public class ZeissTIFFReader extends BaseZeissReader
Modifier and Type | Class and Description |
---|---|
(package private) class |
ZeissTIFFReader.Channel |
(package private) class |
ZeissTIFFReader.Plane |
(package private) class |
ZeissTIFFReader.Slice |
(package private) class |
ZeissTIFFReader.TIFFInfo |
(package private) class |
ZeissTIFFReader.Timepoint |
BaseZeissReader.Charset, BaseZeissReader.Context, BaseZeissReader.DrawStyle, BaseZeissReader.FeatureType, BaseZeissReader.FillStyle, BaseZeissReader.Layer, BaseZeissReader.LineEndPositions, BaseZeissReader.LineEndStyle, BaseZeissReader.PointStyle, BaseZeissReader.Shape, BaseZeissReader.Tag, BaseZeissReader.TextAlignment
Modifier and Type | Field and Description |
---|---|
(package private) HashMap<Integer,ZeissTIFFReader.Channel> |
channels |
(package private) ArrayList<ZeissTIFFReader.Plane> |
planes
Image planes
|
(package private) HashMap<Integer,ZeissTIFFReader.Slice> |
slices |
static String[] |
TIFF_SUFFIXES |
(package private) ZeissTIFFReader.TIFFInfo |
tiffInfo |
private MinimalTiffReader |
tiffReader
Helper reader for TIFF files.
|
(package private) HashMap<Integer,ZeissTIFFReader.Timepoint> |
timepoints |
static String |
XML_NAME |
bpp, channelColors, channelIndices, channelName, cIndex, colCount, coordinates, detectorGain, detectorOffset, emWavelength, exposureTime, exWavelength, imageDescription, imageFiles, isJPEG, isZlib, lastPlane, layers, nextChName, nextEmWave, nextExWave, offsets, physicalSizeX, physicalSizeY, physicalSizeZ, rawCount, realHeight, realWidth, roiIDs, rowCount, stageX, stageY, tagsToParse, tileIndices, tiles, timepoint, timepointIndices, timestamps, zIndices
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 |
---|
ZeissTIFFReader() |
Modifier and Type | Method and Description |
---|---|
void |
close(boolean fileOnly)
Closes the currently open file.
|
protected void |
countImages() |
protected ZeissTIFFReader.TIFFInfo |
evalFile(String id)
Evaluate the metadata of a TIFF/XML file collection, and return this to the user.
|
int |
fileGroupOption(String id)
Returns an int indicating that we cannot, must, or might group the files
in a given dataset.
|
protected void |
fillMetadataPass1(MetadataStore store)
Read and store basic dimensions in model
|
protected void |
fillMetadataPass2(MetadataStore store)
Read and store basic dimensions in model
|
protected void |
fillMetadataPass5(MetadataStore store)
Read and store basic dimensions in model
|
(package private) ZeissTIFFReader.Channel |
getChannel(int id) |
protected String |
getPrefix(String name) |
String[] |
getSeriesUsedFiles(boolean noPixels)
Returns an array of filenames needed to open the current series.
|
(package private) ZeissTIFFReader.Slice |
getslice(int id) |
(package private) ZeissTIFFReader.Timepoint |
getTimepoint(int id) |
protected void |
initFile(String id)
Initializes the given file (parsing header information, etc.).
|
protected void |
initVars(String id) |
boolean |
isSingleFile(String id)
Returns true if this is a single-file format.
|
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.
|
fillMetadataPass3, fillMetadataPass4, fillMetadataPass6, fillMetadataPass7, get16BitLookupTable, get8BitLookupTable, getOptimalTileHeight, initFileMain, parseColor, parseInt, parseInt, parseMainTags, storeROIs
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, getMarker, getMedium, getMetadataStore, getMetadataStoreRoot, getMetadataValue, getMicrobeamManipulationType, getMicroscopeType, getModuloC, getModuloT, getModuloZ, getNamingConvention, getOptimalTileWidth, 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, 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
public static final String[] TIFF_SUFFIXES
public static final String XML_NAME
ZeissTIFFReader.TIFFInfo tiffInfo
ArrayList<ZeissTIFFReader.Plane> planes
private MinimalTiffReader tiffReader
HashMap<Integer,ZeissTIFFReader.Channel> channels
HashMap<Integer,ZeissTIFFReader.Slice> slices
HashMap<Integer,ZeissTIFFReader.Timepoint> timepoints
public boolean isSingleFile(String id) throws FormatException, IOException
IFormatReader
isSingleFile
in interface IFormatReader
isSingleFile
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 int fileGroupOption(String id) throws FormatException, IOException
IFormatReader
fileGroupOption
in interface IFormatReader
fileGroupOption
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 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 BaseZeissReader
IOException
protected ZeissTIFFReader.TIFFInfo evalFile(String id) throws FormatException, IOException
id
- the filename to evaluate. This may be the top-level or per-plane TIFF, or the XML metadata.FormatException
IOException
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 fileprotected void initVars(String id) throws FormatException, IOException
initVars
in class BaseZeissReader
FormatException
IOException
protected void fillMetadataPass1(MetadataStore store) throws FormatException, IOException
BaseZeissReader
fillMetadataPass1
in class BaseZeissReader
FormatException
IOException
protected void fillMetadataPass2(MetadataStore store) throws FormatException, IOException
BaseZeissReader
fillMetadataPass2
in class BaseZeissReader
FormatException
IOException
protected void fillMetadataPass5(MetadataStore store) throws FormatException, IOException
BaseZeissReader
fillMetadataPass5
in class BaseZeissReader
FormatException
IOException
protected void countImages()
countImages
in class BaseZeissReader
ZeissTIFFReader.Channel getChannel(int id)
ZeissTIFFReader.Slice getslice(int id)
ZeissTIFFReader.Timepoint getTimepoint(int id)
Copyright © 2016 Open Microscopy Environment