loci.formats.in

Class InveonReader

java.lang.Object

loci.formats.FormatHandler

loci.formats.FormatReader

loci.formats.in.InveonReader

All Implemented Interfaces:

Closeable, AutoCloseable, IFormatHandler, IFormatReader, IMetadataConfigurable

public class InveonReader
extends FormatReader

InveonReader is the file format reader for Inveon files.

Field Summary

Fields

Modifier and Type	Field and Description
private ArrayList<Long>	dataPointers
private String	datFile
private static String	HEADER

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
InveonReader() Constructs a new Inveon reader.

Method Summary

Methods

Modifier and Type	Method and Description
void	close(boolean fileOnly) Closes the currently open file.
String[]	getUsedFiles(boolean noPixels) Returns an array of filenames needed to open this dataset.
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.
boolean	isThisType(String name, boolean open) Checks if a file matches the type of this format reader.
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	setDataType(String value)
private String	transformAcquisitionMode(String value)
private String	transformBedControl(String value)
private String	transformBedMotion(String value)
private String	transformCTProjectionInterpolation(String value)
private String	transformCTWarping(String value)
private String	transformEventType(String value)
private String	transformFileType(String value)
private String	transformFilter(String value)
private String	transformGantryRotation(String value)
private String	transformModality(String value)
private String	transformModalityConfiguration(String value)
private String	transformModel(String value)
private String	transformNormalizationApplied(String value)
private String	transformReconAlgorithm(String value)
private String	transformRegistrationAvailable(String value)
private String	transformRotationDirection(String value)
private String	transformSubjectLengthUnits(String value)
private String	transformSubjectOrientation(String value)
private String	transformSubjectWeightUnits(String value)

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, 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, getSeriesUsedFiles, getSizeC, getSizeT, getSizeX, getSizeY, getSizeZ, getSupportedMetadataLevels, getThumbSizeX, getThumbSizeY, getUnderlyingReaders, getUsedFiles, getZCTCoords, getZCTModuloCoords, hasCompanionFiles, hasFlattenedResolutions, isFalseColor, isGroupFiles, isIndexed, isInterleaved, isInterleaved, isLittleEndian, isMetadataComplete, isMetadataFiltered, isNormalized, isOrderCertain, isOriginalMetadataPopulated, isRGB, isSingleFile, 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

HEADER

private static final String HEADER

See Also:

Constant Field Values

datFile

private String datFile

dataPointers

private ArrayList<Long> dataPointers

Constructor Detail

InveonReader

public InveonReader()

Constructs a new Inveon reader.

Method Detail

isThisType

public boolean isThisType(String name,
                 boolean open)

Description copied from class: FormatReader

Checks if a file matches the type of this format reader. Checks filename suffixes against those known for this format. If the suffix check is inconclusive and the open parameter is true, the file is opened and tested with FormatReader.isThisType(RandomAccessInputStream).

Specified by:

isThisType in interface IFormatReader

Overrides:

isThisType in class FormatReader

open - If true, and the file extension is insufficient to determine the file type, the (existing) file is opened for further analysis.

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

getUsedFiles

public String[] getUsedFiles(boolean noPixels)

Description copied from interface: IFormatReader

Returns an array of filenames needed to open this dataset. If the 'noPixels' flag is set, then only files that do not contain pixel data will be returned.

Specified by:

getUsedFiles in interface IFormatReader

Overrides:

getUsedFiles in class FormatReader

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

transformModel

private String transformModel(String value)

transformModality

private String transformModality(String value)

transformModalityConfiguration

private String transformModalityConfiguration(String value)

transformFileType

private String transformFileType(String value)

transformAcquisitionMode

private String transformAcquisitionMode(String value)

transformBedControl

private String transformBedControl(String value)

transformBedMotion

private String transformBedMotion(String value)

transformRegistrationAvailable

private String transformRegistrationAvailable(String value)

transformNormalizationApplied

private String transformNormalizationApplied(String value)

transformReconAlgorithm

private String transformReconAlgorithm(String value)

transformFilter

private String transformFilter(String value)

transformSubjectOrientation

private String transformSubjectOrientation(String value)

transformSubjectLengthUnits

private String transformSubjectLengthUnits(String value)

transformSubjectWeightUnits

private String transformSubjectWeightUnits(String value)

transformGantryRotation

private String transformGantryRotation(String value)

transformRotationDirection

private String transformRotationDirection(String value)

transformCTWarping

private String transformCTWarping(String value)

transformCTProjectionInterpolation

private String transformCTProjectionInterpolation(String value)

transformEventType

private String transformEventType(String value)

setDataType

private void setDataType(String value)