PixelsService (OMERO API)

java.lang.Object
- ome.io.nio.AbstractFileSystemService
- - ome.io.nio.PixelsService

All Implemented Interfaces:

ApplicationEventPublisherAware
```
public class PixelsService
extends AbstractFileSystemService
implements ApplicationEventPublisherAware
```
Since:

OMERO-Beta1.0

Version:

3.0 (Internal version: $Revision$ $Date$)

Author:

Chris Allan callan@blackcat.ca

Field Summary

Fields
Modifier and Type	Field and Description
`protected BackOff`	`backOff` BackOff implementation for calculating MissingPyramidExceptions
`static long`	`MEMOIZER_WAIT` Default of 100 ms for `memoizerWait`
`protected File`	`memoizerDirectory` Location where cached data from the `Memoizer` should be stored.
`protected long`	`memoizerWait` Time in ms. which setId must take before a file is memoized
`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

Constructors
Constructor and Description
`PixelsService(String path)` Constructor.
`PixelsService(String path, File memoizerDirectory, FilePathResolver resolver, BackOff backOff, TileSizes sizes, IQuery iQuery)` Call `PixelsService(String, File, long, FilePathResolver, BackOff, TileSizes, IQuery)` with `MEMOIZER_WAIT`.
`PixelsService(String path, File memoizerDirectory, long memoizerWait, FilePathResolver resolver, BackOff backOff, TileSizes sizes, IQuery iQuery)`
`PixelsService(String path, FilePathResolver resolver)` Constructor.
`PixelsService(String path, FilePathResolver resolver, BackOff backOff, TileSizes sizes, IQuery iQuery)` Constructor.
`PixelsService(String path, long memoizerWait, FilePathResolver resolver, BackOff backOff, TileSizes sizes, IQuery iQuery)` Call `PixelsService(String, File, long, FilePathResolver, BackOff, TileSizes, IQuery)` with `MEMOIZER_WAIT`.

Method Summary

All Methods Instance Methods Concrete Methods Deprecated Methods
Modifier and Type	Method and Description
`PixelBuffer`	`_getPixelBuffer(Pixels pixels, boolean write)`
`protected BfPixelBuffer`	`createBfPixelBuffer(String filePath, int series)` Helper method to properly log any exceptions raised by Bio-Formats.
`protected loci.formats.IFormatReader`	`createBfReader()` Create an `IFormatReader` with the appropriate `ReaderWrapper` instances and `IFormatReader.setFlattenedResolutions(boolean)` set to false.
`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(Pixels pixels)` Creates a PixelBuffer for a given pixels set.
`protected BfPyramidPixelBuffer`	`createPyramidPixelBuffer(Pixels pixels, String filePath, boolean write)` Helper method to properly log any exceptions raised by Bio-Formats.
`protected PixelBuffer`	`createRomioPixelBuffer(String pixelsFilePath, Pixels pixels, boolean allowModification)` Helper method to properlty create a RomioPixelBuffer.
`loci.formats.IFormatReader`	`getBfReader(Pixels pixels)` Short-cut in the FS case where we know that we are dealing with a FS-lite file, and want to retrieve the actual file as opposed to a pyramid or anything else.
`File`	`getMemoizerDirectory()`
`long`	`getMemoizerWait()`
`protected String`	`getOriginalFilePath(Pixels pixels)` Retrieves the original file path for a given set of pixels.
`PixelBuffer`	`getPixelBuffer(Pixels pixels)` Deprecated. In the future callers should use the more descriptive `getPixelBuffer(Pixels, boolean)`.
`PixelBuffer`	`getPixelBuffer(Pixels pixels, boolean write)` Returns a pixel buffer for a given set of pixels.
`protected int`	`getSeries(Pixels pixels)` Retrieves the series for a given set of pixels.
`protected void`	`handleMissingPyramid(Pixels pixels, String pixelsPyramidFilePath)` If the outer loop should continue, this method returns successfully; otherwise it throws a MissingPyramidException.
`protected void`	`handleMissingStatsInfo(Pixels pixels)` If the outer loop should continue, this method returns successfully; otherwise it throws a MissingPyramidException.
`StatsInfo[]`	`makePyramid(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(Pixels pixels)` Returns whether a pyramid should be used for the given `Pixels`.
`void`	`setApplicationEventPublisher(ApplicationEventPublisher pub)`
`void`	`setFilePathResolver(FilePathResolver resolver)`
`void`	`setMetrics(Metrics metrics)`

Methods inherited from class ome.io.nio.AbstractFileSystemService
createSubpath, getFilesPath, getPixelsPath, getThumbnailPath

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

- Field Detail
  - PYRAMID_SUFFIX
```
public static final String PYRAMID_SUFFIX
```
    Suffix for an the image pyramid of a given pixels set.
    
    See Also:
    
    Constant Field Values
  - NULL_PLANE_SIZE
```
public static final int NULL_PLANE_SIZE
```
    Null plane size constant.
    
    See Also:
    
    Constant Field Values
  - MEMOIZER_WAIT
```
public static final long MEMOIZER_WAIT
```
    Default of 100 ms for memoizerWait
    
    See Also:
    
    Constant Field Values
  - resolver
```
protected FilePathResolver resolver
```
    Resolver of archived original file paths for pixels sets.
  - backOff
```
protected final BackOff backOff
```
    BackOff implementation for calculating MissingPyramidExceptions
  - sizes
```
protected final TileSizes sizes
```
    TileSizes implementation for default values
  - memoizerDirectory
```
protected final File memoizerDirectory
```
    Location where cached data from the Memoizer should be stored.
  - memoizerWait
```
protected final long memoizerWait
```
    Time in ms. which setId must take before a file is memoized
  - nullPlane
```
public static final byte[] nullPlane
```
    Null plane byte array.
- Constructor Detail
  - PixelsService
```
public PixelsService(String path)
```
    Constructor.
    
    Parameters:
    
    path - The root of the ROMIO proprietary pixels store. (usually /OMERO/Pixels).
  - PixelsService
```
public PixelsService(String path,
                     FilePathResolver resolver)
```
    Constructor.
    
    Parameters:
    
    path - The root of the ROMIO proprietary pixels store. (usually /OMERO/Pixels).
  - PixelsService
```
public PixelsService(String path,
                     FilePathResolver resolver,
                     BackOff backOff,
                     TileSizes sizes,
                     IQuery iQuery)
```
    Constructor.
    
    Parameters:
    
    path - The root of the ROMIO proprietary pixels store. (usually /OMERO/Pixels).
    
    resolver - Original file path resolver for pixels sets.
  - PixelsService
```
public PixelsService(String path,
                     long memoizerWait,
                     FilePathResolver resolver,
                     BackOff backOff,
                     TileSizes sizes,
                     IQuery iQuery)
```
    Call PixelsService(String, File, long, FilePathResolver, BackOff, TileSizes, IQuery) with MEMOIZER_WAIT.
  - PixelsService
```
public PixelsService(String path,
                     File memoizerDirectory,
                     FilePathResolver resolver,
                     BackOff backOff,
                     TileSizes sizes,
                     IQuery iQuery)
```
    Call PixelsService(String, File, long, FilePathResolver, BackOff, TileSizes, IQuery) with MEMOIZER_WAIT.
  - PixelsService
```
public PixelsService(String path,
                     File memoizerDirectory,
                     long memoizerWait,
                     FilePathResolver resolver,
                     BackOff backOff,
                     TileSizes sizes,
                     IQuery iQuery)
```
- Method Detail
  - setMetrics
```
public void setMetrics(Metrics metrics)
```
  - getMemoizerWait
```
public long getMemoizerWait()
```
  - getMemoizerDirectory
```
public File getMemoizerDirectory()
```
  - setApplicationEventPublisher
```
public void setApplicationEventPublisher(ApplicationEventPublisher pub)
```
    Specified by:
    
    setApplicationEventPublisher in interface ApplicationEventPublisherAware
  - setFilePathResolver
```
public void setFilePathResolver(FilePathResolver resolver)
```
  - createPixelBuffer
```
public PixelBuffer createPixelBuffer(Pixels pixels)
                              throws IOException
```
    Creates a PixelBuffer for a given pixels set.
    
    Parameters:
    
    pixels - Pixels set to create a pixel buffer for.
    
    Returns:
    
    Allocated pixel buffer ready to be used.
    
    Throws:
    
    IOException - If there is an I/O error creating the pixel buffer backing file.
  - makePyramid
```
public StatsInfo[] makePyramid(Pixels pixels)
```
    Creates a pixels pyramid for a given set of pixels. If the pyramid file already exists, then a DEBUG message is logged and this method returns.
    
    Parameters:
    
    pixels - Pixels set to retrieve a pixel buffer for.
    
    Since:
    
    OMERO-Beta4.3
  - getPixelBuffer
```
@Deprecated
public PixelBuffer getPixelBuffer(Pixels pixels)
```
    Deprecated. In the future callers should use the more descriptive getPixelBuffer(Pixels, boolean).
    
    Returns a pixel buffer for a given set of pixels. Either a proprietary ROMIO pixel buffer or a specific pixel buffer implementation.
    
    Parameters:
    
    pixels - Pixels set to retrieve a pixel buffer for.
    
    Returns:
    
    A pixel buffer instance. NOTE: The pixel buffer is initialized as read-write.
    
    Since:
    
    OMERO-Beta4.3
    
    See Also:
    
    getPixelBuffer(Pixels, boolean)
  - getPixelBuffer
```
public PixelBuffer getPixelBuffer(Pixels pixels,
                                  boolean write)
```
    Returns a pixel buffer for a given set of pixels. Either a proprietary ROMIO pixel buffer or a specific pixel buffer implementation.
    
    Parameters:
    
    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.
    
    Returns:
    
    A pixel buffer instance.
    
    Since:
    
    OMERO-Beta4.3
  - _getPixelBuffer
```
public PixelBuffer _getPixelBuffer(Pixels pixels,
                                   boolean write)
```
  - requiresPixelsPyramid
```
public boolean requiresPixelsPyramid(Pixels pixels)
```
    Returns whether a pyramid should be used for the given Pixels. This usually implies that this is a "Big image" and therefore will need tiling.
    
    Parameters:
    
    pixels -
    
    Returns:
    
    true if a pyramid should be used, false otherwise
  - getOriginalFilePath
```
protected String getOriginalFilePath(Pixels pixels)
```
    Retrieves the original file path for a given set of pixels.
    
    Parameters:
    
    pixels - Set of pixels to return an orignal file path for.
    
    Returns:
    
    The original file path or null if the original file path could not be located or the resolver has not been set.
  - getSeries
```
protected int getSeries(Pixels pixels)
```
    Retrieves the series for a given set of pixels.
    
    Parameters:
    
    pixels - Set of pixels to return the series for.
    
    Returns:
    
    The series as specified by the pixels parameters or 0 (the first series).
  - handleMissingStatsInfo
```
protected void handleMissingStatsInfo(Pixels pixels)
```
    If the outer loop should continue, this method returns successfully; otherwise it throws a MissingPyramidException.
    
    Parameters:
    
    pixels -
  - handleMissingPyramid
```
protected void handleMissingPyramid(Pixels pixels,
                                    String pixelsPyramidFilePath)
```
    If the outer loop should continue, this method returns successfully; otherwise it throws a MissingPyramidException.
    
    Parameters:
    
    pixels -
    
    pixelsPyramidFilePath -
    
    Throws:
    
    MissingPyramidException
  - createMinMaxBfPixelBuffer
```
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.
    
    Parameters:
    
    filePath - Non-null.
    
    series - series to use
    
    store - Min/max store to use with the min/max calculator.
  - getBfReader
```
public loci.formats.IFormatReader getBfReader(Pixels pixels)
                                       throws loci.formats.FormatException,
                                              IOException
```
    Short-cut in the FS case where we know that we are dealing with a FS-lite file, and want to retrieve the actual file as opposed to a pyramid or anything else. This may be used to access the original metadata.
    
    Throws:
    
    loci.formats.FormatException
    
    IOException
  - createBfReader
```
protected loci.formats.IFormatReader createBfReader()
```
    Create an IFormatReader with the appropriate ReaderWrapper instances and IFormatReader.setFlattenedResolutions(boolean) set to false.
  - createBfPixelBuffer
```
protected BfPixelBuffer createBfPixelBuffer(String filePath,
                                            int series)
```
    Helper method to properly log any exceptions raised by Bio-Formats.
    
    Parameters:
    
    filePath - Non-null.
    
    series - series to use
    
    Returns:
    
    the initialized BfPixelBuffer
  - createPyramidPixelBuffer
```
protected BfPyramidPixelBuffer createPyramidPixelBuffer(Pixels pixels,
                                                        String filePath,
                                                        boolean write)
```
    Helper method to properly log any exceptions raised by Bio-Formats.
    
    Parameters:
    
    pixels - passed to BfPixelBuffer
    
    filePath - Non-null.
    
    Returns:
    
    the initialized BfPyramidPixelBuffer
  - createRomioPixelBuffer
```
protected PixelBuffer createRomioPixelBuffer(String pixelsFilePath,
                                             Pixels pixels,
                                             boolean allowModification)
```
    Helper method to properlty create a RomioPixelBuffer.
    
    Parameters:
    
    pixelsFilePath -
    
    pixels -
    
    allowModification -
  - removePixels
```
public void removePixels(List<Long> pixelIds)
```
    Removes files from data repository based on a parameterized List of Long pixels ids
    
    Parameters:
    
    pixelIds - Long file keys to be deleted
    
    Throws:
    
    ResourceError - If deletion fails.

Class PixelsService

Field Summary

Fields inherited from class ome.io.nio.AbstractFileSystemService

Constructor Summary

Method Summary

Methods inherited from class ome.io.nio.AbstractFileSystemService

Methods inherited from class java.lang.Object

Field Detail

PYRAMID_SUFFIX

NULL_PLANE_SIZE

MEMOIZER_WAIT

resolver

backOff

sizes

memoizerDirectory

memoizerWait

nullPlane

Constructor Detail

PixelsService

PixelsService

PixelsService

PixelsService

PixelsService

PixelsService

Method Detail

setMetrics

getMemoizerWait

getMemoizerDirectory

setApplicationEventPublisher

setFilePathResolver

createPixelBuffer

makePyramid

getPixelBuffer

getPixelBuffer

_getPixelBuffer

requiresPixelsPyramid

getOriginalFilePath

getSeries

handleMissingStatsInfo

handleMissingPyramid

createMinMaxBfPixelBuffer

getBfReader

createBfReader

createBfPixelBuffer

createPyramidPixelBuffer

createRomioPixelBuffer

removePixels