Package adams.data.io.input

Class OpusSpectrumReader

  • 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 OpusSpectrumReader
extends AbstractSpectrumReader
    Reads spectra in OPUS format. 

    -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
 
    -sample-id <java.lang.String> (property: sampleID)
    ID|Field1|Field2|Field3|[prefix]
    default: SNM
 
    -start <int> (property: start)
    Spectrum number to start loading from.
    default: 1
 
    -max <int> (property: max)
    Maximum spectra to load.
    default: -1
 
    -add-trace-to-report <boolean> (property: addTraceToReport)
    If enabled the trace of identified blocks etc gets added to the report,
    using prefix Trace..
    default: false
    Author:
    fracpete (fracpete at waikato dot ac dot nz)
    See Also:
    Serialized Form

    • Field Detail

      • BLOCKS_OFFSET

        public static int BLOCKS_OFFSET

      • PREFIX_TRACE

        public static String PREFIX_TRACE
        the prefix for the trace values in the report.

      • m_SampleID

        protected String m_SampleID
        where to get sample id from. see param defs

      • m_Start

        protected int m_Start
        starting spectrum.

      • m_Max

        protected int m_Max
        maximum to load.

      • m_Trace

        protected HashMap<String,​Object> m_Trace
        trace of data that was retrieved from byte array.

      • m_AddTraceToReport

        protected boolean m_AddTraceToReport
        whether to add the trace to the report.

    • Constructor Detail

      • OpusSpectrumReader

        public OpusSpectrumReader()

    • 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

      • 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(s) (without the dot!)

      • 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

      • setMax

        public void setMax​(int value)
        Sets the nth point setting.
        Parameters:
        value - the nth point to use

      • getMax

        public int getMax()
        Returns the nth point setting.
        Returns:
        the nth point

      • maxTipText

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

      • setStart

        public void setStart​(int value)
        Sets the start point setting.
        Parameters:
        value - the nth point to use

      • getStart

        public int getStart()
        Returns the start point setting.
        Returns:
        the nth point

      • startTipText

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

      • getSampleID

        public String getSampleID()
        Get id field.
        Returns:
        id field

      • setSampleID

        public void setSampleID​(String value)
        Set id field.
        Parameters:
        value -

      • sampleIDTipText

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

      • getAddTraceToReport

        public boolean getAddTraceToReport()
        Returns whether to add the trace to the report.
        Returns:
        true if to add the trace

      • setAddTraceToReport

        public void setAddTraceToReport​(boolean value)
        Sets whether to add the trace to the report.
        Parameters:
        value - true if to add the trace

      • addTraceToReportTipText

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

      • getInt

        protected int getInt​(byte[] b,
                     int offset)
        Get int from 4bytes, LSByte first
        Parameters:
        b - byte array
        offset - grab from
        Returns:
        integer

      • getNirArray

        protected double[] getNirArray​(byte[] file_image)
        Get array of nir data from byte array of bruker file image
        Parameters:
        file_image - byte array
        Returns:
        nir data array

      • getBlockOffset

        protected int getBlockOffset​(byte[] buf,
                             byte byte1,
                             byte byte2,
                             byte byte3,
                             byte byte4)
        Starting from blocks_offset, find sequence of bytes Return position of sequence, or -1 if not found
        Parameters:
        buf - byte array
        byte1 - the first byte
        byte2 - the second byte
        byte3 - the third byte
        byte4 - the fourth byte
        Returns:
        position of sequence, or -1 if not found

      • getBlockOffsetReverse

        protected int getBlockOffsetReverse​(byte[] buf,
                                    int start,
                                    byte byte1,
                                    byte byte2,
                                    byte byte3,
                                    byte byte4)
        Starting from blocks_offset, find sequence of bytes Return position of sequence, or -1 if not found
        Parameters:
        buf - byte array
        byte1 - the first byte
        byte2 - the second byte
        byte3 - the third byte
        byte4 - the fourth byte
        Returns:
        position of sequence, or -1 if not found

      • getABOffset

        protected int getABOffset​(byte[] buf)
        Find position of AB Block offset
        Parameters:
        buf - byte array
        Returns:
        AB Block offset

      • getTextOffset

        protected int getTextOffset​(byte[] buf)
        Find position of Text Block offset
        Parameters:
        buf - byte array
        Returns:
        Text Block offset

      • getABCount

        protected int getABCount​(byte[] buf)
        Get number of spectral values
        Parameters:
        buf - byte array
        Returns:
        number of spectral values

      • getWaveNumbers

        protected double[] getWaveNumbers​(byte[] buf)

      • getTextBlockOffset

        protected int getTextBlockOffset​(byte[] buf)
        Get position of Text Data.
        Parameters:
        buf - byte array
        Returns:
        the text data pos

      • getTextBlockSize

        protected int getTextBlockSize​(byte[] buf)
        Size of Text Block (in 4-byte words).
        Parameters:
        buf - byte array of bruker file image
        Returns:
        the text block size (in 4-byte words)

      • getABDataOffset

        protected int getABDataOffset​(byte[] buf)
        Get position of nir data.
        Parameters:
        buf - byte array of file image
        Returns:
        nir data pos

      • find

        protected boolean find​(String find,
                       byte[] buf,
                       int start)
        Find a given string in byte array, from a starting pos.
        Parameters:
        find - the string to find
        buf - the byte array
        start - the starting offset
        Returns:
        found?

      • split

        public static String[] split​(String s)
        Attempts to split a string, using the specified delimiter character. A delimiter gets ignored if inside double quotes.
        Parameters:
        s - the string to split
        Returns:
        the parts (single array element if no range)

      • getMetaData

        protected HashMap<String,​Object> getMetaData​(byte[] buf)
        Returns the meta-data from the buffer.
        Parameters:
        buf - the buffer to read from
        Returns:
        the meta data

      • getValueFor

        protected String getValueFor​(String key,
                             byte[] buf)
        Get value for key, from Text Block. Or null if not found.
        Parameters:
        key - the key to look up
        buf - byte array
        Returns:
        the value

      • byte2UByte

        protected int byte2UByte​(byte b)
        Convert byte to unsigned byte.
        Parameters:
        b - the byte
        Returns:
        the unsigned byte

      • convertToLong

        protected long convertToLong​(byte[] buf,
                             int offset)
        Convert 4 bytes to long. LSByte first.
        Parameters:
        buf - byte array
        offset - starting pos
        Returns:
        the long value

      • convert8ToDouble

        protected double convert8ToDouble​(byte[] buf,
                                  int offset)
        Convert 8 bytes to long. LSByte first.
        Parameters:
        buf - byte array
        offset - starting pos
        Returns:
        the double value

      • 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