From 34a1c3243889e01a5994d6cf70239a8242663c64 Mon Sep 17 00:00:00 2001
From: Thomas MUSSET <thomas.musset@pasteur.fr>
Date: Wed, 5 Apr 2023 18:28:32 +0200
Subject: [PATCH] update pom parent, add .DS_Store in gitignore, update some
classes
---
.gitignore | 3 +-
pom.xml | 15 +-
.../LabelExtractor$ConnectedComponent.class | Bin 748 -> 0 bytes
.../roi/LabelExtractor$ExtractionType.class | Bin 1885 -> 0 bytes
.../plugins/adufour/roi/LabelExtractor.java | 284 +++++++-----------
5 files changed, 117 insertions(+), 185 deletions(-)
delete mode 100644 src/main/java/plugins/adufour/roi/LabelExtractor$ConnectedComponent.class
delete mode 100644 src/main/java/plugins/adufour/roi/LabelExtractor$ExtractionType.class
diff --git a/.gitignore b/.gitignore
index 5abffee..b2f15ce 100644
--- a/.gitignore
+++ b/.gitignore
@@ -7,4 +7,5 @@ bin/
*.jar
.classpath
.project
-export.jardesc
\ No newline at end of file
+export.jardesc
+**/.DS_Store
\ No newline at end of file
diff --git a/pom.xml b/pom.xml
index 260c6d6..f39c844 100644
--- a/pom.xml
+++ b/pom.xml
@@ -6,12 +6,12 @@
<parent>
<groupId>org.bioimageanalysis.icy</groupId>
- <artifactId>parent-pom-plugin</artifactId>
- <version>1.0.8</version>
+ <artifactId>pom-icy</artifactId>
+ <version>2.2.0</version>
</parent>
<artifactId>label-extractor</artifactId>
- <version>1.5.1</version>
+ <version>1.5.2</version>
<packaging>jar</packaging>
@@ -23,11 +23,14 @@
<dependencies>
<dependency>
<groupId>org.bioimageanalysis.icy</groupId>
- <artifactId>blocks</artifactId>
- <version>5.3.0</version>
+ <artifactId>ezplug</artifactId>
+ </dependency>
+ <dependency>
+ <groupId>org.bioimageanalysis.icy</groupId>
+ <artifactId>protocols</artifactId>
</dependency>
</dependencies>
-
+
<repositories>
<repository>
<id>icy</id>
diff --git a/src/main/java/plugins/adufour/roi/LabelExtractor$ConnectedComponent.class b/src/main/java/plugins/adufour/roi/LabelExtractor$ConnectedComponent.class
deleted file mode 100644
index 2e92845d9f571e9292fe1a9f4c4de7ae0263956a..0000000000000000000000000000000000000000
GIT binary patch
literal 0
HcmV?d00001
literal 748
zcmbVJO>fgc5PcIT4RzckBv8Iu2&K?A2P`2W4j?Wml_CNhT1Dz{<1E3&u_Jq3@lOzN
zMdHE*iGsv|D-u5n@z#kDhyxM_@0*<&zc=&t`;RYQ0o=k?6(zy#S(H!0IP=vwf12c}
zpC+L{P$L~Zcwtf%m?YioC2_0+qsP5uI!j_5n<~nJ=8-y9ex%}w|73K;27wz+)kF_f
zlxu<P3Tj5B6Kx7YX8MB0JoAf6aA)veGu#y{-3#N;+!s`~cl$d-LAjTVwF?Ig4>dFe
z&i2l58G@FF3YKhi#zPgSIL9E2_2Yax(&>R3MVz-aNCFiNRT|p+B3U-i!i)mP^PMV@
zwMJ0qQU|}UMxnl?U-z&K*JX6Y!$n*Ytn3>VJb$ES3r2UJHV1kyw3_Wdt-fh36?lCb
zp7tV@Wjd?kx?tnq7IA^U9||2#;_$s4G_3=SVD~SOgAz;pYVg>%!sw8lWn!cI8TIbg
z2~Ky{Ptg8QG@j+zD#|Z;zT&2@QO6ssGT$j=8aP*wk^tu^Czc8qC}@YE9}Ag>L|a?!
ze#F{0xP<n*0@gm^@_SYsShYFB+d{#P$Uhbe9mW-u>U+WsuJTgC2CfmU_kvB_fcq1b
C!=F$9
diff --git a/src/main/java/plugins/adufour/roi/LabelExtractor$ExtractionType.class b/src/main/java/plugins/adufour/roi/LabelExtractor$ExtractionType.class
deleted file mode 100644
index 77d8b2abb567ce58c1be04fdcc56c5fbc6efcd4d..0000000000000000000000000000000000000000
GIT binary patch
literal 0
HcmV?d00001
literal 1885
zcmbVMYg5}+5Ir}tEn88E1C0rgwkb8lk0cIxkhXRSMi}ZKOd5e(Pd+fRQHU}^^5~J)
z|EeW3hH0jme$J2Tbg!%gLtrxDgQdIH**$0X?(Vz){(cMKE?OckFwAwWVAr(0lD-o>
zcLKNMI%Y}L+lE#9!*}(L@3`6MWIFa{uWN{iF^s&_U+E=Fw|7f5JJ@3wuQpoSYIUim
zZa1~<rK+;F`gCKfvCME!{cMUd!_}&)4&rGi1CD4<YD#^jt_;32T&y*=*0as3x>eH{
z?ms&hVY1S(OxyGq7=&ED$q-YV9V3aj1ctPX%NS)yR3b<wryf;6^Ig;4E!XqS6k)%V
z5l12kksISOL~bOxF)1U71V3Gqk%Gi<Ni}Vw5$v@McT;a$2E(Z8babn!yC%28KP3oA
zlOF$t=`kdIXTV2Hx%|f}I65oiTTF|XB>^X8E(NBwW4ID>D2T{YZYL2kinz&;@`AP(
zX2y`o)$6Bn<#1a@33nL8SGpA#8_yYLhikLZera_4@~O@<xXbH$kKxL&OH|H$lWTmy
z)y#9mSpvS7@dKu*3w%d)em7i2_YCe?mQle^B+NCsmfoS-W^#&hhLA@x7Ez@O*1KK9
z-eI_Pnxc=Y9Tl@IVFp>cB3s`J@9<<vsi6~Ledq$`bNTahsDz*KSVaB!h4nn&*psma
zl`c$oUA@<Fx;=)%u>9x_>O=D1|3y8^usRHWU;T3o5pTT>-VRR~9t_7+EZy_UL-Zd=
zjta%s2$f0FXbE+U6_XFc*zrYlo1-aD&D^zhKX3_A8w$!JRL&uLfoSErZBy%TorWjk
zSBB|NZ!KDb$5-Rx9L=^s+cma0!IuC)Z<_z`O`{K_C;8wLB2KH|B4omUK~@hjdIHrq
zV6D*+;Q*IjV=OeT#6lwz8du|?F_HL(aKb*uv{q~%8LbuH$AtD8Q-4vA3;2qjUlTE3
z^AhHX;vvRS#w1Nd7LRZPcj!Au@*i!sNX8tA=kmou@!A2tISQ5_03s)@nIO2%^Pw|s
zn#jFFS@Dp?!U4Wh-(aRy6k>hcIK-_3%oXW)zmJFM?ez6Ne(YnRkEK5eKF}+LuFDjn
z7HZ23LPa!j%tFC35vAz+N<=tMXs$Q2kEzz0P<Y#_@WQMMQ-@f+c@%pfpMA(VMLoJ6
n#V8ODPe>YNg+ny{1v}eMz%QZRr_jRpCbqaI`7<=}+v3Fk_msv!
diff --git a/src/main/java/plugins/adufour/roi/LabelExtractor.java b/src/main/java/plugins/adufour/roi/LabelExtractor.java
index f26e8c4..e9edd05 100644
--- a/src/main/java/plugins/adufour/roi/LabelExtractor.java
+++ b/src/main/java/plugins/adufour/roi/LabelExtractor.java
@@ -25,14 +25,13 @@ import plugins.kernel.roi.roi3d.ROI3DArea;
* Toolbox to extract regions of interest (ROI) from a labeled image or sequence based on its
* connected components.<br>
* This toolbox supersedes the connected components toolbox
- *
+ *
* @author Alexandre Dufour
*/
-public class LabelExtractor extends EzPlug implements Block, EzStoppable
-{
+public class LabelExtractor extends EzPlug implements Block, EzStoppable {
EzVarSequence inSeq = new EzVarSequence("Labeled sequence");
- EzVarEnum<ExtractionType> type = new EzVarEnum<ExtractionType>("Extract", ExtractionType.values());
+ EzVarEnum<ExtractionType> type = new EzVarEnum<>("Extract", ExtractionType.values());
EzVarDouble value = new EzVarDouble("Value");
@@ -42,11 +41,10 @@ public class LabelExtractor extends EzPlug implements Block, EzStoppable
/**
* List of extraction methods suitable for the "ROI Extractor" toolbox
- *
+ *
* @author Alexandre Dufour
*/
- public enum ExtractionType
- {
+ public enum ExtractionType {
/**
* Extract all connected components with a value that is different from the background.<br>
* NB: Touching components with different labels will be <u>fused together</u>
@@ -63,40 +61,34 @@ public class LabelExtractor extends EzPlug implements Block, EzStoppable
SPECIFIC_LABEL;
@Override
- public String toString()
- {
+ public String toString() {
String name = super.toString();
- return name.substring(0, 1) + name.substring(1).toLowerCase().replace('_', ' ');
+ return name.charAt(0) + name.substring(1).toLowerCase().replace('_', ' ');
}
}
@Override
- public void declareInput(VarList inputMap)
- {
+ public void declareInput(VarList inputMap) {
inputMap.add("input sequence", inSeq.getVariable());
inputMap.add("extract mode", type.getVariable());
inputMap.add("value", value.getVariable());
}
@Override
- public void declareOutput(VarList outputMap)
- {
+ public void declareOutput(VarList outputMap) {
outputMap.add("ROI", outROI);
}
@Override
- public void clean()
- {
+ public void clean() {
}
@Override
- protected void execute()
- {
+ protected void execute() {
List<ROI> rois = extractLabels(inSeq.getValue(true), type.getValue(), value.getValue());
- if (getUI() != null)
- {
+ if (getUI() != null) {
Sequence outputSequence = outSeq.getValue(true);
outputSequence.beginUpdate();
@@ -104,15 +96,13 @@ public class LabelExtractor extends EzPlug implements Block, EzStoppable
outputSequence.addROI(roi);
outputSequence.endUpdate();
}
- else
- {
+ else {
outROI.setValue(rois.toArray(new ROI[rois.size()]));
}
}
@Override
- protected void initialize()
- {
+ protected void initialize() {
addEzComponent(inSeq);
addEzComponent(type);
addEzComponent(value);
@@ -122,11 +112,10 @@ public class LabelExtractor extends EzPlug implements Block, EzStoppable
/**
* A temporary component structure used during the extraction process. Many such components may
* be extracted from the sequence, and some are fused into the final extracted ROI
- *
+ *
* @author Alexandre Dufour
*/
- private static class ConnectedComponent
- {
+ private static class ConnectedComponent {
final double imageValue;
/**
@@ -142,25 +131,19 @@ public class LabelExtractor extends EzPlug implements Block, EzStoppable
/**
* Creates a new label with the given value. If no parent is set to this label, the given
* value will be the final one
- *
- * @param value
- * the pixel value
- * @param label
- * the label value
+ *
+ * @param value the pixel value
+ * @param label the label value
*/
- ConnectedComponent(double value, int label)
- {
+ ConnectedComponent(double value, int label) {
this.imageValue = value;
this.targetLabel = label;
}
/**
* Retrieves the final object label (recursively)
- *
- * @return
*/
- int getTargetLabel()
- {
+ int getTargetLabel() {
return targetComponent == null ? targetLabel : targetComponent.getTargetLabel();
}
}
@@ -170,36 +153,30 @@ public class LabelExtractor extends EzPlug implements Block, EzStoppable
* considered in 2D, and 26-connectivity in 3D). The algorithm uses a fast two-pass image
* sweeping technique that builds a list of intermediate connected components which are
* eventually fused according to their connectivity.
- *
- * @param sequence
- * the sequence to extract connected components from
- * @param whatToExtract
- * the type of extraction to conduct (see the {@link ExtractionType} enumeration for
- * available options
- * @param value
- * this value is interpreted differently depending on the <code>whatToExtract</code>
- * parameter:<br>
- * <ul>
- * <li>{@link ExtractionType#ALL_LABELS_VS_BACKGROUND}: the value is that of the
- * background</li>
- * <li>{@link ExtractionType#ANY_LABEL_VS_BACKGROUND}: the value is that of the
- * background</li>
- * <li>{@link ExtractionType#SPECIFIC_LABEL}: the value is that of the structures to
- * extract</li>
- * </ul>
+ *
+ * @param sequence the sequence to extract connected components from
+ * @param whatToExtract the type of extraction to conduct (see the {@link ExtractionType} enumeration for
+ * available options
+ * @param value this value is interpreted differently depending on the <code>whatToExtract</code>
+ * parameter:<br>
+ * <ul>
+ * <li>{@link ExtractionType#ALL_LABELS_VS_BACKGROUND}: the value is that of the
+ * background</li>
+ * <li>{@link ExtractionType#ANY_LABEL_VS_BACKGROUND}: the value is that of the
+ * background</li>
+ * <li>{@link ExtractionType#SPECIFIC_LABEL}: the value is that of the structures to
+ * extract</li>
+ * </ul>
* @return List of ROI
*/
- public static List<ROI> extractLabels(Sequence sequence, ExtractionType whatToExtract, double value)
- {
- ArrayList<ROI> roi = new ArrayList<ROI>();
+ public static List<ROI> extractLabels(Sequence sequence, ExtractionType whatToExtract, double value) {
+ ArrayList<ROI> roi = new ArrayList<>();
int objID = 1;
for (int t = 0; t < sequence.getSizeT(); t++)
- for (int c = 0; c < sequence.getSizeC(); c++)
- {
- for (ROI label : extractLabels(sequence, t, c, whatToExtract, value))
- {
+ for (int c = 0; c < sequence.getSizeC(); c++) {
+ for (ROI label : extractLabels(sequence, t, c, whatToExtract, value)) {
// rename each ROI, but replace the ID
String shortName = label.getName().substring(label.getName().indexOf(" ("));
label.setName("Object #" + objID++ + shortName);
@@ -216,31 +193,25 @@ public class LabelExtractor extends EzPlug implements Block, EzStoppable
* technique that builds a list of intermediate connected components which are eventually fused
* according to their connectivity.<br>
* NB: in 3D, the algorithm caches some intermediate buffers to disk to save RAM
- *
- * @param sequence
- * the sequence to extract connected components from
- * @param t
- * a specific time point where components should be extracted
- * @param c
- * a specific channel where components should be extracted
- * @param whatToExtract
- * the type of extraction to conduct (see the {@link ExtractionType} enumeration for
- * available options
- * @param value
- * this value is interpreted differently depending on the <code>whatToExtract</code>
- * parameter:<br>
- * <ul>
- * <li>{@link ExtractionType#ALL_LABELS_VS_BACKGROUND}: the value is that of the
- * background</li>
- * <li>{@link ExtractionType#ANY_LABEL_VS_BACKGROUND}: the value is that of the
- * background</li>
- * <li>{@link ExtractionType#SPECIFIC_LABEL}: the value is that of the structures to
- * extract</li>
- * </ul>
+ *
+ * @param sequence the sequence to extract connected components from
+ * @param t a specific time point where components should be extracted
+ * @param c a specific channel where components should be extracted
+ * @param whatToExtract the type of extraction to conduct (see the {@link ExtractionType} enumeration for
+ * available options
+ * @param value this value is interpreted differently depending on the <code>whatToExtract</code>
+ * parameter:<br>
+ * <ul>
+ * <li>{@link ExtractionType#ALL_LABELS_VS_BACKGROUND}: the value is that of the
+ * background</li>
+ * <li>{@link ExtractionType#ANY_LABEL_VS_BACKGROUND}: the value is that of the
+ * background</li>
+ * <li>{@link ExtractionType#SPECIFIC_LABEL}: the value is that of the structures to
+ * extract</li>
+ * </ul>
* @return List of ROI
*/
- public static List<ROI> extractLabels(Sequence sequence, int t, int c, ExtractionType whatToExtract, double value)
- {
+ public static List<ROI> extractLabels(Sequence sequence, int t, int c, ExtractionType whatToExtract, double value) {
int width = sequence.getSizeX();
int height = sequence.getSizeY();
int slice = width * height;
@@ -248,8 +219,8 @@ public class LabelExtractor extends EzPlug implements Block, EzStoppable
boolean is3D = depth > 1;
DataType dataType = sequence.getDataType_();
- final Map<Integer, ConnectedComponent> ccs = new HashMap<Integer, LabelExtractor.ConnectedComponent>();
- final Map<Integer, ROI> roiMap = new HashMap<Integer, ROI>();
+ final Map<Integer, ConnectedComponent> ccs = new HashMap<>();
+ final Map<Integer, ROI> roiMap = new HashMap<>();
int[] neighborLabels = new int[13];
int nbNeighbors = 0;
@@ -265,19 +236,15 @@ public class LabelExtractor extends EzPlug implements Block, EzStoppable
// first image pass: naive labeling with simple backward neighborhood
int highestKnownLabel = 0;
- for (int z = 0; z < depth; z++)
- {
+ for (int z = 0; z < depth; z++) {
int[] _labelsHere;
- try
- {
+ try {
_labelsHere = new int[slice];
}
- catch (OutOfMemoryError error)
- {
+ catch (OutOfMemoryError error) {
// not enough memory --> pass in virtual mode
- if (!virtual)
- {
+ if (!virtual) {
labelSequence.setVolatile(true);
virtual = true;
@@ -292,13 +259,11 @@ public class LabelExtractor extends EzPlug implements Block, EzStoppable
Object inputData = sequence.getDataXY(t, z, c);
- for (int y = 0, inOffset = 0; y < height; y++)
- {
+ for (int y = 0, inOffset = 0; y < height; y++) {
if (Thread.currentThread().isInterrupted())
- return new ArrayList<ROI>();
+ return new ArrayList<>();
- for (int x = 0; x < width; x++, inOffset++)
- {
+ for (int x = 0; x < width; x++, inOffset++) {
final double currentImageValue = Array1DUtil.getValue(inputData, inOffset, dataType);
final boolean pixelEqualsUserValue = (currentImageValue == value);
@@ -322,20 +287,16 @@ public class LabelExtractor extends EzPlug implements Block, EzStoppable
// n = valid neighbor
// . = other neighbor
- if (z == 0)
- {
- if (y == 0)
- {
- if (x == 0)
- {
+ if (z == 0) {
+ if (y == 0) {
+ if (x == 0) {
// e e e
// e x .
// e . .
// do nothing
}
- else
- {
+ else {
// e e e
// n x .
// . . .
@@ -344,12 +305,10 @@ public class LabelExtractor extends EzPlug implements Block, EzStoppable
nbNeighbors = 1;
}
}
- else
- {
+ else {
int north = inOffset - width;
- if (x == 0)
- {
+ if (x == 0) {
// e n n
// e x .
// e . .
@@ -358,8 +317,7 @@ public class LabelExtractor extends EzPlug implements Block, EzStoppable
neighborLabels[1] = _labelsHere[north + 1];
nbNeighbors = 2;
}
- else if (x == width - 1)
- {
+ else if (x == width - 1) {
// n n e
// n x e
// . . e
@@ -369,8 +327,7 @@ public class LabelExtractor extends EzPlug implements Block, EzStoppable
neighborLabels[2] = _labelsHere[inOffset - 1];
nbNeighbors = 3;
}
- else
- {
+ else {
// n n n
// n x .
// . . .
@@ -383,14 +340,11 @@ public class LabelExtractor extends EzPlug implements Block, EzStoppable
}
}
}
- else
- {
- if (y == 0)
- {
+ else {
+ if (y == 0) {
int south = inOffset + width;
- if (x == 0)
- {
+ if (x == 0) {
// e e e | e e e
// e n n | e x .
// e n n | e . .
@@ -401,8 +355,7 @@ public class LabelExtractor extends EzPlug implements Block, EzStoppable
neighborLabels[3] = _labelsAbove[south + 1];
nbNeighbors = 4;
}
- else if (x == width - 1)
- {
+ else if (x == width - 1) {
// e e e | e e e
// n n e | n x e
// n n e | . . e
@@ -414,8 +367,7 @@ public class LabelExtractor extends EzPlug implements Block, EzStoppable
neighborLabels[4] = _labelsHere[inOffset - 1];
nbNeighbors = 5;
}
- else
- {
+ else {
// e e e | e e e
// n n n | n x .
// n n n | . . .
@@ -430,12 +382,10 @@ public class LabelExtractor extends EzPlug implements Block, EzStoppable
nbNeighbors = 7;
}
}
- else if (y == height - 1)
- {
+ else if (y == height - 1) {
int north = inOffset - width;
- if (x == 0)
- {
+ if (x == 0) {
// e n n | e n n
// e n n | e x .
// e e e | e e e
@@ -448,8 +398,7 @@ public class LabelExtractor extends EzPlug implements Block, EzStoppable
neighborLabels[5] = _labelsHere[north + 1];
nbNeighbors = 6;
}
- else if (x == width - 1)
- {
+ else if (x == width - 1) {
// n n e | n n e
// n n e | n x e
// e e e | e e e
@@ -463,8 +412,7 @@ public class LabelExtractor extends EzPlug implements Block, EzStoppable
neighborLabels[6] = _labelsHere[inOffset - 1];
nbNeighbors = 7;
}
- else
- {
+ else {
// n n n | n n n
// n n n | n x .
// e e e | e e e
@@ -482,13 +430,11 @@ public class LabelExtractor extends EzPlug implements Block, EzStoppable
nbNeighbors = 10;
}
}
- else
- {
+ else {
int north = inOffset - width;
int south = inOffset + width;
- if (x == 0)
- {
+ if (x == 0) {
// e n n | e n n
// e n n | e x .
// e n n | e . .
@@ -503,8 +449,7 @@ public class LabelExtractor extends EzPlug implements Block, EzStoppable
neighborLabels[7] = _labelsHere[north + 1];
nbNeighbors = 8;
}
- else if (x == width - 1)
- {
+ else if (x == width - 1) {
int northwest = north - 1;
int west = inOffset - 1;
@@ -523,8 +468,7 @@ public class LabelExtractor extends EzPlug implements Block, EzStoppable
neighborLabels[8] = _labelsHere[west];
nbNeighbors = 9;
}
- else
- {
+ else {
int northwest = north - 1;
int west = inOffset - 1;
int northeast = north + 1;
@@ -561,8 +505,7 @@ public class LabelExtractor extends EzPlug implements Block, EzStoppable
int currentLabel = Integer.MAX_VALUE;
- for (int i = 0; i < nbNeighbors; i++)
- {
+ for (int i = 0; i < nbNeighbors; i++) {
int neighborLabel = neighborLabels[i];
// "zero" neighbors belong to the background...
@@ -575,14 +518,12 @@ public class LabelExtractor extends EzPlug implements Block, EzStoppable
// here, the neighbor label is valid
// => check if it is lower
- if (neighborLabel < currentLabel)
- {
+ if (neighborLabel < currentLabel) {
currentLabel = neighborLabel;
}
}
- if (currentLabel == Integer.MAX_VALUE)
- {
+ if (currentLabel == Integer.MAX_VALUE) {
// currentLabel didn't change
// => there is no lower neighbor
// => register a new connected component
@@ -590,8 +531,7 @@ public class LabelExtractor extends EzPlug implements Block, EzStoppable
currentLabel = highestKnownLabel;
ccs.put(currentLabel, new ConnectedComponent(currentImageValue, currentLabel));
}
- else
- {
+ else {
// currentLabel has been modified
// -> browse the neighborhood again
// --> fuse high labels with low labels
@@ -599,8 +539,7 @@ public class LabelExtractor extends EzPlug implements Block, EzStoppable
ConnectedComponent currentCC = ccs.get(currentLabel);
int currentTargetLabel = currentCC.getTargetLabel();
- for (int i = 0; i < nbNeighbors; i++)
- {
+ for (int i = 0; i < nbNeighbors; i++) {
int neighborLabel = neighborLabels[i];
if (neighborLabel == 0)
@@ -617,12 +556,10 @@ public class LabelExtractor extends EzPlug implements Block, EzStoppable
continue;
// fuse the highest with the lowest
- if (neighborTargetLabel > currentTargetLabel)
- {
+ if (neighborTargetLabel > currentTargetLabel) {
ccs.get(neighborTargetLabel).targetComponent = ccs.get(currentTargetLabel);
}
- else
- {
+ else {
ccs.get(currentTargetLabel).targetComponent = ccs.get(neighborTargetLabel);
}
}
@@ -655,7 +592,7 @@ public class LabelExtractor extends EzPlug implements Block, EzStoppable
// (though might not be unique within a given component)
if (Thread.currentThread().isInterrupted())
- return new ArrayList<ROI>();
+ return new ArrayList<>();
// fusion strategy: fuse higher labels with lower ones
// "highestKnownLabel" holds the highest known label
@@ -663,13 +600,11 @@ public class LabelExtractor extends EzPlug implements Block, EzStoppable
int finalLabel = 0;
- for (int currentLabel = highestKnownLabel; currentLabel > 0; currentLabel--)
- {
+ for (int currentLabel = highestKnownLabel; currentLabel > 0; currentLabel--) {
ConnectedComponent currentCC = ccs.get(currentLabel);
// if the target label is higher than or equal to the current label
- if (currentCC.targetLabel >= currentLabel)
- {
+ if (currentCC.targetLabel >= currentLabel) {
// label has same labelValue and targetLabelValue
// -> it cannot be fused to anything
// -> this is a terminal label
@@ -678,8 +613,7 @@ public class LabelExtractor extends EzPlug implements Block, EzStoppable
finalLabel++;
currentCC.targetLabel = finalLabel;
}
- else
- {
+ else {
// the current label should be fused to targetLabel
currentCC.targetComponent = ccs.get(currentCC.targetLabel);
}
@@ -687,18 +621,16 @@ public class LabelExtractor extends EzPlug implements Block, EzStoppable
// 3) second image pass: replace all labels by their final values
- finalPass: for (int z = 0; z < depth; z++)
- {
+ finalPass:
+ for (int z = 0; z < depth; z++) {
// get labels for that slice
final int[] _labelsHere = (int[]) labelSequence.getDataXY(0, z, 0);
- for (int j = 0, offset = 0; j < height; j++)
- {
+ for (int j = 0, offset = 0; j < height; j++) {
if (Thread.currentThread().isInterrupted())
break finalPass;
- for (int i = 0; i < width; i++, offset++)
- {
+ for (int i = 0; i < width; i++, offset++) {
int targetLabel = _labelsHere[offset];
if (targetLabel == 0)
@@ -711,10 +643,8 @@ public class LabelExtractor extends EzPlug implements Block, EzStoppable
targetLabel = ccs.get(targetLabel).getTargetLabel();
// store the current pixel in the component
- if (is3D)
- {
- if (!roiMap.containsKey(targetLabel))
- {
+ if (is3D) {
+ if (!roiMap.containsKey(targetLabel)) {
ROI3DArea roi3D = new ROI3DArea();
roi3D.setName("Object #" + targetLabel + " (value: " + imageValue + ")");
roi3D.setT(t);
@@ -724,10 +654,8 @@ public class LabelExtractor extends EzPlug implements Block, EzStoppable
((ROI3DArea) roiMap.get(targetLabel)).addPoint(i, j, z);
}
- else
- {
- if (!roiMap.containsKey(targetLabel))
- {
+ else {
+ if (!roiMap.containsKey(targetLabel)) {
ROI2DArea roi2D = new ROI2DArea();
roi2D.setName("Object #" + targetLabel + " (value: " + imageValue + ")");
roi2D.setZ(0);
@@ -742,6 +670,6 @@ public class LabelExtractor extends EzPlug implements Block, EzStoppable
}
}
- return new ArrayList<ROI>(roiMap.values());
+ return new ArrayList<>(roiMap.values());
}
}
--
GitLab