unified structure and names, added test for vtk{point/voxel}cloud
This commit is contained in:
Martin Diehl
parent
bbb6ac8852
commit
fc9d290339
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@ -17,12 +17,12 @@ Produce a VTK point cloud dataset based on coordinates given in an ASCIItable.
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""", version = scriptID)
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parser.add_option('-p','--position',
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dest = 'position',
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parser.add_option('-d', '--deformed',
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dest = 'deformed',
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type = 'string', metavar = 'string',
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help = 'column label for coordinates [%default]')
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help = 'deformed coordinate label [%default]')
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parser.set_defaults(position = 'pos',
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parser.set_defaults(deformed = 'ipdeformedcoord'
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)
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(options, filenames) = parser.parse_args()
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@ -36,7 +36,7 @@ for name in filenames:
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table = damask.ASCIItable(name = name,
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buffered = False, readonly = True)
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except: continue
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damask.util.croak(damask.util.emph(scriptName)+(': '+name if name else ''))
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damask.util.report(scriptName,name)
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# --- interpret header ----------------------------------------------------------------------------
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@ -44,8 +44,10 @@ for name in filenames:
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errors = []
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remarks = []
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if table.label_dimension(options.position) != 3: errors.append('columns "{}" have dimension {}'.format(options.position,
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table.label_dimension(options.position)))
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if table.label_dimension(options.deformed) != 3:
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errors.append('columns "{}" have dimension {}'.format(options.deformed,
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table.label_dimension(options.deformed)))
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if remarks != []: damask.util.croak(remarks)
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if errors != []:
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damask.util.croak(errors)
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@ -54,16 +56,16 @@ for name in filenames:
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# ------------------------------------------ process data ---------------------------------------
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table.data_readArray(options.position)
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table.data_readArray(options.deformed)
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Polydata = vtk.vtkPolyData()
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Points = vtk.vtkPoints()
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Vertices = vtk.vtkCellArray()
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for p in table.data:
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id = Points.InsertNextPoint(p)
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pointID = Points.InsertNextPoint(p)
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Vertices.InsertNextCell(1)
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Vertices.InsertCellPoint(id)
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Vertices.InsertCellPoint(pointID)
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Polydata.SetPoints(Points)
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Polydata.SetVerts(Vertices)
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@ -73,24 +75,20 @@ for name in filenames:
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# ------------------------------------------ output result ---------------------------------------
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if name:
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(dir,filename) = os.path.split(name)
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writer = vtk.vtkXMLPolyDataWriter()
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(directory,filename) = os.path.split(name)
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writer.SetDataModeToBinary()
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writer.SetCompressorTypeToZLib()
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writer.SetFileName(os.path.join(dir,os.path.splitext(filename)[0]+'_{}'.format(options.position) \
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writer.SetFileName(os.path.join(directory,os.path.splitext(filename)[0]
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+'.'+writer.GetDefaultFileExtension()))
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if vtk.VTK_MAJOR_VERSION <= 5: writer.SetInput(Polydata)
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else: writer.SetInputData(Polydata)
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writer.Write()
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else:
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writer = vtk.vtkPolyDataWriter()
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writer = vtk.vtkDataSetWriter()
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writer.WriteToOutputStringOn()
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writer.SetFileTypeToASCII()
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writer.SetHeader('# powered by '+scriptID)
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if vtk.VTK_MAJOR_VERSION <= 5: writer.SetInput(Polydata)
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else: writer.SetInputData(Polydata)
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writer.Write()
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sys.stdout.write(writer.GetOutputString()[0:writer.GetOutputStringLength()])
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if name == None: sys.stdout.write(writer.GetOutputString()[0:writer.GetOutputStringLength()])
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table.close() # close input ASCII table
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table.close()
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@ -19,30 +19,20 @@ Create hexahedral voxels around points in an ASCIItable.
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""", version = scriptID)
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parser.add_option('-p', '--positions',
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dest = 'position',
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parser.add_option('-d', '--deformed',
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dest = 'deformed',
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type = 'string', metavar = 'string',
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help = 'coordinate label [%default]')
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parser.add_option('-s', '--size',
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dest = 'size',
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type = 'float', nargs = 3, metavar = 'float float float',
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help = 'x,y,z size of voxel')
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parser.add_option('-o', '--origin',
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dest = 'origin',
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type = 'float', nargs = 3, metavar = 'float float float',
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help = 'x,y,z origin of coordinate system')
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parser.add_option('-g', '--geom',
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dest = 'geom', action='store_true',
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help = 'derive geometry from geom-file header information [%default]')
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parser.set_defaults(position = 'pos',
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origin = (0.0,0.0,0.0),
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geom = False,
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help = 'deformed coordinate label [%default]')
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parser.add_option('-c','--coordinates',
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dest = 'coords',
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type = 'string', metavar='string',
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help = 'undeformed coordinates label [%default]')
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parser.set_defaults(deformed = 'ipdeformedcoord',
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coords = 'ipinitialcoord',
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)
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(options, filenames) = parser.parse_args()
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if options.size == None and not options.geom:
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parser.error('no size specified.')
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# --- loop over input files -------------------------------------------------------------------------
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@ -53,43 +43,32 @@ for name in filenames:
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table = damask.ASCIItable(name = name,
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buffered = False, readonly = True)
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except: continue
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damask.util.croak(damask.util.emph(scriptName)+(': '+name if name else ''))
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# --- interpret header ----------------------------------------------------------------------------
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damask.util.report(scriptName,name)
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# --------------- interprete header -----------------------------------------------------------------
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table.head_read()
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errors=[]
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if table.label_dimension(options.deformed) != 3: errors.append('columns "{}" have dimension {}'.format(options.deformed,
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table.label_dimension(options.deformed)))
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if table.label_dimension(options.coords) != 3: errors.append('coordinates {} are not a vector.'.format(options.coords))
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if options.geom:
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info,extra_header = table.head_getGeom()
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table.data_readArray([options.coords,options.deformed])
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damask.util.croak(['grid a b c: %s'%(' x '.join(map(str,info['grid']))),
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'size x y z: %s'%(' x '.join(map(str,info['size']))),
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'origin x y z: %s'%(' : '.join(map(str,info['origin']))),
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'homogenization: %i'%info['homogenization'],
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'microstructures: %i'%info['microstructures'],
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])
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else:
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info = {}
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info['size'] = np.ones(3)
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info['grid'] = info['size'] / options.size
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info['origin'] = options.origin
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# --------------- figure out size and grid ---------------------------------------------------------
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coords = [{},{},{}]
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for i in xrange(len(table.data)):
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for j in xrange(3):
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coords[j][str(table.data[i,table.label_index(options.coords)+j])] = True
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grid = np.array(map(len,coords),'i')
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size = grid/np.maximum(np.ones(3,'d'),grid-1.0)* \
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np.array([max(map(float,coords[0].keys()))-min(map(float,coords[0].keys())),\
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max(map(float,coords[1].keys()))-min(map(float,coords[1].keys())),\
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max(map(float,coords[2].keys()))-min(map(float,coords[2].keys())),\
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],'d') # size from bounding box, corrected for cell-centeredness
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errors = []
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if table.label_dimension(options.position) != 3: errors.append('columns "{}" have dimension {}'.format(options.position,
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table.label_dimension(options.position)))
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if np.any(info['grid'] < 1): errors.append('invalid grid a b c.')
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if np.any(info['size'] <= 0.0): errors.append('invalid size x y z.')
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if errors != []:
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damask.util.croak(errors)
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table.close(dismiss = True)
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continue
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size = np.where(grid > 1, size, min(size[grid > 1]/grid[grid > 1])) # spacing for grid==1 equal to smallest among other spacings
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# ------------------------------------------ process data ---------------------------------------
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table.data_readArray(options.position)
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table.data[:,0:3] *= info['size']
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table.data[:,0:3] += info['origin']
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hexPoints = np.array([[-1,-1,-1],
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[ 1,-1,-1],
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[ 1, 1,-1],
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@ -100,7 +79,7 @@ for name in filenames:
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[-1, 1, 1],
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])
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halfDelta = 0.5*info['size']/info['grid']
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halfDelta = 0.5*size/grid
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Points = vtk.vtkPoints()
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Hex = vtk.vtkHexahedron()
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@ -108,8 +87,8 @@ for name in filenames:
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for p in table.data:
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for i,h in enumerate(hexPoints):
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id = Points.InsertNextPoint(p+h*halfDelta)
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Hex.GetPointIds().SetId(i,id)
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pointID = Points.InsertNextPoint(p[table.label_index(options.deformed):table.label_index(options.deformed)+3]+h*halfDelta)
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Hex.GetPointIds().SetId(i,pointID)
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uGrid.InsertNextCell(Hex.GetCellType(), Hex.GetPointIds())
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@ -118,25 +97,21 @@ for name in filenames:
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# ------------------------------------------ output result ---------------------------------------
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if name:
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(dir,filename) = os.path.split(name)
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writer = vtk.vtkXMLUnstructuredGridWriter()
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(directory,filename) = os.path.split(name)
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writer.SetDataModeToBinary()
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writer.SetCompressorTypeToZLib()
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writer.SetFileName(os.path.join(dir,os.path.splitext(filename)[0]+'_{}'.format(options.position) \
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writer.SetFileName(os.path.join(directory,os.path.splitext(filename)[0]
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+'.'+writer.GetDefaultFileExtension()))
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if vtk.VTK_MAJOR_VERSION <= 5: writer.SetInput(uGrid)
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else: writer.SetInputData(uGrid)
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writer.Write()
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else:
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writer = vtk.vtkUnstructuredGridWriter()
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writer = vtk.vtkDataSetWriter()
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writer.WriteToOutputStringOn()
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writer.SetFileTypeToASCII()
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writer.SetHeader('# powered by '+scriptID)
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if vtk.VTK_MAJOR_VERSION <= 5: writer.SetInput(uGrid)
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else: writer.SetInputData(uGrid)
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writer.Write()
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sys.stdout.write(writer.GetOutputString()[0:writer.GetOutputStringLength()])
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if name == None: sys.stdout.write(writer.GetOutputString()[0:writer.GetOutputStringLength()])
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table.close() # close input ASCII table
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