BIJutil

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bijnum
Class BIJutil

java.lang.Object
  bijnum.BIJutil

public class BIJutil
extends java.lang.Object
extends java.lang.Object

Constructor Summary
`BIJutil()`

Method Summary
`static void`	`addSlice(java.lang.String label, byte[] img, ij.ImageStack is)` Add an image to a ImageStack of FloatProcessors.
`static void`	`addSlice(java.lang.String label, float[] img, ij.ImageStack is)` Add an image to a ImageStack of FloatProcessors.
`static void`	`addSlice(java.lang.String label, ij.process.ImageProcessor ip, ij.ImageStack is)` Add an image to a ImageStack of FloatProcessors.
`static void`	`addSlice(java.lang.String label, int[] img, ij.ImageStack is)` Add an image to a ImageStack of FloatProcessors.
`static void`	`addSlice(java.lang.String label, short[] img, ij.ImageStack is)` Add an image to a ImageStack of FloatProcessors.
`static void`	`bin(double[] x, int binwidth)` Bin a vector x.
`static float[]`	`center(float[] image0, int width0, float[] image1, int width1, float scaling)` Center a scaled image1 into the center of a larger image0.
`static float[]`	`center(float[] image0, int width0, float[] image1, int width1, float scaling, int offset_x, int offset_y)` Center a scaled image1 into the center of a larger image0 with offset offset_x and offset_y.
`static float[]`	`crop(float[] image, int width, int height, int x, int y, int newwidth, int newheight)` Crop a float image to the rectangular size of a ROI defined by x,y,newwidth,newheight
`static byte[]`	`fit(byte[] image, int width)` Fit a byte image into a new power of 2 size image of newwidth * newwidth.
`static float[]`	`fit(float[] image, int width)` Fit a float image into a new power of 2 size image of newwidth * newwidth.
`static float[]`	`fit(float[] spectrum, int width, int height)` Fit a square image into a smaller image widthxheight, with the center in the center of the new image.
`static float[]`	`getMask(ij.gui.Roi roi, int width, int height)` Make a mask within an image widthxheight for Roi.
`static int`	`getMatrixWidth(ij.ImagePlus imp)` Compute the width of the images in imp, or the ROI if one has been selected.
`static int`	`getMatrixWidth(ij.ImagePlus imp, double scaleFactor)` Compute the width of the images in imp, containing a stack, including scaling.
`static ij.ImageStack`	`imageStackFromMatrix(float[][] a, int width)` Create an ImageJ ImageStack out of a float matrix.
`static ij.ImageStack`	`imageStackFromMatrix(short[][] a, int width)` Create an ImageJ ImageStack out of a float matrix.
`static float[]`	`makePower2(float[] v)` Mirror a vector so that is has power of 2 length and does not contain extra edges.
`static float[][]`	`matrixFromImageStack(ij.ImagePlus imp)` Convert the data in the ImageStack in imp into a float[][] matrix for further processing.
`static float[][]`	`matrixFromImageStack(ij.ImagePlus imp, double scaleFactor)` Convert the data in the ImageStack in imp into a float[][] matrix and scale by scaleFactor on the fly.
`static float[][]`	`matrixFromImageStack(ij.ImageStack is)` Access the data in the ImageStack in imp into a float[][] matrix for further processing.
`static float[][]`	`matrixFromImageStackRoi(ij.ImagePlus imp)` Convert the data only within the rectangular Roi in the ImageStack in imp into a float[][] matrix for further processing.
`static int`	`minPower2(int n)` Find the minimal power of 2 that is larger than n.
`static float[]`	`montage(float[][] a, int awidth, int columns)` Make a montage of all images in a, with columns images per row, so that the width of the returned image will be awidth*columns.
`static boolean`	`saveAsText(float[] v, java.lang.String path)` Save vector v as a text file.
`static boolean`	`saveImagePlusAsTiff(java.lang.String directory, java.lang.String name, ij.ImagePlus imp)`
`static boolean`	`saveImageStackAsTiff(java.lang.String directory, java.lang.String name, ij.ImageStack is)`
`static short[][]`	`shortMatrixFromImageStack(ij.ImagePlus imp)` Convert the data in the ImageStack in imp into a short [][] matrix for further processing.
`static ij.ImagePlus`	`showVectorAsImage(float[] v, int width)`
`static float[]`	`tile(float[] image, int width)` Fit an image into a new image of newwidth * newwidth, where newwidth is next large power of 2 than width.
`static byte[]`	`toByte(float[] img)`
`static float[]`	`tofloat(byte[] v)`
`static float[]`	`tofloat(double[] v)`
`static float[]`	`tofloat(int[] v)`
`static java.lang.String`	`toString(double[] m)`
`static java.lang.String`	`toString(double[][] m)`
`static java.lang.String`	`toString(float[] m)`
`static java.lang.String`	`toString(float[][] m)`
`static java.lang.String`	`toString(int[][] m)`
`static float[]`	`vectorFromImageStack(ij.ImagePlus imp, int i)` Convert the data in the ImagePlus image stack into a float[] vector for further processing.
`static float[]`	`vectorFromImageStack(ij.ImagePlus imp, int i, float scaleFactor)` Convert the data in the ImageStack in imp into a float[][] matrix and scale by scaleFactor on the fly.
`static float[]`	`vectorFromImageStackRoi(ij.ImagePlus imp)` Convert the data in the i'th ImagePlus image into a float[] vector for further processing.
`static float[]`	`vectorFromImageStackRoi(ij.ImagePlus imp, int i)` Convert the data in the i'th ImagePlus image into a float[] vector for further processing.

Methods inherited from class java.lang.Object
`equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait`

Constructor Detail

BIJutil

public BIJutil()

Method Detail

imageStackFromMatrix

public static ij.ImageStack imageStackFromMatrix(float[][] a,
                                                 int width)

Create an ImageJ ImageStack out of a float matrix. width is the width of each image.

Parameters:: a - a float[][] matrix with the images as column vectors.; width - the width of each image in pixels.
Returns:: an ImageStack.

imageStackFromMatrix

public static ij.ImageStack imageStackFromMatrix(short[][] a,
                                                 int width)

Create an ImageJ ImageStack out of a float matrix. width is the width of each image.

Parameters:: a - a float[][] matrix with the images as column vectors.; width - the width of each image in pixels.
Returns:: an ImageStack.

getMatrixWidth

public static int getMatrixWidth(ij.ImagePlus imp)

Compute the width of the images in imp, or the ROI if one has been selected.

Returns:: the width of the images in imp.

getMatrixWidth

public static int getMatrixWidth(ij.ImagePlus imp,
                                 double scaleFactor)

Compute the width of the images in imp, containing a stack, including scaling.

Parameters:: scaleFactor - the scaling factor.
Returns:: the width of the images in imp.

matrixFromImageStack

public static float[][] matrixFromImageStack(ij.ImagePlus imp)

Convert the data in the ImageStack in imp into a float[][] matrix for further processing. Do not use ROI. Uses getFloatPixels(ipp.getPixels()), which converts 16-bit images to

Returns:: a float[][] with the images.

matrixFromImageStack

public static float[][] matrixFromImageStack(ij.ImageStack is)

Access the data in the ImageStack in imp into a float[][] matrix for further processing. Do not use ROI. If the is contains float images, does not convert and the float[][] are the actual pixels. If not, the float[][] are copies of whatever is in the is. Uses getFloatPixels(ipp.getPixels()), which converts 16-bit images to

Returns:: a float[][] with the images.

showVectorAsImage

public static ij.ImagePlus showVectorAsImage(float[] v,
                                             int width)

vectorFromImageStack

public static float[] vectorFromImageStack(ij.ImagePlus imp,
                                           int i)

Convert the data in the ImagePlus image stack into a float[] vector for further processing. Do not use ROI.

Parameters:: imp - the imageplus containing the stack.; i - the image number in the stack, starting with 0.
Returns:: a float[] with the image as a vector.

vectorFromImageStack

public static float[] vectorFromImageStack(ij.ImagePlus imp,
                                           int i,
                                           float scaleFactor)

Convert the data in the ImageStack in imp into a float[][] matrix and scale by scaleFactor on the fly. Do not use Roi.

Parameters:: imp - the imageplus containing the stack.; i - the image number in the stack, starting with 0.; scaleFactor - the scaling factor.
Returns:: a float[] with the image as a vector.

vectorFromImageStackRoi

public static float[] vectorFromImageStackRoi(ij.ImagePlus imp)

Convert the data in the i'th ImagePlus image into a float[] vector for further processing. Use ROI if present.

Returns:: a float[] with the image.

vectorFromImageStackRoi

public static float[] vectorFromImageStackRoi(ij.ImagePlus imp,
                                              int i)

Convert the data in the i'th ImagePlus image into a float[] vector for further processing. Use ROI if present.

Returns:: a float[] with the image.

crop

public static float[] crop(float[] image,
                           int width,
                           int height,
                           int x,
                           int y,
                           int newwidth,
                           int newheight)

Crop a float image to the rectangular size of a ROI defined by x,y,newwidth,newheight

Parameters:: image - a float[] vector image; width - the width in pixels of image; height - the width in pixels of image; x, - y, newwidth, newheight the ROI
Returns:: the cropped image as a float[].

matrixFromImageStack

public static float[][] matrixFromImageStack(ij.ImagePlus imp,
                                             double scaleFactor)

Convert the data in the ImageStack in imp into a float[][] matrix and scale by scaleFactor on the fly. Do not use Roi.

Parameters:: imp - an ImagePlus; scaleFactor - the scalefactor between 100-0.01.
Returns:: a float[][] with the images.

matrixFromImageStackRoi

public static float[][] matrixFromImageStackRoi(ij.ImagePlus imp)

Convert the data only within the rectangular Roi in the ImageStack in imp into a float[][] matrix for further processing.

Returns:: a float[][] with the images. The size of the resulting aray may not conform to that of the imp because it corresponds to the Roi size.

shortMatrixFromImageStack

public static short[][] shortMatrixFromImageStack(ij.ImagePlus imp)

Convert the data in the ImageStack in imp into a short [][] matrix for further processing.

Returns:: a short[][] with the images.

montage

public static float[] montage(float[][] a,
                              int awidth,
                              int columns)

Make a montage of all images in a, with columns images per row, so that the width of the returned image will be awidth*columns. Uses ImageJ library to include lettering etc.

Parameters:: a - a float[][] with the images.; awidth, - the width of each image in pixels.; columns - the number of columns desired.
Returns:: a float[] image containing the montage.

minPower2

public static int minPower2(int n)

Find the minimal power of 2 that is larger than n.

Returns:: the minimal power of 2 that larger than n.

bin

public static void bin(double[] x,
                       int binwidth)

Bin a vector x. By binning is meant add consecutive elements i...i+binwidth and put into elements i...i+binwidth.

makePower2

public static float[] makePower2(float[] v)

Mirror a vector so that is has power of 2 length and does not contain extra edges.

tile

public static float[] tile(float[] image,
                           int width)

Fit an image into a new image of newwidth * newwidth, where newwidth is next large power of 2 than width. The image is centered in the center of the new image and mirrored at the edges to avoid edge artifacts.

Parameters:: image - a float[] with the image; width - the width of image.
Returns:: a float[] with a new tiled image newwidthxnewheight.

fit

public static float[] fit(float[] image,
                          int width)

Fit a float image into a new power of 2 size image of newwidth * newwidth. The image is centered in the center of the new image and NOT mirrored

Parameters:: image - a float[] with the image; width - the width of image.
Returns:: a float[] with a new square image newwidthxnewheight.

fit

public static float[] fit(float[] spectrum,
                          int width,
                          int height)

Fit a square image into a smaller image widthxheight, with the center in the center of the new image.

Parameters:: spectrum - a square image vector.; width - the width in pixels of the new image.; height - the height of the new image.
Returns:: the centered resize spectrum.

fit

public static byte[] fit(byte[] image,
                         int width)

Fit a byte image into a new power of 2 size image of newwidth * newwidth. The image is centered in the center of the new image and NOT mirrored

Parameters:: image - a byte[] with the image; width - the width of image.
Returns:: a byte[] with a new square image newwidthxnewheight.

getMask

public static float[] getMask(ij.gui.Roi roi,
                              int width,
                              int height)

Make a mask within an image widthxheight for Roi. All pixels within Roi will be 1, all others 0. March 2004, update to conform to ImageJ 1.32e and higher, where getMask returns a ByteProcessor.

Parameters:: roi - the roi.; width - the width of the mask.; height - the height of the mask.
Returns:: a float[] containing the mask bytes.

center

public static float[] center(float[] image0,
                             int width0,
                             float[] image1,
                             int width1,
                             float scaling)

Center a scaled image1 into the center of a larger image0. The original image0 will not be modified.

Parameters:: image0 - the base image; width0 - the width in pixels of the base image; image1 - the image to be inserted; width1 - the width in pixels of the new image; scaling - the amount by which image1 will be scaled.
Returns:: a new image of the same size as image0.

center

public static float[] center(float[] image0,
                             int width0,
                             float[] image1,
                             int width1,
                             float scaling,
                             int offset_x,
                             int offset_y)

Center a scaled image1 into the center of a larger image0 with offset offset_x and offset_y. The original image0 will not be modified.

Parameters:: image0 - the base image; width0 - the width in pixels of the base image; image1 - the image to be inserted; width1 - the width in pixels of the new image; scaling - the amount by which image1 will be scaled.
Returns:: a new image of the same size as image0.

saveAsText

public static boolean saveAsText(float[] v,
                                 java.lang.String path)

Save vector v as a text file. Tab separated.

Parameters:: v - the float[] vector; path - a String with the path to save the vector to.
Returns:: true if succesful, false if Exception.

tofloat

public static float[] tofloat(double[] v)

tofloat

public static float[] tofloat(byte[] v)

tofloat

public static float[] tofloat(int[] v)

toString

public static java.lang.String toString(float[][] m)

toString

public static java.lang.String toString(double[][] m)

toString

public static java.lang.String toString(int[][] m)

toString

public static java.lang.String toString(float[] m)

toString

public static java.lang.String toString(double[] m)

saveImageStackAsTiff

public static boolean saveImageStackAsTiff(java.lang.String directory,
                                           java.lang.String name,
                                           ij.ImageStack is)

saveImagePlusAsTiff

public static boolean saveImagePlusAsTiff(java.lang.String directory,
                                          java.lang.String name,
                                          ij.ImagePlus imp)