def generate_mr_signed_in_short_range(out_dir, patient_id):
sb = StudyBuilder(patient_position="HFS",
patient_id=patient_id,
patients_name="MrSigned^InShortRange",
patients_birthdate="20121212")
ct = sb.build_mr(num_voxels=[48, 64, 10],
voxel_size=[4, 3, 4], # [mm]
pixel_representation=get_pixel_representation('signed'))
ct.clear(stored_value=0)
ct.add_box(size=[25, 50, 5], center=[0, 0, 0], stored_value=12345, mode='set')
# Smallest stored value is: 0 (in short range)
# Largest stored value is: 12345 (in short range).
mk_fresh_dir(out_dir)
sb.write(out_dir)
print out_dir
def generate_pt_unsigned_not_in_short_range(out_dir, patient_id):
sb = StudyBuilder(patient_position="HFS",
patient_id=patient_id,
patients_name="PtUnsigned^NotInShortRange",
patients_birthdate="20121212")
pt = sb.build_pt(num_voxels=[48, 64, 10],
voxel_size=[4, 3, 4], # [mm]
pixel_representation=get_pixel_representation('unsigned'),
rescale_slope=1)
pt.clear(stored_value=0)
pt.add_box(size=[25, 50, 5], center=[0, 0, 0], stored_value=54321, mode='set')
# Smallest stored value is: 0 (in short range)
# Largest stored value is: 54321 (greater than 32767).
mk_fresh_dir(out_dir)
sb.write(out_dir)
print out_dir
def generate_ct_unsigned_rescaled_in_short_range(out_dir, patient_id):
sb = StudyBuilder(patient_position="HFS",
patient_id=patient_id,
patients_name="CtUnsigned^InShortRange",
patients_birthdate="20121212")
ct = sb.build_ct(num_voxels=[48, 64, 10],
voxel_size=[4, 3, 4], # [mm]
pixel_representation=get_pixel_representation('unsigned'),
rescale_slope=1,
rescale_intercept=-1024)
ct.clear(stored_value=0)
ct.add_box(size=[25, 50, 5], center=[0, 0, 0], stored_value=12345, mode='set')
# Smallest rescaled value is: 1 * 0 - 1024 = -1024 (in short range)
# Largest rescaled value is: 1 * 54321 - 1024 = 11321 (in short range).
mk_fresh_dir(out_dir)
sb.write(out_dir)
print out_dir
elif series.modality == "RTSTRUCT":
for structure in series.structures:
structure = structure.split(",")
shape = structure[0]
if shape == 'sphere':
name = structure[1]
radius = float(structure[2])
interpreted_type = structure[3]
if len(structure) > 4:
center = [float(c) for c in structure[4].lstrip('[').rstrip(']').split(";")]
else:
center = [0,0,0]
rtstruct.add_sphere(name=name, radius=radius, center=center, interpreted_type=interpreted_type)
elif shape == 'box':
name = structure[1]
size = structure[2]
if size.startswith("[") and size.endswith("]"):
size = [float(c) for c in size.lstrip('[').rstrip(']').split(";")]
else:
size = [float(size),float(size),float(size)]
interpreted_type = structure[3]
if len(structure) > 4:
center = [float(c) for c in structure[4].lstrip('[').rstrip(']').split(";")]
else:
center = [0,0,0]
rtstruct.add_box(name=name, size=size, center=center, interpreted_type=interpreted_type)
elif shape == "external":
rtstruct.add_external_box()
rtstruct.build()
sb.write(args.outdir)
elif series.modality == "RTSTRUCT":
for structure in series.structures:
structure = structure.split(",")
shape = structure[0]
if shape == 'sphere':
name = structure[1]
radius = float(structure[2])
interpreted_type = structure[3]
if len(structure) > 4:
center = [float(c) for c in structure[4].lstrip('[').rstrip(']').split(";")]
else:
center = [0, 0, 0]
rtstruct.add_sphere(name=name, radius=radius, center=center, interpreted_type=interpreted_type)
elif shape == 'box':
name = structure[1]
size = structure[2]
if size.startswith("[") and size.endswith("]"):
size = [float(c) for c in size.lstrip('[').rstrip(']').split(";")]
else:
size = [float(size), float(size), float(size)]
interpreted_type = structure[3]
if len(structure) > 4:
center = [float(c) for c in structure[4].lstrip('[').rstrip(']').split(";")]
else:
center = [0, 0, 0]
rtstruct.add_box(name=name, size=size, center=center, interpreted_type=interpreted_type)
elif shape == "external":
rtstruct.add_external_box()
rtstruct.build()
sb.write(args.outdir)
rtstruct = sb.build_structure_set()
rtstruct.add_external_box()
sph = rtstruct.add_sphere(radius=70,
center=[-50, 0, -100],
name='Sph-Organ',
interpreted_type='CAVITY')
sph2 = rtstruct.add_sphere(radius=25,
center=[0, 0, 0],
name='Sph-PTV',
interpreted_type='PTV')
rtplan = sb.build_static_plan()
b1 = rtplan.build_beam(gantry_angle=180, collimator_angle=15, meterset=100)
b1.conform_to_rectangle(1, 1, [0, 0])
rtplan.build(finalize_mlc=False)
modules.conform_mlc_to_roi(b1.rtbeam, sph.roi_contour, sb.current_study)
modules.conform_mlc_to_roi(b1.rtbeam, sph2.roi_contour, sb.current_study)
b1.finalize_mlc()
sb.write(tmpdir)
print tmpdir
import plotting as p
p.plot_cp(rtplan.datasets[0].Beams[0], rtplan.datasets[0].Beams[0].CPs[0])
p.plot_roi_in_cp(rtplan.datasets[0].Beams[0],
rtplan.datasets[0].Beams[0].CPs[0], sph.roi_contour,
sb.current_study)
pp.axis('image')
ct.add_sphere(radius = 25, center = [0,0,0], real_value = -1000, mode = 'set')
print ct.pixel_array.max(),ct.pixel_array.min()
ct.add_box(size = [25,50,25], center = [0,0,0], stored_value = 300, mode = 'add')
print ct.pixel_array.max(),ct.pixel_array.min()
assert sb.seriesbuilders['CT'] == [ct]
rtstruct = sb.build_structure_set()
rtstruct.add_external_box()
rtstruct.add_sphere(radius = 25, center = [0,0,0], name='Sph-PTV', interpreted_type='PTV')
rtstruct.add_box(size = [25,50,25], center = [0,0,0], name='Box-Organ', interpreted_type='CAVITY')
rtplan = sb.build_static_plan()
b1 = rtplan.build_beam(gantry_angle = 0, meterset = 100)
b1.conform_to_circle(25, [0,0])
b2 = rtplan.build_beam(gantry_angle = 120, meterset = 91)
b2.conform_to_rectangle(25, 50, [0,0])
b3 = rtplan.build_beam(gantry_angle = 240, meterset = 71)
b3.conform_to_rectangle(50, 25, [50,-50])
assert rtplan.beam_builders == [b1,b2,b3]
rtplan.build()
rtdose = sb.build_dose()
for beam in rtplan.beam_builders:
rtdose.add_lightfield(beam.rtbeam, beam.meterset)
sb.write(tmpdir)
print tmpdir
print ct.pixel_array.max(),ct.pixel_array.min()
ct.add_sphere(radius = 25, center = [0,0,0], real_value = -1000, mode = 'set')
print ct.pixel_array.max(),ct.pixel_array.min()
ct.add_box(size = [25,50,25], center = [0,0,0], stored_value = 300, mode = 'add')
print ct.pixel_array.max(),ct.pixel_array.min()
assert sb.seriesbuilders['CT'] == [ct]
rtstruct = sb.build_structure_set()
rtstruct.add_external_box()
rtstruct.add_sphere(radius = 25, center = [0,0,0], name='Sph-PTV', interpreted_type='PTV')
rtstruct.add_box(size = [25,50,25], center = [0,0,0], name='Box-Organ', interpreted_type='CAVITY')
rtplan = sb.build_static_plan()
b1 = rtplan.build_beam(gantry_angle = 0, meterset = 100)
b1.conform_to_circle(25, [0,0])
b2 = rtplan.build_beam(gantry_angle = 120, meterset = 91)
b2.conform_to_rectangle(25, 50, [0,0])
b3 = rtplan.build_beam(gantry_angle = 240, meterset = 71)
b3.conform_to_rectangle(50, 25, [50,-50])
assert rtplan.beam_builders == [b1,b2,b3]
rtplan.build()
rtdose = sb.build_dose()
for beam in rtplan.beam_builders:
rtdose.add_lightfield(beam.rtbeam, beam.meterset)
sb.write("/tmp/studybuilder")