pyglotaran
v0.7.2
Contents:
Introduction
Installation
Quickstart/Cheat-Sheet
Import the data into your project
Changelog
Authors
User Documentation:
Overview
Data IO
Plotting
Modelling
Parameter
Optimizing
Plugins
Command-line Interface
Developer Documentation:
Contributing
API Documentation
Plugin development
pyglotaran
Index
Edit on GitHub
Index
Symbols
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A
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B
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C
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D
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E
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F
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G
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H
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I
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J
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K
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L
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M
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N
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O
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P
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R
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S
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T
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U
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V
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W
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X
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Y
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Z
Symbols
--data
glotaran-optimize command line option
--dataformat
glotaran-optimize command line option
--model_file
glotaran-optimize command line option
glotaran-print command line option
glotaran-validate command line option
--nfev
glotaran-optimize command line option
--nnls
glotaran-optimize command line option
--out
glotaran-optimize command line option
--outformat
glotaran-optimize command line option
--parameters_file
glotaran-optimize command line option
glotaran-print command line option
glotaran-validate command line option
--version
glotaran command line option
--yes
glotaran-optimize command line option
-d
glotaran-optimize command line option
-dfmt
glotaran-optimize command line option
-m
glotaran-optimize command line option
glotaran-print command line option
glotaran-validate command line option
-n
glotaran-optimize command line option
-o
glotaran-optimize command line option
-ofmt
glotaran-optimize command line option
-p
glotaran-optimize command line option
glotaran-print command line option
glotaran-validate command line option
-y
glotaran-optimize command line option
A
a_matrix() (glotaran.builtin.megacomplexes.decay.k_matrix.KMatrix method)
a_matrix_as_markdown() (glotaran.builtin.megacomplexes.decay.k_matrix.KMatrix method)
a_matrix_general() (glotaran.builtin.megacomplexes.decay.k_matrix.KMatrix method)
a_matrix_sequential() (glotaran.builtin.megacomplexes.decay.k_matrix.KMatrix method)
action (glotaran.io.preprocessor.preprocessor.CorrectBaselineAverage attribute)
(glotaran.io.preprocessor.preprocessor.CorrectBaselineValue attribute)
actions (glotaran.io.preprocessor.pipeline.PreProcessingPipeline attribute)
add_data_row() (glotaran.builtin.io.ascii.wavelength_time_explicit_file.TimeExplicitFile method)
(glotaran.builtin.io.ascii.wavelength_time_explicit_file.WavelengthExplicitFile method)
add_instantiated_plugin_to_registry() (in module glotaran.plugin_system.base_registry)
add_model_weight() (glotaran.optimization.data_provider.DataProvider method)
(glotaran.optimization.data_provider.DataProviderLinked method)
add_plugin_to_registry() (in module glotaran.plugin_system.base_registry)
add_svd (glotaran.project.scheme.Scheme attribute)
add_svd_data() (glotaran.optimization.optimization_group.OptimizationGroup static method)
add_svd_to_dataset() (in module glotaran.io.prepare_dataset)
add_weight_to_result_data() (glotaran.optimization.optimization_group.OptimizationGroup method)
additional_penalty (glotaran.project.result.Result attribute)
align_data() (glotaran.optimization.data_provider.DataProviderLinked method)
align_dataset_indices() (glotaran.optimization.data_provider.DataProviderLinked method)
align_full_clp_labels() (glotaran.optimization.matrix_provider.MatrixProviderLinked method)
align_groups() (glotaran.optimization.data_provider.DataProviderLinked static method)
align_index() (glotaran.optimization.data_provider.DataProviderLinked static method)
align_matrices() (glotaran.optimization.matrix_provider.MatrixProviderLinked static method)
align_weights() (glotaran.optimization.data_provider.DataProviderLinked method)
aligned_full_clp_labels (glotaran.optimization.matrix_provider.MatrixProviderLinked property)
aligned_global_axis (glotaran.optimization.data_provider.DataProviderLinked property)
all() (glotaran.parameter.parameters.Parameters method)
amplitude (glotaran.builtin.megacomplexes.spectral.shape.SpectralShapeGaussian attribute)
(glotaran.builtin.megacomplexes.spectral.shape.SpectralShapeSkewedGaussian attribute)
append() (glotaran.parameter.parameter_history.ParameterHistory method)
applies() (glotaran.model.clp_constraint.ClpConstraint method)
(glotaran.model.clp_constraint.OnlyConstraint method)
(glotaran.model.clp_constraint.ZeroConstraint method)
(glotaran.model.clp_relation.ClpRelation method)
(glotaran.model.interval_item.IntervalItem method)
apply() (glotaran.io.preprocessor.pipeline.PreProcessingPipeline method)
(glotaran.io.preprocessor.preprocessor.CorrectBaselineAverage method)
(glotaran.io.preprocessor.preprocessor.CorrectBaselineValue method)
(glotaran.io.preprocessor.preprocessor.PreProcessor method)
apply_constraints() (glotaran.optimization.matrix_provider.MatrixProvider method)
(glotaran.optimization.matrix_provider.MatrixProviderLinked method)
(glotaran.optimization.matrix_provider.MatrixProviderUnlinked method)
apply_relations() (glotaran.optimization.matrix_provider.MatrixProvider method)
(glotaran.optimization.matrix_provider.MatrixProviderLinked method)
(glotaran.optimization.matrix_provider.MatrixProviderUnlinked method)
apply_weight() (glotaran.optimization.matrix_provider.MatrixContainer static method)
arbitrary_types_allowed (glotaran.io.preprocessor.preprocessor.CorrectBaselineAverage.Config attribute)
(glotaran.io.preprocessor.preprocessor.CorrectBaselineValue.Config attribute)
(glotaran.io.preprocessor.preprocessor.PreProcessor.Config attribute)
arity (glotaran.cli.commands.util.ValOrRangeOrList attribute)
as_dict() (glotaran.model.model.Model method)
(glotaran.parameter.parameter.Parameter method)
as_list() (glotaran.parameter.parameter.Parameter method)
AsciiDataIo (class in glotaran.builtin.io.ascii.wavelength_time_explicit_file)
asdict() (in module glotaran.project.dataclass_helpers)
B
backsweep (glotaran.builtin.megacomplexes.decay.irf.IrfGaussian attribute)
(glotaran.builtin.megacomplexes.decay.irf.IrfMultiGaussian attribute)
(glotaran.builtin.megacomplexes.decay.irf.IrfSpectralGaussian attribute)
(glotaran.builtin.megacomplexes.decay.irf.IrfSpectralMultiGaussian attribute)
backsweep_period (glotaran.builtin.megacomplexes.decay.irf.IrfGaussian attribute)
(glotaran.builtin.megacomplexes.decay.irf.IrfMultiGaussian attribute)
(glotaran.builtin.megacomplexes.decay.irf.IrfSpectralGaussian attribute)
(glotaran.builtin.megacomplexes.decay.irf.IrfSpectralMultiGaussian attribute)
BaselineMegacomplex (class in glotaran.builtin.megacomplexes.baseline.baseline_megacomplex)
bool_str_repr() (in module glotaran.plugin_system.io_plugin_utils)
bool_table_repr() (in module glotaran.plugin_system.io_plugin_utils)
C
calculate() (glotaran.builtin.megacomplexes.decay.irf.IrfGaussian method)
(glotaran.builtin.megacomplexes.decay.irf.IrfMultiGaussian method)
(glotaran.builtin.megacomplexes.decay.irf.IrfSpectralGaussian method)
(glotaran.builtin.megacomplexes.decay.irf.IrfSpectralMultiGaussian method)
(glotaran.builtin.megacomplexes.spectral.shape.SpectralShapeGaussian method)
(glotaran.builtin.megacomplexes.spectral.shape.SpectralShapeOne method)
(glotaran.builtin.megacomplexes.spectral.shape.SpectralShapeSkewedGaussian method)
(glotaran.builtin.megacomplexes.spectral.shape.SpectralShapeZero method)
(glotaran.optimization.matrix_provider.MatrixProvider method)
(glotaran.optimization.matrix_provider.MatrixProviderLinked method)
(glotaran.optimization.matrix_provider.MatrixProviderUnlinked method)
(glotaran.optimization.optimization_group.OptimizationGroup method)
calculate_aligned_matrices() (glotaran.optimization.matrix_provider.MatrixProviderLinked method)
calculate_clp_penalties() (glotaran.optimization.estimation_provider.EstimationProvider method)
(glotaran.optimization.estimation_provider.EstimationProviderLinked method)
(glotaran.optimization.estimation_provider.EstimationProviderUnlinked method)
calculate_covariance_matrix_and_standard_errors() (glotaran.optimization.optimizer.Optimizer method)
calculate_damped_oscillation_matrix_gaussian_irf() (in module glotaran.builtin.megacomplexes.damped_oscillation.damped_oscillation_megacomplex)
calculate_damped_oscillation_matrix_gaussian_irf_on_index() (in module glotaran.builtin.megacomplexes.damped_oscillation.damped_oscillation_megacomplex)
calculate_damped_oscillation_matrix_no_irf() (in module glotaran.builtin.megacomplexes.damped_oscillation.damped_oscillation_megacomplex)
calculate_dataset_matrices() (glotaran.optimization.matrix_provider.MatrixProvider method)
(glotaran.optimization.matrix_provider.MatrixProviderLinked method)
(glotaran.optimization.matrix_provider.MatrixProviderUnlinked method)
calculate_dataset_matrix() (glotaran.optimization.matrix_provider.MatrixProvider static method)
(glotaran.optimization.matrix_provider.MatrixProviderLinked static method)
(glotaran.optimization.matrix_provider.MatrixProviderUnlinked static method)
calculate_decay_matrix_gaussian_irf() (in module glotaran.builtin.megacomplexes.decay.decay_matrix_gaussian_irf)
calculate_decay_matrix_gaussian_irf_on_index() (in module glotaran.builtin.megacomplexes.decay.decay_matrix_gaussian_irf)
calculate_decay_matrix_no_irf() (in module glotaran.builtin.megacomplexes.decay.util)
calculate_dispersion() (glotaran.builtin.megacomplexes.decay.irf.IrfSpectralGaussian method)
(glotaran.builtin.megacomplexes.decay.irf.IrfSpectralMultiGaussian method)
calculate_estimation() (glotaran.optimization.estimation_provider.EstimationProviderUnlinked method)
calculate_full_matrices() (glotaran.optimization.matrix_provider.MatrixProviderUnlinked method)
calculate_full_model_estimation() (glotaran.optimization.estimation_provider.EstimationProviderUnlinked method)
calculate_gamma() (in module glotaran.builtin.megacomplexes.decay.k_matrix)
calculate_global_matrices() (glotaran.optimization.matrix_provider.MatrixProviderUnlinked method)
calculate_matrix() (glotaran.builtin.megacomplexes.baseline.baseline_megacomplex.BaselineMegacomplex method)
(glotaran.builtin.megacomplexes.clp_guide.clp_guide_megacomplex.ClpGuideMegacomplex method)
(glotaran.builtin.megacomplexes.coherent_artifact.coherent_artifact_megacomplex.CoherentArtifactMegacomplex method)
(glotaran.builtin.megacomplexes.damped_oscillation.damped_oscillation_megacomplex.DampedOscillationMegacomplex method)
(glotaran.builtin.megacomplexes.decay.decay_megacomplex.DecayMegacomplex method)
(glotaran.builtin.megacomplexes.decay.decay_parallel_megacomplex.DecayParallelMegacomplex method)
(glotaran.builtin.megacomplexes.decay.decay_sequential_megacomplex.DecaySequentialMegacomplex method)
(glotaran.builtin.megacomplexes.spectral.spectral_megacomplex.SpectralMegacomplex method)
(in module glotaran.builtin.megacomplexes.decay.util)
calculate_penalty() (glotaran.optimization.optimizer.Optimizer method)
calculate_prepared_matrices() (glotaran.optimization.matrix_provider.MatrixProviderUnlinked method)
calculate_residual() (glotaran.optimization.estimation_provider.EstimationProvider method)
(glotaran.optimization.estimation_provider.EstimationProviderLinked method)
(glotaran.optimization.estimation_provider.EstimationProviderUnlinked method)
capitalize() (glotaran.utils.ipython.MarkdownStr method)
casefold() (glotaran.utils.ipython.MarkdownStr method)
center (glotaran.builtin.megacomplexes.decay.irf.IrfGaussian attribute)
(glotaran.builtin.megacomplexes.decay.irf.IrfMultiGaussian attribute)
(glotaran.builtin.megacomplexes.decay.irf.IrfSpectralGaussian attribute)
(glotaran.builtin.megacomplexes.decay.irf.IrfSpectralMultiGaussian attribute)
center() (glotaran.utils.ipython.MarkdownStr method)
center_dispersion_coefficients (glotaran.builtin.megacomplexes.decay.irf.IrfSpectralGaussian attribute)
(glotaran.builtin.megacomplexes.decay.irf.IrfSpectralMultiGaussian attribute)
chdir_context() (in module glotaran.utils.io)
check_overdue() (in module glotaran.deprecation.deprecation_utils)
check_qualnames_in_tests() (in module glotaran.deprecation.deprecation_utils)
chi_square (glotaran.project.result.Result attribute)
clear() (glotaran.project.generators.generator.GeneratorArguments method)
(glotaran.utils.io.DatasetMapping method)
clp_constraints (glotaran.model.model.Model attribute)
clp_labels (glotaran.optimization.matrix_provider.MatrixContainer attribute)
clp_link_method (glotaran.project.scheme.Scheme attribute)
clp_link_tolerance (glotaran.project.scheme.Scheme attribute)
clp_penalties (glotaran.model.model.Model attribute)
clp_relations (glotaran.model.model.Model attribute)
ClpConstraint (class in glotaran.model.clp_constraint)
ClpGuideMegacomplex (class in glotaran.builtin.megacomplexes.clp_guide.clp_guide_megacomplex)
ClpPenalty (class in glotaran.model.clp_penalties)
ClpRelation (class in glotaran.model.clp_relation)
CoherentArtifactMegacomplex (class in glotaran.builtin.megacomplexes.coherent_artifact.coherent_artifact_megacomplex)
collect_megacomplexes() (in module glotaran.builtin.megacomplexes.decay.util)
combine() (glotaran.builtin.megacomplexes.decay.k_matrix.KMatrix method)
combine_megacomplex_matrices() (glotaran.optimization.matrix_provider.MatrixProvider static method)
(glotaran.optimization.matrix_provider.MatrixProviderLinked static method)
(glotaran.optimization.matrix_provider.MatrixProviderUnlinked static method)
compartments (glotaran.builtin.megacomplexes.decay.decay_parallel_megacomplex.DecayParallelMegacomplex attribute)
(glotaran.builtin.megacomplexes.decay.decay_sequential_megacomplex.DecaySequentialMegacomplex attribute)
(glotaran.builtin.megacomplexes.decay.initial_concentration.InitialConcentration attribute)
compartments() (glotaran.builtin.megacomplexes.coherent_artifact.coherent_artifact_megacomplex.CoherentArtifactMegacomplex method)
construct() (glotaran.io.preprocessor.pipeline.PreProcessingPipeline class method)
(glotaran.io.preprocessor.preprocessor.CorrectBaselineAverage class method)
(glotaran.io.preprocessor.preprocessor.CorrectBaselineValue class method)
(glotaran.io.preprocessor.preprocessor.PreProcessor class method)
convert() (glotaran.cli.commands.util.ValOrRangeOrList method)
convert_scientific_to_float() (in module glotaran.utils.sanitize)
copy() (glotaran.io.preprocessor.pipeline.PreProcessingPipeline method)
(glotaran.io.preprocessor.preprocessor.CorrectBaselineAverage method)
(glotaran.io.preprocessor.preprocessor.CorrectBaselineValue method)
(glotaran.io.preprocessor.preprocessor.PreProcessor method)
(glotaran.parameter.parameter.Parameter method)
(glotaran.parameter.parameters.Parameters method)
(glotaran.project.generators.generator.GeneratorArguments method)
correct_baseline_average() (glotaran.io.preprocessor.pipeline.PreProcessingPipeline method)
correct_baseline_value() (glotaran.io.preprocessor.pipeline.PreProcessingPipeline method)
CorrectBaselineAverage (class in glotaran.io.preprocessor.preprocessor)
CorrectBaselineAverage.Config (class in glotaran.io.preprocessor.preprocessor)
CorrectBaselineValue (class in glotaran.io.preprocessor.preprocessor)
CorrectBaselineValue.Config (class in glotaran.io.preprocessor.preprocessor)
cost (glotaran.project.result.Result attribute)
count() (glotaran.utils.ipython.MarkdownStr method)
covariance_matrix (glotaran.project.result.Result attribute)
create() (glotaran.project.project.Project static method)
create_aligned_global_axes() (glotaran.optimization.data_provider.DataProviderLinked method)
create_class() (glotaran.model.model.Model class method)
create_class_from_megacomplexes() (glotaran.model.model.Model class method)
create_clp_guide_dataset() (glotaran.project.result.Result method)
(in module glotaran.utils.io)
create_result() (glotaran.optimization.optimizer.Optimizer method)
create_result_data() (glotaran.optimization.optimization_group.OptimizationGroup method)
create_result_run_name() (glotaran.project.project_result_registry.ProjectResultRegistry method)
create_scaled_matrix() (glotaran.optimization.matrix_provider.MatrixContainer method)
create_scheme() (glotaran.project.project.Project method)
create_weighted_matrix() (glotaran.optimization.matrix_provider.MatrixContainer method)
CsvProjectIo (class in glotaran.builtin.io.pandas.csv)
D
DampedOscillationMegacomplex (class in glotaran.builtin.megacomplexes.damped_oscillation.damped_oscillation_megacomplex)
data (glotaran.optimization.optimization_history.OptimizationHistory property)
(glotaran.project.project.Project property)
(glotaran.project.result.Result attribute)
(glotaran.project.scheme.Scheme attribute)
data_filter (glotaran.io.interface.SavingOptions attribute)
data_format (glotaran.io.interface.SavingOptions attribute)
data_io_plugin_table() (in module glotaran.plugin_system.data_io_registration)
DataFileType (class in glotaran.builtin.io.ascii.wavelength_time_explicit_file)
DataIoInterface (class in glotaran.io.interface)
DataProvider (class in glotaran.optimization.data_provider)
DataProviderLinked (class in glotaran.optimization.data_provider)
dataset (glotaran.model.model.Model attribute)
dataset() (glotaran.builtin.io.ascii.wavelength_time_explicit_file.ExplicitFile method)
(glotaran.builtin.io.ascii.wavelength_time_explicit_file.TimeExplicitFile method)
(glotaran.builtin.io.ascii.wavelength_time_explicit_file.WavelengthExplicitFile method)
dataset_groups (glotaran.model.model.Model attribute)
dataset_models (glotaran.model.dataset_group.DatasetGroup attribute)
DatasetGroup (class in glotaran.model.dataset_group)
DatasetGroupModel (class in glotaran.model.dataset_group)
DatasetMapping (class in glotaran.utils.io)
DatasetModel (class in glotaran.model.dataset_model)
datasets (glotaran.model.weight.Weight attribute)
decay_matrix_implementation_index_dependent() (in module glotaran.builtin.megacomplexes.decay.util)
decay_matrix_implementation_index_independent() (in module glotaran.builtin.megacomplexes.decay.util)
DecayDatasetModel (class in glotaran.builtin.megacomplexes.decay.decay_megacomplex)
(class in glotaran.builtin.megacomplexes.decay.decay_parallel_megacomplex)
DecayMegacomplex (class in glotaran.builtin.megacomplexes.decay.decay_megacomplex)
DecayParallelMegacomplex (class in glotaran.builtin.megacomplexes.decay.decay_parallel_megacomplex)
DecaySequentialMegacomplex (class in glotaran.builtin.megacomplexes.decay.decay_sequential_megacomplex)
degrees_of_freedom (glotaran.project.result.Result attribute)
deprecate() (in module glotaran.deprecation.deprecation_utils)
deprecate_dict_entry() (in module glotaran.deprecation.deprecation_utils)
deprecate_module_attribute() (in module glotaran.deprecation.deprecation_utils)
deprecate_submodule() (in module glotaran.deprecation.deprecation_utils)
deserialize_options() (in module glotaran.parameter.parameter)
dict() (glotaran.io.preprocessor.pipeline.PreProcessingPipeline method)
(glotaran.io.preprocessor.preprocessor.CorrectBaselineAverage method)
(glotaran.io.preprocessor.preprocessor.CorrectBaselineValue method)
(glotaran.io.preprocessor.preprocessor.PreProcessor method)
dimension (glotaran.builtin.megacomplexes.baseline.baseline_megacomplex.BaselineMegacomplex attribute)
(glotaran.builtin.megacomplexes.clp_guide.clp_guide_megacomplex.ClpGuideMegacomplex attribute)
(glotaran.builtin.megacomplexes.coherent_artifact.coherent_artifact_megacomplex.CoherentArtifactMegacomplex attribute)
(glotaran.builtin.megacomplexes.damped_oscillation.damped_oscillation_megacomplex.DampedOscillationMegacomplex attribute)
(glotaran.builtin.megacomplexes.decay.decay_megacomplex.DecayMegacomplex attribute)
(glotaran.builtin.megacomplexes.decay.decay_parallel_megacomplex.DecayParallelMegacomplex attribute)
(glotaran.builtin.megacomplexes.decay.decay_sequential_megacomplex.DecaySequentialMegacomplex attribute)
(glotaran.builtin.megacomplexes.spectral.spectral_megacomplex.SpectralMegacomplex attribute)
directory (glotaran.project.project_data_registry.ProjectDataRegistry property)
(glotaran.project.project_model_registry.ProjectModelRegistry property)
(glotaran.project.project_parameter_registry.ProjectParameterRegistry property)
(glotaran.project.project_registry.ProjectRegistry property)
(glotaran.project.project_result_registry.ProjectResultRegistry property)
dispersion_center (glotaran.builtin.megacomplexes.decay.irf.IrfSpectralGaussian attribute)
(glotaran.builtin.megacomplexes.decay.irf.IrfSpectralMultiGaussian attribute)
display_file() (in module glotaran.utils.ipython)
does_interval_item_apply() (glotaran.optimization.matrix_provider.MatrixProvider static method)
(glotaran.optimization.matrix_provider.MatrixProviderLinked static method)
(glotaran.optimization.matrix_provider.MatrixProviderUnlinked static method)
E
eigen() (glotaran.builtin.megacomplexes.decay.k_matrix.KMatrix method)
elements_in_string_of_list (glotaran.utils.regex.RegexPattern attribute)
empty (glotaran.project.project_data_registry.ProjectDataRegistry property)
(glotaran.project.project_model_registry.ProjectModelRegistry property)
(glotaran.project.project_parameter_registry.ProjectParameterRegistry property)
(glotaran.project.project_registry.ProjectRegistry property)
(glotaran.project.project_result_registry.ProjectResultRegistry property)
empty() (glotaran.builtin.megacomplexes.decay.k_matrix.KMatrix class method)
encode() (glotaran.utils.ipython.MarkdownStr method)
endswith() (glotaran.utils.ipython.MarkdownStr method)
envvar_list_splitter (glotaran.cli.commands.util.ValOrRangeOrList attribute)
EqualAreaPenalty (class in glotaran.model.clp_penalties)
estimate() (glotaran.optimization.estimation_provider.EstimationProvider method)
(glotaran.optimization.estimation_provider.EstimationProviderLinked method)
(glotaran.optimization.estimation_provider.EstimationProviderUnlinked method)
EstimationProvider (class in glotaran.optimization.estimation_provider)
EstimationProviderLinked (class in glotaran.optimization.estimation_provider)
EstimationProviderUnlinked (class in glotaran.optimization.estimation_provider)
ExcelProjectIo (class in glotaran.builtin.io.pandas.xlsx)
exclude (glotaran.io.preprocessor.preprocessor.CorrectBaselineAverage attribute)
exclude_from_dict_field() (in module glotaran.project.dataclass_helpers)
exclude_from_normalize (glotaran.builtin.megacomplexes.decay.initial_concentration.InitialConcentration attribute)
ExclusiveMegacomplexIssue (class in glotaran.model.dataset_model)
expandtabs() (glotaran.utils.ipython.MarkdownStr method)
ExplicitFile (class in glotaran.builtin.io.ascii.wavelength_time_explicit_file)
export() (in module glotaran.cli.commands.explore)
expression (glotaran.parameter.parameter.Parameter attribute)
F
fail() (glotaran.cli.commands.util.ValOrRangeOrList method)
file (glotaran.project.project.Project attribute)
file_loadable_field() (in module glotaran.project.dataclass_helpers)
file_loader_factory() (in module glotaran.project.dataclass_helpers)
FileLoadableProtocol (class in glotaran.typing.protocols)
finalize_data() (glotaran.builtin.megacomplexes.baseline.baseline_megacomplex.BaselineMegacomplex method)
(glotaran.builtin.megacomplexes.clp_guide.clp_guide_megacomplex.ClpGuideMegacomplex method)
(glotaran.builtin.megacomplexes.coherent_artifact.coherent_artifact_megacomplex.CoherentArtifactMegacomplex method)
(glotaran.builtin.megacomplexes.damped_oscillation.damped_oscillation_megacomplex.DampedOscillationMegacomplex method)
(glotaran.builtin.megacomplexes.decay.decay_megacomplex.DecayMegacomplex method)
(glotaran.builtin.megacomplexes.decay.decay_parallel_megacomplex.DecayParallelMegacomplex method)
(glotaran.builtin.megacomplexes.decay.decay_sequential_megacomplex.DecaySequentialMegacomplex method)
(glotaran.builtin.megacomplexes.spectral.spectral_megacomplex.SpectralMegacomplex method)
(in module glotaran.builtin.megacomplexes.decay.util)
finalize_dataset_model() (in module glotaran.model.dataset_model)
find() (glotaran.utils.ipython.MarkdownStr method)
flatten_parameter_dict() (in module glotaran.parameter.parameters)
flush() (glotaran.utils.tee.TeeContext method)
folder (glotaran.project.project.Project attribute)
FolderProjectIo (class in glotaran.builtin.io.folder.folder_plugin)
force_index_dependent (glotaran.builtin.megacomplexes.decay.decay_megacomplex.DecayDatasetModel attribute)
(glotaran.builtin.megacomplexes.decay.decay_parallel_megacomplex.DecayDatasetModel attribute)
(glotaran.builtin.megacomplexes.spectral.spectral_megacomplex.SpectralDatasetModel attribute)
(glotaran.model.dataset_model.DatasetModel attribute)
format() (glotaran.utils.ipython.MarkdownStr method)
format_map() (glotaran.utils.ipython.MarkdownStr method)
free_parameter_labels (glotaran.project.result.Result attribute)
frequencies (glotaran.builtin.megacomplexes.damped_oscillation.damped_oscillation_megacomplex.DampedOscillationMegacomplex attribute)
from_csv() (glotaran.optimization.optimization_history.OptimizationHistory class method)
(glotaran.parameter.parameter_history.ParameterHistory class method)
from_dataframe() (glotaran.parameter.parameter_history.ParameterHistory class method)
(glotaran.parameter.parameters.Parameters class method)
from_dict() (glotaran.parameter.parameters.Parameters class method)
from_list() (glotaran.parameter.parameter.Parameter class method)
(glotaran.parameter.parameters.Parameters class method)
from_orm() (glotaran.io.preprocessor.pipeline.PreProcessingPipeline class method)
(glotaran.io.preprocessor.preprocessor.CorrectBaselineAverage class method)
(glotaran.io.preprocessor.preprocessor.CorrectBaselineValue class method)
(glotaran.io.preprocessor.preprocessor.PreProcessor class method)
from_parameter_dict_list() (glotaran.parameter.parameters.Parameters class method)
from_stdout_str() (glotaran.optimization.optimization_history.OptimizationHistory class method)
fromdict() (in module glotaran.project.dataclass_helpers)
fromkeys() (glotaran.project.generators.generator.GeneratorArguments method)
ftol (glotaran.project.scheme.Scheme attribute)
full() (glotaran.builtin.megacomplexes.decay.k_matrix.KMatrix method)
full_plugin_name() (in module glotaran.plugin_system.base_registry)
G
generate_model() (glotaran.project.project.Project method)
(glotaran.project.project_model_registry.ProjectModelRegistry method)
(in module glotaran.project.generators.generator)
generate_model_yml() (in module glotaran.project.generators.generator)
generate_parallel_decay_model() (in module glotaran.project.generators.generator)
generate_parallel_spectral_decay_model() (in module glotaran.project.generators.generator)
generate_parameters() (glotaran.model.model.Model method)
(glotaran.project.project.Project method)
(glotaran.project.project_parameter_registry.ProjectParameterRegistry method)
generate_sequential_decay_model() (in module glotaran.project.generators.generator)
generate_sequential_spectral_decay_model() (in module glotaran.project.generators.generator)
GeneratorArguments (class in glotaran.project.generators.generator)
get() (glotaran.parameter.parameters.Parameters method)
(glotaran.project.generators.generator.GeneratorArguments method)
(glotaran.project.project_registry.ItemMapping method)
(glotaran.utils.io.DatasetMapping method)
get_a_matrix() (glotaran.builtin.megacomplexes.decay.decay_megacomplex.DecayMegacomplex method)
(glotaran.builtin.megacomplexes.decay.decay_parallel_megacomplex.DecayParallelMegacomplex method)
(glotaran.builtin.megacomplexes.decay.decay_sequential_megacomplex.DecaySequentialMegacomplex method)
get_additional_penalties() (glotaran.optimization.estimation_provider.EstimationProvider method)
(glotaran.optimization.estimation_provider.EstimationProviderLinked method)
(glotaran.optimization.estimation_provider.EstimationProviderUnlinked method)
(glotaran.optimization.optimization_group.OptimizationGroup method)
get_aligned_data() (glotaran.optimization.data_provider.DataProviderLinked method)
get_aligned_dataset_indices() (glotaran.optimization.data_provider.DataProviderLinked method)
get_aligned_group_label() (glotaran.optimization.data_provider.DataProviderLinked method)
get_aligned_matrix_container() (glotaran.optimization.matrix_provider.MatrixProviderLinked method)
get_aligned_weight() (glotaran.optimization.data_provider.DataProviderLinked method)
get_axis_slice_from_interval() (glotaran.optimization.data_provider.DataProvider static method)
(glotaran.optimization.data_provider.DataProviderLinked static method)
get_compartments() (glotaran.builtin.megacomplexes.decay.decay_megacomplex.DecayMegacomplex method)
(glotaran.builtin.megacomplexes.decay.decay_parallel_megacomplex.DecayParallelMegacomplex method)
(glotaran.builtin.megacomplexes.decay.decay_sequential_megacomplex.DecaySequentialMegacomplex method)
get_current_optimization_iteration() (glotaran.optimization.optimizer.Optimizer static method)
get_data() (glotaran.optimization.data_provider.DataProvider method)
(glotaran.optimization.data_provider.DataProviderLinked method)
get_data_file_format() (in module glotaran.builtin.io.ascii.wavelength_time_explicit_file)
get_data_io() (in module glotaran.plugin_system.data_io_registration)
get_data_row() (glotaran.builtin.io.ascii.wavelength_time_explicit_file.ExplicitFile method)
(glotaran.builtin.io.ascii.wavelength_time_explicit_file.TimeExplicitFile method)
(glotaran.builtin.io.ascii.wavelength_time_explicit_file.WavelengthExplicitFile method)
get_dataloader() (in module glotaran.plugin_system.data_io_registration)
get_datasaver() (in module glotaran.plugin_system.data_io_registration)
get_dataset_groups() (glotaran.model.model.Model method)
get_dataset_model_model_dimension() (in module glotaran.model.dataset_model)
get_dataset_model_type() (glotaran.builtin.megacomplexes.baseline.baseline_megacomplex.BaselineMegacomplex class method)
(glotaran.builtin.megacomplexes.clp_guide.clp_guide_megacomplex.ClpGuideMegacomplex class method)
(glotaran.builtin.megacomplexes.coherent_artifact.coherent_artifact_megacomplex.CoherentArtifactMegacomplex class method)
(glotaran.builtin.megacomplexes.damped_oscillation.damped_oscillation_megacomplex.DampedOscillationMegacomplex class method)
(glotaran.builtin.megacomplexes.decay.decay_megacomplex.DecayMegacomplex class method)
(glotaran.builtin.megacomplexes.decay.decay_parallel_megacomplex.DecayParallelMegacomplex class method)
(glotaran.builtin.megacomplexes.decay.decay_sequential_megacomplex.DecaySequentialMegacomplex class method)
(glotaran.builtin.megacomplexes.spectral.spectral_megacomplex.SpectralMegacomplex class method)
get_explicit_axis() (glotaran.builtin.io.ascii.wavelength_time_explicit_file.ExplicitFile method)
(glotaran.builtin.io.ascii.wavelength_time_explicit_file.TimeExplicitFile method)
(glotaran.builtin.io.ascii.wavelength_time_explicit_file.WavelengthExplicitFile method)
get_flattened_data() (glotaran.optimization.data_provider.DataProvider method)
(glotaran.optimization.data_provider.DataProviderLinked method)
get_flattened_weight() (glotaran.optimization.data_provider.DataProvider method)
(glotaran.optimization.data_provider.DataProviderLinked method)
get_format_name() (glotaran.builtin.io.ascii.wavelength_time_explicit_file.ExplicitFile method)
(glotaran.builtin.io.ascii.wavelength_time_explicit_file.TimeExplicitFile method)
(glotaran.builtin.io.ascii.wavelength_time_explicit_file.WavelengthExplicitFile method)
get_from_dataset() (glotaran.optimization.data_provider.DataProvider static method)
(glotaran.optimization.data_provider.DataProviderLinked static method)
get_full_matrix() (glotaran.optimization.matrix_provider.MatrixProviderUnlinked method)
get_full_penalty() (glotaran.optimization.estimation_provider.EstimationProvider method)
(glotaran.optimization.estimation_provider.EstimationProviderLinked method)
(glotaran.optimization.estimation_provider.EstimationProviderUnlinked method)
(glotaran.optimization.optimization_group.OptimizationGroup method)
get_global_axis() (glotaran.optimization.data_provider.DataProvider method)
(glotaran.optimization.data_provider.DataProviderLinked method)
get_global_dimension() (glotaran.optimization.data_provider.DataProvider method)
(glotaran.optimization.data_provider.DataProviderLinked method)
get_global_matrix_container() (glotaran.optimization.matrix_provider.MatrixProviderUnlinked method)
get_initial_concentration() (glotaran.builtin.megacomplexes.decay.decay_megacomplex.DecayMegacomplex method)
(glotaran.builtin.megacomplexes.decay.decay_parallel_megacomplex.DecayParallelMegacomplex method)
(glotaran.builtin.megacomplexes.decay.decay_sequential_megacomplex.DecaySequentialMegacomplex method)
get_interval_number() (in module glotaran.builtin.io.ascii.wavelength_time_explicit_file)
get_irf_parameter() (glotaran.builtin.megacomplexes.coherent_artifact.coherent_artifact_megacomplex.CoherentArtifactMegacomplex method)
get_issues() (glotaran.model.model.Model method)
get_item_type() (glotaran.builtin.megacomplexes.baseline.baseline_megacomplex.BaselineMegacomplex class method)
(glotaran.builtin.megacomplexes.clp_guide.clp_guide_megacomplex.ClpGuideMegacomplex class method)
(glotaran.builtin.megacomplexes.coherent_artifact.coherent_artifact_megacomplex.CoherentArtifactMegacomplex class method)
(glotaran.builtin.megacomplexes.damped_oscillation.damped_oscillation_megacomplex.DampedOscillationMegacomplex class method)
(glotaran.builtin.megacomplexes.decay.decay_megacomplex.DecayMegacomplex class method)
(glotaran.builtin.megacomplexes.decay.decay_parallel_megacomplex.DecayParallelMegacomplex class method)
(glotaran.builtin.megacomplexes.decay.decay_sequential_megacomplex.DecaySequentialMegacomplex class method)
(glotaran.builtin.megacomplexes.decay.irf.Irf class method)
(glotaran.builtin.megacomplexes.decay.irf.IrfGaussian class method)
(glotaran.builtin.megacomplexes.decay.irf.IrfMultiGaussian class method)
(glotaran.builtin.megacomplexes.decay.irf.IrfSpectralGaussian class method)
(glotaran.builtin.megacomplexes.decay.irf.IrfSpectralMultiGaussian class method)
(glotaran.builtin.megacomplexes.spectral.shape.SpectralShape class method)
(glotaran.builtin.megacomplexes.spectral.shape.SpectralShapeGaussian class method)
(glotaran.builtin.megacomplexes.spectral.shape.SpectralShapeOne class method)
(glotaran.builtin.megacomplexes.spectral.shape.SpectralShapeSkewedGaussian class method)
(glotaran.builtin.megacomplexes.spectral.shape.SpectralShapeZero class method)
(glotaran.builtin.megacomplexes.spectral.spectral_megacomplex.SpectralMegacomplex class method)
(glotaran.model.clp_constraint.ClpConstraint class method)
(glotaran.model.clp_constraint.OnlyConstraint class method)
(glotaran.model.clp_constraint.ZeroConstraint class method)
(glotaran.model.clp_penalties.ClpPenalty class method)
(glotaran.model.clp_penalties.EqualAreaPenalty class method)
get_item_type_class() (glotaran.builtin.megacomplexes.baseline.baseline_megacomplex.BaselineMegacomplex class method)
(glotaran.builtin.megacomplexes.clp_guide.clp_guide_megacomplex.ClpGuideMegacomplex class method)
(glotaran.builtin.megacomplexes.coherent_artifact.coherent_artifact_megacomplex.CoherentArtifactMegacomplex class method)
(glotaran.builtin.megacomplexes.damped_oscillation.damped_oscillation_megacomplex.DampedOscillationMegacomplex class method)
(glotaran.builtin.megacomplexes.decay.decay_megacomplex.DecayMegacomplex class method)
(glotaran.builtin.megacomplexes.decay.decay_parallel_megacomplex.DecayParallelMegacomplex class method)
(glotaran.builtin.megacomplexes.decay.decay_sequential_megacomplex.DecaySequentialMegacomplex class method)
(glotaran.builtin.megacomplexes.decay.irf.Irf class method)
(glotaran.builtin.megacomplexes.decay.irf.IrfGaussian class method)
(glotaran.builtin.megacomplexes.decay.irf.IrfMultiGaussian class method)
(glotaran.builtin.megacomplexes.decay.irf.IrfSpectralGaussian class method)
(glotaran.builtin.megacomplexes.decay.irf.IrfSpectralMultiGaussian class method)
(glotaran.builtin.megacomplexes.spectral.shape.SpectralShape class method)
(glotaran.builtin.megacomplexes.spectral.shape.SpectralShapeGaussian class method)
(glotaran.builtin.megacomplexes.spectral.shape.SpectralShapeOne class method)
(glotaran.builtin.megacomplexes.spectral.shape.SpectralShapeSkewedGaussian class method)
(glotaran.builtin.megacomplexes.spectral.shape.SpectralShapeZero class method)
(glotaran.builtin.megacomplexes.spectral.spectral_megacomplex.SpectralMegacomplex class method)
(glotaran.model.clp_constraint.ClpConstraint class method)
(glotaran.model.clp_constraint.OnlyConstraint class method)
(glotaran.model.clp_constraint.ZeroConstraint class method)
(glotaran.model.clp_penalties.ClpPenalty class method)
(glotaran.model.clp_penalties.EqualAreaPenalty class method)
get_item_types() (glotaran.builtin.megacomplexes.baseline.baseline_megacomplex.BaselineMegacomplex class method)
(glotaran.builtin.megacomplexes.clp_guide.clp_guide_megacomplex.ClpGuideMegacomplex class method)
(glotaran.builtin.megacomplexes.coherent_artifact.coherent_artifact_megacomplex.CoherentArtifactMegacomplex class method)
(glotaran.builtin.megacomplexes.damped_oscillation.damped_oscillation_megacomplex.DampedOscillationMegacomplex class method)
(glotaran.builtin.megacomplexes.decay.decay_megacomplex.DecayMegacomplex class method)
(glotaran.builtin.megacomplexes.decay.decay_parallel_megacomplex.DecayParallelMegacomplex class method)
(glotaran.builtin.megacomplexes.decay.decay_sequential_megacomplex.DecaySequentialMegacomplex class method)
(glotaran.builtin.megacomplexes.decay.irf.Irf class method)
(glotaran.builtin.megacomplexes.decay.irf.IrfGaussian class method)
(glotaran.builtin.megacomplexes.decay.irf.IrfMultiGaussian class method)
(glotaran.builtin.megacomplexes.decay.irf.IrfSpectralGaussian class method)
(glotaran.builtin.megacomplexes.decay.irf.IrfSpectralMultiGaussian class method)
(glotaran.builtin.megacomplexes.spectral.shape.SpectralShape class method)
(glotaran.builtin.megacomplexes.spectral.shape.SpectralShapeGaussian class method)
(glotaran.builtin.megacomplexes.spectral.shape.SpectralShapeOne class method)
(glotaran.builtin.megacomplexes.spectral.shape.SpectralShapeSkewedGaussian class method)
(glotaran.builtin.megacomplexes.spectral.shape.SpectralShapeZero class method)
(glotaran.builtin.megacomplexes.spectral.spectral_megacomplex.SpectralMegacomplex class method)
(glotaran.model.clp_constraint.ClpConstraint class method)
(glotaran.model.clp_constraint.OnlyConstraint class method)
(glotaran.model.clp_constraint.ZeroConstraint class method)
(glotaran.model.clp_penalties.ClpPenalty class method)
(glotaran.model.clp_penalties.EqualAreaPenalty class method)
get_k_matrix() (glotaran.builtin.megacomplexes.decay.decay_megacomplex.DecayMegacomplex method)
(glotaran.builtin.megacomplexes.decay.decay_parallel_megacomplex.DecayParallelMegacomplex method)
(glotaran.builtin.megacomplexes.decay.decay_sequential_megacomplex.DecaySequentialMegacomplex method)
get_label_value_and_bounds_arrays() (glotaran.parameter.parameters.Parameters method)
get_latest_result_path() (glotaran.project.project.Project method)
get_matrix_container() (glotaran.optimization.matrix_provider.MatrixProvider method)
(glotaran.optimization.matrix_provider.MatrixProviderLinked method)
(glotaran.optimization.matrix_provider.MatrixProviderUnlinked method)
get_megacomplex() (in module glotaran.plugin_system.megacomplex_registration)
get_megacomplex_issues() (in module glotaran.model.dataset_model)
get_metavar() (glotaran.cli.commands.util.ValOrRangeOrList method)
get_method_from_plugin() (in module glotaran.plugin_system.base_registry)
get_missing_message() (glotaran.cli.commands.util.ValOrRangeOrList method)
get_model_axis() (glotaran.optimization.data_provider.DataProvider method)
(glotaran.optimization.data_provider.DataProviderLinked method)
get_model_dimension() (glotaran.optimization.data_provider.DataProvider method)
(glotaran.optimization.data_provider.DataProviderLinked method)
get_models_directory() (glotaran.project.project.Project method)
get_observations() (glotaran.builtin.io.ascii.wavelength_time_explicit_file.ExplicitFile method)
(glotaran.builtin.io.ascii.wavelength_time_explicit_file.TimeExplicitFile method)
(glotaran.builtin.io.ascii.wavelength_time_explicit_file.WavelengthExplicitFile method)
get_parameter_labels() (glotaran.model.model.Model method)
get_parameters() (glotaran.parameter.parameter_history.ParameterHistory method)
get_parameters_directory() (glotaran.project.project.Project method)
get_plugin_from_registry() (in module glotaran.plugin_system.base_registry)
get_prepared_matrix_container() (glotaran.optimization.matrix_provider.MatrixProviderUnlinked method)
get_project_io() (in module glotaran.plugin_system.project_io_registration)
get_project_io_method() (in module glotaran.plugin_system.project_io_registration)
get_result() (glotaran.optimization.estimation_provider.EstimationProvider method)
(glotaran.optimization.estimation_provider.EstimationProviderLinked method)
(glotaran.optimization.estimation_provider.EstimationProviderUnlinked method)
(glotaran.optimization.matrix_provider.MatrixProvider method)
(glotaran.optimization.matrix_provider.MatrixProviderLinked method)
(glotaran.optimization.matrix_provider.MatrixProviderUnlinked method)
get_result_path() (glotaran.project.project.Project method)
get_scheme() (glotaran.project.result.Result method)
get_script_dir() (in module glotaran.utils.io)
get_secondary_axis() (glotaran.builtin.io.ascii.wavelength_time_explicit_file.ExplicitFile method)
(glotaran.builtin.io.ascii.wavelength_time_explicit_file.TimeExplicitFile method)
(glotaran.builtin.io.ascii.wavelength_time_explicit_file.WavelengthExplicitFile method)
get_value_and_bounds_for_optimization() (glotaran.parameter.parameter.Parameter method)
get_weight() (glotaran.optimization.data_provider.DataProvider method)
(glotaran.optimization.data_provider.DataProviderLinked method)
global_interval (glotaran.model.weight.Weight attribute)
global_megacomplex (glotaran.builtin.megacomplexes.decay.decay_megacomplex.DecayDatasetModel attribute)
(glotaran.builtin.megacomplexes.decay.decay_parallel_megacomplex.DecayDatasetModel attribute)
(glotaran.builtin.megacomplexes.spectral.spectral_megacomplex.SpectralDatasetModel attribute)
(glotaran.model.dataset_model.DatasetModel attribute)
global_megacomplex_scale (glotaran.builtin.megacomplexes.decay.decay_megacomplex.DecayDatasetModel attribute)
(glotaran.builtin.megacomplexes.decay.decay_parallel_megacomplex.DecayDatasetModel attribute)
(glotaran.builtin.megacomplexes.spectral.spectral_megacomplex.SpectralDatasetModel attribute)
(glotaran.model.dataset_model.DatasetModel attribute)
glotaran
module
glotaran command line option
--version
glotaran-optimize command line option
--data
--dataformat
--model_file
--nfev
--nnls
--out
--outformat
--parameters_file
--yes
-d
-dfmt
-m
-n
-o
-ofmt
-p
-y
SCHEME_FILE
glotaran-print command line option
--model_file
--parameters_file
-m
-p
SCHEME_FILE
glotaran-validate command line option
--model_file
--parameters_file
-m
-p
SCHEME_FILE
glotaran.analysis
module
glotaran.builtin
module
glotaran.builtin.io
module
glotaran.builtin.io.ascii
module
glotaran.builtin.io.ascii.wavelength_time_explicit_file
module
glotaran.builtin.io.folder
module
glotaran.builtin.io.folder.folder_plugin
module
glotaran.builtin.io.netCDF
module
glotaran.builtin.io.netCDF.netCDF
module
glotaran.builtin.io.pandas
module
glotaran.builtin.io.pandas.csv
module
glotaran.builtin.io.pandas.tsv
module
glotaran.builtin.io.pandas.xlsx
module
glotaran.builtin.io.sdt
module
glotaran.builtin.io.sdt.sdt_file_reader
module
glotaran.builtin.io.yml
module
glotaran.builtin.io.yml.utils
module
glotaran.builtin.io.yml.yml
module
glotaran.builtin.megacomplexes
module
glotaran.builtin.megacomplexes.baseline
module
glotaran.builtin.megacomplexes.baseline.baseline_megacomplex
module
glotaran.builtin.megacomplexes.clp_guide
module
glotaran.builtin.megacomplexes.clp_guide.clp_guide_megacomplex
module
glotaran.builtin.megacomplexes.coherent_artifact
module
glotaran.builtin.megacomplexes.coherent_artifact.coherent_artifact_megacomplex
module
glotaran.builtin.megacomplexes.damped_oscillation
module
glotaran.builtin.megacomplexes.damped_oscillation.damped_oscillation_megacomplex
module
glotaran.builtin.megacomplexes.decay
module
glotaran.builtin.megacomplexes.decay.decay_matrix_gaussian_irf
module
glotaran.builtin.megacomplexes.decay.decay_megacomplex
module
glotaran.builtin.megacomplexes.decay.decay_parallel_megacomplex
module
glotaran.builtin.megacomplexes.decay.decay_sequential_megacomplex
module
glotaran.builtin.megacomplexes.decay.initial_concentration
module
glotaran.builtin.megacomplexes.decay.irf
module
glotaran.builtin.megacomplexes.decay.k_matrix
module
glotaran.builtin.megacomplexes.decay.util
module
glotaran.builtin.megacomplexes.spectral
module
glotaran.builtin.megacomplexes.spectral.shape
module
glotaran.builtin.megacomplexes.spectral.spectral_megacomplex
module
glotaran.cli
module
glotaran.cli.commands
module
glotaran.cli.commands.explore
module
glotaran.cli.commands.export
module
glotaran.cli.commands.optimize
module
glotaran.cli.commands.pluginlist
module
glotaran.cli.commands.print
module
glotaran.cli.commands.util
module
glotaran.cli.commands.validate
module
glotaran.deprecation
module
glotaran.deprecation.deprecation_utils
module
glotaran.deprecation.modules
module
glotaran.deprecation.modules.builtin_io_yml
module
glotaran.deprecation.modules.examples
module
glotaran.deprecation.modules.examples.sequential
module
glotaran.io
module
glotaran.io.interface
module
glotaran.io.prepare_dataset
module
glotaran.io.preprocessor
module
glotaran.io.preprocessor.pipeline
module
glotaran.io.preprocessor.preprocessor
module
glotaran.model
module
glotaran.model.clp_constraint
module
glotaran.model.clp_penalties
module
glotaran.model.clp_relation
module
glotaran.model.dataset_group
module
glotaran.model.dataset_model
module
glotaran.model.interval_item
module
glotaran.model.model
module
glotaran.model.weight
module
glotaran.optimization
module
glotaran.optimization.data_provider
module
glotaran.optimization.estimation_provider
module
glotaran.optimization.matrix_provider
module
glotaran.optimization.nnls
module
glotaran.optimization.optimization_group
module
glotaran.optimization.optimization_history
module
glotaran.optimization.optimize
module
glotaran.optimization.optimizer
module
glotaran.optimization.variable_projection
module
glotaran.parameter
module
glotaran.parameter.parameter
module
glotaran.parameter.parameter_history
module
glotaran.parameter.parameters
module
glotaran.plugin_system
module
glotaran.plugin_system.base_registry
module
glotaran.plugin_system.data_io_registration
module
glotaran.plugin_system.io_plugin_utils
module
glotaran.plugin_system.megacomplex_registration
module
glotaran.plugin_system.project_io_registration
module
glotaran.project
module
glotaran.project.dataclass_helpers
module
glotaran.project.generators
module
glotaran.project.generators.generator
module
glotaran.project.project
module
glotaran.project.project_data_registry
module
glotaran.project.project_model_registry
module
glotaran.project.project_parameter_registry
module
glotaran.project.project_registry
module
glotaran.project.project_result_registry
module
glotaran.project.result
module
glotaran.project.scheme
module
glotaran.simulation
module
glotaran.simulation.simulation
module
glotaran.testing
module
glotaran.testing.plugin_system
module
glotaran.testing.simulated_data
module
glotaran.testing.simulated_data.parallel_spectral_decay
module
glotaran.testing.simulated_data.sequential_spectral_decay
module
glotaran.testing.simulated_data.shared_decay
module
glotaran.typing
module
glotaran.typing.protocols
module
glotaran.typing.types
module
glotaran.utils
module
glotaran.utils.attrs_helper
module
glotaran.utils.helpers
module
glotaran.utils.io
module
glotaran.utils.ipython
module
glotaran.utils.regex
module
glotaran.utils.sanitize
module
glotaran.utils.tee
module
glotaran_version (glotaran.project.result.Result attribute)
glotaran_version() (in module glotaran.deprecation.deprecation_utils)
group (glotaran.builtin.megacomplexes.decay.decay_megacomplex.DecayDatasetModel attribute)
(glotaran.builtin.megacomplexes.decay.decay_parallel_megacomplex.DecayDatasetModel attribute)
(glotaran.builtin.megacomplexes.spectral.spectral_megacomplex.SpectralDatasetModel attribute)
(glotaran.model.dataset_model.DatasetModel attribute)
(glotaran.optimization.estimation_provider.EstimationProvider property)
(glotaran.optimization.estimation_provider.EstimationProviderLinked property)
(glotaran.optimization.estimation_provider.EstimationProviderUnlinked property)
(glotaran.optimization.matrix_provider.MatrixProvider property)
(glotaran.optimization.matrix_provider.MatrixProviderLinked property)
(glotaran.optimization.matrix_provider.MatrixProviderUnlinked property)
(glotaran.utils.regex.RegexPattern attribute)
group_definitions (glotaran.optimization.data_provider.DataProviderLinked property)
gtol (glotaran.project.scheme.Scheme attribute)
H
has() (glotaran.parameter.parameters.Parameters method)
has_data (glotaran.project.project.Project property)
has_dataset_model_global_model() (in module glotaran.model.dataset_model)
has_interval() (glotaran.model.clp_constraint.ClpConstraint method)
(glotaran.model.clp_constraint.OnlyConstraint method)
(glotaran.model.clp_constraint.ZeroConstraint method)
(glotaran.model.clp_relation.ClpRelation method)
(glotaran.model.interval_item.IntervalItem method)
has_models (glotaran.project.project.Project property)
has_parameters (glotaran.project.project.Project property)
has_results (glotaran.project.project.Project property)
I
import_data() (glotaran.project.project.Project method)
(glotaran.project.project_data_registry.ProjectDataRegistry method)
index() (glotaran.utils.ipython.MarkdownStr method)
index_dependent() (in module glotaran.builtin.megacomplexes.decay.util)
infer_file_format() (in module glotaran.plugin_system.io_plugin_utils)
infer_global_dimension() (glotaran.optimization.data_provider.DataProvider static method)
(glotaran.optimization.data_provider.DataProviderLinked static method)
init_file_loadable_fields() (in module glotaran.project.dataclass_helpers)
initial_concentration (glotaran.builtin.megacomplexes.decay.decay_megacomplex.DecayDatasetModel attribute)
initial_parameters (glotaran.project.result.Result attribute)
InitialConcentration (class in glotaran.builtin.megacomplexes.decay.initial_concentration)
interval (glotaran.model.clp_constraint.ClpConstraint attribute)
(glotaran.model.clp_constraint.OnlyConstraint attribute)
(glotaran.model.clp_constraint.ZeroConstraint attribute)
(glotaran.model.clp_relation.ClpRelation attribute)
(glotaran.model.interval_item.IntervalItem attribute)
IntervalItem (class in glotaran.model.interval_item)
involved_compartments() (glotaran.builtin.megacomplexes.decay.k_matrix.KMatrix method)
Irf (class in glotaran.builtin.megacomplexes.decay.irf)
irf (glotaran.builtin.megacomplexes.decay.decay_megacomplex.DecayDatasetModel attribute)
(glotaran.builtin.megacomplexes.decay.decay_parallel_megacomplex.DecayDatasetModel attribute)
(glotaran.project.generators.generator.GeneratorArguments attribute)
IrfGaussian (class in glotaran.builtin.megacomplexes.decay.irf)
IrfMultiGaussian (class in glotaran.builtin.megacomplexes.decay.irf)
IrfSpectralGaussian (class in glotaran.builtin.megacomplexes.decay.irf)
IrfSpectralMultiGaussian (class in glotaran.builtin.megacomplexes.decay.irf)
is_composite (glotaran.cli.commands.util.ValOrRangeOrList attribute)
is_index_dependent (glotaran.optimization.matrix_provider.MatrixContainer property)
is_index_dependent() (glotaran.builtin.megacomplexes.decay.irf.IrfGaussian method)
(glotaran.builtin.megacomplexes.decay.irf.IrfMultiGaussian method)
(glotaran.builtin.megacomplexes.decay.irf.IrfSpectralGaussian method)
(glotaran.builtin.megacomplexes.decay.irf.IrfSpectralMultiGaussian method)
is_item() (glotaran.project.project_data_registry.ProjectDataRegistry method)
(glotaran.project.project_model_registry.ProjectModelRegistry method)
(glotaran.project.project_parameter_registry.ProjectParameterRegistry method)
(glotaran.project.project_registry.ProjectRegistry method)
(glotaran.project.project_result_registry.ProjectResultRegistry method)
is_known_data_format() (in module glotaran.plugin_system.data_io_registration)
is_known_megacomplex() (in module glotaran.plugin_system.megacomplex_registration)
is_known_project_format() (in module glotaran.plugin_system.project_io_registration)
is_linkable() (glotaran.model.dataset_group.DatasetGroup method)
is_registered_plugin() (in module glotaran.plugin_system.base_registry)
is_sequential() (glotaran.builtin.megacomplexes.decay.k_matrix.KMatrix method)
isalnum() (glotaran.utils.ipython.MarkdownStr method)
isalpha() (glotaran.utils.ipython.MarkdownStr method)
isascii() (glotaran.utils.ipython.MarkdownStr method)
isdecimal() (glotaran.utils.ipython.MarkdownStr method)
isdigit() (glotaran.utils.ipython.MarkdownStr method)
isidentifier() (glotaran.utils.ipython.MarkdownStr method)
islower() (glotaran.utils.ipython.MarkdownStr method)
isnumeric() (glotaran.utils.ipython.MarkdownStr method)
isprintable() (glotaran.utils.ipython.MarkdownStr method)
isspace() (glotaran.utils.ipython.MarkdownStr method)
istitle() (glotaran.utils.ipython.MarkdownStr method)
isupper() (glotaran.utils.ipython.MarkdownStr method)
item() (in module glotaran.model)
ItemMapping (class in glotaran.project.project_registry)
items (glotaran.project.project_data_registry.ProjectDataRegistry property)
(glotaran.project.project_model_registry.ProjectModelRegistry property)
(glotaran.project.project_parameter_registry.ProjectParameterRegistry property)
(glotaran.project.project_registry.ProjectRegistry property)
(glotaran.project.project_result_registry.ProjectResultRegistry property)
items() (glotaran.project.generators.generator.GeneratorArguments method)
(glotaran.project.project_registry.ItemMapping method)
(glotaran.utils.io.DatasetMapping method)
iterate_all_items() (glotaran.model.model.Model method)
iterate_dataset_model_global_megacomplexes() (in module glotaran.model.dataset_model)
iterate_dataset_model_megacomplexes() (in module glotaran.model.dataset_model)
iterate_items() (glotaran.model.model.Model method)
J
jacobian (glotaran.project.result.Result attribute)
join() (glotaran.utils.ipython.MarkdownStr method)
json() (glotaran.io.preprocessor.pipeline.PreProcessingPipeline method)
(glotaran.io.preprocessor.preprocessor.CorrectBaselineAverage method)
(glotaran.io.preprocessor.preprocessor.CorrectBaselineValue method)
(glotaran.io.preprocessor.preprocessor.PreProcessor method)
K
k_matrix (glotaran.builtin.megacomplexes.decay.decay_megacomplex.DecayMegacomplex attribute)
keys() (glotaran.project.generators.generator.GeneratorArguments method)
(glotaran.project.project_registry.ItemMapping method)
(glotaran.utils.io.DatasetMapping method)
KMatrix (class in glotaran.builtin.megacomplexes.decay.k_matrix)
known_data_formats() (in module glotaran.plugin_system.data_io_registration)
known_megacomplex_names() (in module glotaran.plugin_system.megacomplex_registration)
known_project_formats() (in module glotaran.plugin_system.project_io_registration)
L
label (glotaran.builtin.megacomplexes.baseline.baseline_megacomplex.BaselineMegacomplex attribute)
(glotaran.builtin.megacomplexes.clp_guide.clp_guide_megacomplex.ClpGuideMegacomplex attribute)
(glotaran.builtin.megacomplexes.coherent_artifact.coherent_artifact_megacomplex.CoherentArtifactMegacomplex attribute)
(glotaran.builtin.megacomplexes.damped_oscillation.damped_oscillation_megacomplex.DampedOscillationMegacomplex attribute)
(glotaran.builtin.megacomplexes.decay.decay_megacomplex.DecayDatasetModel attribute)
(glotaran.builtin.megacomplexes.decay.decay_megacomplex.DecayMegacomplex attribute)
(glotaran.builtin.megacomplexes.decay.decay_parallel_megacomplex.DecayDatasetModel attribute)
(glotaran.builtin.megacomplexes.decay.decay_parallel_megacomplex.DecayParallelMegacomplex attribute)
(glotaran.builtin.megacomplexes.decay.decay_sequential_megacomplex.DecaySequentialMegacomplex attribute)
(glotaran.builtin.megacomplexes.decay.initial_concentration.InitialConcentration attribute)
(glotaran.builtin.megacomplexes.decay.irf.Irf attribute)
(glotaran.builtin.megacomplexes.decay.irf.IrfGaussian attribute)
(glotaran.builtin.megacomplexes.decay.irf.IrfMultiGaussian attribute)
(glotaran.builtin.megacomplexes.decay.irf.IrfSpectralGaussian attribute)
(glotaran.builtin.megacomplexes.decay.irf.IrfSpectralMultiGaussian attribute)
(glotaran.builtin.megacomplexes.decay.k_matrix.KMatrix attribute)
(glotaran.builtin.megacomplexes.spectral.shape.SpectralShape attribute)
(glotaran.builtin.megacomplexes.spectral.shape.SpectralShapeGaussian attribute)
(glotaran.builtin.megacomplexes.spectral.shape.SpectralShapeOne attribute)
(glotaran.builtin.megacomplexes.spectral.shape.SpectralShapeSkewedGaussian attribute)
(glotaran.builtin.megacomplexes.spectral.shape.SpectralShapeZero attribute)
(glotaran.builtin.megacomplexes.spectral.spectral_megacomplex.SpectralDatasetModel attribute)
(glotaran.builtin.megacomplexes.spectral.spectral_megacomplex.SpectralMegacomplex attribute)
(glotaran.model.dataset_group.DatasetGroupModel attribute)
(glotaran.model.dataset_model.DatasetModel attribute)
(glotaran.parameter.parameter.Parameter attribute)
label_short (glotaran.parameter.parameter.Parameter property)
labels (glotaran.builtin.megacomplexes.damped_oscillation.damped_oscillation_megacomplex.DampedOscillationMegacomplex attribute)
(glotaran.parameter.parameters.Parameters property)
LegacyProjectIo (class in glotaran.builtin.io.folder.folder_plugin)
link_clp (glotaran.model.dataset_group.DatasetGroup attribute)
(glotaran.model.dataset_group.DatasetGroupModel attribute)
list_string_to_tuple() (in module glotaran.utils.sanitize)
list_with_tuples (glotaran.utils.regex.RegexPattern attribute)
ljust() (glotaran.utils.ipython.MarkdownStr method)
load_data() (glotaran.project.project.Project method)
load_dataset() (glotaran.builtin.io.ascii.wavelength_time_explicit_file.AsciiDataIo method)
(glotaran.builtin.io.netCDF.netCDF.NetCDFDataIo method)
(glotaran.builtin.io.sdt.sdt_file_reader.SdtDataIo method)
(glotaran.io.interface.DataIoInterface method)
(in module glotaran.plugin_system.data_io_registration)
load_dataset_file() (in module glotaran.cli.commands.util)
load_datasets() (in module glotaran.utils.io)
load_dict() (in module glotaran.builtin.io.yml.utils)
load_item() (glotaran.project.project_data_registry.ProjectDataRegistry method)
(glotaran.project.project_model_registry.ProjectModelRegistry method)
(glotaran.project.project_parameter_registry.ProjectParameterRegistry method)
(glotaran.project.project_registry.ProjectRegistry method)
(glotaran.project.project_result_registry.ProjectResultRegistry method)
load_latest_result() (glotaran.project.project.Project method)
load_model() (glotaran.builtin.io.folder.folder_plugin.FolderProjectIo method)
(glotaran.builtin.io.folder.folder_plugin.LegacyProjectIo method)
(glotaran.builtin.io.pandas.csv.CsvProjectIo method)
(glotaran.builtin.io.pandas.tsv.TsvProjectIo method)
(glotaran.builtin.io.pandas.xlsx.ExcelProjectIo method)
(glotaran.builtin.io.yml.yml.YmlProjectIo method)
(glotaran.io.interface.ProjectIoInterface method)
(glotaran.project.project.Project method)
(in module glotaran.plugin_system.project_io_registration)
load_model_file() (in module glotaran.cli.commands.util)
load_parameter_file() (in module glotaran.cli.commands.util)
load_parameters() (glotaran.builtin.io.folder.folder_plugin.FolderProjectIo method)
(glotaran.builtin.io.folder.folder_plugin.LegacyProjectIo method)
(glotaran.builtin.io.pandas.csv.CsvProjectIo method)
(glotaran.builtin.io.pandas.tsv.TsvProjectIo method)
(glotaran.builtin.io.pandas.xlsx.ExcelProjectIo method)
(glotaran.builtin.io.yml.yml.YmlProjectIo method)
(glotaran.io.interface.ProjectIoInterface method)
(glotaran.project.project.Project method)
(in module glotaran.plugin_system.project_io_registration)
load_plugins() (in module glotaran.plugin_system.base_registry)
load_result() (glotaran.builtin.io.folder.folder_plugin.FolderProjectIo method)
(glotaran.builtin.io.folder.folder_plugin.LegacyProjectIo method)
(glotaran.builtin.io.pandas.csv.CsvProjectIo method)
(glotaran.builtin.io.pandas.tsv.TsvProjectIo method)
(glotaran.builtin.io.pandas.xlsx.ExcelProjectIo method)
(glotaran.builtin.io.yml.yml.YmlProjectIo method)
(glotaran.io.interface.ProjectIoInterface method)
(glotaran.project.project.Project method)
(in module glotaran.plugin_system.project_io_registration)
load_scheme() (glotaran.builtin.io.folder.folder_plugin.FolderProjectIo method)
(glotaran.builtin.io.folder.folder_plugin.LegacyProjectIo method)
(glotaran.builtin.io.pandas.csv.CsvProjectIo method)
(glotaran.builtin.io.pandas.tsv.TsvProjectIo method)
(glotaran.builtin.io.pandas.xlsx.ExcelProjectIo method)
(glotaran.builtin.io.yml.yml.YmlProjectIo method)
(glotaran.io.interface.ProjectIoInterface method)
(in module glotaran.plugin_system.project_io_registration)
load_scheme_file() (in module glotaran.cli.commands.util)
loader (glotaran.typing.protocols.FileLoadableProtocol attribute)
loader() (glotaran.model.model.Model method)
(glotaran.optimization.optimization_history.OptimizationHistory class method)
(glotaran.parameter.parameter_history.ParameterHistory class method)
(glotaran.parameter.parameters.Parameters method)
(glotaran.project.result.Result method)
(glotaran.project.scheme.Scheme method)
(glotaran.utils.io.DatasetMapping class method)
location (glotaran.builtin.megacomplexes.spectral.shape.SpectralShapeGaussian attribute)
(glotaran.builtin.megacomplexes.spectral.shape.SpectralShapeSkewedGaussian attribute)
lower() (glotaran.utils.ipython.MarkdownStr method)
lstrip() (glotaran.utils.ipython.MarkdownStr method)
M
main (in module glotaran.cli)
make_path_absolute_if_relative() (in module glotaran.utils.io)
maketrans() (glotaran.utils.ipython.MarkdownStr method)
markdown() (glotaran.model.model.Model method)
(glotaran.parameter.parameter.Parameter method)
(glotaran.parameter.parameters.Parameters method)
(glotaran.project.project.Project method)
(glotaran.project.project_data_registry.ProjectDataRegistry method)
(glotaran.project.project_model_registry.ProjectModelRegistry method)
(glotaran.project.project_parameter_registry.ProjectParameterRegistry method)
(glotaran.project.project_registry.ProjectRegistry method)
(glotaran.project.project_result_registry.ProjectResultRegistry method)
(glotaran.project.result.Result method)
(glotaran.project.scheme.Scheme method)
MarkdownStr (class in glotaran.utils.ipython)
matrix (glotaran.builtin.megacomplexes.decay.k_matrix.KMatrix attribute)
(glotaran.optimization.matrix_provider.MatrixContainer attribute)
matrix_as_markdown() (glotaran.builtin.megacomplexes.decay.k_matrix.KMatrix method)
MatrixContainer (class in glotaran.optimization.matrix_provider)
MatrixProvider (class in glotaran.optimization.matrix_provider)
MatrixProviderLinked (class in glotaran.optimization.matrix_provider)
MatrixProviderUnlinked (class in glotaran.optimization.matrix_provider)
maximum (glotaran.parameter.parameter.Parameter attribute)
maximum_number_function_evaluations (glotaran.project.scheme.Scheme attribute)
megacomplex (glotaran.builtin.megacomplexes.decay.decay_megacomplex.DecayDatasetModel attribute)
(glotaran.builtin.megacomplexes.decay.decay_parallel_megacomplex.DecayDatasetModel attribute)
(glotaran.builtin.megacomplexes.spectral.spectral_megacomplex.SpectralDatasetModel attribute)
(glotaran.model.dataset_model.DatasetModel attribute)
(glotaran.model.model.Model attribute)
megacomplex() (in module glotaran.model)
megacomplex_plugin_table() (in module glotaran.plugin_system.megacomplex_registration)
megacomplex_scale (glotaran.builtin.megacomplexes.decay.decay_megacomplex.DecayDatasetModel attribute)
(glotaran.builtin.megacomplexes.decay.decay_parallel_megacomplex.DecayDatasetModel attribute)
(glotaran.builtin.megacomplexes.spectral.spectral_megacomplex.SpectralDatasetModel attribute)
(glotaran.model.dataset_model.DatasetModel attribute)
methods_differ_from_baseclass() (in module glotaran.plugin_system.base_registry)
methods_differ_from_baseclass_table() (in module glotaran.plugin_system.base_registry)
minimum (glotaran.parameter.parameter.Parameter attribute)
Model (class in glotaran.model.model)
model (glotaran.model.dataset_group.DatasetGroup attribute)
(glotaran.project.result.Result property)
(glotaran.project.scheme.Scheme attribute)
model_computed_fields (glotaran.io.preprocessor.pipeline.PreProcessingPipeline property)
(glotaran.io.preprocessor.preprocessor.CorrectBaselineAverage property)
(glotaran.io.preprocessor.preprocessor.CorrectBaselineValue property)
(glotaran.io.preprocessor.preprocessor.PreProcessor property)
model_config (glotaran.io.preprocessor.pipeline.PreProcessingPipeline attribute)
(glotaran.io.preprocessor.preprocessor.CorrectBaselineAverage attribute)
(glotaran.io.preprocessor.preprocessor.CorrectBaselineValue attribute)
(glotaran.io.preprocessor.preprocessor.PreProcessor attribute)
model_construct() (glotaran.io.preprocessor.pipeline.PreProcessingPipeline class method)
(glotaran.io.preprocessor.preprocessor.CorrectBaselineAverage class method)
(glotaran.io.preprocessor.preprocessor.CorrectBaselineValue class method)
(glotaran.io.preprocessor.preprocessor.PreProcessor class method)
model_copy() (glotaran.io.preprocessor.pipeline.PreProcessingPipeline method)
(glotaran.io.preprocessor.preprocessor.CorrectBaselineAverage method)
(glotaran.io.preprocessor.preprocessor.CorrectBaselineValue method)
(glotaran.io.preprocessor.preprocessor.PreProcessor method)
model_dispersion_with_wavenumber (glotaran.builtin.megacomplexes.decay.irf.IrfSpectralGaussian attribute)
(glotaran.builtin.megacomplexes.decay.irf.IrfSpectralMultiGaussian attribute)
model_dump() (glotaran.io.preprocessor.pipeline.PreProcessingPipeline method)
(glotaran.io.preprocessor.preprocessor.CorrectBaselineAverage method)
(glotaran.io.preprocessor.preprocessor.CorrectBaselineValue method)
(glotaran.io.preprocessor.preprocessor.PreProcessor method)
model_dump_json() (glotaran.io.preprocessor.pipeline.PreProcessingPipeline method)
(glotaran.io.preprocessor.preprocessor.CorrectBaselineAverage method)
(glotaran.io.preprocessor.preprocessor.CorrectBaselineValue method)
(glotaran.io.preprocessor.preprocessor.PreProcessor method)
model_extra (glotaran.io.preprocessor.pipeline.PreProcessingPipeline property)
(glotaran.io.preprocessor.preprocessor.CorrectBaselineAverage property)
(glotaran.io.preprocessor.preprocessor.CorrectBaselineValue property)
(glotaran.io.preprocessor.preprocessor.PreProcessor property)
model_fields (glotaran.io.preprocessor.pipeline.PreProcessingPipeline attribute)
(glotaran.io.preprocessor.preprocessor.CorrectBaselineAverage attribute)
(glotaran.io.preprocessor.preprocessor.CorrectBaselineValue attribute)
(glotaran.io.preprocessor.preprocessor.PreProcessor attribute)
model_fields_set (glotaran.io.preprocessor.pipeline.PreProcessingPipeline property)
(glotaran.io.preprocessor.preprocessor.CorrectBaselineAverage property)
(glotaran.io.preprocessor.preprocessor.CorrectBaselineValue property)
(glotaran.io.preprocessor.preprocessor.PreProcessor property)
model_interval (glotaran.model.weight.Weight attribute)
model_json_schema() (glotaran.io.preprocessor.pipeline.PreProcessingPipeline class method)
(glotaran.io.preprocessor.preprocessor.CorrectBaselineAverage class method)
(glotaran.io.preprocessor.preprocessor.CorrectBaselineValue class method)
(glotaran.io.preprocessor.preprocessor.PreProcessor class method)
model_parametrized_name() (glotaran.io.preprocessor.pipeline.PreProcessingPipeline class method)
(glotaran.io.preprocessor.preprocessor.CorrectBaselineAverage class method)
(glotaran.io.preprocessor.preprocessor.CorrectBaselineValue class method)
(glotaran.io.preprocessor.preprocessor.PreProcessor class method)
model_post_init() (glotaran.io.preprocessor.pipeline.PreProcessingPipeline method)
(glotaran.io.preprocessor.preprocessor.CorrectBaselineAverage method)
(glotaran.io.preprocessor.preprocessor.CorrectBaselineValue method)
(glotaran.io.preprocessor.preprocessor.PreProcessor method)
model_rebuild() (glotaran.io.preprocessor.pipeline.PreProcessingPipeline class method)
(glotaran.io.preprocessor.preprocessor.CorrectBaselineAverage class method)
(glotaran.io.preprocessor.preprocessor.CorrectBaselineValue class method)
(glotaran.io.preprocessor.preprocessor.PreProcessor class method)
model_spec_deprecations() (in module glotaran.deprecation.modules.builtin_io_yml)
model_validate() (glotaran.io.preprocessor.pipeline.PreProcessingPipeline class method)
(glotaran.io.preprocessor.preprocessor.CorrectBaselineAverage class method)
(glotaran.io.preprocessor.preprocessor.CorrectBaselineValue class method)
(glotaran.io.preprocessor.preprocessor.PreProcessor class method)
model_validate_json() (glotaran.io.preprocessor.pipeline.PreProcessingPipeline class method)
(glotaran.io.preprocessor.preprocessor.CorrectBaselineAverage class method)
(glotaran.io.preprocessor.preprocessor.CorrectBaselineValue class method)
(glotaran.io.preprocessor.preprocessor.PreProcessor class method)
model_validate_strings() (glotaran.io.preprocessor.pipeline.PreProcessingPipeline class method)
(glotaran.io.preprocessor.preprocessor.CorrectBaselineAverage class method)
(glotaran.io.preprocessor.preprocessor.CorrectBaselineValue class method)
(glotaran.io.preprocessor.preprocessor.PreProcessor class method)
models (glotaran.project.project.Project property)
module
glotaran
glotaran.analysis
glotaran.builtin
glotaran.builtin.io
glotaran.builtin.io.ascii
glotaran.builtin.io.ascii.wavelength_time_explicit_file
glotaran.builtin.io.folder
glotaran.builtin.io.folder.folder_plugin
glotaran.builtin.io.netCDF
glotaran.builtin.io.netCDF.netCDF
glotaran.builtin.io.pandas
glotaran.builtin.io.pandas.csv
glotaran.builtin.io.pandas.tsv
glotaran.builtin.io.pandas.xlsx
glotaran.builtin.io.sdt
glotaran.builtin.io.sdt.sdt_file_reader
glotaran.builtin.io.yml
glotaran.builtin.io.yml.utils
glotaran.builtin.io.yml.yml
glotaran.builtin.megacomplexes
glotaran.builtin.megacomplexes.baseline
glotaran.builtin.megacomplexes.baseline.baseline_megacomplex
glotaran.builtin.megacomplexes.clp_guide
glotaran.builtin.megacomplexes.clp_guide.clp_guide_megacomplex
glotaran.builtin.megacomplexes.coherent_artifact
glotaran.builtin.megacomplexes.coherent_artifact.coherent_artifact_megacomplex
glotaran.builtin.megacomplexes.damped_oscillation
glotaran.builtin.megacomplexes.damped_oscillation.damped_oscillation_megacomplex
glotaran.builtin.megacomplexes.decay
glotaran.builtin.megacomplexes.decay.decay_matrix_gaussian_irf
glotaran.builtin.megacomplexes.decay.decay_megacomplex
glotaran.builtin.megacomplexes.decay.decay_parallel_megacomplex
glotaran.builtin.megacomplexes.decay.decay_sequential_megacomplex
glotaran.builtin.megacomplexes.decay.initial_concentration
glotaran.builtin.megacomplexes.decay.irf
glotaran.builtin.megacomplexes.decay.k_matrix
glotaran.builtin.megacomplexes.decay.util
glotaran.builtin.megacomplexes.spectral
glotaran.builtin.megacomplexes.spectral.shape
glotaran.builtin.megacomplexes.spectral.spectral_megacomplex
glotaran.cli
glotaran.cli.commands
glotaran.cli.commands.explore
glotaran.cli.commands.export
glotaran.cli.commands.optimize
glotaran.cli.commands.pluginlist
glotaran.cli.commands.print
glotaran.cli.commands.util
glotaran.cli.commands.validate
glotaran.deprecation
glotaran.deprecation.deprecation_utils
glotaran.deprecation.modules
glotaran.deprecation.modules.builtin_io_yml
glotaran.deprecation.modules.examples
glotaran.deprecation.modules.examples.sequential
glotaran.io
glotaran.io.interface
glotaran.io.prepare_dataset
glotaran.io.preprocessor
glotaran.io.preprocessor.pipeline
glotaran.io.preprocessor.preprocessor
glotaran.model
glotaran.model.clp_constraint
glotaran.model.clp_penalties
glotaran.model.clp_relation
glotaran.model.dataset_group
glotaran.model.dataset_model
glotaran.model.interval_item
glotaran.model.model
glotaran.model.weight
glotaran.optimization
glotaran.optimization.data_provider
glotaran.optimization.estimation_provider
glotaran.optimization.matrix_provider
glotaran.optimization.nnls
glotaran.optimization.optimization_group
glotaran.optimization.optimization_history
glotaran.optimization.optimize
glotaran.optimization.optimizer
glotaran.optimization.variable_projection
glotaran.parameter
glotaran.parameter.parameter
glotaran.parameter.parameter_history
glotaran.parameter.parameters
glotaran.plugin_system
glotaran.plugin_system.base_registry
glotaran.plugin_system.data_io_registration
glotaran.plugin_system.io_plugin_utils
glotaran.plugin_system.megacomplex_registration
glotaran.plugin_system.project_io_registration
glotaran.project
glotaran.project.dataclass_helpers
glotaran.project.generators
glotaran.project.generators.generator
glotaran.project.project
glotaran.project.project_data_registry
glotaran.project.project_model_registry
glotaran.project.project_parameter_registry
glotaran.project.project_registry
glotaran.project.project_result_registry
glotaran.project.result
glotaran.project.scheme
glotaran.simulation
glotaran.simulation.simulation
glotaran.testing
glotaran.testing.plugin_system
glotaran.testing.simulated_data
glotaran.testing.simulated_data.parallel_spectral_decay
glotaran.testing.simulated_data.sequential_spectral_decay
glotaran.testing.simulated_data.shared_decay
glotaran.typing
glotaran.typing.protocols
glotaran.typing.types
glotaran.utils
glotaran.utils.attrs_helper
glotaran.utils.helpers
glotaran.utils.io
glotaran.utils.ipython
glotaran.utils.regex
glotaran.utils.sanitize
glotaran.utils.tee
module_attribute() (in module glotaran.deprecation.deprecation_utils)
monkeypatch_plugin_registry() (in module glotaran.testing.plugin_system)
monkeypatch_plugin_registry_data_io() (in module glotaran.testing.plugin_system)
monkeypatch_plugin_registry_megacomplex() (in module glotaran.testing.plugin_system)
monkeypatch_plugin_registry_project_io() (in module glotaran.testing.plugin_system)
N
name (glotaran.cli.commands.util.ValOrRangeOrList attribute)
nan_or_equal() (in module glotaran.utils.helpers)
NetCDFDataIo (class in glotaran.builtin.io.netCDF.netCDF)
no_default_vals_in_repr() (in module glotaran.utils.attrs_helper)
non_negative (glotaran.parameter.parameter.Parameter attribute)
normalize (glotaran.builtin.megacomplexes.decay.irf.IrfGaussian attribute)
(glotaran.builtin.megacomplexes.decay.irf.IrfMultiGaussian attribute)
(glotaran.builtin.megacomplexes.decay.irf.IrfSpectralGaussian attribute)
(glotaran.builtin.megacomplexes.decay.irf.IrfSpectralMultiGaussian attribute)
normalized() (glotaran.builtin.megacomplexes.decay.initial_concentration.InitialConcentration method)
not_implemented_to_value_error() (in module glotaran.plugin_system.io_plugin_utils)
nr_compartments (glotaran.project.generators.generator.GeneratorArguments attribute)
number (glotaran.utils.regex.RegexPattern attribute)
number_of_clps (glotaran.optimization.matrix_provider.MatrixProvider property)
(glotaran.optimization.matrix_provider.MatrixProviderLinked property)
(glotaran.optimization.matrix_provider.MatrixProviderUnlinked property)
(glotaran.optimization.optimization_group.OptimizationGroup property)
(glotaran.project.result.Result attribute)
number_of_data_points (glotaran.project.result.Result property)
number_of_free_parameters (glotaran.project.result.Result attribute)
number_of_function_evaluations (glotaran.project.result.Result attribute)
number_of_jacobian_evaluations (glotaran.project.result.Result attribute)
number_of_parameters (glotaran.project.result.Result property)
number_of_records (glotaran.parameter.parameter_history.ParameterHistory property)
number_of_residuals (glotaran.project.result.Result attribute)
number_scientific (glotaran.utils.regex.RegexPattern attribute)
O
objective_function() (glotaran.optimization.optimizer.Optimizer method)
OnlyConstraint (class in glotaran.model.clp_constraint)
open() (glotaran.project.project.Project class method)
optimality (glotaran.project.result.Result attribute)
optimization_history (glotaran.project.result.Result attribute)
optimization_method (glotaran.project.scheme.Scheme attribute)
optimization_stdout (glotaran.utils.regex.RegexPattern attribute)
OptimizationGroup (class in glotaran.optimization.optimization_group)
OptimizationHistory (class in glotaran.optimization.optimization_history)
optimize() (glotaran.optimization.optimizer.Optimizer method)
(glotaran.project.project.Project method)
(in module glotaran.optimization.optimize)
optimize_cmd() (in module glotaran.cli.commands.optimize)
optimized_parameters (glotaran.project.result.Result attribute)
Optimizer (class in glotaran.optimization.optimizer)
order (glotaran.builtin.megacomplexes.coherent_artifact.coherent_artifact_megacomplex.CoherentArtifactMegacomplex attribute)
OscillationParameterIssue (class in glotaran.builtin.megacomplexes.damped_oscillation.damped_oscillation_megacomplex)
P
param_dict_to_markdown() (in module glotaran.parameter.parameters)
Parameter (class in glotaran.parameter.parameter)
parameter (glotaran.model.clp_penalties.EqualAreaPenalty attribute)
(glotaran.model.clp_relation.ClpRelation attribute)
parameter() (glotaran.builtin.megacomplexes.decay.irf.IrfGaussian method)
(glotaran.builtin.megacomplexes.decay.irf.IrfMultiGaussian method)
(glotaran.builtin.megacomplexes.decay.irf.IrfSpectralGaussian method)
(glotaran.builtin.megacomplexes.decay.irf.IrfSpectralMultiGaussian method)
parameter_format (glotaran.io.interface.SavingOptions attribute)
parameter_history (glotaran.project.result.Result attribute)
parameter_labels (glotaran.parameter.parameter_history.ParameterHistory property)
ParameterHistory (class in glotaran.parameter.parameter_history)
Parameters (class in glotaran.parameter.parameters)
parameters (glotaran.builtin.megacomplexes.decay.initial_concentration.InitialConcentration attribute)
(glotaran.model.dataset_group.DatasetGroup attribute)
(glotaran.parameter.parameter_history.ParameterHistory property)
(glotaran.project.project.Project property)
(glotaran.project.scheme.Scheme attribute)
parse_file() (glotaran.io.preprocessor.pipeline.PreProcessingPipeline class method)
(glotaran.io.preprocessor.preprocessor.CorrectBaselineAverage class method)
(glotaran.io.preprocessor.preprocessor.CorrectBaselineValue class method)
(glotaran.io.preprocessor.preprocessor.PreProcessor class method)
parse_obj() (glotaran.io.preprocessor.pipeline.PreProcessingPipeline class method)
(glotaran.io.preprocessor.preprocessor.CorrectBaselineAverage class method)
(glotaran.io.preprocessor.preprocessor.CorrectBaselineValue class method)
(glotaran.io.preprocessor.preprocessor.PreProcessor class method)
parse_raw() (glotaran.io.preprocessor.pipeline.PreProcessingPipeline class method)
(glotaran.io.preprocessor.preprocessor.CorrectBaselineAverage class method)
(glotaran.io.preprocessor.preprocessor.CorrectBaselineValue class method)
(glotaran.io.preprocessor.preprocessor.PreProcessor class method)
parse_version() (in module glotaran.deprecation.deprecation_utils)
partition() (glotaran.utils.ipython.MarkdownStr method)
plugin_list_cmd() (in module glotaran.cli.commands.pluginlist)
pop() (glotaran.project.generators.generator.GeneratorArguments method)
(glotaran.utils.io.DatasetMapping method)
popitem() (glotaran.project.generators.generator.GeneratorArguments method)
(glotaran.utils.io.DatasetMapping method)
prepare_time_trace_dataset() (in module glotaran.io.prepare_dataset)
PreProcessingPipeline (class in glotaran.io.preprocessor.pipeline)
PreProcessor (class in glotaran.io.preprocessor.preprocessor)
PreProcessor.Config (class in glotaran.io.preprocessor.preprocessor)
pretty_format_numerical() (in module glotaran.utils.sanitize)
previous_result_paths() (glotaran.project.project_result_registry.ProjectResultRegistry method)
print_cmd() (in module glotaran.cli.commands.print)
Project (class in glotaran.project.project)
project_io_list_supporting_plugins() (in module glotaran.cli.commands.util)
project_io_plugin_table() (in module glotaran.plugin_system.project_io_registration)
ProjectDataRegistry (class in glotaran.project.project_data_registry)
ProjectIoInterface (class in glotaran.io.interface)
ProjectModelRegistry (class in glotaran.project.project_model_registry)
ProjectParameterRegistry (class in glotaran.project.project_parameter_registry)
ProjectRegistry (class in glotaran.project.project_registry)
ProjectResultRegistry (class in glotaran.project.project_result_registry)
protect_from_overwrite() (in module glotaran.plugin_system.io_plugin_utils)
R
raise_deprecation_error() (in module glotaran.deprecation.deprecation_utils)
rates (glotaran.builtin.megacomplexes.damped_oscillation.damped_oscillation_megacomplex.DampedOscillationMegacomplex attribute)
(glotaran.builtin.megacomplexes.decay.decay_parallel_megacomplex.DecayParallelMegacomplex attribute)
(glotaran.builtin.megacomplexes.decay.decay_sequential_megacomplex.DecaySequentialMegacomplex attribute)
rates() (glotaran.builtin.megacomplexes.decay.k_matrix.KMatrix method)
read() (glotaran.builtin.io.ascii.wavelength_time_explicit_file.ExplicitFile method)
(glotaran.builtin.io.ascii.wavelength_time_explicit_file.TimeExplicitFile method)
(glotaran.builtin.io.ascii.wavelength_time_explicit_file.WavelengthExplicitFile method)
(glotaran.utils.tee.TeeContext method)
recreate() (glotaran.project.result.Result method)
reduce_matrix() (glotaran.optimization.matrix_provider.MatrixProvider method)
(glotaran.optimization.matrix_provider.MatrixProviderLinked method)
(glotaran.optimization.matrix_provider.MatrixProviderUnlinked method)
reduced() (glotaran.builtin.megacomplexes.decay.k_matrix.KMatrix method)
reduced_chi_square (glotaran.project.result.Result attribute)
RegexPattern (class in glotaran.utils.regex)
register_data_io() (in module glotaran.plugin_system.data_io_registration)
register_megacomplex() (in module glotaran.plugin_system.megacomplex_registration)
register_project_io() (in module glotaran.plugin_system.project_io_registration)
registered_plugins() (in module glotaran.plugin_system.base_registry)
relative_posix_path() (in module glotaran.utils.io)
removeprefix() (glotaran.utils.ipython.MarkdownStr method)
removesuffix() (glotaran.utils.ipython.MarkdownStr method)
replace() (glotaran.utils.ipython.MarkdownStr method)
report (glotaran.io.interface.SavingOptions attribute)
residual_function (glotaran.model.dataset_group.DatasetGroup attribute)
(glotaran.model.dataset_group.DatasetGroupModel attribute)
residual_nnls() (in module glotaran.optimization.nnls)
residual_variable_projection() (in module glotaran.optimization.variable_projection)
Result (class in glotaran.project.result)
result_path (glotaran.project.scheme.Scheme attribute)
result_pattern (glotaran.project.project_result_registry.ProjectResultRegistry attribute)
results (glotaran.project.project.Project property)
retrieve_clps() (glotaran.optimization.estimation_provider.EstimationProvider method)
(glotaran.optimization.estimation_provider.EstimationProviderLinked method)
(glotaran.optimization.estimation_provider.EstimationProviderUnlinked method)
retrieve_decay_associated_data() (in module glotaran.builtin.megacomplexes.decay.util)
retrieve_initial_concentration() (in module glotaran.builtin.megacomplexes.decay.util)
retrieve_irf() (in module glotaran.builtin.megacomplexes.decay.util)
retrieve_species_associated_data() (in module glotaran.builtin.megacomplexes.decay.util)
rfind() (glotaran.utils.ipython.MarkdownStr method)
rindex() (glotaran.utils.ipython.MarkdownStr method)
rjust() (glotaran.utils.ipython.MarkdownStr method)
root_mean_square_error (glotaran.project.result.Result attribute)
rpartition() (glotaran.utils.ipython.MarkdownStr method)
rsplit() (glotaran.utils.ipython.MarkdownStr method)
rstrip() (glotaran.utils.ipython.MarkdownStr method)
S
safe_dataframe_fillna() (in module glotaran.utils.io)
safe_dataframe_replace() (in module glotaran.utils.io)
sanitize_dict_keys() (in module glotaran.utils.sanitize)
sanitize_dict_values() (in module glotaran.utils.sanitize)
sanitize_list_with_broken_tuples() (in module glotaran.utils.sanitize)
sanitize_parameter_list() (in module glotaran.utils.sanitize)
sanitize_yaml() (in module glotaran.utils.sanitize)
sanity_scientific_notation_conversion() (in module glotaran.utils.sanitize)
save() (glotaran.project.project_result_registry.ProjectResultRegistry method)
(glotaran.project.result.Result method)
save_dataset() (glotaran.builtin.io.ascii.wavelength_time_explicit_file.AsciiDataIo method)
(glotaran.builtin.io.netCDF.netCDF.NetCDFDataIo method)
(glotaran.builtin.io.sdt.sdt_file_reader.SdtDataIo method)
(glotaran.io.interface.DataIoInterface method)
(in module glotaran.plugin_system.data_io_registration)
save_model() (glotaran.builtin.io.folder.folder_plugin.FolderProjectIo method)
(glotaran.builtin.io.folder.folder_plugin.LegacyProjectIo method)
(glotaran.builtin.io.pandas.csv.CsvProjectIo method)
(glotaran.builtin.io.pandas.tsv.TsvProjectIo method)
(glotaran.builtin.io.pandas.xlsx.ExcelProjectIo method)
(glotaran.builtin.io.yml.yml.YmlProjectIo method)
(glotaran.io.interface.ProjectIoInterface method)
(in module glotaran.plugin_system.project_io_registration)
save_parameters() (glotaran.builtin.io.folder.folder_plugin.FolderProjectIo method)
(glotaran.builtin.io.folder.folder_plugin.LegacyProjectIo method)
(glotaran.builtin.io.pandas.csv.CsvProjectIo method)
(glotaran.builtin.io.pandas.tsv.TsvProjectIo method)
(glotaran.builtin.io.pandas.xlsx.ExcelProjectIo method)
(glotaran.builtin.io.yml.yml.YmlProjectIo method)
(glotaran.io.interface.ProjectIoInterface method)
(in module glotaran.plugin_system.project_io_registration)
save_result() (glotaran.builtin.io.folder.folder_plugin.FolderProjectIo method)
(glotaran.builtin.io.folder.folder_plugin.LegacyProjectIo method)
(glotaran.builtin.io.pandas.csv.CsvProjectIo method)
(glotaran.builtin.io.pandas.tsv.TsvProjectIo method)
(glotaran.builtin.io.pandas.xlsx.ExcelProjectIo method)
(glotaran.builtin.io.yml.yml.YmlProjectIo method)
(glotaran.io.interface.ProjectIoInterface method)
(in module glotaran.plugin_system.project_io_registration)
save_scheme() (glotaran.builtin.io.folder.folder_plugin.FolderProjectIo method)
(glotaran.builtin.io.folder.folder_plugin.LegacyProjectIo method)
(glotaran.builtin.io.pandas.csv.CsvProjectIo method)
(glotaran.builtin.io.pandas.tsv.TsvProjectIo method)
(glotaran.builtin.io.pandas.xlsx.ExcelProjectIo method)
(glotaran.builtin.io.yml.yml.YmlProjectIo method)
(glotaran.io.interface.ProjectIoInterface method)
(in module glotaran.plugin_system.project_io_registration)
SavingOptions (class in glotaran.io.interface)
scale (glotaran.builtin.megacomplexes.decay.decay_megacomplex.DecayDatasetModel attribute)
(glotaran.builtin.megacomplexes.decay.decay_parallel_megacomplex.DecayDatasetModel attribute)
(glotaran.builtin.megacomplexes.decay.irf.IrfGaussian attribute)
(glotaran.builtin.megacomplexes.decay.irf.IrfMultiGaussian attribute)
(glotaran.builtin.megacomplexes.decay.irf.IrfSpectralGaussian attribute)
(glotaran.builtin.megacomplexes.decay.irf.IrfSpectralMultiGaussian attribute)
(glotaran.builtin.megacomplexes.spectral.spectral_megacomplex.SpectralDatasetModel attribute)
(glotaran.model.dataset_model.DatasetModel attribute)
schema() (glotaran.io.preprocessor.pipeline.PreProcessingPipeline class method)
(glotaran.io.preprocessor.preprocessor.CorrectBaselineAverage class method)
(glotaran.io.preprocessor.preprocessor.CorrectBaselineValue class method)
(glotaran.io.preprocessor.preprocessor.PreProcessor class method)
schema_json() (glotaran.io.preprocessor.pipeline.PreProcessingPipeline class method)
(glotaran.io.preprocessor.preprocessor.CorrectBaselineAverage class method)
(glotaran.io.preprocessor.preprocessor.CorrectBaselineValue class method)
(glotaran.io.preprocessor.preprocessor.PreProcessor class method)
Scheme (class in glotaran.project.scheme)
scheme (glotaran.project.result.Result attribute)
SCHEME_FILE
glotaran-optimize command line option
glotaran-print command line option
glotaran-validate command line option
SdtDataIo (class in glotaran.builtin.io.sdt.sdt_file_reader)
select (glotaran.io.preprocessor.preprocessor.CorrectBaselineAverage attribute)
select_data() (in module glotaran.cli.commands.util)
select_name() (in module glotaran.cli.commands.util)
serialize_options() (in module glotaran.parameter.parameter)
set_data_plugin() (in module glotaran.plugin_system.data_io_registration)
set_explicit_axis() (glotaran.builtin.io.ascii.wavelength_time_explicit_file.ExplicitFile method)
(glotaran.builtin.io.ascii.wavelength_time_explicit_file.TimeExplicitFile method)
(glotaran.builtin.io.ascii.wavelength_time_explicit_file.WavelengthExplicitFile method)
set_from_history() (glotaran.parameter.parameters.Parameters method)
set_from_label_and_value_arrays() (glotaran.parameter.parameters.Parameters method)
set_megacomplex_plugin() (in module glotaran.plugin_system.megacomplex_registration)
set_parameters() (glotaran.model.dataset_group.DatasetGroup method)
set_plugin() (in module glotaran.plugin_system.base_registry)
set_project_plugin() (in module glotaran.plugin_system.project_io_registration)
set_transformed_expression() (in module glotaran.parameter.parameter)
set_value_from_optimization() (glotaran.parameter.parameter.Parameter method)
setdefault() (glotaran.project.generators.generator.GeneratorArguments method)
(glotaran.utils.io.DatasetMapping method)
shape (glotaran.builtin.megacomplexes.spectral.spectral_megacomplex.SpectralMegacomplex attribute)
shell_complete() (glotaran.cli.commands.util.ValOrRangeOrList method)
shift (glotaran.builtin.megacomplexes.decay.irf.IrfGaussian attribute)
(glotaran.builtin.megacomplexes.decay.irf.IrfMultiGaussian attribute)
(glotaran.builtin.megacomplexes.decay.irf.IrfSpectralGaussian attribute)
(glotaran.builtin.megacomplexes.decay.irf.IrfSpectralMultiGaussian attribute)
show_data_io_method_help() (in module glotaran.plugin_system.data_io_registration)
show_method_help() (in module glotaran.plugin_system.base_registry)
show_model_definition() (glotaran.project.project.Project method)
show_parameters_definition() (glotaran.project.project.Project method)
show_project_io_method_help() (in module glotaran.plugin_system.project_io_registration)
signature_analysis() (in module glotaran.cli.commands.util)
simulate() (in module glotaran.simulation.simulation)
simulate_from_clp() (in module glotaran.simulation.simulation)
simulate_full_model() (in module glotaran.simulation.simulation)
skewness (glotaran.builtin.megacomplexes.spectral.shape.SpectralShapeSkewedGaussian attribute)
source (glotaran.model.clp_penalties.EqualAreaPenalty attribute)
(glotaran.model.clp_relation.ClpRelation attribute)
source_intervals (glotaran.model.clp_penalties.EqualAreaPenalty attribute)
source_path (glotaran.model.model.Model attribute)
(glotaran.project.result.Result attribute)
(glotaran.project.scheme.Scheme attribute)
(glotaran.typing.protocols.FileLoadableProtocol attribute)
(glotaran.utils.io.DatasetMapping property)
spectral_axis_inverted (glotaran.builtin.megacomplexes.spectral.spectral_megacomplex.SpectralDatasetModel attribute)
spectral_axis_scale (glotaran.builtin.megacomplexes.spectral.spectral_megacomplex.SpectralDatasetModel attribute)
SpectralDatasetModel (class in glotaran.builtin.megacomplexes.spectral.spectral_megacomplex)
SpectralMegacomplex (class in glotaran.builtin.megacomplexes.spectral.spectral_megacomplex)
SpectralShape (class in glotaran.builtin.megacomplexes.spectral.shape)
SpectralShapeGaussian (class in glotaran.builtin.megacomplexes.spectral.shape)
SpectralShapeOne (class in glotaran.builtin.megacomplexes.spectral.shape)
SpectralShapeSkewedGaussian (class in glotaran.builtin.megacomplexes.spectral.shape)
SpectralShapeZero (class in glotaran.builtin.megacomplexes.spectral.shape)
split() (glotaran.utils.ipython.MarkdownStr method)
split_envvar_value() (glotaran.cli.commands.util.ValOrRangeOrList method)
splitlines() (glotaran.utils.ipython.MarkdownStr method)
standard_error (glotaran.parameter.parameter.Parameter attribute)
startswith() (glotaran.utils.ipython.MarkdownStr method)
string_to_tuple() (in module glotaran.utils.sanitize)
strip() (glotaran.utils.ipython.MarkdownStr method)
success (glotaran.project.result.Result attribute)
supported_file_extensions() (in module glotaran.plugin_system.base_registry)
supported_file_extensions_data_io() (in module glotaran.plugin_system.data_io_registration)
supported_file_extensions_project_io() (in module glotaran.plugin_system.project_io_registration)
swapcase() (glotaran.utils.ipython.MarkdownStr method)
T
target (glotaran.builtin.megacomplexes.clp_guide.clp_guide_megacomplex.ClpGuideMegacomplex attribute)
(glotaran.model.clp_constraint.ClpConstraint attribute)
(glotaran.model.clp_constraint.OnlyConstraint attribute)
(glotaran.model.clp_constraint.ZeroConstraint attribute)
(glotaran.model.clp_penalties.EqualAreaPenalty attribute)
(glotaran.model.clp_relation.ClpRelation attribute)
target_intervals (glotaran.model.clp_penalties.EqualAreaPenalty attribute)
TeeContext (class in glotaran.utils.tee)
termination_reason (glotaran.project.result.Result attribute)
time_explicit (glotaran.builtin.io.ascii.wavelength_time_explicit_file.DataFileType attribute)
TimeExplicitFile (class in glotaran.builtin.io.ascii.wavelength_time_explicit_file)
times() (glotaran.builtin.io.ascii.wavelength_time_explicit_file.WavelengthExplicitFile method)
title() (glotaran.utils.ipython.MarkdownStr method)
to_csv() (glotaran.optimization.optimization_history.OptimizationHistory method)
(glotaran.parameter.parameter_history.ParameterHistory method)
to_dataframe() (glotaran.parameter.parameter_history.ParameterHistory method)
(glotaran.parameter.parameters.Parameters method)
to_info_dict() (glotaran.cli.commands.util.ValOrRangeOrList method)
to_parameter_dict_list() (glotaran.parameter.parameters.Parameters method)
to_parameter_dict_or_list() (glotaran.parameter.parameters.Parameters method)
to_string() (glotaran.builtin.megacomplexes.damped_oscillation.damped_oscillation_megacomplex.OscillationParameterIssue method)
(glotaran.model.dataset_model.ExclusiveMegacomplexIssue method)
(glotaran.model.dataset_model.UniqueMegacomplexIssue method)
transformed_expression (glotaran.parameter.parameter.Parameter attribute)
translate() (glotaran.utils.ipython.MarkdownStr method)
TsvProjectIo (class in glotaran.builtin.io.pandas.tsv)
tuple_number (glotaran.utils.regex.RegexPattern attribute)
tuple_word (glotaran.utils.regex.RegexPattern attribute)
type (glotaran.builtin.megacomplexes.baseline.baseline_megacomplex.BaselineMegacomplex attribute)
(glotaran.builtin.megacomplexes.clp_guide.clp_guide_megacomplex.ClpGuideMegacomplex attribute)
(glotaran.builtin.megacomplexes.coherent_artifact.coherent_artifact_megacomplex.CoherentArtifactMegacomplex attribute)
(glotaran.builtin.megacomplexes.damped_oscillation.damped_oscillation_megacomplex.DampedOscillationMegacomplex attribute)
(glotaran.builtin.megacomplexes.decay.decay_megacomplex.DecayMegacomplex attribute)
(glotaran.builtin.megacomplexes.decay.decay_parallel_megacomplex.DecayParallelMegacomplex attribute)
(glotaran.builtin.megacomplexes.decay.decay_sequential_megacomplex.DecaySequentialMegacomplex attribute)
(glotaran.builtin.megacomplexes.decay.irf.Irf attribute)
(glotaran.builtin.megacomplexes.decay.irf.IrfGaussian attribute)
(glotaran.builtin.megacomplexes.decay.irf.IrfMultiGaussian attribute)
(glotaran.builtin.megacomplexes.decay.irf.IrfSpectralGaussian attribute)
(glotaran.builtin.megacomplexes.decay.irf.IrfSpectralMultiGaussian attribute)
(glotaran.builtin.megacomplexes.spectral.shape.SpectralShape attribute)
(glotaran.builtin.megacomplexes.spectral.shape.SpectralShapeGaussian attribute)
(glotaran.builtin.megacomplexes.spectral.shape.SpectralShapeOne attribute)
(glotaran.builtin.megacomplexes.spectral.shape.SpectralShapeSkewedGaussian attribute)
(glotaran.builtin.megacomplexes.spectral.shape.SpectralShapeZero attribute)
(glotaran.builtin.megacomplexes.spectral.spectral_megacomplex.SpectralMegacomplex attribute)
(glotaran.model.clp_constraint.ClpConstraint attribute)
(glotaran.model.clp_constraint.OnlyConstraint attribute)
(glotaran.model.clp_constraint.ZeroConstraint attribute)
(glotaran.model.clp_penalties.ClpPenalty attribute)
(glotaran.model.clp_penalties.EqualAreaPenalty attribute)
U
UniqueMegacomplexIssue (class in glotaran.model.dataset_model)
update() (glotaran.project.generators.generator.GeneratorArguments method)
(glotaran.utils.io.DatasetMapping method)
update_forward_refs() (glotaran.io.preprocessor.pipeline.PreProcessingPipeline class method)
(glotaran.io.preprocessor.preprocessor.CorrectBaselineAverage class method)
(glotaran.io.preprocessor.preprocessor.CorrectBaselineValue class method)
(glotaran.io.preprocessor.preprocessor.PreProcessor class method)
update_parameter_expression() (glotaran.parameter.parameters.Parameters method)
upper() (glotaran.utils.ipython.MarkdownStr method)
V
valid() (glotaran.model.model.Model method)
(glotaran.project.scheme.Scheme method)
valid_label() (in module glotaran.parameter.parameter)
validate() (glotaran.io.preprocessor.pipeline.PreProcessingPipeline class method)
(glotaran.io.preprocessor.preprocessor.CorrectBaselineAverage class method)
(glotaran.io.preprocessor.preprocessor.CorrectBaselineValue class method)
(glotaran.io.preprocessor.preprocessor.PreProcessor class method)
(glotaran.model.model.Model method)
(glotaran.project.project.Project method)
(glotaran.project.scheme.Scheme method)
validate_cmd() (in module glotaran.cli.commands.validate)
validate_global_megacomplexes() (in module glotaran.model.dataset_model)
validate_megacomplexes() (in module glotaran.model.dataset_model)
validate_oscillation_parameter() (in module glotaran.builtin.megacomplexes.damped_oscillation.damped_oscillation_megacomplex)
ValOrRangeOrList (class in glotaran.cli.commands.util)
value (glotaran.io.preprocessor.preprocessor.CorrectBaselineValue attribute)
(glotaran.model.weight.Weight attribute)
(glotaran.parameter.parameter.Parameter attribute)
values() (glotaran.project.generators.generator.GeneratorArguments method)
(glotaran.project.project_registry.ItemMapping method)
(glotaran.utils.io.DatasetMapping method)
vary (glotaran.parameter.parameter.Parameter attribute)
verify() (glotaran.project.result.Result method)
version (glotaran.project.project.Project attribute)
W
warn_deprecated() (in module glotaran.deprecation.deprecation_utils)
wavelength_explicit (glotaran.builtin.io.ascii.wavelength_time_explicit_file.DataFileType attribute)
WavelengthExplicitFile (class in glotaran.builtin.io.ascii.wavelength_time_explicit_file)
wavelengths() (glotaran.builtin.io.ascii.wavelength_time_explicit_file.WavelengthExplicitFile method)
Weight (class in glotaran.model.weight)
weight (glotaran.model.clp_penalties.EqualAreaPenalty attribute)
weights (glotaran.model.model.Model attribute)
width (glotaran.builtin.megacomplexes.coherent_artifact.coherent_artifact_megacomplex.CoherentArtifactMegacomplex attribute)
(glotaran.builtin.megacomplexes.decay.irf.IrfGaussian attribute)
(glotaran.builtin.megacomplexes.decay.irf.IrfMultiGaussian attribute)
(glotaran.builtin.megacomplexes.decay.irf.IrfSpectralGaussian attribute)
(glotaran.builtin.megacomplexes.decay.irf.IrfSpectralMultiGaussian attribute)
(glotaran.builtin.megacomplexes.spectral.shape.SpectralShapeGaussian attribute)
(glotaran.builtin.megacomplexes.spectral.shape.SpectralShapeSkewedGaussian attribute)
width_dispersion_coefficients (glotaran.builtin.megacomplexes.decay.irf.IrfSpectralGaussian attribute)
(glotaran.builtin.megacomplexes.decay.irf.IrfSpectralMultiGaussian attribute)
word (glotaran.utils.regex.RegexPattern attribute)
write() (glotaran.builtin.io.ascii.wavelength_time_explicit_file.ExplicitFile method)
(glotaran.builtin.io.ascii.wavelength_time_explicit_file.TimeExplicitFile method)
(glotaran.builtin.io.ascii.wavelength_time_explicit_file.WavelengthExplicitFile method)
(glotaran.utils.tee.TeeContext method)
write_data() (in module glotaran.cli.commands.util)
write_dict() (in module glotaran.builtin.io.yml.utils)
X
xtol (glotaran.project.scheme.Scheme attribute)
Y
YmlProjectIo (class in glotaran.builtin.io.yml.yml)
Z
ZeroConstraint (class in glotaran.model.clp_constraint)
zfill() (glotaran.utils.ipython.MarkdownStr method)
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