def run_generate_automatic_segmentation_leave_one_out(
modalities=('T1', 'FA'),
suffix_result='automaticMulti',
tag_suffix='Multi'):
assert os.path.exists(ph.pfo_mutli_atlas_leave_one_out)
atlas_subjects = ph.atlas_subjects
for target_chart_name in [ph.selected_target]:
atlas_without_one = np.sort(
list(set(atlas_subjects) - {ph.selected_target}))
print(
'\n\nLeave one out segmentation [START]:\nSub-template is {0}\nTarget is {1}\n Spot target started!!\n'
'\n'.format(atlas_without_one, target_chart_name))
assert target_chart_name not in atlas_without_one
spot_sj = SpotDS(atlas_pfo=ph.pfo_mutli_atlas_leave_one_out,
target_pfo=ph.pfo_target,
target_name=target_chart_name,
parameters_tag='CrossValidation' + tag_suffix)
# Template parameters:
spot_sj.atlas_name = 'Multi Atlas Newborn Rabbit' # Multi Atlas Newborn Rabbit
spot_sj.atlas_list_charts_names = atlas_without_one
spot_sj.atlas_list_suffix_modalities = ['T1', 'S0', 'V1', 'MD', 'FA']
spot_sj.atlas_list_suffix_masks = ['roi_mask', 'roi_reg_mask']
spot_sj.atlas_reference_chart_name = '1305'
spot_sj.atlas_segmentation_suffix = 'segm'
spot_sj.arch_suffix_masks = ['roi_mask', 'reg_mask', 'reg_mask']
spot_sj.arch_automatic_segmentations_name_folder = suffix_result
# --- target parameters
spot_sj.target_list_suffix_modalities = ['T1', 'S0', 'V1', 'MD', 'FA']
spot_sj.target_name = target_chart_name
# --- Utils
spot_sj.bfc_corrector_cmd = ph.bfc_corrector_cmd
# --- Propagator option
spot_sj.propagation_options['Affine_modalities'] = modalities
spot_sj.propagation_options['Affine_reg_masks'] = (
) # if (), there is a single mask for all mods
spot_sj.propagation_options['Affine_parameters'] = ' -speeeeed '
spot_sj.propagation_options[
'N_rigid_modalities'] = modalities # if empty, no non-rigid step.
spot_sj.propagation_options['N_rigid_reg_masks'] = (
) # if [], same mask for all modalities
spot_sj.propagation_options['N_rigid_slim_reg_mask'] = False
spot_sj.propagation_options['N_rigid_mod_diff_bfc'] = (
'T1', ) # empty list no diff bfc. - put a comma!!
spot_sj.propagation_options[
'N_rigid_parameters'] = ' -be 0.5 -ln 6 -lp 4 -smooR 0.07 -smooF 0.07 '
spot_sj.propagation_options['N_rigid_same_mask_moving'] = False
spot_sj.propagation_options[
'N_reg_mask_target'] = 0 # 0 roi_mask, 1 reg_mask
spot_sj.propagation_options[
'N_reg_mask_moving'] = 1 # 0 roi_mask, 1 reg_mask
spot_sj.propagation_options['Final_smoothing_factor'] = 0
# --- Propagator controller
spot_sj.propagation_controller['Aff_alignment'] = True
spot_sj.propagation_controller['Propagate_aff_to_segm'] = True
spot_sj.propagation_controller['Propagate_aff_to_mask'] = True
spot_sj.propagation_controller['Get_N_rigid_slim_mask'] = True
spot_sj.propagation_controller['Get_differential_BFC'] = True
spot_sj.propagation_controller['N_rigid_alignment'] = True
spot_sj.propagation_controller['Propagate_n_rigid'] = True
spot_sj.propagation_controller['Smooth_results'] = True
spot_sj.propagation_controller['Stack_warps_and_segms'] = True
# --- Fuser option
spot_sj.fuser_options['Fusion_methods'] = ['MV', 'STEPS', 'STAPLE'
] # 'MV', multi atlas only.
spot_sj.fuser_options['Tp_mod_to_stack'] = 0
spot_sj.fuser_options['STAPLE_params'] = OrderedDict([('pr_1', None)])
spot_sj.fuser_options['STEPS_params'] = OrderedDict([
('pr_{0}_{1}'.format(k, n), [k, n, 0.4]) for n in [5, 7, 9]
for k in [5, 7, 10]
])
# --- Fuser controller
spot_sj.fuser_controller['Fuse'] = True
spot_sj.fuser_controller['Save_results'] = True
spot_sj.spot_on_target_initialise()
spot_sj.propagate()
spot_sj.fuse()
print('\n\nAutomatic initialisation [END] for subject {0} '
'\n Complete atlas chart was {1} \n'.format(
target_chart_name, atlas_without_one))
def spot_a_list_of_rabbits(subjects_list):
for sj_target in subjects_list:
print(
'\nAutomatic segmentation with SPOT-A-NeonatalRabbit - subject {} started.\n'
.format(sj_target))
sj_parameters = pickle.load(
open(jph(pfo_subjects_parameters, sj_target), 'r'))
study = sj_parameters['study']
category = sj_parameters['category']
pfo_target = jph(root_study_rabbits, 'A_data', study, category,
sj_target, 'stereotaxic')
# Parameter tag z-SPOT_<TAG>
if study == 'W8':
parameters_tag = 'P3'
multi_atlas_subjects_list = multi_atlas_W8_subjects
pfo_sj_atlas = jph(root_study_rabbits, 'A_MultiAtlas_W8',
sj_target)
root_multi_atlas = root_atlas_W8
elif study == 'ACS' or study == 'PTB' or study == 'TestStudy':
parameters_tag = 'P2'
multi_atlas_subjects_list = multi_atlas_subjects
pfo_sj_atlas = jph(root_study_rabbits, 'A_MultiAtlas', sj_target)
root_multi_atlas = root_atlas
else:
raise IOError(
'Study for subject {} not feasible.'.format(sj_target))
# parameters_tag = 'P2'
if sj_parameters['in_atlas']:
# SPOT only the rabbits not already in the atlas.
print(
'Subject {} already in atlas. No automatic segmentation needed'
.format(sj_target))
pfi_T1_segm_from_atlas = jph(pfo_sj_atlas, 'segm',
'{}_segm.nii.gz'.format(sj_target))
assert os.path.exists(pfi_T1_segm_from_atlas)
cmd0 = 'mkdir -p {}'.format(jph(pfo_target, 'segm'))
cmd1 = 'cp {} {}'.format(
pfi_T1_segm_from_atlas,
jph(pfo_target, 'segm', '{}_segm.nii.gz'.format(sj_target)))
print_and_run(cmd0)
print_and_run(cmd1)
return
# --- initialise the class spot:
spot_sj = SpotDS(atlas_pfo=root_multi_atlas,
target_pfo=pfo_target,
target_name=sj_target,
parameters_tag=parameters_tag)
"""
Parameters tag -> correspondence:
'P1' -> Mono modal T1 + BFC on T1.
'P2' -> Multi modal T1 affine only.
"""
# Template parameters:
spot_sj.atlas_name = 'MANRround3' # Multi Atlas Newborn Rabbit
spot_sj.atlas_list_charts_names = multi_atlas_subjects_list
spot_sj.atlas_list_suffix_modalities = ['T1', 'S0', 'V1', 'MD', 'FA']
spot_sj.atlas_list_suffix_masks = [
'roi_mask', 'roi_reg_mask', 'brain_mask'
]
spot_sj.atlas_segmentation_suffix = 'segm'
# Architecture names - default 'automatic'.
spot_sj.arch_automatic_segmentations_name_folder = sj_parameters[
'names_architecture']['final_segm_strx']
# --- target parameters
spot_sj.target_list_suffix_modalities = ['T1', 'S0', 'V1', 'MD', 'FA']
spot_sj.target_name = sj_target
# --- Utils
spot_sj.bfc_corrector_cmd = bfc_corrector_cmd
spot_sj.num_cores_run = num_cores_run
if sj_parameters['options_brain_mask']['method'] is None:
use_slim_mask = False
else:
use_slim_mask = True
if sj_parameters['category'] == 'ex_vivo' or sj_parameters[
'category'] == 'ex_vivo01' or sj_parameters[
'category'] == 'ex_vivo02':
# --- Propagator option
spot_sj.atlas_reference_chart_name = '1305'
spot_sj.propagation_options['Affine_modalities'] = ('T1', 'FA')
spot_sj.propagation_options['Affine_reg_masks'] = (
'T1', 'S0') # if (), there is a single mask for all modalities
spot_sj.propagation_options['Affine_parameters'] = ' -speeeeed '
spot_sj.propagation_options['Affine_slim_reg_mask'] = use_slim_mask
spot_sj.propagation_options['N_rigid_modalities'] = (
) # ('T1', 'FA') # if empty, no non-rigid step.
spot_sj.propagation_options['N_rigid_reg_masks'] = (
) #('T1', 'S0') # if [], same mask for all modalities
spot_sj.propagation_options[
'N_rigid_slim_reg_mask'] = use_slim_mask
spot_sj.propagation_options['N_rigid_mod_diff_bfc'] = (
'T1',
) # empty list no diff bfc. - PUT A COMMA IF ONLY ONE SUBJECT!!
spot_sj.propagation_options[
'N_rigid_parameters'] = ' -be 0.9 -ln 6 -lp 1 -smooR 0.07 -smooF 0.07 '
spot_sj.propagation_options['N_rigid_same_mask_moving'] = False
spot_sj.propagation_options[
'N_reg_mask_target'] = 0 # 0 roi_mask, 1 reg_mask
spot_sj.propagation_options[
'N_reg_mask_moving'] = 1 # 0 roi_mask, 1 reg_mask
spot_sj.propagation_options['Final_smoothing_factor'] = 0
elif sj_parameters['category'] == 'in_vivo':
# --- Propagator option
spot_sj.atlas_reference_chart_name = '1305'
spot_sj.propagation_options['Affine_modalities'] = ('T1', )
spot_sj.propagation_options['Affine_reg_masks'] = (
'T1', ) # if (), there is a single mask for all modalities
spot_sj.propagation_options['Affine_parameters'] = ' -speeeeed '
spot_sj.propagation_options['Affine_slim_reg_mask'] = use_slim_mask
spot_sj.propagation_options['N_rigid_modalities'] = (
) # if empty, no non-rigid step. - first attempt with only an affine step.
spot_sj.propagation_options['N_rigid_reg_masks'] = (
) # if [], same mask for all modalities
spot_sj.propagation_options[
'N_rigid_slim_reg_mask'] = use_slim_mask
spot_sj.propagation_options['N_rigid_mod_diff_bfc'] = (
) # empty list no diff bfc. - PUT A COMMA IF ONLY ONE SUBJECT!!
spot_sj.propagation_options[
'N_rigid_parameters'] = ' -be 0.9 -ln 6 -lp 1 -smooR 0.07 -smooF 0.07 '
spot_sj.propagation_options['N_rigid_same_mask_moving'] = False
spot_sj.propagation_options[
'N_reg_mask_target'] = 0 # 0 roi_mask, 1 reg_mask
spot_sj.propagation_options[
'N_reg_mask_moving'] = 1 # 0 roi_mask, 1 reg_mask
spot_sj.propagation_options['Final_smoothing_factor'] = 1
elif sj_parameters['category'] == 'first_trial' or sj_parameters[
'category'] == 'second_trial' or sj_parameters[
'category'] == 'third_trial':
# --- Propagator option
spot_sj.atlas_reference_chart_name = '12503'
spot_sj.propagation_options['Affine_modalities'] = ('T1', 'FA')
spot_sj.propagation_options['Affine_reg_masks'] = (
'T1', 'S0') # if (), there is a single mask for all modalities
spot_sj.propagation_options['Affine_parameters'] = ' -speeeeed '
spot_sj.propagation_options['Affine_slim_reg_mask'] = use_slim_mask
spot_sj.propagation_options['N_rigid_modalities'] = (
'T1', ) # if empty, no non-rigid step.
spot_sj.propagation_options['N_rigid_reg_masks'] = (
'T1', ) # if [], same mask for all modalities
spot_sj.propagation_options[
'N_rigid_slim_reg_mask'] = use_slim_mask
spot_sj.propagation_options['N_rigid_mod_diff_bfc'] = (
) # empty list no diff bfc. - PUT A COMMA EVEN IF ONLY ONE SUBJECT!!
spot_sj.propagation_options[
'N_rigid_parameters'] = ' -be 0.8 -vel -smooR 0.07 -smooF 0.07 '
spot_sj.propagation_options['N_rigid_same_mask_moving'] = False
spot_sj.propagation_options[
'N_reg_mask_target'] = 0 # 0 roi_mask, 1 reg_mask
spot_sj.propagation_options[
'N_reg_mask_moving'] = 1 # 0 roi_mask, 1 reg_mask
spot_sj.propagation_options['Final_smoothing_factor'] = 0
else:
raise IOError(
'Given subject category not recognised for subject {} and category {}.'
.format(sj_target, sj_parameters['category']))
# --- Propagator controller
spot_sj.propagation_controller['Aff_alignment'] = True
spot_sj.propagation_controller['Propagate_aff_to_segm'] = True
spot_sj.propagation_controller['Propagate_aff_to_mask'] = True
spot_sj.propagation_controller['Get_N_rigid_slim_mask'] = True
spot_sj.propagation_controller['Get_differential_BFC'] = True
spot_sj.propagation_controller['N_rigid_alignment'] = True
spot_sj.propagation_controller['Propagate_n_rigid'] = True
spot_sj.propagation_controller['Smooth_results'] = True
spot_sj.propagation_controller['Stack_warps_and_segms'] = True
# --- Fuser option
spot_sj.fuser_options['Fusion_methods'] = [
'MV',
'STAPLE',
'STEPS',
] # ['STAPLE', 'STEPS', ] # 'STAPLE', 'STEPS'
spot_sj.fuser_options['STAPLE_params'] = OrderedDict([('pr1', None)])
spot_sj.fuser_options['STEPS_params'] = OrderedDict([
('pr{0}.{1}'.format(k, n), [k, n, 4]) for n in [9]
for k in [5, 11]
])
# --- Fuser controller
spot_sj.fuser_controller['Fuse'] = True
spot_sj.fuser_controller['Save_results'] = True
spot_sj.spot_on_target_initialise()
t = time.time()
spot_sj.propagate()
spot_sj.fuse()
elapsed = time.time() - t
print('Time to spot subject {} is : {}'.format(sj_target, elapsed))
from collections import OrderedDict
from os.path import join as jph
from spot.tools.system_parameters import bfc_corrector_cmd
from spot.spotter import SpotDS
if __name__ == '__main__':
root_rabbit = '/Volumes/sebastianof/rabbits'
# --- initialise the class spot:
target_name = '4501'
spot_sj = SpotDS(
atlas_pfo=jph(root_rabbit,
'A_atlas'), # here path to the folder with the atlas.
target_pfo=jph(
root_rabbit,
'A_data/PTB/ex_vivo/{0}/stereotaxic'.format(target_name)),
target_name=target_name,
parameters_tag='test')
# Template parameters:
spot_sj.atlas_name = 'MANRround3' # Multi Atlas Newborn Rabbit
spot_sj.atlas_list_charts_names = [
'1201', '1203', '1305', '1404', '1507', '1510', '1702', '1805', '2002',
'2502', '3301', '3404'
]
spot_sj.atlas_list_suffix_modalities = ['T1', 'S0', 'V1', 'MD', 'FA']
spot_sj.atlas_list_suffix_masks = ['roi_mask', 'roi_reg_mask']
spot_sj.atlas_reference_chart_name = '1305'
spot_sj.atlas_segmentation_suffix = 'approved_round3'
for k in sp.fuser_controller.keys():
f.write('{0:<40} : {1} \n'.format(k, sp.fuser_controller[k]))
# f.write('\n--- Stereotaxic alignment options:\n')
# for k in sp.stereotaxic_alignment_options.keys():
# f.write('{0:<40} : {1} \n'.format(k, sp.stereotaxic_alignment_options[k]))
#
# f.write('\n--- Stereotaxic alignment controller:\n')
# for k in sp.stereotaxic_alignment_controller.keys():
# f.write('{0:<40} : {1} \n'.format(k, sp.stereotaxic_alignment_controller[k]))
if __name__ == '__main__':
from spot.spotter import SpotDS
from collections import OrderedDict
sp = SpotDS('', '', '', '') # dummy test!
# extra utils:
sp.bfc_corrector_cmd = ''
sp.num_cores_run = 8
# Output tagging and intermediate files
sp.parameters_tag = 'OP1'
sp.target_scaffoldings_folder_name = sp.arch_scaffoldings_name_folder + '_' + sp.parameters_tag
sp.scaffoldings_pfo = '/Users/sebastiano/Desktop/test_scaffoldings'
sp.stack_anatomies_pfi = jph(sp.scaffoldings_pfo, 'res_4d_seg.nii.gz')
sp.stack_segmentations_pfi = jph(sp.scaffoldings_pfo, 'res_4d_warp.nii.gz')
# Options and controller for propagation, fuser and stereotaxic alignment:
sp.propagation_options = OrderedDict({
'Rigid_modalities': ['T1', 'S0inT1', 'FAinT1'],
'Rigid_masks': ['T1', 'S0inT1', 'S0inT1'],
PATH_MULTI_ATLAS = jph(PATH_DIR, 'MultiAtlas')
PATH_TARGETS = jph(PATH_DIR, 'Targets')
MULTI_ATLAS_NAME_PREFIX = 'sj'
TARGET_NAME_SUFFIX = 'ta'
N = 8
RS = 0.3
RN = 0.4
if __name__ == '__main__':
global PATH_DIR
generate_phantom_dataset(PATH_DIR)
# --- initialise the class spot:
target_name = '{}01'.format(TARGET_NAME_SUFFIX)
spot_sj = SpotDS(atlas_pfo=PATH_MULTI_ATLAS,
target_pfo=PATH_TARGETS,
target_name=target_name,
parameters_tag='MyTag')
# Template parameters:
spot_sj.atlas_name = 'test' # Multi Atlas Newborn Rabbit
spot_sj.atlas_list_charts_names = [
MULTI_ATLAS_NAME_PREFIX + str(n + 1).zfill(len(str(N)) + 1)
for n in range(N)
]
spot_sj.atlas_list_suffix_modalities = ['mod1', 'mod2']
spot_sj.atlas_list_suffix_masks = ['roi_mask', 'roi_reg_mask']
spot_sj.atlas_reference_chart_name = 'sj02'
spot_sj.atlas_segmentation_suffix = 'segm_GT'
# --- target parameters
spot_sj.target_list_suffix_modalities = ['mod1', 'mod2']
def test_standard_experiment_with_phantom():
global PATH_DIR
generate_phantom_dataset(PATH_DIR)
# # --- initialise the class spot:
target_name = '{}01'.format(TARGET_NAME_SUFFIX)
spot_sj = SpotDS(atlas_pfo=PATH_MULTI_ATLAS,
target_pfo=PATH_TARGETS,
target_name=target_name,
parameters_tag='MyTag')
# Template parameters:
spot_sj.atlas_name = 'test' # Multi Atlas Newborn Rabbit
spot_sj.atlas_list_charts_names = [
MULTI_ATLAS_NAME_PREFIX + str(n + 1).zfill(len(str(N)) + 1)
for n in range(N)
]
spot_sj.atlas_list_suffix_modalities = ['mod1', 'mod2']
spot_sj.atlas_list_suffix_masks = ['roi_mask', 'roi_reg_mask']
spot_sj.atlas_reference_chart_name = 'sj02'
spot_sj.atlas_segmentation_suffix = 'segm_GT'
# --- target parameters
spot_sj.target_list_suffix_modalities = ['mod1', 'mod2']
# --- Utils
spot_sj.bfc_corrector_cmd = bfc_corrector_cmd
# --- Propagator option
spot_sj.propagation_options['Affine_modalities'] = ('mod1', 'mod2')
spot_sj.propagation_options['Affine_reg_masks'] = (
) # if (), there is a single mask for all modalities
spot_sj.propagation_options['Affine_parameters'] = ' -speeeeed '
spot_sj.propagation_options['N_rigid_modalities'] = (
'mod1', 'mod2') # if empty, no non-rigid step.
spot_sj.propagation_options['N_rigid_reg_masks'] = (
) # if (), same mask for all modalities
spot_sj.propagation_options['N_rigid_slim_reg_mask'] = True
spot_sj.propagation_options['N_rigid_mod_diff_bfc'] = (
'mod2', ) # empty list no diff bfc. - put a comma!!
spot_sj.propagation_options[
'N_rigid_parameters'] = ' -vel -be 0.5 -ln 6 -lp 2 -smooR 1.5 -smooF 1.5 '
spot_sj.propagation_options['N_rigid_same_mask_moving'] = True
spot_sj.propagation_options['Final_smoothing_factor'] = 0
# --- Propagator controller
spot_sj.propagation_controller['Aff_alignment'] = True
spot_sj.propagation_controller['Propagate_aff_to_segm'] = True
spot_sj.propagation_controller['Propagate_aff_to_mask'] = True
spot_sj.propagation_controller['Get_N_rigid_slim_mask'] = True
spot_sj.propagation_controller['Get_differential_BFC'] = True
spot_sj.propagation_controller['N_rigid_alignment'] = True
spot_sj.propagation_controller['Propagate_n_rigid'] = True
spot_sj.propagation_controller['Smooth_results'] = True
spot_sj.propagation_controller['Stack_warps_and_segms'] = True
# --- Fuser option
spot_sj.fuser_options['Fusion_methods'] = ['MV', 'STAPLE', 'STEPS']
spot_sj.fuser_options['Tp_mod_to_stack'] = 0
spot_sj.fuser_options['STAPLE_params'] = OrderedDict([('pr1', None)])
spot_sj.fuser_options['STEPS_params'] = OrderedDict([
('pr{0}_{1}'.format(k, n), [k, n, 4]) for n in [9] for k in [5, 11]
])
# --- Fuser controller
spot_sj.fuser_controller['Fuse'] = True
spot_sj.fuser_controller['Save_results'] = True
if not os.path.exists(
jph(PATH_TARGETS, spot_sj.arch_segmentations_name_folder,
spot_sj.arch_automatic_segmentations_name_folder)):
spot_sj.spot_on_target_initialise()
spot_sj.propagate()
spot_sj.fuse()
#
pfi_ground_truth_segm = jph(
PATH_TARGETS, spot_sj.arch_segmentations_name_folder,
'{0}_{1}.nii.gz'.format(target_name,
spot_sj.atlas_segmentation_suffix))
pri_result_MV = jph(
PATH_TARGETS, spot_sj.arch_segmentations_name_folder,
spot_sj.arch_automatic_segmentations_name_folder,
'{0}_{1}_{2}.nii.gz'.format(target_name, 'MV', spot_sj.parameters_tag))
im_segm_gt = nib.load(pfi_ground_truth_segm)
im_segm_mv = nib.load(pri_result_MV)
assert global_dice_score(im_segm_gt, im_segm_mv) > 0.9
def test_standard_experiments_with_phantom_broken_input_tag():
global PATH_DIR
generate_phantom_dataset(PATH_DIR)
target_name = '{}01'.format(TARGET_NAME_SUFFIX)
with npt.assert_raises(TypeError):
SpotDS(atlas_pfo=PATH_MULTI_ATLAS,
target_pfo=PATH_TARGETS,
target_name=target_name,
parameters_tag=None) # error here
spot_sj = SpotDS(atlas_pfo=PATH_MULTI_ATLAS,
target_pfo=PATH_TARGETS,
target_name=target_name,
parameters_tag='') # error here
spot_sj.spot_on_target_initialise()
with npt.assert_raises(IOError):
spot_sj.propagate()
spot_sj = SpotDS(atlas_pfo=PATH_MULTI_ATLAS,
target_pfo=PATH_TARGETS,
target_name=target_name,
parameters_tag='a_b') # error here
spot_sj.spot_on_target_initialise()
with npt.assert_raises(IOError):
spot_sj.propagate()
def run_update_automatic_segmentation_for_atlas():
pfo_multi_atlas_third_round = jph(path_manager.pfo_root,
'C_atlas_third_round')
assert os.path.exists(pfo_multi_atlas_third_round)
atlas_subjects = path_manager.atlas_subjects
# atlas flipped created with benchmarking/cross_validation/flipper
atlas_charts_flipped = [sj + 'flip' for sj in atlas_subjects]
atlas_chart_complete = [
item for pair in zip(atlas_subjects, atlas_charts_flipped + [0])
for item in pair
]
for target_name in atlas_subjects:
print(
'\n\nAutomatic initialisation [START]: \nSub-template is {0} \n Target is {1} \n Spot target started!!\n'
'\n'.format(atlas_chart_complete, target_name))
atlas_pfo = pfo_multi_atlas_third_round,
target_pfo = jph(pfo_multi_atlas_third_round, target_name)
spot_sj = SpotDS(atlas_pfo=atlas_pfo,
target_pfo=target_pfo,
target_name=target_name,
parameters_tag='AutoRound3')
# Template parameters:
spot_sj.atlas_name = 'AutoRound3' # Automatic round 3
spot_sj.atlas_list_charts_names = atlas_chart_complete
spot_sj.atlas_list_suffix_modalities = ['T1', 'S0', 'V1', 'MD', 'FA']
spot_sj.atlas_list_suffix_masks = ['roi_mask', 'roi_reg_mask']
spot_sj.atlas_reference_chart_name = '1305'
spot_sj.atlas_segmentation_suffix = 'approved_round3'
# --- target parameters
spot_sj.target_list_suffix_modalities = ['T1', 'S0', 'V1', 'MD', 'FA']
spot_sj.target_name = target_name
# --- Utils
spot_sj.bfc_corrector_cmd = bfc_corrector_cmd
# --- Propagator option
spot_sj.propagation_options['Affine_modalities'] = ('T1', 'FA')
spot_sj.propagation_options['Affine_reg_masks'] = (
'T1', 'S0') # if (), there is a single mask for all modalities
spot_sj.propagation_options['Affine_parameters'] = ' -speeeeed '
spot_sj.propagation_options['N_rigid_modalities'] = (
'T1', 'FA') # if empty, no non-rigid step.
spot_sj.propagation_options['N_rigid_reg_masks'] = (
'T1', 'S0') # if [], same mask for all modalities
spot_sj.propagation_options['N_rigid_slim_reg_mask'] = True
spot_sj.propagation_options['N_rigid_mod_diff_bfc'] = (
'T1', ) # empty list no diff bfc. - put a comma!!
spot_sj.propagation_options[
'N_rigid_parameters'] = ' -be 0.5 -ln 6 -lp 4 -smooR 1.5 -smooF 1.5 '
spot_sj.propagation_options['N_rigid_same_mask_moving'] = True
spot_sj.propagation_options['Final_smoothing_factor'] = 0
# --- Propagator controller
spot_sj.propagation_controller['Aff_alignment'] = False
spot_sj.propagation_controller['Propagate_aff_to_segm'] = False
spot_sj.propagation_controller['Propagate_aff_to_mask'] = False
spot_sj.propagation_controller['Get_N_rigid_slim_mask'] = True
spot_sj.propagation_controller['Get_differential_BFC'] = True
spot_sj.propagation_controller['N_rigid_alignment'] = True
spot_sj.propagation_controller['Propagate_n_rigid'] = True
spot_sj.propagation_controller['Smooth_results'] = True
spot_sj.propagation_controller['Stack_warps_and_segms'] = True
# --- Fuser option
spot_sj.fuser_options['Fusion_methods'] = ['MV'] # 'MV', 'STAPLE',
spot_sj.fuser_options['Tp_mod_to_stack'] = 0
spot_sj.fuser_options['STAPLE_params'] = OrderedDict([('pr1', None)])
spot_sj.fuser_options['STEPS_params'] = OrderedDict([
('pr{0}_{1}'.format(k, n), [k, n, 4]) for n in [9]
for k in [5, 11]
])
# --- Fuser controller
spot_sj.fuser_controller['Fuse'] = True
spot_sj.fuser_controller['Save_results'] = True
spot_sj.spot_on_target_initialise()
spot_sj.propagate()
spot_sj.fuse()
print('\n\nAutomatic initialisation [END] for subject {0} '
'\n Complete atlas chart was {1} \n'.format(
target_name, atlas_chart_complete))
def run_generate_automatic_segmentation_leave_one_out():
assert os.path.exists(path_manager.pfo_atlas_validation_leave_one_out)
# atlas flipped created with benchmarking/cross_validation/flipper
atlas_charts_flipped = [sj + 'flip' for sj in path_manager.atlas_subjects]
atlas_chart_complete = [item
for pair in zip(path_manager.atlas_subjects, atlas_charts_flipped + [0]) for item in pair]
for target_chart_name in path_manager.atlas_subjects:
sub_atlas_charts_with_flipped = np.sort(list(set(atlas_chart_complete) -
{target_chart_name, target_chart_name + 'flip'}))
print('\n\nLeave one out segmentation [START]:\nSub-template is {0}\nTarget is {1}\n Spot target started!!\n'
'\n'.format(sub_atlas_charts_with_flipped, target_chart_name))
assert target_chart_name not in sub_atlas_charts_with_flipped
spot_sj = SpotDS(atlas_pfo=path_manager.pfo_atlas_validation_leave_one_out,
target_pfo=jph(path_manager.pfo_atlas_validation_leave_one_out, target_chart_name),
target_name=target_chart_name,
parameters_tag='CrossValidation')
# Template parameters:
spot_sj.atlas_name = 'CrossValidationWithFlipped' # Multi Atlas Newborn Rabbit
spot_sj.atlas_list_charts_names = sub_atlas_charts_with_flipped
spot_sj.atlas_list_suffix_modalities = ['T1', 'S0', 'V1', 'MD', 'FA']
spot_sj.atlas_list_suffix_masks = ['roi_mask', 'roi_reg_mask']
spot_sj.atlas_reference_chart_name = '1305'
spot_sj.atlas_segmentation_suffix = 'segm'
# --- target parameters
spot_sj.target_list_suffix_modalities = ['T1', 'S0', 'V1', 'MD', 'FA']
spot_sj.target_name = target_chart_name
# --- Utils
spot_sj.bfc_corrector_cmd = path_manager.bfc_corrector_cmd
# --- Propagator option
spot_sj.propagation_options['Affine_modalities'] = ('T1', 'FA')
spot_sj.propagation_options['Affine_reg_masks'] = () # if (), there is a single mask for all mods
spot_sj.propagation_options['Affine_parameters'] = ' '
spot_sj.propagation_options['N_rigid_modalities'] = ('T1', 'FA') # if empty, no non-rigid step.
spot_sj.propagation_options['N_rigid_reg_masks'] = () # if [], same mask for all modalities
spot_sj.propagation_options['N_rigid_slim_reg_mask'] = False
spot_sj.propagation_options['N_rigid_mod_diff_bfc'] = ('T1',) # empty list no diff bfc. - put a comma!!
spot_sj.propagation_options['N_rigid_parameters'] = ' -vel -be 0.5 -ln 6 -lp 4 -smooR 0.07 -smooF 0.07 '
spot_sj.propagation_options['N_rigid_same_mask_moving'] = False
spot_sj.propagation_options['N_reg_mask_target'] = 0 # 0 roi_mask, 1 reg_mask
spot_sj.propagation_options['N_reg_mask_moving'] = 1 # 0 roi_mask, 1 reg_mask
spot_sj.propagation_options['Final_smoothing_factor'] = 0
# --- Propagator controller
spot_sj.propagation_controller['Aff_alignment'] = True
spot_sj.propagation_controller['Propagate_aff_to_segm'] = True
spot_sj.propagation_controller['Propagate_aff_to_mask'] = True
spot_sj.propagation_controller['Get_N_rigid_slim_mask'] = True
spot_sj.propagation_controller['Get_differential_BFC'] = True
spot_sj.propagation_controller['N_rigid_alignment'] = True
spot_sj.propagation_controller['Propagate_n_rigid'] = True
spot_sj.propagation_controller['Smooth_results'] = True
spot_sj.propagation_controller['Stack_warps_and_segms'] = True
# --- Fuser option
spot_sj.fuser_options['Fusion_methods'] = ['MV'] # 'MV', multi atlas only.
spot_sj.fuser_options['Tp_mod_to_stack'] = 0
spot_sj.fuser_options['STAPLE_params'] = OrderedDict([('pr_1', None)])
spot_sj.fuser_options['STEPS_params'] = OrderedDict([('pr_{0}_{1}'.format(k, n), [k, n, 0.4])
for n in [5, 7, 9]
for k in [5, 11]])
# --- Fuser controller
spot_sj.fuser_controller['Fuse'] = True
spot_sj.fuser_controller['Save_results'] = True
spot_sj.spot_on_target_initialise()
spot_sj.propagate()
spot_sj.fuse()
print('\n\nAutomatic initialisation [END] for subject {0} '
'\n Complete atlas chart was {1} \n'.format(target_chart_name, sub_atlas_charts_with_flipped))