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raytrace.py
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raytrace.py
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"""
This file is part of LightRayRider, a fast column density computation tool.
Author: Johannes Buchner (C) 2013-2017
License: AGPLv3
See README and LICENSE file.
"""
from __future__ import print_function, division
import numpy
from ctypes import *
from numpy.ctypeslib import ndpointer
import os
if int(os.environ.get('OMP_NUM_THREADS', '1')) > 1:
lib = cdll.LoadLibrary(os.path.join(os.path.dirname(__file__), './ray-parallel.so'))
print("""
You are using the LightRayRider library, which provides optimized calls for
photon propagation and column density computations.
Please cite: Buchner & Bauer (2017), http://adsabs.harvard.edu/abs/2017MNRAS.465.4348B
Parallelisation enabled.
""")
else:
lib = cdll.LoadLibrary(os.path.join(os.path.dirname(__file__), './ray.so'))
print("""
You are using the LightRayRider library, which provides optimized calls for
photon propagation and column density computations.
Please cite: Buchner & Bauer (2017), http://adsabs.harvard.edu/abs/2017MNRAS.465.4348B
Parallelisation disabled (use OMP_NUM_THREADS to enable).
""")
lib.sphere_raytrace.argtypes = [
ndpointer(dtype=numpy.float64, ndim=1, flags='C_CONTIGUOUS'),
ndpointer(dtype=numpy.float64, ndim=1, flags='C_CONTIGUOUS'),
ndpointer(dtype=numpy.float64, ndim=1, flags='C_CONTIGUOUS'),
ndpointer(dtype=numpy.float64, ndim=1, flags='C_CONTIGUOUS'),
ndpointer(dtype=numpy.float64, ndim=1, flags='C_CONTIGUOUS'),
c_int,
ndpointer(dtype=numpy.float64, ndim=1, flags='C_CONTIGUOUS'),
ndpointer(dtype=numpy.float64, ndim=1, flags='C_CONTIGUOUS'),
ndpointer(dtype=numpy.float64, ndim=1, flags='C_CONTIGUOUS'),
c_int,
ndpointer(dtype=numpy.float64, ndim=1, flags='C_CONTIGUOUS'),
c_int,
ndpointer(dtype=numpy.float64, ndim=1, flags='C_CONTIGUOUS'),
]
def sphere_raytrace(xx, yy, zz, RR, rho, a, b, c, mindistances):
"""
ray tracing using sphere intersections.
Parameters regarding the spheres:
xx: double array: coordinates
yy: double array: coordinates
zz: double array: coordinates
RR: double array: sphere radius
rho: double array: density for conversion from length to column density
* n: length of xx, yy, zz, RR
a: double array: direction vector
b: double array: direction vector
c: double array: direction vector
* m: length of a, b, c
mindistances double array: only consider intersections beyond these values
* int l length of mindistances
NHout double array: output; of size n * l
"""
NHout = numpy.zeros(shape=(len(a)*len(mindistances))) - 1
lenxx = len(xx)
lena = len(a)
lenmd = len(mindistances)
r = lib.sphere_raytrace(xx, yy, zz, RR, rho, lenxx, a, b, c, lena, mindistances, lenmd, NHout)
if r != 0:
raise Exception("Calculation failed")
return NHout.reshape((len(mindistances), -1))
lib.sphere_raytrace_count_between.argtypes = [
ndpointer(dtype=numpy.float64, ndim=1, flags='C_CONTIGUOUS'),
ndpointer(dtype=numpy.float64, ndim=1, flags='C_CONTIGUOUS'),
ndpointer(dtype=numpy.float64, ndim=1, flags='C_CONTIGUOUS'),
ndpointer(dtype=numpy.float64, ndim=1, flags='C_CONTIGUOUS'),
c_int,
ndpointer(dtype=numpy.float64, ndim=1, flags='C_CONTIGUOUS'),
ndpointer(dtype=numpy.float64, ndim=1, flags='C_CONTIGUOUS'),
ndpointer(dtype=numpy.float64, ndim=1, flags='C_CONTIGUOUS'),
c_int,
ndpointer(dtype=numpy.float64, ndim=1, flags='C_CONTIGUOUS'),
]
def sphere_raytrace_count_between(xx, yy, zz, RR, rho, a, b, c):
NHout = numpy.zeros(len(a)) - 1
lenxx = len(xx)
lena = len(a)
r = lib.sphere_raytrace_count_between(xx, yy, zz, RR, lenxx, a, b, c, lena, NHout)
if r != 0:
raise Exception("Calculation failed")
return NHout
lib.grid_raytrace.argtypes = [
ndpointer(dtype=numpy.float64, ndim=1, flags='C_CONTIGUOUS'),
c_int,
ndpointer(dtype=numpy.float64, ndim=1, flags='C_CONTIGUOUS'),
ndpointer(dtype=numpy.float64, ndim=1, flags='C_CONTIGUOUS'),
ndpointer(dtype=numpy.float64, ndim=1, flags='C_CONTIGUOUS'),
ndpointer(dtype=numpy.float64, ndim=1, flags='C_CONTIGUOUS'),
ndpointer(dtype=numpy.float64, ndim=1, flags='C_CONTIGUOUS'),
ndpointer(dtype=numpy.float64, ndim=1, flags='C_CONTIGUOUS'),
c_int,
ndpointer(dtype=numpy.float64, ndim=1, flags='C_CONTIGUOUS'),
]
def grid_raytrace_flat(rho_flat, lenrho, x, y, z, a, b, c):
"""
ray tracing on a grid
Parameters regarding the spheres:
rho: double array: density for conversion from length to column density
* n: length of rho
x: double array: start vector
y: double array: start vector
z: double array: start vector
a: double array: direction vector
b: double array: direction vector
c: double array: direction vector
* m: length of a, b, c, x, y, z
NHout double array: output; of size m
"""
lena = len(a)
NHout = numpy.zeros(shape=lena) - 1
r = lib.grid_raytrace(rho_flat, lenrho, x, y, z, a, b, c, lena, NHout)
if r != 0:
raise Exception("Calculation failed")
return NHout
def grid_raytrace(rho, x, y, z, a, b, c):
"""
ray tracing on a grid
Parameters regarding the spheres:
rho: double array: density for conversion from length to column density
* n: length of rho
x: double array: start vector
y: double array: start vector
z: double array: start vector
a: double array: direction vector
b: double array: direction vector
c: double array: direction vector
* m: length of a, b, c, x, y, z
NHout double array: output; of size m
"""
lenrho = len(rho)
rho_flat = numpy.array(rho.flatten())
return grid_raytrace_flat(rho_flat, lenrho, x, y, z, a, b, c)
lib.voronoi_raytrace.argtypes = [
ndpointer(dtype=numpy.float64, ndim=1, flags='C_CONTIGUOUS'),
ndpointer(dtype=numpy.float64, ndim=1, flags='C_CONTIGUOUS'),
ndpointer(dtype=numpy.float64, ndim=1, flags='C_CONTIGUOUS'),
ndpointer(dtype=numpy.float64, ndim=1, flags='C_CONTIGUOUS'),
ndpointer(dtype=numpy.float64, ndim=1, flags='C_CONTIGUOUS'),
c_int,
ndpointer(dtype=numpy.float64, ndim=1, flags='C_CONTIGUOUS'),
ndpointer(dtype=numpy.float64, ndim=1, flags='C_CONTIGUOUS'),
ndpointer(dtype=numpy.float64, ndim=1, flags='C_CONTIGUOUS'),
c_int,
ndpointer(dtype=numpy.float64, ndim=1, flags='C_CONTIGUOUS'),
c_int,
ndpointer(dtype=numpy.float64, ndim=1, flags='C_CONTIGUOUS'),
]
def voronoi_raytrace(xx, yy, zz, RR, rho, a, b, c, mindistances):
"""
ray tracing using nearest point density.
Parameters regarding the points:
xx: double array: coordinates
yy: double array: coordinates
zz: double array: coordinates
RR: double array: sphere radius
rho: double array: density for conversion from length to column density
* n: length of xx, yy, zz, RR
Parameters regarding the integration direction:
a: double array: direction vector
b: double array: direction vector
c: double array: direction vector
* m: length of a, b, c
mindistances double array: only consider intersections beyond these values
* int l length of mindistances
NHout double array: output; of size n * l
"""
NHout = numpy.zeros(shape=(len(a)*len(mindistances))) - 1
lenxx = len(xx)
lena = len(a)
lenmd = len(mindistances)
assert xx.shape == (lenxx,), xx.shape
assert yy.shape == (lenxx,), yy.shape
assert zz.shape == (lenxx,), zz.shape
assert RR.shape == (lenxx,), RR.shape
assert rho.shape == (lenxx,), rho.shape
assert a.shape == (lena,), a.shape
assert b.shape == (lena,), b.shape
assert c.shape == (lena,), c.shape
assert mindistances.shape == (lenmd,), mindistances.shape
assert NHout.shape == (lena*lenmd,), NHout.shape
r = lib.voronoi_raytrace(xx, yy, zz, RR, rho, lenxx, a, b, c, lena, mindistances, lenmd, NHout)
if r != 0:
raise Exception("Interpolation failed")
#for (k = 0; k < l; k++) {
# NHout[i * l + k] = NHtotal[k];
return NHout.reshape((len(mindistances), -1))
#return NHout
lib.sphere_sphere_collisions.argtypes = [
ndpointer(dtype=numpy.float64, ndim=1, flags='C_CONTIGUOUS'),
ndpointer(dtype=numpy.float64, ndim=1, flags='C_CONTIGUOUS'),
ndpointer(dtype=numpy.float64, ndim=1, flags='C_CONTIGUOUS'),
ndpointer(dtype=numpy.float64, ndim=1, flags='C_CONTIGUOUS'),
c_int,
c_int,
ndpointer(dtype=numpy.float64, ndim=1, flags='C_CONTIGUOUS'),
]
def sphere_sphere_collisions(xx, yy, zz, RR, k):
"""
marks the first kstop non-intersecting spheres
Parameters regarding the spheres:
xx: double array: coordinates
yy: double array: coordinates
zz: double array: coordinates
RR: double array: sphere radius
k: int: number of spheres desired
NHout double array: output; same size as xx
"""
lenxx = len(xx)
NHout = numpy.zeros(lenxx) - 1
r = lib.sphere_sphere_collisions(xx, yy, zz, RR, lenxx, k, NHout)
if r != 0:
raise Exception("Calculation failed")
return NHout
lib.sphere_raytrace_finite.argtypes = [
ndpointer(dtype=numpy.float64, ndim=1, flags='C_CONTIGUOUS'),
ndpointer(dtype=numpy.float64, ndim=1, flags='C_CONTIGUOUS'),
ndpointer(dtype=numpy.float64, ndim=1, flags='C_CONTIGUOUS'),
ndpointer(dtype=numpy.float64, ndim=1, flags='C_CONTIGUOUS'),
ndpointer(dtype=numpy.float64, ndim=1, flags='C_CONTIGUOUS'),
c_int,
ndpointer(dtype=numpy.float64, ndim=1, flags='C_CONTIGUOUS'),
ndpointer(dtype=numpy.float64, ndim=1, flags='C_CONTIGUOUS'),
ndpointer(dtype=numpy.float64, ndim=1, flags='C_CONTIGUOUS'),
ndpointer(dtype=numpy.float64, ndim=1, flags='C_CONTIGUOUS'),
ndpointer(dtype=numpy.float64, ndim=1, flags='C_CONTIGUOUS'),
ndpointer(dtype=numpy.float64, ndim=1, flags='C_CONTIGUOUS'),
c_int,
ndpointer(dtype=numpy.float64, ndim=1, flags='C_CONTIGUOUS'),
ndpointer(dtype=numpy.float64, ndim=1, flags='C_CONTIGUOUS'),
]
def sphere_raytrace_finite(xx, yy, zz, RR, rho, x, y, z, a, b, c, NHmax):
"""
ray tracing using sphere intersections.
Parameters regarding the spheres:
xx: double array: coordinates
yy: double array: coordinates
zz: double array: coordinates
RR: double array: sphere radius
rho: double array: density for conversion from length to column density
* n: length of xx, yy, zz, RR, rho
x: double array: position vector
y: double array: position vector
z: double array: position vector
a: double array: direction vector
b: double array: direction vector
c: double array: direction vector
* m: length of a, b, c
NHmax double array: stop at this NH
Returns:
t double array: end position along direction vector. -1 if infinite
"""
lenxx = len(xx)
lena = len(a)
t = numpy.zeros(shape=lena)
assert len(b) == lena
assert len(c) == lena
assert len(x) == lena
assert len(y) == lena
assert len(z) == lena
assert len(yy) == lenxx
assert len(zz) == lenxx
assert len(RR) == lenxx
assert len(rho) == lenxx
r = lib.sphere_raytrace_finite(xx, yy, zz, RR, rho, lenxx, x, y, z, a, b, c, lena, NHmax, t)
if r != 0:
raise Exception("Calculation failed")
return t
lib.cone_raytrace_finite.argtypes = [
ndpointer(dtype=numpy.float64, ndim=1, flags='C_CONTIGUOUS'),
ndpointer(dtype=numpy.float64, ndim=1, flags='C_CONTIGUOUS'),
c_int,
ndpointer(dtype=numpy.float64, ndim=1, flags='C_CONTIGUOUS'),
ndpointer(dtype=numpy.float64, ndim=1, flags='C_CONTIGUOUS'),
ndpointer(dtype=numpy.float64, ndim=1, flags='C_CONTIGUOUS'),
ndpointer(dtype=numpy.float64, ndim=1, flags='C_CONTIGUOUS'),
ndpointer(dtype=numpy.float64, ndim=1, flags='C_CONTIGUOUS'),
ndpointer(dtype=numpy.float64, ndim=1, flags='C_CONTIGUOUS'),
c_int,
ndpointer(dtype=numpy.float64, ndim=1, flags='C_CONTIGUOUS'),
ndpointer(dtype=numpy.float64, ndim=1, flags='C_CONTIGUOUS'),
]
def cone_raytrace_finite(thetas, rhos, x, y, z, a, b, c, d):
"""
* ray tracing through a sphere/cone cuts
*
* Sphere radius is 1, each cone angle defines a region of a certain density.
*
* This function raytraces from the starting coordinates in the direction
* given and compute the column density of the intersecting segments.
* Then it will go along the ray in the positive direction until the
* column density d is reached. The coordinates of that point are stored into
* (x, y, z)
*
* Parameters regarding the cones:
* thetas: double array: cone opening angle
* rhos: double array: density of each cone from length to column density
* n: number of cones
* Parameters regarding the integration direction:
* x: double array: coordinates
* y: double array: coordinates
* z: double array: coordinates
* a: double array: direction vector
* b: double array: direction vector
* c: double array: direction vector
* d: double array: distance to travel
* m: length of (a, b, c) and (x,y,z)
* Output:
* t double array: end position along direction vector. -1 if infinite
"""
n = len(thetas)
assert len(rhos) == n
lena = len(a)
assert len(b) == lena
assert len(c) == lena
assert len(x) == lena
assert len(y) == lena
assert len(z) == lena
assert len(d) == lena
t = numpy.zeros(shape=lena)
r = lib.cone_raytrace_finite(thetas, rhos, n, x, y, z, a, b, c, lena, d, t)
if r != 0:
raise Exception("Calculation failed")
return t
lib.grid_raytrace_finite.argtypes = [
ndpointer(dtype=numpy.float64, ndim=1, flags='C_CONTIGUOUS'),
c_int,
ndpointer(dtype=numpy.float64, ndim=1, flags='C_CONTIGUOUS'),
ndpointer(dtype=numpy.float64, ndim=1, flags='C_CONTIGUOUS'),
ndpointer(dtype=numpy.float64, ndim=1, flags='C_CONTIGUOUS'),
ndpointer(dtype=numpy.float64, ndim=1, flags='C_CONTIGUOUS'),
ndpointer(dtype=numpy.float64, ndim=1, flags='C_CONTIGUOUS'),
ndpointer(dtype=numpy.float64, ndim=1, flags='C_CONTIGUOUS'),
c_int,
ndpointer(dtype=numpy.float64, ndim=1, flags='C_CONTIGUOUS'),
ndpointer(dtype=numpy.float64, ndim=1, flags='C_CONTIGUOUS'),
]
def grid_raytrace_finite_flat(rho_flat, lenrho, x, y, z, a, b, c, d):
"""
ray tracing on a grid
Parameters regarding the spheres:
rho: double array: density for conversion from length to column density
lenrho: length of rho
x: double array: start vector
y: double array: start vector
z: double array: start vector
a: double array: direction vector
b: double array: direction vector
c: double array: direction vector
* m: length of a, b, c, x, y, z
NHmax double array: stop at this NH
Returns:
t double array: end position along direction vector. -1 if infinite
"""
lena = len(a)
assert len(b) == lena
assert len(c) == lena
assert len(x) == lena
assert len(y) == lena
assert len(z) == lena
assert len(d) == lena
t = numpy.zeros(shape=lena)
r = lib.grid_raytrace_finite(rho_flat, lenrho, x, y, z, a, b, c, lena, d, t)
if r != 0:
raise Exception("Calculation failed")
return t
def grid_raytrace_finite(rho, x, y, z, a, b, c, d):
"""
ray tracing on a grid
Parameters regarding the spheres:
rho: double array: density for conversion from length to column density
* n: length of rho
x: double array: start vector
y: double array: start vector
z: double array: start vector
a: double array: direction vector
b: double array: direction vector
c: double array: direction vector
* m: length of a, b, c, x, y, z
NHmax double array: stop at this NH
Returns:
t double array: end position along direction vector. -1 if infinite
"""
lenrho = len(rho)
rho_flat = numpy.array(rho.flatten())
return grid_raytrace_finite_flat(rho_flat, lenrho, x, y, z, a, b, c, d)