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pNbody/pNbody/geometry.py
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geometry.py
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from numpy import *
def norm(x):
'''
return the norm of vector x
'''
return sqrt(x[0]**2+x[1]**2+x[2]**2)
def rotate(x,angle=0,axis=[1,0,0],point=[0,0,0]):
'''
Rotate the positions and/or the velocities of the object around a specific axis
with respect to a specific point
angle : rotation angle in radian
axis : [x,y,z] : around this axis
point : [x,y,z] : rotation origin
use the euler rotation matrix
'''
# center point
x = x-point
# construction of the rotation matrix
norm = sqrt(axis[0]**2 + axis[1]**2 + axis[2]**2)
if norm == 0:
return x
sn = sin(-angle/2.)
e0 = cos(-angle/2.)
e1 = axis[0]*sn/norm
e2 = axis[1]*sn/norm
e3 = axis[2]*sn/norm
a = zeros((3,3),float)
a[0,0] = e0**2 + e1**2 - e2**2 - e3**2
a[1,0] = 2.*(e1*e2 + e0*e3)
a[2,0] = 2.*(e1*e3 - e0*e2)
a[0,1] = 2.*(e1*e2 - e0*e3)
a[1,1] = e0**2 - e1**2 + e2**2 - e3**2
a[2,1] = 2.*(e2*e3 + e0*e1)
a[0,2] = 2.*(e1*e3 + e0*e2)
a[1,2] = 2.*(e2*e3 - e0*e1)
a[2,2] = e0**2 - e1**2 - e2**2 + e3**2
a = a.astype(float)
# multiply x
x = dot(x,a)
# decenter point
return x+point
def align(x,axis1=[1,0,0],axis2=[0,0,1],point=[0,0,0]):
'''
Rotate the object around point in order to align the axis 'axis1' with the axis 'axis2'.
axis1 : [x,y,z]
axis2 : [x,y,z]
'''
a1 = array(axis1,float)
a2 = array(axis2,float)
a3 = array([0,0,0],float)
a3[0] = a1[1]*a2[2] - a1[2]*a2[1]
a3[1] = a1[2]*a2[0] - a1[0]*a2[2]
a3[2] = a1[0]*a2[1] - a1[1]*a2[0]
n1 = sqrt(a1[0]**2 + a1[1]**2 + a1[2]**2)
n2 = sqrt(a2[0]**2 + a2[1]**2 + a2[2]**2)
angle = arccos(inner(a1,a2)/(n1*n2))
return rotate(x,angle=angle,axis=a3,point=point)
def expose(obj,obs,eye=None,dist_eye=None,foc=None):
"""
Rotate and translate the object in order to be seen as if the
observer was in x0, looking at a point in xp.
obj : object array to expose
obs : representation of the observer
eye : 'right' or 'left'
dist_eye : distance between eyes (separation = angle))
foc : focal
"""
# first : put x0 at the origin
obj = obj - obs[0]
obs = obs - obs[0]
# second : anti-align e1 with z
obj = align(obj,axis1=obs[1],axis2=[0,0,-1])
obs = align(obs,axis1=obs[1],axis2=[0,0,-1])
# third : align e3 with y
obj = align(obj,axis1=obs[3],axis2=[0,1,0])
# fourth if eye is defined
if eye=='right':
if foc!=None:
Robs = foc
else:
Robs = sqrt((obs[0][0]-obs[1][0])**2 + (obs[0][1]-obs[1][1])**2 + (obs[0][2]-obs[1][2])**2)
phi = -arctan(dist_eye)
obj = rotate(obj,-phi,axis=[0,1,0],point=[0,0,-Robs])
elif eye=='left':
if foc!=None:
Robs = foc
else:
Robs = sqrt((obs[0][0]-obs[1][0])**2 + (obs[0][1]-obs[1][1])**2 + (obs[0][2]-obs[1][2])**2)
phi = -arctan(dist_eye)
obj = rotate(obj,+phi,axis=[0,1,0],point=[0,0,-Robs])
return obj
def perspective(r_obs=100.,foc=50.,view='xz'):
'''
Project the N-body model in order to get a perspective view.
r_obs = distance of the observer to the looking point
foc = focal
view = 'xz' , 'xy' , 'yz'
'''
from Nbody.nbodymodule import perspective as perspec
if view=='xz':
view=1
elif view=='xy':
view=2
elif view=='yz':
view=3
elif view!='xz'and view!='xy'and view!='yz':
view=1
return perspec(pos,r_obs,foc,view)
def frustum(pos,clip,size):
'''
Project using a frustrum matrix
clip = near and far planes
size = size of the box
'''
tmp = ones((pos.shape[0],pos.shape[1]+1),float)
tmp[:,:-1] = pos
pos = tmp
n = float(clip[0])
f = float(clip[1])
l = -float(size[0])
r = float(size[0])
b = -float(size[1])
t = float(size[1])
# frustum
m1 = zeros((4,4),float)
m1[0,0] = 2.*n/(r-l)
m1[1,0] = 0.
m1[2,0] = (r+l)/(r-l)
m1[3,0] = 0.
m1[0,1] = 0.
m1[1,1] = 2.*n/(t-b)
m1[2,1] = (t+b)/(t-b)
m1[3,1] = 0.
m1[0,2] = 0.
m1[1,2] = 0.
m1[2,2] = -(f+n)/(f-n)
m1[3,2] = -(2.*f*n)/(f-n)
m1[0,3] = 0.
m1[1,3] = 0.
m1[2,3] = -1
m1[3,3] = 0.
m1 = m1.astype(float)
posc = dot(pos,m1)
posc = transpose(transpose(posc)/posc[:,3])[:,:-1]
return posc
def ortho(pos,clip,size):
'''
Project using an ortho matrix
clip = near and far planes
size = size of the box
'''
tmp = ones((pos.shape[0],pos.shape[1]+1),float)
tmp[:,:-1] = pos
pos = tmp
n = float(clip[0])
f = float(clip[1])
l = -float(size[0])
r = float(size[0])
b = -float(size[1])
t = float(size[1])
# ortho
m1 = zeros((4,4),float)
m1[0,0] = 2./(r-l)
m1[1,0] = 0.
m1[2,0] = 0.
m1[3,0] = -(r+l)/(r-l)
m1[0,1] = 0.
m1[1,1] = 2./(t-b)
m1[2,1] = 0
m1[3,1] = -(t+b)/(t-b)
m1[0,2] = 0.
m1[1,2] = 0.
m1[2,2] = -2./(f-n)
m1[3,2] = -(f+n)/(f-n)
m1[0,3] = 0.
m1[1,3] = 0.
m1[2,3] = 0.
m1[3,3] = 1.
m1 = m1.astype(float)
posc = dot(pos,m1)
posc = transpose(transpose(posc)/posc[:,3])[:,:-1]
return posc
def viewport(xn,shape=None):
'''
viewport transformation
xn = position (output from frustum or ortho)
shape = shape of the image
'''
x = xn[:,0]
y = xn[:,1]
z = xn[:,2]
if shape==None:
wx = 1
wy = 1
else:
wx = shape[0]
wy = shape[1]
winx = (x+1)/2. * wx
winy = -(y-1)/2. * wy
winz = (z+1)/2.
return transpose(array([winx,winy,winz]))
def inv_viewport(xw,yw,zw,shape):
'''
viewport transformation
xn = position (output from frustum or ortho)
shape = shape of the image
'''
wx = shape[0]
wy = shape[1]
x = 2.*xw/wx - 1
y = -2.*yw/wy + 1
z = 2.*zw-1
return x,y,z
def boxcut(pos,args):
'''
Return only particles that are inside box 1:1:1
'''
c = logical_not((fabs(pos[:,0])>1) | (fabs(pos[:,1])>1) | (fabs(pos[:,2])>1))
pos = compress(c,pos,axis=0)
newargs = ()
for arg in args:
newargs = newargs + (compress(c,arg,axis=0),)
return pos,newargs
def boxcut_segments(pos,args):
'''
Return only particles that are inside box 1:1:1
'''
n = len(pos)
p = int(n/2)
newpos = zeros(pos.shape)
cs = zeros(len(pos))
np = 0
for j in xrange(p):
i = 2*j
f0=False
f1=False
if (fabs(pos[i ,0]) > 1) or (fabs(pos[i ,1]) > 1) or (fabs(pos[i ,2]) > 1):
f0=True
if (fabs(pos[i+1,0]) > 1) or (fabs(pos[i+1,1]) > 1) or (fabs(pos[i+1,2]) > 1):
f1=True
if f0 and f1:
# both outside : remove the segment
#print "remove"
pass
elif f0 and not f1:
# 0 outside 1 inside : change 0
#print "change 0"
newpos[i] = pos[i]
newpos[i+1] = pos[i+1]
cs[i] = 0 # remove
cs[i+1] = 0
np+=2
elif not f0 and f1:
# 0 inside 1 outside : change 1
#print "change 1"
newpos[i] = pos[i]
newpos[i+1] = pos[i+1]
cs[i] = 0 # remove
cs[i+1] = 0
np+=2
else:
# both inside : keep
newpos[i] = pos[i]
newpos[i+1] = pos[i+1]
cs[i] = 1
cs[i+1] = 1
np+=2
pos = compress(cs,newpos,axis=0)
newargs = ()
for arg in args:
newargs = newargs + (compress(cs,arg,axis=0),)
return pos,newargs
def get_obs(x0=[0.,-50.,0.],xp=[0.,0.,0.],alpha=0,view='xz',r_obs=50):
'''
From some parameters, return an obs matrix
x0,xp,alpha
or
xz
'''
# use view and r_obs
if (x0==None or xp==None or alpha==None) and (view!=None and r_obs != None):
if view=='xz':
e0 = array([ 0,-r_obs,0],float)
e1 = array([ 0, 0,0],float)
e2 = array([-1,-r_obs,0],float)
e3 = array([ 0,-r_obs,1],float)
elif view=='xy':
e0 = array([ 0, 0,r_obs],float)
e1 = array([ 0, 0, 0],float)
e2 = array([-1, 0,r_obs],float)
e3 = array([ 0, 1,r_obs],float)
elif view=='yz':
e0 = array([r_obs, 0,0],float)
e1 = array([ 0, 0,0],float)
e2 = array([r_obs,-1,0],float)
e3 = array([r_obs, 0,1],float)
else:
e0 = array([ 0,-r_obs,0],float)
e1 = array([ 0, 0,0],float)
e2 = array([-1,-r_obs,0],float)
e3 = array([ 0,-r_obs,1],float)
# create the matrix
obs = array([e0,e1,e2,e3],float)
# center xp
if xp!= None:
obs = obs + xp
# use x0,xp,alpha
else:
x0 = array(x0,float)
xp = array(xp,float)
Robs = sqrt((x0[0]-xp[0])**2 + (x0[1]-xp[1])**2 + (x0[2]-xp[2])**2)
e0 = array([0,0,0],float)
e1 = array([Robs,0,0],float)
e2 = array([0,1,0],float)
e3 = array([0,0,1],float)
# create the matrix
obs = array([e0,e1,e2,e3],float)
#####################
yp = xp-x0
rxy = sqrt(yp[0]**2+yp[1]**2)
z = yp[2]
a = arctan2(yp[1],yp[0])
if rxy!=0:
b = arctan(z/rxy)
else:
b = 0.
# rotate azimuth
obs = rotate(obs,angle=a,axis=[0,0,1])
# rotate elevation
obs = rotate(obs,angle=-b,axis=obs[2])
# rotate (xa around e1)
obs = rotate(obs,angle=alpha,axis=obs[1])
# translate to x0
obs = obs + x0
'''
# old version (bad)
# create the matrix
obs = array([e0,e1,e2,e3],float)
# rotate (align e1 with xp-x0 )
obs = align(obs,axis1=obs[1],axis2=xp-x0)
# rotate (xa around e1)
obs = rotate(obs,angle=alpha,axis=obs[1])
# translate to x0
obs = obs + x0
'''
# !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
# !!! e2 may not be parallel to the plane z=0 !!!
# !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
return obs
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