allLines = infile.readlines()
pointLine = False
cleanLines = [x.strip() for x in allLines]
for line in cleanLines:
if line is '{':
pointLine = True
elif line is '}':
pointLine = False
pass
elif pointLine:
ptList.append(map(float, line.split(' ')))
else:
pass
ptList
s1 = Shape(ptList)
f, ((ax1, ax2), (ax3, ax4)) = plt.subplots(2, 2)
## Original shape (input)
cmShape = ASM.centroid(s1)
plotAll(ax1, s1)
############## Calc transformations ###################
## Translate
t = [[-cmShape.x], [-cmShape.y]]
for pt in s1.shapePoints:
pt.translate(t)
s1.update()
plotAll(ax2, s1)
from ActiveShapeModels import ASM, Point, Shape
import matplotlib.pyplot as plt
import seaborn as sns
import math
import numpy as np
s1 = Shape([Point(200, 300), Point(100, 200), Point(300, 50)])
s2 = Shape([Point(150, 250), Point(50, 100), Point(250, 0)])
f, ((ax1, ax2), (ax3, ax4)) = plt.subplots(2, 2, sharex=True, sharey=True)
s1.draw(sns.xkcd_palette(["light blue"]), ax1)
s2.draw(sns.xkcd_palette(["light blue"]), ax2)
cmShape = ASM.centroid(s1)
cmMeanShape = ASM.centroid(s2)
ax1.scatter(cmShape.x, cmShape.y, c='r')
ax2.scatter(cmMeanShape.x, cmMeanShape.y, c='r')
ax1.plot([s1.shapePoints[0].x, s1.shapePoints[1].x],
[s1.shapePoints[0].y, s1.shapePoints[1].y],
color='r',
ls='-')
ax2.plot([s2.shapePoints[0].x, s2.shapePoints[1].x],
[s2.shapePoints[0].y, s2.shapePoints[1].y],
color='r',
lw=1,
ls='-')
t = [[cmShape.x - cmMeanShape.x], [cmShape.y - cmMeanShape.y]]
from ActiveShapeModels import ASM, Point, Shape
import matplotlib.pyplot as plt
import seaborn as sns
import math
import numpy as np
s1 = Shape( [ Point(200,300), Point(100, 200), Point(300, 50 ) ] )
s2 = Shape( [ Point(150,250), Point(50, 100 ), Point(250, 0) ] )
f, ((ax1,ax2),(ax3,ax4)) = plt.subplots(2,2, sharex =True, sharey = True)
s1.draw( sns.xkcd_palette( ["light blue" ]), ax1)
s2.draw( sns.xkcd_palette( ["light blue"] ), ax2)
cmShape = ASM.centroid( s1)
cmMeanShape = ASM.centroid( s2 )
ax1.scatter( cmShape.x, cmShape.y, c='r')
ax2.scatter( cmMeanShape.x, cmMeanShape.y, c='r')
ax1.plot( [s1.shapePoints[0].x, s1.shapePoints[1].x],
[s1.shapePoints[0].y, s1.shapePoints[1].y],
color= 'r', ls = '-')
ax2.plot( [s2.shapePoints[0].x, s2.shapePoints[1].x],
[s2.shapePoints[0].y, s2.shapePoints[1].y],
color= 'r', lw = 1, ls = '-')
from ActiveShapeModels import ASM, Point, Shape
import matplotlib.pyplot as plt
import seaborn as sns
import math
import numpy as np
#s1 = Shape( [ Point(200,300), Point(100, 200), Point(300, 50 ) ] )
#s2 = Shape( [ Point(150,250), Point(50, 100 ), Point(250, 0) ] )
s1 = Shape( [ Point(857, -129), Point(89,-409), Point(-404,254), Point( 96,957), Point(877,712) ])
f, ((ax1,ax2),(ax3,ax4)) = plt.subplots(2,2)
s1.draw( sns.xkcd_palette( ["light blue" ]), 0, ax1)
#s2.draw( sns.xkcd_palette( ["light blue"] ), ax2)
cmShape = ASM.centroid( s1 )
#cmMeanShape = ASM.centroid( s2 )
ax1.scatter( cmShape.x, cmShape.y, c='r')
#ax2.scatter( cmMeanShape.x, cmMeanShape.y, c='r')
ax1.plot( [s1.shapePoints[0].x, s1.shapePoints[1].x],
[s1.shapePoints[0].y, s1.shapePoints[1].y],
color= 'r', ls = '-')
#ax2.plot( [s2.shapePoints[0].x, s2.shapePoints[1].x],
# [s2.shapePoints[0].y, s2.shapePoints[1].y],
# color= 'r', lw = 1, ls = '-')
from ActiveShapeModels import ASM, Point, Shape
import matplotlib.pyplot as plt
import seaborn as sns
import math
import numpy as np
#s1 = Shape( [ Point(200,300), Point(100, 200), Point(300, 50 ) ] )
#s2 = Shape( [ Point(150,250), Point(50, 100 ), Point(250, 0) ] )
s1 = Shape([
Point(857, -129),
Point(89, -409),
Point(-404, 254),
Point(96, 957),
Point(877, 712)
])
f, ((ax1, ax2), (ax3, ax4)) = plt.subplots(2, 2)
s1.draw(sns.xkcd_palette(["light blue"]), 0, ax1)
#s2.draw( sns.xkcd_palette( ["light blue"] ), ax2)
cmShape = ASM.centroid(s1)
#cmMeanShape = ASM.centroid( s2 )
ax1.scatter(cmShape.x, cmShape.y, c='r')
#ax2.scatter( cmMeanShape.x, cmMeanShape.y, c='r')
ax1.plot([s1.shapePoints[0].x, s1.shapePoints[1].x],
[s1.shapePoints[0].y, s1.shapePoints[1].y],
color='r',
ls='-')
def calcMeanShape(self):
xList = [el.xs for el in self.allShapes]
yList = [el.ys for el in self.allShapes]
meanPointsList = zip(np.mean(xList, 0), np.mean(yList, 0))
self.meanShape = Shape(meanPointsList)
class ASMB(object):
def __init__(self, refIndices, numIterations):
self.allShapes = []
self.n = 0
self.refIxs = refIndices
self.nIters = numIterations
@property
def I(self):
return len(self.allShapes)
def addShape(self, s):
if len(self.allShapes) == 0:
self.allShapes.append(s)
self.n = s.n
else:
assert (s.n == self.n)
self.allShapes.append(s)
@property
def V(self):
"""
Variance in distance matrix amongst all shapes
"""
V = []
for k in range(self.n):
row = []
for l in range(self.n):
col = []
for i in range(len(self.allShapes)):
col.append(self.allShapes[i].R[k][l])
row.append(np.var(col))
V.append(row)
return V
@property
def W(self):
"""
Point weights as diagonal matrix
"""
return np.diag(self.w)
@property
def w(self):
"""
Point weights as array
"""
s = map(sum, self.V)
return [math.pow(j, -1) for j in s]
def Zgen(self, shape):
return sum([
self.w[k] * (shape.xs[k]**2 + shape.xs[k]**2)
for k in range(self.n)
])
def Xgen(self, shape):
return sum([self.w[k] * shape.xs[k] for k in range(self.n)])
def Ygen(self, shape):
return sum([self.w[k] * shape.ys[k] for k in range(self.n)])
def Wgen(self):
return sum([self.w[k] for k in range(self.n)])
def C1gen(self, shape1, shape2):
return sum([
self.w[k] *
(shape1.xs[k] * shape2.xs[k] + shape1.ys[k] * shape2.ys[k])
for k in range(self.n)
])
def C2gen(self, shape1, shape2):
return sum([
self.w[k] *
(shape1.ys[k] * shape2.xs[k] + shape1.xs[k] * shape2.ys[k])
for k in range(self.n)
])
def calcMeanShape(self):
xList = [el.xs for el in self.allShapes]
yList = [el.ys for el in self.allShapes]
meanPointsList = zip(np.mean(xList, 0), np.mean(yList, 0))
self.meanShape = Shape(meanPointsList)
def iterateAlignment(self):
# Setup drawing
#colors = ["purple", "light purple",
# "blue", "cyan", "neon blue"]
#"red", "rose",
#"green", "bright green", "mint"]
# roygbv
co = [
'lightish red', 'yellowish orange', 'canary yellow', 'lime', 'cyan'
] #,'lavender]
pal = sns.xkcd_palette(co)
for i in range(self.nIters):
f, (ax1, ax2) = plt.subplots(1, 2) #, sharex= True, sharey=True)
## Calculate mean shape
self.calcMeanShape()
ax1.plot(self.meanShape.xs, self.meanShape.ys, 'k')
## Normalize mean shape
self.normMeanShape()
for sh in self.allShapes:
sh.draw(pal, ax1)
## Realign
self.alignAllShapes()
for sh in self.allShapes:
sh.draw(pal, ax2)
ax2.plot(self.meanShape.xs, self.meanShape.ys, 'k')
# Draw change
self.calcMeanShape()
f.savefig("C:/Users/Valerie/Desktop/stars/plots5/%d.png" % i)
f.clear()
plt.close()
i += 1
# Show
# f.show()
# def isConverged( self ):
def alignAllShapes(self):
import pathos.multiprocessing as mp
start = time.time()
pool = Pool()
self.allShapes = pool.map(self.alignOneShape, self.allShapes)
# for sh in self.allShapes:
# self.alignOneShape( sh )
print 'alignAllShapes: %f' % (time.time() - start)
return
def alignOneShape(self, shape):
start = time.time()
transDict = self.calcAlignTrans(shape)
shape.applyTrans(transDict)
return shape
@staticmethod
def centroid(shape1):
return Point(np.mean(shape1.xs), np.mean(shape1.ys))
@staticmethod
def unitV(v):
return v / np.linalg.norm(v)
@staticmethod
def angleV(v1, v2):
return math.atan2(v1[0], v1[1]) - math.atan2(v2[0], v2[1])
def normMeanShape(self):
############## Calc transformations ###################
## Translate
cmShape = ASMB.centroid(self.meanShape)
t = [[-cmShape.x], [-cmShape.y]]
self.meanShape.translate(t)
self.meanShape.update()
leftEyeIx = self.refIxs[0]
rightEyeIx = self.refIxs[1]
## Scale
# distance between two "eyes"
d = self.meanShape.shapePoints[leftEyeIx].dist(
self.meanShape.shapePoints[rightEyeIx])
s = float(1) / float(d)
## Rotation
xDiff = self.meanShape.shapePoints[
rightEyeIx].x - self.meanShape.shapePoints[leftEyeIx].x
yDiff = self.meanShape.shapePoints[
rightEyeIx].y - self.meanShape.shapePoints[leftEyeIx].y
p0 = [
xDiff, yDiff
] #self.meanShape.shapePoints[0].x, self.meanShape.shapePoints[0].y ]
axisVector = [1, 0]
thetaP = ASMB.angleV(p0, axisVector)
thetaRot = thetaP
rot = [[math.cos(thetaRot), -math.sin(thetaRot)],
[math.sin(thetaRot), math.cos(thetaRot)]]
self.meanShape.rotate(rot)
self.meanShape.update()
self.meanShape.scale(s)
self.meanShape.update()
return
def calcAlignTrans(self, shape):
start = time.time()
coeffs = np.array(
[[self.Xgen(shape), -self.Ygen(shape),
self.Wgen(), 0],
[self.Ygen(shape),
self.Xgen(shape), 0,
self.Wgen()],
[self.Zgen(shape), 0,
self.Xgen(shape),
self.Ygen(shape)],
[0, self.Zgen(shape), -self.Ygen(shape),
self.Xgen(shape)]])
eqs = np.array([
self.Xgen(self.meanShape),
self.Ygen(self.meanShape),
self.C1gen(self.meanShape, shape),
self.C2gen(self.meanShape, shape)
])
sol = np.linalg.solve(coeffs, eqs)
# d = ax = s cos 0
# e = ay = s sin 0
# f = tx
# g = ty
rot = [[sol[0], -sol[1]], [sol[1], sol[0]]]
t = [[sol[2]], [sol[3]]]
return {'rot': rot, 't': t}
def drawAll(self, axis, palette):
i = 0
for el in self.allShapes:
el.draw(palette, i, axis)
i += 1
axis.plot(self.meanShape.xs, self.meanShape.ys, c='k')
allLines = infile.readlines()
pointLine = False
cleanLines = [ x.strip() for x in allLines]
for line in cleanLines:
if line is '{':
pointLine = True
elif line is '}':
pointLine = False
pass
elif pointLine:
ptList.append( map( float, line.split(' ') ) )
else:
pass
ptList
s1 = Shape( ptList )
f, ((ax1,ax2),(ax3,ax4)) = plt.subplots(2,2)
## Original shape (input)
cmShape = ASM.centroid( s1 )
plotAll( ax1, s1 )
############## Calc transformations ###################
## Translate
t = [[ -cmShape.x ], [ -cmShape.y ]]
for pt in s1.shapePoints:
pt.translate( t )
s1.update()
plotAll( ax2, s1)
def calcMeanShape( self ):
xList = [ el.xs for el in self.allShapes ]
yList = [ el.ys for el in self.allShapes ]
meanPointsList = zip( np.mean(xList, 0), np.mean(yList, 0) )
self.meanShape = Shape( meanPointsList )
class ASMB( object ):
def __init__( self, refIndices, numIterations ):
self.allShapes = []
self.n = 0
self.refIxs = refIndices
self.nIters = numIterations
@property
def I( self ):
return len( self.allShapes )
def addShape( self, s ):
if len( self.allShapes ) == 0:
self.allShapes.append( s )
self.n = s.n
else:
assert( s.n == self.n )
self.allShapes.append( s )
@property
def V( self ):
"""
Variance in distance matrix amongst all shapes
"""
V = []
for k in range(self.n):
row = []
for l in range(self.n):
col = []
for i in range(len( self.allShapes )):
col.append( self.allShapes[i].R[k][l])
row.append( np.var(col) )
V.append(row)
return V
@property
def W( self ):
"""
Point weights as diagonal matrix
"""
return np.diag(self.w)
@property
def w( self ):
"""
Point weights as array
"""
s = map( sum, self.V)
return [ math.pow( j, -1) for j in s]
def Zgen( self, shape ):
return sum( [ self.w[k] * ( shape.xs[k] **2 +
shape.xs[k] **2 )
for k in range( self.n ) ] )
def Xgen( self, shape ):
return sum( [ self.w[k] * shape.xs[k]
for k in range( self.n ) ] )
def Ygen( self, shape ):
return sum( [ self.w[k] * shape.ys[k]
for k in range( self.n ) ] )
def Wgen( self ):
return sum( [ self.w[k] for k in range( self.n ) ] )
def C1gen( self, shape1, shape2):
return sum( [ self.w[k] *
( shape1.xs[k] * shape2.xs[k] +
shape1.ys[k] * shape2.ys[k] )
for k in range( self.n) ] )
def C2gen( self, shape1, shape2):
return sum( [ self.w[k] *
( shape1.ys[k] * shape2.xs[k] +
shape1.xs[k] * shape2.ys[k] )
for k in range( self.n) ] )
def calcMeanShape( self ):
xList = [ el.xs for el in self.allShapes ]
yList = [ el.ys for el in self.allShapes ]
meanPointsList = zip( np.mean(xList, 0), np.mean(yList, 0) )
self.meanShape = Shape( meanPointsList )
def iterateAlignment( self ):
# Setup drawing
#colors = ["purple", "light purple",
# "blue", "cyan", "neon blue"]
#"red", "rose",
#"green", "bright green", "mint"]
# roygbv
co = ['lightish red', 'yellowish orange', 'canary yellow', 'lime', 'cyan']#,'lavender]
pal = sns.xkcd_palette( co )
for i in range( self.nIters ):
f, (ax1,ax2) = plt.subplots(1,2)#, sharex= True, sharey=True)
## Calculate mean shape
self.calcMeanShape( )
ax1.plot( self.meanShape.xs, self.meanShape.ys, 'k' )
## Normalize mean shape
self.normMeanShape( )
for sh in self.allShapes:
sh.draw( pal, ax1)
## Realign
self.alignAllShapes( )
for sh in self.allShapes:
sh.draw( pal, ax2 )
ax2.plot( self.meanShape.xs, self.meanShape.ys, 'k' )
# Draw change
self.calcMeanShape()
f.savefig( "C:/Users/Valerie/Desktop/stars/plots5/%d.png" % i )
f.clear()
plt.close()
i += 1
# Show
# f.show()
# def isConverged( self ):
def alignAllShapes( self ):
import pathos.multiprocessing as mp
start = time.time()
pool = Pool()
self.allShapes = pool.map( self.alignOneShape, self.allShapes )
# for sh in self.allShapes:
# self.alignOneShape( sh )
print 'alignAllShapes: %f' % (time.time() - start )
return
def alignOneShape( self, shape ):
start = time.time()
transDict = self.calcAlignTrans( shape )
shape.applyTrans( transDict )
return shape
@staticmethod
def centroid( shape1 ):
return Point( np.mean( shape1.xs ) , np.mean( shape1.ys ) )
@staticmethod
def unitV( v ):
return v / np.linalg.norm( v )
@staticmethod
def angleV( v1, v2 ):
return math.atan2( v1[0], v1[1] ) - math.atan2( v2[0], v2[1] )
def normMeanShape( self ):
############## Calc transformations ###################
## Translate
cmShape = ASMB.centroid( self.meanShape )
t = [[ -cmShape.x ], [ -cmShape.y ]]
self.meanShape.translate( t )
self.meanShape.update( )
leftEyeIx = self.refIxs[0]
rightEyeIx = self.refIxs[1]
## Scale
# distance between two "eyes"
d = self.meanShape.shapePoints[leftEyeIx].dist( self.meanShape.shapePoints[rightEyeIx] )
s = float(1)/float(d)
## Rotation
xDiff = self.meanShape.shapePoints[rightEyeIx].x - self.meanShape.shapePoints[leftEyeIx].x
yDiff = self.meanShape.shapePoints[rightEyeIx].y - self.meanShape.shapePoints[leftEyeIx].y
p0 = [ xDiff, yDiff ] #self.meanShape.shapePoints[0].x, self.meanShape.shapePoints[0].y ]
axisVector = [ 1, 0]
thetaP = ASMB.angleV( p0, axisVector )
thetaRot = thetaP
rot = [[ math.cos( thetaRot ), -math.sin( thetaRot ) ],
[ math.sin( thetaRot ), math.cos( thetaRot ) ] ]
self.meanShape.rotate( rot )
self.meanShape.update( )
self.meanShape.scale( s )
self.meanShape.update( )
return
def calcAlignTrans( self, shape ):
start = time.time()
coeffs = np.array( [
[ self.Xgen( shape ), - self.Ygen( shape ), self.Wgen(), 0],
[ self.Ygen( shape ), self.Xgen( shape ), 0, self.Wgen()],
[ self.Zgen( shape ), 0, self.Xgen( shape ), self.Ygen( shape )],
[ 0, self.Zgen( shape ), - self.Ygen( shape ), self.Xgen( shape )]
])
eqs = np.array([ self.Xgen(self.meanShape) , self.Ygen(self.meanShape), self.C1gen(self.meanShape, shape), self.C2gen(self.meanShape, shape) ] )
sol = np.linalg.solve( coeffs, eqs )
# d = ax = s cos 0
# e = ay = s sin 0
# f = tx
# g = ty
rot = [[ sol[0], - sol[1]],
[ sol[1], sol[0]] ]
t = [[ sol[2]],[sol[3]]]
return { 'rot': rot, 't':t}
def drawAll( self, axis, palette ):
i = 0
for el in self.allShapes:
el.draw( palette, i, axis)
i += 1
axis.plot( self.meanShape.xs, self.meanShape.ys, c = 'k' )