Thanks, I'll try to get a look at it. This appears to be what I
needed to find. No promises, as I'm pretty swamped, but now I have
somewhere to start.
Jonathan
On Nov 3, 1:02 am, Jason Grout <jason-s...@creativetrax.com> wrote:
> Jonathan wrote:
> > Jason,
> > I think this is a great idea. As I use Sage a bit in my teaching,
> > it would be nice to have a primitive with separate items for axes,
> > axes' labels, axes scale (the numbers on the axes). Then buttons
> > could be added to turn these on and off at the user request. If some
> > things can be passed to Jmol as functions, they will render well at
> > any zoom level. It would also be easier to use the slab function for
> > slicing 3-D objects.
> > That said there are some serious problems with how the notebook/
> > plot3D uses Jmol presently, that have little to do with whether a
> > primitive exists or not. I'm willing to help fix them, but need to
> > understand where in the code the html and javascript for Jmol is
> > generated. The way it is presently done the following things are a
> > problem:
>
> > 1) It does not work in Firefox on Macs. Since I never have trouble
> > with this, I'm assuming something abnormal is being done with the
> > javascript that controls Jmol. Again, I bet I can help with this, but
> > I could not easily find where the code was generated. All I can do is
> > look at a web page.
> > 2) Since people are running into memory problems, I suggest that only
> > a limited number of live Jmols (present default JavaVM configurations
> > support about 8 - 10 per page) be allowed in any given notebook. I
> > provided some example code that does not require any server
> > intervention that does this. I could help fold this in, if I could
> > figure out how you are generating the javascript to control Jmol.
> > 3) Since there is room next to Jmol in the notebook, I suggest that
> > simple instructions on what Jmol can do and how to access the pop-up
> > be added and maybe a link to more extensive documentation (the Jmol
> > Site?). I'm an expert with Jmol and found it difficult to do anything
> > but rotate the image without significant experimentation.
> > 4) It also might be worth loading only a static image first with a
> > link to make live. This saves a lot of bandwidth and will decrease
> > the time users have to wait to see their plots.
> > 5) It would probably be a good idea to upgrade Jmol to the latest
> > stable release 11.8. I will try slipping that into a copy of 4.2 I
> > just downloaded.
>
> > These are just some thoughts. The key thing is I think I could help,
> > but do not have time to wade through the code to figure out how
> > everything is connected. Can someone just tell me were to look?
>
> Here's what I found by poking around for a bit. Everything has changed
> since the new notebook, so someone that knows, *please* correct me if
> I'm wrong.
>
> In Sage 4.2, it looks like the jmol-invoking javascript code is in:
>
> local/lib/python2.6/site-packages/sagenb/data/sage/js/jmol_lib.js
>
> That appears to be the code that actually sets up a jmol applet and
> makes the "Get Image" link.
>
> That file is loaded in
> local/lib/python2.6/site-packages/sagenb/data/sage/js/notebook_lib.js
>
> Jmol is initialized at the bottom of the template file:
>
> local/lib/python2.6/site-packages/sagenb/data/sage/html/notebook/head.tmpl
>
> The actual jmol application is in:
>
> local/lib/python2.6/site-packages/sagenb/data/jmol
>
> The jmol code gets invoked when a ".jmol" file is created by a 3d plot.
> The notebook then comes by, sees the .jmol file, and creates the jmol
> applet. The code that does this is in
> local/lib/python2.6/site-packages/sagenb/notebook/cell.py (search for
> jmol).
>
> The code in Sage that generates the .jmol files is (I believe) in
> devel/sage/sage/plot/plot3d/base.pyx (see the show method, starting with
> the following code. EMBEDDED_MODE is True when you are inside the
> notebook, and False if you are not executing inside the notebook.)
>
> if DOCTEST_MODE or viewer=='jmol':
> # Temporary hack: encode the desired applet size in the end
> of the filename:
> # (This will be removed once we have dynamic resizing of
> applets in the browser.)
> base, ext = os.path.splitext(filename)
> fg = figsize[0]
> #if fg >= 2:
> # fg = 2
> filename = '%s-size%s%s'%(base, fg*100, ext)
> ext = "jmol"
> archive_name = "%s.%s.zip" % (filename, ext)
> if EMBEDDED_MODE:
> # jmol doesn't seem to correctly parse the ?params part
> of a URL
> archive_name = "%s-%s.%s.zip" % (filename, randint(0, 1
> << 30), ext)
>
> T = self._prepare_for_jmol(frame, axes, frame_aspect_ratio,
> aspect_ratio, zoom)
> T.export_jmol(archive_name, force_reload=EMBEDDED_MODE,
> zoom=zoom*100, **kwds)
> viewer_app = "sage-native-execute " +
> os.path.join(sage.misc.misc.SAGE_LOCAL, "bin/jmol")
>
> # We need a script to load the file
> f = open(filename + '.jmol', 'w')
> f.write('set defaultdirectory "%s"\n' % archive_name)
> f.write('script SCRIPT\n')
> f.close()
>
> I hope this helps.
>
> Thanks,
>
> Jason
>
> --
> Jason Grout
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