omero::api::RawPixelsStore
Overview
[ "ami", "amd" ]
interface RawPixelsStore extends PyramidService
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 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.
Operation Index
- setPixelsId
-
Initializes the stateful service for a given Pixels set.
- getPixelsId
-
Returns the current Pixels set identifier.
- getPixelsPath
-
Returns the current Pixels path.
- 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.
- getTile
-
Retrieves a tile from this pixel buffer.
- getHypercube
-
Retrieves a n-dimensional block from 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.
- setTile
-
Sets a tile in this pixel buffer.
- 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.
- save
-
Save the current state of the pixels, updating the SHA1.
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.
See "read-only caveat" under RawPixelsStore
Returns the current Pixels set identifier.
Return Value
See above.
Returns the current Pixels path.
Return Value
See above.
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.
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).
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)
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).
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).
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).
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.
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.
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.
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 getTile(int z, int c, int t, int x, int y, int w, int h) throws ServerError
Retrieves a tile from this pixel buffer.
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.
- x
-
Top left corner of the tile, X offset.
- y
-
Top left corner of the tile, Y offset.
- w
-
Width of the tile.
- h
-
Height of the tile.
Return Value
buffer containing the data.
Retrieves a n-dimensional block from this pixel store.
Parameters
- start
-
offset for each dimension within pixel store.
- size
-
of each dimension (dependent on dimension).
- step
-
needed of each dimension (dependent on dimension).
Return Value
buffer containing the data.
::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.
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.
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 setTile(::Ice::ByteSeq 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
- buf
-
A byte array of the data.
- 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.
- x
-
Top left corner of the tile, X offset.
- y
-
Top left corner of the tile, Y offset.
- w
-
Width of the tile.
- h
-
Height of the tile.
Exceptions
- 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
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.
See "read-only caveat" under RawPixelsStore
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.
See "read-only caveat" under RawPixelsStore
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.
See "read-only caveat" under RawPixelsStore
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.
See "read-only caveat" under RawPixelsStore
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.
See "read-only caveat" under RawPixelsStore
Returns the byte width for the pixel store.
Return Value
See above.
Returns whether or not the pixel store has signed pixels.
Return Value
See above.
Returns whether or not the pixel buffer has floating point pixels.
Calculates a SHA-1 message digest for the entire pixel store.
Return Value
byte array containing the message digest.
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.