def profileDistances(ID, biniter):
histo=getDendriticProfiles(ID, biniter)
xhisto=histo[0]
yhisto=histo[1]
zhisto=histo[2]
xdistance=[]
ydistance=[]
zdistance=[]
tree = Display.getFront().getLayerSet().findById(ID)
coords = Matrix(getNodeCoordinates(tree))
m=coords.getRowDimension()
for i in range(0, m):
xdist = coords.get(i, 1 )
if xdist > 0 :
xdistance.append(xdist)
else:
xdistance.append((-1)*xdist)
for i in range(0, m):
ydist = coords.get(i, 0 )
if ydist > 0 :
ydistance.append(ydist)
else:
ydistance.append((-1)*ydist)
for i in range(0, m):
zdist = sqrt(coords.get(i, 0)**2 + coords.get(i,1)**2)
zdistance.append(zdist)
return xdistance, ydistance, zdistance
from ini.trakem2.display import Display
from jarray import array
import sys
sys.path.append("/Users/berthola/Desktop/Fiji Scripts")
from matrixoperator import Matrix
from javax.media.j3d import Transform3D
from javax.vecmath import Point3d
from ij.io import FileSaver
from profilingFixedCoordinates import getDendriticProfiles
from profilingFixedCoordinates import getNodeCoordinates
#----------------PLOT histograms-----------------------------------
ID=75408
tree = Display.getFront().getLayerSet().findById(ID)
coords = Matrix(getNodeCoordinates(tree))
#Define axis vectors and origin
xnorm = Matrix([[1,0,0]])
ynorm = Matrix([[0,1,0]])
znorm = Matrix([[0,0,1]])
center= Matrix([[0,0,0]])
#Project nodes onto axis
dpx=[]
dpy=[]
dpz=[]
m=coords.getRowDimension()
for i in range(0, m):
xstore = Matrix([coords.getRow( i )]) * xnorm.transpose()
ystore = Matrix([coords.getRow( i )]) * ynorm.transpose()
def sumDist(id1, biniter):
distance=profileDistances(id1, biniter)
xdistance=distance[0]
ydistance=distance[1]
zdistance=distance[2]
tree = Display.getFront().getLayerSet().findById(id1)
coords = Matrix(getNodeCoordinates(tree))
m=coords.getRowDimension()
xdist=[]
ydist=[]
zdist=[]
#Initialize interval size and fix iterations to a specific coordinate position
xbinleft = -34600.0
ybinleft = -24200.0
zbinleft = 0
#----------PARAMETER FOR MACHINE LEARNING-----
iterations =biniter
#---------------------------------------------
xlength = int((35600.0+34600.0)/iterations + 0.5)
ylength = int((21300.0+24200.0)/iterations + 0.5)
zlength = int((22500)/iterations + 0.5)
xbinright = xbinleft + xlength
ybinright = ybinleft + ylength
zbinright = zbinleft + zlength
sumdist=0.0
for i in range(0, iterations):
for i in range(0, len(xdistance)):
if xdistance[i] <= xbinright and xdistance[i] >= xbinleft:
sumdist += xdistance[i]
xdist.append(sumdist)
sumdist=0.0
xbinleft += xlength
xbinright += xlength
for i in range(0, iterations):
for i in range(0, len(ydistance)):
if ydistance[i] <= ybinright and ydistance[i] >= ybinleft:
sumdist += ydistance[i]
ydist.append(sumdist)
sumdist=0.0
ybinleft += ylength
ybinright += ylength
for i in range(0, iterations):
for i in range(0, len(zdistance)):
if zdistance[i] <= zbinright and zdistance[i] >= zbinleft:
sumdist += zdistance[i]
zdist.append(sumdist)
sumdist=0.0
zbinleft += zlength
zbinright += zlength
sumdistance=[]
sumdistance= [xdist, ydist, zdist]
return sumdistance