loci.formats.in

Class InveonReader

java.lang.Object

loci.formats.FormatHandler

loci.formats.FormatReader

loci.formats.in.InveonReader

All Implemented Interfaces:

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

public class InveonReader
extends FormatReader

InveonReader is the file format reader for Inveon files.

Field Summary

Fields

Modifier and Type	Field and Description
private java.util.ArrayList<java.lang.Long>	dataPointers
private java.lang.String	datFile
private static java.lang.String	HEADER

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
InveonReader() Constructs a new Inveon reader.

Method Summary

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

Field Detail

HEADER

private static final java.lang.String HEADER

See Also:

Constant Field Values

datFile

private java.lang.String datFile

dataPointers

private java.util.ArrayList<java.lang.Long> dataPointers

Constructor Detail

InveonReader

public InveonReader()

Constructs a new Inveon reader.

Method Detail

isThisType

public boolean isThisType(java.lang.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(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

getUsedFiles

public java.lang.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. 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:

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,
                        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

transformModel

private java.lang.String transformModel(java.lang.String value)

transformModality

private java.lang.String transformModality(java.lang.String value)

transformModalityConfiguration

private java.lang.String transformModalityConfiguration(java.lang.String value)

transformFileType

private java.lang.String transformFileType(java.lang.String value)

transformAcquisitionMode

private java.lang.String transformAcquisitionMode(java.lang.String value)

transformBedControl

private java.lang.String transformBedControl(java.lang.String value)

transformBedMotion

private java.lang.String transformBedMotion(java.lang.String value)

transformRegistrationAvailable

private java.lang.String transformRegistrationAvailable(java.lang.String value)

transformNormalizationApplied

private java.lang.String transformNormalizationApplied(java.lang.String value)

transformReconAlgorithm

private java.lang.String transformReconAlgorithm(java.lang.String value)

transformFilter

private java.lang.String transformFilter(java.lang.String value)

transformSubjectOrientation

private java.lang.String transformSubjectOrientation(java.lang.String value)

transformSubjectLengthUnits

private java.lang.String transformSubjectLengthUnits(java.lang.String value)

transformSubjectWeightUnits

private java.lang.String transformSubjectWeightUnits(java.lang.String value)

transformGantryRotation

private java.lang.String transformGantryRotation(java.lang.String value)

transformRotationDirection

private java.lang.String transformRotationDirection(java.lang.String value)

transformCTWarping

private java.lang.String transformCTWarping(java.lang.String value)

transformCTProjectionInterpolation

private java.lang.String transformCTProjectionInterpolation(java.lang.String value)

transformEventType

private java.lang.String transformEventType(java.lang.String value)

setDataType

private void setDataType(java.lang.String value)