ZeissCZIReader (Bio-Formats API)

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

All Implemented Interfaces:

java.io.Closeable, java.lang.AutoCloseable, IFormatHandler, IFormatReader, IMetadataConfigurable, IPyramidHandler
```
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 java.lang.String`	`acquiredDate`
`private int`	`acquisitions`
`private java.lang.String`	`airPressure`
`private static int`	`ALIGNMENT`
`static boolean`	`ALLOW_AUTOSTITCHING_DEFAULT`
`static java.lang.String`	`ALLOW_AUTOSTITCHING_KEY`
`private int`	`angles`
`private static int`	`BGR_24`
`private static int`	`BGR_48`
`private static int`	`BGR_FLOAT`
`private static int`	`BGRA_8`
`private java.util.ArrayList<java.lang.String>`	`binnings`
`private static int`	`BUFFER_SIZE`
`private java.util.ArrayList<ZeissCZIReader.Channel>`	`channels`
`private java.lang.String`	`co2Percent`
`private static int`	`COMPLEX`
`private static int`	`COMPLEX_FLOAT`
`private java.lang.String`	`correctionCollar`
`private static java.lang.String`	`CZI_MAGIC_STRING`
`private java.lang.String`	`description`
`private java.util.ArrayList<java.lang.String>`	`detectorRefs`
`private java.util.ArrayList<ZeissCZIReader.Attachment>`	`extraImages`
`private java.lang.String`	`gain`
`private java.util.ArrayList<java.lang.String>`	`gains`
`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 java.lang.String`	`humidity`
`private java.lang.String[]`	`illuminationLabels`
`private int`	`illuminations`
`private java.lang.String`	`imageName`
`static boolean`	`INCLUDE_ATTACHMENTS_DEFAULT`
`static java.lang.String`	`INCLUDE_ATTACHMENTS_KEY`
`private java.util.HashMap<ZeissCZIReader.Coordinate,java.util.ArrayList<java.lang.Integer>>`	`indexIntoPlanes`
`private static int`	`JPEG`
`private static int`	`JPEGXR`
`private static int`	`LZW`
`private int`	`maxResolution`
`private java.lang.String`	`medium`
`private int`	`mosaics`
`private java.lang.String`	`objectiveSettingsID`
`private javax.xml.parsers.DocumentBuilder`	`parser`
`private java.lang.String[]`	`phaseLabels`
`private int`	`phases`
`private java.util.HashMap<java.lang.Integer,java.lang.String>`	`pixels`
`private java.util.ArrayList<ZeissCZIReader.SubBlock>`	`planes`
`private int`	`plateColumns`
`private java.util.ArrayList<java.lang.String>`	`platePositions`
`private int`	`plateRows`
`private int`	`positions`
`private ome.units.quantity.Length[]`	`positionsX`
`private ome.units.quantity.Length[]`	`positionsY`
`private ome.units.quantity.Length[]`	`positionsZ`
`private java.lang.Boolean`	`prestitched`
`private int`	`previousChannel`
`private java.lang.String`	`refractiveIndex`
`static boolean`	`RELATIVE_POSITIONS_DEFAULT`
`static java.lang.String`	`RELATIVE_POSITIONS_KEY`
`private java.lang.String[]`	`rotationLabels`
`private int`	`rotations`
`private int`	`scaleFactor`
`private int`	`scanDim`
`private java.util.ArrayList<ZeissCZIReader.Segment>`	`segments`
`private MetadataStore`	`store`
`private java.lang.String`	`temperature`
`private int[]`	`tileHeight`
`private int[]`	`tileWidth`
`private ome.units.quantity.Time`	`timeIncrement`
`private java.util.ArrayList<java.lang.Double>`	`timestamps`
`static boolean`	`TRIM_DIMENSIONS_DEFAULT`
`static java.lang.String`	`TRIM_DIMENSIONS_KEY`
`private static int`	`UNCOMPRESSED` Compression constants.
`private java.lang.String`	`userDisplayName`
`private java.lang.String`	`userEmail`
`private java.lang.String`	`userFirstName`
`private java.lang.String`	`userInstitution`
`private java.lang.String`	`userLastName`
`private java.lang.String`	`userMiddleName`
`private java.lang.String`	`userName`
`private java.lang.String`	`zoom`
`private ome.units.quantity.Length`	`zStep`

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

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

All Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`boolean`	`allowAutostitching()`
`private void`	`assignPlaneIndices()`
`private void`	`calculateDimensions()`
`private void`	`calculateDimensions(int coreIndex, boolean xyOnly)`
`boolean`	`canReadAttachments()`
`private boolean`	`checkPALM(java.lang.String xml)`
`void`	`close(boolean fileOnly)` Closes the currently open file.
`private void`	`convertPixelType(CoreMetadata ms0, int pixelType)`
`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.
`protected java.util.ArrayList<java.lang.String>`	`getAvailableOptions()` Returns the list of available metadata options.
`private org.w3c.dom.Element`	`getFirstNode(org.w3c.dom.Element root, java.lang.String name)`
`private java.lang.String`	`getFirstNodeValue(org.w3c.dom.Element root, java.lang.String name)`
`private org.w3c.dom.NodeList`	`getGrandchildren(org.w3c.dom.Element root, java.lang.String name)`
`private org.w3c.dom.NodeList`	`getGrandchildren(org.w3c.dom.Element root, java.lang.String child, java.lang.String name)`
`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`	`isThisType(loci.common.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(org.w3c.dom.NodeList objectives)`
`private int`	`populateCircles(org.w3c.dom.NodeList circles, int roi, int shape)`
`private int`	`populateLines(org.w3c.dom.NodeList lines, int roi, int shape)`
`private void`	`populateOriginalMetadata(org.w3c.dom.Element root, java.util.Deque<java.lang.String> nameStack)`
`private int`	`populatePolylines(org.w3c.dom.NodeList polylines, int roi, int shape, boolean closed)`
`private int`	`populateRectangles(org.w3c.dom.NodeList rectangles, int roi, int shape)`
`private void`	`readAttachments()`
`private ZeissCZIReader.Segment`	`readSegment(java.lang.String filename)`
`private void`	`readSegments(java.lang.String id)`
`boolean`	`storeRelativePositions()`
`private void`	`translateDisplaySettings(org.w3c.dom.Element root)`
`private void`	`translateExperiment(org.w3c.dom.Element root)`
`private void`	`translateHardwareSettings(org.w3c.dom.Element root)`
`private void`	`translateInformation(org.w3c.dom.Element root)`
`private void`	`translateLayers(org.w3c.dom.Element root)`
`private void`	`translateMetadata(java.lang.String xml)`
`private void`	`translateScaling(org.w3c.dom.Element root)`
`boolean`	`trimDimensions()`

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, 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, 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, isSingleFile, 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, updateMetadataLists

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

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

Methods inherited from interface loci.formats.IMetadataConfigurable
getMetadataOptions, getSupportedMetadataLevels, setMetadataOptions

Field Detail

ALLOW_AUTOSTITCHING_KEY

public static final java.lang.String ALLOW_AUTOSTITCHING_KEY

See Also:: Constant Field Values

ALLOW_AUTOSTITCHING_DEFAULT
```
public static final boolean ALLOW_AUTOSTITCHING_DEFAULT
```
See Also:

Constant Field Values

INCLUDE_ATTACHMENTS_KEY

public static final java.lang.String INCLUDE_ATTACHMENTS_KEY

See Also:: Constant Field Values

INCLUDE_ATTACHMENTS_DEFAULT
```
public static final boolean INCLUDE_ATTACHMENTS_DEFAULT
```
See Also:

Constant Field Values

TRIM_DIMENSIONS_KEY

public static final java.lang.String TRIM_DIMENSIONS_KEY

See Also:: Constant Field Values

TRIM_DIMENSIONS_DEFAULT
```
public static final boolean TRIM_DIMENSIONS_DEFAULT
```
See Also:

Constant Field Values

RELATIVE_POSITIONS_KEY

public static final java.lang.String RELATIVE_POSITIONS_KEY

See Also:: Constant Field Values

RELATIVE_POSITIONS_DEFAULT
```
public static final boolean RELATIVE_POSITIONS_DEFAULT
```
See Also:

Constant Field Values

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 java.lang.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 java.util.HashMap<java.lang.Integer,java.lang.String> pixels

segments

private java.util.ArrayList<ZeissCZIReader.Segment> segments

planes

private java.util.ArrayList<ZeissCZIReader.SubBlock> planes

indexIntoPlanes

private java.util.HashMap<ZeissCZIReader.Coordinate,java.util.ArrayList<java.lang.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
```

maxResolution
```
private int maxResolution
```

imageName
```
private java.lang.String imageName
```

acquiredDate
```
private java.lang.String acquiredDate
```

description
```
private java.lang.String description
```

userDisplayName

private java.lang.String userDisplayName

userName
```
private java.lang.String userName
```

userFirstName
```
private java.lang.String userFirstName
```

userLastName
```
private java.lang.String userLastName
```

userMiddleName

private java.lang.String userMiddleName

userEmail
```
private java.lang.String userEmail
```

userInstitution

private java.lang.String userInstitution

temperature
```
private java.lang.String temperature
```

airPressure
```
private java.lang.String airPressure
```

humidity
```
private java.lang.String humidity
```

co2Percent
```
private java.lang.String co2Percent
```

correctionCollar

private java.lang.String correctionCollar

medium
```
private java.lang.String medium
```

refractiveIndex

private java.lang.String refractiveIndex

timeIncrement

private transient ome.units.quantity.Time timeIncrement

zoom
```
private java.lang.String zoom
```

gain
```
private java.lang.String gain
```

channels

private java.util.ArrayList<ZeissCZIReader.Channel> channels

binnings

private java.util.ArrayList<java.lang.String> binnings

detectorRefs

private java.util.ArrayList<java.lang.String> detectorRefs

timestamps

private java.util.ArrayList<java.lang.Double> timestamps

gains

private transient java.util.ArrayList<java.lang.String> gains

positionsX

private ome.units.quantity.Length[] positionsX

positionsY

private ome.units.quantity.Length[] positionsY

positionsZ

private ome.units.quantity.Length[] positionsZ

previousChannel
```
private int previousChannel
```

prestitched
```
private java.lang.Boolean prestitched
```

objectiveSettingsID

private java.lang.String objectiveSettingsID

hasDetectorSettings
```
private boolean hasDetectorSettings
```

scanDim
```
private int scanDim
```

rotationLabels

private java.lang.String[] rotationLabels

phaseLabels
```
private java.lang.String[] phaseLabels
```

illuminationLabels

private java.lang.String[] illuminationLabels

parser

private transient javax.xml.parsers.DocumentBuilder parser

extraImages

private java.util.ArrayList<ZeissCZIReader.Attachment> extraImages

tileWidth
```
private int[] tileWidth
```

tileHeight
```
private int[] tileHeight
```

scaleFactor
```
private int scaleFactor
```

zStep

private transient ome.units.quantity.Length zStep

plateRows
```
private transient int plateRows
```

plateColumns
```
private transient int plateColumns
```

platePositions

private transient java.util.ArrayList<java.lang.String> platePositions

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

Method Detail
- isThisType
```
public boolean isThisType(loci.common.RandomAccessInputStream stream)
                   throws java.io.IOException
```
  Description copied from interface: IFormatReader
  
  Checks if the given stream is a valid stream for this file format. The number of bytes read is format-dependent.
  
  Specified by:
  
  isThisType in interface IFormatReader
  
  Overrides:
  
  isThisType in class FormatReader
  
  Parameters:
  
  stream - A RandomAccessInputStream representing the file to check. The first byte in the stream is assumed to be the first byte in the file.
  
  Returns:
  
  true if the file represented by the stream can be read by this reader; false otherwise.
  
  Throws:
  
  java.io.IOException
  
  See Also:
  
  IFormatReader.isThisType(RandomAccessInputStream)
- getSeriesUsedFiles
```
public java.lang.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. The first element in the array is expected to be the path passed to 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.
  
  Specified by:
  
  getSeriesUsedFiles in interface IFormatReader
  
  Overrides:
  
  getSeriesUsedFiles in class FormatReader
  
  See Also:
  
  IFormatReader.getSeriesUsedFiles(boolean)
- get8BitLookupTable
```
public byte[][] get8BitLookupTable()
                            throws FormatException,
                                   java.io.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
  
  java.io.IOException
- get16BitLookupTable
```
public short[][] get16BitLookupTable()
                              throws FormatException,
                                     java.io.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
  
  java.io.IOException
- openBytes
```
public byte[] openBytes(int no,
                        byte[] buf,
                        int x,
                        int y,
                        int w,
                        int h)
                 throws FormatException,
                        java.io.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 plane index within the current series.
  
  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.
  
  java.io.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 java.io.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:
  
  java.io.IOException
- getOptimalTileWidth
```
public int getOptimalTileWidth()
```
  Description copied from interface: IFormatReader
  
  Returns the optimal sub-image width for use with openBytes.
  
  Specified by:
  
  getOptimalTileWidth in interface IFormatReader
  
  Overrides:
  
  getOptimalTileWidth in class FormatReader
- getOptimalTileHeight
```
public int getOptimalTileHeight()
```
  Description copied from interface: IFormatReader
  
  Returns the optimal sub-image height for use with openBytes.
  
  Specified by:
  
  getOptimalTileHeight in interface IFormatReader
  
  Overrides:
  
  getOptimalTileHeight in class FormatReader
- getAvailableOptions
```
protected java.util.ArrayList<java.lang.String> getAvailableOptions()
```
  Description copied from class: FormatReader
  
  Returns the list of available metadata options.
  
  Overrides:
  
  getAvailableOptions in class FormatReader
- initFile
```
protected void initFile(java.lang.String id)
                 throws FormatException,
                        java.io.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.
  
  java.io.IOException - if an I/O error occurs processing the file
- allowAutostitching
```
public boolean allowAutostitching()
```
- canReadAttachments
```
public boolean canReadAttachments()
```
- trimDimensions
```
public boolean trimDimensions()
```
- storeRelativePositions
```
public boolean storeRelativePositions()
```
- readSegments
```
private void readSegments(java.lang.String id)
                   throws java.io.IOException
```
  Throws:
  
  java.io.IOException
- readAttachments
```
private void readAttachments()
                      throws FormatException,
                             java.io.IOException
```
  Throws:
  
  FormatException
  
  java.io.IOException
- calculateDimensions
```
private void calculateDimensions()
```
- calculateDimensions
```
private void calculateDimensions(int coreIndex,
                                 boolean xyOnly)
```
- assignPlaneIndices
```
private void assignPlaneIndices()
```
- translateMetadata
```
private void translateMetadata(java.lang.String xml)
                        throws FormatException,
                               java.io.IOException
```
  Throws:
  
  FormatException
  
  java.io.IOException
- checkPALM
```
private boolean checkPALM(java.lang.String xml)
                   throws FormatException,
                          java.io.IOException
```
  Throws:
  
  FormatException
  
  java.io.IOException
- translateInformation
```
private void translateInformation(org.w3c.dom.Element root)
                           throws FormatException
```
  Throws:
  
  FormatException
- translateScaling
```
private void translateScaling(org.w3c.dom.Element root)
```
- translateDisplaySettings
```
private void translateDisplaySettings(org.w3c.dom.Element root)
                               throws FormatException
```
  Throws:
  
  FormatException
- translateLayers
```
private void translateLayers(org.w3c.dom.Element root)
```
- translateHardwareSettings
```
private void translateHardwareSettings(org.w3c.dom.Element root)
                                throws FormatException
```
  Throws:
  
  FormatException
- populateRectangles
```
private int populateRectangles(org.w3c.dom.NodeList rectangles,
                               int roi,
                               int shape)
```
- populatePolylines
```
private int populatePolylines(org.w3c.dom.NodeList polylines,
                              int roi,
                              int shape,
                              boolean closed)
```
- populateLines
```
private int populateLines(org.w3c.dom.NodeList lines,
                          int roi,
                          int shape)
```
- populateCircles
```
private int populateCircles(org.w3c.dom.NodeList circles,
                            int roi,
                            int shape)
```
- translateExperiment
```
private void translateExperiment(org.w3c.dom.Element root)
                          throws FormatException
```
  Throws:
  
  FormatException
- getFirstNode
```
private org.w3c.dom.Element getFirstNode(org.w3c.dom.Element root,
                                         java.lang.String name)
```
- getGrandchildren
```
private org.w3c.dom.NodeList getGrandchildren(org.w3c.dom.Element root,
                                              java.lang.String name)
```
- getGrandchildren
```
private org.w3c.dom.NodeList getGrandchildren(org.w3c.dom.Element root,
                                              java.lang.String child,
                                              java.lang.String name)
```
- getFirstNodeValue
```
private java.lang.String getFirstNodeValue(org.w3c.dom.Element root,
                                           java.lang.String name)
```
- populateOriginalMetadata
```
private void populateOriginalMetadata(org.w3c.dom.Element root,
                                      java.util.Deque<java.lang.String> nameStack)
```
- readSegment
```
private ZeissCZIReader.Segment readSegment(java.lang.String filename)
                                    throws java.io.IOException
```
  Throws:
  
  java.io.IOException
- convertPixelType
```
private void convertPixelType(int pixelType)
                       throws FormatException
```
  Throws:
  
  FormatException
- convertPixelType
```
private void convertPixelType(CoreMetadata ms0,
                              int pixelType)
                       throws FormatException
```
  Throws:
  
  FormatException
- parseObjectives
```
private void parseObjectives(org.w3c.dom.NodeList objectives)
                      throws FormatException
```
  Throws:
  
  FormatException
- decode12BitCamera
```
private byte[] decode12BitCamera(byte[] data,
                                 int maxBytes)
                          throws java.io.IOException
```
  Throws:
  
  java.io.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

Methods inherited from interface loci.formats.IMetadataConfigurable

Field Detail

ALLOW_AUTOSTITCHING_KEY

ALLOW_AUTOSTITCHING_DEFAULT

INCLUDE_ATTACHMENTS_KEY

INCLUDE_ATTACHMENTS_DEFAULT

TRIM_DIMENSIONS_KEY

TRIM_DIMENSIONS_DEFAULT

RELATIVE_POSITIONS_KEY

RELATIVE_POSITIONS_DEFAULT

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

maxResolution

imageName

acquiredDate

description

userDisplayName

userName

userFirstName

userLastName

userMiddleName

userEmail

userInstitution

temperature

airPressure

humidity

co2Percent

correctionCollar

medium

refractiveIndex

timeIncrement

zoom

gain

channels

binnings

detectorRefs

timestamps

gains

positionsX