loci.formats.in

Class GatanReader

java.lang.Object

loci.formats.FormatHandler

loci.formats.FormatReader

loci.formats.in.GatanReader

All Implemented Interfaces:

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

public class GatanReader
extends FormatReader

GatanReader is the file format reader for Gatan files.

Author:

Melissa Linkert melissa at glencoesoftware.com

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
(package private) class	GatanReader.ROIShape

Field Summary

Fields

Modifier and Type	Field and Description
private boolean	adjustEndianness
private static int	ARRAY Data types.
private static int	BYTE
private static int	CHAR
static int	DM3_MAGIC_BYTES
static int	DM4_MAGIC_BYTES
private static int	DOUBLE
private static int	ELLIPSE
private static int	FLOAT
private boolean	foundMontage
private double	gamma
private static int	GROUP Tag types.
private java.lang.String	info
private static int	INT
private static int	LINE Shape types
private double	mag
private long	numPixelBytes
private long	pixelOffset Offset to pixel data.
private java.util.List<java.lang.Double>	pixelSizes List of pixel sizes.
private ome.units.quantity.Length	posX
private ome.units.quantity.Length	posY
private ome.units.quantity.Length	posZ
private static int	RECTANGLE
private double	sampleTime
private java.util.List<GatanReader.ROIShape>	shapes
private static int	SHORT
private boolean	signed
static java.lang.String	SPLIT_MONTAGE
static boolean	SPLIT_MONTAGE_DEFAULT
private java.util.List<ome.units.quantity.Length>	stageX
private java.util.List<ome.units.quantity.Length>	stageY
private java.util.List<ome.units.quantity.Length>	stageZ
private static int	TEXT
private long	timestamp
private static int	UBYTE
private static int	UINT
private java.util.List<java.lang.String>	units
private static int	UNKNOWN
private static int	UNKNOWN2
private static int	USHORT
private static int	VALUE
private int	version
private double	voltage

Fields inherited from class loci.formats.FormatReader

core, coreIndex, datasetDescription, domains, fillColor, 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
GatanReader() Constructs a new Gatan reader.

Method Summary

Modifier and Type	Method and Description
void	close(boolean fileOnly) Closes the currently open file.
private ome.units.unit.Unit<ome.units.quantity.Length>	convertUnits(java.lang.String units)
private java.lang.String	createROI(MetadataStore store, int index) Create an empty ROI and link it to the Image.
protected java.util.ArrayList<java.lang.String>	getAvailableOptions() Returns the list of available metadata options.
private int	getNumBytes(int type)
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	parseTags(int numTags, java.lang.String parent, java.lang.String indent) Parses Gatan DM3 tags.
private double	readValue(int type)
private void	skipPadding()
boolean	splitMontage()

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, get8BitLookupTable, getAcquisitionMode, getAdvancedSeriesUsedFiles, getAdvancedUsedFiles, getArcType, getBinning, getBitsPerPixel, getCompression, getContrastMethod, getCoreIndex, getCoreMetadataList, getCorrection, getCurrentCore, getCurrentFile, getDatasetStructureDescription, getDetectorType, getDimensionOrder, getDimensionOrder, getDomains, getEffectiveSizeC, getExperimentType, getFilamentType, getFillColor, 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, getTileColumns, getTileRows, 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, readPlane, reopenFile, seriesToCoreIndex, setCoreIndex, setFillColor, 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

Methods inherited from interface loci.formats.ICompressedTileReader

getTileCodec, getTileCodecOptions, openCompressedBytes, openCompressedBytes

Field Detail

DM3_MAGIC_BYTES

public static final int DM3_MAGIC_BYTES

See Also:

Constant Field Values

DM4_MAGIC_BYTES

public static final int DM4_MAGIC_BYTES

See Also:

Constant Field Values

GROUP

private static final int GROUP

Tag types.

See Also:

Constant Field Values

VALUE

private static final int VALUE

See Also:

Constant Field Values

ARRAY

private static final int ARRAY

Data types.

See Also:

Constant Field Values

SHORT

private static final int SHORT

See Also:

Constant Field Values

USHORT

private static final int USHORT

See Also:

Constant Field Values

INT

private static final int INT

See Also:

Constant Field Values

UINT

private static final int UINT

See Also:

Constant Field Values

FLOAT

private static final int FLOAT

See Also:

Constant Field Values

DOUBLE

private static final int DOUBLE

See Also:

Constant Field Values

BYTE

private static final int BYTE

See Also:

Constant Field Values

UBYTE

private static final int UBYTE

See Also:

Constant Field Values

CHAR

private static final int CHAR

See Also:

Constant Field Values

UNKNOWN

private static final int UNKNOWN

See Also:

Constant Field Values

UNKNOWN2

private static final int UNKNOWN2

See Also:

Constant Field Values

LINE

private static final int LINE

Shape types

See Also:

Constant Field Values

RECTANGLE

private static final int RECTANGLE

See Also:

Constant Field Values

ELLIPSE

private static final int ELLIPSE

See Also:

Constant Field Values

TEXT

private static final int TEXT

See Also:

Constant Field Values

SPLIT_MONTAGE

public static final java.lang.String SPLIT_MONTAGE

See Also:

Constant Field Values

SPLIT_MONTAGE_DEFAULT

public static final boolean SPLIT_MONTAGE_DEFAULT

See Also:

Constant Field Values

pixelOffset

private long pixelOffset

Offset to pixel data.

pixelSizes

private java.util.List<java.lang.Double> pixelSizes

List of pixel sizes.

units

private java.util.List<java.lang.String> units

numPixelBytes

private long numPixelBytes

signed

private boolean signed

timestamp

private long timestamp

gamma

private double gamma

mag

private double mag

voltage

private double voltage

info

private java.lang.String info

posX

private ome.units.quantity.Length posX

posY

private ome.units.quantity.Length posY

posZ

private ome.units.quantity.Length posZ

sampleTime

private double sampleTime

adjustEndianness

private boolean adjustEndianness

version

private int version

shapes

private transient java.util.List<GatanReader.ROIShape> shapes

foundMontage

private transient boolean foundMontage

stageX

private transient java.util.List<ome.units.quantity.Length> stageX

stageY

private transient java.util.List<ome.units.quantity.Length> stageY

stageZ

private transient java.util.List<ome.units.quantity.Length> stageZ

Constructor Detail

GatanReader

public GatanReader()

Constructs a new Gatan 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

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

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

splitMontage

public boolean splitMontage()

parseTags

private void parseTags(int numTags,
                       java.lang.String parent,
                       java.lang.String indent)
                throws FormatException,
                       java.io.IOException,
                       java.text.ParseException

Parses Gatan DM3 tags. Information on the DM3 structure found at: http://rsb.info.nih.gov/ij/plugins/DM3Format.gj.html and http://www-hrem.msm.cam.ac.uk/~cbb/info/dmformat/ The basic structure is this: the file is comprised of a list of tags. Each tag is either a data tag or a group tag. Group tags are simply containers for more group and data tags, where data tags contain actual metadata. Each data tag is comprised of a type (byte, short, etc.), a label, and a value.

Throws:

FormatException

java.io.IOException

java.text.ParseException

readValue

private double readValue(int type)
                  throws java.io.IOException

Throws:

java.io.IOException

getNumBytes

private int getNumBytes(int type)

skipPadding

private void skipPadding()
                  throws java.io.IOException

Throws:

java.io.IOException

convertUnits

private ome.units.unit.Unit<ome.units.quantity.Length> convertUnits(java.lang.String units)

createROI

private java.lang.String createROI(MetadataStore store,
                                   int index)

Create an empty ROI and link it to the Image.

Parameters:

store - MetadataStore in which to create the ROI

index - ROI index

Returns:

corresponding Shape ID to be used with the new ROI