icy.sequence

Class SequenceUtil

java.lang.Object

icy.sequence.SequenceUtil

public class SequenceUtil
extends java.lang.Object

Sequence utilities class.
You can find here tools to manipulate the sequence organization, its data type, its size...

Author:

Stephane

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	SequenceUtil.AddTHelper
static class	SequenceUtil.AddZHelper
static class	SequenceUtil.AdjustZTHelper
static class	SequenceUtil.MergeCHelper
static class	SequenceUtil.MergeTHelper
static class	SequenceUtil.MergeZHelper

Constructor Summary

Constructors

Constructor and Description
SequenceUtil()

Method Summary

Methods

Modifier and Type	Method and Description
static void	addT(Sequence sequence, int num) Add one or severals frames at position t.
static void	addT(Sequence sequence, int num, boolean copyLast) Add one or severals frames at position t.
static void	addT(Sequence sequence, int t, int num) Add one or severals frames at position t.
static void	addT(Sequence sequence, int t, int num, int copyLast) Add one or severals frames at position t.
static void	addZ(Sequence sequence, int num) Add one or severals slices at position z.
static void	addZ(Sequence sequence, int num, boolean copyLast) Add one or severals slices at position z.
static void	addZ(Sequence sequence, int z, int num) Add one or severals slices at position z.
static void	addZ(Sequence sequence, int z, int num, int copyLast) Add one or severals slices at position z.
static void	adjustZT(Sequence sequence, int newSizeZ, int newSizeT, boolean reverseOrder) Adjust Z and T dimension of the sequence.
static Sequence	concatC(Sequence[] sequences) Create and returns a new sequence by concatenating all given sequences on C dimension.
static Sequence	concatC(Sequence[] sequences, boolean fillEmpty, boolean rescale) Create and returns a new sequence by concatenating all given sequences on C dimension.
static Sequence	concatC(Sequence[] sequences, boolean fillEmpty, boolean rescale, ProgressListener pl) Create and returns a new sequence by concatenating all given sequences on C dimension.
static Sequence	concatC(Sequence[] sequences, int[] channels, boolean fillEmpty, boolean rescale, ProgressListener pl) Create and returns a new sequence by concatenating all given sequences on C dimension.
static Sequence	concatT(Sequence[] sequences) Create and returns a new sequence by concatenating all given sequences on T dimension.
static Sequence	concatT(Sequence[] sequences, boolean interlaced, boolean fillEmpty, boolean rescale) Create and returns a new sequence by concatenating all given sequences on T dimension.
static Sequence	concatT(Sequence[] sequences, boolean interlaced, boolean fillEmpty, boolean rescale, ProgressListener pl) Create and returns a new sequence by concatenating all given sequences on T dimension.
static Sequence	concatZ(Sequence[] sequences) Create and returns a new sequence by concatenating all given sequences on Z dimension.
static Sequence	concatZ(Sequence[] sequences, boolean interlaced, boolean fillEmpty, boolean rescale) Create and returns a new sequence by concatenating all given sequences on Z dimension.
static Sequence	concatZ(Sequence[] sequences, boolean interlaced, boolean fillEmpty, boolean rescale, ProgressListener pl) Create and returns a new sequence by concatenating all given sequences on Z dimension.
static Sequence	convertColor(Sequence source, int imageType, LUT lut) Do color conversion of the specified Sequence into the specified type.
static java.awt.geom.Point2D	convertPoint(java.awt.geom.Point2D pt, int inputResolution, int outputResolution) Convert the given Point2D coordinate from an input resolution and a wanted output resolution level (0/1/2/3/...)
static java.awt.geom.Point2D	convertPoint(java.awt.geom.Point2D pt, Sequence source, Sequence destination) Convert the given Point2D coordinate from the source Sequence to the destination Sequence.
static Point3D	convertPoint(Point3D pt, Sequence source, Sequence destination) Convert the given Point2D coordinate from the source Sequence to the destination Sequence.
static java.awt.geom.Rectangle2D	convertRectangle(java.awt.geom.Rectangle2D rect, int inputResolution, int outputResolution) Convert the given Rectangle2D from an input resolution and a wanted output resolution level (0/1/2/3/...)
static java.awt.geom.Rectangle2D	convertRectangle(java.awt.geom.Rectangle2D rect, Sequence source, Sequence destination) Convert the given Rectangle2D from the source Sequence to the destination Sequence.
static Rectangle3D	convertRectangle(Rectangle3D rect, Sequence source, Sequence destination) Convert the given Rectangle3D from the source Sequence to the destination Sequence.
static void	convertToStack(Sequence sequence) Set all images of the sequence in Z dimension.
static void	convertToTime(Sequence sequence) Set all images of the sequence in T dimension.
static Sequence	convertToType(Sequence source, DataType dataType, boolean rescale) Converts the source sequence to the specified data type.
static Sequence	convertToType(Sequence source, DataType dataType, boolean rescale, boolean useDataBounds) Converts the source sequence to the specified data type.
static Sequence	convertToType(Sequence source, DataType dataType, Scaler scaler) Deprecated. Use convertType(Sequence, DataType, Scaler[]) instead.
static void	convertToVolume(Sequence sequence) Deprecated. Use convertToStack(Sequence) instead.
static Sequence	convertType(Sequence source, DataType dataType, Scaler[] scalers) Converts the source sequence to the specified data type.
static Sequence	extractChannel(Sequence source, int channel) Build a new single channel sequence (grey) from the specified channel of the source sequence.
static Sequence	extractChannels(Sequence source, int... channels) Build a new sequence by extracting the specified channels from the source sequence.
static Sequence	extractChannels(Sequence source, java.util.List<java.lang.Integer> channels) Deprecated. Use extractChannels(Sequence, int...) instead.
static Sequence	extractFrame(Sequence source, int t) Build a new sequence by extracting the specified T frame from the source sequence.
static Sequence	extractSlice(Sequence source, int z) Build a new sequence by extracting the specified Z slice from the source sequence.
static Sequence	getCopy(Sequence source) Creates and return a copy of the sequence.
static Sequence	getCopy(Sequence source, boolean copyROI, boolean copyOverlay, boolean nameSuffix) Creates and return a copy of the sequence.
static int	getMaxDim(Sequence[] sequences, DimensionId dim) Returns the max size of specified dimension for the given sequences.
static java.awt.Point	getOriginPoint(java.awt.Point pt, Sequence source) Convert the given Point coordinate from the source Sequence into the original image coordinate (pixel) This method use the Sequence.getOriginResolution() and Sequence.getOriginXYRegion() informations to compute the original image position.
static java.awt.Rectangle	getOriginRectangle(java.awt.Rectangle rect, Sequence source) Convert the given Rectangle region from the source Sequence into the original image region coordinates (pixel) This method use the Sequence.getOriginResolution() and Sequence.getOriginXYRegion() informations to compute the original image region coordinates.
static Sequence	getSubSequence(Sequence source, int startX, int startY, int startZ, int startT, int sizeX, int sizeY, int sizeZ, int sizeT) Deprecated. Use getSubSequence(Sequence, icy.type.rectangle.Rectangle5D.Integer) instead.
static Sequence	getSubSequence(Sequence source, int startX, int startY, int startC, int startZ, int startT, int sizeX, int sizeY, int sizeC, int sizeZ, int sizeT) Deprecated. Use getSubSequence(Sequence, icy.type.rectangle.Rectangle5D.Integer) instead.
static Sequence	getSubSequence(Sequence source, Rectangle5D.Integer region) Creates a new sequence from the specified region of the source sequence.
static Sequence	getSubSequence(Sequence source, ROI roi) Creates a new sequence which is a sub part of the source sequence defined by the specified ROI bounds.
static Sequence	getSubSequence(Sequence source, ROI roi, double nullValue) Creates a new sequence which is a sub part of the source sequence defined by the specified ROI bounds.
static void	moveT(Sequence sequence, int t, int newT) Modify frame position.
static void	moveT(Sequence sequence, int from, int to, int offset) Modify T position of a range of frame by the specified offset
static void	moveZ(Sequence sequence, int z, int newZ) Modify slice position.
static void	moveZ(Sequence sequence, int from, int to, int offset) Modify Z position of a range of slice by the specified offset
static void	removeChannel(Sequence source, int channel) Remove the specified channel from the source sequence.
static void	removeT(Sequence sequence, int t) Remove a frame at position t.
static void	removeTAndShift(Sequence sequence, int t) Remove a frame at position t and shift all the further t by -1.
static void	removeZ(Sequence sequence, int z) Remove a slice at position Z.
static void	removeZAndShift(Sequence sequence, int z) Remove a slice at position t and shift all the further t by -1.
static void	reverseT(Sequence sequence) Reverse T frames order.
static void	reverseZ(Sequence sequence) Reverse Z slices order.
static Sequence	rotate(Sequence source, double angle) Return a rotated version of the source Sequence with specified parameters.
static Sequence	rotate(Sequence source, double xOrigin, double yOrigin, double angle, IcyBufferedImageUtil.FilterType filterType) Return a rotated version of the source sequence with specified parameters.
static Sequence	rotate(Sequence source, double angle, IcyBufferedImageUtil.FilterType filterType) Return a rotated version of the source Sequence with specified parameters.
static Sequence	scale(Sequence source, int width, int height) Return a copy of the sequence with specified size.
static Sequence	scale(Sequence source, int width, int height, boolean resizeContent, int xAlign, int yAlign) Return a copy of the sequence with specified size.
static Sequence	scale(Sequence source, int width, int height, boolean resizeContent, int xAlign, int yAlign, IcyBufferedImageUtil.FilterType filterType) Return a copy of the source sequence with specified size, alignment rules and filter type.
static Sequence	scale(Sequence source, int width, int height, IcyBufferedImageUtil.FilterType filterType) Return a copy of the sequence with specified size.
static void	swapT(Sequence sequence, int t1, int t2) Exchange 2 frames position on the sequence.
static void	swapZ(Sequence sequence, int z1, int z2) Exchange 2 slices position on the sequence.
static Sequence	toARGB(Sequence source) Convert the specified sequence to ARGB sequence (4 channels)
static Sequence	toGray(Sequence source) Convert the specified sequence to gray sequence (single channel)
static Sequence	toRGB(Sequence source) Convert the specified sequence to RGB sequence (3 channels)

Methods inherited from class java.lang.Object

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

Constructor Detail

SequenceUtil

public SequenceUtil()

Method Detail

addT

public static void addT(Sequence sequence,
        int t,
        int num,
        int copyLast)

Add one or severals frames at position t.

Parameters:

t - Position where to add frame(s)

num - Number of frame to add

copyLast - Number of last frame(s) to copy to fill added frames.
0 means that new frames are empty.
1 means we duplicate the last frame.
2 means we duplicate the two last frames.
and so on...

addT

public static void addT(Sequence sequence,
        int t,
        int num)

Add one or severals frames at position t.

Parameters:

t - Position where to add frame(s)

num - Number of frame to add

addT

public static void addT(Sequence sequence,
        int num)

Add one or severals frames at position t.

Parameters:

num - Number of frame to add

addT

public static void addT(Sequence sequence,
        int num,
        boolean copyLast)

Add one or severals frames at position t.

Parameters:

num - Number of frame to add

copyLast - If true then the last frame is copied in added frames.

swapT

public static void swapT(Sequence sequence,
         int t1,
         int t2)

Exchange 2 frames position on the sequence.

moveT

public static void moveT(Sequence sequence,
         int t,
         int newT)

Modify frame position.
The previous frame present at newT position is lost.

Parameters:

sequence -

t - current t position

newT - wanted t position

moveT

public static void moveT(Sequence sequence,
         int from,
         int to,
         int offset)

Modify T position of a range of frame by the specified offset

Parameters:

sequence -

from - start of range (t position)

to - end of range (t position)

offset - position shift

removeT

public static void removeT(Sequence sequence,
           int t)

Remove a frame at position t.

Parameters:

sequence -

t -

removeTAndShift

public static void removeTAndShift(Sequence sequence,
                   int t)

Remove a frame at position t and shift all the further t by -1.

Parameters:

sequence -

t -

reverseT

public static void reverseT(Sequence sequence)

Reverse T frames order.

addZ

public static void addZ(Sequence sequence,
        int z,
        int num,
        int copyLast)

Add one or severals slices at position z.

Parameters:

z - Position where to add slice(s)

num - Number of slice to add

copyLast - Number of last slice(s) to copy to fill added slices.
0 means that new slices are empty.
1 means we duplicate the last slice.
2 means we duplicate the two last slices.
and so on...

addZ

public static void addZ(Sequence sequence,
        int z,
        int num)

Add one or severals slices at position z.

Parameters:

z - Position where to add slice(s)

num - Number of slice to add

addZ

public static void addZ(Sequence sequence,
        int num)

Add one or severals slices at position z.

Parameters:

num - Number of slice to add

addZ

public static void addZ(Sequence sequence,
        int num,
        boolean copyLast)

Add one or severals slices at position z.

Parameters:

num - Number of slice to add

copyLast - If true then the last slice is copied in added slices.

swapZ

public static void swapZ(Sequence sequence,
         int z1,
         int z2)

Exchange 2 slices position on the sequence.

moveZ

public static void moveZ(Sequence sequence,
         int z,
         int newZ)

Modify slice position.
The previous slice present at newZ position is lost.

Parameters:

sequence -

z - current z position

newZ - wanted z position

moveZ

public static void moveZ(Sequence sequence,
         int from,
         int to,
         int offset)

Modify Z position of a range of slice by the specified offset

Parameters:

sequence -

from - start of range (z position)

to - end of range (z position)

offset - position shift

removeZ

public static void removeZ(Sequence sequence,
           int z)

Remove a slice at position Z.

Parameters:

sequence -

z -

removeZAndShift

public static void removeZAndShift(Sequence sequence,
                   int z)

Remove a slice at position t and shift all the further t by -1.

Parameters:

sequence -

z -

reverseZ

public static void reverseZ(Sequence sequence)

Reverse Z slices order.

convertToTime

public static void convertToTime(Sequence sequence)

Set all images of the sequence in T dimension.

convertToStack

public static void convertToStack(Sequence sequence)

Set all images of the sequence in Z dimension.

convertToVolume

@Deprecated
public static void convertToVolume(Sequence sequence)

Deprecated. Use convertToStack(Sequence) instead.

removeChannel

public static void removeChannel(Sequence source,
                 int channel)

Remove the specified channel from the source sequence.

Parameters:

source - Source sequence

channel - Channel index to remove

getMaxDim

public static int getMaxDim(Sequence[] sequences,
            DimensionId dim)

Returns the max size of specified dimension for the given sequences.

concatC

public static Sequence concatC(Sequence[] sequences,
               int[] channels,
               boolean fillEmpty,
               boolean rescale,
               ProgressListener pl)
                        throws java.lang.IllegalArgumentException

Create and returns a new sequence by concatenating all given sequences on C dimension.

Parameters:

sequences - Sequences to concatenate (use array order).

channels - Selected channel for each sequence (channels.length = sequences.length)
If you want to select 2 or more channels from a sequence, just duplicate the sequence entry in the sequences parameter :
sequences[n] = Sequence1; channels[n] = 0;
sequences[n+1] = Sequence1; channels[n+1] = 2;
...

fillEmpty - Replace empty image by the previous non empty one.

rescale - Images are scaled to all fit in the same XY dimension.

pl - ProgressListener to indicate processing progress.

Throws:

java.lang.IllegalArgumentException - if sequences contains incompatible sequence for merge operation.

concatC

public static Sequence concatC(Sequence[] sequences,
               boolean fillEmpty,
               boolean rescale,
               ProgressListener pl)

Create and returns a new sequence by concatenating all given sequences on C dimension.

Parameters:

sequences - Sequences to concatenate (use array order).

fillEmpty - Replace empty image by the previous non empty one.

rescale - Images are scaled to all fit in the same XY dimension.

pl - ProgressListener to indicate processing progress.

concatC

public static Sequence concatC(Sequence[] sequences,
               boolean fillEmpty,
               boolean rescale)

Create and returns a new sequence by concatenating all given sequences on C dimension.

Parameters:

sequences - Sequences to concatenate (use array order).

fillEmpty - Replace empty image by the previous non empty one.

rescale - Images are scaled to all fit in the same XY dimension.

concatC

public static Sequence concatC(Sequence[] sequences)

Create and returns a new sequence by concatenating all given sequences on C dimension.

Parameters:

sequences - Sequences to concatenate (use array order).

concatZ

public static Sequence concatZ(Sequence[] sequences,
               boolean interlaced,
               boolean fillEmpty,
               boolean rescale,
               ProgressListener pl)

Create and returns a new sequence by concatenating all given sequences on Z dimension.

Parameters:

sequences - Sequences to concatenate (use array order).

interlaced - Interlace images.
normal : 1,1,1,2,2,2,3,3,..
interlaced : 1,2,3,1,2,3,..

fillEmpty - Replace empty image by the previous non empty one.

rescale - Images are scaled to all fit in the same XY dimension.

pl - ProgressListener to indicate processing progress.

concatZ

public static Sequence concatZ(Sequence[] sequences,
               boolean interlaced,
               boolean fillEmpty,
               boolean rescale)

Create and returns a new sequence by concatenating all given sequences on Z dimension.

Parameters:

sequences - Sequences to concatenate (use array order).

interlaced - Interlace images.
normal : 1,1,1,2,2,2,3,3,..
interlaced : 1,2,3,1,2,3,..

fillEmpty - Replace empty image by the previous non empty one.

rescale - Images are scaled to all fit in the same XY dimension.

concatZ

public static Sequence concatZ(Sequence[] sequences)

Create and returns a new sequence by concatenating all given sequences on Z dimension.

Parameters:

sequences - Sequences to concatenate (use array order).

concatT

public static Sequence concatT(Sequence[] sequences,
               boolean interlaced,
               boolean fillEmpty,
               boolean rescale,
               ProgressListener pl)

Create and returns a new sequence by concatenating all given sequences on T dimension.

Parameters:

sequences - sequences to concatenate (use array order).

interlaced - interlace images.
normal : 1,1,1,2,2,2,3,3,..
interlaced : 1,2,3,1,2,3,..

fillEmpty - replace empty image by the previous non empty one.

rescale - Images are scaled to all fit in the same XY dimension.

pl - ProgressListener to indicate processing progress.

concatT

public static Sequence concatT(Sequence[] sequences,
               boolean interlaced,
               boolean fillEmpty,
               boolean rescale)

Create and returns a new sequence by concatenating all given sequences on T dimension.

Parameters:

sequences - Sequences to concatenate (use array order).

interlaced - Interlace images.
normal : 1,1,1,2,2,2,3,3,..
interlaced : 1,2,3,1,2,3,..

fillEmpty - Replace empty image by the previous non empty one.

rescale - Images are scaled to all fit in the same XY dimension.

concatT

public static Sequence concatT(Sequence[] sequences)

Create and returns a new sequence by concatenating all given sequences on T dimension.

Parameters:

sequences - Sequences to concatenate (use array order).

adjustZT

public static void adjustZT(Sequence sequence,
            int newSizeZ,
            int newSizeT,
            boolean reverseOrder)

Adjust Z and T dimension of the sequence.

Parameters:

reverseOrder - Means that images are T-Z ordered instead of Z-T ordered

newSizeZ - New Z size of the sequence

newSizeT - New T size of the sequence

extractChannel

public static Sequence extractChannel(Sequence source,
                      int channel)

Build a new single channel sequence (grey) from the specified channel of the source sequence.

Parameters:

source - Source sequence

channel - Channel index to extract from the source sequence.

Returns:

Sequence

extractChannels

@Deprecated
public static Sequence extractChannels(Sequence source,
                                  java.util.List<java.lang.Integer> channels)

Deprecated. Use extractChannels(Sequence, int...) instead.

extractChannels

public static Sequence extractChannels(Sequence source,
                       int... channels)

Build a new sequence by extracting the specified channels from the source sequence.

Parameters:

source - Source sequence

channels - Channel indexes to extract from the source sequence.

Returns:

Sequence

extractSlice

public static Sequence extractSlice(Sequence source,
                    int z)

Build a new sequence by extracting the specified Z slice from the source sequence.

Parameters:

source - Source sequence

z - Slice index to extract from the source sequence.

Returns:

Sequence

extractFrame

public static Sequence extractFrame(Sequence source,
                    int t)

Build a new sequence by extracting the specified T frame from the source sequence.

Parameters:

source - Source sequence

t - Frame index to extract from the source sequence.

Returns:

Sequence

convertToType

public static Sequence convertToType(Sequence source,
                     DataType dataType,
                     boolean rescale,
                     boolean useDataBounds)

Converts the source sequence to the specified data type.
This method returns a new sequence (the source sequence is not modified).

Parameters:

source - Source sequence to convert

dataType - Data type wanted

rescale - Indicate if we want to scale data value according to data (or data type) range

useDataBounds - Only used when rescale parameter is true.
Specify if we use the data bounds for rescaling instead of data type bounds.

Returns:

converted sequence

convertToType

public static Sequence convertToType(Sequence source,
                     DataType dataType,
                     boolean rescale)

Converts the source sequence to the specified data type.
This method returns a new sequence (the source sequence is not modified).

Parameters:

source - Source sequence to convert

dataType - data type wanted

rescale - indicate if we want to scale data value according to data type range

Returns:

converted sequence

convertToType

@Deprecated
public static Sequence convertToType(Sequence source,
                                DataType dataType,
                                Scaler scaler)

Deprecated. Use convertType(Sequence, DataType, Scaler[]) instead.

convertType

public static Sequence convertType(Sequence source,
                   DataType dataType,
                   Scaler[] scalers)

Converts the source sequence to the specified data type.
This method returns a new sequence (the source sequence is not modified).

Parameters:

source - Source sequence to convert

dataType - data type wanted.

scalers - scalers for scaling internal data during conversion (1 scaler per channel).
Can be set to null to avoid value conversion.

Returns:

converted image

rotate

public static Sequence rotate(Sequence source,
              double xOrigin,
              double yOrigin,
              double angle,
              IcyBufferedImageUtil.FilterType filterType)

Return a rotated version of the source sequence with specified parameters.

Parameters:

source - source image

xOrigin - X origin for the rotation

yOrigin - Y origin for the rotation

angle - rotation angle in radian

filterType - filter resampling method used

rotate

public static Sequence rotate(Sequence source,
              double angle,
              IcyBufferedImageUtil.FilterType filterType)

Return a rotated version of the source Sequence with specified parameters.

Parameters:

source - source image

angle - rotation angle in radian

filterType - filter resampling method used

rotate

public static Sequence rotate(Sequence source,
              double angle)

Return a rotated version of the source Sequence with specified parameters.

Parameters:

source - source image

angle - rotation angle in radian

scale

public static Sequence scale(Sequence source,
             int width,
             int height,
             boolean resizeContent,
             int xAlign,
             int yAlign,
             IcyBufferedImageUtil.FilterType filterType)

Return a copy of the source sequence with specified size, alignment rules and filter type.

Parameters:

source - source sequence

resizeContent - indicate if content should be resized or not (empty area are 0 filled)

xAlign - horizontal image alignment (SwingConstants.LEFT / CENTER / RIGHT)
(used only if resizeContent is false)

yAlign - vertical image alignment (SwingConstants.TOP / CENTER / BOTTOM)
(used only if resizeContent is false)

filterType - filter method used for scale (used only if resizeContent is true)

scale

public static Sequence scale(Sequence source,
             int width,
             int height,
             boolean resizeContent,
             int xAlign,
             int yAlign)

Return a copy of the sequence with specified size.
By default the FilterType.BILINEAR is used as filter method if resizeContent is true

Parameters:

source - source sequence

resizeContent - indicate if content should be resized or not (empty area are 0 filled)

xAlign - horizontal image alignment (SwingConstants.LEFT / CENTER / RIGHT)
(used only if resizeContent is false)

yAlign - vertical image alignment (SwingConstants.TOP / CENTER / BOTTOM)
(used only if resizeContent is false)

scale

public static Sequence scale(Sequence source,
             int width,
             int height,
             IcyBufferedImageUtil.FilterType filterType)

Return a copy of the sequence with specified size.

Parameters:

source - source sequence

filterType - filter method used for scale (used only if resizeContent is true)

scale

public static Sequence scale(Sequence source,
             int width,
             int height)

Return a copy of the sequence with specified size.
By default the FilterType.BILINEAR is used as filter method.

getSubSequence

public static Sequence getSubSequence(Sequence source,
                      Rectangle5D.Integer region)

Creates a new sequence from the specified region of the source sequence.

getSubSequence

@Deprecated
public static Sequence getSubSequence(Sequence source,
                                 int startX,
                                 int startY,
                                 int startC,
                                 int startZ,
                                 int startT,
                                 int sizeX,
                                 int sizeY,
                                 int sizeC,
                                 int sizeZ,
                                 int sizeT)

Deprecated. Use getSubSequence(Sequence, icy.type.rectangle.Rectangle5D.Integer) instead.

getSubSequence

@Deprecated
public static Sequence getSubSequence(Sequence source,
                                 int startX,
                                 int startY,
                                 int startZ,
                                 int startT,
                                 int sizeX,
                                 int sizeY,
                                 int sizeZ,
                                 int sizeT)

Deprecated. Use getSubSequence(Sequence, icy.type.rectangle.Rectangle5D.Integer) instead.

getSubSequence

public static Sequence getSubSequence(Sequence source,
                      ROI roi,
                      double nullValue)

Creates a new sequence which is a sub part of the source sequence defined by the specified ROI bounds.

Parameters:

source - the source sequence

roi - used to define to region to retain.

nullValue - the returned sequence is created by using the ROI rectangular bounds.
if nullValue is different of Double.NaN then any pixel outside the ROI region will be set to nullValue

getSubSequence

public static Sequence getSubSequence(Sequence source,
                      ROI roi)

Creates a new sequence which is a sub part of the source sequence defined by the specified ROI bounds.

getCopy

public static Sequence getCopy(Sequence source,
               boolean copyROI,
               boolean copyOverlay,
               boolean nameSuffix)

Creates and return a copy of the sequence.

Parameters:

source - the source sequence to copy

copyROI - Copy the ROI from source sequence.
Warning: by doing that the ROI will retain the result sequence as long the source sequence is alive.

copyOverlay - Copy the Overlay from source sequence.
Warning: by doing that the Overlay will retain the result sequence as long the source sequence is alive.

nameSuffix - add the suffix " (copy)" to the new Sequence name to distinguish it

getCopy

public static Sequence getCopy(Sequence source)

Creates and return a copy of the sequence.
Note that only data and metadata are copied, overlays and ROIs are not preserved.

toGray

public static Sequence toGray(Sequence source)

Convert the specified sequence to gray sequence (single channel)

toRGB

public static Sequence toRGB(Sequence source)

Convert the specified sequence to RGB sequence (3 channels)

toARGB

public static Sequence toARGB(Sequence source)

Convert the specified sequence to ARGB sequence (4 channels)

convertColor

public static Sequence convertColor(Sequence source,
                    int imageType,
                    LUT lut)

Do color conversion of the specified Sequence into the specified type.
The resulting Sequence will have 4, 3 or 1 channel(s) depending the selected type.

Parameters:

source - source sequence

imageType - wanted image type, only the following is accepted :
BufferedImage.TYPE_INT_ARGB (4 channels)
BufferedImage.TYPE_INT_RGB (3 channels)
BufferedImage.TYPE_BYTE_GRAY (1 channel)

lut - lut used for color calculation (source sequence lut is used if null)

convertPoint

public static java.awt.geom.Point2D convertPoint(java.awt.geom.Point2D pt,
                                 int inputResolution,
                                 int outputResolution)

Convert the given Point2D coordinate from an input resolution and a wanted output resolution level (0/1/2/3/...)

See Also:

Sequence.getOriginResolution()

convertRectangle

public static java.awt.geom.Rectangle2D convertRectangle(java.awt.geom.Rectangle2D rect,
                                         int inputResolution,
                                         int outputResolution)

Convert the given Rectangle2D from an input resolution and a wanted output resolution level (0/1/2/3/...)

See Also:

Sequence.getOriginResolution()

convertPoint

public static Point3D convertPoint(Point3D pt,
                   Sequence source,
                   Sequence destination)

Convert the given Point2D coordinate from the source Sequence to the destination Sequence.
It internally uses the Sequence.getPosition() and Sequence.getPixelSize() information to do the coordinate conversion.

convertPoint

public static java.awt.geom.Point2D convertPoint(java.awt.geom.Point2D pt,
                                 Sequence source,
                                 Sequence destination)

Convert the given Point2D coordinate from the source Sequence to the destination Sequence.
It internally uses the Sequence.getPosition() and Sequence.getPixelSize() information to do the coordinate conversion.

convertRectangle

public static Rectangle3D convertRectangle(Rectangle3D rect,
                           Sequence source,
                           Sequence destination)

Convert the given Rectangle3D from the source Sequence to the destination Sequence.
It internally uses the Sequence.getPosition() and Sequence.getPixelSize() information to do the coordinate conversion.

convertRectangle

public static java.awt.geom.Rectangle2D convertRectangle(java.awt.geom.Rectangle2D rect,
                                         Sequence source,
                                         Sequence destination)

Convert the given Rectangle2D from the source Sequence to the destination Sequence.
It internally uses the Sequence.getPosition() and Sequence.getPixelSize() information to do the coordinate conversion.

getOriginPoint

public static java.awt.Point getOriginPoint(java.awt.Point pt,
                            Sequence source)

Convert the given Point coordinate from the source Sequence into the original image coordinate (pixel)
This method use the Sequence.getOriginResolution() and Sequence.getOriginXYRegion() informations to compute the original image position.

See Also:

Sequence.getOriginResolution(), Sequence.getOriginXYRegion()

getOriginRectangle

public static java.awt.Rectangle getOriginRectangle(java.awt.Rectangle rect,
                                    Sequence source)

Convert the given Rectangle region from the source Sequence into the original image region coordinates (pixel)
This method use the Sequence.getOriginResolution() and Sequence.getOriginXYRegion() informations to compute the original image region coordinates.

See Also:

Sequence.getOriginResolution(), Sequence.getOriginXYRegion()