loci.formats

Class MinMaxCalculator

java.lang.Object

loci.formats.ReaderWrapper

loci.formats.MinMaxCalculator

All Implemented Interfaces:

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

public class MinMaxCalculator
extends ReaderWrapper

Logic to compute minimum and maximum values for each channel.

Field Summary

Fields

Modifier and Type	Field and Description
protected double[][]	chanMax Max values for each channel.
protected double[][]	chanMin Min values for each channel.
protected int[]	minMaxDone Number of planes for which min/max computations have been completed.
protected IMinMaxStore	minMaxStore Consumer of channel global minima and maxima
protected double[][]	planeMax Max values for each plane.
protected double[][]	planeMin Min values for each plane.

Fields inherited from class loci.formats.ReaderWrapper

reader

Fields inherited from interface loci.formats.IFormatReader

CAN_GROUP, CANNOT_GROUP, MUST_GROUP

Constructor Summary

Constructors

Constructor and Description
MinMaxCalculator() Constructs a MinMaxCalculator around a new image reader.
MinMaxCalculator(IFormatReader r) Constructs a MinMaxCalculator with the given reader.

Method Summary

Modifier and Type	Method and Description
void	close(boolean fileOnly) Closes the currently open file.
java.lang.Double	getChannelGlobalMaximum(int theC) Retrieves a specified channel's global maximum.
java.lang.Double	getChannelGlobalMinimum(int theC) Retrieves a specified channel's global minimum.
java.lang.Double	getChannelKnownMaximum(int theC) Retrieves the specified channel's maximum based on the images that have been read.
java.lang.Double	getChannelKnownMinimum(int theC) Retrieves the specified channel's minimum based on the images that have been read.
IMinMaxStore	getMinMaxStore() Retrieves the current active min-max store for the calculator.
java.lang.Class<?>	getNativeDataType() Returns the native data type of image planes for this reader, as returned by IFormatReader.openPlane(int, int, int, int, int) or IFormatWriter.savePlane(int, java.lang.Object).
java.lang.Double[]	getPlaneMaximum(int no) Retrieves the maximum pixel value for the specified plane.
java.lang.Double[]	getPlaneMinimum(int no) Retrieves the minimum pixel value for the specified plane.
protected void	initMinMax() Ensures internal min/max variables are initialized properly.
boolean	isMinMaxPopulated() Returns true if the values returned by getChannelGlobalMinimum/Maximum can be trusted.
static MinMaxCalculator	makeMinMaxCalculator(IFormatReader r) Converts the given reader into a MinMaxCalculator, wrapping if needed.
byte[]	openBytes(int no) Obtains the specified image plane from the current file as a byte array.
byte[]	openBytes(int no, byte[] buf) Obtains the specified image plane from the current file into a pre-allocated byte array of (sizeX * sizeY * bytesPerPixel * RGB channel count).
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[]	openBytes(int no, int x, int y, int w, int h) Obtains a sub-image of the specified image plane, whose upper-left corner is given by (x, y).
void	setMinMaxStore(IMinMaxStore store) Sets the active min-max store for the calculator.
protected void	updateMinMax(int no, byte[] buf, int len) Updates min/max values based on the given byte array.

Methods inherited from class loci.formats.ReaderWrapper

close, coreIndexToSeries, duplicate, fileGroupOption, get16BitLookupTable, get8BitLookupTable, getAdvancedSeriesUsedFiles, getAdvancedUsedFiles, getBitsPerPixel, getCoreIndex, getCoreMetadataList, getCurrentFile, getDatasetStructureDescription, getDimensionOrder, getDomains, getEffectiveSizeC, getFillColor, getFormat, getGlobalMetadata, getImageCount, getIndex, getIndex, getMetadataOptions, getMetadataStore, getMetadataStoreRoot, getMetadataValue, getModuloC, getModuloT, getModuloZ, getOptimalTileHeight, getOptimalTileWidth, getPixelType, getPossibleDomains, getReader, getRequiredDirectories, getResolution, getResolutionCount, getRGBChannelCount, getSeries, getSeriesCount, getSeriesMetadata, getSeriesMetadataValue, getSeriesUsedFiles, getSeriesUsedFiles, getSizeC, getSizeT, getSizeX, getSizeY, getSizeZ, getSuffixes, getSupportedMetadataLevels, 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, isThisType, isThumbnailSeries, openPlane, openThumbBytes, reopenFile, seriesToCoreIndex, setCoreIndex, setFillColor, setFlattenedResolutions, setGroupFiles, setId, setMetadataFiltered, setMetadataOptions, setMetadataStore, setNormalized, setOriginalMetadataPopulated, setResolution, setSeries, unwrap, unwrap, unwrap

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

chanMin

protected double[][] chanMin

Min values for each channel.

chanMax

protected double[][] chanMax

Max values for each channel.

planeMin

protected double[][] planeMin

Min values for each plane.

planeMax

protected double[][] planeMax

Max values for each plane.

minMaxDone

protected int[] minMaxDone

Number of planes for which min/max computations have been completed.

minMaxStore

protected IMinMaxStore minMaxStore

Consumer of channel global minima and maxima

Constructor Detail

MinMaxCalculator

public MinMaxCalculator()

Constructs a MinMaxCalculator around a new image reader.

MinMaxCalculator

public MinMaxCalculator(IFormatReader r)

Constructs a MinMaxCalculator with the given reader.

Method Detail

makeMinMaxCalculator

public static MinMaxCalculator makeMinMaxCalculator(IFormatReader r)

Converts the given reader into a MinMaxCalculator, wrapping if needed.

setMinMaxStore

public void setMinMaxStore(IMinMaxStore store)

Sets the active min-max store for the calculator. Whenever a channel's global minimum and maximum calculation has been completed this store is notified.

Parameters:

store - See above.

getMinMaxStore

public IMinMaxStore getMinMaxStore()

Retrieves the current active min-max store for the calculator.

Returns:

See above.

getChannelGlobalMinimum

public java.lang.Double getChannelGlobalMinimum(int theC)
                                         throws FormatException,
                                                java.io.IOException

Retrieves a specified channel's global minimum. Returns null if some of the image planes have not been read.

Throws:

java.io.IOException - Not actually thrown.

FormatException

getChannelGlobalMaximum

public java.lang.Double getChannelGlobalMaximum(int theC)
                                         throws FormatException,
                                                java.io.IOException

Retrieves a specified channel's global maximum. Returns null if some of the image planes have not been read.

Throws:

java.io.IOException - Not actually thrown.

FormatException

getChannelKnownMinimum

public java.lang.Double getChannelKnownMinimum(int theC)
                                        throws FormatException,
                                               java.io.IOException

Retrieves the specified channel's minimum based on the images that have been read. Returns null if no image planes have been read yet.

Throws:

FormatException - Not actually thrown.

java.io.IOException - Not actually thrown.

getChannelKnownMaximum

public java.lang.Double getChannelKnownMaximum(int theC)
                                        throws FormatException,
                                               java.io.IOException

Retrieves the specified channel's maximum based on the images that have been read. Returns null if no image planes have been read yet.

Throws:

FormatException - Not actually thrown.

java.io.IOException - Not actually thrown.

getPlaneMinimum

public java.lang.Double[] getPlaneMinimum(int no)
                                   throws FormatException,
                                          java.io.IOException

Retrieves the minimum pixel value for the specified plane. If each image plane contains more than one channel (i.e., ReaderWrapper.getRGBChannelCount() > 1), returns the maximum value for each embedded channel. Returns null if the plane has not already been read.

Throws:

FormatException - Not actually thrown.

java.io.IOException - Not actually thrown.

getPlaneMaximum

public java.lang.Double[] getPlaneMaximum(int no)
                                   throws FormatException,
                                          java.io.IOException

Retrieves the maximum pixel value for the specified plane. If each image plane contains more than one channel (i.e., ReaderWrapper.getRGBChannelCount() > 1), returns the maximum value for each embedded channel. Returns null if the plane has not already been read.

Throws:

FormatException - Not actually thrown.

java.io.IOException - Not actually thrown.

isMinMaxPopulated

public boolean isMinMaxPopulated()
                          throws FormatException,
                                 java.io.IOException

Returns true if the values returned by getChannelGlobalMinimum/Maximum can be trusted.

Throws:

FormatException - Not actually thrown.

java.io.IOException - Not actually thrown.

openBytes

public byte[] openBytes(int no)
                 throws FormatException,
                        java.io.IOException

Description copied from interface: IFormatReader

Obtains the specified image plane from the current file as a byte array.

Specified by:

openBytes in interface IFormatReader

Overrides:

openBytes in class ReaderWrapper

Throws:

FormatException

java.io.IOException

See Also:

IFormatReader.openBytes(int, byte[])

openBytes

public byte[] openBytes(int no,
                        byte[] buf)
                 throws FormatException,
                        java.io.IOException

Description copied from interface: IFormatReader

Obtains the specified image plane from the current file into a pre-allocated byte array of (sizeX * sizeY * bytesPerPixel * RGB channel count).

Specified by:

openBytes in interface IFormatReader

Overrides:

openBytes in class ReaderWrapper

Parameters:

no - the plane index within the current series.

buf - a pre-allocated buffer.

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.

openBytes

public byte[] openBytes(int no,
                        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, whose upper-left corner is given by (x, y).

Specified by:

openBytes in interface IFormatReader

Overrides:

openBytes in class ReaderWrapper

Throws:

FormatException

java.io.IOException

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

Overrides:

openBytes in class ReaderWrapper

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.

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 ReaderWrapper

Throws:

java.io.IOException

getNativeDataType

public java.lang.Class<?> getNativeDataType()

Description copied from interface: IFormatHandler

Returns the native data type of image planes for this reader, as returned by IFormatReader.openPlane(int, int, int, int, int) or IFormatWriter.savePlane(int, java.lang.Object). For most readers this type will be a byte array; however, some readers call external APIs that work with other types such as BufferedImage.

Specified by:

getNativeDataType in interface IFormatHandler

Overrides:

getNativeDataType in class ReaderWrapper

updateMinMax

protected void updateMinMax(int no,
                            byte[] buf,
                            int len)
                     throws FormatException,
                            java.io.IOException

Updates min/max values based on the given byte array.

Parameters:

no - the plane index within the series.

buf - a pre-allocated buffer.

len - as buf may be larger than the actual pixel count having been written to it, the length (in bytes) of the those pixels.

Throws:

FormatException

java.io.IOException

initMinMax

protected void initMinMax()
                   throws FormatException,
                          java.io.IOException

Ensures internal min/max variables are initialized properly.

Throws:

FormatException - Not actually thrown.

java.io.IOException - Not actually thrown.