public class ScanrReader extends FormatReader
Modifier and Type | Class and Description |
---|---|
(package private) class |
ScanrReader.ScanrHandler |
Modifier and Type | Field and Description |
---|---|
private static java.lang.String |
ACQUISITION_FILE |
private java.util.List<java.lang.String> |
channelNames |
private java.lang.Double |
deltaT |
private static java.lang.String |
EXPERIMENT_FILE |
private java.util.List<java.lang.Double> |
exposures |
private int |
fieldColumns |
private ome.units.quantity.Length[] |
fieldPositionX |
private ome.units.quantity.Length[] |
fieldPositionY |
private int |
fieldRows |
private boolean |
foundPositions |
private static java.lang.String[] |
METADATA_SUFFIXES |
private java.util.List<java.lang.String> |
metadataFiles |
private java.lang.Double |
pixelSize |
private java.lang.String |
plateName |
private MinimalTiffReader |
reader |
private java.util.Map<java.lang.Integer,java.lang.String[]> |
seriesFiles |
static java.lang.String |
SKIP_MISSING_WELLS |
static boolean |
SKIP_MISSING_WELLS_DEFAULT |
private java.lang.String[] |
tiffs |
private int |
tileHeight |
private int |
tileWidth |
private int |
wellColumns |
private int |
wellCount |
private java.util.Map<java.lang.String,java.lang.Integer> |
wellLabels |
private java.util.Map<java.lang.Integer,java.lang.Integer> |
wellNumbers |
private int |
wellRows |
private static java.lang.String |
XML_FILE |
core, coreIndex, datasetDescription, domains, fillColor, 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 |
---|
ScanrReader()
Constructs a new ScanR reader.
|
Modifier and Type | Method and Description |
---|---|
private void |
adjustWellDimensions() |
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 java.util.ArrayList<java.lang.String> |
getAvailableOptions()
Returns the list of available metadata options.
|
private java.lang.String |
getBlock(int index,
java.lang.String axis) |
int |
getOptimalTileHeight()
Returns the optimal sub-image height for use with openBytes.
|
int |
getOptimalTileWidth()
Returns the optimal sub-image width for use with openBytes.
|
java.lang.String[] |
getSeriesUsedFiles(boolean noPixels)
Returns an array of filenames needed to open the current series.
|
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 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.
|
boolean |
skipMissingWells() |
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, 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, getPixelType, getPixelType, getPossibleDomains, getPulse, getRequiredDirectories, getResolution, getResolutionCount, getRGBChannelCount, getRotationTransform, getSeries, getSeriesCount, getSeriesMeta, getSeriesMetadata, getSeriesMetadataValue, getSeriesUsedFiles, getSizeC, getSizeT, getSizeX, getSizeY, getSizeZ, getThumbSizeX, getThumbSizeY, getTileColumns, getTileRows, 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, readPlane, reopenFile, seriesToCoreIndex, setCoreIndex, setFillColor, setFlattenedResolutions, setGroupFiles, setId, setMetadataFiltered, setMetadataStore, setNormalized, setOriginalMetadataPopulated, setResolution, setSeries, 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
getTileCodec, getTileCodecOptions, openCompressedBytes, openCompressedBytes
private static final java.lang.String XML_FILE
private static final java.lang.String EXPERIMENT_FILE
private static final java.lang.String ACQUISITION_FILE
private static final java.lang.String[] METADATA_SUFFIXES
public static final java.lang.String SKIP_MISSING_WELLS
public static final boolean SKIP_MISSING_WELLS_DEFAULT
private final java.util.List<java.lang.String> metadataFiles
private int wellRows
private int wellColumns
private int fieldRows
private int fieldColumns
private int wellCount
private final java.util.List<java.lang.String> channelNames
private java.util.Map<java.lang.String,java.lang.Integer> wellLabels
private java.util.Map<java.lang.Integer,java.lang.Integer> wellNumbers
private java.lang.String plateName
private java.lang.Double pixelSize
private int tileWidth
private int tileHeight
private java.lang.String[] tiffs
private MinimalTiffReader reader
private boolean foundPositions
private ome.units.quantity.Length[] fieldPositionX
private ome.units.quantity.Length[] fieldPositionY
private final java.util.List<java.lang.Double> exposures
private java.lang.Double deltaT
private java.util.Map<java.lang.Integer,java.lang.String[]> seriesFiles
public boolean isSingleFile(java.lang.String id) throws FormatException, java.io.IOException
IFormatReader
isSingleFile
in interface IFormatReader
isSingleFile
in class FormatReader
FormatException
java.io.IOException
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 boolean isThisType(loci.common.RandomAccessInputStream stream) throws java.io.IOException
IFormatReader
isThisType
in interface IFormatReader
isThisType
in class FormatReader
stream
- 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.IOException
public java.lang.String[] getSeriesUsedFiles(boolean noPixels)
IFormatReader
IFormatHandler.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.getSeriesUsedFiles
in interface IFormatReader
getSeriesUsedFiles
in class FormatReader
public void close(boolean fileOnly) throws java.io.IOException
IFormatReader
Closeable.close()
.close
in interface IFormatReader
close
in class FormatReader
java.io.IOException
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 FormatReader
no
- 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 int getOptimalTileWidth()
IFormatReader
getOptimalTileWidth
in interface IFormatReader
getOptimalTileWidth
in class FormatReader
public int getOptimalTileHeight()
IFormatReader
getOptimalTileHeight
in interface IFormatReader
getOptimalTileHeight
in class FormatReader
protected java.util.ArrayList<java.lang.String> getAvailableOptions()
FormatReader
getAvailableOptions
in class FormatReader
protected void initFile(java.lang.String id) throws FormatException, java.io.IOException
FormatReader
initFile
in class FormatReader
FormatException
- if a parsing error occurs processing the file.java.io.IOException
- if an I/O error occurs processing the filepublic boolean skipMissingWells()
private java.lang.String getBlock(int index, java.lang.String axis)
private void adjustWellDimensions()
Copyright © 2024 Open Microscopy Environment