Add MSC.Marc to VTK conversion support
marc_to_vtk.py takes Marc input file, subdivides it and creates a vtkUnstructuredGrid .vtu file with the resulting geometry. Currently supports hexahedron elements. vtk_addGridData.py adds nodal/cell data to some VTK grid. It is essentially vtk_addRectilinearGridData with support for unstructured grid (.vtu) format, which is marc_to_vtk.py's output.
This commit is contained in:
brendanvk
parent
beedd27a16
commit
a03bb1ec3e
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#!/usr/bin/env python2.7
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# -*- coding: UTF-8 no BOM -*-
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import os,re
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import argparse
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import damask
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import vtk, numpy as np
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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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parser = argparse.ArgumentParser(description='Convert from Marc input file format to VTK', version = scriptID)
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parser.add_argument('filename', type=str, nargs='+', help='files to convert')
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args = parser.parse_args()
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files = args.filename
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if type(files) is str:
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files = [files]
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for f in files:
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with open(f, 'r') as marcfile:
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marctext = marcfile.read();
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# Extract connectivity chunk from file...
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connectivity_text = re.findall(r'connectivity[\n\r]+(.*?)[\n\r]+[a-zA-Z]', marctext, flags=(re.MULTILINE | re.DOTALL))[0]
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connectivity_lines = re.split(r'[\n\r]+', connectivity_text, flags=(re.MULTILINE | re.DOTALL))
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connectivity_header = connectivity_lines[0]
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connectivity_lines = connectivity_lines[1:]
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# Construct element map
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elements = dict(map(lambda line:
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(
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int(line[0:10]), # index
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{
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'type': int(line[10:20]),
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'verts': list(map(int, re.split(r' +', line[20:].strip())))
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}
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), connectivity_lines))
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# Extract coordinate chunk from file
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coordinates_text = re.findall(r'coordinates[\n\r]+(.*?)[\n\r]+[a-zA-Z]', marctext, flags=(re.MULTILINE | re.DOTALL))[0]
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coordinates_lines = re.split(r'[\n\r]+', coordinates_text, flags=(re.MULTILINE | re.DOTALL))
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coordinates_header = coordinates_lines[0]
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coordinates_lines = coordinates_lines[1:]
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# marc input file does not use "e" in scientific notation, this adds it and converts
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fl_format = lambda string: float(re.sub(r'(\d)([\+\-])', r'\1e\2', string))
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# Construct coordinate map
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coordinates = dict(map(lambda line:
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(
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int(line[0:10]),
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np.array([
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fl_format(line[10:30]),
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fl_format(line[30:50]),
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fl_format(line[50:70])
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])
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), coordinates_lines))
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# Subdivide volumes
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grid = vtk.vtkUnstructuredGrid()
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vertex_count = len(coordinates)
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edge_to_vert = dict() # when edges are subdivided, a new vertex in the middle is produced and placed in here
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ordered_pair = lambda a, b: (a, b) if a < b else (b, a) # edges are bidirectional
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def subdivide_edge(vert1, vert2):
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edge = ordered_pair(vert1, vert2)
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if edge in edge_to_vert:
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return edge_to_vert[edge]
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newvert = len(coordinates) + 1
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coordinates[newvert] = 0.5 * (coordinates[vert1] + coordinates[vert2]) # Average
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edge_to_vert[edge] = newvert;
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return newvert;
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for el_id in range(1, len(elements) + 1):
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el = elements[el_id]
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if el['type'] == 7:
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# Hexahedron, subdivided
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# There may be a better way to iterate over these, but this is consistent
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# with the ordering scheme provided at https://damask.mpie.de/pub/Documentation/ElementType
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subverts = np.zeros((3,3,3), dtype=int)
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# Get corners
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subverts[0, 0, 0] = el['verts'][0]
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subverts[2, 0, 0] = el['verts'][1]
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subverts[2, 2, 0] = el['verts'][2]
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subverts[0, 2, 0] = el['verts'][3]
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subverts[0, 0, 2] = el['verts'][4]
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subverts[2, 0, 2] = el['verts'][5]
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subverts[2, 2, 2] = el['verts'][6]
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subverts[0, 2, 2] = el['verts'][7]
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# lower edges
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subverts[1, 0, 0] = subdivide_edge(subverts[0, 0, 0], subverts[2, 0, 0])
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subverts[2, 1, 0] = subdivide_edge(subverts[2, 0, 0], subverts[2, 2, 0])
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subverts[1, 2, 0] = subdivide_edge(subverts[2, 2, 0], subverts[0, 2, 0])
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subverts[0, 1, 0] = subdivide_edge(subverts[0, 2, 0], subverts[0, 0, 0])
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# middle edges
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subverts[0, 0, 1] = subdivide_edge(subverts[0, 0, 0], subverts[0, 0, 2])
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subverts[2, 0, 1] = subdivide_edge(subverts[2, 0, 0], subverts[2, 0, 2])
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subverts[2, 2, 1] = subdivide_edge(subverts[2, 2, 0], subverts[2, 2, 2])
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subverts[0, 2, 1] = subdivide_edge(subverts[0, 2, 0], subverts[0, 2, 2])
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# top edges
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subverts[1, 0, 2] = subdivide_edge(subverts[0, 0, 2], subverts[2, 0, 2])
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subverts[2, 1, 2] = subdivide_edge(subverts[2, 0, 2], subverts[2, 2, 2])
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subverts[1, 2, 2] = subdivide_edge(subverts[2, 2, 2], subverts[0, 2, 2])
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subverts[0, 1, 2] = subdivide_edge(subverts[0, 2, 2], subverts[0, 0, 2])
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# then faces... The edge_to_vert addition is due to there being two ways
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# to calculate a face, depending which opposite vertices are used to subdivide
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subverts[1, 1, 0] = subdivide_edge(subverts[1, 0, 0], subverts[1, 2, 0])
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edge_to_vert[ordered_pair(subverts[0, 1, 0], subverts[2, 1, 0])] = subverts[1, 1, 0]
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subverts[1, 0, 1] = subdivide_edge(subverts[1, 0, 0], subverts[1, 0, 2])
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edge_to_vert[ordered_pair(subverts[0, 0, 1], subverts[2, 0, 1])] = subverts[1, 0, 1]
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subverts[2, 1, 1] = subdivide_edge(subverts[2, 1, 0], subverts[2, 1, 2])
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edge_to_vert[ordered_pair(subverts[2, 0, 1], subverts[2, 2, 1])] = subverts[2, 1, 1]
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subverts[1, 2, 1] = subdivide_edge(subverts[1, 2, 0], subverts[1, 2, 2])
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edge_to_vert[ordered_pair(subverts[0, 2, 1], subverts[2, 2, 1])] = subverts[1, 2, 1]
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subverts[0, 1, 1] = subdivide_edge(subverts[0, 1, 0], subverts[0, 1, 2])
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edge_to_vert[ordered_pair(subverts[0, 0, 1], subverts[0, 2, 1])] = subverts[0, 1, 1]
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subverts[1, 1, 2] = subdivide_edge(subverts[1, 0, 2], subverts[1, 2, 2])
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edge_to_vert[ordered_pair(subverts[0, 1, 2], subverts[2, 1, 2])] = subverts[1, 1, 2]
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# and finally the center. There are three ways to calculate, but elements should
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# not intersect, so the edge_to_vert part isn't needed here.
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subverts[1, 1, 1] = subdivide_edge(subverts[1, 1, 0], subverts[1, 1, 2])
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# Now make the hexahedron subelements
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# order in which vtk expects vertices for a hexahedron
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order = np.array([(0,0,0),(1,0,0),(1,1,0),(0,1,0),(0,0,1),(1,0,1),(1,1,1),(0,1,1)])
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for z in range(2):
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for y in range(2):
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for x in range(2):
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hex_ = vtk.vtkHexahedron()
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for vert_id in range(8):
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coord = order[vert_id] + (x, y, z)
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hex_.GetPointIds().SetId(vert_id, subverts[coord[0], coord[1], coord[2]] - 1) # minus one, since vtk starts at zero but marc starts at one
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grid.InsertNextCell(hex_.GetCellType(), hex_.GetPointIds())
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else:
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damask.util.croak('Unsupported Marc element type: {} (skipping)'.format(el['type']))
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# Load all points
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points = vtk.vtkPoints()
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for point in range(1, len(coordinates) + 1): # marc indices start at 1
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points.InsertNextPoint(coordinates[point].tolist())
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grid.SetPoints(points)
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# grid now contains the elements from the given marc file
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writer = vtk.vtkXMLUnstructuredGridWriter()
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writer.SetFileName(re.sub(r'\..+', ".vtu", f)) # *.vtk extension does not work in paraview
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#writer.SetCompressorTypeToZLib()
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if vtk.VTK_MAJOR_VERSION <= 5: writer.SetInput(grid)
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else: writer.SetInputData(grid)
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writer.Write()
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#!/usr/bin/env python2.7
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# -*- coding: UTF-8 no BOM -*-
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import os,vtk
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import damask
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from vtk.util import numpy_support
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from collections import defaultdict
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from optparse import OptionParser
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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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# MAIN
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# --------------------------------------------------------------------
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msg = "Add scalars, vectors, and/or an RGB tuple from"
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msg += "an ASCIItable to existing VTK grid (.vtr/.vtk/.vtu)."
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parser = OptionParser(option_class=damask.extendableOption,
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usage='%prog options [file[s]]',
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description = msg,
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version = scriptID)
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parser.add_option( '--vtk',
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dest = 'vtk',
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type = 'string', metavar = 'string',
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help = 'VTK file name')
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parser.add_option( '--inplace',
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dest = 'inplace',
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action = 'store_true',
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help = 'modify VTK file in-place')
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parser.add_option('-r', '--render',
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dest = 'render',
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action = 'store_true',
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help = 'open output in VTK render window')
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parser.add_option('-d', '--data',
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dest = 'data',
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action = 'extend', metavar = '<string LIST>',
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help = 'scalar/vector value(s) label(s)')
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parser.add_option('-t', '--tensor',
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dest = 'tensor',
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action = 'extend', metavar = '<string LIST>',
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help = 'tensor (3x3) value label(s)')
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parser.add_option('-c', '--color',
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dest = 'color',
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action = 'extend', metavar = '<string LIST>',
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help = 'RGB color tuple label')
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parser.set_defaults(data = [],
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tensor = [],
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color = [],
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inplace = False,
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render = False,
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)
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(options, filenames) = parser.parse_args()
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if not options.vtk: parser.error('No VTK file specified.')
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if not os.path.exists(options.vtk): parser.error('VTK file does not exist.')
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if os.path.splitext(options.vtk)[1] == '.vtr':
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reader = vtk.vtkXMLRectilinearGridReader()
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reader.SetFileName(options.vtk)
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reader.Update()
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rGrid = reader.GetOutput()
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writer = vtk.vtkXMLRectilinearGridWriter()
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writer.SetFileName(os.path.splitext(options.vtk)[0]+('.vtr' if options.inplace else '_added.vtr'))
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elif os.path.splitext(options.vtk)[1] == '.vtk':
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reader = vtk.vtkGenericDataObjectReader()
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reader.SetFileName(options.vtk)
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reader.Update()
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rGrid = reader.GetRectilinearGridOutput()
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writer = vtk.vtkXMLRectilinearGridWriter()
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writer.SetFileName(os.path.splitext(options.vtk)[0]+('.vtr' if options.inplace else '_added.vtr'))
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elif os.path.splitext(options.vtk)[1] == '.vtu':
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reader = vtk.vtkXMLUnstructuredGridReader()
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reader.SetFileName(options.vtk)
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reader.Update()
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rGrid = reader.GetOutput()
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writer = vtk.vtkXMLUnstructuredGridWriter()
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writer.SetFileName(os.path.splitext(options.vtk)[0]+('.vtu' if options.inplace else '_added.vtu'))
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else:
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parser.error('Unsupported VTK file type extension.')
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Npoints = rGrid.GetNumberOfPoints()
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Ncells = rGrid.GetNumberOfCells()
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damask.util.croak('{}: {} points and {} cells...'.format(options.vtk,Npoints,Ncells))
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# --- loop over input files -------------------------------------------------------------------------
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if filenames == []: filenames = [None]
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for name in filenames:
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try: table = damask.ASCIItable(name = name,
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buffered = False,
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readonly = True)
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except: continue
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damask.util.report(scriptName, name)
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# --- interpret header ----------------------------------------------------------------------------
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table.head_read()
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remarks = []
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errors = []
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VTKarray = {}
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active = defaultdict(list)
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for datatype,dimension,label in [['data',99,options.data],
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['tensor',9,options.tensor],
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['color' ,3,options.color],
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]:
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for i,dim in enumerate(table.label_dimension(label)):
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me = label[i]
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if dim == -1: remarks.append('{} "{}" not found...'.format(datatype,me))
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elif dim > dimension: remarks.append('"{}" not of dimension {}...'.format(me,dimension))
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else:
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remarks.append('adding {} "{}"...'.format(datatype,me))
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active[datatype].append(me)
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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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table.close(dismiss = True)
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continue
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# ------------------------------------------ process data ---------------------------------------
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table.data_readArray([item for sublist in active.values() for item in sublist]) # read all requested data
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for datatype,labels in active.items(): # loop over scalar,color
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for me in labels: # loop over all requested items
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VTKtype = vtk.VTK_DOUBLE
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VTKdata = table.data[:, table.label_indexrange(me)].copy() # copy to force contiguous layout
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if datatype == 'color':
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VTKtype = vtk.VTK_UNSIGNED_CHAR
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VTKdata = (VTKdata*255).astype(int) # translate to 0..255 UCHAR
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elif datatype == 'tensor':
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VTKdata[:,1] = VTKdata[:,3] = 0.5*(VTKdata[:,1]+VTKdata[:,3])
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VTKdata[:,2] = VTKdata[:,6] = 0.5*(VTKdata[:,2]+VTKdata[:,6])
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VTKdata[:,5] = VTKdata[:,7] = 0.5*(VTKdata[:,5]+VTKdata[:,7])
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VTKarray[me] = numpy_support.numpy_to_vtk(num_array=VTKdata,deep=True,array_type=VTKtype)
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VTKarray[me].SetName(me)
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table.close() # close input ASCII table
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# ------------------------------------------ add data ---------------------------------------
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if len(table.data) == Npoints: mode = 'point'
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elif len(table.data) == Ncells: mode = 'cell'
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else:
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damask.util.croak('Data count is incompatible with grid...')
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continue
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damask.util.croak('{} mode...'.format(mode))
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for datatype,labels in active.items(): # loop over scalar,color
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if datatype == 'color':
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if mode == 'cell': rGrid.GetCellData().SetScalars(VTKarray[active['color'][0]])
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elif mode == 'point': rGrid.GetPointData().SetScalars(VTKarray[active['color'][0]])
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for me in labels: # loop over all requested items
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if mode == 'cell': rGrid.GetCellData().AddArray(VTKarray[me])
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elif mode == 'point': rGrid.GetPointData().AddArray(VTKarray[me])
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rGrid.Modified()
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if vtk.VTK_MAJOR_VERSION <= 5: rGrid.Update()
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# ------------------------------------------ output result ---------------------------------------
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writer.SetDataModeToBinary()
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writer.SetCompressorTypeToZLib()
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if vtk.VTK_MAJOR_VERSION <= 5: writer.SetInput(rGrid)
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else: writer.SetInputData(rGrid)
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writer.Write()
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# ------------------------------------------ render result ---------------------------------------
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if options.render:
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mapper = vtk.vtkDataSetMapper()
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mapper.SetInputData(rGrid)
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actor = vtk.vtkActor()
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actor.SetMapper(mapper)
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# Create the graphics structure. The renderer renders into the
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# render window. The render window interactor captures mouse events
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# and will perform appropriate camera or actor manipulation
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# depending on the nature of the events.
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ren = vtk.vtkRenderer()
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renWin = vtk.vtkRenderWindow()
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renWin.AddRenderer(ren)
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ren.AddActor(actor)
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ren.SetBackground(1, 1, 1)
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renWin.SetSize(200, 200)
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iren = vtk.vtkRenderWindowInteractor()
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iren.SetRenderWindow(renWin)
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iren.Initialize()
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renWin.Render()
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iren.Start()
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