public class InveonReader extends FormatReader
Modifier and Type | Field and Description |
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private java.util.ArrayList<java.lang.Long> |
dataPointers |
private java.lang.String |
datFile |
private static java.lang.String |
HEADER |
core, coreIndex, datasetDescription, domains, filterMetadata, flattenedResolutions, group, hasCompanionFiles, in, indexedAsRGB, metadata, metadataStore, normalizeData, resolution, saveOriginalMetadata, series, suffixNecessary, suffixSufficient, THUMBNAIL_DIMENSION
COMPRESSION_SUFFIXES, currentId, format, LOGGER, metadataOptions, suffixes
CAN_GROUP, CANNOT_GROUP, MUST_GROUP
Constructor and Description |
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InveonReader()
Constructs a new Inveon reader.
|
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) |
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, 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, reopenFile, seriesToCoreIndex, setCoreIndex, setFlattenedResolutions, setGroupFiles, setId, setMetadataFiltered, setMetadataStore, setNormalized, setOriginalMetadataPopulated, setResolution, setSeries, updateMetadataLists
checkSuffix, checkSuffix, getFormat, getMetadataOptions, getNativeDataType, getSuffixes, getSupportedMetadataLevels, setMetadataOptions
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
getFormat, getNativeDataType, getSuffixes
getMetadataOptions, getSupportedMetadataLevels, setMetadataOptions
private static final java.lang.String HEADER
private java.lang.String datFile
private java.util.ArrayList<java.lang.Long> dataPointers
public boolean isThisType(java.lang.String name, boolean open)
FormatReader
FormatReader.isThisType(RandomAccessInputStream)
.isThisType
in interface IFormatReader
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.public boolean isThisType(loci.common.RandomAccessInputStream stream) throws java.io.IOException
IFormatReader
isThisType
in interface IFormatReader
isThisType
in class FormatReader
stream
- A RandomAccessInputStream representing the file to check.
The first byte in the stream is assumed to be the first byte
in the file.java.io.IOException
public java.lang.String[] getUsedFiles(boolean noPixels)
IFormatReader
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.getUsedFiles
in interface IFormatReader
getUsedFiles
in class FormatReader
public byte[] openBytes(int no, byte[] buf, int x, int y, int w, int h) throws FormatException, java.io.IOException
IFormatReader
openBytes
in interface IFormatReader
openBytes
in class FormatReader
no
- the image index within the file.buf
- a pre-allocated buffer.x
- X coordinate of the upper-left corner of the sub-imagey
- Y coordinate of the upper-left corner of the sub-imagew
- width of the sub-imageh
- height of the sub-imagebuf
for convenience.FormatException
- if there was a problem parsing the metadata of the
file.java.io.IOException
- if there was a problem reading the file.IFormatReader.openBytes(int, byte[], int, int, int, int)
public void close(boolean fileOnly) throws java.io.IOException
IFormatReader
Closeable.close()
.close
in interface IFormatReader
close
in class FormatReader
java.io.IOException
protected void initFile(java.lang.String id) throws FormatException, java.io.IOException
FormatReader
initFile
in class FormatReader
FormatException
- if a parsing error occurs processing the file.java.io.IOException
- if an I/O error occurs processing the fileprivate java.lang.String transformModel(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 transformFileType(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 transformRegistrationAvailable(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 transformFilter(java.lang.String value)
private java.lang.String transformSubjectOrientation(java.lang.String value)
private java.lang.String transformSubjectLengthUnits(java.lang.String value)
private java.lang.String transformSubjectWeightUnits(java.lang.String value)
private java.lang.String transformGantryRotation(java.lang.String value)
private java.lang.String transformRotationDirection(java.lang.String value)
private java.lang.String transformCTWarping(java.lang.String value)
private java.lang.String transformCTProjectionInterpolation(java.lang.String value)
private java.lang.String transformEventType(java.lang.String value)
private void setDataType(java.lang.String value)
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