OmeroJava API
@Transactional(readOnly=true) public class PixelsImpl extends AbstractLevel2Service implements IPixels
| Modifier and Type | Field and Description |
|---|---|
static String |
RENDERING_DEF_QUERY_PREFIX
Standard rendering definition HQL query prefix
|
iQuery, iUpdate, metadata, queryFactory, sec| Constructor and Description |
|---|
PixelsImpl() |
| Modifier and Type | Method and Description |
|---|---|
Long |
copyAndResizeImage(long imageId,
Integer sizeX,
Integer sizeY,
Integer sizeZ,
Integer sizeT,
List<Integer> channelList,
String name,
boolean copyStats)
Copies the metadata, and only the metadata linked to a Image
object into a new Image object of equal or differing size across one
or many of its three physical dimensions or temporal dimension.
|
Long |
copyAndResizePixels(long pixelsId,
Integer sizeX,
Integer sizeY,
Integer sizeZ,
Integer sizeT,
List<Integer> channelList,
String methodology,
boolean copyStats)
Copies the metadata, and only the metadata linked to a Pixels
object into a new Pixels object of equal or differing size across one
or many of its three physical dimensions or temporal dimension.
|
Long |
createImage(int sizeX,
int sizeY,
int sizeZ,
int sizeT,
List<Integer> channelList,
PixelsType pixelsType,
String name,
String description)
Creates the metadata, and only the metadata linked to an Image
object.
|
<T extends IObject> |
getAllEnumerations(Class<T> klass)
Deprecated.
|
int |
getBitDepth(PixelsType pixelsType)
Bit depth for a given pixel type.
|
<T extends IObject> |
getEnumeration(Class<T> klass,
String value)
Deprecated.
|
Class<? extends ServiceInterface> |
getServiceInterface()
Returns the interface this implementation is for.
|
RenderingDef |
loadRndSettings(long renderingDefId)
Loads a specific set of rendering settings with the following objects
pre-linked:
renderingDef.quantization
renderingDef.model
renderingDef.waveRendering
renderingDef.waveRendering.color
renderingDef.waveRendering.family
renderingDef.spatialDomainEnhancement
|
List<IObject> |
retrieveAllRndSettings(long pixId,
long userId)
Retrieves all the rendering settings for a given pixels set and the
passed user with the following objects pre-linked:
renderingDef.quantization
renderingDef.model
renderingDef.waveRendering
renderingDef.waveRendering.color
renderingDef.waveRendering.family
renderingDef.spatialDomainEnhancement
|
Pixels |
retrievePixDescription(long pixId)
Retrieves the pixels metadata with the following objects pre-linked:
pixels.pixelsType
pixels.pixelsDimensions
pixels.channels
pixels.channnels.statsInfo
pixels.channnels.colorComponent
pixels.channnels.logicalChannel
pixels.channnels.logicalChannel.photometricInterpretation
|
RenderingDef |
retrieveRndSettings(long pixId)
Retrieves the rendering settings for a given pixels set and the currently
logged in user.
|
RenderingDef |
retrieveRndSettingsFor(long pixId,
long userId)
Retrieves the rendering settings for a given pixels set and the passed
user with the following objects pre-linked:
renderingDef.quantization
renderingDef.model
renderingDef.waveRendering
renderingDef.waveRendering.color
renderingDef.waveRendering.family
renderingDef.spatialDomainEnhancement
|
void |
saveRndSettings(RenderingDef rndSettings)
Saves the specified rendering settings.
|
void |
setChannelGlobalMinMax(long pixelsId,
int channelIndex,
double min,
double max)
Sets the channel global (all 2D optical sections corresponding to a
particular channel) minimum and maximum for a Pixels set.
|
getBeanHelper, getExtendedMetadata, getQueryFactory, getSecuritySystem, selfConfigure, setExtendedMetadata, setQueryFactory, setQueryService, setSecuritySystem, setUpdateServicepublic static final String RENDERING_DEF_QUERY_PREFIX
public Class<? extends ServiceInterface> getServiceInterface()
getServiceInterface in interface SelfConfigurableServiceSelfConfigurableService.getServiceInterface()public Pixels retrievePixDescription(long pixId)
IPixelsretrievePixDescription in interface IPixelspixId - Pixels id.public RenderingDef retrieveRndSettingsFor(long pixId, long userId)
IPixelsretrieveRndSettingsFor in interface IPixelspixId - Pixels id.userId - The id of the user.public List<IObject> retrieveAllRndSettings(long pixId, long userId)
IPixelsretrieveAllRndSettings in interface IPixelspixId - Pixels id.userId - The id of the user.public RenderingDef retrieveRndSettings(long pixId)
IPixelsRenderingDef, and the
user is an administrator, then a RenderingDef may be returned
for the owner of the Pixels. This matches the behavior of the
Rendering service.
The following objects will be pre-linked:
retrieveRndSettings in interface IPixelspixId - Pixels id.public RenderingDef loadRndSettings(long renderingDefId)
IPixelsloadRndSettings in interface IPixelsrenderingDefId - Rendering definition id.@Transactional(readOnly=false) public Long copyAndResizePixels(long pixelsId, Integer sizeX, Integer sizeY, Integer sizeZ, Integer sizeT, List<Integer> channelList, String methodology, boolean copyStats)
IPixelsRawPixelsStore or to add
and link PlaneInfo and/or other Pixels set
specific metadata.
It is also assumed that the caller wishes the pixels dimensions and
PixelsType to remain the same;
changing these is outside the scope of this method. NOTE: As
Channel objects are only able to apply to a
single set of Pixels any annotations or linkage to these objects will
be lost.copyAndResizePixels in interface IPixelspixelsId - The source Pixels set id.sizeX - The new size across the X-axis. null if the
copy should maintain the same size.sizeY - The new size across the Y-axis. null if the
copy should maintain the same size.sizeZ - The new size across the Z-axis. null if the
copy should maintain the same size.sizeT - The new number of timepoints. null if the
copy should maintain the same number.channelList - The channels that should be copied into the new Pixels
set.methodology - An optional string signifying the methodology that
will be used to produce this new Pixels set.copyStats - Whether or not to copy the StatsInfo for each
channel.null on
failure.@Transactional(readOnly=false) public Long copyAndResizeImage(long imageId, Integer sizeX, Integer sizeY, Integer sizeZ, Integer sizeT, List<Integer> channelList, String name, boolean copyStats)
IPixelsRawPixelsStore or to add
and link PlaneInfo and/or other Pixels set specific metadata.
It is also assumed that the caller wishes the pixels dimensions and
PixelsType to remain the same;
changing these is outside the scope of this method. NOTE: As
Channel objects are only able to apply to a single set of
Pixels any annotations or linkage to these objects will be lost.copyAndResizeImage in interface IPixelsimageId - The source Image id.sizeX - The new size across the X-axis. null if the
copy should maintain the same size.sizeY - The new size across the Y-axis. null if the
copy should maintain the same size.sizeZ - The new size across the Z-axis. null if the
copy should maintain the same size.sizeT - The new number of timepoints. null if the
copy should maintain the same number.channelList - The channels that should be copied into the new Pixels
set.name - The name of the new Image.copyStats - Whether or not to copy the StatsInfo for each
channel.null on
failure.@Transactional(readOnly=false) public Long createImage(int sizeX, int sizeY, int sizeZ, int sizeT, List<Integer> channelList, PixelsType pixelsType, String name, String description)
IPixelsRawPixelsStore
or to add and link PlaneInfo or StatsInfo objects
and/or other Pixels set specific metadata. It is also up to the caller
to update the pixels dimensions.createImage in interface IPixelssizeX - The new size across the X-axis.sizeY - The new size across the Y-axis.sizeZ - The new size across the Z-axis.sizeT - The new number of timepoints.channelList - The channels (emission wavelength in nanometers) that
should be added to the new Pixels set.name - The name of the new Image.description - The description of the new Image.null on
failure.@Transactional(readOnly=false)
public void setChannelGlobalMinMax(long pixelsId,
int channelIndex,
double min,
double max)
IPixelssetChannelGlobalMinMax in interface IPixelspixelsId - The source Pixels set id.channelIndex - The channel index within the Pixels set.min - The channel global minimum.max - The channel global maximum.@Transactional(readOnly=false) public void saveRndSettings(RenderingDef rndSettings)
IPixelssaveRndSettings in interface IPixelsrndSettings - Rendering settings.public int getBitDepth(PixelsType pixelsType)
IPixelsgetBitDepth in interface IPixelspixelsType - Pixels type.@Deprecated public <T extends IObject> T getEnumeration(Class<T> klass, String value)
IPixelsgetEnumeration in interface IPixelsklass - Enumeration class.value - Enumeration string value.@Deprecated public <T extends IObject> List<T> getAllEnumerations(Class<T> klass)
IPixelsgetAllEnumerations in interface IPixelsklass - Enumeration class.
OmeroJava API
Version: 5.3.5-ice35-b73
Copyright © 2017 The University of Dundee & Open Microscopy Environment. All Rights Reserved.