- all length in nag file in micrometer
- "size" option replaced by "scale": uniform scaling of all length - default normal in negative z-direction - more output in verbose mode - ang file numbering starts with 1 - positions in ang file in TSL, not lab frame
This commit is contained in:
Christoph Kords
parent
278198121d
commit
9656d06fcc
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@ -2,7 +2,7 @@
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# -*- coding: utf-8 -*-
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#
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import os,numpy,string,math
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import os,numpy,string,math,sys
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from optparse import OptionParser, Option
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from vtk import vtkUnstructuredGridReader, \
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vtkWarpVector, \
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@ -21,7 +21,7 @@ from vtk import vtkUnstructuredGridReader, \
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def getHeader(filename,sizeFastIndex,sizeSlowIndex,stepsize):
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# -----------------------------
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# returns header for ang file
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#
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# step size in micrometer
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return '\n'.join([ \
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'# TEM_PIXperUM 1.000000', \
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@ -41,8 +41,8 @@ def getHeader(filename,sizeFastIndex,sizeSlowIndex,stepsize):
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'# Categories 0 0 0 0 0 ', \
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'#', \
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'# GRID: SqrGrid', \
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'# XSTEP: ' + str(stepsize), \
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'# YSTEP: ' + str(stepsize), \
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'# XSTEP: ' + str(stepsize*1e6), \
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'# YSTEP: ' + str(stepsize*1e6), \
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'# NCOLS_ODD: ' + str(sizeFastIndex), \
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'# NCOLS_EVEN: ' + str(sizeFastIndex), \
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'# NROWS: ' + str(sizeSlowIndex), \
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@ -70,14 +70,15 @@ def positiveRadians(angle):
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# -----------------------------
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def getDataLine(angles,position,validData=True):
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def getDataLine(angles,x,y,validData=True):
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# -----------------------------
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# returns string of one line in ang file
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# convention in ang file: y coordinate comes first and is fastest index
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# positions in micrometer
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info = {True: (9999.9, 1.0, 0,99999,0.0),
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False: ( -1.0,-1.0,-1, -1,1.0)}
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return '%9.5f %9.5f %9.5f %12.5f %12.5f %6.1f %6.3f %2i %6i %6.3f \n'%(tuple(map(positiveRadians,angles))+tuple(position[1::-1])+info[validData])
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return '%9.5f %9.5f %9.5f %12.5f %12.5f %6.1f %6.3f %2i %6i %6.3f \n'%(tuple(map(positiveRadians,angles))+(y*1e6,x*1e6)+info[validData])
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@ -104,14 +105,12 @@ parser.add_option('-i','--slices', dest='Nslices', type='int', \
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help='number of slices [%default]')
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parser.add_option('-d','--distance', dest='distance', type='float', \
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help='slice distance [%default]')
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parser.add_option('-s','--size', dest='size', type='float', nargs=3, \
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help='physical size of ang file [%default]')
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parser.add_option('-s','--scale', dest='scale', type='float', \
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help='scale length from vtk file [%default]')
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parser.add_option('-r','--resolution', dest='resolution', type='float',
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help='scaling factor for resolution [%default]')
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parser.add_option('--hex','--hexagonal', dest='hexagonal', action='store_true',
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help='use in plane hexagonal grid [%default]')
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parser.add_option('--ds','--dispscaling', dest='dispScaling', type='float', \
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help='scaling of displacements [%default]')
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parser.add_option('--interpolation', dest='interpolation', type='int', \
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help='number of points for linear interpolation [%default]')
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parser.add_option('--verbose', dest='verbose', action='store_true',
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@ -120,11 +119,11 @@ parser.add_option('--verbose', dest='verbose', action='store_true',
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parser.set_defaults(dispLabel = 'displacement')
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parser.set_defaults(eulerLabel = ['1_eulerangles','2_eulerangles','3_eulerangles'])
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parser.set_defaults(hexagonal = False)
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parser.set_defaults(normal = [0.0,0.0,1.0])
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parser.set_defaults(normal = [0.0,0.0,-1.0])
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parser.set_defaults(up = [0.0,1.0,0.0])
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parser.set_defaults(Nslices = 1)
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parser.set_defaults(distance = 0.0)
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parser.set_defaults(size = [1.0,1.0,0.0])
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parser.set_defaults(scale = 1.0)
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parser.set_defaults(resolution = 1.0)
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parser.set_defaults(dispScaling = 1.0)
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parser.set_defaults(verbose = False)
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@ -164,22 +163,24 @@ for filename in filenames:
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# Read the source file
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if options.verbose: sys.stdout.write("\nREADING VTK FILE\n")
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reader = vtkUnstructuredGridReader()
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reader.SetFileName(filename)
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reader.ReadAllScalarsOn()
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reader.ReadAllVectorsOn()
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reader.Update()
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undeformedMesh = reader.GetOutput()
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# Get euler angles from cell data
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if options.verbose: sys.stdout.write("\nGETTING EULER ANGLES\n")
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angles = {}
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Nscalars = reader.GetNumberOfScalarsInFile()
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for i in range(Nscalars):
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for i in range(reader.GetNumberOfScalarsInFile()):
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scalarName = reader.GetScalarsNameInFile(i)
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if scalarName in options.eulerLabel:
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angles[scalarName] = undeformedMesh.GetCellData().GetScalars(scalarName)
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if options.verbose: sys.stdout.write(" found scalar with name %s\n"%scalarName)
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if len(angles) < 3: # found data for all three euler angles?
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for label in options.eulerLabel:
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if not label in angles.keys():
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@ -188,23 +189,22 @@ for filename in filenames:
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# Get deformed mesh
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if options.verbose: sys.stdout.write("\nDEFORM MESH\n")
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warpVector = vtkWarpVector()
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warpVector.SetScaleFactor(options.dispScaling)
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warpVector.SetInput(undeformedMesh)
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warpVector.Update()
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deformedMesh = warpVector.GetOutput() # todo: not clear how to choose other vector data than the first entry
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box = deformedMesh.GetBounds() # bounding box in mesh system
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if options.verbose:
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print ''
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print 'MESH SYSTEM'
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print ' bounding box'
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print ' x ',[box[0],box[1]]
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print ' y ',[box[2],box[3]]
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print ' z ',[box[4],box[5]]
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sys.stdout.write(" bounding box in lab system\n")
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sys.stdout.write(" x (% .8f % .8f)\n"%(box[0],box[1]))
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sys.stdout.write(" y (% .8f % .8f)\n"%(box[2],box[3]))
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sys.stdout.write(" z (% .8f % .8f)\n"%(box[4],box[5]))
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# Get cell centers of deformed mesh (position of ips)
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if options.verbose: sys.stdout.write("\nGETTING CELL CENTERS OF DEFORMED MESH\n")
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cellCenter = vtkCellCenters()
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cellCenter.SetVertexCells(0) # do not generate vertex cells, just points
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cellCenter.SetInput(deformedMesh)
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@ -214,6 +214,7 @@ for filename in filenames:
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# Get outer surface of deformed mesh
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if options.verbose: sys.stdout.write("\nGETTING OUTER SURFACE OF DEFORMED MESH\n")
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surfaceFilter = vtkDataSetSurfaceFilter()
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surfaceFilter.SetInput(deformedMesh)
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surfaceFilter.Update()
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@ -225,16 +226,23 @@ for filename in filenames:
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# x-vector corresponds to the up-direction
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# "R" rotates coordinates from the mesh system into the TSL system
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if options.verbose: sys.stdout.write("\nGETTING COORDINATE SYSTEM FOR ANG FILES\n")
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z = numpy.array(options.normal,dtype='float')
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z = z / numpy.linalg.norm(z)
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x = numpy.array(options.up,dtype='float')
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x = x / numpy.linalg.norm(x)
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y = numpy.cross(z,x)
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R = numpy.array([x,y,z])
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if options.verbose:
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sys.stdout.write(" axis (x: up direction, z: slice normal)\n")
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sys.stdout.write(" x (% .8f % .8f % .8f)\n"%tuple(x))
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sys.stdout.write(" y (% .8f % .8f % .8f)\n"%tuple(y))
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sys.stdout.write(" z (% .8f % .8f % .8f)\n"%tuple(z))
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# Get bounding box in rotated system (x,y,z)
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if options.verbose: sys.stdout.write("\nGETTING BOUNDING BOX IN ROTATED SYSTEM\n")
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rotatedbox = [[numpy.inf,-numpy.inf] for i in range(3)] # bounding box in rotated TSL system
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for n in range(8): # loop over eight vertices of mesh bounding box
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vert = numpy.array([box[0+(n/1)%2],
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@ -244,11 +252,17 @@ for filename in filenames:
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for i in range(3):
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rotatedbox[i][0] = min(rotatedbox[i][0],rotatedvert[i])
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rotatedbox[i][1] = max(rotatedbox[i][1],rotatedvert[i])
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if options.verbose:
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sys.stdout.write(" bounding box in rotated system\n")
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sys.stdout.write(" x (% .8f % .8f)\n"%tuple(rotatedbox[0]))
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sys.stdout.write(" y (% .8f % .8f)\n"%tuple(rotatedbox[1]))
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sys.stdout.write(" z (% .8f % .8f)\n"%tuple(rotatedbox[2]))
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# Correct bounding box so that a multiplicity of the resolution fits into it
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# and get number of points and extent in each (rotated) axis direction
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if options.verbose: sys.stdout.write("\nCORRECTING EXTENT OF BOUNDING BOX IN ROTATED SYSTEM\n")
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correction = []
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Npoints = []
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extent = [rotatedbox[i][1] - rotatedbox[i][0] for i in range(3)]
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@ -266,28 +280,20 @@ for filename in filenames:
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rotatedbox[i][0] = rotatedbox[i][0] - 0.5 * correction[i]
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rotatedbox[i][1] = rotatedbox[i][1] + 0.5 * correction[i]
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extent[i] = rotatedbox[i][1] - rotatedbox[i][0]
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NpointsPerSlice = Npoints[0] * Npoints[1]
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totalNpoints = NpointsPerSlice * Npoints[2]
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if options.verbose:
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print ''
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print 'ROTATED SYSTEM'
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print ' axis (x: up direction, z: slice normal)'
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print ' x ',list(x)
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print ' y ',list(y)
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print ' z ',list(z)
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print ' bounding box'
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print ' x ',rotatedbox[0]
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print ' y ',rotatedbox[1]
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print ' z ',rotatedbox[2]
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print ' number of points per slice'
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print ' x ',Npoints[0]
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print ' y ',Npoints[1]
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print ' number of slices'
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print ' z ',Npoints[2]
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sys.stdout.write(" corrected bounding box in rotated system\n")
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sys.stdout.write(" x (% .8f % .8f)\n"%tuple(rotatedbox[0]))
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sys.stdout.write(" y (% .8f % .8f)\n"%tuple(rotatedbox[1]))
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sys.stdout.write(" z (% .8f % .8f)\n"%tuple(rotatedbox[2]))
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# Generate new regular point grid for ang files
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# Use "polydata" object with points as single vertices
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# beware of TSL convention: y direction is fastest index
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if options.verbose: sys.stdout.write("\nGENERATING POINTS FOR POINT GRID")
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points = vtkPoints()
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for k in xrange(Npoints[2]):
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for j in xrange(Npoints[0]):
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@ -297,13 +303,26 @@ for filename in filenames:
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rotatedbox[2][0] + (float(k) + 0.5) * options.distance ]) # point in rotated system
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point = numpy.dot(R.T,rotatedpoint) # point in mesh system
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points.InsertNextPoint(list(point))
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if options.verbose:
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sys.stdout.write("\rGENERATING POINTS FOR POINT GRID %d%%" %(100*(Npoints[1]*(k*Npoints[0]+j)+i+1)/totalNpoints))
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sys.stdout.flush()
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if options.verbose:
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sys.stdout.write("\n number of slices: %i\n"%Npoints[2])
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sys.stdout.write(" slice spacing: %.8f\n"%options.distance)
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sys.stdout.write(" number of points per slice: %i = %i rows * %i points in row\n"%(NpointsPerSlice,Npoints[0],Npoints[1]))
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sys.stdout.write(" grid resolution: %.8f\n"%options.resolution)
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if options.verbose: sys.stdout.write("\nGENERATING VERTICES FOR POINT GRID")
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vertices = vtkCellArray()
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for i in xrange(Npoints[0]*Npoints[1]*Npoints[2]):
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for i in xrange(totalNpoints):
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vertex = vtkVertex()
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vertex.GetPointIds().SetId(0,i) # each vertex consists of exactly one (index 0) point with ID "i"
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vertices.InsertNextCell(vertex)
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if options.verbose:
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sys.stdout.write("\rGENERATING VERTICES FOR POINT GRID %d%%" %(100*(i+1)/totalNpoints))
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sys.stdout.flush()
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if options.verbose: sys.stdout.write("\n\nGENERATING POINT GRID\n")
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pointgrid = vtkPolyData()
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pointgrid.SetPoints(points)
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pointgrid.SetVerts(vertices)
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@ -312,6 +331,7 @@ for filename in filenames:
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# Find out which points reside inside mesh geometry
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if options.verbose: sys.stdout.write("\nIDENTIFYING POINTS INSIDE MESH GEOMETRY\n")
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enclosedPoints = vtkSelectEnclosedPoints()
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enclosedPoints.SetSurface(surface)
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enclosedPoints.SetInput(pointgrid)
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@ -321,29 +341,41 @@ for filename in filenames:
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# Build kdtree from mesh IPs and match mesh IPs to point grid
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# could also be done with nearest neighbor search from damask.core, would possibly be faster ?
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if options.verbose: sys.stdout.write("\nBUILDING MAPPING OF GRID POINTS")
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kdTree = vtkKdTree()
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kdTree.BuildLocatorFromPoints(meshIPs.GetPoints())
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gridToMesh = []
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ids = vtkIdList()
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NenclosedPoints = 0
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for i in range(pointgrid.GetNumberOfPoints()):
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gridToMesh.append([])
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if enclosedPoints.IsInside(i):
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NenclosedPoints += 1
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kdTree.FindClosestNPoints(options.interpolation,pointgrid.GetPoint(i),ids) # here one could use faster(?) "FindClosestPoint" if only first nearest neighbor required
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for j in range(ids.GetNumberOfIds()):
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gridToMesh[-1].extend([ids.GetId(j)])
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if options.verbose:
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sys.stdout.write("\rBUILDING MAPPING OF GRID POINTS %d%%" %(100*(i+1)/totalNpoints))
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sys.stdout.flush()
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if options.verbose:
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sys.stdout.write("\n Number of points inside mesh geometry %i\n"%NenclosedPoints)
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sys.stdout.write(" Number of points outside mesh geometry %i\n"%(totalNpoints - NenclosedPoints))
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# ITERATE OVER SLICES AND CREATE ANG FILE
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NpointsPerSlice = Npoints[0] * Npoints[1]
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if options.verbose:
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sys.stdout.write("\nWRITING OUT ANG FILES\n")
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sys.stdout.write(" scaling all length with %f\n"%options.scale)
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for sliceN in range(Npoints[2]):
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# Open file and write header
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angfilename = eval('"'+eval("'%%s_slice%%0%ii.ang'%(math.log10(Npoints[2])+1)")+'"%(os.path.splitext(filename)[0],sliceN)')
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angfilename = eval('"'+eval("'%%s_slice%%0%ii.ang'%(math.log10(Npoints[2])+1)")+'"%(os.path.splitext(filename)[0],sliceN+1)')
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with open(angfilename,'w') as angfile:
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angfile.write(getHeader(filename,Npoints[1],Npoints[0],options.resolution))
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if options.verbose: sys.stdout.write(" %s\n"%angfilename)
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angfile.write(getHeader(filename,Npoints[1],Npoints[0],options.resolution*options.scale))
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for i in xrange(sliceN*NpointsPerSlice,(sliceN+1)*NpointsPerSlice): # Iterate over points on slice
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@ -368,5 +400,8 @@ for filename in filenames:
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# write data to ang file
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angfile.write(getDataLine(interpolatedPhi,pointgrid.GetPoint(i),enclosedPoints.IsInside(i)))
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x,y,z = numpy.dot(R,pointgrid.GetPoint(i)) # point in rotated TSL system
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x *= options.scale
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y *= options.scale
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angfile.write(getDataLine(interpolatedPhi,x,y,enclosedPoints.IsInside(i)))
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