if fidLine[0] == "#":
temp = fidLine.split()
#print np.shape(temp)
areas[count] = float(temp[8])
CS[count] = float(temp[6])
count = count + 1
fid.close()
legend.append(line.rstrip())
peakTime.append(np.argmin(areas))
areasAll.append(areas)
zPos, numContours, contours = IT.readContourFile(workingDir + region +
'/' + line.rstrip() +
'/' + line.rstrip() +
'_' +
contraction.rstrip())
cRest.append(contours[0])
cCont.append(contours[np.argmin(areas)])
print np.size(cRest), np.shape(cCont)
f, ax1 = plt.subplots(1, 1)
flib = 1
#Going to try flipping 6905_07 -> [1:3]
#it flipped it back, cause of the landmark numbering lol
ax1.plot(cRest[flib][:, 0], cRest[flib][:, 1] * -1, 'ob')
ax1.plot(cCont[flib][:, 0], cCont[flib][:, 1] * -1, 'or')
workingDir = './../imageToolsTestSpace/'
#we will have a control file that has all of the contour groups we are planning to use
activeContours = open(workingDir + 'ContourList').readlines()
#read in the contraction map
CMap = np.loadtxt(workingDir + 'contractionMap')
#set up infromation arrays
contourData = []
contourInformation = []
#loop through activeContours
for line in activeContours:
print 'Opening contour:', line.rstrip()
zPos, numContours, contours = IT.readContourFile(workingDir +
line.rstrip() +
'/Results.txt')
#store the zPos and numContous in contourInformation
contourInformation = contourInformation + [[zPos, numContours]]
contourData = contourData + [contours]
contractionMatrix, endtime = IT.createContractionMatrix(
activeContours, contourInformation, contourData, CMap)
#lets make a nxm spatial array for the first time point, where n=(x,y,z) and m are the nodes
cMshape = np.shape(contractionMatrix)
# fititng parameters for host mesh fitting
host_mesh_pad = 10.0 # host mesh padding around slave points
host_elem_type = 'quad333' # quadrilateral cubic host elements
host_elems = [1, 1, 3] # a single element host mesh
import numpy as np
import matplotlib.pyplot as plt
import imageTools as IT
from fieldwork.field.tools import fitting_tools
plt.switch_backend('TkAgg')
print '\nRunning script registerZeroPositionToSpiral...'
workingDir = './../imageToolsTestSpace/'
filename='6948_02'
#import the xyzPositions for corresponding spiral contour
spiralContour=np.loadtxt(workingDir+filename+'/CorrespondingSpiral/spiralControlPoints')
#import zero position contour from results
zPos,numContours,contours=IT.readContourFile(workingDir+filename+'/Results.txt')
#Ditch it all but keep the first contour
deformContour=contours[0]
xOpt,transformedContour=fitting_tools.fitTranslation(deformContour, spiralContour, xtol=1e-5, maxfev=0, sample=None, verbose=0, outputErrors=0)
#plot for sanity check
fig=plt.figure()
ax = fig.add_subplot(111)
ax.scatter(spiralContour[:,0],spiralContour[:,1]*-1,facecolors='g', edgecolors='g')
ax.scatter(deformContour[:,0],deformContour[:,1]*-1,facecolors='r', edgecolors='r')
#ax.scatter(transformedContour[:,0],transformedContour[:,1]*-1,facecolors='b', edgecolors='b')
ax.axis('equal')
for i in range(np.shape(spiralContour)[0]):
print spiralContour[i,0]
