Package loci.plugins.macro

Class LociFunctions

java.lang.Object
loci.plugins.macro.MacroFunctions
loci.plugins.macro.LociFunctions
All Implemented Interfaces:
ij.macro.MacroExtension, ij.plugin.PlugIn
public class LociFunctions extends MacroFunctions
This class provides macro extensions in ImageJ for Bio-Formats. Currently, it is a fairly tight mirror to the IFormatReader interface, with some additional functions to control the type of format reader used. Note that public methods in this class can only accept parameters of String, Double, String[], Double[], and Object[] types. Anything else will prevent the method from being usable within a macro.
Author:
Curtis Rueden ctrueden at wisc.edu

  • Field Details

    • URL_JAVADOCS

      public static final String URL_JAVADOCS
      URL for Javadocs.

    • r

      private ImageProcessorReader r

    • series

      private int series

  • Constructor Details

    • LociFunctions

      public LociFunctions()

  • Method Details

    • getRevision

      public void getRevision(String[] revision)

    • getBuildDate

      public void getBuildDate(String[] date)

    • getVersionNumber

      public void getVersionNumber(String[] version)

    • getImageCount

      public void getImageCount(Double[] imageCount)

    • getSizeX

      public void getSizeX(Double[] sizeX)

    • getSizeY

      public void getSizeY(Double[] sizeY)

    • getSizeZ

      public void getSizeZ(Double[] sizeZ)

    • getSizeC

      public void getSizeC(Double[] sizeC)

    • getSizeT

      public void getSizeT(Double[] sizeT)

    • getPixelType

      public void getPixelType(String[] pixelType)

    • getEffectiveSizeC

      public void getEffectiveSizeC(Double[] effectiveSizeC)

    • getRGBChannelCount

      public void getRGBChannelCount(Double[] rgbChannelCount)

    • isIndexed

      public void isIndexed(String[] indexed)

    • getChannelDimCount

      public void getChannelDimCount(Double[] channelDimCount)

    • getChannelDimLength

      public void getChannelDimLength(Double i, Double[] channelDimLength)

    • getChannelDimType

      public void getChannelDimType(Double i, String[] channelDimType)

    • isLittleEndian

      public void isLittleEndian(String[] littleEndian)

    • getDimensionOrder

      public void getDimensionOrder(String[] dimOrder)

    • isOrderCertain

      public void isOrderCertain(String[] orderCertain)

    • isInterleaved

      public void isInterleaved(String[] interleaved)

    • isInterleavedSubC

      public void isInterleavedSubC(Double subC, String[] interleaved)

    • openImagePlus

      public void openImagePlus(String path)

    • openThumbImagePlus

      public void openThumbImagePlus(String path)

    • openThumbImage

      public void openThumbImage(String title, Double no) throws FormatException, IOException
      Throws:
      FormatException
      IOException

    • openImage

      public void openImage(String title, Double no) throws FormatException, IOException
      Throws:
      FormatException
      IOException

    • openSubImage

      public void openSubImage(String title, Double no, Double x, Double y, Double w, Double h) throws FormatException, IOException
      Throws:
      FormatException
      IOException

    • close

      public void close() throws IOException
      Throws:
      IOException

    • closeFileOnly

      public void closeFileOnly() throws IOException
      Throws:
      IOException

    • getSeriesCount

      public void getSeriesCount(Double[] seriesCount)

    • setSeries

      public void setSeries(Double seriesNum)

    • getSeries

      public void getSeries(Double[] seriesNum)

    • setNormalized

      public void setNormalized(Boolean normalize)

    • isNormalized

      public void isNormalized(Boolean[] normalize)

    • setOriginalMetadataPopulated

      public void setOriginalMetadataPopulated(Boolean populate)

    • isOriginalMetadataPopulated

      public void isOriginalMetadataPopulated(Boolean[] populate)

    • setGroupFiles

      public void setGroupFiles(String groupFiles)

    • isGroupFiles

      public void isGroupFiles(String[] groupFiles)

    • isMetadataComplete

      public void isMetadataComplete(String[] complete)

    • fileGroupOption

      public void fileGroupOption(String id, String[] fileGroupOption) throws FormatException, IOException
      Throws:
      FormatException
      IOException

    • getUsedFileCount

      public void getUsedFileCount(Double[] count)

    • getUsedFile

      public void getUsedFile(Double i, String[] used)

    • getCurrentFile

      public void getCurrentFile(String[] file)

    • getIndex

      public void getIndex(Double z, Double c, Double t, Double[] index)

    • getZCTCoords

      public void getZCTCoords(Double index, Double[] z, Double[] c, Double[] t)

    • getMetadataValue

      public void getMetadataValue(String field, String[] value)

    • getSeriesMetadataValue

      public void getSeriesMetadataValue(String field, String[] value)

    • setMetadataFiltered

      public void setMetadataFiltered(String metadataFiltered)

    • isMetadataFiltered

      public void isMetadataFiltered(String[] metadataFiltered)

    • getFormat

      public void getFormat(String id, String[] format) throws FormatException, IOException
      Throws:
      FormatException
      IOException

    • setId

      public void setId(String id) throws FormatException, IOException
      Throws:
      FormatException
      IOException

    • isThisType

      public void isThisType(String name, String[] thisType)

    • isThisTypeFast

      public void isThisTypeFast(String name, String[] thisType)

    • getSeriesName

      public void getSeriesName(String[] seriesName)

    • getImageCreationDate

      public void getImageCreationDate(String[] creationDate)

    • getPlaneTimingDeltaT

      public void getPlaneTimingDeltaT(Double[] deltaT, Double no)

    • getPlaneTimingExposureTime

      public void getPlaneTimingExposureTime(Double[] exposureTime, Double no)

    • getPlanePositionX

      public void getPlanePositionX(Double[] positionX, Double no)

    • getPlanePositionY

      public void getPlanePositionY(Double[] positionY, Double no)

    • getPlanePositionZ

      public void getPlanePositionZ(Double[] positionZ, Double no)

    • getPixelsPhysicalSizeX

      public void getPixelsPhysicalSizeX(Double[] sizeX)

    • getPixelsPhysicalSizeY

      public void getPixelsPhysicalSizeY(Double[] sizeY)

    • getPixelsPhysicalSizeZ

      public void getPixelsPhysicalSizeZ(Double[] sizeZ)

    • getPixelsTimeIncrement

      public void getPixelsTimeIncrement(Double[] sizeT)

    • run

      public void run(String arg)
      Specified by:
      run in interface ij.plugin.PlugIn
      Overrides:
      run in class MacroFunctions

    • getPlaneIndex

      private static int getPlaneIndex(IFormatReader r, int no)
      Finds the Plane index corresponding to the given image plane number.