bdv.img.openconnectome

Class OpenConnectomeVolatileArrayLoader

java.lang.Object

bdv.img.openconnectome.OpenConnectomeVolatileArrayLoader

All Implemented Interfaces:

CacheArrayLoader<VolatileByteArray>

public class OpenConnectomeVolatileArrayLoader
extends Object
implements CacheArrayLoader<VolatileByteArray>

Constructor Summary

Constructors

Constructor and Description
OpenConnectomeVolatileArrayLoader(String baseUrl, String token, String mode, long zMin) Create a CacheArrayLoader for a source provided by the Open Connectome Volume Cutout Service.

Method Summary

Modifier and Type	Method and Description
int	getBytesPerElement() How many bytes does one element (voxel) occupy? This is used only for statistics, i.e., estimating I/O bandwidth.
VolatileByteArray	loadArray(int timepoint, int setup, int level, int[] dimensions, long[] min) Load cell data into memory.
VolatileByteArray	tryLoadArray(int timepoint, int setup, int level, int[] dimensions, long[] min)

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Methods inherited from interface bdv.img.cache.CacheArrayLoader

getEmptyArrayCreator

Constructor Detail

OpenConnectomeVolatileArrayLoader

public OpenConnectomeVolatileArrayLoader(String baseUrl,
                                         String token,
                                         String mode,
                                         long zMin)

Create a CacheArrayLoader for a source provided by the Open Connectome Volume Cutout Service.

It is created with a base URL, e.g. http://openconnecto.me/ocp/ca/kasthuri11 the cell dimensions, and an offset in z. This offset constitutes the 0-coordinate in z and should point to the first slice of the dataset.

Parameters:

baseUrl - e.g. http://openconnecto.me/ocp/ca

token - e.g. "kasthuri11"

mode - z-scaling mode, either of [null, "", "neariso"]

zMin - first z-index at scale level 0

Method Detail

getBytesPerElement

public int getBytesPerElement()

Description copied from interface: CacheArrayLoader

How many bytes does one element (voxel) occupy? This is used only for statistics, i.e., estimating I/O bandwidth. Implementing classes can return an estimate if element size is varying or unknown.

Specified by:

getBytesPerElement in interface CacheArrayLoader<VolatileByteArray>

Returns:

number of bytes required to store one element.

loadArray

public VolatileByteArray loadArray(int timepoint,
                                   int setup,
                                   int level,
                                   int[] dimensions,
                                   long[] min)
                            throws InterruptedException

Description copied from interface: CacheArrayLoader

Load cell data into memory. This method blocks until data is successfully loaded. If it completes normally, the returned data is always valid. If anything goes wrong, an InterruptedException is thrown.

Parameters specify the image within the data set and the location of the cell within the image: timepoint, setup, and level define the stack, where setup is a combination of angle, channel, etc., and level is the resolution level (for multi-resolution data). dimensions is the size of the block to load (in voxels). min is the starting coordinate of the block in the stack (in voxels).

Usually, the CacheArrayLoader interface is implemented in conjunction with implementing a ViewerImgLoader for a BDV data back-end. You do not need to be able to load blocks of arbitrary sizes and offsets here -- just the ones that you will use from the images returned by your ViewerImgLoader. For an example, look at CatmaidImageLoader. There, the blockDimensions are defined in the constructor, according to the tile size of the data set. These blockDimensions are then used for every image that the CatmaidImageLoader provides. Therefore, all calls to CacheArrayLoader.loadArray(int, int, int, int[], long[]) will have predictable dimensions (corresponding to tile size of the data set) and min offsets (multiples of the tile size).

The only exception to this rule is at the (max) border of the stack. The boundary cells may have a truncated shape. For example, if your image size is 20x20x1 and your cell size is 16x16x1, you will have cell sizes
(16x16x1), (4x16x1)
(16x4x1), (4x4x1)

Specified by:

loadArray in interface CacheArrayLoader<VolatileByteArray>

Parameters:

timepoint - the timepoint of the stack.

setup - the setup of the stack.

level - the resolution level of the stack (0 for full resolution).

dimensions - the size of the block to load (in voxels).

min - the min coordinate of the block in the stack (in voxels).

Returns:

loaded cell data.

Throws:

InterruptedException

tryLoadArray

public VolatileByteArray tryLoadArray(int timepoint,
                                      int setup,
                                      int level,
                                      int[] dimensions,
                                      long[] min)
                               throws InterruptedException

Throws:

InterruptedException