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generation_rays.py
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#used only to generate rays from the trd element till the end of the lossless
from ray import Ray
import create_topology as tp
import numpy as np
from scipy import special
import intersection as inters
import reflection_refraction as rf
import intersection as inter
from numpy import linalg as LA
# trd is an object of the Class transducer
# r_1 is the first zero bessel 3.8317
# top is the list of objects of the class Topology
# This Function is called for every trd element -> 256 times for Sonalleve transducer
def generation_rays_lossless(trd, top, Nrays, final_geometry, initial_geometry, index_trd, AA, k_r, index): # r_1 first zero bessel
ptrd_1 = 0
start = ([trd.coord[index_trd, 1], trd.coord[index_trd, 2], trd.coord[index_trd, 3]])
start = np.asanyarray(start)
normal = - start / LA.norm(start)
v2 = ([-normal[2], 0, normal[0]])
v2_norm = v2 / LA.norm(v2)
v3 = np.cross(v2_norm, normal)
v3 = v3 / LA.norm(v3)
r_loss = []
# file_vray = open('vray_cylinder.txt', 'w')
# vray_x, vray_y, vray_z = np.genfromtxt('vray_cylinder.txt', unpack=True)
for j in range(0, Nrays):
rd = np.random.random_sample()
# rd = 0.07
theta = np.arccos(1 - AA*rd)
phi = 2 * np.pi * np.random.random_sample()
# phi = 2 * np.pi * 0.06
vray = normal + np.tan(theta)*(np.cos(phi)*v2_norm + np.sin(phi)*v3)
# vray = np.asarray([vray_x[j], vray_y[j], vray_z[j]])
# vray_trd = np.real(vray)
# vray_trd = vray_trd.tolist()
# vray_trd = ' '.join(str(e) for e in vray_trd)
# file_vray.write(vray_trd + '\n')
B = k_r * np.sin(theta)
if B == 0:
scaling = 1
else:
scaling = (2 * special.j1(B) / B)**2
I0 = scaling
ptrd_1 = ptrd_1 + I0
next_obj, end, nn, lambda_int, stop_ray = inter.intersection(start, vray, top,
index,
final_geometry,
initial_geometry)
path = []
path.append(index)
phi_initial = 0
phase_shift = 0
real_dist = np.dot((end - start), nn)/np.dot(vray, nn)
phi_final = phi_initial + top[index].material.k * lambda_int
r = Ray(start, end, vray, path, I0, phi_initial, phi_final, phase_shift,
0, index, next_obj, nn, I0)
r_loss.append(r)
# file_vray.close()
return r_loss, ptrd_1
def Generation_ray(top, ray, final_geometry, initial_geometry):
son = []
I_limit = 0.0001
control = ray
while len(control) != 0:
processing = control
control = []
for o in range(0, len(processing)):
# NEXT MATERIAL IS SOFT?
if top[processing[o].next_obj].material.type == 'liquid': # next material is soft
# ACTUAL MATERIAL IS SOFT?
if top[processing[o].obj_index].material.type == 'liquid': # actual material soft SOFT->SOFT
nn = processing[o].nn
refr, v_out = rf.refraction0(processing[o].vray, nn, top[processing[o].obj_index].material.c * 0.01, top[processing[o].next_obj].material.c * 0.01)
if top[processing[o].obj_index].material.name == 'lossless': # ray is in lossless
T = 1
R = 0
Ph_refl = 0
Ph_tr = 0
else:
T, R, Ph_refl, Ph_tr = rf.coefficient_ll(processing[o].vray, nn,
top[processing[o].obj_index].material.c * 1e-2,
top[processing[o].next_obj].material.c * 1e-2,
top[processing[o].obj_index].material.rho * 1e6,
top[processing[o].next_obj].material.rho * 1e6)
#refraction In soft tissue
if processing[o].IF > I_limit:
if refr == True and top[processing[o].next_obj].material.name != 'lossless': # I have refraction
start = processing[o].end
I0 = processing[o].IF * T
vray = v_out / LA.norm(v_out)
next_obj, end, possible_nn, lambda_int, stop_ray = inter.intersection(start, vray, top,
processing[o].next_obj,
final_geometry,
initial_geometry)
# if np.abs(next_obj - processing[o].next_obj) == 2:
# # processing[o].next_obj = int(np.abs((next_obj + processing[o].next_obj)) / 2)
# print("Buggy1.1\n")
# stop_ray = True
# elif next_obj == processing[o].next_obj and not isinstance(possible_nn, str):
# # processing[o].next_obj += 1
# print("Buggy1.2\n")
# stop_ray = True
# elif processing[o].next_obj == 2 and isinstance(possible_nn, str):
# # processing[o].next_obj = 1
# print("Buggy1.3\n")
# stop_ray = True
# elif (end[0] == -8 or end[0] == 2) and processing[o].next_obj == 2:
# print("Buggy1.4\n")
# stop_ray = True
# else:
# stop_ray = False
if stop_ray is False:
if isinstance(possible_nn, str): # if possible nn is a string and not a vector
IF = 0
else:
IF = I0 * np.exp(-2 * top[processing[o].next_obj].material.alpha * lambda_int)
lst = []
lst.append(processing[o].next_obj)
path = processing[o].path + lst
phi_initial = processing[o].phase_final + Ph_tr
phi_final = phi_initial + top[processing[o].next_obj].material.k * lambda_int
phase_shift = processing[o].phase_shift + Ph_tr
sn = Ray(start, end, vray, path, I0, phi_initial, phi_final, phase_shift, 0, processing[o].next_obj, next_obj, possible_nn, IF, 0, False)
son.append(sn)
if IF > I_limit:
control.append(sn)
if R != 0 and top[processing[o].next_obj].material.name != 'lossless':
if processing[o].IF > I_limit:
v_out = rf.reflection(processing[o].vray, nn)
vray = v_out / LA.norm(v_out)
start = processing[o].end
I0 = processing[o].IF * R
next_obj, end, possible_nn, lambda_int, stop_ray = inter.intersection(start, vray, top,
processing[o].obj_index,
final_geometry,
initial_geometry)
# if np.abs(next_obj - processing[o].obj_index) == 2:
# # processing[o].obj_index = int(np.abs((next_obj + processing[o].obj_index)) / 2)
# print("Buggy2.1\n")
# stop_ray = True
# elif next_obj == processing[o].obj_index and not isinstance(possible_nn, str):
# # processing[o].obj_index += 1
# print("Buggy2.2\n")
# stop_ray = True
# elif processing[o].obj_index == 2 and isinstance(possible_nn, str):
# # processing[o].obj_index = 1
# print("Buggy2.3\n")
# stop_ray = True
# elif (end[0] == -8 or end[0] == -1) and processing[o].obj_index == 2:
# print("Buggy2.4\n")
# stop_ray = True
# else:
# stop_ray = False
if stop_ray is False:
if isinstance(possible_nn, str): # if possible nn is a string and not a vector
IF = 0
else:
IF = I0 * np.exp(-2 * top[processing[o].obj_index].material.alpha * lambda_int)
lst = []
lst.append(processing[o].obj_index)
path = (processing[o].path) + lst
phi_initial = processing[o].phase_final + Ph_refl
phi_final = phi_initial + top[processing[o].obj_index].material.k * lambda_int
phase_shift = processing[o].phase_shift + Ph_refl
sn = Ray(start, end, vray, path, I0, phi_initial, phi_final, phase_shift,
0, processing[o].obj_index, next_obj, possible_nn, IF,0, False)
son.append(sn)
if IF > I_limit:
control.append(sn)
# ACTUAL MATERIAL IS NOT SOFT! RAY IS IN BONE!!
else:
#print('coming here?')
#print('actual material is not soft???')
#print(processing[o].end)
#print(processing[o].start)
#print(processing[o].nn)
nn = processing[o].nn
alpha_in = np.arccos(np.abs(np.dot(nn, processing[o].vray)))
rho_liquid = top[processing[o].next_obj].material.rho * 1e6
rho_solid = top[processing[o].obj_index].material.rho * 1e6
c_long_liquid = top[processing[o].next_obj].material.c * 1e-2
c_long_solid = top[processing[o].obj_index].material.cL * 1e-2
c_shear_solid = top[processing[o].obj_index].material.cS * 1e-2
# IT's a LONGITUDINAL RAY: REFL LONG - REFL SHEAR -REFRACT LONG
if processing[o].shear == False: # IT's a LONGITUDINAL RAY: REFL LONG - REFL SHEAR -REFRACT LONG
Refl_long, Refl_shear, Transm_long = rf.B2MCoef_long(alpha_in, rho_liquid,
rho_solid, c_long_liquid,
c_long_solid, c_shear_solid)
intens_long_reflect = processing[o].IF * Refl_long
intens_shear_reflec = processing[o].IF * Refl_shear
intens_long_refract = processing[o].IF * Transm_long
#REFLECTED LONG RAY
if intens_long_reflect > I_limit:
v_out = rf.reflection(processing[o].vray, nn)
vray = v_out / LA.norm(v_out)
start = processing[o].end
next_obj, end, possible_nn, lambda_int, stop_ray = inter.intersection(start, vray, top,
processing[o].obj_index,
final_geometry,
initial_geometry)
# if np.abs(next_obj - processing[o].obj_index) == 2:
# # processing[o].obj_index = int(np.abs((next_obj + processing[o].obj_index)) / 2)
# print("Buggy3.1\n")
# stop_ray = True
# elif next_obj == processing[o].obj_index and not isinstance(possible_nn, str):
# # processing[o].obj_index += 1
# print("Buggy3.2\n")
# stop_ray = True
# elif processing[o].obj_index == 2 and isinstance(possible_nn, str):
# # processing[o].obj_index = 1
# print("Buggy3.3\n")
# stop_ray = True
# elif (end[0] == -8 or end[0] == 2) and processing[o].obj_index == 2:
# print("Buggy3.4\n")
# stop_ray = True
# else:
# stop_ray = False
if stop_ray is False:
IF = intens_long_reflect * np.exp(-2 * top[processing[o].obj_index].material.alphaL * lambda_int)
lst = []
lst.append(processing[o].obj_index)
path = processing[o].path + lst
Ph_refl_long = 0 # to change!!!! Maybe there's a phase shift
phi_initial = processing[o].phase_final + Ph_refl_long
phi_final = phi_initial + top[processing[o].obj_index].material.kL * lambda_int
phase_shift = processing[o].phase_shift + Ph_refl_long
sn = Ray(start, end, vray, path, intens_long_reflect, phi_initial, phi_final, phase_shift,
0, processing[o].obj_index, next_obj, possible_nn, IF, 0, False)
son.append(sn)
if IF > I_limit:
control.append(sn)
# REFLECTED SHEAR
if intens_shear_reflec > I_limit:
refl, v_out, poldir = rf.reflection2(processing[o].vray, nn, c_long_solid, c_long_liquid)
vray = v_out / LA.norm(v_out)
start = processing[o].end
next_obj, end, possible_nn, lambda_int, stop_ray = inter.intersection(start, vray, top,
processing[o].obj_index,
final_geometry,
initial_geometry)
# if np.abs(next_obj - processing[o].obj_index) == 2:
# # processing[o].obj_index = int(np.abs((next_obj + processing[o].obj_index)) / 2)
# print("Buggy4.1\n")
# stop_ray = True
# elif next_obj == processing[o].obj_index and not isinstance(possible_nn, str):
# # processing[o].obj_index += 1
# print("Buggy4.2\n")
# stop_ray = True
# elif processing[o].obj_index == 2 and isinstance(possible_nn, str):
# # processing[o].obj_index = 1
# print("Buggy4.3\n")
# stop_ray = True
# elif (end[0] == -8 or end[0] == 2) and processing[o].obj_index == 2:
# print("Buggy4.4\n")
# stop_ray = True
# else:
# stop_ray = False
if stop_ray is False:
IF = intens_long_reflect * np.exp(-2 * top[processing[o].obj_index].material.alphaS * lambda_int)
lst = []
lst.append(processing[o].obj_index)
path = (processing[o].path) + lst
Ph_refl_shear = 0 # to change!!!! Maybe there's a phase shift
phi_initial = processing[o].phase_final + Ph_refl_shear
phi_final = phi_initial + top[processing[o].obj_index].material.kS * lambda_int
phase_shift = processing[o].phase_shift + Ph_refl_shear
sn = Ray(start, end, vray, path, intens_long_reflect, phi_initial, phi_final, phase_shift,
0, processing[o].obj_index, next_obj, possible_nn, IF, poldir, True)
son.append(sn)
if IF > I_limit:
control.append(sn)
# REFRACTED LONGITUDINAL
if intens_long_refract > I_limit:
refr, v_out, useless = rf.refraction(processing[o].vray, nn, c_long_solid, c_long_liquid)
if refr == True: # I have refraction
start = processing[o].end
vray = v_out / LA.norm(v_out)
next_obj, end, possible_nn, lambda_int, stop_ray = inter.intersection(start, vray, top,
processing[o].next_obj,
final_geometry,
initial_geometry)
# if np.abs(next_obj - processing[o].next_obj) == 2:
# # processing[o].next_obj = int(np.abs((next_obj + processing[o].next_obj)) / 2)
# print("Buggy5.1\n")
# stop_ray = True
# elif next_obj == processing[o].next_obj and not isinstance(possible_nn, str):
# # processing[o].next_obj += 1
# print("Buggy5.2\n")
# stop_ray = True
# elif processing[o].next_obj == 2 and isinstance(possible_nn, str):
# # processing[o].next_obj = 1
# print("Buggy5.3\n")
# stop_ray = True
# elif (end[0] == -8 or end[0] == 2) and processing[o].next_obj == 2:
# print("Buggy5.4\n")
# stop_ray = True
# else:
# stop_ray = False
if stop_ray is False:
if isinstance(possible_nn, str): # if possible_nn is a string and not a vector
IF = 0
else:
IF = intens_long_refract * np.exp(-2 * top[processing[o].next_obj].material.alpha * lambda_int)
lst = []
lst.append(processing[o].next_obj)
path = (processing[o].path) + lst
Ph_tr_shift = 0 #TO CHANGE!!! CAN BE DIFFERENT
phi_initial = processing[o].phase_final + Ph_tr_shift
phi_final = phi_initial + top[processing[o].next_obj].material.k * lambda_int
phase_shift = processing[o].phase_shift + Ph_tr_shift
sn = Ray(start, end, vray, path, intens_long_refract, phi_initial, phi_final, phase_shift, 0,
processing[o].next_obj, next_obj, possible_nn, IF, 0, False)
son.append(sn)
if IF > I_limit:
control.append(sn)
else: # it's a shear wave. Shear: reflected shear horiz pol, reflected shear vert pol, reflected long, refracted long
v_out, vpol_dir_in, vpol_dir_refl, hpol_dir = rf.reflection3(processing[o].vray, nn)
pol_dir_in = processing[o].poldir
cosvert = np.dot(pol_dir_in, vpol_dir_in)
coshor = np.dot(pol_dir_in, hpol_dir)
intensity_horcomp = processing[o].IF * coshor ** 2
intensity_vertcomp = processing[o].IF * cosvert ** 2
# SHEAR HORIZONATAL REFLECTED
if intensity_horcomp > I_limit: # SHEAR HORIZONATAL REFLECTED
vray = v_out / LA.norm(v_out)
start = processing[o].end
next_obj, end, possible_nn, lambda_int, stop_ray = inter.intersection(start, vray, top,
processing[o].obj_index,
final_geometry,
initial_geometry)
# if np.abs(next_obj - processing[o].obj_index) == 2:
# # processing[o].obj_index = int(np.abs((next_obj + processing[o].obj_index)) / 2)
# print("Buggy6.1\n")
# stop_ray = True
# elif next_obj == processing[o].obj_index and not isinstance(possible_nn, str):
# # processing[o].obj_index += 1
# print("Buggy6.2\n")
# stop_ray = True
# elif processing[o].obj_index == 2 and isinstance(possible_nn, str):
# # processing[o].obj_index = 1
# print("Buggy6.3\n")
# stop_ray = True
# elif (end[0] == -8 or end[0] == 2) and processing[o].obj_index == 2:
# print("Buggy6.4\n")
# stop_ray = True
# else:
# stop_ray = False
if stop_ray is False:
IF = intensity_horcomp * np.exp(
-2 * top[processing[o].obj_index].material.alphaS * lambda_int)
lst = []
lst.append(processing[o].obj_index)
path = (processing[o].path) + lst
Ph_refl_shear = 0 # to change!!!! Maybe there's a phase shift
phi_initial = processing[o].phase_final + Ph_refl_shear
phi_final = phi_initial + top[processing[o].obj_index].material.kS * lambda_int
phase_shift = processing[o].phase_shift + Ph_refl_shear
sn = Ray(start, end, vray, path, intensity_horcomp, phi_initial, phi_final, phase_shift,
0, processing[o].obj_index, next_obj, possible_nn, IF, hpol_dir, True)
son.append(sn)
if IF > I_limit:
control.append(sn)
Refl_long, Refl_shear, Transm_long = rf.B2MCoef_shear(alpha_in, rho_liquid,
rho_solid, c_long_liquid,
c_long_solid,
c_shear_solid)
intensity_vert_shear_reflected = Refl_shear * intensity_vertcomp
# SHEAR VERTICAL REFLECTED
if intensity_vert_shear_reflected > I_limit: # SHEAR VERTICAL REFLECTED
vray = v_out / LA.norm(v_out)
start = processing[o].end
next_obj, end, possible_nn, lambda_int, stop_ray = inter.intersection(start, vray, top,
processing[o].obj_index,
final_geometry,
initial_geometry)
# if np.abs(next_obj - processing[o].obj_index) == 2:
# # processing[o].obj_index = int(np.abs((next_obj + processing[o].obj_index)) / 2)
# print("Buggy7.1\n")
# stop_ray = True
# elif next_obj == processing[o].obj_index and not isinstance(possible_nn, str):
# # processing[o].obj_index += 1
# print("Buggy7.2\n")
# stop_ray = True
# elif processing[o].obj_index == 2 and isinstance(possible_nn, str):
# # processing[o].obj_index = 1
# print("Buggy7.3\n")
# stop_ray = True
# elif (end[0] == -8 or end[0] == 2) and processing[o].obj_index == 2:
# print("Buggy7.4\n")
# stop_ray = True
# else:
# stop_ray = False
if stop_ray is False:
IF = intensity_vert_shear_reflected * np.exp(
-2 * top[processing[o].obj_index].material.alphaS * lambda_int)
lst = []
lst.append(processing[o].obj_index)
path = (processing[o].path) + lst
Ph_refl_shear = 0 # to change!!!! Maybe there's a phase shift
phi_initial = processing[o].phase_final + Ph_refl_shear
phi_final = phi_initial + top[processing[o].obj_index].material.kS * lambda_int
phase_shift = processing[o].phase_shift + Ph_refl_shear
sn = Ray(start, end, vray, path, intensity_horcomp, phi_initial, phi_final, phase_shift,
0, processing[o].obj_index, next_obj, possible_nn, IF, vpol_dir_refl, True)
son.append(sn)
if IF > I_limit:
control.append(sn)
#print(processing[o].start)
# longitudinal REFLECTED
longrefl_possible, v_out, poldir = rf.reflection2(processing[o].vray, nn, c_shear_solid,
c_long_solid)
intensity_longit_reflected = Refl_long * intensity_vertcomp
if longrefl_possible == 1 and intensity_longit_reflected > I_limit:
v_out = rf.reflection(processing[o].vray, nn)
vray = v_out / LA.norm(v_out)
start = processing[o].end
next_obj, end, possible_nn, lambda_int, stop_ray = inter.intersection(start, vray, top,
processing[o].obj_index,
final_geometry,
initial_geometry)
# if np.abs(next_obj - processing[o].obj_index) == 2:
# # processing[o].obj_index = int(np.abs((next_obj + processing[o].obj_index)) / 2)
# print("Buggy8.1\n")
# stop_ray = True
# elif next_obj == processing[o].obj_index and not isinstance(possible_nn, str):
# # processing[o].obj_index += 1
# print("Buggy8.2\n")
# stop_ray = True
# elif processing[o].obj_index == 2 and isinstance(possible_nn, str):
# # processing[o].obj_index = 1
# print("Buggy8.3\n")
# stop_ray = True
# elif (end[0] == -8 or end[0] == 2) and processing[o].obj_index == 2:
# print("Buggy8.4\n")
# stop_ray = True
# else:
# stop_ray = False
if stop_ray is False:
if isinstance(possible_nn, str): # if possible nn is a string and not a vector
IF = 0
else:
IF = intensity_longit_reflected * np.exp(
-2 * top[processing[o].obj_index].material.alphaL * lambda_int)
lst = []
lst.append(processing[o].obj_index)
path = processing[o].path + lst
Ph_refl_long = 0 # to change!!!! Maybe there's a phase shift
phi_initial = processing[o].phase_final + Ph_refl_long
phi_final = phi_initial + top[processing[o].obj_index].material.kL * lambda_int
phase_shift = processing[o].phase_shift + Ph_refl_long
sn = Ray(start, end, vray, path, intensity_longit_reflected, phi_initial, phi_final, phase_shift,
0, processing[o].obj_index, next_obj, possible_nn, IF, 0, False)
son.append(sn)
if IF > I_limit:
control.append(sn)
# LONGITUDINAL REFRACTED
refr, v_out, poldir = rf.refraction(processing[o].vray, nn, c_shear_solid, c_long_liquid)
intensity_longit_refracted = Transm_long * intensity_vertcomp
if intensity_longit_refracted > I_limit and refr ==1:
start = processing[o].end
vray = v_out / LA.norm(v_out)
next_obj, end, possible_nn, lambda_int, stop_ray = inter.intersection(start, vray, top,
processing[o].next_obj,
final_geometry,
initial_geometry)
# if np.abs(next_obj - processing[o].next_obj) == 2:
# # processing[o].next_obj = int(np.abs((next_obj + processing[o].next_obj)) / 2)
# print("Buggy9.1\n")
# stop_ray = True
# elif next_obj == processing[o].next_obj and not isinstance(possible_nn, str):
# # processing[o].next_obj += 1
# print("Buggy9.2\n")
# stop_ray = True
# elif processing[o].next_obj == 2 and isinstance(possible_nn, str):
# # processing[o].next_obj = 1
# print("Buggy9.3\n")
# stop_ray = True
# elif (end[0] == -8 or end[0] == 2) and processing[o].next_obj == 2:
# print("Buggy9.4\n")
# stop_ray = True
# else:
# stop_ray = False
if stop_ray is False:
if isinstance(possible_nn, str): # if possible nn is a string and not a vector
IF = 0
else:
IF = intensity_longit_refracted * np.exp(
-2 * top[processing[o].next_obj].material.alpha * lambda_int)
lst = []
lst.append(processing[o].next_obj)
path = (processing[o].path) + lst
Ph_tr_shift = 0 # TO CHANGE!!! CAN BE DIFFERENT
phi_initial = processing[o].phase_final + Ph_tr_shift
phi_final = phi_initial + top[processing[o].next_obj].material.k * lambda_int
phase_shift = processing[o].phase_shift + Ph_tr_shift
sn = Ray(start, end, vray, path, intensity_longit_refracted, phi_initial, phi_final, phase_shift, 0,
processing[o].next_obj, next_obj, possible_nn, IF, 0, False)
son.append(sn)
if IF > I_limit:
control.append(sn)
# SOFT -> BONE
else:
# NEXT MATERIAL IS BONE
nn = processing[o].nn
alpha_in = np.arccos(np.abs(np.dot(nn,processing[o].vray)))
rho_liquid = top[processing[o].obj_index].material.rho * 1e6
rho_solid = top[processing[o].next_obj].material.rho * 1e6
c_long_liquid = top[processing[o].obj_index].material.c * 1e-2
c_long_solid = top[processing[o].next_obj].material.cL * 1e-2
c_shear_solid = top[processing[o].next_obj].material.cS * 1e-2
Refl, Transm_long, Transm_shear, Ph_refl, Ph_tr_long, Ph_tr_shear = rf.M2BCoef(alpha_in,
rho_liquid, rho_solid,
c_long_liquid,
c_long_solid,
c_shear_solid)
# REFLECTED RAY IN SOFT
intens_long_refl = processing[o].IF * Refl
if intens_long_refl > I_limit:
v_out = rf.reflection(processing[o].vray, nn)
vray = v_out / LA.norm(v_out)
start = processing[o].end
next_obj, end, possible_nn, lambda_int, stop_ray = inter.intersection(start, vray, top,
processing[o].obj_index,
final_geometry,
initial_geometry)
# if np.abs(next_obj - processing[o].obj_index) == 2:
# # processing[o].obj_index = int(np.abs((next_obj + processing[o].obj_index)) / 2)
# print("Buggy10.1\n")
# stop_ray = True
# elif next_obj == processing[o].obj_index and not isinstance(possible_nn, str):
# # processing[o].obj_index += 1
# print("Buggy10.2\n")
# stop_ray = True
# elif processing[o].obj_index == 2 and isinstance(possible_nn, str):
# # processing[o].obj_index = 1
# print("Buggy10.3\n")
# stop_ray = True
# elif (end[0] == -8 or end[0] == 2) and processing[o].obj_index == 2:
# print("Buggy10.4\n")
# stop_ray = True
# else:
# stop_ray = False
if stop_ray is False:
if isinstance(possible_nn, str): # if possible nn is a string and not a vector
IF = 0
else:
IF = intens_long_refl * np.exp(-2 * top[processing[o].obj_index].material.alpha * lambda_int)
lst = []
lst.append(processing[o].obj_index)
path = (processing[o].path) + lst
phi_initial = processing[o].phase_final + Ph_refl
phi_final = phi_initial + top[processing[o].obj_index].material.k * lambda_int
sn = Ray(start, end, vray, path, intens_long_refl, phi_initial, phi_final, Ph_refl, 0, processing[o].obj_index,
next_obj, possible_nn, IF,0, False)
son.append(sn)
if IF > I_limit:
control.append(sn)
# REFRACTED LONGITUDINAL RAY IN BONE
longrefrac_possible, v_out, pp = rf.refraction(processing[o].vray, nn, c_long_liquid, c_long_solid)
intens_long_refrac = processing[o].IF * Transm_long
if longrefrac_possible == True and intens_long_refrac > I_limit:
start = processing[o].end
I0 = intens_long_refrac
vray = v_out / LA.norm(v_out)
next_obj, end, possible_nn, lambda_int, stop_ray = inter.intersection(start, vray, top,
processing[o].next_obj,
final_geometry,
initial_geometry)
# if np.abs(next_obj - processing[o].next_obj) == 2:
# # processing[o].next_obj = int(np.abs((next_obj + processing[o].next_obj)) / 2)
# print("Buggy11.1\n")
# stop_ray = True
# elif next_obj == processing[o].next_obj and not isinstance(possible_nn, str):
# # processing[o].next_obj += 1
# print("Buggy11.2\n")
# stop_ray = True
# elif processing[o].next_obj == 2 and isinstance(possible_nn, str):
# # processing[o].next_obj = 1
# print("Buggy11.3\n")
# stop_ray = True
# elif (end[0] == -8 or end[0] == 2) and processing[o].next_obj == 2:
# print("Buggy11.4\n")
# stop_ray = True
# else:
# stop_ray = False
if stop_ray is False:
if isinstance(possible_nn, str):
IF = 0
else:
IF = I0 * np.exp(-2 * top[processing[o].next_obj].material.alphaL * lambda_int)
lst = []
lst.append(processing[o].next_obj)
path = (processing[o].path) + lst
phi_initial = processing[o].phase_final + Ph_tr_long
phi_final = phi_initial + top[processing[o].next_obj].material.kL * lambda_int
phase_shift = processing[o].phase_shift + Ph_tr_long
sn = Ray(start, end, vray, path, I0, phi_initial, phi_final, phase_shift, 0, processing[o].next_obj,
next_obj, possible_nn, IF,0, False)
son.append(sn)
if IF > I_limit:
control.append(sn)
# if np.abs(start[0] - end[0]) < 0.00001:
# print('something wrong in long')
# REFRACTED SHEAR RAY IN BONE
shearrefrac_possible, v_out, poldir = rf.refraction(processing[o].vray, nn, c_long_liquid, c_shear_solid)
if shearrefrac_possible == True:
intens_shear_refrac = processing[o].IF * Transm_shear
if intens_shear_refrac > I_limit:
start = processing[o].end
I0 = intens_shear_refrac
vray = v_out / LA.norm(v_out)
poldir = poldir / LA.norm(poldir)
next_obj, end, possible_nn, lambda_int, stop_ray = inter.intersection(start, vray, top,
processing[o].next_obj,
final_geometry,
initial_geometry)
# if np.abs(next_obj - processing[o].next_obj) == 2:
# # processing[o].next_obj = int(np.abs((next_obj + processing[o].next_obj)) / 2)
# print("Buggy12.1\n")
# stop_ray = True
# elif next_obj == processing[o].next_obj and not isinstance(possible_nn, str):
# # processing[o].next_obj += 1
# print("Buggy12.2\n")
# stop_ray = True
# elif processing[o].next_obj == 2 and isinstance(possible_nn, str):
# # processing[o].next_obj = 1
# print("Buggy12.3\n")
# stop_ray = True
# elif (end[0] == -8 or end[0] == 2) and processing[o].next_obj == 2:
# print("Buggy12.4\n")
# stop_ray = True
# else:
# stop_ray = False
if stop_ray is False:
if isinstance(possible_nn, str): # if possible_nn is a string
IF = 0
else:
IF = I0 * np.exp(-2 * top[processing[o].next_obj].material.alphaS * lambda_int)
lst = []
lst.append(processing[o].next_obj)
path = (processing[o].path) + lst
phi_initial = processing[o].phase_final + Ph_tr_shear
phi_final = phi_initial + top[processing[o].next_obj].material.kL * lambda_int
phase_shift = processing[o].phase_shift + Ph_tr_shear
sn = Ray(start, end, vray, path, I0, phi_initial, phi_final, phase_shift, 0,
processing[o].next_obj,
next_obj, possible_nn, IF, poldir, True)
son.append(sn)
if IF > I_limit:
control.append(sn)
# if np.abs(start[0] - end[0]) < 0.00001:
# print('something wrong in shear')
return son