stereodisc
Class Conventions

java.lang.Object
  stereodisc.Conventions

public class Conventions
extends java.lang.Object

Class with defaults and conventions for stereo disk file size, names, directories, etc. Copyright (c) 1999-2004, Michael Abramoff. All rights reserved.

Field Summary

static java.lang.String	classificationName
static java.lang.String	reportName
static java.lang.String	rsName

Constructor Summary

Conventions()

Method Summary

static java.lang.String	clsDirectory()
static byte[]	convertImageToResult(ij.process.ColorProcessor ip, int binning) Convert a ColorProcessor with an image containing different colors for different classes into an array with 0...number of classes for each pixel.
static java.lang.String	ftTempDirectory()
static java.lang.String	ftTrainDirectory()
static java.lang.String	ftUnseenDirectory()
static java.lang.String	getBase()
static java.lang.String	getBasename(java.lang.String cname) Get the name of the original file that was observed for name.
static java.lang.String[]	getBasenames(java.lang.String directory) Return a list of all unique basenames in directory.
static java.lang.String[]	getBasenamesFromFile() Return a list of basenames coming from a file in TEXT format.
static java.lang.String[]	getBasenamesFromFile(java.lang.String directory, java.lang.String fileName) Return a list of basenames coming from a file in TEXT format.
static java.lang.String	getBaseNoExtension(java.lang.String basename) Get the name of the original file that was observed for name,.
static java.lang.String[]	getFeaturenames() Return a list of all feature files in directory.
static java.lang.String[]	getFilenames(java.lang.String directory)
static int	getGroundTruthObserverIndex(java.lang.String name) Get the index of the observer that observed file name.
static ij.ImagePlus	getImagePlus(java.lang.String directory, java.lang.String name) Read image file with name making sure it is a JPEG, TIFF or JPS image.
static ij.process.ImageProcessor	getLeftProcessor(ij.process.ImageProcessor ip) Get the left half of an image that contains a stereo pair.
static ij.ImagePlus	getObservationImagePlus(java.lang.String basename, int observer) Get the image that is the observation by observer of the image basename.
static java.lang.String[]	getObservationnames(java.lang.String directory) Return a list of all observation stack files in directory.
static int[]	getObservers() Get the number of observers that made ground truth files in directory.
static java.awt.geom.Point2D.Float[]	getPointsFromFile(java.lang.String directory, java.lang.String filename)
static ij.process.ImageProcessor	getRightProcessor(ij.process.ImageProcessor ip) Get the left half of an image that contains a stereo pair.
static ij.ImagePlus	getStereoPairImagePlus(java.lang.String basename) Return an ImagePlus for the sterep pair (single image) in directory with basename.
static java.lang.String	imageDirectory()
static boolean	isGroundTruthBackground(java.awt.Color pixel)
static boolean	isGroundTruthCup(java.awt.Color pixel) Cups are somewhat *&%$&^ yellowish, i.e., G >= 253 and B < = 5.
static boolean	isGroundTruthDisk(java.awt.Color pixel) Disks are somewhat *&%$&^ red, i.e..
static boolean	isOD(java.lang.String name)
static boolean	isOS(java.lang.String name)
static double	lcdr(float[] v) Calculate linear cup to disc ratio for a float image.
static ij.process.ImageProcessor	loadImage(java.lang.String directory, java.lang.String name, int i) Load an image from directory/filename
static ij.ImageStack	loadImageStack(java.lang.String directory, java.lang.String name) Load an image stack from directory/filename
static java.lang.String	makeFeaturesName(java.lang.String basename) Make a features filename for basename.
static java.lang.String	makeFeaturesName(java.lang.String directory, java.lang.String basestart) Make a features filename for a basename that starts with basestart.
static java.lang.String	makeGroundTruthName(java.lang.String basename) Make a ground truth filename for basename.
static java.lang.String	makeStereoPairName(java.lang.String basename) Make a stereopair filename for basename.
static java.lang.String	obsCompiledDirectory()
static java.lang.String	obsDirectory()
static java.lang.String	resultsDirectory()
static double	rre(float[] rs, float[] obs) Calculate relative rim error (rimn = class 1).
static java.lang.String	rsDirectory()
static void	setBase(java.lang.String b)
static java.lang.String	slidesDirectory()
static java.lang.String	stacksDirectory()
static void	useArgs(java.lang.String[] args, java.lang.String exename)
static void	useBase(java.lang.String b)

Methods inherited from class java.lang.Object

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

Field Detail

rsName

public static final java.lang.String rsName

See Also:

Constant Field Values

reportName

public static final java.lang.String reportName

See Also:

Constant Field Values

classificationName

public static final java.lang.String classificationName

See Also:

Constant Field Values

Constructor Detail

Conventions

public Conventions()

Method Detail

useArgs

public static void useArgs(java.lang.String[] args,
                           java.lang.String exename)

useBase

public static void useBase(java.lang.String b)

getBase

public static java.lang.String getBase()

setBase

public static void setBase(java.lang.String b)

resultsDirectory

public static java.lang.String resultsDirectory()

rsDirectory

public static java.lang.String rsDirectory()

ftTrainDirectory

public static java.lang.String ftTrainDirectory()

ftUnseenDirectory

public static java.lang.String ftUnseenDirectory()

ftTempDirectory

public static java.lang.String ftTempDirectory()

clsDirectory

public static java.lang.String clsDirectory()

obsDirectory

public static java.lang.String obsDirectory()

obsCompiledDirectory

public static java.lang.String obsCompiledDirectory()

imageDirectory

public static java.lang.String imageDirectory()

slidesDirectory

public static java.lang.String slidesDirectory()

stacksDirectory

public static java.lang.String stacksDirectory()

getFilenames

public static java.lang.String[] getFilenames(java.lang.String directory)

lcdr

public static double lcdr(float[] v)

Calculate linear cup to disc ratio for a float image. Requires cup pixels to be 2 and rim pixels 1.

rre

public static double rre(float[] rs,
                         float[] obs)

Calculate relative rim error (rimn = class 1). Determine all pixels in rs that have class 1 and do not have class 1 in obs.

Parameters:

rs - float[]

obs - float[]

Returns:

double

getBasenamesFromFile

public static java.lang.String[] getBasenamesFromFile()
                                               throws java.lang.Exception

Return a list of basenames coming from a file in TEXT format.

Returns:

a String[] with the s.

Throws:

java.lang.Exception

getBasenamesFromFile

public static java.lang.String[] getBasenamesFromFile(java.lang.String directory,
                                                      java.lang.String fileName)
                                               throws java.lang.Exception

Return a list of basenames coming from a file in TEXT format.

Returns:

a String[] with the s.

Throws:

java.lang.Exception

getBasenames

public static java.lang.String[] getBasenames(java.lang.String directory)

Return a list of all unique basenames in directory. In the directory there can be multiple variations on , for example observations and ground truth files, which all have the same

Returns:

a String[] with the s.

getFeaturenames

public static java.lang.String[] getFeaturenames()
                                          throws java.io.IOException

Return a list of all feature files in directory. Chop off the fts- part.

Returns:

a String[] with the s.

Throws:

java.io.IOException

getObservationnames

public static java.lang.String[] getObservationnames(java.lang.String directory)

Return a list of all observation stack files in directory. The observation files have the format obs-.

Returns:

a String[] with all obs-.

isGroundTruthCup

public static boolean isGroundTruthCup(java.awt.Color pixel)

Cups are somewhat *&%$&^ yellowish, i.e., G >= 253 and B < = 5.

isGroundTruthDisk

public static boolean isGroundTruthDisk(java.awt.Color pixel)

Disks are somewhat *&%$&^ red, i.e..

isGroundTruthBackground

public static boolean isGroundTruthBackground(java.awt.Color pixel)

getObservers

public static int[] getObservers()

Get the number of observers that made ground truth files in directory.

Returns:

the number of observers.

convertImageToResult

public static byte[] convertImageToResult(ij.process.ColorProcessor ip,
                                          int binning)

Convert a ColorProcessor with an image containing different colors for different classes into an array with 0...number of classes for each pixel. In this case, hardwired for three classes.

Returns:

a byte array with the class index for each pixel.

getGroundTruthObserverIndex

public static int getGroundTruthObserverIndex(java.lang.String name)

Get the index of the observer that observed file name. The format is -. where n is the number of the observer.

Returns:

n, -1 if no observer.

getBasename

public static java.lang.String getBasename(java.lang.String cname)

Get the name of the original file that was observed for name. The format is -. where n is the number of the observer, and a possible prefix "gt-".

Returns:

the base-name.

getBaseNoExtension

public static java.lang.String getBaseNoExtension(java.lang.String basename)

Get the name of the original file that was observed for name,. without extension. The format is -. where n is the number of the observer, and a possible prefix "gt-".

Returns:

the base-name.

getLeftProcessor

public static ij.process.ImageProcessor getLeftProcessor(ij.process.ImageProcessor ip)

Get the left half of an image that contains a stereo pair.

getRightProcessor

public static ij.process.ImageProcessor getRightProcessor(ij.process.ImageProcessor ip)

Get the left half of an image that contains a stereo pair.

makeGroundTruthName

public static java.lang.String makeGroundTruthName(java.lang.String basename)

Make a ground truth filename for basename. The format is ..

Returns:

..

makeFeaturesName

public static java.lang.String makeFeaturesName(java.lang.String basename)

Make a features filename for basename. The format is ..

Returns:

..

makeFeaturesName

public static java.lang.String makeFeaturesName(java.lang.String directory,
                                                java.lang.String basestart)

Make a features filename for a basename that starts with basestart. Usually basestart will be a number ex. 500, and then the feature filename "fts_500_xxx" will be returned. The format is ..

Returns:

., null if no name can be found.

makeStereoPairName

public static java.lang.String makeStereoPairName(java.lang.String basename)

Make a stereopair filename for basename. The format is ..

Returns:

..

getObservationImagePlus

public static ij.ImagePlus getObservationImagePlus(java.lang.String basename,
                                                   int observer)

Get the image that is the observation by observer of the image basename. The format is -. where n is the number of the observer. can be jpeg, jpg or tiff or tif.

Parameters:

directory - String

basename - String

observer - int

Returns:

ImagePlus normalized to OD.

getStereoPairImagePlus

public static ij.ImagePlus getStereoPairImagePlus(java.lang.String basename)

Return an ImagePlus for the sterep pair (single image) in directory with basename. Flips OS image to OD if necessary. must be jpeg, jpg or tiff or tif.

Parameters:

directory - String the directory from where to obtain the image

basename - String a name of the form od. etc.

Returns:

ImagePlus normalized to OD.

getImagePlus

public static ij.ImagePlus getImagePlus(java.lang.String directory,
                                        java.lang.String name)

Read image file with name making sure it is a JPEG, TIFF or JPS image. Normalize to OD image.

Parameters:

directory - String where the image file is located.

name - String the basename of the image file

Returns:

ImagePlus, if it was an OS image, will be OD.

isOD

public static boolean isOD(java.lang.String name)

isOS

public static boolean isOS(java.lang.String name)

getPointsFromFile

public static java.awt.geom.Point2D.Float[] getPointsFromFile(java.lang.String directory,
                                                              java.lang.String filename)
                                                       throws java.lang.Exception

Throws:

java.lang.Exception

loadImage

public static ij.process.ImageProcessor loadImage(java.lang.String directory,
                                                  java.lang.String name,
                                                  int i)

Load an image from directory/filename

Parameters:

directory -

name -

i -

Returns:

ImageProcessor containing desired image... or null

loadImageStack

public static ij.ImageStack loadImageStack(java.lang.String directory,
                                           java.lang.String name)

Load an image stack from directory/filename

Parameters:

directory -

name -

Returns:

ImageStack containing desired images... or null