def get_baseconf_settings( baseconf_settings_filename = None ):
"""
Returns the basic configuration settings as a parameter structure.
:param baseconf_settings_filename: loads the settings from the specified filename, otherwise from the default filename or in the absence of such a file creates default settings from scratch.
:return: parameter structure
"""
# These are the parameters for the general I/O and example cases
baseconf_params = pars.ParameterDict()
baseconf_params[('baseconf',{},'determines if settings should be loaded from file and visualization options')]
if baseconf_settings_filename is not None:
print( 'Loading baseconf configuration from: ' + baseconf_settings_filename )
baseconf_params.load_JSON( baseconf_settings_filename )
return baseconf_params
else:
print( 'Using default baseconf settings from config_parser.py')
baseconf_params['baseconf'][('load_default_settings_from_default_setting_files',False,'if set to True default configuration files (in settings directory) are first loaded')]
baseconf_params['baseconf'][('load_settings_from_file',True,'if set to True configuration settings are loaded from file')]
baseconf_params['baseconf'][('save_settings_to_file',True,'if set to True configuration settings are saved to file')]
if not baseconf_params['baseconf']['load_default_settings_from_default_setting_files']:
print('HINT: Only compute_settings.json and baseconf_settings.json will be read from file by default.')
print('HINT: Set baseconf.load_default_settings_from_default_setting_files to True if you want to use the other setting files in directory settings.')
print('HINT: Otherwise the defaults will be as defined in config_parser.py.')
return baseconf_params
def analyze_on_single_res(pair,pair_name, expr_folder=None, color_image=False,model_name='rdmm'):
moving, target, spacing, moving_init_weight, phi,m = get_analysis_input(pair,expr_folder,pair_name,color_image=color_image,model_name=model_name)
lmoving, ltarget =get_labeled_image(pair)
params = pars.ParameterDict()
params.load_JSON(os.path.join(expr_folder,'mermaid_setting.json'))
individual_parameters = dict(m=m,local_weights=moving_init_weight)
sz = np.array(moving.shape)
saving_folder = os.path.join(expr_folder, 'analysis')
saving_folder = os.path.join(saving_folder, pair_name)
saving_folder = os.path.join(saving_folder,'res_analysis')
os.makedirs(saving_folder,exist_ok=True)
extra_info = None
visual_param = None
extra_info = {'fname':[pair_name],'saving_folder':[saving_folder]}
visual_param = setting_visual_saving(expr_folder, pair_name,folder_name='color')
res= evaluate_model(moving, target, sz, spacing,
use_map=True,
compute_inverse_map=False,
map_low_res_factor=0.5,
compute_similarity_measure_at_low_res=False,
spline_order=1,
individual_parameters=individual_parameters,
shared_parameters=None, params=params, extra_info=extra_info,visualize=False,visual_param=visual_param, given_weight=True)
phi = res[1]
lres = utils.compute_warped_image_multiNC(lmoving, phi, spacing, 0, zero_boundary=True)
scores = get_multi_metric(lres,ltarget,rm_bg=True)
avg_jacobi = compute_jacobi(phi,spacing)
return scores['label_batch_avg_res']['dice'], avg_jacobi
def create_mermaid_model(mermaid_json_pth,
img_sz,
compute_inverse=True):
import mermaid.model_factory as py_mf
spacing = 1. / (np.array(img_sz[2:]) - 1)
params = pars.ParameterDict()
params.load_JSON(
mermaid_json_pth) # ''../easyreg/cur_settings_svf.json')
model_name = params['model']['registration_model']['type']
params.print_settings_off()
mermaid_low_res_factor = 0.5
lowResSize = get_res_size_from_size(img_sz, mermaid_low_res_factor)
lowResSpacing = get_res_spacing_from_spacing(
spacing, img_sz, lowResSize)
##
mf = py_mf.ModelFactory(img_sz, spacing, lowResSize, lowResSpacing)
model, criterion = mf.create_registration_model(
model_name, params['model'], compute_inverse_map=True)
lowres_id = identity_map_multiN(lowResSize, lowResSpacing)
lowResIdentityMap = torch.from_numpy(lowres_id).cuda()
_id = identity_map_multiN(img_sz, spacing)
identityMap = torch.from_numpy(_id).cuda()
mermaid_unit_st = model.cuda()
mermaid_unit_st.associate_parameters_with_module()
return mermaid_unit_st, criterion, lowResIdentityMap, lowResSize, lowResSpacing, identityMap, spacing
def add_texture_on_img(im_orig,
texture_gaussian_smoothness=0.1,
texture_magnitude=0.3):
# do this separately for each integer intensity level
levels = np.unique((np.floor(im_orig)).astype('int'))
im = np.zeros_like(im_orig)
for current_level in levels:
sz = im_orig.shape
rand_noise = np.random.random(sz[2:]).astype('float32') - 0.5
rand_noise = rand_noise.view().reshape(sz)
r_params = pars.ParameterDict()
r_params['smoother']['type'] = 'gaussian'
r_params['smoother']['gaussian_std'] = texture_gaussian_smoothness
spacing = 1.0 / (np.array(sz[2:]).astype('float32') - 1)
s_r = sf.SmootherFactory(sz[2::], spacing).create_smoother(r_params)
rand_noise_smoothed = s_r.smooth(AdaptVal(
torch.from_numpy(rand_noise))).detach().cpu().numpy()
rand_noise_smoothed /= rand_noise_smoothed.max()
rand_noise_smoothed *= texture_magnitude
c_indx = (im_orig >= current_level - 0.5)
im[c_indx] = im_orig[c_indx] + rand_noise_smoothed[c_indx]
return torch.Tensor(im)
def _none_if_empty(par):
if type(par) == type(pars.ParameterDict()):
if par.isempty():
return None
else:
return par
else:
return par
def get_setting(path, output_path, setting_name="mermaid"):
params = pars.ParameterDict()
params.load_JSON(path)
os.makedirs(output_path, exist_ok=True)
output_path = os.path.join(output_path,
'{}_setting.json'.format(setting_name))
params.write_JSON(output_path, save_int=False)
return params
def setting_visual_saving(expr_folder,pair_name,expr_name='',folder_name='intermid'):
extra_info = pars.ParameterDict()
extra_info['expr_name'] = expr_name
extra_info['visualize']=False
extra_info['save_fig']=True
extra_info['save_fig_path']=os.path.join(expr_folder,folder_name)
extra_info['save_fig_num'] = -1
extra_info['save_excel'] =False
extra_info['pair_name'] = [pair_name]
return extra_info
def test_lddmm_shooting_scalar_momentum_image_multi_scale(self):
self.params = pars.ParameterDict()
self.params.load_JSON('./json/test_lddmm_shooting_scalar_momentum_image_multi_scale_config.json')
self.createImage()
mo = MO.SimpleMultiScaleRegistration(self.ISource, self.ITarget, self.spacing, self.sz, self.params)
mo.get_optimizer().set_visualization(False)
mo.register()
# E=[ 0.03197587], similarityE=[ 0.02087387], regE=[ 0.01110199], relF=[ 0.00138645]
energy = mo.get_energy()
npt.assert_almost_equal(energy[0], 0.03184246, decimal=4 )
npt.assert_almost_equal(energy[1], 0.0207199, decimal=4 )
npt.assert_almost_equal(energy[2], 0.01112256, decimal=4 )
def test_lddmm_shooting_scalar_momentum_image_single_scale(self):
self.params = pars.ParameterDict()
self.params.load_JSON('./json/test_lddmm_shooting_scalar_momentum_image_single_scale_config.json')
self.createImage()
so = MO.SimpleSingleScaleRegistration(self.ISource, self.ITarget, self.spacing, self.sz, self.params)
so.get_optimizer().set_visualization(False)
so.register()
# E = [0.03198373], similarityE = [0.0210261], regE = [0.01095762], relF = [0.]
energy = so.get_energy()
npt.assert_almost_equal(energy[0], 0.03198373, decimal=4 )
npt.assert_almost_equal(energy[1], 0.0210261, decimal=4 )
npt.assert_almost_equal(energy[2], 0.01095762, decimal=4 )
def test_lddmm_shooting_scalar_momentum_map_multi_scale(self):
self.params = pars.ParameterDict()
self.params.load_JSON('./json/test_lddmm_shooting_scalar_momentum_map_multi_scale_config.json')
self.createImage()
mo = MO.SimpleMultiScaleRegistration(self.ISource, self.ITarget, self.spacing, self.sz, self.params)
mo.get_optimizer().set_visualization(False)
mo.register()
# E = [0.08930502], simE = [0.08034889], regE = [0.00895613], optParE = [0.], relF = [0.03883468]
energy = mo.get_energy()
npt.assert_almost_equal(energy[0], 0.04333755, decimal=4 )
npt.assert_almost_equal(energy[1], 0.03237363, decimal=4 )
npt.assert_almost_equal(energy[2], 0.010963925, decimal=4 )
def test_svf_image_single_scale(self):
self.params = pars.ParameterDict()
self.params.load_JSON('./json/test_svf_image_single_scale_config.json')
self.createImage( 32 )
so = MO.SimpleSingleScaleRegistration( self.ISource, self.ITarget, self.spacing, self.sz, self.params)
so.get_optimizer().set_visualization(False)
so.register()
# E=[ 1.80229616], similarityE=[ 0.71648604], regE=[ 1.08581007], relF=[ 0.0083105]
energy = so.get_energy()
npt.assert_almost_equal( energy[0], 1.7918575, decimal=1 )
npt.assert_almost_equal( energy[1], 0.5308577, decimal=1 )
npt.assert_almost_equal( energy[2], 1.2609998, decimal=1 )
def test_lddmm_shooting_map_multi_scale(self):
self.params = pars.ParameterDict()
self.params.load_JSON('./json/test_lddmm_shooting_map_multi_scale_config.json')
self.createImage()
mo = MO.SimpleMultiScaleRegistration(self.ISource, self.ITarget, self.spacing, self.sz, self.params)
mo.get_optimizer().set_visualization(False)
mo.register()
# E = [0.07970674], simE = [0.06657108], regE = [0.01313565], optParE = [0.], relF = [0.02088663]
energy = mo.get_energy()
npt.assert_almost_equal(energy[0], 0.07360865, decimal=4 )
npt.assert_almost_equal(energy[1], 0.06016802, decimal=4 )
npt.assert_almost_equal(energy[2], 0.01344063, decimal=4 )
def test_svf_map_single_scale(self):
self.params = pars.ParameterDict()
self.params.load_JSON('./json/test_svf_map_single_scale_config.json')
self.createImage( 32 )
so = MO.SimpleSingleScaleRegistration( self.ISource, self.ITarget, self.spacing, self.sz, self.params)
so.get_optimizer().set_visualization(False)
so.register()
# E = [36.42594528], similarityE = [16.22630882], regE = [20.19963646], relF = [0.0422723]
energy = so.get_energy()
npt.assert_almost_equal( energy[0], 16.957407, decimal=0 )
npt.assert_almost_equal( energy[1], 6.718715, decimal=0 )
npt.assert_almost_equal( energy[2], 10.238692, decimal=0 )
def test_lddmm_shooting_map_single_scale(self):
self.params = pars.ParameterDict()
self.params.load_JSON('./json/test_lddmm_shooting_map_single_scale_config.json')
self.createImage()
so = MO.SimpleSingleScaleRegistration( self.ISource, self.ITarget, self.spacing, self.sz, self.params)
so.get_optimizer().set_visualization(False)
so.register()
# E = [0.05674197], similarityE = [0.04364978], regE = [0.01309219], relF = [0.01391943]
energy = so.get_energy()
npt.assert_almost_equal( energy[0], 0.05927172, decimal=3 )
npt.assert_almost_equal( energy[1], 0.04580842, decimal=3 )
npt.assert_almost_equal( energy[2], 0.013463295, decimal=3 )
def test_lddmm_shooting_image_single_scale(self):
self.params = pars.ParameterDict()
self.params.load_JSON('./json/test_lddmm_shooting_image_single_scale_config.json')
self.createImage()
so = MO.SimpleSingleScaleRegistration(self.ISource, self.ITarget, self.spacing, self.sz, self.params)
so.get_optimizer().set_visualization(False)
so.register()
# E=[ 0.02896098], similarityE=[ 0.0170299], regE=[ 0.01193108], relF=[ 0.00193194]
energy = so.get_energy()
npt.assert_almost_equal(energy[0], 0.02896098, decimal=2 )
npt.assert_almost_equal(energy[1], 0.0170299, decimal=2 )
npt.assert_almost_equal(energy[2], 0.01193108, decimal=2 )
def test_lddmm_shooting_image_multi_scale(self):
self.params = pars.ParameterDict()
self.params.load_JSON('./json/test_lddmm_shooting_image_multi_scale_config.json')
self.createImage()
mo = MO.SimpleMultiScaleRegistration(self.ISource, self.ITarget, self.spacing, self.sz, self.params)
mo.get_optimizer().set_visualization(False)
mo.register()
# E = [0.04338037], similarityE = [0.03070126], regE = [0.01267911], relF = [0.01936091]
energy = mo.get_energy()
npt.assert_almost_equal(energy[0], 0.04338037, decimal=4 )
npt.assert_almost_equal(energy[1], 0.03070126, decimal=4 )
npt.assert_almost_equal(energy[2], 0.01267911, decimal=4 )
def test_svf_vector_momentum_map_single_scale(self):
self.params = pars.ParameterDict()
self.params.load_JSON('./json/svf_momentum_base_config.json')
self.params['model']['deformation']['use_map'] = True
self.params['model']['registration_model']['type'] = 'svf_vector_momentum_map'
self.createImage()
so = MO.SimpleSingleScaleRegistration(self.ISource, self.ITarget, self.spacing, self.sz, self.params)
so.get_optimizer().set_visualization(False)
so.register()
# E=[0.03567663], simE=[0.02147915], regE=0.01419747807085514
energy = so.get_energy()
npt.assert_almost_equal(energy[0], 0.03706806, decimal = 4)
npt.assert_almost_equal(energy[1], 0.02302469, decimal = 4)
npt.assert_almost_equal(energy[2], 0.014043369330, decimal = 4)
def test_svf_scalar_momentum_image_single_scale(self):
self.params = pars.ParameterDict()
self.params.load_JSON('./json/svf_momentum_base_config.json')
self.params['model']['deformation']['use_map'] = False
self.params['model']['registration_model']['type'] = 'svf_scalar_momentum_image'
self.createImage()
so = MO.SimpleSingleScaleRegistration(self.ISource, self.ITarget, self.spacing, self.sz, self.params)
so.get_optimizer().set_visualization(False)
so.register()
# E=[0.12413108], simE=[0.11151054], regE=0.012620546855032444
energy = so.get_energy()
npt.assert_almost_equal(energy[0], 0.12428085, decimal=4)
npt.assert_almost_equal(energy[1], 0.11166441, decimal=4)
npt.assert_almost_equal(energy[2], 0.012616440653800964, decimal=4)
def test_svf_scalar_momentum_map_single_scale(self):
self.params = pars.ParameterDict()
self.params.load_JSON('./json/svf_momentum_base_config.json')
self.params['model']['deformation']['use_map'] = True
self.params['model']['registration_model']['type'] = 'svf_scalar_momentum_map'
self.createImage()
self.setUp()
so = MO.SimpleSingleScaleRegistration(self.ISource, self.ITarget, self.spacing, self.sz, self.params)
so.get_optimizer().set_visualization(False)
so.register()
# E=[0.16388921], simE=[0.15010326], regE=0.013785961084067822
energy = so.get_energy()
npt.assert_almost_equal(energy[0], 0.16180025, decimal = 4)
npt.assert_almost_equal(energy[1], 0.14811447, decimal = 4)
npt.assert_almost_equal(energy[2], 0.01368578, decimal = 4)
def test_svf_vector_momentum_image_single_scale(self):
self.params = pars.ParameterDict()
self.params.load_JSON('./json/svf_momentum_base_config.json')
self.params['model']['deformation']['use_map'] = False
self.params['model']['registration_model']['type'] = 'svf_vector_momentum_image'
self.createImage()
self.setUp()
so = MO.SimpleSingleScaleRegistration(self.ISource, self.ITarget, self.spacing, self.sz, self.params)
so.get_optimizer().set_visualization(False)
so.register()
# E=[ 0.02504558], similarityE=[ 0.01045385], regE=[ 0.01459173], relF=[ 0.00203472]
energy = so.get_energy()
npt.assert_almost_equal(energy[0], 0.02504558, decimal = 2)
npt.assert_almost_equal(energy[1], 0.01045385, decimal = 2)
npt.assert_almost_equal(energy[2], 0.01459173, decimal = 2)
def get_respro_settings(respro_settings_filename = None):
respro_params = pars.ParameterDict()
respro_params[('respro', {}, 'settings for the results process')]
if respro_settings_filename is not None:
print( 'Loading respro configuration from: ' + respro_settings_filename )
respro_params.load_JSON(respro_settings_filename)
return respro_params
else:
print( 'Using default respro settings from config_parser.py')
respro_params['respro'][('expr_name', 'reg', 'name of experiment')]
respro_params['respro'][('visualize', True, 'if set to true intermediate results are visualized')]
respro_params['respro'][('visualize_step', 5, 'Number of iterations between visualization output')]
respro_params['respro'][('save_fig', False, 'save visualized results')]
respro_params['respro'][('save_fig_path', '../data/saved_results', 'path of saved figures')]
respro_params['respro'][('save_excel', True, 'save results in excel')]
return respro_params
def get_democonf_settings( democonf_settings_filename = None ):
"""
Returns the configuration settings for the demo data as a parameter structure.
:param democonf_settings_filename: loads the settings from the specified filename, otherwise from the default filename or in the absence of such a file creates default settings from scratch.
:return: parameter structure
"""
# These are the parameters for the general I/O and example cases
democonf_params = pars.ParameterDict()
democonf_params[('democonf', {}, 'settings for demo images/examples')]
if democonf_settings_filename is not None:
print( 'Loading democonf configuration from: ' + democonf_settings_filename )
democonf_params.load_JSON( democonf_settings_filename )
return democonf_params
else:
print( 'Using default democonf settings from config_parser.py' )
democonf_params['democonf'][('dim', 2, 'Spatial dimension for demo examples 1/2/3')]
democonf_params['democonf'][('example_img_len', 128, 'side length of image cube for example')]
democonf_params['democonf'][('use_real_images', False, 'if set to true using real and otherwise synthetic images')]
return democonf_params
def get_mermaid_setting(path, output_path):
params = pars.ParameterDict()
params.load_JSON(path)
os.makedirs(output_path, exist_ok=True)
output_path = os.path.join(output_path, 'mermaid_setting.json')
params.write_JSON(output_path, save_int=False)
def get_algconf_settings( algconf_settings_filename = None ):
"""
Returns the registration algorithm configuration settings as a parameter structure.
:param algconf_settings_filename: loads the settings from the specified filename, otherwise from the default filename or in the absence of such a file creates default settings from scratch.
:return: parameter structure
"""
# These are the parameters for the general I/O and example cases
algconf_params = pars.ParameterDict()
algconf_params[('algconf',{},'settings for the registration algorithms')]
if algconf_settings_filename is not None:
print( 'Loading algconf configuration from: ' + algconf_settings_filename )
algconf_params.load_JSON( algconf_settings_filename )
return algconf_params
else:
print( 'Using default algconf settings from config_parser.py')
algconf_params['algconf'][('optimizer', {}, 'optimizer settings')]
algconf_params['algconf']['optimizer'][('name', 'lbfgs_ls', 'name of the optimizer: [lbfgs_ls|adam]')]
algconf_params['algconf']['optimizer'][('single_scale', {}, 'single scale settings')]
algconf_params['algconf']['optimizer']['single_scale'][('nr_of_iterations', 20, 'number of iterations')]
algconf_params['algconf']['optimizer'][('multi_scale', {}, 'multi scale settings')]
algconf_params['algconf']['optimizer']['multi_scale'][('use_multiscale', False, 'use multi-scale optimizer')]
algconf_params['algconf']['optimizer']['multi_scale'][('scale_factors', [1.0, 0.5, 0.25], 'how images are scaled')]
algconf_params['algconf']['optimizer']['multi_scale'][('scale_iterations', [10, 20, 20], 'number of iterations per scale')]
algconf_params['algconf'][('model', {}, 'general model settings')]
algconf_params['algconf']['model'][('deformation', {}, 'model describing the desired deformation model')]
algconf_params['algconf']['model']['deformation'][('name', 'lddmm_shooting', "['svf'|'svf_quasi_momentum'|'lddmm_shooting'|'lddmm_shooting_scalar_momentum'] all with '_map' or '_image' suffix")]
algconf_params['algconf']['model']['deformation'][('use_map', True, '[True|False] either do computations via a map or directly using the image')]
algconf_params['algconf']['model']['deformation'][('map_low_res_factor',1.0,'Set to a value in (0,1) if a map-based solution should be computed at a lower internal resolution (image matching is still at full resolution')]
algconf_params['algconf']['model'][('registration_model', {}, 'general settings for the registration model')]
algconf_params['algconf']['model']['registration_model'][('forward_model', {}, 'Holds the parameters for the forward model')]
algconf_params['algconf']['model']['registration_model']['forward_model'][('number_of_time_steps', 10, 'Number of time steps for integration (if applicable)')]
algconf_params['algconf']['model']['registration_model']['forward_model'][('smoother', {}, 'how the smoothing of velocity fields is done')]
#algconf_params['algconf']['model']['registration_model']['forward_model']['smoother'][('type', 'multiGaussian', 'type of smoothing')]
#algconf_params['algconf']['model']['registration_model']['forward_model']['smoother'][('multi_gaussian_stds', [0.05,0.1,0.15,0.2,0.25], 'standard deviations for smoothing')]
algconf_params['algconf']['model']['registration_model']['forward_model']['smoother'][
('type', 'gaussian', 'type of smoothing')]
algconf_params['algconf']['model']['registration_model']['forward_model']['smoother'][
('gaussian_std', 0.15, 'standard deviations for smoothing')]
algconf_params['algconf']['model']['registration_model'][('similarity_measure', {}, 'model describing the similarity measure')]
algconf_params['algconf']['model']['registration_model']['similarity_measure'][('sigma', 0.1, '1/sigma^2 weighting')]
algconf_params['algconf']['model']['registration_model']['similarity_measure'][('type', 'ssd', '[ssd|ncc]')]
algconf_params['algconf']['model']['registration_model']['similarity_measure'][('develop_mod_on', False, 'if true would allow develop settings ')]
algconf_params['algconf']['model']['registration_model']['similarity_measure'][('develop_mod', {}, 'developing mode ')]
algconf_params['algconf']['model']['registration_model']['similarity_measure']['develop_mod'][('smoother', {}, 'how the smoothing of velocity fields is done ')]
algconf_params['algconf']['model']['registration_model']['similarity_measure']['develop_mod']['smoother'][('type', 'gaussian', 'type of smoothing')]
algconf_params['algconf']['model']['registration_model']['similarity_measure']['develop_mod']['smoother'][('gaussian_std', 0.1, 'standard deviation for smoothing')]
algconf_params['algconf'][('image_smoothing', {}, 'image smoothing settings')]
algconf_params['algconf']['image_smoothing'][('smooth_images', True, '[True|False]; smoothes the images before registration')]
algconf_params['algconf']['image_smoothing'][('smoother',{},'settings for the image smoothing')]
algconf_params['algconf']['image_smoothing']['smoother'][('gaussian_std', 0.01, 'how much smoothing is done')]
algconf_params['algconf']['image_smoothing']['smoother'][('type', 'gaussian', "['gaussianSpatial'|'gaussian'|'diffusion']")]
return algconf_params
def get_single_gaussian_smoother(gaussian_std, sz, spacing):
s_m_params = pars.ParameterDict()
s_m_params['smoother']['type'] = 'gaussian'
s_m_params['smoother']['gaussian_std'] = gaussian_std
s_m = sf.SmootherFactory(sz, spacing).create_smoother(s_m_params)
return s_m
print('Specifying directories based on SYNTH main directory: {:s}'.
format(args.main_synth_directory))
validation_dataset_name = 'SYNTH'
input_image_directory = os.path.join(args.main_synth_directory,
'brain_affine_icbm')
image_pair_config_pt = os.path.join(args.main_synth_directory,
'used_image_pairs.pt')
validation_dataset_directory = args.main_synth_directory
# if this is not synth data, we first check if a JSON file was used to specify the directories
elif args.dataset_config is not None:
print('Reading dataset configuration from: {:s}'.format(
args.dataset_config))
data_params = pars.ParameterDict()
save_dataset_config = False
if not os.path.exists(args.dataset_config):
print(
'INFO: config file {:s} does not exist. Creating a generic one.'
.format(args.dataset_config))
input_image_directory_default = 'synthetic_example_out/brain_affine_icbm'
image_pair_config_pt_default = 'synthetic_example_out/used_image_pairs.pt'
output_base_directory_default = 'experimental_results_synth_2d'
validation_dataset_directory_default = 'synthetic_example_out'
validation_dataset_name_default = 'SYNTH'
save_dataset_config = True
else:
input_image_directory_default = None
image_pair_config_pt_default = None
# first do the torch imports
import set_pyreg_paths
import torch
from torch.autograd import Variable
from mermaid.data_wrapper import AdaptVal
import numpy as np
import mermaid.module_parameters as MP
import mermaid.example_generation as eg
import mermaid.utils as utils
import mermaid.smoother_factory as SF
import matplotlib.pyplot as plt
params = MP.ParameterDict()
dim = 2
szEx = np.tile(64, dim)
I0, I1, spacing = eg.CreateSquares(dim).create_image_pair(
szEx, params) # create a default image size with two sample squares
sz = np.array(I0.shape)
# create the source and target image as pyTorch variables
ISource = AdaptVal(torch.from_numpy(I0.copy()))
smoother = SF.MySingleGaussianFourierSmoother(sz[2:], spacing, params)
g_std = smoother.get_gaussian_std()
import numpy as np
import matplotlib.pyplot as plt
import mermaid.simple_interface as SI
import mermaid.example_generation as EG
import mermaid.module_parameters as pars
################################
# Creating some example data
# ^^^^^^^^^^^^^^^^^^^^^^^^^^
#
# We can use ``mermaid.example_generation`` to create some test data as follows:
#
# We first generate a parameter object to hold settings
params = pars.ParameterDict()
# We select if we want to create synthetic image pairs or would prefer a real image pair
use_synthetic_test_case = True
# Desired dimension (mermaid supports 1D, 2D, and 3D registration)
dim = 2
# If we want to add some noise to the background (for synthetic examples)
add_noise_to_bg = True
# and now create it
if use_synthetic_test_case:
length = 64
# size of the desired images: (sz)^dim
szEx = np.tile(length, dim )
def init_mermaid_env(self):
"""
setup the mermaid environemnt
* saving the settings into record folder
* initialize model from model, criterion and related variables
"""
spacing = self.spacing
params = pars.ParameterDict()
params.load_JSON(
self.mermaid_net_json_pth) #''../easyreg/cur_settings_svf.json')
print(" The mermaid setting from {} included:".format(
self.mermaid_net_json_pth))
print(params)
model_name = params['model']['registration_model']['type']
use_map = params['model']['deformation']['use_map']
compute_similarity_measure_at_low_res = params['model']['deformation'][
('compute_similarity_measure_at_low_res', False,
'to compute Sim at lower resolution')]
params['model']['registration_model']['similarity_measure'][
'type'] = self.loss_type
params.print_settings_off()
self.mermaid_low_res_factor = self.low_res_factor
smoother_type = params['model']['registration_model']['forward_model'][
'smoother']['type']
self.use_adaptive_smoother = smoother_type == 'learned_multiGaussianCombination'
lowResSize = None
lowResSpacing = None
##
if self.mermaid_low_res_factor == 1.0 or self.mermaid_low_res_factor == [
1., 1., 1.
]:
self.mermaid_low_res_factor = None
self.lowResSize = self.img_sz
self.lowResSpacing = spacing
##
if self.mermaid_low_res_factor is not None:
lowResSize = get_res_size_from_size(self.img_sz,
self.mermaid_low_res_factor)
lowResSpacing = get_res_spacing_from_spacing(
spacing, self.img_sz, lowResSize)
self.lowResSize = lowResSize
self.lowResSpacing = lowResSpacing
if self.mermaid_low_res_factor is not None:
# computes model at a lower resolution than the image similarity
if compute_similarity_measure_at_low_res:
mf = py_mf.ModelFactory(lowResSize, lowResSpacing, lowResSize,
lowResSpacing)
else:
mf = py_mf.ModelFactory(self.img_sz, spacing, lowResSize,
lowResSpacing)
else:
# computes model and similarity at the same resolution
mf = py_mf.ModelFactory(self.img_sz, spacing, self.img_sz, spacing)
model, criterion = mf.create_registration_model(
model_name,
params['model'],
compute_inverse_map=self.compute_inverse_map)
if use_map:
# create the identity map [0,1]^d, since we will use a map-based implementation
_id = py_utils.identity_map_multiN(self.img_sz, spacing)
self.identityMap = torch.from_numpy(_id).cuda()
if self.mermaid_low_res_factor is not None:
# create a lower resolution map for the computations
lowres_id = py_utils.identity_map_multiN(
lowResSize, lowResSpacing)
self.lowResIdentityMap = torch.from_numpy(lowres_id).cuda()
print(torch.min(self.lowResIdentityMap))
self.lowRes_fn = partial(get_resampled_image,
spacing=spacing,
desiredSize=lowResSize,
zero_boundary=False,
identity_map=self.lowResIdentityMap)
self.mermaid_unit_st = model.cuda()
self.criterion = criterion
self.mermaid_unit_st.associate_parameters_with_module()
self.save_cur_mermaid_settings(params)
def get_default_algconf_settings_filenames():
"""Returns the filename string where the configuration for the registration algorithm will be read from.
:return: filename string
"""
return (_algconf_settings_filename,_algconf_settings_filename_comments)
def get_default_respro_settings_filenames():
return (_respro_settings_filename,_respro_settings_filename_comments)
# First get the computational settings that will be used in various parts of the library
compute_params = pars.ParameterDict()
compute_params.print_settings_off()
compute_params.load_JSON(get_default_compute_settings_filenames()[0])
compute_params[('compute',{},'how computations are done')]
CUDA_ON = compute_params['compute'][('CUDA_ON',False,'Determines if the code should be run on the GPU')]
"""If set to True CUDA will be used, otherwise it will not be used"""
USE_FLOAT16 = compute_params['compute'][('USE_FLOAT16',False,'if set to True uses half-precision - not recommended')]
"""If set to True 16 bit computations will be used -- not recommended and not actively supported"""
nr_of_threads = compute_params['compute'][('nr_of_threads',mp.cpu_count(),'set the maximal number of threads')]
"""Specifies the number of threads"""
MATPLOTLIB_AGG = compute_params['compute'][('MATPLOTLIB_AGG',False,'Determines how matplotlib plots images. Set to True for remote debugging')]
"""If set to True matplotlib's AGG graphics renderer will be used; this should be set to True if run on a server and to False if visualization are desired as part of an interactive compute session"""
