you exactly replaced Maxima by writing it over in Python,
> Yes. It would be a waste of effort.
>
This rewrite definitely has potential to be wasted effort. William
has provided some reasons why it might not be. Is there a complete
list of reasons somewhere? Sometimes migrating existing co
post it there.
Jonathan
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ask? The issue there is most users might not know how to shut it
down if they don't want it running.
Since nobody has told me how to post it, and the script is short, I'll
just include the applescript below. I just had scripteditor save it
as an application in the sage directory.
Jonatha
package I've
written for myself).
This is essentially what I did when using Maple and Mathematica as
well. The unit package for Mathematic didn't exist at the time I was
using it and, as mentioned, Maple's is hard to use.
Jonathan
def SI_units():
var('
On Aug 13, 12:01 pm, "Dr. David Kirkby"
wrote:
> Jonathan wrote:
> > As a physical scientists I am definitely excited about this. I think
> > the basic plans are sound.
>
> > I presently do units as symbolic variable defined in terms of a list
> > of
l function that does this and can show all the intermediate steps
at user request. I always make my students show me they can do it by
hand (or manually using SAGE). Once they do that I provide them with
the function.
Jonathan
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To post to thi
On Aug 13, 2:11 pm, "Dr. David Kirkby"
wrote:
> Jonathan wrote:
>
> > On Aug 13, 12:01 pm, "Dr. David Kirkby"
> > wrote:
> >> Jonathan wrote:
> >>> As a physical scientists I am definitely excited about this. I think
> >>
necessary). These
wouldn't be too hard to do, but I don't really understand how (or
where) in the notebook code the Jmol stuff is fed to the web browser.
After the notebook is separated out, if somebody can give me some
direction, I'd be willing to look at the generation of the that
cont
o I don't think transit time would be a problem. I'll ask
around on the Jmol lists.
Jonathan
On Sep 26, 2:38 am, Robert Bradshaw
wrote:
> On Sep 25, 2009, at 10:30 AM, Jason Grout wrote:
>
>
>
> > William Stein wrote:
>
> >> We could try changing how jmo
time to devote to this it may take a while, but I
will give it a shot.
The behavior is suggestive of a security problem making it so that
Jmol cannot read the input file/data.
Jonathan
On Sep 25, 2:07 pm, Bill Page wrote:
> On Fri, Sep 25, 2009 at 2:35 PM, Alfredo Portes wrote:
>
> &g
the
notebook, I don't think I can actually do the coding now. If I get a
chance later I will try it on a plain vanilla test page and pass along
the javascript that works for that.
Jonathan
On Sep 26, 7:24 am, Jonathan wrote:
> A few things related to the memory constraints:
>
> 1) Th
mises.
Jonathan
On Sep 26, 12:45 pm, Jonathan wrote:
> I have my own answer to #3. I think that using document.write to
> replace the applet with a picture when not in use should work. I
> haven't investigated yet to see if it really saves memory. My
> suggestion is to u
java applet console? Do you see
all the information about the applet load, file calls? We may have to
up the debug level to get the information we need. This will require
a recompile of the applet.
Jonathan
On Sep 28, 3:38 pm, Bill Page wrote:
> On Mon, Sep 28, 2009 at 1:07 PM, Jason Grout
er stuff. If it is this hard to set up your
program for things most people expect to be standard, I think you have
real problems. Thus always try to make sure there is only one central
place where settings can get changed, and that dialogs that purport to
change things actually do.
Jonathan
On
I and my students may be able to help with testing, but I don't think
I can commit to any coding. I just don't have time. I'll watch for
requests to test this, but whomever works on it might want to give me
a buzz when they want some testing.
Jonathan
On Oct 4, 1:56 pm, Willi
systems of differential equations involved in
chemical kinetics through the "interact" operation.
Jonathan
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sag
se 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?
Jonathan
On Oct 22, 2:01 am
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 wrote:
> Jonathan wrote:
> > Jason,
> > I think this is a great idea.
? Is anybody aware of
implementations of something like this that is open source? Or
something non-open source that we could look at for ideas about how
things should behave? We would also welcome more input on the 3D
object properties.
Jonathan
a small part of the Jmol development team
--
To
On Dec 20, 12:37 am, Christopher Olah
wrote:
> On Sat, Dec 19, 2009 at 11:24 PM, Jonathan wrote:
> > Dear SAGE community:
> > The Jmol development team is starting to build a plot object into
> > Jmol that SAGE could just pass a group of surfaces/meshes to for
> >
On Dec 20, 9:43 am, Jonathan wrote:
> > Another thing that comes to mind is that if you move beyond three
> > dimensions, you will have to give up your triangle based meshes and
> > move to higher-dimensional equivalents. ...
>
> yeah...I haven't thought too hard
at works, my suggestion is that the signed
version be included in the Sage distribution.
I will also try using a more recent Jmol release. Maybe we've fixed
something that is causing this.
Jonathan
On Dec 7, 9:23 pm, "William Stein" wrote:
> On Sun, Dec 7, 2008 at 7:20 PM, Ronan
o use with sage.
Jonathan
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y the notebook. This may be the problem. If
someone can point me to the code that generates the jmol parts of
pages for the notebook, I can take a look. However, I make no
promises.
Jonathan
a Jmol developer
On Dec 26 2008, 10:18 am, Kathy Gerber wrote:
> I am not able to resolve the probl
tedly on the move. The time dependent graphs are cute, but
not all that useful.
Jonathan
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For
things being worked on for the Jmol
based 3-D views see:
https://141.233.197.45:4443/home/pub/0/
This test server has a self-signed security certificate so you will
get a bunch of security warning. Just accept the certificate.
Comments appreciated.
Jonathan
On Apr 17, 5:49 pm, Dox wrote:
> Hi g
his little script available. I just need to know where to
put it. It runs which ever Sage is in the directory you put it in.
This has the advantage that the Sage directory structure is not
hidden.
Jonathan
On Jun 10, 1:53 am, "Georg S. Weber"
wrote:
> On 10 Jun., 02:37, Jason Grout w
ou
get a chance please test with the official Sun Java and let me know
the results.
Thanks,
Jonathan
On Jun 14, 9:15 pm, Dan Drake wrote:
> I tried Jason's spkg with 4.4.4.alpha0, and I never actually got my plot
> to display. The control panel showed up, and Jmol appeared to load,
I've now tested Sage 4.4.3 with sun java and ubuntu 10.04 32 bit
(don't have a 64 bit version installed). The 32 bit works fine.
On Jun 14, 9:15 pm, Dan Drake wrote:
> I tried Jason's spkg with 4.4.4.alpha0, and I never actually got my plot
> to display. The control panel showed up, and Jmol app
uding it, so that we can start getting feedback.
Jonathan
On Jul 13, 6:49 pm, William Stein wrote:
> Hi Sage Developers,
>
> I'm setting the Sage-5.0 target date for August 31, 2010
> (seehttp://trac.sagemath.org/sage_trac/milestone/sage-5.0). The goals
> a
are of is the issue I reported with Jmol not
working in FF on Macs when the worksheet is not published. That
appeared to be a notebook problem with keeping track of logins (I
assume cookies). I have no idea if that problem has been solved.
Jonathan
On Jul 14, 8:42 am, William Stein wrote:
>
Does it work if you install the new version of Jmol? See trac # 9238
(http://trac.sagemath.org/sage_trac/ticket/9238). I think this broke
when the notebook was put inside an egg. I took that into account
with the new version of Jmol
On Jul 14, 1:15 pm, Volker Braun wrote:
> For the record, Jmo
d greatest".
I also know that this fixes Jmol from the command line, which has
stopped working since the notebook was moved inside of an .egg.
Jonathan
Try it at:
http://www.uwosh.edu/faculty_staff/gutow/Jmol_for_SageNoteBook-1.1.spkg
On Jul 14, 9:22 pm, Robert Bradshaw
wrote:
> On Wed,
Open the java console. I think you are still getting some java errors
of some kind.
On Jul 19, 9:23 am, Jan Groenewald wrote:
> Hi
>
> Re: jmol via SAGE on lucid using openjdk
>
> Progress! The error has reduced. I still get:
>
> 2010-07-19 14:26:15+0200 [HTTPChannel,14,127.0.0.1] Request error:
Jmol does have the ability to show the intersection curve of two
planes. At the moment that requires using the Jmol command line
interface. I will put it on the list of things to figure out how to
make a GUI to control that.
On Nov 7, 9:03 am, mmarco wrote:
> I don't know if it is already done,
On Nov 6, 8:22 pm, Jason Grout wrote:
> This would be cool too. Along these lines, it would be cool to "ride" a
> parametric curve, for example, to show how motion works in 3d (T,N,B
> vectors, for example).
That is one of the places I am interested in going as in chemistry we
think about chemi
On Nov 6, 11:17 pm, Oscar Lazo wrote:
> On Nov 6, 7:49 pm, Jonathan Gutow wrote:
>
>
>
> > 2) Development of a plot4d command allowing time dependent 3-D plots. I
> > believe this requires a little work on Jmol, but mostly a reworking of how
> > sage sends data
Second +1
Jonathan
On Nov 13, 9:07 pm, "Dr. David Kirkby"
wrote:
> On 11/14/10 02:54 AM, Eviatar wrote:
>
> > Anyway, I made an updated version (linking seems to work now):
>
> >http://oi55.tinypic.com/rclh5l.jpg
>
> I think that's better. At least the
user control of frame rate and the ability
to step back and forth, it just requires building the input data
sets. Nobody has done that yet.
Jonathan
On Sep 25, 8:02 am, Aielyn wrote:
> I feel I should start by noting that I'm new to Sage itself, and I'm
> no developer.
>
&g
provide insight into Jmol, just not much coding time.
I personally think the interactive version may be higher priority.
Jonathan
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Fo
. I've posted it to the logo section of the
Sage Wiki. What do people think? You can see it at this link:
http://wiki.sagemath.org/logos?action=AttachFile&do=view&target=Sage+logo+3D.png
Jonathan
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e upon it.
First we have to chase some bugs out of Jmol. I had to do a little
fussing to make this work.
Jonathan
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Create a ticket listing the files you think should be removed.
On Oct 16, 5:29 am, Keshav Kini wrote:
> Hi all,
>
> I was browsing through $SAGE_ROOT/devel/sage/.hgignore and noticed that some
> specific filenames are mentioned which don't seem to exist in my
> installation of Sage (4.7.2.alpha3
A version of the 3-D logo that can be downloaded and manipulated in
the Jmol application is now available. Still not working inside of
Sage...That will come. The link is:
http://wiki.sagemath.org/logos?action=AttachFile&do=view&target=Sage+Logo+2.jmol
Jonathan
--
To post to this gro
ably be converted to a special version of an interact, but as
proof of principle this is a start. Any comments?
Jonathan
-
def calctable(exprID,nrows):
"""
This function creates an interactive table (mini spreadsheet) with
columns into
which you can enter multiple
On Dec 11, 8:26 pm, William Stein wrote:
>
> Can you please post your code athttp://pastebin.com/or something,
> since putting it in email results in it getting all mangled by some
> email clients?
>
> Thanks!
>
> William
Sure thing.
A sage worksheet can be downloaded here:
http://www.uwosh.e
ight it be
cleaner to include the jmol_lib in the spkg?
Jonathan
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also agree that you should be looking at supporting other rendering
methods as the world of web interfaces is constantly shifting.
Jonathan
On Jan 28, 12:15 pm, William Stein wrote:
> Sorry to trouble you, but I think it is time to move past jmol. We could
> keep jmol as an
That looks much better than the previous webgl stuff!
Jonathan
On Jan 31, 8:57 am, Jason Grout wrote:
>
> No problem. Here is the demo that I'm basing my work on:
>
> http://sage.math.washington.edu/home/jason/threejsboilerplate/
>
> You can get a screenshot by doing &#
not. When the flask-
notebook is incorporated, do we need to add the openssl package to the
compilation dependencies in the Sage readme, or does the flask
notebook spkg need to include or build those dependencies?
Thanks,
Jonathan
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ndary license (yes they have two inconsistent ones)
does not allow distribution under a GPL license. Still I see no
problem with depending on the package as it is open source. I agree
that distributing as part of Sage might be a problem.
Jonathan
On Feb 11, 8:59 am, Alex Kramer wrote:
> On Sat
On Feb 11, 2:12 pm, Volker Braun wrote:
> If you want to compile the flask notebook then I think we should recommend
> installing openssl-dev but not require it. So on machines without ssl it'll
> just build without ssl support, easy.
So you are suggesting that the openssl support be automatica
working in the Sage notebook. There is also a significant learning
curve associated with setting up these proxys even with
VirtualHostMonster.
This is not easy. I put Sage behind an SSL proxy and had significant
problems. I found it better to serve SSL directly from Sage.
Jonathan
On Feb 11
On Feb 11, 3:18 pm, Jason Grout wrote:
>
> That sounds reasonable. I *think* OpenSSL is also a requirement for
> OpenID, so they'd lose that as well.
>
> So exactly what error happens when you try to install sagenb on a system
> with the headers? I assume we need to work around that, and then
never tried using it for straight unencrypted reverse
proxy, which in my experience is a little easier.
On Feb 11, 4:04 pm, Michael Orlitzky wrote:
> On 02/11/2012 04:37 PM, Jonathan wrote:
>
> > Making Sage work well with a proxy is no simple matter. I run a
> > number of w
On Feb 12, 3:00 am, Jeroen Demeyer wrote:
> On 2012-02-12 03:30, Jonathan wrote:> This does not work cleanly with Sage
> because the css and js
> The *only* problem I found was the URL displayed when you publish a
> worksheet which is wrong.
I also found problems with URLs necess
I think people
can use that and just have to link to OpenSSL as a system service.
Jonathan
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erving other stuff as
well.
Jonathan
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URL: http://www.sagemath.org
m aware of this bug, but I think it should be a separate ticket for
code clean-up and I will keep looking for it as all it does is produce
the javascript error/warning.
Will you make a ticket or should I?
Jonathan
On Feb 14, 7:00 am, Jason Grout wrote:
> When I look at a 3d plot o
On Feb 15, 7:43 am, Jonathan wrote:
> Will you make a ticket or should I?
I've created a ticket here:
http://trac.sagemath.org/sage_trac/ticket/12523
Jonathan
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sa
could manually change it, but
I'm wondering what happened. Any ideas?
Thanks,
Jonathan
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I used Mercurial, which is why I am confused. I would like to figure
out why this happened to avoid the problem in the future.
Jonathan
On Feb 19, 11:41 pm, Keshav Kini wrote:
> Jonathan writes:
> > For example I'm trying to patch base.pyx inside SAGE_ROOT/devel/sage/
> >
? I haven't had time to build a more recent beta.
Jonathan
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structure or object might work even better. The trick would be to default
to the mean value when doing calculations.
I think this would be useful.
Jonathan
On Friday, March 16, 2012 11:03:55 PM UTC-5, Eviatar wrote:
>
> Thank you, that's what I thought. I'll do it outside of GS
wraps up the values and
uncertainties as they claim that it works with standard python expressions.
Jonathan
On Saturday, March 17, 2012 3:55:57 PM UTC-5, Eviatar wrote:
>
> @Jonathan
> Thank you for the ideas. I had previously just implemented it by copying
> the current NIST va
s
as well, but it is pretty extensive.
That said, integrating the uncertainties package into Sage would probably
be useful to many scientists and engineers.
Jonathan
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I want the answer in particular
units I just divide the answer by the units I want. I sometimes use a function
I call factorout that prints the numerical answer multiplied by the units I
divided by.
Is that what you are asking about?
Jonathan
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Oops! I see a typo...I meant input "10.0*cm"
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I build them as necessary.
Jonathan
On Sunday, March 18, 2012 2:49:08 PM UTC-5, William wrote:
>
> On Sun, Mar 18, 2012 at 11:33 AM, Jonathan wrote:
> > I simply define my fundamental unit system and define all units
> relative to that. Typically I use SI units kg, m and s. Then
. They
should be translated by the Javascript into normal Sage functions. Once
users get used to the pythonic function syntax, I doubt they will make much
use of the palette, except for generating typeset expressions.
Jonathan
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Sage, I
would suggest that this inherit from the symbolic expression class or maybe
the derivative class as it really is a formula based on gradients.
Jonathan
On Thursday, March 29, 2012 9:17:22 PM UTC-5, Eviatar wrote:
>
> Hello,
>
> I'm working on implementing an error
Scroll back in this discussion. The math/arithmetic problems, other than
getting good symbolic expression, have been solved in the "uncertainties"
package ( http://pypi.python.org/pypi/uncertainties/) you mentioned before.
Jonathan
On Friday, March 30, 2012 7:11:20 PM UTC-5, Evi
have to do a thorough review of the literature and
probably recalculate the correlations to make sure they have things correct.
Jonathan
On Saturday, March 31, 2012 6:47:45 PM UTC-5, Eviatar wrote:
>
> Now that I look through
> http://physics.nist.gov/cuu/Constants/RevModPhys_80_0006
python power of Sage provides pretty wide
open access to anything available to the user the instance of sage is
running under.
Jonathan
On Tuesday, April 3, 2012 8:32:56 PM UTC-5, kcrisman wrote:
>
> With respect to Jmol, there seems to be a lot of traffic about older
> Java ver
an also be produced. Jmol is
capable of displaying animations that you can zoom and manipulate while the
animation proceeds, but the information needs to be passed to it properly.
Anyway, contact me off-list at gu...@uwosh.edu and we should get organized.
Jonathan
On Monday, April 9, 2012 4:02:4
I got my answer in the sage-notebook list. Thanks.
Jonathan
On Jan 21, 11:49 am, Jonathan Gutow wrote:
> I just downloaded 4.6.1 and tried to install the
> Jmol_for_SageNoteBook.spkg which I've been working on. The .spkg
> properly updated the files in the site-packages subdi
e willing to stick with it and prod it
along over the long term. People who are not serious won't do this.
My example may be a little slower than many people's because I also
have very little time to contribute to this, but I still think you are
unlikely to get really bad code included using
Tim,
Your point that the code should be well structured and documented is
important for long term usefulness. However, even well documented
code will not remain useful if someone does not maintain it. One of
the goals of the leaders of the SAGE project should be to groom new
leaders.
Jonathan
Ivan,
I am aware that you've been working on this. However, I have not had
any time to look at it. If things go well with my classes and
administrative responsibilities in the next couple of weeks I may get
a chance. I am very glad you have worked on this.
Jonathan
On Jan 30, 3:46 pm,
mercurial. The mercurial model seems good,
but the tools appear to be much less developed than SVN.
Jonathan
On Feb 21, 1:29 pm, Volker Braun wrote:
> I'm all in favor of updating jmol, but I don't see the plan here. Do you
> want to break out jmol from the sagenb spkg into a s
is only
tested against the Sun/Oracle VM.
*We are working on patches to Jmol in the present notebook. There are
still some asychronicity issues that I think I've almost got a handle
on. Let's not try to move this stuff to the new notebook until that
is solved. I hope today :)
Jonath
some comments on how
it works.
Thanks,
Jonathan
On Mar 30, 12:02 am, jtyard wrote:
> I am having issues with sage notebooks that contain more than five
> instances of the Jmol viewer. In short, if I create a notebook with
> more than 5 Jmol viewers, save, then reload it, I get an unr
Your description sounds like you are doing a hg_sagenb.commit(), not a
hg_sagenb.apply("http://.patch"). If you just copy
the link to the listed patches as shown above they should work.
That's what I do.
Jonathan
P.S. Great name!
On Mar 31, 11:32 am, jtyard wrote
happening. Would a pop-up
progress window indicating which applet is loading help with the way
it feels? Long term, I will probably make it so that old pages load
with all the applets replaced by static images, but this requires
changes to the plot3d functions. I was worrying about the interface
first.
quire some
reworking of how 3-D plots are generated.
Jonathan
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Oracle/Sun release.
I just destroyed my Ubuntu VM so can't check this right now.
Jonathan
On May 20, 5:15 pm, RegB <2regburg...@earthlink.net> wrote:
> From the fact that plot3d worked previously from the terminal and that
> 2d plots still work from the terminal with UBUNTU 11.04
le version.
Jonathan
On May 21, 9:26 am, Jonathan wrote:
> Which java do you have installed? The default with Ubuntu is
> IcedTea. Last time I checked this was working with the patch, but
> that could be the problem. Jmol (the 3D application that is launched)
> is only verified
OpenJDK VM (used to be IceTea) is the default with Ubuntu and it does
work with Jmol. So if things don't work after the patch there is
something else wrong with your installation.
Jonathan
On May 21, 9:36 am, Jonathan wrote:
> OK, I found an Ubuntu VM (11.04) that I hadn't kill
This is also a great example of the difference between '=' and '=='.
If the statement a = b, where to precede everything, then Sage would
know that a - b = 0, and would convert the statement 'a==b' to 'b==b',
which would frustrate the proof.
Jonathan
On Ma
ns and have the spreadsheet do simple math locally.
My 2p.
Jonathan
On Jun 26, 8:16 pm, mhampton wrote:
> That looks fantastically useful. It is impossible to overstate how
> big a draw this could be.
>
> -Marshall
>
> On Jun 25, 10:41 pm, Rob Beezer wrote:
>
>
&g
od if you don't choose too much
compression in the application. This is harder to control from the
applet.
Jonathan
(a Jmol developer)
On Sep 8, 9:37 pm, Nils Bruin wrote:
> On Sep 8, 6:02 pm, Sébastien Labbé wrote:
>
> > Hi,
>
> > I have been asked this question since
If you are doing everything through Sage, would having Jmol print the
rotation information to the web page be enough? Then the user could
do a cut and paste to use with the renderer they want. Completely
automating things would require more fiddling.
Jonathan
On Sep 9, 12:04 pm, Nils Bruin
sage: var('x y z p q A B C')
sage: solve((A + p^B),p)
results in:
...
TypeError: ECL says: Maxima asks: Is B an integer?
Shouldn't it result in:
[p = (-A)^(1/p)]
Jonathan
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Jonathan
On Monday, May 21, 2012 3:21:19 PM UTC-5, Benjamin Jones wrote:
>
> On Mon, May 21, 2012 at 3:10 PM, Jonathan wrote:
> > sage: var('x y z p q A B C')
> > sage: solve((A + p^B),p)
> >
> > results in:
> >
It is Jonathan G and I will try to open a ticket. I'm running 3 workshops
on computer software and hardware for our Chemistry, Physics and Math
departments over the next few days, so we'll see when I can squeeze it in.
I agree that maybe forcing Maxima to do purely symbolics mi
On Tuesday, June 12, 2012 10:20:20 AM UTC-5, kcrisman wrote:
>
>
>> I would also say that high quality should be turned on by default, the
>> plots look so much better. I also shared a worksheet with you (kcrisman)
>> which had several 3d plots that you can test (we used it here a couple of
>>
is is to plot a surface. Turn
on the black mess and start it spinning. Then toggle the "high quality" on
and off.
Jonathan
> Was it the high quality (i.e., antialiasing) that caused all the white
> speckles to appear all the time?
>
> Jason
>
>
>
>
--
T
nch in the browsers. Is that the case? If so, that is my experience.
See
http://www.webupd8.org/2012/01/install-oracle-java-jdk-7-in-ubuntu-via.html
for what looks like an easy way to install the Oracle Java under Ubuntu.
Jonathan
On Tuesday, June 12, 2012 6:48:31 PM UTC-5, Eviatar wrote:
>
Just had a power outage. My test server will be down until after I get a
chance to eat dinnersorry
Jonathan
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Test server at http://gutow.no-ip.org:8080 is up again.
On Tuesday, June 12, 2012 7:31:27 PM UTC-5, Eviatar wrote:
>
> The applet does work on IcedTea 6, but some of the mesh and color options
> don't, as I mentioned. But yes, I'll try out Java 6 and see how that goes.
I may have to try it again
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