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Added volume export
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added export of meshes to CATMAID
minor improvements
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@schlegelp
schlegelp committed Nov 3, 2016
1 parent f136122 commit 7422122
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241 changes: 187 additions & 54 deletions CATMAIDImport.py
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Original file line number Diff line number Diff line change
Expand Up @@ -366,19 +366,45 @@ def draw(self, context):

row = layout.row(align=True)
row.alignment = 'EXPAND'
row.operator("check.version", text = "Check Versions", icon ='VISIBLE_IPO_ON')
row.operator("check.version", text = "Check Versions", icon ='VISIBLE_IPO_ON')


layout.label('Calculate Similarity:')
layout.label('CATMAID Import:')

row = layout.row(align=True)
row.alignment = 'EXPAND'
row.operator_context = 'INVOKE_DEFAULT'
row.operator("calc.similarity_modal", text = "Start Calculation", icon ='PARTICLE_PATH')
row.alignment = 'EXPAND'
row.operator("connect.to_catmaid", text = "Connect 2 CATMAID", icon = 'PLUGIN')#.number=1

row = layout.row(align=True)
row.alignment = 'EXPAND'
row.operator("calc.similarity_modal_settings", text = "Settings", icon ='MODIFIER')
row.operator("display.help", text = "", icon ='QUESTION').entry = 'color.by_similarity'

row.operator("retrieve.neuron", text = "Import Neuron(s)", icon = 'ARMATURE_DATA')#.number=1

#row = layout.row(align=True)
#row.alignment = 'EXPAND'
#row.operator("retrieve.by_annotation", text = "Retrieve by Annotation", icon = 'OUTLINER_DATA_FONT')#.number=1

row = layout.row(align=True)
row.alignment = 'EXPAND'
row.operator("retrieve.partners", text = "Retrieve Partners", icon = 'AUTOMERGE_ON')#.number=1

row = layout.row(align=True)
row.alignment = 'EXPAND'
row.operator("retrieve.by_pairs", text = "Retrieve Paired", icon = 'MOD_ARRAY')#.number=1
row.operator("display.help", text = "", icon ='QUESTION').entry = 'retrieve.by_pairs'

row = layout.row(align=True)
row.alignment = 'EXPAND'
row.operator("retrieve.in_volume", text = "Retrieve in Volume", icon = 'BBOX')#.number=1

row = layout.row(align=True)
row.alignment = 'EXPAND'
row.operator("reload.neurons", text = "Reload Neurons", icon = 'FILE_REFRESH')#.number=1

row = layout.row(align=True)
row.alignment = 'EXPAND'
row.operator("retrieve.connectors", text = "Retrieve Connectors", icon = 'PMARKER_SEL')#.number=1
row.operator("display.help", text = "", icon ='QUESTION').entry = 'retrieve.connectors'

layout.label('Materials:')

row = layout.row(align=True)
Expand Down Expand Up @@ -423,66 +449,47 @@ def draw(self, context):
row = layout.row(align=True)
row.alignment = 'EXPAND'
row.operator("for_render.all_materials", text = "Setup 4 Render", icon ='SCENE')


layout.label('CATMAID Import:')

layout.label(text="Export to SVG:")

row = layout.row(align=True)
row.alignment = 'EXPAND'
row.operator("connect.to_catmaid", text = "Connect 2 CATMAID", icon = 'PLUGIN')#.number=1
row.operator("exportall.to_svg", text = 'Export Morphology', icon = 'EXPORT')

row = layout.row(align=True)
row.alignment = 'EXPAND'
row.operator("retrieve.neuron", text = "Import Neuron(s)", icon = 'ARMATURE_DATA')#.number=1

#row = layout.row(align=True)
#row.alignment = 'EXPAND'
#row.operator("retrieve.by_annotation", text = "Retrieve by Annotation", icon = 'OUTLINER_DATA_FONT')#.number=1
row.operator("connectors.to_svg", text = 'Export Connectors', icon = 'EXPORT')

row = layout.row(align=True)
row.alignment = 'EXPAND'
row.operator("retrieve.partners", text = "Retrieve Partners", icon = 'AUTOMERGE_ON')#.number=1
layout.label('Select:')

row = layout.row(align=True)
row.alignment = 'EXPAND'
row.operator("retrieve.by_pairs", text = "Retrieve Paired", icon = 'MOD_ARRAY')#.number=1
row.operator("display.help", text = "", icon ='QUESTION').entry = 'retrieve.by_pairs'
row.operator("select.by_annotation", text = 'By Annotation', icon = 'BORDER_RECT')

row = layout.row(align=True)
row.alignment = 'EXPAND'
row.operator("retrieve.in_volume", text = "Retrieve in Volume", icon = 'BBOX')#.number=1

row = layout.row(align=True)
row.alignment = 'EXPAND'
row.operator("reload.neurons", text = "Reload Neurons", icon = 'FILE_REFRESH')#.number=1
layout.label('Analyze:')

row = layout.row(align=True)
row.alignment = 'EXPAND'
row.operator("retrieve.connectors", text = "Retrieve Connectors", icon = 'PMARKER_SEL')#.number=1
row.operator("display.help", text = "", icon ='QUESTION').entry = 'retrieve.connectors'
row.operator("analyze.statistics", text = 'Get Statistics', icon = 'BORDER_RECT')


layout.label(text="Export to SVG:")

row = layout.row(align=True)
row.alignment = 'EXPAND'
row.operator("exportall.to_svg", text = 'Export Morphology', icon = 'EXPORT')
layout.label('Calculate Similarity:')

row = layout.row(align=True)
row.alignment = 'EXPAND'
row.operator("connectors.to_svg", text = 'Export Connectors', icon = 'EXPORT')

layout.label('Select:')

row.alignment = 'EXPAND'
row.operator_context = 'INVOKE_DEFAULT'
row.operator("calc.similarity_modal", text = "Start Calculation", icon ='PARTICLE_PATH')
row = layout.row(align=True)
row.alignment = 'EXPAND'
row.operator("select.by_annotation", text = 'By Annotation', icon = 'BORDER_RECT')
row.operator("calc.similarity_modal_settings", text = "Settings", icon ='MODIFIER')
row.operator("display.help", text = "", icon ='QUESTION').entry = 'color.by_similarity'

layout.label('Analyze:')
layout.label('Export to CATMAID:')

row = layout.row(align=True)
row.alignment = 'EXPAND'
row.operator("analyze.statistics", text = 'Get Statistics', icon = 'BORDER_RECT')
row.operator("export.volume", text = 'Export Volume', icon = 'BORDER_RECT')


class VersionManager(bpy.types.PropertyGroup):
Expand Down Expand Up @@ -702,6 +709,10 @@ def search_url(self,tag,pid):
def get_skeletons_from_neuron_id(self,neuron_id,pid):
return self.djangourl("/" + str(pid) + "/neuron/" + str(neuron_id) + '/get-all-skeletons' )

#Use to parse url for adding volumes
def add_volume(self, pid):
return self.djangourl("/" + str(pid) + "/volumes/add")

def search_neuron_names(tag, allow_partial = True):
search_url = remote_instance.get_annotated_url( project_id )
annotation_post = { 'name': str(tag) , 'rangey_start': 0, 'range_length':500, 'with_annotations':False }
Expand Down Expand Up @@ -1346,10 +1357,11 @@ def execute(self, context):
retrieve_by_names = [str(e) for e in retrieve_by_names]

if not retrieve_by_names:
print('WARNING: Search tag(s) not found!')
self.report({'ERROR'},'Search tag(s) not found!')
osd.show("WARNING: Search tag(s) not found!")
print('WARNING: Search tag(s) not found! Import stopped')
self.report({'ERROR'},'Search tag(s) not found! Import stopped')
osd.show("WARNING: Search tag(s) not found! Import stopped")
bpy.ops.wm.redraw_timer(type='DRAW_WIN_SWAP', iterations=1)
return{'FINISHED'}

if self.skeleton_ids:
retrieve_by_skids = [x.strip() for x in self.skeleton_ids.split(',')]
Expand All @@ -1358,14 +1370,23 @@ def execute(self, context):
annotations_to_retrieve = [x.strip() for x in self.annotations.split(',')]
retrieve_by_annotations = self.retrieve_annotated( annotations_to_retrieve )

if not retrieve_by_annotations:
print('ERROR: No matching anotation(s) found! Import stopped')
self.report({'ERROR'},'No matching anotation(s) found! Import stopped')
osd.show("ERROR: No matching anotation(s) found! Import stopped")
bpy.ops.wm.redraw_timer(type='DRAW_WIN_SWAP', iterations=1)
return{'FINISHED'}


if self.intersect and self.annotations and self.names:
skeletons_to_retrieve = list( set( [ e for e in retrieve_by_names + retrieve_by_annotations if e in retrieve_by_names and e in retrieve_by_annotations ] + retrieve_by_skids ) )

if not skeletons_to_retrieve:
print('WARNING: No neurons left after intersection!')
self.report({'ERROR'},'Intersection empty!')
osd.show("WARNING: Intersection empty!")
print('WARNING: No neurons left after intersection! Import stopped')
self.report({'ERROR'},'Intersection empty! Import stopped')
osd.show("WARNING: Intersection empty! Import stopped")
bpy.ops.wm.redraw_timer(type='DRAW_WIN_SWAP', iterations=1)
return{'FINISHED'}

else:
skeletons_to_retrieve = list( set( retrieve_by_skids + retrieve_by_names + retrieve_by_annotations ) )
Expand Down Expand Up @@ -1421,11 +1442,7 @@ def retrieve_annotated(self, annotations_to_retrieve):
annotation_ids = [ x['id'] for x in an_list['annotations'] if True in [ y.lower() in x['name'].lower() for y in annotations_to_retrieve ] ]
annotation_names = [ x['name'] for x in an_list['annotations'] if True in [ y.lower() in x['name'].lower() for y in annotations_to_retrieve ] ]

if not annotation_ids:
print('ERROR: No matching anotation(s) found!')
self.report({'ERROR'},'No matching anotation(s) found!')
osd.show("ERROR: No matching anotation(s) found!")
bpy.ops.wm.redraw_timer(type='DRAW_WIN_SWAP', iterations=1)
if not annotation_ids:
return []

#Now retrieve annotated skids
Expand Down Expand Up @@ -10520,6 +10537,122 @@ def execute(self,context):
def invoke(self, context, event):
return context.window_manager.invoke_props_dialog(self, width = 500)

class ExportVolume(Operator):
"""Takes a volume (mesh) and exports it to CATMAID"""
bl_idname = "export.volume"
bl_label = "Export mesh to CATMAID"
bl_options = {'UNDO'}

volume_name = StringProperty( name= 'Name',
default = '',
description = 'Exporte mesh will show up under this name in CATMAID.'
)


def execute(self,context):
conversion_factor = context.user_preferences.addons['CATMAIDImport'].preferences.conversion_factor
obj = bpy.context.active_object

if type(obj) == type(None):
print("No active object found!")
osd.show("No active object found!")
osd_timed = ClearOSDAfter(3)
osd_timed.start()
return{'FINISHED'}

if self.volume_name == '':
print("No name entered! Please enter a name for the volume.")
osd.show("No name entered! Please enter a name for the volume.")
osd_timed = ClearOSDAfter(3)
osd_timed.start()
return{'FINISHED'}

if obj.type != 'MESH':
print("Object to export has to be a MESH!x Active object is %s" % obj.type )
osd.show("Object to export has to be a MESH!x Active object is %s" % obj.type )
osd_timed = ClearOSDAfter(3)
osd_timed.start()
return{'FINISHED'}

#Check if mesh is trimesh:
if [f for f in obj.data.polygons if len(f.vertices) != 3]:
print('Mesh not a trimesh - trying to convert')

#First go out of edit mode and select all vertices while in object mode:
if obj.mode != 'OBJECT':
bpy.ops.object.mode_set(mode='OBJECT')

for v in obj.data.vertices:
v.select = True

#Now go to edit mode and convert to trimesh
bpy.ops.object.mode_set(mode='EDIT')
bpy.ops.mesh.quads_convert_to_tris()
bpy.ops.object.mode_set(mode='OBJECT')

#Check if again mesh is trimesh:
if not [f for f in obj.data.polygons if len(f.vertices) != 3]:
print('MESH successfully converted to trimesh!')
else:
print("Error during conversion to trimesh - try manually!" )
osd.show("Error during conversion to trimesh - try manually!" )
osd_timed = ClearOSDAfter(3)
osd_timed.start()
return{'FINISHED'}

#Now create postdata
verts = [ list(obj.matrix_world * v.co) for v in obj.data.vertices ]
#Multiply by conversion factor, switch y and z coordinates and invert z
verts = [ [ round( v[0] * conversion_factor), round( v[2] * -conversion_factor ) , round ( v[1] * conversion_factor ) ] for v in verts]
faces = [ list(p.vertices) for p in obj.data.polygons ]

mesh = [ verts, faces ]

postdata = {'title': self.volume_name,
'type': 'trimesh',
'mesh': mesh
}

add_volume_url = remote_instance.add_volume( project_id )

response = remote_instance.fetch ( add_volume_url, postdata )

if response['success'] is True:
print("Export successful")
osd.show("Export successful" )
osd_timed = ClearOSDAfter(3)
osd_timed.start()
else:
print("Something went wrong - see console.")
osd.show("Something went wrong - see console." )
print(response)
osd_timed = ClearOSDAfter(3)
osd_timed.start()

return{'FINISHED'}


def invoke(self, context, event):
try:
self.volume_name = bpy.context.active_object.name
except:
pass
return context.window_manager.invoke_props_dialog(self, width = 500)

def draw(self, context):
layout = self.layout
layout.label(text="This will export the ACTIVE object. Will then show up in CATMAID 3D viewer and volume manager.")
layout.label(text="Requires CATMAID version 2016.04.18 or higher. Meshes will be converted into trimesh - please")
layout.label(text="save before clicking OK.")
layout.prop(self, "volume_name")

@classmethod
def poll(cls, context):
if connected:
return True
else:
return False


class DisplayHelp(Operator):
"""Displays popup with additional help"""
Expand Down
2 changes: 1 addition & 1 deletion update.txt
View file
Original file line number Diff line number Diff line change
Expand Up @@ -3,5 +3,5 @@

current_version = {5.5}
last_stable = {4.1}
new_features = {improved neuron import; improved ui; check for CATMAID server version}
new_features = {added volume export;improved neuron import; improved ui; check for CATMAID server version}
message = {}

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