Skip to main content

Using PCA in MDP


I found mdp on sourceforge. I needed to do PCA for some of my simulations. The mdp.pca function is easy to handle. The input is a m x n matrix, n is the dimension of the space, and m are the observations (rows = observations, cols = dimensions. The doc string is confused as to this point)

The output is a matrix also m x n, but the vectors have been transformed, so that the first column is along the direction with greatest variance etc.

An example is below:


import pylab as m
import matplotlib.axes3d as m3
import mdp

x1 = m.rand(10,3)
x2 = m.rand(10,3) + m.array([[2.,-2.,0.]])
x = m.concatenate((x1,x2))
y = mdp.pca(x)

fig = m.figure()
ax = m3.Axes3D(fig)
ax.scatter3D(x[:10,0].squeeze().T, x[:10,1].squeeze().T, x[:10,2].squeeze().T, marker = '^')
ax.scatter3D(x[10:,0].squeeze().T, x[10:,1].squeeze().T, x[10:,2].squeeze().T, marker = 'o')
m.axis('scaled')
m.axes([.7, .8, .2, .2])
m.plot(y[:10,0], y[:10,1],'k^')
m.plot(y[10:,0], y[10:,1],'b.')
m.axis('scaled')
m.title('2 D')

m.axes([.7, .6, .2, .2])
m.plot(y[:10,0],'k^')
m.plot(y[10:,0],'b.')
m.axis('scaled')
m.title('1 D')

Comments

  1. For anyone reading this, the code needs to be updated for the latest version of matplotlib:
    line 2 should be:
    import mpl_toolkits.mplot3d as m3

    also add m.show() at the end to display the results.

    ReplyDelete

Post a Comment

Popular posts from this blog

Python: Multiprocessing: passing multiple arguments to a function

Write a wrapper function to unpack the arguments before calling the real function. Lambda won't work, for some strange un-Pythonic reason.


import multiprocessing as mp def myfun(a,b): print a + b def mf_wrap(args): return myfun(*args) p = mp.Pool(4) fl = [(a,b) for a in range(3) for b in range(2)] #mf_wrap = lambda args: myfun(*args) -> this sucker, though more pythonic and compact, won't work p.map(mf_wrap, fl)

Flowing text in inkscape (Poster making)

You can flow text into arbitrary shapes in inkscape. (From a hint here).

You simply create a text box, type your text into it, create a frame with some drawing tool, select both the text box and the frame (click and shift) and then go to text->flow into frame.

UPDATE:

The omnipresent anonymous asked:
Trying to enter sentence so that text forms the number three...any ideas?
The solution:
Type '3' using the text toolConvert to path using object->pathSize as necessaryRemove fillUngroupType in actual text in new text boxSelect the text and the '3' pathFlow the text

Running a task in a separate thread in a Tkinter app.

Use Queues to communicate between main thread and sub-threadUse wm_protocol/protocol to handle quit eventUse Event to pass a message to sub-threadimport Tkinter as tki, threading, Queue, time def thread(q, stop_event): """q is a Queue object, stop_event is an Event. stop_event from http://stackoverflow.com/questions/6524459/stopping-a-thread-python """ while(not stop_event.is_set()): if q.empty(): q.put(time.strftime('%H:%M:%S')) class App(object): def __init__(self): self.root = tki.Tk() self.win = tki.Text(self.root, undo=True, width=10, height=1) self.win.pack(side='left') self.queue = Queue.Queue(maxsize=1) self.poll_thread_stop_event = threading.Event() self.poll_thread = threading.Thread(target=thread, name='Thread', args=(self.queue,self.poll_thread_stop_event)) self.poll_thread.start() self.poll_interval = 250 self.poll() self.root.wm_protocol("WM_DELETE…