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 List<FV1000Reader.ChannelData> |
channels |
private static int |
CIRCLE |
private String[] |
code |
private static int |
COLOR_BAR |
private String |
creationDate |
static String |
DATE_FORMAT |
private static int |
ELLIPSE |
private Map<Integer,String> |
filenames |
private static int |
FREE_LINE |
private static int |
FREE_SHAPE |
static String |
FV1000_MAGIC_STRING_1 |
static String |
FV1000_MAGIC_STRING_2 |
static String[] |
FV1000_SUFFIXES |
private static int |
GRID |
private ArrayList<IFDList> |
ifds |
private List<String> |
illuminations |
private int |
imageDepth |
private boolean |
isOIB
Flag indicating this is an OIB dataset.
|
private int |
lastChannel |
private String |
lensNA |
private String |
line |
private static int |
LINE |
private short[][][] |
lut |
private List<String> |
lutNames |
private String |
magnification |
private static int |
NUM_DIMENSIONS |
private String |
objectiveName |
static String[] |
OIB_SUFFIX |
private Map<String,String> |
oibMapping
File mappings for OIB file.
|
static String[] |
OIF_SUFFIX |
private IniParser |
parser |
private String |
pinholeSize |
private Double[] |
pixelSize |
private double |
pixelSizeT |
private String |
pixelSizeX |
private String |
pixelSizeY |
private double |
pixelSizeZ |
private List<FV1000Reader.PlaneData> |
planes |
private POIService |
poi |
private static int |
POINT
ROI types.
|
private static int |
POLYGON |
private static int |
POLYLINE |
static String[] |
PREVIEWNAME_PREFIXES |
private List<String> |
previewNames |
private String |
ptyEnd |
private String |
ptyPattern |
private String |
ptyStart |
private static int |
RECTANGLE |
private Map<Integer,String> |
roiFilenames |
private static String |
ROTATION |
private static int |
SCALE |
private String[] |
size |
private String |
thumbId
Name of thumbnail file.
|
private BMPReader |
thumbReader
Helper reader for thumbnail.
|
private List<String> |
tiffs
Names of every TIFF file to open.
|
private List<String> |
usedFiles
Used file list.
|
private int |
validBits |
private List<Double> |
wavelengths |
private 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(String id)
Returns an int indicating that we cannot, must, or might group the files
in a given dataset.
|
private String |
findOIFFile(String baseFile) |
short[][] |
get16BitLookupTable()
Gets the 16-bit color lookup table associated with
the most recently opened image.
|
private RandomAccessInputStream |
getFile(String name) |
private IniList |
getIniFile(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 RandomAccessInputStream |
getPlane(int seriesIndex,
int planeIndex) |
private Integer |
getPreviewNameIndex(String key) |
String[] |
getSeriesUsedFiles(boolean noPixels)
Returns an array of filenames needed to open the current series.
|
protected void |
initFile(String id)
Initializes the given file (parsing header information, etc.).
|
private void |
initPOIService() |
private boolean |
isPreviewName(String name) |
boolean |
isSingleFile(String id)
Returns true if this is a single-file format.
|
boolean |
isThisType(RandomAccessInputStream stream)
Checks if the given stream is a valid stream for this file format.
|
boolean |
isThisType(String name,
boolean open)
Checks if a file matches the type of this format reader.
|
private 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(String filename,
MetadataStore store,
int nextROI,
int plane) |
private void |
populateMetadataStore(MetadataStore store,
String path) |
private String |
removeGST(String s) |
private String |
replaceExtension(String name,
String oldExt,
String newExt) |
private String |
sanitizeFile(String file,
String path) |
private String |
sanitizeValue(String value) |
private static int[] |
scanFormat(String pattern,
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, 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
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 String FV1000_MAGIC_STRING_1
public static final String FV1000_MAGIC_STRING_2
public static final String[] OIB_SUFFIX
public static final String[] OIF_SUFFIX
public static final String[] FV1000_SUFFIXES
public static final String[] PREVIEWNAME_PREFIXES
public static final 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 String ROTATION
private IniParser parser
private String thumbId
private BMPReader thumbReader
private boolean isOIB
private String[] code
private String[] size
private Double[] pixelSize
private int imageDepth
private String pixelSizeX
private String pixelSizeY
private int validBits
private String pinholeSize
private String magnification
private String lensNA
private String objectiveName
private String workingDistance
private String creationDate
private List<FV1000Reader.ChannelData> channels
private List<FV1000Reader.PlaneData> planes
private transient POIService poi
private short[][][] lut
private int lastChannel
private double pixelSizeZ
private double pixelSizeT
private String ptyStart
private String ptyEnd
private String ptyPattern
private String line
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(String id) throws FormatException, IOException
IFormatReader
isSingleFile
in interface IFormatReader
isSingleFile
in class FormatReader
FormatException
IOException
public boolean isThisType(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(RandomAccessInputStream stream) throws IOException
IFormatReader
isThisType
in interface IFormatReader
isThisType
in class FormatReader
IOException
public int fileGroupOption(String id) throws FormatException, IOException
IFormatReader
fileGroupOption
in interface IFormatReader
fileGroupOption
in class FormatReader
FormatException
IOException
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, 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.IOException
- if there was a problem reading the file.IFormatReader.openBytes(int, byte[], int, int, int, int)
public String[] getSeriesUsedFiles(boolean noPixels)
IFormatReader
getSeriesUsedFiles
in interface IFormatReader
getSeriesUsedFiles
in class FormatReader
public void close(boolean fileOnly) throws IOException
IFormatReader
Closeable.close()
.close
in interface IFormatReader
close
in class FormatReader
IOException
protected void initFile(String id) throws FormatException, IOException
FormatReader
initFile
in class FormatReader
FormatException
- if a parsing error occurs processing the file.IOException
- if an I/O error occurs processing the fileprivate void populateMetadataStore(MetadataStore store, String path) throws FormatException, IOException
FormatException
IOException
private int parseROIFile(String filename, MetadataStore store, int nextROI, int plane) throws FormatException, IOException
FormatException
IOException
private void addPtyFiles() throws FormatException
FormatException
private String findOIFFile(String baseFile) throws FormatException
FormatException
private String mapOIBFiles() throws FormatException, IOException
FormatException
IOException
private void initPOIService() throws FormatException, IOException
FormatException
IOException
private RandomAccessInputStream getFile(String name) throws FormatException, IOException
FormatException
IOException
private RandomAccessInputStream getPlane(int seriesIndex, int planeIndex)
private boolean isPreviewName(String name)
private static int[] scanFormat(String pattern, String string) throws FormatException
FormatException
private IniList getIniFile(String filename) throws FormatException, IOException
FormatException
IOException
Copyright © 2016 Open Microscopy Environment