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DAMASK_EICMD
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WIP: making compatible with python3/vtk9

This commit is contained in:
Martin Diehl 2020-08-08 18:19:04 +02:00
parent 0ad189ea9d
commit 0878302961
1 changed files with 56 additions and 74 deletions
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52
processing/post/vtk2ang.py
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@ -1,4 +1,4 @@
#!/usr/bin/env python2.7 #!/usr/bin/env python3
import os import os
import sys import sys
@ -17,7 +17,7 @@ scriptID = ' '.join([scriptName,damask.version])
# ----------------------------- # -----------------------------
def getHeader(filename,sizeFastIndex,sizeSlowIndex,stepsize): def getHeader(filename,sizeFastIndex,sizeSlowIndex,stepsize):
"""Returns header for ang file step size in micrometer""" """Returns header for ang file step size in micrometer."""
return '\n'.join([ \ return '\n'.join([ \
'# TEM_PIXperUM 1.000000', \ '# TEM_PIXperUM 1.000000', \
'# x-star 1.000000', \ '# x-star 1.000000', \
@ -53,7 +53,7 @@ def getHeader(filename,sizeFastIndex,sizeSlowIndex,stepsize):
# ----------------------------- # -----------------------------
def positiveRadians(angle): def positiveRadians(angle):
"""Returns positive angle in radians from angle in degrees""" """Returns positive angle in radians from angle in degrees."""
angle = math.radians(float(angle)) angle = math.radians(float(angle))
while angle < 0.0: while angle < 0.0:
angle += 2.0 * math.pi angle += 2.0 * math.pi
@ -67,7 +67,7 @@ def getDataLine(angles,x,y,validData=True):
Returns string of one line in ang file. Returns string of one line in ang file.
Convention in ang file: y coordinate comes first and is fastest index Convention in ang file: y coordinate comes first and is fastest index
positions in micrometer positions in micrometer.
""" """
info = {True: (9999.9, 1.0, 0,99999,0.0), info = {True: (9999.9, 1.0, 0,99999,0.0),
False: ( -1.0,-1.0,-1, -1,1.0)} False: ( -1.0,-1.0,-1, -1,1.0)}
@ -75,11 +75,9 @@ def getDataLine(angles,x,y,validData=True):
%(tuple(map(positiveRadians,angles))+(y*1e6,x*1e6)+info[validData]) %(tuple(map(positiveRadians,angles))+(y*1e6,x*1e6)+info[validData])
# -------------------------------------------------------------------- # --------------------------------------------------------------------
# MAIN FUNCTION STARTS HERE # MAIN FUNCTION STARTS HERE
# -------------------------------------------------------------------- # --------------------------------------------------------------------
parser = OptionParser(usage='%prog options [file[s]]', description = """ parser = OptionParser(usage='%prog options [file[s]]', description = """
Builds a ang files from a vtk file. Builds a ang files from a vtk file.
@ -110,11 +108,6 @@ parser.add_option('-s','--scale', dest='scale', type='float',
parser.add_option('-r','--resolution', dest='resolution', type='float', parser.add_option('-r','--resolution', dest='resolution', type='float',
metavar ='float', metavar ='float',
help='scaling factor for resolution [%default]') help='scaling factor for resolution [%default]')
parser.add_option('--hex','--hexagonal', dest='hexagonal', action='store_true',
help='use in plane hexagonal grid')
parser.add_option('--interpolation', dest='interpolation', type='int',
metavar='float',
help='number of points for linear interpolation [%default]')
parser.add_option('--verbose', dest='verbose', action='store_true', parser.add_option('--verbose', dest='verbose', action='store_true',
help='verbose mode') help='verbose mode')
parser.add_option('--visualize', dest='visualize', action='store_true', parser.add_option('--visualize', dest='visualize', action='store_true',
@ -122,7 +115,6 @@ parser.add_option('--visualize', dest='visualize', action='store_true
parser.set_defaults(dispLabel = 'displacement') parser.set_defaults(dispLabel = 'displacement')
parser.set_defaults(eulerLabel = ['1_1_eulerangles','1_2_eulerangles','1_3_eulerangles']) 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(normal = [0.0,0.0,-1.0])
parser.set_defaults(up = [0.0,1.0,0.0]) parser.set_defaults(up = [0.0,1.0,0.0])
parser.set_defaults(Nslices = 1) parser.set_defaults(Nslices = 1)
@ -130,7 +122,6 @@ parser.set_defaults(distance = 0.0)
parser.set_defaults(scale = 1.0) parser.set_defaults(scale = 1.0)
parser.set_defaults(resolution = 1.0) parser.set_defaults(resolution = 1.0)
parser.set_defaults(dispScaling = 1.0) parser.set_defaults(dispScaling = 1.0)
parser.set_defaults(interpolation = 1)
parser.set_defaults(verbose = False) parser.set_defaults(verbose = False)
parser.set_defaults(visualize = False) parser.set_defaults(visualize = False)
(options,filenames) = parser.parse_args() (options,filenames) = parser.parse_args()
@ -153,15 +144,6 @@ if np.dot(np.array(options.normal),np.array(options.up)) > 1e-3:
parser.error('normal vector and up vector have to be orthogonal') 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 #--- ITERATE OVER FILES AND PROCESS THEM
for filename in filenames: for filename in filenames:
@ -180,8 +162,8 @@ for filename in filenames:
if options.verbose: sys.stdout.write("\nGETTING EULER ANGLES\n") if options.verbose: sys.stdout.write("\nGETTING EULER ANGLES\n")
angles = {} angles = {}
for i in range(reader.GetNumberOfScalarsInFile()): for i in range(undeformedMesh.GetPointData().GetNumberOfArrays()):
scalarName = reader.GetScalarsNameInFile(i) scalarName = undeformedMesh.GetPointData().GetArrayName(i)
if scalarName in options.eulerLabel: if scalarName in options.eulerLabel:
angles[scalarName] = undeformedMesh.GetCellData().GetScalars(scalarName) angles[scalarName] = undeformedMesh.GetCellData().GetScalars(scalarName)
if options.verbose: sys.stdout.write(" found scalar with name %s\n"%scalarName) if options.verbose: sys.stdout.write(" found scalar with name %s\n"%scalarName)
@ -196,7 +178,7 @@ for filename in filenames:
if options.verbose: sys.stdout.write("\nDEFORM MESH\n") if options.verbose: sys.stdout.write("\nDEFORM MESH\n")
warpVector = vtk.vtkWarpVector() warpVector = vtk.vtkWarpVector()
undeformedMesh.GetPointData().SetActiveVectors(options.dispLabel) undeformedMesh.GetPointData().SetActiveVectors(options.dispLabel)
warpVector.SetInput(undeformedMesh) warpVector.SetInputData(undeformedMesh)
warpVector.Update() warpVector.Update()
deformedMesh = warpVector.GetOutput() deformedMesh = warpVector.GetOutput()
box = deformedMesh.GetBounds() # bounding box in mesh system box = deformedMesh.GetBounds() # bounding box in mesh system
@ -212,7 +194,7 @@ for filename in filenames:
if options.verbose: sys.stdout.write("\nGETTING CELL CENTERS OF DEFORMED MESH\n") if options.verbose: sys.stdout.write("\nGETTING CELL CENTERS OF DEFORMED MESH\n")
cellCenter = vtk.vtkCellCenters() cellCenter = vtk.vtkCellCenters()
cellCenter.SetVertexCells(0) # do not generate vertex cells, just points cellCenter.SetVertexCells(0) # do not generate vertex cells, just points
cellCenter.SetInput(deformedMesh) cellCenter.SetInputData(deformedMesh)
cellCenter.Update() cellCenter.Update()
meshIPs = cellCenter.GetOutput() meshIPs = cellCenter.GetOutput()
@ -221,7 +203,7 @@ for filename in filenames:
if options.verbose: sys.stdout.write("\nGETTING OUTER SURFACE OF DEFORMED MESH\n") if options.verbose: sys.stdout.write("\nGETTING OUTER SURFACE OF DEFORMED MESH\n")
surfaceFilter = vtk.vtkDataSetSurfaceFilter() surfaceFilter = vtk.vtkDataSetSurfaceFilter()
surfaceFilter.SetInput(deformedMesh) surfaceFilter.SetInputData(deformedMesh)
surfaceFilter.Update() surfaceFilter.Update()
surface = surfaceFilter.GetOutput() surface = surfaceFilter.GetOutput()
@ -250,9 +232,9 @@ for filename in filenames:
if options.verbose: sys.stdout.write("\nGETTING BOUNDING BOX IN ROTATED SYSTEM\n") if options.verbose: sys.stdout.write("\nGETTING BOUNDING BOX IN ROTATED SYSTEM\n")
rotatedbox = [[np.inf,-np.inf] for i in range(3)] # bounding box in rotated TSL system 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 for n in range(8): # loop over eight vertices of mesh bounding box
vert = np.array([box[0+(n/1)%2], vert = np.array([box[0+(n//1)%2],
box[2+(n/2)%2], box[2+(n//2)%2],
box[4+(n/4)%2]]) # vertex in mesh system box[4+(n//4)%2]]) # vertex in mesh system
rotatedvert = np.dot(R,vert) # vertex in rotated system rotatedvert = np.dot(R,vert) # vertex in rotated system
for i in range(3): for i in range(3):
rotatedbox[i][0] = min(rotatedbox[i][0],rotatedvert[i]) rotatedbox[i][0] = min(rotatedbox[i][0],rotatedvert[i])
@ -282,8 +264,8 @@ for filename in filenames:
correction.extend([0.0]) correction.extend([0.0])
options.distance = extent[2] / float(options.Nslices) options.distance = extent[2] / float(options.Nslices)
for i in range(3): for i in range(3):
rotatedbox[i][0] = rotatedbox[i][0] - 0.5 * correction[i] rotatedbox[i][0] -= 0.5 * correction[i]
rotatedbox[i][1] = rotatedbox[i][1] + 0.5 * correction[i] rotatedbox[i][1] += 0.5 * correction[i]
extent[i] = rotatedbox[i][1] - rotatedbox[i][0] extent[i] = rotatedbox[i][1] - rotatedbox[i][0]
NpointsPerSlice = Npoints[0] * Npoints[1] NpointsPerSlice = Npoints[0] * Npoints[1]
totalNpoints = NpointsPerSlice * Npoints[2] totalNpoints = NpointsPerSlice * Npoints[2]
@ -304,8 +286,8 @@ for filename in filenames:
for j in range(Npoints[0]): for j in range(Npoints[0]):
for i in range(Npoints[1]): # y is fastest index for i in range(Npoints[1]): # y is fastest index
rotatedpoint = np.array([rotatedbox[0][0] + (float(j) + 0.5) * options.resolution, rotatedpoint = np.array([rotatedbox[0][0] + (float(j) + 0.5) * options.resolution,
rotatedbox[1][0] + (float(i) + 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 rotatedbox[2][0] + (float(k) + 0.5) * options.distance ]) # point in rotated system
point = np.dot(R.T,rotatedpoint) # point in mesh system point = np.dot(R.T,rotatedpoint) # point in mesh system
points.InsertNextPoint(list(point)) points.InsertNextPoint(list(point))
if options.verbose: if options.verbose:
@ -357,7 +339,7 @@ for filename in filenames:
if enclosedPoints.IsInside(i): if enclosedPoints.IsInside(i):
NenclosedPoints += 1 NenclosedPoints += 1
# here one could use faster(?) "FindClosestPoint" if only first nearest neighbor required # here one could use faster(?) "FindClosestPoint" if only first nearest neighbor required
kdTree.FindClosestNPoints(options.interpolation,pointgrid.GetPoint(i),ids) kdTree.FindClosestNPoints(1,pointgrid.GetPoint(i),ids)
for j in range(ids.GetNumberOfIds()): for j in range(ids.GetNumberOfIds()):
gridToMesh[-1].extend([ids.GetId(j)]) gridToMesh[-1].extend([ids.GetId(j)])
if options.verbose: if options.verbose: