Package adams.data.io.input

Class AbstractSpectrumReader

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

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

Direct Known Subclasses:

AbstractJCampSpectrumReader, ASCIIXYSpectrumReader, ASCSpectrumReader, CALSpectrumReader, ColumnWiseSpreadSheetSpectrumReader, DPTSpectrumReader, ExtractIdAndTypeSpectrumReader, FilteredSpectrumReader, JCampDX2SpectrumReader, JsonSpectrumReader, MPSSpectrumReader, OpusSpectrumReader, OpusSpectrumReaderExt, RelabSpectrumReader, RowWiseSpreadSheetSpectrumReader, ScioLabExportSpectrumReader, SimpleSpectrumReader, SoilCaresScannerSpectrumReader, SPASpectrumReader, SPCSpectrumReader, SpecLibSpectrumReader, TrinamixSpectrumJsonReader, TrinamixSpectrumReader, UnscramblerSpectrumReader, ZippedSpectrumReader

public abstract class AbstractSpectrumReader
extends adams.data.io.input.AbstractDataContainerReader<Spectrum>
implements adams.core.Stoppable

Abstract ancestor for readers that read files in various formats and turn them into spectrums.

Author:

fracpete (fracpete at waikato dot ac dot nz)

See Also:

Serialized Form

Field Summary

Fields

Modifier and Type	Field	Description
protected String	m_Format	the form of this data.
protected String	m_Instrument	the instrument this data is from.
protected boolean	m_KeepFormat	whether to not override the format obtained from the file.
protected boolean	m_Stopped	whether reading was stopped.
protected boolean	m_UseAbsoluteSource	whether to use absolute filename for the source report field or just the file's name.
static String	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
AbstractSpectrumReader()

Method Summary

Modifier and Type	Method	Description
protected void	checkData()	Hook method for checking the data.
protected adams.data.report.Report	createDummyReport(Spectrum cont)	Creates a dummy report.
void	defineOptions()	Adds options to the internal list of options.
String	formatTipText()	Returns the tip text for this property.
protected String	getDefaultFormat()	Returns the default format of the spectra.
protected String	getDefaultInstrument()	Returns the default instrument of the spectra.
protected boolean	getDefaultKeepFormat()	Returns the default for keeping the format.
protected boolean	getDefaultUseAbsoluteSource()	Returns the default for using absolute source filename.
String	getFormat()	Returns the format string of the data.
String	getInstrument()	Returns the instrument's name.
boolean	getKeepFormat()	Returns whether to keep the format obtained from the file.
static String[]	getReaders()	Returns a list with classnames of readers.
boolean	getUseAbsoluteSource()	Returns whether to use absolute source filename rather than just name.
String	instrumentTipText()	Returns the tip text for this property.
String	keepFormatTipText()	Returns the tip text for this property.
protected void	postProcessData()	Performs some post-processing.
static void	runReader(Class env, Class reader, String[] args)	Runs the reader from commandline.
void	setFormat(String value)	Sets the format string of the data (always converted to upper case).
void	setInstrument(String value)	Sets the instrument's name.
void	setKeepFormat(boolean value)	Sets whether to keep the format obtained from the file.
void	setUseAbsoluteSource(boolean value)	Sets whether to use absolute source filename rather than just name.
void	stopExecution()	Stops the execution.
String	useAbsoluteSourceTipText()	Returns the tip text for this property.

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

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

Methods inherited from class adams.core.option.AbstractOptionHandler

cleanUpOptions, finishInit, getDefaultLoggingLevel, getOptionManager, globalInfo, 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

Field Detail

OPTION_OUTPUTDIR

public static final String OPTION_OUTPUTDIR

See Also:

Constant Field Values

m_Instrument

protected String m_Instrument

the instrument this data is from.

m_Format

protected String m_Format

the form of this data.

m_KeepFormat

protected boolean m_KeepFormat

whether to not override the format obtained from the file.

m_UseAbsoluteSource

protected boolean m_UseAbsoluteSource

whether to use absolute filename for the source report field or just the file's name.

m_Stopped

protected boolean m_Stopped

whether reading was stopped.

Constructor Detail

AbstractSpectrumReader

public AbstractSpectrumReader()

Method Detail

defineOptions

public void defineOptions()

Adds options to the internal list of options.

Specified by:

defineOptions in interface adams.core.option.OptionHandler

Overrides:

defineOptions in class adams.data.io.input.AbstractDataContainerReader<Spectrum>

getDefaultInstrument

protected String getDefaultInstrument()

Returns the default instrument of the spectra.

Returns:

the default

getDefaultFormat

protected String getDefaultFormat()

Returns the default format of the spectra.

Returns:

the default

getDefaultKeepFormat

protected boolean getDefaultKeepFormat()

Returns the default for keeping the format.

Returns:

the default

getDefaultUseAbsoluteSource

protected boolean getDefaultUseAbsoluteSource()

Returns the default for using absolute source filename.

Returns:

the default

setInstrument

public void setInstrument(String value)

Sets the instrument's name.

Parameters:

value - the name

getInstrument

public String getInstrument()

Returns the instrument's name.

Returns:

the name

instrumentTipText

public String instrumentTipText()

Returns the tip text for this property.

Returns:

tip text for this property suitable for displaying in the GUI or for listing the options.

setFormat

public void setFormat(String value)

Sets the format string of the data (always converted to upper case). Use null to set default format.

Parameters:

value - the format

getFormat

public String getFormat()

Returns the format string of the data.

Returns:

the format

formatTipText

public String formatTipText()

Returns the tip text for this property.

Returns:

tip text for this property suitable for displaying in the GUI or for listing the options.

setKeepFormat

public void setKeepFormat(boolean value)

Sets whether to keep the format obtained from the file.

Parameters:

value - true if to keep format

getKeepFormat

public boolean getKeepFormat()

Returns whether to keep the format obtained from the file.

Returns:

true if to keep format

keepFormatTipText

public String keepFormatTipText()

Returns the tip text for this property.

Returns:

tip text for this property suitable for displaying in the GUI or for listing the options.

setUseAbsoluteSource

public void setUseAbsoluteSource(boolean value)

Sets whether to use absolute source filename rather than just name.

Parameters:

value - true if to use absolute source

getUseAbsoluteSource

public boolean getUseAbsoluteSource()

Returns whether to use absolute source filename rather than just name.

Returns:

true if to use absolute source

useAbsoluteSourceTipText

public String useAbsoluteSourceTipText()

Returns the tip text for this property.

Returns:

tip text for this property suitable for displaying in the GUI or for listing the options.

checkData

protected void checkData()

Hook method for checking the data.

Overrides:

checkData in class adams.data.io.input.AbstractDataContainerReader<Spectrum>

createDummyReport

protected adams.data.report.Report createDummyReport(Spectrum cont)

Creates a dummy report.

Overrides:

createDummyReport in class adams.data.io.input.AbstractDataContainerReader<Spectrum>

Parameters:

cont - the data container the dummy is for

Returns:

the dummy report or null

See Also:

AbstractDataContainerReader.m_CreateDummyReport, postProcessData()

postProcessData

protected void postProcessData()

Performs some post-processing.

Overrides:

postProcessData in class adams.data.io.input.AbstractDataContainerReader<Spectrum>

stopExecution

public void stopExecution()

Stops the execution.

Specified by:

stopExecution in interface adams.core.Stoppable

getReaders

public static String[] getReaders()

Returns a list with classnames of readers.

Returns:

the reader classnames

runReader

public static void runReader(Class env,
                             Class reader,
                             String[] args)

Runs the reader from commandline.

Parameters:

env - the environment class to use

reader - the reader to execute

args - the commandline arguments, use --input to specify the input file/dir and --output-dir to specify directory to save them as .spec files