#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 gutow):
Replying to [comment:32 kcrisman]:
> > My first attempt at getting this to work showed that
> > * the Tachyon "placeholder" evaluates fine, though I agree with
strogdon from #9238 that it's annoying to always have to make it
interactive, though I understand the reasoning
>
> You were right, it was the Jmol placeholder. I really find that
annoying.
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. One of the problems I consistently have using
the old format where Jmol loads live in interacts is that the interact
starts calling for a new applet before the previous one is finished
loading. I have had some discussions about putting the applet in a special
div that does not get zapped each time a recalculation is done. That's
probably the correct thing to do, but not high on people's list when the
notebook was undergoing major revisions. I would prefer to put this off
as an additional enhancement.
>
> > * Nothing else worked - lots of messages about restarting Jmol and so
forth. At one point I even got a !JmolData java applet starting outside
the browser window.
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.
> Question about implementation. How much work does Jmol have to do to
generate all those static images '''every''' time that one opens a
worksheet?
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.
>
>
> More minor issues.
> * When I sleep an image, it doesn't come back with the advanced
controls if I had them up. Is there any way to "save" that state, or is
it too hard?
Hadn't thought about this. I will look into it.
> * Although it's pretty clear by the content, it's a little hard to see
which tab you are on in the advanced controls sometimes. Maybe the
shading could be slightly different.
I'm using Sage default CSS. I suppose we could define something custom.
> * In interacts, I think there is no point to having the initial static
image. I have no idea if there is a way to detect this, but presumably
one wouldn't have asked for this to be evaluated if one wasn't going to
use it.
As I explained above, only simple interacts where the user does not call
for lots of recalculations work reliably with the present model of loading
Jmol live. Things with sliders are really bad.
> * The opening of the "!JmolData" app each time is a little annoying.
> * When doing
> {{{
>
implicit_plot3d(x^2+y^2+z^2==16,(x,-5,5),(y,-5,5),(z,-5,5),color='green',plot_points=200)
> }}}
> I got
> {{{
> viewer handling error condition: java.lang.OutOfMemoryError: Java heap
space
> }}}
> Maybe I'm being overoptimistic; the docs don't even have any with 100
`plot_points`.
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...
> * On the plus side, the thing where only four Jmols are active at a
time is working fine. I notice that it deactivates the one furthest down
or something, not the oldest one.
Actually it picks the one farthest from the cell you most recently
evaluated that includes a Jmol. It can be above or below the cell you are
working on.
>
> ----
>
> I have to say that I'm by far the most concerned about the "old
worksheets" issue. Second is the "automatically every image is static" -
couldn't at least the ''first'' one be "live"? - but nearly everything
else could be considered an enhancement request. Let me know what stuff
I've mentioned is worth discussing here.
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?
--
Ticket URL: <http://trac.sagemath.org/sage_trac/ticket/12299#comment:35>
Sage <http://www.sagemath.org>
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