polygon3d view in jmol broken

[kcrisman]

polygon3d([[0,0,0], [1,2,3], [3,0,0]]).show(viewer='jmol') 

does not show anything. See this ask.sagemath question.

EDIT: Issue previously reported as #19274. Description from that ticket:

Thomas Fernique reported the following bug by private email: from the console, some flat polygons in three-space lead to an empty picture with jmol (java version), for example:

sage: polygon([(0, 0, 0), (1, 0, 0), (1, 0, 1), (0, 0, 1)])

However, this is correctly displayed with jsmol (javascript version) from the notebook.

I can reproduce this bug on Sage 6.8, Debian GNU/Linux jessie 64 bit, openjdk-7-jre.

Still present in Sage 9.6.beta5, and still after upgrading to 14.32.35 (#30316).

Depends on #30316

CC: @paulmasson @novoselt @mkoeppe

Component: graphics

Keywords: jmol threejs

Issue created by migration from https://trac.sagemath.org/ticket/20978

[tscrim]

comment:2

When I add an arrow3d (for example), then it displays properly:

sage: polygon3d([[0,0,1],[0,1,0],[1,0,0]]) + arrow3d([0,0,0],[1,1,1])
sage: p2.plot() + arrow3d([0,0,0],[1,1,1])

It seems like it is just ignoring the polygon3d when it is the only object:

sage: p = polygon3d([[0,0,1],[0,1,0],[1,0,0]]) + arrow3d([0,0,0],[1,1,1])
sage: rp = p.default_render_params()
sage: rp.output_archive = None
sage: p.jmol_repr(rp)
['pmesh obj_1 "/home/travis/.sage/temp/apricot/5573/tmp_pU6Ppq-obj_1.pmesh"\ncolor pmesh  [0,0,255]']
<type 'sage.plot.plot3d.index_face_set.IndexFaceSet'>

sage: p = polygon3d([[0,0,1],[0,1,0],[1,0,0]]) + arrow3d([0,0,0],[1,1,1])
sage: p.jmol_repr(rp)
[['pmesh obj_2 "/home/travis/.sage/temp/apricot/5573/tmp_pU6Ppq-obj_2.pmesh"\ncolor pmesh  [0,0,255]'],
 [[['\ndraw line_3 width 0.02 {0.0 0.0 0.0} {0.896076951546 0.896076951546 0.896076951546}\ncolor $line_3  [102,102,255]\n'],
   [['pmesh obj_4 "/home/travis/.sage/temp/apricot/5573/tmp_pU6Ppq-obj_4.pmesh"\ncolor pmesh  [102,102,255]']]]]]
sage: type(p)
<class 'sage.plot.plot3d.base.Graphics3dGroup'>

sage: p = arrow3d([0,0,0],[1,1,1])
sage: p.plot()    # This works fine
Launched jmol viewer for Graphics3d Object
sage: p.jmol_repr(rp)
[[['\ndraw line_5 width 0.02 {0.0 0.0 0.0} {0.896076951546 0.896076951546 0.896076951546}\ncolor $line_5  [102,102,255]\n'],
  [['pmesh obj_6 "/home/travis/.sage/temp/apricot/5573/tmp_pU6Ppq-obj_6.pmesh"\ncolor pmesh  [102,102,255]']]]]
sage: type(p)
<class 'sage.plot.plot3d.base.TransformGroup'>

A somewhat strange thing is that the graphics group jmol_repr calls the jmol_repr of the polygon. Perhaps someone has an idea about this (and knows how to read the jmol input).

[egourgoulhon]

comment:3

Works for me with sage 7.3.beta6 on Ubuntu 15.10 for both sage notebook and jupyter notebook (a blue triangle is displayed in the jmol output). Does not work from the sage console (only the bounding box is displayed).

[egourgoulhon]

comment:4

Replying to @egourgoulhon:

Works for me with sage 7.3.beta6 on Ubuntu 15.10 for both sage notebook and jupyter notebook (a blue triangle is displayed in the jmol output). Does not work from the sage console (only the bounding box is displayed).

Addendum: in the sage notebook, the triangle is displayed only after one has clicked on the figure.

[paulmasson]

comment:5

I don't think this is a Sage problem. If you look at the temporary files under the hidden User/.sage directory that are passed to the Jmol viewer, the pmesh files for the polygons are there and included every time in the SCRIPT file in scene.spt.zip. The data for the polygons is exactly the same whether or not the arrow is included.

As a test, run this at the command line:

p=polygon([(0,0,0),(1,0,0),(1,1,0)])
for n in range(1,10):
     p+=polygon([(n,0,0),(n+1,0,0),(n+1,n+1,0)])
     p

When I run it the polygons don't being to appear until there are six of them, and don't appear reliably for higher numbers.

I think this is a Jmol display problem.

[tscrim]

comment:6

Hmmm...perhaps it is time to revive the discussion of moving to a different 3d viewing platform? At least we should probably tell upstream.

[paulmasson]

Description changed:

--- 
+++ 
@@ -3,3 +3,15 @@
 polygon3d([[0,0,0], [1,2,3], [3,0,0]]) 
 ```
 does not show anything.  See [this ask.sagemath question](http://ask.sagemath.org/question/34054/polygon3d-doesnt-work/).
+
+EDIT: Issue previously reported as #19274. Description from that ticket:
+
+Thomas Fernique reported the following bug by private email: from the console, some flat polygons in three-space lead to an empty picture with jmol (java version), for example:
+
+```
+sage: polygon([(0, 0, 0), (1, 0, 0), (1, 0, 1), (0, 0, 1)])
+```
+
+However, this is correctly displayed with jsmol (javascript version) from the notebook.
+
+I can reproduce this bug on Sage 6.8, Debian GNU/Linux jessie 64 bit, openjdk-7-jre.

[paulmasson]

comment:9

On #12402 I've written some basic Three.js support for Graphics3d objects that can handle examples here that fail in Jmol. If there is interest in having an option other than Jmol, feedback on #12402 would be appreciated.

[mkoeppe]

comment:10

Is this usable with sage running in a terminal? Note that the failure documented in this ticket is about the Java version of Jmol, which is the one that is used in this situation.

[paulmasson]

comment:11

Replying to @mkoeppe:

Is this usable with sage running in a terminal?

Yup! That's the entire point: an HTML file is generated at the command line and saved in a temporary file like other plots. It can then be displayed immediately in a browser, or embedded in an iframe for future application in notebooks or the cell server.

[paulmasson]

Changed keywords from none to jmol threejs

[paulmasson]

comment:12

Since Three.js will be the default viewer in Sage 9.0 this ticket can be closed.