From paxton at kitp.ucsb.edu  Thu Jun  1 09:28:57 2006
From: paxton at kitp.ucsb.edu (Bill Paxton)
Date: Thu, 1 Jun 2006 06:28:57 -0700
Subject: [Tioga-users] Tioga 3d axes, making simple things simpler,
	and other good ideas
In-Reply-To: <f64183dc14752.447d9461@9online.fr>
References: <f64183dc14752.447d9461@9online.fr>
Message-ID: <9C6366D1-CD4B-4017-8597-D5A49CE87BF2@kitp.ucsb.edu>

Hello from the airport waiting area in Reykjavik!

I'm on my way back to Santa Barabara after a wonderful trip in a  
converted Russian research ship around Iceland and up to the ice pack  
near Greenland.  Here's one of the many photo's I took -- great fun!

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During the voyage I was out of email contact, so I've been catching  
up this morning.  I'm happy to see the conversations going on  
concerning Tioga.  Here are a few comments.


On May 28, 2006, at 6:48 AM, Edwin wrote:
> I've been working (slowly) on adding 3d plotting capabilities to  
> tioga.
> Till now I've jut plotted a line to represent every axis, but was
> wondering about the best way to get proper axes. As far as I can  
> tell the
> standard axis drawing routines of tioga only allow to draw them  
> horizontal
> or vertical etc. Would it be possible to have a routine that accepts a
> starting point and an ending point and draws an axis complete with
> ticks+labels etc between those?

Edwin: I believe you've quickly reached the crux of the problem with  
3D.  The issues around axes stopped me when I briefly considered  
trying to include 3D for the initial Tioga.  I can only wish you luck  
and suggest that you leave lots of lower-level hooks to let people  
craft special axis layouts for themselves.  Putting some effort into  
getting the defaults "right" is of course important, but there's no  
way to anticipate every case for every user.  BTW: yes, the axis  
routines in Tioga are horizontal and verical only for plotting.  For  
fancier stuff, you'll need to do your own, but perhaps we can find  
some useful utilities in the 2D code that might help.  For example, I  
expect that the routines for picking locations for tick marks should  
be the same.  If you haven't already done so, you should take a look  
at axes.c and see what if anything might be useful for the 3D code.


On May 30, 2006, at 12:43 PM, Edwin wrote:
> To be honest the way tioga
> works with one _big_ figuremaker class is a bit counterintuitve for my
> ruby eyes :)

The "one big class" approach is admittedly a compromise.  I'm hoping  
that Tioga will be a "gentle" introduction to the use of classes and  
methods for those who have not yet had their eyes opened to modern  
programming practices.   Believe it or not, some of my friends still  
think fortran77 and supermongo are the perfect solution for any  
programming problem!   Some of my design decisions where made to  
improve the chances of getting these poor folks to migrate to Tioga/ 
Ruby -- I'll have to ask for patience from the ruby experts for the  
counterintuitive monster class that results!



On Wed, 31 May 2006 01:50:10 +0100, Alex Gutteridge
<alexg at kuicr.kyoto-u.ac.jp> wrote:

> I'd just thought I'd mention that I've been
> thinking along the same lines. Although I really like the flexibility
> and pretty output from Tioga, there's quite a learning curve, even if
> you just want to do simple things.

On May 31, 2006, at 4:47 AM, Edwin wrote:
> Something that I've been thinking about is a simple plot method  
> that just
> plots a couple of dvectors/arrays and automatically opens the pdf  
> file.
> I've created one of those to use gnuplot before, but it would be  
> nice to
> be able to use tioga.

On May 31, 2006, at 8:50 AM, Roy Mayfield wrote:
> I asked Bill about the same thing last summer, and he gently noted  
> that
> that is really easy to do in a ruby script (simpler than his  
> examples).
> It took me awhile to get used to the make_preview_pdf() method, but I
> now agree with him and suggest that Tioga's code space be guarded for
> tough tasks (like your 3D idea, Edwin, which is really cool).

On May 31, 2006, at 9:25 AM, Edwin wrote:
> It is indeed rather simple and I agree that it should not be  
> included in
> the FigureMaker class. On the other hand it doesn't make much sense  
> for
> everyone to write this for himself. That's why it sounds like a  
> good idea
> to make a separate module that provides some simplification methods  
> around
> the tough tasks provided by FigureMaker.

Yes, yes, yes, and yes!  The focus in FigureMaker is to make the hard  
stuff possible and provide enough low-level access to build on for  
the unforeseen future.  I haven't put much effort at all into making  
simple things simple enough, and that's definitely an important  
project.  I expect that user-developers such as yourselves will be  
the source of such things.  I'll be happy to listen to suggestions  
for modifications and extensions to FigureMaker to ease your task.



On May 31, 2006, at 6:04 AM, vincent.fourmond at 9online.fr wrote:
> I also wanted to say that I've been working for a long time on a  
> fully-featured (well, fully enough !) command-line interface for Tioga

Excellent.  My little "irb" interface is just a place holder for  
those unfortunate souls who haven't yet migrated to Mac and the  
wonderful Tioga GUI I've done there!   ; - )


Cheers,
Bill














From edder at tkwsping.nl  Sat Jun  3 16:29:24 2006
From: edder at tkwsping.nl (Edwin)
Date: Sat, 03 Jun 2006 21:29:24 +0100
Subject: [Tioga-users] Tioga3d 0.0.1
Message-ID: <op.tak67aj0ngac0g@localhost>

Most of the basic plotting functionality of my 3d project is finished, so  
I decided to share it in the hope of some feedback :) I attached the  
source code

====The Good====
The good is that the plotting functionality works. Show_plot_3d draws the  
axes, and you should be able to use most default methods by putting _3d  
behind them. This should work at least with all functions that expect xs  
and ys coordinates (show_polyline). Methods that expect dicts (like  
show_marker) should also be covered as long as they use the standard  
coord-notations (at, point, x, y, xs, ys). Other methods might need custom  
wrappers (like show_arrow) which aren't provided yet.

====The Bad====
I only concentrated on plotting, because I don't see a reason to use 3d  
otherwise. This means that I have only concentrated on the plotting  
functions and I can see no reason to support "figure only" things like  
append_arc_to_path. If you disagree please let me know

Testing has been very incomplete and there are probably quite a few  
functions that need customized wrappers, which I don't know about yet or  
have ignored for now (like show_arrow). If you find any "bugs" please let  
me know.

====The Ugly====
The way axes are handled is not nice and they don't look perfect yet. This  
is mostly because I have not yet taken the dive into writing c extensions.  
To be able to draw axes properly I would have to rewrite my show_axis  
function in c, so I can access the PlotAxis struct.
On the plus side I wrote a more versatile show_axis method (called  
show_axis_3d), which should also be usable for 2d axes. The method  
basically needs an origin ([x,y] for 2d and [x,y,z] for 3d), the minimum  
value of the axis, the maximum value, the direction the axis takes ([1,0]  
or [1,0,0] for in the x direction) and the direction of the ticks ([0,1]  
or [0,1,0] are ticks parellel to the y axis)

====Performance====
I haven't checked performance, but the easiest way to gain performance  
would be by implementing the transform_coord method in c. I used the  
gnuplot code as an example and we could just use their code almost  
directly, although I'm not sure if you can use gpl'ed code in lgpl  
projects (prob not)

====Example====
require 'tioga3d.rb'
class Test
   include Tioga
   include FigureConstants
   def initialize
     @figure_maker = FigureMaker.default
     #until the 3d code is part of the official tree you will need to  
initialize some constants separatedly
     t.initialize_3d
     t.save_dir = 'plots_out'
     #for linux users
     $open_command = 'xpdf'
     @cube = t.def_figure( "cube" ) { cube }
     @random = t.def_figure( "random" ) { random }
   end
   def t
     @figure_maker
   end
   def cube
     #t3d.view( 60,245 )
     xs = Dvector[-1,-1,1,1,-1,-1,1,1]
     ys = Dvector[-1,-1,-1,1,1,1,1,-1]
     zs = Dvector[-1,1,1,1,1,-1,-1,-1]
     t.show_plot_3d([xs.min-0.05, xs.max+0.05, ys.min-0.05, ys.max+0.05,  
zs.min, zs.max]) {
       t.append_points_to_path_3d(xs, ys, zs)
			t.append_point_to_path_3d(0,0,0)
       t.stroke
       t.show_polyline_3d([-1,1],[-1,1],[-1,1], Red)
     }
   end
   def random
     t.show_plot_3d() {
       100.times {
         x = rand
         y = rand
         z = rand
         t.show_marker_3d( 'marker' => Bullet, 'at' => [x, y, z], 'scale'  
=> 0.2 )
       }
       t.show_marker_3d( 'marker' => Bullet,
                       'xs' => [0,1,0],
                       'ys'=> [1,0,0],
                       'zs' => [0,0,1],
                       'color' => Red )
     }
   end
end

Test.new
====Future====
First thing I want to do is implement the drawing of a surface from data  
points. I have no experience with this type of thing, but google tells me  
I should use Delaunay triangulations, if anyone knows more, please let me  
know.

The easiest way to go about that is use the qhull library. This will also  
finally teach me how to extend ruby programs in c. If anyone has a good  
tutorial on that please let me know.

After that I'll probably want to fix/rewrite the axes (unless Bill or  
Vincent find time to do it ofcourse :) )
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From paxton at kitp.ucsb.edu  Sat Jun  3 17:59:56 2006
From: paxton at kitp.ucsb.edu (Bill Paxton)
Date: Sat, 3 Jun 2006 14:59:56 -0700
Subject: [Tioga-users] Fwd:  Tioga3d 0.0.1
References: <AACEBEC3-6249-4AE0-95EB-C55ECFB5F6C9@kitp.ucsb.edu>
Message-ID: <38ED3C30-86EC-47B7-A613-ADADFA43D4B7@kitp.ucsb.edu>

I just sent this to Edwin, and then I realized it should probably go  
to the full users list.  It is a comment on the prospects for using  
PDF's ability to do interpolated shading of a triangular mesh -- a  
rather esoteric subject, but one that may turn out to be useful for 3D!

--Bill



Begin forwarded message:

> From: Bill Paxton <paxton at kitp.ucsb.edu>
> Date: June 3, 2006 2:46:42 PM PDT
> To: Edwin <edder at tkwsping.nl>
> Subject: Re: [Tioga-users] Tioga3d 0.0.1
>
>
> On Jun 3, 2006, at 1:29 PM, Edwin wrote:
>
>> First thing I want to do is implement the drawing of a surface  
>> from data points. I have no experience with this type of thing,  
>> but google tells me I should use Delaunay triangulations, if  
>> anyone knows more, please let me know.
>
> Hi Edwin,
>
> Great progress!  I'll download and play with it, but first I wanted  
> to reply to your comment about drawing surfaces.    It sounds like  
> you are on the right track already concerning Delaunay  
> triangulations and qhull, but once you got that working we may want  
> to go one step more and take advantage of the PDF capability for  
> doing Gouraud shaded triangle meshes.   That's something that I  
> skipped on the first round, but it might be worth doing for 3D.    
> In PDF, you can give a triangle mesh with colors at the vertices.   
> The interiors are interpolated (either linear or nonlinear).   The  
> results aren't Pixar quality of course, but they are much nicer  
> than the sharp edges of flat shading.    You should certainly go  
> ahead with flat shading first, but keep in mind the later option of  
> Gouraud.  It will of course mean a shift from treating colors for  
> triangle faces to colors for triangle corners -- but beyond that  
> the main issue will be extending the Tioga PDF code to produce the  
> necessary stuff.    That can't be too hard since the current  
> version of the PDF reference manual is now a mere 1236 pages!   If  
> you don't have a copy, you can get one at http://partners.adobe.com/ 
> public/developer/pdf/index_reference.html#5.  The relevant section  
> starts at page 284.
>
> Cheers,
> Bill
>
>

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From paxton at kitp.ucsb.edu  Sat Jun  3 18:00:22 2006
From: paxton at kitp.ucsb.edu (Bill Paxton)
Date: Sat, 3 Jun 2006 15:00:22 -0700
Subject: [Tioga-users] tutorial on extending ruby in c
In-Reply-To: <op.tak67aj0ngac0g@localhost>
References: <op.tak67aj0ngac0g@localhost>
Message-ID: <E528B50D-8EE2-4A78-BB23-2D54CACC6546@kitp.ucsb.edu>


On Jun 3, 2006, at 1:29 PM, Edwin wrote:

>  This will also finally teach me how to extend ruby programs in c.  
> If anyone has a good tutorial on that please let me know.

Hi Edwin,

A while back I put together a small example in response to another  
Tioga user.  You might want to give this a try.


????
1) create a new folder and place the 4 files in it (no other c files  
please!)

2) do
	ruby extconf.rb
	make
	make install

The 'ruby extconf.rb' should create a Makefile in the folder.
The 'make' should compile spa.c and then create a dynamic lib.
The 'make install' should put the dynamic lib into your Ruby release  
(this may need superuser status of course).

3) check it by
	ruby myspa_test.rb

This should produce terminal output like this:

Loaded suite myspa_test
Started
s.calc * 0.5e-9 is 3.141591
.
Finished in 0.000506 seconds.

1 tests, 4 assertions, 0 failures, 0 errors


If that works, you are off and running!  If not, let me know where  
things go bad.


Cheers,
Bill


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From jilani.khaldi1 at virgilio.it  Thu Jun  8 02:01:32 2006
From: jilani.khaldi1 at virgilio.it (Jilani Khaldi)
Date: Thu, 08 Jun 2006 08:01:32 +0200
Subject: [Tioga-users] [Tioga-news] Tioga 1.1.1 -- the 1st beta release
In-Reply-To: <F898937A-7E01-4CC4-A02B-CE76B3C37726@kitp.ucsb.edu>
References: <F898937A-7E01-4CC4-A02B-CE76B3C37726@kitp.ucsb.edu>
Message-ID: <4487BD3C.9060904@virgilio.it>

Bill Paxton wrote:

> Hi,
>
> After spending a year as an "alpha" release, I think Tioga is ready 
> for a wider audience, and moving it to "beta" status is one way to 
> help that happen.  There will certainly be lots more changes (and 
> perhaps even a bug fix or two), but I think it no longer needs the 
> "use at your own risk" label.   
>
Thank you very very very much Bill! Great job really!

jk



From ifinvers at ucalgary.ca  Wed Jun 28 23:47:44 2006
From: ifinvers at ucalgary.ca (Ivars Finvers)
Date: Wed, 28 Jun 2006 21:47:44 -0600
Subject: [Tioga-users] Setting absolute size of figure
Message-ID: <5CC34D9F-9A29-4EE8-844E-3400CE66F761@ucalgary.ca>

Hi,

I'm a new user of Tioga.

I would like to create a double column wide figure (with 3  
subfigures) for a paper that I'm writing, but I can't find anything  
in the Tioga documentation regarding setting the absolute width of  
the figure. All the sizing commands are in relative dimensions. The  
standard figure width seems to be about 3-3.5 inches (what sets  
this?), while I would like a width of about 7 inches.

Ideally I would like to specify the figure width and the absolute  
size of the font (so that the final figure text matches the rest of  
the paper).

Any suggestions?

Thanks.

Ivars


From paxton at kitp.ucsb.edu  Thu Jun 29 00:33:46 2006
From: paxton at kitp.ucsb.edu (Bill Paxton)
Date: Wed, 28 Jun 2006 21:33:46 -0700
Subject: [Tioga-users] Setting absolute size of figure
In-Reply-To: <5CC34D9F-9A29-4EE8-844E-3400CE66F761@ucalgary.ca>
References: <5CC34D9F-9A29-4EE8-844E-3400CE66F761@ucalgary.ca>
Message-ID: <4255D2C6-B055-4242-A3C9-8A5B8792F353@kitp.ucsb.edu>

Hi Ivars,


On Jun 28, 2006, at 8:47 PM, Ivars Finvers wrote:

> Hi,
>
> I'm a new user of Tioga.

Great!

> I would like to create a double column wide figure (with 3
> subfigures) for a paper that I'm writing, but I can't find anything
> in the Tioga documentation regarding setting the absolute width of
> the figure. All the sizing commands are in relative dimensions. The
> standard figure width seems to be about 3-3.5 inches (what sets
> this?), while I would like a width of about 7 inches.
>
> Ideally I would like to specify the figure width and the absolute
> size of the font (so that the final figure text matches the rest of
> the paper).
>
> Any suggestions?

Coming Soon -- that's exactly the stuff I've been working on lately.   
(It would already be released if we hadn't had RubyForge network  
problems for the last week.)

Here's a sneak preview of what's coming:

for top-level page layout
	set_device_pagesize(width, height) # measured in tenths of points
	set_A4_portrait, set_A4_landscape
	set_A5_portrait, set_A5_landscape
	set_B5_portrait, set_B5_landscape
	set_JB5_portrait, set_JB5_landscape
	set_USLegal_portrait, set_USLegal_landscape
	set_USLetter_portrait, set_USLetter_landscape
	set_frame_sides(left, right, top, bottom) # sizes in page coords [0..1]

for TeX preview page and figure size
	tex_preview_paper_width
	tex_preview_paper_height
	tex_preview_hoffset
	tex_preview_voffset
	tex_preview_figure_width
	tex_preview_figure_height

for TeX preview font selection
         tex_preview_fontsize
         tex_preview_fontfamily
         tex_preview_fontseries
         tex_preview_fontshape

I hope this will prove to be adequate to do what you're after -- but  
if not, please let me know.

> Thanks.
>
> Ivars

Your welcome.  And I hope there will be a new release very soon!

However, iIn case you are impatient (like me), here is an example of  
the new Tioga preview preamble.  You can try cut-and-pasting it into  
your own file in your favorite TeX editor if you'd like to give it a  
try.    Note that you can edit the preview TeX file for things like  
the font family or figure or page size, and then "typeset" the new  
version in the TeX editor to see the changes -- no need to rerun  
Tioga for that.  You can play in the TeX editor until you get what  
you want, and then go back later to edit your Tioga program.

You might even want to do the figures in the paper using the preview  
preamble approach rather than using the preview PDF's themselves --  
i.e., instead of doing 'includegraphics' for the PDF's, use the  
preview preamble commands like TiogaFigureSized and build the figures  
"on the fly" from the pieces when you typeset the document.  That way  
you delay the choice of fonts in the figures until the last moment,  
so if something changes you don't need redo the figures and you can  
also feel sure that the font choice is consistent across the full set.

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Cheers,
Bill



From vincent.fourmond at 9online.fr  Fri Jun 30 02:48:19 2006
From: vincent.fourmond at 9online.fr (vincent.fourmond at 9online.fr)
Date: Fri, 30 Jun 2006 06:48:19 +0000 (GMT)
Subject: [Tioga-users] Setting absolute size of figure
In-Reply-To: <DC4BCDAF-5521-4BE4-987F-2368FB0A3F34@kitp.ucsb.edu>
References: <5CC34D9F-9A29-4EE8-844E-3400CE66F761@ucalgary.ca>
	<4255D2C6-B055-4242-A3C9-8A5B8792F353@kitp.ucsb.edu>
	<23C81F5A-4B5B-4D7A-A4D7-FD7A52894CBA@ucalgary.ca>
	<DC4BCDAF-5521-4BE4-987F-2368FB0A3F34@kitp.ucsb.edu>
Message-ID: <f49fa8723f71.44a4c933@9online.fr>

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From paxton at kitp.ucsb.edu  Fri Jun 30 11:04:17 2006
From: paxton at kitp.ucsb.edu (Bill Paxton)
Date: Fri, 30 Jun 2006 08:04:17 -0700
Subject: [Tioga-users] Setting absolute size of figure
In-Reply-To: <f49fa8723f71.44a4c933@9online.fr>
References: <5CC34D9F-9A29-4EE8-844E-3400CE66F761@ucalgary.ca>
	<4255D2C6-B055-4242-A3C9-8A5B8792F353@kitp.ucsb.edu>
	<23C81F5A-4B5B-4D7A-A4D7-FD7A52894CBA@ucalgary.ca>
	<DC4BCDAF-5521-4BE4-987F-2368FB0A3F34@kitp.ucsb.edu>
	<f49fa8723f71.44a4c933@9online.fr>
Message-ID: <39F59EF5-7483-4902-A2D7-9F9353BD9DA5@kitp.ucsb.edu>

Hi,

This email is a comment on the issue of unintentionally getting  
multiple copies of additions to the tex_preview_preamble string.  I  
now think this is simply a bug in Tioga.  We get extra copies  
appended because the string is not being reset when a file is  
reloaded.  We do automatically call reset_figures to clear the list  
of figures (or else we'd be having the same problem with the list of  
figures as well!) -- so my intention is to add to reset_figures so  
that it resets the entire figuremaker state to defaults.  That fixes  
the preview_preamble problem and also eliminates one possible source  
of nasty confusion in which a Tioga figure gives different results  
depending on how many times the file has been reloaded!

Unless I hear violent objections, that's what I'll do for the next  
release.

Cheers,
Bill




On Jun 29, 2006, at 11:48 PM, vincent.fourmond at 9online.fr wrote:

>
> Hello !
>
> > > I discovered a possible bug (or perhaps it is my usage). If I
> > > include the following line in my .rb file:
> > >
> > > t.tex_preview_preamble = t.tex_preview_preamble +
> > > "\n\t\\usepackage{MyCommonStuff}\n" +
> > > "\n\t\\usepackage{mathtime}\n"
> > >
> > > I end up with repeated occurrences (about 20) of the \usepackage
> > > lines in the .tex file.
>
> I would like to have a little more context however. You're using  
> irb or the graphical interface and you repeatedly try to plot the  
> same things ? Could you send us the file (or an extract) ?
>
> If that really is an annoyance, I propose the creation of a function
>
> def tex_preview_preamble_append(str, unique = true)
> if not unique or tex_preview_preamble.index(str)
> tex_preview_preamble += str
> end
> end
>
> Then, you call it
> tex_preview_preamble_append("your string")
>
> and it will get appended only once.
>
> That's the best I see for now.
>
> Vincent
> _______________________________________________
> Tioga-users mailing list
> Tioga-users at rubyforge.org
> http://rubyforge.org/mailman/listinfo/tioga-users


From vincent.fourmond at 9online.fr  Fri Jun 30 14:16:30 2006
From: vincent.fourmond at 9online.fr (Vincent Fourmond)
Date: Fri, 30 Jun 2006 20:16:30 +0200
Subject: [Tioga-users] Setting absolute size of figure
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  Hello !

> This email is a comment on the issue of unintentionally getting multiple
> copies of additions to the tex_preview_preamble string.  I now think
> this is simply a bug in Tioga.  We get extra copies appended because the
> string is not being reset when a file is reloaded.  We do automatically
> call reset_figures to clear the list of figures (or else we'd be having
> the same problem with the list of figures as well!) -- so my intention
> is to add to reset_figures so that it resets the entire figuremaker
> state to defaults. 

  That's sounds good to me. Then, we probably should name reset_figures
otherwise (reset_state ?) and provide reset_figures as an alias for that ?

	Vincent