vtk files, mainly removed from vtk import *
This commit is contained in:
Martin Diehl
parent
f7fedc4744
commit
9fa49b8584
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@ -4,17 +4,15 @@
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import os,string,math,sys
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import numpy as np
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from optparse import OptionParser
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from vtk import *
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import vtk
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import damask
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scriptName = os.path.splitext(os.path.basename(__file__))[0]
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scriptID = ' '.join([scriptName,damask.version])
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# -----------------------------
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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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# step size in micrometer
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"""returns header for ang file step size in micrometer"""
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return '\n'.join([ \
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'# TEM_PIXperUM 1.000000', \
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'# x-star 1.000000', \
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@ -50,10 +48,7 @@ def getHeader(filename,sizeFastIndex,sizeSlowIndex,stepsize):
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# -----------------------------
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def positiveRadians(angle):
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# -----------------------------
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# returns positive angle in radians
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# gets angle in degrees
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"""returns positive angle in radians from angle in degrees"""
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angle = math.radians(float(angle))
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while angle < 0.0:
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angle += 2.0 * math.pi
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@ -63,11 +58,12 @@ def positiveRadians(angle):
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# -----------------------------
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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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"""
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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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"""
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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))+(y*1e6,x*1e6)+info[validData])
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@ -155,10 +151,9 @@ if options.hexagonal:
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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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# Read the source file
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reader = vtk.vtkUnstructuredGridReader()
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reader.SetFileName(filename)
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reader.ReadAllScalarsOn()
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reader.ReadAllVectorsOn()
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@ -166,7 +161,7 @@ for filename in filenames:
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undeformedMesh = reader.GetOutput()
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# Get euler angles from cell data
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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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@ -177,14 +172,14 @@ for filename in filenames:
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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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if label not in angles.keys():
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parser.error('Could not find scalar data with name %s'%label)
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# Get deformed mesh
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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 = vtk.vtkWarpVector()
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undeformedMesh.GetPointData().SetActiveVectors(options.dispLabel)
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warpVector.SetInput(undeformedMesh)
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warpVector.Update()
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@ -197,29 +192,29 @@ for filename in filenames:
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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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# 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 = vtk.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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cellCenter.Update()
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meshIPs = cellCenter.GetOutput()
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# Get outer surface of deformed mesh
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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 = vtk.vtkDataSetSurfaceFilter()
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surfaceFilter.SetInput(deformedMesh)
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surfaceFilter.Update()
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surface = surfaceFilter.GetOutput()
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# Get coordinate system for ang files
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# z-vector is normal to slices
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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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# Get coordinate system for ang files
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# z-vector is normal to slices
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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 = np.array(options.normal,dtype='float')
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@ -235,7 +230,7 @@ for filename in filenames:
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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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# 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 = [[np.inf,-np.inf] for i in range(3)] # bounding box in rotated TSL system
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@ -254,8 +249,8 @@ for filename in filenames:
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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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# 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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@ -284,12 +279,12 @@ for filename in filenames:
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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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# 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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points = vtk.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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for i in xrange(Npoints[1]): # y is fastest index
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@ -309,9 +304,9 @@ for filename in filenames:
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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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vertices = vtk.vtkCellArray()
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for i in xrange(totalNpoints):
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vertex = vtkVertex()
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vertex = vtk.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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@ -319,34 +314,35 @@ for filename in filenames:
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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 = vtk.vtkPolyData()
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pointgrid.SetPoints(points)
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pointgrid.SetVerts(vertices)
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pointgrid.Update()
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# Find out which points reside inside mesh geometry
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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 = vtk.vtkSelectEnclosedPoints()
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enclosedPoints.SetSurface(surface)
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enclosedPoints.SetInput(pointgrid)
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enclosedPoints.Update()
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# Build kdtree from mesh IPs and match mesh IPs to point grid
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# Build kdtree from mesh IPs and match mesh IPs to point grid
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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 = vtk.vtkKdTree()
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kdTree.BuildLocatorFromPoints(meshIPs.GetPoints())
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gridToMesh = []
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ids = vtkIdList()
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ids = vtk.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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# here one could use faster(?) "FindClosestPoint" if only first nearest neighbor required
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kdTree.FindClosestNPoints(options.interpolation,pointgrid.GetPoint(i),ids)
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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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@ -358,7 +354,7 @@ for filename in filenames:
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# ITERATE OVER SLICES AND CREATE ANG FILE
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# ITERATE OVER SLICES AND CREATE ANG FILE
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if options.verbose:
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sys.stdout.write("\nWRITING OUT ANG FILES\n")
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@ -404,13 +400,13 @@ for filename in filenames:
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angfile.write(getDataLine(interpolatedPhi,x,y,enclosedPoints.IsInside(i)))
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# Visualize slices
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# Visualize slices
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if options.visualize:
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meshMapper = vtkDataSetMapper()
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meshMapper = vtk.vtkDataSetMapper()
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meshMapper.SetInput(surface)
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meshMapper.ScalarVisibilityOff() # do not use scalar data for coloring
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meshActor = vtkActor()
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meshActor = vtk.vtkActor()
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meshActor.SetMapper(meshMapper)
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meshActor.GetProperty().SetOpacity(0.2)
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meshActor.GetProperty().SetColor(1.0,1.0,0)
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@ -418,43 +414,43 @@ for filename in filenames:
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# meshActor.GetProperty().SetEdgeColor(1,1,0.5)
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# meshActor.GetProperty().EdgeVisibilityOn()
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boxpoints = vtkPoints()
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boxpoints = vtk.vtkPoints()
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for n in range(8):
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P = [rotatedbox[0][(n/1)%2],
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rotatedbox[1][(n/2)%2],
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rotatedbox[2][(n/4)%2]]
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boxpoints.InsertNextPoint(list(np.dot(R.T,np.array(P))))
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box = vtkHexahedron()
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box = vtk.vtkHexahedron()
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for n,i in enumerate([0,1,3,2,4,5,7,6]):
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box.GetPointIds().SetId(n,i)
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boxgrid = vtkUnstructuredGrid()
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boxgrid = vtk.vtkUnstructuredGrid()
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boxgrid.SetPoints(boxpoints)
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boxgrid.InsertNextCell(box.GetCellType(), box.GetPointIds())
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boxsurfaceFilter = vtkDataSetSurfaceFilter()
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boxsurfaceFilter = vtk.vtkDataSetSurfaceFilter()
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boxsurfaceFilter.SetInput(boxgrid)
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boxsurfaceFilter.Update()
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boxsurface = boxsurfaceFilter.GetOutput()
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boxMapper = vtkDataSetMapper()
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boxMapper = vtk.vtkDataSetMapper()
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boxMapper.SetInput(boxsurface)
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boxActor = vtkActor()
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boxActor = vtk.vtkActor()
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boxActor.SetMapper(boxMapper)
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boxActor.GetProperty().SetLineWidth(2.0)
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boxActor.GetProperty().SetRepresentationToWireframe()
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gridMapper = vtkDataSetMapper()
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gridMapper = vtk.vtkDataSetMapper()
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gridMapper.SetInput(pointgrid)
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gridActor = vtkActor()
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gridActor = vtk.vtkActor()
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gridActor.SetMapper(gridMapper)
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gridActor.GetProperty().SetColor(0,0,0)
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gridActor.GetProperty().SetPointSize(3)
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renderer = vtkRenderer()
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renderWindow = vtkRenderWindow()
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renderer = vtk.vtkRenderer()
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renderWindow = vtk.vtkRenderWindow()
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renderWindow.FullScreenOn()
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renderWindow.AddRenderer(renderer)
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renderWindowInteractor = vtkRenderWindowInteractor()
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renderWindowInteractor = vtk.vtkRenderWindowInteractor()
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renderWindowInteractor.SetRenderWindow(renderWindow)
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renderer.AddActor(meshActor)
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renderer.AddActor(boxActor)
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@ -462,6 +458,6 @@ for filename in filenames:
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renderer.SetBackground(1,1,1)
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renderWindow.Render()
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renderWindowInteractor.SetInteractorStyle(vtkInteractorStyleTrackballCamera())
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renderWindowInteractor.SetInteractorStyle(vtk.vtkInteractorStyleTrackballCamera())
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renderWindowInteractor.Start()
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@ -10,7 +10,6 @@ scriptID = ' '.join([scriptName,damask.version])
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# -----------------------------
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def findTag(filename,tag):
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# -----------------------------
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with open(filename,'r') as myfile:
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mypattern = re.compile(str(tag))
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@ -4,7 +4,7 @@
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import os,sys,shutil
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import damask
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from optparse import OptionParser
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from vtk import *
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import vtk
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scriptName = os.path.splitext(os.path.basename(__file__))[0]
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scriptID = ' '.join([scriptName,damask.version])
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@ -44,18 +44,16 @@ for filename in filenames:
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for filename in filenames:
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# Read the source file
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sys.stdout.write('read file "%s" ...'%filename)
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sys.stdout.flush()
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suffix = os.path.splitext(filename)[1]
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if suffix == '.vtk':
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reader = vtkUnstructuredGridReader()
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reader = vtk.vtkUnstructuredGridReader()
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reader.ReadAllScalarsOn()
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reader.ReadAllVectorsOn()
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reader.ReadAllTensorsOn()
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elif suffix == '.vtu':
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reader = vtkXMLUnstructuredGridReader()
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reader = vtk.vtkXMLUnstructuredGridReader()
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else:
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parser.error('filetype "%s" not supported'%suffix)
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reader.SetFileName(filename)
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@ -65,7 +63,7 @@ for filename in filenames:
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sys.stdout.flush()
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# Read the scalar data
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# Read the scalar data
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scalarData = {}
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scalarsToBeRemoved = []
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@ -83,19 +81,18 @@ for filename in filenames:
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scalarsToBeRemoved.append(scalarName)
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for scalarName in scalarsToBeRemoved:
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uGrid.GetCellData().RemoveArray(scalarName)
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# uGrid.UpdateData()
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sys.stdout.write('\rread scalar data done\n')
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sys.stdout.flush()
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# Convert the scalar data to vector data
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# Convert the scalar data to vector data
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NscalarData = len(scalarData)
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for n,label in enumerate(scalarData):
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sys.stdout.write("\rconvert to vector data %d%%" %(100*n/NscalarData))
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sys.stdout.flush()
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Nvalues = scalarData[label][0].GetNumberOfTuples()
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vectorData = vtkDoubleArray()
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vectorData = vtk.vtkDoubleArray()
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vectorData.SetName(label)
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vectorData.SetNumberOfComponents(3) # set this before NumberOfTuples !!!
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vectorData.SetNumberOfTuples(Nvalues)
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@ -103,16 +100,15 @@ for filename in filenames:
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for j in range(3):
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vectorData.SetComponent(i,j,scalarData[label][j].GetValue(i))
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uGrid.GetCellData().AddArray(vectorData)
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# uGrid.GetCellData().SetActiveVectors(label)
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sys.stdout.write('\rconvert to vector data done\n')
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# Write to new vtk file
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# Write to new vtk file
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outfilename = os.path.splitext(filename)[0]+'.vtu'
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sys.stdout.write('write to file "%s" ...'%outfilename)
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sys.stdout.flush()
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writer = vtkXMLUnstructuredGridWriter()
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writer = vtk.vtkXMLUnstructuredGridWriter()
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writer.SetFileName(outfilename+'_tmp')
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writer.SetDataModeToAscii()
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writer.SetInput(uGrid)
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