Package adams.data.conversion

Class SpreadSheetRowsToSpectra

  • All Implemented Interfaces:
    adams.core.AdditionalInformationHandler, adams.core.CleanUpHandler, adams.core.Destroyable, adams.core.GlobalInfoSupporter, adams.core.LenientModeSupporter, adams.core.logging.LoggingLevelHandler, adams.core.logging.LoggingSupporter, adams.core.option.OptionHandler, adams.core.QuickInfoSupporter, adams.core.ShallowCopySupporter<adams.data.conversion.AbstractConversion>, adams.core.SizeOfHandler, adams.core.Stoppable, adams.data.conversion.Conversion, Serializable
    public class SpreadSheetRowsToSpectra
extends adams.data.conversion.AbstractConversion
implements adams.core.LenientModeSupporter
    Turns spreadsheet rows into spectra. 

    -logging-level <OFF|SEVERE|WARNING|INFO|CONFIG|FINE|FINER|FINEST> (property: loggingLevel)
    The logging level for outputting errors and debugging output.
    default: WARNING
 
    -row-wave-number <adams.data.spreadsheet.SpreadSheetRowIndex> (property: rowWaveNumber)
    The (optional) row in the spreadsheet that contains the wavenumber information.
    default:
    example: An index is a number starting with 1; the following placeholders can be used as well: first, second, third, last_2, last_1, last
 
    -wave-numbers-in-header <boolean> (property: waveNumbersInHeader)
    Whether the wave numbers are stored in the header.
    default: false
 
    -wave-number-regexp <adams.core.base.BaseRegExp> (property: waveNumberRegExp)
    The regular expression to identify the wave number (1st group is used).
    default: (.*)
    more: https://docs.oracle.com/javase/tutorial/essential/regex/
    https://docs.oracle.com/javase/8/docs/api/java/util/regex/Pattern.html
 
    -cols-amplitude <adams.data.spreadsheet.SpreadSheetColumnRange> (property: columnsAmplitude)
    The columns that contain amplitude information.
    default:
    example: A range is a comma-separated list of single 1-based indices or sub-ranges of indices ('start-end'); 'inv(...)' inverts the range '...'; column names (case-sensitive) as well as the following placeholders can be used: first, second, third, last_2, last_1, last; numeric indices can be enforced by preceding them with '#' (eg '#12'); column names can be surrounded by double quotes.
 
    -rows-amplitude <adams.data.spreadsheet.SpreadSheetRowRange> (property: rowsAmplitude)
    The rows in the spreadsheet that contain the amplitude information.
    default:
    example: A range is a comma-separated list of single 1-based indices or sub-ranges of indices ('start-end'); 'inv(...)' inverts the range '...'; the following placeholders can be used as well: first, second, third, last_2, last_1, last
 
    -row-sampledata-names <adams.data.spreadsheet.SpreadSheetRowIndex> (property: rowSampleDataNames)
    The (optional) row that contains the sample data names.
    default:
    example: An index is a number starting with 1; the following placeholders can be used as well: first, second, third, last_2, last_1, last
 
    -sampledata-names-in-header <boolean> (property: sampleDataNamesInHeader)
    Whether the sample data names are stored in the header.
    default: false
 
    -cols-sampledata <adams.data.spreadsheet.SpreadSheetColumnRange> (property: columnsSampleData)
    The columns that contain sampledata.
    default:
    example: A range is a comma-separated list of single 1-based indices or sub-ranges of indices ('start-end'); 'inv(...)' inverts the range '...'; column names (case-sensitive) as well as the following placeholders can be used: first, second, third, last_2, last_1, last; numeric indices can be enforced by preceding them with '#' (eg '#12'); column names can be surrounded by double quotes.
 
    -col-id <adams.data.spreadsheet.SpreadSheetColumnIndex> (property: columnID)
    The (optional) column that contains the sample ID.
    default:
    example: An index is a number starting with 1; column names (case-sensitive) as well as the following placeholders can be used: first, second, third, last_2, last_1, last; numeric indices can be enforced by preceding them with '#' (eg '#12'); column names can be surrounded by double quotes.
 
    -format <java.lang.String> (property: format)
    The format for the spectrum.
    default: NIR
 
    -instrument <java.lang.String> (property: instrument)
    The instrument for the spectrum.
    default: unknown
 
    -lenient <boolean> (property: lenient)
    If enabled, then errors (e.g., due to corrupt data) will not cause exceptions.
    default: false
    Author:
    fracpete (fracpete at waikato dot ac dot nz)
    See Also:
    Serialized Form

    • Field Summary

      Fields 
      Modifier and Type Field Description
      static String DEFAULT_WAVENO_REGEXP  
      protected adams.data.spreadsheet.SpreadSheetColumnIndex m_ColumnID
      the (optional) row with the sample ID.
      protected adams.data.spreadsheet.SpreadSheetColumnRange m_ColumnsAmplitude
      the rows to get the amplitudes from.
      protected adams.data.spreadsheet.SpreadSheetColumnRange m_ColumnsSampleData
      the rows to get the sample data from.
      protected String m_Format
      the format to use for the spectrum.
      protected String m_Instrument
      the instrument to use for the spectrum.
      protected boolean m_Lenient
      whether to skip over errors.
      protected adams.data.spreadsheet.SpreadSheetRowIndex m_RowSampleDataNames
      the column with the sample data names.
      protected adams.data.spreadsheet.SpreadSheetRowRange m_RowsAmplitude
      the rows with amplitudes.
      protected adams.data.spreadsheet.SpreadSheetRowIndex m_RowWaveNumber
      the (optional) wavenumber row.
      protected boolean m_SampleDataNamesInHeader
      whether the sample data names are in the header row.
      protected adams.core.base.BaseRegExp m_WaveNumberRegExp
      the regular expression to extract the wave number from the header (first group is used).
      protected boolean m_WaveNumbersInHeader
      whether the wavenumbers are in the header row.

      • Fields inherited from class adams.data.conversion.AbstractConversion

        m_Input, m_Output, m_Owner, m_Stopped

      • Fields inherited from class adams.core.option.AbstractOptionHandler

        m_OptionManager

      • Fields inherited from class adams.core.logging.LoggingObject

        m_Logger, m_LoggingIsEnabled, m_LoggingLevel

    • Field Detail

      • m_RowWaveNumber

        protected adams.data.spreadsheet.SpreadSheetRowIndex m_RowWaveNumber
        the (optional) wavenumber row.

      • m_WaveNumbersInHeader

        protected boolean m_WaveNumbersInHeader
        whether the wavenumbers are in the header row.

      • m_WaveNumberRegExp

        protected adams.core.base.BaseRegExp m_WaveNumberRegExp
        the regular expression to extract the wave number from the header (first group is used).

      • m_RowsAmplitude

        protected adams.data.spreadsheet.SpreadSheetRowRange m_RowsAmplitude
        the rows with amplitudes.

      • m_ColumnsAmplitude

        protected adams.data.spreadsheet.SpreadSheetColumnRange m_ColumnsAmplitude
        the rows to get the amplitudes from.

      • m_RowSampleDataNames

        protected adams.data.spreadsheet.SpreadSheetRowIndex m_RowSampleDataNames
        the column with the sample data names.

      • m_SampleDataNamesInHeader

        protected boolean m_SampleDataNamesInHeader
        whether the sample data names are in the header row.

      • m_ColumnsSampleData

        protected adams.data.spreadsheet.SpreadSheetColumnRange m_ColumnsSampleData
        the rows to get the sample data from.

      • m_ColumnID

        protected adams.data.spreadsheet.SpreadSheetColumnIndex m_ColumnID
        the (optional) row with the sample ID.

      • m_Format

        protected String m_Format
        the format to use for the spectrum.

      • m_Instrument

        protected String m_Instrument
        the instrument to use for the spectrum.

      • m_Lenient

        protected boolean m_Lenient
        whether to skip over errors.

    • Constructor Detail

      • SpreadSheetRowsToSpectra

        public SpreadSheetRowsToSpectra()

    • 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 adams.core.option.AbstractOptionHandler

      • setRowWaveNumber

        public void setRowWaveNumber​(adams.data.spreadsheet.SpreadSheetRowIndex value)
        Sets the row with the wavenumber information.
        Parameters:
        value - the row

      • getRowWaveNumber

        public adams.data.spreadsheet.SpreadSheetRowIndex getRowWaveNumber()
        Returns the row with the wavenumber information.
        Returns:
        the row

      • rowWaveNumberTipText

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

      • setWaveNumbersInHeader

        public void setWaveNumbersInHeader​(boolean value)
        Sets whether the wave numbers are in the header.
        Parameters:
        value - true if in header

      • getWaveNumbersInHeader

        public boolean getWaveNumbersInHeader()
        Returns whether the wave numbers are in the header.
        Returns:
        true if in header

      • waveNumbersInHeaderTipText

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

      • setWaveNumberRegExp

        public void setWaveNumberRegExp​(adams.core.base.BaseRegExp value)
        Sets the regular expression to identify the wave number (1st group is used).
        Parameters:
        value - the expression

      • getWaveNumberRegExp

        public adams.core.base.BaseRegExp getWaveNumberRegExp()
        Returns the regular expression to identify the wave number (1st group is used).
        Returns:
        the expression

      • waveNumberRegExpTipText

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

      • setRowsAmplitude

        public void setRowsAmplitude​(adams.data.spreadsheet.SpreadSheetRowRange value)
        Sets the rows with the amplitude information.
        Parameters:
        value - the rows

      • getRowsAmplitude

        public adams.data.spreadsheet.SpreadSheetRowRange getRowsAmplitude()
        Returns the rows with the amplitude information.
        Returns:
        the rows

      • rowsAmplitudeTipText

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

      • setColumnID

        public void setColumnID​(adams.data.spreadsheet.SpreadSheetColumnIndex value)
        Sets the (optional) column that contains the sample ID.
        Parameters:
        value - the column

      • getColumnID

        public adams.data.spreadsheet.SpreadSheetColumnIndex getColumnID()
        Returns the (optional) column that contains the sample ID.
        Returns:
        the column

      • columnIDTipText

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

      • setColumnsAmplitude

        public void setColumnsAmplitude​(adams.data.spreadsheet.SpreadSheetColumnRange value)
        Sets the columns with amplitude information.
        Parameters:
        value - the columns

      • getColumnsAmplitude

        public adams.data.spreadsheet.SpreadSheetColumnRange getColumnsAmplitude()
        Returns the columns with amplitude information.
        Returns:
        the columns

      • columnsAmplitudeTipText

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

      • setRowSampleDataNames

        public void setRowSampleDataNames​(adams.data.spreadsheet.SpreadSheetRowIndex value)
        Sets the row that contains the sample data names.
        Parameters:
        value - the row

      • getRowSampleDataNames

        public adams.data.spreadsheet.SpreadSheetRowIndex getRowSampleDataNames()
        Returns the row that contains the sample data names.
        Returns:
        the row

      • rowSampleDataNamesTipText

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

      • setSampleDataNamesInHeader

        public void setSampleDataNamesInHeader​(boolean value)
        Sets whether the wave numbers are in the header.
        Parameters:
        value - true if in header

      • getSampleDataNamesInHeader

        public boolean getSampleDataNamesInHeader()
        Returns whether the sample data names are in the header.
        Returns:
        true if in header

      • sampleDataNamesInHeaderTipText

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

      • setColumnsSampleData

        public void setColumnsSampleData​(adams.data.spreadsheet.SpreadSheetColumnRange value)
        Sets the columns with sampledata.
        Parameters:
        value - the columns

      • getColumnsSampleData

        public adams.data.spreadsheet.SpreadSheetColumnRange getColumnsSampleData()
        Returns the columns with sampledata.
        Returns:
        the columns

      • columnsSampleDataTipText

        public String columnsSampleDataTipText()
        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 to use for the spectrum.
        Parameters:
        value - the format

      • getFormat

        public String getFormat()
        Returns the format to use for the spectrum.
        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.

      • setInstrument

        public void setInstrument​(String value)
        Sets the instrument to use for the spectrum.
        Parameters:
        value - the instrument

      • getInstrument

        public String getInstrument()
        Returns the instrument to use for the spectrum.
        Returns:
        the instrument

      • 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.

      • setLenient

        public void setLenient​(boolean value)
        Sets whether to skip over errors.
        Specified by:
        setLenient in interface adams.core.LenientModeSupporter
        Parameters:
        value - true if to skip

      • getLenient

        public boolean getLenient()
        Returns whether whether to skip over errors.
        Specified by:
        getLenient in interface adams.core.LenientModeSupporter
        Returns:
        true if to skip

      • lenientTipText

        public String lenientTipText()
        Returns the tip text for this property.
        Specified by:
        lenientTipText in interface adams.core.LenientModeSupporter
        Returns:
        tip text for this property suitable for displaying in the GUI or for listing the options.

      • accepts

        public Class accepts()
        Returns the class that is accepted as input.
        Specified by:
        accepts in interface adams.data.conversion.Conversion
        Specified by:
        accepts in class adams.data.conversion.AbstractConversion
        Returns:
        the class

      • generates

        public Class generates()
        Returns the class that is generated as output.
        Specified by:
        generates in interface adams.data.conversion.Conversion
        Specified by:
        generates in class adams.data.conversion.AbstractConversion
        Returns:
        the class

      • getQuickInfo

        public String getQuickInfo()
        Returns a quick info about the object, which can be displayed in the GUI.
        Specified by:
        getQuickInfo in interface adams.core.QuickInfoSupporter
        Overrides:
        getQuickInfo in class adams.data.conversion.AbstractConversion
        Returns:
        null if no info available, otherwise short string

      • doConvert

        protected Object doConvert()
                    throws Exception
        Performs the actual conversion.
        Specified by:
        doConvert in class adams.data.conversion.AbstractConversion
        Returns:
        the converted data
        Throws:
        Exception - if something goes wrong with the conversion