Package org.anchoranalysis.plugin.io.multifile

Class OpenedMultiFile

Object

OpenedMultiFile

All Implemented Interfaces:

AutoCloseable, OpenedImageFile

public class OpenedMultiFile
extends Object
implements OpenedImageFile

A OpenedImageFile where the image is formed from more than one file on the file-system.

It ignores multiple series.

Author:

Owen Feehan

Constructor Summary

Constructors

Constructor	Description
OpenedMultiFile(StackReader stackReader, ParsedFilePathBag fileBag, ExecutionTimeRecorder executionTimeRecorder)

Method Summary

Modifier and Type	Method	Description
int	bitDepth(Logger logger)	The bit-depth of the image voxels e.g. 8 for 8-bit, 16 for 16-bit etc.
Optional<List<String>>	channelNames(Logger logger)	The names of each channel, if they are known.
void	close()	Closes the opened image-file, removing any intermediate data-structures.
Dimensions	dimensionsForSeries(int seriesIndex, Logger logger)	The Dimensions associated with a particular series.
boolean	isRGB(Logger logger)	Whether the image-file has RGB encoded voxels.
Optional<ImageLocation>	location()	The location associated with the image, if it is known.
int	numberChannels(Logger logger)	The number of channels in the image-file e.g. 1 for grayscale, 3 for RGB.
int	numberFrames(Logger logger)	The number of frames in the image-file i.e. distinct images for a particular time-point.
int	numberSeries()	The number of series (distinct sets of images) in the image-file.
TimeSeries	open(int seriesIndex, Logger logger)	Open when we don't have a specific-type.
Optional<ImagePyramidMetadata>	pyramid()	Metadata to describe an image-pyramid, if it exists for this opened-image.
ImageTimestampsAttributes	timestamps()	The timestamps and file-attributes associated with the image.

Methods inherited from class java.lang.Object

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

Methods inherited from interface org.anchoranalysis.image.io.stack.input.OpenedImageFile

metadata, open, openCheckType

Constructor Details

OpenedMultiFile

public OpenedMultiFile(StackReader stackReader,
 ParsedFilePathBag fileBag,
 ExecutionTimeRecorder executionTimeRecorder)

Method Details

numberSeries

public int numberSeries()

Description copied from interface: OpenedImageFile

The number of series (distinct sets of images) in the image-file.

Specified by:

numberSeries in interface OpenedImageFile

Returns:

the number of series.

open

public TimeSeries open(int seriesIndex,
 Logger logger)
                throws ImageIOException

Description copied from interface: OpenedImageFile

Open when we don't have a specific-type.

Specified by:

open in interface OpenedImageFile

Parameters:

seriesIndex - the index of the series of the open, zero-indexed.

logger - the logger.

Returns:

a time-sequence of images.

Throws:

ImageIOException - if an error occurs reading the image during this operation.

channelNames

public Optional<List<String>> channelNames(Logger logger)

Description copied from interface: OpenedImageFile

The names of each channel, if they are known.

Specified by:

channelNames in interface OpenedImageFile

Parameters:

logger - the logger.

Returns:

a list of the names, which should correspond (and have the same number of items) as OpenedImageFile.numberChannels(Logger).

numberChannels

public int numberChannels(Logger logger)
                   throws ImageIOException

Description copied from interface: OpenedImageFile

The number of channels in the image-file e.g. 1 for grayscale, 3 for RGB.

Specified by:

numberChannels in interface OpenedImageFile

Parameters:

logger - the logger.

Returns:

the number of channels.

Throws:

ImageIOException - if an error occurs reading the image to determine this information.

bitDepth

public int bitDepth(Logger logger)
             throws ImageIOException

Description copied from interface: OpenedImageFile

The bit-depth of the image voxels e.g. 8 for 8-bit, 16 for 16-bit etc.

Specified by:

bitDepth in interface OpenedImageFile

Parameters:

logger - the logger.

Returns:

the bit-depth.

Throws:

ImageIOException - if an error occurs reading the image to determine this information.

isRGB

public boolean isRGB(Logger logger)
              throws ImageIOException

Description copied from interface: OpenedImageFile

Whether the image-file has RGB encoded voxels.

Specified by:

isRGB in interface OpenedImageFile

Parameters:

logger - the logger.

Returns:

true if the image has RGB or RGBA encoded voxels, false otherwise.

Throws:

ImageIOException - if an error occurs reading the image to determine this information.

numberFrames

public int numberFrames(Logger logger)
                 throws ImageIOException

Description copied from interface: OpenedImageFile

The number of frames in the image-file i.e. distinct images for a particular time-point.

Specified by:

numberFrames in interface OpenedImageFile

Parameters:

logger - the logger.

Returns:

the number of frames.

Throws:

ImageIOException - if an error occurs reading the image to determine this information.

timestamps

public ImageTimestampsAttributes timestamps()
                                     throws ImageIOException

Description copied from interface: OpenedImageFile

The timestamps and file-attributes associated with the image.

Specified by:

timestamps in interface OpenedImageFile

Returns:

timestamps and file-attributes, either newly-created or reused.

Throws:

ImageIOException - if an error occurs reading the image to determine this information.

location

public Optional<ImageLocation> location()
                                 throws ImageIOException

Description copied from interface: OpenedImageFile

The location associated with the image, if it is known.

Specified by:

location in interface OpenedImageFile

Returns:

the image location, or Optional.empty() if no location is known.

Throws:

ImageIOException - if an error occurs reading the image to determine this information.

close

public void close()
           throws ImageIOException

Description copied from interface: OpenedImageFile

Closes the opened image-file, removing any intermediate data-structures.

Specified by:

close in interface AutoCloseable

Specified by:

close in interface OpenedImageFile

Throws:

ImageIOException

dimensionsForSeries

public Dimensions dimensionsForSeries(int seriesIndex,
 Logger logger)
                               throws ImageIOException

Description copied from interface: OpenedImageFile

The Dimensions associated with a particular series.

Specified by:

dimensionsForSeries in interface OpenedImageFile

Parameters:

seriesIndex - the index of the series.

logger - a logger for any non-fatal errors. Fatal errors throw an exception.

Returns:

the corresponding dimensions.

Throws:

ImageIOException - if any filesystem-related input-output failure occurs.

pyramid

public Optional<ImagePyramidMetadata> pyramid()
                                       throws ImageIOException

Description copied from interface: OpenedImageFile

Metadata to describe an image-pyramid, if it exists for this opened-image.

Specified by:

pyramid in interface OpenedImageFile

Returns:

the metadata, or Optional.empty() if no pyramid exists.

Throws:

ImageIOException - if an error occurs reading the image to determine this information.