icy.file

Class Loader

java.lang.Object

icy.file.Loader

public class Loader
extends java.lang.Object

Sequence / Image loader class.

Author:

Fabrice de Chaumont & Stephane

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	Loader.FilePosition

Constructor Summary

Constructors

Constructor and Description
Loader()

Method Summary

Methods

Modifier and Type	Method and Description
static boolean	canDiscardImageFile(java.lang.String path) Returns true if the specified path describes a file type (from extension) which is well known to not be an image file.
static void	checkOpening(int resolution, int sizeX, int sizeY, int sizeC, int sizeZ, int sizeT, DataType dataType, java.lang.String messageSuffix) Check if we have enough resource to open the image defined by the given size information and wanted resolution.
static void	checkOpening(loci.formats.ome.OMEXMLMetadata meta, int serie, int resolution, int sizeZ, int sizeT, java.lang.String messageSuffix) Check if we have enough resource to open the image defined by the given metadata information, serie index and wanted resolution.
static void	checkOpening(loci.formats.ome.OMEXMLMetadata meta, int serie, int resolution, java.lang.String messageSuffix) Check if we have enough resource to open the image defined by the given metadata information, serie index and wanted resolution.
static FileImporter	getFileImporter(java.util.List<FileImporter> importers, java.lang.String path, boolean useFirstFound) Returns the appropriate file importer for the specified file.
static FileImporter	getFileImporter(java.lang.String path, boolean useFirstFound) Returns the appropriate file importer for the specified file.
static java.util.List<FileImporter>	getFileImporters() Returns all available resource (non image) importer which take file as input.
static java.util.Map<FileImporter,java.util.List<java.lang.String>>	getFileImporters(java.util.List<FileImporter> importers, java.util.List<java.lang.String> paths, boolean useFirstFound) Returns a Map containing the appropriate file importer for the specified file.
static java.util.List<FileImporter>	getFileImporters(java.util.List<FileImporter> importers, java.lang.String path) Returns all file importer which can open the specified file.
static java.util.Map<FileImporter,java.util.List<java.lang.String>>	getFileImporters(java.util.List<java.lang.String> paths, boolean useFirstFound) Returns a Map containing the appropriate file importer for the specified file.
static java.util.List<FileImporter>	getFileImporters(java.lang.String path) Returns all file importer which can open the specified file.
static java.util.List<Loader.FilePosition>	getFilePositions(java.util.List<java.lang.String> paths, boolean dimOrder) Sort the specified image files from their name and return their corresponding Sequence position information.
static java.util.List<Loader.FilePosition>	getFilePositions(java.util.List<java.lang.String> paths, boolean dimOrder, FileFrame loadingFrame) Sort the specified image files from their name and return their corresponding Sequence position information.
static java.util.List<Importer>	getImporters() Returns all available resource importer.
static loci.formats.ome.OMEXMLMetadataImpl	getMetaData(java.io.File file) Deprecated. Use getMetaData(String) instead.
static loci.formats.ome.OMEXMLMetadataImpl	getMetaData(SequenceFileImporter importer, java.lang.String path) Loads and returns metadata of the specified image file with given importer.
static loci.formats.ome.OMEXMLMetadataImpl	getMetaData(java.lang.String path) Loads and returns metadata of the specified image file.
static loci.formats.IFormatReader	getReader(java.lang.String path) Deprecated. Use getSequenceFileImporters(String) instead.
static SequenceFileImporter	getSequenceFileImporter(java.util.List<SequenceFileImporter> importers, java.lang.String path) Deprecated. Use getSequenceFileImporter(List, String, boolean)
static SequenceFileImporter	getSequenceFileImporter(java.util.List<SequenceFileImporter> importers, java.lang.String path, boolean useFirstFound) Returns the appropriate sequence file importer for the specified file.
static SequenceFileImporter	getSequenceFileImporter(java.lang.String path) Deprecated. Use getSequenceFileImporter(String, boolean)
static SequenceFileImporter	getSequenceFileImporter(java.lang.String path, boolean useFirstFound) Returns the appropriate sequence file importer for the specified file.
static java.util.List<SequenceFileImporter>	getSequenceFileImporters() Returns all available sequence importer which take file as input.
static java.util.Map<SequenceFileImporter,java.util.List<java.lang.String>>	getSequenceFileImporters(java.util.List<SequenceFileImporter> importers, java.util.List<java.lang.String> paths, boolean useFirstFound) Returns a Map containing the appropriate sequence file importer for the specified files.
static java.util.List<SequenceFileImporter>	getSequenceFileImporters(java.util.List<SequenceFileImporter> importers, java.lang.String path) Returns all sequence file importer which can open the specified file.
static java.util.Map<SequenceFileImporter,java.util.List<java.lang.String>>	getSequenceFileImporters(java.util.List<java.lang.String> paths, boolean useFirstFound) Returns a Map containing the appropriate sequence file importer for the specified file.
static java.util.List<SequenceFileImporter>	getSequenceFileImporters(java.lang.String path) Returns all sequence file importer which can open the specified file.
static java.util.List<SequenceIdImporter>	getSequenceIdImporters() Returns all available sequence importer which take id as input.
static java.util.List<SequenceImporter>	getSequenceImporters() Returns all available sequence importer (different from SequenceIdImporter).
static java.util.List<java.lang.String>	getSupportedFiles(SequenceFileImporter importer, java.util.List<java.lang.String> paths) Returns path which are supported by the specified imported for the given list of paths.
static boolean	isImageFile(java.lang.String path) Deprecated. Use isSupportedImageFile(String) instead.
static boolean	isSupportedImageFile(java.lang.String path) Returns true if the specified file is a supported image file.
static void	load(java.io.File file) Deprecated. Use load(String, boolean) instead.
static void	load(java.io.File[] files, boolean separate, boolean autoOrder, boolean showProgress) Deprecated. Use load(List, boolean, boolean, boolean) instead.
static void	load(java.io.File file, boolean showProgress) Deprecated. Use load(String, boolean) instead.
static void	load(FileImporter importer, java.util.List<java.lang.String> paths, boolean showProgress) Load the specified files with the given FileImporter.
static void	load(java.util.List<java.io.File> files) Deprecated. Use load(List, boolean, boolean, boolean) instead.
static void	load(java.util.List<java.io.File> files, boolean separate) Deprecated. Use load(List, boolean, boolean, boolean) instead.
static void	load(java.util.List<java.io.File> files, boolean separate, boolean showProgress) Deprecated. Use load(List, boolean, boolean, boolean) instead.
static void	load(java.util.List<java.lang.String> paths, boolean separate, boolean autoOrder, boolean showProgress) Load the specified files (asynchronous process) by using automatically the appropriate FileImporter or SequenceFileImporter.
static void	load(SequenceFileImporter importer, java.util.List<java.lang.String> paths, boolean separate, boolean autoOrder, boolean showProgress) Load the specified image files with the given SequenceFileImporter.
static void	load(SequenceFileImporter importer, java.lang.String path, int serie, int resolution, java.awt.Rectangle region, int minZ, int maxZ, int minT, int maxT, int channel, boolean addToRecent, boolean showProgress) Load the specified image file with the given SequenceFileImporter.
static void	load(java.lang.String path, boolean showProgress) Load the specified file (asynchronous process) by using automatically the appropriate FileImporter or SequenceFileImporter.
static IcyBufferedImage	loadImage(java.io.File file) Deprecated. Use loadImage(String) instead.
static IcyBufferedImage	loadImage(java.io.File file, int z, int t) Deprecated. Use loadImage(String, int, int) instead.
static IcyBufferedImage	loadImage(loci.formats.IFormatReader reader) Deprecated. Use IcyBufferedImage.createFrom(IFormatReader, int, int) with Z and T parameters set to 0.
static IcyBufferedImage	loadImage(loci.formats.IFormatReader reader, int z, int t) Deprecated. Use IcyBufferedImage.createFrom(IFormatReader, int, int) instead.
static IcyBufferedImage	loadImage(SequenceFileImporter importer, java.lang.String path, int serie, int z, int t) Load and return the image at given position from the specified file path.
static IcyBufferedImage	loadImage(java.lang.String path) Load and return a single image from the specified file path.
static IcyBufferedImage	loadImage(java.lang.String path, int z, int t) Deprecated. Use loadImage(String, int, int, int) instead.
static IcyBufferedImage	loadImage(java.lang.String path, int serie, int z, int t) Load and return the image at given position from the specified file path.
static Sequence	loadSequence(java.io.File file) Deprecated. Use loadSequence(File, int, boolean) instead.
static Sequence	loadSequence(java.io.File[] files, int serie, boolean showProgress) Deprecated.
static Sequence	loadSequence(java.io.File file, boolean showProgress) Deprecated. Use loadSequence(File, int, boolean) instead.
static Sequence	loadSequence(java.io.File file, int serie, boolean showProgress) Deprecated. Use loadSequence(String, int, boolean) instead.
static Sequence	loadSequence(java.util.List<java.io.File> files) Deprecated. Use loadSequence(File[], int, boolean) instead.
static Sequence	loadSequence(java.util.List<java.io.File> files, boolean showProgress) Deprecated. Use loadSequence(File[], int, boolean) instead.
static Sequence	loadSequence(java.util.List<java.io.File> files, boolean display, boolean addToRecent) Deprecated. Use loadSequence(File[], int, boolean) instead or load(File, boolean) if you want to display the resulting sequence.
static Sequence	loadSequence(java.util.List<java.lang.String> paths, int serie, boolean showProgress) Load a sequence from the specified list of file and returns it.
static Sequence	loadSequence(SequenceFileImporter importer, java.util.List<java.lang.String> paths, int serie, boolean showProgress) Load a sequence from the specified list of file and returns it.
static Sequence	loadSequence(SequenceFileImporter importer, java.util.List<java.lang.String> paths, int serie, boolean addToRecent, boolean showProgress) Load a sequence from the specified list of file and returns it.
static Sequence	loadSequence(SequenceFileImporter importer, java.lang.String path, int serie, boolean showProgress) Load a sequence from the specified file.
static Sequence	loadSequence(SequenceFileImporter importer, java.lang.String path, int serie, boolean addToRecent, boolean showProgress) Loads the specified image file and return it as a Sequence, it can return null if an error occured.
static Sequence	loadSequence(SequenceFileImporter importer, java.lang.String path, int serie, int resolution, java.awt.Rectangle region, int minZ, int maxZ, int minT, int maxT, int channel, boolean addToRecent, boolean showProgress) Loads the specified image file and return it as a Sequence, it can return null if an error occured.
static Sequence	loadSequence(java.lang.String path, int serie, boolean showProgress) Load a sequence from the specified file.
static Sequence[]	loadSequences(java.io.File[] files, int[] series, boolean separate, boolean autoOrder, boolean showProgress) Deprecated. Use loadSequences(File[], int, boolean, boolean, boolean) instead.
static Sequence[]	loadSequences(java.io.File[] files, int serie, boolean separate, boolean autoOrder, boolean showProgress) Deprecated. Use loadSequences(List, int, boolean, boolean, boolean, boolean) instead.
static Sequence[]	loadSequences(java.io.File file, int[] series, boolean showProgress) Deprecated. Use loadSequence(File, int, boolean) instead.
static java.util.List<Sequence>	loadSequences(java.io.File file, java.util.List<java.lang.Integer> series) Deprecated. Use loadSequences(File, int[], boolean) instead.
static java.util.List<Sequence>	loadSequences(java.io.File file, java.util.List<java.lang.Integer> series, boolean showProgress) Deprecated. Use loadSequences(File, int[], boolean) instead.
static java.util.List<Sequence>	loadSequences(java.io.File file, java.util.List<java.lang.Integer> series, boolean display, boolean addToRecent) Deprecated. Use loadSequences(File, int[], boolean) instead.
static java.util.List<Sequence>	loadSequences(java.util.List<java.io.File> files, boolean separate) Deprecated. Use loadSequences(File[], int[], boolean, boolean, boolean) instead.
static java.util.List<Sequence>	loadSequences(java.util.List<java.io.File> files, boolean separate, boolean showProgress) Deprecated. Use loadSequences(File[], int[], boolean, boolean, boolean) instead.
static java.util.List<Sequence>	loadSequences(java.util.List<java.io.File> files, boolean separate, boolean display, boolean addToRecent) Deprecated. Use loadSequences(File[], int[], boolean, boolean, boolean) instead.
static java.util.List<Sequence>	loadSequences(java.util.List<java.io.File> files, java.util.List<java.lang.Integer> series) Deprecated. Use loadSequences(File[], int[], boolean, boolean, boolean) instead.
static java.util.List<Sequence>	loadSequences(java.util.List<java.io.File> files, java.util.List<java.lang.Integer> series, boolean separate) Deprecated. Use loadSequences(File[], int[], boolean, boolean, boolean) instead.
static java.util.List<Sequence>	loadSequences(java.util.List<java.io.File> files, java.util.List<java.lang.Integer> series, boolean separate, boolean showProgress) Deprecated. Use loadSequences(File[], int[], boolean, boolean, boolean) instead.
static java.util.List<Sequence>	loadSequences(java.util.List<java.io.File> files, java.util.List<java.lang.Integer> series, boolean separate, boolean autoOrder, boolean showProgress) Deprecated. Use loadSequences(File[], int[], boolean, boolean, boolean) instead.
static java.util.List<Sequence>	loadSequences(java.util.List<java.lang.String> paths, int serie, boolean separate, boolean autoOrder, boolean addToRecent, boolean showProgress) Loads a list of sequence from the specified list of file and returns them.
static java.util.List<Sequence>	loadSequences(SequenceFileImporter importer, java.util.List<java.lang.String> paths, int serie, boolean separate, boolean autoOrder, boolean addToRecent, boolean showProgress) Load a list of sequence from the specified list of file with the given SequenceFileImporter and returns them.
static IcyBufferedImage	loadThumbnail(SequenceFileImporter importer, java.lang.String path, int serie) Returns a thumbnail of the specified image file path.
static IcyBufferedImage	loadThumbnail(java.lang.String path, int serie) Returns a thumbnail of the specified image file path.
static FileImporter	selectFileImporter(java.util.List<FileImporter> importers, java.lang.String path) Display a dialog to let the user select the appropriate file importer for the specified file.
static SequenceFileImporter	selectSequenceFileImporter(java.util.List<SequenceFileImporter> importers, java.lang.String path) Display a dialog to let the user select the appropriate sequence file importer for the specified file.
static int	selectSerie(SequenceFileImporter importer, java.lang.String path, loci.formats.ome.OMEXMLMetadataImpl meta, int defaultSerie) Deprecated. Use selectSerie(SequenceFileImporter, String, OMEXMLMetadata, int) instead
static int	selectSerie(SequenceFileImporter importer, java.lang.String path, loci.formats.ome.OMEXMLMetadata meta, int defaultSerie) Display the Serie Selection frame for the given image and return the selected serie (single selection).
static int[]	selectSeries(SequenceFileImporter importer, java.lang.String path, loci.formats.ome.OMEXMLMetadataImpl meta, int defaultSerie, boolean singleSelection) Display the Serie Selection frame for the given image and returns selected serie(s).
static int[]	selectSeries(SequenceFileImporter importer, java.lang.String path, loci.formats.ome.OMEXMLMetadata meta, int defaultSerie, boolean singleSelection) Display the Serie Selection frame for the given image and returns selected serie(s).
static void	setupSequence(Sequence sequence, java.lang.String path, boolean multiSerie, int serie, java.awt.Rectangle region, int resolution, int sizeZ, int sizeT, int sizeC, int minZ, int maxZ, int minT, int maxT, int channel) Setup the specified sequence object given the different opening informations

Methods inherited from class java.lang.Object

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

Constructor Detail

Loader

public Loader()

Method Detail

getImporters

public static java.util.List<Importer> getImporters()

Returns all available resource importer.

getFileImporters

public static java.util.List<FileImporter> getFileImporters()

Returns all available resource (non image) importer which take file as input.

getFileImporters

public static java.util.Map<FileImporter,java.util.List<java.lang.String>> getFileImporters(java.util.List<FileImporter> importers,
                                                                            java.util.List<java.lang.String> paths,
                                                                            boolean useFirstFound)

Returns a Map containing the appropriate file importer for the specified file.
A file can be absent from the returned Map when no importer support it.

Parameters:

importers - the base list of importer we want to test to open file.

paths - the list of file we want to retrieve importer for.

useFirstFound - if set to true then the first matching importer is automatically selected otherwise a dialog appears to let the user to choose the correct importer when severals importers match for a file.

getFileImporters

public static java.util.Map<FileImporter,java.util.List<java.lang.String>> getFileImporters(java.util.List<java.lang.String> paths,
                                                                            boolean useFirstFound)

Returns a Map containing the appropriate file importer for the specified file.
A file can be absent from the returned Map when no importer support it.

Parameters:

paths - the list of file we want to retrieve importer for.

useFirstFound - if set to true then the first matching importer is automatically selected otherwise a dialog appears to let the user to choose the correct importer when severals importers match for a file.

getFileImporters

public static java.util.List<FileImporter> getFileImporters(java.util.List<FileImporter> importers,
                                            java.lang.String path)

Returns all file importer which can open the specified file.

getFileImporters

public static java.util.List<FileImporter> getFileImporters(java.lang.String path)

Returns all file importer which can open the specified file.

getFileImporter

public static FileImporter getFileImporter(java.util.List<FileImporter> importers,
                           java.lang.String path,
                           boolean useFirstFound)

Returns the appropriate file importer for the specified file.
Returns null if no importer can open the file.

Parameters:

importers - the base list of importer we want to test to open file.

path - the file we want to retrieve importer for.

useFirstFound - if set to true then the first matching importer is automatically selected otherwise a dialog appears to let the user to choose the correct importer when severals importers match.

See Also:

getFileImporters(List, String)

getFileImporter

public static FileImporter getFileImporter(java.lang.String path,
                           boolean useFirstFound)

Returns the appropriate file importer for the specified file.
Returns null if no importer can open the file.

Parameters:

path - the file we want to retrieve importer for.

useFirstFound - if set to true then the first matching importer is automatically selected otherwise a dialog appears to let the user to choose the correct importer when severals importers match.

See Also:

getFileImporters(String)

selectFileImporter

public static FileImporter selectFileImporter(java.util.List<FileImporter> importers,
                              java.lang.String path)

Display a dialog to let the user select the appropriate file importer for the specified file.

getSequenceImporters

public static java.util.List<SequenceImporter> getSequenceImporters()

Returns all available sequence importer (different from SequenceIdImporter).

getSequenceIdImporters

public static java.util.List<SequenceIdImporter> getSequenceIdImporters()

Returns all available sequence importer which take id as input.

getSequenceFileImporters

public static java.util.List<SequenceFileImporter> getSequenceFileImporters()

Returns all available sequence importer which take file as input.

getSequenceFileImporters

public static java.util.Map<SequenceFileImporter,java.util.List<java.lang.String>> getSequenceFileImporters(java.util.List<SequenceFileImporter> importers,
                                                                                            java.util.List<java.lang.String> paths,
                                                                                            boolean useFirstFound)

Returns a Map containing the appropriate sequence file importer for the specified files.
A file can be absent from the returned Map when no importer support it.

Parameters:

importers - the base list of importer we want to test to open file.

paths - the list of file we want to retrieve importer for.

useFirstFound - if set to true then the first matching importer is automatically selected otherwise a dialog appears to let the user to choose the correct importer when severals importers match for a file.

getSequenceFileImporters

public static java.util.Map<SequenceFileImporter,java.util.List<java.lang.String>> getSequenceFileImporters(java.util.List<java.lang.String> paths,
                                                                                            boolean useFirstFound)

Returns a Map containing the appropriate sequence file importer for the specified file.
A file can be absent from the returned Map when no importer support it.

Parameters:

paths - the list of file we want to retrieve importer for.

useFirstFound - if set to true then the first matching importer is automatically selected otherwise a dialog appears to let the user to choose the correct importer when severals importers match for a file.

getSequenceFileImporters

public static java.util.List<SequenceFileImporter> getSequenceFileImporters(java.util.List<SequenceFileImporter> importers,
                                                            java.lang.String path)

Returns all sequence file importer which can open the specified file.

getSequenceFileImporters

public static java.util.List<SequenceFileImporter> getSequenceFileImporters(java.lang.String path)

Returns all sequence file importer which can open the specified file.

getSequenceFileImporter

public static SequenceFileImporter getSequenceFileImporter(java.util.List<SequenceFileImporter> importers,
                                           java.lang.String path,
                                           boolean useFirstFound)

Returns the appropriate sequence file importer for the specified file.
Depending the parameters it will open a dialog to let the user choose the importer to use when severals match.
Returns null if no importer can open the file.

Parameters:

importers - the base list of importer we want to test to open file.

path - the file we want to retrieve importer for.

useFirstFound - if set to true then the first matching importer is automatically selected otherwise a dialog appears to let the user to choose the correct importer when severals importers match.

See Also:

getSequenceFileImporters(List, String)

getSequenceFileImporter

public static SequenceFileImporter getSequenceFileImporter(java.lang.String path,
                                           boolean useFirstFound)

Returns the appropriate sequence file importer for the specified file.
Depending the parameters it will open a dialog to let the user choose the importer to use when severals match.
Returns null if no importer can open the file.

Parameters:

path - the file we want to retrieve importer for.

useFirstFound - if set to true then the first matching importer is automatically selected otherwise a dialog appears to let the user to choose the correct importer when severals importers match.

See Also:

getSequenceFileImporters(String)

getSequenceFileImporter

@Deprecated
public static SequenceFileImporter getSequenceFileImporter(java.util.List<SequenceFileImporter> importers,
                                                      java.lang.String path)

Deprecated. Use getSequenceFileImporter(List, String, boolean)

getSequenceFileImporter

@Deprecated
public static SequenceFileImporter getSequenceFileImporter(java.lang.String path)

Deprecated. Use getSequenceFileImporter(String, boolean)

selectSequenceFileImporter

public static SequenceFileImporter selectSequenceFileImporter(java.util.List<SequenceFileImporter> importers,
                                              java.lang.String path)

Display a dialog to let the user select the appropriate sequence file importer for the specified file.

canDiscardImageFile

public static boolean canDiscardImageFile(java.lang.String path)

Returns true if the specified path describes a file type (from extension) which is well known to not be an image file.
For instance .exe, .wav or .doc file cannot specify an image file so we can quickly discard them (extension based exclusion)

isSupportedImageFile

public static boolean isSupportedImageFile(java.lang.String path)

Returns true if the specified file is a supported image file.

isImageFile

@Deprecated
public static boolean isImageFile(java.lang.String path)

Deprecated. Use isSupportedImageFile(String) instead.

getSupportedFiles

public static java.util.List<java.lang.String> getSupportedFiles(SequenceFileImporter importer,
                                                 java.util.List<java.lang.String> paths)

Returns path which are supported by the specified imported for the given list of paths.

checkOpening

public static void checkOpening(int resolution,
                int sizeX,
                int sizeY,
                int sizeC,
                int sizeZ,
                int sizeT,
                DataType dataType,
                java.lang.String messageSuffix)
                         throws java.lang.UnsupportedOperationException,
                                java.lang.OutOfMemoryError

Check if we have enough resource to open the image defined by the given size information and wanted resolution.
If the image is too large to be displayed at full resolution (XY plane size > 2^31) or if we don't have enough memory to store the whole image the method throw an exception with an informative error message about the encountered limitation.

Parameters:

resolution - wanted image resolution: a value of 0 means full resolution of the original image while value 1 correspond to the resolution / 2.
Formula: resolution / 2^value

sizeX - width of the image region we want to load

sizeY - height of the image region we want to load

sizeC - number of channel we want to load

sizeZ - number of slice we want to load (can be different from original image sizeZ)

sizeT - number of frame we want to load (can be different from original image sizeT)

dataType - pixel data type of the image we want to load

messageSuffix - message suffix for the exception if wanted

Throws:

java.lang.UnsupportedOperationException - if the XY plane size is >= 2^31 pixels

java.lang.OutOfMemoryError - if there is not enough memory to open the image

checkOpening

public static void checkOpening(loci.formats.ome.OMEXMLMetadata meta,
                int serie,
                int resolution,
                int sizeZ,
                int sizeT,
                java.lang.String messageSuffix)
                         throws java.lang.UnsupportedOperationException,
                                java.lang.OutOfMemoryError

Check if we have enough resource to open the image defined by the given metadata information, serie index and wanted resolution.
If the image is too large to be displayed at full resolution (XY plane size > 2^31) or if we don't have enough memory to store the whole image the method throw an exception with an informative error message about the encountered limitation.

Parameters:

meta - metadata of the image

serie - serie index

resolution - wanted image resolution: a value of 0 means full resolution of the original image while value 1 correspond to the resolution / 2.
Formula: resolution / 2^value

sizeZ - number of slice we want to load (can be different from original image sizeZ)

sizeT - number of frame we want to load (can be different from original image sizeT)

messageSuffix - message suffix for the exception if wanted

Throws:

java.lang.UnsupportedOperationException - if the XY plane size is >= 2^31 pixels

java.lang.OutOfMemoryError - if there is not enough memory to open the image

checkOpening

public static void checkOpening(loci.formats.ome.OMEXMLMetadata meta,
                int serie,
                int resolution,
                java.lang.String messageSuffix)
                         throws java.lang.UnsupportedOperationException,
                                java.lang.OutOfMemoryError

Check if we have enough resource to open the image defined by the given metadata information, serie index and wanted resolution.
If the image is too large to be displayed at full resolution (XY plane size > 2^31) or if we don't have enough memory to store the whole image the method throw an exception with an informative error message about the encountered limitation.

Parameters:

meta - metadata of the image

serie - serie index

resolution - wanted image resolution: a value of 0 means full resolution of the original image while value 1 correspond to the resolution / 2.
Formula: resolution / 2^value

messageSuffix - message suffix for the exception if wanted

Throws:

java.lang.UnsupportedOperationException - if the XY plane size is >= 2^31 pixels

java.lang.OutOfMemoryError - if there is not enough memory to open the image

getReader

@Deprecated
public static loci.formats.IFormatReader getReader(java.lang.String path)
                                            throws loci.formats.FormatException,
                                                   java.io.IOException

Deprecated. Use getSequenceFileImporters(String) instead.

Throws:

loci.formats.FormatException

java.io.IOException

getMetaData

public static loci.formats.ome.OMEXMLMetadataImpl getMetaData(SequenceFileImporter importer,
                                              java.lang.String path)
                                                       throws UnsupportedFormatException,
                                                              java.io.IOException

Loads and returns metadata of the specified image file with given importer.
It can returns null if the specified file is not a valid or supported) image file.

Throws:

UnsupportedFormatException

java.io.IOException

getMetaData

public static loci.formats.ome.OMEXMLMetadataImpl getMetaData(java.lang.String path)
                                                       throws UnsupportedFormatException,
                                                              java.io.IOException

Loads and returns metadata of the specified image file.

Throws:

UnsupportedFormatException

java.io.IOException

getMetaData

@Deprecated
public static loci.formats.ome.OMEXMLMetadataImpl getMetaData(java.io.File file)
                                                       throws UnsupportedFormatException,
                                                              java.io.IOException

Deprecated. Use getMetaData(String) instead.

Throws:

UnsupportedFormatException

java.io.IOException

loadThumbnail

public static IcyBufferedImage loadThumbnail(SequenceFileImporter importer,
                             java.lang.String path,
                             int serie)
                                      throws UnsupportedFormatException,
                                             java.io.IOException

Returns a thumbnail of the specified image file path.
It can return null if the specified file is not a valid or supported image file.

Parameters:

importer - Importer used to open and load the thumbnail from the image file.

path - image file path.

serie - Serie index we want to retrieve thumbnail from (for multi serie image).
Set to 0 if unsure.

Throws:

UnsupportedFormatException

java.io.IOException

loadThumbnail

public static IcyBufferedImage loadThumbnail(java.lang.String path,
                             int serie)
                                      throws UnsupportedFormatException,
                                             java.io.IOException

Returns a thumbnail of the specified image file path.

Parameters:

path - image file path.

serie - Serie index we want to retrieve thumbnail from (for multi serie image).
Set to 0 if unsure.

Throws:

UnsupportedFormatException

java.io.IOException

loadImage

@Deprecated
public static IcyBufferedImage loadImage(loci.formats.IFormatReader reader,
                                    int z,
                                    int t)
                                  throws loci.formats.FormatException,
                                         java.io.IOException

Deprecated. Use IcyBufferedImage.createFrom(IFormatReader, int, int) instead.

Throws:

loci.formats.FormatException

java.io.IOException

loadImage

@Deprecated
public static IcyBufferedImage loadImage(loci.formats.IFormatReader reader)
                                  throws loci.formats.FormatException,
                                         java.io.IOException

Deprecated. Use IcyBufferedImage.createFrom(IFormatReader, int, int) with Z and T parameters set to 0.

Throws:

loci.formats.FormatException

java.io.IOException

loadImage

@Deprecated
public static IcyBufferedImage loadImage(java.io.File file,
                                    int z,
                                    int t)
                                  throws loci.formats.FormatException,
                                         java.io.IOException

Deprecated. Use loadImage(String, int, int) instead.

Throws:

loci.formats.FormatException

java.io.IOException

loadImage

@Deprecated
public static IcyBufferedImage loadImage(java.io.File file)
                                  throws UnsupportedFormatException,
                                         java.io.IOException

Deprecated. Use loadImage(String) instead.

Throws:

UnsupportedFormatException

java.io.IOException

loadImage

@Deprecated
public static IcyBufferedImage loadImage(java.lang.String path,
                                    int z,
                                    int t)
                                  throws loci.formats.FormatException,
                                         java.io.IOException

Deprecated. Use loadImage(String, int, int, int) instead.

Throws:

loci.formats.FormatException

java.io.IOException

loadImage

public static IcyBufferedImage loadImage(SequenceFileImporter importer,
                         java.lang.String path,
                         int serie,
                         int z,
                         int t)
                                  throws UnsupportedFormatException,
                                         java.io.IOException

Load and return the image at given position from the specified file path.
For lower image level access, you can use importer methods.

Parameters:

importer - Importer used to open and load the image file.

path - image file path.

serie - Serie index we want to retrieve image from (for multi serie image).
Set to 0 if unsure (default).

z - Z position of the image to open.

t - T position of the image to open.

Throws:

java.io.IOException

UnsupportedFormatException

loadImage

public static IcyBufferedImage loadImage(java.lang.String path,
                         int serie,
                         int z,
                         int t)
                                  throws UnsupportedFormatException,
                                         java.io.IOException

Load and return the image at given position from the specified file path.
For lower image level access, you can use getSequenceFileImporter(String, boolean) method and directly work through the returned ImageProvider interface.

Parameters:

path - image file path.

serie - Serie index we want to retrieve image from (for multi serie image).
Set to 0 if unsure (default).

z - Z position of the image to open.

t - T position of the image to open.

Throws:

java.io.IOException

UnsupportedFormatException

loadImage

public static IcyBufferedImage loadImage(java.lang.String path)
                                  throws UnsupportedFormatException,
                                         java.io.IOException

Load and return a single image from the specified file path.
If the specified file contains severals image the first image is returned.

Throws:

UnsupportedFormatException

java.io.IOException

loadSequences

@Deprecated
public static Sequence[] loadSequences(java.io.File[] files,
                                  int[] series,
                                  boolean separate,
                                  boolean autoOrder,
                                  boolean showProgress)

Deprecated. Use loadSequences(File[], int, boolean, boolean, boolean) instead.

loadSequences

@Deprecated
public static java.util.List<Sequence> loadSequences(java.util.List<java.io.File> files,
                                                java.util.List<java.lang.Integer> series,
                                                boolean separate,
                                                boolean autoOrder,
                                                boolean showProgress)

Deprecated. Use loadSequences(File[], int[], boolean, boolean, boolean) instead.

loadSequences

@Deprecated
public static java.util.List<Sequence> loadSequences(java.util.List<java.io.File> files,
                                                java.util.List<java.lang.Integer> series,
                                                boolean separate,
                                                boolean showProgress)

Deprecated. Use loadSequences(File[], int[], boolean, boolean, boolean) instead.

loadSequences

@Deprecated
public static java.util.List<Sequence> loadSequences(java.util.List<java.io.File> files,
                                                java.util.List<java.lang.Integer> series,
                                                boolean separate)

Deprecated. Use loadSequences(File[], int[], boolean, boolean, boolean) instead.

loadSequences

@Deprecated
public static java.util.List<Sequence> loadSequences(java.util.List<java.io.File> files,
                                                java.util.List<java.lang.Integer> series)

Deprecated. Use loadSequences(File[], int[], boolean, boolean, boolean) instead.

loadSequences

@Deprecated
public static java.util.List<Sequence> loadSequences(java.util.List<java.io.File> files,
                                                boolean separate,
                                                boolean showProgress)

Deprecated. Use loadSequences(File[], int[], boolean, boolean, boolean) instead.

loadSequences

@Deprecated
public static java.util.List<Sequence> loadSequences(java.util.List<java.io.File> files,
                                                boolean separate)

Deprecated. Use loadSequences(File[], int[], boolean, boolean, boolean) instead.

loadSequences

@Deprecated
public static java.util.List<Sequence> loadSequences(java.util.List<java.io.File> files,
                                                boolean separate,
                                                boolean display,
                                                boolean addToRecent)

Deprecated. Use loadSequences(File[], int[], boolean, boolean, boolean) instead.

loadSequences

@Deprecated
public static Sequence[] loadSequences(java.io.File file,
                                  int[] series,
                                  boolean showProgress)

Deprecated. Use loadSequence(File, int, boolean) instead.

loadSequences

@Deprecated
public static java.util.List<Sequence> loadSequences(java.io.File file,
                                                java.util.List<java.lang.Integer> series,
                                                boolean showProgress)

Deprecated. Use loadSequences(File, int[], boolean) instead.

loadSequences

@Deprecated
public static java.util.List<Sequence> loadSequences(java.io.File file,
                                                java.util.List<java.lang.Integer> series)

Deprecated. Use loadSequences(File, int[], boolean) instead.

loadSequences

@Deprecated
public static java.util.List<Sequence> loadSequences(java.io.File file,
                                                java.util.List<java.lang.Integer> series,
                                                boolean display,
                                                boolean addToRecent)

Deprecated. Use loadSequences(File, int[], boolean) instead.

loadSequence

@Deprecated
public static Sequence loadSequence(java.util.List<java.io.File> files,
                               boolean showProgress)

Deprecated. Use loadSequence(File[], int, boolean) instead.

loadSequence

@Deprecated
public static Sequence loadSequence(java.util.List<java.io.File> files)

Deprecated. Use loadSequence(File[], int, boolean) instead.

loadSequence

@Deprecated
public static Sequence loadSequence(java.util.List<java.io.File> files,
                               boolean display,
                               boolean addToRecent)

Deprecated. Use loadSequence(File[], int, boolean) instead or load(File, boolean) if you want to display the resulting sequence.

loadSequence

@Deprecated
public static Sequence loadSequence(java.io.File file,
                               boolean showProgress)

Deprecated. Use loadSequence(File, int, boolean) instead.

loadSequence

@Deprecated
public static Sequence loadSequence(java.io.File file)

Deprecated. Use loadSequence(File, int, boolean) instead.

loadSequences

@Deprecated
public static Sequence[] loadSequences(java.io.File[] files,
                                  int serie,
                                  boolean separate,
                                  boolean autoOrder,
                                  boolean showProgress)

Deprecated. Use loadSequences(List, int, boolean, boolean, boolean, boolean) instead.

loadSequence

@Deprecated
public static Sequence loadSequence(java.io.File[] files,
                               int serie,
                               boolean showProgress)

Deprecated.

Load a sequence from the specified list of file and returns it.
As the function can take sometime you should not call it from the AWT EDT.
The function can return null if no sequence can be loaded from the specified files.

Parameters:

files - List of image file to load.

serie - Serie index to load (for multi serie sequence), set to 0 if unsure (default).

showProgress - Show progression of loading process.

loadSequence

@Deprecated
public static Sequence loadSequence(java.io.File file,
                               int serie,
                               boolean showProgress)

Deprecated. Use loadSequence(String, int, boolean) instead.

loadSequences

public static java.util.List<Sequence> loadSequences(SequenceFileImporter importer,
                                     java.util.List<java.lang.String> paths,
                                     int serie,
                                     boolean separate,
                                     boolean autoOrder,
                                     boolean addToRecent,
                                     boolean showProgress)

Load a list of sequence from the specified list of file with the given SequenceFileImporter and returns them.
As the function can take sometime you should not call it from the AWT EDT.
The method returns an empty array if an error occurred or if no file could be opened (not supported).
If the user cancelled the action (serie selection dialog) then it returns null.

Parameters:

importer - Importer used to open and load image files.
If set to null the loader will search for a compatible importer and if several importers match the user will have to select the appropriate one from a selection dialog.

paths - List of image file to load.

serie - Serie index to load (for multi serie sequence), set to 0 if unsure (default).
-1 is a special value so it gives a chance to the user
to select the serie to open from a serie selector dialog.

separate - Force image to be loaded in separate sequence.

autoOrder - Try to order image in sequence from their filename

addToRecent - If set to true the files list will be traced in recent opened sequence.

showProgress - Show progression of loading process.

loadSequences

public static java.util.List<Sequence> loadSequences(java.util.List<java.lang.String> paths,
                                     int serie,
                                     boolean separate,
                                     boolean autoOrder,
                                     boolean addToRecent,
                                     boolean showProgress)

Loads a list of sequence from the specified list of file and returns them.
As the function can take sometime you should not call it from the AWT EDT.
The method returns an empty array if an error occurred or if no file could not be opened (not supported).
If several importers match to open a file the user will have to select the appropriate one from a selection dialog.

Parameters:

paths - List of image file to load.

serie - Serie index to load (for multi serie sequence), set to 0 if unsure (default).
-1 is a special value so it gives a chance to the user
to select the serie to open from a serie selector dialog.

separate - Force image to be loaded in separate sequence.

autoOrder - Try to order image in sequence from their filename

addToRecent - If set to true the files list will be traced in recent opened sequence.

showProgress - Show progression of loading process.

loadSequence

public static Sequence loadSequence(SequenceFileImporter importer,
                    java.util.List<java.lang.String> paths,
                    int serie,
                    boolean addToRecent,
                    boolean showProgress)

Load a sequence from the specified list of file and returns it.
As the function can take sometime you should not call it from the AWT EDT.
The function can return null if no sequence can be loaded from the specified files.

Parameters:

importer - Importer used to load the image file (shouldn't be null).

paths - List of image file to load.

serie - Serie index to load (for multi serie sequence), set to 0 if unsure (default).
-1 is a special value so it gives a chance to the user to select series to open from a serie selector dialog.

addToRecent - If set to true the files list will be traced in recent opened sequence.

showProgress - Show progression of loading process.

See Also:

getSequenceFileImporter(String, boolean)

loadSequence

public static Sequence loadSequence(SequenceFileImporter importer,
                    java.util.List<java.lang.String> paths,
                    int serie,
                    boolean showProgress)

Load a sequence from the specified list of file and returns it.
As the function can take sometime you should not call it from the AWT EDT.
The function can return null if no sequence can be loaded from the specified files.

Parameters:

importer - Importer used to load the image file (shouldn't be null).

paths - List of image file to load.

serie - Serie index to load (for multi serie sequence), set to 0 if unsure (default).

showProgress - Show progression of loading process.

See Also:

getSequenceFileImporter(String, boolean)

loadSequence

public static Sequence loadSequence(java.util.List<java.lang.String> paths,
                    int serie,
                    boolean showProgress)

Load a sequence from the specified list of file and returns it.
As the function can take sometime you should not call it from the AWT EDT.
The function can return null if no sequence can be loaded from the specified files.
If several importers match to open a file the user will have to select the appropriate one from a selection dialog.

Parameters:

paths - List of image file to load.

serie - Serie index to load (for multi serie sequence), set to 0 if unsure (default).

showProgress - Show progression of loading process.

See Also:

getSequenceFileImporter(String, boolean)

loadSequence

public static Sequence loadSequence(SequenceFileImporter importer,
                    java.lang.String path,
                    int serie,
                    boolean addToRecent,
                    boolean showProgress)

Loads the specified image file and return it as a Sequence, it can return null if an error occured.
As this method can take sometime, you should not call it from the EDT.

Parameters:

importer - Importer used to load the image file.
If set to null the loader will search for a compatible importer and if several importers match the user will have to select the appropriate one from a selection dialog if showProgress parameter is set to true otherwise the first compatible importer will be automatically used.

path - Image file to load.

serie - Serie index to load (for multi serie sequence), set to 0 if unsure (default).
-1 is a special value so it gives a chance to the user to select serie to open from a serie selector dialog.

addToRecent - If set to true the path will be traced in recent opened sequence.

showProgress - Show progression of loading process.

loadSequence

public static Sequence loadSequence(SequenceFileImporter importer,
                    java.lang.String path,
                    int serie,
                    boolean showProgress)

Load a sequence from the specified file.
As the function can take sometime you should not call it from the AWT EDT.

Parameters:

importer - Importer used to load the image file.
If set to null the loader will search for a compatible importer and if several importers match the user will have to select the appropriate one from a selection dialog if showProgress parameter is set to true otherwise the first compatible importer will be automatically used.

path - Image file to load.

serie - Serie index to load (for multi serie sequence), set to 0 if unsure (default).

showProgress - Show progression of loading process.

loadSequence

public static Sequence loadSequence(java.lang.String path,
                    int serie,
                    boolean showProgress)

Load a sequence from the specified file.
As the function can take sometime you should not call it from the AWT EDT.
If several importers match to open the file the user will have to select the appropriate one from a selection dialog if showProgress parameter is set to true otherwise the first compatible importer is automatically used.

Parameters:

path - Image file to load.

serie - Serie index to load (for multi serie sequence), set to 0 if unsure (default).

showProgress - Show progression of loading process.

load

@Deprecated
public static void load(java.util.List<java.io.File> files)

Deprecated. Use load(List, boolean, boolean, boolean) instead.

load

@Deprecated
public static void load(java.util.List<java.io.File> files,
                   boolean separate)

Deprecated. Use load(List, boolean, boolean, boolean) instead.

load

@Deprecated
public static void load(java.util.List<java.io.File> files,
                   boolean separate,
                   boolean showProgress)

Deprecated. Use load(List, boolean, boolean, boolean) instead.

load

@Deprecated
public static void load(java.io.File file)

Deprecated. Use load(String, boolean) instead.

load

@Deprecated
public static void load(java.io.File[] files,
                   boolean separate,
                   boolean autoOrder,
                   boolean showProgress)

Deprecated. Use load(List, boolean, boolean, boolean) instead.

load

@Deprecated
public static void load(java.io.File file,
                   boolean showProgress)

Deprecated. Use load(String, boolean) instead.

load

public static void load(FileImporter importer,
        java.util.List<java.lang.String> paths,
        boolean showProgress)

Load the specified files with the given FileImporter.
The loading process is asynchronous.
The FileImporter is responsible to make the loaded files available in the application.
This method should be used only for non image file.

Parameters:

importer - Importer used to open and load files.
If set to null the loader will search for a compatible importer and if several importers match the user will have to select the appropriate one from a selection dialog.

paths - list of file to load

showProgress - Show progression in loading process

load

public static void load(SequenceFileImporter importer,
        java.lang.String path,
        int serie,
        int resolution,
        java.awt.Rectangle region,
        int minZ,
        int maxZ,
        int minT,
        int maxT,
        int channel,
        boolean addToRecent,
        boolean showProgress)

Load the specified image file with the given SequenceFileImporter.
The loading process is asynchronous.
The resulting sequence is automatically displayed when the process complete.

Parameters:

importer - Importer used to load the image file.
If set to null the loader will search for a compatible importer and if several importers match the user will have to select the appropriate one from a selection dialog if showProgress parameter is set to true otherwise the first compatible importer will be automatically used.

path - image file to load

serie - Serie index to load (for multi serie sequence), set to 0 if unsure (default).
-1 is a special value so it gives a chance to the user to select serie to open from a serie selector dialog.

resolution - Wanted resolution level for the image (use 0 if unsure), useful for large image
The retrieved image resolution is equal to image.resolution / (2^resolution)
So for instance level 0 is the default/full image resolution while level 1 is base image resolution / 2 and so on...

region - The 2D region of the image we want to retrieve.
If set to null then the whole XY plane of the image is returned.

minZ - the minimum Z position of the image (slice) we want retrieve (inclusive).
Set to -1 to retrieve the whole stack.

maxZ - the maximum Z position of the image (slice) we want retrieve (inclusive).
Set to -1 to retrieve the whole stack.

minT - the minimum T position of the image (frame) we want retrieve (inclusive).
Set to -1 to retrieve the whole timelaps.

maxT - the maximum T position of the image (frame) we want retrieve (inclusive).
Set to -1 to retrieve the whole timelaps.

channel - C position of the image (channel) we want retrieve (-1 means all channel).

addToRecent - If set to true the files list will be traced in recent opened sequence.

showProgress - Show progression in loading process

load

public static void load(SequenceFileImporter importer,
        java.util.List<java.lang.String> paths,
        boolean separate,
        boolean autoOrder,
        boolean showProgress)

Load the specified image files with the given SequenceFileImporter.
The loading process is asynchronous.
If separate is false the loader try to set image in the same sequence.
If separate is true each image is loaded in a separate sequence.
The resulting sequences are automatically displayed when the process complete.

Parameters:

importer - Importer used to open and load image files.
If set to null the loader will search for a compatible importer and if several importers match the user will have to select the appropriate one from a selection dialog.

paths - list of image file to load

separate - Force image to be loaded in separate sequence

autoOrder - Try to order image in sequence from their filename

showProgress - Show progression in loading process

load

public static void load(java.util.List<java.lang.String> paths,
        boolean separate,
        boolean autoOrder,
        boolean showProgress)

Load the specified files (asynchronous process) by using automatically the appropriate FileImporter or SequenceFileImporter. If several importers match to open the file the user will have to select the appropriate one from a selection dialog.

If the specified files are image files:
When separate is false the loader try to set image in the same sequence.
When separate is true each image is loaded in a separate sequence.
The resulting sequences are automatically displayed when the process complete.

Parameters:

paths - list of file to load

separate - Force image to be loaded in separate sequence (image files only)

autoOrder - Try to order image in sequence from their filename (image files only)

showProgress - Show progression in loading process

load

public static void load(java.lang.String path,
        boolean showProgress)

Load the specified file (asynchronous process) by using automatically the appropriate FileImporter or SequenceFileImporter. If several importers match to open the file the user will have to select the appropriate one from a selection dialog.

If the specified file is an image file, the resulting sequence is automatically displayed when process complete.

Parameters:

path - file to load

showProgress - Show progression of loading process.

loadSequence

public static Sequence loadSequence(SequenceFileImporter importer,
                    java.lang.String path,
                    int serie,
                    int resolution,
                    java.awt.Rectangle region,
                    int minZ,
                    int maxZ,
                    int minT,
                    int maxT,
                    int channel,
                    boolean addToRecent,
                    boolean showProgress)

Loads the specified image file and return it as a Sequence, it can return null if an error occured.
As this method can take sometime, you should not call it from the EDT.

Parameters:

importer - Importer used to load the image file.
If set to null the loader will search for a compatible importer and if several importers match the user will have to select the appropriate one from a selection dialog if showProgress parameter is set to true otherwise the first compatible importer will be automatically used.

path - image file to load

serie - Serie index to load (for multi serie sequence), set to 0 if unsure (default).
-1 is a special value so it gives a chance to the user to select series to open from a serie selector dialog.

resolution - Wanted resolution level for the image (use 0 if unsure), useful for large image
The retrieved image resolution is equal to image.resolution / (2^resolution)
So for instance level 0 is the default/full image resolution while level 1 is base image resolution / 2 and so on...

region - The 2D region of the image we want to retrieve.
If set to null then the whole XY plane of the image is returned.

minZ - the minimum Z position of the image (slice) we want retrieve (inclusive).
Set to -1 to retrieve the whole stack.

maxZ - the maximum Z position of the image (slice) we want retrieve (inclusive).
Set to -1 to retrieve the whole stack.

minT - the minimum T position of the image (frame) we want retrieve (inclusive).
Set to -1 to retrieve the whole timelaps.

maxT - the maximum T position of the image (frame) we want retrieve (inclusive).
Set to -1 to retrieve the whole timelaps.

channel - C position of the image (channel) we want retrieve (-1 means all channel).

addToRecent - If set to true the files list will be traced in recent opened sequence.

showProgress - Show progression in loading process

setupSequence

public static void setupSequence(Sequence sequence,
                 java.lang.String path,
                 boolean multiSerie,
                 int serie,
                 java.awt.Rectangle region,
                 int resolution,
                 int sizeZ,
                 int sizeT,
                 int sizeC,
                 int minZ,
                 int maxZ,
                 int minT,
                 int maxT,
                 int channel)

Setup the specified sequence object given the different opening informations

Parameters:

sequence - sequence to adjust properties

path - image path

multiSerie - true if this Sequence comes from a multi serie dataset

serie - serie index

region - Rectangle region we want to load from original image

resolution - Resolution level to open

sizeZ - original image sizeZ

sizeT - original image sizeT

sizeC - original image sizeC

minZ - minimum Z slice wanted

maxZ - maximum Z slice wanted

minT - minimum T frame wanted

maxT - maximum T frame wanted

channel - channel we want to load (-1 for all)

selectSeries

public static int[] selectSeries(SequenceFileImporter importer,
                 java.lang.String path,
                 loci.formats.ome.OMEXMLMetadata meta,
                 int defaultSerie,
                 boolean singleSelection)
                          throws UnsupportedFormatException,
                                 java.io.IOException

Display the Serie Selection frame for the given image and returns selected serie(s).
Returns a 0 length array if user canceled serie selection.

Throws:

UnsupportedFormatException

java.io.IOException

selectSeries

public static int[] selectSeries(SequenceFileImporter importer,
                 java.lang.String path,
                 loci.formats.ome.OMEXMLMetadataImpl meta,
                 int defaultSerie,
                 boolean singleSelection)
                          throws UnsupportedFormatException,
                                 java.io.IOException

Display the Serie Selection frame for the given image and returns selected serie(s).
Returns a 0 length array if user canceled serie selection.

Throws:

UnsupportedFormatException

java.io.IOException

selectSerie

public static int selectSerie(SequenceFileImporter importer,
              java.lang.String path,
              loci.formats.ome.OMEXMLMetadata meta,
              int defaultSerie)
                       throws UnsupportedFormatException,
                              java.io.IOException

Display the Serie Selection frame for the given image and return the selected serie (single selection).
Returns -1 if user canceled serie selection.

Throws:

UnsupportedFormatException

java.io.IOException

selectSerie

@Deprecated
public static int selectSerie(SequenceFileImporter importer,
                         java.lang.String path,
                         loci.formats.ome.OMEXMLMetadataImpl meta,
                         int defaultSerie)
                       throws UnsupportedFormatException,
                              java.io.IOException

Deprecated. Use selectSerie(SequenceFileImporter, String, OMEXMLMetadata, int) instead

Throws:

UnsupportedFormatException

java.io.IOException

getFilePositions

public static java.util.List<Loader.FilePosition> getFilePositions(java.util.List<java.lang.String> paths,
                                                   boolean dimOrder,
                                                   FileFrame loadingFrame)

Sort the specified image files from their name and return their corresponding Sequence position information.

Parameters:

paths - image files we want to sort

dimOrder - if true we try to determine the Z, T and C image position as well else only simple T ordering is done.

loadingFrame - Loading dialog if any to show progress

getFilePositions

public static java.util.List<Loader.FilePosition> getFilePositions(java.util.List<java.lang.String> paths,
                                                   boolean dimOrder)

Sort the specified image files from their name and return their corresponding Sequence position information.

Parameters:

paths - image files we want to sort

dimOrder - if true we try to determine the Z, T and C image position as well else only simple T ordering is done.