icy.roi

Class ROIDescriptor

java.lang.Object

icy.roi.ROIDescriptor

Direct Known Subclasses:

ROIAreaDescriptor, ROIColorDescriptor, ROIContourDescriptor, ROIGroupIdDescriptor, ROIIconDescriptor, ROIInteriorDescriptor, ROIMassCenterCDescriptor, ROIMassCenterTDescriptor, ROIMassCenterXDescriptor, ROIMassCenterYDescriptor, ROIMassCenterZDescriptor, ROIMaxIntensityDescriptor, ROIMeanIntensityDescriptor, ROIMinIntensityDescriptor, ROINameDescriptor, ROIOpacityDescriptor, ROIPerimeterDescriptor, ROIPositionCDescriptor, ROIPositionTDescriptor, ROIPositionXDescriptor, ROIPositionYDescriptor, ROIPositionZDescriptor, ROIReadOnlyDescriptor, ROISizeCDescriptor, ROISizeTDescriptor, ROISizeXDescriptor, ROISizeYDescriptor, ROISizeZDescriptor, ROIStandardDeviationDescriptor, ROISumIntensityDescriptor, ROISurfaceAreaDescriptor, ROIVolumeDescriptor

public abstract class ROIDescriptor
extends java.lang.Object

Abstract class providing the basic methods to retrieve properties and compute a specific descriptor for a region of interest (ROI)

Author:

Stephane Dallongeville, Alexandre Dufour

Method Summary

Methods

Modifier and Type	Method and Description
abstract java.lang.Object	compute(ROI roi, Sequence sequence) Computes the descriptor on the specified ROI and return the result.
static java.lang.Object	computeDescriptor(java.util.Collection<ROIDescriptor> roiDescriptors, java.lang.String descriptorId, ROI roi, Sequence sequence) Computes the specified descriptor from the input ROIDescriptor set on given ROI and returns the result (or null if the descriptor is not found).
static java.lang.Object	computeDescriptor(java.lang.String descriptorId, ROI roi, Sequence sequence) Computes the specified descriptor on given ROI and returns the result (or null if the descriptor is not found).
boolean	equals(java.lang.Object obj)
abstract java.lang.String	getDescription() Returns a single line description (used as tooltip) for this descriptor
static ROIDescriptor	getDescriptor(java.util.Collection<ROIDescriptor> descriptors, java.lang.String id) Returns the descriptor identified by the given id from the given list of ROIDescriptor.
static ROIDescriptor	getDescriptor(java.lang.String id) Returns the descriptor identified by the given id from the given list of ROIDescriptor.
static java.util.Map<ROIDescriptor,PluginROIDescriptor>	getDescriptors() Returns all available ROI descriptors (see ROIDescriptor) and their attached plugin (see PluginROIDescriptor).
java.lang.String	getId() Returns the id of this descriptor.
java.lang.String	getName() Returns the name of this descriptor.
java.lang.Class<?>	getType() Returns the type of result for this descriptor
java.lang.String	getUnit(Sequence sequence) Returns the unit of this descriptor (ex: "px", "mm", "µm2"...
int	hashCode()
boolean	needRecompute(ROIEvent change) Returns true if this descriptor need to be recomputed when the specified ROI change event happen.
boolean	needRecompute(SequenceEvent change) Returns true if this descriptor need to be recomputed when the specified Sequence change event happen.
boolean	separateChannel() Returns true if this descriptor compute its result on Sequence data and *per channel* (as pixel intensity information).
java.lang.String	toString()

Methods inherited from class java.lang.Object

getClass, notify, notifyAll, wait, wait, wait

Method Detail

getDescriptors

public static java.util.Map<ROIDescriptor,PluginROIDescriptor> getDescriptors()

Returns all available ROI descriptors (see ROIDescriptor) and their attached plugin (see PluginROIDescriptor).
This list can be extended by installing new plugin(s) implementing the PluginROIDescriptor interface.

See Also:

compute(ROI, Sequence), PluginROIDescriptor.compute(ROI, Sequence)

getDescriptor

public static ROIDescriptor getDescriptor(java.util.Collection<ROIDescriptor> descriptors,
                          java.lang.String id)

Returns the descriptor identified by the given id from the given list of ROIDescriptor.
It can return null if the descriptor is not found in the given list.

Parameters:

id - the id of the descriptor (ROIBasicMeasureDescriptorsPlugin.ID_VOLUME for instance) @see #getDescriptors()

See Also:

computeDescriptor(String, ROI, Sequence)

getDescriptor

public static ROIDescriptor getDescriptor(java.lang.String id)

Returns the descriptor identified by the given id from the given list of ROIDescriptor.
It can return null if the descriptor is not found in the given list.

Parameters:

id - the id of the descriptor (ROIBasicMeasureDescriptorsPlugin.ID_VOLUME for instance) @see #getDescriptors()

See Also:

computeDescriptor(String, ROI, Sequence)

computeDescriptor

public static java.lang.Object computeDescriptor(java.util.Collection<ROIDescriptor> roiDescriptors,
                                 java.lang.String descriptorId,
                                 ROI roi,
                                 Sequence sequence)

Computes the specified descriptor from the input ROIDescriptor set on given ROI and returns the result (or null if the descriptor is not found).

Parameters:

roiDescriptors - the input ROIDescriptor set (see getDescriptors() method)

descriptorId - the id of the descriptor we want to compute (ROIBasicMeasureDescriptorsPlugin.ID_VOLUME for instance)

roi - the ROI on which the descriptor(s) should be computed

sequence - an optional sequence where the pixel size can be retrieved

Returns:

the computed descriptor or null if the descriptor if not found in the specified set

Throws:

java.lang.UnsupportedOperationException - if the type of the given ROI is not supported by this descriptor, or if sequence is null while the calculation requires it, or if the specified Z, T or C position are not supported by the descriptor

computeDescriptor

public static java.lang.Object computeDescriptor(java.lang.String descriptorId,
                                 ROI roi,
                                 Sequence sequence)

Computes the specified descriptor on given ROI and returns the result (or null if the descriptor is not found).

Parameters:

descriptorId - the id of the descriptor we want to compute (ROIBasicMeasureDescriptorsPlugin.ID_VOLUME for instance)

roi - the ROI on which the descriptor(s) should be computed

sequence - an optional sequence where the pixel size can be retrieved

Returns:

the computed descriptor or null if the descriptor if not found in the specified set

Throws:

java.lang.UnsupportedOperationException - if the type of the given ROI is not supported by this descriptor, or if sequence is null while the calculation requires it, or if the specified Z, T or C position are not supported by the descriptor

getId

public java.lang.String getId()

Returns the id of this descriptor.
By default it uses the descriptor's name but it can be overridden to be different.

getName

public java.lang.String getName()

Returns the name of this descriptor.
The name is used as title (column header) in the ROI panel so keep it short and self explanatory.

getDescription

public abstract java.lang.String getDescription()

Returns a single line description (used as tooltip) for this descriptor

getUnit

public java.lang.String getUnit(Sequence sequence)

Returns the unit of this descriptor (ex: "px", "mm", "µm2"...).
It can return an empty or null string (default implementation) if there is no specific unit attached to the descriptor.
Note that unit is concatenated to the name to build the title (column header) in the ROI panel.

Parameters:

sequence - the sequence on which we want to compute the descriptor (if required) to get access to the pixel size informations and return according unit

getType

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

Returns the type of result for this descriptor

See Also:

compute(ROI, Sequence)

separateChannel

public boolean separateChannel()

Returns true if this descriptor compute its result on Sequence data and *per channel* (as pixel intensity information).
By default it returns false, override this method if a descriptor require per channel computation.

See Also:

compute(ROI, Sequence)

needRecompute

public boolean needRecompute(SequenceEvent change)

Returns true if this descriptor need to be recomputed when the specified Sequence change event happen.
By default it returns false, override this method if a descriptor need a specific implementation.

See Also:

compute(ROI, Sequence)

needRecompute

public boolean needRecompute(ROIEvent change)

Returns true if this descriptor need to be recomputed when the specified ROI change event happen.
By default it returns true on ROI content change, override this method if a descriptor need a specific implementation.

See Also:

compute(ROI, Sequence)

compute

public abstract java.lang.Object compute(ROI roi,
                       Sequence sequence)
                                  throws java.lang.UnsupportedOperationException

Computes the descriptor on the specified ROI and return the result.

Parameters:

roi - the ROI on which the descriptor(s) should be computed

sequence - an optional sequence where the pixel informations can be retrieved (see separateChannel())

Returns:

the result of this descriptor computed from the specified parameters.

Throws:

java.lang.UnsupportedOperationException - if the type of the given ROI is not supported by this descriptor, or if sequence is null while the calculation requires it

equals

public boolean equals(java.lang.Object obj)

Overrides:

equals in class java.lang.Object

hashCode

public int hashCode()

Overrides:

hashCode in class java.lang.Object

toString

public java.lang.String toString()

Overrides:

toString in class java.lang.Object