public class SVSReader extends BaseTiffReader
Modifier and Type | Field and Description |
---|---|
static String |
APERIO_IMAGE_DESCRIPTION_PREFIX
TIFF image description prefix for Aperio SVS files.
|
private String[] |
comments |
private String |
date |
private static String |
DATE_FORMAT |
private Double |
emissionWavelength |
private Double |
excitationWavelength |
private Double |
exposureScale |
private Double |
exposureTime |
private int[] |
ifdmap |
private static org.slf4j.Logger |
LOGGER
Logger for this class.
|
private Double |
magnification |
private Length[] |
pixelSize |
private String |
time |
DATE_FORMATS
equalStrips, ifds, lastPlane, noSubresolutions, subResolutionIFDs, thumbnailIFDs, tiffParser, use64Bit
core, coreIndex, datasetDescription, domains, filterMetadata, flattenedResolutions, group, hasCompanionFiles, in, indexedAsRGB, metadata, metadataOptions, metadataStore, normalizeData, resolution, saveOriginalMetadata, series, suffixNecessary, suffixSufficient, THUMBNAIL_DIMENSION
COMPRESSION_SUFFIXES, currentId, format, suffixes
CAN_GROUP, CANNOT_GROUP, MUST_GROUP
Constructor and Description |
---|
SVSReader()
Constructs a new SVS reader.
|
Modifier and Type | Method and Description |
---|---|
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.
|
protected Timestamp |
getDatestamp() |
protected Length |
getEmission() |
protected Length |
getExcitation() |
protected Double |
getExposureTime() |
private int |
getIFDIndex(int coreIndex) |
protected double |
getMagnification() |
int |
getOptimalTileHeight()
Returns the optimal sub-image height for use with openBytes.
|
int |
getOptimalTileWidth()
Returns the optimal sub-image width for use with openBytes.
|
protected Length[] |
getPhysicalSizes() |
protected void |
initMetadataStore()
Populates the metadata store using the data parsed in
BaseTiffReader.initStandardMetadata() along with some further parsing done in
the method itself. |
protected void |
initStandardMetadata()
Parses standard metadata.
|
boolean |
isThisType(String name,
boolean open)
Checks if a file matches the type of this format reader.
|
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[] |
openThumbBytes(int no)
Obtains a thumbnail for the specified image plane from the current file,
as a byte array.
|
protected void |
reorderResolutions()
Validate the order of resolutions for the current series, in
decending order of size.
|
getExifTagName, getImageCreationDate, initFile, initMetadata, put, put, put, put, put, put, put, put, put, put, putInt, putString
get16BitLookupTable, get8BitLookupTable, getIFDs, getThumbnailIFDs, getThumbSizeX, getThumbSizeY, initTiffParser, isThisType, reopenFile, setResolutionLevel
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, 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, getLineCap, getMarker, getMedium, getMetadataOptions, getMetadataStore, getMetadataStoreRoot, getMetadataValue, getMicrobeamManipulationType, getMicroscopeType, getModuloC, getModuloT, getModuloZ, getNamingConvention, getPixelType, getPixelType, getPossibleDomains, getPulse, getRequiredDirectories, getResolution, getResolutionCount, getRGBChannelCount, getRotationTransform, getSeries, getSeriesCount, getSeriesMeta, getSeriesMetadata, getSeriesMetadataValue, getSeriesUsedFiles, getSeriesUsedFiles, getSizeC, getSizeT, getSizeX, getSizeY, getSizeZ, getSupportedMetadataLevels, getUnderlyingReaders, getUsedFiles, getUsedFiles, getZCTCoords, getZCTModuloCoords, hasCompanionFiles, hasFlattenedResolutions, isFalseColor, isGroupFiles, isIndexed, isInterleaved, isInterleaved, isLittleEndian, isMetadataComplete, isMetadataFiltered, isNormalized, isOrderCertain, isOriginalMetadataPopulated, isRGB, isSingleFile, isThisType, isThisType, isThumbnailSeries, isUsedFile, makeFilterMetadata, openBytes, openBytes, openBytes, openPlane, readPlane, readPlane, seriesToCoreIndex, setCoreIndex, setFlattenedResolutions, setGroupFiles, setId, setMetadataFiltered, setMetadataOptions, setMetadataStore, setNormalized, setOriginalMetadataPopulated, setResolution, setSeries
checkSuffix, checkSuffix, getFormat, getNativeDataType, getSuffixes
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
getFormat, getNativeDataType, getSuffixes
private static final org.slf4j.Logger LOGGER
public static final String APERIO_IMAGE_DESCRIPTION_PREFIX
private static final String DATE_FORMAT
private Length[] pixelSize
private String[] comments
private int[] ifdmap
private Double emissionWavelength
private Double excitationWavelength
private Double exposureTime
private Double exposureScale
private Double magnification
private String date
private String time
public int fileGroupOption(String id) throws FormatException, IOException
IFormatReader
fileGroupOption
in interface IFormatReader
fileGroupOption
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 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 MinimalTiffReader
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 byte[] openThumbBytes(int no) throws FormatException, IOException
IFormatReader
openThumbBytes
in interface IFormatReader
openThumbBytes
in class MinimalTiffReader
FormatException
IOException
public void close(boolean fileOnly) throws IOException
IFormatReader
Closeable.close()
.close
in interface IFormatReader
close
in class MinimalTiffReader
IOException
public int getOptimalTileWidth()
IFormatReader
getOptimalTileWidth
in interface IFormatReader
getOptimalTileWidth
in class MinimalTiffReader
public int getOptimalTileHeight()
IFormatReader
getOptimalTileHeight
in interface IFormatReader
getOptimalTileHeight
in class MinimalTiffReader
protected void initStandardMetadata() throws FormatException, IOException
BaseTiffReader
initStandardMetadata
in class BaseTiffReader
FormatException
IOException
protected void initMetadataStore() throws FormatException
BaseTiffReader
BaseTiffReader.initStandardMetadata()
along with some further parsing done in
the method itself.
All calls to the active MetadataStore
should be made in this
method and only in this method. This is especially important for
sub-classes that override the getters for pixel set array size, etc.initMetadataStore
in class BaseTiffReader
FormatException
private int getIFDIndex(int coreIndex)
protected void reorderResolutions()
protected Length getEmission()
protected Length getExcitation()
protected Double getExposureTime()
protected Timestamp getDatestamp()
protected Length[] getPhysicalSizes()
protected double getMagnification()
Copyright © 2016 Open Microscopy Environment