#!/usr/bin/env python # -*- coding: utf-8 -*- # import os,numpy,string,math,sys from optparse import OptionParser, Option from vtk import vtkUnstructuredGridReader, \ vtkWarpVector, \ vtkCellCenters, \ vtkDataSetSurfaceFilter, \ vtkPoints, \ vtkCellArray, \ vtkVertex, \ vtkPolyData, \ vtkSelectEnclosedPoints, \ vtkKdTree, \ vtkIdList # ----------------------------- def getHeader(filename,sizeFastIndex,sizeSlowIndex,stepsize): # ----------------------------- # returns header for ang file # step size in micrometer return '\n'.join([ \ '# TEM_PIXperUM 1.000000', \ '# x-star 1.000000', \ '# y-star 1.000000', \ '# z-star 1.000000', \ '# WorkingDistance 18.000000', \ '#', \ '# Phase 1', \ '# MaterialName XX', \ '# Formula XX', \ '# Info', \ '# Symmetry 43', \ '# LatticeConstants 2.870 2.870 2.870 90.000 90.000 90.000', \ '# NumberFamilies 1', \ '# hklFamilies 1 1 0 1 0.000000 1', \ '# Categories 0 0 0 0 0 ', \ '#', \ '# GRID: SqrGrid', \ '# XSTEP: ' + str(stepsize*1e6), \ '# YSTEP: ' + str(stepsize*1e6), \ '# NCOLS_ODD: ' + str(sizeFastIndex), \ '# NCOLS_EVEN: ' + str(sizeFastIndex), \ '# NROWS: ' + str(sizeSlowIndex), \ '#', \ '# OPERATOR: ' + string.replace('$Id$','\n','\\n'), \ '#', \ '# SAMPLEID: %s'%filename, \ '#', \ '# SCANID: ', \ '#', \ ]) + '\n' # ----------------------------- def positiveRadians(angle): # ----------------------------- # returns positive angle in radians # gets angle in degrees angle = math.radians(float(angle)) while angle < 0.0: angle += 2.0 * math.pi return angle # ----------------------------- def getDataLine(angles,x,y,validData=True): # ----------------------------- # returns string of one line in ang file # convention in ang file: y coordinate comes first and is fastest index # positions in micrometer info = {True: (9999.9, 1.0, 0,99999,0.0), False: ( -1.0,-1.0,-1, -1,1.0)} 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]) # -------------------------------------------------------------------- # MAIN FUNCTION STARTS HERE # -------------------------------------------------------------------- parser = OptionParser(usage='%prog options [file[s]]', description = """ Builds a ang files from a vtk file. """ + string.replace('$Id$','\n','\\n') ) parser.add_option('--disp','--displacement',dest='dispLabel', type='string', \ help='label of displacements [%default]') parser.add_option('--euler', dest='eulerLabel', type='string', nargs=3, \ help='labels of euler angles [%default]') parser.add_option('-n','--normal', dest='normal', type='float', nargs=3, \ help='normal of slices in direction of increasing slice numbers [%default]') parser.add_option('-u','--up', dest='up', type='float', nargs=3, help='up direction of slices [%default]') parser.add_option('-i','--slices', dest='Nslices', type='int', \ help='number of slices [%default]') parser.add_option('-d','--distance', dest='distance', type='float', \ help='slice distance [%default]') parser.add_option('-s','--scale', dest='scale', type='float', \ help='scale length from vtk file [%default]') parser.add_option('-r','--resolution', dest='resolution', type='float', help='scaling factor for resolution [%default]') parser.add_option('--hex','--hexagonal', dest='hexagonal', action='store_true', help='use in plane hexagonal grid [%default]') parser.add_option('--interpolation', dest='interpolation', type='int', \ help='number of points for linear interpolation [%default]') parser.add_option('--verbose', dest='verbose', action='store_true', help='verbose mode [%default]') parser.set_defaults(dispLabel = 'displacement') parser.set_defaults(eulerLabel = ['1_eulerangles','2_eulerangles','3_eulerangles']) parser.set_defaults(hexagonal = False) parser.set_defaults(normal = [0.0,0.0,-1.0]) parser.set_defaults(up = [0.0,1.0,0.0]) parser.set_defaults(Nslices = 1) parser.set_defaults(distance = 0.0) parser.set_defaults(scale = 1.0) parser.set_defaults(resolution = 1.0) parser.set_defaults(dispScaling = 1.0) parser.set_defaults(verbose = False) parser.set_defaults(interpolation = 1) (options,filenames) = parser.parse_args() #--- SANITY CHECKS # check for valid filenames for filename in filenames: if not os.path.exists(filename): parser.error('file "%s" does not exist'%filename) if not os.path.splitext(filename)[1] == '.vtk': parser.error('"%s": need vtk file'%filename) # check for othogonality of normal and up vector if numpy.dot(numpy.array(options.normal),numpy.array(options.up)) > 1e-3: parser.error('normal vector and up vector have to be orthogonal') # check for options that are not yet implemented if options.interpolation > 1: parser.error('interpolation not yet supported') if options.hexagonal: parser.error('hexagonal grid not yet supported') #--- ITERATE OVER FILES AND PROCESS THEM for filename in filenames: # Read the source file if options.verbose: sys.stdout.write("\nREADING VTK FILE\n") reader = vtkUnstructuredGridReader() reader.SetFileName(filename) reader.ReadAllScalarsOn() reader.ReadAllVectorsOn() reader.Update() undeformedMesh = reader.GetOutput() # Get euler angles from cell data if options.verbose: sys.stdout.write("\nGETTING EULER ANGLES\n") angles = {} for i in range(reader.GetNumberOfScalarsInFile()): scalarName = reader.GetScalarsNameInFile(i) if scalarName in options.eulerLabel: angles[scalarName] = undeformedMesh.GetCellData().GetScalars(scalarName) if options.verbose: sys.stdout.write(" found scalar with name %s\n"%scalarName) if len(angles) < 3: # found data for all three euler angles? for label in options.eulerLabel: if not label in angles.keys(): parser.error('Could not find scalar data with name %s'%label) # Get deformed mesh if options.verbose: sys.stdout.write("\nDEFORM MESH\n") warpVector = vtkWarpVector() warpVector.SetInput(undeformedMesh) warpVector.Update() deformedMesh = warpVector.GetOutput() # todo: not clear how to choose other vector data than the first entry box = deformedMesh.GetBounds() # bounding box in mesh system if options.verbose: sys.stdout.write(" bounding box in lab system\n") sys.stdout.write(" x (% .8f % .8f)\n"%(box[0],box[1])) sys.stdout.write(" y (% .8f % .8f)\n"%(box[2],box[3])) sys.stdout.write(" z (% .8f % .8f)\n"%(box[4],box[5])) # Get cell centers of deformed mesh (position of ips) if options.verbose: sys.stdout.write("\nGETTING CELL CENTERS OF DEFORMED MESH\n") cellCenter = vtkCellCenters() cellCenter.SetVertexCells(0) # do not generate vertex cells, just points cellCenter.SetInput(deformedMesh) cellCenter.Update() meshIPs = cellCenter.GetOutput() # Get outer surface of deformed mesh if options.verbose: sys.stdout.write("\nGETTING OUTER SURFACE OF DEFORMED MESH\n") surfaceFilter = vtkDataSetSurfaceFilter() surfaceFilter.SetInput(deformedMesh) surfaceFilter.Update() surface = surfaceFilter.GetOutput() # Get coordinate system for ang files # z-vector is normal to slices # x-vector corresponds to the up-direction # "R" rotates coordinates from the mesh system into the TSL system if options.verbose: sys.stdout.write("\nGETTING COORDINATE SYSTEM FOR ANG FILES\n") z = numpy.array(options.normal,dtype='float') z = z / numpy.linalg.norm(z) x = numpy.array(options.up,dtype='float') x = x / numpy.linalg.norm(x) y = numpy.cross(z,x) R = numpy.array([x,y,z]) if options.verbose: sys.stdout.write(" axis (x: up direction, z: slice normal)\n") sys.stdout.write(" x (% .8f % .8f % .8f)\n"%tuple(x)) sys.stdout.write(" y (% .8f % .8f % .8f)\n"%tuple(y)) sys.stdout.write(" z (% .8f % .8f % .8f)\n"%tuple(z)) # Get bounding box in rotated system (x,y,z) if options.verbose: sys.stdout.write("\nGETTING BOUNDING BOX IN ROTATED SYSTEM\n") rotatedbox = [[numpy.inf,-numpy.inf] for i in range(3)] # bounding box in rotated TSL system for n in range(8): # loop over eight vertices of mesh bounding box vert = numpy.array([box[0+(n/1)%2], box[2+(n/2)%2], box[4+(n/4)%2]]) # vertex in mesh system rotatedvert = numpy.dot(R,vert) # vertex in rotated system for i in range(3): rotatedbox[i][0] = min(rotatedbox[i][0],rotatedvert[i]) rotatedbox[i][1] = max(rotatedbox[i][1],rotatedvert[i]) if options.verbose: sys.stdout.write(" bounding box in rotated system\n") sys.stdout.write(" x (% .8f % .8f)\n"%tuple(rotatedbox[0])) sys.stdout.write(" y (% .8f % .8f)\n"%tuple(rotatedbox[1])) sys.stdout.write(" z (% .8f % .8f)\n"%tuple(rotatedbox[2])) # Correct bounding box so that a multiplicity of the resolution fits into it # and get number of points and extent in each (rotated) axis direction if options.verbose: sys.stdout.write("\nCORRECTING EXTENT OF BOUNDING BOX IN ROTATED SYSTEM\n") correction = [] Npoints = [] extent = [rotatedbox[i][1] - rotatedbox[i][0] for i in range(3)] for i in range(2): Npoints.extend([int(math.ceil(extent[i] / options.resolution))]) correction.extend([float(Npoints[i]) * options.resolution - extent[i]]) if options.distance > 0.0: Npoints.extend([int(math.ceil(extent[2] / options.distance))]) correction.extend([float(Npoints[2]) * options.distance - extent[2]]) else: Npoints.extend([options.Nslices]) correction.extend([0.0]) options.distance = extent[2] / float(options.Nslices) for i in range(3): rotatedbox[i][0] = rotatedbox[i][0] - 0.5 * correction[i] rotatedbox[i][1] = rotatedbox[i][1] + 0.5 * correction[i] extent[i] = rotatedbox[i][1] - rotatedbox[i][0] NpointsPerSlice = Npoints[0] * Npoints[1] totalNpoints = NpointsPerSlice * Npoints[2] if options.verbose: sys.stdout.write(" corrected bounding box in rotated system\n") sys.stdout.write(" x (% .8f % .8f)\n"%tuple(rotatedbox[0])) sys.stdout.write(" y (% .8f % .8f)\n"%tuple(rotatedbox[1])) sys.stdout.write(" z (% .8f % .8f)\n"%tuple(rotatedbox[2])) # Generate new regular point grid for ang files # Use "polydata" object with points as single vertices # beware of TSL convention: y direction is fastest index if options.verbose: sys.stdout.write("\nGENERATING POINTS FOR POINT GRID") points = vtkPoints() for k in xrange(Npoints[2]): for j in xrange(Npoints[0]): for i in xrange(Npoints[1]): # y is fastest index rotatedpoint = numpy.array([rotatedbox[0][0] + (float(j) + 0.5) * options.resolution, rotatedbox[1][0] + (float(i) + 0.5) * options.resolution, rotatedbox[2][0] + (float(k) + 0.5) * options.distance ]) # point in rotated system point = numpy.dot(R.T,rotatedpoint) # point in mesh system points.InsertNextPoint(list(point)) if options.verbose: sys.stdout.write("\rGENERATING POINTS FOR POINT GRID %d%%" %(100*(Npoints[1]*(k*Npoints[0]+j)+i+1)/totalNpoints)) sys.stdout.flush() if options.verbose: sys.stdout.write("\n number of slices: %i\n"%Npoints[2]) sys.stdout.write(" slice spacing: %.8f\n"%options.distance) sys.stdout.write(" number of points per slice: %i = %i rows * %i points in row\n"%(NpointsPerSlice,Npoints[0],Npoints[1])) sys.stdout.write(" grid resolution: %.8f\n"%options.resolution) if options.verbose: sys.stdout.write("\nGENERATING VERTICES FOR POINT GRID") vertices = vtkCellArray() for i in xrange(totalNpoints): vertex = vtkVertex() vertex.GetPointIds().SetId(0,i) # each vertex consists of exactly one (index 0) point with ID "i" vertices.InsertNextCell(vertex) if options.verbose: sys.stdout.write("\rGENERATING VERTICES FOR POINT GRID %d%%" %(100*(i+1)/totalNpoints)) sys.stdout.flush() if options.verbose: sys.stdout.write("\n\nGENERATING POINT GRID\n") pointgrid = vtkPolyData() pointgrid.SetPoints(points) pointgrid.SetVerts(vertices) pointgrid.Update() # Find out which points reside inside mesh geometry if options.verbose: sys.stdout.write("\nIDENTIFYING POINTS INSIDE MESH GEOMETRY\n") enclosedPoints = vtkSelectEnclosedPoints() enclosedPoints.SetSurface(surface) enclosedPoints.SetInput(pointgrid) enclosedPoints.Update() # Build kdtree from mesh IPs and match mesh IPs to point grid # could also be done with nearest neighbor search from damask.core, would possibly be faster ? if options.verbose: sys.stdout.write("\nBUILDING MAPPING OF GRID POINTS") kdTree = vtkKdTree() kdTree.BuildLocatorFromPoints(meshIPs.GetPoints()) gridToMesh = [] ids = vtkIdList() NenclosedPoints = 0 for i in range(pointgrid.GetNumberOfPoints()): gridToMesh.append([]) if enclosedPoints.IsInside(i): NenclosedPoints += 1 kdTree.FindClosestNPoints(options.interpolation,pointgrid.GetPoint(i),ids) # here one could use faster(?) "FindClosestPoint" if only first nearest neighbor required for j in range(ids.GetNumberOfIds()): gridToMesh[-1].extend([ids.GetId(j)]) if options.verbose: sys.stdout.write("\rBUILDING MAPPING OF GRID POINTS %d%%" %(100*(i+1)/totalNpoints)) sys.stdout.flush() if options.verbose: sys.stdout.write("\n Number of points inside mesh geometry %i\n"%NenclosedPoints) sys.stdout.write(" Number of points outside mesh geometry %i\n"%(totalNpoints - NenclosedPoints)) # ITERATE OVER SLICES AND CREATE ANG FILE if options.verbose: sys.stdout.write("\nWRITING OUT ANG FILES\n") sys.stdout.write(" scaling all length with %f\n"%options.scale) for sliceN in range(Npoints[2]): # Open file and write header angfilename = eval('"'+eval("'%%s_slice%%0%ii.ang'%(math.log10(Npoints[2])+1)")+'"%(os.path.splitext(filename)[0],sliceN+1)') with open(angfilename,'w') as angfile: if options.verbose: sys.stdout.write(" %s\n"%angfilename) angfile.write(getHeader(filename,Npoints[1],Npoints[0],options.resolution*options.scale)) for i in xrange(sliceN*NpointsPerSlice,(sliceN+1)*NpointsPerSlice): # Iterate over points on slice # Get euler angles of closest IDs if enclosedPoints.IsInside(i): phi = [] for j in range(len(gridToMesh[i])): IP = gridToMesh[i][j] phi.append([]) for k in range(3): phi[-1].extend([angles[options.eulerLabel[k]].GetValue(IP)]) else: phi = [[720,720,720]] # fake angles # Interpolate Euler angle # NOT YET IMPLEMENTED, simply take the nearest neighbors values interpolatedPhi = phi[0] # write data to ang file x,y,z = numpy.dot(R,pointgrid.GetPoint(i)) # point in rotated TSL system x *= options.scale y *= options.scale angfile.write(getDataLine(interpolatedPhi,x,y,enclosedPoints.IsInside(i)))