DAMASK_EICMD/processing/post/vtk2ang.py

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#!/usr/bin/env python2
# -*- coding: UTF-8 no BOM -*-
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import os,string,math,sys
import numpy as np
from optparse import OptionParser
import vtk
import damask
scriptName = os.path.splitext(os.path.basename(__file__))[0]
scriptID = ' '.join([scriptName,damask.version])
# -----------------------------
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 from 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.
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""", version = scriptID)
parser.add_option('--disp','--displacement',dest='dispLabel', \
help='label of displacements [%default]')
parser.add_option('--euler', dest='eulerLabel', 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.add_option('--visualize', dest='visualize', action='store_true',
help='visualize geometry [%default]')
parser.set_defaults(dispLabel = 'displacement')
parser.set_defaults(eulerLabel = ['1_1_eulerangles','1_2_eulerangles','1_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(interpolation = 1)
parser.set_defaults(verbose = False)
parser.set_defaults(visualize = False)
(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
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if np.dot(np.array(options.normal),np.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:
if options.verbose: sys.stdout.write("\nREADING VTK FILE\n")
# Read the source file
reader = vtk.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 label not 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 = vtk.vtkWarpVector()
undeformedMesh.GetPointData().SetActiveVectors(options.dispLabel)
warpVector.SetInput(undeformedMesh)
warpVector.Update()
deformedMesh = warpVector.GetOutput()
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 = vtk.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 = vtk.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")
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z = np.array(options.normal,dtype='float')
z = z / np.linalg.norm(z)
x = np.array(options.up,dtype='float')
x = x / np.linalg.norm(x)
y = np.cross(z,x)
R = np.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")
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rotatedbox = [[np.inf,-np.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
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vert = np.array([box[0+(n/1)%2],
box[2+(n/2)%2],
box[4+(n/4)%2]]) # vertex in mesh system
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rotatedvert = np.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 = vtk.vtkPoints()
for k in xrange(Npoints[2]):
for j in xrange(Npoints[0]):
for i in xrange(Npoints[1]): # y is fastest index
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rotatedpoint = np.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
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point = np.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)
if Npoints[2] > 1:
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 = vtk.vtkCellArray()
for i in xrange(totalNpoints):
vertex = vtk.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 = vtk.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 = vtk.vtkSelectEnclosedPoints()
enclosedPoints.SetSurface(surface)
enclosedPoints.SetInput(pointgrid)
enclosedPoints.Update()
# Build kdtree from mesh IPs and match mesh IPs to point grid
if options.verbose: sys.stdout.write("\nBUILDING MAPPING OF GRID POINTS")
kdTree = vtk.vtkKdTree()
kdTree.BuildLocatorFromPoints(meshIPs.GetPoints())
gridToMesh = []
ids = vtk.vtkIdList()
NenclosedPoints = 0
for i in range(pointgrid.GetNumberOfPoints()):
gridToMesh.append([])
if enclosedPoints.IsInside(i):
NenclosedPoints += 1
# here one could use faster(?) "FindClosestPoint" if only first nearest neighbor required
kdTree.FindClosestNPoints(options.interpolation,pointgrid.GetPoint(i),ids)
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)
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x0,y0,z0 = np.dot(R,pointgrid.GetPoint(0)) # first point on slice defines origin
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
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x,y,z = np.dot(R,pointgrid.GetPoint(i)) # point in rotated TSL system
x -= x0 # first point on slice defines origin
y -= y0 # first point on slice defines origin
x *= options.scale
y *= options.scale
angfile.write(getDataLine(interpolatedPhi,x,y,enclosedPoints.IsInside(i)))
# Visualize slices
if options.visualize:
meshMapper = vtk.vtkDataSetMapper()
meshMapper.SetInput(surface)
meshMapper.ScalarVisibilityOff() # do not use scalar data for coloring
meshActor = vtk.vtkActor()
meshActor.SetMapper(meshMapper)
meshActor.GetProperty().SetOpacity(0.2)
meshActor.GetProperty().SetColor(1.0,1.0,0)
meshActor.GetProperty().BackfaceCullingOn()
# meshActor.GetProperty().SetEdgeColor(1,1,0.5)
# meshActor.GetProperty().EdgeVisibilityOn()
boxpoints = vtk.vtkPoints()
for n in range(8):
P = [rotatedbox[0][(n/1)%2],
rotatedbox[1][(n/2)%2],
rotatedbox[2][(n/4)%2]]
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boxpoints.InsertNextPoint(list(np.dot(R.T,np.array(P))))
box = vtk.vtkHexahedron()
for n,i in enumerate([0,1,3,2,4,5,7,6]):
box.GetPointIds().SetId(n,i)
boxgrid = vtk.vtkUnstructuredGrid()
boxgrid.SetPoints(boxpoints)
boxgrid.InsertNextCell(box.GetCellType(), box.GetPointIds())
boxsurfaceFilter = vtk.vtkDataSetSurfaceFilter()
boxsurfaceFilter.SetInput(boxgrid)
boxsurfaceFilter.Update()
boxsurface = boxsurfaceFilter.GetOutput()
boxMapper = vtk.vtkDataSetMapper()
boxMapper.SetInput(boxsurface)
boxActor = vtk.vtkActor()
boxActor.SetMapper(boxMapper)
boxActor.GetProperty().SetLineWidth(2.0)
boxActor.GetProperty().SetRepresentationToWireframe()
gridMapper = vtk.vtkDataSetMapper()
gridMapper.SetInput(pointgrid)
gridActor = vtk.vtkActor()
gridActor.SetMapper(gridMapper)
gridActor.GetProperty().SetColor(0,0,0)
gridActor.GetProperty().SetPointSize(3)
renderer = vtk.vtkRenderer()
renderWindow = vtk.vtkRenderWindow()
renderWindow.FullScreenOn()
renderWindow.AddRenderer(renderer)
renderWindowInteractor = vtk.vtkRenderWindowInteractor()
renderWindowInteractor.SetRenderWindow(renderWindow)
renderer.AddActor(meshActor)
renderer.AddActor(boxActor)
renderer.AddActor(gridActor)
renderer.SetBackground(1,1,1)
renderWindow.Render()
renderWindowInteractor.SetInteractorStyle(vtk.vtkInteractorStyleTrackballCamera())
renderWindowInteractor.Start()