public abstract class BaseZeissReader extends FormatReader
Modifier and Type | Class and Description |
---|---|
(package private) static class |
BaseZeissReader.Charset |
static class |
BaseZeissReader.Context |
(package private) static class |
BaseZeissReader.DrawStyle
Line drawing styles.
|
(package private) static class |
BaseZeissReader.FeatureType
Feature types.
|
(package private) static class |
BaseZeissReader.FillStyle
Fill styles.
|
(package private) class |
BaseZeissReader.Layer
Layer class representing an AxioVision layer; used to contain a
collection of shapes.
|
(package private) static class |
BaseZeissReader.LineEndPositions |
(package private) static class |
BaseZeissReader.LineEndStyle
Line ending styles.
|
(package private) static class |
BaseZeissReader.PointStyle
Point styles.
|
(package private) class |
BaseZeissReader.Shape
Shape class representing the metadata within an AxioVision Shape ROI
|
class |
BaseZeissReader.Tag
Content of a single tag from a Tags block.
|
(package private) static class |
BaseZeissReader.TextAlignment |
Modifier and Type | Field and Description |
---|---|
protected ome.xml.model.primitives.Timestamp |
acquisitionDate |
protected int |
bpp
Number of bytes per pixel.
|
protected int[] |
channelColors |
protected java.util.Set<java.lang.Integer> |
channelIndices |
protected java.util.Map<java.lang.Integer,java.lang.String> |
channelName |
protected int |
cIndex |
protected int |
colCount |
protected int[][] |
coordinates |
protected java.util.Map<java.lang.Integer,java.lang.Double> |
detectorGain |
protected java.util.Map<java.lang.Integer,java.lang.Double> |
detectorOffset |
protected java.util.Map<java.lang.Integer,ome.units.quantity.Length> |
emWavelength |
protected java.util.Map<java.lang.Integer,java.lang.String> |
exposureTime |
protected java.util.Map<java.lang.Integer,ome.units.quantity.Length> |
exWavelength |
protected java.lang.String |
imageDescription |
protected java.lang.String[] |
imageFiles |
protected boolean |
isJPEG |
protected boolean |
isZlib |
protected int |
lastPlane |
java.util.ArrayList<BaseZeissReader.Layer> |
layers |
protected int |
nextChName |
protected int |
nextEmWave |
protected int |
nextExWave |
protected int[] |
offsets |
protected java.lang.Double |
physicalSizeX |
protected java.lang.Double |
physicalSizeY |
protected java.lang.Double |
physicalSizeZ |
protected int |
rawCount |
protected int |
realHeight |
protected int |
realWidth |
protected java.util.List<java.lang.String> |
roiIDs |
protected int |
rowCount |
protected java.util.Map<java.lang.Integer,ome.units.quantity.Length> |
stageX |
protected java.util.Map<java.lang.Integer,ome.units.quantity.Length> |
stageY |
protected java.util.List<java.lang.String> |
tagsToParse |
protected java.util.Set<java.lang.Integer> |
tileIndices |
protected java.util.Map<java.lang.Integer,java.lang.Integer> |
tiles |
protected int |
timepoint |
protected java.util.Set<java.lang.Integer> |
timepointIndices |
protected java.util.Map<java.lang.Integer,java.lang.String> |
timestamps |
protected java.util.Set<java.lang.Integer> |
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 |
---|
BaseZeissReader(java.lang.String name,
java.lang.String suffix)
Constructs a new ZeissZVI reader.
|
BaseZeissReader(java.lang.String name,
java.lang.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(java.lang.String id) |
protected void |
initVars(java.lang.String id) |
protected static int |
parseColor(byte r,
byte g,
byte b) |
protected static int |
parseInt(java.lang.String number)
Parse an Integer from a String.
|
protected static int |
parseInt(java.lang.String number,
int defaultnum)
Parse an Integer from a String.
|
(package private) void |
parseMainTags(int image,
MetadataStore store,
java.util.ArrayList<BaseZeissReader.Tag> tags) |
private long |
parseTimestamp(java.lang.String s)
Parse timestamp from string.
|
protected void |
storeROIs(MetadataStore store)
Store basic dimensions in model
|
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, getAcquisitionMode, getAdvancedSeriesUsedFiles, getAdvancedUsedFiles, getArcType, getBinning, getBitsPerPixel, getCompression, getContrastMethod, getCoreIndex, getCoreMetadataList, getCorrection, getCurrentCore, 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, getSeriesUsedFiles, getSizeC, getSizeT, getSizeX, getSizeY, getSizeZ, getThumbSizeX, getThumbSizeY, getUnderlyingReaders, getUsedFiles, getUsedFiles, getZCTCoords, getZCTModuloCoords, 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, reopenFile, seriesToCoreIndex, setCoreIndex, 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
protected int bpp
protected java.lang.String[] imageFiles
protected int[] offsets
protected int[][] coordinates
protected transient ome.xml.model.primitives.Timestamp acquisitionDate
protected java.util.Map<java.lang.Integer,java.lang.String> timestamps
protected java.util.Map<java.lang.Integer,java.lang.String> exposureTime
protected int cIndex
protected boolean isJPEG
protected boolean isZlib
protected int realWidth
protected int realHeight
protected java.util.List<java.lang.String> tagsToParse
protected int nextEmWave
protected int nextExWave
protected int nextChName
protected final java.util.Map<java.lang.Integer,ome.units.quantity.Length> stageX
protected final java.util.Map<java.lang.Integer,ome.units.quantity.Length> stageY
protected int timepoint
protected int[] channelColors
protected int lastPlane
protected final java.util.Map<java.lang.Integer,java.lang.Integer> tiles
protected final java.util.Map<java.lang.Integer,java.lang.Double> detectorGain
protected final java.util.Map<java.lang.Integer,java.lang.Double> detectorOffset
protected final java.util.Map<java.lang.Integer,ome.units.quantity.Length> emWavelength
protected final java.util.Map<java.lang.Integer,ome.units.quantity.Length> exWavelength
protected final java.util.Map<java.lang.Integer,java.lang.String> channelName
protected java.lang.Double physicalSizeX
protected java.lang.Double physicalSizeY
protected java.lang.Double physicalSizeZ
protected int rowCount
protected int colCount
protected int rawCount
protected java.lang.String imageDescription
protected java.util.Set<java.lang.Integer> channelIndices
protected java.util.Set<java.lang.Integer> zIndices
protected java.util.Set<java.lang.Integer> timepointIndices
protected java.util.Set<java.lang.Integer> tileIndices
protected java.util.List<java.lang.String> roiIDs
public java.util.ArrayList<BaseZeissReader.Layer> layers
public BaseZeissReader(java.lang.String name, java.lang.String suffix)
public BaseZeissReader(java.lang.String name, java.lang.String[] suffixes)
protected void initFileMain(java.lang.String id) throws FormatException, java.io.IOException
FormatException
java.io.IOException
protected void initVars(java.lang.String id) throws FormatException, java.io.IOException
FormatException
java.io.IOException
protected void countImages()
protected void fillMetadataPass1(MetadataStore store) throws FormatException, java.io.IOException
store
- FormatException
java.io.IOException
protected void fillMetadataPass2(MetadataStore store) throws FormatException, java.io.IOException
store
- FormatException
java.io.IOException
protected void fillMetadataPass3(MetadataStore store) throws FormatException, java.io.IOException
store
- FormatException
java.io.IOException
protected void fillMetadataPass4(MetadataStore store) throws FormatException, java.io.IOException
store
- FormatException
java.io.IOException
protected void fillMetadataPass5(MetadataStore store) throws FormatException, java.io.IOException
store
- FormatException
java.io.IOException
protected void fillMetadataPass6(MetadataStore store) throws FormatException, java.io.IOException
store
- FormatException
java.io.IOException
protected void fillMetadataPass7(MetadataStore store) throws FormatException, java.io.IOException
store
- FormatException
java.io.IOException
public int getOptimalTileHeight()
IFormatReader
getOptimalTileHeight
in interface IFormatReader
getOptimalTileHeight
in class FormatReader
protected void storeROIs(MetadataStore store) throws FormatException, java.io.IOException
store
- FormatException
java.io.IOException
public byte[][] get8BitLookupTable() throws FormatException, java.io.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
java.io.IOException
public short[][] get16BitLookupTable() throws FormatException, java.io.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
java.io.IOException
public void close(boolean fileOnly) throws java.io.IOException
IFormatReader
Closeable.close()
.close
in interface IFormatReader
close
in class FormatReader
java.io.IOException
void parseMainTags(int image, MetadataStore store, java.util.ArrayList<BaseZeissReader.Tag> tags) throws FormatException, java.io.IOException
FormatException
java.io.IOException
protected static int parseInt(java.lang.String number)
number
- the number to parseprotected static int parseInt(java.lang.String number, int defaultnum)
number
- the number to parsedefaultnum
- the number to return if number is null or emptyprivate long parseTimestamp(java.lang.String s)
s
- protected static int parseColor(byte r, byte g, byte b)
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