def mu_density_per_patient_and_display(filepaths,
display=True,
grid_resolution=1,
max_leaf_gap=400,
leaf_pair_widths=[5] * 80):
print('Starting')
print('...calculating beam no. 0')
mu_density = mu_density_per_beam_and_display(
filepaths[0],
display=True,
grid_resolution=grid_resolution,
max_leaf_gap=max_leaf_gap,
leaf_pair_widths=leaf_pair_widths)
if len(filepaths) > 1:
for i in range(len(filepaths) - 1):
print('...calculating beam no. ' + str(i + 1))
mu_density += mu_density_per_beam_and_display(
filepaths[i + 1],
display=True,
grid_resolution=grid_resolution,
max_leaf_gap=max_leaf_gap,
leaf_pair_widths=leaf_pair_widths)
if display:
grid = mudensity.get_grid(max_leaf_gap=max_leaf_gap,
grid_resolution=grid_resolution,
leaf_pair_widths=leaf_pair_widths)
mudensity.display_mu_density(grid, mu_density)
print('Total MU density of Current Case')
plt.show()
return mu_density
def calc_mu_density_per_segment_and_display(data,
check_mlc=True,
display=True,
grid_resolution=1,
max_leaf_gap=400,
leaf_pair_widths=[5] * 80):
mu = data.loc[:, 'Step Dose/Actual Value (Mu)'].to_numpy()
mlc_1 = np.expand_dims(data.loc[:, [
'Y1 Leaf ' + str(i + 1) + '/Scaled Actual (mm)'
for i in range(len(leaf_pair_widths))
]].to_numpy(),
axis=-1)
mlc_2 = np.expand_dims(data.loc[:, [
'Y2 Leaf ' + str(i + 1) + '/Scaled Actual (mm)'
for i in range(len(leaf_pair_widths))
]].to_numpy(),
axis=-1)
mlc = np.append(mlc_1, mlc_2, 2)
jaw = data.loc[:, [
'X1 Diaphragm/Scaled Actual (mm)', 'X2 Diaphragm/Scaled Actual (mm)'
]].to_numpy()
jaw = np.clip(jaw, -200, 200)
if check_mlc:
print(
'.........showing the setup MLC-jaw positions of current segment')
# Check MLC and jaw coordinates
plt.plot(mlc[0] * np.array([-1, 1]), np.arange(-200, 200, 5))
plt.axhline(-jaw[0, 0], xmin=-200, xmax=200, color='red')
plt.axhline(jaw[0, 1], xmin=-200, xmax=200, color='green')
plt.xlim(-200, 200)
plt.ylim(200, -200)
plt.show()
mu_density = mudensity.calc_mu_density(mu,
mlc,
jaw,
grid_resolution=grid_resolution,
max_leaf_gap=max_leaf_gap,
leaf_pair_widths=leaf_pair_widths)
if display:
grid = mudensity.get_grid(max_leaf_gap=max_leaf_gap,
grid_resolution=grid_resolution,
leaf_pair_widths=leaf_pair_widths)
mudensity.display_mu_density(grid, mu_density)
print('......MU Density of Current Segment')
plt.show()
return mu_density
def calc_mu_density_per_segment_and_display(cp,
current_weight,
total_mu,
check_mlc=True,
display=True,
grid_resolution=1,
max_leaf_gap=400,
leaf_pair_widths=[5] * 80):
# Ref: correlate the DICOM MLC leaf positions with Monaco display
# multipling by [-1, 1]
raw_mlc = np.array(
[cp.BeamLimitingDevicePositionSequence[1].LeafJawPositions])
mlc = np.swapaxes(raw_mlc.reshape(1, 2, len(leaf_pair_widths)), 1,
2) * np.array([-1, 1])
mlc = np.append(mlc, mlc, 0)
jaw = np.array([cp.BeamLimitingDevicePositionSequence[0].LeafJawPositions
]) * np.array([-1, 1])
jaw = np.append(jaw, jaw, 0)
mu = [current_weight * total_mu, cp.CumulativeMetersetWeight * total_mu]
if check_mlc:
print(
'.........showing the setup MLC-jaw positions of current segment')
# Check MLC and jaw coordinates
plt.plot(mlc[0] * np.array([-1, 1]), np.arange(-200, 200, 5))
plt.axhline(-jaw[0, 0], xmin=-200, xmax=200, color='red')
plt.axhline(jaw[0, 1], xmin=-200, xmax=200, color='green')
plt.xlim(-200, 200)
plt.ylim(200, -200)
plt.show()
mu_density = mudensity.calc_mu_density(mu,
mlc,
jaw,
grid_resolution=grid_resolution,
max_leaf_gap=max_leaf_gap,
leaf_pair_widths=leaf_pair_widths)
current_weight = cp.CumulativeMetersetWeight
if display:
grid = mudensity.get_grid(max_leaf_gap=max_leaf_gap,
grid_resolution=grid_resolution,
leaf_pair_widths=leaf_pair_widths)
mudensity.display_mu_density(grid, mu_density)
print('......MU Density of Current Segment')
plt.show()
return mu_density
def mu_density_per_beam_and_display(beam,
total_mu,
display=True,
grid_resolution=1,
max_leaf_gap=400,
leaf_pair_widths=[5] * 80):
N_CP = beam.NumberOfControlPoints
print('......calculating segment no. 0')
mu_density = calc_mu_density_per_segment_and_display(
beam.ControlPointSequence[0],
0,
total_mu=total_mu,
check_mlc=True,
display=True,
grid_resolution=grid_resolution,
max_leaf_gap=max_leaf_gap,
leaf_pair_widths=leaf_pair_widths)
if N_CP > 1:
current_weight = beam.ControlPointSequence[0].CumulativeMetersetWeight
for i in range(N_CP - 1):
print('......calculating segment no. ' + str(i + 1))
mu_density += calc_mu_density_per_segment_and_display(
beam.ControlPointSequence[i + 1],
current_weight,
total_mu=total_mu,
check_mlc=False,
display=False,
grid_resolution=grid_resolution,
max_leaf_gap=max_leaf_gap,
leaf_pair_widths=leaf_pair_widths)
current_weight = beam.ControlPointSequence[
i + 1].CumulativeMetersetWeight
if display:
grid = mudensity.get_grid(max_leaf_gap=max_leaf_gap,
grid_resolution=grid_resolution,
leaf_pair_widths=leaf_pair_widths)
mudensity.display_mu_density(grid, mu_density)
print('...MU Density of Current Beam')
plt.show()
print('..............................................')
return mu_density
def mu_density_per_patient_and_display(file,
fraction_group,
display=True,
grid_resolution=1,
max_leaf_gap=400,
leaf_pair_widths=[5] * 80):
print('Starting')
print('...calculating beam no. 0')
total_mu = fraction_group.ReferencedBeamSequence[0].BeamMeterset
mu_density = mu_density_per_beam_and_display(
file.BeamSequence[0],
total_mu,
display=True,
grid_resolution=grid_resolution,
max_leaf_gap=max_leaf_gap,
leaf_pair_widths=leaf_pair_widths)
if fraction_group.NumberOfBeams > 1:
for i in range(fraction_group.NumberOfBeams - 1):
print('...calculating beam no. ' + str(i + 1))
total_mu = fraction_group.ReferencedBeamSequence[i +
1].BeamMeterset
mu_density += mu_density_per_beam_and_display(
file.BeamSequence[i + 1],
total_mu,
display=True,
grid_resolution=grid_resolution,
max_leaf_gap=max_leaf_gap,
leaf_pair_widths=leaf_pair_widths)
if display:
grid = mudensity.get_grid(max_leaf_gap=max_leaf_gap,
grid_resolution=grid_resolution,
leaf_pair_widths=leaf_pair_widths)
mudensity.display_mu_density(grid, mu_density)
print('Total MU density of Current Case')
plt.show()
return mu_density
def mu_density_per_beam_and_display(filepath,
display=True,
grid_resolution=1,
max_leaf_gap=400,
leaf_pair_widths=[5] * 80):
data = _read_beam_log_data(filepath)
print('......calculating segment no. 0')
mu_density = calc_mu_density_per_segment_and_display(
data[data['Segment'] == 1],
check_mlc=True,
display=True,
grid_resolution=grid_resolution,
max_leaf_gap=max_leaf_gap,
leaf_pair_widths=leaf_pair_widths)
if np.amax(data['Segment']) > 1:
for i in range(np.amax(data['Segment']) - 1):
print('......calculating segment no. ' + str(i + 1))
mu_density += calc_mu_density_per_segment_and_display(
data[data['Segment'] == (i + 2)],
check_mlc=False,
display=False,
grid_resolution=grid_resolution,
max_leaf_gap=max_leaf_gap,
leaf_pair_widths=leaf_pair_widths)
if display:
grid = mudensity.get_grid(max_leaf_gap=max_leaf_gap,
grid_resolution=grid_resolution,
leaf_pair_widths=leaf_pair_widths)
mudensity.display_mu_density(grid, mu_density)
print('...MU Density of Current Beam')
plt.show()
print('..............................................')
return mu_density
dicom_out_filepath = '{}{}.mudensity.png'.format(
prepend_string, dicom_filename)
filepath_mu_density_map[dicom_out_filepath] = dicom
diff_filepath = '{}[{}]-[{}].mudensity_diff.png'.format(
prepend_string, trf_filename, dicom_filename)
filepath_mu_density_diff_map[diff_filepath] = diff
maximum_mudensity = np.max(
[mudensity for _, mudensity in filepath_mu_density_map.items()])
grid = get_grid(grid_resolution=grid_resolution)
for filepath, mudensity in filepath_mu_density_map.items():
plt.figure()
display_mu_density(grid, mudensity, vmin=0, vmax=maximum_mudensity)
plt.savefig(filepath, dpi=image_dpi)
maximum_diff = np.max(
np.abs([
mudensity_diff
for _, mudensity_diff in filepath_mu_density_diff_map.items()
]))
for filepath, mudensity_diff in filepath_mu_density_diff_map.items():
plt.figure()
display_mu_density(grid,
mudensity_diff,
vmin=-maximum_diff,
vmax=maximum_diff,
cmap='seismic')
from pymedphys.mudensity import calc_mu_density, get_grid, display_mu_density
leaf_pair_widths = (5, 5, 5)
max_leaf_gap = 10
mu = [0, 2, 5, 10]
mlc = [[[1, 1], [2, 2], [3, 3]], [[2, 2], [3, 3], [4, 4]],
[[-2, 3], [-2, 4], [-2, 5]], [[0, 0], [0, 0], [0, 0]]]
jaw = [[7.5, 7.5], [7.5, 7.5], [-2, 7.5], [0, 0]]
grid = get_grid(max_leaf_gap=max_leaf_gap, leaf_pair_widths=leaf_pair_widths)
mu_density = calc_mu_density(mu,
mlc,
jaw,
max_leaf_gap=max_leaf_gap,
leaf_pair_widths=leaf_pair_widths)
display_mu_density(grid, mu_density)
# In[12]:
mu_density_dicom = np.loadtxt(
'C:/Users/sjiae08541/Documents/Project_MU_density/mu_density_dicom.txt')
# In[13]:
grid_resolution = 1
max_leaf_gap = 400
leaf_pair_widths = [5] * 80
grid = mudensity.get_grid(max_leaf_gap=max_leaf_gap,
grid_resolution=grid_resolution,
leaf_pair_widths=leaf_pair_widths)
mudensity.display_mu_density(grid, -mu_density + np.flip(mu_density_dicom))
# In[ ]:
# In[14]:
### Lulu's Implementation with PyMedPhys
from pymedphys import Delivery
# In[15]:
delivery_data = Delivery.from_logfile(filepaths[0])
mu = delivery_data.monitor_units
mlc = delivery_data.mlc
jaw = delivery_data.jaw