|
||||||||||
PREV CLASS NEXT CLASS | FRAMES NO FRAMES | |||||||||
SUMMARY: NESTED | FIELD | CONSTR | METHOD | DETAIL: FIELD | CONSTR | METHOD |
public interface IFormatReader
Interface for all biological file format readers.
Field Summary | |
---|---|
static int |
CAN_GROUP
|
static int |
CANNOT_GROUP
|
static int |
MUST_GROUP
File grouping options. |
Method Summary | |
---|---|
void |
close(boolean fileOnly)
Closes the currently open file. |
int |
fileGroupOption(String id)
Returns an int indicating that we cannot, must, or might group the files in a given dataset. |
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. |
int[] |
getChannelDimLengths()
Gets the lengths of each subdimension of C, in fastest-to-sloweset rasterization order. |
int[] |
getChannelDimLengths(String id)
Deprecated. Replaced by getChannelDimLengths() |
String[] |
getChannelDimTypes()
Gets the name of each subdimension of C, in fastest-to-slowest rasterization order. |
String[] |
getChannelDimTypes(String id)
Deprecated. Replaced by getChannelDimTypes() |
CoreMetadata |
getCoreMetadata()
Obtains the core metadata values for the current file. |
CoreMetadata |
getCoreMetadata(String id)
Deprecated. Replaced by getCoreMetadata() |
String |
getCurrentFile()
Returns the current file. |
String |
getDimensionOrder()
Gets a five-character string representing the dimension order within the file. |
String |
getDimensionOrder(String id)
Deprecated. Replaced by getDimensionOrder() |
int |
getEffectiveSizeC()
Gets the effective size of the C dimension, guaranteeing that getEffectiveSizeC() * getSizeZ() * getSizeT() == getImageCount() regardless of the result of isRGB(). |
int |
getEffectiveSizeC(String id)
Deprecated. Replaced by getEffectiveSizeC() |
int |
getImageCount()
Determines the number of images in the current file. |
int |
getImageCount(String id)
Deprecated. Replaced by getImageCount() |
int |
getIndex(int z,
int c,
int t)
Gets the rasterized index corresponding to the given Z, C and T coordinates. |
int |
getIndex(String id,
int z,
int c,
int t)
Deprecated. Replaced by getIndex(int, int, int) |
Hashtable |
getMetadata()
Obtains the hashtable containing the metadata field/value pairs from the current file. |
Hashtable |
getMetadata(String id)
Deprecated. Replaced by getMetadata() |
MetadataStore |
getMetadataStore()
Retrieves the current metadata store for this reader. |
MetadataStore |
getMetadataStore(String id)
Deprecated. Replaced by getMetadataStore() |
Object |
getMetadataStoreRoot()
Retrieves the current metadata store's root object. |
Object |
getMetadataStoreRoot(String id)
Deprecated. Replaced by getMetadataStoreRoot() |
Object |
getMetadataValue(String field)
Obtains the specified metadata field's value for the current file. |
Object |
getMetadataValue(String id,
String field)
Deprecated. Replaced by getMetadataValue(String) |
int |
getPixelType()
Gets the pixel type. |
int |
getPixelType(String id)
Deprecated. Replaced by getPixelType() |
int |
getRGBChannelCount()
Gets the number of channels per RGB image (if not RGB, this returns 1). |
int |
getRGBChannelCount(String id)
Deprecated. Replaced by getRGBChannelCount() |
int |
getSeries()
Gets the currently active series. |
int |
getSeries(String id)
Deprecated. Replaced by getSeries() |
int |
getSeriesCount()
Gets the number of series in this file. |
int |
getSeriesCount(String id)
Deprecated. Replaced by getSeriesCount() |
int |
getSizeC()
Gets the size of the C dimension. |
int |
getSizeC(String id)
Deprecated. Replaced by getSizeC() |
int |
getSizeT()
Gets the size of the T dimension. |
int |
getSizeT(String id)
Deprecated. Replaced by getSizeT() |
int |
getSizeX()
Gets the size of the X dimension. |
int |
getSizeX(String id)
Deprecated. Replaced by getSizeX() |
int |
getSizeY()
Gets the size of the Y dimension. |
int |
getSizeY(String id)
Deprecated. Replaced by getSizeY() |
int |
getSizeZ()
Gets the size of the Z dimension. |
int |
getSizeZ(String id)
Deprecated. Replaced by getSizeZ() |
int |
getThumbSizeX()
Get the size of the X dimension for the thumbnail. |
int |
getThumbSizeX(String id)
Deprecated. Replaced by getThumbSizeX() |
int |
getThumbSizeY()
Get the size of the Y dimension for the thumbnail. |
int |
getThumbSizeY(String id)
Deprecated. Replaced by getThumbSizeY() |
String[] |
getUsedFiles()
Returns an array of filenames needed to open this dataset. |
String[] |
getUsedFiles(String id)
Deprecated. Replaced by getUsedFiles() |
int[] |
getZCTCoords(int index)
Gets the Z, C and T coordinates corresponding to the given rasterized index value. |
int[] |
getZCTCoords(String id,
int index)
Deprecated. Replaced by getZCTCoords(int) |
boolean |
isFalseColor()
Returns false if isIndexed is false, or if isIndexed is true and the lookup table represents "real" color data. |
boolean |
isGroupFiles()
Returns true if we should group files in multi-file formats. |
boolean |
isIndexed()
Gets whether the images are indexed color. |
boolean |
isInterleaved()
Gets whether or not the channels are interleaved. |
boolean |
isInterleaved(int subC)
Gets whether or not the given sub-channel is interleaved. |
boolean |
isInterleaved(String id)
Deprecated. Replaced by isInterleaved() |
boolean |
isInterleaved(String id,
int subC)
Deprecated. Replaced by isInterleaved(int) |
boolean |
isLittleEndian()
Gets whether the data is in little-endian format. |
boolean |
isLittleEndian(String id)
Deprecated. Replaced by isLittleEndian() |
boolean |
isMetadataCollected()
Returns true if we should collect metadata. |
boolean |
isMetadataComplete()
Returns true if this format's metadata is completely parsed. |
boolean |
isMetadataFiltered()
Returns true if ugly metadata (entries with unprintable characters, and extremely large entries) are discarded from the metadata table. |
boolean |
isNormalized()
Returns true if we should normalize float data. |
boolean |
isOrderCertain()
Gets whether the dimension order and sizes are known, or merely guesses. |
boolean |
isOrderCertain(String id)
Deprecated. Replaced by isOrderCertain() |
boolean |
isOriginalMetadataPopulated()
Returns true if we should save proprietary metadata in the MetadataStore. |
boolean |
isRGB()
Checks if the images in the file are RGB. |
boolean |
isRGB(String id)
Deprecated. Replaced by isRGB() |
boolean |
isThisType(byte[] block)
Checks if the given block is a valid header for this file format. |
byte[] |
openBytes(int no)
Obtains the specified image from the current file as a byte array. |
byte[] |
openBytes(int no,
byte[] buf)
Obtains the specified image from the current file into a pre-allocated byte array of (sizeX * sizeY * bytesPerPixel). |
byte[] |
openBytes(String id,
int no)
Deprecated. Replaced by openBytes(int) |
byte[] |
openBytes(String id,
int no,
byte[] buf)
Deprecated. Replaced by openBytes(int, byte[]) |
BufferedImage |
openImage(int no)
Obtains the specified image from the current file. |
BufferedImage |
openImage(String id,
int no)
Deprecated. Replaced by openImage(int) |
byte[] |
openThumbBytes(int no)
Obtains a thumbnail for the specified image from the current file, as a byte array. |
byte[] |
openThumbBytes(String id,
int no)
Deprecated. Replaced by openThumbBytes(int) |
BufferedImage |
openThumbImage(int no)
Obtains a thumbnail for the specified image from the current file. |
BufferedImage |
openThumbImage(String id,
int no)
Deprecated. Replaced by openThumbImage(int) |
void |
setGroupFiles(boolean group)
Specifies whether or not to force grouping in multi-file formats. |
void |
setMetadataCollected(boolean collect)
Specifies whether or not to collect metadata. |
void |
setMetadataFiltered(boolean filter)
Specifies whether ugly metadata (entries with unprintable characters, and extremely large entries) should be discarded from the metadata table. |
void |
setMetadataStore(MetadataStore store)
Sets the default metadata store for this reader. |
void |
setNormalized(boolean normalize)
Specifies whether or not to normalize float data. |
void |
setOriginalMetadataPopulated(boolean populate)
Specifies whether or not to save proprietary metadata in the MetadataStore. |
void |
setSeries(int no)
Activates the specified series. |
void |
setSeries(String id,
int no)
Deprecated. Replaced by setSeries(int) |
Methods inherited from interface loci.formats.IFormatHandler |
---|
close, getFormat, getSuffixes, isThisType, isThisType, setId, setId |
Methods inherited from interface loci.formats.StatusReporter |
---|
addStatusListener, getStatusListeners, removeStatusListener |
Field Detail |
---|
static final int MUST_GROUP
static final int CAN_GROUP
static final int CANNOT_GROUP
Method Detail |
---|
boolean isThisType(byte[] block)
int getImageCount()
boolean isRGB()
int getSizeX()
int getSizeY()
int getSizeZ()
int getSizeC()
int getSizeT()
int getPixelType()
FormatTools
static pixel types such as INT8
.int getEffectiveSizeC()
int getRGBChannelCount()
boolean isIndexed()
boolean isFalseColor()
byte[][] get8BitLookupTable() throws FormatException, IOException
INT8
or UINT8
, this method will return null.
FormatException
IOException
short[][] get16BitLookupTable() throws FormatException, IOException
INT16
or UINT16
, this method will return null.
FormatException
IOException
int[] getChannelDimLengths()
String[] getChannelDimTypes()
FormatTools
.
int getThumbSizeX()
int getThumbSizeY()
boolean isLittleEndian()
String getDimensionOrder()
isInterleaved(String)
method will return true.
boolean isOrderCertain()
boolean isInterleaved()
boolean isInterleaved(int subC)
SDTReader
handles spectral-lifetime data with
the interleaved lifetime bins and non-interleaved spectral channels.
byte[] openBytes(int no) throws FormatException, IOException
FormatException
IOException
byte[] openBytes(int no, byte[] buf) throws FormatException, IOException
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.BufferedImage openImage(int no) throws FormatException, IOException
FormatException
IOException
byte[] openThumbBytes(int no) throws FormatException, IOException
FormatException
IOException
BufferedImage openThumbImage(int no) throws FormatException, IOException
FormatException
IOException
void close(boolean fileOnly) throws IOException
IFormatHandler.close()
.
IOException
int getSeriesCount()
void setSeries(int no)
int getSeries()
void setNormalized(boolean normalize)
boolean isNormalized()
void setMetadataCollected(boolean collect)
boolean isMetadataCollected()
void setOriginalMetadataPopulated(boolean populate)
boolean isOriginalMetadataPopulated()
void setGroupFiles(boolean group)
boolean isGroupFiles()
boolean isMetadataComplete()
int fileGroupOption(String id) throws FormatException, IOException
FormatException
IOException
String[] getUsedFiles()
String getCurrentFile()
int getIndex(int z, int c, int t)
int[] getZCTCoords(int index)
Object getMetadataValue(String field)
field
- the name associated with the metadata field
Hashtable getMetadata()
CoreMetadata getCoreMetadata()
void setMetadataFiltered(boolean filter)
boolean isMetadataFiltered()
void setMetadataStore(MetadataStore store)
store
- a metadata store implementation.MetadataStore getMetadataStore()
null
metadata store.
Object getMetadataStoreRoot()
int getImageCount(String id) throws FormatException, IOException
getImageCount()
FormatException
IOException
boolean isRGB(String id) throws FormatException, IOException
isRGB()
FormatException
IOException
int getSizeX(String id) throws FormatException, IOException
getSizeX()
FormatException
IOException
int getSizeY(String id) throws FormatException, IOException
getSizeY()
FormatException
IOException
int getSizeZ(String id) throws FormatException, IOException
getSizeZ()
FormatException
IOException
int getSizeC(String id) throws FormatException, IOException
getSizeC()
FormatException
IOException
int getSizeT(String id) throws FormatException, IOException
getSizeT()
FormatException
IOException
int getPixelType(String id) throws FormatException, IOException
getPixelType()
FormatException
IOException
int getEffectiveSizeC(String id) throws FormatException, IOException
getEffectiveSizeC()
FormatException
IOException
int getRGBChannelCount(String id) throws FormatException, IOException
getRGBChannelCount()
FormatException
IOException
int[] getChannelDimLengths(String id) throws FormatException, IOException
getChannelDimLengths()
FormatException
IOException
String[] getChannelDimTypes(String id) throws FormatException, IOException
getChannelDimTypes()
FormatException
IOException
int getThumbSizeX(String id) throws FormatException, IOException
getThumbSizeX()
FormatException
IOException
int getThumbSizeY(String id) throws FormatException, IOException
getThumbSizeY()
FormatException
IOException
boolean isLittleEndian(String id) throws FormatException, IOException
isLittleEndian()
FormatException
IOException
String getDimensionOrder(String id) throws FormatException, IOException
getDimensionOrder()
FormatException
IOException
boolean isOrderCertain(String id) throws FormatException, IOException
isOrderCertain()
FormatException
IOException
boolean isInterleaved(String id) throws FormatException, IOException
isInterleaved()
FormatException
IOException
boolean isInterleaved(String id, int subC) throws FormatException, IOException
isInterleaved(int)
FormatException
IOException
BufferedImage openImage(String id, int no) throws FormatException, IOException
openImage(int)
FormatException
IOException
byte[] openBytes(String id, int no) throws FormatException, IOException
openBytes(int)
FormatException
IOException
byte[] openBytes(String id, int no, byte[] buf) throws FormatException, IOException
openBytes(int, byte[])
FormatException
IOException
BufferedImage openThumbImage(String id, int no) throws FormatException, IOException
openThumbImage(int)
FormatException
IOException
byte[] openThumbBytes(String id, int no) throws FormatException, IOException
openThumbBytes(int)
FormatException
IOException
int getSeriesCount(String id) throws FormatException, IOException
getSeriesCount()
FormatException
IOException
void setSeries(String id, int no) throws FormatException, IOException
setSeries(int)
FormatException
IOException
int getSeries(String id) throws FormatException, IOException
getSeries()
FormatException
IOException
String[] getUsedFiles(String id) throws FormatException, IOException
getUsedFiles()
FormatException
IOException
int getIndex(String id, int z, int c, int t) throws FormatException, IOException
getIndex(int, int, int)
FormatException
IOException
int[] getZCTCoords(String id, int index) throws FormatException, IOException
getZCTCoords(int)
FormatException
IOException
Object getMetadataValue(String id, String field) throws FormatException, IOException
getMetadataValue(String)
FormatException
IOException
Hashtable getMetadata(String id) throws FormatException, IOException
getMetadata()
FormatException
IOException
CoreMetadata getCoreMetadata(String id) throws FormatException, IOException
getCoreMetadata()
FormatException
IOException
MetadataStore getMetadataStore(String id) throws FormatException, IOException
getMetadataStore()
FormatException
IOException
Object getMetadataStoreRoot(String id) throws FormatException, IOException
getMetadataStoreRoot()
FormatException
IOException
|
||||||||||
PREV CLASS NEXT CLASS | FRAMES NO FRAMES | |||||||||
SUMMARY: NESTED | FIELD | CONSTR | METHOD | DETAIL: FIELD | CONSTR | METHOD |