IM3Reader (Bio-Formats API)

java.lang.Object
- loci.formats.FormatHandler
- - loci.formats.FormatReader
  - - loci.formats.in.IM3Reader

All Implemented Interfaces:

Closeable, AutoCloseable, IFormatHandler, IFormatReader, IMetadataConfigurable
```
public class IM3Reader
extends FormatReader
```
Author:

Lee Kamentsky This is a FormatReader for the Perkin-Elmer Nuance line of multispectral imaging microscopes' .im3 file format. The .im3 format stores 63 planes representing intensity measurements taken on separate spectral bands. The pixel intensity at a single band might be used as a proxy for fluorophore presence, but the best results are obtained if the whole spectrum is used to synthesize an intensity. The most efficient strategy is to use IM3Reader.openRaw() to fetch the entire image which may then be scanned sequentially to create one planar image per desired signal. IM3Reader may be run as a Java application to dump a per-record description of the file to standard output

Nested Class Summary

Nested Classes
Modifier and Type	Class and Description
`protected static class`	`IM3Reader.BooleanIM3Record` A record containing boolean values
`protected static class`	`IM3Reader.ContainerRecord`
`protected static class`	`IM3Reader.FloatIM3Record`
`protected static class`	`IM3Reader.IM3Record`
`protected static class`	`IM3Reader.IntIM3Record`
`static class`	`IM3Reader.Spectrum`
`protected static class`	`IM3Reader.StringIM3Record`

Field Summary

Fields
Modifier and Type	Field and Description
`private static int`	`COOKIE` First 4 bytes of file is "1985"
`private byte[]`	`data`
`private List<IM3Reader.ContainerRecord>`	`dataSets`
`private static String`	`EMPTY_STRING`
`private static String`	`FIELD_AUX_FLAGS`
`private static String`	`FIELD_BAND_INDEX`
`private static String`	`FIELD_BANDS`
`private static String`	`FIELD_CLASS_ID`
`private static String`	`FIELD_DATA`
`private static String`	`FIELD_DATA_SET`
`private static String`	`FIELD_EXPOSURE`
`private static String`	`FIELD_FILE_VERSION`
`private static String`	`FIELD_FILTER_PAIR`
`private static String`	`FIELD_FIXED_FILTER`
`private static String`	`FIELD_HOMOGENEOUS`
`private static String`	`FIELD_MAGNITUDES`
`private static String`	`FIELD_MANUFACTURER`
`private static String`	`FIELD_MILLIMETERS_PER_PIXEL`
`private static String`	`FIELD_NAME`
`private static String`	`FIELD_NUANCE_FLAGS`
`private static String`	`FIELD_OBJECTIVE`
`private static String`	`FIELD_PART_NUMBER`
`private static String`	`FIELD_PROTOCOL`
`private static String`	`FIELD_PROXY_PARENT_FILE_NAME`
`private static String`	`FIELD_SAMPLE_ID`
`private static String`	`FIELD_SHAPE`
`private static String`	`FIELD_SOURCE_FILE_NAME`
`private static String`	`FIELD_SPECTRA`
`private static String`	`FIELD_SPECTRAL_BASIS_INFO`
`private static String`	`FIELD_SPECTRAL_LIBRARY`
`private static String`	`FIELD_SPECTRUM`
`private static String`	`FIELD_THUMBNAIL`
`private static String`	`FIELD_TIMESTAMP`
`private static String`	`FIELD_TYPE_ID`
`private static String`	`FIELD_USER_COMMENTS`
`private static String`	`FIELD_VALUES`
`private static String`	`FIELD_WAVELENGTH`
`private static String`	`FIELD_WAVELENGTHS`
`private static org.slf4j.Logger`	`LOGGER` Logger for outputting summary diagnostics.
`private static int`	`REC_BOOLEAN`
`private static int`	`REC_CONTAINER` A record that is a container of other records.
`private static int`	`REC_FLOAT`
`private static int`	`REC_IMAGE` Image format int: pixel type? 3 = RGBA int: width int: height int: depth data bytes follow
`private static int`	`REC_INT` 32-bit integer values
`private static int`	`REC_NESTED` A nested record of records
`private static int`	`REC_STRING` A string int: ? int: length 8-byte characters follow
`private List<IM3Reader.IM3Record>`	`records`
`private List<IM3Reader.Spectrum>`	`spectra`

Fields inherited from class loci.formats.FormatReader
core, coreIndex, datasetDescription, domains, 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, metadataOptions, suffixes

Fields inherited from interface loci.formats.IFormatReader
CAN_GROUP, CANNOT_GROUP, MUST_GROUP

Constructor Summary

Constructors
Constructor and Description

IM3Reader()
Construct an uninitialized reader of .im3 files.

Constructors
Constructor and Description
`IM3Reader()` Construct an uninitialized reader of .im3 files.

Method Summary

All Methods Static Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`void`	`close(boolean fileOnly)` Closes the currently open file.
`List<IM3Reader.Spectrum>`	`getSpectra()` If a Nuance file is a spectral library set (.csl) file, there is a spectral library inside that contains a profile of spectral bin magnitudes for each of several measured fluorophores (or auto fluorescence).
`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.
`static void`	`main(String[] args)` Write a summary of each record to STDOUT
`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.
`byte[]`	`openRaw()` Open the current series in raw-mode, returning the interleaved image bytes.
`private static IM3Reader.IM3Record`	`parseRecord(loci.common.IRandomAccess is)` Parse an IM3 record at the current file pointer location
`protected static String`	`parseString(loci.common.IRandomAccess is)` Parse a string from the IM3 file at the current file pointer loc
`void`	`setSeries(int no)` Activates the specified series.
`void`	`writeSummary()` Write a summary of each field in the IM3 file to the writer

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, 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, 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, reopenFile, seriesToCoreIndex, setCoreIndex, setFlattenedResolutions, setGroupFiles, setId, setMetadataFiltered, setMetadataStore, setNormalized, setOriginalMetadataPopulated, setResolution

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
  - LOGGER
```
private static final org.slf4j.Logger LOGGER
```
    Logger for outputting summary diagnostics.
  - COOKIE
```
private static final int COOKIE
```
    First 4 bytes of file is "1985"
    
    See Also:
    
    Constant Field Values
  - REC_CONTAINER
```
private static final int REC_CONTAINER
```
    A record that is a container of other records.
    
    See Also:
    
    Constant Field Values
  - REC_IMAGE
```
private static final int REC_IMAGE
```
    Image format int: pixel type? 3 = RGBA int: width int: height int: depth data bytes follow
    
    See Also:
    
    Constant Field Values
  - REC_NESTED
```
private static final int REC_NESTED
```
    A nested record of records
    
    See Also:
    
    Constant Field Values
  - REC_INT
```
private static final int REC_INT
```
    32-bit integer values
    
    See Also:
    
    Constant Field Values
  - REC_FLOAT
```
private static final int REC_FLOAT
```
    See Also:
    
    Constant Field Values
  - REC_BOOLEAN
```
private static final int REC_BOOLEAN
```
    See Also:
    
    Constant Field Values
  - REC_STRING
```
private static final int REC_STRING
```
    A string int: ? int: length 8-byte characters follow
    
    See Also:
    
    Constant Field Values
  - FIELD_DATA_SET
```
private static final String FIELD_DATA_SET
```
    See Also:
    
    Constant Field Values
  - FIELD_TIMESTAMP
```
private static final String FIELD_TIMESTAMP
```
    See Also:
    
    Constant Field Values
  - FIELD_AUX_FLAGS
```
private static final String FIELD_AUX_FLAGS
```
    See Also:
    
    Constant Field Values
  - FIELD_NUANCE_FLAGS
```
private static final String FIELD_NUANCE_FLAGS
```
    See Also:
    
    Constant Field Values
  - FIELD_SPECTRA
```
private static final String FIELD_SPECTRA
```
    See Also:
    
    Constant Field Values
  - FIELD_VALUES
```
private static final String FIELD_VALUES
```
    See Also:
    
    Constant Field Values
  - FIELD_PROTOCOL
```
private static final String FIELD_PROTOCOL
```
    See Also:
    
    Constant Field Values
  - FIELD_OBJECTIVE
```
private static final String FIELD_OBJECTIVE
```
    See Also:
    
    Constant Field Values
  - FIELD_SPECTRAL_BASIS_INFO
```
private static final String FIELD_SPECTRAL_BASIS_INFO
```
    See Also:
    
    Constant Field Values
  - FIELD_FILTER_PAIR
```
private static final String FIELD_FILTER_PAIR
```
    See Also:
    
    Constant Field Values
  - FIELD_FIXED_FILTER
```
private static final String FIELD_FIXED_FILTER
```
    See Also:
    
    Constant Field Values
  - FIELD_BANDS
```
private static final String FIELD_BANDS
```
    See Also:
    
    Constant Field Values
  - FIELD_SPECTRAL_LIBRARY
```
private static final String FIELD_SPECTRAL_LIBRARY
```
    See Also:
    
    Constant Field Values
  - FIELD_SPECTRUM
```
private static final String FIELD_SPECTRUM
```
    See Also:
    
    Constant Field Values
  - FIELD_THUMBNAIL
```
private static final String FIELD_THUMBNAIL
```
    See Also:
    
    Constant Field Values
  - FIELD_DATA
```
private static final String FIELD_DATA
```
    See Also:
    
    Constant Field Values
  - FIELD_FILE_VERSION
```
private static final String FIELD_FILE_VERSION
```
    See Also:
    
    Constant Field Values
  - FIELD_CLASS_ID
```
private static final String FIELD_CLASS_ID
```
    See Also:
    
    Constant Field Values
  - FIELD_TYPE_ID
```
private static final String FIELD_TYPE_ID
```
    See Also:
    
    Constant Field Values
  - FIELD_SHAPE
```
private static final String FIELD_SHAPE
```
    See Also:
    
    Constant Field Values
  - FIELD_BAND_INDEX
```
private static final String FIELD_BAND_INDEX
```
    See Also:
    
    Constant Field Values
  - FIELD_NAME
```
private static final String FIELD_NAME
```
    See Also:
    
    Constant Field Values
  - FIELD_SAMPLE_ID
```
private static final String FIELD_SAMPLE_ID
```
    See Also:
    
    Constant Field Values
  - FIELD_USER_COMMENTS
```
private static final String FIELD_USER_COMMENTS
```
    See Also:
    
    Constant Field Values
  - FIELD_SOURCE_FILE_NAME
```
private static final String FIELD_SOURCE_FILE_NAME
```
    See Also:
    
    Constant Field Values
  - FIELD_PROXY_PARENT_FILE_NAME
```
private static final String FIELD_PROXY_PARENT_FILE_NAME
```
    See Also:
    
    Constant Field Values
  - FIELD_MANUFACTURER
```
private static final String FIELD_MANUFACTURER
```
    See Also:
    
    Constant Field Values
  - FIELD_PART_NUMBER
```
private static final String FIELD_PART_NUMBER
```
    See Also:
    
    Constant Field Values
  - FIELD_MILLIMETERS_PER_PIXEL
```
private static final String FIELD_MILLIMETERS_PER_PIXEL
```
    See Also:
    
    Constant Field Values
  - FIELD_EXPOSURE
```
private static final String FIELD_EXPOSURE
```
    See Also:
    
    Constant Field Values
  - FIELD_WAVELENGTH
```
private static final String FIELD_WAVELENGTH
```
    See Also:
    
    Constant Field Values
  - FIELD_WAVELENGTHS
```
private static final String FIELD_WAVELENGTHS
```
    See Also:
    
    Constant Field Values
  - FIELD_MAGNITUDES
```
private static final String FIELD_MAGNITUDES
```
    See Also:
    
    Constant Field Values
  - FIELD_HOMOGENEOUS
```
private static final String FIELD_HOMOGENEOUS
```
    See Also:
    
    Constant Field Values
  - records
```
private List<IM3Reader.IM3Record> records
```
  - dataSets
```
private List<IM3Reader.ContainerRecord> dataSets
```
  - spectra
```
private List<IM3Reader.Spectrum> spectra
```
  - data
```
private byte[] data
```
  - EMPTY_STRING
```
private static final String EMPTY_STRING
```
- Constructor Detail
  - IM3Reader
```
public IM3Reader()
```
    Construct an uninitialized reader of .im3 files.
- Method Detail
  - 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.
  - openRaw
```
public byte[] openRaw()
               throws IOException
```
    Open the current series in raw-mode, returning the interleaved image bytes. The data format for a pixel is a run of 63 unsigned short little endian values.
    
    Returns:
    
    a byte array containing the data organized by spectral channel, then x, then y. Returns null if, for some incomprehensible reason, the DATA block was missing.
    
    Throws:
    
    IOException
  - getSpectra
```
public List<IM3Reader.Spectrum> getSpectra()
```
    If a Nuance file is a spectral library set (.csl) file, there is a spectral library inside that contains a profile of spectral bin magnitudes for each of several measured fluorophores (or auto fluorescence). This method finds the spectral library and returns the spectra inside.
    
    Returns:
    
    a list of the Spectrum records contained in the library
  - 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
  - parseString
```
protected static String parseString(loci.common.IRandomAccess is)
                             throws IOException
```
    Parse a string from the IM3 file at the current file pointer loc
    
    Parameters:
    
    is - stream to read from
    
    Returns:
    
    parsed string or null for string of zero length
    
    Throws:
    
    IOException
  - parseRecord
```
private static IM3Reader.IM3Record parseRecord(loci.common.IRandomAccess is)
                                        throws IOException
```
    Parse an IM3 record at the current file pointer location
    
    Parameters:
    
    is - random access stream, pointing at the record's start (the length-quadword of the record's tag name)
    
    Returns:
    
    an IM3Record or subclass depending on the record's type
    
    Throws:
    
    IOException - on file misparsing leading to overrun and other
  - 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.
    
    Specified by:
    
    isThisType in interface IFormatReader
    
    Overrides:
    
    isThisType in class FormatReader
    
    Throws:
    
    IOException
  - setSeries
```
public void setSeries(int no)
```
    Description copied from interface: IFormatReader
    
    Activates the specified series. This also resets the resolution to 0.
    
    Specified by:
    
    setSeries in interface IFormatReader
    
    Overrides:
    
    setSeries in class FormatReader
  - 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
  - writeSummary
```
public void writeSummary()
                  throws IOException
```
    Write a summary of each field in the IM3 file to the writer
    
    Throws:
    
    IOException
  - main
```
public static void main(String[] args)
                 throws IOException
```
    Write a summary of each record to STDOUT
    
    Parameters:
    
    args -
    
    Throws:
    
    IOException

Class IM3Reader

Nested Class Summary

Field Summary

Fields inherited from class loci.formats.FormatReader

Fields inherited from class loci.formats.FormatHandler

Fields inherited from interface loci.formats.IFormatReader

Constructor Summary

Method Summary

Methods inherited from class loci.formats.FormatReader

Methods inherited from class loci.formats.FormatHandler

Methods inherited from class java.lang.Object

Methods inherited from interface loci.formats.IFormatHandler

Methods inherited from interface loci.formats.IMetadataConfigurable

Field Detail

LOGGER

COOKIE

REC_CONTAINER

REC_IMAGE

REC_NESTED

REC_INT

REC_FLOAT

REC_BOOLEAN

REC_STRING

FIELD_DATA_SET

FIELD_TIMESTAMP

FIELD_AUX_FLAGS

FIELD_NUANCE_FLAGS

FIELD_SPECTRA

FIELD_VALUES

FIELD_PROTOCOL

FIELD_OBJECTIVE

FIELD_SPECTRAL_BASIS_INFO

FIELD_FILTER_PAIR

FIELD_FIXED_FILTER

FIELD_BANDS

FIELD_SPECTRAL_LIBRARY

FIELD_SPECTRUM

FIELD_THUMBNAIL

FIELD_DATA

FIELD_FILE_VERSION

FIELD_CLASS_ID

FIELD_TYPE_ID

FIELD_SHAPE

FIELD_BAND_INDEX

FIELD_NAME

FIELD_SAMPLE_ID

FIELD_USER_COMMENTS

FIELD_SOURCE_FILE_NAME

FIELD_PROXY_PARENT_FILE_NAME

FIELD_MANUFACTURER

FIELD_PART_NUMBER

FIELD_MILLIMETERS_PER_PIXEL

FIELD_EXPOSURE

FIELD_WAVELENGTH

FIELD_WAVELENGTHS

FIELD_MAGNITUDES

FIELD_HOMOGENEOUS

records

dataSets

spectra

data

EMPTY_STRING

Constructor Detail

IM3Reader

Method Detail

openBytes

openRaw

getSpectra

initFile

parseString

parseRecord

isThisType

setSeries

close

writeSummary

main