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 build_orientation(patient_position,
column_direction,
row_direction,
frame_of_reference_uid=None):
sb = StudyBuilder(patient_position=patient_position,
patient_id="oblique_mr_x_z",
patient_name="Amanda^Grayson^Mother^Of^Spock",
patient_birthdate="20121212")
if frame_of_reference_uid != None:
sb.current_study['FrameOfReferenceUID'] = frame_of_reference_uid
print "building %s..." % (patient_position, )
print "ct"
ct = sb.build_mr(num_voxels=[7, 7, 7],
voxel_size=[4, 4, 4],
pixel_representation=0,
row_direction=row_direction,
column_direction=column_direction)
ct.clear(stored_value=0)
ct.add_box(size=[4, 4, 4], center=[-12, -12, -12], stored_value=100)
ct.add_box(size=[4, 4, 4], center=[-12, -12, -8], stored_value=200)
ct.add_box(size=[4, 4, 4], center=[-12, -12, -4], stored_value=300)
ct.add_box(size=[4, 4, 4], center=[-12, -12, 0], stored_value=400)
ct.add_box(size=[4, 4, 4], center=[-12, -12, 4], stored_value=500)
ct.add_box(size=[4, 4, 4], center=[-12, -12, 8], stored_value=600)
ct.add_box(size=[4, 4, 4], center=[-12, -12, 12], stored_value=700)
ct.add_box(size=[4, 4, 4], center=[0, 0, -12], stored_value=450)
ct.add_box(size=[4, 4, 4], center=[0, 0, -8], stored_value=450)
ct.add_box(size=[4, 4, 4], center=[0, 0, -4], stored_value=450)
ct.add_box(size=[4, 4, 4], center=[0, 0, 0], stored_value=450)
ct.add_box(size=[4, 4, 4], center=[0, 0, 4], stored_value=450)
ct.add_box(size=[4, 4, 4], center=[0, 0, 8], stored_value=450)
ct.add_box(size=[4, 4, 4], center=[0, 0, 12], stored_value=450)
ct.add_box(size=[4, 4, 4], center=[12, -12, -12], stored_value=100)
ct.add_box(size=[4, 4, 4], center=[12, -8, -12], stored_value=200)
ct.add_box(size=[4, 4, 4], center=[12, -4, -12], stored_value=300)
ct.add_box(size=[4, 4, 4], center=[12, -0, -12], stored_value=400)
ct.add_box(size=[4, 4, 4], center=[12, 4, -12], stored_value=500)
ct.add_box(size=[4, 4, 4], center=[12, 8, -12], stored_value=600)
ct.add_box(size=[4, 4, 4], center=[12, 12, -12], stored_value=700)
ct.build()
return sb
parser.error("Patient position must be specified when writing CT images!")
ib = sb.build_ct(
num_voxels=num_voxels,
voxel_size=voxel_size,
pixel_representation=pixel_representations[series.pixel_representation],
rescale_slope=series.rescale_slope,
rescale_intercept=series.rescale_intercept,
center=np.array(series.center))
elif series.modality == "MR":
if 'PatientPosition' not in sb.current_study:
parser.error("Patient position must be specified when writing MR images!")
ib = sb.build_mr(
num_voxels=num_voxels,
voxel_size=voxel_size,
pixel_representation=pixel_representations[series.pixel_representation],
center=np.array(series.center))
elif series.modality == "PT":
if 'PatientPosition' not in sb.current_study:
parser.error("Patient position must be specified when writing MR images!")
ib = sb.build_pt(
num_voxels=num_voxels,
voxel_size=voxel_size,
pixel_representation=pixel_representations[series.pixel_representation],
rescale_slope=series.rescale_slope,
center=np.array(series.center))
elif series.modality == "RTDOSE":
ib = sb.build_dose(
num_voxels=num_voxels,
parser.error("Patient position must be specified when writing CT images!")
ib = sb.build_ct(
num_voxels=num_voxels,
voxel_size=voxel_size,
pixel_representation=pixel_representations[series.pixel_representation],
rescale_slope=series.rescale_slope,
rescale_intercept=series.rescale_intercept,
center=np.array(series.center))
elif series.modality == "MR":
if 'PatientPosition' not in sb.current_study:
parser.error("Patient position must be specified when writing MR images!")
ib = sb.build_mr(
num_voxels=num_voxels,
voxel_size=voxel_size,
pixel_representation=pixel_representations[series.pixel_representation],
center=np.array(series.center))
elif series.modality == "PT":
if 'PatientPosition' not in sb.current_study:
parser.error("Patient position must be specified when writing MR images!")
ib = sb.build_pt(
num_voxels=num_voxels,
voxel_size=voxel_size,
pixel_representation=pixel_representations[series.pixel_representation],
rescale_slope=series.rescale_slope,
center=np.array(series.center))
elif series.modality == "RTDOSE":
ib = sb.build_dose(
num_voxels=num_voxels,