magpie.data.materials

Class ElementDataset

java.lang.Object

magpie.data.Dataset

magpie.data.MultiPropertyDataset

magpie.data.materials.ElementDataset

All Implemented Interfaces:

java.io.Serializable, java.lang.Cloneable, Citable, Commandable, Options, Printable, Savable

public class ElementDataset
extends MultiPropertyDataset

Store elemental properties. For example, this could be the dilute solution solution energies of elements in zirconia (see: Meredig and Wolvertion, 2014).

Input files should have element abbreviations as the first column, and measured property values as the next columns. If a property is known for a certain entry, list a string that doesn't parse to a number (e.g., "None"). The header should be a list of property names. If a property has multiple classes, list them inside {}'s (ex: stability{Yes,No}). An example data file could look like:

element sln_energy valency{2+,3+,4+}
Al 0.78 3+
Ni None 2+
Fe 0.39 None

By default, this class uses the properties of an element as attributes.

Implemented Commands:

attributes properties - List which elemental properties are used to generate attributes

attributes properties add <names...> - Add elemental properties to use when generating attributes
name...: Name of a elemental properties

attributes properties add set <name> - Add in all elemental properties from a pre-defined set
name: Name of the pre-defined set

attributes properties remove <names...> - Remove properties from list of those used when generating attributes
names...: Name of properties to remove

attributes properties <directory> - Specify directory that contains the elemental property lookup files
directory: Desired directory

Usage: *No options*

See Also:

Serialized Form

Field Summary

Fields

Modifier and Type	Field and Description
java.util.List<java.lang.String>	ElementalProperties List of elemental properties used when computing attributes
java.lang.String	LookupDirectory Directory containing elemental property lookup tables
java.util.Map<java.lang.String,double[]>	PropertyData Lookup table of elemental properties

Fields inherited from class magpie.data.Dataset

AttributeName, Entries, Expanders, Generators

Constructor Summary

Constructors

Constructor and Description
ElementDataset() Create a dataset using the default attribute generators: ElementalPropertyAttributeGenerator
ElementDataset(boolean useDefaultGenerators) Create a blank dataset.

Method Summary

Modifier and Type	Method and Description
void	addElementalProperty(java.lang.String name) Add an elemental property to the list of those used when computing attributes.
void	addElementalPropertySet(java.lang.String setName) Add a set of elemental properties to the list of those used when computing attributes.
BaseEntry	addEntry(java.lang.String entry) A new entry by parsing an input string.
protected void	calculateAttributes() Compute attributes that are specific to this class.
ElementDataset	createTemplate() Create a template designed to be saved using serialization
ElementDataset	emptyClone() Creates a new instance with the same class and attribute names, but without any entries.
java.util.List<java.lang.String>	getElementalProperties() Get the list of elemental properties to be used to compute attributes.
ElementEntry	getEntry(int index) Retrieve a single entry from the dataset
double[]	getLookupTable(java.lang.String prop) Get an elemental property lookup table
void	importText(java.lang.String filename, java.lang.Object[] options) Imports data from a text file.
java.lang.String	printEntryDescription(boolean htmlFormat) Print out what the entries to this dataset are.
boolean	removeElementalProperty(java.lang.String name) Remove an elemental property from the list of those used when computing attributes.
protected java.lang.Object	runAttributeCommand(java.util.List<java.lang.Object> Command) Run commands related to attributes of each entry.
protected java.lang.Object	runPropertyCommand(java.util.List<java.lang.Object> Command) Run commands that control which elemental properties are used when generating attributes
void	setElementalProperties(java.util.List<java.lang.String> properties) Define the list of elemental properties to be used to compute attributes.

Methods inherited from class magpie.data.MultiPropertyDataset

addEntries, addEntries, addEntry, addProperty, addProperty, clearPropertyData, combine, definePropertyNames, getClassNames, getMeasuredPropertyArray, getMeasuredPropertyArray, getPredictedPropertyArray, getPredictedPropertyArray, getPropertyClassCount, getPropertyClasses, getPropertyClasses, getPropertyIndex, getPropertyName, getPropertyNames, getTargetPropertyIndex, getTargetPropertyName, hasProperty, importEntryProperties, importPropertyNames, NClasses, NProperties, runCommand, saveCommand, setClassNames, setPropertyClasses, setTargetProperty, setTargetProperty, toJSON, toString, usingPropertyAsClass

Methods inherited from class magpie.data.Dataset

about, addAttribute, addAttributeExpander, addAttributeGenerator, addAttributes, clearAttributeExpanders, clearAttributeGenerators, clearAttributes, clearData, clone, combine, combine, containsEntry, deleteMeasuredClasses, deletePredictedClasses, finalizeGeneration, generateAttributes, getAttributeArray, getAttributeExpanders, getAttributeGenerators, getAttributeIndex, getAttributeName, getAttributeNames, getCitations, getClassName, getClassProbabilityArray, getDistribution, getDistributionCount, getDuplicates, getEntries, getEntriesWriteAccess, getEntryArray, getMeasuredClassArray, getPredictedClassArray, getRandomSplit, getRandomSplit, getRandomSplit, getRandomSplit, getRandomSubset, getRandomSubset, getSingleAttributeArray, getSubset, getTrainingExamples, getUniqueEntries, loadState, matchEntries, NAttributes, NEntries, partition, partition, printAttributeDescription, printCommand, printDescription, printDistribution, printEntries, printUsage, removeDuplicates, resolveDuplicates, restoreAttributes, runAttributeExpanders, runAttributeExpansionCommand, runAttributeGeneratorCommand, runAttributeGenerators, saveState, saveTemplate, setAttributeNames, setClassProbabilities, setMeasuredClasses, setOptions, setPredictedClasses, splitForThreading, splitIntoFolds, splitIntoFolds, subtract, transferToWeka

Methods inherited from class java.lang.Object

equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Field Detail

LookupDirectory

public java.lang.String LookupDirectory

Directory containing elemental property lookup tables

ElementalProperties

public java.util.List<java.lang.String> ElementalProperties

List of elemental properties used when computing attributes

PropertyData

public java.util.Map<java.lang.String,double[]> PropertyData

Lookup table of elemental properties

Constructor Detail

ElementDataset

public ElementDataset()

Create a dataset using the default attribute generators:

1. ElementalPropertyAttributeGenerator

ElementDataset

public ElementDataset(boolean useDefaultGenerators)

Create a blank dataset.

Parameters:

useDefaultGenerators - Whether to use default attribute generators

See Also:

ElementDataset()

Method Detail

emptyClone

public ElementDataset emptyClone()

Description copied from class: Dataset

Creates a new instance with the same class and attribute names, but without any entries.

Overrides:

emptyClone in class MultiPropertyDataset

Returns:

Dataset with same properties, no entries

createTemplate

public ElementDataset createTemplate()

Description copied from class: Dataset

Create a template designed to be saved using serialization

Overrides:

createTemplate in class MultiPropertyDataset

Returns:

An empty clone of the dataset, with any additional changes made

importText

public void importText(java.lang.String filename,
                       java.lang.Object[] options)
                throws java.lang.Exception

Description copied from class: Dataset

Imports data from a text file. Expected format for file:

Attribute1Name, Attribute2Name, ..., AttributeNName, Class
Attribute1, Attribute2, ..., AttributeN, ClassVariable

Overrides:

importText in class Dataset

Parameters:

filename - Path to data file

options - Any options used to control import

Throws:

java.lang.Exception - If text import fails

addEntry

public BaseEntry addEntry(java.lang.String entry)
                   throws java.lang.Exception

Description copied from class: Dataset

A new entry by parsing an input string. After using this operation, it may be necessary to recalculate attributes.

Overrides:

addEntry in class Dataset

Parameters:

entry - String describing the entry

Returns:

Entry representing the parsed string.

Throws:

java.lang.Exception - If conversion fails

getEntry

public ElementEntry getEntry(int index)

Description copied from class: Dataset

Retrieve a single entry from the dataset

Overrides:

getEntry in class MultiPropertyDataset

Parameters:

index - Index of entry

Returns:

Specified entry

setElementalProperties

public void setElementalProperties(java.util.List<java.lang.String> properties)

Define the list of elemental properties to be used to compute attributes.

Parameters:

properties - List of elemental properties

getElementalProperties

public java.util.List<java.lang.String> getElementalProperties()

Get the list of elemental properties to be used to compute attributes.

Returns:

List of elemental properties

addElementalProperty

public void addElementalProperty(java.lang.String name)

Add an elemental property to the list of those used when computing attributes.

Parameters:

name - Name of elemental property

removeElementalProperty

public boolean removeElementalProperty(java.lang.String name)

Remove an elemental property from the list of those used when computing attributes.

Parameters:

name - Name of elemental property to be removed

Returns:

Whether anything was moved

addElementalPropertySet

public void addElementalPropertySet(java.lang.String setName)
                             throws java.lang.Exception

Add a set of elemental properties to the list of those used when computing attributes.

Parameters:

setName - Name of set

Throws:

java.lang.Exception

See Also:

PropertyLists.getPropertySet(java.lang.String)

getLookupTable

public double[] getLookupTable(java.lang.String prop)
                        throws java.lang.Exception

Get an elemental property lookup table

Parameters:

prop - Name of property

Returns:

Elemental properties, ordered by atomic number

Throws:

java.lang.Exception

calculateAttributes

protected void calculateAttributes()
                            throws java.lang.Exception

Description copied from class: Dataset

Compute attributes that are specific to this class.

Overrides:

calculateAttributes in class Dataset

Throws:

java.lang.Exception - If attribute calculation fails

runAttributeCommand

protected java.lang.Object runAttributeCommand(java.util.List<java.lang.Object> Command)
                                        throws java.lang.Exception

Description copied from class: Dataset

Run commands related to attributes of each entry. Starts with the action to perform on the attributes

Overrides:

runAttributeCommand in class Dataset

Parameters:

Command - Operation to be run on/about attributes

Returns:

Any output (null if nothing is created)

Throws:

java.lang.Exception - On any error

runPropertyCommand

protected java.lang.Object runPropertyCommand(java.util.List<java.lang.Object> Command)
                                       throws java.lang.Exception

Run commands that control which elemental properties are used when generating attributes

Parameters:

Command - Command to act on

Returns:

Any output from operation (null if no output)

Throws:

java.lang.Exception

printEntryDescription

public java.lang.String printEntryDescription(boolean htmlFormat)

Description copied from class: Dataset

Print out what the entries to this dataset are.

Overrides:

printEntryDescription in class Dataset

Parameters:

htmlFormat - Whether to print in HTML format

Returns:

Description of each entry (i.e., what kind of data is this).