java.lang.Object
ij.ImageStack
- Direct Known Subclasses:
VirtualStack
This class represents an expandable array of images.
- See Also:
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Field Summary
Fields -
Constructor Summary
ConstructorsConstructorDescriptionDefault constructor.ImageStack
(int width, int height) Creates a new, empty image stack.ImageStack
(int width, int height, int size) Creates a new, empty image stack with a capacity of 'size'.ImageStack
(int width, int height, ColorModel cm) Creates a new, empty image stack using the specified color model. -
Method Summary
Modifier and TypeMethodDescriptionvoid
Adds the image in 'ip' to the end of the stack.void
addSlice
(String sliceLabel, ImageProcessor ip) Adds the image in 'ip' to the end of the stack, setting the string 'sliceLabel' as the slice metadata.void
addSlice
(String sliceLabel, ImageProcessor ip, int n) Adds the image in 'ip' to the stack following slice 'n'.void
Adds an image in the form of a pixel array to the end of the stack.void
addUnsignedShortSlice
(String sliceLabel, Object pixels) Deprecated.Short images are always unsigned.Creates a float version of this stack.static ImageStack
create
(int width, int height, int depth, int bitdepth) Creates a new ImageStack.static ImageStack
Creates an ImageStack from an ImagePlus array.crop
(int x, int y, int z, int width, int height, int depth) Creates a new stack by cropping this one.void
Deletes the last slice in the stack.void
deleteSlice
(int n) Deletes the specified slice, where 1<=n<=nslices.void
drawSphere
(double radius, int xc, int yc, int zc) ExperimentalDuplicates this stack.int
Returns the bit depth (8=byte, 16=short, 24=RGB, 32=float).Returns this stack's color model.int
Object[]
Returns the stack as an array of 1D pixel arrays.getPixels
(int n) Returns the pixel array for the specified slice, where 1<=n<=nslices.getProcessor
(int n) Returns an ImageProcessor for the specified slice, where 1<=n<=nslices.getRoi()
getShortSliceLabel
(int n) Returns a shortened version (up to the first 60 characters or first newline), with the extension removed, of the specified slice label, or null if the slice does not have a label.getShortSliceLabel
(int n, int max) Returns a shortened version (up to the first 'max' characters or first newline), with the extension removed, of the specified slice label, or null if the slice does not have a label.int
getSize()
getSliceLabel
(int n) Returns the label of the specified slice, where 1<=n<=nslices.String[]
Returns the slice labels as an array of Strings.final double
getVoxel
(int x, int y, int z) Returns, as a double, the value of the specified voxel.float[]
getVoxels
(int x0, int y0, int z0, int w, int h, int d, float[] voxels) float[]
getVoxels
(int x0, int y0, int z0, int w, int h, int d, float[] voxels, int channel) int
getWidth()
boolean
isHSB()
Returns true if this is a 3-slice HSB stack.boolean
isHSB32()
Returns true if this is a 3-slice 32-bit HSB stack.boolean
isLab()
Returns true if this is a Lab stack.boolean
isRGB()
Returns true if this is a 3-slice, 8-bit RGB stack.boolean
Returns true if this is a virtual (disk resident) stack.void
setBitDepth
(int depth) Sets the bit depth (8=byte, 16=short, 24=RGB, 32=float).void
Assigns a new color model to this stack.void
setOptions
(String options) void
Assigns a pixel array to the specified slice, where 1<=n<=nslices.void
setProcessor
(ImageProcessor ip, int n) Assigns the pixel array of an ImageProcessor to the specified slice, where 1<=n<=nslices.void
void
setSliceLabel
(String label, int n) Sets the label of the specified slice, where 1<=n<=nslices.final void
setVoxel
(int x, int y, int z, double value) void
setVoxels
(int x0, int y0, int z0, int w, int h, int d, float[] voxels) Experimentalvoid
setVoxels
(int x0, int y0, int z0, int w, int h, int d, float[] voxels, int channel) Experimentalint
size()
Returns the number of slices in this stack.toString()
void
trim()
Frees memory by deleting a few slices from the end of the stack.void
update
(ImageProcessor ip) Updates this stack so its attributes, such as min, max, calibration table and color model, are the same as 'ip'.
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Field Details
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cTable
protected float[] cTable
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Constructor Details
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ImageStack
public ImageStack()Default constructor. -
ImageStack
public ImageStack(int width, int height) Creates a new, empty image stack. -
ImageStack
public ImageStack(int width, int height, int size) Creates a new, empty image stack with a capacity of 'size'. All 'size' slices and labels of this image stack are initially null. -
ImageStack
Creates a new, empty image stack using the specified color model.
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Method Details
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addSlice
Adds an image in the form of a pixel array to the end of the stack. -
addUnsignedShortSlice
Deprecated.Short images are always unsigned. -
addSlice
Adds the image in 'ip' to the end of the stack. -
addSlice
Adds the image in 'ip' to the end of the stack, setting the string 'sliceLabel' as the slice metadata. -
addSlice
Adds the image in 'ip' to the stack following slice 'n'. Adds the slice to the beginning of the stack if 'n' is zero. -
deleteSlice
public void deleteSlice(int n) Deletes the specified slice, where 1<=n<=nslices. -
deleteLastSlice
public void deleteLastSlice()Deletes the last slice in the stack. -
getWidth
public int getWidth() -
getHeight
public int getHeight() -
setRoi
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getRoi
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update
Updates this stack so its attributes, such as min, max, calibration table and color model, are the same as 'ip'. -
getPixels
Returns the pixel array for the specified slice, where 1<=n<=nslices. -
setPixels
Assigns a pixel array to the specified slice, where 1<=n<=nslices. -
getImageArray
Returns the stack as an array of 1D pixel arrays. Note that the size of the returned array may be greater than the number of slices currently in the stack, with unused elements set to null. -
size
public int size()Returns the number of slices in this stack. -
getSize
public int getSize() -
getSliceLabels
Returns the slice labels as an array of Strings. Note that the size of the returned array may be greater than the number of slices currently in the stack. Returns null if the stack is empty or the label of the first slice is null. -
getSliceLabel
Returns the label of the specified slice, where 1<=n<=nslices. Returns null if the slice does not have a label or 'n'; is out of range. For DICOM and FITS stacks, labels may contain header information. -
getShortSliceLabel
Returns a shortened version (up to the first 60 characters or first newline), with the extension removed, of the specified slice label, or null if the slice does not have a label. -
getShortSliceLabel
Returns a shortened version (up to the first 'max' characters or first newline), with the extension removed, of the specified slice label, or null if the slice does not have a label. -
setSliceLabel
Sets the label of the specified slice, where 1<=n<=nslices. -
getProcessor
Returns an ImageProcessor for the specified slice, where 1<=n<=nslices. Returns null if the stack is empty. -
setProcessor
Assigns the pixel array of an ImageProcessor to the specified slice, where 1<=n<=nslices. -
setColorModel
Assigns a new color model to this stack. -
getColorModel
Returns this stack's color model. May return null. -
isRGB
public boolean isRGB()Returns true if this is a 3-slice, 8-bit RGB stack. -
isHSB
public boolean isHSB()Returns true if this is a 3-slice HSB stack. -
isHSB32
public boolean isHSB32()Returns true if this is a 3-slice 32-bit HSB stack. -
isLab
public boolean isLab()Returns true if this is a Lab stack. -
isVirtual
public boolean isVirtual()Returns true if this is a virtual (disk resident) stack. This method is overridden by the VirtualStack subclass. -
trim
public void trim()Frees memory by deleting a few slices from the end of the stack. -
toString
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getVoxel
public final double getVoxel(int x, int y, int z) Returns, as a double, the value of the specified voxel. Throws an IndexOutOfBoundsException if x, y or z are beyond the stack limits. Use the ImagePlus.getStackIndex() method to convert a C,Z,T hyperstack position (one-based) into a z index (zero-based).- See Also:
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setVoxel
public final void setVoxel(int x, int y, int z, double value) -
getVoxels
public float[] getVoxels(int x0, int y0, int z0, int w, int h, int d, float[] voxels) -
getVoxels
public float[] getVoxels(int x0, int y0, int z0, int w, int h, int d, float[] voxels, int channel) -
setVoxels
public void setVoxels(int x0, int y0, int z0, int w, int h, int d, float[] voxels) Experimental -
setVoxels
public void setVoxels(int x0, int y0, int z0, int w, int h, int d, float[] voxels, int channel) Experimental -
drawSphere
public void drawSphere(double radius, int xc, int yc, int zc) Experimental -
getBitDepth
public int getBitDepth()Returns the bit depth (8=byte, 16=short, 24=RGB, 32=float). -
setBitDepth
public void setBitDepth(int depth) Sets the bit depth (8=byte, 16=short, 24=RGB, 32=float). -
create
Creates a new ImageStack.- Parameters:
width
- width in pixelsheight
- height in pixelsdepth
- number of imagesbitdepth
- 8, 16, 32 (float) or 24 (RGB)
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create
Creates an ImageStack from an ImagePlus array. -
duplicate
Duplicates this stack. -
crop
Creates a new stack by cropping this one. -
convertToFloat
Creates a float version of this stack. -
setOptions
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