Tuesday, September 23, 2008
Sunday, March 16, 2008
Wednesday, January 30, 2008
Tuesday, January 29, 2008
easy_install -f http://rieke-server.physiol.washington.edu/~barry/python/ scikits.annif you're on OS X 10.5.
I've also made an egg for OS X that statically links the ANN library. You should be able to install via (one line):
easy_install -f http://rieke-server.physiol.washington.edu/~barry/python scigpl.ann
Of course, you can still get it via the scikits SVN.
Here's how the new API looks:
>>> import scigpl.ann as ann
>>> import numpy as np
(array([]), array([[ 0.04]]))
(array([[0, 1]]), array([[ 0.04, 1.04]]))
[1, 2]]), array([[ 0.04, 1.04],
[ 1.96, 4.01],
[ 3.25, 5. ],
[ 1. , 6.25]]))
(array([[ 0, 1, 2],
[ 2, 0, 1],
[ 2, 1, 0],
[ 1, 2, -1]]), array([[ 4.00000000e-002, 1.04000000e+000, 5.49000000e+000],
[ 1.96000000e+000, 4.01000000e+000, 4.81000000e+000],
[ 3.25000000e+000, 5.00000000e+000, 1.00000000e+001],
[ 1.00000000e+000, 6.25000000e+000, 1.79769313e+308]]))
Friday, January 18, 2008
Tuesday, January 1, 2008
ANN is licensed under the LGPL and we've licensed the scikits.ann wrapper under the BSD license. If you need a kd-tree implementation for Python/numpy, check it out.
The author of numpy, Travis Oliphant recently moved from Utah to Texas to work with Enthought. One of the many contributions Enthought has made to the scientific software community is developing a whole suite of tools (in Python) that make developing cross-platform scientific applications much easier. In a recenet post, Travis talks at length about what makes a "good" UI. Travis has obviously thought a lot about UI's for scientific computing and his discussion is very interesting. Definitely worth a read. Briefly, Travis notes that the user interface of an app is not just the buttons and menus, but the entire application framework—persistence, undo/redo, safe exploration, workflow, etc.
In scientific software, I think "workflow" is the most important part of an application's user interface. Application frameworks such as Apple's Cocoa, Microsoft's .NET, Trolltech's Qt, etc. have solved many of the applicaiton framework UI issues that Travis mentions (in fact, this is why we use Cocoa and Qt for most of our work at Physion). Apple's Cocoa framework is particularly impressive in this regard. An application with undo/redo, persistence to an SQLite database, automatic network discovery of distributed computing resources, you-name-it, is virtually code-free for the developer. But, none of these frameworks have solved the scientific workflow problem. That's because we know how undo/redo should work. We've known for decades how a database should work (for the most part), but science is about the new and very often discovering something new involves creating the entire workflow anew.
One reason why new workflow and new experiments often go together is because a workflow implicitly defines a world model—an idea about what objects in the world mater and how they interact—and new experiments also define a new world model. Therefore, new experiment, new workflow. Only by matching the workflow to the experiment, can we make software that becomes invisible to the researcher while facilitating new discoveries.