loci.formats.in

Class PictReader

java.lang.Object

loci.formats.FormatHandler

loci.formats.FormatReader

loci.formats.in.PictReader

All Implemented Interfaces:

java.io.Closeable, java.lang.AutoCloseable, IFormatHandler, IFormatReader, IMetadataConfigurable, IPyramidHandler

public class PictReader
extends FormatReader

PictReader is the file format reader for Apple PICT files. Most of this code was adapted from the PICT readers in JIMI (http://java.sun.com/products/jimi/index.html), ImageMagick (http://www.imagemagick.org), and Java QuickDraw.

Field Summary

Fields

Modifier and Type	Field and Description
private static byte[]	EXPANSION_TABLE Table used in expanding pixels that use less than 8 bits.
private java.util.Vector<java.lang.Long>	jpegOffsets
private boolean	legacy
protected byte[][]	lookup Color lookup table for palette color images.
private static int	PICT_9A
private static int	PICT_BITSRECT
private static int	PICT_BITSRGN
private static int	PICT_CLIP_RGN
private static int	PICT_END
private static int	PICT_JPEG
private static int	PICT_LONGCOMMENT
private static int	PICT_PACKBITSRECT
private static int	PICT_PACKBITSRGN
private static int	PICT_TYPE_1
private static int	PICT_TYPE_2
protected LegacyQTTools	qtTools Helper reader in case this one fails.
protected int	rowBytes Number of bytes in a row of pixel data (variable).
protected java.util.Vector	strips Vector of byte arrays representing individual rows.
protected boolean	versionOne Whether or not the file is PICT v1.

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
PictReader() Constructs a new PICT reader.

Method Summary

Modifier and Type	Method and Description
void	close(boolean fileOnly) Closes the currently open file.
private boolean	drivePictDecoder(int opcode) Handles the opcodes in the PICT file.
private void	expandPixels(int bitSize, byte[] ib, byte[] ob, int outLen) Expand an array of bytes.
byte[][]	get8BitLookupTable() Gets the 8-bit color lookup table associated with the most recently opened image.
private void	handleBitmap(int opcode) Extract the image data in a PICT bitmap structure.
private void	handlePixmap(int opcode) Extracts the image data in a PICT pixmap structure.
private void	handlePixmap(int pixelSize, int compCount) Handles the unpacking of the image data.
protected void	initFile(java.lang.String id) Initializes the given file (parsing header information, etc.).
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	readImageHeader(int opcode)
void	setLegacy(boolean legacy) Control whether or not legacy reader (QT Java) is used.
private void	unpackBits(byte[] ib, int[] ob) PackBits variant that outputs an int array.

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, get16BitLookupTable, getAcquisitionMode, getAdvancedSeriesUsedFiles, getAdvancedUsedFiles, getArcType, getAvailableOptions, 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, getOptimalTileHeight, 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, isFalseColor, isGroupFiles, isIndexed, isInterleaved, isInterleaved, isLittleEndian, isMetadataComplete, isMetadataFiltered, isNormalized, isOrderCertain, isOriginalMetadataPopulated, isRGB, isSingleFile, isThisType, 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

PICT_CLIP_RGN

private static final int PICT_CLIP_RGN

See Also:

Constant Field Values

PICT_BITSRECT

private static final int PICT_BITSRECT

See Also:

Constant Field Values

PICT_BITSRGN

private static final int PICT_BITSRGN

See Also:

Constant Field Values

PICT_PACKBITSRECT

private static final int PICT_PACKBITSRECT

See Also:

Constant Field Values

PICT_PACKBITSRGN

private static final int PICT_PACKBITSRGN

See Also:

Constant Field Values

PICT_9A

private static final int PICT_9A

See Also:

Constant Field Values

PICT_END

private static final int PICT_END

See Also:

Constant Field Values

PICT_LONGCOMMENT

private static final int PICT_LONGCOMMENT

See Also:

Constant Field Values

PICT_JPEG

private static final int PICT_JPEG

See Also:

Constant Field Values

PICT_TYPE_1

private static final int PICT_TYPE_1

See Also:

Constant Field Values

PICT_TYPE_2

private static final int PICT_TYPE_2

See Also:

Constant Field Values

EXPANSION_TABLE

private static final byte[] EXPANSION_TABLE

Table used in expanding pixels that use less than 8 bits.

rowBytes

protected int rowBytes

Number of bytes in a row of pixel data (variable).

strips

protected java.util.Vector strips

Vector of byte arrays representing individual rows.

versionOne

protected boolean versionOne

Whether or not the file is PICT v1.

lookup

protected byte[][] lookup

Color lookup table for palette color images.

qtTools

protected LegacyQTTools qtTools

Helper reader in case this one fails.

legacy

private boolean legacy

jpegOffsets

private java.util.Vector<java.lang.Long> jpegOffsets

Constructor Detail

PictReader

public PictReader()

Constructs a new PICT reader.

Method Detail

setLegacy

public void setLegacy(boolean legacy)

Control whether or not legacy reader (QT Java) is used.

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

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

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

drivePictDecoder

private boolean drivePictDecoder(int opcode)
                          throws FormatException,
                                 java.io.IOException

Handles the opcodes in the PICT file.

Throws:

FormatException

java.io.IOException

readImageHeader

private void readImageHeader(int opcode)
                      throws java.io.IOException

Throws:

java.io.IOException

handleBitmap

private void handleBitmap(int opcode)
                   throws FormatException,
                          java.io.IOException

Extract the image data in a PICT bitmap structure.

Throws:

FormatException

java.io.IOException

handlePixmap

private void handlePixmap(int opcode)
                   throws FormatException,
                          java.io.IOException

Extracts the image data in a PICT pixmap structure.

Throws:

FormatException

java.io.IOException

handlePixmap

private void handlePixmap(int pixelSize,
                          int compCount)
                   throws FormatException,
                          java.io.IOException

Handles the unpacking of the image data.

Throws:

FormatException

java.io.IOException

expandPixels

private void expandPixels(int bitSize,
                          byte[] ib,
                          byte[] ob,
                          int outLen)
                   throws FormatException

Expand an array of bytes.

Throws:

FormatException

unpackBits

private void unpackBits(byte[] ib,
                        int[] ob)

PackBits variant that outputs an int array.