ZeissCZIReader (Bio-Formats API)

java.lang.Object
- loci.formats.FormatHandler
- - loci.formats.FormatReader
  - - loci.formats.in.ZeissCZIReader

All Implemented Interfaces:

Closeable, AutoCloseable, IFormatHandler, IFormatReader, IMetadataConfigurable
```
public class ZeissCZIReader
extends FormatReader
```
ZeissCZIReader is the file format reader for Zeiss .czi files.

Nested Class Summary

Nested Classes
Modifier and Type	Class and Description
`(package private) class`	`ZeissCZIReader.Attachment` Segment with ID "ZISRAWATTACH".
`(package private) class`	`ZeissCZIReader.AttachmentDirectory` Segment with ID "ZISRAWATTDIR".
`(package private) static class`	`ZeissCZIReader.AttachmentEntry`
`(package private) static class`	`ZeissCZIReader.Channel`
`(package private) static class`	`ZeissCZIReader.Coordinate`
`(package private) static class`	`ZeissCZIReader.DimensionEntry`
`(package private) class`	`ZeissCZIReader.Directory` Segment with ID "ZISRAWDIRECTORY".
`(package private) class`	`ZeissCZIReader.DirectoryEntry`
`(package private) class`	`ZeissCZIReader.FileHeader` Segment with ID "ZISRAWFILE".
`(package private) class`	`ZeissCZIReader.Metadata` Segment with ID "ZISRAWMETADATA".
`(package private) class`	`ZeissCZIReader.Segment` Top-level class that implements logic common to all types of Segment.
`(package private) class`	`ZeissCZIReader.SubBlock` Segment with ID "ZISRAWSUBBLOCK".

Field Summary

Fields
Modifier and Type	Field and Description
`private String`	`acquiredDate`
`private int`	`acquisitions`
`private String`	`airPressure`
`private static int`	`ALIGNMENT`
`private int`	`angles`
`private static int`	`BGR_24`
`private static int`	`BGR_48`
`private static int`	`BGR_FLOAT`
`private static int`	`BGRA_8`
`private ArrayList<String>`	`binnings`
`private static int`	`BUFFER_SIZE`
`private ArrayList<ZeissCZIReader.Channel>`	`channels`
`private String`	`co2Percent`
`private static int`	`COMPLEX`
`private static int`	`COMPLEX_FLOAT`
`private String`	`correctionCollar`
`private static String`	`CZI_MAGIC_STRING`
`private String`	`description`
`private ArrayList<String>`	`detectorRefs`
`private String`	`gain`
`private static int`	`GRAY_DOUBLE`
`private static int`	`GRAY_FLOAT`
`private static int`	`GRAY16`
`private static int`	`GRAY32`
`private static int`	`GRAY8` Pixel type constants.
`private boolean`	`hasDetectorSettings`
`private static int`	`HEADER_SIZE`
`private String`	`humidity`
`private String[]`	`illuminationLabels`
`private int`	`illuminations`
`private String`	`imageName`
`private HashMap<ZeissCZIReader.Coordinate,ArrayList<Integer>>`	`indexIntoPlanes`
`private static int`	`JPEG`
`private static int`	`JPEGXR`
`private static int`	`LZW`
`private String`	`medium`
`private int`	`mosaics`
`private String`	`objectiveSettingsID`
`private DocumentBuilder`	`parser`
`private String[]`	`phaseLabels`
`private int`	`phases`
`private HashMap<Integer,String>`	`pixels`
`private ArrayList<ZeissCZIReader.SubBlock>`	`planes`
`private int`	`positions`
`private Length[]`	`positionsX`
`private Length[]`	`positionsY`
`private Length[]`	`positionsZ`
`private Boolean`	`prestitched`
`private int`	`previousChannel`
`private String`	`refractiveIndex`
`private String[]`	`rotationLabels`
`private int`	`rotations`
`private int`	`scanDim`
`private ArrayList<ZeissCZIReader.Segment>`	`segments`
`private MetadataStore`	`store`
`private String`	`temperature`
`private ArrayList<Double>`	`timestamps`
`private static int`	`UNCOMPRESSED` Compression constants.
`private String`	`userDisplayName`
`private String`	`userEmail`
`private String`	`userFirstName`
`private String`	`userInstitution`
`private String`	`userLastName`
`private String`	`userMiddleName`
`private String`	`userName`
`private String`	`zoom`

Fields inherited from class loci.formats.FormatReader
core, coreIndex, datasetDescription, domains, filterMetadata, flattenedResolutions, group, hasCompanionFiles, in, indexedAsRGB, metadata, metadataOptions, metadataStore, normalizeData, resolution, saveOriginalMetadata, series, suffixNecessary, suffixSufficient, THUMBNAIL_DIMENSION

Fields inherited from class loci.formats.FormatHandler
COMPRESSION_SUFFIXES, currentId, format, LOGGER, suffixes

Fields inherited from interface loci.formats.IFormatReader
CAN_GROUP, CANNOT_GROUP, MUST_GROUP

Constructor Summary

Constructors
Constructor and Description

ZeissCZIReader()
Constructs a new Zeiss .czi reader.

Constructors
Constructor and Description
`ZeissCZIReader()` Constructs a new Zeiss .czi reader.

Method Summary

Methods
Modifier and Type	Method and Description
`private void`	`assignPlaneIndices()`
`private void`	`calculateDimensions()`
`void`	`close(boolean fileOnly)` Closes the currently open file.
`private void`	`convertPixelType(int pixelType)`
`private byte[]`	`decode12BitCamera(byte[] data, int maxBytes)`
`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.
`private Element`	`getFirstNode(Element root, String name)`
`private String`	`getFirstNodeValue(Element root, String name)`
`private NodeList`	`getGrandchildren(Element root, String name)`
`private NodeList`	`getGrandchildren(Element root, String child, String name)`
`String[]`	`getSeriesUsedFiles(boolean noPixels)` Returns an array of filenames needed to open the current series.
`protected void`	`initFile(String id)` Initializes the given file (parsing header information, etc.).
`boolean`	`isThisType(RandomAccessInputStream stream)` Checks if the given stream is a valid stream for this file format.
`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`	`parseObjectives(NodeList objectives)`
`private int`	`populateCircles(NodeList circles, int roi, int shape)`
`private int`	`populateLines(NodeList lines, int roi, int shape)`
`private void`	`populateOriginalMetadata(Element root, Deque<String> nameStack)`
`private int`	`populatePolylines(NodeList polylines, int roi, int shape, boolean closed)`
`private int`	`populateRectangles(NodeList rectangles, int roi, int shape)`
`private ZeissCZIReader.Segment`	`readSegment(String filename)`
`private void`	`readSegments(String id)`
`private void`	`translateDisplaySettings(Element root)`
`private void`	`translateExperiment(Element root)`
`private void`	`translateHardwareSettings(Element root)`
`private void`	`translateInformation(Element root)`
`private void`	`translateLayers(Element root)`
`private void`	`translateMetadata(String xml)`
`private void`	`translateScaling(Element root)`

Methods inherited from class loci.formats.FormatReader
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, getCurrentFile, getDatasetStructureDescription, getDetectorType, getDimensionOrder, getDimensionOrder, getDomains, getEffectiveSizeC, getExperimentType, getFilamentType, getFillRule, getFilterType, getFontFamily, getFontStyle, getGlobalMeta, getGlobalMetadata, getIlluminationType, getImageCount, getImmersion, getIndex, getIndex, getLaserMedium, getLaserType, getLineCap, getMarker, getMedium, getMetadataOptions, getMetadataStore, getMetadataStoreRoot, getMetadataValue, getMicrobeamManipulationType, getMicroscopeType, getModuloC, getModuloT, getModuloZ, getNamingConvention, getOptimalTileHeight, getOptimalTileWidth, getPixelType, getPixelType, getPossibleDomains, getPulse, getRequiredDirectories, getResolution, getResolutionCount, getRGBChannelCount, getRotationTransform, getSeries, getSeriesCount, getSeriesMeta, getSeriesMetadata, getSeriesMetadataValue, getSeriesUsedFiles, getSizeC, getSizeT, getSizeX, getSizeY, getSizeZ, getSupportedMetadataLevels, getThumbSizeX, getThumbSizeY, getUnderlyingReaders, getUsedFiles, getUsedFiles, getZCTCoords, getZCTModuloCoords, hasCompanionFiles, hasFlattenedResolutions, isFalseColor, isGroupFiles, isIndexed, isInterleaved, isInterleaved, isLittleEndian, isMetadataComplete, isMetadataFiltered, isNormalized, isOrderCertain, isOriginalMetadataPopulated, isRGB, isSingleFile, isThisType, isThisType, isThisType, isThumbnailSeries, isUsedFile, makeFilterMetadata, openBytes, openBytes, openBytes, openPlane, openThumbBytes, readPlane, readPlane, reopenFile, seriesToCoreIndex, setCoreIndex, setFlattenedResolutions, setGroupFiles, setId, setMetadataFiltered, setMetadataOptions, setMetadataStore, setNormalized, setOriginalMetadataPopulated, setResolution, setSeries

Methods inherited from class loci.formats.FormatHandler
checkSuffix, checkSuffix, getFormat, getNativeDataType, getSuffixes

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Methods inherited from interface loci.formats.IFormatHandler
getFormat, getNativeDataType, getSuffixes

Field Detail

ALIGNMENT
```
private static final int ALIGNMENT
```
See Also:
Constant Field Values

HEADER_SIZE
```
private static final int HEADER_SIZE
```
See Also:
Constant Field Values

CZI_MAGIC_STRING

private static final String CZI_MAGIC_STRING

See Also:: Constant Field Values

BUFFER_SIZE
```
private static final int BUFFER_SIZE
```
See Also:
Constant Field Values

UNCOMPRESSED
```
private static final int UNCOMPRESSED
```
Compression constants.

See Also:
Constant Field Values

JPEG
```
private static final int JPEG
```
See Also:
Constant Field Values

LZW
```
private static final int LZW
```
See Also:
Constant Field Values

JPEGXR
```
private static final int JPEGXR
```
See Also:
Constant Field Values

GRAY8
```
private static final int GRAY8
```
Pixel type constants.

See Also:
Constant Field Values

GRAY16
```
private static final int GRAY16
```
See Also:
Constant Field Values

GRAY_FLOAT
```
private static final int GRAY_FLOAT
```
See Also:
Constant Field Values

BGR_24
```
private static final int BGR_24
```
See Also:
Constant Field Values

BGR_48
```
private static final int BGR_48
```
See Also:
Constant Field Values

BGR_FLOAT
```
private static final int BGR_FLOAT
```
See Also:
Constant Field Values

BGRA_8
```
private static final int BGRA_8
```
See Also:
Constant Field Values

COMPLEX
```
private static final int COMPLEX
```
See Also:
Constant Field Values

COMPLEX_FLOAT
```
private static final int COMPLEX_FLOAT
```
See Also:
Constant Field Values

GRAY32
```
private static final int GRAY32
```
See Also:
Constant Field Values

GRAY_DOUBLE
```
private static final int GRAY_DOUBLE
```
See Also:
Constant Field Values

store
```
private MetadataStore store
```

pixels
```
private HashMap<Integer,String> pixels
```

segments

private ArrayList<ZeissCZIReader.Segment> segments

planes

private ArrayList<ZeissCZIReader.SubBlock> planes

indexIntoPlanes

private HashMap<ZeissCZIReader.Coordinate,ArrayList<Integer>> indexIntoPlanes

rotations
```
private int rotations
```

positions
```
private int positions
```

illuminations
```
private int illuminations
```

acquisitions
```
private int acquisitions
```

mosaics
```
private int mosaics
```

phases
```
private int phases
```

angles
```
private int angles
```

imageName
```
private String imageName
```

acquiredDate
```
private String acquiredDate
```

description
```
private String description
```

userDisplayName
```
private String userDisplayName
```

userName
```
private String userName
```

userFirstName
```
private String userFirstName
```

userLastName
```
private String userLastName
```

userMiddleName
```
private String userMiddleName
```

userEmail
```
private String userEmail
```

userInstitution
```
private String userInstitution
```

temperature
```
private String temperature
```

airPressure
```
private String airPressure
```

humidity
```
private String humidity
```

co2Percent
```
private String co2Percent
```

correctionCollar
```
private String correctionCollar
```

medium
```
private String medium
```

refractiveIndex
```
private String refractiveIndex
```

zoom
```
private String zoom
```

gain
```
private String gain
```

channels

private ArrayList<ZeissCZIReader.Channel> channels

binnings
```
private ArrayList<String> binnings
```

detectorRefs
```
private ArrayList<String> detectorRefs
```

timestamps
```
private ArrayList<Double> timestamps
```

positionsX
```
private Length[] positionsX
```

positionsY
```
private Length[] positionsY
```

positionsZ
```
private Length[] positionsZ
```

previousChannel
```
private int previousChannel
```

prestitched
```
private Boolean prestitched
```

objectiveSettingsID
```
private String objectiveSettingsID
```

hasDetectorSettings
```
private boolean hasDetectorSettings
```

scanDim
```
private int scanDim
```

rotationLabels
```
private String[] rotationLabels
```

phaseLabels
```
private String[] phaseLabels
```

illuminationLabels
```
private String[] illuminationLabels
```

parser

private transient DocumentBuilder parser

Constructor Detail
- ZeissCZIReader
```
public ZeissCZIReader()
```
  Constructs a new Zeiss .czi reader.

Method Detail
- isThisType
```
public boolean isThisType(RandomAccessInputStream stream)
                   throws IOException
```
  Description copied from interface: IFormatReader
  
  Checks if the given stream is a valid stream for this file format.
  
  Specified by:
  
  isThisType in interface IFormatReader
  
  Overrides:
  
  isThisType in class FormatReader
  
  Throws:
  
  IOException
  See Also:
  IFormatReader.isThisType(RandomAccessInputStream)
- getSeriesUsedFiles
```
public String[] getSeriesUsedFiles(boolean noPixels)
```
  Description copied from interface: IFormatReader
  
  Returns an array of filenames needed to open the current series. If the 'noPixels' flag is set, then only files that do not contain pixel data will be returned.
  
  Specified by:
  
  getSeriesUsedFiles in interface IFormatReader
  
  Overrides:
  
  getSeriesUsedFiles in class FormatReader
  
  See Also:
  IFormatReader.getSeriesUsedFiles(boolean)
- get8BitLookupTable
```
public byte[][] get8BitLookupTable()
                            throws FormatException,
                                   IOException
```
  Description copied from interface: IFormatReader
  
  Gets the 8-bit color lookup table associated with the most recently opened image. If no image planes have been opened, or if 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.
  
  Specified by:
  
  get8BitLookupTable in interface IFormatReader
  
  Overrides:
  
  get8BitLookupTable in class FormatReader
  
  Throws:
  
  FormatException
  
  IOException
- get16BitLookupTable
```
public short[][] get16BitLookupTable()
                              throws FormatException,
                                     IOException
```
  Description copied from interface: IFormatReader
  
  Gets the 16-bit color lookup table associated with the most recently opened image. If no image planes have been opened, or if 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.
  
  Specified by:
  
  get16BitLookupTable in interface IFormatReader
  
  Overrides:
  
  get16BitLookupTable in class FormatReader
  
  Throws:
  
  FormatException
  
  IOException
- openBytes
```
public byte[] openBytes(int no,
               byte[] buf,
               int x,
               int y,
               int w,
               int h)
                 throws FormatException,
                        IOException
```
  Description copied from interface: IFormatReader
  
  Obtains a sub-image of the specified image plane into a pre-allocated byte array.
  
  Specified by:
  
  openBytes in interface IFormatReader
  
  Specified by:
  
  openBytes in class FormatReader
  
  Parameters:
  no - the image index within the file.
  buf - a pre-allocated buffer.
  x - X coordinate of the upper-left corner of the sub-image
  y - Y coordinate of the upper-left corner of the sub-image
  w - width of the sub-image
  h - height of the sub-image
  
  Returns:
  the pre-allocated buffer buf for convenience.
  
  Throws:
  
  FormatException - if there was a problem parsing the metadata of the file.
  
  IOException - if there was a problem reading the file.
  See Also:
  IFormatReader.openBytes(int, byte[], int, int, int, int)
- close
```
public void close(boolean fileOnly)
           throws IOException
```
  Description copied from interface: IFormatReader
  
  Closes the currently open file. If the flag is set, this is all that happens; if unset, it is equivalent to calling Closeable.close().
  
  Specified by:
  
  close in interface IFormatReader
  
  Overrides:
  
  close in class FormatReader
  
  Throws:
  
  IOException
- initFile
```
protected void initFile(String id)
                 throws FormatException,
                        IOException
```
  Description copied from class: FormatReader
  
  Initializes the given file (parsing header information, etc.). Most subclasses should override this method to perform initialization operations such as parsing metadata.
  
  Overrides:
  
  initFile in class FormatReader
  
  Throws:
  
  FormatException - if a parsing error occurs processing the file.
  
  IOException - if an I/O error occurs processing the file
- readSegments
```
private void readSegments(String id)
                   throws IOException
```
  Throws:
  
  IOException
- calculateDimensions
```
private void calculateDimensions()
```
- assignPlaneIndices
```
private void assignPlaneIndices()
```
- translateMetadata
```
private void translateMetadata(String xml)
                        throws FormatException,
                               IOException
```
  Throws:
  
  FormatException
  
  IOException
- translateInformation
```
private void translateInformation(Element root)
                           throws FormatException
```
  Throws:
  
  FormatException
- translateScaling
```
private void translateScaling(Element root)
```
- translateDisplaySettings
```
private void translateDisplaySettings(Element root)
                               throws FormatException
```
  Throws:
  
  FormatException
- translateLayers
```
private void translateLayers(Element root)
```
- translateHardwareSettings
```
private void translateHardwareSettings(Element root)
                                throws FormatException
```
  Throws:
  
  FormatException
- populateRectangles
```
private int populateRectangles(NodeList rectangles,
                     int roi,
                     int shape)
```
- populatePolylines
```
private int populatePolylines(NodeList polylines,
                    int roi,
                    int shape,
                    boolean closed)
```
- populateLines
```
private int populateLines(NodeList lines,
                int roi,
                int shape)
```
- populateCircles
```
private int populateCircles(NodeList circles,
                  int roi,
                  int shape)
```
- translateExperiment
```
private void translateExperiment(Element root)
                          throws FormatException
```
  Throws:
  
  FormatException
- getFirstNode
```
private Element getFirstNode(Element root,
                   String name)
```
- getGrandchildren
```
private NodeList getGrandchildren(Element root,
                        String name)
```
- getGrandchildren
```
private NodeList getGrandchildren(Element root,
                        String child,
                        String name)
```
- getFirstNodeValue
```
private String getFirstNodeValue(Element root,
                       String name)
```
- populateOriginalMetadata
```
private void populateOriginalMetadata(Element root,
                            Deque<String> nameStack)
```
- readSegment
```
private ZeissCZIReader.Segment readSegment(String filename)
                                    throws IOException
```
  Throws:
  
  IOException
- convertPixelType
```
private void convertPixelType(int pixelType)
                       throws FormatException
```
  Throws:
  
  FormatException
- parseObjectives
```
private void parseObjectives(NodeList objectives)
                      throws FormatException
```
  Throws:
  
  FormatException
- decode12BitCamera
```
private byte[] decode12BitCamera(byte[] data,
                       int maxBytes)
                          throws IOException
```
  Throws:
  
  IOException

Class ZeissCZIReader

Nested Class Summary

Field Summary

Fields inherited from class loci.formats.FormatReader

Fields inherited from class loci.formats.FormatHandler

Fields inherited from interface loci.formats.IFormatReader

Constructor Summary

Method Summary

Methods inherited from class loci.formats.FormatReader

Methods inherited from class loci.formats.FormatHandler

Methods inherited from class java.lang.Object

Methods inherited from interface loci.formats.IFormatHandler

Field Detail

ALIGNMENT

HEADER_SIZE

CZI_MAGIC_STRING

BUFFER_SIZE

UNCOMPRESSED

JPEG

LZW

JPEGXR

GRAY8

GRAY16

GRAY_FLOAT

BGR_24

BGR_48

BGR_FLOAT

BGRA_8

COMPLEX

COMPLEX_FLOAT

GRAY32

GRAY_DOUBLE

store

pixels

segments

planes

indexIntoPlanes

rotations

positions

illuminations

acquisitions

mosaics

phases

angles

imageName

acquiredDate

description

userDisplayName

userName

userFirstName

userLastName

userMiddleName

userEmail

userInstitution

temperature

airPressure

humidity

co2Percent

correctionCollar

medium

refractiveIndex

zoom

gain

channels

binnings

detectorRefs

timestamps

positionsX

positionsY

positionsZ

previousChannel

prestitched

objectiveSettingsID

hasDetectorSettings

scanDim

rotationLabels

phaseLabels

illuminationLabels

parser

Constructor Detail