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java.lang.Objectome.io.bioformats.BfPixelsWrapper
public class BfPixelsWrapper
Constructor Summary | |
---|---|
BfPixelsWrapper(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? |
Method Summary | |
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void |
checkBounds(Integer x,
Integer y,
Integer z,
Integer c,
Integer t)
|
void |
close()
|
int |
getByteWidth()
|
byte[] |
getCol(Integer x,
Integer z,
Integer c,
Integer t,
byte[] buffer)
|
Integer |
getColSize()
|
byte[] |
getHypercube(List<Integer> offset,
List<Integer> size,
List<Integer> step,
byte[] buffer)
|
Integer |
getHypercubeSize(List<Integer> offset,
List<Integer> size,
List<Integer> step)
|
long |
getId()
|
byte[] |
getMessageDigest()
|
String |
getPath()
|
String |
getPixelsType()
cgb - created from the methods below? |
byte[] |
getPlane(Integer z,
Integer c,
Integer t,
byte[] buffer)
|
Long |
getPlaneOffset(Integer z,
Integer c,
Integer t)
|
byte[] |
getPlaneRegion(Integer z,
Integer c,
Integer t,
Integer count,
Integer offset,
byte[] buffer)
|
Integer |
getPlaneSize()
|
byte[] |
getRegion(Integer size,
Long offset,
byte[] buffer)
|
byte[] |
getRow(Integer y,
Integer z,
Integer c,
Integer t,
byte[] buffer)
|
Long |
getRowOffset(Integer y,
Integer z,
Integer c,
Integer t)
|
Integer |
getRowSize()
|
int |
getSizeC()
|
int |
getSizeT()
|
int |
getSizeX()
|
int |
getSizeY()
|
int |
getSizeZ()
|
byte[] |
getStack(Integer c,
Integer t,
byte[] buffer)
|
Long |
getStackOffset(Integer c,
Integer t)
|
Integer |
getStackSize()
|
byte[] |
getTile(int z,
int c,
int t,
int x,
int y,
int w,
int h,
byte[] buffer)
|
byte[] |
getTimepoint(Integer t,
byte[] buffer)
|
Long |
getTimepointOffset(Integer t)
|
Integer |
getTimepointSize()
|
Integer |
getTotalSize()
|
boolean |
isFloat()
|
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 |
---|
public BfPixelsWrapper(String path, loci.formats.IFormatReader reader) throws IOException, loci.formats.FormatException
IOException
loci.formats.FormatException
Method Detail |
---|
public byte[] getMessageDigest() throws IOException
IOException
public void checkBounds(Integer x, Integer y, Integer z, Integer c, Integer t) throws DimensionsOutOfBoundsException
DimensionsOutOfBoundsException
public void close() throws IOException
IOException
public long getId()
public String getPath()
public int getSizeC()
public int getSizeT()
public int getSizeX()
public int getSizeY()
public int getSizeZ()
public int getByteWidth()
public Integer getRowSize()
public Integer getColSize()
public Integer getPlaneSize()
public Integer getStackSize()
public Integer getTimepointSize()
public Integer getTotalSize()
public Integer getHypercubeSize(List<Integer> offset, List<Integer> size, List<Integer> step) throws DimensionsOutOfBoundsException
DimensionsOutOfBoundsException
public Long getRowOffset(Integer y, Integer z, Integer c, Integer t) throws DimensionsOutOfBoundsException
DimensionsOutOfBoundsException
public Long getPlaneOffset(Integer z, Integer c, Integer t) throws DimensionsOutOfBoundsException
DimensionsOutOfBoundsException
public Long getStackOffset(Integer c, Integer t) throws DimensionsOutOfBoundsException
DimensionsOutOfBoundsException
public Long getTimepointOffset(Integer t) throws DimensionsOutOfBoundsException
DimensionsOutOfBoundsException
public byte[] getCol(Integer x, Integer z, Integer c, Integer t, byte[] buffer) throws IOException, DimensionsOutOfBoundsException
IOException
DimensionsOutOfBoundsException
public byte[] getPlane(Integer z, Integer c, Integer t, byte[] buffer) throws IOException, DimensionsOutOfBoundsException
IOException
DimensionsOutOfBoundsException
public byte[] getPlaneRegion(Integer z, Integer c, Integer t, Integer count, Integer offset, byte[] buffer) throws IOException, DimensionsOutOfBoundsException
IOException
DimensionsOutOfBoundsException
public byte[] getRegion(Integer size, Long offset, byte[] buffer) throws IOException
IOException
public byte[] getRow(Integer y, Integer z, Integer c, Integer t, byte[] buffer) throws IOException, DimensionsOutOfBoundsException
IOException
DimensionsOutOfBoundsException
public byte[] getStack(Integer c, Integer t, byte[] buffer) throws IOException, DimensionsOutOfBoundsException
IOException
DimensionsOutOfBoundsException
public byte[] getTimepoint(Integer t, byte[] buffer) throws IOException, DimensionsOutOfBoundsException
IOException
DimensionsOutOfBoundsException
public byte[] getHypercube(List<Integer> offset, List<Integer> size, List<Integer> step, byte[] buffer) throws IOException, DimensionsOutOfBoundsException
IOException
DimensionsOutOfBoundsException
public byte[] getTile(int z, int c, int t, int x, int y, int w, int h, byte[] buffer) throws loci.formats.FormatException, IOException
loci.formats.FormatException
IOException
public String getPixelsType()
public boolean isFloat()
public boolean isSigned()
public byte[] swapIfRequired(byte[] bytes) throws loci.formats.FormatException, IOException
bytes
- The byte array to check and modify if required.
IOException
- if there is an error read from the file.
loci.formats.FormatException
- if there is an error during metadata parsing.
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Version: 4.3.3-00d1137e-b2894
Copyright © 2009 The University of Dundee. All Rights Reserved.