Package | Description |
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Contains base Icy canvas and related classes
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Contains all classes and components related to the Icy inspector
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Contains graphic components and objects for the main interface
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Contains specific graphic components related to menu actions
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Contains all Image related stuff as the Icy image data structure, ColorModel, ColorSpace, ColorMap, Image tools...
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All supported plugin interface to specialize plugin in a specific task (Canvas, ROI, file importer...)
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Contains all ROI (Region Of Interest) related classes and tools
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Contains Icy Sequence structure definition and associated objects / tools.
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Contains all 2D ROI classes included in the kernel
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Contains all 2D ROI plugin classes included in the kernel
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Contains all 3D ROI classes included in the kernel
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Contains all 4D ROI classes included in the kernel
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Contains all 5D ROI classes included in the kernel
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Modifier and Type | Method and Description |
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() |
Modifier and Type | Method and Description |
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( roi)
Find the layer corresponding to the specified ROI (use the ROI overlay internally).
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protected void |
( roi,
type)
sequence roi has changed
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Modifier and Type | Method and Description |
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() |
Modifier and Type | Method and Description |
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<> |
()
Get the selected ROI in the ROI control panel.
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(package private) <> |
()
Get the selected ROI in the ROI control panel
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<> |
()
Returns the visible ROI in the ROI control panel.
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(package private) <> |
()
Get the visible ROI in the ROI control panel
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Modifier and Type | Method and Description |
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( roi)
Returns the ROI informations for the specified ROI.
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(package private) int |
( roi)
Return index of specified ROI in the model
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Modifier and Type | Method and Description |
---|---|
protected void |
(<ROI> newSelected) |
Constructor and Description |
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( roi) |
Modifier and Type | Method and Description |
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( overlay) |
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( overlay) |
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( overlay)
Returns the ROI containing the specified overlay (if any)
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( painter)
Deprecated.
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( painter)
Deprecated.
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( painter)
Deprecated.
Use instead.
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Modifier and Type | Method and Description |
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<> |
() |
<> |
() |
<> |
()
Returns all active ROI
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Modifier and Type | Method and Description |
---|---|
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( roi) |
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( roi) |
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( roi)
Returns the first active sequence containing the specified ROI
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( roi)
Deprecated.
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( roi) |
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( roi)
Deprecated.
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( roi) |
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( roi) |
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( roi)
Returns first viewer for the sequence containing specified ROI
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<> |
( roi) |
<> |
( roi) |
<> |
( roi)
Returns all active sequence containing the specified ROI
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void |
( roi)
A ROI was just added to its first sequence
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void |
( roi)
A ROI was just removed from its last sequence
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Modifier and Type | Method and Description |
---|---|
static boolean |
( viewer,
roi) |
Constructor and Description |
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( image,
roi)
Deprecated.
Use instead.
You can use the method to
retrieve the boolean mask from the ROI.
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Modifier and Type | Method and Description |
---|---|
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()
Create and return a new ROI.
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( pt)
Create and return a new ROI for interactive mode.
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Modifier and Type | Class and Description |
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class |
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class |
3D ROI base class
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class |
4D ROI base class.
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class |
5D ROI base class.
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Modifier and Type | Method and Description |
---|---|
protected |
( roi,
op)
Compute the specified boolean operation with the specified
ROI and return result
in a new ROI . |
static |
( className)
Create a ROI from its class name or class name.
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static |
( className,
imagePoint)
Deprecated.
Use instead
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static |
( className,
imagePoint)
Create a ROI from its class name or class name (interactive mode).
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static |
( className,
seq,
imagePoint,
boolean creation)
Deprecated.
Use instead.
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static |
( node)
Create a ROI from a xml definition
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() |
static |
(<? extends ROI> rois)
Builds and returns a ROI corresponding to the exclusive union of the specified ROI list.
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( roi)
Compute exclusive union with specified
ROI and return result in a new
ROI . |
static |
(<? extends ROI> rois)
Builds and returns a ROI corresponding to the intersection of the specified ROI list.
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( roi)
Compute intersection with specified
ROI and return result in a new
ROI . |
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() |
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( roi)
Subtract the specified
ROI and return result in a new ROI . |
static |
(<? extends ROI> rois)
Builds and returns a ROI corresponding to the union of the specified ROI list.
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( roi)
Compute union with specified
ROI and return result in a new ROI . |
static |
(<? extends ROI> rois,
operator)
Merge the specified array of with the given .
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( roi,
op)
Compute the boolean operation with specified
ROI and return result in a new
ROI . |
static |
( roi1,
roi2)
Subtract the content of the roi2 from the roi1 and return the result as a new .
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Modifier and Type | Method and Description |
---|---|
static <> |
(<? extends ROI> rois,
<? extends > clazz)
Deprecated.
Use instead.
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static <> |
(<? extends ROI> rois,
<? extends > clazz)
Return ROI of specified type from the ROI list
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static <> |
([] rois,
<? extends > clazz)
Deprecated.
Use instead.
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static <> |
( node)
Deprecated.
Use instead.
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static <> |
( node)
Return a list of ROI from a XML node.
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Modifier and Type | Method and Description |
---|---|
int |
( roi1,
roi2) |
protected |
( roi,
op)
Compute the specified boolean operation with the specified
ROI and return result
in a new ROI . |
boolean |
( roi) |
boolean |
( roi) |
boolean |
( roi) |
boolean |
( roi) |
abstract boolean |
( roi)
Tests if the
ROI entirely contains the specified ROI . |
static |
( sequence,
roi)
Return area of the specified ROI.
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static |
( sequence,
roi,
int roundSignificant)
Return area of the specified ROI.
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static |
( sequence,
double contourPoints,
roi,
int dim,
int roundSignificant)
Returns the contour size for specified sequence and dimension from a given number of contour
points.
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static |
( sequence,
roi,
int dim)
Returns the ROI contour size for specified sequence and dimension.
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static |
( sequence,
roi,
int dim,
int roundSignificant)
Returns the ROI contour size for specified sequence and dimension.
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( roi)
Compute exclusive union with specified
ROI and return result in a new
ROI . |
static |
( sequence,
roi)
Returns the min, max, mean intensity for the specified sequence region.
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static |
( sequence,
roi,
int z,
int t,
int c)
Computes and returns the min, max, mean intensity for the specified sequence region.
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static |
( sequence,
double interiorPoints,
roi,
int dim,
int roundSignificant)
Returns the ROI interior size for specified sequence and dimension from a given number of
interior points.
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static |
( sequence,
roi,
int dim)
Returns the ROI interior size for specified sequence and dimension.
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static |
( sequence,
roi,
int dim,
int roundSignificant)
Returns the ROI interior size for specified sequence and dimension.
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( roi)
Compute intersection with specified
ROI and return result in a new
ROI . |
protected |
( roi,
boolean throwException)
Compute the resulting bounds for intersection operation with the specified ROI.
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static double |
( sequence,
roi)
Returns the maximum pixel intensity contained in the ROI of specified sequence.
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static double |
( sequence,
roi,
int z,
int t,
int c)
Returns the maximum pixel intensity contained in the ROI of specified sequence.
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static double |
( sequence,
roi)
Returns the mean pixel intensity contained in the ROI of specified sequence.
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static double |
( sequence,
roi,
int z,
int t,
int c)
Returns the mean pixel intensity contained in the ROI of specified sequence.
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static double |
( sequence,
roi)
Returns the minimum pixel intensity contained in the ROI of specified sequence.
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static double |
( sequence,
roi,
int z,
int t,
int c)
Returns the minimum pixel intensity contained in the ROI of specified sequence.
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static long |
( sequence,
roi)
Returns the number of pixel contained in the ROI of specified sequence.
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static long |
( sequence,
roi,
int z,
int t,
int c)
Returns the number of pixel contained in the ROI of specified sequence.
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static |
( sequence,
roi)
Return perimeter of the specified ROI with the correct unit.
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static |
( sequence,
roi,
int roundSignificant)
Return perimeter of the specified ROI with the correct unit.
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static [] |
([] rois)
Deprecated.
Use instead.
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static <> |
([] rois,
<? extends > clazz)
Deprecated.
Use instead.
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static double |
( sequence,
roi,
int z,
int t,
int c)
Computes and returns the standard deviation for the specified sequence region.
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( roi)
Subtract the specified
ROI and return result in a new ROI . |
static double |
( sequence,
roi)
Returns the sum of all pixel intensity contained in the ROI of specified sequence.
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static double |
( sequence,
roi,
int z,
int t,
int c)
Returns the sum of all pixel intensity contained in the ROI of specified sequence.
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static |
( sequence,
roi)
Return surface area of the specified ROI.
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static |
( sequence,
roi,
int roundSignificant)
Return surface area of the specified ROI.
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|
( roi)
Compute union with specified
ROI and return result in a new ROI . |
protected |
( roi,
boolean throwException)
Compute the resulting bounds for union operation with the specified ROI.
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static |
( sequence,
roi)
Return volume of the specified ROI.
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static |
( sequence,
roi,
int roundSignificant)
Return volume of the specified ROI.
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boolean |
( roi) |
boolean |
( roi) |
boolean |
( roi) |
boolean |
( roi) |
abstract boolean |
( roi)
Tests if the interior of the
ROI intersects the interior of a specified
ROI |
|
( roi,
op)
Compute the boolean operation with specified
ROI and return result in a new
ROI . |
static |
( roi1,
roi2)
Subtract the content of the roi2 from the roi1 and return the result as a new .
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Modifier and Type | Method and Description |
---|---|
static |
(<? extends ROI> rois)
Builds and returns a ROI corresponding to the exclusive union of the specified ROI list.
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static |
(<? extends ROI> rois)
Builds and returns a ROI corresponding to the intersection of the specified ROI list.
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static <> |
(<ROI> rois)
Deprecated.
Use instead.
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static <> |
(<ROI> rois)
Return ROI2D of ROI list.
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static <> |
(<ROI> rois)
Deprecated.
Use instead.
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static <> |
(<ROI> rois)
Return all 3D ROI from the ROI list
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static <> |
(<ROI> rois)
Deprecated.
Use instead.
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static <> |
(<ROI> rois)
Return all 4D ROI from the ROI list
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static <> |
(<ROI> rois)
Deprecated.
Use instead.
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static <> |
(<ROI> rois)
Return all 5D ROI from the ROI list
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static <> |
(<? extends ROI> rois,
<? extends > clazz)
Deprecated.
Use instead.
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static <> |
(<? extends ROI> rois,
<? extends > clazz)
Deprecated.
Use instead.
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static <> |
(<? extends ROI> rois,
<? extends > clazz)
Return ROI of specified type from the ROI list
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static <> |
(<? extends ROI> rois,
<? extends > clazz)
Return ROI of specified type from the ROI list
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static <> |
([] rois,
<? extends > clazz)
Deprecated.
Use instead.
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static |
(<? extends ROI> rois)
Builds and returns a ROI corresponding to the union of the specified ROI list.
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static |
(<? extends ROI> rois,
operator)
Merge the specified array of with the given .
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static void |
( node,
<> rois)
Set a list of ROI to a XML node.
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static void |
( node,
<> rois)
Deprecated.
Use instead
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Constructor and Description |
---|
( source,
type) |
( source,
type,
pointEventType,
point)
Deprecated.
Use constructor instead
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( source,
propertyName) |
Modifier and Type | Field and Description |
---|---|
protected |
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Modifier and Type | Field and Description |
---|---|
(package private) <> |
ROIs
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Modifier and Type | Method and Description |
---|---|
|
()
Returns the current focused ROI (null if no ROI focused)
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() |
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() |
|
()
Returns the first selected ROI found (null if no ROI selected)
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Modifier and Type | Method and Description |
---|---|
<> |
() |
<> |
() |
<> |
()
Returns all ROIs attached to this sequence
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<> |
(<? extends ROI> roiClass)
Returns ROIs of specified class attached to this sequence
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<> |
()
Returns all ROIs attached to this sequence (HashSet form)
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<> |
()
Returns all selected ROI
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Modifier and Type | Method and Description |
---|---|
boolean |
( roi)
Add the specified ROI to the sequence.
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boolean |
( roi,
boolean canUndo)
Add the specified ROI to the sequence.
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boolean |
( roi)
Returns true if the sequence contains the specified ROI
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static |
( source,
roi)
Creates a new sequence which is a sub part of the source sequence defined by the specified
.
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boolean |
( roi)
Remove the specified ROI from the sequence.
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boolean |
( roi,
boolean canUndo)
Remove the specified ROI from the sequence.
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boolean |
( roi)
Set the focused ROI
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boolean |
( roi)
Set the selected ROI (exclusive selection).
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boolean |
( roi,
boolean exclusive)
Deprecated.
Use instead.
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Modifier and Type | Method and Description |
---|---|
int |
(<? extends ROI> roiClass)
Returns the number of ROI of specified ROI class attached to the sequence.
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<> |
(<? extends ROI> roiClass)
Returns ROIs of specified class attached to this sequence
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boolean |
(<? extends ROI> roiClass)
Returns true if the sequence contains ROI of specified ROI class.
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void |
(<ROI> selected)
Deprecated.
Use instead.
|
void |
(<? extends ROI> selected)
Set selected ROI (unselected all others)
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Constructor and Description |
---|
( sequence,
roi)
Create a new SequenceData iterator to iterate data through the specified ROI.
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( sequence,
roi,
boolean inclusive)
Create a new SequenceData iterator to iterate data through the specified ROI.
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( sequence,
roi,
boolean inclusive,
int z,
int t,
int c)
Create a new SequenceData iterator to iterate data through the specified ROI.
|
( sequence,
source) |
( sequence,
source) |
Constructor and Description |
---|
( sequence,
<> source) |
( sequence,
<> source) |
Modifier and Type | Class and Description |
---|---|
class |
ROI Area type.
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class |
|
class |
ROI 2D Line.
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class |
ROI Path.
|
class |
ROI 2D Point class.
|
class |
ROI 2D polygon class.
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class |
|
class |
|
class |
Base class for rectangular shape ROI.
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class |
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Modifier and Type | Method and Description |
---|---|
protected |
( roi,
op) |
Modifier and Type | Method and Description |
---|---|
protected |
( roi,
op) |
boolean |
( roi) |
boolean |
( roi) |
Modifier and Type | Method and Description |
---|---|
|
() |
|
() |
|
() |
|
() |
|
() |
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() |
|
() |
|
( pt) |
|
( pt) |
|
( pt) |
|
( pt) |
|
( pt) |
|
( pt) |
|
( pt) |
Modifier and Type | Class and Description |
---|---|
class |
3D Area ROI.
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class |
<R extends >
Abstract class defining a generic 3D ROI as a stack of individual 2D ROI slices.
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Modifier and Type | Class and Description |
---|---|
class |
4D Area ROI.
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class |
<R extends >
Abstract class defining a generic 4D ROI as a stack of individual 3D ROI slices.
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Modifier and Type | Class and Description |
---|---|
class |
5D Area ROI.
|
class |
<R extends >
Abstract class defining a generic 5D ROI as a stack of individual 4D ROI slices.
|