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Bioimage Analysis
Active Contour
Commits
85635c59
Commit
85635c59
authored
Sep 16, 2020
by
Jean-Yves TINEVEZ
Browse files
Fix javadoc errors.
parent
b0005ce0
Changes
3
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src/main/java/plugins/adufour/activecontours/ActiveContour.java
View file @
85635c59
...
...
@@ -52,7 +52,7 @@ public abstract class ActiveContour extends Detection implements Iterable<Point3
}
@SuppressWarnings
(
"unchecked"
)
protected
ActiveContour
(
Var
<
Double
>
sampling
,
SlidingWindow
convergenceWindow
)
protected
ActiveContour
(
Var
<
Double
>
sampling
,
final
SlidingWindow
convergenceWindow
)
{
super
(
0
,
0
,
0
,
0
);
...
...
@@ -77,7 +77,7 @@ public abstract class ActiveContour extends Detection implements Iterable<Point3
return
name
;
}
public
void
setName
(
String
name
)
public
void
setName
(
final
String
name
)
{
this
.
name
=
name
;
}
...
...
@@ -91,7 +91,6 @@ public abstract class ActiveContour extends Detection implements Iterable<Point3
*
* @param p
* the point to add
* @return the index indicating where the point has been inserted in the internal list
*/
protected
abstract
void
addPoint
(
Point3d
p
);
...
...
@@ -183,8 +182,6 @@ public abstract class ActiveContour extends Detection implements Iterable<Point3
*
* @param imageData
* the data on which the average intensity should be computed
* @param channel
* the channel on which the average intensity should be computed
* @param mask
* the boolean mask where all contours (including the current one) have already been
* rasterised
...
...
@@ -193,51 +190,52 @@ public abstract class ActiveContour extends Detection implements Iterable<Point3
public
abstract
double
computeBackgroundIntensity
(
Sequence
imageData
,
BooleanMask3D
mask
);
/**
* Tests whether the given point is inside the contour, and if so returns
the penetration depth
*
of this point. <br>
*
* @param p
*
a point to test
* @return
* <ul>
* <li
/
>if <code>p</code> is outside: <code>0</code>
* <li
/
>if <code>p</code> is inside: the distance from <code>p</code>
to the contour
* edge
* </ul>
*/
* Tests whether the given point is inside the contour, and if so returns
* the penetration depth
of this point. <br>
*
* @param p
*
a point to test
* @return
* <ul>
* <li>if <code>p</code> is outside: <code>0</code>
* <li>if <code>p</code> is inside: the distance from <code>p</code>
*
to the contour
edge
* </ul>
*/
public
abstract
double
getDistanceToEdge
(
Point3d
p
);
/**
* @param order
*
the dimension (a.k.a. norm) to compute:
<br/>
*
<ul>
*
<li>0: number of points,</li>
*
<li>1: perimeter (2D) or surface area (3D),</li>
*
<li>2: surface (2D) or volume (3D)</li>
*
</ul>
* @return the dimension for the specified order
*/
* @param order
*
the dimension (a.k.a. norm) to compute:
*
<ul>
*
<li>0: number of points,</li>
*
<li>1: perimeter (2D) or surface area (3D),</li>
*
<li>2: surface (2D) or volume (3D)</li>
*
</ul>
* @return the dimension for the specified order
*/
public
abstract
double
getDimension
(
int
order
);
abstract
void
move
(
ROI
boundField
,
double
timeStep
);
/**
* Re-samples the Contour according to an 'average distance between points' criterion. This
* method ensures that the distance between two consecutive points is strictly comprised between
* a minimum value and a maximum value. In order to avoid oscillatory behavior, 'max' and 'min'
* should verify the following relations: min < 1, max > 1, 2*min <= max.
*
* @param minFactor
* the minimum distance between two points.
* @param maxFactor
* the maximum distance between two points.
*/
* Re-samples the Contour according to an 'average distance between points'
* criterion. This method ensures that the distance between two consecutive
* points is strictly comprised between a minimum value and a maximum value.
* In order to avoid oscillatory behavior, 'max' and 'min' should verify the
* following relations: min < 1, max > 1, 2*min <= max.
*
* @param minFactor
* the minimum distance between two points.
* @param maxFactor
* the maximum distance between two points.
*/
public
abstract
void
reSample
(
double
minFactor
,
double
maxFactor
)
throws
TopologyException
;
/**
* @return a ROI representing the contour
* @deprecated use {@link #toROI(ROIType)} instead
*/
* @return a ROI representing the contour
* @deprecated use {@link #toROI(ROIType
, Sequence
)} instead
*/
@Deprecated
public
abstract
ROI
toROI
();
...
...
@@ -262,19 +260,20 @@ public abstract class ActiveContour extends Detection implements Iterable<Point3
public
abstract
void
toSequence
(
Sequence
output
,
double
value
);
/**
* Updates the contour's meta-data (i.e. data that can be computed directly from the actual
* contour data, but stored locally for fast repetitive access). This includes:<br/>
* <ul>
* <li>bounding box</li>
* <li>bounding sphere</li>
* <li>contour normals</li>
* <li>center of mass</li>
* </ul>
*/
* Updates the contour's meta-data (i.e. data that can be computed directly
* from the actual contour data, but stored locally for fast repetitive
* access). This includes:
* <ul>
* <li>bounding box</li>
* <li>bounding sphere</li>
* <li>contour normals</li>
* <li>center of mass</li>
* </ul>
*/
protected
void
updateMetaData
()
{
// center of mass
Point3d
center
=
new
Point3d
();
final
Point3d
center
=
new
Point3d
();
// bounding sphere
double
radius
=
0
;
...
...
@@ -289,7 +288,7 @@ public abstract class ActiveContour extends Detection implements Iterable<Point3
// center calculation
double
nbPts
=
0
;
for
(
Point3d
p
:
this
)
for
(
final
Point3d
p
:
this
)
{
nbPts
++;
...
...
@@ -322,9 +321,9 @@ public abstract class ActiveContour extends Detection implements Iterable<Point3
boundingSphere
.
setCenter
(
center
);
// radius calculation
for
(
Point3d
p
:
this
)
for
(
final
Point3d
p
:
this
)
{
double
d
=
p
.
distanceSquared
(
center
);
final
double
d
=
p
.
distanceSquared
(
center
);
if
(
d
>
radius
)
radius
=
d
;
...
...
@@ -358,12 +357,12 @@ public abstract class ActiveContour extends Detection implements Iterable<Point3
return
lastConvergedFrame
;
}
public
void
setLastConvergedFrame
(
int
frame
)
public
void
setLastConvergedFrame
(
final
int
frame
)
{
lastConvergedFrame
=
frame
;
}
public
void
setDivisionSensitivity
(
Var
<
Double
>
divisionSensitivity
)
public
void
setDivisionSensitivity
(
final
Var
<
Double
>
divisionSensitivity
)
{
this
.
divisionSensitivity
=
divisionSensitivity
;
}
...
...
src/main/java/plugins/adufour/activecontours/ActiveContours.java
View file @
85635c59
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src/main/java/plugins/adufour/activecontours/Polygon2D.java
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85635c59
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