Opened 6 years ago
Last modified 6 weeks ago
#20978 needs_info defect
polygon3d view in jmol broken
Reported by: | kcrisman | Owned by: | |
---|---|---|---|
Priority: | minor | Milestone: | sage-9.7 |
Component: | graphics | Keywords: | jmol threejs |
Cc: | paulmasson, novoselt, mkoeppe | Merged in: | |
Authors: | Reviewers: | ||
Report Upstream: | N/A | Work issues: | |
Branch: | Commit: | ||
Dependencies: | #30316 | Stopgaps: |
Description (last modified by )
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).
Change History (29)
comment:1 Changed 6 years ago by
- Cc paulmasson added
comment:2 Changed 6 years ago by
comment:3 follow-up: ↓ 4 Changed 6 years ago by
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).
comment:4 in reply to: ↑ 3 Changed 6 years ago by
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.
comment:5 Changed 6 years ago by
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.
comment:6 Changed 6 years ago by
Hmmm...perhaps it is time to revive the discussion of moving to a different 3d viewing platform? At least we should probably tell upstream.
comment:7 Changed 6 years ago by
- Description modified (diff)
comment:8 Changed 6 years ago by
- Cc novoselt mkoeppe added
comment:9 Changed 6 years ago by
comment:10 follow-up: ↓ 11 Changed 6 years ago by
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.
comment:11 in reply to: ↑ 10 Changed 6 years ago by
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.
comment:12 follow-up: ↓ 13 Changed 3 years ago by
- Keywords jmol threejs added
- Milestone changed from sage-7.3 to sage-duplicate/invalid/wontfix
- Status changed from new to needs_review
Since Three.js will be the default viewer in Sage 9.0 this ticket can be closed.
comment:13 in reply to: ↑ 12 Changed 3 years ago by
- Reviewers set to Eric Gourgoulhon
- Status changed from needs_review to positive_review
Replying to paulmasson:
Since Three.js will be the default viewer in Sage 9.0 this ticket can be closed.
Yes indeed.
comment:14 follow-ups: ↓ 16 ↓ 18 Changed 3 years ago by
- Milestone changed from sage-duplicate/invalid/wontfix to sage-9.0
- Priority changed from critical to minor
- Reviewers Eric Gourgoulhon deleted
- Status changed from positive_review to needs_info
Just because the default changes doesn't mean this is fixed, and some people may still be using Jmol from command line or whatever. But we can certainly modify the ticket.
comment:15 Changed 3 years ago by
- Summary changed from polygon3d view broken to polygon3d view in jmol broken
comment:16 in reply to: ↑ 14 Changed 3 years ago by
Replying to kcrisman:
Just because the default changes doesn't mean this is fixed, and some people may still be using Jmol from command line or whatever.
Yes you are right of course, I've been too fast here.
comment:17 Changed 3 years ago by
For the record, the issue is still there in Sage 9.0.beta0, even after the update of Jmol in #25026.
comment:18 in reply to: ↑ 14 Changed 3 years ago by
Replying to kcrisman:
Just because the default changes doesn't mean this is fixed, and some people may still be using Jmol from command line or whatever. But we can certainly modify the ticket.
As I pointed out three years ago, this is not a Sage problem and won’t get fixed here. Are you keeping the ticket open monitor upstream activity? Otherwise it should be closed.
comment:19 Changed 3 years ago by
We have tons of tickets here that monitor upstream activity, because they impact Sage usability in various contexts. I notice that "Report Upstream" is currently N/A, though, so maybe that should be changed and possibly worked on. I often do this with Maxima bugs but I don't know what the current Jmol upstream reporting process is.
comment:20 Changed 2 years ago by
- Milestone changed from sage-9.0 to sage-9.1
Ticket retargeted after milestone closed
comment:21 Changed 2 years ago by
- Milestone changed from sage-9.1 to sage-9.2
Moving tickets to milestone sage-9.2 based on a review of last modification date, branch status, and severity.
comment:22 Changed 19 months ago by
- Milestone changed from sage-9.2 to sage-9.3
comment:23 Changed 14 months ago by
- Milestone changed from sage-9.3 to sage-9.4
Moving this ticket to 9.4, as it seems unlikely that it will be merged in 9.3, which is in the release candidate stage
comment:24 Changed 10 months ago by
- Milestone changed from sage-9.4 to sage-9.5
Setting a new milestone for this ticket based on a cursory review.
comment:25 Changed 5 months ago by
- Milestone changed from sage-9.5 to sage-9.6
Stalled in needs_review
or needs_info
; likely won't make it into Sage 9.5.
comment:26 Changed 2 months ago by
- Description modified (diff)
comment:27 Changed 2 months ago by
- Dependencies set to #30316
comment:28 Changed 2 months ago by
- Description modified (diff)
comment:29 Changed 6 weeks ago by
- Milestone changed from sage-9.6 to sage-9.7
When I add an
arrow3d
(for example), then it displays properly:It seems like it is just ignoring the polygon3d when it is the only object:
A somewhat strange thing is that the graphics group
jmol_repr
calls thejmol_repr
of the polygon. Perhaps someone has an idea about this (and knows how to read the jmol input).