icy.sequence

Class SequenceDataIterator

java.lang.Object

icy.sequence.SequenceDataIterator

All Implemented Interfaces:

DataIterator

public class SequenceDataIterator
extends java.lang.Object
implements DataIterator

Sequence data iterator.
This class permit to use simple iterator to read / write Sequence data
as double in XYCZT ([T[Z[C[Y[X}}]]]) dimension order.
Whatever is the internal DataType data is returned and set as double.
If the sequence size or type is modified during iteration the iterator becomes invalid and can exception can happen.

Author:

Stephane

Constructor Summary

Constructors

Constructor and Description
SequenceDataIterator(Sequence sequence) Create a new SequenceData iterator to iterate all data.
SequenceDataIterator(Sequence sequence, int z, int t, int c) Create a new SequenceData iterator to iterate data of specified channel.
SequenceDataIterator(Sequence sequence, int startX, int endX, int startY, int endY, int c, int z, int t) Deprecated. Use SequenceDataIterator(Sequence, Rectangle, int, int, int) instead
SequenceDataIterator(Sequence sequence, int startX, int endX, int startY, int endY, int startC, int endC, int startZ, int endZ, int startT, int endT) Deprecated. Use SequenceDataIterator(Sequence, Rectangle5D.Integer) instead
SequenceDataIterator(Sequence sequence, Rectangle5D.Integer bounds5D) Create a new SequenceData iterator to iterate data through the specified 5D region (inclusive).
SequenceDataIterator(Sequence sequence, java.awt.Rectangle XYBounds, int z, int t, int c) Create a new SequenceData iterator to iterate data through the specified dimensions (inclusive).
SequenceDataIterator(Sequence sequence, ROI roi) Create a new SequenceData iterator to iterate data through the specified ROI.
SequenceDataIterator(Sequence sequence, ROI roi, boolean inclusive) Create a new SequenceData iterator to iterate data through the specified ROI.
SequenceDataIterator(Sequence sequence, ROI roi, boolean inclusive, int z, int t, int c) Create a new SequenceData iterator to iterate data through the specified ROI.

Method Summary

Methods

Modifier and Type	Method and Description
boolean	done() Returns true if the iterator has no more elements.
void	flush() Ensure changed data are correctly saved back to original data source (should be called at the end)
double	get() Returns the current element in the iteration.
int	getPositionC() Return current C position.
int	getPositionT() Return current T position.
int	getPositionX() Return current X position.
int	getPositionY() Return current Y position.
int	getPositionZ() Return current Z position.
void	next() Pass to the next element.
void	reset() Reset iterator to initial position.
void	set(double value) Sets the current element in the iteration and pass to the next.

Methods inherited from class java.lang.Object

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

Constructor Detail

SequenceDataIterator

public SequenceDataIterator(Sequence sequence,
                    Rectangle5D.Integer bounds5D)

Create a new SequenceData iterator to iterate data through the specified 5D region (inclusive).

Parameters:

sequence - Sequence we want to iterate data from

bounds5D - the 5D rectangular region we want to iterate

SequenceDataIterator

public SequenceDataIterator(Sequence sequence,
                    java.awt.Rectangle XYBounds,
                    int z,
                    int t,
                    int c)

Create a new SequenceData iterator to iterate data through the specified dimensions (inclusive).

Parameters:

sequence - Sequence we want to iterate data from

XYBounds - XY region to iterate

z - Z position (stack) we want to iterate data

t - T position (time) we want to iterate data

c - C position (channel) we want to iterate data

SequenceDataIterator

@Deprecated
public SequenceDataIterator(Sequence sequence,
                               int startX,
                               int endX,
                               int startY,
                               int endY,
                               int startC,
                               int endC,
                               int startZ,
                               int endZ,
                               int startT,
                               int endT)

Deprecated. Use SequenceDataIterator(Sequence, Rectangle5D.Integer) instead

SequenceDataIterator

@Deprecated
public SequenceDataIterator(Sequence sequence,
                               int startX,
                               int endX,
                               int startY,
                               int endY,
                               int c,
                               int z,
                               int t)

Deprecated. Use SequenceDataIterator(Sequence, Rectangle, int, int, int) instead

SequenceDataIterator

public SequenceDataIterator(Sequence sequence,
                    int z,
                    int t,
                    int c)

Create a new SequenceData iterator to iterate data of specified channel.

Parameters:

sequence - Sequence we want to iterate data from

z - Z position (stack) we want to iterate data

t - T position (time) we want to iterate data

c - C position (channel) we want to iterate data

SequenceDataIterator

public SequenceDataIterator(Sequence sequence)

Create a new SequenceData iterator to iterate all data.

Parameters:

sequence - Sequence we want to iterate data from.

SequenceDataIterator

public SequenceDataIterator(Sequence sequence,
                    ROI roi,
                    boolean inclusive,
                    int z,
                    int t,
                    int c)

Create a new SequenceData iterator to iterate data through the specified ROI.

Parameters:

sequence - Sequence we want to iterate data from.

roi - ROI defining the region to iterate.

inclusive - If true then all partially contained (intersected) pixels in the ROI are included.

z - The specific Z position (slice) we want to iterate or -1 to iterate over the whole ROI Z dimension.

t - The specific T position (frame) we want to iterate or -1 to iterate over the whole ROI T dimension.

c - The specific C position (channel) we want to iterate or -1 to iterate over the whole ROI C dimension.

SequenceDataIterator

public SequenceDataIterator(Sequence sequence,
                    ROI roi,
                    boolean inclusive)

Create a new SequenceData iterator to iterate data through the specified ROI.

Parameters:

sequence - Sequence we want to iterate data from.

roi - ROI defining the region to iterate.

inclusive - If true then all partially contained (intersected) pixels in the ROI are included.

SequenceDataIterator

public SequenceDataIterator(Sequence sequence,
                    ROI roi)

Create a new SequenceData iterator to iterate data through the specified ROI.

Parameters:

sequence - Sequence we want to iterate data from.

roi - ROI defining the region to iterate.

Method Detail

reset

public void reset()

Description copied from interface: DataIterator

Reset iterator to initial position.

Specified by:

reset in interface DataIterator

next

public void next()

Description copied from interface: DataIterator

Pass to the next element.

Specified by:

next in interface DataIterator

done

public boolean done()

Description copied from interface: DataIterator

Returns true if the iterator has no more elements.

Specified by:

done in interface DataIterator

get

public double get()

Description copied from interface: DataIterator

Returns the current element in the iteration.

Specified by:

get in interface DataIterator

Returns:

the current element in the iteration.

set

public void set(double value)

Description copied from interface: DataIterator

Sets the current element in the iteration and pass to the next.

Specified by:

set in interface DataIterator

getPositionX

public int getPositionX()

Return current X position.

getPositionY

public int getPositionY()

Return current Y position.

getPositionC

public int getPositionC()

Return current C position.

getPositionZ

public int getPositionZ()

Return current Z position.

getPositionT

public int getPositionT()

Return current T position.

flush

public void flush()

Ensure changed data are correctly saved back to original data source (should be called at the end)