omero.api

Interface _RawPixelsStoreOperationsNC

All Superinterfaces:

_PyramidServiceOperationsNC, _ServiceInterfaceOperationsNC, _StatefulServiceInterfaceOperationsNC

All Known Subinterfaces:

RawPixelsStore

All Known Implementing Classes:

_RawPixelsStoreDisp, _RawPixelsStoreTie, BfPixelsStoreI

public interface _RawPixelsStoreOperationsNC
extends _PyramidServiceOperationsNC

Binary data provider. Initialized with the ID of a Pixels instance, this service can provide various slices, stacks, regions of the 5-dimensional (X-Y planes with multiple Z-sections and Channels over Time). The byte array returned by the getter methods and passed to the setter methods can and will be interpreted according to results of getByteWidth, isFloat, and isSigned.

Read-only caveat: Mutating methods (set*) are only available during the first access. Once the Pixels data has been successfully saved (via the save or close methods on this interface), then the data should be treated read-only. If Pixels data writing fails and the service is inadvertently closed, delete the Pixels object, and create a new one. Any partially written data will be removed.

Method Summary

Modifier and Type	Method and Description
void	calculateMessageDigest_async(AMD_RawPixelsStore_calculateMessageDigest __cb) Calculates a SHA-1 message digest for the entire pixel store.
void	findMinMax_async(AMD_RawPixelsStore_findMinMax __cb, int[] channels) Find the minimum and maximum pixel values for the specified channels by iterating over a full plane.
void	getByteWidth_async(AMD_RawPixelsStore_getByteWidth __cb) Returns the byte width for the pixel store.
void	getCol_async(AMD_RawPixelsStore_getCol __cb, int x, int z, int c, int t) Retrieves a particular column from this pixel store.
void	getHistogram_async(AMD_RawPixelsStore_getHistogram __cb, int[] channels, int binCount, boolean globalRange, PlaneDef plane) Retrieves the histogram data for the specified plane and channels.
void	getHypercube_async(AMD_RawPixelsStore_getHypercube __cb, java.util.List<java.lang.Integer> offset, java.util.List<java.lang.Integer> size, java.util.List<java.lang.Integer> step) Retrieves a n-dimensional block from this pixel store.
void	getPixelsId_async(AMD_RawPixelsStore_getPixelsId __cb) Returns the current Pixels set identifier.
void	getPixelsPath_async(AMD_RawPixelsStore_getPixelsPath __cb) Returns the current Pixels path.
void	getPlane_async(AMD_RawPixelsStore_getPlane __cb, int z, int c, int t) Retrieves a particular 2D image plane from this pixel store.
void	getPlaneOffset_async(AMD_RawPixelsStore_getPlaneOffset __cb, int z, int c, int t) Retrieves the offset for a particular 2D image plane in this pixel store.
void	getPlaneRegion_async(AMD_RawPixelsStore_getPlaneRegion __cb, int z, int c, int t, int size, int offset) Retrieves a region from a given plane from this pixel store.
void	getPlaneSize_async(AMD_RawPixelsStore_getPlaneSize __cb) Retrieves the in memory size of a 2D image plane in this pixel store.
void	getRegion_async(AMD_RawPixelsStore_getRegion __cb, int size, long offset) Retrieves a region from this pixel store.
void	getRow_async(AMD_RawPixelsStore_getRow __cb, int y, int z, int c, int t) Retrieves a particular row or scanline from this pixel store.
void	getRowOffset_async(AMD_RawPixelsStore_getRowOffset __cb, int y, int z, int c, int t) Retrieves the offset for a particular row or scanline in this pixel store.
void	getRowSize_async(AMD_RawPixelsStore_getRowSize __cb) Retrieves the in memory size of a row or scanline of pixels in this pixel store.
void	getStack_async(AMD_RawPixelsStore_getStack __cb, int c, int t) Retrieves the the entire number of optical sections for a single wavelength or channel at a particular timepoint in this pixel store.
void	getStackOffset_async(AMD_RawPixelsStore_getStackOffset __cb, int c, int t) Retrieves the offset for the entire number of optical sections for a single wavelength or channel at a particular timepoint in this pixel store.
void	getStackSize_async(AMD_RawPixelsStore_getStackSize __cb) Retrieves the in memory size of the entire number of optical sections for a single wavelength or channel at a particular timepoint in this pixel store.
void	getTile_async(AMD_RawPixelsStore_getTile __cb, int z, int c, int t, int x, int y, int w, int h) Retrieves a tile from this pixel buffer.
void	getTimepoint_async(AMD_RawPixelsStore_getTimepoint __cb, int t) Retrieves the entire number of optical sections for all wavelengths or channels at a particular timepoint in this pixel store.
void	getTimepointOffset_async(AMD_RawPixelsStore_getTimepointOffset __cb, int t) Retrieves the in memory size of the entire number of optical sections for all wavelengths or channels at a particular timepoint in this pixel store.
void	getTimepointSize_async(AMD_RawPixelsStore_getTimepointSize __cb) Retrieves the in memory size of the entire number of optical sections for all wavelengths or channels at a particular timepoint in this pixel store.
void	getTotalSize_async(AMD_RawPixelsStore_getTotalSize __cb) Retrieves the in memory size of the entire pixel store.
void	isFloat_async(AMD_RawPixelsStore_isFloat __cb) Returns whether or not the pixel buffer has floating point pixels.
void	isSigned_async(AMD_RawPixelsStore_isSigned __cb) Returns whether or not the pixel store has signed pixels.
void	prepare_async(AMD_RawPixelsStore_prepare __cb, java.util.List<java.lang.Long> pixelsIds) Prepares the stateful service with a cache of loaded Pixels objects.
void	save_async(AMD_RawPixelsStore_save __cb) Save the current state of the pixels, updating the SHA1.
void	setPixelsId_async(AMD_RawPixelsStore_setPixelsId __cb, long pixelsId, boolean bypassOriginalFile) Initializes the stateful service for a given Pixels set.
void	setPlane_async(AMD_RawPixelsStore_setPlane __cb, byte[] buf, int z, int c, int t) Sets a particular 2D image plane in this pixel store.
void	setRegion_async(AMD_RawPixelsStore_setRegion __cb, int size, long offset, byte[] buf) Sets a region in this pixel buffer.
void	setRow_async(AMD_RawPixelsStore_setRow __cb, byte[] buf, int y, int z, int c, int t) Sets a particular row or scanline in this pixel store.
void	setStack_async(AMD_RawPixelsStore_setStack __cb, byte[] buf, int z, int c, int t) Sets the entire number of optical sections for a single wavelength or channel at a particular timepoint in this pixel store.
void	setTile_async(AMD_RawPixelsStore_setTile __cb, byte[] buf, int z, int c, int t, int x, int y, int w, int h) Sets a tile in this pixel buffer.
void	setTimepoint_async(AMD_RawPixelsStore_setTimepoint __cb, byte[] buf, int t) Sets the entire number of optical sections for all wavelengths or channels at a particular timepoint in this pixel store.

Methods inherited from interface omero.api._PyramidServiceOperationsNC

getResolutionDescriptions_async, getResolutionLevel_async, getResolutionLevels_async, getTileSize_async, requiresPixelsPyramid_async, setResolutionLevel_async

Methods inherited from interface omero.api._StatefulServiceInterfaceOperationsNC

activate_async, close_async, getCurrentEventContext_async, passivate_async

Method Detail

setPixelsId_async

void setPixelsId_async(AMD_RawPixelsStore_setPixelsId __cb,
                       long pixelsId,
                       boolean bypassOriginalFile)
                throws ServerError

Initializes the stateful service for a given Pixels set.

Parameters:

__cb - The callback object for the operation.

pixelsId - Pixels set identifier.

Throws:

ServerError

getPixelsId_async

void getPixelsId_async(AMD_RawPixelsStore_getPixelsId __cb)
                throws ServerError

Returns the current Pixels set identifier.

Parameters:

__cb - The callback object for the operation.

Throws:

ServerError

getPixelsPath_async

void getPixelsPath_async(AMD_RawPixelsStore_getPixelsPath __cb)
                  throws ServerError

Returns the current Pixels path.

Parameters:

__cb - The callback object for the operation.

Throws:

ServerError

prepare_async

void prepare_async(AMD_RawPixelsStore_prepare __cb,
                   java.util.List<java.lang.Long> pixelsIds)
            throws ServerError

Prepares the stateful service with a cache of loaded Pixels objects. This method is designed to combat query overhead, where many sets of Pixels are to be read from or written to, by loading all the Pixels sets at once. Multiple calls will result in the existing cache being overwritten.

Parameters:

__cb - The callback object for the operation.

pixelsIds - Pixels IDs to cache.

Throws:

ServerError

getPlaneSize_async

void getPlaneSize_async(AMD_RawPixelsStore_getPlaneSize __cb)
                 throws ServerError

Retrieves the in memory size of a 2D image plane in this pixel store.

Parameters:

__cb - The callback object for the operation.

Throws:

ServerError

getRowSize_async

void getRowSize_async(AMD_RawPixelsStore_getRowSize __cb)
               throws ServerError

Retrieves the in memory size of a row or scanline of pixels in this pixel store.

Parameters:

__cb - The callback object for the operation.

Throws:

ServerError

getStackSize_async

void getStackSize_async(AMD_RawPixelsStore_getStackSize __cb)
                 throws ServerError

Retrieves the in memory size of the entire number of optical sections for a single wavelength or channel at a particular timepoint in this pixel store.

Parameters:

__cb - The callback object for the operation.

Throws:

ServerError

getTimepointSize_async

void getTimepointSize_async(AMD_RawPixelsStore_getTimepointSize __cb)
                     throws ServerError

Retrieves the in memory size of the entire number of optical sections for all wavelengths or channels at a particular timepoint in this pixel store.

Parameters:

__cb - The callback object for the operation.

Throws:

ServerError

getTotalSize_async

void getTotalSize_async(AMD_RawPixelsStore_getTotalSize __cb)
                 throws ServerError

Retrieves the in memory size of the entire pixel store.

Parameters:

__cb - The callback object for the operation.

Throws:

ServerError

getRowOffset_async

void getRowOffset_async(AMD_RawPixelsStore_getRowOffset __cb,
                        int y,
                        int z,
                        int c,
                        int t)
                 throws ServerError

Retrieves the offset for a particular row or scanline in this pixel store.

Parameters:

__cb - The callback object for the operation.

y - offset across the Y-axis of the pixel buffer.

c - offset across the C-axis of the pixel buffer.

Throws:

ServerError

getPlaneOffset_async

void getPlaneOffset_async(AMD_RawPixelsStore_getPlaneOffset __cb,
                          int z,
                          int c,
                          int t)
                   throws ServerError

Retrieves the offset for a particular 2D image plane in this pixel store.

Parameters:

__cb - The callback object for the operation.

z - offset across the Z-axis of the pixel buffer.

t - offset across the T-axis of the pixel buffer.

Throws:

ServerError

getStackOffset_async

void getStackOffset_async(AMD_RawPixelsStore_getStackOffset __cb,
                          int c,
                          int t)
                   throws ServerError

Retrieves the offset for the entire number of optical sections for a single wavelength or channel at a particular timepoint in this pixel store.

Parameters:

__cb - The callback object for the operation.

c - offset across the C-axis of the pixel buffer.

Throws:

ServerError

getTimepointOffset_async

void getTimepointOffset_async(AMD_RawPixelsStore_getTimepointOffset __cb,
                              int t)
                       throws ServerError

Retrieves the in memory size of the entire number of optical sections for all wavelengths or channels at a particular timepoint in this pixel store.

Parameters:

__cb - The callback object for the operation.

t - offset across the T-axis of the pixel buffer.

Throws:

ServerError

getTile_async

void getTile_async(AMD_RawPixelsStore_getTile __cb,
                   int z,
                   int c,
                   int t,
                   int x,
                   int y,
                   int w,
                   int h)
            throws ServerError

Retrieves a tile from this pixel buffer.

Parameters:

__cb - The callback object for the operation.

z - offset across the Z-axis of the pixel buffer.

t - offset across the T-axis of the pixel buffer.

y - Top left corner of the tile, Y offset.

h - Height of the tile.

Throws:

ServerError

getHypercube_async

void getHypercube_async(AMD_RawPixelsStore_getHypercube __cb,
                        java.util.List<java.lang.Integer> offset,
                        java.util.List<java.lang.Integer> size,
                        java.util.List<java.lang.Integer> step)
                 throws ServerError

Retrieves a n-dimensional block from this pixel store.

Parameters:

__cb - The callback object for the operation.

offset - offset for each dimension within pixel store.

step - needed of each dimension (dependent on dimension).

Throws:

ServerError

getRegion_async

void getRegion_async(AMD_RawPixelsStore_getRegion __cb,
                     int size,
                     long offset)
              throws ServerError

Retrieves a region from this pixel store.

Parameters:

__cb - The callback object for the operation.

size - byte width of the region to retrieve.

Throws:

ServerError

getRow_async

void getRow_async(AMD_RawPixelsStore_getRow __cb,
                  int y,
                  int z,
                  int c,
                  int t)
           throws ServerError

Retrieves a particular row or scanline from this pixel store.

Parameters:

__cb - The callback object for the operation.

y - offset across the Y-axis of the pixel store.

c - offset across the C-axis of the pixel store.

Throws:

ServerError

getCol_async

void getCol_async(AMD_RawPixelsStore_getCol __cb,
                  int x,
                  int z,
                  int c,
                  int t)
           throws ServerError

Retrieves a particular column from this pixel store.

Parameters:

__cb - The callback object for the operation.

x - offset across the X-axis of the pixel store.

c - offset across the C-axis of the pixel store.

Throws:

ServerError

getPlane_async

void getPlane_async(AMD_RawPixelsStore_getPlane __cb,
                    int z,
                    int c,
                    int t)
             throws ServerError

Retrieves a particular 2D image plane from this pixel store.

Parameters:

__cb - The callback object for the operation.

z - offset across the Z-axis of the pixel store.

t - offset across the T-axis of the pixel store.

Throws:

ServerError

getPlaneRegion_async

void getPlaneRegion_async(AMD_RawPixelsStore_getPlaneRegion __cb,
                          int z,
                          int c,
                          int t,
                          int size,
                          int offset)
                   throws ServerError

Retrieves a region from a given plane from this pixel store.

Parameters:

__cb - The callback object for the operation.

z - offset across the Z-axis of the pixel store.

t - offset across the T-axis of the pixel store.

offset - the offset at which to retrieve size pixels.

Throws:

ServerError

getStack_async

void getStack_async(AMD_RawPixelsStore_getStack __cb,
                    int c,
                    int t)
             throws ServerError

Retrieves the the entire number of optical sections for a single wavelength or channel at a particular timepoint in this pixel store.

Parameters:

__cb - The callback object for the operation.

c - offset across the C-axis of the pixel store.

Throws:

ServerError

getTimepoint_async

void getTimepoint_async(AMD_RawPixelsStore_getTimepoint __cb,
                        int t)
                 throws ServerError

Retrieves the entire number of optical sections for all wavelengths or channels at a particular timepoint in this pixel store.

Parameters:

__cb - The callback object for the operation.

t - offset across the T-axis of the pixel store.

Throws:

ServerError

setTile_async

void setTile_async(AMD_RawPixelsStore_setTile __cb,
                   byte[] buf,
                   int z,
                   int c,
                   int t,
                   int x,
                   int y,
                   int w,
                   int h)
            throws ServerError

Sets a tile in this pixel buffer.

Parameters:

__cb - The callback object for the operation.

buf - A byte array of the data.

c - offset across the C-axis of the pixel buffer.

x - Top left corner of the tile, X offset.

w - Width of the tile.

Throws:

IOException - if there is a problem writing to the pixel buffer.

BufferOverflowException - if an attempt is made to write off the end of the file. See Read-only caveat under RawPixelsStore

ServerError

setRegion_async

void setRegion_async(AMD_RawPixelsStore_setRegion __cb,
                     int size,
                     long offset,
                     byte[] buf)
              throws ServerError

Sets a region in this pixel buffer.

Parameters:

__cb - The callback object for the operation.

size - byte width of the region to set.

buf - a byte array of the data. See Read-only caveat under RawPixelsStore

Throws:

ServerError

setRow_async

void setRow_async(AMD_RawPixelsStore_setRow __cb,
                  byte[] buf,
                  int y,
                  int z,
                  int c,
                  int t)
           throws ServerError

Sets a particular row or scanline in this pixel store.

Parameters:

__cb - The callback object for the operation.

buf - a byte array of the data comprising this row or scanline.

z - offset across the Z-axis of the pixel store.

t - offset across the T-axis of the pixel store. See Read-only caveat under RawPixelsStore

Throws:

ServerError

setPlane_async

void setPlane_async(AMD_RawPixelsStore_setPlane __cb,
                    byte[] buf,
                    int z,
                    int c,
                    int t)
             throws ServerError

Sets a particular 2D image plane in this pixel store.

Parameters:

__cb - The callback object for the operation.

buf - a byte array of the data comprising this 2D image plane.

c - offset across the C-axis of the pixel store.

Throws:

ServerError

setStack_async

void setStack_async(AMD_RawPixelsStore_setStack __cb,
                    byte[] buf,
                    int z,
                    int c,
                    int t)
             throws ServerError

Sets the entire number of optical sections for a single wavelength or channel at a particular timepoint in this pixel store.

Parameters:

__cb - The callback object for the operation.

buf - a byte array of the data comprising this stack.

t - offset across the T-axis of the pixel store. See Read-only caveat under RawPixelsStore

Throws:

ServerError

setTimepoint_async

void setTimepoint_async(AMD_RawPixelsStore_setTimepoint __cb,
                        byte[] buf,
                        int t)
                 throws ServerError

Sets the entire number of optical sections for all wavelengths or channels at a particular timepoint in this pixel store.

Parameters:

__cb - The callback object for the operation.

buf - a byte array of the data comprising this timepoint.

Throws:

ServerError

getHistogram_async

void getHistogram_async(AMD_RawPixelsStore_getHistogram __cb,
                        int[] channels,
                        int binCount,
                        boolean globalRange,
                        PlaneDef plane)
                 throws ServerError

Retrieves the histogram data for the specified plane and channels. This method can currently only handle non-pyramid images.

Parameters:

__cb - The callback object for the operation.

channels - the channels to generate the histogram data for

plane - the plane (optional, default: whole region of first z/t plane)

Throws:

ServerError

findMinMax_async

void findMinMax_async(AMD_RawPixelsStore_findMinMax __cb,
                      int[] channels)
               throws ServerError

Find the minimum and maximum pixel values for the specified channels by iterating over a full plane. In case of multi-z/t images only the 'middle' plane with index maxZ/2, respectively maxT/2 is taken into account. Note: This method can currently only handle non-pyramid images, otherwise an empty map will be returned.

Parameters:

__cb - The callback object for the operation.

channels - the channels

Throws:

ServerError

getByteWidth_async

void getByteWidth_async(AMD_RawPixelsStore_getByteWidth __cb)
                 throws ServerError

Returns the byte width for the pixel store.

Parameters:

__cb - The callback object for the operation.

Throws:

ServerError

isSigned_async

void isSigned_async(AMD_RawPixelsStore_isSigned __cb)
             throws ServerError

Returns whether or not the pixel store has signed pixels.

Parameters:

__cb - The callback object for the operation.

Throws:

ServerError

isFloat_async

void isFloat_async(AMD_RawPixelsStore_isFloat __cb)
            throws ServerError

Returns whether or not the pixel buffer has floating point pixels.

Parameters:

__cb - The callback object for the operation.

Throws:

ServerError

calculateMessageDigest_async

void calculateMessageDigest_async(AMD_RawPixelsStore_calculateMessageDigest __cb)
                           throws ServerError

Calculates a SHA-1 message digest for the entire pixel store.

Parameters:

__cb - The callback object for the operation.

Throws:

ServerError

save_async

void save_async(AMD_RawPixelsStore_save __cb)
         throws ServerError

Save the current state of the pixels, updating the SHA1. This should only be called AFTER all data is successfully set. Future invocations of set methods may be disallowed. This read-only status will allow background processing (generation of thumbnails, compression, etc.) to begin. More information under RawPixelsStore. A null instance will be returned if no save was performed.

Parameters:

__cb - The callback object for the operation.

Throws:

ServerError