public class FV1000Reader extends FormatReader
Modifier and Type | Class and Description |
---|---|
(package private) class |
FV1000Reader.ChannelData |
(package private) class |
FV1000Reader.PlaneData |
Modifier and Type | Field and Description |
---|---|
private static int |
ARROW |
private java.util.List<FV1000Reader.ChannelData> |
channels |
private static int |
CIRCLE |
private java.lang.String[] |
code |
private static int |
COLOR_BAR |
private java.lang.String |
creationDate |
static java.lang.String |
DATE_FORMAT |
private static int |
ELLIPSE |
private java.util.Map<java.lang.Integer,java.lang.String> |
filenames |
private static int |
FREE_LINE |
private static int |
FREE_SHAPE |
static java.lang.String |
FV1000_MAGIC_STRING_1 |
static java.lang.String |
FV1000_MAGIC_STRING_2 |
static java.lang.String[] |
FV1000_SUFFIXES |
private static int |
GRID |
private java.util.ArrayList<IFDList> |
ifds |
private java.util.List<java.lang.String> |
illuminations |
private int |
imageDepth |
private boolean |
isOIB
Flag indicating this is an OIB dataset.
|
private int |
lastChannel |
private java.lang.String |
lensNA |
private java.lang.String |
line |
private static int |
LINE |
private short[][][] |
lut |
private java.util.List<java.lang.String> |
lutNames |
private java.lang.String |
magnification |
private static int |
NUM_DIMENSIONS |
private java.lang.String |
objectiveName |
static java.lang.String[] |
OIB_SUFFIX |
private java.util.Map<java.lang.String,java.lang.String> |
oibMapping
File mappings for OIB file.
|
static java.lang.String[] |
OIF_SUFFIX |
private loci.common.IniParser |
parser |
private java.lang.String |
pinholeSize |
private java.lang.Double[] |
pixelSize |
private double |
pixelSizeT |
private java.lang.String |
pixelSizeX |
private java.lang.String |
pixelSizeY |
private double |
pixelSizeZ |
private java.util.List<FV1000Reader.PlaneData> |
planes |
private POIService |
poi |
private static int |
POINT
ROI types.
|
private static int |
POLYGON |
private static int |
POLYLINE |
static java.lang.String[] |
PREVIEWNAME_PREFIXES |
private java.util.List<java.lang.String> |
previewNames |
private java.lang.String |
ptyEnd |
private java.lang.String |
ptyPattern |
private java.lang.String |
ptyStart |
private static int |
RECTANGLE |
private java.util.Map<java.lang.Integer,java.lang.String> |
roiFilenames |
private static java.lang.String |
ROTATION |
private static int |
SCALE |
private java.lang.String[] |
size |
private java.lang.String |
thumbId
Name of thumbnail file.
|
private BMPReader |
thumbReader
Helper reader for thumbnail.
|
private java.util.List<java.lang.String> |
tiffs
Names of every TIFF file to open.
|
private java.util.List<java.lang.String> |
usedFiles
Used file list.
|
private int |
validBits |
private java.util.List<java.lang.Double> |
wavelengths |
private java.lang.String |
workingDistance |
core, coreIndex, datasetDescription, domains, filterMetadata, flattenedResolutions, group, hasCompanionFiles, in, indexedAsRGB, metadata, metadataStore, normalizeData, resolution, saveOriginalMetadata, series, suffixNecessary, suffixSufficient, THUMBNAIL_DIMENSION
COMPRESSION_SUFFIXES, currentId, format, LOGGER, metadataOptions, suffixes
CAN_GROUP, CANNOT_GROUP, MUST_GROUP
Constructor and Description |
---|
FV1000Reader()
Constructs a new FV1000 reader.
|
Modifier and Type | Method and Description |
---|---|
private void |
addPtyFiles() |
void |
close(boolean fileOnly)
Closes the currently open file.
|
int |
fileGroupOption(java.lang.String id)
Returns an indication of whether the files in a multi-file dataset can
be handled individually.
|
private java.lang.String |
findOIFFile(java.lang.String baseFile) |
short[][] |
get16BitLookupTable()
Gets the 16-bit color lookup table associated with
the most recently opened image.
|
private loci.common.RandomAccessInputStream |
getFile(java.lang.String name) |
private loci.common.IniList |
getIniFile(java.lang.String filename) |
int |
getOptimalTileHeight()
Returns the optimal sub-image height for use with openBytes.
|
int |
getOptimalTileWidth()
Returns the optimal sub-image width for use with openBytes.
|
private loci.common.RandomAccessInputStream |
getPlane(int seriesIndex,
int planeIndex) |
private java.lang.Integer |
getPreviewNameIndex(java.lang.String key) |
java.lang.String[] |
getSeriesUsedFiles(boolean noPixels)
Returns an array of filenames needed to open the current series.
|
protected void |
initFile(java.lang.String id)
Initializes the given file (parsing header information, etc.).
|
private void |
initPOIService() |
private boolean |
isPreviewName(java.lang.String name) |
boolean |
isSingleFile(java.lang.String id)
Returns true if the named file is expected to be the only
file in the dataset.
|
boolean |
isThisType(loci.common.RandomAccessInputStream stream)
Checks if the given stream is a valid stream for this file format.
|
boolean |
isThisType(java.lang.String name,
boolean open)
Checks if a file matches the type of this format reader.
|
private java.lang.String |
mapOIBFiles() |
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.
|
private int |
parseROIFile(java.lang.String filename,
MetadataStore store,
int nextROI,
int plane) |
private void |
populateMetadataStore(MetadataStore store,
java.lang.String path) |
private java.lang.String |
removeGST(java.lang.String s) |
private java.lang.String |
replaceExtension(java.lang.String name,
java.lang.String oldExt,
java.lang.String newExt) |
private java.lang.String |
sanitizeFile(java.lang.String file,
java.lang.String path) |
private java.lang.String |
sanitizeValue(java.lang.String value) |
private static int[] |
scanFormat(java.lang.String pattern,
java.lang.String string) |
addGlobalMeta, addGlobalMeta, addGlobalMeta, addGlobalMeta, addGlobalMeta, addGlobalMeta, addGlobalMeta, addGlobalMeta, addGlobalMeta, addGlobalMetaList, addMeta, addMetaList, addSeriesMeta, addSeriesMeta, addSeriesMeta, addSeriesMeta, addSeriesMeta, addSeriesMeta, addSeriesMeta, addSeriesMeta, addSeriesMeta, addSeriesMetaList, close, coreIndexToSeries, flattenHashtables, get8BitLookupTable, getAcquisitionMode, getAdvancedSeriesUsedFiles, getAdvancedUsedFiles, getArcType, getBinning, getBitsPerPixel, getCompression, getContrastMethod, getCoreIndex, getCoreMetadataList, getCorrection, getCurrentCore, getCurrentFile, getDatasetStructureDescription, getDetectorType, getDimensionOrder, getDimensionOrder, getDomains, getEffectiveSizeC, getExperimentType, getFilamentType, getFillRule, getFilterType, getFontFamily, getFontStyle, getGlobalMeta, getGlobalMetadata, getIlluminationType, getImageCount, getImmersion, getIndex, getIndex, getLaserMedium, getLaserType, getMarker, getMedium, getMetadataStore, getMetadataStoreRoot, getMetadataValue, getMicrobeamManipulationType, getMicroscopeType, getModuloC, getModuloT, getModuloZ, getNamingConvention, getPixelType, getPixelType, getPossibleDomains, getPulse, getRequiredDirectories, getResolution, getResolutionCount, getRGBChannelCount, getRotationTransform, getSeries, getSeriesCount, getSeriesMeta, getSeriesMetadata, getSeriesMetadataValue, getSeriesUsedFiles, getSizeC, getSizeT, getSizeX, getSizeY, getSizeZ, getThumbSizeX, getThumbSizeY, getUnderlyingReaders, getUsedFiles, getUsedFiles, getZCTCoords, getZCTModuloCoords, hasCompanionFiles, hasFlattenedResolutions, isFalseColor, isGroupFiles, isIndexed, isInterleaved, isInterleaved, isLittleEndian, isMetadataComplete, isMetadataFiltered, isNormalized, isOrderCertain, isOriginalMetadataPopulated, isRGB, isThisType, isThisType, isThumbnailSeries, isUsedFile, makeFilterMetadata, openBytes, openBytes, openBytes, openPlane, openThumbBytes, readPlane, readPlane, reopenFile, seriesToCoreIndex, setCoreIndex, setFlattenedResolutions, setGroupFiles, setId, setMetadataFiltered, setMetadataStore, setNormalized, setOriginalMetadataPopulated, setResolution, setSeries, updateMetadataLists
checkSuffix, checkSuffix, getFormat, getMetadataOptions, getNativeDataType, getSuffixes, getSupportedMetadataLevels, setMetadataOptions
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
getFormat, getNativeDataType, getSuffixes
getMetadataOptions, getSupportedMetadataLevels, setMetadataOptions
public static final java.lang.String FV1000_MAGIC_STRING_1
public static final java.lang.String FV1000_MAGIC_STRING_2
public static final java.lang.String[] OIB_SUFFIX
public static final java.lang.String[] OIF_SUFFIX
public static final java.lang.String[] FV1000_SUFFIXES
public static final java.lang.String[] PREVIEWNAME_PREFIXES
public static final java.lang.String DATE_FORMAT
private static final int NUM_DIMENSIONS
private static final int POINT
private static final int LINE
private static final int POLYLINE
private static final int RECTANGLE
private static final int CIRCLE
private static final int ELLIPSE
private static final int POLYGON
private static final int FREE_SHAPE
private static final int FREE_LINE
private static final int GRID
private static final int ARROW
private static final int COLOR_BAR
private static final int SCALE
private static final java.lang.String ROTATION
private loci.common.IniParser parser
private java.util.List<java.lang.String> tiffs
private java.lang.String thumbId
private BMPReader thumbReader
private java.util.List<java.lang.String> usedFiles
private boolean isOIB
private java.util.Map<java.lang.String,java.lang.String> oibMapping
private java.lang.String[] code
private java.lang.String[] size
private java.lang.Double[] pixelSize
private int imageDepth
private java.util.List<java.lang.String> previewNames
private java.lang.String pixelSizeX
private java.lang.String pixelSizeY
private int validBits
private java.util.List<java.lang.String> illuminations
private java.util.List<java.lang.Double> wavelengths
private java.lang.String pinholeSize
private java.lang.String magnification
private java.lang.String lensNA
private java.lang.String objectiveName
private java.lang.String workingDistance
private java.lang.String creationDate
private java.util.List<FV1000Reader.ChannelData> channels
private java.util.List<java.lang.String> lutNames
private java.util.Map<java.lang.Integer,java.lang.String> filenames
private java.util.Map<java.lang.Integer,java.lang.String> roiFilenames
private java.util.List<FV1000Reader.PlaneData> planes
private transient POIService poi
private short[][][] lut
private int lastChannel
private double pixelSizeZ
private double pixelSizeT
private java.lang.String ptyStart
private java.lang.String ptyEnd
private java.lang.String ptyPattern
private java.lang.String line
private java.util.ArrayList<IFDList> ifds
public int getOptimalTileWidth()
IFormatReader
getOptimalTileWidth
in interface IFormatReader
getOptimalTileWidth
in class FormatReader
public int getOptimalTileHeight()
IFormatReader
getOptimalTileHeight
in interface IFormatReader
getOptimalTileHeight
in class FormatReader
public boolean isSingleFile(java.lang.String id) throws FormatException, java.io.IOException
IFormatReader
isSingleFile
in interface IFormatReader
isSingleFile
in class FormatReader
FormatException
java.io.IOException
public boolean isThisType(java.lang.String name, boolean open)
FormatReader
FormatReader.isThisType(RandomAccessInputStream)
.isThisType
in interface IFormatReader
isThisType
in class FormatReader
open
- If true, and the file extension is insufficient to determine
the file type, the (existing) file is opened for further analysis.public boolean isThisType(loci.common.RandomAccessInputStream stream) throws java.io.IOException
IFormatReader
isThisType
in interface IFormatReader
isThisType
in class FormatReader
stream
- A RandomAccessInputStream representing the file to check.
The first byte in the stream is assumed to be the first byte
in the file.java.io.IOException
public int fileGroupOption(java.lang.String id) throws FormatException, java.io.IOException
IFormatReader
fileGroupOption
in interface IFormatReader
fileGroupOption
in class FormatReader
id
- a file in the multi-file datasetFormatTools.MUST_GROUP
indicates that the
files cannot be handled separately; the reader will always detect and
read all files in the dataset. FormatTools.CAN_GROUP
indicates
that the files may be handled separately, but file grouping must then
be disabled via IFormatReader.setGroupFiles(boolean)
.
FormatTools.CANNOT_GROUP
indicates that the files must be handled
separately; the reader will not attempt to read all files in the dataset
(this is rare).FormatException
java.io.IOException
FormatTools.MUST_GROUP
,
FormatTools.CAN_GROUP
,
FormatTools.CANNOT_GROUP
public short[][] get16BitLookupTable()
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 FormatReader
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 FormatReader
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.IFormatReader.openBytes(int, byte[], int, int, int, int)
public java.lang.String[] getSeriesUsedFiles(boolean noPixels)
IFormatReader
IFormatHandler.setId(String)
, if appropriate based upon 'noPixels'.
The remaining elements are expected to be in a consistent order;
if a directory listing is necessary to build the list then it should
be sorted first.getSeriesUsedFiles
in interface IFormatReader
getSeriesUsedFiles
in class FormatReader
public void close(boolean fileOnly) throws java.io.IOException
IFormatReader
Closeable.close()
.close
in interface IFormatReader
close
in class FormatReader
java.io.IOException
protected void initFile(java.lang.String id) throws FormatException, java.io.IOException
FormatReader
initFile
in class FormatReader
FormatException
- if a parsing error occurs processing the file.java.io.IOException
- if an I/O error occurs processing the fileprivate void populateMetadataStore(MetadataStore store, java.lang.String path) throws FormatException, java.io.IOException
FormatException
java.io.IOException
private int parseROIFile(java.lang.String filename, MetadataStore store, int nextROI, int plane) throws FormatException, java.io.IOException
FormatException
java.io.IOException
private void addPtyFiles() throws FormatException
FormatException
private java.lang.String findOIFFile(java.lang.String baseFile) throws FormatException
FormatException
private java.lang.String mapOIBFiles() throws FormatException, java.io.IOException
FormatException
java.io.IOException
private java.lang.String sanitizeValue(java.lang.String value)
private java.lang.String sanitizeFile(java.lang.String file, java.lang.String path)
private java.lang.String removeGST(java.lang.String s)
private void initPOIService() throws FormatException, java.io.IOException
FormatException
java.io.IOException
private loci.common.RandomAccessInputStream getFile(java.lang.String name) throws FormatException, java.io.IOException
FormatException
java.io.IOException
private loci.common.RandomAccessInputStream getPlane(int seriesIndex, int planeIndex)
private java.lang.Integer getPreviewNameIndex(java.lang.String key)
private boolean isPreviewName(java.lang.String name)
private java.lang.String replaceExtension(java.lang.String name, java.lang.String oldExt, java.lang.String newExt)
private static int[] scanFormat(java.lang.String pattern, java.lang.String string) throws FormatException
FormatException
private loci.common.IniList getIniFile(java.lang.String filename) throws FormatException, java.io.IOException
FormatException
java.io.IOException
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