Package adams.data.io.input

Class NIRSpectrumReader

java.lang.Object

adams.core.logging.LoggingObject

adams.core.logging.CustomLoggingLevelObject

adams.core.option.AbstractOptionHandler

adams.data.io.input.AbstractDataContainerReader<Spectrum>

adams.data.io.input.AbstractSpectrumReader

adams.data.io.input.CALSpectrumReader

adams.data.io.input.NIRSpectrumReader

All Implemented Interfaces:

adams.core.AdditionalInformationHandler, adams.core.CleanUpHandler, adams.core.Destroyable, adams.core.GlobalInfoSupporter, adams.core.io.FileFormatHandler, adams.core.logging.LoggingLevelHandler, adams.core.logging.LoggingSupporter, adams.core.option.OptionHandler, adams.core.ShallowCopySupporter<adams.data.io.input.AbstractDataContainerReader>, adams.core.SizeOfHandler, adams.core.Stoppable, Serializable, Comparable

public class NIRSpectrumReader
extends CALSpectrumReader

Reads spectra in FOSS NIR format.

Valid options are:

-D <int> (property: debugLevel)
    The greater the number the more additional info the scheme may output to
    the console (0 = off).
    default: 0
    minimum: 0
 

-input <adams.core.io.PlaceholderFile> (property: input)
    The file to read and turn into a container.
    default: .
 

-create-dummy-report (property: createDummyReport)
    If true, then a dummy report is created if none present.
 

-instrument <java.lang.String> (property: instrument)
    The name of the instrument that generated the spectra (if not already present
    in data).
    default: unknown
 

-format <java.lang.String> (property: format)
    The data format string.
    default: NIR
 

-typefield <java.lang.String> (property: typefield)
    Code|Field1|Field2|Field3|ID|[sample_type]
    default: Code
 

-idfield <java.lang.String> (property: idfield)
    ID|Field1|Field2|Field3|[prefix]
    default: ID
 

-start <int> (property: start)
    Spectrum number to start loading from.
    default: 1
 

-max <int> (property: max)
    Maximum spectra to load.
    default: -1
 

Author:

dale (dale at waikato dot ac dot nz)

See Also:

Serialized Form

Field Summary

Fields inherited from class adams.data.io.input.CALSpectrumReader

m_max, m_start, sample_id, sample_type

Fields inherited from class adams.data.io.input.AbstractSpectrumReader

m_Format, m_Instrument, m_KeepFormat, m_Stopped, m_UseAbsoluteSource, OPTION_OUTPUTDIR

Fields inherited from class adams.data.io.input.AbstractDataContainerReader

m_CreateDummyReport, m_Input, m_InputIsFile, m_Processed, m_ReadData

Fields inherited from class adams.core.option.AbstractOptionHandler

m_OptionManager

Fields inherited from class adams.core.logging.LoggingObject

m_Logger, m_LoggingIsEnabled, m_LoggingLevel

Constructor Summary

Constructors

Constructor	Description
NIRSpectrumReader()

Method Summary

Modifier and Type	Method	Description
String	getFormatDescription()	Returns a string describing the format (used in the file chooser).
String[]	getFormatExtensions()	Returns the extension(s) of the format.
String	globalInfo()	Returns a string describing the object.
static void	main(String[] args)	Runs the reader from the command-line.

Methods inherited from class adams.data.io.input.CALSpectrumReader

defineOptions, getID, getIdfield, getMax, getSampleType, getStart, getTypefield, idfieldTipText, maxTipText, readData, setIdfield, setMax, setStart, setTypefield, startTipText, typefieldTipText

Methods inherited from class adams.data.io.input.AbstractSpectrumReader

checkData, createDummyReport, formatTipText, getDefaultFormat, getDefaultInstrument, getDefaultKeepFormat, getDefaultUseAbsoluteSource, getFormat, getInstrument, getKeepFormat, getReaders, getUseAbsoluteSource, instrumentTipText, keepFormatTipText, postProcessData, runReader, setFormat, setInstrument, setKeepFormat, setUseAbsoluteSource, stopExecution, useAbsoluteSourceTipText

Methods inherited from class adams.data.io.input.AbstractDataContainerReader

cleanUp, compareTo, createDummyReportTipText, destroy, doRead, equals, getAdditionalInformation, getCreateDummyReport, getDefaultFormatExtension, getInput, initialize, inputTipText, isInputFile, read, reset, setCreateDummyReport, setInput, shallowCopy, shallowCopy

Methods inherited from class adams.core.option.AbstractOptionHandler

cleanUpOptions, finishInit, getDefaultLoggingLevel, getOptionManager, loggingLevelTipText, newOptionManager, setLoggingLevel, toCommandLine, toString

Methods inherited from class adams.core.logging.LoggingObject

configureLogger, getLogger, getLoggingLevel, initializeLogging, isLoggingEnabled, sizeOf

Methods inherited from class java.lang.Object

clone, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Methods inherited from interface adams.core.logging.LoggingLevelHandler

getLoggingLevel

Constructor Detail

NIRSpectrumReader

public NIRSpectrumReader()

Method Detail

globalInfo

public String globalInfo()

Returns a string describing the object.

Specified by:

globalInfo in interface adams.core.GlobalInfoSupporter

Overrides:

globalInfo in class CALSpectrumReader

Returns:

a description suitable for displaying in the gui

getFormatDescription

public String getFormatDescription()

Returns a string describing the format (used in the file chooser).

Specified by:

getFormatDescription in interface adams.core.io.FileFormatHandler

Overrides:

getFormatDescription in class CALSpectrumReader

Returns:

a description suitable for displaying in the file chooser

getFormatExtensions

public String[] getFormatExtensions()

Returns the extension(s) of the format.

Specified by:

getFormatExtensions in interface adams.core.io.FileFormatHandler

Overrides:

getFormatExtensions in class CALSpectrumReader

Returns:

the extension(s) (without the dot!)

main

public static void main(String[] args)

Runs the reader from the command-line. If the option AbstractSpectrumReader.OPTION_OUTPUTDIR is specified then the read spectra get output as .spec files in that directory.

Parameters:

args - the command-line options to use