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 (Internal version: $Rev: 1167 $ $Date: 2006-12-15 10:39:34 +0000 (Fri, 15 Dec 2006) $)
Author:
Chris Allan      callan@blackcat.ca

Field Summary
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
 long projectPixels(long pixelsId, ome.model.enums.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, ome.model.enums.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,
                    ome.model.enums.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()

projectPixels

long projectPixels(long pixelsId,
                   ome.model.enums.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().

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()


OmeroJava Api

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