A B C D E F G H I J K L M N O P Q R S T U V W Z 

A

about() - Method in class magpie.analytics.BaseStatistics
 
about() - Method in class magpie.analytics.ClustererStatistics
 
about() - Method in class magpie.attributes.selectors.BaseAttributeSelector
 
about() - Method in class magpie.cluster.BaseClusterer
 
about() - Method in class magpie.csp.CSPEngine
 
about() - Method in class magpie.csp.CSPPerformanceStats
 
about() - Method in class magpie.data.Dataset
 
about() - Method in class magpie.data.utilities.normalizers.BaseDatasetNormalizer
 
about() - Method in class magpie.data.utilities.splitters.BaseDatasetSplitter
 
about() - Method in class magpie.models.BaseModel
 
about() - Method in class magpie.optimization.analytics.OptimizationStatistics
 
about() - Method in class magpie.optimization.BaseOptimizer
 
about() - Method in interface magpie.utility.interfaces.Printable
Prints a simple status message about this object
about() - Method in class magpie.utility.tools.PhaseDiagramExclusionValidator
 
AbstractClassifier - Interface in magpie.models.classification
Interface that defines what operations a Classifier must fulfill
AbstractNonlinearRegression - Class in magpie.models.regression
Abstract class for models that fit terms using non-linear regression.
AbstractNonlinearRegression() - Constructor for class magpie.models.regression.AbstractNonlinearRegression
 
AbstractParsedNonlinearRegression - Class in magpie.models.regression
Superclass of AbstractNonlinearRegression-based models which parse the equation of interest from text input.
AbstractParsedNonlinearRegression() - Constructor for class magpie.models.regression.AbstractParsedNonlinearRegression
 
AbstractRegressionModel - Interface in magpie.models.regression
Interface for all regression models.
Accuracy - Variable in class magpie.analytics.ClassificationStatistics
Accuracy
ActiveLearningOptimizer - Class in magpie.optimization.algorithms
An active learning scheme that using a machine-learning model to find optimal candidates.
ActiveLearningOptimizer() - Constructor for class magpie.optimization.algorithms.ActiveLearningOptimizer
 
AdaptiveScalarizingEntryRanker - Class in magpie.optimization.rankers
Transforms the values of multiple objectives to a single variable using automatically-determined weights.
AdaptiveScalarizingEntryRanker() - Constructor for class magpie.optimization.rankers.AdaptiveScalarizingEntryRanker
 
addAlloyElement(int, double, double, double) - Method in class magpie.data.utilities.generators.CompositionRangeEntryGenerator
Add alloying element
addAlloyElement(String, double, double, double) - Method in class magpie.data.utilities.generators.CompositionRangeEntryGenerator
Add alloying element
addAlloyingElement(String) - Method in class magpie.data.utilities.generators.AlloyingCompositionEntryGenerator
Add element to list of potential alloying elements
addAlloyingElements(Collection<String>) - Method in class magpie.data.utilities.generators.AlloyingCompositionEntryGenerator
Add elements to list of potential alloying elements
addAttribueExpander(BaseAttributeExpander) - Method in class magpie.data.Dataset
Add a new tool to expand the number of attributes for this dataset.
addAttribueGenerator(BaseAttributeGenerator) - Method in class magpie.data.Dataset
Add a new tool to generate additional attributes
addAttribute(double) - Method in class magpie.data.BaseEntry
Adds attribute value to the end of the list of current attributes
addAttribute(String, double[]) - Method in class magpie.data.Dataset
Add in a new attribute.
addAttributes(Dataset) - Method in class magpie.attributes.generators.BaseAttributeGenerator
Generate new attributes for a dataset.
addAttributes(Dataset) - Method in class magpie.attributes.generators.composition.ElementalPropertyAttributeGenerator
 
addAttributes(Dataset) - Method in class magpie.attributes.generators.composition.ElementFractionAttributeGenerator
 
addAttributes(Dataset) - Method in class magpie.attributes.generators.composition.IonicityAttributeGenerator
 
addAttributes(Dataset) - Method in class magpie.attributes.generators.composition.MeredigAttributeGenerator
 
addAttributes(Dataset) - Method in class magpie.attributes.generators.composition.StoichiometricAttributeGenerator
 
addAttributes(Dataset) - Method in class magpie.attributes.generators.composition.ValenceShellAttributeGenerator
 
addAttributes(Dataset) - Method in class magpie.attributes.generators.element.ElementalPropertyAttributeGenerator
 
addAttributes(Dataset) - Method in class magpie.attributes.generators.LookupTableAttributeGenerator
 
addAttributes(Dataset) - Method in class magpie.attributes.generators.ModelPredictionAttributeGenerator
 
addAttributes(Dataset) - Method in class magpie.attributes.generators.PropertyAsAttributeGenerator
 
addAttributes(double[]) - Method in class magpie.data.BaseEntry
Adds several attributes to the end of the attribute list.
addAttributes(List<String>) - Method in class magpie.data.Dataset
Add new attributes.
addCoefficient(String) - Method in class magpie.models.regression.AbstractNonlinearRegression
Adds a new fitting parameter to function (if not already defined).
addCoefficient(String, Double) - Method in class magpie.models.regression.AbstractNonlinearRegression
Adds a new fitting parameter to function (if not already defined)
addComposition(CompositionEntry) - Method in class magpie.data.utilities.filters.CompositionSetDistanceFilter
Add a new composition to the dataset.
addComposition(CompositionEntry) - Method in class magpie.data.utilities.modifiers.CompositionSetDistanceModifier
Add a new composition to the dataset.
addComposition(CompositionEntry) - Method in class magpie.optimization.rankers.CompositionDistanceRanker
Add a new composition to the dataset.
addCompositionBin(double[], List<String>) - Method in class magpie.csp.diagramdata.PhaseDiagramStatistics
Adds all permutations (i.e.
addCompositions(Collection<CompositionEntry>) - Method in class magpie.data.utilities.filters.CompositionSetDistanceFilter
Add a list of compositions to the set
addCompositions(Collection<CompositionEntry>) - Method in class magpie.data.utilities.modifiers.CompositionSetDistanceModifier
Add a list of compositions to the set
addCompositions(Collection<CompositionEntry>) - Method in class magpie.optimization.rankers.CompositionDistanceRanker
Add a list of compositions to the set
addElementalProperty(String) - Method in class magpie.data.materials.CompositionDataset
Define a new elemental property to use when generating attributes.
addElementalProperty(String) - Method in class magpie.data.materials.ElementDataset
Add an elemental property to the list of those used when computing attributes.
addElementalPropertySet(String) - Method in class magpie.data.materials.ElementDataset
Add a set of elemental properties to the list of those used when computing attributes.
addElementGroup(String) - Method in class magpie.data.utilities.splitters.MultipleElementGroupsSplitter
Add a list of elements to be defined as the same group.
addElementGroup(Collection<String>) - Method in class magpie.data.utilities.splitters.MultipleElementGroupsSplitter
Add a list of elements to be treated as a single group.
addEntries(Collection<? extends BaseEntry>) - Method in class magpie.data.Dataset
Add many entries to a the data set
addEntries(Dataset, boolean) - Method in class magpie.data.Dataset
Add entries from another dataset.
addEntries(Dataset, boolean) - Method in class magpie.data.MultiPropertyDataset
Add entries from another dataset.
addEntries(Collection<? extends BaseEntry>) - Method in class magpie.data.MultiPropertyDataset
 
addEntriesToDataset(Dataset) - Method in class magpie.data.utilities.generators.BaseEntryGenerator
Generate entries, and add them new a dataset.
addEntriesToDataset(Dataset) - Method in class magpie.data.utilities.generators.IonicCompoundGenerator
 
addEntry(BaseEntry) - Method in class magpie.data.Dataset
Add an entry.
addEntry(String) - Method in class magpie.data.Dataset
A new entry by parsing an input string.
addEntry(String) - Method in class magpie.data.materials.CompositionDataset
 
addEntry(String) - Method in class magpie.data.materials.ElementDataset
 
addEntry(String) - Method in class magpie.data.materials.PrototypeDataset
 
addEntry(BaseEntry) - Method in class magpie.data.MultiPropertyDataset
 
addFilter(BaseDatasetFilter) - Method in class magpie.data.utilities.filters.MultiFilter
Append filter to the current list of filters in use
addModel(String, ModelPackage) - Method in class magpie.user.server.thrift.MagpieServerHandler
Add a new model to the server handler
addNewFunction(String) - Method in class magpie.attributes.expanders.FunctionExpander
Add a new function to be used for expansion
addObjectiveFunction(String, BaseEntryRanker) - Method in class magpie.optimization.rankers.AdaptiveScalarizingEntryRanker
Define a new objective function.
addObjectiveFunction(String, BaseEntryRanker) - Method in class magpie.optimization.rankers.RankAggregationRanker
Define a new objective function.
addPhase(CompositionEntry, double) - Method in class magpie.data.materials.util.GCLPCalculator
Add new phase to the list of phases to consider.
addPhases(CompositionDataset) - Method in class magpie.data.materials.util.GCLPCalculator
Set many phase energies.
addPNorm(int) - Method in class magpie.attributes.generators.composition.StoichiometricAttributeGenerator
Add a p norm to be computed
addPNorms(Collection<Integer>) - Method in class magpie.attributes.generators.composition.StoichiometricAttributeGenerator
Add several norms to be computed
addProperty(String) - Method in class magpie.attributes.generators.PropertyAsAttributeGenerator
Add property to list of properties used as attributes.
addProperty(String) - Method in class magpie.data.MultiPropertyDataset
Add a new property to dataset.
addProperty(String, String[]) - Method in class magpie.data.MultiPropertyDataset
Add a new property to dataset.
addProperty() - Method in class magpie.data.MultiPropertyEntry
Add a new property to this entry.
addProperty(double) - Method in class magpie.data.MultiPropertyEntry
Add a new property and define measured property.
addProperty(double, double) - Method in class magpie.data.MultiPropertyEntry
Add a new property to this entry, set measured and predicted values
AddPropertyModifier - Class in magpie.data.utilities.modifiers
Adds properties to a MultiPropertyDataset.
AddPropertyModifier() - Constructor for class magpie.data.utilities.modifiers.AddPropertyModifier
 
addResult(String, List<Pair<String, Double>>) - Method in class magpie.csp.CSPPerformanceStats
Add results of a prediction to performance dataset.
addSite(double, boolean, List<Integer>) - Method in class magpie.data.materials.util.PrototypeSiteInformation
Add a new crystallographic site.
addToEntries(Entry) - Method in class magpie.user.server.thrift.MagpieServer.evaluateProperties_args
 
addToObjs(String) - Method in class magpie.user.server.thrift.MagpieServer.searchMultiObjective_args
 
addToProps(String) - Method in class magpie.user.server.thrift.MagpieServer.evaluateProperties_args
 
addToSuccess(Entry) - Method in class magpie.user.server.thrift.MagpieServer.evaluateProperties_result
 
addToSuccess(Entry) - Method in class magpie.user.server.thrift.MagpieServer.searchMultiObjective_result
 
addToSuccess(Entry) - Method in class magpie.user.server.thrift.MagpieServer.searchSingleObjective_result
 
addVariable(String) - Method in class magpie.models.regression.AbstractNonlinearRegression
Define a variable to be used in the user function (if not already defined)
addVariable(String, Object) - Method in class magpie.user.Workspace
Adds a variable to the workspace.
AllMetalsFilter - Class in magpie.data.utilities.filters
Filter entries based on whether all constituents are metals.
AllMetalsFilter() - Constructor for class magpie.data.utilities.filters.AllMetalsFilter
 
AllMetalsSplitter - Class in magpie.data.utilities.splitters
Splits CompositionDataset based on whether entries contain all metals.
AllMetalsSplitter() - Constructor for class magpie.data.utilities.splitters.AllMetalsSplitter
 
allocateResults(int) - Method in class magpie.optimization.analytics.OptimizationStatistics
Before evaluation, allocate result arrays
AllowedMixing - Variable in class magpie.data.utilities.generators.PrototypeEntryGenerator
Allowed mixing on each site.
AlloyingCompositionEntryGenerator - Class in magpie.data.utilities.generators
Generate entries by adding alloying elements into a set composition.
AlloyingCompositionEntryGenerator() - Constructor for class magpie.data.utilities.generators.AlloyingCompositionEntryGenerator
 
AlloyingElements - Variable in class magpie.data.utilities.generators.AlloyingCompositionEntryGenerator
Set of elements to add into alloy
AlloyStep - Variable in class magpie.data.utilities.generators.AlloyingCompositionEntryGenerator
Step size.
applyClassCutoff(double[], int) - Method in class magpie.analytics.ClassificationStatistics
Takes a continuous class variable and converts it to discrete values that range between [0,nclass).
AreaUnderROCEvaluator - Class in magpie.attributes.evaluators
Ranks entries based on the area under the Receiver Operating Characteristic Curve.
AreaUnderROCEvaluator() - Constructor for class magpie.attributes.evaluators.AreaUnderROCEvaluator
 
assignment(List<String>) - Method in class magpie.user.CommandHandler
Handle variable assignment
AttributeFilter - Class in magpie.data.utilities.filters
Filter entries based on value of a single attribute.
AttributeFilter() - Constructor for class magpie.data.utilities.filters.AttributeFilter
 
AttributeID - Variable in class magpie.data.utilities.splitters.AttributeIntervalSplitter
ID of attribute used for split
AttributeIntervalSplitter - Class in magpie.data.utilities.splitters
This class splits data into multiple properties based on the attributes of each entry.
AttributeIntervalSplitter() - Constructor for class magpie.data.utilities.splitters.AttributeIntervalSplitter
 
AttributeMean - Variable in class magpie.data.utilities.filters.ZScoreOutlierFilter
Means of attributes
AttributeName - Variable in class magpie.data.Dataset
Names of attributes that describe each entry
AttributeName - Variable in class magpie.data.utilities.splitters.AttributeIntervalSplitter
Name of attribute used for split
AttributeNames - Variable in class magpie.data.utilities.filters.ZScoreOutlierFilter
Names of attributes.
AttributeSelector - Variable in class magpie.models.BaseModel
BaseAttributeSelector used to screen attributes during training
AttributeStdDev - Variable in class magpie.data.utilities.filters.ZScoreOutlierFilter
Standard deviation of attributes
Author - Variable in class magpie.user.server.ModelPackage
Author of this model
author - Variable in class magpie.user.server.thrift.ModelInfo
 
Authors - Variable in class magpie.utility.interfaces.Citation
Author(s) associated with this citation

B

BaseAttributeEvaluator - Class in magpie.attributes.evaluators
Base class for objects designed to evaluate the predictive power of single attributes.
BaseAttributeEvaluator() - Constructor for class magpie.attributes.evaluators.BaseAttributeEvaluator
 
BaseAttributeExpander - Class in magpie.attributes.expanders
This class is a template for operations that expand the number of available attributes based on what is already in the dataset.
BaseAttributeExpander() - Constructor for class magpie.attributes.expanders.BaseAttributeExpander
 
BaseAttributeGenerator - Class in magpie.attributes.generators
Base class for objects that generate attributes.
BaseAttributeGenerator() - Constructor for class magpie.attributes.generators.BaseAttributeGenerator
 
BaseAttributeSelector - Class in magpie.attributes.selectors
Interface to select a subset of attributes for a dataset.
BaseAttributeSelector() - Constructor for class magpie.attributes.selectors.BaseAttributeSelector
 
BaseClassifier - Class in magpie.models.classification
Base class for all classification models.
BaseClassifier() - Constructor for class magpie.models.classification.BaseClassifier
 
BaseClusterer - Class in magpie.cluster
Abstract model for all clustering algorithms.
BaseClusterer() - Constructor for class magpie.cluster.BaseClusterer
 
BaseCrossoverFunction - Class in magpie.optimization.algorithms.genetic.operators
Operation that performs crossover for a genetic algorithm.
BaseCrossoverFunction() - Constructor for class magpie.optimization.algorithms.genetic.operators.BaseCrossoverFunction
 
BaseDatasetFilter - Class in magpie.data.utilities.filters
Abstract model for classes that filter undesired entries out of a dataset.
BaseDatasetFilter() - Constructor for class magpie.data.utilities.filters.BaseDatasetFilter
 
BaseDatasetModifier - Class in magpie.data.utilities.modifiers
Perform some kind of manipulation on a Dataset, and all of the entries.
BaseDatasetModifier() - Constructor for class magpie.data.utilities.modifiers.BaseDatasetModifier
 
BaseDatasetNormalizer - Class in magpie.data.utilities.normalizers
Base class for objects designed to scale attributes and or class variable to exist on the same range.
BaseDatasetNormalizer() - Constructor for class magpie.data.utilities.normalizers.BaseDatasetNormalizer
 
BaseDatasetSplitter - Class in magpie.data.utilities.splitters
This class provides an interface to Dataset splitting operations.
BaseDatasetSplitter() - Constructor for class magpie.data.utilities.splitters.BaseDatasetSplitter
 
BaseElement - Variable in class magpie.data.utilities.generators.CompositionRangeEntryGenerator
ID of base element
BaseEntry - Class in magpie.data
This class is designed to store all information related to an entry in a Dataset
BaseEntry() - Constructor for class magpie.data.BaseEntry
Create a blank entry
BaseEntry(String) - Constructor for class magpie.data.BaseEntry
Generate an entry by parsing a text string
BaseEntryGenerator - Class in magpie.data.utilities.generators
Base for classes that generate new entries.
BaseEntryGenerator() - Constructor for class magpie.data.utilities.generators.BaseEntryGenerator
 
BaseEntryRanker - Class in magpie.optimization.rankers
This is a template for classes that rank entries based on some sort of objective function.
BaseEntryRanker() - Constructor for class magpie.optimization.rankers.BaseEntryRanker
 
BaseModel - Class in magpie.models
Base class for any model, regression or classification.
BaseModel() - Constructor for class magpie.models.BaseModel
 
BaseMutationFunction - Class in magpie.optimization.algorithms.genetic.operators
Mutation operations needed for a GeneticAlgorithm, takes a BaseEntry and modifies it slightly.
BaseMutationFunction() - Constructor for class magpie.optimization.algorithms.genetic.operators.BaseMutationFunction
 
BaseOptimizer - Class in magpie.optimization
Basic interface for an optimization algorithm.
BaseOptimizer() - Constructor for class magpie.optimization.BaseOptimizer
Construct an empty BaseOptimizer
BaseOracle - Class in magpie.optimization.oracles
Interface for all Oracle classes, which manage the evaluation of new entries (useful for optimization algorithms)
BaseOracle() - Constructor for class magpie.optimization.oracles.BaseOracle
 
BaseRegression - Class in magpie.models.regression
Base class for all regression models.
BaseRegression() - Constructor for class magpie.models.regression.BaseRegression
 
BaseStatistics - Class in magpie.analytics
This class stores basic statistics about model performance and contains methods to calculate each of these statistics.
BaseStatistics() - Constructor for class magpie.analytics.BaseStatistics
 
BatchModelEvaluator - Class in magpie.utility.tools
Generate attributes and simpleRun models in batches.
BatchModelEvaluator() - Constructor for class magpie.utility.tools.BatchModelEvaluator
 
BestInAlloySystemFilter - Class in magpie.data.utilities.filters
Select only the best N entries from any one phase diagram.
BestInAlloySystemFilter() - Constructor for class magpie.data.utilities.filters.BestInAlloySystemFilter
 
BestIndividualSelector - Class in magpie.attributes.selectors
Selects attributes based on their individual performance.
BestIndividualSelector() - Constructor for class magpie.attributes.selectors.BestIndividualSelector
 
BestSoFar - Variable in class magpie.optimization.analytics.OptimizationStatistics
Best objective function of entries added by all previous generations
BinEdges - Variable in class magpie.data.utilities.splitters.AttributeIntervalSplitter
Values to use as bin edges

C

calculateAttributes() - Method in class magpie.data.Dataset
Compute attributes that are specific to this class.
calculateAttributes() - Method in class magpie.data.materials.CompositionDataset
 
calculateAttributes() - Method in class magpie.data.materials.ElementDataset
 
calculateAttributes() - Method in class magpie.data.materials.PrototypeDataset
 
calculateProbabilities() - Method in class magpie.csp.diagramdata.PhaseDiagramStatistics
Calculate the probability of each compound and element being in a phase diagram.
calculateStructureProbabilities() - Method in class magpie.csp.diagramdata.OnTheFlyPhaseDiagramStatistics
 
calculateStructureProbabilities() - Method in class magpie.csp.diagramdata.PhaseDiagramStatistics
Calculate the probability of each prototype appearing in a phase diagram.
calculateStructureProbabilities() - Method in class magpie.csp.diagramdata.PrecomputedPhaseDiagramStatistics
Deprecated.
Calculate the probability of each prototype appearing in a phase diagram
calculateStructureProbabilities() - Method in class magpie.csp.diagramdata.TernaryPhaseDiagramStatistics
Deprecated.
 
CartesianSumGenerator<Type> - Class in magpie.utility
Generate Cartesian sum of several collections.
CartesianSumGenerator(List<Collection<Type>>) - Constructor for class magpie.utility.CartesianSumGenerator
Define collections to be summed
CartesianSumGenerator(Collection<Type>...) - Constructor for class magpie.utility.CartesianSumGenerator
Define collections to be summed
checkComponents() - Method in class magpie.optimization.algorithms.ActiveLearningOptimizer
 
checkComponents() - Method in class magpie.optimization.BaseOptimizer
Check if all of the necessary components are loaded
checkIfReady() - Method in class magpie.optimization.BaseOptimizer
Throw an error if all components are not ready
checkModelCount(int) - Method in class magpie.models.SplitModel
Checks if enough models are defined.
checkStatus() - Method in class magpie.models.regression.CompositeRegression
 
checkStatus() - Method in class magpie.models.regression.StagedRegression
Verify that this model is ready to be trained
Citable - Interface in magpie.utility.interfaces
Interface for objects that should be referenced if they are used.
Citation - Variable in class magpie.user.server.ModelPackage
Citation for this model
citation - Variable in class magpie.user.server.thrift.ModelInfo
 
Citation - Class in magpie.utility.interfaces
Class used by Citable to define a resource being cited.
Citation(Class, String, String[], String, String, String) - Constructor for class magpie.utility.interfaces.Citation
Create a new citation object.
class_cutoff - Variable in class magpie.analytics.ClassificationStatistics
For binary cases: Probability below above which an entry has class = 0
ClassEliminationModifier - Class in magpie.data.utilities.modifiers
Remove a possible class from a dataset.
ClassEliminationModifier() - Constructor for class magpie.data.utilities.modifiers.ClassEliminationModifier
 
ClassFilter - Class in magpie.data.utilities.filters
Filter entries based on value of class variable.
ClassFilter() - Constructor for class magpie.data.utilities.filters.ClassFilter
 
ClassificationRegression - Class in magpie.models.regression
Use a classification algorithm to perform regression.
ClassificationRegression() - Constructor for class magpie.models.regression.ClassificationRegression
Create a instances of this model that uses ZeroR.
ClassificationStatistics - Class in magpie.analytics
This class handles the calculation of statistics for classifiers.
ClassificationStatistics() - Constructor for class magpie.analytics.ClassificationStatistics
 
classifier - Variable in class magpie.user.server.thrift.ModelInfo
 
ClassIntervalModifier - Class in magpie.data.utilities.modifiers
Transforms a Dataset with a continuous class variable into a dataset with multiple class based on the value of the class variable.
ClassIntervalModifier() - Constructor for class magpie.data.utilities.modifiers.ClassIntervalModifier
 
classIsDiscrete() - Method in class magpie.analytics.ClassificationStatistics
 
classIsDiscrete() - Method in interface magpie.models.classification.AbstractClassifier
 
classIsDiscrete() - Method in class magpie.models.classification.BaseClassifier
 
classIsDiscrete() - Method in class magpie.models.classification.SplitClassifier
 
ClassMean - Variable in class magpie.data.utilities.filters.ZScoreOutlierFilter
Mean of class variable
ClassName - Variable in class magpie.data.utilities.modifiers.DiscreteToContinuousModifier
Name of class for which to compute probability.
ClassNames - Variable in class magpie.analytics.ClassificationStatistics
Names of classes (used when printing)
ClassNames - Variable in class magpie.models.classification.BaseClassifier
Names of classes this model can distinguish between
ClassNames - Variable in class magpie.models.classification.SplitClassifier
Names of classes this model can distinguish between
ClassProbabilityFilter - Class in magpie.data.utilities.filters
Filter based on predicted probability that an entry is a certain class.
ClassProbabilityFilter() - Constructor for class magpie.data.utilities.filters.ClassProbabilityFilter
 
ClassProbabilityRanker - Class in magpie.optimization.rankers
Rank entries based on the probability that they are a certain class.
ClassProbabilityRanker() - Constructor for class magpie.optimization.rankers.ClassProbabilityRanker
 
ClassProbabilityRanker(String) - Constructor for class magpie.optimization.rankers.ClassProbabilityRanker
Create new instance of ranker.
classProbs - Variable in class magpie.user.server.thrift.Entry
 
ClassRangeFilter - Class in magpie.data.utilities.filters
Filter entries that have class variables within or outside a certain range.
ClassRangeFilter() - Constructor for class magpie.data.utilities.filters.ClassRangeFilter
 
ClassStdDev - Variable in class magpie.data.utilities.filters.ZScoreOutlierFilter
Standard deviation of class variable
clear() - Method in class magpie.csp.CSPPerformanceStats
Removes results from previous tests.
clear() - Method in class magpie.user.server.thrift.Entry
 
clear() - Method in exception magpie.user.server.thrift.MagpieException
 
clear() - Method in class magpie.user.server.thrift.MagpieServer.evaluateProperties_args
 
clear() - Method in class magpie.user.server.thrift.MagpieServer.evaluateProperties_result
 
clear() - Method in class magpie.user.server.thrift.MagpieServer.getModelInformation_args
 
clear() - Method in class magpie.user.server.thrift.MagpieServer.getModelInformation_result
 
clear() - Method in class magpie.user.server.thrift.MagpieServer.searchMultiObjective_args
 
clear() - Method in class magpie.user.server.thrift.MagpieServer.searchMultiObjective_result
 
clear() - Method in class magpie.user.server.thrift.MagpieServer.searchSingleObjective_args
 
clear() - Method in class magpie.user.server.thrift.MagpieServer.searchSingleObjective_result
 
clear() - Method in class magpie.user.server.thrift.ModelInfo
 
clearAlloyingElements() - Method in class magpie.data.utilities.generators.CompositionRangeEntryGenerator
Clear the list of elements to be added
clearAttributeExpanders() - Method in class magpie.data.Dataset
Reset the list of attribute expanders
clearAttributeGenerators() - Method in class magpie.data.Dataset
Reset the list of attribute generators
clearAttributes() - Method in class magpie.data.BaseEntry
Clear all currently-set attributes.
clearAttributes() - Method in class magpie.data.Dataset
Clear attribute data.
clearCompositions() - Method in class magpie.data.utilities.filters.CompositionSetDistanceFilter
Clear the list of compositions in set
clearCompositions() - Method in class magpie.data.utilities.modifiers.CompositionSetDistanceModifier
Clear the list of compositions in set
clearCompositions() - Method in class magpie.optimization.rankers.CompositionDistanceRanker
Clear the list of compositions in set
clearData() - Method in class magpie.data.Dataset
Clear out all entries
clearElementGroups() - Method in class magpie.data.utilities.splitters.MultipleElementGroupsSplitter
Clear the current list of element groups
clearElements() - Method in class magpie.data.utilities.generators.AlloyingCompositionEntryGenerator
Clear the list of alloying elements
clearFilters() - Method in class magpie.data.utilities.filters.MultiFilter
Clear list of filters.
clearFunctionList() - Method in class magpie.attributes.expanders.FunctionExpander
Clear list of functions used to generate new attributes.
clearObjectiveFunctions() - Method in class magpie.optimization.rankers.AdaptiveScalarizingEntryRanker
Clear out list of currently-defined objective functions
clearObjectiveFunctions() - Method in class magpie.optimization.rankers.RankAggregationRanker
Clear out list of currently-defined objective functions
clearPNorms() - Method in class magpie.attributes.generators.composition.StoichiometricAttributeGenerator
Clear out the list of p norms to be computed
clearProperties() - Method in class magpie.attributes.generators.PropertyAsAttributeGenerator
Clear the list of properties being used as attributes.
clearPropertyData() - Method in class magpie.data.MultiPropertyDataset
Clear all property information from this dataset.
clearPropertyData() - Method in class magpie.data.MultiPropertyEntry
Remove all information about properties
Clfr - Variable in class magpie.data.utilities.splitters.NonZeroClassificationSplitter
Model to use for splitting
clone() - Method in class magpie.analytics.BaseStatistics
 
clone() - Method in class magpie.analytics.ClassificationStatistics
 
clone() - Method in class magpie.analytics.RegressionStatistics
 
clone() - Method in class magpie.attributes.selectors.BaseAttributeSelector
 
clone() - Method in class magpie.attributes.selectors.UserSpecifiedAttributeSelector
 
clone() - Method in class magpie.attributes.selectors.WekaAttributeSelector
 
clone() - Method in class magpie.cluster.BaseClusterer
 
clone() - Method in class magpie.cluster.WekaClusterer
 
clone() - Method in class magpie.data.BaseEntry
Generates a clone of an entry.
clone() - Method in class magpie.data.Dataset
Creates a new instance of this dataset, and clones of each entry.
clone() - Method in class magpie.data.materials.CompositionEntry
 
clone() - Method in class magpie.data.materials.PrototypeEntry
 
clone() - Method in class magpie.data.materials.util.PrototypeSiteInformation
 
clone() - Method in class magpie.data.MultiPropertyEntry
 
clone() - Method in class magpie.data.utilities.normalizers.BaseDatasetNormalizer
 
clone() - Method in class magpie.data.utilities.normalizers.RescalingNormalizer
 
clone() - Method in class magpie.data.utilities.normalizers.ZScoreNormalizer
 
clone() - Method in class magpie.data.utilities.splitters.AttributeIntervalSplitter
 
clone() - Method in class magpie.data.utilities.splitters.BaseDatasetSplitter
 
clone() - Method in class magpie.data.utilities.splitters.ClustererSplitter
 
clone() - Method in class magpie.data.utilities.splitters.MultipleElementGroupsSplitter
 
clone() - Method in class magpie.data.utilities.splitters.NonZeroClassificationSplitter
 
clone() - Method in class magpie.data.utilities.splitters.ObjectiveFunctionSplitter
 
clone() - Method in class magpie.data.utilities.splitters.PredictedClassIntervalSplitter
 
clone() - Method in class magpie.data.utilities.splitters.SingleElementGroupSplitter
 
clone() - Method in class magpie.models.BaseModel
 
clone() - Method in class magpie.models.classification.BaseClassifier
 
clone() - Method in class magpie.models.classification.SplitClassifier
 
clone() - Method in class magpie.models.classification.WekaClassifier
 
clone() - Method in class magpie.models.regression.BaseRegression
 
clone() - Method in class magpie.models.regression.ClassificationRegression
 
clone() - Method in class magpie.models.regression.CompositeRegression
 
clone() - Method in class magpie.models.regression.LASSORegression
 
clone() - Method in class magpie.models.regression.LinearCorrectedRegression
 
clone() - Method in class magpie.models.regression.MixingRuleRegression
 
clone() - Method in class magpie.models.regression.MultiObjectiveRegression
 
clone() - Method in class magpie.models.regression.PolynomialRegression
 
clone() - Method in class magpie.models.regression.ScikitLearnRegression
 
clone() - Method in class magpie.models.regression.SingleGuessRegression
 
clone() - Method in class magpie.models.regression.SplitRegression
 
clone() - Method in class magpie.models.regression.StagedRegression
 
clone() - Method in class magpie.models.regression.WekaRegression
 
clone() - Method in class magpie.models.SplitModel
 
clone() - Method in class magpie.optimization.analytics.OptimizationStatistics
 
clone() - Method in class magpie.optimization.BaseOptimizer
 
clone() - Method in class magpie.optimization.oracles.BaseOracle
 
clone() - Method in class magpie.optimization.oracles.LookupOracle
 
clone() - Method in class magpie.optimization.rankers.AdaptiveScalarizingEntryRanker
 
clone() - Method in class magpie.optimization.rankers.BaseEntryRanker
 
clone() - Method in class magpie.optimization.rankers.CompositionDistanceRanker
 
clone() - Method in class magpie.optimization.rankers.MultiObjectiveEntryRanker
 
clone() - Method in class magpie.optimization.rankers.PropertyFormulaRanker
 
closeFile() - Method in class magpie.user.InputFileParser
Closes currently open file.
ClustererSplitter - Class in magpie.data.utilities.splitters
Split data based using unsupervised learning.
ClustererSplitter() - Constructor for class magpie.data.utilities.splitters.ClustererSplitter
 
ClustererStatistics - Class in magpie.analytics
Characterize the results from a clusterer.
ClustererStatistics() - Constructor for class magpie.analytics.ClustererStatistics
 
Coefficients - Variable in class magpie.models.regression.LASSORegression
Coefficients for linear model
coefficients - Variable in class magpie.models.regression.PolynomialRegression
Coefficients of each term in the polynomial
collectAnswers(BaseOptimizer) - Method in class magpie.optimization.analytics.OptimizationStatistics
If answers to optimization problem are already known, collect them.
combine(Dataset) - Method in class magpie.data.Dataset
Combine the data structure with another.
combine(Dataset[]) - Method in class magpie.data.Dataset
Combine the data structure with an array of other Datasets.
combine(Collection<Dataset>) - Method in class magpie.data.Dataset
Combine the data structure with a collection of other data structures.
combine(Dataset) - Method in class magpie.data.MultiPropertyDataset
Combine the dataset with another.
combineCompositions(Map<Integer, Double>, Map<Integer, Double>, double) - Method in class magpie.data.materials.CompositionEntry
Add composition from one map to another
Commandable - Interface in magpie.utility.interfaces
Provides interface for classes that can handle commands.
CommandHandler - Class in magpie.user
This class turns text commands into actions.
CommandHandler() - Constructor for class magpie.user.CommandHandler
 
CommonCompositions - Variable in class magpie.csp.diagramdata.PhaseDiagramStatistics
List of common compositions and the names of prototypes found at that composition.
compare() - Method in class magpie.attributes.evaluators.AreaUnderROCEvaluator
 
compare() - Method in class magpie.attributes.evaluators.BaseAttributeEvaluator
Create a comparator that will sort entries from the best to worst
compare() - Method in class magpie.attributes.evaluators.PearsonsCorrelationEvaluator
 
compare() - Method in class magpie.attributes.evaluators.PolynomialFitEvaluator
 
compare() - Method in class magpie.attributes.evaluators.SpearmansCorrelationEvaluator
 
compare(Object, Object) - Method in class magpie.data.BaseEntry
 
compare(Object, Object) - Method in class magpie.data.materials.CompositionEntry
 
compare(Object, Object) - Method in class magpie.data.materials.PrototypeEntry
 
compareTo(Object) - Method in class magpie.data.BaseEntry
 
compareTo(Entry) - Method in class magpie.user.server.thrift.Entry
 
compareTo(MagpieException) - Method in exception magpie.user.server.thrift.MagpieException
 
compareTo(MagpieServer.evaluateProperties_args) - Method in class magpie.user.server.thrift.MagpieServer.evaluateProperties_args
 
compareTo(MagpieServer.evaluateProperties_result) - Method in class magpie.user.server.thrift.MagpieServer.evaluateProperties_result
 
compareTo(MagpieServer.getModelInformation_args) - Method in class magpie.user.server.thrift.MagpieServer.getModelInformation_args
 
compareTo(MagpieServer.getModelInformation_result) - Method in class magpie.user.server.thrift.MagpieServer.getModelInformation_result
 
compareTo(MagpieServer.searchMultiObjective_args) - Method in class magpie.user.server.thrift.MagpieServer.searchMultiObjective_args
 
compareTo(MagpieServer.searchMultiObjective_result) - Method in class magpie.user.server.thrift.MagpieServer.searchMultiObjective_result
 
compareTo(MagpieServer.searchSingleObjective_args) - Method in class magpie.user.server.thrift.MagpieServer.searchSingleObjective_args
 
compareTo(MagpieServer.searchSingleObjective_result) - Method in class magpie.user.server.thrift.MagpieServer.searchSingleObjective_result
 
compareTo(ModelInfo) - Method in class magpie.user.server.thrift.ModelInfo
 
Component - Variable in class magpie.utility.interfaces.Citation
Component this citation is associated with
CompositeRegression - Class in magpie.models.regression
Ensemble of regression models.
CompositeRegression() - Constructor for class magpie.models.regression.CompositeRegression
 
CompositionBasedCSPEngine - Class in magpie.csp
Use machine learning model trained on the composition of the entries.
CompositionBasedCSPEngine() - Constructor for class magpie.csp.CompositionBasedCSPEngine
 
compositionCanFormIonic(CompositionEntry) - Method in class magpie.data.materials.CompositionDataset
Whether a composition can form a neutral compound assuming each element takes only a single oxidation state.
CompositionComparator - Variable in class magpie.csp.diagramdata.PhaseDiagramStatistics
CompositionDataset - Class in magpie.data.materials
This class stores entries that describe a material based solely on its composition.
CompositionDataset() - Constructor for class magpie.data.materials.CompositionDataset
Create a dataset using the default set of attribute generators.
CompositionDataset(boolean) - Constructor for class magpie.data.materials.CompositionDataset
Create a blank dataset.
CompositionDatasetOutput - Class in magpie.data.materials.util
Holds static operations that permit writing composition datasets to disk.
CompositionDatasetOutput() - Constructor for class magpie.data.materials.util.CompositionDatasetOutput
 
CompositionDistanceFilter - Class in magpie.data.utilities.filters
Filter compositions based on distance from a target composition.
CompositionDistanceFilter() - Constructor for class magpie.data.utilities.filters.CompositionDistanceFilter
 
CompositionDistanceRanker - Class in magpie.optimization.rankers
Rank entries based on distance from compositions in a user-provided dataset.
CompositionDistanceRanker() - Constructor for class magpie.optimization.rankers.CompositionDistanceRanker
 
CompositionEntry - Class in magpie.data.materials
Stores several properties about a compound and its composition.
CompositionEntry() - Constructor for class magpie.data.materials.CompositionEntry
Allows the creation of arbitrary constructors for superclasses.
CompositionEntry(String) - Constructor for class magpie.data.materials.CompositionEntry
Make a new instance by parsing the composition of an object, provided by a string.
CompositionEntry(int[], double[]) - Constructor for class magpie.data.materials.CompositionEntry
Given the element numbers (probably Z-1) and fractions, create an entry
CompositionRangeEntryGenerator - Class in magpie.data.utilities.generators
Create compositions in a rectangular, user-specified grid.
CompositionRangeEntryGenerator() - Constructor for class magpie.data.utilities.generators.CompositionRangeEntryGenerator
 
Compositions - Variable in class magpie.data.utilities.modifiers.CompositionSetDistanceModifier
Set of compositions to consider
compositionsAreEqual(double[], double[]) - Method in class magpie.csp.diagramdata.PhaseDiagramStatistics
Determine whether two compositions are equal (within PhaseDiagramStatistics.MinDistance).
CompositionSetDistanceFilter - Class in magpie.data.utilities.filters
Filter based on whether the distance of a composition from any other composition in a dataset is past a threshold.
CompositionSetDistanceFilter() - Constructor for class magpie.data.utilities.filters.CompositionSetDistanceFilter
 
CompositionSetDistanceModifier - Class in magpie.data.utilities.modifiers
Compute the distance of composition from those in a user-supplied dataset, store as a property.
CompositionSetDistanceModifier() - Constructor for class magpie.data.utilities.modifiers.CompositionSetDistanceModifier
 
CompoundCrossover - Class in magpie.optimization.algorithms.genetic.operators
CrossoverFunction designed to deal with CompositionEntry that represent a compound with a fixed number of sites that must contain different elements.
CompoundCrossover() - Constructor for class magpie.optimization.algorithms.genetic.operators.CompoundCrossover
 
computeAttributeStatistics(int, double[]) - Method in class magpie.data.utilities.normalizers.IndependentVariableNormalizer
Compute statistics required to perform normalization/restoration.
computeAttributeStatistics(int, double[]) - Method in class magpie.data.utilities.normalizers.RescalingNormalizer
 
computeAttributeStatistics(int, double[]) - Method in class magpie.data.utilities.normalizers.ZScoreNormalizer
 
computeClassStatistics(double[]) - Method in class magpie.data.utilities.normalizers.IndependentVariableNormalizer
Compute statistics regarding the class variable.
computeClassStatistics(double[]) - Method in class magpie.data.utilities.normalizers.RescalingNormalizer
 
computeClassStatistics(double[]) - Method in class magpie.data.utilities.normalizers.ZScoreNormalizer
 
computeDistance(CompositionEntry, CompositionEntry, int) - Static method in class magpie.data.utilities.filters.CompositionSetDistanceFilter
Compute the distance between two entries.
computeDistance(Collection<CompositionEntry>, CompositionEntry, int) - Static method in class magpie.data.utilities.filters.CompositionSetDistanceFilter
Compute the distance between a composition and a set of other compositions.
computeListLengthCurve(double, int) - Method in class magpie.csp.CSPPerformanceStats
Compute the minimum length of a list required to find the correct structure
computeMixingTerm(CompositionEntry) - Static method in class magpie.data.utilities.normalizers.RegularSolutionNormalizer
Compute the mixing term for a solution model.
configureFunction(Set<BaseEntry>) - Method in class magpie.optimization.algorithms.genetic.operators.BaseMutationFunction
Configure the mutation function based on the search space.
configureFunction(Set<BaseEntry>) - Method in class magpie.optimization.algorithms.genetic.operators.PrototypeMutation
 
configureFunction(Set<BaseEntry>) - Method in class magpie.optimization.algorithms.genetic.operators.SimpleCompoundMutation
 
ConfusionMatrix - Variable in class magpie.analytics.ClassificationStatistics
Description of how often instances are assigned to each class
ContainsElementFilter - Class in magpie.data.utilities.filters
Filter entries that contain certain elements.
ContainsElementFilter() - Constructor for class magpie.data.utilities.filters.ContainsElementFilter
 
containsEntry(BaseEntry) - Method in class magpie.data.Dataset
Determine whether a dataset contains a certain entry
ContingencyTable - Variable in class magpie.analytics.ClassificationStatistics
Contingency table (for binary cases)
convertCommandToString(List<Object>) - Static method in class magpie.user.CommandHandler
Convert a command (List<Object>) to string.
convertToCitation(TechnicalInformation, Class) - Static method in class magpie.utility.WekaUtility
Convert a Weka TechnicalInformation object to a Magpie Citation object.
convertVolumeToLatticeParam(double) - Method in class magpie.data.utilities.modifiers.VolumeToLatticeParamModifier
Calculate the equivalent cubic lattice parameter corresponding to a volume per atom, given the number of atoms in the unit cell
CorrectionFactors - Variable in class magpie.models.regression.MixingRuleRegression
Coefficients used for correction factor.
CrossExpander - Class in magpie.attributes.expanders
Creates new attributes as multiplicative cross terms of currently available ones.
CrossExpander() - Constructor for class magpie.attributes.expanders.CrossExpander
 
crossover(BaseEntry, BaseEntry) - Method in class magpie.optimization.algorithms.genetic.operators.BaseCrossoverFunction
Given two BaseEntry classes, return a third that is a combination of the two
crossover(BaseEntry, BaseEntry) - Method in class magpie.optimization.algorithms.genetic.operators.CompoundCrossover
 
crossover(BaseEntry, BaseEntry) - Method in class magpie.optimization.algorithms.genetic.operators.HeuslerCrossover
 
crossover(BaseEntry, BaseEntry) - Method in class magpie.optimization.algorithms.genetic.operators.PrototypeCrossover
 
crossvalidate(int, int) - Method in class magpie.csp.CSPEngine
Validates predictive ability of this model.
crossValidate(int, Dataset) - Method in class magpie.models.BaseModel
Perform n-fold cross validation
CSPEngine - Class in magpie.csp
Predict what structure is likely to form at a specific composition from a list of possible candidates.
CSPEngine() - Constructor for class magpie.csp.CSPEngine
 
CSPPerformanceStats - Class in magpie.csp
Holds data about the performance of a CSP algorithm.
CSPPerformanceStats() - Constructor for class magpie.csp.CSPPerformanceStats
 
CumulantExpansionClassifier - Class in magpie.models.classification
Predict whether instance of a prototype structure will be a member of one of several mutually-exclusive classes.
CumulantExpansionClassifier() - Constructor for class magpie.models.classification.CumulantExpansionClassifier
 
CurrentComposition - Variable in class magpie.data.materials.util.GCLPCalculator
Composition for which equilibrium is currently computed.
CurrentIteration - Variable in class magpie.optimization.BaseOptimizer
How many iterations have been completed
currentIteration() - Method in class magpie.optimization.BaseOptimizer
 

D

Data - Variable in class magpie.utility.ModelRunningThread
 
DataDirectory - Variable in class magpie.data.materials.CompositionDataset
Location of lookup date files
Dataset - Class in magpie.data
Provides a basic storage container for data-mining tasks.
Dataset() - Constructor for class magpie.data.Dataset
Generate a blank dataset
Dataset - Variable in class magpie.user.server.ModelPackage
Dataset used to generate attributes
DatasetHelper - Class in magpie.data.utilities
This class provides useful operations for handling Datasets (and their derivatives)
DatasetHelper() - Constructor for class magpie.data.utilities.DatasetHelper
 
DatasetOutput - Class in magpie.data.utilities
This class contains operations relating to basic outputs/conversions of the Dataset
DatasetOutput() - Constructor for class magpie.data.utilities.DatasetOutput
 
dataType - Variable in class magpie.user.server.thrift.ModelInfo
 
deepCopy() - Method in class magpie.user.server.thrift.Entry
 
deepCopy() - Method in exception magpie.user.server.thrift.MagpieException
 
deepCopy() - Method in class magpie.user.server.thrift.MagpieServer.evaluateProperties_args
 
deepCopy() - Method in class magpie.user.server.thrift.MagpieServer.evaluateProperties_result
 
deepCopy() - Method in class magpie.user.server.thrift.MagpieServer.getModelInformation_args
 
deepCopy() - Method in class magpie.user.server.thrift.MagpieServer.getModelInformation_result
 
deepCopy() - Method in class magpie.user.server.thrift.MagpieServer.searchMultiObjective_args
 
deepCopy() - Method in class magpie.user.server.thrift.MagpieServer.searchMultiObjective_result
 
deepCopy() - Method in class magpie.user.server.thrift.MagpieServer.searchSingleObjective_args
 
deepCopy() - Method in class magpie.user.server.thrift.MagpieServer.searchSingleObjective_result
 
deepCopy() - Method in class magpie.user.server.thrift.ModelInfo
 
defineCoefficients() - Method in class magpie.models.regression.AbstractNonlinearRegression
Define the names and, if desired, initial guesses of fitting coefficients.
defineCoefficients() - Method in class magpie.models.regression.AbstractParsedNonlinearRegression
 
defineCoefficients() - Method in class magpie.models.regression.nonlinear.SimpleLinearModelExample
 
defineKnownCompounds(String) - Method in class magpie.models.classification.CumulantExpansionClassifier
Define compositions of all known compounds.
definePropertyNames(String[]) - Method in class magpie.data.MultiPropertyDataset
Define all known properties for a dataset.
defineSitePossibilities(int, int, double, Collection<String>) - Method in class magpie.data.utilities.generators.PrototypeEntryGenerator
Define the possible compositions for each site.
defineVariables() - Method in class magpie.models.regression.AbstractNonlinearRegression
Define which attributes are used by the function.
defineVariables(String) - Method in class magpie.models.regression.AbstractParsedNonlinearRegression
Reads an expression and stores the names of all variables.
defineVariables() - Method in class magpie.models.regression.AbstractParsedNonlinearRegression
 
defineVariables() - Method in class magpie.models.regression.nonlinear.SimpleLinearModelExample
 
defineVariables(String) - Method in class magpie.models.regression.NonlinearRegressionExpr
Reads an expression and stores the names of all variables.
deleteMeasuredClass() - Method in class magpie.data.BaseEntry
Delete measured class variable.
deleteMeasuredClass() - Method in class magpie.data.MultiPropertyEntry
 
deleteMeasuredClasses() - Method in class magpie.data.Dataset
Delete all measured classes from entry from entries
deletePredictedClass() - Method in class magpie.data.BaseEntry
Delete predicted class variable.
Description - Variable in class magpie.user.server.ModelPackage
Short description of this model
description - Variable in class magpie.user.server.thrift.ModelInfo
 
DiagramStatistics - Variable in class magpie.csp.CSPEngine
Statistics about phase diagrams with certain number of constituents.
discrete_class - Variable in class magpie.analytics.ClassificationStatistics
Whether class variable should be treated as discrete
DiscreteClass - Variable in class magpie.models.classification.BaseClassifier
Whether the class variable is treated as discrete
DiscreteToContinuousModifier - Class in magpie.data.utilities.modifiers
Convert multiple, discrete class values to single continuous class.
DiscreteToContinuousModifier() - Constructor for class magpie.data.utilities.modifiers.DiscreteToContinuousModifier
 
DistinctPermutationGenerator - Class in magpie.utility
Given a list of objects, generate the set of distinct permutations.
DistinctPermutationGenerator() - Constructor for class magpie.utility.DistinctPermutationGenerator
 
DMSPEngine - Class in magpie.csp
Data-Mining Structure Predictor (DMSP) from Fisher et al.
DMSPEngine() - Constructor for class magpie.csp.DMSPEngine
 
doRobustRegression() - Method in interface magpie.models.regression.AbstractRegressionModel
Whether robust regression is desired.
doRobustRegression() - Method in class magpie.models.regression.BaseRegression
 
doRobustRegression() - Method in class magpie.models.regression.SplitRegression
 

E

EchoCommands - Variable in class magpie.user.CommandHandler
Whether to echo commands to screen
Element - Variable in class magpie.data.materials.CompositionEntry
Elements present in composition
ElementalProperties - Variable in class magpie.data.materials.CompositionDataset
List of properties used when generating attributes
ElementalProperties - Variable in class magpie.data.materials.ElementDataset
List of elemental properties used when computing attributes
ElementalProperties - Static variable in class magpie.data.materials.util.LookupData
Holds elemental property data.
ElementalProperties - Variable in class magpie.user.CommandHandler
Which elemental properties to use when calculating features
ElementalPropertyAttributeGenerator - Class in magpie.attributes.generators.composition
Generate attributes based on elemental property statistics.
ElementalPropertyAttributeGenerator() - Constructor for class magpie.attributes.generators.composition.ElementalPropertyAttributeGenerator
 
ElementalPropertyAttributeGenerator - Class in magpie.attributes.generators.element
Compute attributes based on elemental properties.
ElementalPropertyAttributeGenerator() - Constructor for class magpie.attributes.generators.element.ElementalPropertyAttributeGenerator
 
ElementalPropertyDirectory - Variable in class magpie.user.CommandHandler
Directory that contain elemental property lookup files
ElementDataset - Class in magpie.data.materials
Store elemental properties.
ElementDataset() - Constructor for class magpie.data.materials.ElementDataset
Create a dataset using the default attribute generators: ElementalPropertyAttributeGenerator
ElementDataset(boolean) - Constructor for class magpie.data.materials.ElementDataset
Create a blank dataset.
ElementEntry - Class in magpie.data.materials
Holds identity and properties of an element.
ElementEntry(String) - Constructor for class magpie.data.materials.ElementEntry
Create a new entry
ElementEntry(int, boolean) - Constructor for class magpie.data.materials.ElementEntry
Create an entry given atomic number or element ID.
ElementFractionAttributeGenerator - Class in magpie.attributes.generators.composition
Stores the fraction of each element as attributes.
ElementFractionAttributeGenerator() - Constructor for class magpie.attributes.generators.composition.ElementFractionAttributeGenerator
 
ElementList - Variable in class magpie.data.utilities.filters.ContainsElementFilter
Elements that compounds are not allowed to contain
ElementNames - Variable in class magpie.csp.diagramdata.PhaseDiagramStatistics
Names of each element
ElementNames - Variable in class magpie.data.materials.CompositionDataset
List of element names
ElementNames - Variable in class magpie.data.materials.CompositionEntry
Names of each element
ElementNames - Static variable in class magpie.data.materials.util.LookupData
Name of elements, ordered by atomic number.
ElementProbability - Variable in class magpie.csp.diagramdata.PhaseDiagramStatistics
Probability that each element appears in a phase diagram
Elements - Variable in class magpie.data.utilities.generators.AlloyingCompositionEntryGenerator
Elements of composition to be added to
Elements - Variable in class magpie.data.utilities.generators.PhaseDiagramCompositionEntryGenerator
List of elements to use (id is Z-1)
emptyClone() - Method in class magpie.data.Dataset
Creates a new instance with the same class and attribute names, but without any entries.
emptyClone() - Method in class magpie.data.materials.CompositionDataset
 
emptyClone() - Method in class magpie.data.materials.ElementDataset
 
emptyClone() - Method in class magpie.data.materials.PrototypeDataset
 
emptyClone() - Method in class magpie.data.MultiPropertyDataset
 
Entries - Variable in class magpie.data.Dataset
Internal array that stores entries
entries - Variable in class magpie.user.server.thrift.MagpieServer.evaluateProperties_args
 
EntriesPerGeneration - Variable in class magpie.optimization.BaseOptimizer
How many entries to create per generation
Entry - Class in magpie.user.server.thrift
 
Entry() - Constructor for class magpie.user.server.thrift.Entry
 
Entry(String, Map<String, Double>, Map<String, Double>, Map<String, List<Double>>) - Constructor for class magpie.user.server.thrift.Entry
 
Entry(Entry) - Constructor for class magpie.user.server.thrift.Entry
Performs a deep copy on other.
Entry._Fields - Enum in magpie.user.server.thrift
The set of fields this struct contains, along with convenience methods for finding and manipulating them.
entryContainsElement(CompositionEntry) - Method in class magpie.data.utilities.filters.ContainsElementFilter
Determine whether an entry contains one of the specified elements.
EntryIterator - Variable in class magpie.utility.tools.BatchModelEvaluator
Iterator over entries to be evaluated
EntryRanker - Variable in class magpie.user.CommandHandler
Method used to rank entries
EntryRankerFilter - Class in magpie.data.utilities.filters
Filter entries based on ranking.
EntryRankerFilter() - Constructor for class magpie.data.utilities.filters.EntryRankerFilter
 
Equal - Variable in class magpie.data.utilities.filters.AttributeFilter
Should entries with Feature==Threshold be kept?
Equal - Variable in class magpie.data.utilities.filters.ClassFilter
Should entries with Feature==Threshold be kept?
equals(Object) - Method in class magpie.data.BaseEntry
 
equals(Object) - Method in class magpie.data.materials.CompositionEntry
 
equals(Object) - Method in class magpie.data.materials.PrototypeEntry
 
equals(Object) - Method in class magpie.data.materials.util.PrototypeSiteInformation
 
equals(Object) - Method in class magpie.user.server.thrift.Entry
 
equals(Entry) - Method in class magpie.user.server.thrift.Entry
 
equals(Object) - Method in exception magpie.user.server.thrift.MagpieException
 
equals(MagpieException) - Method in exception magpie.user.server.thrift.MagpieException
 
equals(Object) - Method in class magpie.user.server.thrift.MagpieServer.evaluateProperties_args
 
equals(MagpieServer.evaluateProperties_args) - Method in class magpie.user.server.thrift.MagpieServer.evaluateProperties_args
 
equals(Object) - Method in class magpie.user.server.thrift.MagpieServer.evaluateProperties_result
 
equals(MagpieServer.evaluateProperties_result) - Method in class magpie.user.server.thrift.MagpieServer.evaluateProperties_result
 
equals(Object) - Method in class magpie.user.server.thrift.MagpieServer.getModelInformation_args
 
equals(MagpieServer.getModelInformation_args) - Method in class magpie.user.server.thrift.MagpieServer.getModelInformation_args
 
equals(Object) - Method in class magpie.user.server.thrift.MagpieServer.getModelInformation_result
 
equals(MagpieServer.getModelInformation_result) - Method in class magpie.user.server.thrift.MagpieServer.getModelInformation_result
 
equals(Object) - Method in class magpie.user.server.thrift.MagpieServer.searchMultiObjective_args
 
equals(MagpieServer.searchMultiObjective_args) - Method in class magpie.user.server.thrift.MagpieServer.searchMultiObjective_args
 
equals(Object) - Method in class magpie.user.server.thrift.MagpieServer.searchMultiObjective_result
 
equals(MagpieServer.searchMultiObjective_result) - Method in class magpie.user.server.thrift.MagpieServer.searchMultiObjective_result
 
equals(Object) - Method in class magpie.user.server.thrift.MagpieServer.searchSingleObjective_args
 
equals(MagpieServer.searchSingleObjective_args) - Method in class magpie.user.server.thrift.MagpieServer.searchSingleObjective_args
 
equals(Object) - Method in class magpie.user.server.thrift.MagpieServer.searchSingleObjective_result
 
equals(MagpieServer.searchSingleObjective_result) - Method in class magpie.user.server.thrift.MagpieServer.searchSingleObjective_result
 
equals(Object) - Method in class magpie.user.server.thrift.ModelInfo
 
equals(ModelInfo) - Method in class magpie.user.server.thrift.ModelInfo
 
EqualSumCombinations - Class in magpie.utility
Iterator over all combinations of nonnegative integers that have equal sum.
EqualSumCombinations(int, int) - Constructor for class magpie.utility.EqualSumCombinations
Create an iterator over all possible vectors with a certain number of entries that are all nonnegative integers that sum to the same amount.
errorIfStarted() - Method in class magpie.optimization.BaseOptimizer
Throw an error if the algorithm has started.
ErrorSignalModifier - Class in magpie.data.utilities.modifiers
Subtract the predicted class from a dataset, leaving only the error signal as the measured class variable.
ErrorSignalModifier() - Constructor for class magpie.data.utilities.modifiers.ErrorSignalModifier
 
evaluate(Dataset) - Method in class magpie.analytics.BaseStatistics
Generates statistics about the performance on a model.
evaluate(Dataset) - Method in class magpie.analytics.ClassificationStatistics
 
evaluate(Dataset[]) - Method in class magpie.analytics.ClustererStatistics
Characterize the performance of a cluster
evaluate(Dataset) - Method in class magpie.analytics.RegressionStatistics
 
evaluate(Dataset) - Method in class magpie.analytics.TargetRegressionStatistics
 
evaluate(BaseOptimizer) - Method in class magpie.optimization.analytics.OptimizationStatistics
Evaluate the performance of an optimizer.
evaluate() - Method in class magpie.optimization.BaseOptimizer
Evaluate the results of the run using the internal statistics object
evaluate() - Method in class magpie.utility.ParsedFunction
Evaluate function with current variable values
evaluate(Dataset, BaseEntryGenerator, BaseDatasetFilter) - Method in class magpie.utility.tools.BatchModelEvaluator
Generate entries and store them in a dataset.
evaluate(Dataset) - Method in class magpie.utility.tools.BatchModelEvaluator
Evaluate the model on a dataset in batch mode.
evaluate_protected() - Method in class magpie.optimization.oracles.BaseOracle
Operation which actually does the work
evaluate_protected() - Method in class magpie.optimization.oracles.LookupOracle
 
evaluateAttributes(Dataset) - Method in class magpie.attributes.evaluators.BaseAttributeEvaluator
Calculate the predictive power of each attributes in a dataset
evaluateAttributes_internal(Dataset) - Method in class magpie.attributes.evaluators.AreaUnderROCEvaluator
 
evaluateAttributes_internal(Dataset) - Method in class magpie.attributes.evaluators.BaseAttributeEvaluator
Operation that actually performs the work of evaluating attributes.
evaluateAttributes_internal(Dataset) - Method in class magpie.attributes.evaluators.PearsonsCorrelationEvaluator
 
evaluateAttributes_internal(Dataset) - Method in class magpie.attributes.evaluators.PolynomialFitEvaluator
 
evaluateAttributes_internal(Dataset) - Method in class magpie.attributes.evaluators.SpearmansCorrelationEvaluator
 
EvaluatedSoFar - Variable in class magpie.optimization.analytics.OptimizationStatistics
Number of entries that have been evaluated so far
evaluateEntries(Dataset, Dataset, BaseEntryRanker, int) - Method in class magpie.optimization.analytics.OptimizationStatistics
Given the new entries for a generation and the total population so far, calculate the statistics for this generation
evaluateEntries() - Method in class magpie.optimization.oracles.BaseOracle
Run all necessary calculations to determine the measured class of each entry Throws error if no entries have been imported
evaluateModel(BaseModel, CompositionDataset) - Method in class magpie.utility.tools.PhaseDiagramExclusionValidator
Evaluate predictive accuracy of model by iteratively excluding elements from a certain phase diagram.
evaluateProbability(PrototypeEntry, double[][], double) - Method in class magpie.csp.diagramdata.PhaseDiagramStatistics
Given a prototype entry, generate its probability of having a certain condition.
evaluateProperties(List<Entry>, List<String>, AsyncMethodCallback) - Method in class magpie.user.server.thrift.MagpieServer.AsyncClient
 
evaluateProperties(List<Entry>, List<String>, AsyncMethodCallback) - Method in interface magpie.user.server.thrift.MagpieServer.AsyncIface
 
evaluateProperties(List<Entry>, List<String>) - Method in class magpie.user.server.thrift.MagpieServer.Client
 
evaluateProperties(List<Entry>, List<String>) - Method in interface magpie.user.server.thrift.MagpieServer.Iface
Compute the properties of each entry in a list.
evaluateProperties(List<Entry>, List<String>) - Method in class magpie.user.server.thrift.MagpieServerHandler
 
Evaluator - Variable in class magpie.attributes.selectors.WekaAttributeSelector
Weka class that is used to rank subsets of attributes
evenSpacing - Variable in class magpie.data.utilities.generators.PhaseDiagramCompositionEntryGenerator
Whether to use even spacing or small integers
expand(Dataset) - Method in class magpie.attributes.expanders.BaseAttributeExpander
Generate new attributes based on the attributes already in Dataset
expand(Dataset) - Method in class magpie.attributes.expanders.CrossExpander
 
expand(Dataset) - Method in class magpie.attributes.expanders.FunctionExpander
 
expand(Dataset) - Method in class magpie.attributes.expanders.PowerExpander
 
expandAttributes(double[][], int) - Static method in class magpie.models.regression.PolynomialRegression
Expand attribute array in order to allow it to be used to fit a polynomial model.
Expanders - Variable in class magpie.data.Dataset
Tools to generate new attributes based on existing ones
expandTextCommand(List<String>) - Method in class magpie.user.CommandHandler
Given a text command, change any word marked with a "$" in the front to the corresponding variable.
extendComposition(double[]) - Method in class magpie.csp.diagramdata.PhaseDiagramStatistics
Extend the length of a composition by padding the end with zeros.
externallyValidate(Dataset) - Method in class magpie.models.BaseModel
Use external testing data to validate a model (should not contain any data used to train the model)
extractDataset() - Method in class magpie.optimization.oracles.BaseOracle
If the oracle is finished, returns the dataset with all evaluated entries.
extractVariables(String) - Method in class magpie.optimization.rankers.PropertyFormulaRanker
Parse a formula to find names of properties used as variables.

F

F1 - Variable in class magpie.analytics.ClassificationStatistics
F1 Score
FDR - Variable in class magpie.analytics.ClassificationStatistics
False Detection Rate
fieldForId(int) - Method in class magpie.user.server.thrift.Entry
 
fieldForId(int) - Method in exception magpie.user.server.thrift.MagpieException
 
fieldForId(int) - Method in class magpie.user.server.thrift.MagpieServer.evaluateProperties_args
 
fieldForId(int) - Method in class magpie.user.server.thrift.MagpieServer.evaluateProperties_result
 
fieldForId(int) - Method in class magpie.user.server.thrift.MagpieServer.getModelInformation_args
 
fieldForId(int) - Method in class magpie.user.server.thrift.MagpieServer.getModelInformation_result
 
fieldForId(int) - Method in class magpie.user.server.thrift.MagpieServer.searchMultiObjective_args
 
fieldForId(int) - Method in class magpie.user.server.thrift.MagpieServer.searchMultiObjective_result
 
fieldForId(int) - Method in class magpie.user.server.thrift.MagpieServer.searchSingleObjective_args
 
fieldForId(int) - Method in class magpie.user.server.thrift.MagpieServer.searchSingleObjective_result
 
fieldForId(int) - Method in class magpie.user.server.thrift.ModelInfo
 
fileIsOpen - Variable in class magpie.user.InputFileParser
Whether an input file is open
fillPrototypeEntry(PrototypeEntry, int[]) - Method in class magpie.csp.CSPEngine
Adjust a PrototypeEntry so that each site is occupied by a specific element
filter(Dataset) - Method in class magpie.data.utilities.filters.BaseDatasetFilter
Filters entries out of dataset
Filters - Variable in class magpie.data.utilities.filters.MultiFilter
List of filters currently in use
finalize() - Method in class magpie.models.regression.ScikitLearnRegression
 
finalizeGeneration() - Method in class magpie.data.Dataset
Run after generating attributes.
findAllCompounds() - Method in class magpie.utility.tools.IonicCompoundFinder
Locate all ionic compounds within a certain distance of the target composition.
findByName(String) - Static method in enum magpie.user.server.thrift.Entry._Fields
Find the _Fields constant that matches name, or null if its not found.
findByName(String) - Static method in enum magpie.user.server.thrift.MagpieException._Fields
Find the _Fields constant that matches name, or null if its not found.
findByName(String) - Static method in enum magpie.user.server.thrift.MagpieServer.evaluateProperties_args._Fields
Find the _Fields constant that matches name, or null if its not found.
findByName(String) - Static method in enum magpie.user.server.thrift.MagpieServer.evaluateProperties_result._Fields
Find the _Fields constant that matches name, or null if its not found.
findByName(String) - Static method in enum magpie.user.server.thrift.MagpieServer.getModelInformation_args._Fields
Find the _Fields constant that matches name, or null if its not found.
findByName(String) - Static method in enum magpie.user.server.thrift.MagpieServer.getModelInformation_result._Fields
Find the _Fields constant that matches name, or null if its not found.
findByName(String) - Static method in enum magpie.user.server.thrift.MagpieServer.searchMultiObjective_args._Fields
Find the _Fields constant that matches name, or null if its not found.
findByName(String) - Static method in enum magpie.user.server.thrift.MagpieServer.searchMultiObjective_result._Fields
Find the _Fields constant that matches name, or null if its not found.
findByName(String) - Static method in enum magpie.user.server.thrift.MagpieServer.searchSingleObjective_args._Fields
Find the _Fields constant that matches name, or null if its not found.
findByName(String) - Static method in enum magpie.user.server.thrift.MagpieServer.searchSingleObjective_result._Fields
Find the _Fields constant that matches name, or null if its not found.
findByName(String) - Static method in enum magpie.user.server.thrift.ModelInfo._Fields
Find the _Fields constant that matches name, or null if its not found.
findByThriftId(int) - Static method in enum magpie.user.server.thrift.Entry._Fields
Find the _Fields constant that matches fieldId, or null if its not found.
findByThriftId(int) - Static method in enum magpie.user.server.thrift.MagpieException._Fields
Find the _Fields constant that matches fieldId, or null if its not found.
findByThriftId(int) - Static method in enum magpie.user.server.thrift.MagpieServer.evaluateProperties_args._Fields
Find the _Fields constant that matches fieldId, or null if its not found.
findByThriftId(int) - Static method in enum magpie.user.server.thrift.MagpieServer.evaluateProperties_result._Fields
Find the _Fields constant that matches fieldId, or null if its not found.
findByThriftId(int) - Static method in enum magpie.user.server.thrift.MagpieServer.getModelInformation_args._Fields
Find the _Fields constant that matches fieldId, or null if its not found.
findByThriftId(int) - Static method in enum magpie.user.server.thrift.MagpieServer.getModelInformation_result._Fields
Find the _Fields constant that matches fieldId, or null if its not found.
findByThriftId(int) - Static method in enum magpie.user.server.thrift.MagpieServer.searchMultiObjective_args._Fields
Find the _Fields constant that matches fieldId, or null if its not found.
findByThriftId(int) - Static method in enum magpie.user.server.thrift.MagpieServer.searchMultiObjective_result._Fields
Find the _Fields constant that matches fieldId, or null if its not found.
findByThriftId(int) - Static method in enum magpie.user.server.thrift.MagpieServer.searchSingleObjective_args._Fields
Find the _Fields constant that matches fieldId, or null if its not found.
findByThriftId(int) - Static method in enum magpie.user.server.thrift.MagpieServer.searchSingleObjective_result._Fields
Find the _Fields constant that matches fieldId, or null if its not found.
findByThriftId(int) - Static method in enum magpie.user.server.thrift.ModelInfo._Fields
Find the _Fields constant that matches fieldId, or null if its not found.
findByThriftIdOrThrow(int) - Static method in enum magpie.user.server.thrift.Entry._Fields
Find the _Fields constant that matches fieldId, throwing an exception if it is not found.
findByThriftIdOrThrow(int) - Static method in enum magpie.user.server.thrift.MagpieException._Fields
Find the _Fields constant that matches fieldId, throwing an exception if it is not found.
findByThriftIdOrThrow(int) - Static method in enum magpie.user.server.thrift.MagpieServer.evaluateProperties_args._Fields
Find the _Fields constant that matches fieldId, throwing an exception if it is not found.
findByThriftIdOrThrow(int) - Static method in enum magpie.user.server.thrift.MagpieServer.evaluateProperties_result._Fields
Find the _Fields constant that matches fieldId, throwing an exception if it is not found.
findByThriftIdOrThrow(int) - Static method in enum magpie.user.server.thrift.MagpieServer.getModelInformation_args._Fields
Find the _Fields constant that matches fieldId, throwing an exception if it is not found.
findByThriftIdOrThrow(int) - Static method in enum magpie.user.server.thrift.MagpieServer.getModelInformation_result._Fields
Find the _Fields constant that matches fieldId, throwing an exception if it is not found.
findByThriftIdOrThrow(int) - Static method in enum magpie.user.server.thrift.MagpieServer.searchMultiObjective_args._Fields
Find the _Fields constant that matches fieldId, throwing an exception if it is not found.
findByThriftIdOrThrow(int) - Static method in enum magpie.user.server.thrift.MagpieServer.searchMultiObjective_result._Fields
Find the _Fields constant that matches fieldId, throwing an exception if it is not found.
findByThriftIdOrThrow(int) - Static method in enum magpie.user.server.thrift.MagpieServer.searchSingleObjective_args._Fields
Find the _Fields constant that matches fieldId, throwing an exception if it is not found.
findByThriftIdOrThrow(int) - Static method in enum magpie.user.server.thrift.MagpieServer.searchSingleObjective_result._Fields
Find the _Fields constant that matches fieldId, throwing an exception if it is not found.
findByThriftIdOrThrow(int) - Static method in enum magpie.user.server.thrift.ModelInfo._Fields
Find the _Fields constant that matches fieldId, throwing an exception if it is not found.
findMaxCorrelation(double[][], double[], boolean[]) - Method in class magpie.models.regression.LASSORegression
Finds the feature with the maximum correlation out of all possible candidates
findSuccesses(Dataset) - Method in class magpie.optimization.analytics.OptimizationStatistics
Find all entries in the search space that pass the success filter.
findTopEntries(Dataset, BaseEntryRanker) - Method in class magpie.optimization.analytics.OptimizationStatistics
Set the top entry list with a known list
fitCorrectionFactors(CompositionDataset) - Method in class magpie.models.regression.MixingRuleRegression
Fit correction factors to the mixing rule model.
fitElementProperties(CompositionDataset) - Method in class magpie.models.regression.MixingRuleRegression
Fits properties for elements specified by user.
fitPolynomialModel(double[][], int, double[]) - Static method in class magpie.models.regression.PolynomialRegression
Fit a polynomial model based on a matrix of attribute values.
FittedElements - Variable in class magpie.models.regression.MixingRuleRegression
Elements to fit using least squares
FN - Variable in class magpie.analytics.ClassificationStatistics
Number of False Negatives
FoundAllSuccess - Variable in class magpie.optimization.analytics.OptimizationStatistics
Whether all successful entries have been found
FoundAllTop - Variable in class magpie.optimization.analytics.OptimizationStatistics
Whether all of the top entries have been found
FP - Variable in class magpie.analytics.ClassificationStatistics
Number of False Positives
FPR - Variable in class magpie.analytics.ClassificationStatistics
False Positive Rate
Fraction - Variable in class magpie.data.materials.CompositionEntry
Fraction of each element
FractionCorrect - Variable in class magpie.analytics.ClassificationStatistics
Fraction of entries assigned to correct class
Fractions - Variable in class magpie.data.utilities.generators.AlloyingCompositionEntryGenerator
Fractions of each element of composition to be added to
function(double[], double[]) - Method in class magpie.models.regression.AbstractNonlinearRegression
Function defined by the user.
function(double[], double[]) - Method in class magpie.models.regression.nonlinear.SimpleLinearModelExample
 
function(double[], double[]) - Method in class magpie.models.regression.NonlinearRegressionExpr
 
FunctionExpander - Class in magpie.attributes.expanders
Generates new attributes that are arbitrary functions of other attributes.
FunctionExpander() - Constructor for class magpie.attributes.expanders.FunctionExpander
 

G

gcd(int, int) - Static method in class magpie.utility.MathUtils
Calculate the greatest common denominator of two integers.
GCLPCalculator - Class in magpie.data.materials.util
Grand-Canonical Linear Programming (GCLP) method to compute phase equilibria.
GCLPCalculator() - Constructor for class magpie.data.materials.util.GCLPCalculator
Initialize a GCLP calculator.
generateAll() - Method in class magpie.utility.EqualSumCombinations
Generate all possible vectors
generateAlloyCompositions() - Method in class magpie.data.utilities.generators.PhaseDiagramCompositionEntryGenerator
Generate evenly-spaced compositions.
generateAttributes() - Method in class magpie.data.Dataset
Generate attributes for this dataset
generateCombinations(List<Set<Integer>>, List<Pair<Integer, Double>>) - Static method in class magpie.data.utilities.generators.PrototypeEntryGenerator
Generate all possible combinations of compositions generated using a list of settings.
generateCrystalCompositions() - Method in class magpie.data.utilities.generators.PhaseDiagramCompositionEntryGenerator
Generate compositions with small denominators.
generateEntries() - Method in class magpie.data.utilities.generators.BaseEntryGenerator
Generate a list of new entries according to the currently-defined settings.
generateInfo() - Method in class magpie.user.server.ModelPackage
Generate model info in a format suitable for Thrift interface
generatePairSiteAttributes() - Method in class magpie.data.materials.PrototypeDataset
Generate attributes related to the differences between a pair of sites
generatePermutations(List<Object>) - Static method in class magpie.utility.DistinctPermutationGenerator
Given a list, generate all permutations that are not equal to each other
generatePermutations(double[]) - Static method in class magpie.utility.DistinctPermutationGenerator
Generate all distinct permutations of an array of doubles.
generatePermutations(int[]) - Static method in class magpie.utility.DistinctPermutationGenerator
Generate all distinct permutations of an array of doubles.
generateSingleSiteAttributes() - Method in class magpie.data.materials.PrototypeDataset
Generate attributes based on the mean elemental property for each site group.
GenerationAverage - Variable in class magpie.optimization.analytics.OptimizationStatistics
Average objective function of entries added by the previous generation
GenerationBest - Variable in class magpie.optimization.analytics.OptimizationStatistics
Best objective function of entries added by the previous generation
Generators - Variable in class magpie.data.Dataset
Tools to generate special-purpose attributes
GenericModel - Variable in class magpie.models.regression.CompositeRegression
Generic composite regression model (use wisely)
GenericModel - Variable in class magpie.models.regression.MultiObjectiveRegression
Generic model (in case one has not already been defined)
GenericModel - Variable in class magpie.models.SplitModel
Model used to if a model template for a certain split is not defined
GeneticAlgorithm - Class in magpie.optimization.algorithms.genetic
This class implements a simple genetic algorithm.
GeneticAlgorithm() - Constructor for class magpie.optimization.algorithms.genetic.GeneticAlgorithm
 
genMethod - Variable in class magpie.user.server.thrift.MagpieServer.searchMultiObjective_args
 
genMethod - Variable in class magpie.user.server.thrift.MagpieServer.searchSingleObjective_args
 
getASEvaluator(String, String[]) - Static method in class magpie.attributes.selectors.WekaAttributeSelector
Generates a Weka ASEvaluator object, given name and options
getASSearch(String, String[]) - Static method in class magpie.attributes.selectors.WekaAttributeSelector
Generates a Weka ASSearch object, given names and options
getAsyncClient(TNonblockingTransport) - Method in class magpie.user.server.thrift.MagpieServer.AsyncClient.Factory
 
getAttribute(int) - Method in class magpie.data.BaseEntry
Retrieve a certain attribute for this entry
getAttributeArray() - Method in class magpie.data.Dataset
Output the attributes of each entry into an array
getAttributeExpanders() - Method in class magpie.data.Dataset
Get a copy of the list of currently-employed attribute expanders.
getAttributeGenerators() - Method in class magpie.data.Dataset
Get a copy of the list of currently-employed attribute generators.
getAttributeIndex(String) - Method in class magpie.data.Dataset
Get index of a certain attribute
getAttributeName(int) - Method in class magpie.data.Dataset
Get name of a specific attribute
getAttributeNames() - Method in class magpie.data.Dataset
 
getAttributeRanks(Dataset) - Method in class magpie.attributes.evaluators.BaseAttributeEvaluator
Generate rank of attributes sorted by their predictive power
getAttributes() - Method in class magpie.data.BaseEntry
Retrieve attributes for this entry
getAttributeSelector() - Method in class magpie.models.BaseModel
Return the BaseAttributeSelector used by this model
getAttributeSelector(String) - Method in class magpie.user.Workspace
Get an BaseAttributeSelector out of the Workspace
getAuthor() - Method in class magpie.user.server.thrift.ModelInfo
 
getAverageDeviation(double[]) - Method in class magpie.data.materials.CompositionEntry
Calculate the mean deviation of a property from the average.
getAverageDeviation(double[], double) - Method in class magpie.data.materials.CompositionEntry
Calculate the mean deviation of a property from the average.
getCitation() - Method in class magpie.user.server.thrift.ModelInfo
 
getCitationDescriptions(String) - Method in class magpie.user.CommandHandler
Print out citation information associated with a single variable
getCitations() - Method in class magpie.attributes.expanders.FunctionExpander
 
getCitations() - Method in class magpie.attributes.generators.composition.MeredigAttributeGenerator
 
getCitations() - Method in class magpie.attributes.generators.composition.ValenceShellAttributeGenerator
 
getCitations() - Method in class magpie.data.Dataset
 
getCitations() - Method in class magpie.models.BaseModel
 
getCitations() - Method in class magpie.models.classification.WekaClassifier
 
getCitations() - Method in class magpie.models.regression.WekaRegression
 
getCitations() - Method in interface magpie.utility.interfaces.Citable
Return a list of citations for this object and any underlying objects.
getClassCutoff() - Method in class magpie.analytics.ClassificationStatistics
 
getClassCutoff() - Method in interface magpie.models.classification.AbstractClassifier
 
getClassCutoff() - Method in class magpie.models.classification.BaseClassifier
 
getClassCutoff() - Method in class magpie.models.classification.SplitClassifier
 
getClassName(int) - Method in class magpie.data.Dataset
Get the name of a certain class (for data with multiple possible classes)
getClassNames() - Method in class magpie.data.Dataset
 
getClassNames() - Method in class magpie.data.MultiPropertyDataset
 
getClassNames() - Method in interface magpie.models.classification.AbstractClassifier
Get names of classes this model distinguishes between.
getClassNames() - Method in class magpie.models.classification.BaseClassifier
 
getClassNames() - Method in class magpie.models.classification.SplitClassifier
 
getClassProbabilityArray() - Method in class magpie.data.Dataset
Get an array of class probabilities
getClassProbilities() - Method in class magpie.data.BaseEntry
Get the probability of an entry existing in each class.
getClassProbilities() - Method in class magpie.data.MultiPropertyEntry
 
getClassProbs() - Method in class magpie.user.server.thrift.Entry
 
getClassProbsSize() - Method in class magpie.user.server.thrift.Entry
 
getClient(TProtocol) - Method in class magpie.user.server.thrift.MagpieServer.Client.Factory
 
getClient(TProtocol, TProtocol) - Method in class magpie.user.server.thrift.MagpieServer.Client.Factory
 
getClosestBin(double[]) - Method in class magpie.csp.diagramdata.PhaseDiagramStatistics
Find the composition bin in PhaseDiagramStatistics.CommonCompositions) closest to a certain composition
getCluster(Dataset, int) - Method in class magpie.cluster.BaseClusterer
Retrieve a specific cluster from a dataset.
getClusterer(String) - Method in class magpie.user.Workspace
Get an BaseClusterer out of the Workspace
getClustererDetails(boolean) - Method in class magpie.cluster.BaseClusterer
Get any user-specified options of this clusterer.
getClustererDetails(boolean) - Method in class magpie.cluster.WekaClusterer
 
getCoefficientName(int) - Method in class magpie.models.regression.AbstractNonlinearRegression
Return name of coefficient, given index
getCoefficients() - Method in class magpie.models.regression.PolynomialRegression
Get coefficients of model.
getCommands() - Method in class magpie.user.InputFileParser
From the open input file, read in the next command.
getCommonCompositions(Map<CompositionEntry, String>, int[]) - Method in class magpie.csp.diagramdata.PhaseDiagramStatistics
Determine most common compositions from all structures.
getComponent(String) - Method in class magpie.csp.CSPEngine
Get a clone of a specific component of this CSP engine.
getCompositionIndex(double[]) - Method in class magpie.csp.diagramdata.OnTheFlyPhaseDiagramStatistics
getCompoundVector(int[]) - Method in class magpie.csp.diagramdata.OnTheFlyPhaseDiagramStatistics
 
getCompoundVector(int[]) - Method in class magpie.csp.diagramdata.PhaseDiagramStatistics
Given a list of elements on each site of a structure, determine which prototypes exist on each site of the corresponding phase diagram.
getCompoundVector(int[]) - Method in class magpie.csp.diagramdata.PrecomputedPhaseDiagramStatistics
Deprecated.
 
getCompoundVector(int[]) - Method in class magpie.csp.diagramdata.TernaryPhaseDiagramStatistics
Deprecated.
 
getCumulants(PrototypeDataset, boolean[]) - Method in class magpie.csp.diagramdata.PhaseDiagramStatistics
For a certain training set, calculate the cumulant function between a condition being true and each variable being any allowed condition.
getDataset(String) - Method in class magpie.user.Workspace
Get a dataset out of the variable list
getDataType() - Method in class magpie.user.server.thrift.ModelInfo
 
getDescription() - Method in class magpie.user.server.thrift.ModelInfo
 
getDistribution() - Method in class magpie.data.Dataset
Get the distribution of entries between known classes
getDistributionCount() - Method in class magpie.data.Dataset
Get the distribution of entries between known classes
getElementalProperties() - Method in class magpie.data.materials.CompositionDataset
Get list of elemental properties currently being used to generate attributes.
getElementalProperties() - Method in class magpie.data.materials.ElementDataset
Get the list of elemental properties to be used to compute attributes.
getElementFraction(String) - Method in class magpie.data.materials.CompositionEntry
Return the fraction of a certain element found in an entry
getElementFraction(int) - Method in class magpie.data.materials.CompositionEntry
Return the fraction of a certain element found in an entry
getElementID() - Method in class magpie.data.materials.ElementEntry
Get the ID of this element
getElementIndices(String[]) - Static method in class magpie.data.utilities.filters.ContainsElementFilter
Given a list of elements, return their indices.
getElementIndices(List<String>, CompositionDataset) - Static method in class magpie.data.utilities.splitters.SingleElementGroupSplitter
Given a CompositionDataset, return the index corresponding to each element in a list of element names
getElementNameList() - Method in class magpie.data.materials.CompositionEntry
 
getElementNames(int[]) - Static method in class magpie.utility.tools.PhaseDiagramExclusionValidator
Provided with a list of elements IDs, print out element names.
getElements() - Method in class magpie.data.materials.CompositionEntry
 
getElements(CompositionDataset) - Static method in class magpie.utility.tools.PhaseDiagramExclusionValidator
Provided a CompositionDataset, get list of all included elements.
getEmptyArgsInstance() - Method in class magpie.user.server.thrift.MagpieServer.AsyncProcessor.evaluateProperties
 
getEmptyArgsInstance() - Method in class magpie.user.server.thrift.MagpieServer.AsyncProcessor.getModelInformation
 
getEmptyArgsInstance() - Method in class magpie.user.server.thrift.MagpieServer.AsyncProcessor.searchMultiObjective
 
getEmptyArgsInstance() - Method in class magpie.user.server.thrift.MagpieServer.AsyncProcessor.searchSingleObjective
 
getEmptyArgsInstance() - Method in class magpie.user.server.thrift.MagpieServer.Processor.evaluateProperties
 
getEmptyArgsInstance() - Method in class magpie.user.server.thrift.MagpieServer.Processor.getModelInformation
 
getEmptyArgsInstance() - Method in class magpie.user.server.thrift.MagpieServer.Processor.searchMultiObjective
 
getEmptyArgsInstance() - Method in class magpie.user.server.thrift.MagpieServer.Processor.searchSingleObjective
 
getEmptyDataset() - Method in class magpie.optimization.BaseOptimizer
Get an empty dataset based on initial population.
getEnsembleMean(double[][]) - Method in class magpie.models.regression.CompositeRegression
Get mean prediction by the ensemble for each entry
getEnsembleMean(Dataset) - Method in class magpie.models.regression.CompositeRegression
Get mean prediction by the ensemble for each entry
getEnsemblePredictions(Dataset) - Method in class magpie.models.regression.CompositeRegression
Calculate the predicted class using each model
getEnsembleVariation(double[][]) - Method in class magpie.models.regression.CompositeRegression
Return the variance in predictions for each entry.
getEnsembleVariation(Dataset) - Method in class magpie.models.regression.CompositeRegression
Return the variance in predictions for each entry.
getEntries() - Method in class magpie.data.Dataset
Return copy of list of entries.
getEntries() - Method in class magpie.user.server.thrift.MagpieServer.evaluateProperties_args
 
getEntriesIterator() - Method in class magpie.user.server.thrift.MagpieServer.evaluateProperties_args
 
getEntriesSize() - Method in class magpie.user.server.thrift.MagpieServer.evaluateProperties_args
 
getEntriesWriteAccess() - Method in class magpie.data.Dataset
Get the internal list of entries from this dataset.
getEntry(int) - Method in class magpie.data.Dataset
Retrieve a single entry from the dataset
getEntry(int) - Method in class magpie.data.materials.CompositionDataset
 
getEntry(int) - Method in class magpie.data.materials.ElementDataset
 
getEntry(int) - Method in class magpie.data.materials.PrototypeDataset
 
getEntry(int) - Method in class magpie.data.MultiPropertyDataset
 
getEntryArray() - Method in class magpie.data.Dataset
Output the attributes and class of each entry
getEntryRanker(String, List<String>) - Static method in class magpie.user.server.thrift.MagpieServerHandler
Get an entry ranker for a single property.
getEquivalentArragements() - Method in class magpie.data.materials.util.PrototypeSiteInformation
Get all equivalent orders of sites.
getEquivalentPrototypes() - Method in class magpie.data.materials.PrototypeEntry
Generate a list of prototypes equivalent to this entry.
getFieldName() - Method in enum magpie.user.server.thrift.Entry._Fields
 
getFieldName() - Method in enum magpie.user.server.thrift.MagpieException._Fields
 
getFieldName() - Method in enum magpie.user.server.thrift.MagpieServer.evaluateProperties_args._Fields
 
getFieldName() - Method in enum magpie.user.server.thrift.MagpieServer.evaluateProperties_result._Fields
 
getFieldName() - Method in enum magpie.user.server.thrift.MagpieServer.getModelInformation_args._Fields
 
getFieldName() - Method in enum magpie.user.server.thrift.MagpieServer.getModelInformation_result._Fields
 
getFieldName() - Method in enum magpie.user.server.thrift.MagpieServer.searchMultiObjective_args._Fields
 
getFieldName() - Method in enum magpie.user.server.thrift.MagpieServer.searchMultiObjective_result._Fields
 
getFieldName() - Method in enum magpie.user.server.thrift.MagpieServer.searchSingleObjective_args._Fields
 
getFieldName() - Method in enum magpie.user.server.thrift.MagpieServer.searchSingleObjective_result._Fields
 
getFieldName() - Method in enum magpie.user.server.thrift.ModelInfo._Fields
 
getFieldValue(Entry._Fields) - Method in class magpie.user.server.thrift.Entry
 
getFieldValue(MagpieException._Fields) - Method in exception magpie.user.server.thrift.MagpieException
 
getFieldValue(MagpieServer.evaluateProperties_args._Fields) - Method in class magpie.user.server.thrift.MagpieServer.evaluateProperties_args
 
getFieldValue(MagpieServer.evaluateProperties_result._Fields) - Method in class magpie.user.server.thrift.MagpieServer.evaluateProperties_result
 
getFieldValue(MagpieServer.getModelInformation_args._Fields) - Method in class magpie.user.server.thrift.MagpieServer.getModelInformation_args
 
getFieldValue(MagpieServer.getModelInformation_result._Fields) - Method in class magpie.user.server.thrift.MagpieServer.getModelInformation_result
 
getFieldValue(MagpieServer.searchMultiObjective_args._Fields) - Method in class magpie.user.server.thrift.MagpieServer.searchMultiObjective_args
 
getFieldValue(MagpieServer.searchMultiObjective_result._Fields) - Method in class magpie.user.server.thrift.MagpieServer.searchMultiObjective_result
 
getFieldValue(MagpieServer.searchSingleObjective_args._Fields) - Method in class magpie.user.server.thrift.MagpieServer.searchSingleObjective_args
 
getFieldValue(MagpieServer.searchSingleObjective_result._Fields) - Method in class magpie.user.server.thrift.MagpieServer.searchSingleObjective_result
 
getFieldValue(ModelInfo._Fields) - Method in class magpie.user.server.thrift.ModelInfo
 
getFilter() - Method in class magpie.models.BaseModel
Get filter used before training
getFittedCoefficient(int) - Method in class magpie.models.regression.AbstractNonlinearRegression
Get the value of fitted coefficient
getFractions() - Method in class magpie.data.materials.CompositionEntry
 
getFullDataset(int) - Method in class magpie.optimization.BaseOptimizer
Returns all entries evaluated up a certain iteration.
getFullSet(int) - Method in class magpie.optimization.BaseOptimizer
Return all entries evaluated up a certain iteration.
getGeneration(int) - Method in class magpie.optimization.BaseOptimizer
Get a Dataset representing all entries generated at a certain generation.
getGenerator(String) - Static method in class magpie.user.server.thrift.MagpieServerHandler
Given the first line of user command, get the entry generator.
getGenericModel() - Method in interface magpie.models.interfaces.MultiModel
Get the model template
getGenericModel() - Method in class magpie.models.regression.CompositeRegression
 
getGenericModel() - Method in class magpie.models.regression.StagedRegression
 
getGenericModel() - Method in class magpie.models.SplitModel
 
getGenMethod() - Method in class magpie.user.server.thrift.MagpieServer.searchMultiObjective_args
 
getGenMethod() - Method in class magpie.user.server.thrift.MagpieServer.searchSingleObjective_args
 
getGroupLabel(int) - Method in class magpie.data.materials.util.PrototypeSiteInformation
Generate a label for a certain group of sites.
getGuess() - Method in class magpie.models.regression.SingleGuessRegression
Get the user's guess
getHeader() - Method in class magpie.optimization.analytics.OptimizationStatistics
Print out a header that has all statistics which have been calculated.
getInitialData() - Method in class magpie.optimization.BaseOptimizer
Initial population defined
getInput() - Method in class magpie.utility.ParsedFunction
Get the string that was provided as input
getLookupTable(String) - Method in class magpie.data.materials.ElementDataset
Get an elemental property lookup table
getLookupValue(double[]) - Method in class magpie.data.materials.ElementEntry
Given an elemental-property lookup array, get the property for this entry.
getMAE(double[]) - Static method in class magpie.models.regression.LASSORegression
Get Mean Absolute Error (MAE) given residuals
getMaxDifference(double[]) - Method in class magpie.data.materials.CompositionEntry
Calculate maximum difference between the properties of two elements that are present in this entry
getMaximum(double[]) - Method in class magpie.data.materials.CompositionEntry
Get the maximum of an elemental property
getMaxIter() - Method in class magpie.models.regression.AbstractNonlinearRegression
Get the maximum number of iterations allowed
getMean(double[]) - Method in class magpie.data.materials.CompositionEntry
Calculate the alloy mean of a property
getMeasuredClass() - Method in class magpie.data.BaseEntry
Get the measured class variable
getMeasuredClass() - Method in class magpie.data.MultiPropertyEntry
 
getMeasuredClassArray() - Method in class magpie.data.Dataset
Output an array of the measured classes for each entry
getMeasuredProperties() - Method in class magpie.data.MultiPropertyEntry
Get copy all measured properties.
getMeasuredProperties() - Method in class magpie.user.server.thrift.Entry
 
getMeasuredPropertiesSize() - Method in class magpie.user.server.thrift.Entry
 
getMeasuredProperty(int) - Method in class magpie.data.MultiPropertyEntry
Get a single measured property.
getMeasuredPropertyArray(String) - Method in class magpie.data.MultiPropertyDataset
Get measured values for a certain property for all entries in the dataset.
getMeasuredPropertyArray(int) - Method in class magpie.data.MultiPropertyDataset
Get the measured value for a certain property for all entries in the dataset.
getMinimum(double[]) - Method in class magpie.data.materials.CompositionEntry
Get the minimum of an elemental property
getModel(int) - Method in interface magpie.models.interfaces.MultiModel
Get a specific submodel.
getModel(int) - Method in class magpie.models.regression.CompositeRegression
 
getModel(String) - Method in class magpie.models.regression.MultiObjectiveRegression
Get the model designed to predict a certain property.
getModel(int) - Method in class magpie.models.regression.StagedRegression
 
getModel(int) - Method in class magpie.models.SplitModel
 
getModel(String) - Method in class magpie.user.Workspace
Get a model out of the workspace
getModelFull() - Method in class magpie.models.classification.WekaClassifier
 
getModelFull() - Method in interface magpie.models.interfaces.WekaModel
Return model name and options
getModelFull() - Method in class magpie.models.regression.WekaRegression
Return model name and options
getModelInformation(AsyncMethodCallback) - Method in class magpie.user.server.thrift.MagpieServer.AsyncClient
 
getModelInformation(AsyncMethodCallback) - Method in interface magpie.user.server.thrift.MagpieServer.AsyncIface
 
getModelInformation() - Method in class magpie.user.server.thrift.MagpieServer.Client
 
getModelInformation() - Method in interface magpie.user.server.thrift.MagpieServer.Iface
Get information about available models
getModelInformation() - Method in class magpie.user.server.thrift.MagpieServerHandler
 
getModelName() - Method in class magpie.models.classification.WekaClassifier
 
getModelName() - Method in interface magpie.models.interfaces.WekaModel
Return the model name
getModelName() - Method in class magpie.models.regression.WekaRegression
Return the model name
getModelOptions() - Method in class magpie.models.classification.WekaClassifier
 
getModelOptions() - Method in interface magpie.models.interfaces.WekaModel
Return the model options
getModelOptions() - Method in class magpie.models.regression.WekaRegression
Return the model options
getModelType() - Method in class magpie.user.server.thrift.ModelInfo
 
getMost(double[]) - Method in class magpie.data.materials.CompositionEntry
Get the elemental property of the most-prevalent element.
getName() - Method in class magpie.user.server.thrift.Entry
 
getNClasses() - Method in interface magpie.models.classification.AbstractClassifier
 
getNClasses() - Method in class magpie.models.classification.BaseClassifier
 
getNClasses() - Method in class magpie.models.classification.SplitClassifier
 
getNewCandidates() - Method in class magpie.optimization.algorithms.ActiveLearningOptimizer
 
getNewCandidates() - Method in class magpie.optimization.algorithms.genetic.GeneticAlgorithm
 
getNewCandidates() - Method in class magpie.optimization.BaseOptimizer
Based on the current optimization state, return a list of new candidate entries
getNextComposition(Iterator<List<Double>>) - Method in class magpie.data.utilities.generators.CompositionRangeEntryGenerator
Get the next alloy composition in the sequence.
getNFittingParameters() - Method in class magpie.models.regression.AbstractNonlinearRegression
 
getNFittingParameters() - Method in interface magpie.models.regression.AbstractRegressionModel
Number of fitting parameters in a model.
getNFittingParameters() - Method in class magpie.models.regression.ClassificationRegression
 
getNFittingParameters() - Method in class magpie.models.regression.CompositeRegression
 
getNFittingParameters() - Method in class magpie.models.regression.GuessMeanRegression
 
getNFittingParameters() - Method in class magpie.models.regression.LASSORegression
 
getNFittingParameters() - Method in class magpie.models.regression.LinearCorrectedRegression
 
getNFittingParameters() - Method in class magpie.models.regression.MetallurgicalHeuristicRegression
 
getNFittingParameters() - Method in class magpie.models.regression.MixingRuleRegression
 
getNFittingParameters() - Method in class magpie.models.regression.MultiObjectiveRegression
 
getNFittingParameters() - Method in class magpie.models.regression.PolynomialRegression
 
getNFittingParameters() - Method in class magpie.models.regression.RandomGuessRegression
 
getNFittingParameters() - Method in class magpie.models.regression.ScikitLearnRegression
 
getNFittingParameters() - Method in class magpie.models.regression.SingleGuessRegression
 
getNFittingParameters() - Method in class magpie.models.regression.SplitRegression
 
getNFittingParameters() - Method in class magpie.models.regression.StagedRegression
 
getNFittingParameters() - Method in class magpie.models.regression.WekaRegression
 
getNotes() - Method in class magpie.user.server.thrift.ModelInfo
 
getNumToList() - Method in class magpie.user.server.thrift.MagpieServer.searchMultiObjective_args
 
getNumToList() - Method in class magpie.user.server.thrift.MagpieServer.searchSingleObjective_args
 
getObj() - Method in class magpie.user.server.thrift.MagpieServer.searchSingleObjective_args
 
getObject(String) - Method in class magpie.user.Workspace
Gets an object that has been created by the user
getObjective(String) - Static method in class magpie.user.server.thrift.MagpieServerHandler
Parse objective function command.
getObjectiveFunction() - Method in class magpie.optimization.BaseOptimizer
 
getObjectiveFunction(String) - Method in class magpie.optimization.rankers.AdaptiveScalarizingEntryRanker
Get objective function for a certain property.
getObjectiveFunction(String) - Method in class magpie.optimization.rankers.RankAggregationRanker
Get objective function for a certain property.
getObjectivePercentile() - Method in class magpie.optimization.rankers.AdaptiveScalarizingEntryRanker
 
getObjectives() - Method in class magpie.optimization.rankers.AdaptiveScalarizingEntryRanker
 
getObjectives() - Method in class magpie.optimization.rankers.MultiObjectiveEntryRanker
Get properties currently used in objective functions.
getObjectives() - Method in class magpie.optimization.rankers.PropertyFormulaRanker
 
getObjectives() - Method in class magpie.optimization.rankers.RankAggregationRanker
 
getObjs() - Method in class magpie.user.server.thrift.MagpieServer.searchMultiObjective_args
 
getObjsIterator() - Method in class magpie.user.server.thrift.MagpieServer.searchMultiObjective_args
 
getObjsSize() - Method in class magpie.user.server.thrift.MagpieServer.searchMultiObjective_args
 
getOptimizer(String) - Method in class magpie.user.Workspace
Get an BaseClusterer out of the Workspace
getOuch() - Method in class magpie.user.server.thrift.MagpieServer.evaluateProperties_result
 
getOuch() - Method in class magpie.user.server.thrift.MagpieServer.getModelInformation_result
 
getOuch() - Method in class magpie.user.server.thrift.MagpieServer.searchMultiObjective_result
 
getOuch() - Method in class magpie.user.server.thrift.MagpieServer.searchSingleObjective_result
 
getOxidationStates() - Method in class magpie.data.materials.CompositionDataset
Get the list of known oxidation states
getP() - Method in class magpie.optimization.rankers.AdaptiveScalarizingEntryRanker
Get tradeoff parameter.
getP() - Method in class magpie.user.server.thrift.MagpieServer.searchMultiObjective_args
 
getPossibleStates(CompositionEntry) - Method in class magpie.utility.tools.OxidationStateGuesser
Get list of possible charge states.
getPossibleStructures(String) - Method in class magpie.csp.CSPEngine
Get a list of possible structure types for a structure, given composition.
getPossibleStructures(CompositionEntry) - Method in class magpie.csp.CSPEngine
Get a list of possible structure types for a structure, given composition.
getPredictedClass() - Method in class magpie.data.BaseEntry
Get the predicted class variable
getPredictedClass() - Method in class magpie.data.MultiPropertyEntry
 
getPredictedClassArray() - Method in class magpie.data.Dataset
Get the predicted class for each entry
getPredictedProperties() - Method in class magpie.user.server.thrift.Entry
 
getPredictedPropertiesSize() - Method in class magpie.user.server.thrift.Entry
 
getPredictedProperty(int) - Method in class magpie.data.MultiPropertyEntry
Get the predicted properties for an instance.
getPredictedPropertyArray(String) - Method in class magpie.data.MultiPropertyDataset
Get predicted values for a certain property for all entries in the dataset.
getPredictedPropertyArray(int) - Method in class magpie.data.MultiPropertyDataset
Get the predicted value for a certain property for all entries in the dataset.
getProbabilities(BaseClassifier, List<String>, PrototypeSiteInformation, PrototypeEntry) - Method in class magpie.csp.CompositionBasedCSPEngine
 
getProbabilities(BaseClassifier, List<String>, PrototypeSiteInformation, PrototypeEntry) - Method in class magpie.csp.CSPEngine
Calculate probability that a compound will form as each of the known prototypes.
getPropertiesBeingModeled() - Method in class magpie.models.regression.MultiObjectiveRegression
Get a list of properties for which a model is defined.
getPropertiesToAdd() - Method in class magpie.data.utilities.modifiers.AddPropertyModifier
Retrieve list of properties that would be added to a dataset.
getProperty() - Method in class magpie.user.server.thrift.ModelInfo
 
getPropertyClassCount(int) - Method in class magpie.data.MultiPropertyDataset
Get the number of classes for a certain property
getPropertyClasses(String) - Method in class magpie.data.MultiPropertyDataset
Get list of possible classes for a certain property
getPropertyClasses(int) - Method in class magpie.data.MultiPropertyDataset
Get list of possible classes for a certain property
getPropertyClassProbabilties(int) - Method in class magpie.data.MultiPropertyEntry
Get the predicted class probabilities for a certain property.
getPropertyIndex(String) - Method in class magpie.data.MultiPropertyDataset
Lookup the index of a property.
getPropertyLookupTable(String) - Method in class magpie.data.materials.CompositionDataset
Reads in a data file that contains properties for each element.
getPropertyName(int) - Method in class magpie.data.MultiPropertyDataset
Retrieve the name of a certain property.
getPropertyName() - Method in class magpie.models.regression.MixingRuleRegression
Retrieve the property used for alloy mean
getPropertyNames() - Method in class magpie.data.MultiPropertyDataset
Get the names of each property stored in this dataset.
getPropertySet(String) - Static method in class magpie.data.materials.util.PropertyLists
Generate a list of properties based on pre-defined sets.
getProps() - Method in class magpie.user.server.thrift.MagpieServer.evaluateProperties_args
 
getPropsIterator() - Method in class magpie.user.server.thrift.MagpieServer.evaluateProperties_args
 
getPropsSize() - Method in class magpie.user.server.thrift.MagpieServer.evaluateProperties_args
 
getPrototypeNames(double[]) - Method in class magpie.csp.diagramdata.PhaseDiagramStatistics
Get list of all known prototype structures at a composition.
getR() - Method in class magpie.data.utilities.normalizers.SoftmaxNormalizer
Get the scaling constant
getRandomList(int, int) - Method in class magpie.utility.UtilityOperations
Randomly select number from a list of a certain length
getRandomSubset(int) - Method in class magpie.data.Dataset
Generate a random subset of the original data, which is left intact
getRandomSubset(double) - Method in class magpie.data.Dataset
Generate a random subset of the original data, which is left intact
getResidual(double[][], double[]) - Method in class magpie.models.regression.LASSORegression
Determines the residuals from a model
getResult() - Method in class magpie.user.server.thrift.MagpieServer.AsyncClient.evaluateProperties_call
 
getResult() - Method in class magpie.user.server.thrift.MagpieServer.AsyncClient.getModelInformation_call
 
getResult() - Method in class magpie.user.server.thrift.MagpieServer.AsyncClient.searchMultiObjective_call
 
getResult() - Method in class magpie.user.server.thrift.MagpieServer.AsyncClient.searchSingleObjective_call
 
getResult(I, MagpieServer.evaluateProperties_args) - Method in class magpie.user.server.thrift.MagpieServer.Processor.evaluateProperties
 
getResult(I, MagpieServer.getModelInformation_args) - Method in class magpie.user.server.thrift.MagpieServer.Processor.getModelInformation
 
getResult(I, MagpieServer.searchMultiObjective_args) - Method in class magpie.user.server.thrift.MagpieServer.Processor.searchMultiObjective
 
getResult(I, MagpieServer.searchSingleObjective_args) - Method in class magpie.user.server.thrift.MagpieServer.Processor.searchSingleObjective
 
getResultHandler(AbstractNonblockingServer.AsyncFrameBuffer, int) - Method in class magpie.user.server.thrift.MagpieServer.AsyncProcessor.evaluateProperties
 
getResultHandler(AbstractNonblockingServer.AsyncFrameBuffer, int) - Method in class magpie.user.server.thrift.MagpieServer.AsyncProcessor.getModelInformation
 
getResultHandler(AbstractNonblockingServer.AsyncFrameBuffer, int) - Method in class magpie.user.server.thrift.MagpieServer.AsyncProcessor.searchMultiObjective
 
getResultHandler(AbstractNonblockingServer.AsyncFrameBuffer, int) - Method in class magpie.user.server.thrift.MagpieServer.AsyncProcessor.searchSingleObjective
 
getRobustRegressionQ() - Method in interface magpie.models.regression.AbstractRegressionModel
Get desired False Discovery Rate
getRobustRegressionQ() - Method in class magpie.models.regression.BaseRegression
 
getRobustRegressionQ() - Method in class magpie.models.regression.SplitRegression
 
getROCCurve(double[], double[], int) - Method in class magpie.analytics.BaseStatistics
Generate the receiver operating characteristic curve based on the measured and predicted variables for many instances.
getRSDR(double[], int) - Method in class magpie.analytics.utility.RobustRegressionUtility
Calculate the Robust Standard Deviation of Residuals.
getRSDR(double[], double, int) - Method in class magpie.analytics.utility.RobustRegressionUtility
Calculate RSDR if the mean is already known.
getScale() - Method in class magpie.data.utilities.normalizers.InverseNormalizer
Get scale factor used when inverting data
getSearchSpace() - Method in class magpie.optimization.BaseOptimizer
Retrieve entries that define the search space
getSingleAttributeArray(int) - Method in class magpie.data.Dataset
Output a single attribute for each entry
getSiteComposition(int) - Method in class magpie.data.materials.PrototypeEntry
Get composition of a certain site
getSiteGroup(int) - Method in class magpie.data.materials.util.PrototypeSiteInformation
Get indices of sites in a particular group.
getSiteGroupMean(int, double[]) - Method in class magpie.data.materials.PrototypeEntry
Calculate the mean of an elemental property for a certain site
getSiteInfo() - Method in class magpie.data.materials.PrototypeDataset
Get information about each site in this prototype structure
getSiteMean(int, double[]) - Method in class magpie.data.materials.PrototypeEntry
Calculate the mean of an elemental property for a certain site
getSortingOrder() - Method in class magpie.data.materials.CompositionDataset
Get the order in which elements are sorted when storing a composition.
getSortingOrder() - Method in class magpie.data.materials.CompositionEntry
 
getSplitNames() - Method in class magpie.data.utilities.splitters.AllMetalsSplitter
 
getSplitNames() - Method in class magpie.data.utilities.splitters.AttributeIntervalSplitter
 
getSplitNames() - Method in class magpie.data.utilities.splitters.BaseDatasetSplitter
Get the names of the splits this splitter creates
getSplitNames() - Method in class magpie.data.utilities.splitters.ClustererSplitter
 
getSplitNames() - Method in class magpie.data.utilities.splitters.MeasuredClassSplitter
 
getSplitNames() - Method in class magpie.data.utilities.splitters.MixedMetalsSplitter
 
getSplitNames() - Method in class magpie.data.utilities.splitters.MultipleElementGroupsSplitter
 
getSplitNames() - Method in class magpie.data.utilities.splitters.NonZeroClassificationSplitter
 
getSplitNames() - Method in class magpie.data.utilities.splitters.ObjectiveFunctionSplitter
 
getSplitNames() - Method in class magpie.data.utilities.splitters.PredictedClassIntervalSplitter
 
getSplitNames() - Method in class magpie.data.utilities.splitters.SingleElementGroupSplitter
 
getSplitterDetails(boolean) - Method in class magpie.data.utilities.splitters.AllMetalsSplitter
 
getSplitterDetails(boolean) - Method in class magpie.data.utilities.splitters.AttributeIntervalSplitter
 
getSplitterDetails(boolean) - Method in class magpie.data.utilities.splitters.BaseDatasetSplitter
Get details of splitter.
getSplitterDetails(boolean) - Method in class magpie.data.utilities.splitters.ClustererSplitter
 
getSplitterDetails(boolean) - Method in class magpie.data.utilities.splitters.MeasuredClassSplitter
 
getSplitterDetails(boolean) - Method in class magpie.data.utilities.splitters.MultipleElementGroupsSplitter
 
getSplitterDetails(boolean) - Method in class magpie.data.utilities.splitters.NonZeroClassificationSplitter
 
getSplitterDetails(boolean) - Method in class magpie.data.utilities.splitters.ObjectiveFunctionSplitter
 
getSplitterDetails(boolean) - Method in class magpie.data.utilities.splitters.PredictedClassIntervalSplitter
 
getSplitterDetails(boolean) - Method in class magpie.data.utilities.splitters.SingleElementGroupSplitter
 
getStatistics() - Method in class magpie.analytics.BaseStatistics
Retrieve list of statistics stored in this class.
getStatistics() - Method in class magpie.analytics.ClassificationStatistics
 
getStatistics(double[], double[]) - Method in class magpie.analytics.RegressionStatistics
Calculate regression statistics
getStatistics() - Method in class magpie.analytics.RegressionStatistics
 
getSubList() - Method in class magpie.utility.tools.BatchModelEvaluator
Get list of entries to be evaluated
getSubset(int[]) - Method in class magpie.data.Dataset
Get a specific list of entries from the dataset.
getSuccess() - Method in class magpie.user.server.thrift.MagpieServer.evaluateProperties_result
 
getSuccess() - Method in class magpie.user.server.thrift.MagpieServer.getModelInformation_result
 
getSuccess() - Method in class magpie.user.server.thrift.MagpieServer.searchMultiObjective_result
 
getSuccess() - Method in class magpie.user.server.thrift.MagpieServer.searchSingleObjective_result
 
getSuccessIterator() - Method in class magpie.user.server.thrift.MagpieServer.evaluateProperties_result
 
getSuccessIterator() - Method in class magpie.user.server.thrift.MagpieServer.searchMultiObjective_result
 
getSuccessIterator() - Method in class magpie.user.server.thrift.MagpieServer.searchSingleObjective_result
 
getSuccessSize() - Method in class magpie.user.server.thrift.MagpieServer.evaluateProperties_result
 
getSuccessSize() - Method in class magpie.user.server.thrift.MagpieServer.getModelInformation_result
 
getSuccessSize() - Method in class magpie.user.server.thrift.MagpieServer.searchMultiObjective_result
 
getSuccessSize() - Method in class magpie.user.server.thrift.MagpieServer.searchSingleObjective_result
 
getTargetProperty() - Method in class magpie.data.MultiPropertyEntry
Look up which property is being used as the class variable.
getTargetPropertyIndex() - Method in class magpie.data.MultiPropertyDataset
Get the index of the currently active property.
getTargetPropertyName() - Method in class magpie.data.MultiPropertyDataset
Lookup what target property is being used.
getThriftFieldId() - Method in enum magpie.user.server.thrift.Entry._Fields
 
getThriftFieldId() - Method in enum magpie.user.server.thrift.MagpieException._Fields
 
getThriftFieldId() - Method in enum magpie.user.server.thrift.MagpieServer.evaluateProperties_args._Fields
 
getThriftFieldId() - Method in enum magpie.user.server.thrift.MagpieServer.evaluateProperties_result._Fields
 
getThriftFieldId() - Method in enum magpie.user.server.thrift.MagpieServer.getModelInformation_args._Fields
 
getThriftFieldId() - Method in enum magpie.user.server.thrift.MagpieServer.getModelInformation_result._Fields
 
getThriftFieldId() - Method in enum magpie.user.server.thrift.MagpieServer.searchMultiObjective_args._Fields
 
getThriftFieldId() - Method in enum magpie.user.server.thrift.MagpieServer.searchMultiObjective_result._Fields
 
getThriftFieldId() - Method in enum magpie.user.server.thrift.MagpieServer.searchSingleObjective_args._Fields
 
getThriftFieldId() - Method in enum magpie.user.server.thrift.MagpieServer.searchSingleObjective_result._Fields
 
getThriftFieldId() - Method in enum magpie.user.server.thrift.ModelInfo._Fields
 
getTraining() - Method in class magpie.user.server.thrift.ModelInfo
 
getTrainingExamples() - Method in class magpie.data.Dataset
Get a dataset that only contains entries with a measured class variable.
getTrainingSet(CompositionEntry) - Method in class magpie.csp.CSPEngine
Get a training set of all examples of all possible crystal structures at a certain composition
getTrainTime() - Method in class magpie.models.BaseModel
Return when this model was trained
getTrainTime() - Method in class magpie.user.server.thrift.ModelInfo
 
getUnits() - Method in class magpie.user.server.thrift.ModelInfo
 
getUseInverse() - Method in class magpie.models.regression.MixingRuleRegression
 
getValidationMethod() - Method in class magpie.models.BaseModel
Get a description of how this model was validated
getValMethod() - Method in class magpie.user.server.thrift.ModelInfo
 
getValScore() - Method in class magpie.user.server.thrift.ModelInfo
 
getValScoreSize() - Method in class magpie.user.server.thrift.ModelInfo
 
getVariableName(int) - Method in class magpie.models.regression.AbstractNonlinearRegression
 
getVariableNames() - Method in class magpie.user.Workspace
Get the names of all variables stored in this class
getVariableNames() - Method in class magpie.utility.ParsedFunction
Get the list of variables.
getVariableVector(PrototypeEntry) - Method in class magpie.csp.diagramdata.PhaseDiagramStatistics
For a certain prototype, get a vector that describes the characteristics of its phase diagram.
getWekaObjectCitations(Object, Class) - Static method in class magpie.utility.WekaUtility
Generate citations from a Weka object
getWhy() - Method in exception magpie.user.server.thrift.MagpieException
 
GreaterThan - Variable in class magpie.data.utilities.filters.AttributeFilter
Should entries with Feature < Threshold be kept?
GreaterThan - Variable in class magpie.data.utilities.filters.ClassFilter
Should entries with Feature < Threshold be kept?
GridBaseEntryGenerator - Class in magpie.data.utilities.generators
Generate BaseEntry objects that represent a grid.
GridBaseEntryGenerator() - Constructor for class magpie.data.utilities.generators.GridBaseEntryGenerator
 
groupIsIncludedInAttributes(int) - Method in class magpie.data.materials.util.PrototypeSiteInformation
Determine whether a group sites of should be included in attributes.
Guess - Variable in class magpie.models.regression.SingleGuessRegression
Guess for all classes
GuessMeanRegression - Class in magpie.models.regression
Always guess the mean of the values provided during training.
GuessMeanRegression() - Constructor for class magpie.models.regression.GuessMeanRegression
 

H

handlePrinting(List<String>) - Method in class magpie.user.CommandHandler
Run commands that require printing something to screen.
Handler - Static variable in class magpie.user.server.ServerLauncher
Tool used to handle requests
handleSaving(List<String>) - Method in class magpie.user.CommandHandler
Save objects to disk as various formats.
handleSetCommand(List<Object>) - Method in class magpie.models.BaseModel
Handle setting components of a model via the command interface
handleSettings(List<String>) - Method in class magpie.user.CommandHandler
Handles commands that change global settings
handleSubmodelCommand(BaseModel, List<Object>) - Static method in class magpie.models.utility.MultiModelUtility
Runs commands that are specific to MultiModel-based classes.
handleSubmodelPrintCommand(MultiModel, List<String>) - Static method in class magpie.models.utility.MultiModelUtility
Handles printing commands specific to MultiModels.
hashCode() - Method in class magpie.data.BaseEntry
 
hashCode() - Method in class magpie.data.materials.CompositionEntry
 
hashCode() - Method in class magpie.data.materials.PrototypeEntry
 
hashCode() - Method in class magpie.data.materials.util.PrototypeSiteInformation
 
hashCode() - Method in class magpie.user.server.thrift.Entry
 
hashCode() - Method in exception magpie.user.server.thrift.MagpieException
 
hashCode() - Method in class magpie.user.server.thrift.MagpieServer.evaluateProperties_args
 
hashCode() - Method in class magpie.user.server.thrift.MagpieServer.evaluateProperties_result
 
hashCode() - Method in class magpie.user.server.thrift.MagpieServer.getModelInformation_args
 
hashCode() - Method in class magpie.user.server.thrift.MagpieServer.getModelInformation_result
 
hashCode() - Method in class magpie.user.server.thrift.MagpieServer.searchMultiObjective_args
 
hashCode() - Method in class magpie.user.server.thrift.MagpieServer.searchMultiObjective_result
 
hashCode() - Method in class magpie.user.server.thrift.MagpieServer.searchSingleObjective_args
 
hashCode() - Method in class magpie.user.server.thrift.MagpieServer.searchSingleObjective_result
 
hashCode() - Method in class magpie.user.server.thrift.ModelInfo
 
hasMeasuredProperty(int) - Method in class magpie.data.MultiPropertyEntry
Whether a specific property of this entry has been measured
hasMeasurement() - Method in class magpie.data.BaseEntry
 
hasMeasurement() - Method in class magpie.data.MultiPropertyEntry
 
hasNext() - Method in class magpie.utility.NDGridIterator
 
hasPredictedProperty(int) - Method in class magpie.data.MultiPropertyEntry
Whether an specific property has any predicted value
hasPrediction() - Method in class magpie.data.BaseEntry
 
hasPrediction() - Method in class magpie.data.MultiPropertyEntry
 
hasProperty(String) - Method in class magpie.data.MultiPropertyDataset
Check whether dataset contains a certain property
HasStarted - Variable in class magpie.optimization.BaseOptimizer
Whether the algorithm has started
hasStarted() - Method in class magpie.optimization.BaseOptimizer
 
hasVariable(String) - Method in class magpie.user.Workspace
Test whether the user has created a variable
HeuslerCrossover - Class in magpie.optimization.algorithms.genetic.operators
Crossover function for the Heusler Dataset
HeuslerCrossover() - Constructor for class magpie.optimization.algorithms.genetic.operators.HeuslerCrossover
 
HHICalculationModifier - Class in magpie.data.utilities.modifiers
Calculates the Herfindahl-Hirschman Index (HHI) for compounds, stores as property.
HHICalculationModifier() - Constructor for class magpie.data.utilities.modifiers.HHICalculationModifier
 
HTMLFormat - Variable in class magpie.data.materials.CompositionEntry
Whether to print composition in HTML Format
HTTPServer - Static variable in class magpie.user.server.ServerLauncher
HTTP server

I

importCompoundDataset(String) - Method in class magpie.csp.diagramdata.PhaseDiagramStatistics
Load in file containing composition and prototypes of all known compounds.
importDataset(Dataset) - Method in class magpie.optimization.oracles.BaseOracle
Adds a new dataset to be evaluated.
importEntryProperties(String[]) - Method in class magpie.data.MultiPropertyDataset
Used by Dataset.importText(java.lang.String, java.lang.Object[]) to import property measurments for each entry.
importKnownCompounds(String) - Method in class magpie.csp.CSPEngine
Gather a list of known compounds an their prototypes.
importKnownCompounds(String, int, int[]) - Method in class magpie.csp.diagramdata.PhaseDiagramStatistics
Import all known compounds into phase diagram object
importKnownCompounds(Map<CompositionEntry, String>, int, int[]) - Method in class magpie.csp.diagramdata.PhaseDiagramStatistics
Import list of known compounds into phase diagram object
importPropertyNames(String) - Method in class magpie.data.MultiPropertyDataset
Given the line describing property names in the input file, read in property names and possible classes.
importText(String, Object[]) - Method in class magpie.data.Dataset
Imports data from a text file.
importText(String, Object[]) - Method in class magpie.data.materials.CompositionDataset
Read in an dataset from file.
importText(String, Object[]) - Method in class magpie.data.materials.ElementDataset
 
importText(String, Object[]) - Method in class magpie.data.materials.PrototypeDataset
 
importWekaHome() - Static method in class magpie.utility.WekaUtility
Load in packages that were installed with the package manager.
includeMatching - Variable in class magpie.attributes.selectors.RegexAttributeSelector
Whether to include attributes that match
incrementCounter(int[]) - Method in class magpie.csp.diagramdata.OnTheFlyPhaseDiagramStatistics
Increment a counter that iterates through all combinations of elements in a phase diagram.
incrementCounter(int[]) - Method in class magpie.csp.diagramdata.PrecomputedPhaseDiagramStatistics
Deprecated.
Increment a counter that iterates through all combinations of elements in a phase diagram.
incrementCounter(int[]) - Method in class magpie.csp.diagramdata.TernaryPhaseDiagramStatistics
Deprecated.
Increment a counter that iterates through all combinations of elements in a phase diagram.
incrementCounter(int[]) - Method in class magpie.utility.CartesianSumGenerator
Increment position of counter.
incrementCounter(int[], int) - Static method in class magpie.utility.EqualSumCombinations
Increment a counter that iterates through all possible vectors.
incrementCounter() - Method in class magpie.utility.NDGridIterator
Increment position of counter.
IndependentVariableNormalizer - Class in magpie.data.utilities.normalizers
Base class for normalizers that treat attributes/class independently.
IndependentVariableNormalizer() - Constructor for class magpie.data.utilities.normalizers.IndependentVariableNormalizer
 
InitialData - Variable in class magpie.optimization.BaseOptimizer
Initial population used for algorithm
inputFile - Variable in class magpie.user.InputFileParser
Reader holding the input file
InputFileParser - Class in magpie.user
Parses user input files.
InputFileParser() - Constructor for class magpie.user.InputFileParser
Create an instance that reads from standard in.
instantiateClass(String, List<Object>) - Static method in class magpie.user.CommandHandler
Create new instance of a class given type and options.
instantiateClusterer(String, String[]) - Static method in class magpie.cluster.WekaClusterer
Generate a new instance of a Weka-based clusterer.
instantiateWekaModel(String, String[]) - Static method in class magpie.utility.WekaUtility
Instantiate an AbstractClassifier object from Weka.
integrateROCCurve(double[][]) - Static method in class magpie.analytics.BaseStatistics
Integrate area between ROC curve and random guessing.
Intercept - Variable in class magpie.models.regression.LASSORegression
Intercept of the linear model
InverseNormalizer - Class in magpie.data.utilities.normalizers
Invert the attributes.
InverseNormalizer() - Constructor for class magpie.data.utilities.normalizers.InverseNormalizer
 
IonicCompoundFinder - Class in magpie.utility.tools
Given a nominal composition, find nearby compositions that can be charge neutral.
IonicCompoundFinder() - Constructor for class magpie.utility.tools.IonicCompoundFinder
 
IonicCompoundGenerator - Class in magpie.data.utilities.generators
Generate compositions of ionic compounds.
IonicCompoundGenerator() - Constructor for class magpie.data.utilities.generators.IonicCompoundGenerator
 
IonicityAttributeGenerator - Class in magpie.attributes.generators.composition
Generate attributes based on the "ioncity" of a compound.
IonicityAttributeGenerator() - Constructor for class magpie.attributes.generators.composition.IonicityAttributeGenerator
 
IQROutlierFilter - Class in magpie.data.utilities.filters
Filters entries based on whether the class values are outliers using the interquartile range.
IQROutlierFilter() - Constructor for class magpie.data.utilities.filters.IQROutlierFilter
 
isClassifier() - Method in class magpie.user.server.thrift.ModelInfo
 
isCloserThan(Collection<CompositionEntry>, CompositionEntry, int, double) - Static method in class magpie.data.utilities.filters.CompositionSetDistanceFilter
Check whether an entry is closer to a known set of compounds than a certain threshold.
isComplete() - Method in class magpie.optimization.oracles.BaseOracle
Check whether every entry has been evaluated
isInteger(String) - Static method in class magpie.utility.UtilityOperations
Determine whether a string represents an integer.
isMaximizing() - Method in class magpie.optimization.rankers.BaseEntryRanker
 
isMetal - Variable in class magpie.data.utilities.filters.AllMetalsFilter
List indicating which elements are metals
isMetal - Variable in class magpie.data.utilities.splitters.AllMetalsSplitter
List indicating which elements are metals
isOneway() - Method in class magpie.user.server.thrift.MagpieServer.AsyncProcessor.evaluateProperties
 
isOneway() - Method in class magpie.user.server.thrift.MagpieServer.AsyncProcessor.getModelInformation
 
isOneway() - Method in class magpie.user.server.thrift.MagpieServer.AsyncProcessor.searchMultiObjective
 
isOneway() - Method in class magpie.user.server.thrift.MagpieServer.AsyncProcessor.searchSingleObjective
 
isOneway() - Method in class magpie.user.server.thrift.MagpieServer.Processor.evaluateProperties
 
isOneway() - Method in class magpie.user.server.thrift.MagpieServer.Processor.getModelInformation
 
isOneway() - Method in class magpie.user.server.thrift.MagpieServer.Processor.searchMultiObjective
 
isOneway() - Method in class magpie.user.server.thrift.MagpieServer.Processor.searchSingleObjective
 
isOutlier(Dataset) - Method in class magpie.analytics.utility.RobustRegressionUtility
Determines which entries in a dataset qualify as an outlier.
isOutlier(Dataset, int) - Method in class magpie.analytics.utility.RobustRegressionUtility
Determine which entries in a dataset qualify as an outlier, for nonlinear regression purposes.
isRunning() - Static method in class magpie.user.server.ServerLauncher
Check if the servers are running
isSet() - Method in class magpie.data.utilities.generators.PrototypeEntryGenerator
Check whether this generator is ready to go.
isSet(Entry._Fields) - Method in class magpie.user.server.thrift.Entry
Returns true if field corresponding to fieldID is set (has been assigned a value) and false otherwise
isSet(MagpieException._Fields) - Method in exception magpie.user.server.thrift.MagpieException
Returns true if field corresponding to fieldID is set (has been assigned a value) and false otherwise
isSet(MagpieServer.evaluateProperties_args._Fields) - Method in class magpie.user.server.thrift.MagpieServer.evaluateProperties_args
Returns true if field corresponding to fieldID is set (has been assigned a value) and false otherwise
isSet(MagpieServer.evaluateProperties_result._Fields) - Method in class magpie.user.server.thrift.MagpieServer.evaluateProperties_result
Returns true if field corresponding to fieldID is set (has been assigned a value) and false otherwise
isSet(MagpieServer.getModelInformation_args._Fields) - Method in class magpie.user.server.thrift.MagpieServer.getModelInformation_args
Returns true if field corresponding to fieldID is set (has been assigned a value) and false otherwise
isSet(MagpieServer.getModelInformation_result._Fields) - Method in class magpie.user.server.thrift.MagpieServer.getModelInformation_result
Returns true if field corresponding to fieldID is set (has been assigned a value) and false otherwise
isSet(MagpieServer.searchMultiObjective_args._Fields) - Method in class magpie.user.server.thrift.MagpieServer.searchMultiObjective_args
Returns true if field corresponding to fieldID is set (has been assigned a value) and false otherwise
isSet(MagpieServer.searchMultiObjective_result._Fields) - Method in class magpie.user.server.thrift.MagpieServer.searchMultiObjective_result
Returns true if field corresponding to fieldID is set (has been assigned a value) and false otherwise
isSet(MagpieServer.searchSingleObjective_args._Fields) - Method in class magpie.user.server.thrift.MagpieServer.searchSingleObjective_args
Returns true if field corresponding to fieldID is set (has been assigned a value) and false otherwise
isSet(MagpieServer.searchSingleObjective_result._Fields) - Method in class magpie.user.server.thrift.MagpieServer.searchSingleObjective_result
Returns true if field corresponding to fieldID is set (has been assigned a value) and false otherwise
isSet(ModelInfo._Fields) - Method in class magpie.user.server.thrift.ModelInfo
Returns true if field corresponding to fieldID is set (has been assigned a value) and false otherwise
isSetAuthor() - Method in class magpie.user.server.thrift.ModelInfo
Returns true if field author is set (has been assigned a value) and false otherwise
isSetCitation() - Method in class magpie.user.server.thrift.ModelInfo
Returns true if field citation is set (has been assigned a value) and false otherwise
isSetClassifier() - Method in class magpie.user.server.thrift.ModelInfo
Returns true if field classifier is set (has been assigned a value) and false otherwise
isSetClassProbs() - Method in class magpie.user.server.thrift.Entry
Returns true if field classProbs is set (has been assigned a value) and false otherwise
isSetDataType() - Method in class magpie.user.server.thrift.ModelInfo
Returns true if field dataType is set (has been assigned a value) and false otherwise
isSetDescription() - Method in class magpie.user.server.thrift.ModelInfo
Returns true if field description is set (has been assigned a value) and false otherwise
isSetEntries() - Method in class magpie.user.server.thrift.MagpieServer.evaluateProperties_args
Returns true if field entries is set (has been assigned a value) and false otherwise
isSetGenMethod() - Method in class magpie.user.server.thrift.MagpieServer.searchMultiObjective_args
Returns true if field genMethod is set (has been assigned a value) and false otherwise
isSetGenMethod() - Method in class magpie.user.server.thrift.MagpieServer.searchSingleObjective_args
Returns true if field genMethod is set (has been assigned a value) and false otherwise
isSetMeasuredProperties() - Method in class magpie.user.server.thrift.Entry
Returns true if field measuredProperties is set (has been assigned a value) and false otherwise
isSetModelType() - Method in class magpie.user.server.thrift.ModelInfo
Returns true if field modelType is set (has been assigned a value) and false otherwise
isSetName() - Method in class magpie.user.server.thrift.Entry
Returns true if field name is set (has been assigned a value) and false otherwise
isSetNotes() - Method in class magpie.user.server.thrift.ModelInfo
Returns true if field notes is set (has been assigned a value) and false otherwise
isSetNumToList() - Method in class magpie.user.server.thrift.MagpieServer.searchMultiObjective_args
Returns true if field numToList is set (has been assigned a value) and false otherwise
isSetNumToList() - Method in class magpie.user.server.thrift.MagpieServer.searchSingleObjective_args
Returns true if field numToList is set (has been assigned a value) and false otherwise
isSetObj() - Method in class magpie.user.server.thrift.MagpieServer.searchSingleObjective_args
Returns true if field obj is set (has been assigned a value) and false otherwise
isSetObjs() - Method in class magpie.user.server.thrift.MagpieServer.searchMultiObjective_args
Returns true if field objs is set (has been assigned a value) and false otherwise
isSetOuch() - Method in class magpie.user.server.thrift.MagpieServer.evaluateProperties_result
Returns true if field ouch is set (has been assigned a value) and false otherwise
isSetOuch() - Method in class magpie.user.server.thrift.MagpieServer.getModelInformation_result
Returns true if field ouch is set (has been assigned a value) and false otherwise
isSetOuch() - Method in class magpie.user.server.thrift.MagpieServer.searchMultiObjective_result
Returns true if field ouch is set (has been assigned a value) and false otherwise
isSetOuch() - Method in class magpie.user.server.thrift.MagpieServer.searchSingleObjective_result
Returns true if field ouch is set (has been assigned a value) and false otherwise
isSetP() - Method in class magpie.user.server.thrift.MagpieServer.searchMultiObjective_args
Returns true if field p is set (has been assigned a value) and false otherwise
isSetPredictedProperties() - Method in class magpie.user.server.thrift.Entry
Returns true if field predictedProperties is set (has been assigned a value) and false otherwise
isSetProperty() - Method in class magpie.user.server.thrift.ModelInfo
Returns true if field property is set (has been assigned a value) and false otherwise
isSetProps() - Method in class magpie.user.server.thrift.MagpieServer.evaluateProperties_args
Returns true if field props is set (has been assigned a value) and false otherwise
isSetSuccess() - Method in class magpie.user.server.thrift.MagpieServer.evaluateProperties_result
Returns true if field success is set (has been assigned a value) and false otherwise
isSetSuccess() - Method in class magpie.user.server.thrift.MagpieServer.getModelInformation_result
Returns true if field success is set (has been assigned a value) and false otherwise
isSetSuccess() - Method in class magpie.user.server.thrift.MagpieServer.searchMultiObjective_result
Returns true if field success is set (has been assigned a value) and false otherwise
isSetSuccess() - Method in class magpie.user.server.thrift.MagpieServer.searchSingleObjective_result
Returns true if field success is set (has been assigned a value) and false otherwise
isSetTraining() - Method in class magpie.user.server.thrift.ModelInfo
Returns true if field training is set (has been assigned a value) and false otherwise
isSetTrainTime() - Method in class magpie.user.server.thrift.ModelInfo
Returns true if field trainTime is set (has been assigned a value) and false otherwise
isSetUnits() - Method in class magpie.user.server.thrift.ModelInfo
Returns true if field units is set (has been assigned a value) and false otherwise
isSetValMethod() - Method in class magpie.user.server.thrift.ModelInfo
Returns true if field valMethod is set (has been assigned a value) and false otherwise
isSetValScore() - Method in class magpie.user.server.thrift.ModelInfo
Returns true if field valScore is set (has been assigned a value) and false otherwise
isSetWhy() - Method in exception magpie.user.server.thrift.MagpieException
Returns true if field why is set (has been assigned a value) and false otherwise
isTrained() - Method in class magpie.analytics.ClustererStatistics
 
isTrained() - Method in class magpie.attributes.selectors.BaseAttributeSelector
 
isTrained() - Method in class magpie.cluster.BaseClusterer
 
isTrained() - Method in class magpie.data.utilities.normalizers.BaseDatasetNormalizer
 
isTrained() - Method in class magpie.models.BaseModel
 
isUsingMeasured() - Method in class magpie.optimization.rankers.BaseEntryRanker
 
isValidated() - Method in class magpie.models.BaseModel
 
IterationsEvaluated - Variable in class magpie.optimization.analytics.OptimizationStatistics
Number of iterations that have been evaluated
iterator() - Method in class magpie.data.utilities.generators.AlloyingCompositionEntryGenerator
 
iterator() - Method in class magpie.data.utilities.generators.CompositionRangeEntryGenerator
 
iterator() - Method in class magpie.data.utilities.generators.GridBaseEntryGenerator
 
iterator() - Method in class magpie.data.utilities.generators.IonicCompoundGenerator
 
iterator() - Method in class magpie.data.utilities.generators.PhaseDiagramCompositionEntryGenerator
 
iterator() - Method in class magpie.data.utilities.generators.PrototypeEntryGenerator
 
iterator() - Method in class magpie.utility.CartesianSumGenerator
 
iterator() - Method in class magpie.utility.EqualSumCombinations
 

J

Jitter - Variable in class magpie.models.regression.SingleGuessRegression
Amount of jitter added to the answer

K

K - Variable in class magpie.optimization.rankers.RankAggregationRanker
Number of top entries to be interested in.
Kappa - Variable in class magpie.analytics.ClassificationStatistics
Fraction correct modified such that 0 is random guessing and 1 is perfect classification
KnownCompounds - Variable in class magpie.csp.CSPEngine
List of known compounds (used when making predictions)

L

label(Dataset) - Method in class magpie.cluster.BaseClusterer
Mark the most likely cluster for each entry
label(Dataset) - Method in class magpie.data.utilities.filters.AllMetalsFilter
 
label(Dataset) - Method in class magpie.data.utilities.filters.AttributeFilter
 
label(Dataset) - Method in class magpie.data.utilities.filters.BaseDatasetFilter
Given a dataset, determine which entries passes the filter.
label(Dataset) - Method in class magpie.data.utilities.filters.BestInAlloySystemFilter
 
label(Dataset) - Method in class magpie.data.utilities.filters.ClassFilter
 
label(Dataset) - Method in class magpie.data.utilities.filters.ClassProbabilityFilter
 
label(Dataset) - Method in class magpie.data.utilities.filters.ClassRangeFilter
 
label(Dataset) - Method in class magpie.data.utilities.filters.CompositionDistanceFilter
 
label(Dataset) - Method in class magpie.data.utilities.filters.CompositionSetDistanceFilter
 
label(Dataset) - Method in class magpie.data.utilities.filters.ContainsElementFilter
 
label(Dataset) - Method in class magpie.data.utilities.filters.EntryRankerFilter
 
label(Dataset) - Method in class magpie.data.utilities.filters.IQROutlierFilter
 
label(Dataset) - Method in class magpie.data.utilities.filters.MultiFilter
 
label(Dataset) - Method in class magpie.data.utilities.filters.PhaseDiagramExclusionFilter
 
label(Dataset) - Method in class magpie.data.utilities.filters.PredictionOutlierFilter
 
label(Dataset) - Method in class magpie.data.utilities.filters.PropertyFilter
 
label(Dataset) - Method in class magpie.data.utilities.filters.PropertyRangeFilter
 
label(Dataset) - Method in class magpie.data.utilities.filters.RegressionErrorFilter
 
label(Dataset) - Method in class magpie.data.utilities.filters.StabilityFilter
 
label(Dataset) - Method in class magpie.data.utilities.filters.ZScoreOutlierFilter
 
label(Dataset) - Method in class magpie.data.utilities.splitters.AllMetalsSplitter
 
label(Dataset) - Method in class magpie.data.utilities.splitters.AttributeIntervalSplitter
 
label(Dataset) - Method in class magpie.data.utilities.splitters.BaseDatasetSplitter
Given a dataset, determine which subset each entry should belong to.
label(Dataset) - Method in class magpie.data.utilities.splitters.ClustererSplitter
 
label(Dataset) - Method in class magpie.data.utilities.splitters.MeasuredClassSplitter
 
label(Dataset) - Method in class magpie.data.utilities.splitters.MixedMetalsSplitter
 
label(Dataset) - Method in class magpie.data.utilities.splitters.MultipleElementGroupsSplitter
 
label(Dataset) - Method in class magpie.data.utilities.splitters.NonZeroClassificationSplitter
 
label(Dataset) - Method in class magpie.data.utilities.splitters.ObjectiveFunctionSplitter
 
label(Dataset) - Method in class magpie.data.utilities.splitters.PredictedClassIntervalSplitter
 
label(Dataset) - Method in class magpie.data.utilities.splitters.SingleElementGroupSplitter
 
label_protected(Dataset) - Method in class magpie.cluster.BaseClusterer
label_protected(Dataset) - Method in class magpie.cluster.WekaClusterer
 
LASSORegression - Class in magpie.models.regression
This class enables regression using the LASSO algorithm, as described by this page.
LASSORegression() - Constructor for class magpie.models.regression.LASSORegression
 
LastCompositionBin - Variable in class magpie.csp.CSPEngine
Matched composition bin of last entry evaluated.
LastNComponents - Variable in class magpie.csp.CSPEngine
Number of elements in the last entry evaluated in this class.
LastResults - Variable in class magpie.utility.tools.PhaseDiagramExclusionValidator
Results from previous test.
LastStatistics - Variable in class magpie.utility.tools.PhaseDiagramExclusionValidator
Statistics from last test
LessThan - Variable in class magpie.data.utilities.filters.AttributeFilter
Should entries with Feature > Threshold be kept?
LessThan - Variable in class magpie.data.utilities.filters.ClassFilter
Should entries with Feature > Threshold be kept?
LinearCorrectedRegression - Class in magpie.models.regression
Apply a linear correction to results from another model.
LinearCorrectedRegression() - Constructor for class magpie.models.regression.LinearCorrectedRegression
 
linearFit(double[], double[], boolean) - Static method in class magpie.models.regression.LASSORegression
Find the best linear fit
ListenPort - Static variable in class magpie.user.server.ServerLauncher
Port on which to listen
loadPropertyLookupTable(String, String) - Static method in class magpie.data.materials.util.LookupData
Load in an elemental property lookup table
loadState(String) - Static method in class magpie.data.Dataset
Read the state from file using serialization
loadState(String) - Static method in class magpie.models.BaseModel
Read the state from file using serialization
loadState(String) - Static method in class magpie.utility.UtilityOperations
Read the state from file using serialization
Location - Variable in class magpie.utility.interfaces.Citation
URL of resource being cited.
LookupData - Class in magpie.data.materials.util
Holds data that any CompositionDataset needs to lookup.
LookupData() - Constructor for class magpie.data.materials.util.LookupData
 
LookupData - Variable in class magpie.data.utilities.generators.IonicCompoundGenerator
Dataset used to compute ionic compounds
LookupDirectory - Variable in class magpie.data.materials.ElementDataset
Directory containing elemental property lookup tables
LookupOracle - Class in magpie.optimization.oracles
BaseOracle that looks up measured class properties from a list of already-solved entries.
LookupOracle() - Constructor for class magpie.optimization.oracles.LookupOracle
 
LookupTable - Variable in class magpie.models.regression.MixingRuleRegression
Lookup table for property of interest
LookupTable - Variable in class magpie.optimization.oracles.LookupOracle
Map that links a Dataset entry to one with measured properties
LookupTableAttributeGenerator - Class in magpie.attributes.generators
Tool to add precomputed attributes from a lookup table.
LookupTableAttributeGenerator() - Constructor for class magpie.attributes.generators.LookupTableAttributeGenerator
 

M

MAE - Variable in class magpie.analytics.RegressionStatistics
Mean absolute error
magpie - package magpie
Holds the main class for this program
Magpie - Class in magpie
Main program for text-based interface.
Magpie() - Constructor for class magpie.Magpie
 
magpie.analytics - package magpie.analytics
Classes necessary to generate statistics about model, searcher, clusterer performance.
magpie.analytics.utility - package magpie.analytics.utility
Classes that handle calculation of useful statistics
magpie.attributes.evaluators - package magpie.attributes.evaluators
Methods to evaluate the predictive power of single attributes
magpie.attributes.expanders - package magpie.attributes.expanders
Classes that expand the number of available attributes
magpie.attributes.generators - package magpie.attributes.generators
Objects design to compute new attributes for a dataset.
magpie.attributes.generators.composition - package magpie.attributes.generators.composition
Attributes based on the composition of a material.
magpie.attributes.generators.element - package magpie.attributes.generators.element
Attribute generators for elements from the periodic table.
magpie.attributes.selectors - package magpie.attributes.selectors
Methods to select attribute subsets that might lead to more effective models
magpie.cluster - package magpie.cluster
Separate data into multiple subsets using unsupervised learning
magpie.csp - package magpie.csp
Models that predict what crystal structure will appear under different conditions.
magpie.csp.diagramdata - package magpie.csp.diagramdata
 
magpie.data - package magpie.data
Objects designed to store, manipulate, and output data
magpie.data.materials - package magpie.data.materials
Datasets specifically designed to handle data from OQMD
magpie.data.materials.util - package magpie.data.materials.util
Data structures used by several types of Dataset/Entry
magpie.data.utilities - package magpie.data.utilities
Abstract objects that hold miscellaneous helpful operations for Datasets
magpie.data.utilities.filters - package magpie.data.utilities.filters
Classes that allow for filtering undesired entries out of a Dataset
magpie.data.utilities.generators - package magpie.data.utilities.generators
Holds classes designed to generate entries.
magpie.data.utilities.modifiers - package magpie.data.utilities.modifiers
Operations that make changes to a Dataset and the entries it contains
magpie.data.utilities.normalizers - package magpie.data.utilities.normalizers
Adjust attributes and/or class to all exist on the same range.
magpie.data.utilities.splitters - package magpie.data.utilities.splitters
Operations to partition a Dataset into multiple subsets.
magpie.models - package magpie.models
Templates for different model types
magpie.models.classification - package magpie.models.classification
Models designed to classify data into multiple categories
magpie.models.interfaces - package magpie.models.interfaces
Holds interfaces that define certain classes of models
magpie.models.regression - package magpie.models.regression
Models that predict a single, continuous class variable
magpie.models.regression.nonlinear - package magpie.models.regression.nonlinear
Sample AbstractNonlinearRegression implementations
magpie.models.utility - package magpie.models.utility
Abstract classes that hold operations necessary to run different models
magpie.optimization - package magpie.optimization
Objects necessary for performing optimization tasks
magpie.optimization.algorithms - package magpie.optimization.algorithms
Different kinds of general-purpose optimization algorithms
magpie.optimization.algorithms.genetic - package magpie.optimization.algorithms.genetic
Contains objects related to genetic algorithms
magpie.optimization.algorithms.genetic.operators - package magpie.optimization.algorithms.genetic.operators
 
magpie.optimization.analytics - package magpie.optimization.analytics
Tools to analyze results from optimization algorithms
magpie.optimization.oracles - package magpie.optimization.oracles
Classes that supervise the calculation of new data
magpie.optimization.rankers - package magpie.optimization.rankers
Classes that rank entries based on arbitrary criteria
magpie.user - package magpie.user
Classes that make the user interface possible
magpie.user.server - package magpie.user.server
 
magpie.user.server.thrift - package magpie.user.server.thrift
Classes auto-generated by Thrift
magpie.utility - package magpie.utility
Junk that does not fall under another category
magpie.utility.interfaces - package magpie.utility.interfaces
Interfaces that are useful for a variety of object types.
magpie.utility.tools - package magpie.utility.tools
Utilities that can be used from the command line.
MagpieException - Exception in magpie.user.server.thrift
 
MagpieException() - Constructor for exception magpie.user.server.thrift.MagpieException
 
MagpieException(String) - Constructor for exception magpie.user.server.thrift.MagpieException
 
MagpieException(MagpieException) - Constructor for exception magpie.user.server.thrift.MagpieException
Performs a deep copy on other.
MagpieException._Fields - Enum in magpie.user.server.thrift
The set of fields this struct contains, along with convenience methods for finding and manipulating them.
MagpieServer - Class in magpie.user.server.thrift
 
MagpieServer() - Constructor for class magpie.user.server.thrift.MagpieServer
 
MagpieServer.AsyncClient - Class in magpie.user.server.thrift
 
MagpieServer.AsyncClient(TProtocolFactory, TAsyncClientManager, TNonblockingTransport) - Constructor for class magpie.user.server.thrift.MagpieServer.AsyncClient
 
MagpieServer.AsyncClient.evaluateProperties_call - Class in magpie.user.server.thrift
 
MagpieServer.AsyncClient.evaluateProperties_call(List<Entry>, List<String>, AsyncMethodCallback, TAsyncClient, TProtocolFactory, TNonblockingTransport) - Constructor for class magpie.user.server.thrift.MagpieServer.AsyncClient.evaluateProperties_call
 
MagpieServer.AsyncClient.Factory - Class in magpie.user.server.thrift
 
MagpieServer.AsyncClient.Factory(TAsyncClientManager, TProtocolFactory) - Constructor for class magpie.user.server.thrift.MagpieServer.AsyncClient.Factory
 
MagpieServer.AsyncClient.getModelInformation_call - Class in magpie.user.server.thrift
 
MagpieServer.AsyncClient.getModelInformation_call(AsyncMethodCallback, TAsyncClient, TProtocolFactory, TNonblockingTransport) - Constructor for class magpie.user.server.thrift.MagpieServer.AsyncClient.getModelInformation_call
 
MagpieServer.AsyncClient.searchMultiObjective_call - Class in magpie.user.server.thrift
 
MagpieServer.AsyncClient.searchMultiObjective_call(double, List<String>, String, int, AsyncMethodCallback, TAsyncClient, TProtocolFactory, TNonblockingTransport) - Constructor for class magpie.user.server.thrift.MagpieServer.AsyncClient.searchMultiObjective_call
 
MagpieServer.AsyncClient.searchSingleObjective_call - Class in magpie.user.server.thrift
 
MagpieServer.AsyncClient.searchSingleObjective_call(String, String, int, AsyncMethodCallback, TAsyncClient, TProtocolFactory, TNonblockingTransport) - Constructor for class magpie.user.server.thrift.MagpieServer.AsyncClient.searchSingleObjective_call
 
MagpieServer.AsyncIface - Interface in magpie.user.server.thrift
 
MagpieServer.AsyncProcessor<I extends MagpieServer.AsyncIface> - Class in magpie.user.server.thrift
 
MagpieServer.AsyncProcessor(I) - Constructor for class magpie.user.server.thrift.MagpieServer.AsyncProcessor
 
MagpieServer.AsyncProcessor(I, Map<String, AsyncProcessFunction<I, ? extends TBase, ?>>) - Constructor for class magpie.user.server.thrift.MagpieServer.AsyncProcessor
 
MagpieServer.AsyncProcessor.evaluateProperties<I extends MagpieServer.AsyncIface> - Class in magpie.user.server.thrift
 
MagpieServer.AsyncProcessor.evaluateProperties() - Constructor for class magpie.user.server.thrift.MagpieServer.AsyncProcessor.evaluateProperties
 
MagpieServer.AsyncProcessor.getModelInformation<I extends MagpieServer.AsyncIface> - Class in magpie.user.server.thrift
 
MagpieServer.AsyncProcessor.getModelInformation() - Constructor for class magpie.user.server.thrift.MagpieServer.AsyncProcessor.getModelInformation
 
MagpieServer.AsyncProcessor.searchMultiObjective<I extends MagpieServer.AsyncIface> - Class in magpie.user.server.thrift
 
MagpieServer.AsyncProcessor.searchMultiObjective() - Constructor for class magpie.user.server.thrift.MagpieServer.AsyncProcessor.searchMultiObjective
 
MagpieServer.AsyncProcessor.searchSingleObjective<I extends MagpieServer.AsyncIface> - Class in magpie.user.server.thrift
 
MagpieServer.AsyncProcessor.searchSingleObjective() - Constructor for class magpie.user.server.thrift.MagpieServer.AsyncProcessor.searchSingleObjective
 
MagpieServer.Client - Class in magpie.user.server.thrift
 
MagpieServer.Client(TProtocol) - Constructor for class magpie.user.server.thrift.MagpieServer.Client
 
MagpieServer.Client(TProtocol, TProtocol) - Constructor for class magpie.user.server.thrift.MagpieServer.Client
 
MagpieServer.Client.Factory - Class in magpie.user.server.thrift
 
MagpieServer.Client.Factory() - Constructor for class magpie.user.server.thrift.MagpieServer.Client.Factory
 
MagpieServer.evaluateProperties_args - Class in magpie.user.server.thrift
 
MagpieServer.evaluateProperties_args() - Constructor for class magpie.user.server.thrift.MagpieServer.evaluateProperties_args
 
MagpieServer.evaluateProperties_args(List<Entry>, List<String>) - Constructor for class magpie.user.server.thrift.MagpieServer.evaluateProperties_args
 
MagpieServer.evaluateProperties_args(MagpieServer.evaluateProperties_args) - Constructor for class magpie.user.server.thrift.MagpieServer.evaluateProperties_args
Performs a deep copy on other.
MagpieServer.evaluateProperties_args._Fields - Enum in magpie.user.server.thrift
The set of fields this struct contains, along with convenience methods for finding and manipulating them.
MagpieServer.evaluateProperties_result - Class in magpie.user.server.thrift
 
MagpieServer.evaluateProperties_result() - Constructor for class magpie.user.server.thrift.MagpieServer.evaluateProperties_result
 
MagpieServer.evaluateProperties_result(List<Entry>, MagpieException) - Constructor for class magpie.user.server.thrift.MagpieServer.evaluateProperties_result
 
MagpieServer.evaluateProperties_result(MagpieServer.evaluateProperties_result) - Constructor for class magpie.user.server.thrift.MagpieServer.evaluateProperties_result
Performs a deep copy on other.
MagpieServer.evaluateProperties_result._Fields - Enum in magpie.user.server.thrift
The set of fields this struct contains, along with convenience methods for finding and manipulating them.
MagpieServer.getModelInformation_args - Class in magpie.user.server.thrift
 
MagpieServer.getModelInformation_args() - Constructor for class magpie.user.server.thrift.MagpieServer.getModelInformation_args
 
MagpieServer.getModelInformation_args(MagpieServer.getModelInformation_args) - Constructor for class magpie.user.server.thrift.MagpieServer.getModelInformation_args
Performs a deep copy on other.
MagpieServer.getModelInformation_args._Fields - Enum in magpie.user.server.thrift
The set of fields this struct contains, along with convenience methods for finding and manipulating them.
MagpieServer.getModelInformation_result - Class in magpie.user.server.thrift
 
MagpieServer.getModelInformation_result() - Constructor for class magpie.user.server.thrift.MagpieServer.getModelInformation_result
 
MagpieServer.getModelInformation_result(Map<String, ModelInfo>, MagpieException) - Constructor for class magpie.user.server.thrift.MagpieServer.getModelInformation_result
 
MagpieServer.getModelInformation_result(MagpieServer.getModelInformation_result) - Constructor for class magpie.user.server.thrift.MagpieServer.getModelInformation_result
Performs a deep copy on other.
MagpieServer.getModelInformation_result._Fields - Enum in magpie.user.server.thrift
The set of fields this struct contains, along with convenience methods for finding and manipulating them.
MagpieServer.Iface - Interface in magpie.user.server.thrift
 
MagpieServer.Processor<I extends MagpieServer.Iface> - Class in magpie.user.server.thrift
 
MagpieServer.Processor(I) - Constructor for class magpie.user.server.thrift.MagpieServer.Processor
 
MagpieServer.Processor(I, Map<String, ProcessFunction<I, ? extends TBase>>) - Constructor for class magpie.user.server.thrift.MagpieServer.Processor
 
MagpieServer.Processor.evaluateProperties<I extends MagpieServer.Iface> - Class in magpie.user.server.thrift
 
MagpieServer.Processor.evaluateProperties() - Constructor for class magpie.user.server.thrift.MagpieServer.Processor.evaluateProperties
 
MagpieServer.Processor.getModelInformation<I extends MagpieServer.Iface> - Class in magpie.user.server.thrift
 
MagpieServer.Processor.getModelInformation() - Constructor for class magpie.user.server.thrift.MagpieServer.Processor.getModelInformation
 
MagpieServer.Processor.searchMultiObjective<I extends MagpieServer.Iface> - Class in magpie.user.server.thrift
 
MagpieServer.Processor.searchMultiObjective() - Constructor for class magpie.user.server.thrift.MagpieServer.Processor.searchMultiObjective
 
MagpieServer.Processor.searchSingleObjective<I extends MagpieServer.Iface> - Class in magpie.user.server.thrift
 
MagpieServer.Processor.searchSingleObjective() - Constructor for class magpie.user.server.thrift.MagpieServer.Processor.searchSingleObjective
 
MagpieServer.searchMultiObjective_args - Class in magpie.user.server.thrift
 
MagpieServer.searchMultiObjective_args() - Constructor for class magpie.user.server.thrift.MagpieServer.searchMultiObjective_args
 
MagpieServer.searchMultiObjective_args(double, List<String>, String, int) - Constructor for class magpie.user.server.thrift.MagpieServer.searchMultiObjective_args
 
MagpieServer.searchMultiObjective_args(MagpieServer.searchMultiObjective_args) - Constructor for class magpie.user.server.thrift.MagpieServer.searchMultiObjective_args
Performs a deep copy on other.
MagpieServer.searchMultiObjective_args._Fields - Enum in magpie.user.server.thrift
The set of fields this struct contains, along with convenience methods for finding and manipulating them.
MagpieServer.searchMultiObjective_result - Class in magpie.user.server.thrift
 
MagpieServer.searchMultiObjective_result() - Constructor for class magpie.user.server.thrift.MagpieServer.searchMultiObjective_result
 
MagpieServer.searchMultiObjective_result(List<Entry>, MagpieException) - Constructor for class magpie.user.server.thrift.MagpieServer.searchMultiObjective_result
 
MagpieServer.searchMultiObjective_result(MagpieServer.searchMultiObjective_result) - Constructor for class magpie.user.server.thrift.MagpieServer.searchMultiObjective_result
Performs a deep copy on other.
MagpieServer.searchMultiObjective_result._Fields - Enum in magpie.user.server.thrift
The set of fields this struct contains, along with convenience methods for finding and manipulating them.
MagpieServer.searchSingleObjective_args - Class in magpie.user.server.thrift
 
MagpieServer.searchSingleObjective_args() - Constructor for class magpie.user.server.thrift.MagpieServer.searchSingleObjective_args
 
MagpieServer.searchSingleObjective_args(String, String, int) - Constructor for class magpie.user.server.thrift.MagpieServer.searchSingleObjective_args
 
MagpieServer.searchSingleObjective_args(MagpieServer.searchSingleObjective_args) - Constructor for class magpie.user.server.thrift.MagpieServer.searchSingleObjective_args
Performs a deep copy on other.
MagpieServer.searchSingleObjective_args._Fields - Enum in magpie.user.server.thrift
The set of fields this struct contains, along with convenience methods for finding and manipulating them.
MagpieServer.searchSingleObjective_result - Class in magpie.user.server.thrift
 
MagpieServer.searchSingleObjective_result() - Constructor for class magpie.user.server.thrift.MagpieServer.searchSingleObjective_result
 
MagpieServer.searchSingleObjective_result(List<Entry>, MagpieException) - Constructor for class magpie.user.server.thrift.MagpieServer.searchSingleObjective_result
 
MagpieServer.searchSingleObjective_result(MagpieServer.searchSingleObjective_result) - Constructor for class magpie.user.server.thrift.MagpieServer.searchSingleObjective_result
Performs a deep copy on other.
MagpieServer.searchSingleObjective_result._Fields - Enum in magpie.user.server.thrift
The set of fields this struct contains, along with convenience methods for finding and manipulating them.
MagpieServerHandler - Class in magpie.user.server.thrift
Handles requests for the MagpieServer.
MagpieServerHandler() - Constructor for class magpie.user.server.thrift.MagpieServerHandler
 
main(String[]) - Static method in class magpie.Magpie
Launch Magpie.
main(String[]) - Static method in class magpie.user.server.ServerLauncher
 
makeClassifier(PhaseDiagramStatistics, PrototypeDataset) - Method in class magpie.csp.CompositionBasedCSPEngine
 
makeClassifier(PhaseDiagramStatistics, PrototypeDataset) - Method in class magpie.csp.CSPEngine
Given the dataset of training examples, make a classifier to predict the probability that a prototype will form at a certain composition.
makeClassifier(PhaseDiagramStatistics, PrototypeDataset) - Method in class magpie.csp.DMSPEngine
 
makeObjectiveFunction(Dataset) - Method in class magpie.models.regression.AbstractNonlinearRegression
Generate an anonymous MultivariateFunction object that calculates the error between the equation described by the user as a function of the fitting coefficients.
makeSiteInfo(double[]) - Method in class magpie.csp.CSPEngine
Generate PrototypeSiteInformation appropriate for a certain crystal prototype.
matchEntries(BaseEntry, int) - Method in class magpie.data.Dataset
Find entries in this dataset with attributes closest to a user-provided entry.
MathUtils - Class in magpie.utility
Math operations that are simple and useful for many operations
MathUtils() - Constructor for class magpie.utility.MathUtils
 
MaxAlloying - Variable in class magpie.data.utilities.generators.AlloyingCompositionEntryGenerator
Maximum amount to add.
MaxBaseElement - Variable in class magpie.data.utilities.generators.CompositionRangeEntryGenerator
Set maximum amount of base element
MaxCandidates - Variable in class magpie.analytics.TargetRegressionStatistics
Maximum number of candidates for ranking analysis
MaxEntryEvaluations - Static variable in class magpie.user.server.thrift.MagpieServerHandler
Maximum number of entries to evaluate (precaution measure).
MaxFraction - Variable in class magpie.data.utilities.generators.CompositionRangeEntryGenerator
Maximum fraction of certain element.
maximumIterations() - Method in class magpie.optimization.BaseOptimizer
 
MaxIteration - Variable in class magpie.optimization.BaseOptimizer
Iteration at which optimization stops
MaxNumberTerms - Variable in class magpie.models.regression.LASSORegression
Maximum number of features allowed in model (-1 is unlimited)
MaxOrder - Variable in class magpie.data.utilities.generators.PhaseDiagramCompositionEntryGenerator
Maximum number of constituents
MaxWindowSize - Variable in class magpie.analytics.TargetRegressionStatistics
Maximum tolerance during window size analysis
MCC - Variable in class magpie.analytics.ClassificationStatistics
Matthews Correlation Coefficient
Measured - Variable in class magpie.analytics.BaseStatistics
Measured value of class variable
MeasuredClassSplitter - Class in magpie.data.utilities.splitters
Splits based on measured class variable.
MeasuredClassSplitter() - Constructor for class magpie.data.utilities.splitters.MeasuredClassSplitter
 
measuredProperties - Variable in class magpie.user.server.thrift.Entry
 
MeredigAttributeGenerator - Class in magpie.attributes.generators.composition
Generates several attributes first demonstrated by Meredig & Agrawal et al..
MeredigAttributeGenerator() - Constructor for class magpie.attributes.generators.composition.MeredigAttributeGenerator
 
MeredigAttributeSelector - Class in magpie.attributes.selectors
Select only attributes that were used by Meredig et al.
MeredigAttributeSelector() - Constructor for class magpie.attributes.selectors.MeredigAttributeSelector
 
metaDataMap - Static variable in class magpie.user.server.thrift.Entry
 
metaDataMap - Static variable in exception magpie.user.server.thrift.MagpieException
 
metaDataMap - Static variable in class magpie.user.server.thrift.MagpieServer.evaluateProperties_args
 
metaDataMap - Static variable in class magpie.user.server.thrift.MagpieServer.evaluateProperties_result
 
metaDataMap - Static variable in class magpie.user.server.thrift.MagpieServer.getModelInformation_args
 
metaDataMap - Static variable in class magpie.user.server.thrift.MagpieServer.getModelInformation_result
 
metaDataMap - Static variable in class magpie.user.server.thrift.MagpieServer.searchMultiObjective_args
 
metaDataMap - Static variable in class magpie.user.server.thrift.MagpieServer.searchMultiObjective_result
 
metaDataMap - Static variable in class magpie.user.server.thrift.MagpieServer.searchSingleObjective_args
 
metaDataMap - Static variable in class magpie.user.server.thrift.MagpieServer.searchSingleObjective_result
 
metaDataMap - Static variable in class magpie.user.server.thrift.ModelInfo
 
MetallurgicalHeuristicRegression - Class in magpie.models.regression
Estimate formation energy for ternary+ alloys using a metallurgical heuristic.
MetallurgicalHeuristicRegression() - Constructor for class magpie.models.regression.MetallurgicalHeuristicRegression
 
MinBaseElement - Variable in class magpie.data.utilities.generators.CompositionRangeEntryGenerator
Set minimum amount of base element
MinDistance - Variable in class magpie.csp.diagramdata.PhaseDiagramStatistics
Minimum Manhattan distance between compositions to be considered equal
MinFraction - Variable in class magpie.data.utilities.generators.CompositionRangeEntryGenerator
Minimum fraction of certain element.
MinOrder - Variable in class magpie.data.utilities.generators.PhaseDiagramCompositionEntryGenerator
Minimum number of constituents
MixedMetalsSplitter - Class in magpie.data.utilities.splitters
This class splits a CompositionDataset into three subsets: all metals (0), no metals (1), mixture (2)
MixedMetalsSplitter() - Constructor for class magpie.data.utilities.splitters.MixedMetalsSplitter
 
MixingRuleRegression - Class in magpie.models.regression
Predicts the class of a CompositionEntry based on the composition-weighted mean.
MixingRuleRegression() - Constructor for class magpie.models.regression.MixingRuleRegression
 
Model - Variable in class magpie.models.classification.WekaClassifier
Link to Weka-based model
Model - Variable in class magpie.models.regression.CompositeRegression
Collections of models used by this class
Model - Variable in class magpie.models.regression.WekaRegression
Link to Weka-based model
Model - Variable in class magpie.models.SplitModel
List of of models used by this model
Model - Variable in class magpie.optimization.algorithms.ActiveLearningOptimizer
Internal model used to make predictions
Model - Variable in class magpie.user.server.ModelPackage
Model to be evaluated
Model - Variable in class magpie.utility.ModelRunningThread
 
model_defined - Variable in class magpie.models.classification.WekaClassifier
Whether model type has been defined
model_defined - Variable in class magpie.models.regression.WekaRegression
Whether model type has been defined
Model_Options - Variable in class magpie.models.classification.WekaClassifier
Options supplied when instantiating Model
Model_Options - Variable in class magpie.models.regression.WekaRegression
Options supplied when instantiating Model
Model_Type - Variable in class magpie.models.classification.WekaClassifier
Name of model type currently in use
Model_Type - Variable in class magpie.models.regression.WekaRegression
Name of model type currently in use
ModelInfo - Class in magpie.user.server.thrift
 
ModelInfo() - Constructor for class magpie.user.server.thrift.ModelInfo
 
ModelInfo(String, String, String, String, String, String, String, String, boolean, Map<String, Double>, String, String, String) - Constructor for class magpie.user.server.thrift.ModelInfo
 
ModelInfo(ModelInfo) - Constructor for class magpie.user.server.thrift.ModelInfo
Performs a deep copy on other.
ModelInfo._Fields - Enum in magpie.user.server.thrift
The set of fields this struct contains, along with convenience methods for finding and manipulating them.
ModelInformation - Variable in class magpie.user.server.thrift.MagpieServerHandler
Information about each model
modelIsDefined(String) - Method in class magpie.models.regression.MultiObjectiveRegression
Determine whether a model for a certain property is defined
modelIsTrained(String) - Method in class magpie.models.regression.MultiObjectiveRegression
Whether the model for a certain property is trained.
modelIsValidated(String) - Method in class magpie.models.regression.MultiObjectiveRegression
Whether the model for a certain property is validated
ModelPackage - Class in magpie.user.server
Holds information about a model.
ModelPackage(Dataset, BaseModel) - Constructor for class magpie.user.server.ModelPackage
Initialize model package
ModelPredictionAttributeGenerator - Class in magpie.attributes.generators
Use the result from another model as an attribute.
ModelPredictionAttributeGenerator() - Constructor for class magpie.attributes.generators.ModelPredictionAttributeGenerator
 
ModelRunningThread - Class in magpie.utility
This class serves a sole purpose: asynchronously run a model.
ModelRunningThread(BaseModel, Dataset) - Constructor for class magpie.utility.ModelRunningThread
 
Models - Variable in class magpie.models.regression.MultiObjectiveRegression
Map of property name to model used to predict it.
modelType - Variable in class magpie.user.server.thrift.ModelInfo
 
modifyDataset(Dataset) - Method in class magpie.data.utilities.modifiers.AddPropertyModifier
 
modifyDataset(Dataset) - Method in class magpie.data.utilities.modifiers.BaseDatasetModifier
Apply changes to the Dataset.
modifyDataset(Dataset) - Method in class magpie.data.utilities.modifiers.ClassEliminationModifier
 
modifyDataset(Dataset) - Method in class magpie.data.utilities.modifiers.ClassIntervalModifier
 
modifyDataset(Dataset) - Method in class magpie.data.utilities.modifiers.CompositionSetDistanceModifier
 
modifyDataset(Dataset) - Method in class magpie.data.utilities.modifiers.DiscreteToContinuousModifier
 
modifyDataset(Dataset) - Method in class magpie.data.utilities.modifiers.ErrorSignalModifier
 
modifyDataset(Dataset) - Method in class magpie.data.utilities.modifiers.HHICalculationModifier
 
modifyDataset(Dataset) - Method in class magpie.data.utilities.modifiers.NaNToMeanModifier
 
modifyDataset(Dataset) - Method in class magpie.data.utilities.modifiers.NonZeroClassModifier
 
modifyDataset(Dataset) - Method in class magpie.data.utilities.modifiers.PartitionToClassModifier
 
modifyDataset(Dataset) - Method in class magpie.data.utilities.modifiers.SetClassNamesModifier
 
modifyDataset(Dataset) - Method in class magpie.data.utilities.modifiers.StabilityCalculationModifier
 
modifyDataset(Dataset) - Method in class magpie.data.utilities.modifiers.VolumeToLatticeParamModifier
 
MRE - Variable in class magpie.analytics.RegressionStatistics
Mean relative error
MultiFilter - Class in magpie.data.utilities.filters
Filter that incorporates multiple other filters.
MultiFilter() - Constructor for class magpie.data.utilities.filters.MultiFilter
 
MultiModel - Interface in magpie.models.interfaces
Interface for models that contain submodels.
MultiModelUtility - Class in magpie.models.utility
Contains commands to handle MultiModel operations
MultiModelUtility() - Constructor for class magpie.models.utility.MultiModelUtility
 
MultiObjectiveEntryRanker - Class in magpie.optimization.rankers
Base class for multi-objective entry rankers.
MultiObjectiveEntryRanker() - Constructor for class magpie.optimization.rankers.MultiObjectiveEntryRanker
 
MultiObjectiveRegression - Class in magpie.models.regression
Employs multiple models, each designed to predict a different property that composes the class variable.
MultiObjectiveRegression() - Constructor for class magpie.models.regression.MultiObjectiveRegression
 
MultipleElementGroupsSplitter - Class in magpie.data.utilities.splitters
Splits entries into multiple groups depending on which elements they contain.
MultipleElementGroupsSplitter() - Constructor for class magpie.data.utilities.splitters.MultipleElementGroupsSplitter
 
MultiPropertyDataset - Class in magpie.data
Dataset that can store multiple properties for each entry.
MultiPropertyDataset() - Constructor for class magpie.data.MultiPropertyDataset
 
MultiPropertyEntry - Class in magpie.data
Entry that can have multiple properties.
MultiPropertyEntry() - Constructor for class magpie.data.MultiPropertyEntry
 
MultiPropertyRegression - Class in magpie.models.regression
Extension of MultiObjectiveEntryRanker where one does not care about the class variable.
MultiPropertyRegression() - Constructor for class magpie.models.regression.MultiPropertyRegression
 
mutate(BaseEntry) - Method in class magpie.optimization.algorithms.genetic.operators.BaseMutationFunction
Mutate an entry so that it only somewhat resembles the original
mutate(BaseEntry) - Method in class magpie.optimization.algorithms.genetic.operators.PrototypeMutation
 
mutate(BaseEntry) - Method in class magpie.optimization.algorithms.genetic.operators.SimpleCompoundMutation
 

N

name - Variable in class magpie.user.server.thrift.Entry
 
NaNToMeanModifier - Class in magpie.data.utilities.modifiers
Replace any attributes that are NaN or infinite with the mean value for that attribute.
NaNToMeanModifier() - Constructor for class magpie.data.utilities.modifiers.NaNToMeanModifier
 
NAttributes() - Method in class magpie.data.BaseEntry
Get number of attributes currently set
NAttributes() - Method in class magpie.data.Dataset
 
NBins() - Method in class magpie.data.utilities.modifiers.ClassIntervalModifier
Get number of intervals on which data is split.
NClasses() - Method in class magpie.data.Dataset
 
NClasses() - Method in class magpie.data.MultiPropertyDataset
 
NClasses - Variable in class magpie.models.classification.BaseClassifier
Number of classes to distinguish between
NClasses - Variable in class magpie.models.classification.SplitClassifier
Number of classes model can distinguish between
NClusters() - Method in class magpie.cluster.BaseClusterer
How many different clusters data may be partitioned into
NClusters_protected() - Method in class magpie.cluster.BaseClusterer
Actual implementation of BaseClusterer.NClusters().
NClusters_protected() - Method in class magpie.cluster.WekaClusterer
 
NCoefficients() - Method in class magpie.models.regression.AbstractNonlinearRegression
 
NComponents - Variable in class magpie.csp.diagramdata.PhaseDiagramStatistics
Order of phase diagram
NComponents() - Method in class magpie.csp.diagramdata.PhaseDiagramStatistics
Get the order of the phase diagram (number of elements).
NCompositions() - Method in class magpie.csp.diagramdata.PhaseDiagramStatistics
 
NCompounds - Variable in class magpie.csp.diagramdata.PhaseDiagramStatistics
Number compounds stored by this object
NCompounds() - Method in class magpie.csp.diagramdata.PhaseDiagramStatistics
Get number of compounds stored by this object.
NDGridIterator - Class in magpie.utility
Iterate over a n-dimensional array.
NDGridIterator(int, int) - Constructor for class magpie.utility.NDGridIterator
Create a iterator over a
NDGridIterator(int[]) - Constructor for class magpie.utility.NDGridIterator
Initialize iterator
NElements - Variable in class magpie.csp.diagramdata.PhaseDiagramStatistics
Number of possible elements
NElements - Variable in class magpie.utility.tools.PhaseDiagramExclusionValidator
Number of elements to use.
NEntries() - Method in class magpie.data.Dataset
 
next() - Method in class magpie.utility.NDGridIterator
 
NGroups() - Method in class magpie.data.materials.util.PrototypeSiteInformation
Get the number of groups of equivalent sites.
NModels() - Method in interface magpie.models.interfaces.MultiModel
 
NModels() - Method in class magpie.models.regression.CompositeRegression
Get the number of models in ensemble
NModels() - Method in class magpie.models.regression.StagedRegression
 
NModels() - Method in class magpie.models.SplitModel
Returns the number of model slots currently available
NonlinearRegressionExpr - Class in magpie.models.regression
Performs non-linear regression on a function supplied as a string.
NonlinearRegressionExpr() - Constructor for class magpie.models.regression.NonlinearRegressionExpr
 
NOnSite(int) - Method in class magpie.data.materials.util.PrototypeSiteInformation
Get number of atoms on a certain site
NonZeroClassificationSplitter - Class in magpie.data.utilities.splitters
Split data based on whether an entry is likely to have a non-zero class variable.
NonZeroClassificationSplitter() - Constructor for class magpie.data.utilities.splitters.NonZeroClassificationSplitter
Create a new instances that uses ZeroR to classify.
NonZeroClassModifier - Class in magpie.data.utilities.modifiers
Takes a Dataset with a single class and a continuous class variable and change it into a dataset with two classes.
NonZeroClassModifier() - Constructor for class magpie.data.utilities.modifiers.NonZeroClassModifier
 
normalizationFunction(double, double, double) - Method in class magpie.data.utilities.normalizers.SoftmaxNormalizer
 
normalizationFunction(double, double, double) - Method in class magpie.data.utilities.normalizers.ZScoreNormalizer
Compute the normalized value of a variable
normalize(Dataset) - Method in class magpie.data.utilities.normalizers.BaseDatasetNormalizer
Transform attributes from original to standardized range.
normalizeAttributes(Dataset) - Method in class magpie.data.utilities.normalizers.BaseDatasetNormalizer
Perform the actual normalization on the attributes
normalizeAttributes(Dataset) - Method in class magpie.data.utilities.normalizers.IndependentVariableNormalizer
 
normalizeAttributes(double[]) - Method in class magpie.data.utilities.normalizers.IndependentVariableNormalizer
Normalize each attribute for an entry
normalizeAttributes(Dataset) - Method in class magpie.data.utilities.normalizers.InverseNormalizer
 
normalizeAttributes(Dataset) - Method in class magpie.data.utilities.normalizers.RegularSolutionNormalizer
 
normalizeAttributes(double[]) - Method in class magpie.data.utilities.normalizers.RescalingNormalizer
 
normalizeAttributes(double[]) - Method in class magpie.data.utilities.normalizers.ZScoreNormalizer
 
normalizeClassVariable(Dataset) - Method in class magpie.data.utilities.normalizers.BaseDatasetNormalizer
Perform the actual normalization on the class variable.
normalizeClassVariable(Dataset) - Method in class magpie.data.utilities.normalizers.IndependentVariableNormalizer
 
normalizeClassVariable(double) - Method in class magpie.data.utilities.normalizers.IndependentVariableNormalizer
Normalize a class variable
normalizeClassVariable(Dataset) - Method in class magpie.data.utilities.normalizers.InverseNormalizer
 
normalizeClassVariable(Dataset) - Method in class magpie.data.utilities.normalizers.RegularSolutionNormalizer
 
normalizeClassVariable(double) - Method in class magpie.data.utilities.normalizers.RescalingNormalizer
 
normalizeClassVariable(double) - Method in class magpie.data.utilities.normalizers.ZScoreNormalizer
 
Notes - Variable in class magpie.user.server.ModelPackage
Long form description of model
notes - Variable in class magpie.user.server.thrift.ModelInfo
 
Notes - Variable in class magpie.utility.interfaces.Citation
Anything else that a user should know about this resource.
NProperties() - Method in class magpie.data.MultiPropertyDataset
 
NProperties() - Method in class magpie.data.MultiPropertyEntry
 
NPV - Variable in class magpie.analytics.ClassificationStatistics
Negative Predictive Value
NResults() - Method in class magpie.csp.CSPPerformanceStats
Number of crystal structure predictions that have been evaluated.
NSites() - Method in class magpie.data.materials.PrototypeDataset
 
NSites() - Method in class magpie.data.materials.PrototypeEntry
 
NSites() - Method in class magpie.data.materials.util.PrototypeSiteInformation
Get the number of sites.
NSuccess - Variable in class magpie.optimization.analytics.OptimizationStatistics
Number of entries pass a success filter
NThreads - Static variable in class magpie.Magpie
Number of threads allowed
NumberCorrect - Variable in class magpie.analytics.ClassificationStatistics
Number of entries assigned to the correct class
NumberInCell - Variable in class magpie.data.materials.CompositionEntry
Number of atoms in cell (used to convert when printing)
NumberTested - Variable in class magpie.analytics.BaseStatistics
Number of entries evaluated
NumberTopEntries - Variable in class magpie.optimization.analytics.OptimizationStatistics
Number of top entries to select
numPhases() - Method in class magpie.data.materials.util.GCLPCalculator
Get the number of phases being considered for GCLP
numToList - Variable in class magpie.user.server.thrift.MagpieServer.searchMultiObjective_args
 
numToList - Variable in class magpie.user.server.thrift.MagpieServer.searchSingleObjective_args
 
numVariables() - Method in class magpie.utility.ParsedFunction
Print the number of variables this function expects
NVariables() - Method in class magpie.models.regression.AbstractNonlinearRegression
 

O

obj - Variable in class magpie.user.server.thrift.MagpieServer.searchSingleObjective_args
 
ObjectiveFunction - Variable in class magpie.optimization.BaseOptimizer
Entry ranker used for objective function
ObjectiveFunction - Variable in class magpie.optimization.rankers.AdaptiveScalarizingEntryRanker
Map of property name to objective function
objectiveFunction(BaseEntry) - Method in class magpie.optimization.rankers.AdaptiveScalarizingEntryRanker
 
objectiveFunction(BaseEntry) - Method in class magpie.optimization.rankers.BaseEntryRanker
Some kind of objective function that returns a double when given an entry.
objectiveFunction(BaseEntry) - Method in class magpie.optimization.rankers.ClassProbabilityRanker
 
objectiveFunction(BaseEntry) - Method in class magpie.optimization.rankers.CompositionDistanceRanker
 
objectiveFunction(BaseEntry) - Method in class magpie.optimization.rankers.PropertyFormulaRanker
 
ObjectiveFunction - Variable in class magpie.optimization.rankers.RankAggregationRanker
Map of property name to objective function
objectiveFunction(BaseEntry) - Method in class magpie.optimization.rankers.RankAggregationRanker
 
objectiveFunction(BaseEntry) - Method in class magpie.optimization.rankers.SimpleEntryRanker
 
objectiveFunction(BaseEntry) - Method in class magpie.optimization.rankers.TargetEntryRanker
 
ObjectiveFunctionSplitter - Class in magpie.data.utilities.splitters
Split based on value of objective function.
ObjectiveFunctionSplitter() - Constructor for class magpie.data.utilities.splitters.ObjectiveFunctionSplitter
 
ObjectiveMaximum - Variable in class magpie.optimization.rankers.AdaptiveScalarizingEntryRanker
Maximum value of each objective function in training data
ObjectiveMinimum - Variable in class magpie.optimization.rankers.AdaptiveScalarizingEntryRanker
Minimum value of each objective function in training data
ObjFunction - Variable in class magpie.models.regression.MultiObjectiveRegression
Objective function used to calculate class variable.
objs - Variable in class magpie.user.server.thrift.MagpieServer.searchMultiObjective_args
 
OnTheFlyPhaseDiagramStatistics - Class in magpie.csp.diagramdata
Calculate phase diagrams as requested.
OnTheFlyPhaseDiagramStatistics() - Constructor for class magpie.csp.diagramdata.OnTheFlyPhaseDiagramStatistics
 
openFile(String) - Method in class magpie.user.InputFileParser
Open an input file
OptimizationHelper - Class in magpie.optimization.algorithms
Operations that can be useful during optimization.
OptimizationHelper() - Constructor for class magpie.optimization.algorithms.OptimizationHelper
 
OptimizationStatistics - Class in magpie.optimization.analytics
Basic statistics about the performance optimization algorithms.
OptimizationStatistics() - Constructor for class magpie.optimization.analytics.OptimizationStatistics
 
Options - Interface in magpie.utility.interfaces
This interface signals that the options of a class can be set by a properly-parsed string.
Oracle - Variable in class magpie.optimization.BaseOptimizer
Oracle used as a method for evaluating new iterations
order - Variable in class magpie.attributes.evaluators.PolynomialFitEvaluator
Order of polynomial used to evaluate attributes
order - Variable in class magpie.models.regression.PolynomialRegression
Desired order of polynomial
orderComposition(int[], double[]) - Method in class magpie.csp.CSPEngine
Ensure that a composition is sorted such that elements are listed in ascending order by atomic fraction
ouch - Variable in class magpie.user.server.thrift.MagpieServer.evaluateProperties_result
 
ouch - Variable in class magpie.user.server.thrift.MagpieServer.getModelInformation_result
 
ouch - Variable in class magpie.user.server.thrift.MagpieServer.searchMultiObjective_result
 
ouch - Variable in class magpie.user.server.thrift.MagpieServer.searchSingleObjective_result
 
OxidationStateGuesser - Class in magpie.utility.tools
Given a composition, guess the most-likely oxidation states for each element.
OxidationStateGuesser() - Constructor for class magpie.utility.tools.OxidationStateGuesser
 
OxidationStates - Variable in class magpie.data.materials.CompositionDataset
Oxidation states of every element
OxidationStates - Static variable in class magpie.data.materials.util.LookupData
Holds oxidation states of individual elements

P

P - Variable in class magpie.optimization.rankers.AdaptiveScalarizingEntryRanker
Trade-off between best in single objective, and generally-good
p - Variable in class magpie.user.server.thrift.MagpieServer.searchMultiObjective_args
 
parallelLabel(Dataset) - Method in class magpie.data.utilities.filters.BaseDatasetFilter
Label entries in parallel.
parallelMinimum() - Method in class magpie.data.utilities.filters.BaseDatasetFilter
Minimum number of entries to label in parallel.
parallelMinimum() - Method in class magpie.data.utilities.filters.BestInAlloySystemFilter
 
parallelMinimum() - Method in class magpie.data.utilities.filters.CompositionSetDistanceFilter
 
parallelMinimum() - Method in class magpie.data.utilities.filters.StabilityFilter
 
ParsedFunction - Class in magpie.utility
Parses a function from text string.
ParsedFunction(String) - Constructor for class magpie.utility.ParsedFunction
Parse a function from a text string.
parseFormula(String) - Method in class magpie.models.regression.AbstractParsedNonlinearRegression
Parse formula to use as model.
parseInput(String[]) - Static method in class magpie.user.server.ServerLauncher
Handle input passed to the server.
partition(int[]) - Method in class magpie.data.Dataset
Given a list of labels, separate Dataset into multiple subsets
partition(int[], int) - Method in class magpie.data.Dataset
Given a list of labels, separate Dataset into multiple subsets (some may be empty)
partitionDataset(Dataset) - Method in class magpie.cluster.BaseClusterer
Separate the Dataset based on predicted classes.
Partitioner - Variable in class magpie.models.SplitModel
Class used to partition data into similar groups
PartitionToClassModifier - Class in magpie.data.utilities.modifiers
Changes the class variable of an entry to be what partition a BaseDatasetSplitter assigns it to.
PartitionToClassModifier() - Constructor for class magpie.data.utilities.modifiers.PartitionToClassModifier
 
PearsonsCorrelationEvaluator - Class in magpie.attributes.evaluators
Evaluate attributes based on Pearson's Correlation Coefficient, which is the "R^2" correlation value that you are likely familiar with.
PearsonsCorrelationEvaluator() - Constructor for class magpie.attributes.evaluators.PearsonsCorrelationEvaluator
 
PerformanceStats - Variable in class magpie.csp.CSPEngine
Holds statistics about CSP algorithm performance.
PhaseDiagramCompositionEntryGenerator - Class in magpie.data.utilities.generators
Generate composition entries at many points in many phase diagrams.
PhaseDiagramCompositionEntryGenerator() - Constructor for class magpie.data.utilities.generators.PhaseDiagramCompositionEntryGenerator
 
PhaseDiagramExclusionFilter - Class in magpie.data.utilities.filters
Filter entries from certain phase diagrams.
PhaseDiagramExclusionFilter() - Constructor for class magpie.data.utilities.filters.PhaseDiagramExclusionFilter
 
PhaseDiagramExclusionValidator - Class in magpie.utility.tools
Validate a model by using data each phase diagram as test set.
PhaseDiagramExclusionValidator() - Constructor for class magpie.utility.tools.PhaseDiagramExclusionValidator
 
PhaseDiagramStatistics - Class in magpie.csp.diagramdata
Holds what compounds exist in phase diagrams.
PhaseDiagramStatistics() - Constructor for class magpie.csp.diagramdata.PhaseDiagramStatistics
Create a blank instance of this class.
Phases - Variable in class magpie.data.materials.util.GCLPCalculator
Phases to consider for equilibria and their energy.
PNorms - Variable in class magpie.attributes.generators.composition.StoichiometricAttributeGenerator
List of p norms to compute
PolynomialFitEvaluator - Class in magpie.attributes.evaluators
Evaluate an attribute based on the RMSE of polynomial model using that attribute.
PolynomialFitEvaluator() - Constructor for class magpie.attributes.evaluators.PolynomialFitEvaluator
 
PolynomialRegression - Class in magpie.models.regression
Performs linear regression using all attributes in a Dataset raised to integer exponents.
PolynomialRegression() - Constructor for class magpie.models.regression.PolynomialRegression
 
PowerExpander - Class in magpie.attributes.expanders
This class creates new attributes that are functions of single, already-existing attributes by simply raising them to a specified power
PowerExpander() - Constructor for class magpie.attributes.expanders.PowerExpander
 
PPV - Variable in class magpie.analytics.ClassificationStatistics
Positive Predictive Value
PrecomputedPhaseDiagramStatistics - Class in magpie.csp.diagramdata
Deprecated. 
PrecomputedPhaseDiagramStatistics() - Constructor for class magpie.csp.diagramdata.PrecomputedPhaseDiagramStatistics
Deprecated.
 
Predicted - Variable in class magpie.analytics.BaseStatistics
Predicted value of class variable
PredictedClassIntervalSplitter - Class in magpie.data.utilities.splitters
Splits data based on whether the class variable is predicted to be within certain intervals.
PredictedClassIntervalSplitter() - Constructor for class magpie.data.utilities.splitters.PredictedClassIntervalSplitter
Create a new instances that uses ZeroR to predict interval.
predictedProperties - Variable in class magpie.user.server.thrift.Entry
 
PredictionOutlierFilter - Class in magpie.data.utilities.filters
Filters entries based on whether they are outliers.
PredictionOutlierFilter() - Constructor for class magpie.data.utilities.filters.PredictionOutlierFilter
 
predictStructure(String) - Method in class magpie.csp.CSPEngine
Predict what structure is most likely at a certain composition
predictStructure(CompositionEntry) - Method in class magpie.csp.CSPEngine
Predict what structure is most likely at a certain composition
prepareAttributeArrays(int) - Method in class magpie.data.utilities.normalizers.IndependentVariableNormalizer
Prepare arrays that will hold attribute statistics.
prepareAttributeArrays(int) - Method in class magpie.data.utilities.normalizers.RescalingNormalizer
 
prepareAttributeArrays(int) - Method in class magpie.data.utilities.normalizers.ZScoreNormalizer
 
prepareEvaluator(String) - Method in class magpie.models.regression.AbstractParsedNonlinearRegression
Define the internal Evaluator and parse the user-defined function
prepareEvaluator(String) - Method in class magpie.models.regression.NonlinearRegressionExpr
Define the internal Evaluator and parse the user-defined function
Printable - Interface in magpie.utility.interfaces
Dictates commands that must be fulfilled for an object to be "printable".
printAttributeDescription(boolean) - Method in class magpie.data.Dataset
Print out description of attributes.
printAttributes() - Method in class magpie.analytics.ClustererStatistics
Print the name and separation power of all attributes used during clustering
printAttributes(int) - Method in class magpie.analytics.ClustererStatistics
Print the name and separation power of a certain number of attributes
printCandidateAnalysis() - Method in class magpie.analytics.TargetRegressionStatistics
Print results of the candidate ranking analysis.
printCitations(List<String>) - Method in class magpie.user.CommandHandler
Run command to print out citations.
printClassInformation(Set<Class<? extends Object>>, boolean) - Static method in class magpie.user.CommandHandler
Given a list of classes, print the names of non-abstract classes and their options (if they implement Options)
printClusters() - Method in class magpie.analytics.ClustererStatistics
Print out attributes name, separation power, and mean for each cluster for all attributes used in clustering
printClusters(int) - Method in class magpie.analytics.ClustererStatistics
Print out attributes name, separation power, and mean for each cluster for a certain number of attributes
printCommand(List<String>) - Method in class magpie.analytics.BaseStatistics
 
printCommand(List<String>) - Method in class magpie.analytics.ClassificationStatistics
 
printCommand(List<String>) - Method in class magpie.analytics.ClustererStatistics
 
printCommand(List<String>) - Method in class magpie.analytics.TargetRegressionStatistics
 
printCommand(List<String>) - Method in class magpie.attributes.selectors.BaseAttributeSelector
 
printCommand(List<String>) - Method in class magpie.cluster.BaseClusterer
 
printCommand(List<String>) - Method in class magpie.csp.CSPEngine
 
printCommand(List<String>) - Method in class magpie.csp.CSPPerformanceStats
 
printCommand(List<String>) - Method in class magpie.data.Dataset
 
printCommand(List<String>) - Method in class magpie.data.utilities.normalizers.BaseDatasetNormalizer
 
printCommand(List<String>) - Method in class magpie.data.utilities.splitters.BaseDatasetSplitter
 
printCommand(List<String>) - Method in class magpie.models.BaseModel
 
printCommand(List<String>) - Method in class magpie.models.classification.CumulantExpansionClassifier
 
printCommand(List<String>) - Method in class magpie.models.regression.MixingRuleRegression
 
printCommand(List<String>) - Method in class magpie.models.regression.StagedRegression
 
printCommand(List<String>) - Method in class magpie.models.SplitModel
 
printCommand(List<String>) - Method in class magpie.optimization.analytics.OptimizationStatistics
 
printCommand(List<String>) - Method in class magpie.optimization.BaseOptimizer
 
printCommand(List<String>) - Method in interface magpie.utility.interfaces.Printable
Handles more complicated printing commands.
printCommand(List<String>) - Method in class magpie.utility.tools.PhaseDiagramExclusionValidator
 
printContingencyTable() - Method in class magpie.analytics.ClassificationStatistics
Print out the contingency table
printCumulants(double[][], int) - Method in class magpie.csp.diagramdata.PhaseDiagramStatistics
Print out values of each cumulant and their names.
printData(int) - Method in class magpie.optimization.analytics.OptimizationStatistics
Print out the data for a single iteration
printDescription(boolean) - Method in class magpie.analytics.BaseStatistics
 
printDescription(boolean) - Method in class magpie.analytics.ClustererStatistics
 
printDescription(boolean) - Method in class magpie.attributes.generators.BaseAttributeGenerator
Print out description of attributes.
printDescription(boolean) - Method in class magpie.attributes.generators.composition.ElementalPropertyAttributeGenerator
 
printDescription(boolean) - Method in class magpie.attributes.generators.composition.ElementFractionAttributeGenerator
 
printDescription(boolean) - Method in class magpie.attributes.generators.composition.IonicityAttributeGenerator
 
printDescription(boolean) - Method in class magpie.attributes.generators.composition.MeredigAttributeGenerator
 
printDescription(boolean) - Method in class magpie.attributes.generators.composition.StoichiometricAttributeGenerator
 
printDescription(boolean) - Method in class magpie.attributes.generators.composition.ValenceShellAttributeGenerator
 
printDescription(boolean) - Method in class magpie.attributes.generators.element.ElementalPropertyAttributeGenerator
 
printDescription(boolean) - Method in class magpie.attributes.generators.LookupTableAttributeGenerator
 
printDescription(boolean) - Method in class magpie.attributes.generators.ModelPredictionAttributeGenerator
 
printDescription(boolean) - Method in class magpie.attributes.generators.PropertyAsAttributeGenerator
 
printDescription(boolean) - Method in class magpie.attributes.selectors.BaseAttributeSelector
 
printDescription(boolean) - Method in class magpie.cluster.BaseClusterer
 
printDescription(boolean) - Method in class magpie.csp.CSPEngine
 
printDescription(boolean) - Method in class magpie.csp.CSPPerformanceStats
 
printDescription(boolean) - Method in class magpie.data.Dataset
Print out name of dataset and what attributes are generated.
printDescription(boolean) - Method in class magpie.data.utilities.normalizers.BaseDatasetNormalizer
 
printDescription(boolean) - Method in class magpie.data.utilities.splitters.BaseDatasetSplitter
 
printDescription(boolean) - Method in class magpie.models.BaseModel
 
printDescription(boolean) - Method in class magpie.optimization.analytics.OptimizationStatistics
 
printDescription(boolean) - Method in class magpie.optimization.BaseOptimizer
 
printDescription(boolean) - Method in interface magpie.utility.interfaces.Printable
Print full name of object, and a simple description of the options.
printDescription(boolean) - Method in class magpie.utility.tools.PhaseDiagramExclusionValidator
 
printDistribution() - Method in class magpie.analytics.ClustererStatistics
Print the distribution between each cluster
printDistribution() - Method in class magpie.data.Dataset
Print out the distribution of entries in the known classes
printEntries(int[]) - Method in class magpie.data.Dataset
Print out data regarding a list of entries.
printEntryDescription(boolean) - Method in class magpie.data.Dataset
Print out what the entries to this dataset are.
printEntryDescription(boolean) - Method in class magpie.data.materials.CompositionDataset
 
printEntryDescription(boolean) - Method in class magpie.data.materials.ElementDataset
 
printForStatistics(Dataset, String) - Static method in class magpie.data.utilities.DatasetOutput
Print out the measured and predicted class for each entry in a dataset.
printForStatistics_Tab(Dataset, String) - Static method in class magpie.data.utilities.DatasetOutput
Print out the measured and predicted class for each entry in a dataset.
printImplmentingClasses(Class, boolean) - Static method in class magpie.user.CommandHandler
Print the names and options (if applicable) of all classes that are subtypes of a certain class.
printImplmentingClasses(Class, boolean) - Static method in class magpie.utility.WekaUtility
Print the names and options (if applicable) of all classes that are subtypes of a certain class.
printInformation() - Method in class magpie.utility.interfaces.Citation
Print out a description of this citation.
printLastResults() - Method in class magpie.utility.tools.PhaseDiagramExclusionValidator
Print last results as formatted text.
printModel() - Method in class magpie.models.BaseModel
If a model is trained, return it formatted as a string.
printModel_protected() - Method in class magpie.models.BaseModel
Internal method that handles printing the model as a string.
printModel_protected() - Method in class magpie.models.classification.CumulantExpansionClassifier
 
printModel_protected() - Method in class magpie.models.classification.WekaClassifier
 
printModel_protected() - Method in class magpie.models.regression.AbstractParsedNonlinearRegression
 
printModel_protected() - Method in class magpie.models.regression.ClassificationRegression
 
printModel_protected() - Method in class magpie.models.regression.CompositeRegression
 
printModel_protected() - Method in class magpie.models.regression.LASSORegression
 
printModel_protected() - Method in class magpie.models.regression.LinearCorrectedRegression
 
printModel_protected() - Method in class magpie.models.regression.MetallurgicalHeuristicRegression
 
printModel_protected() - Method in class magpie.models.regression.MixingRuleRegression
 
printModel_protected() - Method in class magpie.models.regression.MultiObjectiveRegression
 
printModel_protected() - Method in class magpie.models.regression.nonlinear.SimpleLinearModelExample
 
printModel_protected() - Method in class magpie.models.regression.PolynomialRegression
 
printModel_protected() - Method in class magpie.models.regression.RandomGuessRegression
 
printModel_protected() - Method in class magpie.models.regression.ScikitLearnRegression
 
printModel_protected() - Method in class magpie.models.regression.SingleGuessRegression
 
printModel_protected() - Method in class magpie.models.regression.StagedRegression
 
printModel_protected() - Method in class magpie.models.regression.WekaRegression
 
printModel_protected() - Method in class magpie.models.SplitModel
 
printModelDescriptionDetails(boolean) - Method in class magpie.models.BaseModel
Print details of the model.
printModelDescriptionDetails(boolean) - Method in class magpie.models.classification.CumulantExpansionClassifier
 
printModelDescriptionDetails(boolean) - Method in class magpie.models.classification.WekaClassifier
 
printModelDescriptionDetails(boolean) - Method in class magpie.models.regression.AbstractParsedNonlinearRegression
 
printModelDescriptionDetails(boolean) - Method in class magpie.models.regression.ClassificationRegression
 
printModelDescriptionDetails(boolean) - Method in class magpie.models.regression.CompositeRegression
 
printModelDescriptionDetails(boolean) - Method in class magpie.models.regression.LASSORegression
 
printModelDescriptionDetails(boolean) - Method in class magpie.models.regression.LinearCorrectedRegression
 
printModelDescriptionDetails(boolean) - Method in class magpie.models.regression.MetallurgicalHeuristicRegression
 
printModelDescriptionDetails(boolean) - Method in class magpie.models.regression.MixingRuleRegression
 
printModelDescriptionDetails(boolean) - Method in class magpie.models.regression.MultiObjectiveRegression
 
printModelDescriptionDetails(boolean) - Method in class magpie.models.regression.nonlinear.SimpleLinearModelExample
 
printModelDescriptionDetails(boolean) - Method in class magpie.models.regression.PolynomialRegression
 
printModelDescriptionDetails(boolean) - Method in class magpie.models.regression.RandomGuessRegression
 
printModelDescriptionDetails(boolean) - Method in class magpie.models.regression.ScikitLearnRegression
 
printModelDescriptionDetails(boolean) - Method in class magpie.models.regression.SingleGuessRegression
 
printModelDescriptionDetails(boolean) - Method in class magpie.models.regression.StagedRegression
 
printModelDescriptionDetails(boolean) - Method in class magpie.models.regression.WekaRegression
 
printModelDescriptionDetails(boolean) - Method in class magpie.models.SplitModel
 
printNumber(double[], double) - Static method in class magpie.data.materials.CompositionEntry
Print out the number of atoms in a formula unit for each element given its fraction
printRankings(Dataset, int) - Method in class magpie.attributes.evaluators.BaseAttributeEvaluator
Print the predictive powers of the top attributes
printResults() - Method in class magpie.optimization.analytics.OptimizationStatistics
Print out all results into a neatly-formated table
printROCCurve() - Method in class magpie.analytics.BaseStatistics
Print the ROC Curve as a plottable string.
printRunTime(long) - Static method in class magpie.utility.UtilityOperations
Print elapsed time to screen
printSelections() - Method in class magpie.attributes.selectors.BaseAttributeSelector
This operation prints out the names of attributes that were selected
printStates(int[], int[]) - Method in class magpie.utility.tools.OxidationStateGuesser
Print out the elements and charges in a nice way.
printStatistics(Dataset, String) - Static method in class magpie.data.utilities.DatasetOutput
Print out statistics for each feature to a datafile
PrintStatus - Variable in class magpie.optimization.BaseOptimizer
Whether status messages should be printed
printTopEntries(Dataset, BaseEntryRanker, int) - Static method in class magpie.data.utilities.DatasetOutput
Print top entries in a dataset based on an objective function
printTypes(List<String>) - Method in class magpie.user.CommandHandler
Run a command to print out variable types
printUsage() - Method in class magpie.analytics.BaseStatistics
 
printUsage() - Method in class magpie.analytics.TargetRegressionStatistics
 
printUsage() - Method in class magpie.attributes.evaluators.AreaUnderROCEvaluator
 
printUsage() - Method in class magpie.attributes.evaluators.PearsonsCorrelationEvaluator
 
printUsage() - Method in class magpie.attributes.evaluators.PolynomialFitEvaluator
 
printUsage() - Method in class magpie.attributes.evaluators.SpearmansCorrelationEvaluator
 
printUsage() - Method in class magpie.attributes.expanders.CrossExpander
 
printUsage() - Method in class magpie.attributes.expanders.FunctionExpander
 
printUsage() - Method in class magpie.attributes.expanders.PowerExpander
 
printUsage() - Method in class magpie.attributes.generators.composition.ElementalPropertyAttributeGenerator
 
printUsage() - Method in class magpie.attributes.generators.composition.ElementFractionAttributeGenerator
 
printUsage() - Method in class magpie.attributes.generators.composition.IonicityAttributeGenerator
 
printUsage() - Method in class magpie.attributes.generators.composition.MeredigAttributeGenerator
 
printUsage() - Method in class magpie.attributes.generators.composition.StoichiometricAttributeGenerator
 
printUsage() - Method in class magpie.attributes.generators.composition.ValenceShellAttributeGenerator
 
printUsage() - Method in class magpie.attributes.generators.element.ElementalPropertyAttributeGenerator
 
printUsage() - Method in class magpie.attributes.generators.LookupTableAttributeGenerator
 
printUsage() - Method in class magpie.attributes.generators.ModelPredictionAttributeGenerator
 
printUsage() - Method in class magpie.attributes.generators.PropertyAsAttributeGenerator
 
printUsage() - Method in class magpie.attributes.selectors.BestIndividualSelector
 
printUsage() - Method in class magpie.attributes.selectors.MeredigAttributeSelector
 
printUsage() - Method in class magpie.attributes.selectors.RegexAttributeSelector
 
printUsage() - Method in class magpie.attributes.selectors.UserSpecifiedAttributeSelector
 
printUsage() - Method in class magpie.attributes.selectors.WekaAttributeSelector
 
printUsage() - Method in class magpie.cluster.WekaClusterer
 
printUsage() - Method in class magpie.csp.CompositionBasedCSPEngine
 
printUsage() - Method in class magpie.csp.DMSPEngine
 
printUsage() - Method in class magpie.data.Dataset
 
printUsage() - Method in class magpie.data.materials.PrototypeDataset
 
printUsage() - Method in class magpie.data.utilities.filters.AllMetalsFilter
 
printUsage() - Method in class magpie.data.utilities.filters.AttributeFilter
 
printUsage() - Method in class magpie.data.utilities.filters.BestInAlloySystemFilter
 
printUsage() - Method in class magpie.data.utilities.filters.ClassFilter
 
printUsage() - Method in class magpie.data.utilities.filters.ClassProbabilityFilter
 
printUsage() - Method in class magpie.data.utilities.filters.ClassRangeFilter
 
printUsage() - Method in class magpie.data.utilities.filters.CompositionDistanceFilter
 
printUsage() - Method in class magpie.data.utilities.filters.CompositionSetDistanceFilter
 
printUsage() - Method in class magpie.data.utilities.filters.ContainsElementFilter
 
printUsage() - Method in class magpie.data.utilities.filters.EntryRankerFilter
 
printUsage() - Method in class magpie.data.utilities.filters.IQROutlierFilter
 
printUsage() - Method in class magpie.data.utilities.filters.MultiFilter
 
printUsage() - Method in class magpie.data.utilities.filters.PredictionOutlierFilter
 
printUsage() - Method in class magpie.data.utilities.filters.PropertyFilter
 
printUsage() - Method in class magpie.data.utilities.filters.PropertyRangeFilter
 
printUsage() - Method in class magpie.data.utilities.filters.RegressionErrorFilter
 
printUsage() - Method in class magpie.data.utilities.filters.StabilityFilter
 
printUsage() - Method in class magpie.data.utilities.filters.ZScoreOutlierFilter
 
printUsage() - Method in class magpie.data.utilities.generators.AlloyingCompositionEntryGenerator
 
printUsage() - Method in class magpie.data.utilities.generators.CompositionRangeEntryGenerator
 
printUsage() - Method in class magpie.data.utilities.generators.GridBaseEntryGenerator
 
printUsage() - Method in class magpie.data.utilities.generators.IonicCompoundGenerator
 
printUsage() - Method in class magpie.data.utilities.generators.PhaseDiagramCompositionEntryGenerator
 
printUsage() - Method in class magpie.data.utilities.generators.PrototypeEntryGenerator
 
printUsage() - Method in class magpie.data.utilities.modifiers.AddPropertyModifier
 
printUsage() - Method in class magpie.data.utilities.modifiers.ClassEliminationModifier
 
printUsage() - Method in class magpie.data.utilities.modifiers.ClassIntervalModifier
 
printUsage() - Method in class magpie.data.utilities.modifiers.CompositionSetDistanceModifier
 
printUsage() - Method in class magpie.data.utilities.modifiers.DiscreteToContinuousModifier
 
printUsage() - Method in class magpie.data.utilities.modifiers.ErrorSignalModifier
 
printUsage() - Method in class magpie.data.utilities.modifiers.HHICalculationModifier
 
printUsage() - Method in class magpie.data.utilities.modifiers.NaNToMeanModifier
 
printUsage() - Method in class magpie.data.utilities.modifiers.NonZeroClassModifier
 
printUsage() - Method in class magpie.data.utilities.modifiers.PartitionToClassModifier
 
printUsage() - Method in class magpie.data.utilities.modifiers.SetClassNamesModifier
 
printUsage() - Method in class magpie.data.utilities.modifiers.StabilityCalculationModifier
 
printUsage() - Method in class magpie.data.utilities.modifiers.VolumeToLatticeParamModifier
 
printUsage() - Method in class magpie.data.utilities.normalizers.InverseNormalizer
 
printUsage() - Method in class magpie.data.utilities.normalizers.RegularSolutionNormalizer
 
printUsage() - Method in class magpie.data.utilities.normalizers.RescalingNormalizer
 
printUsage() - Method in class magpie.data.utilities.normalizers.SoftmaxNormalizer
 
printUsage() - Method in class magpie.data.utilities.normalizers.ZScoreNormalizer
 
printUsage() - Method in class magpie.data.utilities.splitters.AllMetalsSplitter
 
printUsage() - Method in class magpie.data.utilities.splitters.AttributeIntervalSplitter
 
printUsage() - Method in class magpie.data.utilities.splitters.ClustererSplitter
 
printUsage() - Method in class magpie.data.utilities.splitters.MeasuredClassSplitter
 
printUsage() - Method in class magpie.data.utilities.splitters.MultipleElementGroupsSplitter
 
printUsage() - Method in class magpie.data.utilities.splitters.NonZeroClassificationSplitter
 
printUsage() - Method in class magpie.data.utilities.splitters.ObjectiveFunctionSplitter
 
printUsage() - Method in class magpie.data.utilities.splitters.PredictedClassIntervalSplitter
 
printUsage() - Method in class magpie.data.utilities.splitters.SingleElementGroupSplitter
 
printUsage() - Method in class magpie.models.classification.CumulantExpansionClassifier
 
printUsage() - Method in class magpie.models.classification.WekaClassifier
 
printUsage() - Method in class magpie.models.regression.AbstractNonlinearRegression
 
printUsage() - Method in class magpie.models.regression.AbstractParsedNonlinearRegression
 
printUsage() - Method in class magpie.models.regression.ClassificationRegression
 
printUsage() - Method in class magpie.models.regression.CompositeRegression
 
printUsage() - Method in class magpie.models.regression.GuessMeanRegression
 
printUsage() - Method in class magpie.models.regression.LASSORegression
 
printUsage() - Method in class magpie.models.regression.LinearCorrectedRegression
 
printUsage() - Method in class magpie.models.regression.MetallurgicalHeuristicRegression
 
printUsage() - Method in class magpie.models.regression.MixingRuleRegression
 
printUsage() - Method in class magpie.models.regression.MultiObjectiveRegression
 
printUsage() - Method in class magpie.models.regression.MultiPropertyRegression
 
printUsage() - Method in class magpie.models.regression.PolynomialRegression
 
printUsage() - Method in class magpie.models.regression.RandomGuessRegression
 
printUsage() - Method in class magpie.models.regression.ScikitLearnRegression
 
printUsage() - Method in class magpie.models.regression.SingleGuessRegression
 
printUsage() - Method in class magpie.models.regression.StagedRegression
 
printUsage() - Method in class magpie.models.regression.WekaRegression
 
printUsage() - Method in class magpie.models.SplitModel
 
printUsage() - Method in class magpie.optimization.algorithms.ActiveLearningOptimizer
 
printUsage() - Method in class magpie.optimization.algorithms.genetic.GeneticAlgorithm
 
printUsage() - Method in class magpie.optimization.oracles.LookupOracle
 
printUsage() - Method in class magpie.optimization.rankers.AdaptiveScalarizingEntryRanker
 
printUsage() - Method in class magpie.optimization.rankers.ClassProbabilityRanker
 
printUsage() - Method in class magpie.optimization.rankers.CompositionDistanceRanker
 
printUsage() - Method in class magpie.optimization.rankers.PropertyFormulaRanker
 
printUsage() - Method in class magpie.optimization.rankers.RankAggregationRanker
 
printUsage() - Method in class magpie.optimization.rankers.SimpleEntryRanker
 
printUsage() - Method in class magpie.optimization.rankers.TargetEntryRanker
 
printUsage() - Method in interface magpie.utility.interfaces.Options
Print out required format for options.
printUsage() - Method in class magpie.utility.tools.BatchModelEvaluator
 
printUsage() - Method in class magpie.utility.tools.OxidationStateGuesser
 
printUsage() - Method in class magpie.utility.tools.PhaseDiagramExclusionValidator
 
printWindowAnalysis() - Method in class magpie.analytics.TargetRegressionStatistics
Print results of the tolerance size analysis.
printWorkspace() - Method in class magpie.user.Workspace
Prints a table containing all variables currently in Workspace.
ProbabilityThreshold - Variable in class magpie.data.utilities.splitters.NonZeroClassificationSplitter
Probability of being of class #0 below which entry gets placed in entry #1
processCompounds(Map<CompositionEntry, String>) - Method in class magpie.csp.diagramdata.OnTheFlyPhaseDiagramStatistics
 
processCompounds(Map<CompositionEntry, String>) - Method in class magpie.csp.diagramdata.PhaseDiagramStatistics
Given a list of compounds, mark which phase diagrams they appear in.
processCompounds(Map<CompositionEntry, String>) - Method in class magpie.csp.diagramdata.PrecomputedPhaseDiagramStatistics
Deprecated.
 
processCompounds(Map<CompositionEntry, String>) - Method in class magpie.csp.diagramdata.TernaryPhaseDiagramStatistics
Deprecated.
 
Properties - Variable in class magpie.attributes.generators.PropertyAsAttributeGenerator
List of properties to use as attributes.
Property - Variable in class magpie.user.server.ModelPackage
Name of property being modeled.
property - Variable in class magpie.user.server.thrift.ModelInfo
 
PropertyAsAttributeGenerator - Class in magpie.attributes.generators
Use measured property of entry as an attribute.
PropertyAsAttributeGenerator() - Constructor for class magpie.attributes.generators.PropertyAsAttributeGenerator
 
PropertyData - Variable in class magpie.data.materials.CompositionDataset
Map of elemental property names to values
PropertyData - Variable in class magpie.data.materials.ElementDataset
Lookup table of elemental properties
PropertyFilter - Class in magpie.data.utilities.filters
Filter entries based on a measured or predicted property.
PropertyFilter() - Constructor for class magpie.data.utilities.filters.PropertyFilter
 
PropertyFormulaRanker - Class in magpie.optimization.rankers
Use a formula of several properties.
PropertyFormulaRanker() - Constructor for class magpie.optimization.rankers.PropertyFormulaRanker
 
PropertyIndex - Variable in class magpie.optimization.rankers.AdaptiveScalarizingEntryRanker
Index of each property of interest
PropertyIndex - Variable in class magpie.optimization.rankers.RankAggregationRanker
Index of each property of interest
PropertyLists - Class in magpie.data.materials.util
Supplies lists of properties used when generating attributes.
PropertyLists() - Constructor for class magpie.data.materials.util.PropertyLists
 
PropertyName - Variable in class magpie.models.regression.MixingRuleRegression
Property used for weighting
PropertyRangeFilter - Class in magpie.data.utilities.filters
Filter entries that have property variables within or outside a certain range.
PropertyRangeFilter() - Constructor for class magpie.data.utilities.filters.PropertyRangeFilter
 
props - Variable in class magpie.user.server.thrift.MagpieServer.evaluateProperties_args
 
PrototypeCrossover - Class in magpie.optimization.algorithms.genetic.operators
Perform crossover for a PrototypeEntry.
PrototypeCrossover() - Constructor for class magpie.optimization.algorithms.genetic.operators.PrototypeCrossover
 
PrototypeDataset - Class in magpie.data.materials
Dataset designed to store composition data about compounds based on a single crystal structure prototype.
PrototypeDataset() - Constructor for class magpie.data.materials.PrototypeDataset
 
PrototypeEntry - Class in magpie.data.materials
Entry in a PrototypeCompositionDataset.
PrototypeEntry(PrototypeSiteInformation, String) - Constructor for class magpie.data.materials.PrototypeEntry
Create a new PrototypeEntry.
PrototypeEntry(PrototypeSiteInformation) - Constructor for class magpie.data.materials.PrototypeEntry
Create a Prototype entry without specifying composition.
PrototypeEntryGenerator - Class in magpie.data.utilities.generators
Generate PrototypeEntry with certain elements (or combination of elements on each site).
PrototypeEntryGenerator() - Constructor for class magpie.data.utilities.generators.PrototypeEntryGenerator
 
PrototypeMutation - Class in magpie.optimization.algorithms.genetic.operators
 
PrototypeMutation() - Constructor for class magpie.optimization.algorithms.genetic.operators.PrototypeMutation
 
PrototypeSiteInformation - Class in magpie.data.materials.util
Stores information about all sites in a prototype crystal structure.
PrototypeSiteInformation() - Constructor for class magpie.data.materials.util.PrototypeSiteInformation
 
putToClassProbs(String, List<Double>) - Method in class magpie.user.server.thrift.Entry
 
putToMeasuredProperties(String, double) - Method in class magpie.user.server.thrift.Entry
 
putToPredictedProperties(String, double) - Method in class magpie.user.server.thrift.Entry
 
putToSuccess(String, ModelInfo) - Method in class magpie.user.server.thrift.MagpieServer.getModelInformation_result
 
putToValScore(String, double) - Method in class magpie.user.server.thrift.ModelInfo
 

Q

Q - Variable in class magpie.analytics.utility.RobustRegressionUtility
Threshold for considering an entry an outlier.

R

R - Variable in class magpie.analytics.RegressionStatistics
Pearson's correlation coefficient
RandomFraction - Variable in class magpie.optimization.algorithms.ActiveLearningOptimizer
Fraction of new entries to select randomly
RandomGuessRegression - Class in magpie.models.regression
Randomly assign class values.
RandomGuessRegression() - Constructor for class magpie.models.regression.RandomGuessRegression
 
randomSplit(int) - Method in class magpie.data.Dataset
Split off a certain number of entries into a separate dataset.
randomSplit(double) - Method in class magpie.data.Dataset
Split off a certain number of entries into a separate dataset.
RankAggregationRanker - Class in magpie.optimization.rankers
Rank entries based on multiple objectives using the Rank Aggregation.
RankAggregationRanker() - Constructor for class magpie.optimization.rankers.RankAggregationRanker
 
rankEntries(Dataset, double[]) - Method in class magpie.optimization.rankers.BaseEntryRanker
Return the rank of entries that were sorted based on the objective function defined in this class (also depends on the settings for Maximize and Measured.
rankEntries(Dataset) - Method in class magpie.optimization.rankers.BaseEntryRanker
Calculate the rank of entries based on this objective function
rankEntries(Dataset, boolean) - Method in class magpie.optimization.rankers.BaseEntryRanker
Calculate the rank of entries based on this objective function
rankEntries(Dataset, double[]) - Method in class magpie.optimization.rankers.RankAggregationRanker
 
read(TProtocol) - Method in class magpie.user.server.thrift.Entry
 
read(TProtocol) - Method in exception magpie.user.server.thrift.MagpieException
 
read(TProtocol) - Method in class magpie.user.server.thrift.MagpieServer.evaluateProperties_args
 
read(TProtocol) - Method in class magpie.user.server.thrift.MagpieServer.evaluateProperties_result
 
read(TProtocol) - Method in class magpie.user.server.thrift.MagpieServer.getModelInformation_args
 
read(TProtocol) - Method in class magpie.user.server.thrift.MagpieServer.getModelInformation_result
 
read(TProtocol) - Method in class magpie.user.server.thrift.MagpieServer.searchMultiObjective_args
 
read(TProtocol) - Method in class magpie.user.server.thrift.MagpieServer.searchMultiObjective_result
 
read(TProtocol) - Method in class magpie.user.server.thrift.MagpieServer.searchSingleObjective_args
 
read(TProtocol) - Method in class magpie.user.server.thrift.MagpieServer.searchSingleObjective_result
 
read(TProtocol) - Method in class magpie.user.server.thrift.ModelInfo
 
readAttributeTable(String) - Method in class magpie.attributes.generators.LookupTableAttributeGenerator
Read in lookup table containing attribute names and values for selected entries.
readFile(String) - Method in class magpie.user.CommandHandler
Reads commands from a text file
readFromFile(String) - Static method in class magpie.data.materials.util.PrototypeSiteInformation
Read site information from a specially-formatted file.
readInformationFile(String) - Static method in class magpie.user.server.ServerLauncher
Given model information file, configure the handler
readLine() - Method in class magpie.user.InputFileParser
Gets a complete, nonempty line out of the input stream.
readModel(InputStream) - Method in class magpie.models.regression.ScikitLearnRegression
Read model from an input stream
readOxidationStates() - Method in class magpie.data.materials.CompositionDataset
Reads in a data file that contains known oxidation states for each element.
readStructureInformation(String) - Method in class magpie.data.materials.PrototypeDataset
Read information about a prototype crystal structure from file.
rectifyEntry(boolean) - Method in class magpie.data.materials.CompositionEntry
Makes sure this entry is in a proper format.
recv_evaluateProperties() - Method in class magpie.user.server.thrift.MagpieServer.Client
 
recv_getModelInformation() - Method in class magpie.user.server.thrift.MagpieServer.Client
 
recv_searchMultiObjective() - Method in class magpie.user.server.thrift.MagpieServer.Client
 
recv_searchSingleObjective() - Method in class magpie.user.server.thrift.MagpieServer.Client
 
regex - Variable in class magpie.attributes.selectors.RegexAttributeSelector
Regular expression to be matched
RegexAttributeSelector - Class in magpie.attributes.selectors
Selects attributes based on whether their name matches a regular expression.
RegexAttributeSelector() - Constructor for class magpie.attributes.selectors.RegexAttributeSelector
 
RegressionErrorFilter - Class in magpie.data.utilities.filters
Filter entries based on absolute error.
RegressionErrorFilter() - Constructor for class magpie.data.utilities.filters.RegressionErrorFilter
 
RegressionStatistics - Class in magpie.analytics
This class contains methods to calculate statistics about regression models.
RegressionStatistics() - Constructor for class magpie.analytics.RegressionStatistics
 
RegularSolutionNormalizer - Class in magpie.data.utilities.normalizers
Normalize data using regular solution model.
RegularSolutionNormalizer() - Constructor for class magpie.data.utilities.normalizers.RegularSolutionNormalizer
 
remove() - Method in class magpie.utility.NDGridIterator
 
removeDuplicates() - Method in class magpie.data.Dataset
Remove all duplicate entries
removeElementalProperty(String) - Method in class magpie.data.materials.CompositionDataset
Remove an elemental property from the list used when generating attributes
removeElementalProperty(String) - Method in class magpie.data.materials.ElementDataset
Remove an elemental property from the list of those used when computing attributes.
removeKnownCompoundsContainingElements(List<String>) - Method in class magpie.csp.CSPEngine
Given a list of elements, remove all entries that contain those elements from the list of known compounds.
removeVariable(String) - Method in class magpie.user.Workspace
Removes a variable from the workspace
RescalingNormalizer - Class in magpie.data.utilities.normalizers
Scale variables using the maximum and minimum values of the training set.
RescalingNormalizer() - Constructor for class magpie.data.utilities.normalizers.RescalingNormalizer
 
resetModel() - Method in class magpie.models.BaseModel
Mark this model as untrained and unvalidated
restorationFunction(double, double, double) - Method in class magpie.data.utilities.normalizers.SoftmaxNormalizer
 
restorationFunction(double, double, double) - Method in class magpie.data.utilities.normalizers.ZScoreNormalizer
Compute the restored value a variable
restore(Dataset) - Method in class magpie.data.utilities.normalizers.BaseDatasetNormalizer
Restore attributes from scaled to original range.
restoreAttributes(Instances) - Method in class magpie.data.Dataset
Restore attribute data to each entry.
restoreAttributes(Dataset) - Method in class magpie.data.utilities.normalizers.BaseDatasetNormalizer
Perform the actual restoration on the attributes
restoreAttributes(Dataset) - Method in class magpie.data.utilities.normalizers.IndependentVariableNormalizer
 
restoreAttributes(double[]) - Method in class magpie.data.utilities.normalizers.IndependentVariableNormalizer
Restore each attribute for an entry
restoreAttributes(Dataset) - Method in class magpie.data.utilities.normalizers.InverseNormalizer
 
restoreAttributes(Dataset) - Method in class magpie.data.utilities.normalizers.RegularSolutionNormalizer
 
restoreAttributes(double[]) - Method in class magpie.data.utilities.normalizers.RescalingNormalizer
 
restoreAttributes(double[]) - Method in class magpie.data.utilities.normalizers.ZScoreNormalizer
 
restoreClassVariable(Dataset) - Method in class magpie.data.utilities.normalizers.BaseDatasetNormalizer
Perform the actual restoration on the class variables (measured and predicted!)
restoreClassVariable(Dataset) - Method in class magpie.data.utilities.normalizers.IndependentVariableNormalizer
 
restoreClassVariable(double) - Method in class magpie.data.utilities.normalizers.IndependentVariableNormalizer
Restore a class variable
restoreClassVariable(Dataset) - Method in class magpie.data.utilities.normalizers.InverseNormalizer
 
restoreClassVariable(Dataset) - Method in class magpie.data.utilities.normalizers.RegularSolutionNormalizer
 
restoreClassVariable(double) - Method in class magpie.data.utilities.normalizers.RescalingNormalizer
 
restoreClassVariable(double) - Method in class magpie.data.utilities.normalizers.ZScoreNormalizer
 
Rho - Variable in class magpie.analytics.RegressionStatistics
Spearman's correlation coefficient
RMSE - Variable in class magpie.analytics.RegressionStatistics
Root mean squared error
RobustRegressionUtility - Class in magpie.analytics.utility
Calculates statistics useful to robust regression.
RobustRegressionUtility() - Constructor for class magpie.analytics.utility.RobustRegressionUtility
 
robustTraining(Dataset) - Method in interface magpie.models.regression.AbstractRegressionModel
Robustly train a model.
robustTraining(Dataset) - Method in class magpie.models.regression.BaseRegression
 
robustTraining(Dataset) - Method in class magpie.models.regression.SplitRegression
 
ROC - Variable in class magpie.analytics.BaseStatistics
Receiver operating characteristic curve
ROC_AUC - Variable in class magpie.analytics.BaseStatistics
Area under receiver operating characteristic curve normalized such that 1.0 is a perfect classifier and 0.0 is a perfectly-random classifier.
roundComposition(double[]) - Method in class magpie.csp.diagramdata.PhaseDiagramStatistics
Round a compound such that it's composition exactly equals that of a common composition, and return the index of that composition
run(Dataset) - Method in class magpie.attributes.selectors.BaseAttributeSelector
Adjust the attribute list of a dataset, based on a trained selection algorithm
run(Dataset) - Method in class magpie.models.BaseModel
Run a model on provided data.
run(Dataset) - Method in class magpie.models.classification.BaseClassifier
 
run() - Method in class magpie.optimization.BaseOptimizer
Run the optimization algorithm until it either the Oracle is unable to evaluate all new candidates, or the algorithm completes
run() - Method in class magpie.utility.ModelRunningThread
 
run_protected(Dataset) - Method in class magpie.models.BaseModel
Run a model without checking if stuff is trained (use carefully)
run_protected(Dataset) - Method in class magpie.models.classification.CumulantExpansionClassifier
 
run_protected(Dataset) - Method in class magpie.models.classification.SplitClassifier
 
run_protected(Dataset) - Method in class magpie.models.classification.WekaClassifier
 
run_protected(Dataset) - Method in class magpie.models.regression.AbstractNonlinearRegression
 
run_protected(Dataset) - Method in class magpie.models.regression.ClassificationRegression
 
run_protected(Dataset) - Method in class magpie.models.regression.CompositeRegression
 
run_protected(Dataset) - Method in class magpie.models.regression.LASSORegression
 
run_protected(Dataset) - Method in class magpie.models.regression.LinearCorrectedRegression
 
run_protected(Dataset) - Method in class magpie.models.regression.MetallurgicalHeuristicRegression
 
run_protected(Dataset) - Method in class magpie.models.regression.MixingRuleRegression
 
run_protected(Dataset) - Method in class magpie.models.regression.MultiObjectiveRegression
 
run_protected(Dataset) - Method in class magpie.models.regression.PolynomialRegression
 
run_protected(Dataset) - Method in class magpie.models.regression.RandomGuessRegression
 
run_protected(Dataset) - Method in class magpie.models.regression.ScikitLearnRegression
 
run_protected(Dataset) - Method in class magpie.models.regression.SingleGuessRegression
 
run_protected(Dataset) - Method in class magpie.models.regression.StagedRegression
 
run_protected(Dataset) - Method in class magpie.models.regression.WekaRegression
 
run_protected(Dataset) - Method in class magpie.models.SplitModel
 
runAndFilter(BaseModel, Dataset, BaseDatasetFilter) - Method in class magpie.utility.tools.BatchModelEvaluator
Create entries, evaluate them, filter out acceptable candidates
runAttributeCommand(List<Object>) - Method in class magpie.data.Dataset
Run commands related to attributes of each entry.
runAttributeCommand(List<Object>) - Method in class magpie.data.materials.CompositionDataset
 
runAttributeCommand(List<Object>) - Method in class magpie.data.materials.ElementDataset
 
runAttributeExpanders() - Method in class magpie.data.Dataset
Expand the list of attributes using the currently-set list of attribute expanders.
runAttributeExpansionCommand(List<Object>) - Method in class magpie.data.Dataset
Run commands relating to expanding the attribute pool.
runAttributeGeneratorCommand(List<Object>) - Method in class magpie.data.Dataset
Run commands relating to generating new attributes.
runAttributeGenerators() - Method in class magpie.data.Dataset
Expand the list of attributes using the currently-set list of attribute generators.
runCandidateAnalysis(double[], double[]) - Method in class magpie.analytics.TargetRegressionStatistics
Perform a candidate selection analysis (described in documentation for this class as a whole).
runCommand(List<Object>) - Method in class magpie.analytics.BaseStatistics
 
runCommand(List<Object>) - Method in class magpie.attributes.selectors.BaseAttributeSelector
 
runCommand(List<Object>) - Method in class magpie.cluster.BaseClusterer
 
runCommand(List<Object>) - Method in class magpie.csp.CompositionBasedCSPEngine
 
runCommand(List<Object>) - Method in class magpie.csp.CSPEngine
 
runCommand(List<Object>) - Method in class magpie.data.Dataset
 
runCommand(List<Object>) - Method in class magpie.data.materials.CompositionDataset
 
runCommand(List<Object>) - Method in class magpie.data.MultiPropertyDataset
 
runCommand(List<Object>) - Method in class magpie.data.utilities.normalizers.BaseDatasetNormalizer
 
runCommand(List<Object>) - Method in class magpie.data.utilities.splitters.BaseDatasetSplitter
 
runCommand(List<Object>) - Method in class magpie.models.BaseModel
 
runCommand(List<Object>) - Method in class magpie.models.regression.AbstractNonlinearRegression
 
runCommand(List<Object>) - Method in class magpie.models.regression.BaseRegression
 
runCommand(List<Object>) - Method in class magpie.models.regression.CompositeRegression
 
runCommand(List<Object>) - Method in class magpie.models.regression.MultiObjectiveRegression
 
runCommand(List<Object>) - Method in class magpie.models.regression.SplitRegression
 
runCommand(List<Object>) - Method in class magpie.models.regression.StagedRegression
 
runCommand(List<Object>) - Method in class magpie.models.SplitModel
 
runCommand(List<Object>) - Method in class magpie.optimization.BaseOptimizer
 
runCommand(List<String>) - Method in class magpie.user.CommandHandler
Given a command, run some actions
runCommand(List<Object>) - Method in interface magpie.utility.interfaces.Commandable
Process some command described by a list of Objects.
runCommand(List<Object>) - Method in class magpie.utility.tools.BatchModelEvaluator
 
runCommand(List<Object>) - Method in class magpie.utility.tools.IonicCompoundFinder
 
runCommand(List<Object>) - Method in class magpie.utility.tools.OxidationStateGuesser
 
runCommand(List<Object>) - Method in class magpie.utility.tools.PhaseDiagramExclusionValidator
 
runCommandOnVariable(String, List<Object>) - Method in class magpie.user.CommandHandler
Pass commands to variables.
runEvaluationCommand(List<Object>) - Static method in class magpie.user.CommandHandler
Run an evaluation command.
runExclusionTest(int[], BaseModel, CompositionDataset) - Static method in class magpie.utility.tools.PhaseDiagramExclusionValidator
Evaluate model by using excluding certain combinations of elements from a dataset, and using the excluded data as a test set.
runGCLP(CompositionEntry) - Method in class magpie.data.materials.util.GCLPCalculator
Compute the ground state phase equilibria for a certain composition.
runModel(double[][]) - Method in class magpie.models.regression.LASSORegression
Runs the model contained within object
runNonlinearCommand(List<Object>) - Method in class magpie.models.regression.AbstractNonlinearRegression
Handle commands for nonliear models
runObjectiveFunction(Dataset) - Method in class magpie.optimization.rankers.BaseEntryRanker
Evaluate every entry in a dataset using the objective function
runPolynomialModel(double[][], int, double[]) - Static method in class magpie.models.regression.PolynomialRegression
Run a polynomial model based on a matrix of attribute values.
runPropertyCommand(List<Object>) - Method in class magpie.data.materials.CompositionDataset
Run commands that control which elemental properties are used when generating attributes
runPropertyCommand(List<Object>) - Method in class magpie.data.materials.ElementDataset
Run commands that control which elemental properties are used when generating attributes
runStatisticsCommand(List<Object>) - Method in class magpie.optimization.BaseOptimizer
Handle commands related to controlling what statistics are generated
runSubmodelCommand(List<Object>) - Method in class magpie.models.regression.MultiObjectiveRegression
Run commands associated with operating on submodels
runTimerCommand(List<String>) - Method in class magpie.user.CommandHandler
Run a certain time command.
runWindowAnalysis(double[], double[]) - Method in class magpie.analytics.TargetRegressionStatistics
Perform a window-size analysis.
runWriteCommand(List<Object>) - Method in class magpie.optimization.BaseOptimizer
Run commands devoted to writing out data

S

Savable - Interface in magpie.utility.interfaces
Dictates commands that must be fulfilled for an object to be "savable".
saveARFF(Dataset, String) - Static method in class magpie.data.utilities.DatasetOutput
Write out to an ARFF-formatted file.
saveCommand(String, String) - Method in class magpie.analytics.BaseStatistics
 
saveCommand(String, String) - Method in class magpie.data.Dataset
 
saveCommand(String, String) - Method in class magpie.data.materials.CompositionDataset
 
saveCommand(String, String) - Method in class magpie.data.MultiPropertyDataset
 
saveCommand(String, String) - Method in class magpie.models.BaseModel
 
saveCommand(String, String) - Method in class magpie.models.classification.CumulantExpansionClassifier
 
saveCommand(String, String) - Method in interface magpie.utility.interfaces.Savable
Handles complicated saving commands.
saveCommand(String, String) - Method in class magpie.utility.tools.PhaseDiagramExclusionValidator
 
saveCompositionProperties(CompositionDataset, String) - Static method in class magpie.data.materials.util.CompositionDatasetOutput
Writes a comma-delimited file containing measured and predicted properties.
saveDelimited(Dataset, String, String) - Static method in class magpie.data.utilities.DatasetOutput
Saves a Dataset as a string-delimited file.
savePerformanceData(String) - Method in class magpie.analytics.BaseStatistics
Write out measured and predicted class variables used to compute statistics.
saveProperties(MultiPropertyDataset, String) - Static method in class magpie.data.utilities.DatasetOutput
Writes a comma-delimited file containing measured and predicted properties.
saveState(String) - Method in class magpie.data.Dataset
Save the state of this object using serialization
saveState(String) - Method in class magpie.models.BaseModel
Save the state of this object using serialization
saveState(Object, String) - Static method in class magpie.utility.UtilityOperations
Use serialization to save object state to file
ScikitLearnRegression - Class in magpie.models.regression
Uses Scikit-learn to train a regression model.
ScikitLearnRegression() - Constructor for class magpie.models.regression.ScikitLearnRegression
 
ScikitServer - Variable in class magpie.models.regression.ScikitLearnRegression
Scikit server process
ScreenAttributes - Variable in class magpie.data.utilities.filters.ZScoreOutlierFilter
Whether to screen based on attributes
ScreenClass - Variable in class magpie.data.utilities.filters.ZScoreOutlierFilter
Whether to screen based on class variable
Searcher - Variable in class magpie.attributes.selectors.WekaAttributeSelector
Weka class used to populate a list of attributes
searchMultiObjective(double, List<String>, String, int, AsyncMethodCallback) - Method in class magpie.user.server.thrift.MagpieServer.AsyncClient
 
searchMultiObjective(double, List<String>, String, int, AsyncMethodCallback) - Method in interface magpie.user.server.thrift.MagpieServer.AsyncIface
 
searchMultiObjective(double, List<String>, String, int) - Method in class magpie.user.server.thrift.MagpieServer.Client
 
searchMultiObjective(double, List<String>, String, int) - Method in interface magpie.user.server.thrift.MagpieServer.Iface
Search for optimal materials based on a multiple objectives in a user-defined space.
searchMultiObjective(double, List<String>, String, int) - Method in class magpie.user.server.thrift.MagpieServerHandler
 
searchSingleObjective(String, String, int, AsyncMethodCallback) - Method in class magpie.user.server.thrift.MagpieServer.AsyncClient
 
searchSingleObjective(String, String, int, AsyncMethodCallback) - Method in interface magpie.user.server.thrift.MagpieServer.AsyncIface
 
searchSingleObjective(String, String, int) - Method in class magpie.user.server.thrift.MagpieServer.Client
 
searchSingleObjective(String, String, int) - Method in interface magpie.user.server.thrift.MagpieServer.Iface
Search for optimal materials based on a single objective in a user-defined space _How to Define Objective Function_ The first word in the objective function input should be the name of the property being optimized, followed by whether to minimize or maximize the objective function, then the name of EntryRanker, and (finally) its options.
searchSingleObjective(String, String, int) - Method in class magpie.user.server.thrift.MagpieServerHandler
 
SearchSpace - Variable in class magpie.optimization.BaseOptimizer
Entries that are acceptable to search
selectAttributes(List<String>) - Method in class magpie.attributes.selectors.MeredigAttributeSelector
 
selectAttributes(List<String>) - Method in class magpie.attributes.selectors.UserSpecifiedAttributeSelector
Define a list of attributes that will be used when training a model
selectAttributes(List<String>) - Method in class magpie.attributes.selectors.UserSpecifiedExcludingAttributeSelector
Define list of attributes that will be excluded before training a model.
SelectedAttributes - Variable in class magpie.attributes.selectors.UserSpecifiedAttributeSelector
Names of attributes to be used
send_evaluateProperties(List<Entry>, List<String>) - Method in class magpie.user.server.thrift.MagpieServer.Client
 
send_getModelInformation() - Method in class magpie.user.server.thrift.MagpieServer.Client
 
send_searchMultiObjective(double, List<String>, String, int) - Method in class magpie.user.server.thrift.MagpieServer.Client
 
send_searchSingleObjective(String, String, int) - Method in class magpie.user.server.thrift.MagpieServer.Client
 
Sensitivity - Variable in class magpie.analytics.ClassificationStatistics
Sensitivity (aka True Positive Rate
ServerLauncher - Class in magpie.user.server
Main class for launching a Magpie server.
ServerLauncher() - Constructor for class magpie.user.server.ServerLauncher
 
setAlloyStep(double) - Method in class magpie.data.utilities.generators.AlloyingCompositionEntryGenerator
Set the step size
setAttribute(int, double) - Method in class magpie.data.BaseEntry
Set a certain attribute for this entry
setAttributeName(String) - Method in class magpie.data.utilities.splitters.AttributeIntervalSplitter
Define which attribute to use for splitting
setAttributeNames(List<String>) - Method in class magpie.data.Dataset
Set the names of each attributes.
setAttributes(double[]) - Method in class magpie.data.BaseEntry
Sets attributes for this entry
setAttributeSelector(BaseAttributeSelector) - Method in class magpie.cluster.BaseClusterer
Define an attribute selector to be used before clustering
setAttributeSelector(BaseAttributeSelector) - Method in class magpie.models.BaseModel
Define an attribute selector that will force this model to only use a subset of the attributes supplied with a Dataset
setAuthor(String) - Method in class magpie.user.server.thrift.ModelInfo
 
setAuthorIsSet(boolean) - Method in class magpie.user.server.thrift.ModelInfo
 
setBaseElement(int, double, double) - Method in class magpie.data.utilities.generators.CompositionRangeEntryGenerator
Set the base element.
setBaseElement(String, double, double) - Method in class magpie.data.utilities.generators.CompositionRangeEntryGenerator
Set the base element.
setBatchSize(int) - Method in class magpie.utility.tools.BatchModelEvaluator
Define how many entries to evaluate at once.
setBinaryConvexHulls(CompositionDataset) - Method in class magpie.models.regression.MetallurgicalHeuristicRegression
Define binary convex hull data.
setBinEdges(double[]) - Method in class magpie.data.utilities.splitters.AttributeIntervalSplitter
Define the edges of bins on which to split data.
setCitation(String) - Method in class magpie.user.server.thrift.ModelInfo
 
setCitationIsSet(boolean) - Method in class magpie.user.server.thrift.ModelInfo
 
setClassContinuous() - Method in class magpie.analytics.ClassificationStatistics
Set that the class variable is continuous
setClassContinuous() - Method in interface magpie.models.classification.AbstractClassifier
Allow the class variable to be treated as continuous
setClassContinuous() - Method in class magpie.models.classification.BaseClassifier
 
setClassContinuous() - Method in class magpie.models.classification.SplitClassifier
 
setClassCutoff(double) - Method in class magpie.analytics.ClassificationStatistics
Set the class cutoff used when calculating statistics.
setClassCutoff(double) - Method in interface magpie.models.classification.AbstractClassifier
Set the class cutoff used when calculating statistics.
setClassCutoff(double) - Method in class magpie.models.classification.BaseClassifier
Set the class cutoff used when calculating statistics.
setClassCutoff(double) - Method in class magpie.models.classification.SplitClassifier
 
setClassDiscrete() - Method in class magpie.analytics.ClassificationStatistics
Set that the class variable is discrete
setClassDiscrete() - Method in interface magpie.models.classification.AbstractClassifier
Allow the class variable to be treated as discrete
setClassDiscrete() - Method in class magpie.models.classification.BaseClassifier
 
setClassDiscrete() - Method in class magpie.models.classification.SplitClassifier
 
setClassifier(BaseModel) - Method in class magpie.data.utilities.splitters.PredictedClassIntervalSplitter
Define the classifier used to predict on which interval a class variable most likely lies.
setClassifier(BaseModel) - Method in class magpie.models.regression.ClassificationRegression
Classifier behind this regression algorithm
setClassifier(boolean) - Method in class magpie.user.server.thrift.ModelInfo
 
setClassifierIsSet(boolean) - Method in class magpie.user.server.thrift.ModelInfo
 
setClassifierTempate(BaseClassifier) - Method in class magpie.csp.CompositionBasedCSPEngine
Define a template for the classifier used by this class
setClassName(String) - Method in class magpie.data.utilities.filters.ClassProbabilityFilter
Set the name of the class considered for filtering.
setClassName(String) - Method in class magpie.data.utilities.modifiers.DiscreteToContinuousModifier
Set name of class for which to compute probability.
setClassNames(String[]) - Method in class magpie.data.Dataset
Set name of class variable (or possible classes)
setClassNames(String[]) - Method in class magpie.data.MultiPropertyDataset
 
setClassNames(String[]) - Method in class magpie.data.utilities.modifiers.SetClassNamesModifier
Define the new class names
SetClassNamesModifier - Class in magpie.data.utilities.modifiers
Sets the class names of a Dataset.
SetClassNamesModifier() - Constructor for class magpie.data.utilities.modifiers.SetClassNamesModifier
 
setClassProbabilities(double[]) - Method in class magpie.data.BaseEntry
Set the predicted probability of a entry existing in each class
setClassProbabilities(double[][]) - Method in class magpie.data.Dataset
Set class probabilities for each entry
setClassProbabilities(double[]) - Method in class magpie.data.MultiPropertyEntry
 
setClassProbs(Map<String, List<Double>>) - Method in class magpie.user.server.thrift.Entry
 
setClassProbsIsSet(boolean) - Method in class magpie.user.server.thrift.Entry
 
setClassToEliminate(String) - Method in class magpie.data.utilities.modifiers.ClassEliminationModifier
Define the name of the class to eliminate.
setClusterer(BaseClusterer) - Method in class magpie.data.utilities.splitters.ClustererSplitter
Set the clusterer used for splitting.
setComparisonOperator(String) - Method in class magpie.data.utilities.filters.ClassFilter
Define comparison operator.
setComponent(String, Object) - Method in class magpie.models.BaseModel
Set a specific component of a model
setComponent(List<Object>) - Method in class magpie.optimization.algorithms.ActiveLearningOptimizer
 
setComponent(List<Object>) - Method in class magpie.optimization.BaseOptimizer
Set a specific component or setting of an optimizer.
setComposition(int[], double[], boolean) - Method in class magpie.data.materials.CompositionEntry
Set the composition of this entry.
setComposition(CompositionEntry) - Method in class magpie.data.utilities.generators.AlloyingCompositionEntryGenerator
Set starting composition for alloys
setCompositions(CompositionDataset) - Method in class magpie.data.utilities.filters.CompositionSetDistanceFilter
Set the list of compositions to be considered
setCompositions(CompositionDataset) - Method in class magpie.data.utilities.modifiers.CompositionSetDistanceModifier
Set the list of compositions to be considered
setCompositions(CompositionDataset) - Method in class magpie.optimization.rankers.CompositionDistanceRanker
Set the list of compositions to be considered
setCompounds(CompositionDataset) - Method in class magpie.data.utilities.filters.StabilityFilter
Define the data used to compute stability.
setCompounds(CompositionDataset) - Method in class magpie.data.utilities.modifiers.StabilityCalculationModifier
Define the data used to compute stability.
setCompressionLevel(int) - Method in class magpie.models.regression.ScikitLearnRegression
Define how well model is compressed after training.
setCrossoverFunction(BaseCrossoverFunction) - Method in class magpie.optimization.algorithms.genetic.GeneticAlgorithm
Define the cross-over function to be used with this algorithm.
setDataDirectory(String) - Method in class magpie.data.materials.CompositionDataset
Define whether to look for elemental property lookup tables.
setDataType(String) - Method in class magpie.user.server.thrift.ModelInfo
 
setDataTypeIsSet(boolean) - Method in class magpie.user.server.thrift.ModelInfo
 
setDescription(String) - Method in class magpie.user.server.thrift.ModelInfo
 
setDescriptionIsSet(boolean) - Method in class magpie.user.server.thrift.ModelInfo
 
setDimension(int) - Method in class magpie.data.utilities.generators.GridBaseEntryGenerator
Define dimension of grid.
setDistanceThreshold(double) - Method in class magpie.data.utilities.filters.CompositionDistanceFilter
Define the threshold composition distance.
setDistanceThreshold(double) - Method in class magpie.data.utilities.filters.CompositionSetDistanceFilter
Set the distance threshold
setEdges(double[]) - Method in class magpie.data.utilities.modifiers.ClassIntervalModifier
Set the Edges that define the class intervals on which data is discretized.
setEdges(double[]) - Method in class magpie.data.utilities.splitters.PredictedClassIntervalSplitter
Define edges describing different values of the class variable on which entries are partitioned.
setElectronegativity(double[]) - Method in class magpie.utility.tools.OxidationStateGuesser
Set the lookup table for electronegativity values.
setElectronegativity(String) - Method in class magpie.utility.tools.OxidationStateGuesser
Set the lookup table for electronegativity values.
setElementalProperties(List<String>) - Method in class magpie.data.materials.ElementDataset
Define the list of elemental properties to be used to compute attributes.
setElementList(String[]) - Method in class magpie.data.utilities.filters.ContainsElementFilter
Define list of elements to use for filter.
setElements(List<String>) - Method in class magpie.data.utilities.splitters.SingleElementGroupSplitter
Define list of elements to define the split.
setElementsByIndex(Set<Integer>) - Method in class magpie.data.utilities.generators.PhaseDiagramCompositionEntryGenerator
Define the lit of elements included in the phase diagrams.
setElementsByName(Set<String>) - Method in class magpie.data.utilities.generators.PhaseDiagramCompositionEntryGenerator
Define the lit of elements included in the phase diagrams.
setEnergyName(String) - Method in class magpie.data.utilities.modifiers.StabilityCalculationModifier
Define the name of the property containing energy data
setEntries(List<Entry>) - Method in class magpie.user.server.thrift.MagpieServer.evaluateProperties_args
 
setEntriesIsSet(boolean) - Method in class magpie.user.server.thrift.MagpieServer.evaluateProperties_args
 
setEntriesPerGeneration(int) - Method in class magpie.optimization.BaseOptimizer
Set the number of new entries created per iteration
setEvaluator(String, String[]) - Method in class magpie.attributes.selectors.WekaAttributeSelector
Set the method used to evaluate subsets of entries.
setEvenSpacing(boolean) - Method in class magpie.data.utilities.generators.IonicCompoundGenerator
Not applicable for this class.
setEvenSpacing(boolean) - Method in class magpie.data.utilities.generators.PhaseDiagramCompositionEntryGenerator
Set whether to use evenly-spaced compositions (or low-denominator).
setExclude(boolean) - Method in class magpie.data.utilities.filters.BaseDatasetFilter
Define whether entries that pass should be removed, or whether an entry must pass the filter to be kept.
setFieldValue(Entry._Fields, Object) - Method in class magpie.user.server.thrift.Entry
 
setFieldValue(MagpieException._Fields, Object) - Method in exception magpie.user.server.thrift.MagpieException
 
setFieldValue(MagpieServer.evaluateProperties_args._Fields, Object) - Method in class magpie.user.server.thrift.MagpieServer.evaluateProperties_args
 
setFieldValue(MagpieServer.evaluateProperties_result._Fields, Object) - Method in class magpie.user.server.thrift.MagpieServer.evaluateProperties_result
 
setFieldValue(MagpieServer.getModelInformation_args._Fields, Object) - Method in class magpie.user.server.thrift.MagpieServer.getModelInformation_args
 
setFieldValue(MagpieServer.getModelInformation_result._Fields, Object) - Method in class magpie.user.server.thrift.MagpieServer.getModelInformation_result
 
setFieldValue(MagpieServer.searchMultiObjective_args._Fields, Object) - Method in class magpie.user.server.thrift.MagpieServer.searchMultiObjective_args
 
setFieldValue(MagpieServer.searchMultiObjective_result._Fields, Object) - Method in class magpie.user.server.thrift.MagpieServer.searchMultiObjective_result
 
setFieldValue(MagpieServer.searchSingleObjective_args._Fields, Object) - Method in class magpie.user.server.thrift.MagpieServer.searchSingleObjective_args
 
setFieldValue(MagpieServer.searchSingleObjective_result._Fields, Object) - Method in class magpie.user.server.thrift.MagpieServer.searchSingleObjective_result
 
setFieldValue(ModelInfo._Fields, Object) - Method in class magpie.user.server.thrift.ModelInfo
 
setFilter(BaseDatasetFilter) - Method in class magpie.models.BaseModel
Set filter used to clean data before training
setFittedElements(List<String>) - Method in class magpie.models.regression.MixingRuleRegression
Set which elements to fit.
setFormula(String) - Method in class magpie.optimization.rankers.PropertyFormulaRanker
Define the formula used by this class.
setGenericModel(BaseModel) - Method in class magpie.models.classification.SplitClassifier
 
setGenericModel(BaseModel) - Method in interface magpie.models.interfaces.MultiModel
Set the model template
setGenericModel(BaseModel) - Method in class magpie.models.regression.CompositeRegression
 
setGenericModel(BaseModel) - Method in class magpie.models.regression.MultiObjectiveRegression
Define the model to be used for a property if one is not specifically defined.
setGenericModel(BaseModel) - Method in class magpie.models.regression.SplitRegression
 
setGenericModel(BaseModel) - Method in class magpie.models.regression.StagedRegression
 
setGenericModel(BaseModel) - Method in class magpie.models.SplitModel
Set the model template
setGenMethod(String) - Method in class magpie.user.server.thrift.MagpieServer.searchMultiObjective_args
 
setGenMethod(String) - Method in class magpie.user.server.thrift.MagpieServer.searchSingleObjective_args
 
setGenMethodIsSet(boolean) - Method in class magpie.user.server.thrift.MagpieServer.searchMultiObjective_args
 
setGenMethodIsSet(boolean) - Method in class magpie.user.server.thrift.MagpieServer.searchSingleObjective_args
 
setGridSpacing(double) - Method in class magpie.data.utilities.generators.GridBaseEntryGenerator
Define grid step size.
setGroupIncludedInAttribute(int, boolean) - Method in class magpie.data.materials.util.PrototypeSiteInformation
Define whether a group of sites should be included when generating attributes.
setGuess(double) - Method in class magpie.models.regression.SingleGuessRegression
Sets the user's guess
setIncludeMatching(boolean) - Method in class magpie.attributes.selectors.RegexAttributeSelector
Set whether to include (or exclude) attributes whose name matches the pattern.
setInitialData(Dataset) - Method in class magpie.optimization.BaseOptimizer
Define the initial population
setInitialGuess(String, double) - Method in class magpie.models.regression.AbstractNonlinearRegression
Set the initial guess for a coefficient
setK(int) - Method in class magpie.data.utilities.filters.PredictionOutlierFilter
Define number of fitting parameters in model.
setK(int) - Method in class magpie.optimization.rankers.RankAggregationRanker
Define the maximum number of entries to be interested in.
setKnownCompounds(Map<CompositionEntry, String>) - Method in class magpie.csp.CSPEngine
Define the composition and prototype of already-known compounds.
setLookupData(CompositionDataset) - Method in class magpie.data.utilities.generators.IonicCompoundGenerator
Define the dataset used to lookup oxidation states.
setLookupTable(Dataset) - Method in class magpie.optimization.oracles.LookupOracle
Define the lookup table used by this oracle.
setMaxAlloying(double) - Method in class magpie.data.utilities.generators.AlloyingCompositionEntryGenerator
Set the maximum amount of element to add.
setMaxCandidates(int) - Method in class magpie.analytics.TargetRegressionStatistics
Set the maximum number of candidates for an analysis of how the number of candidates affects prediction accuracy.
setMaxFormulaUnitSize(int) - Method in class magpie.utility.tools.IonicCompoundFinder
Set maximum number of atoms in formula unit.
setMaximizeFunction(boolean) - Method in class magpie.optimization.rankers.BaseEntryRanker
Set whether this entry ranker will maximize objective function
setMaximumDistance(double) - Method in class magpie.utility.tools.IonicCompoundFinder
Set the maximum allowed distance from the target value.
setMaxIterations(int) - Method in class magpie.models.regression.AbstractNonlinearRegression
Define the maximum number of iterations allowed.
setMaxIterations(int) - Method in class magpie.optimization.BaseOptimizer
Set the maximum number of iterations the algorithm is allowed.
setMaxNumberTerms(int) - Method in class magpie.models.regression.LASSORegression
 
setMaxValue(double) - Method in class magpie.data.utilities.generators.GridBaseEntryGenerator
Define maximum value in all directions
setMaxWindowSize(double) - Method in class magpie.analytics.TargetRegressionStatistics
Set the maximum window size for an analysis of how tolerance window size affects prediction accuracy.
setMeasuredClass(double) - Method in class magpie.data.BaseEntry
Set the measured class variable
setMeasuredClass(double) - Method in class magpie.data.MultiPropertyEntry
 
setMeasuredClasses(double[]) - Method in class magpie.data.Dataset
Set measured class for each entry, given an array of measurements
setMeasuredProperties(double[]) - Method in class magpie.data.MultiPropertyEntry
Define the values of all measured properties of this entry.
setMeasuredProperties(Map<String, Double>) - Method in class magpie.user.server.thrift.Entry
 
setMeasuredPropertiesIsSet(boolean) - Method in class magpie.user.server.thrift.Entry
 
setMeasuredProperty(int, double) - Method in class magpie.data.MultiPropertyEntry
Set the measured value of a specific property of this entry.
setMinValue(double) - Method in class magpie.data.utilities.generators.GridBaseEntryGenerator
Define minimum value in all directions.
setModel(String, BaseModel, Dataset) - Method in class magpie.attributes.generators.ModelPredictionAttributeGenerator
Set the model used to create attribute(s).
setModel(BaseModel) - Method in class magpie.data.utilities.modifiers.ErrorSignalModifier
Set the model used to make predictions.
setModel(BaseModel) - Method in class magpie.data.utilities.splitters.NonZeroClassificationSplitter
Define the model used to split data.
setModel(int, BaseModel) - Method in class magpie.models.classification.SplitClassifier
 
setModel(String, String[]) - Method in class magpie.models.classification.WekaClassifier
 
setModel(int, BaseModel) - Method in interface magpie.models.interfaces.MultiModel
Set a specific submodel.
setModel(String, String[]) - Method in interface magpie.models.interfaces.WekaModel
Set the underlying Weka-based model
setModel(int, BaseModel) - Method in class magpie.models.regression.CompositeRegression
 
setModel(String, BaseModel) - Method in class magpie.models.regression.MultiObjectiveRegression
Define a model for a certain property.
setModel(int, BaseModel) - Method in class magpie.models.regression.SplitRegression
 
setModel(int, BaseModel) - Method in class magpie.models.regression.StagedRegression
 
setModel(String, String[]) - Method in class magpie.models.regression.WekaRegression
Set the underlying Weka-based model
setModel(int, BaseModel) - Method in class magpie.models.SplitModel
 
setModel(CompositeRegression) - Method in class magpie.optimization.algorithms.ActiveLearningOptimizer
Define the model used to perform the active learning
setModel(BaseModel) - Method in class magpie.utility.tools.BatchModelEvaluator
Define which model this class is used to evaluate
setModelType(String) - Method in class magpie.user.server.thrift.ModelInfo
 
setModelTypeIsSet(boolean) - Method in class magpie.user.server.thrift.ModelInfo
 
setMu(String, double) - Method in class magpie.data.materials.util.GCLPCalculator
Define the chemical potential of an element
setMutationFunction(BaseMutationFunction) - Method in class magpie.optimization.algorithms.genetic.GeneticAlgorithm
Define the mutation function to use with this algorithm
setMutationProbability(double) - Method in class magpie.optimization.algorithms.genetic.GeneticAlgorithm
Probability that a candidate will be mutated after cross-over
setName(String) - Method in class magpie.user.server.thrift.Entry
 
setNameIsSet(boolean) - Method in class magpie.user.server.thrift.Entry
 
setNBins(int[]) - Method in class magpie.models.classification.CumulantExpansionClassifier
Define number of desired bins of common compositions.
setNComponents(int) - Method in class magpie.models.classification.CumulantExpansionClassifier
Set the number of components in the material being considered.
setNElements(int) - Method in class magpie.utility.tools.PhaseDiagramExclusionValidator
Set the number of elements in phase diagrams being iterated through
setNewClassName(String) - Method in class magpie.data.utilities.modifiers.ClassEliminationModifier
Define the name of the new class for entries measured to exist in the undesired class.
setNominalComposition(CompositionEntry) - Method in class magpie.utility.tools.IonicCompoundFinder
Set the target composition of the ionic compound.
setNotes(String) - Method in class magpie.user.server.thrift.ModelInfo
 
setNotesIsSet(boolean) - Method in class magpie.user.server.thrift.ModelInfo
 
setNPerDiagram(int) - Method in class magpie.data.utilities.filters.BestInAlloySystemFilter
Set number of entries to collect per diagram
setNProperties(int) - Method in class magpie.data.MultiPropertyEntry
Define the number of properties this entry can support.
setNSteps(int) - Method in class magpie.analytics.TargetRegressionStatistics
Set the number of steps to use when calculating model performance for ranking or filtering.
setNumberElite(int) - Method in class magpie.optimization.algorithms.genetic.GeneticAlgorithm
Define how many elite entries to keep in breeding pool
setNumberOfModels(int) - Method in interface magpie.models.interfaces.MultiModel
Defines the number of models to be trained.
setNumberOfModels(int) - Method in class magpie.models.regression.CompositeRegression
 
setNumberOfModels(int) - Method in class magpie.models.regression.StagedRegression
 
setNumberOfModels(int) - Method in class magpie.models.SplitModel
 
setNumberToFilter(int) - Method in class magpie.data.utilities.filters.EntryRankerFilter
Define how many entries will pass this filter
setNumberTopEntries(int) - Method in class magpie.optimization.analytics.OptimizationStatistics
Define the number of top entries to hold for statistical purposes.
setNumToList(int) - Method in class magpie.user.server.thrift.MagpieServer.searchMultiObjective_args
 
setNumToList(int) - Method in class magpie.user.server.thrift.MagpieServer.searchSingleObjective_args
 
setNumToListIsSet(boolean) - Method in class magpie.user.server.thrift.MagpieServer.searchMultiObjective_args
 
setNumToListIsSet(boolean) - Method in class magpie.user.server.thrift.MagpieServer.searchSingleObjective_args
 
setObj(String) - Method in class magpie.user.server.thrift.MagpieServer.searchSingleObjective_args
 
setObjectiveFunction(BaseEntryRanker) - Method in class magpie.data.utilities.splitters.ObjectiveFunctionSplitter
Define objective function by which to split entries
setObjectiveFunction(BaseEntryRanker) - Method in class magpie.models.regression.ClassificationRegression
Define the objective function used to order entries
setObjectiveFunction(MultiObjectiveEntryRanker) - Method in class magpie.models.regression.MultiObjectiveRegression
Define the objective function used to calculate perform of each entry.
setObjectiveFunction(BaseEntryRanker) - Method in class magpie.optimization.BaseOptimizer
Define the objective function
setObjectivePercentile(double) - Method in class magpie.optimization.rankers.AdaptiveScalarizingEntryRanker
Define percentile to use for approximating the minimum value of each objective function.
setObjIsSet(boolean) - Method in class magpie.user.server.thrift.MagpieServer.searchSingleObjective_args
 
setObjs(List<String>) - Method in class magpie.user.server.thrift.MagpieServer.searchMultiObjective_args
 
setObjsIsSet(boolean) - Method in class magpie.user.server.thrift.MagpieServer.searchMultiObjective_args
 
setOptions(List<Object>) - Method in class magpie.analytics.BaseStatistics
 
setOptions(List<Object>) - Method in class magpie.analytics.TargetRegressionStatistics
 
setOptions(List<Object>) - Method in class magpie.attributes.evaluators.AreaUnderROCEvaluator
 
setOptions(List<Object>) - Method in class magpie.attributes.evaluators.PearsonsCorrelationEvaluator
 
setOptions(List<Object>) - Method in class magpie.attributes.evaluators.PolynomialFitEvaluator
 
setOptions(List<Object>) - Method in class magpie.attributes.evaluators.SpearmansCorrelationEvaluator
 
setOptions(List<Object>) - Method in class magpie.attributes.expanders.CrossExpander
 
setOptions(List<Object>) - Method in class magpie.attributes.expanders.FunctionExpander
 
setOptions(List<Object>) - Method in class magpie.attributes.expanders.PowerExpander
 
setOptions(List<Object>) - Method in class magpie.attributes.generators.composition.ElementalPropertyAttributeGenerator
 
setOptions(List<Object>) - Method in class magpie.attributes.generators.composition.ElementFractionAttributeGenerator
 
setOptions(List<Object>) - Method in class magpie.attributes.generators.composition.IonicityAttributeGenerator
 
setOptions(List<Object>) - Method in class magpie.attributes.generators.composition.MeredigAttributeGenerator
 
setOptions(List<Object>) - Method in class magpie.attributes.generators.composition.StoichiometricAttributeGenerator
 
setOptions(List<Object>) - Method in class magpie.attributes.generators.composition.ValenceShellAttributeGenerator
 
setOptions(List<Object>) - Method in class magpie.attributes.generators.element.ElementalPropertyAttributeGenerator
 
setOptions(List<Object>) - Method in class magpie.attributes.generators.LookupTableAttributeGenerator
 
setOptions(List<Object>) - Method in class magpie.attributes.generators.ModelPredictionAttributeGenerator
 
setOptions(List<Object>) - Method in class magpie.attributes.generators.PropertyAsAttributeGenerator
 
setOptions(List<Object>) - Method in class magpie.attributes.selectors.BestIndividualSelector
 
setOptions(List<Object>) - Method in class magpie.attributes.selectors.MeredigAttributeSelector
 
setOptions(List<Object>) - Method in class magpie.attributes.selectors.RegexAttributeSelector
 
setOptions(List<Object>) - Method in class magpie.attributes.selectors.UserSpecifiedAttributeSelector
Sets the object to select only attributes listed in input
setOptions(List<Object>) - Method in class magpie.attributes.selectors.WekaAttributeSelector
 
setOptions(List<Object>) - Method in class magpie.cluster.WekaClusterer
 
setOptions(List<Object>) - Method in class magpie.csp.CompositionBasedCSPEngine
 
setOptions(List<Object>) - Method in class magpie.csp.DMSPEngine
 
setOptions(List<Object>) - Method in class magpie.data.Dataset
 
setOptions(List<Object>) - Method in class magpie.data.materials.PrototypeDataset
 
setOptions(List<Object>) - Method in class magpie.data.utilities.filters.AllMetalsFilter
 
setOptions(List<Object>) - Method in class magpie.data.utilities.filters.AttributeFilter
 
setOptions(String, String, String) - Method in class magpie.data.utilities.filters.AttributeFilter
Configure the filter by defining which entries should be kept
setOptions(List<Object>) - Method in class magpie.data.utilities.filters.BestInAlloySystemFilter
 
setOptions(List<Object>) - Method in class magpie.data.utilities.filters.ClassFilter
 
setOptions(String, String, String) - Method in class magpie.data.utilities.filters.ClassFilter
Configure the filter by defining which entries should be kept
setOptions(List<Object>) - Method in class magpie.data.utilities.filters.ClassProbabilityFilter
 
setOptions(List<Object>) - Method in class magpie.data.utilities.filters.ClassRangeFilter
 
setOptions(List<Object>) - Method in class magpie.data.utilities.filters.CompositionDistanceFilter
 
setOptions(List<Object>) - Method in class magpie.data.utilities.filters.CompositionSetDistanceFilter
 
setOptions(List<Object>) - Method in class magpie.data.utilities.filters.ContainsElementFilter
 
setOptions(List<Object>) - Method in class magpie.data.utilities.filters.EntryRankerFilter
 
setOptions(List<Object>) - Method in class magpie.data.utilities.filters.IQROutlierFilter
 
setOptions(List<Object>) - Method in class magpie.data.utilities.filters.MultiFilter
 
setOptions(List<Object>) - Method in class magpie.data.utilities.filters.PredictionOutlierFilter
 
setOptions(List<Object>) - Method in class magpie.data.utilities.filters.PropertyFilter
 
setOptions(List<Object>) - Method in class magpie.data.utilities.filters.PropertyRangeFilter
 
setOptions(List) - Method in class magpie.data.utilities.filters.RegressionErrorFilter
 
setOptions(List<Object>) - Method in class magpie.data.utilities.filters.StabilityFilter
 
setOptions(List<Object>) - Method in class magpie.data.utilities.filters.ZScoreOutlierFilter
 
setOptions(List<Object>) - Method in class magpie.data.utilities.generators.AlloyingCompositionEntryGenerator
 
setOptions(List<Object>) - Method in class magpie.data.utilities.generators.CompositionRangeEntryGenerator
 
setOptions(List<Object>) - Method in class magpie.data.utilities.generators.GridBaseEntryGenerator
 
setOptions(List<Object>) - Method in class magpie.data.utilities.generators.IonicCompoundGenerator
 
setOptions(List<Object>) - Method in class magpie.data.utilities.generators.PhaseDiagramCompositionEntryGenerator
 
setOptions(List<Object>) - Method in class magpie.data.utilities.generators.PrototypeEntryGenerator
 
setOptions(List<Object>) - Method in class magpie.data.utilities.modifiers.AddPropertyModifier
 
setOptions(List<Object>) - Method in class magpie.data.utilities.modifiers.ClassEliminationModifier
 
setOptions(List) - Method in class magpie.data.utilities.modifiers.ClassIntervalModifier
 
setOptions(List<Object>) - Method in class magpie.data.utilities.modifiers.CompositionSetDistanceModifier
 
setOptions(List<Object>) - Method in class magpie.data.utilities.modifiers.DiscreteToContinuousModifier
 
setOptions(List) - Method in class magpie.data.utilities.modifiers.ErrorSignalModifier
 
setOptions(List<Object>) - Method in class magpie.data.utilities.modifiers.HHICalculationModifier
 
setOptions(List<Object>) - Method in class magpie.data.utilities.modifiers.NaNToMeanModifier
 
setOptions(List) - Method in class magpie.data.utilities.modifiers.NonZeroClassModifier
 
setOptions(List<Object>) - Method in class magpie.data.utilities.modifiers.PartitionToClassModifier
 
setOptions(List<Object>) - Method in class magpie.data.utilities.modifiers.SetClassNamesModifier
 
setOptions(List<Object>) - Method in class magpie.data.utilities.modifiers.StabilityCalculationModifier
 
setOptions(List) - Method in class magpie.data.utilities.modifiers.VolumeToLatticeParamModifier
 
setOptions(List<Object>) - Method in class magpie.data.utilities.normalizers.InverseNormalizer
 
setOptions(List<Object>) - Method in class magpie.data.utilities.normalizers.RegularSolutionNormalizer
 
setOptions(List<Object>) - Method in class magpie.data.utilities.normalizers.RescalingNormalizer
 
setOptions(List<Object>) - Method in class magpie.data.utilities.normalizers.SoftmaxNormalizer
 
setOptions(List<Object>) - Method in class magpie.data.utilities.normalizers.ZScoreNormalizer
 
setOptions(List) - Method in class magpie.data.utilities.splitters.AllMetalsSplitter
 
setOptions(List) - Method in class magpie.data.utilities.splitters.AttributeIntervalSplitter
 
setOptions(List) - Method in class magpie.data.utilities.splitters.ClustererSplitter
 
setOptions(List) - Method in class magpie.data.utilities.splitters.MeasuredClassSplitter
 
setOptions(List) - Method in class magpie.data.utilities.splitters.MultipleElementGroupsSplitter
 
setOptions(List) - Method in class magpie.data.utilities.splitters.NonZeroClassificationSplitter
 
setOptions(List<Object>) - Method in class magpie.data.utilities.splitters.ObjectiveFunctionSplitter
 
setOptions(List<Object>) - Method in class magpie.data.utilities.splitters.PredictedClassIntervalSplitter
 
setOptions(List) - Method in class magpie.data.utilities.splitters.SingleElementGroupSplitter
 
setOptions(List<Object>) - Method in class magpie.models.classification.CumulantExpansionClassifier
 
setOptions(List) - Method in class magpie.models.classification.SplitClassifier
 
setOptions(List) - Method in class magpie.models.classification.WekaClassifier
 
setOptions(List) - Method in class magpie.models.regression.AbstractNonlinearRegression
 
setOptions(List) - Method in class magpie.models.regression.AbstractParsedNonlinearRegression
 
setOptions(List<Object>) - Method in class magpie.models.regression.ClassificationRegression
 
setOptions(List) - Method in class magpie.models.regression.CompositeRegression
 
setOptions(List) - Method in class magpie.models.regression.GuessMeanRegression
 
setOptions(List) - Method in class magpie.models.regression.LASSORegression
 
setOptions(List<Object>) - Method in class magpie.models.regression.LinearCorrectedRegression
 
setOptions(List<Object>) - Method in class magpie.models.regression.MetallurgicalHeuristicRegression
 
setOptions(List) - Method in class magpie.models.regression.MixingRuleRegression
 
setOptions(List<Object>) - Method in class magpie.models.regression.MultiObjectiveRegression
 
setOptions(List<Object>) - Method in class magpie.models.regression.MultiPropertyRegression
 
setOptions(List) - Method in class magpie.models.regression.PolynomialRegression
 
setOptions(List) - Method in class magpie.models.regression.RandomGuessRegression
 
setOptions(List<Object>) - Method in class magpie.models.regression.ScikitLearnRegression
 
setOptions(List) - Method in class magpie.models.regression.SingleGuessRegression
 
setOptions(List) - Method in class magpie.models.regression.StagedRegression
 
setOptions(List) - Method in class magpie.models.regression.WekaRegression
 
setOptions(List) - Method in class magpie.models.SplitModel
 
setOptions(List) - Method in class magpie.optimization.algorithms.ActiveLearningOptimizer
 
setOptions(List) - Method in class magpie.optimization.algorithms.genetic.GeneticAlgorithm
 
setOptions(List) - Method in class magpie.optimization.oracles.LookupOracle
 
setOptions(List<Object>) - Method in class magpie.optimization.rankers.AdaptiveScalarizingEntryRanker
 
setOptions(List<Object>) - Method in class magpie.optimization.rankers.ClassProbabilityRanker
 
setOptions(List<Object>) - Method in class magpie.optimization.rankers.CompositionDistanceRanker
 
setOptions(List<Object>) - Method in class magpie.optimization.rankers.PropertyFormulaRanker
 
setOptions(List<Object>) - Method in class magpie.optimization.rankers.RankAggregationRanker
 
setOptions(List) - Method in class magpie.optimization.rankers.SimpleEntryRanker
 
setOptions(List) - Method in class magpie.optimization.rankers.TargetEntryRanker
 
setOptions(List<Object>) - Method in interface magpie.utility.interfaces.Options
Set any options for this object.
setOptions(List<Object>) - Method in class magpie.utility.tools.BatchModelEvaluator
 
setOptions(List<Object>) - Method in class magpie.utility.tools.OxidationStateGuesser
 
setOptions(List<Object>) - Method in class magpie.utility.tools.PhaseDiagramExclusionValidator
 
setOracle(BaseOracle) - Method in class magpie.optimization.BaseOptimizer
Define BaseOracle used to evaluate properties/class variable
setOrder(int, int) - Method in class magpie.data.utilities.generators.PhaseDiagramCompositionEntryGenerator
Define the order of generated phase diagrams
setOrder(int) - Method in class magpie.models.regression.PolynomialRegression
Define order of polynomial.
setOuch(MagpieException) - Method in class magpie.user.server.thrift.MagpieServer.evaluateProperties_result
 
setOuch(MagpieException) - Method in class magpie.user.server.thrift.MagpieServer.getModelInformation_result
 
setOuch(MagpieException) - Method in class magpie.user.server.thrift.MagpieServer.searchMultiObjective_result
 
setOuch(MagpieException) - Method in class magpie.user.server.thrift.MagpieServer.searchSingleObjective_result
 
setOuchIsSet(boolean) - Method in class magpie.user.server.thrift.MagpieServer.evaluateProperties_result
 
setOuchIsSet(boolean) - Method in class magpie.user.server.thrift.MagpieServer.getModelInformation_result
 
setOuchIsSet(boolean) - Method in class magpie.user.server.thrift.MagpieServer.searchMultiObjective_result
 
setOuchIsSet(boolean) - Method in class magpie.user.server.thrift.MagpieServer.searchSingleObjective_result
 
setOxidationStates(int[][]) - Method in class magpie.utility.tools.OxidationStateGuesser
Set the oxidation states
setOxidationStates(double[][]) - Method in class magpie.utility.tools.OxidationStateGuesser
Set the oxidation states
setOxidationStates(String) - Method in class magpie.utility.tools.OxidationStateGuesser
Set the oxidation states
setP(int) - Method in class magpie.data.utilities.filters.CompositionSetDistanceFilter
Set the p-norm to use when computing distance between compositions.
setP(int) - Method in class magpie.data.utilities.modifiers.CompositionSetDistanceModifier
Set the p-norm to use when computing distance between compositions.
setP(double) - Method in class magpie.optimization.rankers.AdaptiveScalarizingEntryRanker
Set tradeoff parameter between optimal in single category and decent in all
setP(int) - Method in class magpie.optimization.rankers.CompositionDistanceRanker
Set the p-norm to use when computing distance between compositions.
setP(double) - Method in class magpie.user.server.thrift.MagpieServer.searchMultiObjective_args
 
setPartitioner(BaseDatasetSplitter) - Method in class magpie.models.SplitModel
Set the partitioner.
setPerCell(int) - Method in class magpie.data.utilities.modifiers.VolumeToLatticeParamModifier
Set number of atoms in unit cell.
setPhaseDiagramStats(PhaseDiagramStatistics) - Method in class magpie.models.classification.CumulantExpansionClassifier
Define the phase diagram statistics object used to make predictions.
setPIsSet(boolean) - Method in class magpie.user.server.thrift.MagpieServer.searchMultiObjective_args
 
setPredictedClass(double) - Method in class magpie.data.BaseEntry
Set the predicted class variable
setPredictedClass(double) - Method in class magpie.data.MultiPropertyEntry
 
setPredictedClasses(double[]) - Method in class magpie.data.Dataset
Set predicted class for each entry, given an array of predictions
setPredictedProperties(Map<String, Double>) - Method in class magpie.user.server.thrift.Entry
 
setPredictedPropertiesIsSet(boolean) - Method in class magpie.user.server.thrift.Entry
 
setPredictedProperty(int, double) - Method in class magpie.data.MultiPropertyEntry
Directly set the predicted value of a property.
setPredictedProperty(int, double[]) - Method in class magpie.data.MultiPropertyEntry
Directly set the probabilities of an entry existing in multiple classes.
setPreviousIterations(int) - Method in class magpie.optimization.algorithms.genetic.GeneticAlgorithm
Set the number of previous iterations to include in breeding pool
setProbabilityThreshold(double) - Method in class magpie.data.utilities.splitters.NonZeroClassificationSplitter
Define the probability of being in class 0 on which to partition data.
setPropertiesToAdd(List<String>) - Method in class magpie.data.utilities.modifiers.AddPropertyModifier
Define list of properties to add to a dataset.
setProperty(String) - Method in class magpie.user.server.thrift.ModelInfo
 
setPropertyClasses(int, String[]) - Method in class magpie.data.MultiPropertyDataset
Define possible classes for a certain property (like "Metal" or "Nonmetal")
setPropertyIsSet(boolean) - Method in class magpie.user.server.thrift.ModelInfo
 
setPropertyName(String) - Method in class magpie.models.regression.MixingRuleRegression
Define which property to use for alloy mean
setProps(List<String>) - Method in class magpie.user.server.thrift.MagpieServer.evaluateProperties_args
 
setPropsIsSet(boolean) - Method in class magpie.user.server.thrift.MagpieServer.evaluateProperties_args
 
setQ(double) - Method in class magpie.analytics.utility.RobustRegressionUtility
Define the target False Discovery Rate for outlier selection
setQ(double) - Method in class magpie.data.utilities.filters.PredictionOutlierFilter
Set target False Discovery rate.
setR(double) - Method in class magpie.data.utilities.normalizers.SoftmaxNormalizer
Set the scaling constant
setRandomFraction(double) - Method in class magpie.optimization.algorithms.ActiveLearningOptimizer
Define what fraction of new entries should be randomly selected.
setRanker(BaseEntryRanker) - Method in class magpie.data.utilities.filters.BestInAlloySystemFilter
Set how to rank entries
setRanker(BaseEntryRanker) - Method in class magpie.data.utilities.filters.EntryRankerFilter
Define the ranker used to filter entries.
setRankingWeight(double) - Method in class magpie.optimization.algorithms.genetic.GeneticAlgorithm
Define weighting parameter used when selecting better-performing entries.
setRegex(String) - Method in class magpie.attributes.selectors.RegexAttributeSelector
Define the regular expression.
setRobustRegressionQ(double) - Method in interface magpie.models.regression.AbstractRegressionModel
Set the desired False Discovery Rate for outlier detection.
setRobustRegressionQ(double) - Method in class magpie.models.regression.BaseRegression
 
setRobustRegressionQ(double) - Method in class magpie.models.regression.SplitRegression
 
setScale(double) - Method in class magpie.data.utilities.normalizers.InverseNormalizer
Define scale of attributes / class.
setScreenAttributes(boolean) - Method in class magpie.data.utilities.filters.ZScoreOutlierFilter
Set whether to screen based on whether any attribute value is an outlier.
setScreenClass(boolean) - Method in class magpie.data.utilities.filters.ZScoreOutlierFilter
Set whether to screen based on whether measured class value is an outlier
setSearcher(String, String[]) - Method in class magpie.attributes.selectors.WekaAttributeSelector
Set the method used to search for optimal subsets.
setSearchSpace(Dataset) - Method in class magpie.optimization.algorithms.genetic.GeneticAlgorithm
 
setSearchSpace(Dataset) - Method in class magpie.optimization.BaseOptimizer
Define the search space over which the algorithm is allowed to sample.
setSiteComposition(int, CompositionEntry) - Method in class magpie.data.materials.PrototypeEntry
Set the composition of a certain site
setSiteInfo(PrototypeSiteInformation) - Method in class magpie.data.materials.PrototypeDataset
Define information about the prototypes contained by this dataset.
setSiteInfo(PrototypeSiteInformation) - Method in class magpie.data.utilities.generators.PrototypeEntryGenerator
Define the information about the sites in the prototype.
setSize(int) - Method in class magpie.data.utilities.generators.PhaseDiagramCompositionEntryGenerator
Define the number of points per binary diagram (in using even spacing) or the maximum denominator (for low-denominator)
setSplitAbove(boolean) - Method in class magpie.data.utilities.splitters.ObjectiveFunctionSplitter
Set whether class #0 should be entries above a threshold
setSplitter(BaseDatasetSplitter) - Method in class magpie.data.utilities.modifiers.PartitionToClassModifier
Set the splitter used to generate new class variables.
setStabilityName(String) - Method in class magpie.data.utilities.modifiers.StabilityCalculationModifier
Set the name of the property in which to store stability data
setSubmodel(BaseModel) - Method in class magpie.models.regression.LinearCorrectedRegression
Define the model that this class corrects.
setSuccess(List<Entry>) - Method in class magpie.user.server.thrift.MagpieServer.evaluateProperties_result
 
setSuccess(Map<String, ModelInfo>) - Method in class magpie.user.server.thrift.MagpieServer.getModelInformation_result
 
setSuccess(List<Entry>) - Method in class magpie.user.server.thrift.MagpieServer.searchMultiObjective_result
 
setSuccess(List<Entry>) - Method in class magpie.user.server.thrift.MagpieServer.searchSingleObjective_result
 
setSuccessFilter(BaseDatasetFilter) - Method in class magpie.optimization.analytics.OptimizationStatistics
Define a filter to define when the optimization algorithm has found an acceptable entry.
setSuccessIsSet(boolean) - Method in class magpie.user.server.thrift.MagpieServer.evaluateProperties_result
 
setSuccessIsSet(boolean) - Method in class magpie.user.server.thrift.MagpieServer.getModelInformation_result
 
setSuccessIsSet(boolean) - Method in class magpie.user.server.thrift.MagpieServer.searchMultiObjective_result
 
setSuccessIsSet(boolean) - Method in class magpie.user.server.thrift.MagpieServer.searchSingleObjective_result
 
setTarget(double) - Method in class magpie.analytics.TargetRegressionStatistics
Define target value of class variable.
setTargetClass(String) - Method in class magpie.attributes.evaluators.AreaUnderROCEvaluator
Define the class for which the ability to classify is being assessed.
setTargetClass(String) - Method in class magpie.optimization.rankers.ClassProbabilityRanker
Set the name of the class of interest
setTargetComposition(CompositionEntry) - Method in class magpie.data.utilities.filters.CompositionDistanceFilter
Define the target composition
setTargetProperty(String, boolean) - Method in class magpie.data.MultiPropertyDataset
Define which property to use as the class variable.
setTargetProperty(int, boolean) - Method in class magpie.data.MultiPropertyDataset
Define which property to set as the measured class of each entry.
setTargetProperty(int) - Method in class magpie.data.MultiPropertyEntry
Define which property to use as the class variable.
setTestFraction(double) - Method in class magpie.analytics.utility.RobustRegressionUtility
Define the fraction of entries that will be tested as potential outliers.
setThreshold(double) - Method in class magpie.data.utilities.filters.ClassFilter
Set the comparison threshold.
setThreshold(double) - Method in class magpie.data.utilities.filters.ClassProbabilityFilter
Set the probability threshold used for filtering.
setThreshold(double) - Method in class magpie.data.utilities.filters.IQROutlierFilter
Define number of IQRs away from the median that an entries is an outliers.
setThreshold(double) - Method in class magpie.data.utilities.filters.StabilityFilter
Set threshold at which compounds are declared "unstable".
setThreshold(double) - Method in class magpie.data.utilities.splitters.ObjectiveFunctionSplitter
Set threshold on which to partition entries
setThreshold(double) - Method in class magpie.models.regression.ClassificationRegression
Define threshold of objective function on which to split entries.
setTolerance(double) - Method in class magpie.analytics.TargetRegressionStatistics
Define the error threshold that is considered a successful prediction.
setTolerance(double) - Method in class magpie.data.utilities.filters.ZScoreOutlierFilter
Set the tolerance defining what is an outlier.
setToNormalizeAttributes(boolean) - Method in class magpie.data.utilities.normalizers.BaseDatasetNormalizer
Set whether to normalize attributes
setToNormalizeClass(boolean) - Method in class magpie.data.utilities.normalizers.BaseDatasetNormalizer
Set whether to normalize class variable
setTraining(String) - Method in class magpie.user.server.thrift.ModelInfo
 
setTrainingIsSet(boolean) - Method in class magpie.user.server.thrift.ModelInfo
 
setTrainTime(String) - Method in class magpie.user.server.thrift.ModelInfo
 
setTrainTimeIsSet(boolean) - Method in class magpie.user.server.thrift.ModelInfo
 
setUnits(String) - Method in class magpie.user.server.thrift.ModelInfo
 
setUnitsIsSet(boolean) - Method in class magpie.user.server.thrift.ModelInfo
 
setUseCorrection(boolean) - Method in class magpie.models.regression.MetallurgicalHeuristicRegression
Set whether to employ correction factors
setUseCorrection(boolean) - Method in class magpie.models.regression.MixingRuleRegression
Whether to fit a linear model to correct differences between the alloy mean and class variable
setUseInverse(boolean) - Method in class magpie.models.regression.MixingRuleRegression
Define whether to take the average of the property, or the average of the inverse of the property.
setUseMeasured(boolean) - Method in class magpie.data.utilities.filters.ClassFilter
Set whether to use the measured class variable.
setUseMeasured(boolean) - Method in class magpie.optimization.rankers.AdaptiveScalarizingEntryRanker
 
setUseMeasured(boolean) - Method in class magpie.optimization.rankers.BaseEntryRanker
Set whether to used measured (or predicted) class values
setUseMeasured(boolean) - Method in class magpie.optimization.rankers.RankAggregationRanker
 
setUsePredicted(boolean) - Method in class magpie.data.utilities.filters.StabilityFilter
Set whether to use the measured or predicted class variable.
setValMethod(String) - Method in class magpie.user.server.thrift.ModelInfo
 
setValMethodIsSet(boolean) - Method in class magpie.user.server.thrift.ModelInfo
 
setValScore(Map<String, Double>) - Method in class magpie.user.server.thrift.ModelInfo
 
setValScoreIsSet(boolean) - Method in class magpie.user.server.thrift.ModelInfo
 
setVariable(String, double) - Method in class magpie.utility.ParsedFunction
Define the value of a certain variable in this expression
setVariable(int, double) - Method in class magpie.utility.ParsedFunction
Define the value of a certain variable in this expression
setWhy(String) - Method in exception magpie.user.server.thrift.MagpieException
 
setWhyIsSet(boolean) - Method in exception magpie.user.server.thrift.MagpieException
 
setWorstFraction(double) - Method in class magpie.optimization.algorithms.ActiveLearningOptimizer
Define what fraction of new entries are to come from entries with the least-reliable predictions
SimpleCompoundMutation - Class in magpie.optimization.algorithms.genetic.operators
Mutate a CompositionEntry that represents a compound by only changing which elements are present.
SimpleCompoundMutation() - Constructor for class magpie.optimization.algorithms.genetic.operators.SimpleCompoundMutation
 
SimpleEntryRanker - Class in magpie.optimization.rankers
BaseEntryRanker that ranks entries based on class variable.
SimpleEntryRanker() - Constructor for class magpie.optimization.rankers.SimpleEntryRanker
 
SimpleLinearModelExample - Class in magpie.models.regression.nonlinear
Example for the AbstractNonlinearRegression Class.
SimpleLinearModelExample() - Constructor for class magpie.models.regression.nonlinear.SimpleLinearModelExample
 
simpleRun(BaseModel, Dataset) - Method in class magpie.utility.tools.BatchModelEvaluator
Evaluate all entries in serial mode.
SingleElementGroupSplitter - Class in magpie.data.utilities.splitters
Split dataset into two groups based on whether it contains certain elements.
SingleElementGroupSplitter() - Constructor for class magpie.data.utilities.splitters.SingleElementGroupSplitter
 
SingleGuessRegression - Class in magpie.models.regression
Guess a single, user-specified value for the class variable of all entries.
SingleGuessRegression() - Constructor for class magpie.models.regression.SingleGuessRegression
 
SiteComp - Variable in class magpie.data.materials.PrototypeEntry
Composition of each site
SiteElements - Variable in class magpie.data.utilities.generators.PrototypeEntryGenerator
Lists of possible elements on each site
SiteInfo - Variable in class magpie.data.materials.PrototypeDataset
Stores information about each site
SiteInfo - Variable in class magpie.data.materials.PrototypeEntry
Link to site information from corresponding dataset
SiteInfo - Variable in class magpie.data.utilities.generators.PrototypeEntryGenerator
Description of sites on prototype
siteIsIncludedInAttributes(int) - Method in class magpie.data.materials.util.PrototypeSiteInformation
 
size - Variable in class magpie.data.utilities.generators.PhaseDiagramCompositionEntryGenerator
Either number of stops in each direction or max denominator
SocketServer - Static variable in class magpie.user.server.ServerLauncher
Socket server
SoftmaxNormalizer - Class in magpie.data.utilities.normalizers
Normalization using the "softmax" method.
SoftmaxNormalizer() - Constructor for class magpie.data.utilities.normalizers.SoftmaxNormalizer
 
sortAndGetRanks(double[], boolean) - Static method in class magpie.optimization.algorithms.OptimizationHelper
Sort an array and return the original indices of the each value.
sortAndGetRanks(double[], Comparator<Double>) - Static method in class magpie.optimization.algorithms.OptimizationHelper
Sort an array and return the original index of each member.
SortingOrder - Variable in class magpie.data.materials.CompositionDataset
Order in which elements are sorted (used when printing)
SortingOrder - Variable in class magpie.data.materials.CompositionEntry
Rank of each element (used in display order)
SortingOrder - Static variable in class magpie.data.materials.util.LookupData
Order in which to sort elements.
SpearmansCorrelationEvaluator - Class in magpie.attributes.evaluators
Evaluate attributes based on Spearson's Correlation Coefficient, which is simply the Pearson's Correlation Coefficient between the measured and predicted ranks of entries.
SpearmansCorrelationEvaluator() - Constructor for class magpie.attributes.evaluators.SpearmansCorrelationEvaluator
 
Specificity - Variable in class magpie.analytics.ClassificationStatistics
Specificity (True Negative Rate)
split(Dataset, Predicate) - Static method in class magpie.data.utilities.DatasetHelper
Split a dataset given a predicate (see Apache Common's Collections) Predicate returns a boolean about whether an entry should be moved
split(Dataset) - Method in class magpie.data.utilities.splitters.BaseDatasetSplitter
Splits a dataset into several partitions.
split(Dataset, boolean) - Method in class magpie.data.utilities.splitters.BaseDatasetSplitter
Split a dataset into several partitions.
SplitClassifier - Class in magpie.models.classification
Model that uses several other models to model different parts of a dataset.
SplitClassifier() - Constructor for class magpie.models.classification.SplitClassifier
Create a blank SplitClassifier
splitForThreading(int) - Method in class magpie.data.Dataset
Split for threading purposes.
splitIntoFolds(int) - Method in class magpie.data.Dataset
Split the dataset into multiple folds for cross-validation, empties the original test set
SplitModel - Class in magpie.models
Abstract class for a model that splits the dataset and trains several submodels.
SplitModel() - Constructor for class magpie.models.SplitModel
 
SplitRegression - Class in magpie.models.regression
Abstract class for models that use multiple submodels.
SplitRegression() - Constructor for class magpie.models.regression.SplitRegression
Create a blank split regression model
StabilityCalculationModifier - Class in magpie.data.utilities.modifiers
Use GCLP compute the stability with respect to other phases.
StabilityCalculationModifier() - Constructor for class magpie.data.utilities.modifiers.StabilityCalculationModifier
 
StabilityFilter - Class in magpie.data.utilities.filters
Filter based on computed stability.
StabilityFilter() - Constructor for class magpie.data.utilities.filters.StabilityFilter
 
StagedRegression - Class in magpie.models.regression
Composite regression where the error signal from a model is used to train the next.
StagedRegression() - Constructor for class magpie.models.regression.StagedRegression
 
start(I, MagpieServer.evaluateProperties_args, AsyncMethodCallback<List<Entry>>) - Method in class magpie.user.server.thrift.MagpieServer.AsyncProcessor.evaluateProperties
 
start(I, MagpieServer.getModelInformation_args, AsyncMethodCallback<Map<String, ModelInfo>>) - Method in class magpie.user.server.thrift.MagpieServer.AsyncProcessor.getModelInformation
 
start(I, MagpieServer.searchMultiObjective_args, AsyncMethodCallback<List<Entry>>) - Method in class magpie.user.server.thrift.MagpieServer.AsyncProcessor.searchMultiObjective
 
start(I, MagpieServer.searchSingleObjective_args, AsyncMethodCallback<List<Entry>>) - Method in class magpie.user.server.thrift.MagpieServer.AsyncProcessor.searchSingleObjective
 
startScikitServer() - Method in class magpie.models.regression.ScikitLearnRegression
Start the server hosting the Scikit model.
startServer() - Static method in class magpie.user.server.ServerLauncher
Given the current settings, start the Magpie server
StartTime - Variable in class magpie.user.CommandHandler
Holds start time of default timer
Statistics - Variable in class magpie.optimization.BaseOptimizer
Statistics about the run
StepFraction - Variable in class magpie.data.utilities.generators.CompositionRangeEntryGenerator
Fraction step size of certain element.
StoichiometricAttributeGenerator - Class in magpie.attributes.generators.composition
Generate attributes based on stoichiometry of material.
StoichiometricAttributeGenerator() - Constructor for class magpie.attributes.generators.composition.StoichiometricAttributeGenerator
 
stopServer() - Static method in class magpie.user.server.ServerLauncher
Stop the servers
StructureProbability - Variable in class magpie.csp.diagramdata.PhaseDiagramStatistics
For each composition, probability of each structure existing in a phase diagram.
subtract(Dataset) - Method in class magpie.data.Dataset
Remove all entries that are in another dataset from this dataset
success - Variable in class magpie.user.server.thrift.MagpieServer.evaluateProperties_result
 
success - Variable in class magpie.user.server.thrift.MagpieServer.getModelInformation_result
 
success - Variable in class magpie.user.server.thrift.MagpieServer.searchMultiObjective_result
 
success - Variable in class magpie.user.server.thrift.MagpieServer.searchSingleObjective_result
 
SuccessFilter - Variable in class magpie.optimization.analytics.OptimizationStatistics
Defines when an entry is considered successful
SuccessfulEntries - Variable in class magpie.optimization.analytics.OptimizationStatistics
A list of entries that pass the SuccessFilter (if defined)

T

Target - Variable in class magpie.analytics.TargetRegressionStatistics
Target value of class variable
Target - Variable in class magpie.optimization.rankers.TargetEntryRanker
Target value of class
TargetAttribute - Variable in class magpie.data.utilities.filters.AttributeFilter
Name of feature to base filter on
TargetEntryRanker - Class in magpie.optimization.rankers
Rank entries based on the distance of their class variable from a target.
TargetEntryRanker(double) - Constructor for class magpie.optimization.rankers.TargetEntryRanker
Create a new instance while specifying the target
TargetEntryRanker() - Constructor for class magpie.optimization.rankers.TargetEntryRanker
Create a new instance the target set to 0.0
TargetRegressionStatistics - Class in magpie.analytics
Statistics for the ability of a model to find entries with a class near a target value.
TargetRegressionStatistics() - Constructor for class magpie.analytics.TargetRegressionStatistics
 
Tau - Variable in class magpie.analytics.RegressionStatistics
Kendall's rank correlation coefficient
TermNames - Variable in class magpie.models.regression.LASSORegression
Names of terms used in the model
Terms - Variable in class magpie.models.regression.LASSORegression
Terms used in the model
TernaryPhaseDiagramStatistics - Class in magpie.csp.diagramdata
Deprecated. 
TernaryPhaseDiagramStatistics() - Constructor for class magpie.csp.diagramdata.TernaryPhaseDiagramStatistics
Deprecated.
 
test(Dataset) - Method in class magpie.data.utilities.normalizers.BaseDatasetNormalizer
Check whether the normalize/restore operations are reversible.
testCriteria(double[]) - Method in class magpie.data.utilities.filters.AttributeFilter
Evaluate the filtering criteria on each member of an array
testCriteria(double[]) - Method in class magpie.data.utilities.filters.ClassFilter
Evaluate the filtering criteria on each member of an array
TestFraction - Variable in class magpie.analytics.utility.RobustRegressionUtility
What fraction of the population to test
Threshold - Variable in class magpie.data.utilities.filters.AttributeFilter
Threshold value
Threshold - Variable in class magpie.data.utilities.filters.ClassFilter
Threshold value
Title - Variable in class magpie.utility.interfaces.Citation
Title of resource being cited.
TN - Variable in class magpie.analytics.ClassificationStatistics
Number of True Negatives
ToEvaluate - Variable in class magpie.optimization.oracles.BaseOracle
Dataset containing entries currently being evaluated
toExclude() - Method in class magpie.data.utilities.filters.BaseDatasetFilter
 
toHTMLString() - Method in class magpie.data.BaseEntry
Print entry in a HTML-friendly format.
toHTMLString() - Method in class magpie.data.materials.CompositionEntry
 
toHTMLString() - Method in class magpie.data.materials.ElementEntry
 
toHTMLString() - Method in class magpie.data.materials.PrototypeEntry
 
Tolerance - Variable in class magpie.analytics.TargetRegressionStatistics
Tolerance for successful prediction
Tolerance - Variable in class magpie.data.utilities.filters.ZScoreOutlierFilter
Number of standard deviation away from mean used when defining outliers
TopEntries - Variable in class magpie.optimization.analytics.OptimizationStatistics
A list of top entries that optimization algorithm is designed to find.
TopEntriesFound - Variable in class magpie.optimization.analytics.OptimizationStatistics
Number of top entries found in the population for each iteration
toString() - Method in class magpie.analytics.ClassificationStatistics
 
toString() - Method in class magpie.analytics.RegressionStatistics
 
toString() - Method in class magpie.data.BaseEntry
 
toString() - Method in class magpie.data.Dataset
 
toString() - Method in class magpie.data.materials.CompositionEntry
 
toString() - Method in class magpie.data.materials.ElementEntry
 
toString() - Method in class magpie.data.materials.PrototypeEntry
 
toString() - Method in class magpie.data.MultiPropertyDataset
 
toString() - Method in class magpie.models.classification.WekaClassifier
 
toString() - Method in class magpie.models.regression.WekaRegression
 
toString() - Method in class magpie.user.server.thrift.Entry
 
toString() - Method in exception magpie.user.server.thrift.MagpieException
 
toString() - Method in class magpie.user.server.thrift.MagpieServer.evaluateProperties_args
 
toString() - Method in class magpie.user.server.thrift.MagpieServer.evaluateProperties_result
 
toString() - Method in class magpie.user.server.thrift.MagpieServer.getModelInformation_args
 
toString() - Method in class magpie.user.server.thrift.MagpieServer.getModelInformation_result
 
toString() - Method in class magpie.user.server.thrift.MagpieServer.searchMultiObjective_args
 
toString() - Method in class magpie.user.server.thrift.MagpieServer.searchMultiObjective_result
 
toString() - Method in class magpie.user.server.thrift.MagpieServer.searchSingleObjective_args
 
toString() - Method in class magpie.user.server.thrift.MagpieServer.searchSingleObjective_result
 
toString() - Method in class magpie.user.server.thrift.ModelInfo
 
toString() - Method in class magpie.utility.interfaces.Citation
 
TP - Variable in class magpie.analytics.ClassificationStatistics
Number of True Positives
train(Dataset) - Method in class magpie.attributes.selectors.BaseAttributeSelector
Train an attribute selection algorithm on a dataset.
train(Dataset) - Method in class magpie.cluster.BaseClusterer
Train the clusterer
train(Dataset) - Method in class magpie.data.utilities.filters.AllMetalsFilter
 
train(Dataset) - Method in class magpie.data.utilities.filters.AttributeFilter
 
train(Dataset) - Method in class magpie.data.utilities.filters.BaseDatasetFilter
Train a dataset splitter, if necessary
train(Dataset) - Method in class magpie.data.utilities.filters.BestInAlloySystemFilter
 
train(Dataset) - Method in class magpie.data.utilities.filters.ClassFilter
 
train(Dataset) - Method in class magpie.data.utilities.filters.ClassProbabilityFilter
 
train(Dataset) - Method in class magpie.data.utilities.filters.ClassRangeFilter
 
train(Dataset) - Method in class magpie.data.utilities.filters.CompositionDistanceFilter
 
train(Dataset) - Method in class magpie.data.utilities.filters.CompositionSetDistanceFilter
 
train(Dataset) - Method in class magpie.data.utilities.filters.ContainsElementFilter
 
train(Dataset) - Method in class magpie.data.utilities.filters.EntryRankerFilter
 
train(Dataset) - Method in class magpie.data.utilities.filters.IQROutlierFilter
 
train(Dataset) - Method in class magpie.data.utilities.filters.MultiFilter
 
train(Dataset) - Method in class magpie.data.utilities.filters.PredictionOutlierFilter
 
train(Dataset) - Method in class magpie.data.utilities.filters.PropertyRangeFilter
 
train(Dataset) - Method in class magpie.data.utilities.filters.RegressionErrorFilter
 
train(Dataset) - Method in class magpie.data.utilities.filters.StabilityFilter
 
train(Dataset) - Method in class magpie.data.utilities.filters.ZScoreOutlierFilter
 
train(Dataset) - Method in class magpie.data.utilities.normalizers.BaseDatasetNormalizer
Train the normalizer.
train(Dataset) - Method in class magpie.data.utilities.splitters.AllMetalsSplitter
 
train(Dataset) - Method in class magpie.data.utilities.splitters.AttributeIntervalSplitter
 
train(Dataset) - Method in class magpie.data.utilities.splitters.BaseDatasetSplitter
Train a dataset splitter, if necessary
train(Dataset) - Method in class magpie.data.utilities.splitters.ClustererSplitter
 
train(Dataset) - Method in class magpie.data.utilities.splitters.MeasuredClassSplitter
 
train(Dataset) - Method in class magpie.data.utilities.splitters.NonZeroClassificationSplitter
Train a classifier for determining which entries have a non-zero class
train(Dataset) - Method in class magpie.data.utilities.splitters.ObjectiveFunctionSplitter
 
train(Dataset) - Method in class magpie.data.utilities.splitters.PredictedClassIntervalSplitter
 
train(Dataset) - Method in class magpie.data.utilities.splitters.SingleElementGroupSplitter
 
train(Dataset) - Method in class magpie.models.BaseModel
Train a model on a specified training set and then evaluate performance on the training set.
train(Dataset, boolean) - Method in class magpie.models.BaseModel
Train a model on a specified training set and then evaluate performance on the training set, if desired
train(Dataset, boolean) - Method in class magpie.models.classification.BaseClassifier
 
train(MultiPropertyDataset) - Method in class magpie.optimization.rankers.AdaptiveScalarizingEntryRanker
 
train(Dataset) - Method in class magpie.optimization.rankers.BaseEntryRanker
Train ranker.
train(Dataset) - Method in class magpie.optimization.rankers.ClassProbabilityRanker
 
train(Dataset) - Method in class magpie.optimization.rankers.CompositionDistanceRanker
 
train(MultiPropertyDataset) - Method in class magpie.optimization.rankers.MultiObjectiveEntryRanker
Train the entry ranker.
train(Dataset) - Method in class magpie.optimization.rankers.MultiObjectiveEntryRanker
 
train(MultiPropertyDataset) - Method in class magpie.optimization.rankers.PropertyFormulaRanker
 
train(MultiPropertyDataset) - Method in class magpie.optimization.rankers.RankAggregationRanker
 
train(Dataset) - Method in class magpie.optimization.rankers.SimpleEntryRanker
 
train(Dataset) - Method in class magpie.optimization.rankers.TargetEntryRanker
 
train_protected(Dataset) - Method in class magpie.attributes.selectors.BaseAttributeSelector
Operation that actually does the work for training.
train_protected(Dataset) - Method in class magpie.attributes.selectors.BestIndividualSelector
 
train_protected(Dataset) - Method in class magpie.attributes.selectors.MeredigAttributeSelector
 
train_protected(Dataset) - Method in class magpie.attributes.selectors.RegexAttributeSelector
 
train_protected(Dataset) - Method in class magpie.attributes.selectors.UserSpecifiedAttributeSelector
 
train_protected(Dataset) - Method in class magpie.attributes.selectors.UserSpecifiedExcludingAttributeSelector
 
train_protected(Dataset) - Method in class magpie.attributes.selectors.WekaAttributeSelector
 
train_protected(Dataset) - Method in class magpie.cluster.BaseClusterer
Perform the actual training.
train_protected(Dataset) - Method in class magpie.cluster.WekaClusterer
 
train_protected(Dataset) - Method in class magpie.models.BaseModel
Train a model without evaluating performance
train_protected(Dataset) - Method in class magpie.models.classification.CumulantExpansionClassifier
 
train_protected(Dataset) - Method in class magpie.models.classification.SplitClassifier
 
train_protected(Dataset) - Method in class magpie.models.classification.WekaClassifier
 
train_protected(Dataset) - Method in class magpie.models.regression.AbstractNonlinearRegression
 
train_protected(Dataset) - Method in class magpie.models.regression.ClassificationRegression
 
train_protected(Dataset) - Method in class magpie.models.regression.CompositeRegression
 
train_protected(Dataset) - Method in class magpie.models.regression.GuessMeanRegression
 
train_protected(Dataset) - Method in class magpie.models.regression.LASSORegression
 
train_protected(Dataset) - Method in class magpie.models.regression.LinearCorrectedRegression
 
train_protected(Dataset) - Method in class magpie.models.regression.MetallurgicalHeuristicRegression
 
train_protected(Dataset) - Method in class magpie.models.regression.MixingRuleRegression
 
train_protected(Dataset) - Method in class magpie.models.regression.MultiObjectiveRegression
 
train_protected(Dataset) - Method in class magpie.models.regression.PolynomialRegression
 
train_protected(Dataset) - Method in class magpie.models.regression.RandomGuessRegression
 
train_protected(Dataset) - Method in class magpie.models.regression.ScikitLearnRegression
 
train_protected(Dataset) - Method in class magpie.models.regression.SingleGuessRegression
 
train_protected(Dataset) - Method in class magpie.models.regression.StagedRegression
 
train_protected(Dataset) - Method in class magpie.models.regression.WekaRegression
 
train_protected(Dataset) - Method in class magpie.models.SplitModel
 
trained - Variable in class magpie.attributes.selectors.BaseAttributeSelector
Whether this BaseAttributeSelector has been trained
Trained - Variable in class magpie.data.utilities.filters.ZScoreOutlierFilter
Whether this class has been trained
trained - Variable in class magpie.models.BaseModel
Records whether model has been trained
training - Variable in class magpie.user.server.thrift.ModelInfo
 
TrainingSet - Variable in class magpie.user.server.ModelPackage
Training set description
TrainingStats - Variable in class magpie.models.BaseModel
Statistics about performance on training set
TrainingStatsPtr - Variable in class magpie.models.classification.SplitClassifier
Pointer to ClassificationStatistics interface of TrainingStats
trainOnAttributes(Dataset) - Method in class magpie.data.utilities.normalizers.BaseDatasetNormalizer
Perform the actual training work for attributes.
trainOnAttributes(Dataset) - Method in class magpie.data.utilities.normalizers.IndependentVariableNormalizer
 
trainOnAttributes(Dataset) - Method in class magpie.data.utilities.normalizers.InverseNormalizer
 
trainOnAttributes(Dataset) - Method in class magpie.data.utilities.normalizers.RegularSolutionNormalizer
 
trainOnMeasuredClass(Dataset) - Method in class magpie.data.utilities.normalizers.BaseDatasetNormalizer
Perform the actual training work for the class variable.
trainOnMeasuredClass(Dataset) - Method in class magpie.data.utilities.normalizers.IndependentVariableNormalizer
 
trainOnMeasuredClass(Dataset) - Method in class magpie.data.utilities.normalizers.InverseNormalizer
 
trainOnMeasuredClass(Dataset) - Method in class magpie.data.utilities.normalizers.RegularSolutionNormalizer
 
trainTime - Variable in class magpie.user.server.thrift.ModelInfo
 
transferToWeka(boolean, boolean) - Method in class magpie.data.Dataset
Convert to Weka Instances object, delete attribute information in each entry.
transform(Dataset) - Method in class magpie.data.utilities.modifiers.BaseDatasetModifier
Apply some change to the dataset and all of its entries
transpose(double[][]) - Static method in class magpie.utility.MathUtils
Transpose a rectangular array
Type - Variable in class magpie.utility.interfaces.Citation
Type of resource being cited.

U

Units - Variable in class magpie.user.server.ModelPackage
Units for property
units - Variable in class magpie.user.server.thrift.ModelInfo
 
unsetAuthor() - Method in class magpie.user.server.thrift.ModelInfo
 
unsetCitation() - Method in class magpie.user.server.thrift.ModelInfo
 
unsetClassifier() - Method in class magpie.user.server.thrift.ModelInfo
 
unsetClassProbs() - Method in class magpie.user.server.thrift.Entry
 
unsetDataType() - Method in class magpie.user.server.thrift.ModelInfo
 
unsetDescription() - Method in class magpie.user.server.thrift.ModelInfo
 
unsetEntries() - Method in class magpie.user.server.thrift.MagpieServer.evaluateProperties_args
 
unsetGenMethod() - Method in class magpie.user.server.thrift.MagpieServer.searchMultiObjective_args
 
unsetGenMethod() - Method in class magpie.user.server.thrift.MagpieServer.searchSingleObjective_args
 
unsetMeasuredProperties() - Method in class magpie.user.server.thrift.Entry
 
unsetModelType() - Method in class magpie.user.server.thrift.ModelInfo
 
unsetName() - Method in class magpie.user.server.thrift.Entry
 
unsetNotes() - Method in class magpie.user.server.thrift.ModelInfo
 
unsetNumToList() - Method in class magpie.user.server.thrift.MagpieServer.searchMultiObjective_args
 
unsetNumToList() - Method in class magpie.user.server.thrift.MagpieServer.searchSingleObjective_args
 
unsetObj() - Method in class magpie.user.server.thrift.MagpieServer.searchSingleObjective_args
 
unsetObjs() - Method in class magpie.user.server.thrift.MagpieServer.searchMultiObjective_args
 
unsetOuch() - Method in class magpie.user.server.thrift.MagpieServer.evaluateProperties_result
 
unsetOuch() - Method in class magpie.user.server.thrift.MagpieServer.getModelInformation_result
 
unsetOuch() - Method in class magpie.user.server.thrift.MagpieServer.searchMultiObjective_result
 
unsetOuch() - Method in class magpie.user.server.thrift.MagpieServer.searchSingleObjective_result
 
unsetP() - Method in class magpie.user.server.thrift.MagpieServer.searchMultiObjective_args
 
unsetPredictedProperties() - Method in class magpie.user.server.thrift.Entry
 
unsetProperty() - Method in class magpie.user.server.thrift.ModelInfo
 
unsetProps() - Method in class magpie.user.server.thrift.MagpieServer.evaluateProperties_args
 
unsetSuccess() - Method in class magpie.user.server.thrift.MagpieServer.evaluateProperties_result
 
unsetSuccess() - Method in class magpie.user.server.thrift.MagpieServer.getModelInformation_result
 
unsetSuccess() - Method in class magpie.user.server.thrift.MagpieServer.searchMultiObjective_result
 
unsetSuccess() - Method in class magpie.user.server.thrift.MagpieServer.searchSingleObjective_result
 
unsetTraining() - Method in class magpie.user.server.thrift.ModelInfo
 
unsetTrainTime() - Method in class magpie.user.server.thrift.ModelInfo
 
unsetUnits() - Method in class magpie.user.server.thrift.ModelInfo
 
unsetValMethod() - Method in class magpie.user.server.thrift.ModelInfo
 
unsetValScore() - Method in class magpie.user.server.thrift.ModelInfo
 
unsetWhy() - Method in exception magpie.user.server.thrift.MagpieException
 
useAbsoluteError() - Method in class magpie.data.utilities.modifiers.ErrorSignalModifier
Set filter to compute absolute error.
useAbsoluteError() - Method in class magpie.models.regression.StagedRegression
Set to train subsequent models on absolute error from previous.
useCompositionAsAttributes(boolean) - Method in class magpie.data.materials.CompositionDataset
Set whether to use composition (i.e.
UseCorrection - Variable in class magpie.models.regression.MixingRuleRegression
Whether to apply correction factors
UseInverse - Variable in class magpie.models.regression.MixingRuleRegression
Whether to compute harmonic mean.
UseMeasured - Variable in class magpie.data.utilities.filters.ClassFilter
Whether to use measured class variable
UseMeasured - Variable in class magpie.data.utilities.filters.PropertyFilter
Whether to use measured or predicted property values
useRelativeError() - Method in class magpie.data.utilities.modifiers.ErrorSignalModifier
Set filter to computer relative error.
useRelativeError() - Method in class magpie.models.regression.StagedRegression
Set model to train subsequent models on relative error from previous.
UserFormula - Variable in class magpie.models.regression.AbstractParsedNonlinearRegression
Stores the user-provided formula
UserSpecifiedAttributeSelector - Class in magpie.attributes.selectors
Use only attributes with a specified name or ID number.
UserSpecifiedAttributeSelector() - Constructor for class magpie.attributes.selectors.UserSpecifiedAttributeSelector
 
UserSpecifiedExcludingAttributeSelector - Class in magpie.attributes.selectors
Exclude attributes with a certain name
UserSpecifiedExcludingAttributeSelector() - Constructor for class magpie.attributes.selectors.UserSpecifiedExcludingAttributeSelector
 
usingPropertyAsClass() - Method in class magpie.data.MultiPropertyDataset
 
usingPropertyAsClass() - Method in class magpie.data.MultiPropertyEntry
 
UtilityOperations - Class in magpie.utility
This is only a class full of useful static methods.
UtilityOperations() - Constructor for class magpie.utility.UtilityOperations
 

V

ValenceShellAttributeGenerator - Class in magpie.attributes.generators.composition
Generate attributes based on fraction of electrons in valence shell of constituent elements.
ValenceShellAttributeGenerator() - Constructor for class magpie.attributes.generators.composition.ValenceShellAttributeGenerator
 
validate() - Method in class magpie.user.server.thrift.Entry
 
validate() - Method in exception magpie.user.server.thrift.MagpieException
 
validate() - Method in class magpie.user.server.thrift.MagpieServer.evaluateProperties_args
 
validate() - Method in class magpie.user.server.thrift.MagpieServer.evaluateProperties_result
 
validate() - Method in class magpie.user.server.thrift.MagpieServer.getModelInformation_args
 
validate() - Method in class magpie.user.server.thrift.MagpieServer.getModelInformation_result
 
validate() - Method in class magpie.user.server.thrift.MagpieServer.searchMultiObjective_args
 
validate() - Method in class magpie.user.server.thrift.MagpieServer.searchMultiObjective_result
 
validate() - Method in class magpie.user.server.thrift.MagpieServer.searchSingleObjective_args
 
validate() - Method in class magpie.user.server.thrift.MagpieServer.searchSingleObjective_result
 
validate() - Method in class magpie.user.server.thrift.ModelInfo
 
validated - Variable in class magpie.models.BaseModel
Records whether model has been validated
ValidationStats - Variable in class magpie.models.BaseModel
Statistics generated during model validation
ValidationStatsPtr - Variable in class magpie.models.classification.SplitClassifier
Pointer to ClassificationStatistics interface of ValidationStates
valMethod - Variable in class magpie.user.server.thrift.ModelInfo
 
valScore - Variable in class magpie.user.server.thrift.ModelInfo
 
value(double[]) - Method in class magpie.utility.ParsedFunction
 
valueOf(String) - Static method in enum magpie.user.server.thrift.Entry._Fields
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum magpie.user.server.thrift.MagpieException._Fields
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum magpie.user.server.thrift.MagpieServer.evaluateProperties_args._Fields
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum magpie.user.server.thrift.MagpieServer.evaluateProperties_result._Fields
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum magpie.user.server.thrift.MagpieServer.getModelInformation_args._Fields
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum magpie.user.server.thrift.MagpieServer.getModelInformation_result._Fields
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum magpie.user.server.thrift.MagpieServer.searchMultiObjective_args._Fields
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum magpie.user.server.thrift.MagpieServer.searchMultiObjective_result._Fields
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum magpie.user.server.thrift.MagpieServer.searchSingleObjective_args._Fields
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum magpie.user.server.thrift.MagpieServer.searchSingleObjective_result._Fields
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum magpie.user.server.thrift.ModelInfo._Fields
Returns the enum constant of this type with the specified name.
values() - Static method in enum magpie.user.server.thrift.Entry._Fields
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum magpie.user.server.thrift.MagpieException._Fields
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum magpie.user.server.thrift.MagpieServer.evaluateProperties_args._Fields
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum magpie.user.server.thrift.MagpieServer.evaluateProperties_result._Fields
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum magpie.user.server.thrift.MagpieServer.getModelInformation_args._Fields
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum magpie.user.server.thrift.MagpieServer.getModelInformation_result._Fields
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum magpie.user.server.thrift.MagpieServer.searchMultiObjective_args._Fields
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum magpie.user.server.thrift.MagpieServer.searchMultiObjective_result._Fields
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum magpie.user.server.thrift.MagpieServer.searchSingleObjective_args._Fields
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum magpie.user.server.thrift.MagpieServer.searchSingleObjective_result._Fields
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum magpie.user.server.thrift.ModelInfo._Fields
Returns an array containing the constants of this enum type, in the order they are declared.
Variables - Variable in class magpie.user.Workspace
Map of variable name to object
VolumeToLatticeParamModifier - Class in magpie.data.utilities.modifiers
Add a new property to a CompositionDataset that represents a cubic lattice parameter.
VolumeToLatticeParamModifier() - Constructor for class magpie.data.utilities.modifiers.VolumeToLatticeParamModifier
 

W

WekaAttributeSelector - Class in magpie.attributes.selectors
Encapsulates Weka's ASSearch routines for attribute selection.
WekaAttributeSelector() - Constructor for class magpie.attributes.selectors.WekaAttributeSelector
Generates a WekaAttributeSelector with default methods
WekaClassifier - Class in magpie.models.classification
Classifier that uses algorithms from Weka.
WekaClassifier(String, String[]) - Constructor for class magpie.models.classification.WekaClassifier
Create a Weka model with a specified model and options
WekaClassifier() - Constructor for class magpie.models.classification.WekaClassifier
Create a WekaClassifier using a "rules.ZeroR" model
WekaClusterer - Class in magpie.cluster
Use Weka to cluster data.
WekaClusterer() - Constructor for class magpie.cluster.WekaClusterer
 
WekaModel - Interface in magpie.models.interfaces
Operations that a Weka-based model must implement.
WekaRegression - Class in magpie.models.regression
Implementation of WekaModel for regression purposes.
WekaRegression(String, String[]) - Constructor for class magpie.models.regression.WekaRegression
Create a Weka model with a specified model and options
WekaRegression() - Constructor for class magpie.models.regression.WekaRegression
Create a WekaRegression model based on the "rules.ZeroR" algorithm
WekaUtility - Class in magpie.utility
Holds static methods useful for Weka-based models/clusterers.
WekaUtility() - Constructor for class magpie.utility.WekaUtility
 
why - Variable in exception magpie.user.server.thrift.MagpieException
 
willNormalizeAttributes() - Method in class magpie.data.utilities.normalizers.BaseDatasetNormalizer
 
willNormalizeClass() - Method in class magpie.data.utilities.normalizers.BaseDatasetNormalizer
 
Workspace - Variable in class magpie.user.CommandHandler
Keep track of which variables have been created
Workspace - Class in magpie.user
Keeps track of variables produced by user interface.
Workspace() - Constructor for class magpie.user.Workspace
Create a Workspace with an empty variable list
WorstFraction - Variable in class magpie.optimization.algorithms.ActiveLearningOptimizer
Fraction of entries to select from the worst predictions
write(TProtocol) - Method in class magpie.user.server.thrift.Entry
 
write(TProtocol) - Method in exception magpie.user.server.thrift.MagpieException
 
write(TProtocol) - Method in class magpie.user.server.thrift.MagpieServer.evaluateProperties_args
 
write(TProtocol) - Method in class magpie.user.server.thrift.MagpieServer.evaluateProperties_result
 
write(TProtocol) - Method in class magpie.user.server.thrift.MagpieServer.getModelInformation_args
 
write(TProtocol) - Method in class magpie.user.server.thrift.MagpieServer.getModelInformation_result
 
write(TProtocol) - Method in class magpie.user.server.thrift.MagpieServer.searchMultiObjective_args
 
write(TProtocol) - Method in class magpie.user.server.thrift.MagpieServer.searchMultiObjective_result
 
write(TProtocol) - Method in class magpie.user.server.thrift.MagpieServer.searchSingleObjective_args
 
write(TProtocol) - Method in class magpie.user.server.thrift.MagpieServer.searchSingleObjective_result
 
write(TProtocol) - Method in class magpie.user.server.thrift.ModelInfo
 
write_args(TProtocol) - Method in class magpie.user.server.thrift.MagpieServer.AsyncClient.evaluateProperties_call
 
write_args(TProtocol) - Method in class magpie.user.server.thrift.MagpieServer.AsyncClient.getModelInformation_call
 
write_args(TProtocol) - Method in class magpie.user.server.thrift.MagpieServer.AsyncClient.searchMultiObjective_call
 
write_args(TProtocol) - Method in class magpie.user.server.thrift.MagpieServer.AsyncClient.searchSingleObjective_call
 
writeModel(String) - Method in class magpie.models.regression.ScikitLearnRegression
Write stored model to disk.

Z

ZScoreNormalizer - Class in magpie.data.utilities.normalizers
Scale variables by calculating their Z scores.
ZScoreNormalizer() - Constructor for class magpie.data.utilities.normalizers.ZScoreNormalizer
 
ZScoreOutlierFilter - Class in magpie.data.utilities.filters
Remove entries that are outliers based on Z-score.
ZScoreOutlierFilter() - Constructor for class magpie.data.utilities.filters.ZScoreOutlierFilter
 
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