FormatTools (Bio-Formats API)

java.lang.Object
- loci.formats.FormatTools

```
public final class FormatTools
extends Object
```
A utility class for format reader and writer implementations.

Field Summary

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

Constructor Summary

Constructors
Modifier Constructor and Description

private FormatTools()

Constructors
Modifier	Constructor and Description
`private`	`FormatTools()`

Method Summary

Methods
Modifier and Type	Method and Description
`static void`	`assertId(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, String outputFile)` Convenience method for writing all of the images and metadata obtained from the specified IFormatReader into the specified IFormatWriter.
`static void`	`convert(String input, String output)` Convenience method for converting the specified input file to the specified output file.
`static Angle`	`createAngle(Double value, Unit<Angle> valueUnit)`
`static Angle`	`createAngle(Integer value, Unit<Angle> valueUnit)`
`static <T extends PrimitiveNumber> Angle`	`createAngle(T value, Unit<Angle> valueUnit)`
`static ElectricPotential`	`createElectricPotential(Double value, Unit<ElectricPotential> valueUnit)`
`static ElectricPotential`	`createElectricPotential(Integer value, Unit<ElectricPotential> valueUnit)`
`static <T extends PrimitiveNumber> ElectricPotential`	`createElectricPotential(T value, Unit<ElectricPotential> valueUnit)`
`static Frequency`	`createFrequency(Double value, Unit<Frequency> valueUnit)`
`static Frequency`	`createFrequency(Integer value, Unit<Frequency> valueUnit)`
`static <T extends PrimitiveNumber> Frequency`	`createFrequency(T value, Unit<Frequency> valueUnit)`
`static Length`	`createLength(Double value, Unit<Length> valueUnit)`
`static Length`	`createLength(Integer value, Unit<Length> valueUnit)`
`static <T extends PrimitiveNumber> Length`	`createLength(T value, Unit<Length> valueUnit)`
`static Power`	`createPower(Double value, Unit<Power> valueUnit)`
`static Power`	`createPower(Integer value, Unit<Power> valueUnit)`
`static <T extends PrimitiveNumber> Power`	`createPower(T value, Unit<Power> valueUnit)`
`static Pressure`	`createPressure(Double value, Unit<Pressure> valueUnit)`
`static Pressure`	`createPressure(Integer value, Unit<Pressure> valueUnit)`
`static <T extends PrimitiveNumber> Pressure`	`createPressure(T value, Unit<Pressure> valueUnit)`
`static Temperature`	`createTemperature(Double value, Unit<Temperature> valueUnit)`
`static Temperature`	`createTemperature(Integer value, Unit<Temperature> valueUnit)`
`static <T extends PrimitiveNumber> Temperature`	`createTemperature(T value, Unit<Temperature> valueUnit)`
`static Time`	`createTime(Double value, Unit<Time> valueUnit)`
`static Time`	`createTime(Integer value, Unit<Time> valueUnit)`
`static <T extends PrimitiveNumber> Time`	`createTime(T value, Unit<Time> valueUnit)`
`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(String pixelType)` Retrieves the number of bytes per pixel in the current plane.
`static Length`	`getCutIn(Double value)`
`static Length`	`getCutOut(Double value)`
`static Length`	`getEmissionWavelength(Double value)`
`static Length`	`getExcitationWavelength(Double value)`
`static String`	`getFilename(int series, int image, IFormatReader r, String pattern)`
`static String[]`	`getFilenames(String pattern, IFormatReader r)`
`static Length`	`getFontSize(Integer value)`
`static int`	`getImagesPerFile(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 (real sizes).
`static int`	`getIndex(IFormatReader reader, int z, int c, int t, int moduloZ, int moduloC, int moduloT)` Gets the rasterized index corresponding to the given Z, C, T, ModuloZ, ModuloC and ModuloT coordinates (effective sizes).
`static int`	`getIndex(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 (real sizes).
`static int`	`getIndex(String order, int zSize, int cSize, int tSize, int moduloZSize, int moduloCSize, int moduloTSize, int num, int z, int c, int t, int moduloZ, int moduloC, int moduloT)` Gets the rasterized index corresponding to the given Z, C, T, ModuloZ, ModuloC, ModuloT coordinates (effective sizes).
`static PositiveInteger`	`getMaxFieldCount(Integer value)`
`static Length`	`getPhysicalSize(Double value, String unit)`
`static Length`	`getPhysicalSizeX(Double value)` Formats the input value for the physical size in X into a length in microns
`static Length`	`getPhysicalSizeX(Double value, String unit)` Formats the input value for the physical size in X into a length of the given unit.
`static Length`	`getPhysicalSizeX(Double value, Unit<Length> unit)` Formats the input value for the physical size in X into a length of the given unit.
`static Length`	`getPhysicalSizeY(Double value)` Formats the input value for the physical size in Y into a length in microns
`static Length`	`getPhysicalSizeY(Double value, String unit)` Formats the input value for the physical size in Y into a length of the given unit.
`static Length`	`getPhysicalSizeY(Double value, Unit<Length> unit)` Formats the input value for the physical size in Y into a length of the given unit.
`static Length`	`getPhysicalSizeZ(Double value)` Formats the input value for the physical size in Z into a length in microns
`static Length`	`getPhysicalSizeZ(Double value, String unit)` Formats the input value for the physical size in Z into a length of the given unit.
`static Length`	`getPhysicalSizeZ(Double value, Unit<Length> unit)` Formats the input value for the physical size in Z into a length of the given unit.
`static 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, Class<? extends IFormatReader> c)` Recursively look for the first underlying reader that is an instance of the given class.
`static int`	`getReorderedIndex(IFormatReader reader, String newOrder, int newIndex)` Converts index from the given dimension order to the reader's native one.
`static int`	`getReorderedIndex(String origOrder, String newOrder, int zSize, int cSize, int tSize, int num, int newIndex)` Converts index from one dimension order to another.
`static String`	`getTileFilename(int tileX, int tileY, int tileIndex, String pattern)`
`static Time`	`getTime(Double value, String unit)` Formats the input value for the time into a length of the given unit.
`static Length`	`getWavelength(Double value)`
`static Length`	`getWavelength(Double value, String unit)` Formats the input value for the wavelength into a length of the given unit.
`static int[]`	`getZCTCoords(IFormatReader reader, int index)` Gets the Z, C and T coordinates corresponding to the given rasterized index value (real sizes).
`static int[]`	`getZCTCoords(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 (real sizes).
`static int[]`	`getZCTCoords(String order, int zSize, int cSize, int tSize, int moduloZSize, int moduloCSize, int moduloTSize, int num, int index)` Gets the Z, C and T coordinates corresponding to the given rasterized index value.
`static int[]`	`getZCTModuloCoords(IFormatReader reader, int index)` Gets the Z, C, T, ModuloZ, ModuloC and ModuloZ coordinates corresponding to the given rasterized index value (effective sizes).
`static boolean`	`isFloatingPoint(IFormatReader reader)` Determines whether the given reader represents any floating point data.
`static boolean`	`isFloatingPoint(int pixelType)` Determines whether the given pixel type is floating point or integer.
`static boolean`	`isPositiveValue(Double value)`
`static boolean`	`isSigned(int pixelType)` Determines whether the given pixel type is signed or unsigned.
`(package private) static Properties`	`loadProperties()`
`(package private) static String[]`	`makePixelTypes()`
`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(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
  - BIT
```
public static final int BIT
```
    Identifies the BIT data type used to store pixel values.
    
    See Also:
    Constant Field Values
  - pixelTypes
```
private static final String[] pixelTypes
```
    Human readable pixel type.
  - CHANNEL
```
public static final String CHANNEL
```
    Identifies the Channel dimensional type, representing a generic channel dimension.
    
    See Also:
    Constant Field Values
  - SPECTRA
```
public static final String SPECTRA
```
    Identifies the Spectra dimensional type, representing a dimension consisting of spectral channels.
    
    See Also:
    Constant Field Values
  - LIFETIME
```
public static final String LIFETIME
```
    Identifies the Lifetime dimensional type, representing a dimension consisting of a lifetime histogram.
    
    See Also:
    Constant Field Values
  - POLARIZATION
```
public static final String POLARIZATION
```
    Identifies the Polarization dimensional type, representing a dimension consisting of polarization states.
    
    See Also:
    Constant Field Values
  - PHASE
```
public static final String PHASE
```
    Identifies the Phase dimensional type, representing a dimension consisting of phases.
    
    See Also:
    Constant Field Values
  - FREQUENCY
```
public static final String FREQUENCY
```
    Identifies the Frequency dimensional type, representing a dimension consisting of frequencies.
    
    See Also:
    Constant Field Values
  - ROTATION
```
public static final String ROTATION
```
    Identifies the Rotation dimensional type, representing a dimension consisting of rotations.
    
    See Also:
    Constant Field Values
  - ILLUMINATION
```
public static final 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 String SERIES_NUM
```
    Patterns to be used when constructing a pattern for output filenames.
    
    See Also:
    Constant Field Values
  - SERIES_NAME
```
public static final String SERIES_NAME
```
    See Also:
    Constant Field Values
  - CHANNEL_NUM
```
public static final String CHANNEL_NUM
```
    See Also:
    Constant Field Values
  - CHANNEL_NAME
```
public static final String CHANNEL_NAME
```
    See Also:
    Constant Field Values
  - Z_NUM
```
public static final String Z_NUM
```
    See Also:
    Constant Field Values
  - T_NUM
```
public static final String T_NUM
```
    See Also:
    Constant Field Values
  - TIMESTAMP
```
public static final String TIMESTAMP
```
    See Also:
    Constant Field Values
  - TILE_X
```
public static final String TILE_X
```
    See Also:
    Constant Field Values
  - TILE_Y
```
public static final String TILE_Y
```
    See Also:
    Constant Field Values
  - TILE_NUM
```
public static final String TILE_NUM
```
    See Also:
    Constant Field Values
  - VERSION_PROPERTIES
```
public static final Properties VERSION_PROPERTIES
```
  - VCS_REVISION
```
public static final String VCS_REVISION
```
    Current VCS revision.
  - VCS_SHORT_REVISION
```
public static final String VCS_SHORT_REVISION
```
    Current VCS revision (short form).
  - DATE
```
public static final String DATE
```
    Date on which this release was built.
  - YEAR
```
public static final String YEAR
```
    Year in which this release was built.
  - VERSION
```
public static final String VERSION
```
    Version number of this release.
  - PROPERTY_FILE
```
public static final String PROPERTY_FILE
```
    See Also:
    Constant Field Values
  - HCS_DOMAIN
```
public static final String HCS_DOMAIN
```
    Identifies the high content screening domain.
    
    See Also:
    Constant Field Values
  - LM_DOMAIN
```
public static final String LM_DOMAIN
```
    Identifies the light microscopy domain.
    
    See Also:
    Constant Field Values
  - EM_DOMAIN
```
public static final String EM_DOMAIN
```
    Identifies the electron microscopy domain.
    
    See Also:
    Constant Field Values
  - SPM_DOMAIN
```
public static final String SPM_DOMAIN
```
    Identifies the scanning probe microscopy domain.
    
    See Also:
    Constant Field Values
  - SEM_DOMAIN
```
public static final String SEM_DOMAIN
```
    Identifies the scanning electron microscopy domain.
    
    See Also:
    Constant Field Values
  - FLIM_DOMAIN
```
public static final String FLIM_DOMAIN
```
    Identifies the fluorescence-lifetime domain.
    
    See Also:
    Constant Field Values
  - MEDICAL_DOMAIN
```
public static final String MEDICAL_DOMAIN
```
    Identifies the medical imaging domain.
    
    See Also:
    Constant Field Values
  - HISTOLOGY_DOMAIN
```
public static final String HISTOLOGY_DOMAIN
```
    Identifies the histology domain.
    
    See Also:
    Constant Field Values
  - GEL_DOMAIN
```
public static final String GEL_DOMAIN
```
    Identifies the gel and blot imaging domain.
    
    See Also:
    Constant Field Values
  - ASTRONOMY_DOMAIN
```
public static final String ASTRONOMY_DOMAIN
```
    Identifies the astronomy domain.
    
    See Also:
    Constant Field Values
  - GRAPHICS_DOMAIN
```
public static final 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 String UNKNOWN_DOMAIN
```
    Identifies an unknown domain.
    
    See Also:
    Constant Field Values
  - NON_GRAPHICS_DOMAINS
```
public static final String[] NON_GRAPHICS_DOMAINS
```
    List of non-graphics domains.
  - NON_HCS_DOMAINS
```
public static final String[] NON_HCS_DOMAINS
```
    List of non-HCS domains.
  - NON_SPECIAL_DOMAINS
```
public static final 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 String[] ALL_DOMAINS
```
    List of all supported domains.
  - URL_BIO_FORMATS
```
public static final String URL_BIO_FORMATS
```
    URL of Bio-Formats web page.
    
    See Also:
    Constant Field Values
  - URL_BIO_FORMATS_LIBRARIES
```
public static final 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 String URL_OME_TIFF
```
    URL of OME-TIFF web page.
    
    See Also:
    Constant Field Values
- Constructor Detail
  - FormatTools
```
private FormatTools()
```
- Method Detail
  - makePixelTypes
```
static String[] makePixelTypes()
```
  - loadProperties
```
static Properties loadProperties()
```
  - 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 (real sizes).
  - getIndex
```
public static int getIndex(IFormatReader reader,
           int z,
           int c,
           int t,
           int moduloZ,
           int moduloC,
           int moduloT)
```
    Gets the rasterized index corresponding to the given Z, C, T, ModuloZ, ModuloC and ModuloT coordinates (effective sizes). Note that the Z, C and T coordinates take the modulo dimension sizes into account. The effective size for each of these dimensions is limited to the total size of the dimension divided by the modulo size.
  - getIndex
```
public static int getIndex(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 (real sizes).
    
    Parameters:
    order - Dimension order.
    zSize - Total number of focal planes (real size).
    cSize - Total number of channels (real size).
    tSize - Total number of time points (real size).
    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 (real size).
    c - C coordinate of ZCT coordinate triple to convert to 1D index (real size).
    t - T coordinate of ZCT coordinate triple to convert to 1D index (real size).
  - getIndex
```
public static int getIndex(String order,
           int zSize,
           int cSize,
           int tSize,
           int moduloZSize,
           int moduloCSize,
           int moduloTSize,
           int num,
           int z,
           int c,
           int t,
           int moduloZ,
           int moduloC,
           int moduloT)
```
    Gets the rasterized index corresponding to the given Z, C, T, ModuloZ, ModuloC, ModuloT coordinates (effective sizes). Note that the Z, C and T coordinates take the modulo dimension sizes into account. The effective size for each of these dimensions is limited to the total size of the dimension divided by the modulo size.
    
    Parameters:
    order - Dimension order.
    zSize - Total number of focal planes (real size).
    cSize - Total number of channels (real size).
    tSize - Total number of time points (real size).
    moduloZSize - Total number of ModuloZ planes (real size).
    moduloCSize - Total number of ModuloC planes (real size).
    moduloTSize - Total number of ModuloT planes (real size).
    num - Total number of image planes (zSize * cSize * tSize), specified as a consistency check.
    z - Z coordinate of ZCTmZmCmT coordinate sextuple to convert to 1D index (effective size).
    c - C coordinate of ZCTmZmCmT coordinate sextuple to convert to 1D index (effective size).
    t - T coordinate of ZCTmZmCmT coordinate sextuple to convert to 1D index (effective size).
    moduloZ - ModuloZ coordinate of ZCTmZmCmT coordinate sextuple to convert to 1D index (effective size).
    moduloC - ModuloC coordinate of ZCTmZmCmT coordinate sextuple to convert to 1D index (effective size).
    moduloT - ModuloT coordinate of ZCTmZmCmT coordinate sextuple to convert to 1D index (effective size).
  - getZCTCoords
```
public static int[] getZCTCoords(IFormatReader reader,
                 int index)
```
    Gets the Z, C and T coordinates corresponding to the given rasterized index value (real sizes).
  - getZCTModuloCoords
```
public static int[] getZCTModuloCoords(IFormatReader reader,
                       int index)
```
    Gets the Z, C, T, ModuloZ, ModuloC and ModuloZ coordinates corresponding to the given rasterized index value (effective sizes). Note that the Z, C and T coordinates are not the same as those returned by getZCTCoords(IFormatReader, int) because the size of the modulo dimensions is taken into account. The effective size for each of these dimensions is limited to the total size of the dimension divided by the modulo size.
  - getZCTCoords
```
public static int[] getZCTCoords(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 (real sizes).
    
    Parameters:
    order - Dimension order.
    zSize - Total number of focal planes (real size).
    cSize - Total number of channels (real size).
    tSize - Total number of time points (real size).
    num - Total number of image planes (zSize * cSize * tSize), specified as a consistency check.
    index - 1D (rasterized) index to convert to ZCT coordinate triple.
  - getZCTCoords
```
public static int[] getZCTCoords(String order,
                 int zSize,
                 int cSize,
                 int tSize,
                 int moduloZSize,
                 int moduloCSize,
                 int moduloTSize,
                 int num,
                 int index)
```
    Gets the Z, C and T coordinates corresponding to the given rasterized index value. Note that the Z, C and T coordinates are not the same as those returned by getZCTCoords(String, int, int, int, int, int) because the size of the modulo dimensions is taken into account. The effective size for each of these dimensions is limited to the total size of the dimension divided by the modulo size.
    
    Parameters:
    order - Dimension order.
    zSize - Total number of focal planes (real size).
    cSize - Total number of channels (real size).
    tSize - Total number of time points (real size).
    moduloZSize - Total number of ModuloZ planes (real size).
    moduloCSize - Total number of ModuloC planes (real size).
    moduloTSize - Total number of ModuloT planes (real size).
    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,
                    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(String origOrder,
                    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 (real size).
    cSize - Total number of channels (real size).
    tSize - Total number of time points (real size).
    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(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 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(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(IFormatReader reader)
```
    Determines whether the given reader represents any floating point data.
    
    Parameters:
    reader - the reader to check
    
    Returns:
    true if any of the reader's series have a floating point pixel type
    See Also:
    isFloatingPoint(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(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 IOException
```
    Returns true if the given RandomAccessInputStream conatins at least 'len' bytes.
    
    Throws:
    
    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.
  - getTileFilename
```
public static String getTileFilename(int tileX,
                     int tileY,
                     int tileIndex,
                     String pattern)
```
  - getFilename
```
public static String getFilename(int series,
                 int image,
                 IFormatReader r,
                 String pattern)
                          throws FormatException,
                                 IOException
```
    Throws:
    
    FormatException - Never actually thrown.
    
    IOException - Never actually thrown.
  - getFilenames
```
public static String[] getFilenames(String pattern,
                    IFormatReader r)
                             throws FormatException,
                                    IOException
```
    Throws:
    
    FormatException
    
    IOException
  - getImagesPerFile
```
public static int getImagesPerFile(String pattern,
                   IFormatReader r)
                            throws FormatException,
                                   IOException
```
    Throws:
    
    FormatException
    
    IOException
  - getReader
```
public static IFormatReader getReader(IFormatReader r,
                      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,
                                    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
    
    IOException
  - convert
```
public static void convert(String input,
           String output)
                    throws FormatException,
                           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.
    
    IOException - if there is an I/O-related error.
    See Also:
    convert(IFormatReader, IFormatWriter, String).
  - convert
```
public static void convert(IFormatReader input,
           IFormatWriter output,
           String outputFile)
                    throws FormatException,
                           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.
    
    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.
    
    Returns:
    an array containing the min and max as elements 0 and 1, respectively.
    
    Throws:
    
    IOException - if the pixel type is floating point or invalid.
  - isPositiveValue
```
public static boolean isPositiveValue(Double value)
```
  - getWavelength
```
public static Length getWavelength(Double value,
                   String unit)
```
    Formats the input value for the wavelength into a length of the given unit.
    
    Parameters:
    value - the value of the wavelength
    unit - the unit of the wavelength. If null will default to Nanometre
    
    Returns:
    the wavelength formatted as a Length
  - getTime
```
public static Time getTime(Double value,
           String unit)
```
    Formats the input value for the time into a length of the given unit.
    
    Parameters:
    value - the value of the time
    unit - the unit of the time. If null will default to Seconds
    
    Returns:
    the wavelength formatted as a Length
  - getPhysicalSize
```
public static Length getPhysicalSize(Double value,
                     String unit)
```
  - getPhysicalSizeX
```
public static Length getPhysicalSizeX(Double value)
```
    Formats the input value for the physical size in X into a length in microns
    
    Parameters:
    value - the value of the physical size in X in microns
    
    Returns:
    the physical size formatted as a Length
  - getPhysicalSizeX
```
public static Length getPhysicalSizeX(Double value,
                      String unit)
```
    Formats the input value for the physical size in X into a length of the given unit.
    
    Parameters:
    value - the value of the physical size in X
    unit - the unit of the physical size in X. If null, default to microns.
    
    Returns:
    the physical size formatted as a Length
  - getPhysicalSizeX
```
public static Length getPhysicalSizeX(Double value,
                      Unit<Length> unit)
```
    Formats the input value for the physical size in X into a length of the given unit.
    
    Parameters:
    value - the value of the physical size in X
    unit - the unit of the physical size in X
    
    Returns:
    the physical size formatted as a Length
  - getPhysicalSizeY
```
public static Length getPhysicalSizeY(Double value)
```
    Formats the input value for the physical size in Y into a length in microns
    
    Parameters:
    value - the value of the physical size in Y in microns
    
    Returns:
    the physical size formatted as a Length
  - getPhysicalSizeY
```
public static Length getPhysicalSizeY(Double value,
                      String unit)
```
    Formats the input value for the physical size in Y into a length of the given unit.
    
    Parameters:
    value - the value of the physical size in Y
    unit - the unit of the physical size in Y. If null, default to microns.
    
    Returns:
    the physical size formatted as a Length
  - getPhysicalSizeY
```
public static Length getPhysicalSizeY(Double value,
                      Unit<Length> unit)
```
    Formats the input value for the physical size in Y into a length of the given unit.
    
    Parameters:
    value - the value of the physical size in Y
    unit - the unit of the physical size in Y
    
    Returns:
    the physical size formatted as a Length
  - getPhysicalSizeZ
```
public static Length getPhysicalSizeZ(Double value)
```
    Formats the input value for the physical size in Z into a length in microns
    
    Parameters:
    value - the value of the physical size in Z in microns
    
    Returns:
    the physical size formatted as a Length
  - getPhysicalSizeZ
```
public static Length getPhysicalSizeZ(Double value,
                      String unit)
```
    Formats the input value for the physical size in Z into a length of the given unit.
    
    Parameters:
    value - the value of the physical size in Z
    unit - the unit of the physical size in Z. If null, default to microns.
    
    Returns:
    the physical size formatted as a Length
  - getPhysicalSizeZ
```
public static Length getPhysicalSizeZ(Double value,
                      Unit<Length> unit)
```
    Formats the input value for the physical size in Z into a length of the given unit.
    
    Parameters:
    value - the value of the physical size in Z
    unit - the unit of the physical size in Z
    
    Returns:
    the physical size formatted as a Length
  - getEmissionWavelength
```
public static Length getEmissionWavelength(Double value)
```
  - getExcitationWavelength
```
public static Length getExcitationWavelength(Double value)
```
  - getWavelength
```
public static Length getWavelength(Double value)
```
  - getMaxFieldCount
```
public static PositiveInteger getMaxFieldCount(Integer value)
```
  - getCutIn
```
public static Length getCutIn(Double value)
```
  - getCutOut
```
public static Length getCutOut(Double value)
```
  - getFontSize
```
public static Length getFontSize(Integer value)
```
  - createAngle
```
public static Angle createAngle(Double value,
                Unit<Angle> valueUnit)
```
  - createAngle
```
public static Angle createAngle(Integer value,
                Unit<Angle> valueUnit)
```
  - createAngle
```
public static <T extends PrimitiveNumber> Angle createAngle(T value,
                                            Unit<Angle> valueUnit)
```
  - createElectricPotential
```
public static ElectricPotential createElectricPotential(Double value,
                                        Unit<ElectricPotential> valueUnit)
```
  - createElectricPotential
```
public static ElectricPotential createElectricPotential(Integer value,
                                        Unit<ElectricPotential> valueUnit)
```
  - createElectricPotential
```
public static <T extends PrimitiveNumber> ElectricPotential createElectricPotential(T value,
                                                                    Unit<ElectricPotential> valueUnit)
```
  - createFrequency
```
public static Frequency createFrequency(Double value,
                        Unit<Frequency> valueUnit)
```
  - createFrequency
```
public static Frequency createFrequency(Integer value,
                        Unit<Frequency> valueUnit)
```
  - createFrequency
```
public static <T extends PrimitiveNumber> Frequency createFrequency(T value,
                                                    Unit<Frequency> valueUnit)
```
  - createPower
```
public static Power createPower(Double value,
                Unit<Power> valueUnit)
```
  - createPower
```
public static Power createPower(Integer value,
                Unit<Power> valueUnit)
```
  - createPower
```
public static <T extends PrimitiveNumber> Power createPower(T value,
                                            Unit<Power> valueUnit)
```
  - createLength
```
public static Length createLength(Double value,
                  Unit<Length> valueUnit)
```
  - createLength
```
public static Length createLength(Integer value,
                  Unit<Length> valueUnit)
```
  - createLength
```
public static <T extends PrimitiveNumber> Length createLength(T value,
                                              Unit<Length> valueUnit)
```
  - createPressure
```
public static Pressure createPressure(Double value,
                      Unit<Pressure> valueUnit)
```
  - createPressure
```
public static Pressure createPressure(Integer value,
                      Unit<Pressure> valueUnit)
```
  - createPressure
```
public static <T extends PrimitiveNumber> Pressure createPressure(T value,
                                                  Unit<Pressure> valueUnit)
```
  - createTemperature
```
public static Temperature createTemperature(Double value,
                            Unit<Temperature> valueUnit)
```
  - createTemperature
```
public static Temperature createTemperature(Integer value,
                            Unit<Temperature> valueUnit)
```
  - createTemperature
```
public static <T extends PrimitiveNumber> Temperature createTemperature(T value,
                                                        Unit<Temperature> valueUnit)
```
  - createTime
```
public static Time createTime(Double value,
              Unit<Time> valueUnit)
```
  - createTime
```
public static Time createTime(Integer value,
              Unit<Time> valueUnit)
```
  - createTime
```
public static <T extends PrimitiveNumber> Time createTime(T value,
                                          Unit<Time> valueUnit)
```

Class FormatTools

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

LOGGER

INT8

UINT8

INT16

UINT16

INT32

UINT32

FLOAT

DOUBLE

BIT

pixelTypes

CHANNEL

SPECTRA

LIFETIME

POLARIZATION

PHASE

FREQUENCY

ROTATION

ILLUMINATION

MUST_GROUP

CAN_GROUP

CANNOT_GROUP

SERIES_NUM

SERIES_NAME

CHANNEL_NUM

CHANNEL_NAME

Z_NUM

T_NUM

TIMESTAMP

TILE_X

TILE_Y

TILE_NUM

VERSION_PROPERTIES

VCS_REVISION

VCS_SHORT_REVISION

DATE

YEAR

VERSION

PROPERTY_FILE

HCS_DOMAIN

LM_DOMAIN

EM_DOMAIN

SPM_DOMAIN

SEM_DOMAIN

FLIM_DOMAIN

MEDICAL_DOMAIN

HISTOLOGY_DOMAIN

GEL_DOMAIN

ASTRONOMY_DOMAIN

GRAPHICS_DOMAIN

UNKNOWN_DOMAIN

NON_GRAPHICS_DOMAINS

NON_HCS_DOMAINS

NON_SPECIAL_DOMAINS

ALL_DOMAINS

URL_BIO_FORMATS

URL_BIO_FORMATS_LIBRARIES

URL_OME_TIFF

Constructor Detail

FormatTools

Method Detail

makePixelTypes

loadProperties

getIndex

getIndex

getIndex

getIndex

getZCTCoords

getZCTModuloCoords

getZCTCoords

getZCTCoords

getReorderedIndex

getReorderedIndex

positionToRaster