Package adams.data.io.input

Class SimpleImageHeatmapReader

  • 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.DataContainerReader>, adams.core.SizeOfHandler, adams.data.io.input.DataContainerReader<Heatmap>, Serializable, Comparable
    public class SimpleImageHeatmapReader
extends AbstractHeatmapReader
    Reads an image with the specified reader and turns the grayscale version of the image into a heatmap. 

    -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
 
    -reader <adams.data.io.input.AbstractImageReader> (property: reader)
    The image reader to use.
    default: adams.data.io.input.JAIImageReader
    Author:
    fracpete (fracpete at waikato dot ac dot nz)
    See Also:
    Serialized Form

    • Field Summary

      Fields 
      Modifier and Type Field Description
      protected adams.data.io.input.ImageReader m_Reader
      the image reader to use.

      • 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

    • Method Summary

      All Methods Instance Methods Concrete Methods 
      Modifier and Type Method Description
      Class[] accepts()
      Returns the class that the consumer accepts.
      void defineOptions()
      Adds options to the internal list of options.
      String getFormatDescription()
      Returns a string describing the format (used in the file chooser).
      String[] getFormatExtensions()
      Returns the extension(s) of the format.
      adams.data.io.input.ImageReader getReader()
      Returns the reader to use.
      String globalInfo()
      Returns a string describing the object.
      protected void readData()
      Performs the actual reading.
      String readerTipText()
      Returns the tip text for this property.
      void setReader​(adams.data.io.input.ImageReader value)
      Sets the reader to use.

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

        checkData, cleanUp, compareTo, createDummyReport, createDummyReportTipText, destroy, doRead, equals, getAdditionalInformation, getCreateDummyReport, getDefaultFormatExtension, getInput, initialize, inputTipText, isInputFile, read, reset, setCreateDummyReport, setInput, shallowCopy, shallowCopy

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

        cleanUpOptions, finishInit, getDefaultLoggingLevel, getOptionManager, loggingLevelTipText, newOptionManager, setLoggingLevel, toCommandLine, toString

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

        configureLogger, getLogger, getLoggingLevel, initializeLogging, isLoggingEnabled, sizeOf

      • Methods inherited from interface adams.core.logging.LoggingLevelHandler

        getLoggingLevel

      • Methods inherited from interface adams.core.option.OptionHandler

        cleanUpOptions, getOptionManager, toCommandLine

    • Field Detail

      • m_Reader

        protected adams.data.io.input.ImageReader m_Reader
        the image reader to use.

    • Constructor Detail

      • SimpleImageHeatmapReader

        public SimpleImageHeatmapReader()

    • 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 AbstractHeatmapReader

      • setReader

        public void setReader​(adams.data.io.input.ImageReader value)
        Sets the reader to use.
        Parameters:
        value - the reader

      • getReader

        public adams.data.io.input.ImageReader getReader()
        Returns the reader to use.
        Returns:
        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.

      • accepts

        public Class[] accepts()
        Returns the class that the consumer accepts.
        Returns:
        the Class of objects that can be processed

      • 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<Heatmap>
        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<Heatmap>
        Returns:
        the extension(s) (without the dot!)

      • readData

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