def isodose_plot():
"""
Description:
Takes any number of .3ddose files and plots a plethora of diagnostic plots
from the data
Inputs:
:name list_file: a list of file names that are to be loaded
:type list_file: list
"""
pwd = getcwd()
# target_dir = '/Users/JLucero/MPhysProj/results_not_to_git' # for home
target_dir = '/Users/student/research/results_not_to_git' # for work
file_list = [
target_dir + '/mlwa_0shield_{0}_sim_sux.phantom.3ddose',
target_dir + '/mlwa_90shield_{0}_sim_sux.phantom.3ddose',
target_dir + '/mlwa_180shield_{0}_sim_sux.phantom.3ddose',
target_dir + '/mlwa_270shield_{0}_sim_sux.phantom.3ddose',
]
label_list = [
'Unshielded', '90 degree shield', '180 degree shield',
'270 degree shield'
]
vox_size_list = [
# '0.5mm',
'1mm',
# '2mm',
]
for fig_index in xrange(len(vox_size_list)):
fig, ax = subplots(2, 2, figsize=(10, 10), sharex='all', sharey='all')
fig2, ax2 = subplots(2,
2,
figsize=(10, 10),
sharex='all',
sharey='all')
for file_index, file_name in enumerate(file_list):
if file_index == 0:
pass
else:
full_data = DoseFile(file_name.format(
vox_size_list[fig_index]))
if file_index == 0:
ax_x, ax_y = 0, 0
elif file_index == 1:
ax_x, ax_y = 0, 1
elif file_index == 2:
ax_x, ax_y = 1, 0
else:
ax_x, ax_y = 1, 1
Nx, Ny, Nz = full_data.shape
# full_data.dose *= 2.2861e14 # scale to total treatment time
# full_data.dose *= 8.2573429808917e13 # scale to maximum individual dwell time
full_data.dose /= 5 # normalize to desired dose of 5 Gy
full_data.dose *= 100 # express in percent. Should see 100% at x=-2cm
x_min, x_max = full_data.x_extent
y_min, y_max = full_data.y_extent
z_min, z_max = full_data.z_extent
xy_contour = ax[ax_x,
ax_y].contourf(linspace(x_min, x_max, Nx),
linspace(y_min, y_max, Ny),
full_data.dose[Nz // 2, :, :],
arange(0, 110, 10),
cmap=cm.Purples)
xz_contour = ax2[ax_x,
ax_y].contourf(linspace(x_min, x_max, Nx),
linspace(z_min, z_max, Nz),
full_data.dose[:, Ny // 2, :],
arange(0, 110, 10),
cmap=cm.Purples)
for n in xrange(2):
for m in xrange(2):
if n == 0 and m == 0:
title_index = 0
elif n == 0 and m == 1:
title_index = 1
elif n == 1 and m == 0:
title_index = 2
else:
title_index = 3
if title_index == 0:
pass
else:
ax[n, m].grid(True)
ax[n, m].xaxis.set_tick_params(labelsize=14)
ax[n, m].yaxis.set_tick_params(labelsize=14)
# ax[n, m].set_xticks(arange(x_min, x_max + 1, 2))
# ax[n, m].set_yticks(arange(y_min, y_max + 1, 2))
ax[n, m].vlines([-2, 2],
-10,
10,
linestyles='dashed',
lw=2.0)
ax[n, m].hlines([-2, 2],
-10,
10,
linestyles='dashed',
lw=2.0)
ax[n, m].set_title(label_list[title_index])
ax2[n, m].grid(True)
ax2[n, m].xaxis.set_tick_params(labelsize=14)
ax2[n, m].yaxis.set_tick_params(labelsize=14)
# ax2[n ,m].set_xticks(arange(x_min, x_max + 1, 2))
# ax2[n ,m].set_yticks(arange(y_min, y_max + 1, 2))
ax2[n, m].vlines([-2, 2],
-10,
10,
linestyles='dashed',
lw=2.0)
ax2[n, m].set_title(label_list[title_index])
fig.text(0.01,
0.51,
'y-axis (cm)',
fontsize=27,
rotation='vertical',
va='center')
fig.text(0.43, 0.03, 'x-axis (cm)', fontsize=27, va='center')
fig.text(0.52,
0.95,
'Isodose Contours \n Suxer Data',
fontsize=27,
va='center',
ha='center')
cax = fig.add_axes([0.91, 0.13, 0.01, 0.7])
cbar1 = fig.colorbar(xy_contour,
cax=cax,
orientation='vertical',
ax=ax)
cbar1.set_label('Percentage Isodose (%)', fontsize=24)
cbar1.ax.tick_params(labelsize=14)
fig.tight_layout()
left = 0.1 # the left side of the subplots of the figure
right = 0.89 # the right side of the subplots of the figure
bottom = 0.09 # the bottom of the subplots of the figure
top = 0.90 # the top of the subplots of the figure
wspace = 0.2 # the amount of width reserved for blank space between subplots
hspace = 0.2 # the amount of height reserved for white space between subplotss
fig.subplots_adjust(left=left, bottom=bottom, right=right, top=top)
fig.savefig(pwd + '/xy_isodose_profile_' + vox_size_list[fig_index] +
'_suxer.pdf')
fig2.text(0.01,
0.51,
'z-axis (cm)',
fontsize=27,
rotation='vertical',
va='center')
fig2.text(0.43, 0.03, 'x-axis (cm)', fontsize=27, va='center')
fig2.text(0.52,
0.95,
'Isodose Contours \n Suxer Data',
fontsize=27,
va='center',
ha='center')
cax2 = fig2.add_axes([0.91, 0.13, 0.01, 0.7])
cbar2 = fig2.colorbar(xz_contour,
cax=cax2,
orientation='vertical',
ax=ax)
cbar2.set_label('Percentage Isodose (%)', fontsize=24)
cbar2.set_clim([0, 100])
cbar2.ax.tick_params(labelsize=14)
fig2.tight_layout()
left = 0.1 # the left side of the subplots of the figure
right = 0.89 # the right side of the subplots of the figure
bottom = 0.09 # the bottom of the subplots of the figure
top = 0.90 # the top of the subplots of the figure
wspace = 0.2 # the amount of width reserved for blank space between subplots
hspace = 0.2 # the amount of height reserved for white space between subplotss
fig2.subplots_adjust(left=left, bottom=bottom, right=right, top=top)
fig2.savefig(pwd + '/xz_isodose_profile_' + vox_size_list[fig_index] +
'_suxer.pdf')
def dose_position_plots():
"""
Description:
Takes any number of .3ddose files and plots a plethora of diagnostic plots
from the data
Inputs:
:name list_file: a list of file names that are to be loaded
:type list_file: list
"""
pwd = getcwd()
# target_dir = '/Users/JLucero/MPhysProj/results_not_to_git' for home
target_dir = '/Users/student/research/results_not_to_git' # for work
file_list = [
# target_dir +
# '/mlwa_0shield_{0}_sim.phantom_wo_applicator_wo_box.3ddose',
target_dir + '/mlwa_90shield_{0}_sim_sux.phantom.3ddose',
target_dir + '/mlwa_180shield_{0}_sim_sux.phantom.3ddose',
target_dir + '/mlwa_270shield_{0}_sim_sux.phantom.3ddose',
]
label_list = [
# 'Unshielded',
'90 degree shield',
'180 degree shield',
'270 degree shield'
]
vox_size_list = [
# '0.5mm',
'1mm',
# '2mm',
]
color_list = ['darkgreen', 'purple', 'darkorange', 'saddlebrown']
title_list = ['X - axis', 'Y - axis', 'Z - axis']
for fig_index in xrange(1):
fig, ax = subplots(3, 1, figsize=(10, 10), sharex='col')
for index2 in xrange(3): # iterate through shield types
full_data = DoseFile(file_list[index2].format(
vox_size_list[fig_index]))
Nx, Ny, Nz = full_data.shape
# full_data.dose *= 2.2861e14 # scale to total treatment time
# full_data.dose *= 8.2573429808917e13 # scale to maximum individual dwell time
x_min, x_max = full_data.x_extent
y_min, y_max = full_data.y_extent
z_min, z_max = full_data.z_extent
for index1 in xrange(3): # iterate through axes
if index1 == 0:
ax[index1].plot(
linspace(x_min, x_max, Nx),
full_data.dose[Nz // 2, Ny // 2, :],
# yerr=full_data.uncertainty[Nz // 2, Ny // 2, :],
lw=3.0,
label=label_list[index2])
elif index1 == 1:
ax[index1].plot(
linspace(y_min, y_max, Ny),
full_data.dose[Nz // 2, :, Nx // 2],
# yerr=full_data.uncertainty[Nz // 2, :, Nx // 2],
lw=3.0)
else:
ax[index1].plot(
linspace(z_min, z_max, Nz),
full_data.dose[:, Ny // 2, Nx // 2],
# yerr=full_data.uncertainty[:, Ny // 2, Nx // 2],
lw=3.0)
for n in xrange(3):
ax[n].grid(True)
ax[n].set_title(title_list[n], fontsize=20)
if n == 0:
ax[n].legend(loc=0, prop={'size': 8})
ax[n].xaxis.set_tick_params(labelsize=14)
ax[n].yaxis.set_tick_params(labelsize=14)
# if n == 2:
# ax[n].set_xticks(arange(z_min, z_max, 5))
fig.text(0.01,
0.51,
'Dose (Gy)',
fontsize=27,
rotation='vertical',
va='center')
fig.text(0.43, 0.03, 'Position (cm)', fontsize=27, va='center')
fig.text(0.52,
0.95,
'Absolute Dose vs. Position \n Suxer Data',
fontsize=27,
va='center',
ha='center')
fig.tight_layout()
left = 0.125 # the left side of the subplots of the figure
right = 0.95 # the right side of the subplots of the figure
bottom = 0.09 # the bottom of the subplots of the figure
top = 0.87 # the top of the subplots of the figure
wspace = 0.2 # the amount of width reserved for blank space between subplots
hspace = 0.2 # the amount of height reserved for white space between subplotss
fig.subplots_adjust(left=left, bottom=bottom, right=right, top=top)
fig.savefig(pwd + '/dosage_comparison_' + vox_size_list[fig_index] +
'_suxer.pdf')
def rel_dose_position_plot():
"""
Description:
Takes any number of .3ddose files and plots a plethora of diagnostic plots
from the data
Inputs:
:name list_file: a list of file names that are to be loaded
:type list_file: list
"""
pwd = getcwd()
# target_dir = '/Users/JLucero/MPhysProj/results_not_to_git' for home
target_dir = '/Users/student/research/results_not_to_git' # for work
# unshielded_file = target_dir + \
# '/mlwa.phantom_wo_applicator.3ddose'
shielded_file_90 = target_dir + \
'/mlwa_90shield_1mm_sim_sux.phantom.3ddose'
shielded_file_180 = target_dir + \
'/mlwa_180shield_1mm_sim_sux.phantom.3ddose'
shielded_file_270 = target_dir + \
'/mlwa_270shield_1mm_sim_sux.phantom.3ddose'
fig, ax = subplots(1, 1, figsize=(10, 10), sharex='col')
ax_twin = ax.twinx()
# unshielded_full_data = DoseFile(unshielded_file)
shield_90_data = DoseFile(shielded_file_90)
shield_180_data = DoseFile(shielded_file_180)
shield_270_data = DoseFile(shielded_file_270)
Nx, Ny, Nz = shield_90_data.shape
# shield_90_data.dose /= unshielded_full_data.dose
# shield_180_data.dose /= unshielded_full_data.dose
# shield_270_data.dose /= unshielded_full_data.dose
x_min, x_max = shield_90_data.x_extent
y_min, y_max = shield_90_data.y_extent
z_min, z_max = shield_90_data.z_extent
ax.plot(linspace(x_min, -1.5, (Nx // 2 - 8) // 2),
shield_90_data.dose[Nz // 2, Ny // 2, :Nx // 2 - 8][::2],
lw=0.0,
label='90 degrees',
color='darkgreen',
marker='o',
markersize=10)
ax_twin.plot(linspace(1.5, x_max, (Nx // 2 - 8) // 2 + 1),
shield_90_data.dose[Nz // 2, Ny // 2, Nx // 2 + 8:][::2],
lw=0.0,
color='darkgreen',
marker='o',
markersize=10)
ax.plot(linspace(x_min, -1.5, (Nx // 2 - 8) // 2),
shield_180_data.dose[Nz // 2, Ny // 2, :Nx // 2 - 8][::2],
lw=0.0,
label='180 degrees',
color='purple',
marker='s',
markersize=10)
ax_twin.plot(linspace(1.5, x_max, (Nx // 2 - 8) // 2 + 1),
shield_180_data.dose[Nz // 2, Ny // 2, Nx // 2 + 8:][::2],
lw=0.0,
color='purple',
marker='s',
markersize=10)
ax.plot(linspace(x_min, -1.5, (Nx // 2 - 8) // 2),
shield_270_data.dose[Nz // 2, Ny // 2, :Nx // 2 - 8][::2],
lw=0.0,
label='270 degrees',
color='darkorange',
marker='^',
markersize=10)
ax_twin.plot(linspace(1.5, x_max, (Nx // 2 - 8) // 2 + 1),
shield_270_data.dose[Nz // 2, Ny // 2, Nx // 2 + 8:][::2],
lw=0.0,
color='darkorange',
marker='^',
markersize=10)
ax.legend(loc=0, prop={'size': 18})
ax.grid(True)
ax.set_title('X - axis', fontsize=20)
ax.set_ylim([0.8, 1.05])
ax.xaxis.set_tick_params(labelsize=17)
ax.yaxis.set_tick_params(labelsize=17)
ax_twin.set_ylim([0.0, 0.5])
ax_twin.yaxis.set_tick_params(labelsize=17)
ax_twin.vlines([-1.5, 1.5], 0, 1.0)
# ax.set_xticks(arange(z_min, z_max + 1, 2))
fig.text(0.01,
0.48,
'Relative Dose',
fontsize=27,
rotation='vertical',
va='center')
fig.text(0.96,
0.51,
'Effective Transmission',
fontsize=27,
rotation='vertical',
va='center')
fig.text(0.43, 0.03, 'Position (cm)', fontsize=27, va='center')
fig.text(0.52,
0.95,
'Relative Dose vs. Position \n Suxer Data',
fontsize=27,
va='center',
ha='center')
fig.tight_layout()
left = 0.11 # the left side of the subplots of the figure
right = 0.9 # the right side of the subplots of the figure
bottom = 0.09 # the bottom of the subplots of the figure
top = 0.87 # the top of the subplots of the figure
wspace = 0.2 # the amount of width reserved for blank space between subplots
hspace = 0.2 # the amount of height reserved for white space between subplotss
fig.subplots_adjust(left=left, bottom=bottom, right=right, top=top)
fig.savefig(pwd + '/relative_dosage_comparison_suxer.pdf')
def generate_tdvh_mlwa():
pwd = getcwd()
# target_dir = '/Users/JLucero/MPhysProj/results_not_to_git' # for home
target_dir = '/Users/student/research/results_not_to_git' # for work
# file_no_shield_0point5mm = target_dir + \
# '/mlwa_0shield_0.5mm_sim.phantom_wo_applicator_wo_box.egsinp'
# file_no_shield_1point0mm = target_dir + \
# '/mlwa_0shield_1mm_sim.phantom_wo_applicator_wo_box.egsinp'
# file_no_shield_2point0mm = target_dir + \
# '/mlwa_0shield_2mm_sim_sux.phantom_wo_applicator_wo_box.egsinp'
# file_90_shield_0point5mm = target_dir + \
# '/mlwa_90shield_0.5mm_sim.phantom_wo_applicator_wo_box.egsinp'
file_90_shield_1point0mm = target_dir + \
'/mlwa_90shield_1mm_sim_sux.phatom.3ddose'
# file_90_shield_2point0mm = target_dir + \
# '/mlwa_90shield_2mm_sim_sux.phantom.3ddose'
# file_180_shield_0point5mm = target_dir + \
# '/mlwa_180shield_0.5mm_sim.phantom_wo_applicator_wo_box.egsinp'
file_180_shield_1point0mm = target_dir + \
'/mlwa_180shield_1mm_sim_sux.phatom.3ddose'
# file_180_shield_2point0mm = target_dir + \
# '/mlwa_180shield_2mm_sim_sux.phantom.3ddose'
# file_270_shield_0point5mm = target_dir + \
# '/mlwa_270shield_0.5mm_sim.phantom_wo_applicator_wo_box.egsinp'
file_270_shield_1point0mm = target_dir + \
'/mlwa_270shield_1mm_sim_sux.phatom.3ddose'
# file_270_shield_2point0mm = target_dir + \
# '/mlwa_270shield_2mm_sim_sux.phantom.3ddose'
file_list = [
file_90_shield_2point0mm, file_180_shield_2point0mm,
file_270_shield_2point0mm
]
color_list = ['darkgreen', 'purple', 'darkorange', 'saddlebrown']
label_list = [
# 'Unshielded',
'90 degree shield',
'180 degree shield',
'270 degree shield'
]
fig, ax = subplots(3, 1, figsize=(10, 10), sharex='all', sharey='all')
fig2, ax2 = subplots(3, 1, figsize=(10, 10), sharex='all', sharey='all')
for index in xrange(3):
main_data = DoseFile(file_list[index])
# data_base_flat = main_base_data.dose.flatten() * 2.2861e14 # converts to Gy; norm to treatment time
data_flat = main_data.dose.flatten(
) # converts to Gy; norm to individual max dwell time
n, bins, __ = ax[index].hist(
data_flat,
bins=500,
# color=color_list[index],
# label=label_list[index],
weights=zeros_like(data_flat) + 1. / data_flat.size * 100,
alpha=0.4)
n_cum_base = n[::-1].cumsum()[::-1]
ax2[index].loglog(
bins[:-1],
n_cum_base,
# color=color_list[index],
# label=label_list[index]
)
for i in xrange(3):
ax[i].legend(loc=0, prop={'size': 10})
ax[i].set_title(label_list[i], fontsize=20)
ax[i].xaxis.set_tick_params(labelsize=17)
ax[i].yaxis.set_tick_params(labelsize=17)
ax2[i].legend(loc=0, prop={'size': 10})
ax2[i].set_title(label_list[i], fontsize=20)
ax2[i].xaxis.set_tick_params(labelsize=17)
ax2[i].yaxis.set_tick_params(labelsize=17)
fig.text(0.03,
0.51,
'Volume (%)',
fontsize=22,
rotation='vertical',
va='center')
fig.text(0.46, 0.03, 'Dose (Gy)', fontsize=22, va='center')
fig.text(0.52,
0.95,
'Dose Volume Histograms \n Suxer Results',
fontsize=22,
va='center',
ha='center')
fig.tight_layout()
left = 0.125 # the left side of the subplots of the figure
right = 0.9 # the right side of the subplots of the figure
bottom = 0.09 # the bottom of the subplots of the figure
top = 0.88 # the top of the subplots of the figure
wspace = 0.2 # the amount of width reserved for blank space between subplots
hspace = 0.2 # the amount of height reserved for white space between subplotss
fig.subplots_adjust(left=left, top=top, right=right, bottom=bottom)
fig.savefig(pwd + '/dose_volume_histogram_suxer.pdf')
fig2.text(0.03,
0.51,
'Volume (%)',
fontsize=22,
rotation='vertical',
va='center')
fig2.text(0.45, 0.03, 'Dose (Gy)', fontsize=22, va='center')
fig2.text(0.52,
0.95,
'Dose Volume Histograms \n With Volume Correction; ncase = 1E9',
fontsize=22,
va='center',
ha='center')
fig2.tight_layout()
left = 0.125 # the left side of the subplots of the figure
right = 0.9 # the right side of the subplots of the figure
bottom = 0.09 # the bottom of the subplots of the figure
top = 0.88 # the top of the subplots of the figure
wspace = 0.2 # the amount of width reserved for blank space between subplots
hspace = 0.2 # the amount of height reserved for white space between subplotss
fig2.subplots_adjust(left=left, top=top, right=right, bottom=bottom)
fig2.savefig(pwd + '/cumulative_dose_volume_histogram_suxer.pdf')
def isodose_plot_compare():
"""
Description:
Takes any number of .3ddose files and plots a plethora of diagnostic plots
from the data
Inputs:
:name list_file: a list of file names that are to be loaded
:type list_file: list
"""
pwd = getcwd()
# target_dir = '/Users/JLucero/MPhysProj/results_not_to_git' # for home
target_dir = '/Users/student/research/results_not_to_git' # for work
# file_name_template = target_dir + \
# '/tg43_applicator_{0}_sim.phantom_wo_applicator_wo_box.3ddose'
file_name_template = target_dir + \
'/tg43_{0}_{1}.phantom_wo_box.3ddose'
vox_size_list = [
# '0.5mm',
# '1mm',
'2mm'
]
vox_size_txt_list = [
# '0.5mm',
# '1pt0mm',
# '2pt0mm'
'2mm'
]
sources = ['Flexisource', 'microSelectronV1', 'microSelectronV2']
fig, ax = subplots(1, 1, figsize=(10, 10), sharex='all', sharey='all')
fig2, ax2 = subplots(1, 1, figsize=(10, 10), sharex='all', sharey='all')
fig3, ax3 = subplots(1, 1, figsize=(10, 10), sharex='all', sharey='all')
# source = 'Flexi-V2Compare'
# source = 'Flexi-V1Compare'
source = 'V2-V1Compare'
if source is 'V2-V1Compare':
print "Source is:", source
data1 = DoseFile(target_dir +
'/tg43_microSelectronV2_2mm.phantom_wo_box.3ddose.gz')
data2 = DoseFile(target_dir +
'/tg43_microSelectronV1_2mm.phantom_wo_box.3ddose.gz')
comparison_matrix = calc_per_diff(data1.dose * 82583025662064.77,
data2.dose * 82105378673169.89)
sup_title = 'microSelectron-v1 to microSelectron-v2\n Dose Comparison'
elif source is 'Flexi-V1Compare':
print "Source is:", source
data1 = DoseFile(target_dir +
'/tg43_Flexisource_2mm.phantom_wo_box.3ddose.gz')
data2 = DoseFile(target_dir +
'/tg43_microSelectronV1_2mm.phantom_wo_box.3ddose.gz')
comparison_matrix = calc_per_diff(data1.dose * 79906971237618.34,
data2.dose * 82105378673169.89)
sup_title = 'Flexisource to microSelectron-v1\n Dose Comparison'
elif source is 'Flexi-V2Compare':
print "Source is:", source
data1 = DoseFile(target_dir +
'/tg43_Flexisource_2mm.phantom_wo_box.3ddose.gz')
data2 = DoseFile(target_dir +
'/tg43_microSelectronV2_2mm.phantom_wo_box.3ddose.gz')
comparison_matrix = calc_per_diff(data1.dose * 79906971237618.34,
data2.dose * 82583025662064.77)
sup_title = 'Flexisource to microSelectron-v2\n Dose Comparison'
else:
print "Prompt not understood."
exit(1)
Nx, Ny, Nz = data1.shape
x_min, x_max = data1.x_extent
y_min, y_max = data1.y_extent
z_min, z_max = data1.z_extent
x_pos = array(data1.positions[0])
y_pos = array(data1.positions[1])
z_pos = array(data1.positions[2])
x_pos_mid = (x_pos[:-1] + x_pos[1:]) / 2.0
y_pos_mid = (y_pos[:-1] + y_pos[1:]) / 2.0
z_pos_mid = (z_pos[:-1] + z_pos[1:]) / 2.0
xy_contour = ax.contourf(
x_pos_mid,
y_pos_mid,
comparison_matrix[:, :, position_to_index(0.0, z_pos)].transpose(),
arange(-7, 10.5, 0.5),
# [5, 10, 20, 50, 100]
cmap=get_cmap('spectral'))
# ax.set_title(vox_size_list,fontsize=14)
xz_contour = ax2.contourf(
x_pos_mid,
z_pos_mid,
comparison_matrix[:, position_to_index(0.0, y_pos), :].transpose(),
arange(-7, 10.5, 0.5),
# [5, 10, 20, 50, 100]
cmap=get_cmap('spectral'))
# ax2.set_title(vox_size_list, fontsize=14)
xy_hist_data = ax3.hist(comparison_matrix[:, :, :].flatten(),
bins='auto',
density=True)
# ax.grid(True)
ax.xaxis.set_tick_params(labelsize=14)
ax.yaxis.set_tick_params(labelsize=14)
ax.set_xticks(arange(-10, 10 + 1, 2))
ax.set_xlim([-10, 10])
ax.set_yticks(arange(-10, 10 + 1, 2))
ax.set_ylim([-10, 10])
# ax.vlines([-2, 2], -10, 10, linestyles='dashed', lw=2.0)
# ax.hlines([-2, 2], -10, 10, linestyles='dashed', lw=2.0)
# ax2.grid(True)
ax2.xaxis.set_tick_params(labelsize=14)
ax2.yaxis.set_tick_params(labelsize=14)
ax2.set_xticks(arange(-10, 10 + 1, 2))
ax2.set_xlim([-10, 10])
ax2.set_yticks(arange(-10, 10 + 1, 2))
ax2.set_ylim([-10, 10])
# ax2.vlines([-2, 2], -10, 10, linestyles='dashed', lw=2.0)
ax3.grid(True)
ax3.xaxis.set_tick_params(labelsize=14)
ax3.yaxis.set_tick_params(labelsize=14)
ax3.set_xticks(arange(-5, 5 + 1, 1))
ax3.set_xlim([-5, 5])
ax3.set_yticks(arange(0, 2.1 + 1, 0.5))
ax3.set_ylim([0, 1])
# ax2.vlines([-2, 2], -10, 10, linestyles='dashed', lw=2.0)
fig.text(0.01,
0.51,
'y-axis (cm)',
fontsize=27,
rotation='vertical',
va='center')
fig.text(0.43, 0.03, 'x-axis (cm)', fontsize=27, va='center')
fig.text(0.52, 0.95, sup_title, fontsize=27, va='center', ha='center')
cax = fig.add_axes([0.91, 0.09, 0.01, 0.79])
cbar1 = fig.colorbar(xy_contour,
cax=cax,
orientation='vertical',
ax=ax,
ticks=arange(0, 15, 1))
cbar1.set_label('Percentage difference (%)', fontsize=24)
cbar1.ax.tick_params(labelsize=14)
fig.tight_layout()
left = 0.1 # the left side of the subplots of the figure
right = 0.89 # the right side of the subplots of the figure
bottom = 0.09 # the bottom of the subplots of the figure
top = 0.88 # the top of the subplots of the figure
# wspace = 0.2 # the amount of width reserved for blank space between subplots
# hspace = 0.2 # the amount of height reserved for white space between subplotss
fig.subplots_adjust(left=left, bottom=bottom, right=right, top=top)
fig.savefig(pwd + '/tg43_' + source + '_xy_isodose_profile_subplots.pdf')
fig2.text(0.01,
0.51,
'z-axis (cm)',
fontsize=27,
rotation='vertical',
va='center')
fig2.text(0.43, 0.03, 'x-axis (cm)', fontsize=27, va='center')
fig2.text(0.52, 0.95, sup_title, fontsize=27, va='center', ha='center')
cax2 = fig2.add_axes([0.90, 0.09, 0.01, 0.79])
cbar2 = fig2.colorbar(xz_contour,
cax=cax2,
orientation='vertical',
ax=ax2,
ticks=arange(0, 15, 1))
cbar2.set_label('Percentage difference (%)', fontsize=24)
# cbar2.set_clim([0, 100])
cbar2.ax.tick_params(labelsize=14)
fig2.tight_layout()
left = 0.1 # the left side of the subplots of the figure
right = 0.888 # the right side of the subplots of the figure
bottom = 0.09 # the bottom of the subplots of the figure
top = 0.88 # the top of the subplots of the figure
# wspace = 0.2 # the amount of width reserved for blank space between subplots
# hspace = 0.2 # the amount of height reserved for white space between subplotss
fig2.subplots_adjust(left=left, bottom=bottom, right=right, top=top)
fig2.savefig(pwd + '/tg43_' + source + '_xz_isodose_profile_subplots.pdf')
fig3.text(0.03,
0.51,
'Probability density',
fontsize=27,
rotation='vertical',
va='center',
ha='center')
fig3.text(0.56,
0.03,
'Percentage difference (%)',
fontsize=27,
va='center',
ha='center')
fig3.text(0.52, 0.95, sup_title, fontsize=27, va='center', ha='center')
fig3.tight_layout()
left = 0.1 # the left side of the subplots of the figure
right = 0.95 # the right side of the subplots of the figure
bottom = 0.09 # the bottom of the subplots of the figure
top = 0.88 # the top of the subplots of the figure
# wspace = 0.2 # the amount of width reserved for blank space between subplots
# hspace = 0.2 # the amount of height reserved for white space between subplotss
fig3.subplots_adjust(left=left, bottom=bottom, right=right, top=top)
fig3.savefig(pwd + '/tg43_' + source + '_comparison_histograms.pdf')
def isodose_plot(place='work', mode='appl'):
"""
Description:
Takes any number of .3ddose files and plots a plethora of diagnostic plots
from the data
Inputs:
:name list_file: a list of file names that are to be loaded
:type list_file: list
"""
pwd = getcwd()
if place == 'home':
target_dir = '/Users/JLucero/MPhysProj/results_not_to_git' # for home
else:
target_dir = '/Users/student/research/results_not_to_git' # for work
if mode == 'pure':
file_name_template = '/tg43_{0}pt0mm_sim.phantom_wo_box.3ddose.gz'
else:
file_name_template = '/tg43appl_{1}mmOut_{0}pt0mm_sim.phantom_wo_applicator_wo_box.3ddose.gz'
vox_size_list = ['1', '2']
fig, ax = subplots(1, 1, figsize=(10, 10), sharex='all', sharey='all')
fig2, ax2 = subplots(1, 1, figsize=(10, 10), sharex='all', sharey='all')
air_kerma = 326.05715
air_kerma_per_hist = 1.1584e-13
max_dwell_time = 0.02917
for voxel_size in vox_size_list:
full_data = DoseFile(target_dir +
file_name_template.format(voxel_size, '30'))
full_data.dose *= get_conversion_factor(
air_kerma, air_kerma_per_hist,
max_dwell_time) # normalize to desired dose of 5 Gy
full_data.dose /= 5 # normalize to desired dose of 5 Gy
full_data.dose *= 100 # normalize to desired dose of 5 Gy
x_min, x_max = full_data.x_extent
y_min, y_max = full_data.y_extent
z_min, z_max = full_data.z_extent
x_pos = array(full_data.positions[0])
y_pos = array(full_data.positions[1])
z_pos = array(full_data.positions[2])
x_pos_mid = (x_pos[:-1] + x_pos[1:]) / 2.0
y_pos_mid = (y_pos[:-1] + y_pos[1:]) / 2.0
z_pos_mid = (z_pos[:-1] + z_pos[1:]) / 2.0
# print x_pos_mid.size, y_pos_mid.size, full_data.dose[:, :, position_to_index(0.0, z_pos)].size
# exit(0)
xy_contour = ax.contourf(
x_pos_mid,
y_pos_mid,
full_data.dose[:, :, position_to_index(0.0, z_pos)].transpose(),
arange(0, 110, 10),
# [5, 10, 20, 50, 100]
# cmap=get_cmap('Purples')
)
# ax.set_title(vox_size_list,fontsize=14)
xz_contour = ax2.contourf(
x_pos_mid,
z_pos_mid,
full_data.dose[:, position_to_index(0.0, y_pos), :].transpose(),
arange(0, 110, 10),
# [5, 10, 20, 50, 100]
# cmap=get_cmap('Purples')
)
# ax2.set_title(vox_size_list, fontsize=14)
# ax.grid(True)
ax.xaxis.set_tick_params(labelsize=14)
ax.yaxis.set_tick_params(labelsize=14)
ax.set_xticks(arange(-10, 10 + 1, 2))
ax.set_xlim([-10, 10])
ax.set_yticks(arange(-10, 10 + 1, 2))
ax.set_ylim([-10, 10])
# ax.vlines([-2, 2], -10, 10, linestyles='dashed', lw=2.0)
# ax.hlines([-2, 2], -10, 10, linestyles='dashed', lw=2.0)
# ax2.grid(True)
ax2.xaxis.set_tick_params(labelsize=14)
ax2.yaxis.set_tick_params(labelsize=14)
ax2.set_xticks(arange(-10, 10 + 1, 2))
ax2.set_xlim([-10, 10])
ax2.set_yticks(arange(-10, 10 + 1, 2))
ax2.set_ylim([-10, 10])
# ax2.vlines([-2, 2], -10, 10, linestyles='dashed', lw=2.0)
fig.text(0.01,
0.51,
'y-axis (cm)',
fontsize=27,
rotation='vertical',
va='center')
fig.text(0.43, 0.03, 'x-axis (cm)', fontsize=27, va='center')
# fig.text(
# 0.52, 0.95,
# ,
# fontsize=27, va='center', ha='center'
# )
cax = fig.add_axes([0.91, 0.09, 0.01, 0.79])
cbar1 = fig.colorbar(xy_contour,
cax=cax,
orientation='vertical',
ax=ax,
ticks=arange(0, 110, 10))
cbar1.set_label('Percentage Dose (%)', fontsize=24)
cbar1.ax.tick_params(labelsize=14)
fig.tight_layout()
left = 0.1 # the left side of the subplots of the figure
right = 0.89 # the right side of the subplots of the figure
bottom = 0.09 # the bottom of the subplots of the figure
top = 0.88 # the top of the subplots of the figure
# wspace = 0.2 # the amount of width reserved for blank space between subplots
# hspace = 0.2 # the amount of height reserved for white space between subplotss
fig.subplots_adjust(left=left, bottom=bottom, right=right, top=top)
fig.savefig(pwd + '/tg43_' + voxel_size +
'_xy_isodose_profile_subplots.pdf')
fig2.text(0.01,
0.51,
'z-axis (cm)',
fontsize=27,
rotation='vertical',
va='center')
fig2.text(0.43, 0.03, 'x-axis (cm)', fontsize=27, va='center')
# fig2.text(
# 0.52, 0.95,
# sup_title,
# fontsize=27, va='center', ha='center'
# )
cax2 = fig2.add_axes([0.90, 0.09, 0.01, 0.86])
cbar2 = fig2.colorbar(xz_contour,
cax=cax2,
orientation='vertical',
ax=ax2,
ticks=arange(0, 110, 10))
cbar2.set_label('Percentage Dose (%)', fontsize=24)
# cbar2.set_clim([0, 100])
cbar2.ax.tick_params(labelsize=14)
fig2.tight_layout()
left = 0.1 # the left side of the subplots of the figure
right = 0.888 # the right side of the subplots of the figure
bottom = 0.09 # the bottom of the subplots of the figure
top = 0.95 # the top of the subplots of the figure
# wspace = 0.2 # the amount of width reserved for blank space between subplots
# hspace = 0.2 # the amount of height reserved for white space between subplotss
fig2.subplots_adjust(left=left, bottom=bottom, right=right, top=top)
fig2.savefig(pwd + '/tg43_' + voxel_size +
'mm_xz_isodose_profile_subplots.pdf')
close(fig)
close(fig2)
def generate_tdvh_tg43():
pwd = getcwd()
# target_dir = '/Users/JLucero/MPhysProj/results_not_to_git' # for home
target_dir = '/Users/student/research/results_not_to_git' # for work
file_tg43_0point5mm = target_dir + \
'/tg43_0shield_0.5mm_sim.phantom_wo_box.3ddose'
file_tg43_1point0mm = target_dir + \
'/tg43_0shield_1mm_sim.phantom_wo_box.3ddose'
file_tg43_2point0mm = target_dir + \
'/tg43_0shield_2mm_sim.phantom_wo_box.3ddose'
file_tg43_applicator_0point5mm = target_dir + \
'/tg43_applicator_0.5mm_sim.phantom_wo_applicator_wo_box.3ddose'
file_tg43_applicator_1point0mm = target_dir + \
'/tg43_applicator_1mm_sim.phantom_wo_applicator_wo_box.3ddose'
file_tg43_applicator_2point0mm = target_dir + \
'/tg43_applicator_2mm_sim.phantom_wo_applicator_wo_box.3ddose'
file_dict = {
(0, 0): file_tg43_0point5mm,
(0, 1): file_tg43_1point0mm,
(0, 2): file_tg43_2point0mm,
(1, 0): file_tg43_applicator_0point5mm,
(1, 1): file_tg43_applicator_1point0mm,
(1, 2): file_tg43_applicator_2point0mm
}
color_list = ['darkgreen', 'purple', 'darkorange', 'saddlebrown']
shield_type_list = [
'Unshielded', '90 degree shield', '180 degree shield',
'270 degree shield'
]
vxl_size_lst = [
'Voxel size = (0.5 mm)^{3}', 'Voxel size = (1.0 mm)^{3}',
'Voxel size = (2.0 mm)^{3}'
]
fig, ax = subplots(2, 1, figsize=(10, 10), sharex='all', sharey='all')
fig2, ax2 = subplots(2, 1, figsize=(10, 10), sharex='all', sharey='all')
for index1 in xrange(2):
for index2 in xrange(3):
if index1 == 0:
pass
else:
main_data = DoseFile(file_dict[(index1, index2)])
# converts to Gy; norm to individual max dwell time
data_flat = main_data.dose.flatten() * 8.2573429808917e13
n, bins, __ = ax[index1].hist(data_flat,
bins=500,
color=color_list[index1],
label=shield_type_list[index1],
weights=zeros_like(data_flat) +
1. / data_flat.size * 100,
alpha=0.4)
n_cum_base = n[::-1].cumsum()[::-1]
ax2[index1].loglog(bins[:-1],
n_cum_base,
color=color_list[index1],
label=shield_type_list[index1])
for i in xrange(3):
ax[i].legend(loc=0, prop={'size': 10})
ax[i].set_title(vxl_size_lst[i], fontsize=20)
ax[i].xaxis.set_tick_params(labelsize=17)
ax[i].yaxis.set_tick_params(labelsize=17)
ax2[i].legend(loc=0, prop={'size': 10})
ax2[i].set_title(vxl_size_lst[i], fontsize=20)
ax2[i].xaxis.set_tick_params(labelsize=17)
ax2[i].yaxis.set_tick_params(labelsize=17)
fig.text(0.03,
0.51,
'Volume (%)',
fontsize=22,
rotation='vertical',
va='center')
fig.text(0.46, 0.03, 'Dose (Gy)', fontsize=22, va='center')
fig.text(0.52,
0.95,
'Dose Volume Histograms \n With Volume Correction; ncase = 1E9',
fontsize=22,
va='center',
ha='center')
fig.tight_layout()
left = 0.125 # the left side of the subplots of the figure
right = 0.9 # the right side of the subplots of the figure
bottom = 0.09 # the bottom of the subplots of the figure
top = 0.88 # the top of the subplots of the figure
# wspace = 0.2 # the amount of width reserved for blank space between subplots
# hspace = 0.2 # the amount of height reserved for white space between subplotss
fig.subplots_adjust(left=left, top=top, right=right, bottom=bottom)
fig.savefig(pwd + '/dose_volume_histogram.pdf')
fig2.text(0.03,
0.51,
'Volume (%)',
fontsize=22,
rotation='vertical',
va='center')
fig2.text(0.45, 0.03, 'Dose (Gy)', fontsize=22, va='center')
fig2.text(0.52,
0.95,
'Dose Volume Histograms \n With Volume Correction; ncase = 1E9',
fontsize=22,
va='center',
ha='center')
fig2.tight_layout()
left = 0.125 # the left side of the subplots of the figure
right = 0.9 # the right side of the subplots of the figure
bottom = 0.09 # the bottom of the subplots of the figure
top = 0.88 # the top of the subplots of the figure
# wspace = 0.2 # the amount of width reserved for blank space between subplots
# hspace = 0.2 # the amount of height reserved for white space between subplotss
fig2.subplots_adjust(left=left, top=top, right=right, bottom=bottom)
fig2.savefig(pwd + '/cumulative_dose_volume_histogram.pdf')
def dose_position_plots():
"""
Description:
Takes any number of .3ddose files and plots a plethora of diagnostic plots
from the data
Inputs:
:name list_file: a list of file names that are to be loaded
:type list_file: list
"""
pwd = getcwd()
# target_dir = '/Users/JLucero/MPhysProj/results_not_to_git' for home
target_dir = '/Users/student/research/results_not_to_git' # for work
file_template = target_dir + \
'/tg43_applicator_{0}_sim.phantom_wo_applicator_wo_box.3ddose'
vox_size_list = ['0.5mm', '1mm', '2mm']
title_list = ['X - axis', 'Y - axis', 'Z - axis']
for fig_index in xrange(3): # iterate through voxel sizes
fig, ax = subplots(3, 1, figsize=(10, 10), sharex='col')
full_data = DoseFile(file_template.format(vox_size_list[fig_index]))
Nx, Ny, Nz = full_data.shape
# full_data.dose *= 2.2861e14 # scale to total treatment time
full_data.dose *= 8.2573429808917e13 # scale to maximum individual dwell time
x_min, x_max = full_data.x_extent
y_min, y_max = full_data.y_extent
z_min, z_max = full_data.z_extent
for index1 in xrange(3): # iterate through axes
if index1 == 0:
ax[index1].plot(
linspace(x_min, x_max, Nx),
full_data.dose[Nz // 2, Ny // 2, :],
# yerr=full_data.uncertainty[Nz // 2, Ny // 2, :],
lw=3.0)
elif index1 == 1:
ax[index1].plot(
linspace(y_min, y_max, Ny),
full_data.dose[Nz // 2, :, Nx // 2],
# yerr=full_data.uncertainty[Nz // 2, :, Nx // 2],
lw=3.0)
else:
ax[index1].plot(
linspace(z_min, z_max, Nz),
full_data.dose[:, Ny // 2, Nx // 2],
# yerr=full_data.uncertainty[:, Ny // 2, Nx // 2],
lw=3.0)
for n in xrange(3):
# ax[n].legend(loc=0,prop={'size':8})
ax[n].grid(True)
ax[n].set_title(title_list[n], fontsize=20)
ax[n].xaxis.set_tick_params(labelsize=14)
ax[n].yaxis.set_tick_params(labelsize=14)
# if n == 2:
# ax[n].set_xticks(arange(z_min, z_max))
fig.text(0.01,
0.51,
'Dose (Gy)',
fontsize=27,
rotation='vertical',
va='center')
fig.text(0.43, 0.03, 'Position (cm)', fontsize=27, va='center')
fig.text(
0.52, 0.95,
'Absolute Dose vs. Position (' + \
vox_size_list[fig_index] + ')^{3} \n With Volume Correction; ncase = 1E10',
fontsize=27, va='center', ha='center'
)
fig.tight_layout()
left = 0.125 # the left side of the subplots of the figure
right = 0.95 # the right side of the subplots of the figure
bottom = 0.09 # the bottom of the subplots of the figure
top = 0.87 # the top of the subplots of the figure
# wspace = 0.2 # the amount of width reserved for blank space between subplots
# hspace = 0.2 # the amount of height reserved for white space between subplotss
fig.subplots_adjust(left=left,
bottom=bottom,
right=right,
top=top
# wspace=wspace, hspace=hspace
)
fig.savefig(pwd + '/tg43_applicator_dosage_comparison_' +
vox_size_list[fig_index] + '.pdf')