icy.file

Class Saver

java.lang.Object

icy.file.Saver

public class Saver
extends java.lang.Object

Sequence / Image saver class.

Supported save format are the following : TIFF (preferred), PNG, JPG and AVI. When sequence is saved as multiple file the following naming convention is used :
filename-tttt-zzzz

Author:

Stephane & Fab

Constructor Summary

Constructors

Constructor and Description
Saver()

Method Summary

Methods

Modifier and Type	Method and Description
static loci.formats.ome.OMEXMLMetadata	generateMetaData(int sizeX, int sizeY, int sizeC, DataType dataType) Deprecated. use OMEUtil.generateMetaData(int, int, int, DataType, boolean) instead
static loci.formats.ome.OMEXMLMetadata	generateMetaData(int sizeX, int sizeY, int sizeC, int dataType, boolean signedDataType) Deprecated. use OMEUtil.generateMetaData(int, int, int, DataType, boolean) instead
static loci.formats.ome.OMEXMLMetadata	generateMetaData(int sizeX, int sizeY, int sizeC, int sizeZ, int sizeT, DataType dataType) Deprecated. use OMEUtil.generateMetaData(int, int, int, int, int, DataType, boolean) instead
static loci.formats.ome.OMEXMLMetadata	generateMetaData(int sizeX, int sizeY, int sizeC, int sizeZ, int sizeT, int dataType, boolean signedDataType) Deprecated. use OMEUtil.generateMetaData(int, int, int, int, int, DataType, boolean) instead
static IcyColorModel	getCompatibleColorModel(loci.formats.IFormatWriter writer, IcyColorModel colorModel) Return the closest compatible IcyColorModel supported by writer from the specified IcyColorModel.
static IcyColorModel	getCompatibleColorModel(loci.formats.IFormatWriter writer, int numChannel, DataType dataType) Return the closest compatible IcyColorModel supported by writer from the specified image description.
static IcyColorModel	getCompatibleColorModel(ImageFileFormat imageFileFormat, IcyColorModel colorModel) Return the closest compatible IcyColorModel supported by the specified image file format from the specified IcyColorModel.
static IcyColorModel	getCompatibleColorModel(ImageFileFormat imageFileFormat, int numChannel, DataType dataType) Return the closest compatible IcyColorModel supported by the specified ImageFileFormat from the specified image description.
static Sequence	getCompatibleSequenceForWriter(loci.formats.IFormatWriter writer, Sequence sequence, int posT, int posZ) Returns a compatible Sequence representing the input sequence so it can be saved with the specified writer.
static FileFormat	getFileFormat(loci.formats.IFormatWriter writer, FileFormat defaultValue) Deprecated. Use getImageFileFormat(IFormatWriter, ImageFileFormat) instead.
static ImageFileFormat	getImageFileFormat(loci.formats.IFormatWriter writer, ImageFileFormat defaultValue) Returns the ImageFileFormat corresponding to specified IFormatWriter.
static loci.formats.IFormatWriter	getWriter(java.io.File file) Deprecated. Use getWriter(File, FileFormat) instead.
static loci.formats.IFormatWriter	getWriter(java.io.File file, FileFormat defaultFormat) Deprecated. Use getWriter(File, ImageFileFormat) instead.
static loci.formats.IFormatWriter	getWriter(FileFormat fileFormat) Deprecated. Use getWriter(ImageFileFormat) instead.
static loci.formats.IFormatWriter	getWriter(java.io.File file, ImageFileFormat defaultFormat) Return the writer to use for the specified file.
static loci.formats.IFormatWriter	getWriter(ImageFileFormat format) Return the writer to use for the specified ImageFileFormat.
static loci.formats.IFormatWriter	getWriter(java.lang.String ext) Deprecated. Use getWriter(String, FileFormat) instead.
static loci.formats.IFormatWriter	getWriter(java.lang.String ext, FileFormat defaultFormat) Deprecated. Use getWriter(String, ImageFileFormat) instead.
static loci.formats.IFormatWriter	getWriter(java.lang.String ext, ImageFileFormat defaultFormat) Return the writer to use for the specified filename extension.
static boolean	isCompatible(loci.formats.IFormatWriter writer, IcyColorModel colorModel) Return true if the specified writer is compatible with the given IcyColorModel.
static boolean	isCompatible(loci.formats.IFormatWriter writer, int numChannel, boolean alpha, DataType dataType) Return true if the specified writer is compatible with the image description.
static boolean	isCompatible(loci.formats.IFormatWriter writer, Sequence sequence) Return true if the specified writer is compatible to save the given Sequence.
static boolean	isCompatible(ImageFileFormat imageFileFormat, IcyColorModel colorModel) Return true if the specified image file format is compatible with the given IcyColorModel.
static boolean	isCompatible(ImageFileFormat imageFileFormat, int numChannel, boolean alpha, DataType dataType) Return true if the specified image file format is compatible with the image description.
static boolean	isCompatible(ImageFileFormat imageFileFormat, Sequence sequence) Return true if the specified image file format is compatible to save the given Sequence.
static void	save(loci.formats.IFormatWriter formatWriter, Sequence sequence, java.io.File file, int fps, boolean multipleFile, boolean showProgress, boolean addToRecent) Save the specified sequence in the specified file.
static void	save(loci.formats.IFormatWriter formatWriter, Sequence sequence, java.io.File file, int zMin, int zMax, int tMin, int tMax, int fps, boolean multipleFile, boolean showProgress) Deprecated. Use save(IFormatWriter, Sequence, File, int, boolean, boolean, boolean) instead.
static void	save(loci.formats.IFormatWriter formatWriter, Sequence sequence, java.io.File file, int zMin, int zMax, int tMin, int tMax, int fps, boolean multipleFile, boolean showProgress, boolean addToRecent) Deprecated. Use save(IFormatWriter, Sequence, File, int, boolean, boolean, boolean) instead.
static void	save(Sequence sequence, java.io.File file) Save the specified sequence in the specified file.
static void	save(Sequence sequence, java.io.File file, boolean multipleFiles) Deprecated. Use save(Sequence, File, boolean, boolean) instead.
static void	save(Sequence sequence, java.io.File file, boolean multipleFiles, boolean showProgress) Save the specified sequence in the specified file.
static void	save(Sequence sequence, java.io.File file, int fps, boolean multipleFile, boolean showProgress) Save the specified sequence in the specified file.
static void	save(Sequence sequence, java.io.File file, int zMin, int zMax, int tMin, int tMax, int fps, boolean multipleFiles) Deprecated. Use save(Sequence, File, int, boolean, boolean) instead.
static void	save(Sequence sequence, java.io.File file, int zMin, int zMax, int tMin, int tMax, int fps, boolean multipleFile, boolean showProgress) Deprecated. Use save(Sequence, File, int, boolean, boolean) instead.
static void	saveImage(byte[] data, int width, int height, int numChannel, DataType dataType, java.io.File file, boolean force) Save a single image from bytes buffer to the specified file.
static void	saveImage(byte[] data, int width, int height, int numChannel, int dataType, boolean signedDataType, java.io.File file, boolean force) Deprecated. Use saveImage(byte[], int, int, int, DataType, File, boolean) instead
static void	saveImage(IcyBufferedImage image, java.io.File file, boolean force) Save a single image to the specified file

Methods inherited from class java.lang.Object

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

Constructor Detail

Saver

public Saver()

Method Detail

generateMetaData

@Deprecated
public static loci.formats.ome.OMEXMLMetadata generateMetaData(int sizeX,
                                                          int sizeY,
                                                          int sizeC,
                                                          int sizeZ,
                                                          int sizeT,
                                                          DataType dataType)
                                                        throws loci.common.services.ServiceException

Deprecated. use OMEUtil.generateMetaData(int, int, int, int, int, DataType, boolean) instead

Throws:

loci.common.services.ServiceException

generateMetaData

@Deprecated
public static loci.formats.ome.OMEXMLMetadata generateMetaData(int sizeX,
                                                          int sizeY,
                                                          int sizeC,
                                                          int sizeZ,
                                                          int sizeT,
                                                          int dataType,
                                                          boolean signedDataType)
                                                        throws loci.common.services.ServiceException

Deprecated. use OMEUtil.generateMetaData(int, int, int, int, int, DataType, boolean) instead

Throws:

loci.common.services.ServiceException

generateMetaData

@Deprecated
public static loci.formats.ome.OMEXMLMetadata generateMetaData(int sizeX,
                                                          int sizeY,
                                                          int sizeC,
                                                          DataType dataType)
                                                        throws loci.common.services.ServiceException

Deprecated. use OMEUtil.generateMetaData(int, int, int, DataType, boolean) instead

Throws:

loci.common.services.ServiceException

generateMetaData

@Deprecated
public static loci.formats.ome.OMEXMLMetadata generateMetaData(int sizeX,
                                                          int sizeY,
                                                          int sizeC,
                                                          int dataType,
                                                          boolean signedDataType)
                                                        throws loci.common.services.ServiceException

Deprecated. use OMEUtil.generateMetaData(int, int, int, DataType, boolean) instead

Throws:

loci.common.services.ServiceException

getImageFileFormat

public static ImageFileFormat getImageFileFormat(loci.formats.IFormatWriter writer,
                                 ImageFileFormat defaultValue)

Returns the ImageFileFormat corresponding to specified IFormatWriter.
defaultValue is returned if no matching format is found.

getFileFormat

@Deprecated
public static FileFormat getFileFormat(loci.formats.IFormatWriter writer,
                                  FileFormat defaultValue)

Deprecated. Use getImageFileFormat(IFormatWriter, ImageFileFormat) instead.

getWriter

public static loci.formats.IFormatWriter getWriter(ImageFileFormat format)

Return the writer to use for the specified ImageFileFormat.

The following writer are currently supported :
OMETiffWriter : TIFF image file (default)
APNGWriter : PNG image file
JPEGWriter : JPG image file
AVIWriter : AVI video file

Parameters:

format - ImageFileFormat we want to retrieve the saver.
Accepted values:
ImageFileFormat.TIFF
ImageFileFormat.PNG
ImageFileFormat.JPG
ImageFileFormat.AVI
null

getWriter

@Deprecated
public static loci.formats.IFormatWriter getWriter(FileFormat fileFormat)

Deprecated. Use getWriter(ImageFileFormat) instead.

getWriter

public static loci.formats.IFormatWriter getWriter(java.lang.String ext,
                                   ImageFileFormat defaultFormat)

Return the writer to use for the specified filename extension.

The following writer are currently supported :
OMETiffWriter : TIFF image file (default)
APNGWriter : PNG image file
JPEGWriter : JPG image file
AVIWriter : AVI video file

Parameters:

ext - Extension we want to retrieve the corresponding image writer.

defaultFormat - default ImageFileFormat to use if ext is not recognized.
Accepted values:
ImageFileFormat.TIFF
ImageFileFormat.PNG
ImageFileFormat.JPG
ImageFileFormat.AVI
null

getWriter

@Deprecated
public static loci.formats.IFormatWriter getWriter(java.lang.String ext,
                                              FileFormat defaultFormat)

Deprecated. Use getWriter(String, ImageFileFormat) instead.

getWriter

@Deprecated
public static loci.formats.IFormatWriter getWriter(java.lang.String ext)

Deprecated. Use getWriter(String, FileFormat) instead.

getWriter

public static loci.formats.IFormatWriter getWriter(java.io.File file,
                                   ImageFileFormat defaultFormat)

Return the writer to use for the specified file.

The following writer are currently supported :
OMETiffWriter : TIFF image file (default)
APNGWriter : PNG image file
JPEGWriter : JPG image file
AVIWriter : AVI video file

Parameters:

file - File we want to retrieve the corresponding image writer.

defaultFormat - default ImageFileFormat to use if file is not recognized.
Accepted values:
ImageFileFormat.TIFF
ImageFileFormat.PNG
ImageFileFormat.JPG
ImageFileFormat.AVI
null

getWriter

@Deprecated
public static loci.formats.IFormatWriter getWriter(java.io.File file,
                                              FileFormat defaultFormat)

Deprecated. Use getWriter(File, ImageFileFormat) instead.

getWriter

@Deprecated
public static loci.formats.IFormatWriter getWriter(java.io.File file)

Deprecated. Use getWriter(File, FileFormat) instead.

getCompatibleColorModel

public static IcyColorModel getCompatibleColorModel(ImageFileFormat imageFileFormat,
                                    int numChannel,
                                    DataType dataType)

Return the closest compatible IcyColorModel supported by the specified ImageFileFormat from the specified image description.
That means this file format is able to save the data described by the returned IcyColorModel without any loss or conversion.

Parameters:

imageFileFormat - Image file format we want to test compatibility

numChannel - number of channel of the image

dataType - image data type

getCompatibleColorModel

public static IcyColorModel getCompatibleColorModel(ImageFileFormat imageFileFormat,
                                    IcyColorModel colorModel)

Return the closest compatible IcyColorModel supported by the specified image file format from the specified IcyColorModel.
That means this image file format supports saving data described by the returned IcyColorModel without any loss or conversion.

Parameters:

imageFileFormat - Image file format we want to test compatibility

colorModel - the colorModel describing data / image format

isCompatible

public static boolean isCompatible(ImageFileFormat imageFileFormat,
                   int numChannel,
                   boolean alpha,
                   DataType dataType)

Return true if the specified image file format is compatible with the image description.
That means this image file format supports saving data without any loss or conversion.

Parameters:

imageFileFormat - Image file format we want to test compatibility

numChannel - number of channel of the image

alpha - true if the image has an alpha channel

dataType - image data type

isCompatible

public static boolean isCompatible(ImageFileFormat imageFileFormat,
                   IcyColorModel colorModel)

Return true if the specified image file format is compatible with the given IcyColorModel.
That means this image file format supports saving data described by the returned IcyColorModel without any loss or conversion.
The color map data are never preserved, they are always restored to their default.

isCompatible

public static boolean isCompatible(ImageFileFormat imageFileFormat,
                   Sequence sequence)

Return true if the specified image file format is compatible to save the given Sequence.
That means this image file format supports saving all original data (3D/4D/5D) without any loss or conversion.

getCompatibleColorModel

public static IcyColorModel getCompatibleColorModel(loci.formats.IFormatWriter writer,
                                    int numChannel,
                                    DataType dataType)

Return the closest compatible IcyColorModel supported by writer from the specified image description.
That means the writer is able to save the data described by the returned IcyColorModel without any loss or conversion.

Parameters:

writer - IFormatWriter we want to test compatibility

numChannel - number of channel of the image

dataType - image data type

getCompatibleColorModel

public static IcyColorModel getCompatibleColorModel(loci.formats.IFormatWriter writer,
                                    IcyColorModel colorModel)

Return the closest compatible IcyColorModel supported by writer from the specified IcyColorModel.
That means the writer is able to save the data described by the returned IcyColorModel without any loss or conversion.

Parameters:

writer - IFormatWriter we want to test compatibility

colorModel - the colorModel describing data / image format

isCompatible

public static boolean isCompatible(loci.formats.IFormatWriter writer,
                   int numChannel,
                   boolean alpha,
                   DataType dataType)

Return true if the specified writer is compatible with the image description.
That means the writer is able to save the data without any loss or conversion.

Parameters:

numChannel - number of channel of the image

alpha - true if the image has an alpha channel

dataType - image data type

isCompatible

public static boolean isCompatible(loci.formats.IFormatWriter writer,
                   IcyColorModel colorModel)

Return true if the specified writer is compatible with the given IcyColorModel.
That means the writer is able to save the data described by the colorModel without any loss or conversion.
The color map data are never preserved, they are always restored to their default.

isCompatible

public static boolean isCompatible(loci.formats.IFormatWriter writer,
                   Sequence sequence)

Return true if the specified writer is compatible to save the given Sequence.
That means the writer is able to save all original data (3D/4D/5D) without any loss or conversion.

save

public static void save(Sequence sequence,
        java.io.File file)

Save the specified sequence in the specified file.
If sequence contains severals images then file is used as a directory
to store all single images.

Parameters:

sequence - sequence to save

file - file where we want to save sequence

save

@Deprecated
public static void save(Sequence sequence,
                   java.io.File file,
                   boolean multipleFiles)

Deprecated. Use save(Sequence, File, boolean, boolean) instead.

save

public static void save(Sequence sequence,
        java.io.File file,
        boolean multipleFiles,
        boolean showProgress)

Save the specified sequence in the specified file.
When the sequence contains severals image the multiFile flag is used to indicate
if images are saved in severals files (file then specify a directory) or in a single file.

Parameters:

sequence - sequence to save

file - file where we want to save sequence

multipleFiles - flag to indicate if images are saved in separate file

showProgress - show progress bar

save

@Deprecated
public static void save(Sequence sequence,
                   java.io.File file,
                   int zMin,
                   int zMax,
                   int tMin,
                   int tMax,
                   int fps,
                   boolean multipleFiles)

Deprecated. Use save(Sequence, File, int, boolean, boolean) instead.

save

@Deprecated
public static void save(Sequence sequence,
                   java.io.File file,
                   int zMin,
                   int zMax,
                   int tMin,
                   int tMax,
                   int fps,
                   boolean multipleFile,
                   boolean showProgress)

Deprecated. Use save(Sequence, File, int, boolean, boolean) instead.

save

public static void save(Sequence sequence,
        java.io.File file,
        int fps,
        boolean multipleFile,
        boolean showProgress)

Save the specified sequence in the specified file.
When the sequence contains severals image the multipleFile flag is used to indicate
if images are saved as separate files (file then specify a directory) or not.
zMin - zMax and tMin - tMax define the Z and T images range to save.

Parameters:

sequence - sequence to save

file - file where we want to save sequence

fps - frame rate for AVI sequence save

multipleFile - flag to indicate if images are saved in separate file

showProgress - show progress bar

save

@Deprecated
public static void save(loci.formats.IFormatWriter formatWriter,
                   Sequence sequence,
                   java.io.File file,
                   int zMin,
                   int zMax,
                   int tMin,
                   int tMax,
                   int fps,
                   boolean multipleFile,
                   boolean showProgress)

Deprecated. Use save(IFormatWriter, Sequence, File, int, boolean, boolean, boolean) instead.

save

@Deprecated
public static void save(loci.formats.IFormatWriter formatWriter,
                   Sequence sequence,
                   java.io.File file,
                   int zMin,
                   int zMax,
                   int tMin,
                   int tMax,
                   int fps,
                   boolean multipleFile,
                   boolean showProgress,
                   boolean addToRecent)

Deprecated. Use save(IFormatWriter, Sequence, File, int, boolean, boolean, boolean) instead.

save

public static void save(loci.formats.IFormatWriter formatWriter,
        Sequence sequence,
        java.io.File file,
        int fps,
        boolean multipleFile,
        boolean showProgress,
        boolean addToRecent)

Save the specified sequence in the specified file.
When the sequence contains severals image the multipleFile flag is used to indicate if images are saved as separate files (file then specify a directory) or not.
zMin - zMax and tMin - tMax define the Z and T images range to save.

Parameters:

formatWriter - writer used to save sequence (define the image format).
If set to null then writer is determined from the file extension.
If destination file does not have a valid extension (for folder for instance) then you have to specify a valid Writer to write the image file (see getWriter(ImageFileFormat))

sequence - sequence to save

file - file where we want to save sequence.
Depending the formatWriter the file extension may be modified.
That is preferred as saving an image with a wrong extension may result in error on future read (wrong reader detection).

fps - frame rate for AVI sequence save

multipleFile - flag to indicate if images are saved in separate file.
When multiple file is enabled the file parameter is considerer as a folder if it doens't have any extension

showProgress - show progress bar

addToRecent - add the saved sequence to recent opened sequence list

saveImage

public static void saveImage(byte[] data,
             int width,
             int height,
             int numChannel,
             DataType dataType,
             java.io.File file,
             boolean force)
                      throws loci.formats.FormatException,
                             java.io.IOException

Save a single image from bytes buffer to the specified file.

Throws:

loci.formats.FormatException

java.io.IOException

saveImage

@Deprecated
public static void saveImage(byte[] data,
                        int width,
                        int height,
                        int numChannel,
                        int dataType,
                        boolean signedDataType,
                        java.io.File file,
                        boolean force)
                      throws loci.formats.FormatException,
                             java.io.IOException

Deprecated. Use saveImage(byte[], int, int, int, DataType, File, boolean) instead

Throws:

loci.formats.FormatException

java.io.IOException

saveImage

public static void saveImage(IcyBufferedImage image,
             java.io.File file,
             boolean force)
                      throws loci.formats.FormatException,
                             java.io.IOException

Save a single image to the specified file

Parameters:

image -

Throws:

java.io.IOException

loci.formats.FormatException

getCompatibleSequenceForWriter

public static Sequence getCompatibleSequenceForWriter(loci.formats.IFormatWriter writer,
                                      Sequence sequence,
                                      int posT,
                                      int posZ)

Returns a compatible Sequence representing the input sequence so it can be saved with the specified writer.
If the writer support the input sequence then the input sequence is directly returned.

Parameters:

writer - writer used to save sequence (define the image format, cannot be null)

sequence - sequence to save

posT - frame index to keep (-1 for all frame)

posZ - slice index to keep (-1 for all slice)

Returns:

the compatible sequence for given Writer