public class ChannelFiller extends ReaderWrapper
Modifier and Type | Field and Description |
---|---|
protected java.lang.Boolean |
filled
Whether to fill in the indices.
|
protected int |
lutLength
Number of LUT components.
|
reader
CAN_GROUP, CANNOT_GROUP, MUST_GROUP
Constructor and Description |
---|
ChannelFiller()
Constructs a ChannelFiller around a new image reader.
|
ChannelFiller(IFormatReader r)
Constructs a ChannelFiller with a given reader.
|
Modifier and Type | Method and Description |
---|---|
short[][] |
get16BitLookupTable()
Gets the 16-bit color lookup table associated with
the most recently opened image.
|
byte[][] |
get8BitLookupTable()
Gets the 8-bit color lookup table associated with
the most recently opened image.
|
private int |
getLookupTableComponentCount()
Gets the number of color components in the lookup table.
|
java.lang.Class<?> |
getNativeDataType()
Returns the native data type of image planes for this reader, as returned
by
IFormatReader.openPlane(int, int, int, int, int) or IFormatWriter.savePlane(int, java.lang.Object) . |
int |
getSizeC()
Gets the size of the C dimension.
|
boolean |
isFilled()
Returns true if the indices are being factored out.
|
boolean |
isIndexed()
Gets whether the image planes are indexed color.
|
boolean |
isRGB()
Checks if the image planes in the file have more than one channel per
IFormatReader.openBytes(int) call. |
static ChannelFiller |
makeChannelFiller(IFormatReader r)
Converts the given reader into a ChannelFiller, wrapping if needed.
|
byte[] |
openBytes(int no)
Obtains the specified image plane from the current file as a byte array.
|
byte[] |
openBytes(int no,
byte[] buf)
Obtains the specified image plane from the current file into a
pre-allocated byte array of
(sizeX * sizeY * bytesPerPixel * RGB channel count).
|
byte[] |
openBytes(int no,
byte[] buf,
int x,
int y,
int w,
int h)
Obtains a sub-image of the specified image plane
into a pre-allocated byte array.
|
byte[] |
openBytes(int no,
int x,
int y,
int w,
int h)
Obtains a sub-image of the specified image plane,
whose upper-left corner is given by (x, y).
|
void |
setFilled(boolean filled)
Toggles whether the indices should be factored out.
|
void |
setId(java.lang.String id)
Sets the current file name.
|
close, close, coreIndexToSeries, duplicate, fileGroupOption, getAdvancedSeriesUsedFiles, getAdvancedUsedFiles, getBitsPerPixel, getCoreIndex, getCoreMetadataList, getCurrentFile, getDatasetStructureDescription, getDimensionOrder, getDomains, getEffectiveSizeC, getFormat, getGlobalMetadata, getImageCount, getIndex, getIndex, getMetadataOptions, getMetadataStore, getMetadataStoreRoot, getMetadataValue, getModuloC, getModuloT, getModuloZ, getOptimalTileHeight, getOptimalTileWidth, getPixelType, getPossibleDomains, getReader, getRequiredDirectories, getResolution, getResolutionCount, getRGBChannelCount, getSeries, getSeriesCount, getSeriesMetadata, getSeriesMetadataValue, getSeriesUsedFiles, getSeriesUsedFiles, getSizeT, getSizeX, getSizeY, getSizeZ, getSuffixes, getSupportedMetadataLevels, getThumbSizeX, getThumbSizeY, getUnderlyingReaders, getUsedFiles, getUsedFiles, getZCTCoords, getZCTModuloCoords, hasCompanionFiles, hasFlattenedResolutions, isFalseColor, isGroupFiles, isInterleaved, isInterleaved, isLittleEndian, isMetadataComplete, isMetadataFiltered, isNormalized, isOrderCertain, isOriginalMetadataPopulated, isSingleFile, isThisType, isThisType, isThisType, isThisType, isThumbnailSeries, openPlane, openThumbBytes, reopenFile, seriesToCoreIndex, setCoreIndex, setFlattenedResolutions, setGroupFiles, setMetadataFiltered, setMetadataOptions, setMetadataStore, setNormalized, setOriginalMetadataPopulated, setResolution, setSeries, unwrap, unwrap, unwrap
protected java.lang.Boolean filled
protected int lutLength
public ChannelFiller()
public ChannelFiller(IFormatReader r)
public static ChannelFiller makeChannelFiller(IFormatReader r)
public boolean isFilled()
public void setFilled(boolean filled)
public int getSizeC()
IFormatReader
getSizeC
in interface IFormatReader
getSizeC
in class ReaderWrapper
public boolean isRGB()
IFormatReader
IFormatReader.openBytes(int)
call.
This method returns true if and only if IFormatReader.getRGBChannelCount()
returns a value greater than 1.isRGB
in interface IFormatReader
isRGB
in class ReaderWrapper
public boolean isIndexed()
IFormatReader
IFormatReader.getSizeC()
,
IFormatReader.getEffectiveSizeC()
or IFormatReader.getRGBChannelCount()
.isIndexed
in interface IFormatReader
isIndexed
in class ReaderWrapper
public byte[][] get8BitLookupTable() throws FormatException, java.io.IOException
IFormatReader
IFormatReader.isIndexed()
returns
false, then this may return null. Also, if IFormatReader.getPixelType()
returns
anything other than FormatTools.INT8
or FormatTools.UINT8
,
this method will return null.get8BitLookupTable
in interface IFormatReader
get8BitLookupTable
in class ReaderWrapper
FormatException
java.io.IOException
public short[][] get16BitLookupTable() throws FormatException, java.io.IOException
IFormatReader
IFormatReader.isIndexed()
returns
false, then this may return null. Also, if IFormatReader.getPixelType()
returns
anything other than FormatTools.INT16
or FormatTools.UINT16
, this method will return null.get16BitLookupTable
in interface IFormatReader
get16BitLookupTable
in class ReaderWrapper
FormatException
java.io.IOException
public byte[] openBytes(int no) throws FormatException, java.io.IOException
IFormatReader
openBytes
in interface IFormatReader
openBytes
in class ReaderWrapper
FormatException
java.io.IOException
IFormatReader.openBytes(int, byte[])
public byte[] openBytes(int no, byte[] buf) throws FormatException, java.io.IOException
IFormatReader
openBytes
in interface IFormatReader
openBytes
in class ReaderWrapper
no
- the image index within the file.buf
- a pre-allocated buffer.buf
for convenience.FormatException
- if there was a problem parsing the metadata of the
file.java.io.IOException
- if there was a problem reading the file.public byte[] openBytes(int no, int x, int y, int w, int h) throws FormatException, java.io.IOException
IFormatReader
openBytes
in interface IFormatReader
openBytes
in class ReaderWrapper
FormatException
java.io.IOException
public byte[] openBytes(int no, byte[] buf, int x, int y, int w, int h) throws FormatException, java.io.IOException
IFormatReader
openBytes
in interface IFormatReader
openBytes
in class ReaderWrapper
no
- the image index within the file.buf
- a pre-allocated buffer.x
- X coordinate of the upper-left corner of the sub-imagey
- Y coordinate of the upper-left corner of the sub-imagew
- width of the sub-imageh
- height of the sub-imagebuf
for convenience.FormatException
- if there was a problem parsing the metadata of the
file.java.io.IOException
- if there was a problem reading the file.public java.lang.Class<?> getNativeDataType()
IFormatHandler
IFormatReader.openPlane(int, int, int, int, int)
or IFormatWriter.savePlane(int, java.lang.Object)
.
For most readers this type will be a byte array; however, some readers
call external APIs that work with other types such as
BufferedImage
.getNativeDataType
in interface IFormatHandler
getNativeDataType
in class ReaderWrapper
public void setId(java.lang.String id) throws FormatException, java.io.IOException
IFormatHandler
setId
in interface IFormatHandler
setId
in class ReaderWrapper
FormatException
java.io.IOException
private int getLookupTableComponentCount() throws FormatException, java.io.IOException
FormatException
java.io.IOException
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