Package loci.formats.in

Class GatanReader

java.lang.Object

loci.formats.FormatHandler

loci.formats.FormatReader

loci.formats.in.GatanReader

All Implemented Interfaces:

Closeable, 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	Description
(package private) class	GatanReader.ROIShape

Field Summary

Fields

Modifier and Type	Field	Description
private boolean	adjustEndianness
private static final int	ARRAY	Data types.
private static final int	BYTE
private static final int	CHAR
static final int	DM3_MAGIC_BYTES
static final int	DM4_MAGIC_BYTES
private static final int	DOUBLE
private static final int	ELLIPSE
private static final int	FLOAT
private boolean	foundMontage
private double	gamma
private static final int	GROUP	Tag types.
private String	info
private static final int	INT
private static final int	LINE	Shape types
private double	mag
private long	numPixelBytes
private long	pixelOffset	Offset to pixel data.
private List<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 final int	RECTANGLE
private double	sampleTime
private List<GatanReader.ROIShape>	shapes
private static final int	SHORT
private boolean	signed
static final String	SPLIT_MONTAGE
static final boolean	SPLIT_MONTAGE_DEFAULT
private List<ome.units.quantity.Length>	stageX
private List<ome.units.quantity.Length>	stageY
private List<ome.units.quantity.Length>	stageZ
private static final int	TEXT
private long	timestamp
private static final int	UBYTE
private static final int	UINT
private List<String>	units
private static final int	UNKNOWN
private static final int	UNKNOWN2
private static final int	USHORT
private static final 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	Description
GatanReader()	Constructs a new Gatan reader.

Method Summary

Modifier and Type	Method	Description
void	close(boolean fileOnly)	Closes the currently open file.
private ome.units.unit.Unit<ome.units.quantity.Length>	convertUnits(String units)
private String	createROI(MetadataStore store, int index)	Create an empty ROI and link it to the Image.
protected ArrayList<String>	getAvailableOptions()	Returns the list of available metadata options.
private int	getNumBytes(int type)
protected void	initFile(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, String parent, 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.ICompressedTileReader

getTileCodec, getTileCodecOptions, openCompressedBytes, openCompressedBytes

Methods inherited from interface loci.formats.IFormatHandler

getFormat, getNativeDataType, getSuffixes

Methods inherited from interface loci.formats.IMetadataConfigurable

getMetadataOptions, getSupportedMetadataLevels, setMetadataOptions

Field Details

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 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 List<Double> pixelSizes

List of pixel sizes.

units

private List<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 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 List<GatanReader.ROIShape> shapes

foundMontage

private transient boolean foundMontage

stageX

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

stageY

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

stageZ

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

Constructor Details

GatanReader

public GatanReader()

Constructs a new Gatan reader.

Method Details

isThisType

public boolean isThisType(loci.common.RandomAccessInputStream stream)
                   throws 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:

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 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.

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

getAvailableOptions

protected ArrayList<String> getAvailableOptions()

Description copied from class: FormatReader

Returns the list of available metadata options.

Overrides:

getAvailableOptions in class FormatReader

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

splitMontage

public boolean splitMontage()

parseTags

private void parseTags(int numTags,
 String parent,
 String indent)
                throws FormatException,
IOException,
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

IOException

ParseException

readValue

private double readValue(int type)
                  throws IOException

Throws:

IOException

getNumBytes

private int getNumBytes(int type)

skipPadding

private void skipPadding()
                  throws IOException

Throws:

IOException

convertUnits

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

createROI

private 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