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 Summary

Fields

Modifier and Type	Field and Description
private ImageProcessorReader	r
private int	series
static java.lang.String	URL_JAVADOCS URL for Javadocs.

Fields inherited from class loci.plugins.macro.MacroFunctions

extensions

Fields inherited from interface ij.macro.MacroExtension

ARG_ARRAY, ARG_NUMBER, ARG_OPTIONAL, ARG_OUTPUT, ARG_STRING

Constructor Summary

Constructors

Constructor and Description
LociFunctions()

Method Summary

Modifier and Type	Method and Description
void	close()
void	closeFileOnly()
void	fileGroupOption(java.lang.String id, java.lang.String[] fileGroupOption)
void	getBuildDate(java.lang.String[] date)
void	getChannelDimCount(java.lang.Double[] channelDimCount)
void	getChannelDimLength(java.lang.Double i, java.lang.Double[] channelDimLength)
void	getChannelDimType(java.lang.Double i, java.lang.Double[] channelDimType)
void	getCurrentFile(java.lang.String[] file)
void	getDimensionOrder(java.lang.String[] dimOrder)
void	getEffectiveSizeC(java.lang.Double[] effectiveSizeC)
void	getFormat(java.lang.String id, java.lang.String[] format)
void	getImageCount(java.lang.Double[] imageCount)
void	getImageCreationDate(java.lang.String[] creationDate)
void	getIndex(java.lang.Double z, java.lang.Double c, java.lang.Double t, java.lang.Double[] index)
void	getMetadataValue(java.lang.String field, java.lang.String[] value)
void	getPixelsPhysicalSizeX(java.lang.Double[] sizeX)
void	getPixelsPhysicalSizeY(java.lang.Double[] sizeY)
void	getPixelsPhysicalSizeZ(java.lang.Double[] sizeZ)
void	getPixelsTimeIncrement(java.lang.Double[] sizeT)
void	getPixelType(java.lang.String[] pixelType)
private static int	getPlaneIndex(IFormatReader r, int no) Finds the Plane index corresponding to the given image plane number.
void	getPlanePositionX(java.lang.Double[] positionX, java.lang.Double no)
void	getPlanePositionY(java.lang.Double[] positionY, java.lang.Double no)
void	getPlanePositionZ(java.lang.Double[] positionZ, java.lang.Double no)
void	getPlaneTimingDeltaT(java.lang.Double[] deltaT, java.lang.Double no)
void	getPlaneTimingExposureTime(java.lang.Double[] exposureTime, java.lang.Double no)
void	getRevision(java.lang.String[] revision)
void	getRGBChannelCount(java.lang.Double[] rgbChannelCount)
void	getSeries(java.lang.Double[] seriesNum)
void	getSeriesCount(java.lang.Double[] seriesCount)
void	getSeriesMetadataValue(java.lang.String field, java.lang.String[] value)
void	getSeriesName(java.lang.String[] seriesName)
void	getSizeC(java.lang.Double[] sizeC)
void	getSizeT(java.lang.Double[] sizeT)
void	getSizeX(java.lang.Double[] sizeX)
void	getSizeY(java.lang.Double[] sizeY)
void	getSizeZ(java.lang.Double[] sizeZ)
void	getUsedFile(java.lang.Double i, java.lang.String[] used)
void	getUsedFileCount(java.lang.Double[] count)
void	getVersionNumber(java.lang.String[] version)
void	getZCTCoords(java.lang.Double index, java.lang.Double[] z, java.lang.Double[] c, java.lang.Double[] t)
void	isGroupFiles(java.lang.String[] groupFiles)
void	isIndexed(java.lang.String[] indexed)
void	isInterleaved(java.lang.String[] interleaved)
void	isInterleavedSubC(java.lang.Double subC, java.lang.String[] interleaved)
void	isLittleEndian(java.lang.String[] littleEndian)
void	isMetadataComplete(java.lang.String[] complete)
void	isMetadataFiltered(java.lang.String[] metadataFiltered)
void	isNormalized(java.lang.Boolean[] normalize)
void	isOrderCertain(java.lang.String[] orderCertain)
void	isOriginalMetadataPopulated(java.lang.Boolean[] populate)
void	isThisType(java.lang.String name, java.lang.String[] thisType)
void	isThisTypeFast(java.lang.String name, java.lang.String[] thisType)
void	openImage(java.lang.String title, java.lang.Double no)
void	openImagePlus(java.lang.String path)
void	openSubImage(java.lang.String title, java.lang.Double no, java.lang.Double x, java.lang.Double y, java.lang.Double w, java.lang.Double h)
void	openThumbImage(java.lang.String title, java.lang.Double no)
void	openThumbImagePlus(java.lang.String path)
void	run(java.lang.String arg)
void	setGroupFiles(java.lang.String groupFiles)
void	setId(java.lang.String id)
void	setMetadataFiltered(java.lang.String metadataFiltered)
void	setNormalized(java.lang.Boolean normalize)
void	setOriginalMetadataPopulated(java.lang.Boolean populate)
void	setSeries(java.lang.Double seriesNum)

Methods inherited from class loci.plugins.macro.MacroFunctions

buildExtensions, getExtensionFunctions, handleExtension

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

URL_JAVADOCS

public static final java.lang.String URL_JAVADOCS

URL for Javadocs.

r

private ImageProcessorReader r

series

private int series

Constructor Detail

LociFunctions

public LociFunctions()

Method Detail

getRevision

public void getRevision(java.lang.String[] revision)

getBuildDate

public void getBuildDate(java.lang.String[] date)

getVersionNumber

public void getVersionNumber(java.lang.String[] version)

getImageCount

public void getImageCount(java.lang.Double[] imageCount)

getSizeX

public void getSizeX(java.lang.Double[] sizeX)

getSizeY

public void getSizeY(java.lang.Double[] sizeY)

getSizeZ

public void getSizeZ(java.lang.Double[] sizeZ)

getSizeC

public void getSizeC(java.lang.Double[] sizeC)

getSizeT

public void getSizeT(java.lang.Double[] sizeT)

getPixelType

public void getPixelType(java.lang.String[] pixelType)

getEffectiveSizeC

public void getEffectiveSizeC(java.lang.Double[] effectiveSizeC)

getRGBChannelCount

public void getRGBChannelCount(java.lang.Double[] rgbChannelCount)

isIndexed

public void isIndexed(java.lang.String[] indexed)

getChannelDimCount

public void getChannelDimCount(java.lang.Double[] channelDimCount)

getChannelDimLength

public void getChannelDimLength(java.lang.Double i,
                                java.lang.Double[] channelDimLength)

getChannelDimType

public void getChannelDimType(java.lang.Double i,
                              java.lang.Double[] channelDimType)

isLittleEndian

public void isLittleEndian(java.lang.String[] littleEndian)

getDimensionOrder

public void getDimensionOrder(java.lang.String[] dimOrder)

isOrderCertain

public void isOrderCertain(java.lang.String[] orderCertain)

isInterleaved

public void isInterleaved(java.lang.String[] interleaved)

isInterleavedSubC

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

openImagePlus

public void openImagePlus(java.lang.String path)

openThumbImagePlus

public void openThumbImagePlus(java.lang.String path)

openThumbImage

public void openThumbImage(java.lang.String title,
                           java.lang.Double no)
                    throws FormatException,
                           java.io.IOException

Throws:

FormatException

java.io.IOException

openImage

public void openImage(java.lang.String title,
                      java.lang.Double no)
               throws FormatException,
                      java.io.IOException

Throws:

FormatException

java.io.IOException

openSubImage

public void openSubImage(java.lang.String title,
                         java.lang.Double no,
                         java.lang.Double x,
                         java.lang.Double y,
                         java.lang.Double w,
                         java.lang.Double h)
                  throws FormatException,
                         java.io.IOException

Throws:

FormatException

java.io.IOException

close

public void close()
           throws java.io.IOException

Throws:

java.io.IOException

closeFileOnly

public void closeFileOnly()
                   throws java.io.IOException

Throws:

java.io.IOException

getSeriesCount

public void getSeriesCount(java.lang.Double[] seriesCount)

setSeries

public void setSeries(java.lang.Double seriesNum)

getSeries

public void getSeries(java.lang.Double[] seriesNum)

setNormalized

public void setNormalized(java.lang.Boolean normalize)

isNormalized

public void isNormalized(java.lang.Boolean[] normalize)

setOriginalMetadataPopulated

public void setOriginalMetadataPopulated(java.lang.Boolean populate)

isOriginalMetadataPopulated

public void isOriginalMetadataPopulated(java.lang.Boolean[] populate)

setGroupFiles

public void setGroupFiles(java.lang.String groupFiles)

isGroupFiles

public void isGroupFiles(java.lang.String[] groupFiles)

isMetadataComplete

public void isMetadataComplete(java.lang.String[] complete)

fileGroupOption

public void fileGroupOption(java.lang.String id,
                            java.lang.String[] fileGroupOption)
                     throws FormatException,
                            java.io.IOException

Throws:

FormatException

java.io.IOException

getUsedFileCount

public void getUsedFileCount(java.lang.Double[] count)

getUsedFile

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

getCurrentFile

public void getCurrentFile(java.lang.String[] file)

getIndex

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

getZCTCoords

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

getMetadataValue

public void getMetadataValue(java.lang.String field,
                             java.lang.String[] value)

getSeriesMetadataValue

public void getSeriesMetadataValue(java.lang.String field,
                                   java.lang.String[] value)

setMetadataFiltered

public void setMetadataFiltered(java.lang.String metadataFiltered)

isMetadataFiltered

public void isMetadataFiltered(java.lang.String[] metadataFiltered)

getFormat

public void getFormat(java.lang.String id,
                      java.lang.String[] format)
               throws FormatException,
                      java.io.IOException

Throws:

FormatException

java.io.IOException

setId

public void setId(java.lang.String id)
           throws FormatException,
                  java.io.IOException

Throws:

FormatException

java.io.IOException

isThisType

public void isThisType(java.lang.String name,
                       java.lang.String[] thisType)

isThisTypeFast

public void isThisTypeFast(java.lang.String name,
                           java.lang.String[] thisType)

getSeriesName

public void getSeriesName(java.lang.String[] seriesName)

getImageCreationDate

public void getImageCreationDate(java.lang.String[] creationDate)

getPlaneTimingDeltaT

public void getPlaneTimingDeltaT(java.lang.Double[] deltaT,
                                 java.lang.Double no)

getPlaneTimingExposureTime

public void getPlaneTimingExposureTime(java.lang.Double[] exposureTime,
                                       java.lang.Double no)

getPlanePositionX

public void getPlanePositionX(java.lang.Double[] positionX,
                              java.lang.Double no)

getPlanePositionY

public void getPlanePositionY(java.lang.Double[] positionY,
                              java.lang.Double no)

getPlanePositionZ

public void getPlanePositionZ(java.lang.Double[] positionZ,
                              java.lang.Double no)

getPixelsPhysicalSizeX

public void getPixelsPhysicalSizeX(java.lang.Double[] sizeX)

getPixelsPhysicalSizeY

public void getPixelsPhysicalSizeY(java.lang.Double[] sizeY)

getPixelsPhysicalSizeZ

public void getPixelsPhysicalSizeZ(java.lang.Double[] sizeZ)

getPixelsTimeIncrement

public void getPixelsTimeIncrement(java.lang.Double[] sizeT)

run

public void run(java.lang.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.