public class SlideBook7Reader extends FormatReader
| Modifier and Type | Field and Description |
|---|---|
static org.slf4j.Logger |
LOGGER |
(package private) SlideBook7Reader.DataLoader |
mDataLoader |
core, coreIndex, datasetDescription, domains, fillColor, filterMetadata, flattenedResolutions, group, hasCompanionFiles, in, indexedAsRGB, metadata, metadataStore, normalizeData, resolution, saveOriginalMetadata, series, suffixNecessary, suffixSufficient, THUMBNAIL_DIMENSIONCOMPRESSION_SUFFIXES, currentId, format, metadataOptions, suffixesCAN_GROUP, CANNOT_GROUP, MUST_GROUP| Constructor and Description |
|---|
SlideBook7Reader() |
| Modifier and Type | Method and Description |
|---|---|
protected int |
addAnnotation(MetadataStore store,
SlideBook7Reader.CAnnotation70 inAnn,
int inCapture,
int inRegionIndex,
int inRoiManagerRoiIndex) |
void |
close(boolean fileOnly)
Closes the currently open file.
|
private void |
findAllFiles(loci.common.Location root,
java.util.ArrayList<java.lang.String> files,
boolean noPixels) |
java.lang.String[] |
getUsedFiles(boolean noPixels)
Returns an array of filenames needed to open this dataset.
|
protected void |
initFile(java.lang.String id)
Initializes the given file (parsing header information, etc.).
|
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 file,
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.
|
addGlobalMeta, addGlobalMeta, addGlobalMeta, addGlobalMeta, addGlobalMeta, addGlobalMeta, addGlobalMeta, addGlobalMeta, addGlobalMeta, addGlobalMetaList, addMeta, addMetaList, addSeriesMeta, addSeriesMeta, addSeriesMeta, addSeriesMeta, addSeriesMeta, addSeriesMeta, addSeriesMeta, addSeriesMeta, addSeriesMeta, addSeriesMetaList, close, coreIndexToSeries, fileGroupOption, flattenHashtables, get16BitLookupTable, get8BitLookupTable, getAcquisitionMode, getAdvancedSeriesUsedFiles, getAdvancedUsedFiles, getArcType, getAvailableOptions, getBinning, getBitsPerPixel, getCompression, getContrastMethod, getCoreIndex, getCoreMetadataList, getCorrection, getCurrentCore, getCurrentFile, getDatasetStructureDescription, getDetectorType, getDimensionOrder, getDimensionOrder, getDomains, getEffectiveSizeC, getExperimentType, getFilamentType, getFillColor, getFillRule, getFilterType, getFontFamily, getFontStyle, getGlobalMeta, getGlobalMetadata, getIlluminationType, getImageCount, getImmersion, getIndex, getIndex, getLaserMedium, getLaserType, getMarker, getMedium, getMetadataStore, getMetadataStoreRoot, getMetadataValue, getMicrobeamManipulationType, getMicroscopeType, getModuloC, getModuloT, getModuloZ, getNamingConvention, getOptimalTileHeight, getOptimalTileWidth, getPixelType, getPixelType, getPossibleDomains, getPulse, getRequiredDirectories, getResolution, getResolutionCount, getRGBChannelCount, getRotationTransform, getSeries, getSeriesCount, getSeriesMeta, getSeriesMetadata, getSeriesMetadataValue, getSeriesUsedFiles, getSeriesUsedFiles, getSizeC, getSizeT, getSizeX, getSizeY, getSizeZ, getThumbSizeX, getThumbSizeY, getTileColumns, getTileRows, getUnderlyingReaders, 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, readPlane, reopenFile, seriesToCoreIndex, setCoreIndex, setFillColor, setFlattenedResolutions, setGroupFiles, setId, setMetadataFiltered, setMetadataStore, setNormalized, setOriginalMetadataPopulated, setResolution, setSeries, updateMetadataListscheckSuffix, checkSuffix, getFormat, getMetadataOptions, getNativeDataType, getSuffixes, getSupportedMetadataLevels, setMetadataOptionsclone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, waitgetFormat, getNativeDataType, getSuffixesgetMetadataOptions, getSupportedMetadataLevels, setMetadataOptionsgetTileCodec, getTileCodecOptions, openCompressedBytes, openCompressedBytespublic static org.slf4j.Logger LOGGER
SlideBook7Reader.DataLoader mDataLoader
public boolean isThisType(loci.common.RandomAccessInputStream stream)
throws java.io.IOException
IFormatReaderisThisType in interface IFormatReaderisThisType in class FormatReaderstream - 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.IOExceptionpublic boolean isThisType(java.lang.String file,
boolean open)
FormatReaderFormatReader.isThisType(RandomAccessInputStream).isThisType in interface IFormatReaderisThisType in class FormatReaderopen - If true, and the file extension is insufficient to determine
the file type, the (existing) file is opened for further analysis.public boolean isSingleFile(java.lang.String id)
throws FormatException,
java.io.IOException
IFormatReaderisSingleFile in interface IFormatReaderisSingleFile in class FormatReaderFormatExceptionjava.io.IOExceptionprivate void findAllFiles(loci.common.Location root,
java.util.ArrayList<java.lang.String> files,
boolean noPixels)
public java.lang.String[] getUsedFiles(boolean noPixels)
IFormatReaderIFormatHandler.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.getUsedFiles in interface IFormatReadergetUsedFiles in class FormatReaderpublic byte[] openBytes(int no,
byte[] buf,
int x,
int y,
int w,
int h)
throws FormatException,
java.io.IOException
IFormatReaderopenBytes in interface IFormatReaderopenBytes in class FormatReaderno - the plane index within the current series.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 void close(boolean fileOnly)
throws java.io.IOException
IFormatReaderCloseable.close().close in interface IFormatReaderclose in class FormatReaderjava.io.IOExceptionprotected int addAnnotation(MetadataStore store, SlideBook7Reader.CAnnotation70 inAnn, int inCapture, int inRegionIndex, int inRoiManagerRoiIndex)
protected void initFile(java.lang.String id)
throws FormatException,
java.io.IOException
FormatReaderinitFile in class FormatReaderFormatException - if a parsing error occurs processing the file.java.io.IOException - if an I/O error occurs processing the fileCopyright © 2025 Open Microscopy Environment