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java.lang.Objectome.io.nio.AbstractFileSystemService
ome.io.nio.PixelsService
public class PixelsService
Field Summary | |
---|---|
protected BackOff |
backOff
BackOff implementation for calculating MissingPyramidExceptions |
static String |
DV_FORMAT
The DeltaVision file format enumeration value |
static int |
NULL_PLANE_SIZE
Null plane size constant. |
static byte[] |
nullPlane
Null plane byte array. |
static String |
PYRAMID_SUFFIX
Suffix for an the image pyramid of a given pixels set. |
protected FilePathResolver |
resolver
Resolver of archived original file paths for pixels sets. |
protected TileSizes |
sizes
TileSizes implementation for default values |
Fields inherited from class ome.io.nio.AbstractFileSystemService |
---|
FILES_PATH, PIXELS_PATH, ROOT_DEFAULT, THUMBNAILS_PATH |
Constructor Summary | |
---|---|
PixelsService(String path)
Constructor. |
|
PixelsService(String path,
FilePathResolver resolver)
Constructor. |
|
PixelsService(String path,
FilePathResolver resolver,
BackOff backOff,
TileSizes sizes)
Constructor. |
Method Summary | |
---|---|
protected PixelBuffer |
createBfPixelBuffer(String filePath,
int series)
Helper method to properly log any exceptions raised by Bio-Formats. |
protected BfPixelBuffer |
createMinMaxBfPixelBuffer(String filePath,
int series,
loci.formats.meta.IMinMaxStore store)
Helper method to properly log any exceptions raised by Bio-Formats and add a min/max calculator wrapper to the reader stack. |
PixelBuffer |
createPixelBuffer(ome.model.core.Pixels pixels)
Creates a PixelBuffer for a given pixels set. |
protected BfPyramidPixelBuffer |
createPyramidPixelBuffer(ome.model.core.Pixels pixels,
String filePath,
boolean write)
Helper method to properly log any exceptions raised by Bio-Formats. |
protected PixelBuffer |
createRomioPixelBuffer(String pixelsFilePath,
ome.model.core.Pixels pixels,
boolean allowModification)
Helper method to properlty create a RomioPixelBuffer. |
protected String |
getOriginalFilePath(ome.model.core.Pixels pixels)
Retrieves the original file path for a given set of pixels. |
PixelBuffer |
getPixelBuffer(ome.model.core.Pixels pixels)
Deprecated. In the future callers should use the more descriptive getPixelBuffer(Pixels, boolean) . |
PixelBuffer |
getPixelBuffer(ome.model.core.Pixels pixels,
boolean write)
Returns a pixel buffer for a given set of pixels. |
protected int |
getSeries(ome.model.core.Pixels pixels)
Retrieves the series for a given set of pixels. |
protected void |
handleMissingPyramid(ome.model.core.Pixels pixels,
String pixelsPyramidFilePath)
If the outer loop should continue, this method returns successfully; otherwise it throws a MissingPyramidException. |
ome.model.stats.StatsInfo[] |
makePyramid(ome.model.core.Pixels pixels)
Creates a pixels pyramid for a given set of pixels. |
void |
removePixels(List<Long> pixelIds)
Removes files from data repository based on a parameterized List of Long pixels ids |
boolean |
requiresPixelsPyramid(ome.model.core.Pixels pixels)
Returns true if a pyramid should be used for the given Pixels . |
void |
setApplicationEventPublisher(org.springframework.context.ApplicationEventPublisher pub)
|
void |
setFilePathResolver(FilePathResolver resolver)
|
Methods inherited from class ome.io.nio.AbstractFileSystemService |
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createSubpath, getFilesPath, getPixelsPath, getThumbnailPath |
Methods inherited from class java.lang.Object |
---|
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Field Detail |
---|
public static final String DV_FORMAT
public static final String PYRAMID_SUFFIX
public static final int NULL_PLANE_SIZE
protected FilePathResolver resolver
protected BackOff backOff
protected TileSizes sizes
public static final byte[] nullPlane
Constructor Detail |
---|
public PixelsService(String path)
path
- The root of the ROMIO proprietary pixels store. (usually
/OMERO/Pixels
).public PixelsService(String path, FilePathResolver resolver)
path
- The root of the ROMIO proprietary pixels store. (usually
/OMERO/Pixels
).public PixelsService(String path, FilePathResolver resolver, BackOff backOff, TileSizes sizes)
path
- The root of the ROMIO proprietary pixels store. (usually
/OMERO/Pixels
).resolver
- Original file path resolver for pixels sets.Method Detail |
---|
public void setApplicationEventPublisher(org.springframework.context.ApplicationEventPublisher pub)
setApplicationEventPublisher
in interface org.springframework.context.ApplicationEventPublisherAware
public void setFilePathResolver(FilePathResolver resolver)
public PixelBuffer createPixelBuffer(ome.model.core.Pixels pixels) throws IOException
pixels
- Pixels set to create a pixel buffer for.
IOException
- If there is an I/O error creating the pixel buffer
backing file.public ome.model.stats.StatsInfo[] makePyramid(ome.model.core.Pixels pixels)
pixels
- Pixels set to retrieve a pixel buffer for.@Deprecated public PixelBuffer getPixelBuffer(ome.model.core.Pixels pixels)
getPixelBuffer(Pixels, boolean)
.
pixels
- Pixels set to retrieve a pixel buffer for.
getPixelBuffer(Pixels, boolean)
public PixelBuffer getPixelBuffer(ome.model.core.Pixels pixels, boolean write)
pixels
- Pixels set to retrieve a pixel buffer for.write
- Whether or not to open the pixel buffer as read-write.
true
opens as read-write, false
opens as
read-only.
public boolean requiresPixelsPyramid(ome.model.core.Pixels pixels)
Pixels
.
This usually implies that this is a "Big image" and therefore will
need tiling.
pixels
-
protected String getOriginalFilePath(ome.model.core.Pixels pixels)
pixels
- Set of pixels to return an orignal file path for.
null
if the original file
path could not be located or the resolver
has not been set.protected int getSeries(ome.model.core.Pixels pixels)
pixels
- Set of pixels to return the series for.
0
(the first series).protected void handleMissingPyramid(ome.model.core.Pixels pixels, String pixelsPyramidFilePath)
pixels
- pixelsPyramidFilePath
-
ome.conditions.MissingPyramidException
protected BfPixelBuffer createMinMaxBfPixelBuffer(String filePath, int series, loci.formats.meta.IMinMaxStore store)
filePath
- Non-null.store
- Min/max store to use with the min/max calculator.series
- series to usereader
- passed to BfPixelBuffer
protected PixelBuffer createBfPixelBuffer(String filePath, int series)
filePath
- Non-null.reader
- passed to BfPixelBuffer
series
- series to use
protected BfPyramidPixelBuffer createPyramidPixelBuffer(ome.model.core.Pixels pixels, String filePath, boolean write)
filePath
- Non-null.reader
- passed to BfPixelBuffer
protected PixelBuffer createRomioPixelBuffer(String pixelsFilePath, ome.model.core.Pixels pixels, boolean allowModification)
pixelsFilePath
- pixels
- allowModification
-
public void removePixels(List<Long> pixelIds)
pixelsIds
- Long file keys to be deleted
ome.conditions.ResourceError
- If deletion fails.
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Version: 4.3.3-00d1137e-b2894
Copyright © 2009 The University of Dundee. All Rights Reserved.