Package adams.data.io.input

Class ExtractIdAndTypeSpectrumReader

  • 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 ExtractIdAndTypeSpectrumReader
extends AbstractSpectrumReader
    Uses the specified ID and group extractor to obtain and update sample ID and type of the spectra read by the specified base reader. 

    -logging-level <OFF|SEVERE|WARNING|INFO|CONFIG|FINE|FINER|FINEST> (property: loggingLevel)
    The logging level for outputting errors and debugging output.
    default: WARNING
 
    -input <adams.core.io.PlaceholderFile> (property: input)
    The file to read and turn into a container.
    default: ${CWD}
 
    -create-dummy-report <boolean> (property: createDummyReport)
    If true, then a dummy report is created if none present.
    default: false
 
    -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
 
    -keep-format <boolean> (property: keepFormat)
    If enabled the format obtained from the file is not replaced by the format
    defined here.
    default: false
 
    -use-absolute-source <boolean> (property: useAbsoluteSource)
    If enabled the source report field stores the absolute file name rather
    than just the name.
    default: false
 
    -reader <adams.data.io.input.AbstractSpectrumReader> (property: reader)
    The base reader to use.
    default: adams.data.io.input.SimpleSpectrumReader
 
    -id-extraction <adams.data.idextraction.IDExtractor> (property: IDExtraction)
    The ID extractor to use.
    default: adams.data.idextraction.Null
 
    -group-extraction <adams.data.groupextraction.GroupExtractor> (property: groupExtraction)
    For extracting the sample type from the spectra.
    default: adams.data.groupextraction.Null
    Author:
    FracPete (fracpete at waikato dot ac dot nz)
    See Also:
    Serialized Form

    • Field Detail

      • m_IDExtraction

        protected adams.data.idextraction.IDExtractor m_IDExtraction
        the ID extractor.

      • m_GroupExtraction

        protected adams.data.groupextraction.GroupExtractor m_GroupExtraction
        the group extractor.

    • Constructor Detail

      • ExtractIdAndTypeSpectrumReader

        public ExtractIdAndTypeSpectrumReader()

    • Method Detail

      • globalInfo

        public String globalInfo()
        Returns a string describing the object.
        Specified by:
        globalInfo in interface adams.core.GlobalInfoSupporter
        Specified by:
        globalInfo in class adams.core.option.AbstractOptionHandler
        Returns:
        a description suitable for displaying in the gui

      • 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 AbstractSpectrumReader

      • setReader

        public void setReader​(AbstractSpectrumReader value)
        Sets the base reader to use.
        Parameters:
        value - the reader

      • readerTipText

        public String readerTipText()
        Returns the tip text for this property.
        Returns:
        tip text for this property suitable for displaying in the GUI or for listing the options.

      • setIDExtraction

        public void setIDExtraction​(adams.data.idextraction.IDExtractor value)
        Sets the sample ID extractor to use.
        Parameters:
        value - the extractor

      • getIDExtraction

        public adams.data.idextraction.IDExtractor getIDExtraction()
        Returns the sample ID extractor to use.
        Returns:
        the extractor

      • IDExtractionTipText

        public String IDExtractionTipText()
        Returns the tip text for this property.
        Returns:
        tip text for this property suitable for displaying in the GUI or for listing the options.

      • setGroupExtraction

        public void setGroupExtraction​(adams.data.groupextraction.GroupExtractor value)
        Sets the scheme for extracting the sample type.
        Parameters:
        value - the extractor

      • getGroupExtraction

        public adams.data.groupextraction.GroupExtractor getGroupExtraction()
        Returns the scheme for extracting the sample type.
        Returns:
        the extractor

      • groupExtractionTipText

        public String groupExtractionTipText()
        Returns the tip text for this property.
        Returns:
        tip text for this property suitable for displaying in the GUI or for listing the options.

      • getFormatDescription

        public String getFormatDescription()
        Returns a string describing the format (used in the file chooser).
        Specified by:
        getFormatDescription in interface adams.core.io.FileFormatHandler
        Specified by:
        getFormatDescription in class adams.data.io.input.AbstractDataContainerReader<Spectrum>
        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
        Specified by:
        getFormatExtensions in class adams.data.io.input.AbstractDataContainerReader<Spectrum>
        Returns:
        the extension (without the dot!)

      • readData

        protected void readData()
        Performs the actual reading.
        Specified by:
        readData in class adams.data.io.input.AbstractDataContainerReader<Spectrum>

      • 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