geomfile — pyFormex 1.0.5 documentation

# Source code for geomfile

    #
    ##
    ##  This file is part of pyFormex 1.0.5  (Sat Feb 16 10:40:32 CET 2019)
    ##  pyFormex is a tool for generating, manipulating and transforming 3D
    ##  geometrical models by sequences of mathematical operations.
    ##  Home page: http://pyformex.org
    ##  Project page:  http://savannah.nongnu.org/projects/pyformex/
    ##  Copyright 2004-2018 (C) Benedict Verhegghe (benedict.verhegghe@ugent.be)
    ##  Distributed under the GNU General Public License version 3 or later.
    ##
    ##  This program is free software: you can redistribute it and/or modify
    ##  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
    ##  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
    ##  GNU General Public License for more details.
    ##
    ##  You should have received a copy of the GNU General Public License
    ##  along with this program.  If not, see http://www.gnu.org/licenses/.
    ##

    """Handling pyFormex Geometry Files

    This module defines a class to work with files in the native
    pyFormex Geometry File Format.
    """
    from __future__ import absolute_import, division, print_function

    import os
    import re
    from distutils.version import StrictVersion as Version
    import numpy as np

    import pyformex as pf
    from pyformex import utils
    from pyformex import filewrite
    from pyformex.odict import OrderedDict
    from pyformex import arraytools as at
    from pyformex.formex import Formex
    from pyformex.mesh import Mesh
    # We need to import the Mesh subclasses that can be read !
    from pyformex.trisurface import TriSurface

    class GeometryFile(object):
        """A class to handle files in the pyFormex Geometry File format.

        The pyFormex Geometry File (PGF) format allows the persistent storage
        of most of the geometrical objects available in pyFormex using a format
        that is independent of the pyFormex version. It guarantees a possible read
        back in future versions. The format is simple and public, and hence
        also allows read back from other software.

        See http://pyformex.org/doc/file_format for a full description
        of the file format(s). Older file formats are supported for reading.

        Other than just geometry, the pyFormex Geometry File format can also
        store some attributes of the objects, like names and colors.
        Future versions will also allow to store field variables.

        The GeometryFile class uses the utils.File class to access the files,
        and thus provides for transparent compression and decompression of the
        files. When making use of the compression, the PGF files will remain small
        even for complex models.

        A PGF file starts with a specific header identifying the format and
        version. When opening a file for reading, the PGF header is read
        automatically, and the file is thus positioned ready for reading
        the objects. When opening a file for writing (not appending!), the
        header is automatically written, and the file is ready for writing objects.

        In append mode however, nothing is currently done with the header.
        This means that it is possible to append to a file using a format
        different from that used to create the file initially. This is not a
        good practice, as it may hinder the proper read back of the data.
        Therefore, append mode should only be used when you are sure that
        your current pyFormex uses the same format as the already stored file.
        As a reminder, warning is written when opening the file in append mode.

        The `filename`, `mode`, `compr`, `level` and `delete_temp` arguments are
        passed to the utils.File class. See :class:`utils.File` for more
        details.

        Parameters:

        - `filename`: string: the name of the file to open.
          If the file name ends with '.gz' or '.bz2', transparent (de)compression
          will be used, as provided by the :class:`utils.File` class.
        - `mode`: one of 'r', 'w' or 'a': specifies that the file should be
          opened in read, write or append mode. If omitted, an
          existing file will be opened in read mode and a non-existing in write
          mode. Opening an existing file in 'w' mode will overwrite the file,
          while opening it in 'a' mode will allow to append to the file.
        - `compr`: string, one of 'gz' or 'bz2': identifies the compression
          algorithm to be used: gzip or bzip2. If the file name is ending with
          '.gz' or '.bz2', `compr` is set automatically from the extension.
        - `level`: an integer from 1..9: gzip/bzip2 compression level.
          Higher values result in smaller files, but require longer compression
          times. The default of 5 gives already a fairly good compression ratio.
        - `delete_temp`: bool: if True (default), the temporary files needed to
          do the (de)compression are deleted when the GeometryFile is closed.
        - `sep`: string: separator string to be used when writing numpy arrays
          to the file. An empty string will make the arrays being written in
          binary format. Any other string will force text mode, and the `sep`
          string is used as a separator between subsequent array elements.
          See also :func:`numpy.tofile`.
        - `ifmt` and `ffmt` are present for historical and development reasons,
          but currently inactive.
        - `version`: if specified, write according to old version standard.
          Available: '1.9', '2.0'(default)
        """

        _version_ = '2.0'

        def __init__(self,filename,mode=None,compr=None,level=5,delete_temp=True,
                     sep=' ',ifmt=' ',ffmt=' ',version=None):
            """Create the GeometryFile object."""
            if version is None:
                version = GeometryFile._version_
            if not version in [ '1.9', '2.0' ]:
                raise ValueError("Can not write GeometryFile of version %s" % version)
            self.version = version

            if mode is None:
                if os.path.exists(filename):
                    mode = 'r'
                else:
                    mode = 'w'

            self.file = utils.File(filename,mode,compr,level,delete_temp)
            self._autoname = None

            if self.writing:
                self.sep = sep
                self.fmt = {'i':ifmt,'f':ffmt}

            self.open()

        @property
        def writing(self):
            return self.file.mode[0:1] in 'wa'

        @property
        def autoname(self):
            if self._autoname is None:
                self._autoname = utils.NameSequence(utils.projectName(self.file.name)+'-0')
            return self._autoname

        def open(self):
            self.fil = self.file.open()
            if self.writing:
                self.writeHeader()
            else:
                self.readHeader()

        def reopen(self,mode='r'):
            """Reopen the file, possibly changing the mode.

            The default mode for the reopen is 'r'
            """
            self.fil = self.file.reopen(mode)
            if self.writing:
                self.writeHeader()
            else:
                self.readHeader()

        def close(self):
            """Close the file.

            """
            self.file.close()

        def checkWritable(self):
            if not self.writing:
                raise RuntimeError("File is not opened for writing")
            if not self.header_done:
                self.writeHeader()

        def writeHeader(self):
            """Write the header of a pyFormex geometry file.

            The header identifies the file as a pyFormex geometry file
            and sets the following global values:

            - `version`: the version of the geometry file format
            - `sep`: the default separator to be used when not specified in
              the data block
            """
            self.fil.write("# pyFormex Geometry File (http://pyformex.org) version='%s'; sep='%s'\n" % (self.version, self.sep))
            self.header_done = True

        def writeData(self,data,sep,fmt=None):
            """Write an array of data to a pyFormex geometry file.

            If fmt is None, the data are written using numpy.tofile, with
            the specified separator. If sep is an empty string, the data block
            is written in binary mode, leading to smaller files.
            If fmt is specified, each
            """
            if not self.writing:
                raise RuntimeError("File is not opened for writing")
            #kind = data.dtype.kind
            #if fmt is None:
            #    fmt = self.fmt[kind]
            filewrite.writeData(self.fil, data, sep, end='\n')

        def write(self,geom,name=None,sep=None):
            """Write a collection of Geometry objects to the Geometry File.

            Parameters:

            - `geom`: an object of one the supported Geometry data types
              or a list or dict of such objects, or a WebGL objdict.
              Currently exported geometry objects are
              :class:`Coords`, :class:`Formex`, :class:`Mesh`,
              :class:`PolyLine`, :class:`BezierSpline`.

            Returns the number of objects written.
            """
            self.checkWritable()
            nobj = 0
            if isinstance(geom, dict):
                for name in geom:
                    nobj += self.writeGeometry(geom[name], name)
            elif isinstance(geom, list):
                for obj in geom:
                    ## if hasattr(obj, 'obj'):
                    ##     # This must be a WebGL object dict
                    ##     nobj += self.writeDict(obj)
                    ## else:
                    nobj += self.writeGeometry(obj,sep=sep)
            else:
                nobj += self.writeGeometry(geom,name,sep)

            return nobj

        def writeGeometry(self,geom,name=None,sep=None):
            """Write a single Geometry object to the Geometry File.

            Writes a single Geometry object to the Geometry File, using the
            specified name and separator.

            Parameters:

            - `geom`: a supported Geometry type object.
              Currently supported Geometry objects are
              :class:`Coords`,
              :class:`Formex`,
              :class:`Mesh`,
              :class:`PolyLine`,
              :class:`BezierSpline`.
              Other types are skipped, and a message is written, but processing
              continues.
            - `name`: string: the name of the object to be stored in the file.
              If not specified, and the object has an `attrib` dict containing
              a name, that value is used. Else an object name is generated
              from the file name.
              On readback, the object names are used as keys to store the objects
              in a dict.
            - `sep`: string: defines the separator to be used for writing this
              object. If not specified, the value given in the constructor will
              be used. This argument allows to override it on a per object base.

            Returns 1 if the object has been written, 0 otherwise.
            """
            self.checkWritable()

            try:
                writefunc = getattr(self, 'write'+geom.__class__.__name__)
            except:
                pf.warning("Can not (yet) write objects of type %s to geometry file: skipping" % type(geom))
                return 1

            if name is None:
                name = geom.attrib.name
            if name is None:
                name = next(self.autoname)

            try:
                writefunc(geom, name, sep)
            except:
                pf.warning("Error while writing objects of type %s to geometry file: skipping" % type(geom))
                raise

            if geom.attrib and Version(self.version) >= Version('2.0'):
                try:
                    self.writeAttrib(geom.attrib)
                except:
                    pf.warning("Error while writing objects of type %s to geometry file: skipping" % type(geom))
                    raise

            return 0

        def writeAttrib(self,attrib):
            """Write the Attributes block of the Geometry

            attrib: the Attributes dict of a Geometry object

            Beware: this is work in progress. Not all Attributes can currently
            be stored in the PGF format.
            """
            def filter_attrib(attrib):
                """Filter the storable attributes.

                Currently, only bool, int, float and str types are stored.
                """
                okkeys = [ k for k in attrib
                               if k is not 'color' and (
                                   isinstance(attrib[k],(bool,int,float,str))
                                   or isInt(attrib[k]) or isFloat(attrib[k]) ) ]
                return utils.selectDict(attrib,okkeys)

            # We rely on Attributes __repr__ method, but multiple line
            # representations are coerced to a single line to allow readback

            # Select the exportable attributes
            okattr = filter_attrib(attrib)
            if okattr:
                # In case we would allow array attributes, We need to set
                # numpy printoptions to display the full array, not a truncated one
                opt = np.get_printoptions()
                np.set_printoptions(threshold=np.inf)
                # Get a reversible representation of the attrib dict
                s = repr(filter_attrib(okattr))
                # Restore the numpy printoptions
                np.set_printoptions(**opt)
                # Remove the newlines, so everything can be read as a single line
                s = re.sub('\n *','',s)
                # In case arrays are stored, remove the dtype (only int and float
                # dtypes are supported, and type is obvious from the stored values)
                s = re.sub(', *dtype=[^)]*\)',')',s)
                # Write the result to the file
                self.fil.write("# attrib = %s\n" % s)

        def writeMesh(self,F,name=None,sep=None,objtype='Mesh'):
            """Write a Mesh to a pyFormex geometry file.

            This writes a header line with these attributes and arguments:
            objtype, ncoords, nelems, nplex, props(True/False),
            eltype, normals(True/False), color, sep, name.
            This is followed by the array data for: coords, elems, prop,
            normals, color

            The objtype can/should be overridden for subclasses.
            """
            if objtype is None:
                objtype = 'Mesh'
            if sep is None:
                sep = self.sep
            hasprop = F.prop is not None
            hasnorm = hasattr(F, 'normals') and isinstance(F.normals, np.ndarray) and F.normals.shape == (F.nelems(), F.nplex(), 3)
            color = None
            colormap = None
            Fc = F.attrib['color']
            if Fc is not None:
                if isinstance(Fc,(str,unicode)):
                    color = Fc
                else:
                    try:
                        Fc = at.checkArray(Fc,kind='f')
                        colormap = None
                        colorshape = Fc.shape
                    except:
                        Fc = at.checkArray(Fc,kind='i')
                        colormap = 'default'
                        colorshape = Fc.shape + (3,)
                    if colorshape == (3,):
                        color = tuple(Fc)
                    elif colorshape == (F.nelems(), 3):
                        color = 'element'
                    elif colorshape == (F.nelems(), F.nplex(), 3):
                        color = 'vertex'
                    else:
                        raise ValueError("Incorrect color shape: %s" % str(colorshape))

            head = "# objtype='%s'; ncoords=%s; nelems=%s; nplex=%s; props=%s; normals=%s; color=%r; sep='%s'" % (objtype, F.npoints(), F.nelems(), F.nplex(), hasprop, hasnorm, color, sep)
            if name:
                head += "; name='%s'" % name
            if F.elName():
                head += "; eltype='%s'" % F.elName()
            if colormap:
                head += "; colormap='%s'" % colormap

            self.fil.write(head+'\n')

            # Apply a fix to avoid a fewgl bug
            #
            # pyFormex webgl exporter exports in pgf format.
            # Unfortunately, due to a bug in fewgl pgf reader, geometries
            # having a first value in the coords block that starts with a
            # bit pattern corresponding with a '#' byte, (dec 35), can not
            # be read back. The solution is to force the first bit (the least
            # significant bit of the mantisse) to zero. This will make sure
            # the bit pattern does not match dec 35 ('#'), and have a
            # neglectable influence on the value. (Still the solution below
            # resets the original value).
            if pf.cfg['webgl/avoid_fewgl_read_pgf_bug']:
                save_first = F.coords[0,0]
                F.coords.view(np.int32)[0, 0] &= -2  # Force least significant bit of the first byte to zero
            self.writeData(F.coords, sep)
            if pf.cfg['webgl/avoid_fewgl_read_pgf_bug']:
                F.coords[0,0] = save_first

            if not objtype == 'Formex':
                self.writeData(F.elems, sep)
            if hasprop:
                self.writeData(F.prop, sep)
            if hasnorm:
                self.writeData(F.normals, sep)
            if color == 'element' or color == 'vertex':
                print("COLOR IS TYPE %s" % Fc.dtype)
                self.writeData(Fc, sep)
            for field in F.fields:
                fld = F.fields[field]
                head = "# field='%s'; fldtype='%s'; shape=%r; sep='%s'" % (fld.fldname, fld.fldtype,fld.data.shape, sep)
                self.fil.write(head+'\n')
                self.writeData(fld.data, sep)

        def writeFormex(self,F,name=None,sep=None):
            """Write a Formex to the geometry file.

            This is equivalent to writeMesh(F,name,sep,objtype='Formex')
            """
            self.writeMesh(F, name=name, sep=sep, objtype='Formex')

        def writeTriSurface(self,F,name=None,sep=None):
            """Write a TriSurface to a pyFormex geometry file.

            This is equivalent to writeMesh(F,name,sep,objtype='TriSurface')
            """
            self.writeMesh(F, name=name, sep=sep, objtype='TriSurface')

        def writeCurve(self,F,name=None,sep=None,objtype=None,extra=None):
            """Write a Curve to a pyFormex geometry file.

            This function writes any curve type to the geometry file.
            The `objtype` is automatically detected but can be overridden.

            The following attributes and arguments are written in the header:
            ncoords, closed, name, sep.
            The following attributes are written as arrays: coords
            """
            if sep is None:
                sep = self.sep
            head = "# objtype='%s'; ncoords=%s; closed=%s; sep='%s'" % (F.__class__.__name__, F.coords.shape[0], F.closed, sep)
            if name:
                head += "; name='%s'" % name
            if extra:
                head += extra
            self.fil.write(head+'\n')
            self.writeData(F.coords, sep)

        def writePolyLine(self,F,name=None,sep=None):
            """Write a PolyLine to a pyFormex geometry file.

            This is equivalent to writeCurve(F,name,sep,objtype='PolyLine')
            """
            self.writeCurve(F, name=name, sep=sep, objtype='PolyLine')

        def writeBezierSpline(self,F,name=None,sep=None):
            """Write a BezierSpline to a pyFormex geometry file.

            This is equivalent to writeCurve(F,name,sep,objtype='BezierSpline')
            """
            self.writeCurve(F, name=name, sep=sep, objtype='BezierSpline', extra="; degree=%s" % F.degree)

        def writeNurbsCurve(self,F,name=None,sep=None,extra=None):
            """Write a NurbsCurve to a pyFormex geometry file.

            This function writes a NurbsCurve instance to the geometry file.

            The following attributes and arguments are written in the header:
            ncoords, nknots, closed, name, sep.
            The following attributes are written as arrays: coords, knots
            """
            if sep is None:
                sep = self.sep
            head = "# objtype='%s'; ncoords=%s; nknots=%s; closed=%s; sep='%s'" % (F.__class__.__name__, F.coords.shape[0], F.knots.shape[0], F.closed, sep)
            if name:
                head += "; name='%s'" % name
            if extra:
                head += extra
            self.fil.write(head+'\n')
            self.writeData(F.coords, sep)
            self.writeData(F.knots, sep)

        def writeNurbsSurface(self,F,name=None,sep=None,extra=None):
            """Write a NurbsSurface to a pyFormex geometry file.

            This function writes a NurbsSurface instance to the geometry file.

            The following attributes and arguments are written in the header:
            ncoords, nknotsu, nknotsv, closedu, closedv, name, sep.
            The following attributes are written as arrays: coords, knotsu, knotsv
            """
            if sep is None:
                sep = self.sep
            head = "# objtype='%s'; ncoords=%s; nuknots=%s; nvknots=%s; uclosed=%s; vclosed=%s; sep='%s'" % (F.__class__.__name__, F.coords.shape[0], F.uknots.shape[0], F.uknots.shape[0], F.closed[0], F.closed[1], sep)
            if name:
                head += "; name='%s'" % name
            if extra:
                head += extra
            self.fil.write(head+'\n')
            self.writeData(F.coords, sep)
            self.writeData(F.uknots, sep)
            self.writeData(F.vknots, sep)

    ###########################################################################
            ### READING ###

        def read(self,count=-1,warn_version=True):
            """Read objects from a pyFormex Geometry File.

            This function reads objects from a Geometry File until the file
            ends, or until `count` objects have been read.
            The File should have been opened for reading.

            A count may be specified to limit the number of objects read.

            Returns a dict with the objects read. The keys of the dict are the
            object names found in the file. If the file does not contain
            object names, they will be autogenerated from the file name.

            Note that PGF files of version 1.0 are no longer supported.
            The use of formats 1.1 to 1.5 is deprecated, and users are
            urged to upgrade these files to a newer format. Support for
            these formats may be removed in future.
            """
            if self.writing:
                print("File is opened for writing, not reading.")
                return {}

            self.results = OrderedDict()
            self.geometry = None # used to make sure fields follow geom block

            if Version(self.version) < Version('1.6'):
                if warn_version:
                    pf.warning("This is an old PGF format (%s). We recommend you to convert it to a newer format. The geometry import menu contains an item to upgrade a PGF file to the latest format (%s)." % (self.version,GeometryFile._version_))
                return self.readLegacy(count)

            while True:
                s = self.fil.readline()

                if len(s) == 0:   # end of file
                    break

                if s.startswith('#'):

                    # Remove the leading '#' and space
                    s = s[1:].strip()

                    if s.startswith('objtype'):
                        if count > 0 and len(self.results) >= count:
                            break
                        self.readGeometry(**self.decode(s))

                    elif s.startswith('field'):
                        self.readField(**self.decode(s))

                    elif s.startswith('attrib'):
                        self.readAttrib(**self.decode(s))

                    elif s.startswith('pyFormex Geometry File'):
                        # we have a new header line
                        self.readHeader(s)

                # Unrecognized lines are silently ignored, whether starting
                # with a '#' or not.
                # We recommend to start all comments lines with a '#' though.

            self.file.close()

            return self.results

        def decode(self,s):
            """Decode the announcement line.

            Returns a dict with the interpreted values of the line.
            """
            # Empty dict for return value
            kargs = {}
            # Dict with defined symbols used in the string repr in PGF format
            loc = { 'array':np.array }
            try:
                exec(s,loc,kargs)
            except:
                raise RuntimeError("This does not look like a regular pyFormex geometry file. I got stuck on the following line:\n==> %s" % s)
            return kargs

        def readHeader(self,s=None):
            """Read the header of a pyFormex geometry file.

            Without argument, reads a line from the file and interpretes it as
            a header line. This is normally used to read the first line of the
            file. A string `s` may be specified to interprete further lines as
            a header line.
            """
            if s is None:
                s = self.fil.readline()

            pos = s.rfind(')')
            s = s[pos+1:].strip()
            kargs = self.decode(s)
            self.version = kargs['version']
            self.sep = kargs['sep']
            self.header_done = True

        def doHeader(self,version='1.1',sep='',**kargs):
            """Read the header of a pyFormex geometry file.

            Sets detected default values
            """

            self.version = version
            self.sep = sep
            self.header_done = True

        def readGeometry(self,objtype='Formex',name=None,nelems=None,ncoords=None,nplex=None,props=None,eltype=None,normals=None,color=None,colormap=None,closed=None,degree=None,nknots=None,sep=None,**kargs):
            """Read a geometry record of a pyFormex geometry file.

            If an object was succesfully read, it is set in self.geometry
            """
            pf.debug("Reading object of type %s" % objtype, pf.DEBUG.INFO)
            self.geometry = None

            if objtype == 'Formex':
                obj = self.readFormex(nelems, nplex, props, eltype, sep)
            elif objtype in ['Mesh', 'TriSurface']:
                obj = self.readMesh(ncoords, nelems, nplex, props, eltype, normals, sep, objtype)
            elif objtype == 'PolyLine':
                obj = self.readPolyLine(ncoords, closed, sep)
            elif objtype == 'BezierSpline':
                obj = self.readBezierSpline(ncoords, closed, degree, sep)
            elif objtype == 'NurbsCurve':
                obj = self.readNurbsCurve(ncoords, nknots, closed, sep)
            elif objtype in globals() and hasattr(globals()[objtype], 'read_geom'):
                obj = globals()[objtype].read_geom(self,**kargs)
            else:
                print("Can not (yet) read objects of type %s from geometry file: skipping" % objtype)

            if obj is not None:
                if color is not None:
                    if isinstance(color,str):
                        # Check for special values:
                        if color == 'element':
                            colorshape = (nelems,)
                        elif color == 'vertex':
                            colorshape = (nelems,nplex,)
                        elif color == '':
                            # Fix for pre 1.9 versions using color='' for no color
                            color = colorshape = None
                        else:
                            # string should be a color name
                            colorshape = None

                        if colorshape:
                            if colormap == 'default':
                                colortype = at.Int
                            else:
                                colortype = at.Float
                                colorshape += ( 3,)

                            try:
                                # Read the color array
                                color = at.readArray(self.fil, colortype, colorshape, sep=sep)
                            except Exception as e:
                                print("Invalid color array on PGF file: skipped. Traceback: %s" % e)
                                color = None

                    else:
                        # A single color encoded in the attribute
                        if colormap == 'default':
                            colortype = 'i'
                        else:
                            colortype = 'f'
                        colorshape = (3,)
                        try:
                            color = at.checkArray(color, colorshape, colortype)
                        except Exception as e:
                            print("Invalid color attribute on PGF file: skipped. Traceback: %s" % e)
                            color = None

                obj.attrib.color = color

                # store the geometry object, and remember as last
                if name is None:
                    name = next(self.autoname)
                self.results[name] = self.geometry = obj

        def readField(self,field=None,fldtype=None,shape=None,sep=None,**kargs):
            """Read a Field defined on the last read geometry.

            """
            data = at.readArray(self.fil, at.Float, shape, sep=sep)
            self.geometry.addField(fldtype,data,field)

        def readAttrib(self,attrib=None,**kargs):
            """Read an Attributes dict defined on the last read geometry.

            """
            try:
                self.geometry.attrib(**attrib)
            except:
                # Attributes readback may produce an error with
                # complex data types, e.g. vertex color array
                pf.warning("GeometryFile.read: Error while reading an Attribute block. The current version does not support the readback of some complex attribute data types (like a vertex color array). All attributes in this block will be skipped.")

        def readFormex(self, nelems, nplex, props, eltype, sep):
            """Read a Formex from a pyFormex geometry file.

            The coordinate array for nelems*nplex points is read from the file.
            If present, the property numbers for nelems elements are read.
            From the coords and props a Formex is created and returned.
            """
            ndim = 3
            f = at.readArray(self.fil, at.Float, (nelems, nplex, ndim), sep=sep)
            if props:
                p = at.readArray(self.fil, at.Int, (nelems,), sep=sep)
            else:
                p = None
            return Formex(f, p, eltype)

        def readMesh(self,ncoords,nelems,nplex,props,eltype,normals,sep,objtype='Mesh'):
            """Read a Mesh from a pyFormex geometry file.

            The following arrays are read from the file:
            - a coordinate array with `ncoords` points,
            - a connectivity array with `nelems` elements of plexitude `nplex`,
            - if present, a property number array for `nelems` elements.

            Returns the Mesh constructed from these data, or a subclass if
            an objtype is specified.
            """

            ndim = 3
            x = at.readArray(self.fil, at.Float, (ncoords, ndim), sep=sep)
            e = at.readArray(self.fil, at.Int, (nelems, nplex), sep=sep)
            if props:
                p = at.readArray(self.fil, at.Int, (nelems,), sep=sep)
            else:
                p = None
            M = Mesh(x, e, p, eltype)
            if objtype != 'Mesh':
                try:
                    clas = locals()[objtype]
                except:
                    clas = globals()[objtype]
                M = clas(M)
            if normals:
                n = at.readArray(self.fil, at.Float, (nelems, nplex, ndim), sep=sep)
                M.normals = n
            return M

        def readPolyLine(self, ncoords, closed, sep):
            """Read a Curve from a pyFormex geometry file.

            The coordinate array for ncoords points is read from the file
            and a Curve of type `objtype` is returned.
            """
            from pyformex.plugins.curve import PolyLine
            ndim = 3
            coords = at.readArray(self.fil, at.Float, (ncoords, ndim), sep=sep)
            return PolyLine(control=coords, closed=closed)

        def readBezierSpline(self, ncoords, closed, degree, sep):
            """Read a BezierSpline from a pyFormex geometry file.

            The coordinate array for ncoords points is read from the file
            and a BezierSpline of the given degree is returned.
            """
            from pyformex.plugins.curve import BezierSpline
            ndim = 3
            coords = at.readArray(self.fil, at.Float, (ncoords, ndim), sep=sep)
            return BezierSpline(control=coords, closed=closed, degree=degree)

        def readNurbsCurve(self, ncoords, nknots, closed, sep):
            """Read a NurbsCurve from a pyFormex geometry file.

            The coordinate array for ncoords control points and the nknots
            knot values are read from the file.
            A NurbsCurve of degree p = nknots - ncoords - 1 is returned.
            """
            from pyformex.plugins.nurbs import NurbsCurve
            ndim = 4
            coords = at.readArray(self.fil, at.Float, (ncoords, ndim), sep=sep)
            knots = at.readArray(self.fil, at.Float, (nknots,), sep=sep)
            return NurbsCurve(control=coords, knots=knots, closed=closed)

        def readNurbsSurface(self, ncoords, nuknots, nvknots, uclosed, vclosed, sep):
            """Read a NurbsSurface from a pyFormex geometry file.

            The coordinate array for ncoords control points and the nuknots and
            nvknots values of uknots and vknots are read from the file.
            A NurbsSurface of degree ``pu = nuknots - ncoords - 1``  and
            ``pv = nvknots - ncoords - 1`` is returned.
            """
            from pyformex.plugins.nurbs import NurbsSurface
            ndim = 4
            coords = at.readArray(self.fil, at.Float, (ncoords, ndim), sep=sep)
            uknots = at.readArray(self.fil, at.Float, (nuknots,), sep=sep)
            vknots = at.readArray(self.fil, at.Float, (nvknots,), sep=sep)
            return NurbsSurface(control=coords, knots=(uknots, vknots), closed=(uclosed, vclosed))

    ###########################################################################
            ### OLD READ FUNCTIONS ###

        def readLegacy(self,count=-1):
            """Read the objects from a pyFormex Geometry File format <= 1.7.

            This function reads all the objects of a Geometry File.
            The File should have been opened for reading, and the header
            should have been read previously.

            A count may be specified to limit the number of objects read.

            Returns a dict with the objects read. The keys of the dict are the
            object names found in the file. If the file does not contain
            object names, they will be autogenerated from the file name.
            """
            if not self.header_done:
                self.readHeader()
            eltype = None # for compatibility with pre 1.1 .formex files
            #ndim = 3
            while True:
                objtype = 'Formex' # the default obj type
                obj = None
                nelems = None
                nplex = None
                ncoords = None
                sep = self.sep
                name = None
                normals = None
                color = None
                props = None
                closed = None
                nparts = None
                nknots = None
                s = self.fil.readline()

                if len(s) == 0:   # end of file
                    break

                if not s.startswith('#'):  # not a header: skip
                    continue

                ###
                ###  THIS WILL USE UNDEFINED VALUES FROM A PREVIOUS OBJECT
                ###  THIS SHOULD THEREFORE BE CHANGED !!!!
                ###
                try:
                    exec(s[1:].strip())
                    #pf.debug("READ COLOR: %s" % str(color),pf.DEBUG.INFO)
                except:
                    nelems = ncoords = None

                if nelems is None and ncoords is None:
                    # For historical reasons, this is a certain way to test
                    # that no geom data block is following
                    pf.debug("SKIPPING %s" % s, pf.DEBUG.LEGACY)
                    continue  # not a legal header: skip

                pf.debug("Reading object of type %s" % objtype, pf.DEBUG.INFO)

                # OK, we have a legal header, try to read data
                if objtype == 'Formex':
                    obj = self.readFormex(nelems, nplex, props, eltype, sep)
                elif objtype in ['Mesh', 'TriSurface']:
                    obj = self.readMesh(ncoords, nelems, nplex, props, eltype, normals, sep, objtype)
                elif objtype == 'PolyLine':
                    obj = self.readPolyLine(ncoords, closed, sep)
                elif objtype == 'BezierSpline':
                    if 'nparts' in s:
                        # This looks like a version 1.3 BezierSpline
                        obj = self.oldReadBezierSpline(ncoords, nparts, closed, sep)
                    else:
                        if not 'degree' in s:
                            # compatibility with 1.4  BezierSpline records
                            degree = 3
                        obj = self.readBezierSpline(ncoords, closed, degree, sep)
                elif objtype == 'NurbsCurve':
                    obj = self.readNurbsCurve(ncoords, nknots, closed, sep)
                elif objtype in globals() and hasattr(globals()[objtype], 'read_geom'):
                    obj = globals()[objtype].read_geom(self)
                else:
                    print("Can not (yet) read objects of type %s from geometry file: skipping" % objtype)
                    continue # skip to next header

                if obj is not None:
                    try:
                        color = at.checkArray(color, (3,), 'f')
                        obj.color = color
                    except:
                        pass

                    if name is None:
                        name = next(self.autoname)
                    self.results[name] = obj

                if count > 0 and len(self.results) >= count:
                    break

            self.file.close()

            return self.results

        def oldReadBezierSpline(self, ncoords, nparts, closed, sep):
            """Read a BezierSpline from a pyFormex geometry file version 1.3.

            The coordinate array for ncoords points and control point array
            for (nparts,2) control points are read from the file.
            A BezierSpline is constructed and returned.
            """
            from pyformex.plugins.curve import BezierSpline
            ndim = 3
            coords = at.readArray(self.fil, at.Float, (ncoords, ndim), sep=sep)
            control = at.readArray(self.fil, at.Float, (nparts, 2, ndim), sep=sep)
            return BezierSpline(coords, control=control, closed=closed)

        def rewrite(self):
            """Convert the geometry file to the latest format.

            The conversion is done by reading all objects from the geometry file
            and writing them back. Parts that could not be succesfully read will
            be skipped.
            """
            self.reopen('r')
            obj = self.read(warn_version=False)
            self.version = GeometryFile._version_
            if obj is not None:
                self.reopen('w')
                self.write(obj)
            self.close()

    # End