public class SVSReader extends BaseTiffReader
Modifier and Type | Field and Description |
---|---|
private static java.lang.String |
APERIO_IMAGE_DESCRIPTION_PREFIX
TIFF image description prefix for Aperio SVS files.
|
private java.lang.String[] |
comments |
private java.lang.String |
date |
private static java.lang.String |
DATE_FORMAT |
private ome.xml.model.primitives.Color |
displayColor |
private java.util.ArrayList<java.lang.String> |
dyeNames |
private java.lang.Double |
emissionWavelength |
private java.lang.Double |
excitationWavelength |
private java.lang.Double |
exposureScale |
private java.lang.Double |
exposureTime |
private static org.slf4j.Logger |
LOGGER
Logger for this class.
|
private java.lang.Double |
magnification |
private java.lang.String |
time |
private java.lang.Double[] |
zPosition |
DATE_FORMATS
canSeparateSeries, equalStrips, ifds, lastPlane, mergeSubIFDs, noSubresolutions, seriesToIFD, subResolutionIFDs, thumbnailIFDs, tiffParser, use64Bit
core
coreIndex, datasetDescription, domains, filterMetadata, flattenedResolutions, group, hasCompanionFiles, in, indexedAsRGB, metadata, metadataStore, normalizeData, resolution, saveOriginalMetadata, series, suffixNecessary, suffixSufficient, THUMBNAIL_DIMENSION
COMPRESSION_SUFFIXES, currentId, format, metadataOptions, suffixes
CAN_GROUP, CANNOT_GROUP, MUST_GROUP
Constructor and Description |
---|
SVSReader()
Constructs a new SVS reader.
|
SVSReader(java.lang.String name,
java.lang.String[] suffixes) |
Modifier and Type | Method and Description |
---|---|
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.
|
protected ome.xml.model.primitives.Timestamp |
getDatestamp() |
protected ome.xml.model.primitives.Color |
getDisplayColor() |
protected java.util.ArrayList<java.lang.String> |
getDyeNames() |
protected ome.units.quantity.Length |
getEmission() |
protected ome.units.quantity.Length |
getExcitation() |
protected java.lang.Double |
getExposureTime() |
private int |
getIFDIndex(int coreIndex,
int no) |
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 ome.units.quantity.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(java.lang.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.
|
getExifTagName, getImageCreationDate, initFile, initMetadata, put, put, put, put, put, put, put, put, put, put, putDouble, putInt, putString
get16BitLookupTable, get8BitLookupTable, getIFDs, getThumbnailIFDs, getThumbSizeX, getThumbSizeY, initTiffParser, isThisType, reopenFile, setResolutionLevel
coreIndexToSeries, flattenHashtables, getCoreIndex, getCoreMetadataList, getCurrentCore, getResolution, getResolutionCount, getSeries, getSeriesCount, seriesToCoreIndex, setCoreIndex, setResolution, setSeries
addGlobalMeta, addGlobalMeta, addGlobalMeta, addGlobalMeta, addGlobalMeta, addGlobalMeta, addGlobalMeta, addGlobalMeta, addGlobalMeta, addGlobalMetaList, addMeta, addMetaList, addSeriesMeta, addSeriesMeta, addSeriesMeta, addSeriesMeta, addSeriesMeta, addSeriesMeta, addSeriesMeta, addSeriesMeta, addSeriesMeta, addSeriesMetaList, close, getAcquisitionMode, getAdvancedSeriesUsedFiles, getAdvancedUsedFiles, getArcType, getBinning, getBitsPerPixel, getCompression, getContrastMethod, 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, getRGBChannelCount, getRotationTransform, getSeriesMeta, getSeriesMetadata, getSeriesMetadataValue, getSeriesUsedFiles, getSeriesUsedFiles, getSizeC, getSizeT, getSizeX, getSizeY, getSizeZ, 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, setFlattenedResolutions, setGroupFiles, setId, setMetadataFiltered, setMetadataStore, setNormalized, setOriginalMetadataPopulated, 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
private static final org.slf4j.Logger LOGGER
private static final java.lang.String APERIO_IMAGE_DESCRIPTION_PREFIX
private static final java.lang.String DATE_FORMAT
private java.lang.Double[] zPosition
private java.lang.String[] comments
private java.lang.Double emissionWavelength
private java.lang.Double excitationWavelength
private java.lang.Double exposureTime
private java.lang.Double exposureScale
private java.lang.Double magnification
private java.lang.String date
private java.lang.String time
private java.util.ArrayList<java.lang.String> dyeNames
private transient ome.xml.model.primitives.Color displayColor
public SVSReader()
public SVSReader(java.lang.String name, java.lang.String[] suffixes)
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 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 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 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.java.io.IOException
- if there was a problem reading the file.IFormatReader.openBytes(int, byte[], int, int, int, int)
public byte[] openThumbBytes(int no) throws FormatException, java.io.IOException
IFormatReader
openThumbBytes
in interface IFormatReader
openThumbBytes
in class MinimalTiffReader
FormatException
java.io.IOException
public void close(boolean fileOnly) throws java.io.IOException
IFormatReader
Closeable.close()
.close
in interface IFormatReader
close
in class MinimalTiffReader
java.io.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, java.io.IOException
BaseTiffReader
initStandardMetadata
in class BaseTiffReader
FormatException
java.io.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, int no)
protected ome.units.quantity.Length getEmission()
protected ome.units.quantity.Length getExcitation()
protected java.lang.Double getExposureTime()
protected ome.xml.model.primitives.Timestamp getDatestamp()
protected ome.units.quantity.Length[] getPhysicalSizes()
protected double getMagnification()
protected java.util.ArrayList<java.lang.String> getDyeNames()
protected ome.xml.model.primitives.Color getDisplayColor()
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