From 0c97e389031781f33cc2a0b69ca88c714887743d Mon Sep 17 00:00:00 2001
From: Daniel Gonzalez <dgonzale@pasteur.fr>
Date: Mon, 10 Aug 2020 10:50:54 +0200
Subject: [PATCH] Code commit
---
RandomCrops/.classpath | 9 ++
RandomCrops/.gitignore | 3 +
RandomCrops/.project | 17 +++
RandomCrops/export.jardesc | 18 +++
.../randomcrops/RandomRectangleGenerator.java | 120 +++++++++++++++
.../randomcrops/GenerateRandomCrops.java | 142 ++++++++++++++++++
.../GenerateRandomRectangleRois.java | 138 +++++++++++++++++
icon100px.png | Bin 0 -> 1211 bytes
8 files changed, 447 insertions(+)
create mode 100644 RandomCrops/.classpath
create mode 100644 RandomCrops/.gitignore
create mode 100644 RandomCrops/.project
create mode 100644 RandomCrops/export.jardesc
create mode 100644 RandomCrops/src/main/java/danyfel80/randomcrops/RandomRectangleGenerator.java
create mode 100644 RandomCrops/src/main/java/plugins/danyfel80/randomcrops/GenerateRandomCrops.java
create mode 100644 RandomCrops/src/main/java/plugins/danyfel80/randomcrops/GenerateRandomRectangleRois.java
create mode 100644 icon100px.png
diff --git a/RandomCrops/.classpath b/RandomCrops/.classpath
new file mode 100644
index 0000000..f2bb7c1
--- /dev/null
+++ b/RandomCrops/.classpath
@@ -0,0 +1,9 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<classpath>
+ <classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-1.8"/>
+ <classpathentry kind="src" path="src/main/java"/>
+ <classpathentry kind="var" path="ICY_JAR"/>
+ <classpathentry kind="var" path="ICY_PLUGINS/adufour/ezplug/EzPlug.jar"/>
+ <classpathentry kind="var" path="ICY_PLUGINS/adufour/blocks/Blocks.jar"/>
+ <classpathentry kind="output" path="bin"/>
+</classpath>
diff --git a/RandomCrops/.gitignore b/RandomCrops/.gitignore
new file mode 100644
index 0000000..c40361a
--- /dev/null
+++ b/RandomCrops/.gitignore
@@ -0,0 +1,3 @@
+/bin/
+/.settings/
+*.jar
\ No newline at end of file
diff --git a/RandomCrops/.project b/RandomCrops/.project
new file mode 100644
index 0000000..f437f6b
--- /dev/null
+++ b/RandomCrops/.project
@@ -0,0 +1,17 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<projectDescription>
+ <name>RandomCrops</name>
+ <comment></comment>
+ <projects>
+ </projects>
+ <buildSpec>
+ <buildCommand>
+ <name>org.eclipse.jdt.core.javabuilder</name>
+ <arguments>
+ </arguments>
+ </buildCommand>
+ </buildSpec>
+ <natures>
+ <nature>org.eclipse.jdt.core.javanature</nature>
+ </natures>
+</projectDescription>
diff --git a/RandomCrops/export.jardesc b/RandomCrops/export.jardesc
new file mode 100644
index 0000000..5052a61
--- /dev/null
+++ b/RandomCrops/export.jardesc
@@ -0,0 +1,18 @@
+<?xml version="1.0" encoding="WINDOWS-1252" standalone="no"?>
+<jardesc>
+ <jar path="RandomCrops/RandomCrops.jar"/>
+ <options buildIfNeeded="true" compress="true" descriptionLocation="/RandomCrops/export.jardesc" exportErrors="false" exportWarnings="true" includeDirectoryEntries="false" overwrite="true" saveDescription="true" storeRefactorings="false" useSourceFolders="false"/>
+ <storedRefactorings deprecationInfo="true" structuralOnly="false"/>
+ <selectedProjects/>
+ <manifest generateManifest="true" manifestLocation="" manifestVersion="1.0" reuseManifest="false" saveManifest="false" usesManifest="true">
+ <sealing sealJar="false">
+ <packagesToSeal/>
+ <packagesToUnSeal/>
+ </sealing>
+ </manifest>
+ <selectedElements exportClassFiles="true" exportJavaFiles="true" exportOutputFolder="false">
+ <javaElement handleIdentifier="=RandomCrops/src\/main\/java"/>
+ <file path="/RandomCrops/.classpath"/>
+ <file path="/RandomCrops/.project"/>
+ </selectedElements>
+</jardesc>
diff --git a/RandomCrops/src/main/java/danyfel80/randomcrops/RandomRectangleGenerator.java b/RandomCrops/src/main/java/danyfel80/randomcrops/RandomRectangleGenerator.java
new file mode 100644
index 0000000..99c8a6d
--- /dev/null
+++ b/RandomCrops/src/main/java/danyfel80/randomcrops/RandomRectangleGenerator.java
@@ -0,0 +1,120 @@
+package danyfel80.randomcrops;
+
+import java.awt.Dimension;
+import java.awt.Rectangle;
+import java.awt.geom.Rectangle2D;
+import java.util.ArrayList;
+import java.util.List;
+import java.util.Objects;
+import java.util.Random;
+import java.util.concurrent.Callable;
+import java.util.function.Supplier;
+
+import icy.roi.ROI2D;
+import plugins.kernel.roi.roi2d.ROI2DRectangle;
+
+public class RandomRectangleGenerator implements Callable<List<ROI2DRectangle>>
+{
+
+ public static class Builder
+ {
+
+ private Dimension rectangleSize;
+ private int rectangleCount;
+ private List<ROI2D> limitingRois;
+
+ public Builder(Dimension rectangleSize, int rectangleCount, List<ROI2D> limitingRois)
+ {
+ Objects.requireNonNull(rectangleSize);
+ Objects.requireNonNull(limitingRois);
+ if (limitingRois.isEmpty())
+ throw new IllegalArgumentException("limitingRois is empty. At least one roi is needed");
+
+ this.rectangleSize = rectangleSize;
+ this.rectangleCount = rectangleCount;
+ this.limitingRois = limitingRois;
+ }
+
+ public RandomRectangleGenerator build()
+ {
+ RandomRectangleGenerator generator = new RandomRectangleGenerator();
+ generator.rectangleSize = rectangleSize;
+ generator.rectangleCount = rectangleCount;
+ generator.limitingRois = limitingRois;
+ return generator;
+ }
+
+ }
+
+ private Random randomValueGenerator;
+ private Dimension rectangleSize;
+ private int rectangleCount;
+ private List<ROI2D> limitingRois;
+
+ private RandomRectangleGenerator()
+ {
+ randomValueGenerator = new Random();
+ }
+
+ @Override
+ public List<ROI2DRectangle> call() throws Exception
+ {
+ computeValueBoundary();
+ if (valueBoundary.getWidth() < rectangleSize.width || valueBoundary.getHeight() < rectangleSize.height)
+ throw new IllegalArgumentException("Rectangle");
+
+ List<ROI2DRectangle> rectangles = new ArrayList<>(rectangleCount);
+ for (int count = 0; count < rectangleCount; count++)
+ {
+ if (Thread.interrupted())
+ throw new InterruptedException();
+
+ rectangles.add(getValidRandomRectangle());
+ }
+ return rectangles;
+ }
+
+ private Rectangle2D valueBoundary;
+ private Supplier<Integer> xGenerator;
+ private Supplier<Integer> yGenerator;
+
+ private void computeValueBoundary()
+ {
+ Rectangle2D seedBounds = limitingRois.get(0).getBounds2D();
+ valueBoundary = new Rectangle2D.Double(seedBounds.getX(), seedBounds.getY(), seedBounds.getWidth(),
+ seedBounds.getHeight());
+ limitingRois.stream().map(ROI2D::getBounds2D)
+ .forEach(rect2d -> Rectangle2D.union(valueBoundary, rect2d, valueBoundary));
+
+ int minX = (int) Math.floor(valueBoundary.getMinX());
+ int maxX = (int) Math.floor(valueBoundary.getMaxX());
+ int xLength = maxX - minX;
+ xGenerator = () -> minX + randomValueGenerator.nextInt(xLength);
+
+ int minY = (int) Math.floor(valueBoundary.getMinY());
+ int maxY = (int) Math.floor(valueBoundary.getMaxY());
+ int yLength = maxY - minY;
+ yGenerator = () -> minY + randomValueGenerator.nextInt(yLength);
+ }
+
+ private ROI2DRectangle getValidRandomRectangle() throws InterruptedException
+ {
+ Rectangle rect = new Rectangle(rectangleSize);
+ do
+ {
+ if (Thread.interrupted())
+ throw new InterruptedException();
+
+ rect.x = xGenerator.get();
+ rect.y = yGenerator.get();
+ }
+ while (!isValidRectangle(rect));
+ return new ROI2DRectangle(rect);
+ }
+
+ private boolean isValidRectangle(Rectangle rect)
+ {
+ return limitingRois.stream().anyMatch(roi -> roi.getBounds2D().contains(rect) && roi.contains(rect));
+ }
+
+}
diff --git a/RandomCrops/src/main/java/plugins/danyfel80/randomcrops/GenerateRandomCrops.java b/RandomCrops/src/main/java/plugins/danyfel80/randomcrops/GenerateRandomCrops.java
new file mode 100644
index 0000000..f499637
--- /dev/null
+++ b/RandomCrops/src/main/java/plugins/danyfel80/randomcrops/GenerateRandomCrops.java
@@ -0,0 +1,142 @@
+package plugins.danyfel80.randomcrops;
+
+import java.awt.Dimension;
+import java.awt.Rectangle;
+import java.util.ArrayList;
+import java.util.List;
+import java.util.stream.Collectors;
+
+import danyfel80.randomcrops.RandomRectangleGenerator;
+import icy.roi.ROI2D;
+import icy.sequence.Sequence;
+import icy.sequence.SequenceUtil;
+import icy.system.IcyHandledException;
+import plugins.adufour.blocks.lang.Block;
+import plugins.adufour.blocks.util.VarList;
+import plugins.adufour.ezplug.EzGroup;
+import plugins.adufour.ezplug.EzPlug;
+import plugins.adufour.ezplug.EzStoppable;
+import plugins.adufour.ezplug.EzVarBoolean;
+import plugins.adufour.ezplug.EzVarInteger;
+import plugins.adufour.ezplug.EzVarSequence;
+import plugins.adufour.vars.lang.VarSequenceArray;
+import plugins.kernel.roi.roi2d.ROI2DRectangle;
+
+public class GenerateRandomCrops extends EzPlug implements Block, EzStoppable
+{
+
+ private EzVarSequence varInSequence;
+ private EzVarInteger varInRectangleWidth;
+ private EzVarInteger varInRectangleHeight;
+ private EzVarInteger varInNumberOfRectangles;
+ private EzVarBoolean varInLimitRectanglesToROIs;
+
+ @Override
+ protected void initialize()
+ {
+ initializeInputVars();
+ addEzComponent(varInSequence);
+ addEzComponent(new EzGroup("Generated rectangles", varInRectangleWidth, varInRectangleHeight,
+ varInNumberOfRectangles));
+ addEzComponent(varInLimitRectanglesToROIs);
+ }
+
+ private void initializeInputVars()
+ {
+ varInSequence = new EzVarSequence("Sequence");
+ varInRectangleWidth = new EzVarInteger("Rectangle width (px)", 512, 1, 10000, 1);
+ varInRectangleHeight = new EzVarInteger("Rectangle height (px)", 512, 1, 10000, 1);
+ varInNumberOfRectangles = new EzVarInteger("Number of rectangles", 10, 0, 10000000, 1);
+ varInLimitRectanglesToROIs = new EzVarBoolean("Limit rectangles to ROIs", false);
+ }
+
+ @Override
+ public void declareInput(VarList inputMap)
+ {
+ initializeInputVars();
+ inputMap.add(varInSequence.name, varInSequence.getVariable());
+ inputMap.add(varInRectangleWidth.name, varInRectangleWidth.getVariable());
+ inputMap.add(varInRectangleHeight.name, varInRectangleHeight.getVariable());
+ inputMap.add(varInNumberOfRectangles.name, varInNumberOfRectangles.getVariable());
+ inputMap.add(varInLimitRectanglesToROIs.name, varInLimitRectanglesToROIs.getVariable());
+ }
+
+ private VarSequenceArray varOutSequences;
+
+ @Override
+ public void declareOutput(VarList outputMap)
+ {
+ varOutSequences = new VarSequenceArray("Random crops");
+ outputMap.add(varOutSequences.getName(), varOutSequences);
+ }
+
+ @Override
+ protected void execute()
+ {
+ readParameters();
+ try
+ {
+ generateRandomRectangles();
+ }
+ catch (Exception e)
+ {
+ throw new IcyHandledException("Error generating random rectangles: " + e.getMessage(), e);
+ }
+ setOutput();
+ }
+
+ private Sequence sequence;
+ private Dimension rectangleSize;
+ private Integer rectangleCount;
+ private Boolean limitRectanglesToRois;
+ private List<ROI2D> limitingRois;
+
+ private void readParameters()
+ {
+ sequence = varInSequence.getValue(true);
+ rectangleSize = new Dimension(varInRectangleWidth.getValue(), varInRectangleHeight.getValue());
+ rectangleCount = varInNumberOfRectangles.getValue();
+ limitRectanglesToRois = varInLimitRectanglesToROIs.getValue();
+ limitingRois = new ArrayList<>();
+ List<ROI2D> sequenceRois = sequence.getROI2Ds();
+ if (!limitRectanglesToRois || sequenceRois.isEmpty())
+ {
+ limitingRois.add(new ROI2DRectangle(new Rectangle(sequence.getWidth(), sequence.getHeight())));
+ }
+ else
+ {
+
+ limitingRois.addAll(sequenceRois);
+ }
+ }
+
+ private List<Sequence> croppedSequences;
+
+ private void generateRandomRectangles() throws Exception
+ {
+ RandomRectangleGenerator rectGenerator = new RandomRectangleGenerator.Builder(rectangleSize, rectangleCount,
+ limitingRois).build();
+ List<ROI2DRectangle> rectangles = rectGenerator.call();
+ croppedSequences = rectangles.stream().map(roi -> SequenceUtil.getSubSequence(sequence, roi))
+ .collect(Collectors.toList());
+ }
+
+ private void setOutput()
+ {
+ if (isHeadLess())
+ {
+ varOutSequences.setValue(croppedSequences.stream().toArray(Sequence[]::new));
+ }
+ else
+
+ {
+ croppedSequences.stream().forEach(seq -> addSequence(seq));
+ }
+ }
+
+ @Override
+ public void clean()
+ {// Nothing to do here
+ }
+
+}
diff --git a/RandomCrops/src/main/java/plugins/danyfel80/randomcrops/GenerateRandomRectangleRois.java b/RandomCrops/src/main/java/plugins/danyfel80/randomcrops/GenerateRandomRectangleRois.java
new file mode 100644
index 0000000..a7bc96e
--- /dev/null
+++ b/RandomCrops/src/main/java/plugins/danyfel80/randomcrops/GenerateRandomRectangleRois.java
@@ -0,0 +1,138 @@
+package plugins.danyfel80.randomcrops;
+
+import java.awt.Dimension;
+import java.awt.Rectangle;
+import java.util.ArrayList;
+import java.util.List;
+
+import danyfel80.randomcrops.RandomRectangleGenerator;
+import icy.roi.ROI;
+import icy.roi.ROI2D;
+import icy.sequence.Sequence;
+import icy.system.IcyHandledException;
+import plugins.adufour.blocks.lang.Block;
+import plugins.adufour.blocks.util.VarList;
+import plugins.adufour.ezplug.EzGroup;
+import plugins.adufour.ezplug.EzPlug;
+import plugins.adufour.ezplug.EzVarBoolean;
+import plugins.adufour.ezplug.EzVarInteger;
+import plugins.adufour.ezplug.EzVarSequence;
+import plugins.adufour.vars.lang.VarROIArray;
+import plugins.kernel.roi.roi2d.ROI2DRectangle;
+
+public class GenerateRandomRectangleRois extends EzPlug implements Block
+{
+
+ private EzVarSequence varInSequence;
+ private EzVarInteger varInRectangleWidth;
+ private EzVarInteger varInRectangleHeight;
+ private EzVarInteger varInNumberOfRectangles;
+ private EzVarBoolean varInLimitRectanglesToROIs;
+
+ @Override
+ protected void initialize()
+ {
+ initializeInputVars();
+ addEzComponent(varInSequence);
+ addEzComponent(new EzGroup("Generated rectangles", varInRectangleWidth, varInRectangleHeight,
+ varInNumberOfRectangles));
+ addEzComponent(varInLimitRectanglesToROIs);
+ }
+
+ private void initializeInputVars()
+ {
+ varInSequence = new EzVarSequence("Sequence");
+ varInRectangleWidth = new EzVarInteger("Rectangle width (px)", 512, 1, 10000, 1);
+ varInRectangleHeight = new EzVarInteger("Rectangle height (px)", 512, 1, 10000, 1);
+ varInNumberOfRectangles = new EzVarInteger("Number of rectangles", 10, 0, 10000000, 1);
+ varInLimitRectanglesToROIs = new EzVarBoolean("Limit rectangles to ROIs", false);
+ }
+
+ @Override
+ public void declareInput(VarList inputMap)
+ {
+ initializeInputVars();
+ inputMap.add(varInSequence.name, varInSequence.getVariable());
+ inputMap.add(varInRectangleWidth.name, varInRectangleWidth.getVariable());
+ inputMap.add(varInRectangleHeight.name, varInRectangleHeight.getVariable());
+ inputMap.add(varInNumberOfRectangles.name, varInNumberOfRectangles.getVariable());
+ inputMap.add(varInLimitRectanglesToROIs.name, varInLimitRectanglesToROIs.getVariable());
+ }
+
+ private VarROIArray varOutRectangles;
+
+ @Override
+ public void declareOutput(VarList outputMap)
+ {
+ varOutRectangles = new VarROIArray("Random rectangles");
+ outputMap.add(varOutRectangles.getName(), varOutRectangles);
+ }
+
+ @Override
+ protected void execute()
+ {
+ readParameters();
+ try
+ {
+ generateRandomRectangles();
+ }
+ catch (Exception e)
+ {
+ throw new IcyHandledException("Error generating random rectangles: " + e.getMessage(), e);
+ }
+ setOutput();
+ }
+
+ private Sequence sequence;
+ private Dimension rectangleSize;
+ private Integer rectangleCount;
+ private Boolean limitRectanglesToRois;
+ private List<ROI2D> limitingRois;
+
+ private void readParameters()
+ {
+ sequence = varInSequence.getValue(true);
+ rectangleSize = new Dimension(varInRectangleWidth.getValue(), varInRectangleHeight.getValue());
+ rectangleCount = varInNumberOfRectangles.getValue();
+ limitRectanglesToRois = varInLimitRectanglesToROIs.getValue();
+ limitingRois = new ArrayList<>();
+ List<ROI2D> sequenceRois = sequence.getROI2Ds();
+ if (!limitRectanglesToRois || sequenceRois.isEmpty())
+ {
+ limitingRois.add(new ROI2DRectangle(new Rectangle(sequence.getWidth(), sequence.getHeight())));
+ }
+ else
+ {
+
+ limitingRois.addAll(sequenceRois);
+ }
+ }
+
+ private List<ROI2DRectangle> rectangles;
+
+ private void generateRandomRectangles() throws Exception
+ {
+ RandomRectangleGenerator rectGenerator = new RandomRectangleGenerator.Builder(rectangleSize, rectangleCount,
+ limitingRois).build();
+ rectangles = rectGenerator.call();
+ }
+
+ private void setOutput()
+ {
+ if (isHeadLess())
+ {
+ varOutRectangles.setValue(rectangles.stream().toArray(ROI[]::new));
+ }
+ else
+ {
+ sequence.addROIs(rectangles, true);
+ }
+
+ }
+
+ @Override
+ public void clean()
+ {// Nothing to do here
+ }
+
+}
diff --git a/icon100px.png b/icon100px.png
new file mode 100644
index 0000000000000000000000000000000000000000..a2b9c1701760295ef4aeeb86276303461a41ef19
GIT binary patch
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