WIP: making compatible with python3/vtk9
This commit is contained in:
Martin Diehl
parent
0ad189ea9d
commit
0878302961
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@ -1,4 +1,4 @@
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#!/usr/bin/env python2.7
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#!/usr/bin/env python3
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import os
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import sys
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@ -17,7 +17,7 @@ scriptID = ' '.join([scriptName,damask.version])
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# -----------------------------
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def getHeader(filename,sizeFastIndex,sizeSlowIndex,stepsize):
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"""Returns header for ang file 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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@ -53,7 +53,7 @@ def getHeader(filename,sizeFastIndex,sizeSlowIndex,stepsize):
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# -----------------------------
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def positiveRadians(angle):
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"""Returns positive angle in radians from 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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@ -67,7 +67,7 @@ def getDataLine(angles,x,y,validData=True):
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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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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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@ -75,11 +75,9 @@ def getDataLine(angles,x,y,validData=True):
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%(tuple(map(positiveRadians,angles))+(y*1e6,x*1e6)+info[validData])
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# --------------------------------------------------------------------
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# MAIN FUNCTION STARTS HERE
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# --------------------------------------------------------------------
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parser = OptionParser(usage='%prog options [file[s]]', description = """
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Builds a ang files from a vtk file.
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@ -110,11 +108,6 @@ parser.add_option('-s','--scale', dest='scale', type='float',
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parser.add_option('-r','--resolution', dest='resolution', type='float',
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metavar ='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')
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parser.add_option('--interpolation', dest='interpolation', type='int',
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metavar='float',
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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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help='verbose mode')
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parser.add_option('--visualize', dest='visualize', action='store_true',
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@ -122,7 +115,6 @@ parser.add_option('--visualize', dest='visualize', action='store_true
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parser.set_defaults(dispLabel = 'displacement')
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parser.set_defaults(eulerLabel = ['1_1_eulerangles','1_2_eulerangles','1_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(up = [0.0,1.0,0.0])
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parser.set_defaults(Nslices = 1)
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@ -130,7 +122,6 @@ parser.set_defaults(distance = 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(interpolation = 1)
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parser.set_defaults(verbose = False)
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parser.set_defaults(visualize = False)
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(options,filenames) = parser.parse_args()
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@ -153,15 +144,6 @@ if np.dot(np.array(options.normal),np.array(options.up)) > 1e-3:
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parser.error('normal vector and up vector have to be orthogonal')
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# check for options that are not yet implemented
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if options.interpolation > 1:
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parser.error('interpolation not yet supported')
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if options.hexagonal:
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parser.error('hexagonal grid not yet supported')
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#--- ITERATE OVER FILES AND PROCESS THEM
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for filename in filenames:
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@ -180,8 +162,8 @@ for filename in filenames:
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if options.verbose: sys.stdout.write("\nGETTING EULER ANGLES\n")
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angles = {}
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for i in range(reader.GetNumberOfScalarsInFile()):
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scalarName = reader.GetScalarsNameInFile(i)
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for i in range(undeformedMesh.GetPointData().GetNumberOfArrays()):
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scalarName = undeformedMesh.GetPointData().GetArrayName(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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@ -196,7 +178,7 @@ for filename in filenames:
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if options.verbose: sys.stdout.write("\nDEFORM MESH\n")
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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.SetInputData(undeformedMesh)
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warpVector.Update()
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deformedMesh = warpVector.GetOutput()
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box = deformedMesh.GetBounds() # bounding box in mesh system
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@ -212,7 +194,7 @@ for filename in filenames:
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if options.verbose: sys.stdout.write("\nGETTING CELL CENTERS OF DEFORMED MESH\n")
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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.SetInputData(deformedMesh)
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cellCenter.Update()
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meshIPs = cellCenter.GetOutput()
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@ -221,7 +203,7 @@ for filename in filenames:
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if options.verbose: sys.stdout.write("\nGETTING OUTER SURFACE OF DEFORMED MESH\n")
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surfaceFilter = vtk.vtkDataSetSurfaceFilter()
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surfaceFilter.SetInput(deformedMesh)
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surfaceFilter.SetInputData(deformedMesh)
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surfaceFilter.Update()
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surface = surfaceFilter.GetOutput()
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@ -250,9 +232,9 @@ for filename in filenames:
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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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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],
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box[2+(n/2)%2],
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box[4+(n/4)%2]]) # vertex in mesh system
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vert = np.array([box[0+(n//1)%2],
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box[2+(n//2)%2],
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box[4+(n//4)%2]]) # vertex in mesh system
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rotatedvert = np.dot(R,vert) # vertex in rotated system
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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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@ -282,8 +264,8 @@ for filename in filenames:
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correction.extend([0.0])
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options.distance = extent[2] / float(options.Nslices)
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for i in range(3):
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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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rotatedbox[i][0] -= 0.5 * correction[i]
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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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@ -304,8 +286,8 @@ for filename in filenames:
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for j in range(Npoints[0]):
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for i in range(Npoints[1]): # y is fastest index
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rotatedpoint = np.array([rotatedbox[0][0] + (float(j) + 0.5) * options.resolution,
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rotatedbox[1][0] + (float(i) + 0.5) * options.resolution,
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rotatedbox[2][0] + (float(k) + 0.5) * options.distance ]) # point in rotated system
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rotatedbox[1][0] + (float(i) + 0.5) * options.resolution,
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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
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points.InsertNextPoint(list(point))
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if options.verbose:
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@ -357,7 +339,7 @@ for filename in filenames:
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if enclosedPoints.IsInside(i):
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NenclosedPoints += 1
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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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kdTree.FindClosestNPoints(1,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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