#12299: Advance Jmol Interactive Features in Flask Notebook
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Reporter: gutow | Owner: jason,
mpatel, was
Type: enhancement | Status:
needs_work
Priority: major | Milestone:
sage-5.2
Component: notebook | Resolution:
Keywords: Jmol, 3D, notebook | Work issues: old
worksheets don't work
Report Upstream: Reported upstream. No feedback yet. | Reviewers:
Karl-Dieter Crisman, Steven Trogdon
Authors: Jonathan Gutow | Merged in:
Dependencies: #11080,#11078,#11503 | Stopgaps:
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Comment (by kcrisman):
> We potentially could get rid of this with significant browser detection
and a complete reworking of how Jmol is called for when a cell is
recalculated. The problem is related to the fact that the applet is
completely reloaded each time a cell is recalculated, rather than just
passing it new data. This means it is very easy to get out of sync with
what the server is sending to the applet. Many of the problems with the
old Jmol relate to this.
Right, and I assume that passing it new info would be a pretty sizable
change in how we use it.
> I would prefer to put this off as an additional enhancement.
Now that I understand the technical issue better, I guess I would agree in
some sense, but I figure it's buyer beware on the @interact cells. Having
to do an extra click every time would get really old really fast with
them. Maybe we could ask on sage-devel about the tradeoff, though perhaps
(as usual with polls on sage-devel) we wouldn't get many takers...
> As your comments below suggest this appears to be a problem with old
worksheets that have not been reevaluated. We might be able to put
something into the notebook code that puts up a message suggesting the
worksheet be re-evaluated if it does not have the data necessary for
static images. I tried to put a message in the "alt" field for the
images, but most browser now seem to ignore that. I think I can put a
check into the cell code that would deal with this. I even have some
ideas for generating images without reevaluation...I'll look into this.
We definitely need to fix this. Again, I even had trouble with some
worksheets even after re-evaluation.
It should be pretty easy for you to test this. Just open an old Sage,
make a new worksheet with Jmols, close it, stop Sage, restart your new
Jmol Sage, and see what happens. I figure you have more diagnostic tools
than I will.
> Jmol only generates the image when a cell is evaluated. When you open a
worksheet that was previously evaluated using these enhancements the
images are already there.
Great.
> The application can certainly handle more. I'll see if I can change the
memory allocation to allow for larger images...That is a little odd as we
use Jmol in web pages to look at things with many more points, atoms and
surfaces...
No, it's 100 points ''per axis'', so one million points are evaluated and
the presumably however many of them are on the sphere must be plotted. I
think that's why we don't even have it in the docs, because it would take
a long time. But it does seem to work in the old Jmol in Sage (just tried
it in vanilla 5.0).
> I agree that this should be a priority. I think there are solutions.
What behavior would be best: 1) A pop-up suggestion to reevaluate old
worksheets to update 3-D plots; 2) Attempt to update plots without
reevaluation; 3) Automatically reevaluate worksheets with 3-D plots in
them?
Definitely not 3. 1 also seems less than desirable unless it was only
when there had been a Jmol before, and one could reliably detect it was
from an earlier version of Jmol. How would 2 work?
----
Some dumb generic review questions.
* So far I've not been able to use this except on Safari on OS X because
of some default I can't get around and logins. What have you tested this
on? In the past you had done some pretty extensive testing. I figure we
should at least test on Safari, FF, Chrome on Mac, FF and Chrome on Linux,
IE and FF on Windows. I don't know how easy that will be for me unless
you set up a remote server again, which I figure would be quite a pain.
* What problems should one be looking for with `secure=True`? It sounds
like you are thinking that there could be different issues in that case,
maybe because of the applets being applets?
--
Ticket URL: <http://trac.sagemath.org/sage_trac/ticket/12299#comment:36>
Sage <http://www.sagemath.org>
Sage: Creating a Viable Open Source Alternative to Magma, Maple, Mathematica,
and MATLAB
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