[chimera-dev] examples of 2-D plotting in plugins?

Randy Heiland heiland at indiana.edu
Wed Jan 14 16:48:21 PST 2009 

This is awesome guys!  I look forward to trying it out...

-Randy

On Jan 14, 2009, at 1:49 PM, Thomas Goddard wrote:

> Matplotlib is in current Mac and Linux Chimera daily builds but not  
> yet
> in Windows.  Should be in Windows within the next week.  I'll send
> another message when it is.
>
> 	Tom
>
>
> Eric Pettersen wrote:
>> Tom Goddard has done the work to get matplotlib to compile with
>> Chimera.  It's now available in the daily builds.
>>
>> --Eric
>>
>> On Dec 16, 2008, at 10:35 AM, Randy Heiland wrote:
>>
>>> Thanks for clarifying, Tom.  Am happy to hear you plan to eventually
>>> include mpl in Chimera.
>>>
>>> Yes, both Charlie (Moad) and I have built it for Windows, but that  
>>> was
>>> several versions back when we did it regularly.  What prompted this
>>> thread initially was my attempt to do it again, but discovered an
>>> apparent mismatch when Chimera jumped to Tcl/Tk 8.5 and mpl still
>>> wanted 8.4.  Perhaps the inclusion of mpl into Chimera will be  
>>> solved
>>> by the passage of time, after the libraries (and stars) align.
>>> Anyway, the only tips I'd have are the obvious ones - to tweak those
>>> checks/settings done in mpl's setup/setupext.py scripts related to  
>>> the
>>> various dependencies (numpy, tcl/tk, etc) before running chimera's
>>> python on setup.py.  Just running:
>>>
>>> ...path-to-chimera-python  setup.py
>>>
>>> will reveal what mpl will attempt to use to build.
>>>
>>> Maybe I'll dust off my Window's laptop :) and make another attempt  
>>> in
>>> the next few days.
>>>
>>> -Randy
>>>
>>>
>>> On Dec 16, 2008, at 1:16 PM, Tom Goddard wrote:
>>>
>>>> Hi Randy,
>>>>
>>>> On the Mac the Chimera python executable finds the Python framework
>>>> and runs it.  When you start Chimera's Python from a shell it is
>>>> finding
>>>> the Mac system Python framework instead of the one included in
>>>> Chimera.app.  The way Chimera gets its own Python framework instead
>>>> of
>>>> the system one is that the start-up script
>>>>
>>>>  Chimera.app/Contents/Resources/bin/chimera
>>>>
>>>> sets the DYLD_FRAMEWORK_PATH environment variable to point to the
>>>> Chimera Python (and Tcl/Tk) frameworks.
>>>>
>>>> We discussed including matplotlib in the Chimera distribution and
>>>> agreed it is a good idea and we plan on doing it though a date has
>>>> not
>>>> been set.  I would like to try using it this month or next month  
>>>> so I
>>>> may add it to Chimera soon.  The trick is to get it to build on all
>>>> platforms (Windows, Linux, Mac).  Have you built it for Chimera on
>>>> Windows.  Any tips?
>>>>
>>>> Thanks,
>>>>
>>>>  Tom
>>>>
>>>>
>>>> Randy Heiland wrote:
>>>>> Hi Eric and others,
>>>>>
>>>>> I've returned to this little exercise of trying to build  
>>>>> matplotlib
>>>>> using Chimera and have a basic question:
>>>>>
>>>>> - using the Chimera-1.3.2577-osx_aqua, when I bring up IDLE, I  
>>>>> see:
>>>>> Python 2.5.2 (r252:60911, Dec  9 2008, 02:00:10)
>>>>> [GCC 4.0.1 (Apple Computer, Inc. build 5370)] on darwin
>>>>>
>>>>> however, when I run Chimera's python manually, I see:
>>>>>
>>>>> $ /Users/heiland/dev/Chimera-1.3.2577-osx_aqua.app/Contents/
>>>>> Resources/
>>>>> bin/python2.5
>>>>> Python 2.5.1 (r251:54869, Apr 18 2007, 22:08:04)
>>>>> [GCC 4.0.1 (Apple Computer, Inc. build 5367)] on darwin
>>>>>
>>>>> Why am I seeing 2 different Python builds?
>>>>>
>>>>> One of the initial things I'm trying to resolve is the ability to
>>>>> 'import Tkinter'.  I can do so from the former, but not the latter
>>>>> (even after setting sys.path to be what it is in the former).
>>>>>
>>>>> thanks, Randy
>>>>>
>>>>>
>>>>> On Nov 3, 2008, at 5:52 PM, Eric Pettersen wrote:
>>>>>
>>>>>
>>>>>> FYI, the last paragraph of my reply below may be of general
>>>>>> interest
>>>>>> to developers interested in plotting data...
>>>>>>
>>>>>> On Oct 31, 2008, at 10:09 AM, Randy Heiland wrote:
>>>>>>
>>>>>> Hi gang,
>>>>>>
>>>>>> For one of the Chimera plugins that I now maintain, I'm  
>>>>>> considering
>>>>>> eliminating the use of matplotlib and wondering if Chimera's
>>>>>> innards
>>>>>> are capable of doing what I want.  For starters, are there any
>>>>>> example plugins, etc that demonstrate how one could do simple
>>>>>> plotting and simple (image) contours?  In addition, I'd need to
>>>>>> handle mouse events, e.g. to retrieve x,y positions on the  
>>>>>> contour
>>>>>> image.
>>>>>>
>>>>>> Hi Randy,
>>>>>> I'm thinking that what Chimera currently provides will not be an
>>>>>> adequate replacement for the capabilities of matplotlib that
>>>>>> NLOPredict uses.  Aside from the basic Tk widgets themselves (the
>>>>>> most salient of which is Canvas) the only relevant widgets I can
>>>>>> think of is an interactive histogram widget in CGLtk.Histogram,  
>>>>>> and
>>>>>> a basic line/point plotting widget available through
>>>>>> Scientific.TkWidgets.TkPlotCanvas
>>>>>> (Scientific.TkWidgets.TkPlotCanvas<http://dirac.cnrs-orleans.fr/ScientificPython/ScientificPythonManual/Scientific.TkWidgets.TkPlotCanvas-module.html
>>>>>>
>>>>>>> ).
>>>>>>>
>>>>>> But I think NLOPredict needs interactive contour and bar graphs.
>>>>>> As
>>>>>> long as you can generate the contour image yourself somehow, I
>>>>>> think
>>>>>> you can pretty easily gin up an interactive contour plot using  
>>>>>> the
>>>>>> Image item of Tk.Canvas.  As for the bar graph, would BLT (A  
>>>>>> User's
>>>>>> Guide to Pmw.Blt<http://heim.ifi.uio.no/~hpl/Pmw.Blt/doc/>)  
>>>>>> provide
>>>>>> enough functionality if we decided to provide that?  It seems to
>>>>>> provide bar charts (A complete reference to the Pmw.Blt plot
>>>>>> widget<http://heim.ifi.uio.no/~hpl/Pmw.Blt/doc/reference.html%23bar_create(...)
>>>>>>
>>>>>>> ).  It also might or might not be easier for you to provide BLT
>>>>>>> for
>>>>>>>
>>>>>> NLOPredict as a stopgap measure.
>>>>>> So the Chimera developers will be discussing possibly providing
>>>>>> some
>>>>>> kind of plotting library at our next weekly meeting.  Clearly,
>>>>>> matplotlib is the "Cadillac" of plotting libraries.  And like a
>>>>>> Cadillac it has the downside of large size -- probably in the  
>>>>>> range
>>>>>> of 60-80MB before compression.  It also has the drawback of
>>>>>> depending on a lot of other packages which we would also have to
>>>>>> include and port to all our supported platforms, including 64-bit
>>>>>> versions thereof.  So I guess the question is whether we could  
>>>>>> get
>>>>>> away with including something smaller like BLT, which we would  
>>>>>> also
>>>>>> be able to deploy more quickly due to the lower effort  
>>>>>> involved, or
>>>>>> do people really need the unique capabilities of matplotlib?
>>>>>> Anybody?
>>>>>>
>>>>>> --Eric
>>>>>>
>>>>>>                     Eric Pettersen
>>>>>>                     UCSF Computer Graphics Lab
>>>>>>                     http://www.cgl.ucsf.edu
>>>>>>
>>>>>>
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