Index
_
|
A
|
B
|
C
|
D
|
E
|
F
|
G
|
H
|
I
|
J
|
L
|
M
|
N
|
O
|
P
|
Q
|
R
|
S
|
T
|
U
|
V
|
W
|
Y
|
Z
_
_builder (mdt.component_templates.base.ComponentTemplate attribute)
_component_type (mdt.component_templates.base.ComponentTemplate attribute)
_constraints (mdt.models.composite.DMRICompositeModel attribute)
_model_priors (mdt.models.composite.DMRICompositeModel attribute)
_proposal_callbacks (mdt.models.composite.DMRICompositeModel attribute)
A
AboutDialog (class in mdt.gui.maps_visualizer.main)
(class in mdt.gui.model_fit.qt_main)
AbsModPiTransform (class in mdt.model_building.parameter_functions.transformations)
AbsModTwoPiTransform (class in mdt.model_building.parameter_functions.transformations)
AbsModXTransform (class in mdt.model_building.parameter_functions.transformations)
AbsSinHalfPrior (class in mdt.model_building.parameter_functions.priors)
AbsSinPrior (class in mdt.model_building.parameter_functions.priors)
AbstractParameterDependency (class in mdt.model_building.parameter_functions.dependencies)
AbstractTransformation (class in mdt.model_building.parameter_functions.transformations)
ActivePostProcessingLoader (class in mdt.configuration)
add_column_to_protocol() (in module mdt.cli_scripts.mdt_create_protocol)
add_component() (in module mdt.lib.components)
add_extra_columns() (in module mdt.cli_scripts.mdt_create_protocol)
add_listener() (mdt.lib.log_handlers.LogDispatchHandler static method)
add_rician_noise() (in module mdt.simulations)
add_sequence_timing_column_to_protocol() (in module mdt.cli_scripts.mdt_create_protocol)
add_template_component() (in module mdt.lib.components)
add_window() (mdt.gui.utils.QtManager static method)
AddProtocolMapDialog (class in mdt.gui.model_fit.tabs.fit_model_tab)
AllSubjects (class in mdt.lib.batch_utils)
AlwaysOne (class in mdt.model_building.parameter_functions.priors)
append() (mdt.utils.PathJoiner method)
append_protocol() (mdt.protocols.Protocol method)
apply() (mdt.configuration.ConfigAction method)
(mdt.configuration.SimpleConfigAction method)
(mdt.configuration.VoidConfigAction method)
(mdt.gui.maps_visualizer.actions.ConfigAction method)
(mdt.gui.maps_visualizer.actions.ModelUpdateAction method)
(mdt.gui.maps_visualizer.actions.NewConfigAction method)
(mdt.gui.maps_visualizer.actions.NewDataAction method)
(mdt.visualization.maps.base.Clipping method)
(mdt.visualization.maps.base.Zoom method)
apply_action() (mdt.gui.maps_visualizer.base.Controller method)
(mdt.gui.maps_visualizer.base.QtController method)
apply_mask() (in module mdt.utils)
apply_mask_to_file() (in module mdt.utils)
apply_to_model() (mdt.utils.InitializationData method)
(mdt.utils.SimpleInitializationData method)
ApplyMask (class in mdt.cli_scripts.mdt_apply_mask)
ARDBeta (class in mdt.model_building.parameter_functions.priors)
ARDGaussian (class in mdt.model_building.parameter_functions.priors)
assignment_code (mdt.model_building.parameter_functions.dependencies.AbstractParameterDependency attribute)
(mdt.model_building.parameter_functions.dependencies.SimpleAssignment attribute)
AssignmentConstructor (class in mdt.model_building.parameter_functions.transformations)
auto_load_protocol() (in module mdt.protocols)
AutoDict (class in mdt.utils)
AutoGridLayout (class in mdt.visualization.layouts)
AxialNormalPDF (class in mdt.model_building.parameter_functions.priors)
AxisData (class in mdt.visualization.maps.matplotlib_renderer)
AzimuthAngleParameterTemplate (class in mdt.component_templates.parameters)
B
base_dir (mdt.gui.model_fit.utils.SharedState attribute)
BasicShellApplication (class in mdt.lib.shell_utils)
batch_apply() (in module mdt.lib.batch_utils)
batch_fit() (in module mdt)
batch_profile_factory() (in module mdt.lib.batch_utils)
BatchFit (class in mdt.cli_scripts.mdt_batch_fit)
BatchFitProtocolLoader (class in mdt.lib.batch_utils)
BatchFitSubjectOutputInfo (class in mdt.lib.batch_utils)
BatchProfile (class in mdt.lib.batch_utils)
BatchProfileBuilder (class in mdt.component_templates.batch_profiles)
BatchProfileTemplate (class in mdt.component_templates.batch_profiles)
BatchSubjectSelection (class in mdt.lib.batch_utils)
bind_function() (in module mdt.component_templates.base)
block_plots() (in module mdt)
blocked_signals() (in module mdt.gui.utils)
blockSignals() (mdt.gui.widgets.composite_widgets.ScientificNumberScroller method)
BooleanConversion (class in mdt.visualization.dict_conversion)
bootstrap_model() (in module mdt)
bound_methods (mdt.component_templates.base.ComponentTemplate attribute)
(mdt.component_templates.batch_profiles.BatchProfileTemplate attribute)
(mdt.component_templates.compartment_models.CompartmentTemplate attribute)
(mdt.component_templates.compartment_models.WeightCompartmentTemplate attribute)
(mdt.component_templates.composite_models.CompositeModelTemplate attribute)
(mdt.component_templates.library_functions.LibraryFunctionTemplate attribute)
(mdt.component_templates.parameters.AzimuthAngleParameterTemplate attribute)
(mdt.component_templates.parameters.FreeParameterTemplate attribute)
(mdt.component_templates.parameters.ParameterTemplate attribute)
(mdt.component_templates.parameters.PolarAngleParameterTemplate attribute)
(mdt.component_templates.parameters.ProtocolParameterTemplate attribute)
(mdt.component_templates.parameters.RotationalAngleParameterTemplate attribute)
(mdt.component_templates.parameters.SphericalCoordinateParameterTemplate attribute)
build_input_data() (mdt.gui.model_fit.tabs.fit_model_tab.InputDataInfo method)
bval_fname (mdt.component_templates.batch_profiles.BatchProfileTemplate attribute)
,
[1]
bvec_fname (mdt.component_templates.batch_profiles.BatchProfileTemplate attribute)
,
[1]
C
cache_info (mdt.component_templates.compartment_models.CompartmentTemplate attribute)
,
[1]
CacheInfo (class in mdt.models.compartments)
calculate_dependent_parameters() (in module mdt.models.composite)
calculate_point_estimate_information_criterions() (in module mdt.utils)
cartesian_to_spherical() (in module mdt.utils)
center_window() (in module mdt.gui.utils)
check_user_components() (in module mdt.utils)
children (mdt.model_building.trees.Tree attribute)
cl_code (mdt.component_templates.compartment_models.CompartmentTemplate attribute)
,
[1]
(mdt.component_templates.compartment_models.WeightCompartmentTemplate attribute)
(mdt.component_templates.library_functions.LibraryFunctionTemplate attribute)
,
[1]
cl_extra (mdt.component_templates.compartment_models.CompartmentTemplate attribute)
,
[1]
(mdt.component_templates.compartment_models.WeightCompartmentTemplate attribute)
(mdt.component_templates.library_functions.LibraryFunctionTemplate attribute)
,
[1]
ClampTransform (class in mdt.model_building.parameter_functions.transformations)
clear_voxel_info() (mdt.gui.maps_visualizer.main.PlottingFrameInfoToStatusBar method)
(mdt.gui.maps_visualizer.renderers.base.NoOptPlottingFrameInfoViewer method)
(mdt.gui.maps_visualizer.renderers.base.PlottingFrameInfoViewer method)
Clipping (class in mdt.visualization.maps.base)
close() (mdt.lib.log_handlers.ModelOutputLogHandler method)
closeEvent() (mdt.gui.model_fit.qt_main.MDTGUISingleModel method)
ColorbarSettings (class in mdt.visualization.maps.base)
column_names (mdt.protocols.Protocol attribute)
combine_dict_to_array() (in module mdt.utils)
CompartmentBuilder (class in mdt.component_templates.compartment_models)
CompartmentContextResults (class in mdt.component_templates.composite_models)
CompartmentModel (class in mdt.models.compartments)
CompartmentModelTree (class in mdt.model_building.trees)
CompartmentTemplate (class in mdt.component_templates.compartment_models)
component_type (mdt.component_templates.base.ComponentTemplate attribute)
(mdt.component_templates.batch_profiles.BatchProfileTemplate attribute)
(mdt.component_templates.compartment_models.CompartmentTemplate attribute)
(mdt.component_templates.compartment_models.WeightCompartmentTemplate attribute)
(mdt.component_templates.composite_models.CompositeModelTemplate attribute)
(mdt.component_templates.library_functions.LibraryFunctionTemplate attribute)
(mdt.component_templates.parameters.AzimuthAngleParameterTemplate attribute)
(mdt.component_templates.parameters.FreeParameterTemplate attribute)
(mdt.component_templates.parameters.ParameterTemplate attribute)
(mdt.component_templates.parameters.PolarAngleParameterTemplate attribute)
(mdt.component_templates.parameters.ProtocolParameterTemplate attribute)
(mdt.component_templates.parameters.RotationalAngleParameterTemplate attribute)
(mdt.component_templates.parameters.SphericalCoordinateParameterTemplate attribute)
ComponentBuilder (class in mdt.component_templates.base)
ComponentTemplate (class in mdt.component_templates.base)
ComponentTemplateMeta (class in mdt.component_templates.base)
CompositeModelFunction (class in mdt.models.composite)
CompositeModelTemplate (class in mdt.component_templates.composite_models)
computations_finished() (mdt.gui.model_fit.qt_main.MDTGUISingleModel method)
computations_started() (mdt.gui.model_fit.qt_main.MDTGUISingleModel method)
compute_covariance_matrix() (mdt.models.composite.DMRICompositeModel method)
compute_fim() (in module mdt)
compute_noddi_dti() (in module mdt.utils)
config_attribute (mdt.gui.maps_visualizer.actions.SetAnnotations attribute)
(mdt.gui.maps_visualizer.actions.SetColorBarNmrTicks attribute)
(mdt.gui.maps_visualizer.actions.SetColorbarLocation attribute)
(mdt.gui.maps_visualizer.actions.SetColormap attribute)
(mdt.gui.maps_visualizer.actions.SetDimension attribute)
(mdt.gui.maps_visualizer.actions.SetFlipud attribute)
(mdt.gui.maps_visualizer.actions.SetFont attribute)
(mdt.gui.maps_visualizer.actions.SetGeneralMask attribute)
(mdt.gui.maps_visualizer.actions.SetInterpolation attribute)
(mdt.gui.maps_visualizer.actions.SetMapClipping attribute)
(mdt.gui.maps_visualizer.actions.SetMapColorbarLabel attribute)
(mdt.gui.maps_visualizer.actions.SetMapColormap attribute)
(mdt.gui.maps_visualizer.actions.SetMapScale attribute)
(mdt.gui.maps_visualizer.actions.SetMapTitle attribute)
(mdt.gui.maps_visualizer.actions.SetMapsToShow attribute)
(mdt.gui.maps_visualizer.actions.SetPlotTitle attribute)
(mdt.gui.maps_visualizer.actions.SetRotate attribute)
(mdt.gui.maps_visualizer.actions.SetShowAxis attribute)
(mdt.gui.maps_visualizer.actions.SetShowPlotColorbars attribute)
(mdt.gui.maps_visualizer.actions.SetShowPlotTitles attribute)
(mdt.gui.maps_visualizer.actions.SetSliceIndex attribute)
(mdt.gui.maps_visualizer.actions.SetVolumeIndex attribute)
(mdt.gui.maps_visualizer.actions.SetZoom attribute)
(mdt.gui.maps_visualizer.actions.SimpleConfigAction attribute)
(mdt.gui.maps_visualizer.actions.SimpleMapSpecificConfigAction attribute)
config_context() (in module mdt.configuration)
ConfigAction (class in mdt.configuration)
(class in mdt.gui.maps_visualizer.actions)
ConfigSectionLoader (class in mdt.configuration)
configure_per_model_logging() (in module mdt.utils)
console_script() (mdt.lib.shell_utils.BasicShellApplication class method)
constraints (mdt.component_templates.compartment_models.CompartmentTemplate attribute)
,
[1]
(mdt.component_templates.composite_models.CompositeModelTemplate attribute)
,
[1]
Controller (class in mdt.gui.maps_visualizer.base)
ConversionSpecification (class in mdt.visualization.dict_conversion)
ConvertDictElements (class in mdt.visualization.dict_conversion)
ConvertDynamicFromModule (class in mdt.visualization.dict_conversion)
ConvertibleConfig (class in mdt.visualization.maps.base)
ConvertListElements (class in mdt.visualization.dict_conversion)
coordinates_to_index() (mdt.visualization.maps.matplotlib_renderer.AxisData method)
copy_with_different_results() (mdt.models.composite.ExtraOptimizationMapsInfo method)
CosSqrClampTransform (class in mdt.model_building.parameter_functions.transformations)
covariance_to_correlation() (in module mdt.utils)
create_2d_sort_matrix() (in module mdt.lib.sorting)
create_4d_sort_matrix() (in module mdt.lib.sorting)
create_assignment() (mdt.model_building.parameter_functions.transformations.AssignmentConstructor method)
(mdt.model_building.parameter_functions.transformations.FormatAssignmentConstructor method)
create_blank_mask() (in module mdt.utils)
create_brain_mask() (in module mdt.utils)
create_class() (mdt.component_templates.base.ComponentBuilder method)
create_covariance_matrix() (in module mdt.utils)
create_extended() (mdt.utils.PathJoiner method)
create_index_matrix() (in module mdt.utils)
create_median_otsu_brain_mask() (in module mdt.lib.masking)
(in module mdt.utils)
create_protocol() (in module mdt.protocols)
create_roi() (in module mdt.utils)
create_signal_estimates() (in module mdt.simulations)
create_slice_roi() (in module mdt.utils)
create_valid() (mdt.visualization.maps.base.MapPlotConfig method)
create_write_median_otsu_brain_mask() (in module mdt.lib.masking)
CreateBvecBval (class in mdt.cli_scripts.mdt_create_bvec_bval)
CreateMask (class in mdt.cli_scripts.mdt_create_mask)
CreateProtocol (class in mdt.cli_scripts.mdt_create_protocol)
CreateRoiSlice (class in mdt.cli_scripts.mdt_create_roi_slice)
D
data (mdt.model_building.trees.Tree attribute)
(mdt.visualization.maps.base.SingleMapInfo attribute)
data_fname (mdt.component_templates.batch_profiles.BatchProfileTemplate attribute)
,
[1]
data_folder (mdt.lib.batch_utils.SimpleSubjectInfo attribute)
(mdt.lib.batch_utils.SubjectInfo attribute)
data_type (mdt.component_templates.parameters.FreeParameterTemplate attribute)
(mdt.component_templates.parameters.ParameterTemplate attribute)
(mdt.component_templates.parameters.ProtocolParameterTemplate attribute)
DataConfigModel (class in mdt.gui.maps_visualizer.base)
DataInfo (class in mdt.visualization.maps.base)
decode() (mdt.model_building.utils.ParameterCodec method)
deepcopy() (mdt.protocols.Protocol method)
DeferredActionDict (class in mdt.lib.deferred_mappings)
DeferredActionTuple (class in mdt.lib.deferred_mappings)
DeferredFunctionDict (class in mdt.lib.deferred_mappings)
dependencies (mdt.component_templates.compartment_models.CompartmentTemplate attribute)
,
[1]
(mdt.component_templates.compartment_models.WeightCompartmentTemplate attribute)
(mdt.component_templates.library_functions.LibraryFunctionTemplate attribute)
,
[1]
description (mdt.component_templates.base.ComponentTemplate attribute)
,
[1]
(mdt.component_templates.batch_profiles.BatchProfileTemplate attribute)
,
[1]
(mdt.component_templates.compartment_models.CompartmentTemplate attribute)
,
[1]
(mdt.component_templates.compartment_models.WeightCompartmentTemplate attribute)
(mdt.component_templates.composite_models.CompositeModelTemplate attribute)
,
[1]
(mdt.component_templates.library_functions.LibraryFunctionTemplate attribute)
,
[1]
(mdt.component_templates.parameters.ParameterTemplate attribute)
dimension_index (mdt.gui.model_fit.utils.SharedState attribute)
DKIMeasures (class in mdt.lib.post_processing)
DMRICompartmentModelFunction (class in mdt.models.compartments)
DMRICompositeModel (class in mdt.models.composite)
DMRICompositeModelBuilder (class in mdt.component_templates.composite_models)
DoubleModelNameException
dragEnterEvent() (mdt.gui.maps_visualizer.main.MapsVisualizerWindow method)
dropEvent() (mdt.gui.maps_visualizer.main.MapsVisualizerWindow method)
DTIMeasures (class in mdt.lib.post_processing)
E
emit() (mdt.gui.utils.ForwardingListener method)
(mdt.lib.log_handlers.LogDispatchHandler method)
(mdt.lib.log_handlers.LogListenerInterface method)
(mdt.lib.log_handlers.ModelOutputLogHandler method)
(mdt.lib.log_handlers.StdOutHandler method)
empty_windows_list() (mdt.gui.utils.QtManager static method)
enable_correct_inputs() (mdt.gui.model_fit.tabs.generate_protocol_tab.LoadColumnDialog method)
enable_pyqt_exception_hook() (in module mdt.gui.utils)
encode() (mdt.model_building.utils.ParameterCodec method)
encode_bounds() (mdt.model_building.parameter_functions.transformations.AbsModXTransform method)
(mdt.model_building.parameter_functions.transformations.AbstractTransformation method)
(mdt.model_building.parameter_functions.transformations.ClampTransform method)
(mdt.model_building.parameter_functions.transformations.CosSqrClampTransform method)
(mdt.model_building.parameter_functions.transformations.IdentityTransform method)
(mdt.model_building.parameter_functions.transformations.PositivityTransform method)
(mdt.model_building.parameter_functions.transformations.ScaleClampTransform method)
(mdt.model_building.parameter_functions.transformations.ScaleTransform method)
(mdt.model_building.parameter_functions.transformations.SinSqrClampTransform method)
(mdt.model_building.parameter_functions.transformations.SqrClampTransform method)
(mdt.model_building.utils.ParameterCodec method)
encode_decode() (mdt.model_building.utils.ParameterCodec method)
enforce_weights_sum_to_one (mdt.component_templates.composite_models.CompositeModelTemplate attribute)
,
[1]
ensure_exists() (in module mdt.configuration)
EstimableModel (class in mdt.models.base)
estimate_noise_std() (in module mdt.utils)
estimated_column_names (mdt.protocols.Protocol attribute)
evaluate() (mdt.models.compartments.DMRICompartmentModelFunction method)
(mdt.models.composite.CompositeModelFunction method)
exec_() (mdt.gui.utils.QtManager static method)
export_image() (mdt.gui.maps_visualizer.renderers.base.PlottingFrame method)
(mdt.gui.maps_visualizer.renderers.matplotlib_renderer.MatplotlibPlotting method)
ExportImageDialog (class in mdt.gui.maps_visualizer.main)
extra_optimization_maps (mdt.component_templates.compartment_models.CompartmentTemplate attribute)
,
[1]
(mdt.component_templates.composite_models.CompositeModelTemplate attribute)
,
[1]
extra_optimization_maps() (mdt.lib.post_processing.DKIMeasures static method)
(mdt.lib.post_processing.DTIMeasures static method)
extra_sampling_maps (mdt.component_templates.compartment_models.CompartmentTemplate attribute)
,
[1]
(mdt.component_templates.composite_models.CompositeModelTemplate attribute)
,
[1]
extra_sampling_maps() (mdt.lib.post_processing.DTIMeasures static method)
extract_volumes() (in module mdt.utils)
ExtraDataDialog (class in mdt.gui.model_fit.tabs.fit_model_tab)
ExtraOptimizationMapsInfo (class in mdt.models.composite)
F
file_path (mdt.visualization.maps.base.SingleMapInfo attribute)
find_all_nifti_files() (in module mdt.visualization.maps.utils)
finished (mdt.gui.model_fit.tabs.fit_model_tab.RunModelWorker attribute)
(mdt.gui.model_fit.tabs.generate_brain_mask_tab.GenerateMaskWorker attribute)
(mdt.gui.model_fit.tabs.generate_roi_mask_tab.GenerateROIMaskWorker attribute)
(mdt.gui.utils.MessageReceiver attribute)
fit_model() (in module mdt)
FitModelTab (class in mdt.gui.model_fit.tabs.fit_model_tab)
fix() (mdt.models.composite.DMRICompositeModel method)
fix_parameter() (mdt.models.composite.ModelFunctionsInformation method)
fixed (mdt.component_templates.parameters.FreeParameterTemplate attribute)
,
[1]
fixed_parameters (mdt.models.composite.SamplingPostProcessingData attribute)
fixes (mdt.component_templates.composite_models.CompositeModelTemplate attribute)
,
[1]
flatten() (in module mdt.utils)
FloatConversion (class in mdt.visualization.dict_conversion)
Font (class in mdt.visualization.maps.base)
font_names() (mdt.visualization.maps.base.Font class method)
FormatAssignmentConstructor (class in mdt.model_building.parameter_functions.transformations)
ForwardingListener (class in mdt.gui.utils)
fractional_anisotropy() (mdt.lib.post_processing.DTIMeasures static method)
fractional_anisotropy_std() (mdt.lib.post_processing.DTIMeasures static method)
FreeParameterTemplate (class in mdt.component_templates.parameters)
from_coords() (mdt.visualization.maps.base.Zoom class method)
from_dict() (mdt.visualization.dict_conversion.ConversionSpecification method)
(mdt.visualization.dict_conversion.ConvertDictElements method)
(mdt.visualization.dict_conversion.ConvertDynamicFromModule method)
(mdt.visualization.dict_conversion.ConvertListElements method)
(mdt.visualization.dict_conversion.OptionalConversionDecorator method)
(mdt.visualization.dict_conversion.SimpleClassConversion method)
(mdt.visualization.dict_conversion.SimpleFunctionConversion method)
(mdt.visualization.dict_conversion.WhiteListConversion method)
(mdt.visualization.maps.base.MapPlotConfig class method)
(mdt.visualization.maps.base.SingleMapConfig class method)
from_file() (mdt.visualization.maps.base.SingleMapInfo class method)
from_object() (mdt.configuration.SetGeneralOptimizer class method)
from_paths() (mdt.visualization.maps.base.SimpleDataInfo class method)
from_yaml() (mdt.visualization.maps.base.MapPlotConfig class method)
(mdt.visualization.maps.base.SingleMapConfig class method)
function_message_decorator() (in module mdt.gui.utils)
G
gamma_h (mdt.protocols.Protocol attribute)
Gaussian (class in mdt.model_building.likelihood_functions)
generate_mask() (mdt.gui.model_fit.tabs.generate_brain_mask_tab.GenerateBrainMaskTab method)
generate_roi_mask() (mdt.gui.model_fit.tabs.generate_roi_mask_tab.GenerateROIMaskTab method)
generate_simple_wm_mask() (in module mdt.lib.masking)
GenerateBrainMaskTab (class in mdt.gui.model_fit.tabs.generate_brain_mask_tab)
GenerateMaskWorker (class in mdt.gui.model_fit.tabs.generate_brain_mask_tab)
GenerateProtocolTab (class in mdt.gui.model_fit.tabs.generate_protocol_tab)
GenerateROIMaskTab (class in mdt.gui.model_fit.tabs.generate_roi_mask_tab)
GenerateROIMaskWorker (class in mdt.gui.model_fit.tabs.generate_roi_mask_tab)
get_active_post_processing() (in module mdt.configuration)
(mdt.models.composite.DMRICompositeModel method)
get_all_columns() (mdt.protocols.Protocol method)
get_all_nifti_data() (in module mdt.lib.nifti)
get_all_protocol_parameters() (mdt.models.composite.ModelFunctionsInformation method)
get_argparse_extension_checker() (in module mdt.lib.shell_utils)
get_available_colormaps() (mdt.visualization.maps.base.MapPlotConfig class method)
(mdt.visualization.maps.base.SingleMapConfig class method)
get_available_interpolations() (mdt.visualization.maps.base.MapPlotConfig class method)
get_axis() (mdt.visualization.layouts.GridLayoutSpecifier method)
get_b_values_shells() (mdt.protocols.Protocol method)
get_batch_profile() (in module mdt.lib.components)
get_best_batch_profile() (in module mdt.lib.batch_utils)
get_bounding_box() (mdt.visualization.maps.base.DataInfo method)
(mdt.visualization.maps.base.SimpleDataInfo method)
(mdt.visualization.maps.base.SingleMapInfo method)
get_cache_init_function() (mdt.models.compartments.CompartmentModel method)
(mdt.models.compartments.DMRICompartmentModelFunction method)
(mdt.models.compartments.WeightCompartment method)
get_cache_struct() (mdt.models.compartments.CompartmentModel method)
(mdt.models.compartments.DMRICompartmentModelFunction method)
(mdt.models.compartments.WeightCompartment method)
get_callback_function() (mdt.models.composite.ProtocolAdaptionCallbacks method)
get_cl_decode() (mdt.model_building.parameter_functions.transformations.AbsModXTransform method)
(mdt.model_building.parameter_functions.transformations.AbstractTransformation method)
(mdt.model_building.parameter_functions.transformations.ClampTransform method)
(mdt.model_building.parameter_functions.transformations.CosSqrClampTransform method)
(mdt.model_building.parameter_functions.transformations.IdentityTransform method)
(mdt.model_building.parameter_functions.transformations.PositivityTransform method)
(mdt.model_building.parameter_functions.transformations.ScaleClampTransform method)
(mdt.model_building.parameter_functions.transformations.ScaleTransform method)
(mdt.model_building.parameter_functions.transformations.SinSqrClampTransform method)
(mdt.model_building.parameter_functions.transformations.SqrClampTransform method)
get_cl_devices() (in module mdt.utils)
get_cl_encode() (mdt.model_building.parameter_functions.transformations.AbsModXTransform method)
(mdt.model_building.parameter_functions.transformations.AbstractTransformation method)
(mdt.model_building.parameter_functions.transformations.ClampTransform method)
(mdt.model_building.parameter_functions.transformations.CosSqrClampTransform method)
(mdt.model_building.parameter_functions.transformations.IdentityTransform method)
(mdt.model_building.parameter_functions.transformations.PositivityTransform method)
(mdt.model_building.parameter_functions.transformations.ScaleClampTransform method)
(mdt.model_building.parameter_functions.transformations.ScaleTransform method)
(mdt.model_building.parameter_functions.transformations.SinSqrClampTransform method)
(mdt.model_building.parameter_functions.transformations.SqrClampTransform method)
get_column() (mdt.protocols.Protocol method)
get_columns() (mdt.protocols.Protocol method)
get_compartment_models() (mdt.model_building.trees.CompartmentModelTree method)
(mdt.models.composite.ModelFunctionsInformation method)
get_component() (in module mdt.lib.components)
get_component_list() (in module mdt.lib.components)
get_composite_model_function() (mdt.models.composite.DMRICompositeModel method)
get_config() (mdt.gui.maps_visualizer.base.DataConfigModel method)
(mdt.gui.maps_visualizer.base.SimpleDataConfigModel method)
get_config_dir() (in module mdt.configuration)
get_config_option() (in module mdt.configuration)
get_constraints_func() (mdt.models.compartments.CompartmentModel method)
(mdt.models.compartments.DMRICompartmentModelFunction method)
(mdt.models.compartments.WeightCompartment method)
get_constraints_function() (mdt.models.base.EstimableModel method)
(mdt.models.composite.DMRICompositeModel method)
get_conversion_info() (mdt.visualization.layouts.GridLayout class method)
(mdt.visualization.maps.base.ConvertibleConfig class method)
(mdt.visualization.maps.base.SimpleConvertibleConfig class method)
get_covariance_output_names() (mdt.models.composite.DMRICompositeModel method)
get_data() (mdt.gui.maps_visualizer.base.DataConfigModel method)
(mdt.gui.maps_visualizer.base.SimpleDataConfigModel method)
get_decode_function() (mdt.model_building.utils.ParameterCodec method)
get_default() (mdt.visualization.maps.base.ColorbarSettings static method)
get_default_parameter_value() (mdt.models.composite.ModelFunctionsInformation method)
get_default_values() (mdt.visualization.maps.base.MapPlotConfig static method)
(mdt.visualization.maps.base.SingleMapConfig static method)
get_dependency_fixed_parameters_list() (mdt.models.composite.ModelFunctionsInformation method)
get_doc_arg_parser() (in module mdt.cli_scripts.MDT)
(in module mdt.cli_scripts.mdt_apply_mask)
(in module mdt.cli_scripts.mdt_batch_fit)
(in module mdt.cli_scripts.mdt_create_bvec_bval)
(in module mdt.cli_scripts.mdt_create_mask)
(in module mdt.cli_scripts.mdt_create_protocol)
(in module mdt.cli_scripts.mdt_create_roi_slice)
(in module mdt.cli_scripts.mdt_estimate_noise_std)
(in module mdt.cli_scripts.mdt_get_example_data)
(in module mdt.cli_scripts.mdt_gui)
(in module mdt.cli_scripts.mdt_info_img)
(in module mdt.cli_scripts.mdt_info_protocol)
(in module mdt.cli_scripts.mdt_init_user_settings)
(in module mdt.cli_scripts.mdt_list_devices)
(in module mdt.cli_scripts.mdt_list_models)
(in module mdt.cli_scripts.mdt_math_img)
(in module mdt.cli_scripts.mdt_math_protocol)
(in module mdt.cli_scripts.mdt_model_fit)
(in module mdt.cli_scripts.mdt_view_maps)
(in module mdt.cli_scripts.mdt_volume_merge)
get_documentation_arg_parser() (mdt.lib.shell_utils.BasicShellApplication method)
get_encode_function() (mdt.model_building.utils.ParameterCodec method)
get_estimable_parameters_list() (mdt.models.composite.ModelFunctionsInformation method)
get_estimable_weights() (mdt.models.composite.ModelFunctionsInformation method)
get_example_data() (in module mdt.utils)
get_extra_optimization_maps_funcs() (mdt.models.compartments.CompartmentModel method)
(mdt.models.compartments.DMRICompartmentModelFunction method)
(mdt.models.compartments.WeightCompartment method)
get_extra_parameters() (mdt.model_building.parameter_functions.priors.ParameterPrior method)
(mdt.model_building.parameter_functions.priors.SimpleParameterPrior method)
get_extra_protocol() (in module mdt.cli_scripts.mdt_model_fit)
get_extra_sampling_maps_funcs() (mdt.models.compartments.CompartmentModel method)
(mdt.models.compartments.DMRICompartmentModelFunction method)
(mdt.models.compartments.WeightCompartment method)
get_file_path() (mdt.visualization.maps.base.DataInfo method)
(mdt.visualization.maps.base.SimpleDataInfo method)
get_file_paths() (mdt.visualization.maps.base.DataInfo method)
(mdt.visualization.maps.base.SimpleDataInfo method)
get_finalize_proposal_function() (mdt.models.base.EstimableModel method)
(mdt.models.composite.DMRICompositeModel method)
get_fixes() (mdt.utils.InitializationData method)
(mdt.utils.SimpleInitializationData method)
get_free_param_names() (mdt.models.base.EstimableModel method)
(mdt.models.composite.DMRICompositeModel method)
get_free_parameters() (mdt.model_building.model_functions.ModelCLFunction method)
(mdt.model_building.model_functions.SimpleModelCLFunction method)
get_free_parameters_list() (mdt.models.composite.ModelFunctionsInformation method)
get_g_columns() (in module mdt.protocols)
get_general_optimizer_name() (in module mdt.configuration)
get_general_optimizer_options() (in module mdt.configuration)
get_general_sampling_settings() (in module mdt.configuration)
get_gridspec() (mdt.visualization.layouts.AutoGridLayout method)
(mdt.visualization.layouts.GridLayout method)
(mdt.visualization.layouts.LowerTriangular method)
(mdt.visualization.layouts.Rectangular method)
(mdt.visualization.layouts.SingleColumn method)
(mdt.visualization.layouts.SingleRow method)
get_index_first_non_zero_slice() (mdt.visualization.maps.base.DataInfo method)
(mdt.visualization.maps.base.SimpleDataInfo method)
(mdt.visualization.maps.base.SingleMapInfo method)
get_indices_bval_in_range() (mdt.protocols.Protocol method)
get_initial_parameters() (mdt.models.base.EstimableModel method)
(mdt.models.composite.DMRICompositeModel method)
get_inits() (mdt.utils.InitializationData method)
(mdt.utils.SimpleInitializationData method)
get_input_data() (mdt.lib.batch_utils.SimpleSubjectInfo method)
(mdt.lib.batch_utils.SubjectInfo method)
(mdt.models.composite.DMRICompositeModel method)
(mdt.models.composite.ExtraOptimizationMapsInfo method)
get_input_data_problems() (mdt.models.base.EstimableModel method)
(mdt.models.composite.DMRICompositeModel method)
get_intermediate_results_path() (in module mdt.utils)
get_kernel_data() (mdt.models.base.EstimableModel method)
(mdt.models.composite.DMRICompositeModel method)
get_kernel_input_data() (mdt.models.composite.ProtocolAdaptionCallbacks method)
get_log_likelihood_function() (mdt.models.base.EstimableModel method)
(mdt.models.composite.DMRICompositeModel method)
get_log_prior_function() (mdt.models.base.EstimableModel method)
(mdt.models.composite.DMRICompositeModel method)
get_logging_configuration_dict() (in module mdt.configuration)
get_lower_bounds() (mdt.models.base.EstimableModel method)
(mdt.models.composite.DMRICompositeModel method)
(mdt.utils.InitializationData method)
(mdt.utils.SimpleInitializationData method)
get_map_data() (mdt.visualization.maps.base.DataInfo method)
(mdt.visualization.maps.base.SimpleDataInfo method)
get_map_names() (mdt.visualization.maps.base.DataInfo method)
(mdt.visualization.maps.base.SimpleDataInfo method)
get_max_dimension() (mdt.visualization.maps.base.DataInfo method)
(mdt.visualization.maps.base.SimpleDataInfo method)
get_max_slice_index() (mdt.visualization.maps.base.DataInfo method)
(mdt.visualization.maps.base.SimpleDataInfo method)
get_max_volume_index() (mdt.visualization.maps.base.DataInfo method)
(mdt.visualization.maps.base.SimpleDataInfo method)
get_max_x_index() (mdt.visualization.maps.base.DataInfo method)
(mdt.visualization.maps.base.SimpleDataInfo method)
(mdt.visualization.maps.base.SingleMapInfo method)
get_max_y_index() (mdt.visualization.maps.base.DataInfo method)
(mdt.visualization.maps.base.SimpleDataInfo method)
(mdt.visualization.maps.base.SingleMapInfo method)
get_meta_info() (in module mdt.lib.components)
get_mle_codec() (mdt.models.base.EstimableModel method)
(mdt.models.composite.DMRICompositeModel method)
get_model() (in module mdt.lib.components)
(mdt.gui.maps_visualizer.base.Controller method)
(mdt.gui.maps_visualizer.base.QtController method)
get_model_config() (in module mdt.configuration)
get_model_eval_function() (mdt.models.composite.DMRICompositeModel method)
get_model_function_parameters() (mdt.models.composite.CompositeModelFunction method)
get_model_function_priors() (mdt.model_building.model_functions.ModelCLFunction method)
(mdt.model_building.model_functions.SimpleModelCLFunction method)
get_model_list() (mdt.models.composite.ModelFunctionsInformation method)
get_model_parameter_by_name() (mdt.models.composite.ModelFunctionsInformation method)
get_model_parameter_list() (mdt.models.composite.CompositeModelFunction method)
(mdt.models.composite.ModelFunctionsInformation method)
get_models_list() (in module mdt)
get_models_meta_info() (in module mdt)
get_new_protocol_with_indices() (mdt.protocols.Protocol method)
get_nmr_observations() (mdt.models.base.EstimableModel method)
(mdt.models.composite.DMRICompositeModel method)
get_nmr_parameters() (mdt.models.base.EstimableModel method)
(mdt.models.composite.DMRICompositeModel method)
get_nmr_shells() (mdt.protocols.Protocol method)
get_noise_std_param() (mdt.models.composite.ModelFunctionsInformation method)
get_objective_function() (mdt.models.base.EstimableModel method)
(mdt.models.composite.DMRICompositeModel method)
get_optimization_inits() (in module mdt)
get_optimizer_for_model() (in module mdt.configuration)
get_parameter_estimable_index() (mdt.models.composite.ModelFunctionsInformation method)
get_parameter_estimable_index_by_name() (mdt.models.composite.ModelFunctionsInformation method)
get_parameter_value() (mdt.models.composite.ModelFunctionsInformation method)
get_post_optimization_output() (mdt.models.base.EstimableModel method)
(mdt.models.composite.DMRICompositeModel method)
get_post_sampling_maps() (mdt.models.base.EstimableModel method)
(mdt.models.composite.DMRICompositeModel method)
get_preferred() (mdt.visualization.maps.base.ColorbarSettings method)
get_prior_parameters() (mdt.model_building.model_functions.ModelCLFunction method)
(mdt.model_building.model_functions.SimpleModelCLFunction method)
get_processing_strategy() (in module mdt.configuration)
get_protocol() (mdt.gui.model_fit.tabs.generate_protocol_tab.LoadGBDialog method)
(mdt.lib.batch_utils.BatchFitProtocolLoader method)
get_protocol_parameter_by_name() (mdt.models.composite.ModelFunctionsInformation method)
get_protocol_parameter_names() (mdt.models.composite.ProtocolAdaptionCallbacks method)
get_qt_application_instance() (mdt.gui.utils.QtManager static method)
get_random_parameter_positions() (mdt.models.base.EstimableModel method)
(mdt.models.composite.DMRICompositeModel method)
get_required_protocol_names() (mdt.models.composite.DMRICompositeModel method)
get_rotated() (mdt.visualization.maps.base.Zoom method)
get_rwm_epsilons() (mdt.models.base.EstimableModel method)
(mdt.models.composite.DMRICompositeModel method)
get_rwm_proposal_stds() (mdt.models.base.EstimableModel method)
(mdt.models.composite.DMRICompositeModel method)
get_script_file_header_text() (in module mdt.gui.utils)
get_section_loader() (in module mdt.configuration)
get_selection() (mdt.lib.batch_utils.AllSubjects method)
(mdt.lib.batch_utils.BatchSubjectSelection method)
(mdt.lib.batch_utils.SelectedSubjects method)
get_sequence_timings() (in module mdt.protocols)
get_shortest_unique_names() (in module mdt.visualization.maps.utils)
get_single_map_info() (mdt.visualization.maps.base.DataInfo method)
(mdt.visualization.maps.base.SimpleDataInfo method)
get_size_in_dimension() (mdt.visualization.maps.base.SingleMapInfo method)
get_slice_in_dimension() (in module mdt.utils)
get_source() (mdt.component_templates.utils.TemplateModifier method)
get_subject_information() (in module mdt.lib.batch_utils)
get_subject_selection() (in module mdt.lib.batch_utils)
get_subjects() (mdt.lib.batch_utils.AllSubjects method)
(mdt.lib.batch_utils.BatchProfile method)
(mdt.lib.batch_utils.BatchSubjectSelection method)
(mdt.lib.batch_utils.SelectedSubjects method)
(mdt.lib.batch_utils.SimpleBatchProfile method)
get_template() (in module mdt.lib.components)
get_temporary_results_dir() (in module mdt.utils)
get_tmp_results_dir() (in module mdt.configuration)
get_unique_protocol_parameters() (mdt.models.composite.ModelFunctionsInformation method)
get_unweighted_indices() (mdt.protocols.Protocol method)
get_updated() (mdt.visualization.maps.base.Clipping method)
(mdt.visualization.maps.base.Font method)
(mdt.visualization.maps.base.Point2d method)
(mdt.visualization.maps.base.Scale method)
(mdt.visualization.maps.base.SimpleDataInfo method)
get_upper_bounds() (mdt.models.base.EstimableModel method)
(mdt.models.composite.DMRICompositeModel method)
(mdt.utils.InitializationData method)
(mdt.utils.SimpleInitializationData method)
get_used_volumes() (mdt.models.base.EstimableModel method)
(mdt.models.composite.DMRICompositeModel method)
get_value() (mdt.visualization.maps.matplotlib_renderer.AxisData method)
get_value_fixed_parameters_list() (mdt.models.composite.ModelFunctionsInformation method)
get_values() (mdt.protocols.SimpleVirtualColumn method)
(mdt.protocols.VirtualColumn method)
(mdt.protocols.VirtualColumnB method)
(mdt.protocols.VirtualColumn_g_spherical method)
get_volume_names() (in module mdt)
get_weighted_indices() (mdt.protocols.Protocol method)
get_weights() (mdt.models.composite.ModelFunctionsInformation method)
GetExampleData (class in mdt.cli_scripts.mdt_get_example_data)
GetExampleDataDialog (class in mdt.gui.model_fit.qt_main)
gradient_deviations_fname (mdt.component_templates.batch_profiles.BatchProfileTemplate attribute)
,
[1]
GridLayout (class in mdt.visualization.layouts)
GridLayoutSpecifier (class in mdt.visualization.layouts)
GUI (class in mdt.cli_scripts.mdt_gui)
(class in mdt.cli_scripts.mdt_view_maps)
GUI_Shortcut (class in mdt.cli_scripts.MDT)
gzip_optimization_results() (in module mdt.configuration)
gzip_sampling_results() (in module mdt.configuration)
H
has_column() (mdt.protocols.Protocol method)
has_component() (in module mdt.lib.components)
has_nan() (mdt.visualization.maps.base.SingleMapInfo method)
has_parameter() (mdt.models.composite.DMRICompositeModel method)
(mdt.models.composite.ModelFunctionsInformation method)
has_protocol_parameter() (mdt.models.composite.ModelFunctionsInformation method)
has_redo() (mdt.gui.maps_visualizer.base.Controller method)
(mdt.gui.maps_visualizer.base.QtController method)
has_undo() (mdt.gui.maps_visualizer.base.Controller method)
(mdt.gui.maps_visualizer.base.QtController method)
I
IdentityTransform (class in mdt.model_building.parameter_functions.transformations)
InfoImg (class in mdt.cli_scripts.mdt_info_img)
InfoProtocol (class in mdt.cli_scripts.mdt_info_protocol)
init() (mdt.models.composite.DMRICompositeModel method)
init_user_settings() (in module mdt.utils)
init_value (mdt.component_templates.parameters.FreeParameterTemplate attribute)
,
[1]
(mdt.component_templates.parameters.RotationalAngleParameterTemplate attribute)
(mdt.component_templates.parameters.SphericalCoordinateParameterTemplate attribute)
InitializationData (class in mdt.utils)
inits (mdt.component_templates.composite_models.CompositeModelTemplate attribute)
,
[1]
InitUserSettings (class in mdt.cli_scripts.mdt_init_user_settings)
InputDataInfo (class in mdt.gui.model_fit.tabs.fit_model_tab)
InputDataProblem (class in mdt.models.base)
InsufficientProtocolError
IntConversion (class in mdt.visualization.dict_conversion)
internal_nodes (mdt.model_building.trees.Tree attribute)
is_column_real() (mdt.protocols.Protocol method)
is_fixed() (mdt.models.composite.ModelFunctionsInformation method)
is_fixed_to_dependency() (mdt.models.composite.ModelFunctionsInformation method)
is_fixed_to_value() (mdt.models.composite.ModelFunctionsInformation method)
is_function (mdt.component_templates.library_functions.LibraryFunctionTemplate attribute)
,
[1]
is_input_data_sufficient() (mdt.models.base.EstimableModel method)
(mdt.models.composite.DMRICompositeModel method)
is_nifti_file() (in module mdt.lib.nifti)
is_parameter_estimable() (mdt.models.composite.ModelFunctionsInformation method)
is_running (mdt.gui.utils.MessageReceiver attribute)
is_scalar() (in module mdt.utils)
is_suitable() (mdt.lib.batch_utils.BatchProfile method)
(mdt.lib.batch_utils.SimpleBatchProfile method)
J
JohnsonNoise (class in mdt.model_building.signal_noise_models)
L
leaves (mdt.model_building.trees.Tree attribute)
length (mdt.protocols.Protocol attribute)
LibraryFunctionsBuilder (class in mdt.component_templates.library_functions)
LibraryFunctionTemplate (class in mdt.component_templates.library_functions)
likelihood_function (mdt.component_templates.composite_models.CompositeModelTemplate attribute)
,
[1]
LikelihoodFunction (class in mdt.model_building.likelihood_functions)
ListDevices (class in mdt.cli_scripts.mdt_list_devices)
ListModels (class in mdt.cli_scripts.mdt_list_models)
load() (mdt.configuration.ActivePostProcessingLoader method)
(mdt.configuration.ConfigSectionLoader method)
(mdt.configuration.LoggingLoader method)
(mdt.configuration.OptimizationSettingsLoader method)
(mdt.configuration.OutputFormatLoader method)
(mdt.configuration.ProcessingStrategySectionLoader method)
(mdt.configuration.RuntimeSettingsLoader method)
(mdt.configuration.SampleSettingsLoader method)
(mdt.configuration.TmpResultsDirSectionLoader method)
load_all_niftis() (in module mdt.lib.nifti)
load_all_npy_files() (in module mdt.lib.file_conversions.npy)
load_brain_mask() (in module mdt.utils)
load_builtin() (in module mdt.configuration)
load_bvec_bval() (in module mdt.protocols)
load_from_dict() (in module mdt.configuration)
load_from_yaml() (in module mdt.configuration)
load_nifti() (in module mdt.lib.nifti)
load_protocol() (in module mdt.protocols)
(mdt.gui.model_fit.tabs.generate_protocol_tab.GenerateProtocolTab method)
load_sample() (in module mdt.utils)
load_samples() (in module mdt.utils)
load_specific() (in module mdt.configuration)
load_user_gui() (in module mdt.configuration)
load_user_home() (in module mdt.configuration)
load_volume_maps() (in module mdt.utils)
LoadColumnDialog (class in mdt.gui.model_fit.tabs.generate_protocol_tab)
LoadGBDialog (class in mdt.gui.model_fit.tabs.generate_protocol_tab)
LogDispatchHandler (class in mdt.lib.log_handlers)
LoggingLoader (class in mdt.configuration)
LogListenerInterface (class in mdt.lib.log_handlers)
lower_bound (mdt.component_templates.parameters.FreeParameterTemplate attribute)
,
[1]
lower_bounds (mdt.component_templates.composite_models.CompositeModelTemplate attribute)
,
[1]
LowerTriangular (class in mdt.visualization.layouts)
M
MainTab (class in mdt.gui.utils)
make_dirs() (mdt.utils.PathJoiner method)
make_path_joiner() (in module mdt)
MapPlotConfig (class in mdt.visualization.maps.base)
MapSpecificOptions (class in mdt.gui.maps_visualizer.config_tabs.tab_map_specific)
MapsVisualizer (class in mdt.visualization.maps.matplotlib_renderer)
MapsVisualizerWindow (class in mdt.gui.maps_visualizer.main)
mask_file_changed() (mdt.gui.model_fit.tabs.generate_roi_mask_tab.GenerateROIMaskTab method)
mask_fname (mdt.component_templates.batch_profiles.BatchProfileTemplate attribute)
,
[1]
MathImg (class in mdt.cli_scripts.mdt_math_img)
MathProtocol (class in mdt.cli_scripts.mdt_math_protocol)
MatplotlibPlotting (class in mdt.gui.maps_visualizer.renderers.matplotlib_renderer)
max() (mdt.visualization.maps.base.SingleMapInfo method)
max_dimension() (mdt.visualization.maps.base.SingleMapInfo method)
max_slice_index() (mdt.visualization.maps.base.SingleMapInfo method)
max_step (mdt.model_building.parameter_functions.numdiff_info.NumDiffInfo attribute)
(mdt.model_building.parameter_functions.numdiff_info.SimpleNumDiffInfo attribute)
max_volume_index() (mdt.visualization.maps.base.SingleMapInfo method)
mdt (module)
mdt.cli_scripts (module)
mdt.cli_scripts.MDT (module)
mdt.cli_scripts.mdt_apply_mask (module)
mdt.cli_scripts.mdt_batch_fit (module)
mdt.cli_scripts.mdt_create_bvec_bval (module)
mdt.cli_scripts.mdt_create_mask (module)
mdt.cli_scripts.mdt_create_protocol (module)
mdt.cli_scripts.mdt_create_roi_slice (module)
mdt.cli_scripts.mdt_estimate_noise_std (module)
mdt.cli_scripts.mdt_get_example_data (module)
mdt.cli_scripts.mdt_gui (module)
mdt.cli_scripts.mdt_info_img (module)
mdt.cli_scripts.mdt_info_protocol (module)
mdt.cli_scripts.mdt_init_user_settings (module)
mdt.cli_scripts.mdt_list_devices (module)
mdt.cli_scripts.mdt_list_models (module)
mdt.cli_scripts.mdt_math_img (module)
mdt.cli_scripts.mdt_math_protocol (module)
mdt.cli_scripts.mdt_model_fit (module)
mdt.cli_scripts.mdt_view_maps (module)
mdt.cli_scripts.mdt_volume_merge (module)
mdt.component_templates (module)
mdt.component_templates.base (module)
mdt.component_templates.batch_profiles (module)
mdt.component_templates.compartment_models (module)
mdt.component_templates.composite_models (module)
mdt.component_templates.library_functions (module)
mdt.component_templates.parameters (module)
mdt.component_templates.utils (module)
mdt.configuration (module)
mdt.gui (module)
mdt.gui.maps_visualizer (module)
mdt.gui.maps_visualizer.actions (module)
mdt.gui.maps_visualizer.base (module)
mdt.gui.maps_visualizer.config_tabs (module)
mdt.gui.maps_visualizer.config_tabs.tab_general (module)
mdt.gui.maps_visualizer.config_tabs.tab_map_specific (module)
mdt.gui.maps_visualizer.config_tabs.tab_textual (module)
mdt.gui.maps_visualizer.design (module)
mdt.gui.maps_visualizer.design.main_rc (module)
mdt.gui.maps_visualizer.design.ui_MainWindow (module)
mdt.gui.maps_visualizer.design.ui_MapSpecificOptions (module)
mdt.gui.maps_visualizer.design.ui_save_image_dialog (module)
mdt.gui.maps_visualizer.design.ui_TabGeneral (module)
mdt.gui.maps_visualizer.design.ui_TabMapSpecific (module)
mdt.gui.maps_visualizer.design.ui_TabTextual (module)
mdt.gui.maps_visualizer.main (module)
mdt.gui.maps_visualizer.renderers (module)
mdt.gui.maps_visualizer.renderers.base (module)
mdt.gui.maps_visualizer.renderers.matplotlib_renderer (module)
mdt.gui.maps_visualizer.widgets (module)
mdt.gui.model_fit (module)
mdt.gui.model_fit.design (module)
mdt.gui.model_fit.design.main_gui_rc (module)
mdt.gui.model_fit.design.ui_about_dialog (module)
mdt.gui.model_fit.design.ui_dialog_get_example_data (module)
mdt.gui.model_fit.design.ui_fit_model_tab (module)
mdt.gui.model_fit.design.ui_generate_brain_mask_tab (module)
mdt.gui.model_fit.design.ui_generate_protocol_load_gb_dialog (module)
mdt.gui.model_fit.design.ui_generate_protocol_tab (module)
mdt.gui.model_fit.design.ui_generate_protocol_update_dialog (module)
mdt.gui.model_fit.design.ui_generate_roi_mask_tab (module)
mdt.gui.model_fit.design.ui_main_gui (module)
mdt.gui.model_fit.design.ui_optimization_extra_data_add_protocol_map_dialog (module)
mdt.gui.model_fit.design.ui_optimization_extra_data_dialog (module)
mdt.gui.model_fit.design.ui_optimization_options_dialog (module)
mdt.gui.model_fit.design.ui_runtime_settings_dialog (module)
mdt.gui.model_fit.qt_main (module)
mdt.gui.model_fit.tabs (module)
mdt.gui.model_fit.tabs.fit_model_tab (module)
mdt.gui.model_fit.tabs.generate_brain_mask_tab (module)
mdt.gui.model_fit.tabs.generate_protocol_tab (module)
mdt.gui.model_fit.tabs.generate_roi_mask_tab (module)
mdt.gui.model_fit.utils (module)
mdt.gui.utils (module)
mdt.gui.widgets (module)
mdt.gui.widgets.composite_widgets (module)
mdt.gui.widgets.decorator_widgets (module)
mdt.gui.widgets.design (module)
mdt.gui.widgets.design.ui_scientific_number_scroller_widget (module)
mdt.lib (module)
mdt.lib.batch_utils (module)
mdt.lib.components (module)
mdt.lib.deferred_mappings (module)
mdt.lib.exceptions (module)
mdt.lib.file_conversions (module)
mdt.lib.file_conversions.npy (module)
mdt.lib.fsl_sampling_routine (module)
mdt.lib.log_handlers (module)
mdt.lib.masking (module)
mdt.lib.nifti (module)
mdt.lib.post_processing (module)
mdt.lib.shell_utils (module)
mdt.lib.sorting (module)
mdt.model_building (module)
mdt.model_building.likelihood_functions (module)
mdt.model_building.model_functions (module)
mdt.model_building.parameter_functions (module)
mdt.model_building.parameter_functions.dependencies (module)
mdt.model_building.parameter_functions.numdiff_info (module)
mdt.model_building.parameter_functions.priors (module)
mdt.model_building.parameter_functions.transformations (module)
mdt.model_building.parameters (module)
mdt.model_building.signal_noise_models (module)
mdt.model_building.trees (module)
mdt.model_building.utils (module)
mdt.models (module)
mdt.models.base (module)
mdt.models.compartments (module)
mdt.models.composite (module)
mdt.protocols (module)
mdt.simulations (module)
mdt.utils (module)
mdt.visualization (module)
mdt.visualization.dict_conversion (module)
mdt.visualization.layouts (module)
mdt.visualization.maps (module)
mdt.visualization.maps.base (module)
mdt.visualization.maps.matplotlib_renderer (module)
mdt.visualization.maps.utils (module)
mdt.visualization.samples (module)
mdt.visualization.utils (module)
MDTGUISingleModel (class in mdt.gui.model_fit.qt_main)
median_otsu() (in module mdt.lib.masking)
merge_dict() (in module mdt.component_templates.base)
MessageReceiver (class in mdt.gui.utils)
meta_info() (mdt.component_templates.base.ComponentTemplate class method)
(mdt.component_templates.composite_models.CompositeModelTemplate class method)
min() (mdt.visualization.maps.base.SingleMapInfo method)
min_max() (mdt.visualization.maps.base.SingleMapInfo method)
MissingProtocolInput (class in mdt.models.base)
model_expression (mdt.component_templates.composite_models.CompositeModelTemplate attribute)
,
[1]
model_output_exists() (in module mdt.utils)
model_updated (mdt.gui.maps_visualizer.base.QtController attribute)
model_updated() (mdt.gui.maps_visualizer.config_tabs.tab_map_specific.TabMapSpecific method)
ModelCLFunction (class in mdt.model_building.model_functions)
ModelFit (class in mdt.cli_scripts.mdt_model_fit)
ModelFunctionsInformation (class in mdt.models.composite)
ModelOutputLogHandler (class in mdt.lib.log_handlers)
ModelUpdateAction (class in mdt.gui.maps_visualizer.actions)
modulus (mdt.component_templates.parameters.RotationalAngleParameterTemplate attribute)
N
name (mdt.component_templates.base.ComponentTemplate attribute)
,
[1]
(mdt.component_templates.batch_profiles.BatchProfileTemplate attribute)
,
[1]
(mdt.component_templates.compartment_models.CompartmentTemplate attribute)
,
[1]
(mdt.component_templates.compartment_models.WeightCompartmentTemplate attribute)
(mdt.component_templates.composite_models.CompositeModelTemplate attribute)
,
[1]
(mdt.component_templates.library_functions.LibraryFunctionTemplate attribute)
,
[1]
(mdt.component_templates.parameters.AzimuthAngleParameterTemplate attribute)
(mdt.component_templates.parameters.FreeParameterTemplate attribute)
(mdt.component_templates.parameters.ParameterTemplate attribute)
(mdt.component_templates.parameters.PolarAngleParameterTemplate attribute)
(mdt.component_templates.parameters.ProtocolParameterTemplate attribute)
(mdt.component_templates.parameters.RotationalAngleParameterTemplate attribute)
(mdt.component_templates.parameters.SphericalCoordinateParameterTemplate attribute)
(mdt.model_building.model_functions.ModelCLFunction attribute)
(mdt.model_building.model_functions.SimpleModelCLFunction attribute)
(mdt.models.base.EstimableModel attribute)
(mdt.models.compartments.DMRICompartmentModelFunction attribute)
(mdt.models.compartments.WeightCompartment attribute)
(mdt.models.composite.DMRICompositeModel attribute)
(mdt.visualization.maps.base.Font attribute)
NamedProtocolProblem (class in mdt.models.base)
natural_key_sort_cb() (in module mdt.utils)
NewConfigAction (class in mdt.gui.maps_visualizer.actions)
NewDataAction (class in mdt.gui.maps_visualizer.actions)
nifti_filepath_resolution() (in module mdt.lib.nifti)
nifti_info (mdt.lib.nifti.NiftiInfoDecorated attribute)
nifti_info_decorate_array() (in module mdt.lib.nifti)
nifti_info_decorate_nibabel_image() (in module mdt.lib.nifti)
NiftiInfo (class in mdt.lib.nifti)
NiftiInfoDecorated (class in mdt.lib.nifti)
no_zoom() (mdt.visualization.maps.base.Zoom class method)
noddi_bingham_extra_optimization_maps() (mdt.lib.post_processing.NODDIMeasures static method)
noddi_bingham_extra_sampling_maps() (mdt.lib.post_processing.NODDIMeasures static method)
noddi_dti_maps() (in module mdt.lib.post_processing)
noddi_watson_extra_optimization_maps() (mdt.lib.post_processing.NODDIMeasures static method)
noddi_watson_extra_sampling_maps() (mdt.lib.post_processing.NODDIMeasures static method)
NODDIMeasures (class in mdt.lib.post_processing)
noise_std_fname (mdt.component_templates.batch_profiles.BatchProfileTemplate attribute)
,
[1]
NoiseStdEstimation (class in mdt.cli_scripts.mdt_estimate_noise_std)
NoiseStdEstimationNotPossible
NonUniqueComponent
NoOptPlottingFrameInfoViewer (class in mdt.gui.maps_visualizer.renderers.base)
NormalPDF (class in mdt.model_building.parameter_functions.priors)
number_of_columns (mdt.protocols.Protocol attribute)
numdiff_info (mdt.component_templates.parameters.FreeParameterTemplate attribute)
,
[1]
(mdt.component_templates.parameters.RotationalAngleParameterTemplate attribute)
(mdt.component_templates.parameters.SphericalCoordinateParameterTemplate attribute)
NumDiffInfo (class in mdt.model_building.parameter_functions.numdiff_info)
O
OffsetGaussian (class in mdt.model_building.likelihood_functions)
optim_routines (mdt.gui.model_fit.tabs.fit_model_tab.OptimOptions attribute)
OptimizationOptionsDialog (class in mdt.gui.model_fit.tabs.fit_model_tab)
OptimizationSettingsLoader (class in mdt.configuration)
OptimOptions (class in mdt.gui.model_fit.tabs.fit_model_tab)
OptionalConversionDecorator (class in mdt.visualization.dict_conversion)
output_file (mdt.lib.log_handlers.ModelOutputLogHandler attribute)
OutputFormatLoader (class in mdt.configuration)
P
param_dict_to_array() (mdt.models.composite.DMRICompositeModel method)
parameter_transform (mdt.component_templates.parameters.FreeParameterTemplate attribute)
,
[1]
ParameterBuilder (class in mdt.component_templates.parameters)
ParameterCodec (class in mdt.model_building.utils)
ParameterDecodingWrapper (class in mdt.model_building.utils)
ParameterPrior (class in mdt.model_building.parameter_functions.priors)
parameters (mdt.component_templates.compartment_models.CompartmentTemplate attribute)
,
[1]
(mdt.component_templates.compartment_models.WeightCompartmentTemplate attribute)
(mdt.component_templates.library_functions.LibraryFunctionTemplate attribute)
,
[1]
ParameterTemplate (class in mdt.component_templates.parameters)
parent (mdt.model_building.trees.Tree attribute)
parse_composite_model_expression() (in module mdt.component_templates.composite_models)
PathJoiner (class in mdt.utils)
per_model_logging_context() (in module mdt.utils)
plot_frame_resized() (mdt.gui.maps_visualizer.main.ExportImageDialog static method)
PlottingFrame (class in mdt.gui.maps_visualizer.renderers.base)
PlottingFrameInfoToStatusBar (class in mdt.gui.maps_visualizer.main)
PlottingFrameInfoViewer (class in mdt.gui.maps_visualizer.renderers.base)
Point2d (class in mdt.visualization.maps.base)
PolarAngleParameterTemplate (class in mdt.component_templates.parameters)
PositivityTransform (class in mdt.model_building.parameter_functions.transformations)
pre_transform_code (mdt.model_building.parameter_functions.dependencies.AbstractParameterDependency attribute)
previous_values (mdt.gui.maps_visualizer.main.ExportImageDialog attribute)
print_info() (mdt.cli_scripts.mdt_info_img.InfoImg method)
(mdt.cli_scripts.mdt_info_protocol.InfoProtocol method)
print_welcome_message() (in module mdt.gui.utils)
prior (mdt.component_templates.compartment_models.CompartmentTemplate attribute)
,
[1]
(mdt.component_templates.composite_models.CompositeModelTemplate attribute)
,
[1]
ProcessingStrategySectionLoader (class in mdt.configuration)
Protocol (class in mdt.protocols)
protocol_auto_dir (mdt.component_templates.batch_profiles.BatchProfileTemplate attribute)
,
[1]
protocol_columns (mdt.component_templates.batch_profiles.BatchProfileTemplate attribute)
,
[1]
protocol_fname (mdt.component_templates.batch_profiles.BatchProfileTemplate attribute)
,
[1]
protocol_merge() (in module mdt.utils)
ProtocolAdaptionCallbacks (class in mdt.models.composite)
ProtocolIOError
ProtocolParameterTemplate (class in mdt.component_templates.parameters)
pyqtSlot() (in module mdt.gui.maps_visualizer.config_tabs.tab_general)
(in module mdt.gui.maps_visualizer.config_tabs.tab_map_specific)
(in module mdt.gui.maps_visualizer.config_tabs.tab_textual)
(in module mdt.gui.maps_visualizer.main)
(in module mdt.gui.maps_visualizer.renderers.matplotlib_renderer)
(in module mdt.gui.maps_visualizer.widgets)
(in module mdt.gui.model_fit.qt_main)
(in module mdt.gui.model_fit.tabs.fit_model_tab)
(in module mdt.gui.model_fit.tabs.generate_brain_mask_tab)
(in module mdt.gui.model_fit.tabs.generate_protocol_tab)
(in module mdt.gui.model_fit.tabs.generate_roi_mask_tab)
(in module mdt.gui.widgets.composite_widgets)
Q
qCleanupResources() (in module mdt.gui.maps_visualizer.design.main_rc)
(in module mdt.gui.model_fit.design.main_gui_rc)
qInitResources() (in module mdt.gui.maps_visualizer.design.main_rc)
(in module mdt.gui.model_fit.design.main_gui_rc)
QtController (class in mdt.gui.maps_visualizer.base)
QtManager (class in mdt.gui.utils)
R
ReciprocalPrior (class in mdt.model_building.parameter_functions.priors)
Rectangular (class in mdt.visualization.layouts)
redo() (mdt.gui.maps_visualizer.base.Controller method)
(mdt.gui.maps_visualizer.base.QtController method)
redraw() (mdt.gui.maps_visualizer.renderers.base.PlottingFrame method)
(mdt.gui.maps_visualizer.renderers.matplotlib_renderer.MatplotlibPlotting method)
reload() (in module mdt.lib.components)
reload_components() (in module mdt)
remove_last_entry() (in module mdt.lib.components)
remove_listener() (mdt.lib.log_handlers.LogDispatchHandler static method)
render() (mdt.visualization.maps.matplotlib_renderer.MapsVisualizer method)
(mdt.visualization.maps.matplotlib_renderer.Renderer method)
Renderer (class in mdt.visualization.maps.matplotlib_renderer)
reset() (mdt.gui.maps_visualizer.config_tabs.tab_map_specific.MapSpecificOptions method)
(mdt.utils.PathJoiner method)
reset_logging() (in module mdt)
resizeEvent() (mdt.gui.maps_visualizer.main.MapsVisualizerWindow method)
restore_volumes() (in module mdt.utils)
results_preselection_names() (in module mdt.gui.model_fit.utils)
retranslateUi() (mdt.gui.maps_visualizer.design.ui_MainWindow.Ui_MapsVisualizer method)
(mdt.gui.maps_visualizer.design.ui_MapSpecificOptions.Ui_MapSpecificOptions method)
(mdt.gui.maps_visualizer.design.ui_TabGeneral.Ui_TabGeneral method)
(mdt.gui.maps_visualizer.design.ui_TabMapSpecific.Ui_TabMapSpecific method)
(mdt.gui.maps_visualizer.design.ui_TabTextual.Ui_TabTextual method)
(mdt.gui.maps_visualizer.design.ui_save_image_dialog.Ui_SaveImageDialog method)
(mdt.gui.model_fit.design.ui_about_dialog.Ui_AboutDialog method)
(mdt.gui.model_fit.design.ui_dialog_get_example_data.Ui_GetExampleDataDialog method)
(mdt.gui.model_fit.design.ui_fit_model_tab.Ui_FitModelTabContent method)
(mdt.gui.model_fit.design.ui_generate_brain_mask_tab.Ui_GenerateBrainMaskTabContent method)
(mdt.gui.model_fit.design.ui_generate_protocol_load_gb_dialog.Ui_LoadGBDialog method)
(mdt.gui.model_fit.design.ui_generate_protocol_tab.Ui_GenerateProtocolTabContent method)
(mdt.gui.model_fit.design.ui_generate_protocol_update_dialog.Ui_UpdateColumnDialog method)
(mdt.gui.model_fit.design.ui_generate_roi_mask_tab.Ui_GenerateROIMaskTabContent method)
(mdt.gui.model_fit.design.ui_main_gui.Ui_MainWindow method)
(mdt.gui.model_fit.design.ui_optimization_extra_data_add_protocol_map_dialog.Ui_AddProtocolMapDialog method)
(mdt.gui.model_fit.design.ui_optimization_extra_data_dialog.Ui_OptimizationExtraDataDialog method)
(mdt.gui.model_fit.design.ui_optimization_options_dialog.Ui_OptimizationOptionsDialog method)
(mdt.gui.model_fit.design.ui_runtime_settings_dialog.Ui_RuntimeSettingsDialog method)
(mdt.gui.widgets.design.ui_scientific_number_scroller_widget.Ui_ScientificScroller method)
return_type (mdt.component_templates.compartment_models.CompartmentTemplate attribute)
,
[1]
(mdt.component_templates.compartment_models.WeightCompartmentTemplate attribute)
(mdt.component_templates.library_functions.LibraryFunctionTemplate attribute)
,
[1]
Rician (class in mdt.model_building.likelihood_functions)
roi_index_to_volume_index() (in module mdt.utils)
rotate90() (mdt.visualization.maps.base.Point2d method)
rotate_orthogonal_vector() (in module mdt.utils)
rotate_vector() (in module mdt.utils)
RotationalAngleParameterTemplate (class in mdt.component_templates.parameters)
run() (mdt.cli_scripts.mdt_apply_mask.ApplyMask method)
(mdt.cli_scripts.mdt_batch_fit.BatchFit method)
(mdt.cli_scripts.mdt_create_bvec_bval.CreateBvecBval method)
(mdt.cli_scripts.mdt_create_mask.CreateMask method)
(mdt.cli_scripts.mdt_create_protocol.CreateProtocol method)
(mdt.cli_scripts.mdt_create_roi_slice.CreateRoiSlice method)
(mdt.cli_scripts.mdt_estimate_noise_std.NoiseStdEstimation method)
(mdt.cli_scripts.mdt_get_example_data.GetExampleData method)
(mdt.cli_scripts.mdt_gui.GUI method)
(mdt.cli_scripts.mdt_info_img.InfoImg method)
(mdt.cli_scripts.mdt_info_protocol.InfoProtocol method)
(mdt.cli_scripts.mdt_init_user_settings.InitUserSettings method)
(mdt.cli_scripts.mdt_list_devices.ListDevices method)
(mdt.cli_scripts.mdt_list_models.ListModels method)
(mdt.cli_scripts.mdt_math_img.MathImg method)
(mdt.cli_scripts.mdt_math_protocol.MathProtocol method)
(mdt.cli_scripts.mdt_model_fit.ModelFit method)
(mdt.cli_scripts.mdt_view_maps.GUI method)
(mdt.cli_scripts.mdt_volume_merge.VolumeMerge method)
(mdt.gui.model_fit.tabs.fit_model_tab.RunModelWorker method)
(mdt.gui.model_fit.tabs.generate_brain_mask_tab.GenerateMaskWorker method)
(mdt.gui.model_fit.tabs.generate_roi_mask_tab.GenerateROIMaskWorker method)
(mdt.gui.utils.MessageReceiver method)
(mdt.lib.shell_utils.BasicShellApplication method)
run_function_on_batch_fit_output() (in module mdt.lib.batch_utils)
RunModelWorker (class in mdt.gui.model_fit.tabs.fit_model_tab)
RuntimeSettingsDialog (class in mdt.gui.model_fit.qt_main)
RuntimeSettingsLoader (class in mdt.configuration)
S
sample_model() (in module mdt)
sampled_parameter_names (mdt.models.composite.SamplingPostProcessingData attribute)
samples (mdt.models.composite.SamplingPostProcessingData attribute)
samples_npy_to_nifti() (in module mdt.lib.file_conversions.npy)
SampleSettingsLoader (class in mdt.configuration)
SampleVisualizer (class in mdt.visualization.samples)
sampling_prior (mdt.component_templates.parameters.FreeParameterTemplate attribute)
,
[1]
sampling_proposal_std (mdt.component_templates.parameters.FreeParameterTemplate attribute)
,
[1]
(mdt.component_templates.parameters.RotationalAngleParameterTemplate attribute)
(mdt.component_templates.parameters.SphericalCoordinateParameterTemplate attribute)
SamplingPostProcessingData (class in mdt.models.composite)
Scale (class in mdt.visualization.maps.base)
ScaleClampTransform (class in mdt.model_building.parameter_functions.transformations)
ScaleTransform (class in mdt.model_building.parameter_functions.transformations)
scaling_factor (mdt.model_building.parameter_functions.numdiff_info.NumDiffInfo attribute)
(mdt.model_building.parameter_functions.numdiff_info.SimpleNumDiffInfo attribute)
ScientificNumberScroller (class in mdt.gui.widgets.composite_widgets)
select_maps_context_menu() (mdt.gui.maps_visualizer.config_tabs.tab_general.TabGeneral method)
SelectedSubjects (class in mdt.lib.batch_utils)
selection_updated() (mdt.gui.model_fit.qt_main.RuntimeSettingsDialog method)
send_sigint() (mdt.gui.maps_visualizer.main.MapsVisualizerWindow method)
(mdt.gui.model_fit.qt_main.MDTGUISingleModel method)
set_args() (mdt.gui.model_fit.tabs.fit_model_tab.RunModelWorker method)
(mdt.gui.model_fit.tabs.generate_brain_mask_tab.GenerateMaskWorker method)
(mdt.gui.model_fit.tabs.generate_roi_mask_tab.GenerateROIMaskWorker method)
set_auto_rendering() (mdt.gui.maps_visualizer.renderers.base.PlottingFrame method)
(mdt.gui.maps_visualizer.renderers.matplotlib_renderer.MatplotlibPlotting method)
set_config_option() (in module mdt.configuration)
set_data() (mdt.gui.maps_visualizer.base.Controller method)
(mdt.gui.maps_visualizer.base.QtController method)
set_initial_parameters() (mdt.models.composite.DMRICompositeModel method)
set_input_data() (mdt.models.base.EstimableModel method)
(mdt.models.composite.DMRICompositeModel method)
set_lower_bound() (mdt.models.composite.DMRICompositeModel method)
set_lower_bounds() (mdt.models.composite.DMRICompositeModel method)
set_new_model() (mdt.gui.maps_visualizer.config_tabs.tab_textual.TabTextual method)
set_parameter_value() (mdt.models.composite.ModelFunctionsInformation method)
set_update_delay() (mdt.gui.widgets.composite_widgets.ScientificNumberScroller method)
set_upper_bound() (mdt.models.composite.DMRICompositeModel method)
set_upper_bounds() (mdt.models.composite.DMRICompositeModel method)
set_voxel() (mdt.visualization.samples.SampleVisualizer method)
set_voxel_info() (mdt.gui.maps_visualizer.main.PlottingFrameInfoToStatusBar method)
(mdt.gui.maps_visualizer.renderers.base.NoOptPlottingFrameInfoViewer method)
(mdt.gui.maps_visualizer.renderers.base.PlottingFrameInfoViewer method)
set_window_title() (mdt.gui.maps_visualizer.main.MapsVisualizerWindow method)
SetAnnotations (class in mdt.gui.maps_visualizer.actions)
SetColorbarLocation (class in mdt.gui.maps_visualizer.actions)
SetColorBarNmrTicks (class in mdt.gui.maps_visualizer.actions)
SetColormap (class in mdt.gui.maps_visualizer.actions)
SetDimension (class in mdt.gui.maps_visualizer.actions)
SetFlipud (class in mdt.gui.maps_visualizer.actions)
SetFont (class in mdt.gui.maps_visualizer.actions)
SetGeneralMask (class in mdt.gui.maps_visualizer.actions)
SetGeneralOptimizer (class in mdt.configuration)
SetGeneralSampler (class in mdt.configuration)
SetInterpolation (class in mdt.gui.maps_visualizer.actions)
SetMapClipping (class in mdt.gui.maps_visualizer.actions)
SetMapColorbarLabel (class in mdt.gui.maps_visualizer.actions)
SetMapColormap (class in mdt.gui.maps_visualizer.actions)
SetMapScale (class in mdt.gui.maps_visualizer.actions)
SetMapsToShow (class in mdt.gui.maps_visualizer.actions)
SetMapTitle (class in mdt.gui.maps_visualizer.actions)
SetPlotTitle (class in mdt.gui.maps_visualizer.actions)
SetRotate (class in mdt.gui.maps_visualizer.actions)
SetShowAxis (class in mdt.gui.maps_visualizer.actions)
SetShowPlotColorbars (class in mdt.gui.maps_visualizer.actions)
SetShowPlotTitles (class in mdt.gui.maps_visualizer.actions)
SetSliceIndex (class in mdt.gui.maps_visualizer.actions)
setup_logging() (in module mdt.utils)
setupUi() (mdt.gui.maps_visualizer.design.ui_MainWindow.Ui_MapsVisualizer method)
(mdt.gui.maps_visualizer.design.ui_MapSpecificOptions.Ui_MapSpecificOptions method)
(mdt.gui.maps_visualizer.design.ui_TabGeneral.Ui_TabGeneral method)
(mdt.gui.maps_visualizer.design.ui_TabMapSpecific.Ui_TabMapSpecific method)
(mdt.gui.maps_visualizer.design.ui_TabTextual.Ui_TabTextual method)
(mdt.gui.maps_visualizer.design.ui_save_image_dialog.Ui_SaveImageDialog method)
(mdt.gui.model_fit.design.ui_about_dialog.Ui_AboutDialog method)
(mdt.gui.model_fit.design.ui_dialog_get_example_data.Ui_GetExampleDataDialog method)
(mdt.gui.model_fit.design.ui_fit_model_tab.Ui_FitModelTabContent method)
(mdt.gui.model_fit.design.ui_generate_brain_mask_tab.Ui_GenerateBrainMaskTabContent method)
(mdt.gui.model_fit.design.ui_generate_protocol_load_gb_dialog.Ui_LoadGBDialog method)
(mdt.gui.model_fit.design.ui_generate_protocol_tab.Ui_GenerateProtocolTabContent method)
(mdt.gui.model_fit.design.ui_generate_protocol_update_dialog.Ui_UpdateColumnDialog method)
(mdt.gui.model_fit.design.ui_generate_roi_mask_tab.Ui_GenerateROIMaskTabContent method)
(mdt.gui.model_fit.design.ui_main_gui.Ui_MainWindow method)
(mdt.gui.model_fit.design.ui_optimization_extra_data_add_protocol_map_dialog.Ui_AddProtocolMapDialog method)
(mdt.gui.model_fit.design.ui_optimization_extra_data_dialog.Ui_OptimizationExtraDataDialog method)
(mdt.gui.model_fit.design.ui_optimization_options_dialog.Ui_OptimizationOptionsDialog method)
(mdt.gui.model_fit.design.ui_runtime_settings_dialog.Ui_RuntimeSettingsDialog method)
(mdt.gui.model_fit.tabs.fit_model_tab.FitModelTab method)
(mdt.gui.model_fit.tabs.generate_brain_mask_tab.GenerateBrainMaskTab method)
(mdt.gui.model_fit.tabs.generate_protocol_tab.GenerateProtocolTab method)
(mdt.gui.model_fit.tabs.generate_roi_mask_tab.GenerateROIMaskTab method)
(mdt.gui.widgets.design.ui_scientific_number_scroller_widget.Ui_ScientificScroller method)
setValue() (mdt.gui.widgets.composite_widgets.ScientificNumberScroller method)
SetVolumeIndex (class in mdt.gui.maps_visualizer.actions)
SetZoom (class in mdt.gui.maps_visualizer.actions)
shape (mdt.visualization.maps.base.SingleMapInfo attribute)
SharedState (class in mdt.gui.model_fit.utils)
show() (mdt.visualization.maps.matplotlib_renderer.MapsVisualizer method)
(mdt.visualization.samples.SampleVisualizer method)
show_header_context_menu() (mdt.gui.model_fit.tabs.generate_protocol_tab.GenerateProtocolTab method)
signal_noise_model (mdt.component_templates.composite_models.CompositeModelTemplate attribute)
,
[1]
SignalNoiseModel (class in mdt.model_building.signal_noise_models)
SimpleAssignment (class in mdt.model_building.parameter_functions.dependencies)
SimpleBatchProfile (class in mdt.lib.batch_utils)
SimpleClassConversion (class in mdt.visualization.dict_conversion)
SimpleConfigAction (class in mdt.configuration)
(class in mdt.gui.maps_visualizer.actions)
SimpleConvertibleConfig (class in mdt.visualization.maps.base)
SimpleDataConfigModel (class in mdt.gui.maps_visualizer.base)
SimpleDataInfo (class in mdt.visualization.maps.base)
SimpleDictConversion (class in mdt.visualization.dict_conversion)
SimpleFunctionConversion (class in mdt.visualization.dict_conversion)
SimpleInitializationData (class in mdt.utils)
SimpleListConversion (class in mdt.visualization.dict_conversion)
SimpleMapSpecificConfigAction (class in mdt.gui.maps_visualizer.actions)
SimpleModelCLFunction (class in mdt.model_building.model_functions)
SimpleNumDiffInfo (class in mdt.model_building.parameter_functions.numdiff_info)
SimpleParameterPrior (class in mdt.model_building.parameter_functions.priors)
SimpleSubjectInfo (class in mdt.lib.batch_utils)
SimpleVirtualColumn (class in mdt.protocols)
SimpleWeight (class in mdt.model_building.model_functions)
simulate_signals() (in module mdt.simulations)
SingleColumn (class in mdt.visualization.layouts)
SingleMapConfig (class in mdt.visualization.maps.base)
SingleMapInfo (class in mdt.visualization.maps.base)
SingleRow (class in mdt.visualization.layouts)
SinSqrClampTransform (class in mdt.model_building.parameter_functions.transformations)
slice_has_data() (mdt.visualization.maps.base.DataInfo method)
(mdt.visualization.maps.base.SimpleDataInfo method)
(mdt.visualization.maps.base.SingleMapInfo method)
slice_index (mdt.gui.model_fit.utils.SharedState attribute)
sort_maps() (in module mdt)
sort_orientations() (in module mdt.lib.sorting)
sort_volumes_per_voxel() (in module mdt.lib.sorting)
spherical_to_cartesian() (in module mdt.utils)
SphericalCoordinateParameterTemplate (class in mdt.component_templates.parameters)
split_array_to_dict() (in module mdt.utils)
split_dataset() (in module mdt.utils)
split_image_path() (in module mdt.utils)
split_long_path_elements() (in module mdt.gui.utils)
SqrClampTransform (class in mdt.model_building.parameter_functions.transformations)
start() (mdt.lib.shell_utils.BasicShellApplication method)
start_gui() (in module mdt)
(in module mdt.gui.maps_visualizer.main)
(in module mdt.gui.model_fit.qt_main)
starting (mdt.gui.model_fit.tabs.fit_model_tab.RunModelWorker attribute)
(mdt.gui.model_fit.tabs.generate_brain_mask_tab.GenerateMaskWorker attribute)
(mdt.gui.model_fit.tabs.generate_roi_mask_tab.GenerateROIMaskWorker attribute)
state_updated_signal (mdt.gui.model_fit.utils.SharedState attribute)
StdOutHandler (class in mdt.lib.log_handlers)
StringConversion (class in mdt.visualization.dict_conversion)
subcomponents (mdt.component_templates.base.ComponentTemplate attribute)
(mdt.component_templates.batch_profiles.BatchProfileTemplate attribute)
(mdt.component_templates.compartment_models.CompartmentTemplate attribute)
(mdt.component_templates.compartment_models.WeightCompartmentTemplate attribute)
(mdt.component_templates.composite_models.CompositeModelTemplate attribute)
(mdt.component_templates.library_functions.LibraryFunctionTemplate attribute)
(mdt.component_templates.parameters.AzimuthAngleParameterTemplate attribute)
(mdt.component_templates.parameters.FreeParameterTemplate attribute)
(mdt.component_templates.parameters.ParameterTemplate attribute)
(mdt.component_templates.parameters.PolarAngleParameterTemplate attribute)
(mdt.component_templates.parameters.ProtocolParameterTemplate attribute)
(mdt.component_templates.parameters.RotationalAngleParameterTemplate attribute)
(mdt.component_templates.parameters.SphericalCoordinateParameterTemplate attribute)
subject_base_folder (mdt.component_templates.batch_profiles.BatchProfileTemplate attribute)
,
[1]
(mdt.lib.batch_utils.SimpleSubjectInfo attribute)
(mdt.lib.batch_utils.SubjectInfo attribute)
subject_id (mdt.lib.batch_utils.SimpleSubjectInfo attribute)
(mdt.lib.batch_utils.SubjectInfo attribute)
SubjectInfo (class in mdt.lib.batch_utils)
T
tab_opened() (mdt.gui.utils.MainTab method)
TabGeneral (class in mdt.gui.maps_visualizer.config_tabs.tab_general)
TabMapSpecific (class in mdt.gui.maps_visualizer.config_tabs.tab_map_specific)
TabTextual (class in mdt.gui.maps_visualizer.config_tabs.tab_textual)
tag (mdt.model_building.trees.Tree attribute)
TemplateModifier (class in mdt.component_templates.utils)
temporary_component_updates() (in module mdt.lib.components)
tensor_cartesian_to_spherical() (in module mdt.utils)
tensor_spherical_to_cartesian() (in module mdt.utils)
text_message_signal (mdt.gui.utils.MessageReceiver attribute)
TmpResultsDirSectionLoader (class in mdt.configuration)
to_dict() (mdt.visualization.dict_conversion.ConversionSpecification method)
(mdt.visualization.dict_conversion.ConvertDictElements method)
(mdt.visualization.dict_conversion.ConvertDynamicFromModule method)
(mdt.visualization.dict_conversion.ConvertListElements method)
(mdt.visualization.dict_conversion.OptionalConversionDecorator method)
(mdt.visualization.dict_conversion.SimpleClassConversion method)
(mdt.visualization.dict_conversion.SimpleFunctionConversion method)
(mdt.visualization.dict_conversion.WhiteListConversion method)
(mdt.visualization.maps.base.MapPlotConfig method)
(mdt.visualization.maps.base.SingleMapConfig method)
to_file() (mdt.visualization.maps.matplotlib_renderer.MapsVisualizer method)
to_normal_dict() (mdt.utils.AutoDict method)
to_yaml() (mdt.visualization.maps.base.MapPlotConfig method)
(mdt.visualization.maps.base.SingleMapConfig method)
Tree (class in mdt.model_building.trees)
U
Ui_AboutDialog (class in mdt.gui.model_fit.design.ui_about_dialog)
Ui_AddProtocolMapDialog (class in mdt.gui.model_fit.design.ui_optimization_extra_data_add_protocol_map_dialog)
Ui_FitModelTabContent (class in mdt.gui.model_fit.design.ui_fit_model_tab)
Ui_GenerateBrainMaskTabContent (class in mdt.gui.model_fit.design.ui_generate_brain_mask_tab)
Ui_GenerateProtocolTabContent (class in mdt.gui.model_fit.design.ui_generate_protocol_tab)
Ui_GenerateROIMaskTabContent (class in mdt.gui.model_fit.design.ui_generate_roi_mask_tab)
Ui_GetExampleDataDialog (class in mdt.gui.model_fit.design.ui_dialog_get_example_data)
Ui_LoadGBDialog (class in mdt.gui.model_fit.design.ui_generate_protocol_load_gb_dialog)
Ui_MainWindow (class in mdt.gui.model_fit.design.ui_main_gui)
Ui_MapSpecificOptions (class in mdt.gui.maps_visualizer.design.ui_MapSpecificOptions)
Ui_MapsVisualizer (class in mdt.gui.maps_visualizer.design.ui_MainWindow)
Ui_OptimizationExtraDataDialog (class in mdt.gui.model_fit.design.ui_optimization_extra_data_dialog)
Ui_OptimizationOptionsDialog (class in mdt.gui.model_fit.design.ui_optimization_options_dialog)
Ui_RuntimeSettingsDialog (class in mdt.gui.model_fit.design.ui_runtime_settings_dialog)
Ui_SaveImageDialog (class in mdt.gui.maps_visualizer.design.ui_save_image_dialog)
Ui_ScientificScroller (class in mdt.gui.widgets.design.ui_scientific_number_scroller_widget)
Ui_TabGeneral (class in mdt.gui.maps_visualizer.design.ui_TabGeneral)
Ui_TabMapSpecific (class in mdt.gui.maps_visualizer.design.ui_TabMapSpecific)
Ui_TabTextual (class in mdt.gui.maps_visualizer.design.ui_TabTextual)
Ui_UpdateColumnDialog (class in mdt.gui.model_fit.design.ui_generate_protocol_update_dialog)
unapply() (mdt.configuration.ConfigAction method)
(mdt.configuration.SimpleConfigAction method)
(mdt.configuration.VoidConfigAction method)
(mdt.gui.maps_visualizer.actions.ConfigAction method)
(mdt.gui.maps_visualizer.actions.ModelUpdateAction method)
(mdt.gui.maps_visualizer.actions.NewConfigAction method)
(mdt.gui.maps_visualizer.actions.NewDataAction method)
undo() (mdt.gui.maps_visualizer.base.Controller method)
(mdt.gui.maps_visualizer.base.QtController method)
undo_sort_volumes_per_voxel() (in module mdt.lib.sorting)
unfix() (mdt.models.composite.DMRICompositeModel method)
(mdt.models.composite.ModelFunctionsInformation method)
UniformWithinBoundsPrior (class in mdt.model_building.parameter_functions.priors)
unzip_nifti() (in module mdt.lib.nifti)
(in module mdt.utils)
update() (mdt.component_templates.utils.TemplateModifier method)
(mdt.configuration.ConfigSectionLoader method)
(mdt.configuration.RuntimeSettingsLoader method)
update_active_post_processing() (mdt.models.base.EstimableModel method)
(mdt.models.composite.DMRICompositeModel method)
update_dimension() (mdt.gui.model_fit.tabs.generate_roi_mask_tab.GenerateROIMaskTab method)
update_gui_config() (in module mdt.configuration)
update_log() (mdt.gui.model_fit.qt_main.MDTGUISingleModel method)
update_model() (mdt.gui.maps_visualizer.config_tabs.tab_general.TabGeneral method)
(mdt.gui.maps_visualizer.main.MapsVisualizerWindow method)
(mdt.gui.maps_visualizer.renderers.matplotlib_renderer.MatplotlibPlotting method)
update_output_file_text() (mdt.gui.model_fit.tabs.generate_roi_mask_tab.GenerateROIMaskTab method)
update_output_folder_text() (mdt.gui.model_fit.tabs.fit_model_tab.FitModelTab method)
update_protocol() (mdt.gui.model_fit.tabs.generate_protocol_tab.LoadColumnDialog method)
update_slice_index() (mdt.gui.model_fit.tabs.generate_roi_mask_tab.GenerateROIMaskTab method)
update_slice_selector() (mdt.gui.model_fit.tabs.generate_roi_mask_tab.GenerateROIMaskTab method)
update_write_config() (in module mdt.configuration)
UpdateDescriptor (class in mdt.gui.utils)
upper_bound (mdt.component_templates.parameters.FreeParameterTemplate attribute)
,
[1]
upper_bounds (mdt.component_templates.composite_models.CompositeModelTemplate attribute)
,
[1]
use() (mdt.gui.maps_visualizer.config_tabs.tab_map_specific.MapSpecificOptions method)
use_bounds (mdt.model_building.parameter_functions.numdiff_info.NumDiffInfo attribute)
(mdt.model_building.parameter_functions.numdiff_info.SimpleNumDiffInfo attribute)
use_lower_bound (mdt.model_building.parameter_functions.numdiff_info.SimpleNumDiffInfo attribute)
use_upper_bound (mdt.model_building.parameter_functions.numdiff_info.SimpleNumDiffInfo attribute)
V
VagueGammaPrior (class in mdt.model_building.parameter_functions.priors)
valid_text_locations (mdt.visualization.maps.base.VoxelAnnotation attribute)
validate() (mdt.visualization.maps.base.MapPlotConfig method)
(mdt.visualization.maps.base.SingleMapConfig method)
(mdt.visualization.maps.base.VoxelAnnotation method)
value (mdt.component_templates.parameters.ProtocolParameterTemplate attribute)
valueChanged (mdt.gui.widgets.composite_widgets.ScientificNumberScroller attribute)
view_maps() (in module mdt)
view_mask() (mdt.gui.model_fit.tabs.generate_brain_mask_tab.GenerateBrainMaskTab method)
(mdt.gui.model_fit.tabs.generate_roi_mask_tab.GenerateROIMaskTab method)
view_result_samples() (in module mdt)
VirtualColumn (class in mdt.protocols)
VirtualColumn_g_spherical (class in mdt.protocols)
VirtualColumnB (class in mdt.protocols)
visible_changes() (mdt.visualization.maps.base.Clipping method)
(mdt.visualization.maps.base.MapPlotConfig method)
(mdt.visualization.maps.base.Scale method)
(mdt.visualization.maps.base.SingleMapConfig method)
VoidConfigAction (class in mdt.configuration)
volume_index_to_roi_index() (in module mdt.utils)
volume_map_npy_to_nifti() (in module mdt.lib.file_conversions.npy)
volume_merge() (in module mdt.utils)
volume_selection (mdt.component_templates.composite_models.CompositeModelTemplate attribute)
,
[1]
VolumeMerge (class in mdt.cli_scripts.mdt_volume_merge)
VoxelAnnotation (class in mdt.visualization.maps.base)
voxelwise_vector_matrix_vector_product() (in module mdt.utils)
W
WeightBuilder (class in mdt.component_templates.compartment_models)
WeightCompartment (class in mdt.models.compartments)
WeightCompartmentTemplate (class in mdt.component_templates.compartment_models)
WeightType (class in mdt.model_building.model_functions)
WhiteListConversion (class in mdt.visualization.dict_conversion)
windows (mdt.gui.utils.QtManager attribute)
with_added_column_from_file() (mdt.protocols.Protocol method)
with_column_removed() (mdt.protocols.Protocol method)
with_columns_removed() (mdt.protocols.Protocol method)
with_logging_to_debug() (in module mdt)
with_new_column() (mdt.protocols.Protocol method)
with_rows_removed() (mdt.protocols.Protocol method)
with_update() (mdt.protocols.Protocol method)
with_updates() (mdt.protocols.Protocol method)
wrap_constraints_function() (mdt.model_building.utils.ParameterDecodingWrapper method)
wrap_input_data() (mdt.model_building.utils.ParameterDecodingWrapper method)
wrap_objective_function() (mdt.model_building.utils.ParameterDecodingWrapper method)
write() (mdt.gui.utils.ForwardingListener method)
write_all_as_nifti() (in module mdt.lib.nifti)
write_bvec_bval() (in module mdt.protocols)
write_config() (mdt.gui.model_fit.tabs.fit_model_tab.AddProtocolMapDialog method)
(mdt.gui.model_fit.tabs.fit_model_tab.ExtraDataDialog method)
(mdt.gui.model_fit.tabs.fit_model_tab.OptimizationOptionsDialog method)
write_nifti() (in module mdt.lib.nifti)
write_protocol() (in module mdt.protocols)
write_slice_roi() (in module mdt.utils)
write_to_file() (mdt.component_templates.utils.TemplateModifier method)
write_volume_maps() (in module mdt)
Y
YamlStringAction (class in mdt.configuration)
yield_nifti_info() (in module mdt.lib.nifti)
Z
zip_nifti() (in module mdt.utils)
Zoom (class in mdt.visualization.maps.base)
MDT
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