FormatTools (SCIFIO Core 0.48.0 API)

java.lang.Object
- io.scif.util.FormatTools

```
public final class FormatTools
extends Object
```
A collection of constants and utility methods applicable for all cycles of image processing within SCIFIO.

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`	`CAN_GROUP`
`static int`	`CANNOT_GROUP`
`static String`	`CHANNEL_NAME`
`static String`	`CHANNEL_NUM`
`static String[]`	`COMPRESSION_SUFFIXES`
`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`	`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 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`	`LM_DOMAIN` Identifies the light microscopy domain.
`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`	`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`	`SPM_DOMAIN` Identifies the scanning probe microscopy domain.
`static String`	`T_NUM`
`static int`	`THUMBNAIL_DIMENSION` Default height and width for thumbnails.
`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`	`Z_NUM`

Method Summary

All Methods Static Methods Concrete Methods
Modifier and Type	Method and Description
`static void`	`assertId(Object id, boolean notNull, int depth)` Asserts that the current file is either null, or not, according to the given flag.
`static void`	`assertStream(org.scijava.io.handle.DataHandle<org.scijava.io.location.Location> stream, boolean notNull, int depth)` Asserts that the current file is either null, or not, according to the given flag.
`static void`	`calibrate(net.imagej.axis.CalibratedAxis axis, double scale, double origin)` Applies the given scale and origin to the provided `CalibratedAxis` , if it is a `LinearAxis`.
`static void`	`calibrate(net.imagej.axis.CalibratedAxis axis, double scale, double origin, String unit)` As `calibrate(CalibratedAxis, double, double)` but also sets the unit of the axis.
`static void`	`calibrate(Metadata m, int imageIndex, double[] scale)` Applies the given scale value, and an origin of 0.0, to each `LinearAxis` in the provided Metadata.
`static void`	`calibrate(Metadata m, int imageIndex, double[] scale, double[] origin)` Applies the given scale and origin values to each `LinearAxis` in the provided Metadata.
`static void`	`checkBufferSize(int imageIndex, Metadata m, int len)` Checks that the given buffer length is long enough to hold planes of the specified image index, using the provided Reader.
`static void`	`checkBufferSize(Metadata m, int len, net.imglib2.Interval bounds, int imageIndex)` Checks that the given buffer size is large enough to hold an image with the given planar lengths.
`static void`	`checkPlaneForReading(Metadata m, int imageIndex, long planeIndex, int bufLength, net.imglib2.Interval bounds)` As `checkPlaneForWriting(io.scif.Metadata, int, long, int, net.imglib2.Interval)` but also asserts that the Metadata has a non-null source attached.
`static void`	`checkPlaneForWriting(Metadata m, int imageIndex, long planeIndex, int bufLength, net.imglib2.Interval bounds)` Convenience method for checking that the plane number, tile size and buffer sizes are all valid for the given Metadata.
`static void`	`checkPlaneNumber(Metadata m, int imageIndex, long planeIndex)` Checks that the given plane number is valid for the given reader.
`static boolean`	`checkSuffix(String name, String suffix)` Performs suffix matching for the given filename.
`static boolean`	`checkSuffix(String name, String[] suffixList)` Performs suffix matching for the given filename.
`static void`	`checkTileSize(Metadata m, net.imglib2.Interval bounds, int imageIndex)` Checks that the given tile size is valid for the given reader.
`static void`	`convert(Reader input, Writer output, String outputFile)` Convenience method for writing all of the images and metadata obtained from the specified Reader into the specified Writer.
`static void`	`convert(Reader input, Writer output, String outputFile, SCIFIOConfig config)` As `convert(Reader, Writer, String)`, with configuration options.
`static net.imagej.axis.CalibratedAxis[]`	`createAxes(net.imagej.axis.AxisType... axisTypes)` Creates an array, wrapping all provided AxisTypes as CalibratedAxis with calibration = 1.0.
`static net.imagej.axis.CalibratedAxis`	`createAxis(net.imagej.axis.AxisType axisType)` Wraps the provided AxisType in a CalibratedAxis with calibration = 1.0.
`static long[]`	`defaultMinMax(ImageMetadata iMeta)` Helper method to get the default range for the specified `ImageMetadata`.
`static long[]`	`defaultMinMax(int pixelType)` Get the default range for the specified pixel type.
`static long[]`	`defaultMinMax(int bitsPerPixel, boolean signed)` Get the default range for the specified bits per pixel.
`static long[]`	`defaultMinMax(int pixelType, int bitsPerPixel)` Helper method to delegate to `defaultMinMax(int, boolean)` or `defaultMinMax(int)` based on the given parameters.
`static int`	`getBitsPerPixel(int pixelType)` Retrieves how many bytes per pixel the current plane or section has.
`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 String`	`getFilename(int imageIndex, int image, Reader r, String pattern)`
`static String[]`	`getFilenames(String pattern, Reader r)`
`static int`	`getImagesPerFile(String pattern, Reader r)`
`static long`	`getNonPlanarAxisPosition(Metadata m, int imageIndex, long planeIndex, net.imagej.axis.AxisType type)` Returns the position of the specified `AxisType` for the given image and plane indices.
`static String`	`getPixelTypeString(int pixelType)` Takes a pixel type value and gets a corresponding string representation.
`static long`	`getPlaneSize(Metadata m, int imageIndex)` Returns the size in bytes of a tile defined by the given Metadata.
`static long`	`getPlaneSize(Metadata m, net.imglib2.Interval bounds, int imageIndex)` Returns the size in bytes of a plane with the given minima and maxima.
`static long`	`getPlaneSize(Metadata m, int width, int height, int imageIndex)` Returns the size in bytes of a w * h tile.
`static long`	`getPlaneSize(Reader r, int imageIndex)` Returns the size in bytes of a single plane read by the given Reader.
`static long`	`getRasterLength(long[] lengths)` Computes the number of raster values for a positional array with the given lengths.
`static double`	`getScale(ImageMetadata imageMeta, net.imagej.axis.AxisType axisType)` Gets the average scale over the specified axis of the given image metadata.
`static double`	`getScale(Metadata m, int imageIndex, net.imagej.axis.AxisType axisType)` Gets the average scale over the specified axis of the given image metadata.
`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 long`	`nextPlaneIndex(int imageIndex, Metadata m, long[] pos, long[] offsets, long[] cropLengths)` Computes the next plane index for a given position, using the current min and max planar values.
`static long`	`nextPlaneIndex(int imageIndex, Reader r, long[] pos, long[] offsets, long[] cropLengths)` Computes the next plane index for a given position, using the current min and max planar values.
`static long`	`nextPlaneIndex(long[] lengths, long[] pos, long[] offsets, long[] cropLengths)` Computes the next plane index for a given position, using the current min and max planar values.
`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 long`	`positionToRaster(int imageIndex, Metadata m, long[] planeIndices)` Computes a unique 1-D index corresponding to the given multidimensional position.
`static long`	`positionToRaster(int imageIndex, Reader reader, long[] planeIndices)` Computes a unique 1-D index corresponding to the given multidimensional position.
`static long`	`positionToRaster(long[] lengths, long[] pos)` Computes a unique 1-D index corresponding to the given multidimensional position.
`static long[]`	`rasterToPosition(int imageIndex, long planeIndex, Metadata m)` Computes a unique N-D position corresponding to the given rasterized index value.
`static long[]`	`rasterToPosition(int imageIndex, long planeIndex, Metadata m, List<net.imagej.axis.CalibratedAxis> expectedAxis)` Computes a unique N-D position corresponding to the given rasterized index value.
`static long[]`	`rasterToPosition(int imageIndex, long planeIndex, Reader reader)` Computes a unique N-D position corresponding to the given rasterized index value.
`static long[]`	`rasterToPosition(long[] lengths, long raster)` Computes a unique N-D position corresponding to the given rasterized index value.
`static long[]`	`rasterToPosition(long[] lengths, long raster, long[] pos)` Computes a unique N-D position corresponding to the given rasterized index value.
`static boolean`	`validStream(org.scijava.io.handle.DataHandle<org.scijava.io.location.Location> handle, int len, boolean littleEndian)` Returns true if the given DataHandle contains at least 'len' bytes.
`static boolean`	`validStream(org.scijava.io.handle.DataHandle<org.scijava.io.location.Location> handle, int len, org.scijava.io.handle.DataHandle.ByteOrder order)` Returns true if the given DataHandle contains at least 'len' bytes.

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

- Field Detail
  - COMPRESSION_SUFFIXES
```
public static final String[] COMPRESSION_SUFFIXES
```
  - THUMBNAIL_DIMENSION
```
public static final int THUMBNAIL_DIMENSION
```
    Default height and width for thumbnails.
    
    See Also:
    
    Constant Field Values
  - 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
  - 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
  - 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.
- Method Detail
  - createAxis
```
public static net.imagej.axis.CalibratedAxis createAxis(net.imagej.axis.AxisType axisType)
```
    Wraps the provided AxisType in a CalibratedAxis with calibration = 1.0.
  - createAxes
```
public static net.imagej.axis.CalibratedAxis[] createAxes(net.imagej.axis.AxisType... axisTypes)
```
    Creates an array, wrapping all provided AxisTypes as CalibratedAxis with calibration = 1.0.
  - calibrate
```
public static void calibrate(Metadata m,
                             int imageIndex,
                             double[] scale)
```
    Applies the given scale value, and an origin of 0.0, to each LinearAxis in the provided Metadata.
  - calibrate
```
public static void calibrate(Metadata m,
                             int imageIndex,
                             double[] scale,
                             double[] origin)
```
    Applies the given scale and origin values to each LinearAxis in the provided Metadata.
  - calibrate
```
public static void calibrate(net.imagej.axis.CalibratedAxis axis,
                             double scale,
                             double origin)
```
    Applies the given scale and origin to the provided CalibratedAxis , if it is a LinearAxis.
    
    Throws:
    
    IllegalArgumentException - if the axis is not a LinearAxis.
  - calibrate
```
public static void calibrate(net.imagej.axis.CalibratedAxis axis,
                             double scale,
                             double origin,
                             String unit)
```
    As calibrate(CalibratedAxis, double, double) but also sets the unit of the axis.
    
    See Also:
    
    CalibratedAxis.setUnit(String)
  - getScale
```
public static double getScale(Metadata m,
                              int imageIndex,
                              net.imagej.axis.AxisType axisType)
```
    Gets the average scale over the specified axis of the given image metadata.
    
    Returns:
    
    the average scale over the axis's values, or 1.0 if the desired axis is null.
  - getScale
```
public static double getScale(ImageMetadata imageMeta,
                              net.imagej.axis.AxisType axisType)
```
    Gets the average scale over the specified axis of the given image metadata.
    
    Returns:
    
    the average scale over the axis's values, or 1.0 if the desired axis is null.
  - getNonPlanarAxisPosition
```
public static long getNonPlanarAxisPosition(Metadata m,
                                            int imageIndex,
                                            long planeIndex,
                                            net.imagej.axis.AxisType type)
```
    Returns the position of the specified AxisType for the given image and plane indices.
    
    Returns:
    
    position of the specified axis type, or 0 if the given axis is planar.
  - rasterToPosition
```
public static long[] rasterToPosition(int imageIndex,
                                      long planeIndex,
                                      Metadata m,
                                      List<net.imagej.axis.CalibratedAxis> expectedAxis)
```
    Computes a unique N-D position corresponding to the given rasterized index value.
    
    Parameters:
    
    imageIndex - image index within dataset
    
    planeIndex - rasterized plane index to convert to axis indices
    
    expectedAxis - determines the size and order of the positions in the returned array.
    
    Returns:
    
    position along each dimensional axis
  - rasterToPosition
```
public static long[] rasterToPosition(int imageIndex,
                                      long planeIndex,
                                      Reader reader)
```
    Computes a unique N-D position corresponding to the given rasterized index value.
    
    Parameters:
    
    imageIndex - image index within dataset
    
    planeIndex - rasterized plane index to convert to axis indices
    
    reader - reader used to open the dataset
    
    Returns:
    
    position along each dimensional axis
  - rasterToPosition
```
public static long[] rasterToPosition(int imageIndex,
                                      long planeIndex,
                                      Metadata m)
```
    Computes a unique N-D position corresponding to the given rasterized index value.
    
    Parameters:
    
    imageIndex - image index within dataset
    
    planeIndex - rasterized plane index to convert to axis indices
    
    m - metadata describing the dataset
    
    Returns:
    
    position along each dimensional axis
  - rasterToPosition
```
public static long[] rasterToPosition(long[] lengths,
                                      long 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 long[] rasterToPosition(long[] lengths,
                                      long raster,
                                      long[] 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
  - nextPlaneIndex
```
public static long nextPlaneIndex(int imageIndex,
                                  Reader r,
                                  long[] pos,
                                  long[] offsets,
                                  long[] cropLengths)
```
    Computes the next plane index for a given position, using the current min and max planar values. Also updates the position array appropriately.
    
    Parameters:
    
    imageIndex - image index within dataset
    
    r - reader used to open the dataset
    
    pos - current position in each dimension
    
    offsets - offsets in each dimension (potentially cropped)
    
    cropLengths - effective lengths in each dimension (potentially cropped)
    
    Returns:
    
    the next plane index, or -1 if the position extends beyond the given min/max
  - nextPlaneIndex
```
public static long nextPlaneIndex(int imageIndex,
                                  Metadata m,
                                  long[] pos,
                                  long[] offsets,
                                  long[] cropLengths)
```
    Computes the next plane index for a given position, using the current min and max planar values. Also updates the position array appropriately.
    
    Parameters:
    
    imageIndex - image index within dataset
    
    m - metadata describing the dataset
    
    pos - current position in each dimension
    
    offsets - offsets in each dimension (potentially cropped)
    
    cropLengths - effective lengths in each dimension (potentially cropped)
    
    Returns:
    
    the next plane index, or -1 if the position extends beyond the given min/max
  - nextPlaneIndex
```
public static long nextPlaneIndex(long[] lengths,
                                  long[] pos,
                                  long[] offsets,
                                  long[] cropLengths)
```
    Computes the next plane index for a given position, using the current min and max planar values. Also updates the position array appropriately.
    
    Parameters:
    
    lengths - actual dimension lengths
    
    pos - current position in each dimension
    
    offsets - offsets in each dimension (potentially cropped)
    
    cropLengths - effective lengths in each dimension (potentially cropped)
    
    Returns:
    
    the next plane index, or -1 if the position extends beyond the given min/max
  - positionToRaster
```
public static long positionToRaster(int imageIndex,
                                    Reader reader,
                                    long[] planeIndices)
```
    Computes a unique 1-D index corresponding to the given multidimensional position.
    
    Parameters:
    
    imageIndex - image index within dataset
    
    reader - reader used to open the dataset
    
    planeIndices - position along each dimensional axis
    
    Returns:
    
    rasterized index value
  - positionToRaster
```
public static long positionToRaster(int imageIndex,
                                    Metadata m,
                                    long[] planeIndices)
```
    Computes a unique 1-D index corresponding to the given multidimensional position.
    
    Parameters:
    
    imageIndex - image index within dataset
    
    m - metadata describing the dataset
    
    planeIndices - position along each dimensional axis
    
    Returns:
    
    rasterized index value
  - positionToRaster
```
public static long positionToRaster(long[] lengths,
                                    long[] 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
  - getRasterLength
```
public static long getRasterLength(long[] lengths)
```
    Computes the number of raster values for a positional array with the given lengths.
  - assertId
```
public static void assertId(Object id,
                            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:
    
    id - 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.
  - assertStream
```
public static void assertStream(org.scijava.io.handle.DataHandle<org.scijava.io.location.Location> stream,
                                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:
    
    stream - Source 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.
  - checkPlaneForReading
```
public static void checkPlaneForReading(Metadata m,
                                        int imageIndex,
                                        long planeIndex,
                                        int bufLength,
                                        net.imglib2.Interval bounds)
                                 throws FormatException
```
    As checkPlaneForWriting(io.scif.Metadata, int, long, int, net.imglib2.Interval) but also asserts that the Metadata has a non-null source attached. If no exception is throwin, these parameters are suitable for reading.
    
    Throws:
    
    FormatException
  - checkPlaneForWriting
```
public static void checkPlaneForWriting(Metadata m,
                                        int imageIndex,
                                        long planeIndex,
                                        int bufLength,
                                        net.imglib2.Interval bounds)
                                 throws FormatException
```
    Convenience method for checking that the plane number, tile size and buffer sizes are all valid for the given Metadata. If 'bufLength' is less than 0, then the buffer length check is not performed. If no exception is thrown, these parameters are suitable for writing.
    
    Throws:
    
    FormatException
  - checkPlaneNumber
```
public static void checkPlaneNumber(Metadata m,
                                    int imageIndex,
                                    long planeIndex)
                             throws FormatException
```
    Checks that the given plane number is valid for the given reader.
    
    Throws:
    
    FormatException
  - checkTileSize
```
public static void checkTileSize(Metadata m,
                                 net.imglib2.Interval bounds,
                                 int imageIndex)
                          throws FormatException
```
    Checks that the given tile size is valid for the given reader.
    
    Throws:
    
    FormatException
  - checkBufferSize
```
public static void checkBufferSize(int imageIndex,
                                   Metadata m,
                                   int len)
                            throws FormatException
```
    Checks that the given buffer length is long enough to hold planes of the specified image index, using the provided Reader.
    
    Throws:
    
    FormatException
  - checkBufferSize
```
public static void checkBufferSize(Metadata m,
                                   int len,
                                   net.imglib2.Interval bounds,
                                   int imageIndex)
                            throws FormatException
```
    Checks that the given buffer size is large enough to hold an image with the given planar lengths.
    
    Throws:
    
    FormatException - if the buffer is too small
  - validStream
```
public static boolean validStream(org.scijava.io.handle.DataHandle<org.scijava.io.location.Location> handle,
                                  int len,
                                  boolean littleEndian)
                           throws IOException
```
    Returns true if the given DataHandle contains at least 'len' bytes.
    
    Throws:
    
    IOException
  - validStream
```
public static boolean validStream(org.scijava.io.handle.DataHandle<org.scijava.io.location.Location> handle,
                                  int len,
                                  org.scijava.io.handle.DataHandle.ByteOrder order)
                           throws IOException
```
    Returns true if the given DataHandle contains at least 'len' bytes.
    
    Throws:
    
    IOException
  - getPlaneSize
```
public static long getPlaneSize(Reader r,
                                int imageIndex)
```
    Returns the size in bytes of a single plane read by the given Reader.
  - getPlaneSize
```
public static long getPlaneSize(Metadata m,
                                int imageIndex)
```
    Returns the size in bytes of a tile defined by the given Metadata.
  - getPlaneSize
```
public static long getPlaneSize(Metadata m,
                                int width,
                                int height,
                                int imageIndex)
```
    Returns the size in bytes of a w * h tile.
  - getPlaneSize
```
public static long getPlaneSize(Metadata m,
                                net.imglib2.Interval bounds,
                                int imageIndex)
```
    Returns the size in bytes of a plane with the given minima and maxima.
  - 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
    
    Returns:
    
    the number of bytes per pixel.
    
    See Also:
    
    ImageMetadata.getPixelType()
  - getBitsPerPixel
```
public static int getBitsPerPixel(int pixelType)
```
    Retrieves how many bytes per pixel the current plane or section has.
    
    Parameters:
    
    pixelType - the pixel type as retrieved from ImageMetadata.getPixelType().
    
    Returns:
    
    the number of bytes per pixel.
    
    See Also:
    
    ImageMetadata.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(int pixelType)
```
    Determines whether the given pixel type is floating point or integer.
    
    Parameters:
    
    pixelType - the pixel type as retrieved from ImageMetadata.getPixelType().
    
    Returns:
    
    true if the pixel type is floating point.
    
    See Also:
    
    ImageMetadata.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 ImageMetadata.getPixelType().
    
    Returns:
    
    true if the pixel type is signed.
    
    See Also:
    
    ImageMetadata.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
  - getFilename
```
public static String getFilename(int imageIndex,
                                 int image,
                                 Reader r,
                                 String pattern)
                          throws FormatException,
                                 IOException
```
    Throws:
    
    FormatException - Never actually thrown.
    
    IOException - Never actually thrown.
  - getFilenames
```
public static String[] getFilenames(String pattern,
                                    Reader r)
                             throws FormatException,
                                    IOException
```
    Throws:
    
    FormatException
    
    IOException
  - getImagesPerFile
```
public static int getImagesPerFile(String pattern,
                                   Reader r)
                            throws FormatException,
                                   IOException
```
    Throws:
    
    FormatException
    
    IOException
  - convert
```
public static void convert(Reader input,
                           Writer output,
                           String outputFile)
                    throws FormatException,
                           IOException
```
    Convenience method for writing all of the images and metadata obtained from the specified Reader into the specified Writer.
    
    Parameters:
    
    input - the pre-initialized Reader used for reading data.
    
    output - the uninitialized Writer 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.
  - convert
```
public static void convert(Reader input,
                           Writer output,
                           String outputFile,
                           SCIFIOConfig config)
                    throws FormatException,
                           IOException
```
    As convert(Reader, Writer, String), with configuration options.
    
    Parameters:
    
    input - the pre-initialized Reader used for reading data.
    
    output - the uninitialized Writer used for writing data.
    
    outputFile - the full path name of the output file to be created.
    
    config - SCIFIOConfig to use for the reading and writing.
    
    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:
    
    IllegalArgumentException - if the pixel type is floating point or invalid.
  - defaultMinMax
```
public static long[] defaultMinMax(int bitsPerPixel,
                                   boolean signed)
```
    Get the default range for the specified bits per pixel. 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.
    
    Returns:
    
    an array containing the min and max as elements 0 and 1, respectively.
    
    Throws:
    
    IllegalArgumentException - if the bits per pixel are non-positive.
  - defaultMinMax
```
public static long[] defaultMinMax(int pixelType,
                                   int bitsPerPixel)
```
    Helper method to delegate to defaultMinMax(int, boolean) or defaultMinMax(int) based on the given parameters. If a valid bitsPerPixel is available, that will be preferred over pixelType.
    
    Returns:
    
    an array containing the min and max as elements 0 and 1, respectively.
  - defaultMinMax
```
public static long[] defaultMinMax(ImageMetadata iMeta)
```
    Helper method to get the default range for the specified ImageMetadata.
    
    Returns:
    
    an array containing the min and max as elements 0 and 1, respectively.
  - checkSuffix
```
public static boolean checkSuffix(String name,
                                  String suffix)
```
    Performs suffix matching for the given filename.
  - checkSuffix
```
public static boolean checkSuffix(String name,
                                  String[] suffixList)
```
    Performs suffix matching for the given filename.

Class FormatTools

Field Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

COMPRESSION_SUFFIXES

THUMBNAIL_DIMENSION

INT8

UINT8

INT16

UINT16

INT32

UINT32

FLOAT

DOUBLE

MUST_GROUP

CAN_GROUP

CANNOT_GROUP

SERIES_NUM

SERIES_NAME

CHANNEL_NUM

CHANNEL_NAME

Z_NUM

T_NUM

TIMESTAMP

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

Method Detail

createAxis

createAxes

calibrate

calibrate

calibrate

calibrate

getScale

getScale

getNonPlanarAxisPosition

rasterToPosition

rasterToPosition

rasterToPosition

rasterToPosition

rasterToPosition

nextPlaneIndex

nextPlaneIndex

nextPlaneIndex

positionToRaster

positionToRaster

positionToRaster

getRasterLength

assertId

assertStream

checkPlaneForReading

checkPlaneForWriting

checkPlaneNumber

checkTileSize

checkBufferSize

checkBufferSize

validStream

validStream

getPlaneSize

getPlaneSize

getPlaneSize

getPlaneSize

pixelTypeFromString

getPixelTypeString

getBytesPerPixel