public abstract class BaseZeissReader extends FormatReader
Modifier and Type | Class and Description |
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static class |
BaseZeissReader.Context |
class |
BaseZeissReader.Tag
Content of a single tag from a Tags block.
|
core, coreIndex, datasetDescription, domains, filterMetadata, flattenedResolutions, group, hasCompanionFiles, in, indexedAsRGB, metadata, metadataOptions, metadataStore, normalizeData, resolution, saveOriginalMetadata, series, suffixNecessary, suffixSufficient, THUMBNAIL_DIMENSION
COMPRESSION_SUFFIXES, currentId, format, LOGGER, suffixes
CAN_GROUP, CANNOT_GROUP, MUST_GROUP
Constructor and Description |
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BaseZeissReader(String name,
String suffix)
Constructs a new ZeissZVI reader.
|
BaseZeissReader(String name,
String[] suffixes)
Constructs a new ZeissZVI reader.
|
Modifier and Type | Method and Description |
---|---|
void |
close(boolean fileOnly)
Closes the currently open file.
|
protected void |
countImages() |
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 |
fillMetadataPass3(MetadataStore store)
Read and store basic dimensions in model
|
protected void |
fillMetadataPass4(MetadataStore store)
Read and store basic dimensions in model
|
protected void |
fillMetadataPass5(MetadataStore store)
Read and store basic dimensions in model
|
protected void |
fillMetadataPass6(MetadataStore store)
Read and store basic dimensions in model
|
protected void |
fillMetadataPass7(MetadataStore store)
Store basic dimensions in model
|
short[][] |
get16BitLookupTable()
Gets the 16-bit color lookup table associated with
the most recently opened image.
|
byte[][] |
get8BitLookupTable()
Gets the 8-bit color lookup table associated with
the most recently opened image.
|
int |
getOptimalTileHeight()
Returns the optimal sub-image height for use with openBytes.
|
protected void |
initFileMain(String id) |
protected void |
initVars(String id) |
protected static int |
parseColor(byte r,
byte g,
byte b) |
protected static int |
parseInt(String number)
Parse an Integer from a String.
|
protected static int |
parseInt(String number,
int defaultnum)
Parse an Integer from a String.
|
protected void |
storeROIs(MetadataStore store)
Store basic dimensions in model
|
addGlobalMeta, addGlobalMeta, addGlobalMeta, addGlobalMeta, addGlobalMeta, addGlobalMeta, addGlobalMeta, addGlobalMeta, addGlobalMeta, addGlobalMetaList, addMeta, addSeriesMeta, addSeriesMeta, addSeriesMeta, addSeriesMeta, addSeriesMeta, addSeriesMeta, addSeriesMeta, addSeriesMeta, addSeriesMeta, addSeriesMetaList, close, coreIndexToSeries, fileGroupOption, flattenHashtables, getAcquisitionMode, getAdvancedSeriesUsedFiles, getAdvancedUsedFiles, getArcType, getBinning, getBitsPerPixel, getChannelDimLengths, getChannelDimTypes, getCompression, getContrastMethod, getCoreIndex, getCoreMetadata, getCoreMetadataList, getCorrection, getCurrentFile, getDatasetStructureDescription, getDetectorType, getDimensionOrder, getDimensionOrder, getDomains, getEffectiveSizeC, getExperimentType, getFilamentType, getFillRule, getFilterType, getFontFamily, getFontStyle, getGlobalMeta, getGlobalMetadata, getIlluminationType, getImageCount, getImmersion, getIndex, getLaserMedium, getLaserType, getLineCap, getMarker, getMedium, getMetadataOptions, 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, getSeriesUsedFiles, getSizeC, getSizeT, getSizeX, getSizeY, getSizeZ, getSupportedMetadataLevels, getThumbSizeX, getThumbSizeY, getUnderlyingReaders, getUsedFiles, getUsedFiles, getZCTCoords, hasCompanionFiles, hasFlattenedResolutions, initFile, isFalseColor, isGroupFiles, isIndexed, isInterleaved, isInterleaved, isLittleEndian, isMetadataComplete, isMetadataFiltered, isNormalized, isOrderCertain, isOriginalMetadataPopulated, isRGB, isSingleFile, isThisType, isThisType, isThisType, isThisType, isThumbnailSeries, isUsedFile, makeFilterMetadata, openBytes, openBytes, openBytes, openBytes, openPlane, openThumbBytes, readPlane, readPlane, seriesToCoreIndex, setCoreIndex, setFlattenedResolutions, setGroupFiles, setId, setMetadataFiltered, setMetadataOptions, setMetadataStore, setNormalized, setOriginalMetadataPopulated, setResolution, setSeries
checkSuffix, checkSuffix, getFormat, getNativeDataType, getSuffixes
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
getFormat, getNativeDataType, getSuffixes
protected int bpp
protected String[] imageFiles
protected int[] offsets
protected int[][] coordinates
protected int cIndex
protected boolean isJPEG
protected boolean isZlib
protected int realWidth
protected int realHeight
protected int nextEmWave
protected int nextExWave
protected int nextChName
protected int timepoint
protected int[] channelColors
protected int lastPlane
protected Hashtable<Integer,PositiveInteger> emWavelength
protected Hashtable<Integer,PositiveInteger> exWavelength
protected Double physicalSizeX
protected Double physicalSizeY
protected Double physicalSizeZ
protected int rowCount
protected int colCount
protected int rawCount
protected String imageDescription
public ArrayList<loci.formats.in.BaseZeissReader.Layer> layers
public BaseZeissReader(String name, String suffix)
protected void initFileMain(String id) throws FormatException, IOException
FormatException
IOException
protected void initVars(String id) throws FormatException, IOException
FormatException
IOException
protected void countImages()
protected void fillMetadataPass1(MetadataStore store) throws FormatException, IOException
store
- FormatException
IOException
protected void fillMetadataPass2(MetadataStore store) throws FormatException, IOException
store
- FormatException
IOException
protected void fillMetadataPass3(MetadataStore store) throws FormatException, IOException
store
- FormatException
IOException
protected void fillMetadataPass4(MetadataStore store) throws FormatException, IOException
store
- FormatException
IOException
protected void fillMetadataPass5(MetadataStore store) throws FormatException, IOException
store
- FormatException
IOException
protected void fillMetadataPass6(MetadataStore store) throws FormatException, IOException
store
- FormatException
IOException
protected void fillMetadataPass7(MetadataStore store) throws FormatException, IOException
store
- FormatException
IOException
public int getOptimalTileHeight()
IFormatReader
getOptimalTileHeight
in interface IFormatReader
getOptimalTileHeight
in class FormatReader
protected void storeROIs(MetadataStore store) throws FormatException, IOException
store
- FormatException
IOException
public byte[][] get8BitLookupTable() throws FormatException, IOException
IFormatReader
IFormatReader.isIndexed()
returns
false, then this may return null. Also, if IFormatReader.getPixelType()
returns
anything other than FormatTools.INT8
or FormatTools.UINT8
,
this method will return null.get8BitLookupTable
in interface IFormatReader
get8BitLookupTable
in class FormatReader
FormatException
IOException
public short[][] get16BitLookupTable() throws FormatException, IOException
IFormatReader
IFormatReader.isIndexed()
returns
false, then this may return null. Also, if IFormatReader.getPixelType()
returns
anything other than FormatTools.INT16
or FormatTools.UINT16
, this method will return null.get16BitLookupTable
in interface IFormatReader
get16BitLookupTable
in class FormatReader
FormatException
IOException
public void close(boolean fileOnly) throws IOException
IFormatReader
Closeable.close()
.close
in interface IFormatReader
close
in class FormatReader
IOException
protected static int parseInt(String number)
number
- the number to parseprotected static int parseInt(String number, int defaultnum)
number
- the number to parsedefaultnum
- the number to return if number is null or emptyprotected static int parseColor(byte r, byte g, byte b)
Copyright © 2014 Open Microscopy Environment