From: Lucian S. <luc...@gm...> - 2016-12-17 22:52:02
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The same issue is present with the rotations in these models as was present in the original: when spatial:rotateAngleInRadians="0", this means 'do not rotate at all'. The order doesn't matter. The rotation is supposed to happen like this: 1) Create a vector from (0,0,0) to (rotateX, rotateY, rotateZ). 2) Rotate the figure around that vector by rotateAngleInRadians. It does *not* mean 'rotate the figure around the X axis by rotateX radians, then do the same for the Y and Z axes', which is how I think you have interpreted the construct. -Lucian On Sat, Dec 17, 2016 at 11:09 AM, Ivan E Cao-Berg <ica...@an...> wrote: > We generated some example synthetic images in CellOrganizer along with > their SBML Spatial representation. > > You can find the examples here > > http://cellorganizer.org/SBML/examples/ > > The examples have been checked using the SBML online validator for syntax. > > As for the rotation issue, the issue is that we probably specified the > operations in the wrong order. What we want to do is start with a sphere, > move it from the origin, scale it to an ellipsoid, and then tilt the > ellipsoid along the line specific by the x, y, and z rotation axes. You > and Jim are correct that the way we wrote it, tilting the sphere along that > line doesn’t change anything. > > > I will update the order of transformations in CellOrganizer to reflect > this feedback. > > I hope this examples are helpful to everyone. > > Ivan > > ------------------------------ > Iván E. Cao-Berg > Senior Research Programmer > Computational Biology Department <http://cbd.cmu.edu> > School of Computer Science <http://www.scs.cmu.edu> > Carnegie Mellon University <http://www.cmu.edu/> > > <http://www.andrew.cmu.edu/~icaoberg/> <http://cbd.cmu.edu> > <http://www.twitter.com/cmucompbio> <https://www.facebook.com/cmucbd> > <https://www.instagram.com/cmucbd/> > <https://plus.google.com/+CMUComputationalBiologyDepartmentPittsburgh> > <https://coderwall.com/icaoberg> <http://www.github.com/icaoberg> > <http://www.bitbucket.com/icaoberg> > > On Dec 16, 2016, at 2:59 PM, Robert F. Murphy <mu...@cm...> wrote: > > We have some more examples that we will send shortly. > > As for the rotation issue, the issue is that we probably specified the > operations in the wrong order. What we want to do is start with a sphere, > move it from the origin, scale it to an ellipsoid, and then tilt the > ellipsoid along the line specific by the x, y, and z rotation axes. You > and Jim are correct that the way we wrote it, tilting the sphere along that > line doesn’t change anything. > > Best, > > Bob > ======================= > Robert F. Murphy, Ph.D. > Ray and Stephanie Lane Professor of Computational Biology and Professor > of Biological Sciences, Biomedical Engineering, and Machine Learning > Head, Computational Biology Department, School of Computer Science, Carnegie > Mellon University > 7723 Gates and Hillman Centers, 5000 Forbes Ave., Pittsburgh, PA 15213 > Phone: 412-268-3480 <(412)%20268-3480>, FAX: 412-268-2977 > <(412)%20268-2977>, email: mu...@cm..., Skype: rfmurphy1953 > Personal: Home Page (http://www.andrew.cmu.edu/user/murphy), Twitter > @murphy2537 > Comp Bio Department: Facebook (cmucbd), Twitter @CMUCompBio > Honorary Professor, University of Freiburg and External Senior Fellow, > Freiburg Institute for Advanced Studies > > > > > On Dec 16, 2016, at 1:54 PM, Lucian Smith <luc...@gm...> > wrote: > > Now that the semantic changes are in, I'm going back over these examples. > Thanks again, Bob! > > I do now see what Jim pointed out: in csg_one_object, you have the > following rotation: > > <spatial:csgRotation spatial:id="rotation" > spatial:rotateX="2.4391" spatial:rotateY="1.5373" spatial:rotateZ="0.58404" > spatial:rotateAngleInRadians="0"> > > In the definition of a csgRotation, you'll see that the X, Y, and Z values > define a vector, from the origin, *around which* the modeler is to rotate > the object, by the amount defined in the rotateAngleInRadians attribute. > However, since in this case the rotateAngle is 0, this rotation does not > actually modify the CSGObject at all. > > Is this what was intended? It seems unlikely. > > -Lucian > > On Mon, Nov 28, 2016 at 8:38 AM, Robert F. Murphy <mu...@cm...> wrote: > >> resending with correct email address for Devin. >> >> Best, >> >> Bob >> ======================= >> Robert F. Murphy, Ph.D. >> Ray and Stephanie Lane Professor of Computational Biology and Professor >> of Biological Sciences, Biomedical Engineering, and Machine Learning >> Head, Computational Biology Department, School of Computer Science, Carnegie >> Mellon University >> 7723 Gates and Hillman Centers, 5000 Forbes Ave., Pittsburgh, PA 15213 >> Phone: 412-268-3480 <(412)%20268-3480>, FAX: 412-268-2977 >> <(412)%20268-2977>, email: mu...@cm..., Skype: rfmurphy1953 >> Personal: Home Page (http://www.andrew.cmu.edu/user/murphy), Twitter >> @murphy2537 >> Comp Bio Department: Facebook (cmucbd), Twitter @CMUCompBio >> Honorary Professor, University of Freiburg and External Senior Fellow, >> Freiburg Institute for Advanced Studies >> >> >> >> >> On Nov 28, 2016, at 11:34 AM, Robert F. Murphy <mu...@cm...> wrote: >> >> attached are some examples we generated with CellOrganizer - they pass >> the online validator and roundtrip through reading and writing with libSBML. >> >> however, they can’t be read by VCell 5.3 (build 29). If anyone else has >> a program that supports SBML spatial, it would be great to see if they can >> be read by it. >> >> We will send some more examples soon, including one with mixed geometry. >> >> Best, >> >> Bob & Ivan >> <SBML spatial samples CellOrganizer.zip> >> >> ======================= >> Robert F. Murphy, Ph.D. >> Ray and Stephanie Lane Professor of Computational Biology and Professor >> of Biological Sciences, Biomedical Engineering, and Machine Learning >> Head, Computational Biology Department, School of Computer Science, Carnegie >> Mellon University >> 7723 Gates and Hillman Centers, 5000 Forbes Ave., Pittsburgh, PA 15213 >> Phone: 412-268-3480 <(412)%20268-3480>, FAX: 412-268-2977 >> <(412)%20268-2977>, email: mu...@cm..., Skype: rfmurphy1953 >> Personal: Home Page (http://www.andrew.cmu.edu/user/murphy), Twitter >> @murphy2537 >> Comp Bio Department: Facebook (cmucbd), Twitter @CMUCompBio >> Honorary Professor, University of Freiburg and External Senior Fellow, >> Freiburg Institute for Advanced Studies >> >> >> >> >> On Nov 16, 2016, at 4:24 PM, Robert F. Murphy <MURPHY@CMU.EDU >> <MU...@cm...>> wrote: >> >> We have generated a lot of examples using different options and are >> testing them using the validator and libSBML and vcell. I'm tied up today >> and tomorrow but will send a report and examples on Friday. >> >> Best, >> >> Bob >> >> Sent from my iPhone >> ================ >> Robert F. Murphy, Ph.D. >> Ray and Stephanie Lane Professor of Computational Biology and Professor >> of Biological Sciences, Biomedical Engineering, and Machine Learning >> Carnegie Mellon University >> 5000 Forbes Ave., Pittsburgh, PA 15213; +1.412.268.3480 >> <(412)%20268-3480> >> >> On Nov 16, 2016, at 1:08 PM, Frank T. Bergmann <fbe...@ca...> >> wrote: >> >> Hello Jim, >> >> as far as I'm aware the current libSBML implementation (experimental) >> implements the latest spec. If you find any issues please let me know >> and i will fix it right away. >> >> best >> Frank >> >> On Wed, Nov 16, 2016 at 9:33 PM, Schaff,Jim <sc...@uc...> wrote: >> Hi All, >> >> Is it true that libSBML does not support the latest SBML Spatial >> specification? I know in theory it is orthogonal, but in practice it is >> essential. >> >> Lucian, do you or Frank know how close libSBML is to the latest spec >> changes? >> >> I'd be willing to take a whack at compliance to the latest spec, >> especially if I don't have to make the libSBML changes. >> >> Jim. >> >> >> ________________________________________ >> From: Lucian Smith <luc...@gm...> >> Sent: Wednesday, November 16, 2016 3:07 PM >> To: The SBML L3 Spatial Processes and Geometries package discussion list >> Subject: [sbml-spatial] Request: example models >> >> Hey, everyone! I have some time to work on the spatial specification >> again, and it looks pretty close to being finished. At this point, >> the main thing it needs is some examples that illustrate both the >> commonly-used aspects of the spec, as well as a few illustrating some >> of the potentially-confusing edge cases. From there, I think it's >> mostly simply a matter of making sure at least one group has >> implemented support for every element in the spec, and it'll be good >> to go! >> >> If anyone has or could put together some simple spatial models that >> follow the current specification, and could send them my way, I think >> we can wrap this thing up and call it finished. Thank you! >> >> As always, if anyone has any comments on the specification itself, >> don't hesitate to bring them up. >> >> -Lucian >> >> ------------------------------------------------------------ >> ------------------ >> _______________________________________________ >> sbml-spatial mailing list >> sbm...@li... >> https://urldefense.proofpoint.com/v2/url?u=https-3A__lists.s >> ourceforge.net_lists_listinfo_sbml-2Dspatial&d=CwICAg&c= >> EZxp_D7cDnouwj5YEFHgXuSKoUq2zVQZ_7Fw9yfotck&r=6W0wBewzLZ4dT2 >> ku5JQeMaL3BGQ7J1CI2zO48jPRDC4&m=D71-76AqMfX4FPnO8tmiPyeCvKXX >> PSbv7fL67OdPOjk&s=zQwyhcdtfpS2YhK0q_zjdryBvhK6vNBFtf_7mAYHpdo&e= >> >> ------------------------------------------------------------ >> ------------------ >> _______________________________________________ >> sbml-spatial mailing list >> sbm...@li... >> https://lists.sourceforge.net/lists/listinfo/sbml-spatial >> >> >> ------------------------------------------------------------ >> ------------------ >> _______________________________________________ >> sbml-spatial mailing list >> sbm...@li... >> https://lists.sourceforge.net/lists/listinfo/sbml-spatial >> >> >> >> >> >> ------------------------------------------------------------ >> ------------------ >> >> _______________________________________________ >> sbml-spatial mailing list >> sbm...@li... >> https://lists.sourceforge.net/lists/listinfo/sbml-spatial >> >> > ------------------------------------------------------------ > ------------------ > Check out the vibrant tech community on one of the world's most > engaging tech sites, SlashDot.org <http://slashdot.org/>! > http://sdm.link/slashdot_______________________________________________ > sbml-spatial mailing list > sbm...@li... > https://lists.sourceforge.net/lists/listinfo/sbml-spatial > > > > ------------------------------------------------------------ > ------------------ > Check out the vibrant tech community on one of the world's most > engaging tech sites, SlashDot.org! http://sdm.link/slashdot > _______________________________________________ > sbml-spatial mailing list > sbm...@li... > https://lists.sourceforge.net/lists/listinfo/sbml-spatial > > |