search

JaneliaSciComp / Neuroptikon

Neuroptikon
Other
9 stars 3 forks source link

Ring as Parent Region #58

Closed dteinferno closed 9 years ago

dteinferno commented 9 years ago

A created 'Ring' region cannot be set as a parentRegion.

csweaver commented 9 years ago

Could you attach a script so I can replicate the problem? I didn't have any trouble setting the ring in 'Ring Segments.py' to parent.

dteinferno commented 9 years ago

I've commented out the relevant parentRegion code in the EB section (e.g. line 136): '''' #############################################################

Neuroptikon Script for Building the

Drosophila Central Complex

#############################################################

Original by Caleb Goertel, Summer 2014

#############################################################

2014/12/24 - Dan Turner-Evans commented, changed cones to demiwedges, added image upload feature

Import necessary libraries

import sys, os, inspect import math from math import pi

flyBrainOnt = library.ontology('Drosophila adult')

sys.path.append('csv') import csv

#############################################################

Create Main Central Complex Regions and Subregions

#############################################################

Add colors and line widths for the arborizations

regions = {} colors = {} lineweight = {} colors['black'] = (0.0,0.0,0.0) colors['white'] = (1.0,1.0,1.0) colors['red'] = (1.0,0.0,0.0) colors['green'] = (0.0,1.0,0.0) colors['blue'] = (0.0,0.0,1.0) colors['purple'] = (0.5,0.0,0.5) colors['yellow'] = (1.0,1.0,0.0) colors['orange'] = (1.0,165.0/255.0,0.0) colors['gray'] = (0.5,0.5,0.5) colors['grey'] = (0.5,0.5,0.45) colors['pink'] = (1.0,192.0/255.0,203.0/255.0) lineweight['xthin'] = 0.444 lineweight['thin'] = 0.666 lineweight['regular'] = 1.000 lineweight['thick'] = 2.000 lineweight['xthick'] = 5.000

#############################################################

PB

regions['protocerebralBridge'] = network.createRegion(ontologyTerm = flyBrainOnt.findTerm(name = 'Protocerebral bridge')) display.setVisiblePosition(regions['protocerebralBridge'], (0.0,2.00,0.0), True) display.setVisibleSize(regions['protocerebralBridge'], (4.0, 0.35, 0.4)) display.setLabel(regions['protocerebralBridge'], regions['protocerebralBridge'].name) display.setLabelPosition(regions['protocerebralBridge'], (0.0,0.75,0.0)) display.setVisibleColor(regions['protocerebralBridge'],colors['blue'])

Left Side

regions['leftProtocerebralBridge'] = network.createRegion(name = 'Left Protocerebral bridge', parentRegion = regions['protocerebralBridge']) display.setLabel(regions['leftProtocerebralBridge'], '') display.setVisibleColor(regions['leftProtocerebralBridge'],colors['blue']) for i in range (9,0,-1): regions['pbL' + str(i)] = network.createRegion(name = 'PB-L' + str(i), ontologyTerm = flyBrainOnt.findTerm(abbreviation = 'pcb' + str(i)), abbreviation = str(i), parentRegion = regions['leftProtocerebralBridge'])

Right Side

regions['rightProtocerebralBridge'] = network.createRegion(name = 'Right Protocerebral bridge', parentRegion = regions['protocerebralBridge']) display.setLabel(regions['rightProtocerebralBridge'], '') display.setVisibleColor(regions['rightProtocerebralBridge'],colors['blue']) for i in range (1,10): regions['pbR' + str(i)] = network.createRegion(name = 'PB-R' + str(i), ontologyTerm = flyBrainOnt.findTerm(abbreviation = 'pcb' + str(i)), abbreviation = str(i), parentRegion = regions['rightProtocerebralBridge'])

display.setArrangedSpacing(regions['protocerebralBridge'], 0.02, recurse = True)

#############################################################

FB

regions['fanshapedBody'] = network.createRegion(ontologyTerm = flyBrainOnt.findTerm(name = 'Fan-shaped body')) display.setVisiblePosition(regions['fanshapedBody'], (0.0,0.756,0.0),True) display.setVisibleSize(regions['fanshapedBody'], (0.5,0.5,0.3)) display.setVisibleShape(regions['fanshapedBody'], None) display.setLabel(regions['fanshapedBody'], regions['fanshapedBody'].name) display.setLabelPosition(regions['fanshapedBody'], (0.0,-0.15,0.0)) display.setArrangedAxis(regions['fanshapedBody'], None) display.setVisibleColor(regions['fanshapedBody'],colors['red'])

Rows

for i in range (9,0,-1): regions['fbL' + str(i)] = network.createRegion(name = 'FB layer ' + str(i), abbreviation = str(i), parentRegion = regions['fanshapedBody']) layerheight = (i-1)_.2 display.setVisiblePosition(regions['fbL' + str(i)], (0,layerheight,0), True) if i == 9: layerwidth = 1.25 elif i == 8: layerwidth = 3 else: layerwidth = 0.75_i display.setVisibleSize(regions['fbL' + str(i)], (layerwidth,0.15,0.3)) display.setVisibleShape(regions['fbL'+ str(i)], shapes['Box']) display.setArrangedAxis(regions['fbL' + str(i)], 'X') display.setVisibleColor(regions['fbL' + str(i)],colors['red'])

Columns

for i in range(5,0,-1): if i == 1: j = 10 else: j = 9 for k in range(1,j): regions['fbL' + str(i) + 'C' + str(k)] = network.createRegion(name ='FBl' + str(i) + str(k), parentRegion = regions['fbL' + str(i)]) display.setLabel(regions['fbL' + str(i) + 'C' + str(k)], '') display.setArrangedSpacing(regions['fbL' + str(i)], 0.02)

#############################################################

EB

regions['ellipsoidBody'] = network.createRegion(ontologyTerm = flyBrainOnt.findTerm(name = 'Ellipsoid Body')) display.setVisiblePosition(regions['ellipsoidBody'], (0.0,-0.5,0.0), True) display.setVisibleShape(regions['ellipsoidBody'], shapes['Ring'](holeSize = 0.0/5.0)) display.setVisibleSize(regions['ellipsoidBody'], (1.4, 1.4,0.7)) display.setVisibleOpacity(regions['ellipsoidBody'], 0.33) display.setLabel(regions['ellipsoidBody'], regions['ellipsoidBody'].name) display.setLabelPosition(regions['ellipsoidBody'], (0.0,-0.6,0.0)) display.setArrangedAxis(regions['ellipsoidBody'], None) display.setVisibleColor(regions['ellipsoidBody'],colors['orange'])

Tiles

letters = ['G','F','E','D','C','B','A','H'] for i in range(0,8): regions['ebT' + letters[i]] = network.createRegion(name = 'EBtile' + letters[i], abbreviation = letters[i])#, parentRegion = regions['ellipsoidBody']) angles = [0, pi/4.00, pi/2.00, 3.00_pi/4.00, pi, 5.00_pi/4.00, 3.00_pi/2.00,7.00_pi/4.00] theta = angles[i] xpos = 0.7_math.cos(theta) ypos = 0.7_math.sin(theta) display.setVisiblePosition(regions['ebT' + letters[i]], (xpos, ypos-0.5, -0.25), True) display.setVisibleShape(regions['ebT' + letters[i]], shapes['Ring'](holeSize = 0.5 / 5.0, startAngle=ipi/4-pi/8, endAngle=%28i+1%29pi/4-pi/8)) display.setVisibleSize(regions['ebT' + letters[i]], (0.6, 0.6, 0.25)) display.setLabel(regions['ebT' + letters[i]], letters[i]) display.setVisibleColor(regions['ebT' + letters[i]],colors['orange'])

Wedges and Demiwedges

names = ['3L','6R','4L','5R','5L','4R','6L','3R','7L','2R','8L','1R','1L','8R','2L','7R'] for i in range(0,16): regions['ebW' + names[i]] = network.createRegion(name = 'EBwedge' + names[i], abbreviation = names[i])#, parentRegion = regions['ellipsoidBody']) angle = math.radians(11.25 + (22.5_i)) xpos = 0.8_math.cos(angle) ypos = 0.8_math.sin(angle)-0.5 display.setVisiblePosition(regions['ebW' + names[i]], (xpos,ypos,0.35), True) display.setVisibleShape(regions['ebW' + names[i]], shapes['Ring'](holeSize = 0.5 / 5.0, startAngle=i*pi/8, endAngle=(i+1)_pi/8)) display.setVisibleSize(regions['ebW' + names[i]], (0.8, 0.8, 0.25)) display.setLabel(regions['ebW' + names[i]], names[i]) display.setVisibleOpacity(regions['ebW' + names[i]], 0.65) display.setVisibleColor(regions['ebW' + names[i]],colors['orange'])

for j in range(1,3):

regions['ebW' + names[i]+str(j)]= network.createRegion(name = 'EBwedge'+names[i]+str(j), abbreviation = names[i] + str(j), parentRegion = regions['ebW' + names[i]])

angle = math.radians(22.5_i+11.25_j)

xpos = 0.70_math.cos(angle)

ypos = 0.70_math.sin(angle)-0.5

display.setVisiblePosition(regions['ebW' + names[i]], (xpos,ypos,0.35), True)

display.setVisibleSize(regions['ebW' + names[i]+str(j)], (0.90, 0.9, 0.25))

display.setLabel(regions['ebW' + names[i]+str(j)], '')

display.setVisibleShape(regions['ebW' + names[i]], shapes['Ring'](holeSize = 0.5 / 5.0, startAngle=ipi/8+%28j-1%29pi/16, endAngle=%28i+1%29pi/8+%28j-1%29pi/16))

Rings

namesRing = ['1','2','3']

for i in range(0,3): regions['ebRing' + namesRing[i]] = network.createRegion(name = 'EB Ring' + namesRing[i], abbreviation = 'ring' + namesRing[i])#, parentRegion = regions['ellipsoidBody']) display.setVisiblePosition(regions['ebRing' + namesRing[i]], (0.0,-0.5,0.15), True) display.setVisibleShape(regions['ebRing' + namesRing[i]], shapes['Ring'](holeSize = %28i+1%29/2.5)) display.setVisibleSize(regions['ebRing' + namesRing[i]], (1.4(i+1)/3, 1.4(i+1)/3,0.4)) display.setLabel(regions['ebRing' + namesRing[i]], regions['ebRing' + namesRing[i]].name) display.setLabelPosition(regions['ebRing' + namesRing[i]], (0.0,-0.6,-0.4))

display.setVisibleOpacity(regions['ebRing' + namesRing[i]], 0.65)

display.setArrangedAxis(regions['ebRing' + namesRing[i]], None)
display.setVisibleColor(regions['ebRing' + namesRing[i]],colors['orange'])

Nubbin and Posterior

regions['EBnubbin'] = network.createRegion(name = 'EB Nubbin', abbreviation = 'Nub')#, parentRegion = regions['ellipsoidBody']) display.setVisiblePosition(regions['EBnubbin'], (0.0,0.09,-0.8), True) display.setVisibleShape(regions['EBnubbin'], shapes['Ball']) display.setVisibleSize(regions['EBnubbin'], (0.75,0.25,0.25)) display.setLabel(regions['EBnubbin'], 'EB Nubbin') display.setVisibleColor(regions['EBnubbin'],colors['orange'])

regions['EBP'] = network.createRegion(name = 'EB Posterior Shell', abbreviation = 'EBP')#, parentRegion = regions['ellipsoidBody'])

display.setVisiblePosition(regions['EBP'], (0.0,-0.5,-0.6), True)

display.setVisibleSize(regions['EBP'], (0.6,0.6,0.1))

display.setVisibleShape(regions['EBP'], shapes['Capsule'])

display.setLabel(regions['EBP'], '')

#############################################################

NO

regions['leftnoduli'] = network.createRegion(name = 'Left Noduli') display.setVisiblePosition(regions['leftnoduli'], (-1.9,-1.8, 0.0), True) display.setVisibleSize(regions['leftnoduli'], (0.5,1.0,0.3)) display.setArrangedAxis(regions['leftnoduli'], 'Y') display.setLabel(regions['leftnoduli'], '') display.setVisibleColor(regions['leftnoduli'],colors['green'])

regions['leftnoduli1'] = network.createRegion(name = 'Left Noduli 1', abbreviation = 'NO1', parentRegion = regions['leftnoduli']) display.setLabel(regions['leftnoduli1'], 'NO1') display.setLabelPosition(regions['leftnoduli1'], (-0.8,0.0,0.0)) display.setArrangedAxis(regions['leftnoduli1'], 'X')

regions['LNO1L'] = network.createRegion(name = 'Left Noduli 1 Lateral', abbreviation = 'LNO1L', parentRegion = regions['leftnoduli1']) display.setLabel(regions['LNO1L'], 'L')

regions['LNO1M'] = network.createRegion(name = 'Left Noduli 1 Medial', abbreviation = 'LNO1M', parentRegion = regions['leftnoduli1']) display.setLabel(regions['LNO1M'], 'M')

display.setArrangedSpacing(regions['leftnoduli1'], 0.05)

regions['leftnoduli2'] = network.createRegion(name = 'Left Noduli 2', abbreviation = 'NO2', parentRegion = regions['leftnoduli']) display.setLabel(regions['leftnoduli2'], 'NO2') display.setLabelPosition(regions['leftnoduli2'], (-0.8,0.0,0.0)) display.setArrangedAxis(regions['leftnoduli2'], 'Y')

regions['LNO2D'] = network.createRegion(name = 'Left Noduli 2 Dorsal', abbreviation = 'LNO2D', parentRegion = regions['leftnoduli2']) display.setLabel(regions['LNO2D'], 'D')

regions['LNO2V'] = network.createRegion(name = 'Left Noduli 2 Ventral', abbreviation = 'LNO2V', parentRegion = regions['leftnoduli2']) display.setLabel(regions['LNO2V'], 'V')

display.setArrangedSpacing(regions['leftnoduli1'], 0.05)

regions['leftnoduli3'] = network.createRegion(name = 'Left Noduli 3', abbreviation = 'NO3', parentRegion = regions['leftnoduli']) display.setLabel(regions['leftnoduli3'], 'NO3') display.setLabelPosition(regions['leftnoduli3'], (-0.8, 0.0, 0.0)) display.setArrangedAxis(regions['leftnoduli3'], 'Z')

regions['LNO3A'] = network.createRegion(name = 'Left Noduli 3 Anterior', abbreviation = 'LNO3A', parentRegion = regions['leftnoduli3']) display.setLabel(regions['LNO3A'], 'A')

regions['LNO3M'] = network.createRegion(name = 'Left Noduli 3 Medial', abbreviation = 'LNO3A', parentRegion = regions['leftnoduli3']) display.setLabel(regions['LNO3M'], 'M')

regions['LNO3P'] = network.createRegion(name = 'Left Noduli 3 Posterior', abbreviation = 'LNO3P', parentRegion = regions['leftnoduli3']) display.setLabel(regions['LNO3P'], 'P')

display.setArrangedSpacing(regions['leftnoduli3'], 0.05)

regions['rightnoduli'] = network.createRegion(name = 'right Noduli') display.setVisiblePosition(regions['rightnoduli'], (1.9,-1.8, 0.0), True) display.setVisibleSize(regions['rightnoduli'], (0.5,1.0,0.3)) display.setArrangedAxis(regions['rightnoduli'], 'Y') display.setLabel(regions['rightnoduli'], '') display.setVisibleColor(regions['rightnoduli'],colors['green'])

regions['rightnoduli1'] = network.createRegion(name = 'right Noduli 1', abbreviation = 'NO1', parentRegion = regions['rightnoduli']) display.setLabel(regions['rightnoduli1'], 'NO1') display.setLabelPosition(regions['rightnoduli1'], (0.8,0.0,0.0)) display.setArrangedAxis(regions['rightnoduli1'], 'X')

regions['RNO1L'] = network.createRegion(name = 'right Noduli 1 Lateral', abbreviation = 'RNO1L', parentRegion = regions['rightnoduli1']) display.setLabel(regions['RNO1L'], 'L')

regions['RNO1M'] = network.createRegion(name = 'right Noduli 1 Medial', abbreviation = 'RNO1M', parentRegion = regions['rightnoduli1']) display.setLabel(regions['RNO1M'], 'M')

display.setArrangedSpacing(regions['rightnoduli1'], 0.05)

regions['rightnoduli2'] = network.createRegion(name = 'right Noduli 2', abbreviation = 'NO2', parentRegion = regions['rightnoduli']) display.setLabel(regions['rightnoduli2'], 'NO2') display.setLabelPosition(regions['rightnoduli2'], (0.8,0.0,0.0)) display.setArrangedAxis(regions['rightnoduli2'], 'Y')

regions['RNO2D'] = network.createRegion(name = 'right Noduli 2 Dorsal', abbreviation = 'RNO2D', parentRegion = regions['rightnoduli2']) display.setLabel(regions['RNO2D'], 'D')

regions['RNO2V'] = network.createRegion(name = 'right Noduli 2 Ventral', abbreviation = 'RNO2V', parentRegion = regions['rightnoduli2']) display.setLabel(regions['RNO2V'], 'V')

display.setArrangedSpacing(regions['rightnoduli2'], 0.05)

regions['rightnoduli3'] = network.createRegion(name = 'right Noduli 3', abbreviation = 'NO3', parentRegion = regions['rightnoduli']) display.setLabel(regions['rightnoduli3'], 'NO3') display.setLabelPosition(regions['rightnoduli3'], (0.8, 0.0, 0.0)) display.setArrangedAxis(regions['rightnoduli3'], 'Z')

regions['RNO3A'] = network.createRegion(name = 'right Noduli 3 Anterior', abbreviation = 'RNO3A', parentRegion = regions['rightnoduli3']) display.setLabel(regions['RNO3A'], 'A')

regions['RNO3M'] = network.createRegion(name = 'right Noduli 3 Medial', abbreviation = 'RNO3A', parentRegion = regions['rightnoduli3']) display.setLabel(regions['RNO3M'], 'M')

regions['RNO3P'] = network.createRegion(name = 'right Noduli 3 Posterior', abbreviation = 'RNO3P', parentRegion = regions['rightnoduli3']) display.setLabel(regions['RNO3P'], 'P')

display.setArrangedSpacing(regions['rightnoduli3'], 0.05)

#############################################################

Other

Lateral Triangles

regions['llateraltriangle'] = network.createRegion(name = 'Left Lateral Triangle', abbreviation = 'LT') display.setVisiblePosition(regions['llateraltriangle'], (-1.9, -0.5,0.0), True) display.setVisibleSize(regions['llateraltriangle'], (0.5,0.8,0.2)) display.setVisibleShape(regions['llateraltriangle'], shapes['Cone']) display.setLabel(regions['llateraltriangle'], 'LT') display.setVisibleRotation(regions['llateraltriangle'], (1,0,0,pi))

regions['rlateraltriangle'] = network.createRegion(name = 'Right Lateral Triangle', abbreviation = 'LT') display.setVisiblePosition(regions['rlateraltriangle'], (1.9, -0.5,0.0), True) display.setVisibleSize(regions['rlateraltriangle'], (0.5,0.8,0.2)) display.setVisibleShape(regions['rlateraltriangle'], shapes['Cone']) display.setLabel(regions['rlateraltriangle'], 'LT') display.setVisibleRotation(regions['rlateraltriangle'], (1,0,0,pi))

Gall and subcompartments

regions['rightgall'] = network.createRegion(name = 'rightgall', abbreviation = 'G') display.setVisiblePosition(regions['rightgall'], (2.75,-0.5,0.0),True) display.setVisibleSize(regions['rightgall'], (0.25,0.5,0.4)) display.setLabel(regions['rightgall'], 'Gall') display.setLabelPosition(regions['rightgall'], (0.0,0.76,0.0)) display.setArrangedAxis(regions['rightgall'], 'Y')

regions['RGallT'] = network.createRegion(name = 'rightgall Tip', abbreviation = 'T', parentRegion = regions['rightgall']) regions['RGallD'] = network.createRegion(name = 'Dorsal rightgall', abbreviation = 'D', parentRegion = regions['rightgall']) regions['RGallV'] = network.createRegion(name = 'Ventral rightgall', abbreviation = 'V', parentRegion = regions['rightgall'])

display.setArrangedSpacing(regions['rightgall'], 0.05)

regions['leftgall'] = network.createRegion(name = 'leftgall', abbreviation = 'G') display.setVisiblePosition(regions['leftgall'], (-2.75,-0.5,0.0),True) display.setVisibleSize(regions['leftgall'], (0.25,0.5,0.4)) display.setLabel(regions['leftgall'], 'Gall') display.setLabelPosition(regions['leftgall'], (0.0,0.76,0.0)) display.setArrangedAxis(regions['leftgall'], 'Y')

regions['LGallT'] = network.createRegion(name = 'leftgall Tip', abbreviation = 'T', parentRegion = regions['leftgall']) regions['LGallD'] = network.createRegion(name = 'Dorsal leftgall', abbreviation = 'D', parentRegion = regions['leftgall']) regions['LGallV'] = network.createRegion(name = 'Ventral leftgall', abbreviation = 'V', parentRegion = regions['leftgall'])

display.setArrangedSpacing(regions['leftgall'], 0.05)

Gall-surround

regions['leftgallsurround'] = network.createRegion(name = 'left gall surround', abbreviation = 'GS') display.setVisiblePosition(regions['leftgallsurround'], (-2.55, -0.5,0.0), True) display.setVisibleSize(regions['leftgallsurround'], (0.1,0.5,0.4)) display.setArrangedAxis(regions['leftgallsurround'], 'Y') display.setLabel(regions['leftgallsurround'], '')

regions['leftDgallsurround'] = network.createRegion(name = 'left dorsal gall surround', abbreviation = 'DGS', parentRegion = regions['leftgallsurround']) regions['leftVgallsurround'] = network.createRegion(name = 'left ventral gall surround', abbreviation = 'VGS', parentRegion = regions['leftgallsurround'])

display.setArrangedSpacing(regions['leftgallsurround'], 0.05)

regions['rightgallsurround'] = network.createRegion(name = 'right gall surround', abbreviation = 'GS') display.setVisiblePosition(regions['rightgallsurround'], (2.55, -0.5,0.0), True) display.setVisibleSize(regions['rightgallsurround'], (0.1,0.5,0.4)) display.setArrangedAxis(regions['rightgallsurround'], 'Y') display.setLabel(regions['rightgallsurround'], '')

regions['rightDgallsurround'] = network.createRegion(name = 'right dorsal gall surround', abbreviation = 'DGS', parentRegion = regions['rightgallsurround']) regions['rightVgallsurround'] = network.createRegion(name = 'right ventral gall surround', abbreviation = 'VGS', parentRegion = regions['rightgallsurround'])

display.setArrangedSpacing(regions['rightgallsurround'], 0.05)

Lateral Accessory Lobe

regions['rightLAL'] = network.createRegion(name = 'rightLAL') display.setVisiblePosition(regions['rightLAL'], (3.2,-0.5,0.0),True) display.setVisibleSize(regions['rightLAL'], (0.75, 0.8, 0.65)) display.setVisibleShape(regions['rightLAL'], shapes['Capsule']) display.setLabel(regions['rightLAL'], 'LAL') display.setLabelPosition(regions['rightLAL'], (0.0,-0.55,0.0))

regions['leftLAL'] = network.createRegion(name = 'leftLAL') display.setVisiblePosition(regions['leftLAL'], (-3.2,-0.5,0.0),True) display.setVisibleSize(regions['leftLAL'], (0.75, 0.8, 0.65)) display.setVisibleShape(regions['leftLAL'], shapes['Capsule']) display.setLabel(regions['leftLAL'], 'LAL') display.setLabelPosition(regions['leftLAL'], (0.0,-0.55,0.0))

Bulb

regions['rightbulb'] = network.createRegion(name = 'right Bulb') display.setVisiblePosition(regions['rightbulb'], (3.2,-0.25, -0.125), True) display.setVisibleSize(regions['rightbulb'], (0.4,0.6,0.3)) display.setVisibleShape(regions['rightbulb'], shapes['Ball']) display.setLabel(regions['rightbulb'], 'BU') display.setLabelPosition(regions['rightbulb'], (0.0,0.55,0.0))

regions['leftbulb'] = network.createRegion(name = 'left Bulb') display.setVisiblePosition(regions['leftbulb'], (-3.2,-0.25, -0.125), True) display.setVisibleSize(regions['leftbulb'], (0.4,0.6,0.3)) display.setVisibleShape(regions['leftbulb'], shapes['Ball']) display.setLabel(regions['leftbulb'], 'BU') display.setLabelPosition(regions['leftbulb'], (0.0,0.55,0.0))

Crepine and Rubus

regions['rightcrepine'] = network.createRegion(name = 'right crepine', abbreviation = 'CRE') display.setVisiblePosition(regions['rightcrepine'], (2.2, 0.95, 0.2), True) display.setVisibleSize(regions['rightcrepine'], (1.00,1.00,1.00)) display.setVisibleShape(regions['rightcrepine'], shapes['Ball']) display.setLabel(regions['rightcrepine'], 'CRE') display.setLabelPosition(regions['rightcrepine'], (0.0,0.6,0.0))

regions['rightrubus'] = network.createRegion(name = 'right rubus')#, parentRegion = regions['rightcrepine']) display.setVisiblePosition(regions['rightrubus'], (2.2, 0.95, 0.7), True) display.setVisibleSize(regions['rightrubus'], (0.65,0.65,0.65)) display.setVisibleShape(regions['rightrubus'], shapes['Ball']) display.setLabel(regions['rightrubus'], 'RB')

regions['leftcrepine'] = network.createRegion(name = 'left crepine', abbreviation = 'CRE') display.setVisiblePosition(regions['leftcrepine'], (-2.2, 0.95, 0.2), True) display.setVisibleSize(regions['leftcrepine'], (1.00,1.00,1.00)) display.setVisibleShape(regions['leftcrepine'], shapes['Ball']) display.setLabel(regions['leftcrepine'], 'CRE') display.setLabelPosition(regions['leftcrepine'], (0.0,0.6,0.0))

regions['leftrubus'] = network.createRegion(name = 'left rubus')#, parentRegion = regions['leftcrepine']) display.setVisiblePosition(regions['leftrubus'], (-2.2, 0.95, 0.7), True) display.setVisibleSize(regions['leftrubus'], (0.65,0.65,0.65)) display.setVisibleShape(regions['leftrubus'], shapes['Ball']) display.setLabel(regions['leftrubus'], 'RB')

Inferior Bridge

regions['inferiorBridge'] = network.createRegion(name = 'Inferior Bridge', abbreviation = 'IB') display.setVisiblePosition(regions['inferiorBridge'], (0.0,-2.05, -0.5), True) display.setVisibleSize(regions['inferiorBridge'], (1.35, 0.7, 0.6)) display.setVisibleShape(regions['inferiorBridge'], shapes['Capsule']) display.setLabel(regions['inferiorBridge'], regions['inferiorBridge'].name)

Posterior Slope

regions['LPS'] = network.createRegion(name = 'Left Posterior Slope', abbreviation = 'LPS') display.setVisiblePosition(regions['LPS'], (-2.2,-3.2,0.0), True) display.setVisibleSize(regions['LPS'], (1.1,1.1,1.1)) display.setArrangedAxis(regions['LPS'], 'Y') display.setLabel(regions['LPS'], '')

regions['LSPS'] = network.createRegion(name = 'Left Superior Posterior Slope', abbreviation = 'LSPS', parentRegion = regions['LPS']) display.setLabel(regions['LSPS'], 'SPS')

regions['LIPS'] = network.createRegion(name = 'Left Inferior Posterior Slope', abbreviation = 'LIPS', parentRegion = regions['LPS']) display.setLabel(regions['LIPS'], 'IPS')

display.setArrangedSpacing(regions['LPS'], 0.05)

regions['RPS'] = network.createRegion(name = 'Right Posterior Slope', abbreviation = 'RPS') display.setVisiblePosition(regions['RPS'], (2.2,-3.2,0.0), True) display.setVisibleSize(regions['RPS'], (1.1,1.1,1.1)) display.setArrangedAxis(regions['RPS'], 'Y') display.setLabel(regions['RPS'], '')

regions['RSPS'] = network.createRegion(name = 'Right Superior Posterior Slope', abbreviation = 'RSPS', parentRegion = regions['RPS']) display.setLabel(regions['RSPS'], 'SPS')

regions['RIPS'] = network.createRegion(name = 'Right Inferior Posterior Slope', abbreviation = 'RIPS', parentRegion = regions['RPS']) display.setLabel(regions['RIPS'], 'IPS')

display.setArrangedSpacing(regions['RPS'], 0.05)

Protocerebrum

regions['rdlProtocerebrum'] = network.createRegion(name = 'Right Dorso-lateral Protocerebrum', abbreviation = 'RDLP') display.setVisiblePosition(regions['rdlProtocerebrum'], (0.5,2.75,0.0), True) display.setVisibleSize(regions['rdlProtocerebrum'], (0.4, 0.4, 0.4))

regions['dfProtocerebrum'] = network.createRegion(name = 'Dorso-Frontal Protocerebrum', abbreviation = 'DFP') display.setVisiblePosition(regions['dfProtocerebrum'], (0.0,2.75,0.0), True) display.setVisibleSize(regions['dfProtocerebrum'], (0.4, 0.4, 0.4))

regions['ldlProtocerebrum'] = network.createRegion(name = 'Left Dorso-lateral Protocerebrum', abbreviation = 'LDLP') display.setVisiblePosition(regions['ldlProtocerebrum'], (-0.5,2.75,0.0), True) display.setVisibleSize(regions['ldlProtocerebrum'], (0.4, 0.4, 0.4))

#############################################################

Create Neurons and Arborizations

#############################################################

csvfile = open('arborizationdata.csv', 'rU') arborizationFile = csv.reader(csvfile) neurons = {}

for row in arborizationFile: columncount = 0

for column in row:
    if column == '':
        columncount += 1
    elif columncount == 0:
        neuron = network.createNeuron(name = column, abbreviation = row[(columncount + 1)], neuronImage=row[(columncount+4)])
        columncount += 1
    elif columncount == 1:
        columncount += 1
    elif columncount == 2:    
        color = colors[column]
        columncount+= 1
    elif columncount == 3:
        weight = lineweight[column]
        columncount += 1            
    elif columncount == 4:
        columncount += 1               
    elif columncount%2 == 0:
        columncount += 1

    elif columncount%2 == 1:

        if column == 'STOP':

            columncount = 0

        else:
            if row[(columncount + 1)] == '.ps':
                sendsOutput = True
                receivesInput = False
            elif row[(columncount + 1)] == '.d':
                receivesInput = True
                sendsOutput = False
            elif row[(columncount + 1)] == '.ps.d':
                receivesInput = True
                sendsOutput = True

            arborization = neuron.arborize(regions[column], sendsOutput, receivesInput)
            display.setVisibleColor(arborization, color)
            display.setVisibleWeight(arborization, weight)
            columncount += 1

display.autoLayout() display.setLabelsFloatOnTop(True)

''''

csweaver commented 9 years ago

I've checked in code that fixes the issue.

You will probably need to edit your script to reposition the child shapes. For example for the tiles section of code I had to modify the x and y to the following:

xpos = 0.5*math.cos(theta)
ypos = 0.5 + 0.5*math.sin(theta)