Subdivide vertex data with geometry when converting Marc input to VTK
This commit is contained in:
Brendan Vande Kieft
parent
f0511e1ecb
commit
ceb0ff09e6
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@ -1,7 +1,7 @@
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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 os,sys,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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@ -9,159 +9,191 @@ 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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parser = argparse.ArgumentParser(description='Convert from Marc input file format (.dat) to VTK format (.vtu)', version = scriptID)
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parser.add_argument('filename', type=str, help='file to convert')
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parser.add_argument('-t', '--table', type=str, help='ASCIItable file containing nodal data to subdivide and interpolate')
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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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with open(args.filename, 'r') as marcfile:
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marctext = marcfile.read();
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# Load table (if any)
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if args.table is not None:
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try:
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table = damask.ASCIItable(
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name=args.table,
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outname='subdivided_{}'.format(args.table),
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buffered=True
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)
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table.head_read()
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table.data_readArray()
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# Python list is faster for appending
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nodal_data = list(table.data)
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except: args.table = None
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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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# Vertex does not exist, create it
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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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# Interpolate nodal data
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if args.table is not None:
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nodal_data.append(0.5 * (nodal_data[vert1 - 1] + nodal_data[vert2 - 1]))
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return newvert;
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for el_id in range(1, len(elements) + 1): # Marc starts counting at 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 vertex, depending on which opposite vertices are used to subdivide.
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# This way, we avoid creating duplicate vertices.
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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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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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# 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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# minus one, since vtk starts at zero but marc starts at one
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hex_.GetPointIds().SetId(vert_id, subverts[coord[0], coord[1], coord[2]] - 1)
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grid.InsertNextCell(hex_.GetCellType(), hex_.GetPointIds())
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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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else:
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damask.util.croak('Unsupported Marc element type: {} (skipping)'.format(el['type']))
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def subdivide_edge(vert1, vert2):
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edge = ordered_pair(vert1, vert2)
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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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if edge in edge_to_vert:
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return edge_to_vert[edge]
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grid.SetPoints(points)
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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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# 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", args.filename)) # *.vtk extension does not work in paraview
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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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if args.table is not None:
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table.info_append([
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scriptID + ' ' + ' '.join(sys.argv[1:]),
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])
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table.head_write()
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table.output_flush()
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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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table.data = np.array(nodal_data)
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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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table.data_writeArray()
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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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table.close()
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