def sinogram():
# SIMULATION PARAMETERS -----------------------------------------------
G = 1.0 # Grueneisen parameter
c0 = 150000. # speed of sound (cm/s)
R = 0.5001
# OBTAIN ABSORBED ENERGY WITHIN SOURCE VOLUME -------------------------
(x,y,z), (x0,y0,z0), Wxyz = modelSourceVolume()
detPos = detectorPositions((x0,z0+0.2),R)
for (phi,xD,zD) in detPos:
sys.stderr.write("# phi=%lf \n"%(phi))
print "# phi, xD, zD = ", phi, xD, zD
print "# D = ", abs(zD-0.1)*2/24/0.15/0.15
# COMPUTE OA EXCESS PRESSURE SIGNAL -----------------------------------
t, p = ps.pressure(((x,y,z),G*Wxyz),(xD,y0,z0+zD),c0)
# LIST RESULTS --------------------------------------------------------
tau = t + zD/c0 # retarded time
print "# (t in s) (c0 tau in cm) (p(tau) in au)"
norm = 1./max(p)
for i in range(tau.size):
print phi, c0*t[i], c0*tau[i], p[i], p[i]*norm
print
def main():
# SIMULATION PARAMETERS -----------------------------------------------
G = 1.0 # Grueneisen parameter
c0 = 150000. # speed of sound (cm/s)
zD = -0.5 # detector location
# OBTAIN ABSORBED ENERGY WITHIN SOURCE VOLUME -------------------------
(x, y, z), (x0, y0, z0), Wxyz = modelSourceVolume()
# COMPUTE OA EXCESS PRESSURE SIGNAL -----------------------------------
t, p = ps.pressure(((x, y, z), G * Wxyz), (x0, y0, z0 + zD), c0)
# LIST RESULTS --------------------------------------------------------
tau = t + zD / c0 # retarded time
print "# (t in s) (c0 tau in cm) (p(tau) in au)"
for i in range(tau.size):
print t[i], c0 * tau[i], p[i]
def main():
# SIMULATION PARAMETERS -----------------------------------------------
G = 1.0 # Grueneisen parameter
c0 = 150000. # speed of sound (cm/s)
zD = -0.12 # detector location
ftd = float(sys.argv[1]) # flat-top diameter (cm)
ma = float(sys.argv[2]) # absorption coefficient (cm^-1)
# OBTAIN ABSORBED ENERGY WITHIN SOURCE VOLUME -------------------------
(x, y, z), (x0, y0, z0), Wxyz = modelSourceVolume(ma, ftd)
# COMPUTE OA EXCESS PRESSURE SIGNAL -----------------------------------
t, p = ps.pressure(((x, y, z), G * Wxyz), (x0, y0, z0 + zD), c0)
# LIST RESULTS --------------------------------------------------------
tau = t + zD / c0 # retarded time
print "# (t in s) (c0 tau in cm) (p(tau) in au)"
for i in range(tau.size):
print t[i], c0 * tau[i], p[i]
def main():
# SIMULATION PARAMETERS -----------------------------------------------
basePath = "../inputData/skinvessel"
G = 0.138 # Grueneisen parameter
c0 = 150000. # speed of sound (cm/s)
xD = float(sys.argv[1]) # detector x-position (cm)
yD = float(sys.argv[2]) # detector y-position (cm)
zD = float(sys.argv[3]) # detector z-position (cm)
# VOLUMETRIC ENERGY DENSITY PER VOXEL ---------------------------------
((x,y,z), Wxyz) = io.mcxyzio.getEnergyDensity(basePath)
# OA EXCESS PRESSURE SIGNAL -------------------------------------------
t, p = ps.pressure(((x,y,z),G*Wxyz),(xD,yD,zD),c0)
tau = t + zD/c0
print "# (c0 tau) (p(tau))"
for i in range(tau.size):
print c0*tau[i],p[i]
def main():
# SIMULATION PARAMETERS -----------------------------------------------
G = 0.11 # Grueneisen parameter
c0 = 150000. # speed of sound (cm/s)
zD = -0.1 # detector location
# OBTAIN ABSORBED ENERGY WITHIN SOURCE VOLUME -------------------------
(x, y, z), (x0, y0, z0), Wxyz = modelSourceVolume()
# STORE SOURCE VOLUME SLICE AT y0 -------------------------------------
#io.gpl.writeROI(x,z,Wxyz[:,y.size/2,:],'./dataUseCase1/Wxy0z.prof')
# COMPUTE OA EXCESS PRESSURE SIGNAL -----------------------------------
t, p = ps.pressure(((x, y, z), G * Wxyz), (x0, y0, z0 + zD), c0)
# LIST RESULTS --------------------------------------------------------
tau = t + zD / c0 # retarded time
print "# (t in s) (c0 tau in cm) (p(tau) in bar)"
for i in range(tau.size):
print t[i], c0 * tau[i], p[i]
def main2():
# SIMULATION PARAMETERS -----------------------------------------------
G = 1.0 # Grueneisen parameter
c0 = 1.5 # speed of sound (cm/s)
zD = 3.250 # detector location
rDList = np.linspace(0., 1.5, 20, endpoint=True)
# OBTAIN ABSORBED ENERGY WITHIN SOURCE VOLUME -------------------------
(x, y, z), (x0, y0, z0), Wxyz = modelSourceVolume()
for idx, rD in enumerate(rDList):
# COMPUTE OA EXCESS PRESSURE SIGNAL -----------------------------------
t, p = ps.pressure(((x, y, z), G * Wxyz), (x0 + rD, y0, zD), c0)
tau = t + zD / c0 # retarded time
print "# (t in s) (c0 tau in cm) (p(tau) in bar)"
for i in range(tau.size):
print rD, t[i], c0 * tau[i], p[i]
print
def main():
# SIMUMATION PARAMETERS -----------------------------------------------
iPath = "../inputData/skinvessel"
G = 0.138 # Grueneisen parameter
c0 = 150000. # speed of sound (cm/s)
# VOLUMETRIC ENERGY DENSITY PER VOXEL ---------------------------------
((x,y,z), Wxyz) = io.mcxyzio.getEnergyDensity(iPath)
# GENERAL FIGURE SETTINGS ---------------------------------------------
plt.rc('font',family='serif',size=12)
plt.figure(figsize=(7.,9.0))
# FIG (a): x-scan -----------------------------------------------------
ax11= plt.subplot2grid((3,2), (0,0))
ax11.set_aspect('equal')
ax11.contourf(y,z,Wxyz[:,:,x.size/2]/1000,100,lw=0.1)
c1 = ax11.contourf(y,z,Wxyz[:,:,x.size/2]/1000,100)
divider1 = make_axes_locatable(ax11)
cax11 = divider1.append_axes("right", "5%", pad="3%")
c1Bar = plt.colorbar(c1,cax=cax11)
c1Bar.set_label('$W(x_0,y,z)$ (kJ/m$^2$)',fontsize=10)
c1Bar.ax.tick_params(labelsize=10)
ax11.set_ylabel('$z$ (cm)')
ax11.set_xlabel('$y$ (cm)')
ax11.text(0.,1.05,'(a)',transform=ax11.transAxes,fontsize=12)
# FIG (b): y-scan -----------------------------------------------------
ax12= plt.subplot2grid((3,2), (0,1))
ax12.set_aspect('equal')
ax12.contour(x,z,Wxyz[:,y.size/2,:]/1000,100,lw=0.1)
c2 = ax12.contourf(x,z,Wxyz[:,y.size/2,:]/1000,100)
divider2 = make_axes_locatable(ax12)
cax12 = divider2.append_axes("right", "5%", pad="3%")
c2Bar = plt.colorbar(c2,cax=cax12)
c2Bar.set_label('$W(x,y_0,z)$ (kJ/m$^2$)',fontsize=10)
c2Bar.ax.tick_params(labelsize=10)
ax12.set_ylabel('$z$ (cm)')
ax12.set_xlabel('$x$ (cm)')
ax12.text(0.,1.05,'(b)',transform=ax12.transAxes,fontsize=12)
# FIG (c): OFF-AXIS OA SIGNALS ----------------------------------------
ax21 = plt.subplot2grid((3,2), (1,0), colspan=2)
ax21.text(0.5,0.75,'$x_D$=0.05 cm\n$z_D$=-0.20 cm',transform=ax21.transAxes,fontsize=10)
xD=0.05
zD=-0.20
for yD in [0.01, 0.03, 0.05]:
t, p = ps.pressure(((x,y,z),G*Wxyz/1000),(xD,yD,zD),c0)
ax21.plot(c0*t+zD,p, label='$y_D$=%3.2lf cm'%(yD))
ax21.set_xlim([-0.002,0.06])
ax21.set_ylabel('$p$ (kPa per J)')
ax21.set_xlabel('$c \\tau$ (cm)')
ax21.axhline(y=0,color='black', ls='--')
ax21.legend(loc='upper right', prop={'size':10}, frameon=False)
ax21.text(0.,1.05,'(c)',transform=ax21.transAxes,fontsize=12)
# FIG (d): ON-AXIS OA SIGNALS -----------------------------------------
ax31 = plt.subplot2grid((3,2), (2,0), colspan=2)
ax31.text(0.5,0.75,'$x_D$=0.05 cm\n$y_D$=0.05 cm',transform=ax31.transAxes,fontsize=10)
xD=0.05
yD=0.05
for zD in [-0.1, -0.4, -1.6]:
t, p = ps.pressure(((x,y,z),G*Wxyz/1000),(xD,yD,zD),c0)
ax31.plot(c0*t+zD,p, label='$z_D$=%3.2lf cm'%(zD))
ax31.set_xlim([-0.002,0.06])
ax31.set_ylabel('$p$ (kPa per J)')
ax31.set_xlabel('$c \\tau$ (cm)')
ax31.axhline(y=0,color='black', ls='--')
ax31.legend(loc='upper right', prop={'size':10}, frameon=False)
ax31.text(0.,1.05,'(d)',transform=ax31.transAxes,fontsize=12)
plt.tight_layout()
plt.savefig('useCase_mcxyz_abcd.eps',dpi=600,format='eps')
def figure():
# SIMULATION PARAMETERS -----------------------------------------------
G = 0.11 # Grueneisen parameter
c0 = 150000. # speed of sound (cm/s)
zD = -0.1 # detector location
# GENERAL FIGURE SETTINGS ---------------------------------------------
plt.rc('font', family='serif', size=12)
plt.figure(figsize=(7., 7.))
#io.gpl.writeROI(x,z,Wxyz[:,y.size/2,:],'./dataUseCase1/Wxy0z.prof')
# FIG (a): FLAT-TOP ISP
ax12 = plt.subplot2grid((2, 2), (0, 0))
ax12.set_aspect('equal')
(x, y, z), (x0, y0, z0), Wxyz = modelSourceVolume(0.025)
ax12.contour(x, z, Wxyz[:, y.size / 2, :] / 10**6, 100, lw=0.1)
c2 = ax12.contourf(x, z, Wxyz[:, y.size / 2, :] / 10**6, 100)
divider2 = make_axes_locatable(ax12)
cax12 = divider2.append_axes("right", "5%", pad="3%")
c2Bar = plt.colorbar(c2, cax=cax12)
c2Bar.set_label('$W(x,y_0,z)$ (MJ/m$^2$)', fontsize=10)
c2Bar.ax.tick_params(labelsize=10)
ax12.set_ylabel('$z$ (cm)')
ax12.set_xlabel('$x$ (cm)')
ax12.text(0., 1.05, '(a)', transform=ax12.transAxes, fontsize=12)
ax12.text(0.05,
0.9,
'$a = 0.025$ cm',
transform=ax12.transAxes,
fontsize=12,
color='white')
# FIG (b): FLAT-TOP ISP
ax13 = plt.subplot2grid((2, 2), (0, 1))
ax13.set_aspect('equal')
(x, y, z), (x0, y0, z0), Wxyz = modelSourceVolume(0.194)
ax13.contour(x, z, Wxyz[:, y.size / 2, :] / 10**6, 100, lw=0.1)
c3 = ax13.contourf(x, z, Wxyz[:, y.size / 2, :] / 10**6, 100)
divider3 = make_axes_locatable(ax13)
cax13 = divider3.append_axes("right", "5%", pad="3%")
c3Bar = plt.colorbar(c3, cax=cax13)
c3Bar.set_label('$W(x,y_0,z)$ (MJ/m$^2$)', fontsize=10)
c3Bar.ax.tick_params(labelsize=10)
ax13.set_ylabel('$z$ (cm)')
ax13.set_xlabel('$x$ (cm)')
ax13.text(0., 1.05, '(b)', transform=ax13.transAxes, fontsize=12)
ax13.text(0.05,
0.9,
'$a = 0.194$ cm',
transform=ax13.transAxes,
fontsize=12,
color='white')
ax21 = plt.subplot2grid((2, 2), (1, 0), colspan=2)
for fta in [0.025, 0.05, 0.075, 0.1, 0.194]:
#for fta in [0.025, 0.194]:
# OBTAIN ABSORBED ENERGY WITHIN SOURCE VOLUME ---------------------
(x, y, z), (x0, y0, z0), Wxyz = modelSourceVolume(fta)
# COMPUTE OA EXCESS PRESSURE SIGNAL -------------------------------
t, p = ps.pressure(((x, y, z), G * Wxyz), (x0, y0, z0 + zD), c0)
# ADD OA SIGNAL TO PLOT -------------------------------------------
ax21.plot((t + zD / c0) * 10**6,
p / 10**5,
label='$a$=%3.2lf cm' % (fta))
ax21.set_xlim([-0.01 * 10**6 / c0, 0.23 * 10**6 / c0])
ax21.set_ylabel('$p$ (bar)')
ax21.set_xlabel('$\\tau$ ($\\mu$s)')
ax21.axhline(y=0, color='black', ls='--')
ax21.legend(loc='upper right', prop={'size': 10}, frameon=False)
ax21.text(0., 1.05, '(c)', transform=ax21.transAxes, fontsize=12)
ax21.text(0.5, 0.92, '$z_D = -0.1$ cm', transform=ax21.transAxes)
plt.tight_layout()
plt.savefig('useCase_pureAbs_abc.eps', dpi=600, format='eps')