ome.api

Interface IProjection

All Superinterfaces:

ServiceInterface

All Known Implementing Classes:

ProjectionBean

public interface IProjection
extends ServiceInterface

Provides methods for performing projections of Pixels sets.

Since:

3.0

Version:

3.0

Author:

Chris Allan callan@blackcat.ca

Field Summary

Fields

Modifier and Type	Field and Description
static int	MAXIMUM_INTENSITY Maximum intensity projection (MIP)
static int	MEAN_INTENSITY Mean intensity projection
static String[]	METHODOLOGY_STRINGS Methodology strings
static int	SUM_INTENSITY Sum intensity projection

Method Summary

Modifier and Type	Method and Description
long	projectPixels(long pixelsId, PixelsType pixelsType, int algorithm, int tStart, int tEnd, List<Integer> channels, int stepping, int zStart, int zEnd, String name) Performs a projection through selected optical sections and optical sections for a given set of time points of a Pixels set.
byte[]	projectStack(long pixelsId, PixelsType pixelsType, int algorithm, int timepoint, int channelIndex, int stepping, int start, int end) Performs a projection through the optical sections of a particular wavelength at a given time point of a Pixels set.

Field Detail

MAXIMUM_INTENSITY

static final int MAXIMUM_INTENSITY

Maximum intensity projection (MIP)

See Also:

Constant Field Values

MEAN_INTENSITY

static final int MEAN_INTENSITY

Mean intensity projection

See Also:

Constant Field Values

SUM_INTENSITY

static final int SUM_INTENSITY

Sum intensity projection

See Also:

Constant Field Values

METHODOLOGY_STRINGS

static final String[] METHODOLOGY_STRINGS

Methodology strings

Method Detail

projectStack

byte[] projectStack(long pixelsId,
                    PixelsType pixelsType,
                    int algorithm,
                    int timepoint,
                    int channelIndex,
                    int stepping,
                    int start,
                    int end)

Performs a projection through the optical sections of a particular wavelength at a given time point of a Pixels set.

Parameters:

pixelsId - The source Pixels set Id.

pixelsType - The destination Pixels type. If null, the source Pixels set pixels type will be used.

algorithm - MAXIMUM_INTENSITY, MEAN_INTENSITY or SUM_INTENSITY. NOTE: When performing a SUM_INTENSITY projection, pixel values will be pinned to the maximum pixel value of the destination Pixels type.

timepoint - Timepoint to perform the projection.

channelIndex - Index of the channel to perform the projection.

stepping - Stepping value to use while calculating the projection. For example, stepping=1 will use every optical section from start to end where stepping=2 will use every other section from start to end to perform the projection.

start - Optical section to start projecting from.

end - Optical section to finish projecting.

Returns:

A byte array of projected pixel values whose length is equal to the Pixels set sizeX * sizeY * bytesPerPixel in big-endian format.

Throws:

ValidationException - Where:

• algorithm is unknown
• timepoint is out of range
• channelIndex is out of range
• start is out of range
• end is out of range
• start > end
• the Pixels set qualified by pixelsId is unlocatable.

See Also:

projectPixels(long, PixelsType, int, int, int, List, int, int, int, String)

projectPixels

long projectPixels(long pixelsId,
                   PixelsType pixelsType,
                   int algorithm,
                   int tStart,
                   int tEnd,
                   List<Integer> channels,
                   int stepping,
                   int zStart,
                   int zEnd,
                   String name)

Performs a projection through selected optical sections and optical sections for a given set of time points of a Pixels set. The Image which is linked to the Pixels set will be copied using IPixels.copyAndResizeImage(long, Integer, Integer, Integer, Integer, List, String, boolean).

Parameters:

pixelsId - The source Pixels set Id.

pixelsType - The destination Pixels type. If null, the source Pixels set pixels type will be used.

algorithm - MAXIMUM_INTENSITY, MEAN_INTENSITY or SUM_INTENSITY. NOTE: When performing a SUM_INTENSITY projection, pixel values will be pinned to the maximum pixel value of the destination Pixels type.

tStart - Timepoint to start projecting from.

tEnd - Timepoint to finish projecting.

channels - List of the channel indexes to use while calculating the projection.

stepping - Stepping value to use while calculating the projection. For example, stepping=1 will use every optical section from start to end where stepping=2 will use every other section from start to end to perform the projection.

zStart - Optical section to start projecting from.

zEnd - Optical section to finish projecting.

name - Name for the newly created image. If null the name of the Image linked to the Pixels qualified by pixelsId will be used with a "Projection" suffix. For example, GFP-H2B Image of HeLa Cells will have an Image name of GFP-H2B Image of HeLa Cells Projection used for the projection.

Returns:

The Id of the newly created Image which has been projected.

Throws:

ValidationException - Where:

• algorithm is unknown
• tStart is out of range
• tEnd is out of range
• tStart > tEnd
• channels is null or has indexes out of range
• zStart is out of range
• zEnd is out of range
• zStart > zEnd
• the Pixels set qualified by pixelsId is unlocatable.

See Also:

projectStack(long, PixelsType, int, int, int, int, int start, int)