factor, v[2] / conversion_factor , v[1] / - conversion_factor ) for v in final_vertices ]

#Now create the mesh
me = bpy.data.meshes.new(mesh_name + '_mesh')
ob = bpy.data.objects.new(mesh_name, me)
#Now create the mesh
me = bpy.data.meshes.new(mesh_name + '_mesh')
ob = bpy.data.objects.new(mesh_name, me)

scn = bpy.context.scene
scn.objects.link(ob)
scn.objects.active = ob
ob.select = True
scn = bpy.context.scene
scn.objects.link(ob)
scn.objects.active = ob
ob.select = True

me.from_pydata(blender_verts, [], final_faces)
me.update()

me.from_pydata(blender_verts, [], final_faces)
me.update()
bpy.ops.object.shade_smooth()

return{'FINISHED'}

Expand All @@ -11259,6 +11286,10 @@ def draw(self,context):
row.label(text="Reconnect to CATMAID server to refresh list")
row = layout.row()
row.prop(self, "volume")
row = layout.row()
row.prop(self, "by_name")
row = layout.row()
row.prop(self, "allow_partial")
"""
def draw(self, context):
layout = self.layout
Expand Down
2 changes: 1 addition & 1 deletion update.txt
View file
Original file line number Diff line number Diff line change
@@ -1,7 +1,7 @@
#Provides current version, last stable version,
#recently added features and a message if need be

current_version = {5.63}
current_version = {5.71}
last_stable = {4.1}
new_features = {UI improvements; code clean-up}
message = {}

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