Package adams.data.io.output

Class NIRSpectrumWriter

  • 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.output.DataContainerWriter>, adams.core.SizeOfHandler, adams.data.io.output.DataContainerWriter<Spectrum>, adams.data.io.output.StreamableBinaryDataContainerWriter<Spectrum>, adams.data.io.output.StreamableDataContainerWriter<Spectrum>, Serializable, Comparable
    Direct Known Subclasses:
    CALSpectrumWriter
    public class NIRSpectrumWriter
extends AbstractSpectrumWriter
implements adams.data.io.output.StreamableBinaryDataContainerWriter<Spectrum>
    Writer that stores spectra in the 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
 
    -output <adams.core.io.PlaceholderFile> (property: output)
    The file to write the container to.
    default: ${TMP}/out.tmp
 
    -instrumentName <java.lang.String> (property: instrumentName)
    Instrument Name.
    default: <not implemented>
 
    -client <java.lang.String> (property: client)
    Client of Sample.
    default: client
 
    -fileID <java.lang.String> (property: fileID)
    File ID.
    default: generated by ADAMS
 
    -sampleID1 <java.lang.String> (property: sampleID1)
    Sample ID1.
    default:
 
    -sampleID2 <java.lang.String> (property: sampleID2)
    Sample ID1.
    default:
 
    -sampleID3 <java.lang.String> (property: sampleID3)
    Sample ID3.
    default:
 
    -serialNo <java.lang.String> (property: serialNo)
    Serial Number of Instrument.
    default: 0000-0000-0000
 
    -master <java.lang.String> (property: master)
    Serial Number of Master Instrument.
    default: 0000-0000-0000
 
    -operator <java.lang.String> (property: operator)
    Instrument Operator.
    default: ADAMS
 
    -productCode <java.lang.String> (property: productCode)
    Either the attribute name with the product code in it, or the actual product
    code to be used.
    default: 01
 
    -productCodeFromField (property: productCodeFromField)
    Regex to find sample id. e.g 'sample_id'
 
    -segments <adams.core.base.BaseInteger> [-segments ...] (property: segments)
    Segments.
    default: 1050
 
    -increment <java.lang.Double> (property: increment)
    Increment
    default: 2.0
 
    -firstXPoint <java.lang.Double> (property: firstXPoint)
    First wavenumber
    default: 3749.3428948242
 
    -lastXPoint <java.lang.Double> (property: lastXPoint)
    Last wavenumber
    default: 9998.2477195313
 
    -EOC <java.lang.Integer> (property: EOC)
    Number of EOC's per rev.
    default: 0
 
    -timestamp <adams.core.base.BaseDateTime> (property: timestamp)
    The timestamp to use in the file; use 'NOW' for current time.
    default: NOW
    Author:
    dale (dale at waikato dot ac dot nz)
    See Also:
    Serialized Form

    • Field Detail

      • m_FileID

        protected String m_FileID
        File ID.

      • m_InstrumentName

        protected String m_InstrumentName
        The instrument name to put in ASC header.

      • m_Serial

        protected String m_Serial
        Serial Number of Instrument.

      • m_SampleID1

        protected String m_SampleID1
        SampleID 1.

      • m_SampleID2

        protected String m_SampleID2
        SampleID 2.

      • m_SampleID3

        protected String m_SampleID3
        SampleID 3.

      • m_Master

        protected String m_Master
        Serial Number of Master Instrument.

      • m_ProductCode

        protected String m_ProductCode
        Either the Field name with the product code in it, or the actual product code. Decided by m_GetProductCodeFromAttribute.

      • m_Operator

        protected String m_Operator
        Operator name.

      • m_Client

        protected String m_Client
        Client name.

      • m_Segments

        protected adams.core.base.BaseInteger[] m_Segments
        Segment points.

      • m_WaveStarts

        protected adams.core.base.BaseFloat[] m_WaveStarts
        Segment starting.

      • m_WaveSteps

        protected adams.core.base.BaseFloat[] m_WaveSteps
        Increments.

      • m_WaveEnds

        protected adams.core.base.BaseFloat[] m_WaveEnds
        Segment ends.

      • m_ProductCodeFromField

        protected Boolean m_ProductCodeFromField
        Get the product code from the Field named ProductCode in the Report? Otherwise use the ProductCode string directly.

      • m_EOC

        protected Integer m_EOC
        Number of EOC's per rev (???).

      • m_Timestamp

        protected adams.core.base.BaseDateTime m_Timestamp
        the timestamp to use in the file.

    • Constructor Detail

      • NIRSpectrumWriter

        public NIRSpectrumWriter()

    • 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.output.AbstractDataContainerWriter<Spectrum>

      • getIncrements

        public adams.core.base.BaseFloat[] getIncrements()
        Get increments.
        Returns:
        increments.

      • setIncrements

        public void setIncrements​(adams.core.base.BaseFloat[] in)
        Set increments.
        Parameters:
        in - increments.

      • incrementsTipText

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

      • getEndPoints

        public adams.core.base.BaseFloat[] getEndPoints()
        Get end points.
        Returns:
        end points.

      • setEndPoints

        public void setEndPoints​(adams.core.base.BaseFloat[] ep)
        Set end points.
        Parameters:
        ep - end points .

      • endPointsTipText

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

      • getStartPoints

        public adams.core.base.BaseFloat[] getStartPoints()
        Get start points.
        Returns:
        start points.

      • setStartPoints

        public void setStartPoints​(adams.core.base.BaseFloat[] sp)
        Set start points.
        Parameters:
        sp - start points .

      • startPointsTipText

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

      • getSegmentWidths

        public adams.core.base.BaseInteger[] getSegmentWidths()
        Get segments.
        Returns:
        segments.

      • setSegmentWidths

        public void setSegmentWidths​(adams.core.base.BaseInteger[] segments)
        Set segments.
        Parameters:
        segments - segments .

      • segmentWidthsTipText

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

      • getProductCodeFromField

        public Boolean getProductCodeFromField()
        Get product code from instance attribute? Or use as string.
        Returns:
        Get product code from instance attribute?

      • setProductCodeFromField

        public void setProductCodeFromField​(Boolean mGetProductCodeFromAttribute)
        Set product code from instance attribute? Or use as string.
        Parameters:
        mGetProductCodeFromAttribute - Set product code from instance attribute?

      • productCodeFromFieldTipText

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

      • getProductCode

        public String getProductCode()
        Get Product Code.
        Returns:
        product code

      • setProductCode

        public void setProductCode​(String productCode)
        Set product code.
        Parameters:
        productCode - product code.

      • productCodeTipText

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

      • getMaster

        public String getMaster()
        Get serial no of master.
        Returns:
        serial no of master.

      • setMaster

        public void setMaster​(String serialNo)
        Set serial no of master.
        Parameters:
        serialNo - serial no of master.

      • masterTipText

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

      • getSerialNo

        public String getSerialNo()
        Get serial no.
        Returns:
        serial no.

      • setSerialNo

        public void setSerialNo​(String serialNo)
        Set serial no.
        Parameters:
        serialNo - serial no.

      • serialNoTipText

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

      • getClient

        public String getClient()
        Get client.
        Returns:
        client.

      • setClient

        public void setClient​(String client)
        Set client.
        Parameters:
        client - client.

      • clientTipText

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

      • getOperator

        public String getOperator()
        Get operator.
        Returns:
        operator.

      • setOperator

        public void setOperator​(String operator)
        Set operator.
        Parameters:
        operator - operator.

      • operatorTipText

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

      • getSampleID1

        public String getSampleID1()
        Get sample id1.
        Returns:
        sample id1.

      • setSampleID1

        public void setSampleID1​(String sampleID)
        Set sample id1.
        Parameters:
        sampleID - sampleID1

      • sampleID1TipText

        public String sampleID1TipText()
        Returns the tip text for this property.
        Returns:
        tip text for this property suitable for displaying in the GUI or for listing the options.

      • getSampleID2

        public String getSampleID2()
        Get sample id2.
        Returns:
        sample id2.

      • setSampleID2

        public void setSampleID2​(String sampleID)
        Set sample id2.
        Parameters:
        sampleID - sampleID2

      • sampleID2TipText

        public String sampleID2TipText()
        Returns the tip text for this property.
        Returns:
        tip text for this property suitable for displaying in the GUI or for listing the options.

      • getSampleID3

        public String getSampleID3()
        Get sample id3.
        Returns:
        sample id3.

      • setSampleID3

        public void setSampleID3​(String sampleID)
        Set sample id3.
        Parameters:
        sampleID - sampleID3

      • sampleID3TipText

        public String sampleID3TipText()
        Returns the tip text for this property.
        Returns:
        tip text for this property suitable for displaying in the GUI or for listing the options.

      • getFileID

        public String getFileID()
        Get file id.
        Returns:
        file id.

      • setFileID

        public void setFileID​(String fileID)
        Set file id.
        Parameters:
        fileID - file ID

      • fileIDTipText

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

      • getInstrumentName

        public String getInstrumentName()
        Get instrument name.
        Returns:
        instrument name

      • setInstrumentName

        public void setInstrumentName​(String mInstrumentName)
        Set instrument name.
        Parameters:
        mInstrumentName - instrument name

      • instrumentNameTipText

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

      • getEOC

        public Integer getEOC()
        Get number of EOC's per rev (whatever that is!!)
        Returns:
        numbe of EOC's per rev

      • setEOC

        public void setEOC​(Integer eoc)
        Set number of EOC's per rev
        Parameters:
        eoc - number of EOC's per rev

      • EOCTipText

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

      • getTimestamp

        public adams.core.base.BaseDateTime getTimestamp()
        Get the timestamp to use in the file.
        Returns:
        the timestamp

      • setTimestamp

        public void setTimestamp​(adams.core.base.BaseDateTime value)
        Set the timestamp to use in the file.
        Parameters:
        value - the timestamp

      • timestampTipText

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

      • 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

      • 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.output.AbstractDataContainerWriter<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.output.AbstractDataContainerWriter<Spectrum>
        Returns:
        the extension(s) (without the dot!)

      • initialize

        protected void initialize()
        Initializes the members.
        Overrides:
        initialize in class adams.core.option.AbstractOptionHandler

      • getSampleHeader

        public FossOutputHelper.SampleHeader getSampleHeader​(Spectrum sp,
                                                     int pos)
        Create a SampleHeader from a Spectrum and position in list/file.
        Parameters:
        sp - spectrum
        pos - position
        Returns:
        SampleHeader

      • getSampleInfo

        public FossOutputHelper.SampleInfo getSampleInfo​(Spectrum sp,
                                                 int pos)
        Create a SampleInfo for the file footer based on a Spectrum and it's position in list/file.
        Parameters:
        sp - Spectrum
        pos - position
        Returns:
        SampleInfo

      • genByteArray

        protected byte[] genByteArray​(List<Spectrum> datalist)
                       throws Exception
        Generate the byte array that makes up the .nir file.
        Parameters:
        datalist - the Spectra to write.
        Returns:
        byte array.
        Throws:
        Exception

      • genByteArray

        protected byte[] genByteArray​(Spectrum data)
        Generate the byte array that makes up the .nir file.
        Parameters:
        data - the data to write
        Returns:
        ASC file as string.

      • canWriteMultiple

        public boolean canWriteMultiple()
        Returns whether writing of multiple containers is supported.
        Specified by:
        canWriteMultiple in interface adams.data.io.output.DataContainerWriter<Spectrum>
        Overrides:
        canWriteMultiple in class AbstractSpectrumWriter
        Returns:
        true if multiple containers are supported

      • writeData

        protected boolean writeData​(List<Spectrum> data)
        Performs the actual writing.
        Specified by:
        writeData in class adams.data.io.output.AbstractDataContainerWriter<Spectrum>
        Parameters:
        data - the data to write
        Returns:
        success

      • write

        public boolean write​(OutputStream stream,
                     Spectrum data)
        Performs checks and writes the data to the stream.
        Specified by:
        write in interface adams.data.io.output.StreamableDataContainerWriter<Spectrum>
        Parameters:
        stream - the stream to write to
        data - the data to write
        Returns:
        true if successfully written
        See Also:
        write(OutputStream stream, List)

      • write

        public boolean write​(OutputStream stream,
                     List<Spectrum> data)
        Performs checks and writes the data to the stream.
        Specified by:
        write in interface adams.data.io.output.StreamableDataContainerWriter<Spectrum>
        Parameters:
        stream - the stream to write to
        data - the data to write
        Returns:
        true if successfully written