ome.io.bioformats

Class BfPixelsWrapper

java.lang.Object

ome.io.bioformats.BfPixelsWrapper

public class BfPixelsWrapper
extends java.lang.Object

Since:

Beta4.3

Constructor Summary

Constructors

Constructor and Description
BfPixelsWrapper(java.lang.String path, loci.formats.IFormatReader reader) We may want a constructor that takes the id of an imported file or that takes a File object? There should ultimately be some sort of check here that the file is in a/the repository.

Method Summary

Modifier and Type	Method and Description
void	checkBounds(java.lang.Integer x, java.lang.Integer y, java.lang.Integer z, java.lang.Integer c, java.lang.Integer t)
void	close()
int	getByteWidth()
byte[]	getCol(java.lang.Integer x, java.lang.Integer z, java.lang.Integer c, java.lang.Integer t, byte[] buffer)
java.lang.Integer	getColSize()
byte[]	getHypercube(java.util.List<java.lang.Integer> offset, java.util.List<java.lang.Integer> size, java.util.List<java.lang.Integer> step, byte[] buffer)
java.lang.Long	getHypercubeSize(java.util.List<java.lang.Integer> offset, java.util.List<java.lang.Integer> size, java.util.List<java.lang.Integer> step)
long	getId()
byte[]	getMessageDigest()
java.lang.String	getPath()
java.lang.String	getPixelsType() cgb - created from the methods below? Retrieves how many bytes per pixel the current plane or section has.
byte[]	getPlane(java.lang.Integer z, java.lang.Integer c, java.lang.Integer t, byte[] buffer)
java.lang.Long	getPlaneOffset(java.lang.Integer z, java.lang.Integer c, java.lang.Integer t)
byte[]	getPlaneRegion(java.lang.Integer z, java.lang.Integer c, java.lang.Integer t, java.lang.Integer count, java.lang.Integer offset, byte[] buffer)
java.lang.Long	getPlaneSize()
byte[]	getRegion(java.lang.Integer size, java.lang.Long offset, byte[] buffer)
byte[]	getRow(java.lang.Integer y, java.lang.Integer z, java.lang.Integer c, java.lang.Integer t, byte[] buffer)
java.lang.Long	getRowOffset(java.lang.Integer y, java.lang.Integer z, java.lang.Integer c, java.lang.Integer t)
java.lang.Integer	getRowSize()
int	getSizeC()
int	getSizeT()
int	getSizeX()
int	getSizeY()
int	getSizeZ()
byte[]	getStack(java.lang.Integer c, java.lang.Integer t, byte[] buffer)
java.lang.Long	getStackOffset(java.lang.Integer c, java.lang.Integer t)
java.lang.Long	getStackSize()
byte[]	getTile(int z, int c, int t, int x, int y, int w, int h, byte[] buffer)
byte[]	getTimepoint(java.lang.Integer t, byte[] buffer)
java.lang.Long	getTimepointOffset(java.lang.Integer t)
java.lang.Long	getTimepointSize()
java.lang.Long	getTotalSize()
boolean	isFloat()
boolean	isLittleEndian()
boolean	isSigned()
byte[]	swapIfRequired(byte[] bytes) cgb - stolen from ImportLibrary - slightly modified Examines a byte array to see if it needs to be byte swapped and modifies the byte array directly.

Methods inherited from class java.lang.Object

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

Constructor Detail

BfPixelsWrapper

public BfPixelsWrapper(java.lang.String path,
                       loci.formats.IFormatReader reader)
                throws java.io.IOException,
                       loci.formats.FormatException

We may want a constructor that takes the id of an imported file or that takes a File object? There should ultimately be some sort of check here that the file is in a/the repository.

Throws:

java.io.IOException

loci.formats.FormatException

Method Detail

getMessageDigest

public byte[] getMessageDigest()
                        throws java.io.IOException

Throws:

java.io.IOException

checkBounds

public void checkBounds(java.lang.Integer x,
                        java.lang.Integer y,
                        java.lang.Integer z,
                        java.lang.Integer c,
                        java.lang.Integer t)
                 throws DimensionsOutOfBoundsException

Throws:

DimensionsOutOfBoundsException

close

public void close()
           throws java.io.IOException

Throws:

java.io.IOException

getId

public long getId()

getPath

public java.lang.String getPath()

getSizeC

public int getSizeC()

getSizeT

public int getSizeT()

getSizeX

public int getSizeX()

getSizeY

public int getSizeY()

getSizeZ

public int getSizeZ()

getByteWidth

public int getByteWidth()

getRowSize

public java.lang.Integer getRowSize()

getColSize

public java.lang.Integer getColSize()

getPlaneSize

public java.lang.Long getPlaneSize()

getStackSize

public java.lang.Long getStackSize()

getTimepointSize

public java.lang.Long getTimepointSize()

getTotalSize

public java.lang.Long getTotalSize()

getHypercubeSize

public java.lang.Long getHypercubeSize(java.util.List<java.lang.Integer> offset,
                                       java.util.List<java.lang.Integer> size,
                                       java.util.List<java.lang.Integer> step)
                                throws DimensionsOutOfBoundsException

Throws:

DimensionsOutOfBoundsException

getRowOffset

public java.lang.Long getRowOffset(java.lang.Integer y,
                                   java.lang.Integer z,
                                   java.lang.Integer c,
                                   java.lang.Integer t)
                            throws DimensionsOutOfBoundsException

Throws:

DimensionsOutOfBoundsException

getPlaneOffset

public java.lang.Long getPlaneOffset(java.lang.Integer z,
                                     java.lang.Integer c,
                                     java.lang.Integer t)
                              throws DimensionsOutOfBoundsException

Throws:

DimensionsOutOfBoundsException

getStackOffset

public java.lang.Long getStackOffset(java.lang.Integer c,
                                     java.lang.Integer t)
                              throws DimensionsOutOfBoundsException

Throws:

DimensionsOutOfBoundsException

getTimepointOffset

public java.lang.Long getTimepointOffset(java.lang.Integer t)
                                  throws DimensionsOutOfBoundsException

Throws:

DimensionsOutOfBoundsException

getCol

public byte[] getCol(java.lang.Integer x,
                     java.lang.Integer z,
                     java.lang.Integer c,
                     java.lang.Integer t,
                     byte[] buffer)
              throws java.io.IOException,
                     DimensionsOutOfBoundsException

Throws:

java.io.IOException

DimensionsOutOfBoundsException

getPlane

public byte[] getPlane(java.lang.Integer z,
                       java.lang.Integer c,
                       java.lang.Integer t,
                       byte[] buffer)
                throws java.io.IOException,
                       DimensionsOutOfBoundsException

Throws:

java.io.IOException

DimensionsOutOfBoundsException

getPlaneRegion

public byte[] getPlaneRegion(java.lang.Integer z,
                             java.lang.Integer c,
                             java.lang.Integer t,
                             java.lang.Integer count,
                             java.lang.Integer offset,
                             byte[] buffer)
                      throws java.io.IOException,
                             DimensionsOutOfBoundsException

Throws:

java.io.IOException

DimensionsOutOfBoundsException

getRegion

public byte[] getRegion(java.lang.Integer size,
                        java.lang.Long offset,
                        byte[] buffer)
                 throws java.io.IOException

Throws:

java.io.IOException

getRow

public byte[] getRow(java.lang.Integer y,
                     java.lang.Integer z,
                     java.lang.Integer c,
                     java.lang.Integer t,
                     byte[] buffer)
              throws java.io.IOException,
                     DimensionsOutOfBoundsException

Throws:

java.io.IOException

DimensionsOutOfBoundsException

getStack

public byte[] getStack(java.lang.Integer c,
                       java.lang.Integer t,
                       byte[] buffer)
                throws java.io.IOException,
                       DimensionsOutOfBoundsException

Throws:

java.io.IOException

DimensionsOutOfBoundsException

getTimepoint

public byte[] getTimepoint(java.lang.Integer t,
                           byte[] buffer)
                    throws java.io.IOException,
                           DimensionsOutOfBoundsException

Throws:

java.io.IOException

DimensionsOutOfBoundsException

getHypercube

public byte[] getHypercube(java.util.List<java.lang.Integer> offset,
                           java.util.List<java.lang.Integer> size,
                           java.util.List<java.lang.Integer> step,
                           byte[] buffer)
                    throws java.io.IOException,
                           DimensionsOutOfBoundsException

Throws:

java.io.IOException

DimensionsOutOfBoundsException

getTile

public byte[] getTile(int z,
                      int c,
                      int t,
                      int x,
                      int y,
                      int w,
                      int h,
                      byte[] buffer)
               throws loci.formats.FormatException,
                      java.io.IOException

Throws:

loci.formats.FormatException

java.io.IOException

getPixelsType

public java.lang.String getPixelsType()

cgb - created from the methods below? Retrieves how many bytes per pixel the current plane or section has.

Returns:

the number of bytes per pixel.

isFloat

public boolean isFloat()

isSigned

public boolean isSigned()

isLittleEndian

public boolean isLittleEndian()

swapIfRequired

public byte[] swapIfRequired(byte[] bytes)
                      throws loci.formats.FormatException,
                             java.io.IOException

cgb - stolen from ImportLibrary - slightly modified Examines a byte array to see if it needs to be byte swapped and modifies the byte array directly.

Parameters:

bytes - The byte array to check and modify if required.

Returns:

the byteArray either swapped or not for convenience.

Throws:

java.io.IOException - if there is an error read from the file.

loci.formats.FormatException - if there is an error during metadata parsing.