Version: Beta4.2.1-r8614-Beta4.2-b41

OmeroBlitz Api
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omero::api::RawPixelsStore

Overview

[ "ami", "amd" ] interface RawPixelsStore extends StatefulServiceInterface

Binary data provider. Initialized with the ID of a omero.model.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 {@link #getByteWidth()}, {@link #isFloat()}, and {@link #isSigned()}.

Operation Index

setPixelsId
Initializes the stateful service for a given Pixels set.
getPixelsId
Returns the current Pixels set identifier.
prepare
Prepares the stateful service with a cache of loaded Pixels objects.
getPlaneSize
Retrieves the in memory size of a 2D image plane in this pixel store.
getRowSize
Retrieves the in memory size of a row or scanline of pixels in this pixel store.
getStackSize
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.
getTimepointSize
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.
getTotalSize
Retrieves the in memory size of the entire pixel store.
getRowOffset
Retrieves the offset for a particular row or scanline in this pixel store.
getPlaneOffset
Retrieves the offset for a particular 2D image plane in this pixel store.
getStackOffset
Retrieves the offset for the entire number of optical sections for a single wavelength or channel at a particular timepoint in this pixel store.
getTimepointOffset
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.
getRegion
Retrieves a region from this pixel store.
getRow
Retrieves a particular row or scanline from this pixel store.
getCol
Retrieves a particular column from this pixel store.
getPlane
Retrieves a particular 2D image plane from this pixel store.
getPlaneRegion
Retrieves a region from a given plane from this pixel store.
getStack
Retrieves the the entire number of optical sections for a single wavelength or channel at a particular timepoint in this pixel store.
getTimepoint
Retrieves the entire number of optical sections for all wavelengths or channels at a particular timepoint in this pixel store.
setRegion
Sets a region in this pixel buffer.
setRow
Sets a particular row or scanline in this pixel store.
setPlane
Sets a particular 2D image plane in this pixel store.
setStack
Sets the entire number of optical sections for a single wavelength or channel at a particular timepoint in this pixel store.
setTimepoint
Sets the entire number of optical sections for all wavelengths or channels at a particular timepoint in this pixel store.
getByteWidth
Returns the byte width for the pixel store.
isSigned
Returns whether or not the pixel store has signed pixels.
isFloat
Returns whether or not the pixel buffer has floating point pixels.
calculateMessageDigest
Calculates a SHA-1 message digest for the entire pixel store.

Operations

void setPixelsId(long pixelsId, bool bypassOriginalFile) throws ServerError

Initializes the stateful service for a given Pixels set.

Parameters

pixelsId
Pixels set identifier.
bypassOriginalFile
Whether or not to bypass checking for an original file to back the pixel buffer used by this service. If requests are predominantly write-only or involve the population of a brand new pixel buffer using true here is a safe optimization otherwise false is expected.

long getPixelsId() throws ServerError

Returns the current Pixels set identifier.

Return Value

See above.

void prepare(sys::LongList 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

pixelsIds
Pixels IDs to cache.

int getPlaneSize() throws ServerError

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

Return Value

2D image plane size in bytes (sizeX*sizeY*ByteWidth).

int getRowSize() throws ServerError

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

Return Value

row or scanline size in bytes (sizeX*ByteWidth)

int getStackSize() 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.

Return Value

stack size in bytes (sizeX*sizeY*sizeZ*ByteWidth).

int getTimepointSize() 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.

Return Value

timepoint size in bytes (sizeX*sizeY*sizeZ*sizeC*ByteWidth).

int getTotalSize() throws ServerError

Retrieves the in memory size of the entire pixel store.

Return Value

total size of the pixel size in bytes (sizeX*sizeY*sizeZ*sizeC*sizeT*ByteWidth).

long getRowOffset(int y, int z, int c, int t) throws ServerError

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

Parameters

y
offset across the Y-axis of the pixel buffer.
z
offset across the Z-axis of the pixel buffer.
c
offset across the C-axis of the pixel buffer.
t
offset across the T-axis of the pixel buffer.

Return Value

offset of the row or scaline.

long getPlaneOffset(int z, int c, int t) throws ServerError

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

Parameters

z
offset across the Z-axis of the pixel buffer.
c
offset across the C-axis of the pixel buffer.
t
offset across the T-axis of the pixel buffer.

Return Value

offset of the 2D image plane.

long getStackOffset(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

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

Return Value

offset of the stack.

long getTimepointOffset(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

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

Return Value

offset of the timepoint.

::Ice::ByteSeq getRegion(int size, long offset) throws ServerError

Retrieves a region from this pixel store.

Parameters

size
byte width of the region to retrieve.
offset
offset within the pixel store.

Return Value

buffer containing the data.

::Ice::ByteSeq getRow(int y, int z, int c, int t) throws ServerError

Retrieves a particular row or scanline from this pixel store.

Parameters

y
offset across the Y-axis of the pixel store.
z
offset across the Z-axis of the pixel store.
c
offset across the C-axis of the pixel store.
t
offset across the T-axis of the pixel store.

Return Value

buffer containing the data which comprises this row or scanline.

::Ice::ByteSeq getCol(int x, int z, int c, int t) throws ServerError

Retrieves a particular column from this pixel store.

Parameters

x
offset across the X-axis of the pixel store.
z
offset across the Z-axis of the pixel store.
c
offset across the C-axis of the pixel store.
t
offset across the T-axis of the pixel store.

Return Value

buffer containing the data which comprises this column.

::Ice::ByteSeq getPlane(int z, int c, int t) throws ServerError

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

Parameters

z
offset across the Z-axis of the pixel store.
c
offset across the C-axis of the pixel store.
t
offset across the T-axis of the pixel store.

Return Value

buffer containing the data which comprises this 2D image plane.

::Ice::ByteSeq getPlaneRegion(int z, int c, int t, int size, int offset) throws ServerError

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

Parameters

z
offset across the Z-axis of the pixel store.
c
offset across the C-axis of the pixel store.
t
offset across the T-axis of the pixel store.
count
the number of pixels to retrieve.
offset
the offset at which to retrieve count pixels.

Return Value

buffer containing the data which comprises the region of the given 2D image plane. It is guaranteed that this buffer will have been byte swapped.

::Ice::ByteSeq getStack(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

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

Return Value

buffer containing the data which comprises this stack.

::Ice::ByteSeq getTimepoint(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

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

void setRegion(int size, long offset, ::Ice::ByteSeq buf) throws ServerError

Sets a region in this pixel buffer.

Parameters

size
byte width of the region to set.
offset
offset within the pixel buffer.
buf
a byte array of the data.

void setRow(::Ice::ByteSeq buf, int y, int z, int c, int t) throws ServerError

Sets a particular row or scanline in this pixel store.

Parameters

buf
a byte array of the data comprising this row or scanline.
y
offset across the Y-axis of the pixel store.
z
offset across the Z-axis of the pixel store.
c
offset across the C-axis of the pixel store.
t
offset across the T-axis of the pixel store.

void setPlane(::Ice::ByteSeq buf, int z, int c, int t) throws ServerError

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

Parameters

buf
a byte array of the data comprising this 2D image plane.
z
offset across the Z-axis of the pixel store.
c
offset across the C-axis of the pixel store.
t
offset across the T-axis of the pixel store.

void setStack(::Ice::ByteSeq 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

buf
a byte array of the data comprising this stack.
c
offset across the C-axis of the pixel store.
t
offset across the T-axis of the pixel store.

void setTimepoint(::Ice::ByteSeq 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

buf
a byte array of the data comprising this timepoint.
t
offset across the T-axis of the pixel buffer.

int getByteWidth() throws ServerError

Returns the byte width for the pixel store.

Return Value

See above.

bool isSigned() throws ServerError

Returns whether or not the pixel store has signed pixels.

Return Value

See above.

bool isFloat() throws ServerError

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

::Ice::ByteSeq calculateMessageDigest() throws ServerError

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

Return Value

byte array containing the message digest.


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