Index

A

add_artefacts() (in module EMCqMRI.core.utilities.dataset_utilities)

apply_gt_noise() (in module EMCqMRI.core.utilities.dataset_utilities) apply_noise() (EMCqMRI.core.models.likelihood.gaussian.Gaussian method)

B

BasicBlock (class in EMCqMRI.core.models.inference.resnet)

C

calculate_snr() (in module EMCqMRI.core.utilities.image_utilities) check_override() (in module EMCqMRI.core.engine.build_model) Configuration (class in EMCqMRI.core.engine.build_model) configure_cuda() (in module EMCqMRI.core.engine.build_model)

convert_argparse_to_attr() (in module EMCqMRI.core.utilities.configuration_utilities) convert_shape_to_pair() (in module EMCqMRI.core.utilities.image_utilities) convert_to_pair_matrix() (in module EMCqMRI.core.utilities.image_utilities) create_dataloader() (in module EMCqMRI.core.engine.data_loader) custom_batch_norm() (in module EMCqMRI.core.models.inference.resnet)

D

Dataset (class in EMCqMRI.core.base.base_dataset) DatasetModel (class in EMCqMRI.core.models.dataset.base)

determine_conv_class() (in module EMCqMRI.core.utilities.torch_utils) determine_conv_functional() (in module EMCqMRI.core.utilities.torch_utils) DictToAttribute (class in EMCqMRI.core.utilities.configuration_utilities)

E

EMCqMRI module EMCqMRI.core module EMCqMRI.core.base module EMCqMRI.core.base.base_dataset module EMCqMRI.core.base.base_inference_model module EMCqMRI.core.base.base_likelihood_model module EMCqMRI.core.base.base_signal_model module EMCqMRI.core.engine module EMCqMRI.core.engine.build_model module EMCqMRI.core.engine.data_loader module EMCqMRI.core.engine.estimate module EMCqMRI.core.engine.train_model module EMCqMRI.core.models module EMCqMRI.core.models.dataset module EMCqMRI.core.models.dataset.base module EMCqMRI.core.models.inference module EMCqMRI.core.models.inference.mle module

EMCqMRI.core.models.inference.resnet module EMCqMRI.core.models.inference.rim module EMCqMRI.core.models.inference.rnn module EMCqMRI.core.models.likelihood module EMCqMRI.core.models.likelihood.gaussian module EMCqMRI.core.models.signal module EMCqMRI.core.models.signal.fse module EMCqMRI.core.models.signal.looklocker module EMCqMRI.core.utilities module EMCqMRI.core.utilities.checkpoint_utilities module EMCqMRI.core.utilities.configuration_utilities module EMCqMRI.core.utilities.core_utilities module EMCqMRI.core.utilities.dataset_utilities module EMCqMRI.core.utilities.image_utilities module EMCqMRI.core.utilities.torch_utils module expansion (EMCqMRI.core.models.inference.resnet.BasicBlock attribute) ExtractPatch (class in EMCqMRI.core.utilities.dataset_utilities)

F

forward() (EMCqMRI.core.base.base_inference_model.InferenceModel method) (EMCqMRI.core.base.base_signal_model.SignalModel method) (EMCqMRI.core.models.inference.mle.Mle method) (EMCqMRI.core.models.inference.resnet.BasicBlock method) (EMCqMRI.core.models.inference.resnet.Resnet method) (EMCqMRI.core.models.inference.rim.Rim method) (EMCqMRI.core.models.inference.rnn.Rnn method) (EMCqMRI.core.models.signal.fse.Fse method) (EMCqMRI.core.models.signal.looklocker.Looklocker method) (EMCqMRI.core.utilities.torch_utils.PixelUnshuffle method) (in module EMCqMRI.core.base.base_inference_model.InferenceModel) (in module EMCqMRI.core.base.base_signal_model.SignalModel)

Fse (class in EMCqMRI.core.models.signal.fse)

G

Gaussian (class in EMCqMRI.core.models.likelihood.gaussian) get_data_information() (in module EMCqMRI.core.utilities.image_utilities) get_engine() (in module EMCqMRI.core.utilities.core_utilities) get_existing_data() (EMCqMRI.core.models.dataset.base.DatasetModel method) get_label() (EMCqMRI.core.base.base_dataset.Dataset method) (EMCqMRI.core.models.dataset.base.DatasetModel method) (in module EMCqMRI.core.base.base_dataset.Dataset) get_length() (EMCqMRI.core.base.base_dataset.Dataset method) (in module EMCqMRI.core.base.base_dataset.Dataset)

get_patch() (EMCqMRI.core.utilities.dataset_utilities.ExtractPatch method) get_rand_seed() (in module EMCqMRI.core.utilities.dataset_utilities) get_signal() (EMCqMRI.core.base.base_dataset.Dataset method) (EMCqMRI.core.models.dataset.base.DatasetModel method) (in module EMCqMRI.core.base.base_dataset.Dataset) gradients() (EMCqMRI.core.base.base_likelihood_model.Likelihood method) (in module EMCqMRI.core.base.base_likelihood_model.Likelihood)

I

imagebrowse_slider() (in module EMCqMRI.core.utilities.image_utilities) index_files() (EMCqMRI.core.base.base_dataset.Dataset method) (in module EMCqMRI.core.base.base_dataset.Dataset) Infer (class in EMCqMRI.core.engine.estimate)

InferenceModel (class in EMCqMRI.core.base.base_inference_model) initialize_parameters() (EMCqMRI.core.base.base_signal_model.SignalModel method) (EMCqMRI.core.models.signal.fse.Fse method) (EMCqMRI.core.models.signal.looklocker.Looklocker method) (in module EMCqMRI.core.base.base_signal_model.SignalModel)

L

Likelihood (class in EMCqMRI.core.base.base_likelihood_model) likelihood() (EMCqMRI.core.base.base_likelihood_model.Likelihood method) (EMCqMRI.core.models.likelihood.gaussian.Gaussian method) (in module EMCqMRI.core.base.base_likelihood_model.Likelihood) load() (in module EMCqMRI.core.utilities.checkpoint_utilities) load_checkpoint() (in module EMCqMRI.core.engine.build_model) load_cost_function() (in module EMCqMRI.core.engine.build_model) load_dataset_model() (in module EMCqMRI.core.engine.build_model) load_ext_module() (in module EMCqMRI.core.utilities.core_utilities)

load_file() (EMCqMRI.core.base.base_dataset.Dataset method) (in module EMCqMRI.core.base.base_dataset.Dataset) load_folder() (EMCqMRI.core.base.base_dataset.Dataset method) (in module EMCqMRI.core.base.base_dataset.Dataset) load_hdf5() (in module EMCqMRI.core.utilities.image_utilities) load_inference_model() (in module EMCqMRI.core.engine.build_model) load_likelihood_model() (in module EMCqMRI.core.engine.build_model) load_optimizer() (in module EMCqMRI.core.engine.build_model) load_signal_model() (in module EMCqMRI.core.engine.build_model) Looklocker (class in EMCqMRI.core.models.signal.looklocker)

M

make() (in module EMCqMRI.core.engine.build_model) Mle (class in EMCqMRI.core.models.inference.mle) module EMCqMRI EMCqMRI.core EMCqMRI.core.base EMCqMRI.core.base.base_dataset EMCqMRI.core.base.base_inference_model EMCqMRI.core.base.base_likelihood_model EMCqMRI.core.base.base_signal_model EMCqMRI.core.engine EMCqMRI.core.engine.build_model EMCqMRI.core.engine.data_loader EMCqMRI.core.engine.estimate EMCqMRI.core.engine.train_model EMCqMRI.core.models EMCqMRI.core.models.dataset EMCqMRI.core.models.dataset.base EMCqMRI.core.models.inference EMCqMRI.core.models.inference.mle EMCqMRI.core.models.inference.resnet EMCqMRI.core.models.inference.rim EMCqMRI.core.models.inference.rnn EMCqMRI.core.models.likelihood EMCqMRI.core.models.likelihood.gaussian EMCqMRI.core.models.signal EMCqMRI.core.models.signal.fse EMCqMRI.core.models.signal.looklocker EMCqMRI.core.utilities EMCqMRI.core.utilities.checkpoint_utilities EMCqMRI.core.utilities.configuration_utilities EMCqMRI.core.utilities.core_utilities EMCqMRI.core.utilities.dataset_utilities EMCqMRI.core.utilities.image_utilities EMCqMRI.core.utilities.torch_utils

O

OptsToAttributes (class in EMCqMRI.core.utilities.configuration_utilities)

P

pad() (in module EMCqMRI.core.utilities.image_utilities) parse_command_line_configuration() (EMCqMRI.core.engine.build_model.Configuration method) parse_configuration() (EMCqMRI.core.utilities.configuration_utilities.ParseConfiguration method) parse_imported_cmd_configuration() (EMCqMRI.core.engine.build_model.Configuration method) parse_json_configuration() (in module EMCqMRI.core.utilities.configuration_utilities) ParseConfiguration (class in EMCqMRI.core.utilities.configuration_utilities)

pixel_unshuffle() (in module EMCqMRI.core.utilities.torch_utils) PixelUnshuffle (class in EMCqMRI.core.utilities.torch_utils) plot_scatter() (in module EMCqMRI.core.utilities.image_utilities) prep_batch() (in module EMCqMRI.core.utilities.core_utilities) ProgressBarWrap() (in module EMCqMRI.core.utilities.core_utilities) ProgressWrapper (class in EMCqMRI.core.utilities.core_utilities)

R

reset() (EMCqMRI.core.utilities.core_utilities.ProgressWrapper method) Resnet (class in EMCqMRI.core.models.inference.resnet) Rim (class in EMCqMRI.core.models.inference.rim)

Rnn (class in EMCqMRI.core.models.inference.rnn) run() (EMCqMRI.core.engine.estimate.Infer method) (EMCqMRI.core.engine.train_model.Trainer method)

S

SampleDatabase (class in EMCqMRI.core.engine.data_loader) save() (in module EMCqMRI.core.utilities.checkpoint_utilities) save_hdf5() (in module EMCqMRI.core.utilities.image_utilities) saveDataPickle() (in module EMCqMRI.core.utilities.image_utilities) saveItermediateResults() (in module EMCqMRI.core.utilities.image_utilities) set_data_path() (EMCqMRI.core.base.base_dataset.Dataset method) (in module EMCqMRI.core.base.base_dataset.Dataset) set_dataset_config() (EMCqMRI.core.engine.build_model.Configuration method)

set_global_config() (EMCqMRI.core.engine.build_model.Configuration method) set_inference_config() (EMCqMRI.core.engine.build_model.Configuration method) set_max() (EMCqMRI.core.utilities.core_utilities.ProgressWrapper method) set_total_sub() (EMCqMRI.core.utilities.core_utilities.ProgressWrapper method) SignalModel (class in EMCqMRI.core.base.base_signal_model) smooth_maps() (in module EMCqMRI.core.utilities.dataset_utilities) str2bool() (in module EMCqMRI.core.utilities.configuration_utilities) str_to_class() (in module EMCqMRI.core.utilities.core_utilities)

T

Trainer (class in EMCqMRI.core.engine.train_model) training (EMCqMRI.core.models.inference.resnet.BasicBlock attribute) (EMCqMRI.core.models.inference.resnet.Resnet attribute) (EMCqMRI.core.models.inference.rim.Rim attribute) (EMCqMRI.core.models.inference.rnn.Rnn attribute) (EMCqMRI.core.utilities.torch_utils.PixelUnshuffle attribute)

U

unpad() (in module EMCqMRI.core.utilities.image_utilities) update() (EMCqMRI.core.utilities.core_utilities.ProgressWrapper method)

update_bar() (EMCqMRI.core.models.inference.mle.Mle method) update_ext_par() (EMCqMRI.core.utilities.core_utilities.ProgressWrapper method)

V

visualise_h5_image() (in module EMCqMRI.core.utilities.image_utilities)