public class ChannelSeparator extends ReaderWrapper
Modifier and Type | Field and Description |
---|---|
private byte[] |
lastImage
Last image opened.
|
private int |
lastImageHeight
Height of last image opened.
|
private int |
lastImageIndex
Index of last image opened.
|
private int |
lastImageSeries
Series of last image opened.
|
private int |
lastImageWidth
Width of last image opened.
|
private int |
lastImageX
X index of last image opened.
|
private int |
lastImageY
Y index of last image opened.
|
reader
CAN_GROUP, CANNOT_GROUP, MUST_GROUP
Constructor and Description |
---|
ChannelSeparator()
Constructs a ChannelSeparator around a new image reader.
|
ChannelSeparator(IFormatReader r)
Constructs a ChannelSeparator with the given reader.
|
Modifier and Type | Method and Description |
---|---|
void |
close(boolean fileOnly)
Closes the currently open file.
|
String |
getDimensionOrder()
Gets a five-character string representing the
dimension order in which planes will be returned.
|
int |
getImageCount()
Determines the number of image planes in the current file.
|
int |
getIndex(int z,
int c,
int t)
Gets the rasterized index corresponding
to the given Z, C and T coordinates (real sizes).
|
int |
getIndex(int z,
int c,
int t,
int moduloZ,
int moduloC,
int moduloT)
Gets the rasterized index corresponding to the given Z, C, T,
moduloZ, moduloC and moduloT coordinates (effective sizes).
|
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 |
getOriginalIndex(int no)
Returns the image number in the original dataset that corresponds to the
given image number.
|
int[] |
getZCTCoords(int index)
Gets the Z, C and T coordinates (real sizes) corresponding to the
given rasterized index value.
|
int[] |
getZCTModuloCoords(int index)
Gets the Z, C, T, moduloZ, moduloC and moduloT coordinates
(effective sizes) corresponding to the given rasterized index
value.
|
boolean |
isRGB()
Checks if the image planes in the file have more than one channel per
IFormatReader.openBytes(int) call. |
static ChannelSeparator |
makeChannelSeparator(IFormatReader r)
Converts the given reader into a ChannelSeparator, 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).
|
byte[] |
openThumbBytes(int no)
Obtains a thumbnail for the specified image plane from the current file,
as a byte array.
|
void |
setId(String id)
Sets the current file name.
|
close, coreIndexToSeries, duplicate, fileGroupOption, get16BitLookupTable, get8BitLookupTable, getAdvancedSeriesUsedFiles, getAdvancedUsedFiles, getBitsPerPixel, getCoreIndex, getCoreMetadataList, getCurrentFile, getDatasetStructureDescription, getDomains, getEffectiveSizeC, getFormat, getGlobalMetadata, getMetadataOptions, getMetadataStore, getMetadataStoreRoot, getMetadataValue, getModuloC, getModuloT, getModuloZ, getOptimalTileHeight, getOptimalTileWidth, getPixelType, getPossibleDomains, getReader, getRequiredDirectories, getResolution, getResolutionCount, getRGBChannelCount, getSeries, getSeriesCount, getSeriesMetadata, getSeriesMetadataValue, getSeriesUsedFiles, getSeriesUsedFiles, getSizeC, getSizeT, getSizeX, getSizeY, getSizeZ, getSuffixes, getSupportedMetadataLevels, getThumbSizeX, getThumbSizeY, getUnderlyingReaders, getUsedFiles, getUsedFiles, hasCompanionFiles, hasFlattenedResolutions, isFalseColor, isGroupFiles, isIndexed, isInterleaved, isInterleaved, isLittleEndian, isMetadataComplete, isMetadataFiltered, isNormalized, isOrderCertain, isOriginalMetadataPopulated, isSingleFile, isThisType, isThisType, isThisType, isThisType, isThumbnailSeries, openPlane, reopenFile, seriesToCoreIndex, setCoreIndex, setFlattenedResolutions, setGroupFiles, setMetadataFiltered, setMetadataOptions, setMetadataStore, setNormalized, setOriginalMetadataPopulated, setResolution, setSeries, unwrap, unwrap, unwrap
private byte[] lastImage
private int lastImageIndex
private int lastImageSeries
private int lastImageX
private int lastImageY
private int lastImageWidth
private int lastImageHeight
public ChannelSeparator()
public ChannelSeparator(IFormatReader r)
public static ChannelSeparator makeChannelSeparator(IFormatReader r)
public int getOriginalIndex(int no)
no
- is an image number greater than or equal to 0 and less than
getImageCount()public int getImageCount()
IFormatReader
getImageCount
in interface IFormatReader
getImageCount
in class ReaderWrapper
public String getDimensionOrder()
IFormatReader
IFormatReader.isInterleaved()
method will return true.getDimensionOrder
in interface IFormatReader
getDimensionOrder
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 byte[] openBytes(int no) throws FormatException, IOException
IFormatReader
openBytes
in interface IFormatReader
openBytes
in class ReaderWrapper
FormatException
IOException
IFormatReader.openBytes(int, byte[])
public byte[] openBytes(int no, byte[] buf) throws FormatException, 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.IOException
- if there was a problem reading the file.public byte[] openBytes(int no, int x, int y, int w, int h) throws FormatException, IOException
IFormatReader
openBytes
in interface IFormatReader
openBytes
in class ReaderWrapper
FormatException
IOException
public byte[] openBytes(int no, byte[] buf, int x, int y, int w, int h) throws FormatException, 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.IOException
- if there was a problem reading the file.public byte[] openThumbBytes(int no) throws FormatException, IOException
IFormatReader
openThumbBytes
in interface IFormatReader
openThumbBytes
in class ReaderWrapper
FormatException
IOException
public void close(boolean fileOnly) throws IOException
IFormatReader
Closeable.close()
.close
in interface IFormatReader
close
in class ReaderWrapper
IOException
public int getIndex(int z, int c, int t)
IFormatReader
getIndex
in interface IFormatReader
getIndex
in class ReaderWrapper
public int getIndex(int z, int c, int t, int moduloZ, int moduloC, int moduloT)
IFormatReader
getIndex
in interface IFormatReader
getIndex
in class ReaderWrapper
public int[] getZCTCoords(int index)
IFormatReader
getZCTCoords
in interface IFormatReader
getZCTCoords
in class ReaderWrapper
public int[] getZCTModuloCoords(int index)
IFormatReader
getZCTModuloCoords
in interface IFormatReader
getZCTModuloCoords
in class ReaderWrapper
public 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(String id) throws FormatException, IOException
IFormatHandler
setId
in interface IFormatHandler
setId
in class ReaderWrapper
FormatException
IOException
Copyright © 2016 Open Microscopy Environment