def density(points):
'''scale is the slice thickness
if 3D and non cubic then scale'''
if size(shape(points)) != 2:
print 'error in points dimensions'
if shape(points)[1] != 3:
if shape(points)[0] != 3:
print 'something wrong'
return
else: #transpose
print 'transposing'
points = points.T
distmat=zeros([size(points ,0), size(points ,0)]);
for i in range(0,size(points,0)):# %get euclid dist between all pairs of points
for ii in range(0,size(points ,0)):
dist = 1/euclid.dist(
points[i,0], points[ii,0],\
points[i,1], points[ii,1], \
points[i,2], points[ii,2]);
if dist == inf:
if i == ii:
distmat[i,ii] = 0
else:
distmat[i,ii] = 1
else:
distmat[i,ii] = dist
return distmat
def proximity(points, scale=None):
'''scale is the slice thickness
if 3D and non cubic then scale'''
distmat=zeros([size(points ,0), size(points ,0)]);
for i in range(0,size(points,0)):# %get euclid dist between all pairs of points
for ii in range(0,size(points ,0)):
distmat[i,ii] = 1/euclid.dist(
points[i,0], points[ii,0],\
points[i,1], points[ii,1], \
points[i,2], points[ii,2]);
return distmat
def sphere(location, gridsize, spacing): # , radius):
"""make 3d sphere grid with given location of center, gridsize, spacing, and radius
g = grid.sphere(array([1,1,1]),12,.5)
makes a grid (g) centered around location 1,1,1 of size 12, with a spacing of 1"""
radius = (gridsize * spacing) / 2.0
cgrid = cube(location, gridsize, spacing)
print cgrid.shape, location
e = np.zeros(np.size(cgrid, 1))
g = np.copy(e)
for i in range(0, np.size(cgrid, 1)):
# e[:,i] = euclid.dist(location[0],cgrid[0][i],location[1],cgrid[1][i],location[2],cgrid[2][i])
e[i] = euclid.dist(location, cgrid[:, i])
# e = e*10
print "diameter", e.max(), "mm"
sgrid = cgrid[:, e < radius].reshape([3, np.size(cgrid[:, e < radius]) / 3])
# cgrid[e > radius].reshape([3,np.size(cgrid[e > radius])/3]) == 0
return sgrid # ,cgrid
import math
from gui.wx import file
fn = file.open()
from pdf2py import pdf
p = pdf.read(fn[0])
p.data.setchannels('meg')
p.data.getdata(0,p.data.pnts_in_file)
p.data.channels.getposition()
#chA1pos = p.data.channels.chlpos[0]
centofsphere = array([0,0,.04]) #center of sphere
chlpos_ = p.data.channels.chlpos - centofsphere
chupos_ = p.data.channels.chupos - centofsphere
from meg import euclid
#Din = euclid.dist(centofsphere, p.data.channels.chlpos)
Din = euclid.dist(array([0,0,0]), chlpos_)
chmin = Din.argmin(); r_min = Din.min()
#Dout = euclid.dist(centofsphere, p.data.channels.chupos)
Dout = euclid.dist(array([0,0,0]), chupos_)
chmax = Dout.argmax(); r_max = Dout.max()
#x = chA1pos[0]; y = chA1pos[1]; z=chA1pos[2]
#r = sqrt((x**2)+(y**2)+(z**2))
x = chlpos_[chmin][0]; y = chlpos_[chmin][1]; z=chlpos_[chmin][2]
phi = math.atan2(z, sqrt(x**2 + y**2)); #phi = arccos(z/r)
theta = math.atan2(y,x)
def cart2sph(chpos):
x = chpos[0]; y = chpos[1]; z=chpos[2]
r = sqrt((x**2)+(y**2)+(z**2))
phi = math.atan2(z, sqrt(x**2 + y**2)); #phi = arccos(z/r)
