pyFormex example scripts — pyFormex v0.8.6 documentation

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# pyFormex example scripts

Warning

This document still needs some cleanup!

Sometimes you learn quicker from studying an example than from reading a tutorial or user guide. To help you we have created this collection of annotated examples. Beware that the script texts presented in this document may differ slightly from the corresponding example coming with the pyFormex distribution.

## WireStent

To get acquainted with the modus operandi of pyFormex, the `WireStent.py` script is studied step by step. The lines are numbered for easy referencing, but are not part of the script itself.

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    # $Id: WireStent.py 2146 2012-01-09 08:57:52Z bverheg $   *** pyformex ***
    ##
    ##  This file is part of pyFormex 0.8.6  (Mon Jan 16 21:15:46 CET 2012)
    ##  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 2004-2011 (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/.
    ##
    """Wirestent.py

    A pyFormex script to generate a geometrical model of a wire stent.

    This version is for inclusion in the pyFormex documentation.
    """

    from formex import *

    class DoubleHelixStent:
        """Constructs a double helix wire stent.

        A stent is a tubular shape such as used for opening obstructed
        blood vessels. This stent is made frome sets of wires spiraling
        in two directions.
        The geometry is defined by the following parameters:
          L  : approximate length of the stent
          De : external diameter of the stent
          D  : average stent diameter
          d  : wire diameter
          be : pitch angle (degrees)
          p  : pitch
          nx : number of wires in one spiral set
          ny : number of modules in axial direction
          ds : extra distance between the wires (default is 0.0 for
               touching wires)
          dz : maximal distance of wire center to average cilinder
          nb : number of elements in a strut (a part of a wire between two
               crossings), default 4
        The stent is created around the z-axis.
        By default, there will be connectors between the wires at each
        crossing. They can be switched off in the constructor.
        The returned formex has one set of wires with property 1, the
        other with property 3. The connectors have property 2. The wire
        set with property 1 is winding positively around the z-axis.
        """
        def __init__(self,De,L,d,nx,be,ds=0.0,nb=4,connectors=True):
            """Create the Wire Stent."""
            D = De - 2*d - ds
            r = 0.5*D
            dz = 0.5*(ds+d)
            p = math.pi*D*tand(be)
            nx = int(nx)
            ny = int(round(nx*L/p))  # The actual length may differ a bit from L
            # a single bumped strut, oriented along the x-axis
            bump_z=lambda x: 1.-(x/nb)**2
            base = Formex(pattern('1')).replic(nb,1.0).bump1(2,[0.,0.,dz],bump_z,0)
            # scale back to size 1.
            base = base.scale([1./nb,1./nb,1.])
            # NE and SE directed struts
            NE = base.shear(1,0,1.)
            SE = base.reflect(2).shear(1,0,-1.)
            NE.setProp(1)
            SE.setProp(3)
            # a unit cell of crossing struts
            cell1 = (NE+SE).rosette(2,180)
            # add a connector between first points of NE and SE
            if connectors:
                cell1 += Formex([[NE[0][0],SE[0][0]]],2)
            # and create its mirror
            cell2 = cell1.reflect(2)
            # and move both to appropriate place
            self.cell1 = cell1.translate([1.,1.,0.])
            self.cell2 = cell2.translate([-1.,-1.,0.])
            # the base pattern cell1+cell2 now has size [-2,-2]..[2,2]
            # Create the full pattern by replication
            dx = 4.
            dy = 4.
            F = (self.cell1+self.cell2).replic2(nx,ny,dx,dy)
            # fold it into a cylinder
            self.F = F.translate([0.,0.,r]).cylindrical(
                dir=[2,0,1],scale=[1.,360./(nx*dx),p/nx/dy])
            self.ny = ny

        def all(self):
            """Return the Formex with all bar elements."""
            return self.F

    if __name__ == "draw":

        # show an example

        wireframe()
        reset()

        D = 10.
        L = 80.
        d = 0.2
        n = 12
        b = 30.
        res = askItems([['Diameter',D],
                        ['Length',L],
                        ['WireDiam',d],
                        ['NWires',n],
                        ['Pitch',b]])

        if not res:
            exit()

        D = float(res['Diameter'])
        L = float(res['Length'])
        d = float(res['WireDiam'])
        n = int(res['NWires'])
        if (n % 2) != 0:
            warning('Number of wires must be even!')
            exit()
        b = float(res['Pitch'])

        H = DoubleHelixStent(D,L,d,n,b).all()
        clear()
        draw(H,view='iso')

        # and save it in a lot of graphics formats
        if ack("Do you want to save this image (in lots of formats) ?"):
            for ext in [ 'bmp', 'jpg', 'pbm', 'png', 'ppm', 'xbm', 'xpm',
                         'eps', 'ps', 'pdf', 'tex' ]:
                image.save('WireStent.'+ext)

    # End

As all pyFormex scripts, it starts with a comments line holding the word `pyformex` (line 1). This is followed more comments lines specifying the copyright and license notices. If you intend to distribute your scripts, you should give these certainly special consideration.

Next is a documentation string explaining the purpose of the script (lines 25-30). The script then starts by importing all definitions from other modules required to run the `WireStent.py` script (line 32).

Subsequently, the class `DoubleHelixStent` is defined which allows the simple use of the geometrical model in other scripts for e.g. parametric, optimization and finite element analyses of braided wire stents. Consequently, the latter scripts do not have to contain the wire stent geometry building and can be condensed and conveniently arranged. The definition of the class starts with a documentation string, explaining its aim and functioning (lines 34-60).

The constructor `__init__` of the `DoubleHelixStent` class requires 8 arguments (line 61):

- stent external diameter (mm).
- stent length (mm).
- wire diameter (mm).
- Number of wires in one spiral set, i.e. wires with the same orientation, (-).
- Pitch angle ().
- Extra radial distance between the crossing wires (mm). By default, is [0.0]mm for crossing wires, corresponding with a centre line distance between two crossing wires of exactly .
- Number of elements in a strut, i.e. part of a wire between two crossings, (-). As every base element is a straight line, multiple elements are required to approximate the curvature of the stent wires. The default value of 4 elements in a strut is a good assumption.
- If `connectors=True`, extra elements are created at the positions where there is physical contact between the crossing wires. These elements are required to enable contact between these wires in finite element analyses.

The virtual construction of the wire stent structure is defined by the following sequence of four operations: (i) Creation of a nearly planar base module of two crossing wires; (ii) Extending the base module with a mirrored and translated copy; (iii) Replicating the extended base module in both directions of the base plane; and (iv) Rolling the nearly planar grid into the cylindrical stent structure, which is easily parametric adaptable.

### Creating the base module

(lines 63-71)

Depending on the specified arguments in the constructor, the mean stent diameter , the average stent radius , the `bump` or curvature of the wires , the pitch and the number of base modules in the axial direction are calculated with the following script. As the wire stent structure is obtained by braiding, the wires have an undulating course and the `bump dz` corresponds to the amplitude of the wave. If no extra distance is specified, there will be exactly one wire diameter between the centre lines of the crossing wires. The number of modules in the axial direction is an integer, therefore, the actual length of the stent model might differ slightly from the specified, desired length . However, this difference has a negligible impact on the numerical results.

Of now, all parameters to describe the stent geometry are specified and available to start the construction of the wire stent. Initially a simple Formex is created using the `pattern()`-function: a straigth line segment of length 1 oriented along the X-axis (East or -direction). The `replic()`-functionality replicates this line segment times with step 1 in the X-direction (-direction). Subsequently, these line segments form a new Formex which is given a one-dimensional `bump` with the `bump1()`-function. The Formex undergoes a deformation in the Z-direction (-direction), forced by the point `[0,0,dz]`. The `bump` intensity is specified by the quadratic `bump_z` function and varies along the X-axis (-axis). The creation of this single bumped strut, oriented along the X-axis is summarized in the next script and depicted in figures A straight line segment, The line segment with replications and A bumped line segment,.

A straight line segment

The line segment with replications

A bumped line segment

The single bumped strut (`base`) is rescaled homothetically in the XY-plane to size one with the `scale()`-function. Subsequently, the `shear()`-functionality generates a new `NE` Formex by skewing the `base` Formex in the Y-direction (-direction) with a `skew` factor of in the YX-plane. As a result, the Y-coordinates of the `base` Formex are altered according to the following rule: . Similarly a `SE` Formex is generated by a `shear()` operation on a mirrored copy of the `base` Formex. The `base` copy, mirrored in the direction of the XY-plane (perpendicular to the -axis), is obtained by the `reflect()` command. Both Formices are given a different property number by the `setProp()`-function, visualised by the different color codes in Figure Unit cell of crossing wires and connectors This number can be used as an entry in a database, which holds some sort of property. The Formex and the database are two seperate entities, only linked by the property numbers. The `rosette()`-function creates a unit cell of crossing struts by rotational replications with an angular step of [180]:math:deg around the Z-axis (the original Formex is the first of the replicas). If specified in the constructor, an additional Formex with property connects the first points of the `NE` and `SE` Formices.

(lines 72-83)

Rescaled bumped strut

Mirrored and skewed bumped strut

Unit cell of crossing wires and connectors

### Extending the base module

Subsequently, a mirrored copy of the base cell is generated (Figure Mirrored unit cell). Both Formices are translated to their appropriate side by side position with the `translate()`-option and form the complete extended base module with 4 by 4 dimensions as depicted in Figure Completed base module. Furthermore, both Formices are defined as an attribute of the `DoubleHelixStent` class by the `self`-statement, allowing their use after every `DoubleHelixStent` initialisation. Such further use is impossible with local variables, such as for example the `NE` and `SE` Formices.

(lines 84-89)

Mirrored unit cell

Completed base module

### Full nearly planar pattern

The fully nearly planar pattern is obtained by copying the base module in two directions and shown in Figure Full planar topology. `replic2()` generates this pattern with and replications with steps and in respectively, the default X- and Y-direction.

(lines 90-93)

Full planar topology

Orthogonal view of the full planar topology

### Cylindrical stent structure

Finally the full pattern is translated over the stent radius in Z-direction and transformed to the cylindrical stent structure by a coordinate transformation with the Z-coordinates as distance , the X-coordinates as angle and the Y-coordinates as height . The `scale()`-operator rescales the stent structure to the correct circumference and length. The resulting stent geometry is depicted in Figure Cylindrical stent. (lines 94-96)

In addition to the stent initialization, the `DoubleHelixStent` class script contains a function `all()` representing the complete stent Formex. Consequently, the `DoubleHelixStent` class has four attributes: the Formices `cell1`, `cell2` and `all`; and the number . (lines 97-100)

Cylindrical stent

Orthogonal view of the cylindrical stent

### Parametric stent geometry

An inherent feature of script-based modeling is the possibility of easily generating lots of variations on the original geometry. This is a huge advantage for parametric analyses and illustrated in figures Stent variant with : these wire stents are all created with the same script, but with other values of the parameters , and . As the script for building the wire stent geometry is defined as a the `DoubleHelixStent` class in the (`WireStent.py`) script, it can easily be imported for e.g. this purpose.

Stent variant with

Stent variant with

Stent variant with

Stent variant with

Stent variant with

Stent variant with

Stent variant with

Stent variant with

    # $Id: WireStentParametricExample.py 2146 2012-01-09 08:57:52Z bverheg $   *** pyformex ***
    ##
    ##  This file is part of pyFormex 0.8.6  (Mon Jan 16 21:15:46 CET 2012)
    ##  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 2004-2011 (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/.
    ##

    from examples.WireStent import DoubleHelixStent

    for De in [16.,32.]:
        for nx in [6,10]:
            for beta in [25,50]:
                stent = DoubleHelixStent(De,40.,0.22,nx,beta).all()
                draw(stent,view='iso')
                pause()
                clear()

Obviously, generating such parametric wire stent geometries with classical CAD methodologies is feasible, though probably (very) time consuming. However, as provides a multitude of features (such as parametric modeling, finite element pre- and postprocessing, optimization strategies, etcetera) in one single consistent environment, it appears to be the obvious way to go when studying the mechanical behavior of braided wire stents.

## Operating on surface meshes

Besides being used for creating geometries, also offers interesting possibilities for executing specialized operations on surface meshes, usually STL type triangulated meshes originating from medical scan (CT) images. Some of the algorithms developed were included in .

### Unroll stent

A stent is a medical device used to reopen narrowed arteries. The vast majority of stents are balloon-expandable, which means that the metal structure is deployed by inflating a balloon, located inside the stent. Figure Triangulated mesh of a Cypher® stent shows an example of such a stent prior to expansion (balloon not shown). The 3D surface is obtained by micro CT and consists of triangles.

Triangulated mesh of a Cypher® stent

The structure of such a device can be quite complex and difficult to analyse. The same functions offers for creating geometries can also be employed to investigate triangulated meshes. A simple unroll operation of the stent gives a much better overview of the complete geometrical structure and allows easier analysis (see figure Result of the unroll operation).

`F = F.toCylindrical().scale([1.,2*radius*pi/360,1.])`

Result of the unroll operation

The unrolled geometry can then be used for further investigations. An important property of such a stent is the circumference of a single stent cell. The `clip()` method can be used to isolate a single stent cell. In order to obtain a line describing the stent cell, the function `intersectionLinesWithPlane()` has been used. The result can be seen in figures Part of the intersection with a plane.

Part of the intersection with a plane

Finally, one connected circumference of a stent cell is selected (figure Circumference of a stent cell) and the `length()` function returns its length, which is 9.19 mm.

Circumference of a stent cell

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