bdv.img.openconnectome

Class OpenConnectomeImageLoader

java.lang.Object

bdv.AbstractViewerSetupImgLoader<net.imglib2.type.numeric.integer.UnsignedByteType,net.imglib2.type.volatiles.VolatileUnsignedByteType>

bdv.img.openconnectome.OpenConnectomeImageLoader

All Implemented Interfaces:

ViewerImgLoader, ViewerSetupImgLoader<net.imglib2.type.numeric.integer.UnsignedByteType,net.imglib2.type.volatiles.VolatileUnsignedByteType>, mpicbg.spim.data.generic.sequence.BasicImgLoader, mpicbg.spim.data.generic.sequence.BasicMultiResolutionImgLoader, mpicbg.spim.data.generic.sequence.BasicMultiResolutionSetupImgLoader<net.imglib2.type.numeric.integer.UnsignedByteType>, mpicbg.spim.data.generic.sequence.BasicSetupImgLoader<net.imglib2.type.numeric.integer.UnsignedByteType>

public class OpenConnectomeImageLoader
extends AbstractViewerSetupImgLoader<net.imglib2.type.numeric.integer.UnsignedByteType,net.imglib2.type.volatiles.VolatileUnsignedByteType>
implements ViewerImgLoader

Field Summary

Fields inherited from class bdv.AbstractViewerSetupImgLoader

type, volatileType

Constructor Summary

Constructors

Constructor and Description
OpenConnectomeImageLoader(String baseUrl, String token, String mode)

Method Summary

Modifier and Type	Method and Description
static OpenConnectomeTokenInfo	fetchTokenInfo(String baseUrl, String token) Fetch information for a token from an OpenConnectome volume cutout service, e.g.
static String[]	fetchTokenList(String baseUrl) Fetch the list of public tokens from an OpenConnectome volume cutout service, e.g.
CacheControl	getCacheControl()
net.imglib2.RandomAccessibleInterval<net.imglib2.type.numeric.integer.UnsignedByteType>	getImage(int timepointId, int level, mpicbg.spim.data.generic.sequence.ImgLoaderHint... hints)
double[][]	getMipmapResolutions()
net.imglib2.realtransform.AffineTransform3D[]	getMipmapTransforms()
ViewerSetupImgLoader<?,?>	getSetupImgLoader(int setupId)
net.imglib2.RandomAccessibleInterval<net.imglib2.type.volatiles.VolatileUnsignedByteType>	getVolatileImage(int timepointId, int level, mpicbg.spim.data.generic.sequence.ImgLoaderHint... hints)
int	numMipmapLevels()
protected <T extends net.imglib2.type.NativeType<T>> VolatileCachedCellImg<T,net.imglib2.img.basictypeaccess.volatiles.array.VolatileByteArray>	prepareCachedImage(int timepointId, int setupId, int level, net.imglib2.cache.volatiles.LoadingStrategy loadingStrategy, T type) Create a VolatileCachedCellImg backed by the cache.
static OpenConnectomeTokenInfo	tryFetchTokenInfo(String baseUrl, String token, int maxNumTrials) Try to fetch information for a token from an OpenConnectome volume cutout service, e.g.
static String[]	tryFetchTokenList(String baseUrl, int maxNumTrials) Try to fetch the list of public tokens from an OpenConnectome volume cutout service, e.g.

Methods inherited from class bdv.AbstractViewerSetupImgLoader

getImage, getImageType, getVolatileImageType

Methods inherited from class java.lang.Object

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

Methods inherited from interface bdv.ViewerImgLoader

setCreatedSharedQueue, setNumFetcherThreads

Constructor Detail

OpenConnectomeImageLoader

public OpenConnectomeImageLoader(String baseUrl,
                                 String token,
                                 String mode)

Method Detail

fetchTokenList

public static final String[] fetchTokenList(String baseUrl)
                                     throws com.google.gson.JsonSyntaxException,
                                            com.google.gson.JsonIOException,
                                            IOException

Fetch the list of public tokens from an OpenConnectome volume cutout service, e.g. "http://openconnecto.me/ocp/ca/public_tokens/".

Parameters:

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

Returns:

a list of Strings

Throws:

com.google.gson.JsonSyntaxException

com.google.gson.JsonIOException

IOException

fetchTokenInfo

public static final OpenConnectomeTokenInfo fetchTokenInfo(String baseUrl,
                                                           String token)
                                                    throws com.google.gson.JsonSyntaxException,
                                                           com.google.gson.JsonIOException,
                                                           IOException

Fetch information for a token from an OpenConnectome volume cutout service, e.g. "http://openconnecto.me/ocp/ca/<token>/info/".

Parameters:

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

token - the token whose information is desired

Returns:

an OpenConnectomeTokenInfo instance that carries the token information

Throws:

com.google.gson.JsonSyntaxException

com.google.gson.JsonIOException

IOException

tryFetchTokenList

public static final String[] tryFetchTokenList(String baseUrl,
                                               int maxNumTrials)

Try to fetch the list of public tokens from an OpenConnectome volume cutout service, e.g. "http://openconnecto.me/ocp/ca/public_tokens/".

Parameters:

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

maxNumTrials - the maximum number of trials

Returns:

a list of Strings or null if maxNumTrials were executed without success

tryFetchTokenInfo

public static final OpenConnectomeTokenInfo tryFetchTokenInfo(String baseUrl,
                                                              String token,
                                                              int maxNumTrials)

Try to fetch information for a token from an OpenConnectome volume cutout service, e.g. "http://openconnecto.me/ocp/ca/<token>/info/".

Parameters:

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

token -

maxNumTrials -

Returns:

an OpenConnectomeTokenInfo instance that carries the token information or null if maxNumTrials were executed without success

getImage

public net.imglib2.RandomAccessibleInterval<net.imglib2.type.numeric.integer.UnsignedByteType> getImage(int timepointId,
                                                                                                        int level,
                                                                                                        mpicbg.spim.data.generic.sequence.ImgLoaderHint... hints)

Specified by:

getImage in interface mpicbg.spim.data.generic.sequence.BasicMultiResolutionSetupImgLoader<net.imglib2.type.numeric.integer.UnsignedByteType>

getVolatileImage

public net.imglib2.RandomAccessibleInterval<net.imglib2.type.volatiles.VolatileUnsignedByteType> getVolatileImage(int timepointId,
                                                                                                                  int level,
                                                                                                                  mpicbg.spim.data.generic.sequence.ImgLoaderHint... hints)

Specified by:

getVolatileImage in interface ViewerSetupImgLoader<net.imglib2.type.numeric.integer.UnsignedByteType,net.imglib2.type.volatiles.VolatileUnsignedByteType>

getMipmapResolutions

public double[][] getMipmapResolutions()

Specified by:

getMipmapResolutions in interface mpicbg.spim.data.generic.sequence.BasicMultiResolutionSetupImgLoader<net.imglib2.type.numeric.integer.UnsignedByteType>

numMipmapLevels

public int numMipmapLevels()

Specified by:

numMipmapLevels in interface mpicbg.spim.data.generic.sequence.BasicMultiResolutionSetupImgLoader<net.imglib2.type.numeric.integer.UnsignedByteType>

getMipmapTransforms

public net.imglib2.realtransform.AffineTransform3D[] getMipmapTransforms()

Specified by:

getMipmapTransforms in interface mpicbg.spim.data.generic.sequence.BasicMultiResolutionSetupImgLoader<net.imglib2.type.numeric.integer.UnsignedByteType>

prepareCachedImage

protected <T extends net.imglib2.type.NativeType<T>> VolatileCachedCellImg<T,net.imglib2.img.basictypeaccess.volatiles.array.VolatileByteArray> prepareCachedImage(int timepointId,
                                                                                                                                                                   int setupId,
                                                                                                                                                                   int level,
                                                                                                                                                                   net.imglib2.cache.volatiles.LoadingStrategy loadingStrategy,
                                                                                                                                                                   T type)

Create a VolatileCachedCellImg backed by the cache. The type should be either ARGBType and VolatileARGBType.

getCacheControl

public CacheControl getCacheControl()

Specified by:

getCacheControl in interface ViewerImgLoader

getSetupImgLoader

public ViewerSetupImgLoader<?,?> getSetupImgLoader(int setupId)

Specified by:

getSetupImgLoader in interface ViewerImgLoader

Specified by:

getSetupImgLoader in interface mpicbg.spim.data.generic.sequence.BasicImgLoader

Specified by:

getSetupImgLoader in interface mpicbg.spim.data.generic.sequence.BasicMultiResolutionImgLoader