icy.roi

Class ROIUtil

java.lang.Object

icy.roi.ROIUtil

public class ROIUtil
extends java.lang.Object

ROI utilities class.

Author:

Stephane

Field Summary

Fields

Modifier and Type	Field and Description
static java.lang.String	MASK_SUFFIX
static java.lang.String	OBJECT_SUFFIX
static java.lang.String	PART_SUFFIX
static java.lang.String	SHAPE_SUFFIX
static java.lang.String	STACK_SUFFIX

Constructor Summary

Constructors

Constructor and Description
ROIUtil()

Method Summary

Methods

Modifier and Type	Method and Description
static ROI	adjustToSequence(ROI roi, Sequence source, Sequence destination) Create a copy of the specified ROI coming from source sequence adjusted to the destination sequence.
static ROI	adjustToSequence(ROI roi, Sequence source, Sequence destination, boolean translate, boolean scale) Create a copy of the specified ROI coming from source sequence adjusted to the destination sequence.
static ROI	adjustToSequence(ROI roi, Sequence source, Sequence destination, boolean translate, boolean scale, boolean ignoreErrorOnScale) Create a copy of the specified ROI coming from source sequence adjusted to the destination sequence.
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.util.Set<ROIDescriptor> roiDescriptors, java.lang.String descriptorId, ROI roi, Sequence sequence) Deprecated. Use ROIDescriptor.computeDescriptor(Collection, String, ROI, Sequence) instead
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).
static ROI2DEllipse	convertToEllipse(ROI roi, double radiusX, double radiusY) Converts the specified ROI to a 2D ellipse type ROI centered on the mass center of the input ROI.
static ROI	convertToMask(ROI roi) Converts the specified ROI to a boolean mask type ROI (ROI Area).
static ROI	convertToPoint(ROI roi) Converts the specified ROI to a ROI Point (ROI2DPoint or ROI3DPoint) representing the mass center of the input ROI.
static ROI2DRectangle	convertToRectangle(ROI roi, double width, double height) Converts the specified ROI to a 2D rectangle type ROI centered on the mass center of the input ROI.
static Sequence	convertToSequence(java.util.List<ROI> inputRois, int sizeX, int sizeY, int sizeC, int sizeZ, int sizeT, DataType dataType, boolean label) Convert a list of ROI into a binary / labeled Sequence.
static Sequence	convertToSequence(java.util.List<ROI> inputRois, Sequence sequence, boolean label) Convert a list of ROI into a binary / labeled Sequence.
static Sequence	convertToSequence(ROI inputRoi, Sequence sequence) Convert a single ROI into a binary / labeled Sequence.
static ROI	convertToShape(ROI roi, double maxDeviation) Converts the specified ROI to a shape type ROI (ROI Polygon or ROI Mesh).
static ROI	convertToStack(ROI2D roi, int zMin, int zMax) Converts the specified 2D ROI to 3D Stack ROI (ROI3DStack) by stacking it along the Z axis given zMin and zMax (inclusive) parameters.
static void	copyROIProperties(ROI source, ROI destination, boolean copyName) Copy properties (name, color...) from source ROI and apply it to destination ROI.
static ROI	get2XScaled(ROI roi, boolean scaleOnZ, boolean down) Create and returns a new ROI which is a 2x up/down scaled version of the input ROI.
static java.lang.String	getArea(Sequence sequence, ROI roi) Deprecated. Use ROIAreaDescriptor or computeDescriptor(String, ROI, Sequence) method instead.
static java.lang.String	getArea(Sequence sequence, ROI roi, int roundSignificant) Deprecated. Use ROIAreaDescriptor or computeDescriptor(String, ROI, Sequence) method instead.
static java.util.List<ROI>	getConnectedComponents(ROI roi) Returns connected component from specified ROI as a list of ROI (Area type).
static java.lang.String	getContourSize(Sequence sequence, double contourPoints, ROI roi, int dim, int roundSignificant) Deprecated. Use ROIContourDescriptor or computeDescriptor(String, ROI, Sequence) method instead.
static java.lang.String	getContourSize(Sequence sequence, ROI roi, int dim) Deprecated. Use ROIContourDescriptor or computeDescriptor(String, ROI, Sequence) method instead.
static java.lang.String	getContourSize(Sequence sequence, ROI roi, int dim, int roundSignificant) Deprecated. Use ROIContourDescriptor or computeDescriptor(String, ROI, Sequence) method instead.
static ROI	getDownscaled(ROI roi, boolean scaleOnZ) Create and returns a new ROI which is a 2x down scaled version of the input ROI.
static int	getEffectiveDimension(Rectangle5D bounds) Returns the effective ROI number of dimension needed for the specified bounds.
static ROI	getExclusiveUnion(java.util.List<? extends ROI> rois) Builds and returns a ROI corresponding to the exclusive union of the specified ROI list.
static ROI	getExclusiveUnion(ROI roi1, ROI roi2) Compute exclusive union of specified ROI and return result in a new ROI.
static IntensityInfo	getIntensityInfo(Sequence sequence, ROI roi) Deprecated. Use ROIIntensityDescriptorsPlugin or computeDescriptor(String, ROI, Sequence) method instead.
static IntensityInfo	getIntensityInfo(Sequence sequence, ROI roi, int z, int t, int c) Deprecated. Use ROIIntensityDescriptorsPlugin or computeDescriptor(String, ROI, Sequence) method instead.
static java.lang.String	getInteriorSize(Sequence sequence, double interiorPoints, ROI roi, int dim, int roundSignificant) Deprecated. Use ROIInteriorDescriptor or computeDescriptor(String, ROI, Sequence) method instead.
static java.lang.String	getInteriorSize(Sequence sequence, ROI roi, int dim) Deprecated. Use ROIInteriorDescriptor or computeDescriptor(String, ROI, Sequence) method instead.
static java.lang.String	getInteriorSize(Sequence sequence, ROI roi, int dim, int roundSignificant) Deprecated. Use ROIInteriorDescriptor or computeDescriptor(String, ROI, Sequence) method instead.
static ROI	getIntersection(java.util.List<? extends ROI> rois) Builds and returns a ROI corresponding to the intersection of the specified ROI list.
static ROI	getIntersection(ROI roi1, ROI roi2) Computes intersection of specified ROI and return result in a new ROI.
static Point5D	getMassCenter(ROI roi) Deprecated. Use ROIMassCenterDescriptorsPlugin or computeDescriptor(String, ROI, Sequence) method instead.
static java.awt.geom.Point2D	getMassCenter(ROI2D roi) Deprecated. Use ROIMassCenterDescriptorsPlugin or computeDescriptor(String, ROI, Sequence) method instead.
static Point3D	getMassCenter(ROI3D roi) Deprecated. Use ROIMassCenterDescriptorsPlugin or computeDescriptor(String, ROI, Sequence) method instead.
static Point4D	getMassCenter(ROI4D roi) Deprecated. Use ROIMassCenterDescriptorsPlugin or computeDescriptor(String, ROI, Sequence) method instead.
static Point5D	getMassCenter(ROI5D roi) Deprecated. Use ROIMassCenterDescriptorsPlugin or computeDescriptor(String, ROI, Sequence) method instead.
static double	getMaxIntensity(Sequence sequence, ROI roi) Deprecated. Use ROIMaxIntensityDescriptor or computeDescriptor(String, ROI, Sequence) method instead.
static double	getMaxIntensity(Sequence sequence, ROI roi, int z, int t, int c) Deprecated. Use ROIMaxIntensityDescriptor or computeDescriptor(String, ROI, Sequence) method instead.
static double	getMeanIntensity(Sequence sequence, ROI roi) Deprecated. Use ROIMeanIntensityDescriptor or computeDescriptor(String, ROI, Sequence) method instead.
static double	getMeanIntensity(Sequence sequence, ROI roi, int z, int t, int c) Deprecated. Use ROIMeanIntensityDescriptor or computeDescriptor(String, ROI, Sequence) method instead.
static double	getMinIntensity(Sequence sequence, ROI roi) Deprecated. Use ROIMinIntensityDescriptor or computeDescriptor(String, ROI, Sequence) method instead.
static double	getMinIntensity(Sequence sequence, ROI roi, int z, int t, int c) Deprecated. Use ROIMinIntensityDescriptor or computeDescriptor(String, ROI, Sequence) method instead.
static long	getNumPixel(Sequence sequence, ROI roi) Returns the number of sequence pixels contained in the specified ROI.
static long	getNumPixel(Sequence sequence, ROI roi, int z, int t, int c) Returns the number of sequence pixels contained in the specified ROI.
static java.lang.String	getPerimeter(Sequence sequence, ROI roi) Deprecated. Use ROIPerimeterDescriptor or computeDescriptor(String, ROI, Sequence) method instead.
static java.lang.String	getPerimeter(Sequence sequence, ROI roi, int roundSignificant) Deprecated. Use ROIPerimeterDescriptor or computeDescriptor(String, ROI, Sequence) method instead.
static java.util.Map<ROIDescriptor,PluginROIDescriptor>	getROIDescriptors() Returns all available ROI descriptors (see ROIDescriptor) and their attached plugin (see PluginROIDescriptor).
static double	getStandardDeviation(Sequence sequence, ROI roi) Deprecated. Use ROIStandardDeviationDescriptor or computeDescriptor(String, ROI, Sequence) method instead.
static double	getStandardDeviation(Sequence sequence, ROI roi, int z, int t, int c) Deprecated. Use ROIStandardDeviationDescriptor or computeDescriptor(String, ROI, Sequence) method instead.
static ROI	getSubtraction(ROI roi1, ROI roi2) Computes the subtraction of roi1 - roi2 and returns result in a new ROI.
static double	getSumIntensity(Sequence sequence, ROI roi) Deprecated. Use ROISumIntensityDescriptor or computeDescriptor(String, ROI, Sequence) method instead.
static double	getSumIntensity(Sequence sequence, ROI roi, int z, int t, int c) Deprecated. Use ROISumIntensityDescriptor or computeDescriptor(String, ROI, Sequence) method instead.
static java.lang.String	getSurfaceArea(Sequence sequence, ROI roi) Deprecated. Use ROISurfaceAreaDescriptor or computeDescriptor(String, ROI, Sequence) method instead.
static java.lang.String	getSurfaceArea(Sequence sequence, ROI roi, int roundSignificant) Deprecated. Use ROISurfaceAreaDescriptor or computeDescriptor(String, ROI, Sequence) method instead.
static ROI	getUnion(java.util.List<? extends ROI> rois) Builds and returns a ROI corresponding to the union of the specified ROI list.
static ROI	getUnion(ROI roi1, ROI roi2) Computes union of specified ROI and return result in a new ROI.
static Rectangle5D	getUnionBounds(ROI roi1, ROI roi2) Compute the resulting bounds for union operation between specified ROIs.
static ROI	getUpscaled(ROI roi, boolean scaleOnZ) Create and returns a new ROI which is a 2x up scaled version of the input ROI.
static java.lang.String	getVolume(Sequence sequence, ROI roi) Deprecated. Use ROIVolumeDescriptor or computeDescriptor(String, ROI, Sequence) method instead.
static java.lang.String	getVolume(Sequence sequence, ROI roi, int roundSignificant) Deprecated. Use ROIVolumeDescriptor or computeDescriptor(String, ROI, Sequence) method instead.
static ROI	merge(java.util.List<? extends ROI> rois, ShapeUtil.BooleanOperator operator) Merge the specified array of ROI with the given ShapeUtil.BooleanOperator.
static void	scale(ROI roi, double scale) Scale the given ROI by specified scale factor.
static void	scale(ROI roi, double scaleX, double scaleY) Scale (2D) the given ROI by specified X/Y factor.
static void	scale(ROI roi, double scaleX, double scaleY, double scaleZ) Scale (3D) the given ROI by specified X,Y,Z factors.
static java.util.List<ROI>	split(ROI roi, java.awt.geom.Line2D line) Cut the specified ROI with the given Line2D (extended to ROI bounds) and return the 2 resulting ROI in a list.
static ROI	subtract(ROI roi1, ROI roi2) Subtract the content of the roi2 from the roi1 and return the result as a new ROI.

Methods inherited from class java.lang.Object

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

Field Detail

STACK_SUFFIX

public static final java.lang.String STACK_SUFFIX

See Also:

Constant Field Values

MASK_SUFFIX

public static final java.lang.String MASK_SUFFIX

See Also:

Constant Field Values

SHAPE_SUFFIX

public static final java.lang.String SHAPE_SUFFIX

See Also:

Constant Field Values

OBJECT_SUFFIX

public static final java.lang.String OBJECT_SUFFIX

See Also:

Constant Field Values

PART_SUFFIX

public static final java.lang.String PART_SUFFIX

See Also:

Constant Field Values

Constructor Detail

ROIUtil

public ROIUtil()

Method Detail

getROIDescriptors

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

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.
This method is an alias of ROIDescriptor.getDescriptors()

See Also:

ROIDescriptor.compute(ROI, Sequence), PluginROIDescriptor.compute(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).
This method is an alias of ROIDescriptor.computeDescriptor(Collection, String, ROI, Sequence)

Parameters:

roiDescriptors - the input ROIDescriptor set (see getROIDescriptors() 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

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

Deprecated. Use ROIDescriptor.computeDescriptor(Collection, String, ROI, Sequence) instead

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).
This method is an alias of ROIDescriptor.computeDescriptor(String, ROI, Sequence)

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

getStandardDeviation

@Deprecated
public static double getStandardDeviation(Sequence sequence,
                                     ROI roi,
                                     int z,
                                     int t,
                                     int c)

Deprecated. Use ROIStandardDeviationDescriptor or computeDescriptor(String, ROI, Sequence) method instead.

getIntensityInfo

@Deprecated
public static IntensityInfo getIntensityInfo(Sequence sequence,
                                        ROI roi,
                                        int z,
                                        int t,
                                        int c)

Deprecated. Use ROIIntensityDescriptorsPlugin or computeDescriptor(String, ROI, Sequence) method instead.

getNumPixel

public static long getNumPixel(Sequence sequence,
               ROI roi,
               int z,
               int t,
               int c)

Returns the number of sequence pixels contained in the specified ROI.

Parameters:

sequence - The sequence we want to get the number of pixel.

roi - The ROI define the region where we want to compute the number of pixel.

z - The specific Z position (slice) where we want to compute the number of pixel or -1 to use the ROI Z dimension information.

t - The specific T position (frame) where we want to compute the number of pixel or -1 to use the ROI T dimension information.

c - The specific C position (channel) where we want to compute the number of pixel or -1 to use the ROI C dimension information.

getMinIntensity

@Deprecated
public static double getMinIntensity(Sequence sequence,
                                ROI roi,
                                int z,
                                int t,
                                int c)

Deprecated. Use ROIMinIntensityDescriptor or computeDescriptor(String, ROI, Sequence) method instead.

getMaxIntensity

@Deprecated
public static double getMaxIntensity(Sequence sequence,
                                ROI roi,
                                int z,
                                int t,
                                int c)

Deprecated. Use ROIMaxIntensityDescriptor or computeDescriptor(String, ROI, Sequence) method instead.

getMeanIntensity

@Deprecated
public static double getMeanIntensity(Sequence sequence,
                                 ROI roi,
                                 int z,
                                 int t,
                                 int c)

Deprecated. Use ROIMeanIntensityDescriptor or computeDescriptor(String, ROI, Sequence) method instead.

getSumIntensity

@Deprecated
public static double getSumIntensity(Sequence sequence,
                                ROI roi,
                                int z,
                                int t,
                                int c)

Deprecated. Use ROISumIntensityDescriptor or computeDescriptor(String, ROI, Sequence) method instead.

getStandardDeviation

@Deprecated
public static double getStandardDeviation(Sequence sequence,
                                     ROI roi)

Deprecated. Use ROIStandardDeviationDescriptor or computeDescriptor(String, ROI, Sequence) method instead.

getIntensityInfo

@Deprecated
public static IntensityInfo getIntensityInfo(Sequence sequence,
                                        ROI roi)

Deprecated. Use ROIIntensityDescriptorsPlugin or computeDescriptor(String, ROI, Sequence) method instead.

getNumPixel

public static long getNumPixel(Sequence sequence,
               ROI roi)

Returns the number of sequence pixels contained in the specified ROI.

getMinIntensity

@Deprecated
public static double getMinIntensity(Sequence sequence,
                                ROI roi)

Deprecated. Use ROIMinIntensityDescriptor or computeDescriptor(String, ROI, Sequence) method instead.

getMaxIntensity

@Deprecated
public static double getMaxIntensity(Sequence sequence,
                                ROI roi)

Deprecated. Use ROIMaxIntensityDescriptor or computeDescriptor(String, ROI, Sequence) method instead.

getMeanIntensity

@Deprecated
public static double getMeanIntensity(Sequence sequence,
                                 ROI roi)

Deprecated. Use ROIMeanIntensityDescriptor or computeDescriptor(String, ROI, Sequence) method instead.

getSumIntensity

@Deprecated
public static double getSumIntensity(Sequence sequence,
                                ROI roi)

Deprecated. Use ROISumIntensityDescriptor or computeDescriptor(String, ROI, Sequence) method instead.

getMassCenter

@Deprecated
public static Point5D getMassCenter(ROI roi)

Deprecated. Use ROIMassCenterDescriptorsPlugin or computeDescriptor(String, ROI, Sequence) method instead.

getMassCenter

@Deprecated
public static java.awt.geom.Point2D getMassCenter(ROI2D roi)

Deprecated. Use ROIMassCenterDescriptorsPlugin or computeDescriptor(String, ROI, Sequence) method instead.

getMassCenter

@Deprecated
public static Point3D getMassCenter(ROI3D roi)

Deprecated. Use ROIMassCenterDescriptorsPlugin or computeDescriptor(String, ROI, Sequence) method instead.

getMassCenter

@Deprecated
public static Point4D getMassCenter(ROI4D roi)

Deprecated. Use ROIMassCenterDescriptorsPlugin or computeDescriptor(String, ROI, Sequence) method instead.

getMassCenter

@Deprecated
public static Point5D getMassCenter(ROI5D roi)

Deprecated. Use ROIMassCenterDescriptorsPlugin or computeDescriptor(String, ROI, Sequence) method instead.

getContourSize

@Deprecated
public static java.lang.String getContourSize(Sequence sequence,
                                         double contourPoints,
                                         ROI roi,
                                         int dim,
                                         int roundSignificant)

Deprecated. Use ROIContourDescriptor or computeDescriptor(String, ROI, Sequence) method instead.

getContourSize

@Deprecated
public static java.lang.String getContourSize(Sequence sequence,
                                         ROI roi,
                                         int dim,
                                         int roundSignificant)

Deprecated. Use ROIContourDescriptor or computeDescriptor(String, ROI, Sequence) method instead.

getContourSize

@Deprecated
public static java.lang.String getContourSize(Sequence sequence,
                                         ROI roi,
                                         int dim)

Deprecated. Use ROIContourDescriptor or computeDescriptor(String, ROI, Sequence) method instead.

getInteriorSize

@Deprecated
public static java.lang.String getInteriorSize(Sequence sequence,
                                          double interiorPoints,
                                          ROI roi,
                                          int dim,
                                          int roundSignificant)

Deprecated. Use ROIInteriorDescriptor or computeDescriptor(String, ROI, Sequence) method instead.

getInteriorSize

@Deprecated
public static java.lang.String getInteriorSize(Sequence sequence,
                                          ROI roi,
                                          int dim,
                                          int roundSignificant)

Deprecated. Use ROIInteriorDescriptor or computeDescriptor(String, ROI, Sequence) method instead.

getInteriorSize

@Deprecated
public static java.lang.String getInteriorSize(Sequence sequence,
                                          ROI roi,
                                          int dim)

Deprecated. Use ROIInteriorDescriptor or computeDescriptor(String, ROI, Sequence) method instead.

getPerimeter

@Deprecated
public static java.lang.String getPerimeter(Sequence sequence,
                                       ROI roi,
                                       int roundSignificant)

Deprecated. Use ROIPerimeterDescriptor or computeDescriptor(String, ROI, Sequence) method instead.

getPerimeter

@Deprecated
public static java.lang.String getPerimeter(Sequence sequence,
                                       ROI roi)

Deprecated. Use ROIPerimeterDescriptor or computeDescriptor(String, ROI, Sequence) method instead.

getArea

@Deprecated
public static java.lang.String getArea(Sequence sequence,
                                  ROI roi,
                                  int roundSignificant)

Deprecated. Use ROIAreaDescriptor or computeDescriptor(String, ROI, Sequence) method instead.

getArea

@Deprecated
public static java.lang.String getArea(Sequence sequence,
                                  ROI roi)

Deprecated. Use ROIAreaDescriptor or computeDescriptor(String, ROI, Sequence) method instead.

getSurfaceArea

@Deprecated
public static java.lang.String getSurfaceArea(Sequence sequence,
                                         ROI roi,
                                         int roundSignificant)

Deprecated. Use ROISurfaceAreaDescriptor or computeDescriptor(String, ROI, Sequence) method instead.

getSurfaceArea

@Deprecated
public static java.lang.String getSurfaceArea(Sequence sequence,
                                         ROI roi)

Deprecated. Use ROISurfaceAreaDescriptor or computeDescriptor(String, ROI, Sequence) method instead.

getVolume

@Deprecated
public static java.lang.String getVolume(Sequence sequence,
                                    ROI roi,
                                    int roundSignificant)

Deprecated. Use ROIVolumeDescriptor or computeDescriptor(String, ROI, Sequence) method instead.

getVolume

@Deprecated
public static java.lang.String getVolume(Sequence sequence,
                                    ROI roi)

Deprecated. Use ROIVolumeDescriptor or computeDescriptor(String, ROI, Sequence) method instead.

getEffectiveDimension

public static int getEffectiveDimension(Rectangle5D bounds)

Returns the effective ROI number of dimension needed for the specified bounds.

getUnionBounds

public static Rectangle5D getUnionBounds(ROI roi1,
                         ROI roi2)
                                  throws java.lang.UnsupportedOperationException

Compute the resulting bounds for union operation between specified ROIs.
It throws an exception if the union operation cannot be done (incompatible dimension).

Throws:

java.lang.UnsupportedOperationException

getUnion

public static ROI getUnion(ROI roi1,
           ROI roi2)
                    throws java.lang.UnsupportedOperationException

Computes union of specified ROI and return result in a new ROI.

Throws:

java.lang.UnsupportedOperationException

getIntersection

public static ROI getIntersection(ROI roi1,
                  ROI roi2)
                           throws java.lang.UnsupportedOperationException

Computes intersection of specified ROI and return result in a new ROI.

Throws:

java.lang.UnsupportedOperationException

getExclusiveUnion

public static ROI getExclusiveUnion(ROI roi1,
                    ROI roi2)
                             throws java.lang.UnsupportedOperationException

Compute exclusive union of specified ROI and return result in a new ROI.

Throws:

java.lang.UnsupportedOperationException

getSubtraction

public static ROI getSubtraction(ROI roi1,
                 ROI roi2)
                          throws java.lang.UnsupportedOperationException

Computes the subtraction of roi1 - roi2 and returns result in a new ROI.

Throws:

java.lang.UnsupportedOperationException

merge

public static ROI merge(java.util.List<? extends ROI> rois,
        ShapeUtil.BooleanOperator operator)
                 throws java.lang.UnsupportedOperationException

Merge the specified array of ROI with the given ShapeUtil.BooleanOperator.

Parameters:

rois - ROIs we want to merge.

operator - ShapeUtil.BooleanOperator to apply.

Returns:

ROI representing the result of the merge operation.

Throws:

java.lang.UnsupportedOperationException

getUnion

public static ROI getUnion(java.util.List<? extends ROI> rois)
                    throws java.lang.UnsupportedOperationException

Builds and returns a ROI corresponding to the union of the specified ROI list.

Throws:

java.lang.UnsupportedOperationException

getExclusiveUnion

public static ROI getExclusiveUnion(java.util.List<? extends ROI> rois)
                             throws java.lang.UnsupportedOperationException

Builds and returns a ROI corresponding to the exclusive union of the specified ROI list.

Throws:

java.lang.UnsupportedOperationException

getIntersection

public static ROI getIntersection(java.util.List<? extends ROI> rois)
                           throws java.lang.UnsupportedOperationException

Builds and returns a ROI corresponding to the intersection of the specified ROI list.

Throws:

java.lang.UnsupportedOperationException

subtract

public static ROI subtract(ROI roi1,
           ROI roi2)
                    throws java.lang.UnsupportedOperationException

Subtract the content of the roi2 from the roi1 and return the result as a new ROI.
This is equivalent to: roi1.getSubtraction(roi2)

Returns:

ROI representing the result of subtraction.

Throws:

java.lang.UnsupportedOperationException

convertToPoint

public static ROI convertToPoint(ROI roi)

Converts the specified ROI to a ROI Point (ROI2DPoint or ROI3DPoint) representing the mass center of the input ROI.

Returns:

the ROI point representing the mass center of the input ROI.

convertToEllipse

public static ROI2DEllipse convertToEllipse(ROI roi,
                            double radiusX,
                            double radiusY)

Converts the specified ROI to a 2D ellipse type ROI centered on the mass center of the input ROI.

Returns:

the 2D ellipse ROI centered on the mass center of the input ROI.

convertToRectangle

public static ROI2DRectangle convertToRectangle(ROI roi,
                                double width,
                                double height)

Converts the specified ROI to a 2D rectangle type ROI centered on the mass center of the input ROI.

Returns:

the 2D rectangle ROI centered on the mass center of the input ROI.

convertToStack

public static ROI convertToStack(ROI2D roi,
                 int zMin,
                 int zMax)

Converts the specified 2D ROI to 3D Stack ROI (ROI3DStack) by stacking it along the Z axis given zMin and zMax (inclusive) parameters.

Returns:

the converted 3D stack ROI or null if the input ROI was null

convertToMask

public static ROI convertToMask(ROI roi)

Converts the specified ROI to a boolean mask type ROI (ROI Area).

Returns:

the ROI Area corresponding to the input ROI.
If the ROI is already of boolean mask type then it's directly returned without any conversion.

convertToShape

public static ROI convertToShape(ROI roi,
                 double maxDeviation)
                          throws java.lang.UnsupportedOperationException

Converts the specified ROI to a shape type ROI (ROI Polygon or ROI Mesh).

Parameters:

roi - the roi to convert to shape type ROI

maxDeviation - maximum allowed deviation/distance of resulting ROI polygon from the input ROI contour (in pixel). Use -1 for automatic maximum deviation calculation.

Returns:

the ROI Polygon or ROI Mesh corresponding to the input ROI.
If the ROI is already of shape type then it's directly returned without any conversion.

Throws:

java.lang.UnsupportedOperationException

getConnectedComponents

public static java.util.List<ROI> getConnectedComponents(ROI roi)
                                                  throws java.lang.UnsupportedOperationException

Returns connected component from specified ROI as a list of ROI (Area type).

Throws:

java.lang.UnsupportedOperationException

split

public static java.util.List<ROI> split(ROI roi,
                        java.awt.geom.Line2D line)

Cut the specified ROI with the given Line2D (extended to ROI bounds) and return the 2 resulting ROI in a list.
If the specified ROI cannot be cut by the given Line2D then null is returned.

convertToSequence

public static Sequence convertToSequence(java.util.List<ROI> inputRois,
                         int sizeX,
                         int sizeY,
                         int sizeC,
                         int sizeZ,
                         int sizeT,
                         DataType dataType,
                         boolean label)

Convert a list of ROI into a binary / labeled Sequence.

Parameters:

inputRois - list of ROI to convert

sizeX - the wanted size X of output Sequence, if set to 0 then Sequence size X is computed automatically from the global ROI bounds.

sizeY - the wanted size Y of output Sequence, if set to 0 then Sequence size Y is computed automatically from the global ROI bounds.

sizeC - the wanted size C of output Sequence, if set to 0 then Sequence size C is computed automatically from the global ROI bounds.

sizeZ - the wanted size Z of output Sequence, if set to 0 then Sequence size Z is computed automatically from the global ROI bounds.

sizeT - the wanted size T of output Sequence, if set to 0 then Sequence size T is computed automatically from the global ROI bounds.

dataType - the wanted dataType of output Sequence

label - if set to true then each ROI will be draw as a separate label (value) in the sequence starting from 1.

convertToSequence

public static Sequence convertToSequence(java.util.List<ROI> inputRois,
                         Sequence sequence,
                         boolean label)

Convert a list of ROI into a binary / labeled Sequence.

Parameters:

inputRois - list of ROI to convert

sequence - the sequence used to define the wanted sequence dimension in return.
If this field is null then the global ROI bounds will be used to define the Sequence dimension

label - if set to true then each ROI will be draw as a separate label (value) in the sequence starting from 1.

convertToSequence

public static Sequence convertToSequence(ROI inputRoi,
                         Sequence sequence)

Convert a single ROI into a binary / labeled Sequence.

Parameters:

inputRoi - ROI to convert

sequence - the sequence used to define the wanted sequence dimension in return.
If this field is null then the global ROI bounds will be used to define the Sequence dimension

scale

public static void scale(ROI roi,
         double scaleX,
         double scaleY,
         double scaleZ)
                  throws java.lang.UnsupportedOperationException

Scale (3D) the given ROI by specified X,Y,Z factors.
Only ROI2DShape and ROI3DShape are supported !

Parameters:

roi - input ROI we want to rescale

Throws:

java.lang.UnsupportedOperationException - if input ROI is not ROI2DShape or ROI3DShape (scaling supported only for these ROI)

scale

public static void scale(ROI roi,
         double scaleX,
         double scaleY)
                  throws java.lang.UnsupportedOperationException

Scale (2D) the given ROI by specified X/Y factor.
Only ROI2DShape and ROI3DShape are supported !

Parameters:

roi - input ROI we want to rescale

Throws:

java.lang.UnsupportedOperationException - if input ROI is not ROI2DShape or ROI3DShape (scaling supported only for these ROI)

scale

public static void scale(ROI roi,
         double scale)
                  throws java.lang.UnsupportedOperationException

Scale the given ROI by specified scale factor.
Only ROI2DShape and ROI3DShape are supported !

Parameters:

roi - input ROI we want to rescale

Throws:

java.lang.UnsupportedOperationException - if input ROI is not ROI2DShape or ROI3DShape (scaling supported only for these ROI)

get2XScaled

public static ROI get2XScaled(ROI roi,
              boolean scaleOnZ,
              boolean down)
                       throws java.lang.UnsupportedOperationException

Create and returns a new ROI which is a 2x up/down scaled version of the input ROI.
Note that the returned ROI can be ROI2DArea or ROI3DArea if original ROI format doesn't support 2X scale operation.

Parameters:

roi - input ROI we want to get the up scaled form

scaleOnZ - Set to true to scale as well on Z dimension (XY dimension only otherwise)

down - Set to true for down scaling and false for up scaling operation

Throws:

java.lang.UnsupportedOperationException - if input ROI is ROI4D or ROI5D (up scaling not supported for these ROI)

getUpscaled

public static ROI getUpscaled(ROI roi,
              boolean scaleOnZ)
                       throws java.lang.UnsupportedOperationException

Create and returns a new ROI which is a 2x up scaled version of the input ROI.
Note that the returned ROI can be ROI2DArea or ROI3DArea if original ROI format doesn't support up scale operation.

Parameters:

roi - input ROI we want to get the up scaled form

scaleOnZ - Set to true to scale as well on Z dimension (XY dimension only otherwise)

Throws:

java.lang.UnsupportedOperationException - if input ROI is ROI4D or ROI5D (up scaling not supported for these ROI)

getDownscaled

public static ROI getDownscaled(ROI roi,
                boolean scaleOnZ)
                         throws java.lang.UnsupportedOperationException

Create and returns a new ROI which is a 2x down scaled version of the input ROI.
Note that the returned ROI can be ROI2DArea or ROI3DArea if original ROI format doesn't support up scale operation.

Parameters:

roi - input ROI we want to get the up scaled form

scaleOnZ - Set to true to scale as well on Z dimension (XY dimension only otherwise)

Throws:

java.lang.UnsupportedOperationException - if input ROI is ROI4D or ROI5D (up scaling not supported for these ROI)

adjustToSequence

public static ROI adjustToSequence(ROI roi,
                   Sequence source,
                   Sequence destination,
                   boolean translate,
                   boolean scale,
                   boolean ignoreErrorOnScale)
                            throws java.lang.UnsupportedOperationException

Create a copy of the specified ROI coming from source sequence adjusted to the destination sequence.
The resulting ROI coordinates can be different if the Sequence.getPosition() are not identical on the 2 sequences.
The resulting ROI can be scaled if the Sequence.getPixelSize() are not identical on the 2 sequences
Note that the returned ROI can have a Boolean Mask format if we can't re-use original ROI format, also the scale operation may not be possible depending the original ROI format.

Parameters:

roi - input ROI we want to adjust

source - the source sequence where the ROI was initially generated (should contains valid origin information, see Sequence#getOriginXXX(} methods)

destination - the destination sequence where we want to copy the ROI (should contains valid origin information, see Sequence#getOriginXXX(} methods)

translate - if we allow the returned ROI to be translated compared to the original ROI

scale - if we allow the returned ROI to be scaled compared to the original ROI

ignoreErrorOnScale - ignore unsupported scaling operation, in which case the result ROI won't be correctly scaled

Returns:

adjusted ROI

Throws:

java.lang.UnsupportedOperationException - if input ROI is ROI4D or ROI5D while scaling is required (scaling not supported for these ROI) and ignoreErrorOnScale is set to FALSE

adjustToSequence

public static ROI adjustToSequence(ROI roi,
                   Sequence source,
                   Sequence destination,
                   boolean translate,
                   boolean scale)
                            throws java.lang.UnsupportedOperationException

Create a copy of the specified ROI coming from source sequence adjusted to the destination sequence.
The resulting ROI coordinates can be different if the Sequence.getPosition() are not identical on the 2 sequences.
The resulting ROI can be scaled if the Sequence.getPixelSize() are not identical on the 2 sequences
Note that the returned ROI can have a Boolean Mask format if we can't re-use original ROI format, also the scale operation may not be possible depending the original ROI format.

Parameters:

roi - input ROI we want to adjust

source - the source sequence where the ROI was initially generated (should contains valid origin information, see Sequence#getOriginXXX(} methods)

destination - the destination sequence where we want to copy the ROI (should contains valid origin information, see Sequence#getOriginXXX(} methods)

translate - if we allow the returned ROI to be translated compared to the original ROI

scale - if we allow the returned ROI to be scaled compared to the original ROI

Returns:

adjusted ROI

Throws:

java.lang.UnsupportedOperationException - if input ROI is ROI4D or ROI5D while scaling is required (scaling not supported for these ROI) and ignoreErrorOnScale is set to FALSE

adjustToSequence

public static ROI adjustToSequence(ROI roi,
                   Sequence source,
                   Sequence destination)
                            throws java.lang.UnsupportedOperationException

Create a copy of the specified ROI coming from source sequence adjusted to the destination sequence.
The resulting ROI coordinates can be different if the Sequence.getPosition() are not identical on the 2 sequences.
The resulting ROI can be scaled if the Sequence.getPixelSize() are not identical on the 2 sequences
Note that the returned ROI can have a Boolean Mask format if we can't re-use original ROI format, also the scale operation may not be possible depending the original ROI format.

Parameters:

roi - input ROI we want to adjust

source - the source sequence where the ROI was initially generated (should contains valid origin information, see Sequence#getOriginXXX(} methods)

destination - the destination sequence where we want to copy the ROI (should contains valid origin information, see Sequence#getOriginXXX(} methods)

Returns:

adjusted ROI

Throws:

java.lang.UnsupportedOperationException - if input ROI is ROI4D or ROI5D while scaling is required (scaling not supported for these ROI)

copyROIProperties

public static void copyROIProperties(ROI source,
                     ROI destination,
                     boolean copyName)

Copy properties (name, color...) from source ROI and apply it to destination ROI.