Notes

from pdf2py import data, channel, pdfread
datapdf = pdfread.guiwin()
datapdf = '/home/danc/vault/decrypted/data/DR_AMwtsup/0003/DR_AMwtsup/04%02%08@09:03/1/e,rfhp0.1Hz,x,n,o,baha001-1AM32,f20lp,o'

ch = channel.index(datapdf, 'meg')
d = data.read(datapdf)
d.getdata(0, d.pnts_in_file, chindex=ch.channelindexhdr)

from meg import megcontour
megcontour.display(d.data_block[170:300:5,:], ch.chanlocs, subplot='on')
wmat=d.data_block[225,:]
from meg import weightfit
from mri import img, viewmri, transform
from pdf2py import channel
nim = img.read('/home/danc/data/standardmri/ch2b.img')
nimstripped = img.read('/home/danc/data/standardmri/ch2b_brain.img')
dec = img.decimate(nimstripped, 10)
rpa=[5,99,27]
lpa=[174,102,22]
nas=[91, 209, 31]
[t,r] = transform.meg2mri(lpa,rpa,nas)
megxyz = transform.mri2meg(t,r,dec.mrixyz)
scaledmegxyz = transform.scalesourcespace(datapdf, megxyz)
from meg import leadfield
ch = channel.index(datapdf, 'meg')
lf = leadfield.calc(datapdf, ch, scaledmegxyz)
w=weightfit.calc(datapdf, lf.leadfield, wmat)

from pylab import *
figure();plot(w.corr_mat.T);show()

from mri import sourcesolution2img
[ssdec, sshires] = sourcesolution2img.build(w.corr_mat,dec)
viewmri.display(ssdec)

mr2vtk.convert(sshires, filename='mrvtk_0003overlay')

ls=array([[44,127,69]]).T
rs=array([[144,127,69]]).T

lmegxyz = transform.mri2meg(t,r,ls)
rmegxyz = transform.mri2meg(t,r,rs)

lfl=leadfield.calc(datapdf, ch, lmegxyz)
lfr=leadfield.calc(datapdf, ch, rmegxyz)

qnr=array([[-.2, -.9, -.8]])
qnl=array([[-.2, .9, -.8]])

datapdf = pdfread.guiwin()
from meg import sourcespaceprojection
sspr=sourcespaceprojection.calc(d.data_block, lfr.leadfield, qnr)
sspl=sourcespaceprojection.calc(d.data_block, lfr.leadfield, qnl)

from meg import timef
t = timef.initialize()
t.calc(datapdf, 'A1', freqrange=[5.0,80])
t.calc(data=sspl, frames=t.frames, trials=t.trials, srate=t.srate, freqrange=[5.0,80])

figure();imshow(abs(t.P), aspect=7, extent=(int(t.timevals[0]), int(t.timevals[-1]), int(t.freqrange[1]), int(t.freqrange[0])));show()

import mayavi
from numpy import *
from pylab import *
from pyvtk import *

z1 = float32(reshape(nim.data, (-1,)))
vtkdata = VtkData(StructuredPoints([181,217,181]), PointData(Scalars(z1)))
vtkdata.tofile('/home/danc/mri_bin', 'binary')

Reader = vtk.vtkStructuredPointsReader()
Reader.SetFileName("/home/danc/mri_bin.vtk")

v = mayavi.mayavi() # create a MayaVi window.
d = v.open_vtk('example2.vtk', conz1 = float32(reshape(nim.data, (-1,)))fig=0) # open the data file
m = v.load_module('SurfaceMap', 0)
a = v.load_module('Axes', 0)
v.Render() # Re-render the scene.
from numpy import *
from mri import img
import pyvtk
nim = img.read('/home/danc/data/standardmri/ch2b.img')

z1 = reshape(nim.data, (-1,))
point_data = pyvtk.PointData(pyvtk.Scalars(z1))
x = nim.data.shape
grid = pyvtk.StructuredPoints((x[0],x[1], x[2]), (1, 1, 1), (1,1 , 1))
data = pyvtk.VtkData(grid, point_data)

import vtk
ren = vtk.vtkRenderer()
renWin = vtk.vtkRenderWindow()
renWin.AddRenderer(ren)
iren = vtk.vtkRenderWindowInteractor()
iren.SetRenderWindow(renWin)
import mayavi
 v = mayavi.mayavi() # create a MayaVi window.
 d = v.open_vtk('/tmp/test.vtk', config=0) # open the data file.
 # The config option turns on/off showing a GUI control for the data/filter/module.
 # load the filters.
 f = v.load_filter('WarpScalar', config=0) 
 n = v.load_filter('PolyDataNormals', 0)
 n.fil.SetFeatureAngle (45) # configure the normals.
 # Load the necessary modules.
 m = v.load_module('SurfaceMap', 0)
 a = v.load_module('Axes', 0)
 a.axes.SetCornerOffset(0.0) # configure the axes module.
 o = v.load_module('Outline', 0)
 v.Render() # Re-render the scene.

MayaVi from the Python interpreter
Format  C-Type        MATLAB      Notes
x     pad-byte                 no value     
c     char               uchar                'c', 'c', 1    
b     signed char             integer     
B     unsigned char             integer     
h     short            int16        integer     'h', 'h', 1    
H     unsigned short     uint16    integer    'H', 'H', 1    
i     int             init32        integer    'i', 'i', 1    
I     unsigned int    uint32    long        'I', 'I', 1    
l     long                    integer
L     unsigned long            long     
q     long long                long     (1)
Q     unsigned long long        long     (1)
f     float            float32    float         'f', 'f', 1    
d     double        double    float         'd', 'd', 1    
s     char[]                string     
p     char[]                string     
P     void *                integer

Format C Type Python Notes
x pad byte no value
c char string of length 1 uchar
b signed char integer
B unsigned char integer
h short int16 integer
H unsigned short uint16 integer
i int init32 integer
I unsigned int uint32 long
l long integer
L unsigned long long
q long long long (1)
Q unsigned long long long (1)
f float float32 float
d double double float
s char[] string
p char[] string
P void * integer

Format C Type Python Notes
x pad byte no value
c char string of length 1 uchar
b signed char integer
B unsigned char integer
h short int16 integer
H unsigned short uint16 integer
i int init32 integer
I unsigned int uint32 long
l long integer
L unsigned long long
q long long long (1)
Q unsigned long long long (1)
f float float32 float
d double float
s char[] string
p char[] string
P void * integer

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