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Re: [sbml-spatial] VTK ordering ...
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From: Schaff,Jim <sc...@uc...> - 2015-05-07 17:00:56
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1) Don’t define a figure 8 – and specify 4 vertices for a quad and 3 for a vertex (there are formats which encode “triangle strips” … this was not the intent). 2) One suggestion is to require (or consider best practice) that the surface “normal” be directed consistently for adjacent polygons on the same surface. If we follow vertex list traversal using right-hand-rule to determine the front/back face of the surface. I’m intentionally not saying “inside and outside”. If a model doesn’t do this, most simulators will have to attempt to correct this … better to do it right the first time. Jim. From: Lucian Smith [mailto:luc...@gm...] Sent: Wednesday, May 06, 2015 6:49 PM To: The SBML L3 Spatial Processes and Geometries package discussion list Subject: Re: [sbml-spatial] VTK ordering ... That sounds great! One question: does 'follow adjacent edges' mean internally for the triangle/quad itself, or 'adjacent' to the previously-defined triangle/quad? In other words, is the only effective restriction, "Don't define your quadrilaterals in a figure eight' or does it mean, 'after you define your first triangle, define your next one so they share an edge'? -Lucian On Wed, May 6, 2015 at 3:31 PM, Schaff,Jim <sc...@uc...<mailto:sc...@uc...>> wrote: Hi all, The VTK ordering refers to the vertex ordering for vtkCellTypes (polygons and polyhedra). If we restrict our attension to polygons (e.g. triangles and quads) then any ordering which follows the edges are fine. See page 9 and 10 of http://www.vtk.org/wp-content/uploads/2015/04/file-formats.pdf for vertex orderings of triangles, quads, and a number of other polygons and polyhedra which we currently are not proposing in SBML spatial. The VTK rationale for this set of vtkCellTypes is that they are simple, computationally efficient, and while not comprehensive they can be used to approximate other shapes.. If we restrict ourselves to triangles and quads for now, then we can remove the language about VTK orderings (just replace it with text which states that the sequence of vertex indices should follow adjacent edges with an implied edge between the first and last vertex of a polygon. If we want room to grow, then for polyhedra, an ordering scheme will be needed - or a hierarchy of shapes, faces, edges, points have to be introduced (the VTK vertex ordering is an efficient approach to simplify the description for a sufficiently large set of simple shapes). Jim. -----Original Message----- From: Frank Bergmann [mailto:fbe...@ca...<mailto:fbe...@ca...>] Sent: Wednesday, May 06, 2015 12:06 PM To: The SBML L3 Spatial Processes and Geometries package discussion list Subject: Re: [sbml-spatial] Examples of spatial models > On May 6, 2015, at 5:28 PM, Weatherby,Gerard <gwe...@uc...<mailto:gwe...@uc...>> wrote: > > Looking at > <spatial:listOfGeometryDefinitions> > <spatial:sampledFieldGeometry spatial:id="mySampledField"> > <spatial:listOfSampledVolumes> > <spatial:sampledVolume spatial:id="Extracellular" spatial:domainType="Extracellular" spatial:sampledValue="0" spatial:minValue="0" spatial:maxValue="0"/> > <spatial:sampledVolume spatial:id="Cytosol" spatial:domainType="Cytosol" spatial:sampledValue="128" spatial:minValue="0" spatial:maxValue="0"/> > <spatial:sampledVolume spatial:id="Nucleus" spatial:domainType="Nucleus" spatial:sampledValue="255" spatial:minValue="0" spatial:maxValue="0"/> > </spatial:listOfSampledVolumes> > </spatial:sampledFieldGeometry> > </spatial:listOfGeometryDefinitions> > from samplefield_3d.xml , the corresponding section from the draft, and existing VCell code: > I’m not getting what the minValue and maxValue is telling us? I think what would make sense, is that you either define a precise value (“sampledValue”) or you specify a range, that everything in the range 120-130 would be the cytosol. (Unless the interpretation of the spec would be +- the sampled value (but i would not like that)). > Are the sampledValue values expected to be unique within a set? within the listOfSampledVolumes they could be unique … it does not make much sense to assign the same sampledValue to multiple domainTypes explicitly. > Should <spatial:sampledFieldGeometry spatial:id="mySampledField"> have a sampledField attribute? (e.g. <spatial:sampledFieldGeometry spatial:id="mySampledField" spatial:sampledField=”imgtest”>? > Yes! Frank > Gerard Weatherby | Application Architect Center for Cell Analysis & > Modeling | UConn Health > 263 Farmington Avenue, Farmington, CT 06030-6406 > Office: 860.679.2065 > uchc.edu<http://uchc.edu> > > > From: Lucian Smith [mailto:luc...@gm...<mailto:luc...@gm...>] > Sent: Wednesday, April 29, 2015 3:11 PM > To: The SBML L3 Spatial Processes and Geometries package discussion > list > Subject: [sbml-spatial] Examples of spatial models > > At HARMONY, Kaito Ii worked on creating some example Spatial models using the latest 0.90 specification. If some of you could take a look (particularly those who are familiar with the parametric geometry piece), that'd be great! > > One issue in particular: nobody at HARMONY knew what 'accepted VTK ordering' was, nor could we find references online--the URL in the specification seems to be out of date, and no longer points to a valid document. > > -Lucian > ---------------------------------------------------------------------- > -------- One dashboard for servers and applications across > Physical-Virtual-Cloud Widest out-of-the-box monitoring support with > 50+ applications Performance metrics, stats and reports that give you > Actionable Insights Deep dive visibility with transaction tracing > using APM Insight. > http://ad.doubleclick.net/ddm/clk/290420510;117567292;y_______________ > ________________________________ > sbml-spatial mailing list > sbm...@li...<mailto:sbm...@li...> > https://lists.sourceforge.net/lists/listinfo/sbml-spatial ------------------------------------------------------------------------------ One dashboard for servers and applications across Physical-Virtual-Cloud Widest out-of-the-box monitoring support with 50+ applications Performance metrics, stats and reports that give you Actionable Insights Deep dive visibility with transaction tracing using APM Insight. http://ad.doubleclick.net/ddm/clk/290420510;117567292;y _______________________________________________ sbml-spatial mailing list sbm...@li...<mailto:sbm...@li...> https://lists.sourceforge.net/lists/listinfo/sbml-spatial ------------------------------------------------------------------------------ One dashboard for servers and applications across Physical-Virtual-Cloud Widest out-of-the-box monitoring support with 50+ applications Performance metrics, stats and reports that give you Actionable Insights Deep dive visibility with transaction tracing using APM Insight. http://ad.doubleclick.net/ddm/clk/290420510;117567292;y _______________________________________________ sbml-spatial mailing list sbm...@li...<mailto:sbm...@li...> https://lists.sourceforge.net/lists/listinfo/sbml-spatial |