Pymeg Data Plot

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2D MEG plot

First use the 4D to python reader as shown here pymeg-data-import
to reiterate to plot for example the 2D data as a simple line plot, use the pylab module for the graphics.

from pdf2py import channel, data

from pylab import *
d=data.read(file)
ch=channel.index(file, 'meg')
d.getdata(0, 200, chindex=ch.channelindexhdr)
from meg import offset
figure();plot(offset.correct(d.data_block));

but before plotting the MEG lets add the trigger channels (trigger and response) to the plot.

ch=channel.index(file, 'trig')
t=data.read(file)
t.getdata(0, 200, chind=ch.channelindexhdr)

but before plotting we should scale the trigger channel, as if too large, will dwarf the MEG channel scale.
we will use the module 'max' from numpy to get the largest scale of both the MEG and triggers to scale by.

from numpy import *
plot(offset.correct(t.data_block/(t.data_block.max()/d.data_block.max())));
show()

Contour plot

leaving where we left off with the 2D plotting of a MEG waveform, lets plot the contour of some data.

first we need the delaunay module from scikits to do the interpolation in the contour.
download from delaunay.tgz
install by extracting

tar -xvzf delaunay.tgz
cd delaunay

and running the install script as root

sudo python setup.py install

now for plotting

from meg import megcontour
ch=channel.index(file, 'meg')
d.data_block=offset.correct(d.data_block)
megcontour.display(d.data_block[100,:], ch.chanlocs)

also the megcontour module does support multiple slices, and will play them back as an animation.
for example, to play a animation of points 100 thru 150…

megcontour.display(d.data_block[100:150,:], ch.chanlocs)

Plot Headshape

Import the module 'pdf' and read the datafile. The datafile is the MEG datafile (ex. e,rfhp1.0Hz….). The pdf module will read the associated config and hs_file from the same dir.

from pdf2py import pdf
p=pdf.read(datapdf)

However, if you only want the headshape (maybe you dont have the MEG data), just import the 'headshape' module and use that.

from pdf2py import headshape
hs=headshape.read('/home/danc/vault/decrypted/programming/python/data/0611SEF/hs_file')

These are the headshape points

p.hs.hs_point

array([[ 0.10589639, -0.01769761, 0.03191416],
[ 0.10719753, -0.01090601, 0.02798972],
[ 0.1073915 , -0.00797158, 0.02596697],
…,
[ 0.02291044, 0.08052011, 0.04076125],
[ 0.03362855, 0.0778126 , 0.03762892],
[ 0.03794358, 0.07627923, 0.03675756]])

from meg import plotvtk
plotvtk.display(hs.hs_point)

Plot Sensors

Plot sensors from configuration file.

from meg import sensors
s=sensors.locations('/home/danc/vault/decrypted/programming/python/data/0611SEF/e,rfhp1.0Hz,n,x,baha001-1SEF,f50lp')
from meg import plotvtk
plotvtk.display(s.megchupos)

or you could plot the lower meg channels by using s.megchlpos

Result

To plot headshape in the sensors…and the indexpoints (lpa, rpa, naision)

ind=hstack([hs.index_lpa,hs.index_rpa,hs.index_nasion]).reshape(3,3)
plotvtk.display(hs.hs_point, s.megchlpos, ind)