コード例 #1
0
    def __init__(self, name='mesh', filename=None, prefix_dir=None, **kwargs):
        """Create a Mesh.

        Parameters
        ----------
        name : str
            Object name.
        filename : str
            Loads a mesh from the specified file, if not None.
        prefix_dir : str
            If not None, the filename is relative to that directory.
        """
        Struct.__init__(self, name=name, **kwargs)

        if filename is None:
            self.io = None
            self.setup_done = 0

        else:
            io = MeshIO.any_from_filename(filename, prefix_dir=prefix_dir)
            output('reading mesh (%s)...' % (io.filename))
            tt = time.clock()
            io.read(self)
            output('...done in %.2f s' % (time.clock() - tt))
            self._set_shape_info()
コード例 #2
0
ファイル: mesh.py プロジェクト: 00liujj/dicom2fem
    def __init__(self, name='mesh', filename=None,
                 prefix_dir=None, **kwargs):
        """Create a Mesh.

        Parameters
        ----------
        name : str
            Object name.
        filename : str
            Loads a mesh from the specified file, if not None.
        prefix_dir : str
            If not None, the filename is relative to that directory.
        """
        Struct.__init__(self, name=name, **kwargs)

        if filename is None:
            self.io = None
            self.setup_done = 0

        else:
            io = MeshIO.any_from_filename(filename, prefix_dir=prefix_dir)
            output( 'reading mesh (%s)...' % (io.filename) )
            tt = time.clock()
            io.read(self)
            output( '...done in %.2f s' % (time.clock() - tt) )
            self._set_shape_info()
コード例 #3
0
ファイル: ioutils.py プロジェクト: olivierverdier/sfepy
def skip_read_line( fd ):
    while 1:
        try:
            line = fd.readline().strip()
        except EOFError:
            break
        except:
            output( "reading " + fd.name + " failed!" )
            raise
        if (len( line ) == 0) or (line[0] == '#'): continue
        return line
コード例 #4
0
ファイル: ioutils.py プロジェクト: GordianStapf/sfepy
def read_list(fd, n_item, dtype):
    vals = []
    ii = 0
    while ii < n_item:
        line = [dtype(ic) for ic in fd.readline().split()]
        vals.append(line)
        ii += len(line)
    if ii > n_item:
        output('corrupted row?', line, ii, n_item)
        raise ValueError

    return vals
コード例 #5
0
ファイル: ioutils.py プロジェクト: rc/dicom2fem
def read_list(fd, n_item, dtype):
    vals = []
    ii = 0
    while ii < n_item:
        line = [dtype(ic) for ic in fd.readline().split()]
        vals.append(line)
        ii += len(line)
    if ii > n_item:
        output('corrupted row?', line, ii, n_item)
        raise ValueError

    return vals
コード例 #6
0
ファイル: ioutils.py プロジェクト: olivierverdier/sfepy
def read_tuple( file, n_item, n_tuple ):

    out = ();
    for it in range( 0, n_tuple ):
        token = ();
        for ii in range( 0, n_item ):
            token = token + (read_token( file ),);
#            print token[ii];
        if (len( token[ii] ) == 0):
            output( "Corrupted file (token %d)!" % ii )
            raise "ERR_CorruptedFile"
        out = out + (token,);

    return out;
コード例 #7
0
ファイル: conf.py プロジェクト: olivierverdier/sfepy
    def validate( self, required = None, other = None ):
        required_left_over, required_missing \
                          = self._validate_helper( required, other )
        other_left_over, other_missing \
                       = self._validate_helper( other, required )

        assert_( required_left_over == other_left_over )

        if other_left_over and self.verbose:
            output( 'left over:', other_left_over )

        if required_missing:
            raise ValueError('required missing: %s' % required_missing)

        return other_missing
コード例 #8
0
ファイル: ioutils.py プロジェクト: olivierverdier/sfepy
def read_array( file, n_row, n_col, dtype ):
    """n_col is basically ignored, n_col == -1 -> intentionally ignored."""
    val = []
    for ir in range( 0, n_row ):
        try:
            while 1:
                line = file.readline().split()
                if (len( line ) == 0) or (line[0] == "#"):
                    continue
                else:
                    break
        except:
            output( "Array (%d, %d) reading failed!" % (n_row, n_col) )
            raise
        row = [float( ii ) for ii in line]
        val.append( row )

    val = array( val, dtype );
    return val
コード例 #9
0
ファイル: conf.py プロジェクト: certik/sfepy
    def validate( self, required = None, other = None ):
        required_left_over, required_missing \
                          = self._validate_helper( required, other )
        other_left_over, other_missing \
                       = self._validate_helper( other, required )

        assert_( required_left_over == other_left_over )

        err = False
        if required_missing:
            err = True
            output( 'error: required missing:', required_missing )

        if other_left_over:
            output( 'left over:', other_left_over )

        if err:
            raise ValueError

        return other_missing
コード例 #10
0
    def from_file(filename=None,
                  io='auto',
                  prefix_dir=None,
                  omit_facets=False):
        """
        Read a mesh from a file.

        Parameters
        ----------
        filename : string or function or MeshIO instance or Mesh instance
            The name of file to read the mesh from. For convenience, a
            mesh creation function or a MeshIO instance or directly a Mesh
            instance can be passed in place of the file name.
        io : *MeshIO instance
            Passing *MeshIO instance has precedence over filename.
        prefix_dir : str
            If not None, the filename is relative to that directory.
        omit_facets : bool
            If True, do not read cells of lower dimension than the space
            dimension (faces and/or edges). Only some MeshIO subclasses
            support this!
        """
        if isinstance(filename, Mesh):
            return filename

        if io == 'auto':
            if filename is None:
                output('filename or io must be specified!')
                raise ValueError
            else:
                io = MeshIO.any_from_filename(filename, prefix_dir=prefix_dir)

        output('reading mesh (%s)...' % (io.filename))
        tt = time.clock()

        trunk = io.get_filename_trunk()
        mesh = Mesh(trunk)
        mesh = io.read(mesh, omit_facets=omit_facets)

        output('...done in %.2f s' % (time.clock() - tt))

        mesh._set_shape_info()

        return mesh
コード例 #11
0
ファイル: mesh.py プロジェクト: 00liujj/dicom2fem
    def from_file(filename=None, io='auto', prefix_dir=None,
                  omit_facets=False):
        """
        Read a mesh from a file.

        Parameters
        ----------
        filename : string or function or MeshIO instance or Mesh instance
            The name of file to read the mesh from. For convenience, a
            mesh creation function or a MeshIO instance or directly a Mesh
            instance can be passed in place of the file name.
        io : *MeshIO instance
            Passing *MeshIO instance has precedence over filename.
        prefix_dir : str
            If not None, the filename is relative to that directory.
        omit_facets : bool
            If True, do not read cells of lower dimension than the space
            dimension (faces and/or edges). Only some MeshIO subclasses
            support this!
        """
        if isinstance(filename, Mesh):
            return filename

        if io == 'auto':
            if filename is None:
                output( 'filename or io must be specified!' )
                raise ValueError
            else:
                io = MeshIO.any_from_filename(filename, prefix_dir=prefix_dir)

        output('reading mesh (%s)...' % (io.filename))
        tt = time.clock()

        trunk = io.get_filename_trunk()
        mesh = Mesh(trunk)
        mesh = io.read(mesh, omit_facets=omit_facets)

        output('...done in %.2f s' % (time.clock() - tt))

        mesh._set_shape_info()

        return mesh
コード例 #12
0
def fix_double_nodes(coor, ngroups, conns, eps):
    """
    Detect and attempt fixing double nodes in a mesh.

    The double nodes are nodes having the same coordinates
    w.r.t. precision given by `eps`.
    """
    n_nod, dim = coor.shape
    cmap = find_map(coor, nm.zeros((0, dim)), eps=eps, allow_double=True)
    if cmap.size:
        output('double nodes in input mesh!')
        output('trying to fix...')

        while cmap.size:
            print cmap.size

            # Just like in Variable.equation_mapping()...
            ii = nm.argsort(cmap[:, 1])
            scmap = cmap[ii]

            eq = nm.arange(n_nod)
            eq[scmap[:, 1]] = -1
            eqi = eq[eq >= 0]
            eq[eqi] = nm.arange(eqi.shape[0])
            remap = eq.copy()
            remap[scmap[:, 1]] = eq[scmap[:, 0]]
            print coor.shape
            coor = coor[eqi]
            ngroups = ngroups[eqi]
            print coor.shape
            ccs = []
            for conn in conns:
                ccs.append(remap[conn])
            conns = ccs
            cmap = find_map(coor,
                            nm.zeros((0, dim)),
                            eps=eps,
                            allow_double=True)
        output('...done')
    return coor, ngroups, conns
コード例 #13
0
ファイル: mesh.py プロジェクト: 00liujj/dicom2fem
def fix_double_nodes(coor, ngroups, conns, eps):
    """
    Detect and attempt fixing double nodes in a mesh.

    The double nodes are nodes having the same coordinates
    w.r.t. precision given by `eps`.
    """
    n_nod, dim = coor.shape
    cmap = find_map( coor, nm.zeros( (0,dim) ), eps = eps, allow_double = True )
    if cmap.size:
        output('double nodes in input mesh!')
        output('trying to fix...')

        while cmap.size:
            print cmap.size

            # Just like in Variable.equation_mapping()...
            ii = nm.argsort( cmap[:,1] )
            scmap = cmap[ii]

            eq = nm.arange( n_nod )
            eq[scmap[:,1]] = -1
            eqi = eq[eq >= 0]
            eq[eqi] = nm.arange( eqi.shape[0] )
            remap = eq.copy()
            remap[scmap[:,1]] = eq[scmap[:,0]]
            print coor.shape
            coor = coor[eqi]
            ngroups = ngroups[eqi]
            print coor.shape
            ccs = []
            for conn in conns:
                ccs.append( remap[conn] )
            conns = ccs
            cmap = find_map( coor, nm.zeros( (0,dim) ), eps = eps,
                            allow_double = True )
        output('...done')
    return coor, ngroups, conns