loci.formats

Class FormatTools

java.lang.Object

loci.formats.FormatTools

public final class FormatTools
extends java.lang.Object

A utility class for format reader and writer implementations.

Source code:

Trac, Gitweb

Field Summary

Fields

Modifier and Type	Field and Description
static java.lang.String[]	ALL_DOMAINS List of all supported domains.
static java.lang.String	ASTRONOMY_DOMAIN Identifies the astronomy domain.
static int	CAN_GROUP
static int	CANNOT_GROUP
static java.lang.String	CHANNEL Identifies the Channel dimensional type, representing a generic channel dimension.
static java.lang.String	CHANNEL_NAME
static java.lang.String	CHANNEL_NUM
static java.lang.String	DATE Date on which this release was built.
static int	DOUBLE Identifies the DOUBLE data type used to store pixel values.
static java.lang.String	EM_DOMAIN Identifies the electron microscopy domain.
static java.lang.String	FLIM_DOMAIN Identifies the fluorescence-lifetime domain.
static int	FLOAT Identifies the FLOAT data type used to store pixel values.
static java.lang.String	FREQUENCY Identifies the Frequency dimensional type, representing a dimension consisting of frequencies.
static java.lang.String	GEL_DOMAIN Identifies the gel and blot imaging domain.
static java.lang.String	GRAPHICS_DOMAIN Identifies the graphics domain.
static java.lang.String	HCS_DOMAIN Identifies the high content screening domain.
static java.lang.String	HISTOLOGY_DOMAIN Identifies the histology domain.
static java.lang.String	ILLUMINATION Identifies the Illumination dimensional type, representing a dimension consisting of illuminations.
static int	INT16 Identifies the INT16 data type used to store pixel values.
static int	INT32 Identifies the INT32 data type used to store pixel values.
static int	INT8 Identifies the INT8 data type used to store pixel values.
static java.lang.String	LIFETIME Identifies the Lifetime dimensional type, representing a dimension consisting of a lifetime histogram.
static java.lang.String	LM_DOMAIN Identifies the light microscopy domain.
protected static org.slf4j.Logger	LOGGER
static java.lang.String	MEDICAL_DOMAIN Identifies the medical imaging domain.
static int	MUST_GROUP File grouping options.
static java.lang.String[]	NON_GRAPHICS_DOMAINS List of non-graphics domains.
static java.lang.String[]	NON_HCS_DOMAINS List of non-HCS domains.
static java.lang.String[]	NON_SPECIAL_DOMAINS List of domains that do not require special handling.
static java.lang.String	PHASE Identifies the Phase dimensional type, representing a dimension consisting of phases.
static java.lang.String	POLARIZATION Identifies the Polarization dimensional type, representing a dimension consisting of polarization states.
static java.lang.String	PROPERTY_FILE
static java.lang.String	ROTATION Identifies the Rotation dimensional type, representing a dimension consisting of rotations.
static java.lang.String	SEM_DOMAIN Identifies the scanning electron microscopy domain.
static java.lang.String	SERIES_NAME
static java.lang.String	SERIES_NUM Patterns to be used when constructing a pattern for output filenames.
static java.lang.String	SPECTRA Identifies the Spectra dimensional type, representing a dimension consisting of spectral channels.
static java.lang.String	SPM_DOMAIN Identifies the scanning probe microscopy domain.
static java.lang.String	T_NUM
static java.lang.String	TIMESTAMP
static int	UINT16 Identifies the UINT16 data type used to store pixel values.
static int	UINT32 Identifies the UINT32 data type used to store pixel values.
static int	UINT8 Identifies the UINT8 data type used to store pixel values.
static java.lang.String	UNKNOWN_DOMAIN Identifies an unknown domain.
static java.lang.String	URL_BIO_FORMATS URL of Bio-Formats web page.
static java.lang.String	URL_BIO_FORMATS_LIBRARIES URL of 'Bio-Formats as a Java Library' web page.
static java.lang.String	URL_OME_TIFF URL of OME-TIFF web page.
static java.lang.String	VCS_REVISION Current VCS revision.
static java.lang.String	VERSION Version number of this release.
static java.util.Properties	VERSION_PROPERTIES
static java.lang.String	YEAR Year in which this release was built.
static java.lang.String	Z_NUM

Method Summary

Methods

Modifier and Type	Method and Description
static void	assertId(java.lang.String currentId, boolean notNull, int depth) Asserts that the current file is either null, or not, according to the given flag.
static void	checkBufferSize(IFormatReader r, int len)
static void	checkBufferSize(IFormatReader r, int len, int w, int h) Checks that the given buffer size is large enough to hold a w * h image as returned by the given reader.
static void	checkPlaneNumber(IFormatReader r, int no) Checks that the given plane number is valid for the given reader.
static void	checkPlaneParameters(IFormatReader r, int no, int bufLength, int x, int y, int w, int h) Convenience method for checking that the plane number, tile size and buffer sizes are all valid for the given reader.
static void	checkTileSize(IFormatReader r, int x, int y, int w, int h) Checks that the given tile size is valid for the given reader.
static void	convert(IFormatReader input, IFormatWriter output, java.lang.String outputFile) Convenience method for writing all of the images and metadata obtained from the specified IFormatReader into the specified IFormatWriter.
static void	convert(java.lang.String input, java.lang.String output) Convenience method for converting the specified input file to the specified output file.
static long[]	defaultMinMax(int pixelType) Get the default range for the specified pixel type.
static boolean	equalReaders(IFormatReader a, IFormatReader b) Check if the two given readers are equal.
static int	getBytesPerPixel(int pixelType) Retrieves how many bytes per pixel the current plane or section has.
static int	getBytesPerPixel(java.lang.String pixelType) Retrieves the number of bytes per pixel in the current plane.
static PositiveInteger	getCutIn(java.lang.Integer value)
static PositiveInteger	getCutOut(java.lang.Integer value)
static PositiveInteger	getEmissionWavelength(java.lang.Integer value)
static PositiveInteger	getExcitationWavelength(java.lang.Integer value)
static java.lang.String	getFilename(int series, int image, IFormatReader r, java.lang.String pattern)
static java.lang.String[]	getFilenames(java.lang.String pattern, IFormatReader r)
static NonNegativeInteger	getFontSize(java.lang.Integer value)
static int	getImagesPerFile(java.lang.String pattern, IFormatReader r)
static int	getIndex(IFormatReader reader, int z, int c, int t) Gets the rasterized index corresponding to the given Z, C and T coordinates.
static int	getIndex(java.lang.String order, int zSize, int cSize, int tSize, int num, int z, int c, int t) Gets the rasterized index corresponding to the given Z, C and T coordinates.
static PositiveInteger	getMaxFieldCount(java.lang.Integer value)
static PositiveFloat	getPhysicalSizeX(java.lang.Double value)
static PositiveFloat	getPhysicalSizeY(java.lang.Double value)
static PositiveFloat	getPhysicalSizeZ(java.lang.Double value)
static java.lang.String	getPixelTypeString(int pixelType) Takes a pixel type value and gets a corresponding string representation.
static int	getPlaneSize(IFormatReader r) Returns the size in bytes of a single plane.
static int	getPlaneSize(IFormatReader r, int w, int h) Returns the size in bytes of a w * h tile.
static int	getRasterLength(int[] lengths) Computes the number of raster values for a positional array with the given lengths.
static IFormatReader	getReader(IFormatReader r, java.lang.Class<? extends IFormatReader> c) Recursively look for the first underlying reader that is an instance of the given class.
static int	getReorderedIndex(IFormatReader reader, java.lang.String newOrder, int newIndex) Converts index from the given dimension order to the reader's native one.
static int	getReorderedIndex(java.lang.String origOrder, java.lang.String newOrder, int zSize, int cSize, int tSize, int num, int newIndex) Converts index from one dimension order to another.
static PositiveInteger	getWavelength(java.lang.Integer value)
static int[]	getZCTCoords(IFormatReader reader, int index) Gets the Z, C and T coordinates corresponding to the given rasterized index value.
static int[]	getZCTCoords(java.lang.String order, int zSize, int cSize, int tSize, int num, int index) Gets the Z, C and T coordinates corresponding to the given rasterized index value.
static boolean	isFloatingPoint(int pixelType) Determines whether the given pixel type is floating point or integer.
static boolean	isSigned(int pixelType) Determines whether the given pixel type is signed or unsigned.
static byte[]	openThumbBytes(IFormatReader reader, int no) Default implementation for IFormatReader.openThumbBytes(int).
static int	pixelTypeFromBytes(int bytes, boolean signed, boolean fp) Returns an appropriate pixel type given the number of bytes per pixel.
static int	pixelTypeFromString(java.lang.String pixelTypeAsString) Takes a string value and maps it to one of the pixel type enumerations.
static int	positionToRaster(int[] lengths, int[] pos) Computes a unique 1-D index corresponding to the given multidimensional position.
static int[]	rasterToPosition(int[] lengths, int raster) Computes a unique N-D position corresponding to the given rasterized index value.
static int[]	rasterToPosition(int[] lengths, int raster, int[] pos) Computes a unique N-D position corresponding to the given rasterized index value.
static boolean	validStream(RandomAccessInputStream stream, int len, boolean littleEndian) Returns true if the given RandomAccessInputStream conatins at least 'len' bytes.

Methods inherited from class java.lang.Object

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

Field Detail

LOGGER

protected static final org.slf4j.Logger LOGGER

INT8

public static final int INT8

Identifies the INT8 data type used to store pixel values.

See Also:

Constant Field Values

UINT8

public static final int UINT8

Identifies the UINT8 data type used to store pixel values.

See Also:

Constant Field Values

INT16

public static final int INT16

Identifies the INT16 data type used to store pixel values.

See Also:

Constant Field Values

UINT16

public static final int UINT16

Identifies the UINT16 data type used to store pixel values.

See Also:

Constant Field Values

INT32

public static final int INT32

Identifies the INT32 data type used to store pixel values.

See Also:

Constant Field Values

UINT32

public static final int UINT32

Identifies the UINT32 data type used to store pixel values.

See Also:

Constant Field Values

FLOAT

public static final int FLOAT

Identifies the FLOAT data type used to store pixel values.

See Also:

Constant Field Values

DOUBLE

public static final int DOUBLE

Identifies the DOUBLE data type used to store pixel values.

See Also:

Constant Field Values

CHANNEL

public static final java.lang.String CHANNEL

Identifies the Channel dimensional type, representing a generic channel dimension.

See Also:

Constant Field Values

SPECTRA

public static final java.lang.String SPECTRA

Identifies the Spectra dimensional type, representing a dimension consisting of spectral channels.

See Also:

Constant Field Values

LIFETIME

public static final java.lang.String LIFETIME

Identifies the Lifetime dimensional type, representing a dimension consisting of a lifetime histogram.

See Also:

Constant Field Values

POLARIZATION

public static final java.lang.String POLARIZATION

Identifies the Polarization dimensional type, representing a dimension consisting of polarization states.

See Also:

Constant Field Values

PHASE

public static final java.lang.String PHASE

Identifies the Phase dimensional type, representing a dimension consisting of phases.

See Also:

Constant Field Values

FREQUENCY

public static final java.lang.String FREQUENCY

Identifies the Frequency dimensional type, representing a dimension consisting of frequencies.

See Also:

Constant Field Values

ROTATION

public static final java.lang.String ROTATION

Identifies the Rotation dimensional type, representing a dimension consisting of rotations.

See Also:

Constant Field Values

ILLUMINATION

public static final java.lang.String ILLUMINATION

Identifies the Illumination dimensional type, representing a dimension consisting of illuminations.

See Also:

Constant Field Values

MUST_GROUP

public static final int MUST_GROUP

File grouping options.

See Also:

Constant Field Values

CAN_GROUP

public static final int CAN_GROUP

See Also:

Constant Field Values

CANNOT_GROUP

public static final int CANNOT_GROUP

See Also:

Constant Field Values

SERIES_NUM

public static final java.lang.String SERIES_NUM

Patterns to be used when constructing a pattern for output filenames.

See Also:

Constant Field Values

SERIES_NAME

public static final java.lang.String SERIES_NAME

See Also:

Constant Field Values

CHANNEL_NUM

public static final java.lang.String CHANNEL_NUM

See Also:

Constant Field Values

CHANNEL_NAME

public static final java.lang.String CHANNEL_NAME

See Also:

Constant Field Values

Z_NUM

public static final java.lang.String Z_NUM

See Also:

Constant Field Values

T_NUM

public static final java.lang.String T_NUM

See Also:

Constant Field Values

TIMESTAMP

public static final java.lang.String TIMESTAMP

See Also:

Constant Field Values

VERSION_PROPERTIES

public static final java.util.Properties VERSION_PROPERTIES

VCS_REVISION

public static final java.lang.String VCS_REVISION

Current VCS revision.

DATE

public static final java.lang.String DATE

Date on which this release was built.

YEAR

public static final java.lang.String YEAR

Year in which this release was built.

VERSION

public static final java.lang.String VERSION

Version number of this release.

PROPERTY_FILE

public static final java.lang.String PROPERTY_FILE

See Also:

Constant Field Values

HCS_DOMAIN

public static final java.lang.String HCS_DOMAIN

Identifies the high content screening domain.

See Also:

Constant Field Values

LM_DOMAIN

public static final java.lang.String LM_DOMAIN

Identifies the light microscopy domain.

See Also:

Constant Field Values

EM_DOMAIN

public static final java.lang.String EM_DOMAIN

Identifies the electron microscopy domain.

See Also:

Constant Field Values

SPM_DOMAIN

public static final java.lang.String SPM_DOMAIN

Identifies the scanning probe microscopy domain.

See Also:

Constant Field Values

SEM_DOMAIN

public static final java.lang.String SEM_DOMAIN

Identifies the scanning electron microscopy domain.

See Also:

Constant Field Values

FLIM_DOMAIN

public static final java.lang.String FLIM_DOMAIN

Identifies the fluorescence-lifetime domain.

See Also:

Constant Field Values

MEDICAL_DOMAIN

public static final java.lang.String MEDICAL_DOMAIN

Identifies the medical imaging domain.

See Also:

Constant Field Values

HISTOLOGY_DOMAIN

public static final java.lang.String HISTOLOGY_DOMAIN

Identifies the histology domain.

See Also:

Constant Field Values

GEL_DOMAIN

public static final java.lang.String GEL_DOMAIN

Identifies the gel and blot imaging domain.

See Also:

Constant Field Values

ASTRONOMY_DOMAIN

public static final java.lang.String ASTRONOMY_DOMAIN

Identifies the astronomy domain.

See Also:

Constant Field Values

GRAPHICS_DOMAIN

public static final java.lang.String GRAPHICS_DOMAIN

Identifies the graphics domain. This includes formats used exclusively by analysis software.

See Also:

Constant Field Values

UNKNOWN_DOMAIN

public static final java.lang.String UNKNOWN_DOMAIN

Identifies an unknown domain.

See Also:

Constant Field Values

NON_GRAPHICS_DOMAINS

public static final java.lang.String[] NON_GRAPHICS_DOMAINS

List of non-graphics domains.

NON_HCS_DOMAINS

public static final java.lang.String[] NON_HCS_DOMAINS

List of non-HCS domains.

NON_SPECIAL_DOMAINS

public static final java.lang.String[] NON_SPECIAL_DOMAINS

List of domains that do not require special handling. Domains that require special handling are GRAPHICS_DOMAIN and HCS_DOMAIN.

ALL_DOMAINS

public static final java.lang.String[] ALL_DOMAINS

List of all supported domains.

URL_BIO_FORMATS

public static final java.lang.String URL_BIO_FORMATS

URL of Bio-Formats web page.

See Also:

Constant Field Values

URL_BIO_FORMATS_LIBRARIES

public static final java.lang.String URL_BIO_FORMATS_LIBRARIES

URL of 'Bio-Formats as a Java Library' web page.

See Also:

Constant Field Values

URL_OME_TIFF

public static final java.lang.String URL_OME_TIFF

URL of OME-TIFF web page.

See Also:

Constant Field Values

Method Detail

getIndex

public static int getIndex(IFormatReader reader,
           int z,
           int c,
           int t)

Gets the rasterized index corresponding to the given Z, C and T coordinates.

getIndex

public static int getIndex(java.lang.String order,
           int zSize,
           int cSize,
           int tSize,
           int num,
           int z,
           int c,
           int t)

Gets the rasterized index corresponding to the given Z, C and T coordinates.

Parameters:

order - Dimension order.

zSize - Total number of focal planes.

cSize - Total number of channels.

tSize - Total number of time points.

num - Total number of image planes (zSize * cSize * tSize), specified as a consistency check.

z - Z coordinate of ZCT coordinate triple to convert to 1D index.

c - C coordinate of ZCT coordinate triple to convert to 1D index.

t - T coordinate of ZCT coordinate triple to convert to 1D index.

getZCTCoords

public static int[] getZCTCoords(IFormatReader reader,
                 int index)

Gets the Z, C and T coordinates corresponding to the given rasterized index value.

getZCTCoords

public static int[] getZCTCoords(java.lang.String order,
                 int zSize,
                 int cSize,
                 int tSize,
                 int num,
                 int index)

Gets the Z, C and T coordinates corresponding to the given rasterized index value.

Parameters:

order - Dimension order.

zSize - Total number of focal planes.

cSize - Total number of channels.

tSize - Total number of time points.

num - Total number of image planes (zSize * cSize * tSize), specified as a consistency check.

index - 1D (rasterized) index to convert to ZCT coordinate triple.

getReorderedIndex

public static int getReorderedIndex(IFormatReader reader,
                    java.lang.String newOrder,
                    int newIndex)
                             throws FormatException

Converts index from the given dimension order to the reader's native one. This method is useful for shuffling the planar order around (rather than eassigning ZCT sizes as DimensionSwapper does).

Throws:

FormatException - Never actually thrown.

getReorderedIndex

public static int getReorderedIndex(java.lang.String origOrder,
                    java.lang.String newOrder,
                    int zSize,
                    int cSize,
                    int tSize,
                    int num,
                    int newIndex)

Converts index from one dimension order to another. This method is useful for shuffling the planar order around (rather than eassigning ZCT sizes as DimensionSwapper does).

Parameters:

origOrder - Original dimension order.

newOrder - New dimension order.

zSize - Total number of focal planes.

cSize - Total number of channels.

tSize - Total number of time points.

num - Total number of image planes (zSize * cSize * tSize), specified as a consistency check.

newIndex - 1D (rasterized) index according to new dimension order.

Returns:

rasterized index according to original dimension order.

positionToRaster

public static int positionToRaster(int[] lengths,
                   int[] pos)

Computes a unique 1-D index corresponding to the given multidimensional position.

Parameters:

lengths - the maximum value for each positional dimension

pos - position along each dimensional axis

Returns:

rasterized index value

rasterToPosition

public static int[] rasterToPosition(int[] lengths,
                     int raster)

Computes a unique N-D position corresponding to the given rasterized index value.

Parameters:

lengths - the maximum value at each positional dimension

raster - rasterized index value

Returns:

position along each dimensional axis

rasterToPosition

public static int[] rasterToPosition(int[] lengths,
                     int raster,
                     int[] pos)

Computes a unique N-D position corresponding to the given rasterized index value.

Parameters:

lengths - the maximum value at each positional dimension

raster - rasterized index value

pos - preallocated position array to populate with the result

Returns:

position along each dimensional axis

getRasterLength

public static int getRasterLength(int[] lengths)

Computes the number of raster values for a positional array with the given lengths.

pixelTypeFromString

public static int pixelTypeFromString(java.lang.String pixelTypeAsString)

Takes a string value and maps it to one of the pixel type enumerations.

Parameters:

pixelTypeAsString - the pixel type as a string.

Returns:

type enumeration value for use with class constants.

getPixelTypeString

public static java.lang.String getPixelTypeString(int pixelType)

Takes a pixel type value and gets a corresponding string representation.

Parameters:

pixelType - the pixel type.

Returns:

string value for human-readable output.

getBytesPerPixel

public static int getBytesPerPixel(int pixelType)

Retrieves how many bytes per pixel the current plane or section has.

Parameters:

pixelType - the pixel type as retrieved from IFormatReader.getPixelType().

Returns:

the number of bytes per pixel.

See Also:

IFormatReader.getPixelType()

getBytesPerPixel

public static int getBytesPerPixel(java.lang.String pixelType)

Retrieves the number of bytes per pixel in the current plane.

Parameters:

pixelType - the pixel type, as a String.

Returns:

the number of bytes per pixel.

See Also:

pixelTypeFromString(String), getBytesPerPixel(int)

isFloatingPoint

public static boolean isFloatingPoint(int pixelType)

Determines whether the given pixel type is floating point or integer.

Parameters:

pixelType - the pixel type as retrieved from IFormatReader.getPixelType().

Returns:

true if the pixel type is floating point.

See Also:

IFormatReader.getPixelType()

isSigned

public static boolean isSigned(int pixelType)

Determines whether the given pixel type is signed or unsigned.

Parameters:

pixelType - the pixel type as retrieved from IFormatReader.getPixelType().

Returns:

true if the pixel type is signed.

See Also:

IFormatReader.getPixelType()

pixelTypeFromBytes

public static int pixelTypeFromBytes(int bytes,
                     boolean signed,
                     boolean fp)
                              throws FormatException

Returns an appropriate pixel type given the number of bytes per pixel.

Parameters:

bytes - number of bytes per pixel.

signed - whether or not the pixel type should be signed.

fp - whether or not these are floating point pixels.

Throws:

FormatException

assertId

public static void assertId(java.lang.String currentId,
            boolean notNull,
            int depth)

Asserts that the current file is either null, or not, according to the given flag. If the assertion fails, an IllegalStateException is thrown.

Parameters:

currentId - File name to test.

notNull - True iff id should be non-null.

depth - How far back in the stack the calling method is; this name is reported as part of the exception message, if available. Use zero to suppress output of the calling method name.

checkPlaneParameters

public static void checkPlaneParameters(IFormatReader r,
                        int no,
                        int bufLength,
                        int x,
                        int y,
                        int w,
                        int h)
                                 throws FormatException

Convenience method for checking that the plane number, tile size and buffer sizes are all valid for the given reader. If 'bufLength' is less than 0, then the buffer length check is not performed.

Throws:

FormatException

checkPlaneNumber

public static void checkPlaneNumber(IFormatReader r,
                    int no)
                             throws FormatException

Checks that the given plane number is valid for the given reader.

Throws:

FormatException

checkTileSize

public static void checkTileSize(IFormatReader r,
                 int x,
                 int y,
                 int w,
                 int h)
                          throws FormatException

Checks that the given tile size is valid for the given reader.

Throws:

FormatException

checkBufferSize

public static void checkBufferSize(IFormatReader r,
                   int len)
                            throws FormatException

Throws:

FormatException

checkBufferSize

public static void checkBufferSize(IFormatReader r,
                   int len,
                   int w,
                   int h)
                            throws FormatException

Checks that the given buffer size is large enough to hold a w * h image as returned by the given reader.

Throws:

FormatException - if the buffer is too small

validStream

public static boolean validStream(RandomAccessInputStream stream,
                  int len,
                  boolean littleEndian)
                           throws java.io.IOException

Returns true if the given RandomAccessInputStream conatins at least 'len' bytes.

Throws:

java.io.IOException

getPlaneSize

public static int getPlaneSize(IFormatReader r)

Returns the size in bytes of a single plane.

getPlaneSize

public static int getPlaneSize(IFormatReader r,
               int w,
               int h)

Returns the size in bytes of a w * h tile.

getFilename

public static java.lang.String getFilename(int series,
                           int image,
                           IFormatReader r,
                           java.lang.String pattern)
                                    throws FormatException,
                                           java.io.IOException

Throws:

FormatException - Never actually thrown.

java.io.IOException - Never actually thrown.

getFilenames

public static java.lang.String[] getFilenames(java.lang.String pattern,
                              IFormatReader r)
                                       throws FormatException,
                                              java.io.IOException

Throws:

FormatException

java.io.IOException

getImagesPerFile

public static int getImagesPerFile(java.lang.String pattern,
                   IFormatReader r)
                            throws FormatException,
                                   java.io.IOException

Throws:

FormatException

java.io.IOException

getReader

public static IFormatReader getReader(IFormatReader r,
                      java.lang.Class<? extends IFormatReader> c)

Recursively look for the first underlying reader that is an instance of the given class.

equalReaders

public static boolean equalReaders(IFormatReader a,
                   IFormatReader b)

Check if the two given readers are equal. To be equal, readers must contain the same stack of wrappers and the same state.

openThumbBytes

public static byte[] openThumbBytes(IFormatReader reader,
                    int no)
                             throws FormatException,
                                    java.io.IOException

Default implementation for IFormatReader.openThumbBytes(int). At the moment, it uses BufferedImage objects to resize thumbnails, so it is not safe for use in headless contexts. In the future, we may reimplement the image scaling logic purely with byte arrays, but handling every case would be substantial effort, so doing so is currently a low priority item.

Throws:

FormatException

java.io.IOException

convert

public static void convert(java.lang.String input,
           java.lang.String output)
                    throws FormatException,
                           java.io.IOException

Convenience method for converting the specified input file to the specified output file. The ImageReader and ImageWriter classes are used for input and output, respectively. To use other IFormatReader or IFormatWriter implementation,

Parameters:

input - the full path name of the existing input file

output - the full path name of the output file to be created

Throws:

FormatException - if there is a general problem reading from or writing to one of the files.

java.io.IOException - if there is an I/O-related error.

See Also:

convert(IFormatReader, IFormatWriter, String).

convert

public static void convert(IFormatReader input,
           IFormatWriter output,
           java.lang.String outputFile)
                    throws FormatException,
                           java.io.IOException

Convenience method for writing all of the images and metadata obtained from the specified IFormatReader into the specified IFormatWriter. It is required that setId(String) be called on the IFormatReader object before it is passed to convert(...). setMetadataStore(...) should also have been called with an appropriate instance of IMetadata. The setId(String) method must not be called on the IFormatWriter object; this is taken care of internally. Additionally, the setMetadataRetrieve(...) method in IFormatWriter should not be called.

Parameters:

input - the pre-initialized IFormatReader used for reading data.

output - the uninitialized IFormatWriter used for writing data.

outputFile - the full path name of the output file to be created.

Throws:

FormatException - if there is a general problem reading from or writing to one of the files.

java.io.IOException - if there is an I/O-related error.

defaultMinMax

public static long[] defaultMinMax(int pixelType)

Get the default range for the specified pixel type. Note that this is not necessarily the minimum and maximum value which may be stored, but the minimum and maximum which should be used for rendering.

Parameters:

pixelType - the pixel type.

Throws:

java.io.IOException - if the pixel type is floating point or invalid.

getPhysicalSizeX

public static PositiveFloat getPhysicalSizeX(java.lang.Double value)

getPhysicalSizeY

public static PositiveFloat getPhysicalSizeY(java.lang.Double value)

getPhysicalSizeZ

public static PositiveFloat getPhysicalSizeZ(java.lang.Double value)

getEmissionWavelength

public static PositiveInteger getEmissionWavelength(java.lang.Integer value)

getExcitationWavelength

public static PositiveInteger getExcitationWavelength(java.lang.Integer value)

getWavelength

public static PositiveInteger getWavelength(java.lang.Integer value)

getMaxFieldCount

public static PositiveInteger getMaxFieldCount(java.lang.Integer value)

getCutIn

public static PositiveInteger getCutIn(java.lang.Integer value)

getCutOut

public static PositiveInteger getCutOut(java.lang.Integer value)

getFontSize

public static NonNegativeInteger getFontSize(java.lang.Integer value)