Dear all, I usual use chimera on my linux box, but for some practicities, I need to use it in windows. I realized though that I can not access the disk F: of my windows box which is a mounted disk from the linux one. Would it be difficult that the file browser of chimera recognize samba mounted disk? Our is ther a trick I miss? All the best, JD On Wed, 2008-04-09 at 12:00 -0700, chimera-dev-request@cgl.ucsf.edu wrote:
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Today's Topics:
1. Re: Multi-touch and Chimera (Tom Goddard) 2. Re: Multi-touch and Chimera (Tom Goddard)
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Message: 1 Date: Tue, 08 Apr 2008 12:39:58 -0700 From: Tom Goddard <goddard@cgl.ucsf.edu> Subject: Re: [chimera-dev] Multi-touch and Chimera To: Gergely Nagy <gergelynagy76@gmail.com> Cc: chimera-dev@cgl.ucsf.edu Message-ID: <47FBCA0E.8090702@cgl.ucsf.edu> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
Hi Greg,
Chimera is written in Python and C++. The C++ is used for OpenGL rendering and for optimizing calculations. The event loop and user interface is all in Python. The touch events and the actions they trigger should definitely be in Python. It looks very reasonable to use Boost Python to wrap the C++ touchlib library or parts of it to make it accessible to Python.
http://wiki.python.org/moin/boost.python/GettingStarted
http://www.boost.org/doc/libs/1_35_0/libs/python/doc/index.html
We use an in-house wrapping program (WrapPy). Wrapping C/C++ for Python is often done with package called SWIG.
We use the Tcl/Tk event loop using the Python/Tk interface module called Tkinter. You can put custom Tk event types such as touch events in the event queue but I haven't figured out a way to do it. The trouble is that you typically will get an event from a callback in C/C++ code. I recently tried passing such an event (for a Space Navigator 6-dof input device) to a Python routine. It resulted in crashes because Tkinter is designed so that only it can call Python code. It has some complicated thread locking code that releases a Python lock and my event handler called into Python without having that Python lock, tried to do some Tk call and crashed. Probably the Python lock can be acquired in the C/C++ callback, but then if that Python code does Tk calls to add an event there may be additional problems with Tkinter's Tk lock which is inaccessible. So some work is needed to figure out how to get the C/C++ callback events into the Tk event loop. Once that is solved everything can be done in Python with event handlers processing those Tk events to cause any desired Chimera actions.
Tom
Gergely Nagy wrote:
Hi Tom,
Thanks for your reply. Our multi-touch interface won't work with touch-pads, since it is based on another technology. The user will need to touch the actual object on the screen since there won't be any pointers. The interaction is direct between the user finger and the programs objects. So basically when the user touches a menu item for example, there is a sort of mouse clicked event at the given coordinates on the screen. Talking about events, there exists a library written in C++ called Touchlib (http://nuigroup.com/touchlib/) that pass those touch events to any program written in C++ and this is what we would like to use. Of course in this case we will need to wrap that code to be able to use it in python. I thought using Boost (http://www.boost.org/users/index.html) for that. I was asking you about the sources because at the end we should have something compiled and working. It doesn't matter if its not the latest version, what would be important is that we will be able to demonstrate the interface working. Would it be possible?
Concerning the atom-atom distance, the user would zoom in on the part he is interested in, after he would choose the appropriate display form and then he would change from moving-zooming mode to selection mode and he would touch the atoms he would like to know the distance between. So you are right, visual feedback would be necessary, as it was the case with a mouse click. So to sum up the interaction events, there would be something like finger_down, finger_up, dragging. And also these events are dispatched by touchlib, so we would need to implement them in Chimera.
What do you think about it?
Thanks a lot for your help!
Regards, Greg
2008/4/8, Tom Goddard <goddard@cgl.ucsf.edu <mailto:goddard@cgl.ucsf.edu>>:
Hi Greg,
Sounds neat. Will a multi-touch interface work with a standard laptop touch-pad?
The source code for Chimera is on the web though it isn't up to date.
http://www.cgl.ucsf.edu/chimera/sourcecode.html
All of the functions you are interested in are implemented in Python code which is included in the distributed Chimera. The Python code is in files (with ".py" suffix) in directories under
chimera/share
or on Mac under directory Chimera.app/Contents/Resources/share. But it is quite difficult to find the Chimera Python routines you need. Our programming reference guide (automatically generated from code comments) is not too useful but we provide programming examples that might help.
http://www.cgl.ucsf.edu/chimera/docs/ProgrammersGuide/Examples/index.html
The easiest approach is to ask us by email for the routines you need, e.g. list all chain identifiers, select chain given id, color equivalent to actions menu, move models, rotate models, show atom-atom distance, find atom under mouse, draw label.... Eric Pettersen is the most familiar with that code and what simple routines already exist to do those things. He is on vacation now but expected back around Thursday.
You are interested in atom-atom distances. Will the user choose an atom through the touch interface? It seems that would require visual feedback in the Chimera window -- equivalent of the mouse pointer. I suppose you could take over the mouse pointer, or you could create a new "cursor" implemented perhaps as a Chimera 2d label.
Tom
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Message: 2 Date: Tue, 08 Apr 2008 12:49:01 -0700 From: Tom Goddard <goddard@cgl.ucsf.edu> Subject: Re: [chimera-dev] Multi-touch and Chimera To: Gergely Nagy <gergelynagy76@gmail.com> Cc: chimera-dev@cgl.ucsf.edu Message-ID: <47FBCC2D.2010402@cgl.ucsf.edu> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
Greg suggest a direct call from C/C++ to queue an event.
Tom
Greg Couch wrote:
Tom,
You need to link with tcl (actually tcl stubs) and use the Tcl_ThreadQueueEvent function.
- Greg
On Tue, 8 Apr 2008, Tom Goddard wrote:
From: Tom Goddard <goddard@cgl.ucsf.edu> Sender: chimera-dev-bounces@cgl.ucsf.edu To: Gergely Nagy <gergelynagy76@gmail.com> Cc: chimera-dev@cgl.ucsf.edu Date: Tue, 08 Apr 2008 12:39:58 -0700 Subject: Re: [chimera-dev] Multi-touch and Chimera Received-SPF: pass (cgl.ucsf.edu: 169.230.27.3 is authenticated by a trusted mechanism) Received-SPF: pass (cgl.ucsf.edu: 169.230.27.3 is authenticated by a trusted mechanism)
Hi Greg,
Chimera is written in Python and C++. The C++ is used for OpenGL rendering and for optimizing calculations. The event loop and user interface is all in Python. The touch events and the actions they trigger should definitely be in Python. It looks very reasonable to use Boost Python to wrap the C++ touchlib library or parts of it to make it accessible to Python.
http://wiki.python.org/moin/boost.python/GettingStarted
http://www.boost.org/doc/libs/1_35_0/libs/python/doc/index.html
We use an in-house wrapping program (WrapPy). Wrapping C/C++ for Python is often done with package called SWIG.
We use the Tcl/Tk event loop using the Python/Tk interface module called Tkinter. You can put custom Tk event types such as touch events in the event queue but I haven't figured out a way to do it. The trouble is that you typically will get an event from a callback in C/C++ code. I recently tried passing such an event (for a Space Navigator 6-dof input device) to a Python routine. It resulted in crashes because Tkinter is designed so that only it can call Python code. It has some complicated thread locking code that releases a Python lock and my event handler called into Python without having that Python lock, tried to do some Tk call and crashed. Probably the Python lock can be acquired in the C/C++ callback, but then if that Python code does Tk calls to add an event there may be additional problems with Tkinter's Tk lock which is inaccessible. So some work is needed to figure out how to get the C/C++ callback events into the Tk event loop. Once that is solved everything can be done in Python with event handlers processing those Tk events to cause any desired Chimera actions.
Tom
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