io.scif.filters

Class MinMaxFilter

java.lang.Object

org.scijava.AbstractContextual

org.scijava.plugin.AbstractRichPlugin

io.scif.AbstractSCIFIOPlugin

io.scif.filters.AbstractFilter<Reader>

io.scif.filters.AbstractReaderFilter

io.scif.filters.MinMaxFilter

All Implemented Interfaces:

Filter, Groupable, HasFormat, HasSource, Reader, SCIFIOPlugin, Comparable<org.scijava.Prioritized>, org.scijava.Contextual, org.scijava.Identifiable, org.scijava.Locatable, org.scijava.log.Logged, org.scijava.plugin.HasPluginInfo, org.scijava.plugin.RichPlugin, org.scijava.plugin.SciJavaPlugin, org.scijava.Prioritized, org.scijava.Versioned

public class MinMaxFilter
extends AbstractReaderFilter

Logic to compute minimum and maximum values for each plane. For each plane, the min/max values for a given value of a specific planar axis can also be queried.

Constructor Summary

Constructors

Constructor and Description
MinMaxFilter()

Method Summary

Modifier and Type	Method and Description
void	close(boolean fileOnly) Closes the image source(s) associated with this component, with a toggle to determine if the component itself is reset.
Double	getAxisGlobalMaximum(int imageIndex, net.imagej.axis.AxisType type, int index) Retrieves a specified planar axis's global maximum.
Double	getAxisGlobalMinimum(int imageIndex, net.imagej.axis.AxisType type, int index) Retrieves a specified planar axis's global minimum.
Double	getAxisKnownMaximum(int imageIndex, net.imagej.axis.AxisType type, int index) Retrieves the specified planar axis's maximum based on the images that have been read.
Double	getAxisKnownMinimum(int imageIndex, net.imagej.axis.AxisType type, int index) Retrieves the specified planar axis's minimum based on the images that have been read.
Class<?>	getNativeDataType()
long	getPlaneCount(int imageIndex) Determines the number of planes in the current file.
Double	getPlaneMaximum(int imageIndex, long planeIndex) Retrieves the maximum pixel value for each planar axis of the specified plane.
Double	getPlaneMinimum(int imageIndex, long planeIndex) Retrieves the minimum pixel value for each planar axis of the specified plane.
boolean	isMinMaxPopulated(int imageIndex) Returns true if the values returned by getAxisGlobalMinimum/Maximum can be trusted.
Plane	openPlane(int imageIndex, long planeIndex) Creates a Plane representation of the pixels at the specified indices.
Plane	openPlane(int imageIndex, long planeIndex, net.imglib2.Interval bounds) Creates a Plane representation of a desired sub-region from the pixels at the specified indices.
Plane	openPlane(int imageIndex, long planeIndex, net.imglib2.Interval bounds, SCIFIOConfig config) As Reader.openPlane(int, long, Interval) with configuration options.
Plane	openPlane(int imageIndex, long planeIndex, Plane plane) Allows a single Plane object to be reused by reference when opening complete planes.
Plane	openPlane(int imageIndex, long planeIndex, Plane plane, net.imglib2.Interval bounds) Allows a single Plane object to be reused by reference when opening sub-regions of planes.
Plane	openPlane(int imageIndex, long planeIndex, Plane plane, net.imglib2.Interval bounds, SCIFIOConfig config) Allows a single Plane object to be reused by reference when opening sub-regions of planes.
Plane	openPlane(int imageIndex, long planeIndex, Plane plane, SCIFIOConfig config) Allows a single Plane object to be reused by reference when opening complete planes.
Plane	openPlane(int imageIndex, long planeIndex, SCIFIOConfig config) As Reader.openPlane(int, long) with configuration options.

Methods inherited from class io.scif.filters.AbstractReaderFilter

castToTypedPlane, cleanUp, close, createPlane, createPlane, fileGroupOption, getContext, getCurrentLocation, getDomains, getFormat, getFormatName, getHandle, getImageCount, getMetadata, getOptimalTileHeight, getOptimalTileWidth, getParentMeta, hasCompanionFiles, isCompatible, isNormalized, isSingleFile, metaCheck, openPlaneHelper, planarBounds, readPlane, readPlane, readPlaneHelper, setContext, setMetadata, setNormalized, setParent, setSource, setSource, setSource, setSource, setSourceHelper, target

Methods inherited from class io.scif.filters.AbstractFilter

enabledDefault, getParent, reset

Methods inherited from class io.scif.AbstractSCIFIOPlugin

getVersion, log

Methods inherited from class org.scijava.plugin.AbstractRichPlugin

getInfo, getPriority, setInfo, setPriority, toString

Methods inherited from class org.scijava.AbstractContextual

context

Methods inherited from class java.lang.Object

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

Methods inherited from interface io.scif.SCIFIOPlugin

getVersion, log

Methods inherited from interface org.scijava.plugin.RichPlugin

getIdentifier

Methods inherited from interface org.scijava.Contextual

context

Methods inherited from interface org.scijava.Prioritized

compareTo, getPriority, setPriority

Methods inherited from interface org.scijava.plugin.HasPluginInfo

getInfo, setInfo

Methods inherited from interface org.scijava.Locatable

getLocation

Constructor Detail

MinMaxFilter

public MinMaxFilter()

Method Detail

getAxisGlobalMinimum

public Double getAxisGlobalMinimum(int imageIndex,
                                   net.imagej.axis.AxisType type,
                                   int index)
                            throws FormatException

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

Throws:

FormatException

getAxisGlobalMaximum

public Double getAxisGlobalMaximum(int imageIndex,
                                   net.imagej.axis.AxisType type,
                                   int index)
                            throws FormatException

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

Throws:

FormatException

getAxisKnownMinimum

public Double getAxisKnownMinimum(int imageIndex,
                                  net.imagej.axis.AxisType type,
                                  int index)

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

getAxisKnownMaximum

public Double getAxisKnownMaximum(int imageIndex,
                                  net.imagej.axis.AxisType type,
                                  int index)

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

getPlaneMinimum

public Double getPlaneMinimum(int imageIndex,
                              long planeIndex)

Retrieves the minimum pixel value for each planar axis of the specified plane. Returns null if the plane has not already been read.

getPlaneMaximum

public Double getPlaneMaximum(int imageIndex,
                              long planeIndex)

Retrieves the maximum pixel value for each planar axis of the specified plane. Returns null if the plane has not already been read.

isMinMaxPopulated

public boolean isMinMaxPopulated(int imageIndex)

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

getPlaneCount

public long getPlaneCount(int imageIndex)

Description copied from interface: Reader

Determines the number of planes in the current file.

Specified by:

getPlaneCount in interface Reader

Overrides:

getPlaneCount in class AbstractReaderFilter

openPlane

public Plane openPlane(int imageIndex,
                       long planeIndex)
                throws FormatException,
                       IOException

Description copied from interface: Reader

Creates a Plane representation of the pixels at the specified indices.

Specified by:

openPlane in interface Reader

Overrides:

openPlane in class AbstractReaderFilter

Parameters:

imageIndex - the image index within the dataset.

planeIndex - the plane index within the image.

Returns:

The complete Plane at the specified indices.

Throws:

FormatException

IOException

openPlane

public Plane openPlane(int imageIndex,
                       long planeIndex,
                       Plane plane)
                throws FormatException,
                       IOException

Description copied from interface: Reader

Allows a single Plane object to be reused by reference when opening complete planes.

Specified by:

openPlane in interface Reader

Overrides:

openPlane in class AbstractReaderFilter

Throws:

FormatException

IOException

See Also:

Reader.openPlane(int, long)

openPlane

public Plane openPlane(int imageIndex,
                       long planeIndex,
                       net.imglib2.Interval bounds)
                throws FormatException,
                       IOException

Description copied from interface: Reader

Creates a Plane representation of a desired sub-region from the pixels at the specified indices.

Specified by:

openPlane in interface Reader

Overrides:

openPlane in class AbstractReaderFilter

Parameters:

imageIndex - the image index within the dataset.

planeIndex - the plane index within the image.

bounds - bounds of the planar axes.

Returns:

The desired sub-region at the specified indices.

Throws:

FormatException

IOException

openPlane

public Plane openPlane(int imageIndex,
                       long planeIndex,
                       Plane plane,
                       net.imglib2.Interval bounds)
                throws FormatException,
                       IOException

Description copied from interface: Reader

Allows a single Plane object to be reused by reference when opening sub-regions of planes.

Specified by:

openPlane in interface Reader

Overrides:

openPlane in class AbstractReaderFilter

Throws:

FormatException

IOException

See Also:

Reader.openPlane(int, long, Interval)

openPlane

public Plane openPlane(int imageIndex,
                       long planeIndex,
                       SCIFIOConfig config)
                throws FormatException,
                       IOException

Description copied from interface: Reader

As Reader.openPlane(int, long) with configuration options.

Specified by:

openPlane in interface Reader

Overrides:

openPlane in class AbstractReaderFilter

Parameters:

imageIndex - the image index within the dataset.

planeIndex - the plane index within the image.

config - Configuration information to use for this read.

Returns:

The complete Plane at the specified indices.

Throws:

FormatException

IOException

openPlane

public Plane openPlane(int imageIndex,
                       long planeIndex,
                       Plane plane,
                       SCIFIOConfig config)
                throws FormatException,
                       IOException

Description copied from interface: Reader

Allows a single Plane object to be reused by reference when opening complete planes.

Specified by:

openPlane in interface Reader

Overrides:

openPlane in class AbstractReaderFilter

Throws:

FormatException

IOException

See Also:

Reader.openPlane(int, long, SCIFIOConfig)

openPlane

public Plane openPlane(int imageIndex,
                       long planeIndex,
                       net.imglib2.Interval bounds,
                       SCIFIOConfig config)
                throws FormatException,
                       IOException

Description copied from interface: Reader

As Reader.openPlane(int, long, Interval) with configuration options.

Specified by:

openPlane in interface Reader

Overrides:

openPlane in class AbstractReaderFilter

Parameters:

imageIndex - the image index within the dataset.

planeIndex - the plane index within the image.

bounds - bounds of the planar axes.

config - Configuration information to use for this read.

Returns:

The desired sub-region at the specified indices.

Throws:

FormatException

IOException

openPlane

public Plane openPlane(int imageIndex,
                       long planeIndex,
                       Plane plane,
                       net.imglib2.Interval bounds,
                       SCIFIOConfig config)
                throws FormatException,
                       IOException

Description copied from interface: Reader

Allows a single Plane object to be reused by reference when opening sub-regions of planes.

Specified by:

openPlane in interface Reader

Overrides:

openPlane in class AbstractReaderFilter

Throws:

FormatException

IOException

See Also:

Reader.openPlane(int, long, Interval, SCIFIOConfig)

close

public void close(boolean fileOnly)
           throws IOException

Description copied from interface: HasSource

Closes the image source(s) associated with this component, with a toggle to determine if the component itself is reset.

Specified by:

close in interface HasSource

Overrides:

close in class AbstractReaderFilter

Parameters:

fileOnly - - If true, only the associated source(s) are closed.

Throws:

IOException

getNativeDataType

public Class<?> getNativeDataType()