Package | Description |
---|---|
ij | |
ij.plugin | |
ij.plugin.filter | |
ij.process | |
ij.util | |
org.physimage |
Modifier and Type | Class and Description |
---|---|
class |
VirtualStack
This class represents an array of disk-resident images.
|
Modifier and Type | Method and Description |
---|---|
ImageStack |
ImageStack.convertToFloat()
Creates a float version of this stack.
|
static ImageStack |
ImageStack.create(int width,
int height,
int depth,
int bitdepth)
Creates a new ImageStack.
|
ImageStack |
ImagePlus.createEmptyStack()
Returns an empty image stack that has the same
width, height and color table as this image.
|
ImageStack |
ImageStack.crop(int x,
int y,
int z,
int width,
int height,
int depth)
Creates a new stack by cropping this one.
|
ImageStack |
ImageStack.duplicate()
Duplicates this stack.
|
ImageStack |
ImagePlus.getImageStack()
Returns the base image stack.
|
ImageStack |
ImagePlus.getStack()
Returns the image stack.
|
ImageStack |
VirtualStack.sortDicom(java.lang.String[] strings,
java.lang.String[] info,
int maxDigits) |
Modifier and Type | Method and Description |
---|---|
void |
ImagePlus.setStack(ImageStack stack)
Replaces the image with the specified stack and updates the display.
|
void |
ImagePlus.setStack(ImageStack stack,
int nChannels,
int nSlices,
int nFrames) |
void |
ImagePlus.setStack(java.lang.String title,
ImageStack newStack)
Replaces the image with the specified stack and updates
the display.
|
Constructor and Description |
---|
ImagePlus(java.lang.String title,
ImageStack stack)
Constructs an ImagePlus from a stack.
|
Modifier and Type | Class and Description |
---|---|
class |
AVI_Reader
ImageJ Plugin for reading an AVI file into an image stack
(one slice per video frame)
Restrictions and Notes:
- Only few formats supported:
- uncompressed 8 bit with palette (=LUT)
- uncompressed 8 & 16 bit grayscale
- uncompressed 24 & 32 bit RGB (alpha channel ignored)
- uncompressed 32 bit AYUV (alpha channel ignored)
- various YUV 4:2:2 and 4:2:0 compressed formats (i.e., formats with
full luminance resolution, but reduced chroma resolution
- png or jpeg-encoded individual frames.
|
class |
FileInfoVirtualStack
This plugin opens a multi-page TIFF file as a virtual stack.
|
class |
ListVirtualStack
This plugin opens images specified by list of file paths as a virtual stack.
|
Modifier and Type | Method and Description |
---|---|
ImageStack |
StackCombiner.combineHorizontally(ImageStack stack1,
ImageStack stack2) |
ImageStack |
StackCombiner.combineVertically(ImageStack stack1,
ImageStack stack2) |
ImageStack |
CanvasResizer.expandStack(ImageStack stackOld,
int wNew,
int hNew,
int xOff,
int yOff) |
static ImageStack |
Filters3D.filter(ImageStack stackorig,
int filter,
float vx,
float vy,
float vz) |
static ImageStack |
ChannelSplitter.getChannel(ImagePlus imp,
int c) |
ImageStack |
StackMaker.makeStack(ImageProcessor ip,
int w,
int h,
int b) |
ImageStack |
AVI_Reader.makeStack(java.lang.String path,
int firstFrame,
int lastFrame,
boolean isVirtual,
boolean convertToGray,
boolean flipVertical)
Create an ImageStack from an avi file with given path.
|
static ImageStack |
RGBStackMerge.mergeStacks(ImageStack red,
ImageStack green,
ImageStack blue,
boolean keepSource) |
ImageStack |
RGBStackMerge.mergeStacks(int w,
int h,
int d,
ImageStack red,
ImageStack green,
ImageStack blue,
boolean keep) |
ImageStack |
PGM_Reader.openFile(java.lang.String path) |
ImageStack |
DICOM_Sorter.sort(ImageStack stack) |
static ImageStack[] |
ChannelSplitter.splitRGB(ImageStack rgb,
boolean keepSource)
Splits the specified RGB stack into three 8-bit grayscale stacks.
|
ImageStack |
Straightener.straightenStack(ImagePlus imp,
Roi roi,
int width) |
Modifier and Type | Method and Description |
---|---|
ImageStack |
StackCombiner.combineHorizontally(ImageStack stack1,
ImageStack stack2) |
ImageStack |
StackCombiner.combineVertically(ImageStack stack1,
ImageStack stack2) |
ImagePlus |
RGBStackMerge.createComposite(int w,
int h,
int d,
ImageStack[] stacks,
boolean keep)
Deprecated; replaced by mergeChannels().
|
ImageStack |
CanvasResizer.expandStack(ImageStack stackOld,
int wNew,
int hNew,
int xOff,
int yOff) |
static ImageStack |
Filters3D.filter(ImageStack stackorig,
int filter,
float vx,
float vy,
float vz) |
static ImageStack |
RGBStackMerge.mergeStacks(ImageStack red,
ImageStack green,
ImageStack blue,
boolean keepSource) |
ImageStack |
RGBStackMerge.mergeStacks(int w,
int h,
int d,
ImageStack red,
ImageStack green,
ImageStack blue,
boolean keep) |
boolean |
StackReducer.showDialog(ImageStack stack) |
ImageStack |
DICOM_Sorter.sort(ImageStack stack) |
static ImageStack[] |
ChannelSplitter.splitRGB(ImageStack rgb,
boolean keepSource)
Splits the specified RGB stack into three 8-bit grayscale stacks.
|
Modifier and Type | Field and Description |
---|---|
ImageStack |
RGBStackSplitter.blue |
ImageStack |
RGBStackSplitter.green |
ImageStack |
RGBStackSplitter.red |
Modifier and Type | Method and Description |
---|---|
void |
Projector.getByteRow(ImageStack stack,
int x,
int y,
int z,
int width1,
int width2,
int[] line) |
void |
Projector.getRGBRow(ImageStack stack,
int x,
int y,
int z,
int width1,
int width2,
int[] line) |
void |
Projector.putByteRow(ImageStack stack,
int y,
int z,
int width,
int[] line) |
void |
Projector.putRGBRow(ImageStack stack,
int y,
int z,
int width,
int[] line) |
void |
RGBStackSplitter.split(ImageStack rgb,
boolean keepSource)
Deprecated; replaced by ChannelSplitter.splitRGB().
|
Modifier and Type | Method and Description |
---|---|
ImageStack |
StackProcessor.crop(int x,
int y,
int width,
int height)
Crops the stack to the specified rectangle.
|
ImageStack |
FHT.getComplexTransform()
Converts this FHT to a complex Fourier transform and returns it as a two slice stack.
|
ImageStack |
ColorProcessor.getHSBStack()
Returns an ImageStack with three 8-bit slices,
representing hue, saturation and brightness
|
ImageStack |
StackProcessor.resize(int newWidth,
int newHeight)
Creates a new stack with dimensions 'newWidth' x 'newHeight'.
|
ImageStack |
StackProcessor.resize(int newWidth,
int newHeight,
boolean averageWhenDownsizing) |
ImageStack |
StackProcessor.rotateLeft() |
ImageStack |
StackProcessor.rotateRight() |
Modifier and Type | Method and Description |
---|---|
void |
StackProcessor.copyBits(ImageStack src,
int xloc,
int yloc,
int mode) |
void |
StackProcessor.filter3D(ImageStack out,
float radx,
float rady,
float radz,
int zmin,
int zmax,
int filter)
3D filter using threads
|
Constructor and Description |
---|
StackProcessor(ImageStack stack)
Constructs a StackProcessor from a stack.
|
StackProcessor(ImageStack stack,
ImageProcessor ip)
Constructs a StackProcessor from a stack.
|
Modifier and Type | Method and Description |
---|---|
static ImageStack |
DicomTools.sort(ImageStack stack)
Sorts a DICOM stack by image number.
|
Modifier and Type | Method and Description |
---|---|
static double |
DicomTools.getVoxelDepth(ImageStack stack)
Calculates the voxel depth of the specified DICOM stack based
on the distance between the first and last slices.
|
static ImageStack |
DicomTools.sort(ImageStack stack)
Sorts a DICOM stack by image number.
|
Modifier and Type | Method and Description |
---|---|
static double[] |
JAH_Utils.getNormalizedZAxisProfile(Analyzer analyzer,
Calibration cal,
ImageStack stack,
Roi roi) |
static double[] |
JAH_Utils.getZAxisProfile(Analyzer analyzer,
Calibration cal,
ImageStack stack,
Roi roi) |
static ImagePlus |
JAH_Utils.makeBackgroundImage(ImageStack stack2,
ImagePlus dupe,
ImagePlus backgroundImage,
int firstIndex,
int lastIndex,
double thresholdToDropFrame) |
static ImagePlus |
JAH_Utils.makeBackgroundImageRolling(ImageStack stack2,
ImagePlus dupe,
ImagePlus backgroundImage,
int firstIndex,
int lastIndex,
int cursor) |
static ImagePlus |
JAH_Utils.makeBackgroundImageRolling(ImageStack stack2,
ImagePlus dupe,
ImagePlus backgroundImage,
int firstIndex,
int lastIndex,
int cursor,
double thresholdToDropFrame) |
static ImagePlus |
JAH_Utils.makeBackgroundImageRolling(ImageStack stack2,
ImagePlus dupe,
ImagePlus backgroundImage,
int firstIndex,
int lastIndex,
int cursor,
double thresholdToDropFrame,
boolean dontDropFrameByThreshold) |