public class BDReader extends FormatReader
Modifier and Type | Field and Description |
---|---|
private String |
binning |
private List<String> |
channelNames |
private double[] |
emWave |
private static String |
EXPERIMENT_FILE |
private double[] |
exposure |
private double[] |
exWave |
private int |
fieldCols |
private int |
fieldRows |
private double[] |
gain |
private static String[] |
META_EXT |
private List<String> |
metadataFiles |
private String |
objective |
private double[] |
offset |
private String |
plateDescription |
private String |
plateName |
private MinimalTiffReader |
reader |
private String |
roiFile |
private String[] |
rootList |
private String[][] |
tiffs |
private int |
wellCols |
private List<String> |
wellLabels |
private List<String[]> |
wellList |
private int |
wellRows |
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 |
---|
BDReader()
Constructs a new ScanR 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.
|
private String |
getFilename(int series,
int no) |
int |
getOptimalTileHeight()
Returns the optimal sub-image height for use with openBytes.
|
int |
getOptimalTileWidth()
Returns the optimal sub-image width for use with openBytes.
|
String[] |
getSeriesUsedFiles(boolean noPixels)
Returns an array of filenames needed to open the current series.
|
private String[][] |
getTiffs() |
private long |
getTimestamp(String file) |
protected void |
initFile(String id)
Initializes the given file (parsing header information, etc.).
|
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 |
locateExperimentFile(String id) |
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 void |
parseChannelData(Location dir) |
private void |
parseROIs(MetadataStore store) |
private IniList |
readMetaData(String id) |
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, get16BitLookupTable, 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
private static final String EXPERIMENT_FILE
private static final String[] META_EXT
private String plateName
private String plateDescription
private String[][] tiffs
private MinimalTiffReader reader
private String roiFile
private double[] emWave
private double[] exWave
private double[] gain
private double[] offset
private double[] exposure
private String binning
private String objective
private int wellRows
private int wellCols
private int fieldRows
private int fieldCols
private String[] rootList
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 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
public int fileGroupOption(String id) throws FormatException, IOException
IFormatReader
fileGroupOption
in interface IFormatReader
fileGroupOption
in class FormatReader
FormatException
IOException
public boolean isSingleFile(String id) throws FormatException, IOException
IFormatReader
isSingleFile
in interface IFormatReader
isSingleFile
in class FormatReader
FormatException
IOException
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 int getOptimalTileWidth()
IFormatReader
getOptimalTileWidth
in interface IFormatReader
getOptimalTileWidth
in class FormatReader
public int getOptimalTileHeight()
IFormatReader
getOptimalTileHeight
in interface IFormatReader
getOptimalTileHeight
in class FormatReader
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 String locateExperimentFile(String id) throws FormatException, IOException
FormatException
IOException
private IniList readMetaData(String id) throws IOException
IOException
private void parseChannelData(Location dir) throws IOException
IOException
private String[][] getTiffs()
private void parseROIs(MetadataStore store) throws IOException
IOException
private String getFilename(int series, int no)
private long getTimestamp(String file) throws FormatException, IOException
FormatException
IOException
Copyright © 2016 Open Microscopy Environment