Add PixelBuffer service methods to API

[cxallan]

A PixelBuffer? service needs to be created, allowing the creation of on disk Pixel buffers and the execution of the setters for Planes, Stacks, etc.

[anonymous]

The relevant api calls seem to be:

PixelsService

• public PixelBuffer createPixelBuffer(Pixels pixels);
• public PixelBuffer getPixelBuffer(Pixels pixels);

PixelBuffer

• public Integer getPlaneSize();
• public Integer getRowSize();
• public Integer getStackSize();
• public Integer getTimepointSize();
• public Integer getTotalSize();
• public Long getRowOffset(Integer y, Integer z, Integer c, Integer t);
• public Long getPlaneOffset(Integer z, Integer c, Integer t);
• public Long getStackOffset(Integer c, Integer t);
• public Long getTimepointOffset(Integer t);
• public MappedByteBuffer? getRegion(Integer size, Long offset);
• public MappedByteBuffer? getRow(Integer y, Integer z, ...
• public MappedByteBuffer? getPlane(Integer z, Integer c, Integer t);
• public MappedByteBuffer? getStack(Integer c, Integer t);
• public MappedByteBuffer? getTimepoint(Integer t);
• public void setRegion(Integer size, Long offset, byte[] buffer);
• public void setRegion(Integer size, Long offset, ByteBuffer? buffer);
• public void setRow(ByteBuffer? buffer, Integer y, Integer z, ...
• public void setPlane(ByteBuffer? buffer, Integer z, Integer c, ...
• public void setPlane(byte[] buffer, Integer z, Integer c, Integer t);
• public void setStack(ByteBuffer? buffer, Integer z, Integer c, ...
• public void setStack(byte[] buffer, Integer z, Integer c, Integer t);
• public void setTimepoint(ByteBuffer? buffer, Integer t);
• public void setTimepoint(byte[] buffer, Integer t);
• public byte[] calculateMessageDigest();
• public static int getBitDepth(PixelsType type);

The PixelsService methods only come into play if we are doing this stateful. We can start off stateless, and see if the creation overhead of the PixelBuffer on each call is significant. A first, stateless solution would be caching. This means all the PixelBuffer calls get a pixelsId as the first parameter.

Of the PixelBuffer methods, a few changes need to be made. All the ones returned MappedByteBuffer need to return byte[]. Make sense? Also, all the duplicate methods taking a ByteBuffer will be omitted. (A setRow(byte[]...) is missing, however.)

As long as the methods are going to be stateless, I'll add them to the existing trunk/components/common/src/ome/api/IPixels.java@723.

[jmoore]

gah! anonymous-silliness.

[jmoore]

Just thinking about this, every single call to the PixelBuffer methods is going to require a hit to the DB if this is stateless. Every call will need to create a session, do iQuery.get(Pixels.class,pixelsId), and then create the delegate PixelBuffer.

Are we sure we don't want to have this stateful? What will be the use cases? How many calls in a row? Calling getTimepoint for t = getTimePointSize. is going to have some serious overhead.

[jmoore]

Decision:

PixelBuffer will get a stateful service (RawPixelsStore?) which holds on the acquired ome.model.core.Pixels and the ome.io.nio.PixelBuffer? instances for performance reasons.

[jmoore]

Initial version committed in r731. Needs testing, etc. Chris, can I turn this over to you now? (Ha, doing it anyway.)

[jmoore]

Working test in r738 : RawPixelStoreTest. All methods not tested, but remoting/sessions/etc. should now work.

[cxallan]

Okay, need to implement the "to byte array" method now to have this thing be semi-complete.

[cxallan]

Completed in r763.

[jmoore]

r783 adds this to source:trunk