Source code for fileread

##  This file is part of pyFormex 1.0.7  (Mon Jun 17 12:20:39 CEST 2019)
##  pyFormex is a tool for generating, manipulating and transforming 3D
##  geometrical models by sequences of mathematical operations.
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##  Copyright 2004-2019 (C) Benedict Verhegghe (
##  Distributed under the GNU General Public License version 3 or later.
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##  it under the terms of the GNU General Public License as published by
##  the Free Software Foundation, either version 3 of the License, or
##  (at your option) any later version.
##  This program is distributed in the hope that it will be useful,
##  but WITHOUT ANY WARRANTY; without even the implied warranty of
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"""Read geometry from file in a whole number of formats.

This module defines basic routines to read geometrical data
from a file and the specialized importers to read files in a number of
well known standardized formats.

The basic routines are very versatile as well as optimized (using the version
in the pyFormex C-library) and allow to easily create new exporters for
other formats.
from __future__ import absolute_import, division, print_function

import numpy as np

import pyformex as pf
from pyformex import Path
import pyformex.arraytools as at
from pyformex.connectivity import Connectivity
from pyformex.coords import Coords
from pyformex.mesh import Mesh
from pyformex import utils

# Global variables used by some funnctions
filename = None
mode = None
nplex = None
offset = None

[docs]def getParams(line): """Strip the parameters from a comment line""" s = line.split() d = {'mode': s.pop(0), 'filename': s.pop(0)} d.update(zip(s[::2], s[1::2])) return d
[docs]def readNodes(fil): """Read a set of nodes from an open mesh file""" a = np.fromfile(fil, sep=" ").reshape(-1, 3) x = Coords(a) return x
[docs]def readElems(fil, nplex): """Read a set of elems of plexitude nplex from an open mesh file""" print("Reading elements of plexitude %s" % nplex) e = np.fromfile(fil, sep=" ", dtype=at.Int).reshape(-1, nplex) e = Connectivity(e) return e
[docs]def readEsets(fil): """Read the eset data of type generate""" data = [] for line in fil: s = line.strip('\n').split() if len(s) == 4: data.append(s[:1] + [int(i) for i in s[1:]]) return data
[docs]def readMeshFile(fn): """Read a nodes/elems model from file. Returns a dict: - `coords`: a Coords with all nodes - `elems`: a list of Connectivities - `esets`: a list of element sets """ d = {} fil = open(fn, 'r') for line in fil: if line[0] == '#': line = line[1:] globals().update(getParams(line)) dfil = open(filename, 'r') if mode == 'nodes': d['coords'] = readNodes(dfil) elif mode == 'elems': elems = d.setdefault('elems', []) e = readElems(dfil, int(nplex)) - int(offset) elems.append(e) elif mode == 'esets': d['esets'] = readEsets(dfil) else: print("Skipping unrecognized line: %s" % line) dfil.close() fil.close() return d
[docs]def extractMeshes(d): """Extract the Meshes read from a .mesh file. """ x = d['coords'] e = d['elems'] M = [Mesh(x, ei) for ei in e] return M
[docs]def convertInp(fn): """Convert an Abaqus .inp to a .mesh set of files""" fn = Path(fn).resolve() converter = pf.cfg['bindir'] / 'read_abq_inp.awk' cmd = 'cd %s;%s %s' % (fn.parent, converter, print(cmd) P = utils.command(cmd, shell=True) print(P.out) print(P.err)
[docs]def readInpFile(filename): """Read the geometry from an Abaqus/Calculix .inp file This is a replacement for the convertInp/readMeshFile combination. It uses the ccxinp plugin to provide a direct import of the Finite Element meshes from an Abaqus or Calculix input file. Currently still experimental and limited in functionality (aimed primarily at Calculix). But also many simple meshes from Abaqus can already be read. Returns an dict. """ from pyformex.plugins import ccxinp, fe ccxinp.skip_unknown_eltype = True model = ccxinp.readInput(filename) print("Number of parts: %s" % len( fem = {} for part in try: coords = Coords(part['coords']) nodid = part['nodid'] nodpos = at.inverseUniqueIndex(nodid) print("nnodes = %s" % coords.shape[0]) print("nodid: %s" % nodid) print("nodpos: %s" % nodpos) for e in part['elems']: print("Orig els %s" % e[1]) print("Trl els %s" % nodpos[e[1]]) elems = [ Connectivity(nodpos[e], eltype=t) for (t, e) in part['elems'] ] print('ELEM TYPES: %s' % [e.eltype for e in elems]) fem[part['name']] = fe.Model(coords, elems) except: print("Skipping part %s" % part['name']) return fem
[docs]def read_off(fn): """Read an OFF surface mesh. The mesh should consist of only triangles! Returns a nodes,elems tuple. """ print("Reading .OFF %s" % fn) with utils.File(fn, 'r') as fil: head = fil.readline().strip() if head != "OFF": print("%s is not an OFF file!" % fn) return None, None nnodes, nelems, nedges = [int(i) for i in fil.readline().split()] nodes = np.fromfile(file=fil, dtype=at.Float, count=3 * nnodes, sep=' ') # elems have number of vertices + 3 vertex numbers elems = np.fromfile(file=fil, dtype=np.int32, count=4 * nelems, sep=' ') print("Read %d nodes and %d elems" % (nnodes, nelems)) return nodes.reshape((-1, 3)), elems.reshape((-1, 4))[:, 1:]
[docs]def read_gts(fn): """Read a GTS surface mesh. Return a coords,edges,faces tuple. """ print("Reading GTS file %s" % fn) with utils.File(fn, 'r') as fil: header = fil.readline().split() ncoords, nedges, nfaces = [int(i) for i in header[:3]] if len(header) >= 7 and header[6].endswith('Binary'): raise RuntimeError( "We can not read binary GTS format yet. See Maybe you should recompile the extra/gts commands." ) sep = '' else: sep = ' ' coords = np.fromfile( fil, dtype=at.Float, count=3 * ncoords, sep=sep ).reshape(-1, 3) edges = np.fromfile( fil, dtype=np.int32, count=2 * nedges, sep=' ' ).reshape(-1, 2) - 1 faces = np.fromfile( fil, dtype=np.int32, count=3 * nfaces, sep=' ' ).reshape(-1, 3) - 1 print("Read %d coords, %d edges, %d faces" % (ncoords, nedges, nfaces)) if coords.shape[0] != ncoords or \ edges.shape[0] != nedges or \ faces.shape[0] != nfaces: print("Error while reading GTS file: the file is probably incorrect!") return coords, edges, faces
[docs]def read_stl_bin(fn): """Read a binary stl. Parameters ---------- fn: str Name of the file to read, holding binary STL data. Returns ------- Coords (ntri,4,3) A Coords with ntri triangles. Each triangle consists of 4 items: the first one is the normal, the other three are the coordinates of the vertices. """ def addTriangle(i): x[i] = np.fromfile(file=fil, dtype=at.Float, count=12).reshape(4, 3) print("Reading binary .STL %s" % fn) fil = open(fn, 'rb') head = if head[:5] == 'solid': raise ValueError("%s looks like an ASCII STL file!" % fn) i = head.find('COLOR=') if i >= 0 and i <= 70: print("HAS COLOR") color = np.fromstring(head[i + 6:i + 10], dtype=np.uint8, count=4) else: color = None ntri = np.fromfile(file=fil, dtype=at.Int, count=1)[0] print("Number of triangles: %s" % ntri) x = np.zeros((ntri, 4, 3), dtype=at.Float) #nbytes = 12*4 + 2 [addTriangle(it) for it in range(ntri)] print("Finished reading binary stl") x = Coords(x) if color is not None: from pyformex.opengl.colors import GLcolor color = GLcolor(color[:3]) return x, color
[docs]def read_gambit_neutral(fn, eltype='tri'): """Read a triangular/hexahedral surface mesh in Gambit neutral format. eltype = 'tri' for triangular, 'hex' for hexahedral mesh. The .neu file nodes are numbered from 1! Returns a nodes,elems tuple. """ fn = Path(fn) if eltype == 'tri': ext = '' nplex = 3 elif eltype == 'hex': ext = '-hex' nplex = 8 else: raise ValueError("Invalid eltype %s" % eltype) scr = pf.cfg['bindir'] / 'gambit-neu' + ext utils.command("%s '%s'" % (scr, fn)) nodesf = fn.with_suffix('.nodes') elemsf = fn.with_suffix('.elems') nodes = np.fromfile(nodesf, sep=' ', dtype=at.Float).reshape((-1, 3)) elems = np.fromfile(elemsf, sep=' ', dtype=at.Int).reshape((-1, nplex)) if eltype == 'hex': # convert to pyFormex numbering order elems = elems[:, (0, 1, 3, 2, 4, 5, 7, 6)] return nodes, elems - 1
#TODO: deprecate this def read_gambit_neutral_hex(fn): return read_gambit_neutral_hex(fn, eltype='hex') # End