loci.formats.services

Interface WlzService

All Superinterfaces:

loci.common.services.Service

All Known Implementing Classes:

WlzServiceImpl

public interface WlzService
extends loci.common.services.Service

Method Summary

Modifier and Type	Method and Description
void	close() Closes the file.
String	getNoWlzMsg() Gets the text string for when Woolz has not been found.
double	getOrgX() Gets column origin.
double	getOrgY() Gets line origin.
double	getOrgZ() Gets plane origin.
int	getPixelType() Gets the image pixel type.
int	getSizeC() Gets number of channels.
int	getSizeT() Gets number of time samples.
int	getSizeX() Gets width in pixels/voxels.
int	getSizeY() Gets height in pixels/voxels.
int	getSizeZ() Gets depth (number of x-y planes) in voxels.
int[]	getSupPixelTypes() Gets supported pixel types.
double	getVoxSzX() Gets voxel width.
double	getVoxSzY() Gets voxel height.
double	getVoxSzZ() Gets voxel depth.
String	getWlzOrgLabelName() Gets the text string used for the Woolz origin label.
boolean	isRGB() Gets boolean for whether image is colour or not.
void	open(String file, String rw) Initializes the service for the given file path.
byte[]	readBytes(int no, byte[] buf, int x, int y, int w, int h) Reads a rectangle of bytes in an x-y plane from the opened Woolz object.
void	saveBytes(int no, byte[] buf, int x, int y, int w, int h) Adds a rectangle of bytes in an x-y plane to the opened Woolz object.
void	setupWrite(int orgX, int orgY, int orgZ, int pixSzX, int pixSzY, int pixSzZ, int pixSzC, int pixSzT, double voxSzX, double voxSzY, double voxSzZ, int gType) Sets up the service, which must have already been opened for writing.

Method Detail

open

void open(String file,
          String rw)
   throws IOException,
          FormatException

Initializes the service for the given file path.

Parameters:

file - File path with which to initialize the service.

Throws:

IOException

FormatException

getNoWlzMsg

String getNoWlzMsg()

Gets the text string for when Woolz has not been found.

getWlzOrgLabelName

String getWlzOrgLabelName()

Gets the text string used for the Woolz origin label.

getSizeX

int getSizeX()

Gets width in pixels/voxels.

Returns:

width.

getSizeY

int getSizeY()

Gets height in pixels/voxels.

Returns:

height.

getSizeZ

int getSizeZ()

Gets depth (number of x-y planes) in voxels.

Returns:

depth.

getSizeC

int getSizeC()

Gets number of channels.

Returns:

channels.

getSizeT

int getSizeT()

Gets number of time samples.

Returns:

time.

isRGB

boolean isRGB()

Gets boolean for whether image is colour or not.

Returns:

true if image is colour.

getPixelType

int getPixelType()

Gets the image pixel type.

Returns:

pixel type.

getVoxSzX

double getVoxSzX()

Gets voxel width.

Returns:

voxel width.

getVoxSzY

double getVoxSzY()

Gets voxel height.

Returns:

voxel height.

getVoxSzZ

double getVoxSzZ()

Gets voxel depth.

Returns:

voxel depth.

getOrgX

double getOrgX()

Gets column origin.

Returns:

column origin.

getOrgY

double getOrgY()

Gets line origin.

Returns:

line origin.

getOrgZ

double getOrgZ()

Gets plane origin.

Returns:

plane origin.

getSupPixelTypes

int[] getSupPixelTypes()

Gets supported pixel types.

Returns:

array of supported pixel types.

setupWrite

void setupWrite(int orgX,
                int orgY,
                int orgZ,
                int pixSzX,
                int pixSzY,
                int pixSzZ,
                int pixSzC,
                int pixSzT,
                double voxSzX,
                double voxSzY,
                double voxSzZ,
                int gType)
         throws FormatException

Sets up the service, which must have already been opened for writing.

Parameters:

orgX - x origin.

orgY - y origin.

orgZ - z origin (set to 0 for 2D).

pixSzX - width.

pixSzY - height.

pixSzZ - depth (number of planes, set to 1 for 2D).

pixSzC - number of channels.

pixSzT - number of time samples.

voxSzX - pixel/voxel width.

voxSzY - pixel/voxel heigth.

voxSzZ - voxel deoth.

gType - image value type.

Throws:

FormatException

close

void close()
    throws IOException

Closes the file.

Throws:

IOException

readBytes

byte[] readBytes(int no,
                 byte[] buf,
                 int x,
                 int y,
                 int w,
                 int h)
          throws FormatException,
                 IOException

Reads a rectangle of bytes in an x-y plane from the opened Woolz object.

Parameters:

no - plane coordinate (set to 0 for 2D).

buf - buffer for bytes.

x - rectangle first column.

y - rectangle first line.

w - rectangle width (in columns).

h - rectangle heigth (in lines).

Returns:

Buffer of bytes read.

Throws:

FormatException

IOException

saveBytes

void saveBytes(int no,
               byte[] buf,
               int x,
               int y,
               int w,
               int h)
        throws FormatException,
               IOException

Adds a rectangle of bytes in an x-y plane to the opened Woolz object.

Parameters:

no - plane coordinate (set to 0 for 2D).

buf - buffer with bytes.

x - rectangle first column.

y - rectangle first line.

w - rectangle width (in columns).

h - rectangle heigth (in lines).

Throws:

FormatException

IOException