diff --git a/.idea/compiler.xml b/.idea/compiler.xml
new file mode 100644
index 0000000..96cc43e
--- /dev/null
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diff --git a/.idea/copyright/profiles_settings.xml b/.idea/copyright/profiles_settings.xml
new file mode 100644
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--- /dev/null
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diff --git a/.idea/libraries/lib.xml b/.idea/libraries/lib.xml
new file mode 100644
index 0000000..e71c7de
--- /dev/null
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diff --git a/.idea/misc.xml b/.idea/misc.xml
new file mode 100644
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--- /dev/null
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diff --git a/.idea/modules.xml b/.idea/modules.xml
new file mode 100644
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--- /dev/null
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diff --git a/.idea/uiDesigner.xml b/.idea/uiDesigner.xml
new file mode 100644
index 0000000..e96534f
--- /dev/null
+++ b/.idea/uiDesigner.xml
@@ -0,0 +1,124 @@
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diff --git a/.idea/vcs.xml b/.idea/vcs.xml
new file mode 100644
index 0000000..35eb1dd
--- /dev/null
+++ b/.idea/vcs.xml
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\ No newline at end of file
diff --git a/.idea/workspace.xml b/.idea/workspace.xml
new file mode 100644
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--- /dev/null
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+ file://$PROJECT_DIR$/test/characterize/CharacterizerTest.java
+ 199
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\ No newline at end of file
diff --git a/karyotyper.iml b/karyotyper.iml
new file mode 100644
index 0000000..076a646
--- /dev/null
+++ b/karyotyper.iml
@@ -0,0 +1,33 @@
+
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\ No newline at end of file
diff --git a/src/characterization/ChromosomeBand.java b/src/characterization/ChromosomeBand.java
index c5ef831..ce5ab4d 100644
--- a/src/characterization/ChromosomeBand.java
+++ b/src/characterization/ChromosomeBand.java
@@ -1,15 +1,15 @@
package characterization;
public class ChromosomeBand {
- public static enum Type {
+ public enum BandType {
BLACK, WHITE, GREY, CENTROMERE
- };
+ }
- private final Type type;
+ private final BandType type;
private final int length;
- public ChromosomeBand(Type type, int length) {
- if (type == this.type.CENTROMERE && length == 0) {
+ public ChromosomeBand(BandType type, int length) {
+ if (type == BandType.CENTROMERE && length == 0) {
throw new IllegalArgumentException("Length of a centromere band cannot be non-zero.");
}
@@ -17,7 +17,7 @@ public ChromosomeBand(Type type, int length) {
this.length = length;
}
- public Type type() {
+ public BandType type() {
return type;
}
diff --git a/src/idiogram/IdiogramMap.java b/src/idiogram/IdiogramMap.java
index a9c9866..0a24115 100644
--- a/src/idiogram/IdiogramMap.java
+++ b/src/idiogram/IdiogramMap.java
@@ -8,7 +8,7 @@
import java.util.regex.Pattern;
import characterization.ChromosomeBand;
-import characterization.ChromosomeBand.Type;
+import characterization.ChromosomeBand.BandType;
/**
* Wrapper for a Java HashMap that maps an idiogram to a chromosome number.
@@ -60,7 +60,7 @@ private void idiogramSheetParser(File file) {
String token = null;
int chromosomeNumber = 0;
- ChromosomeBand.Type bandType;
+ ChromosomeBand.BandType bandType;
int bandLength = 0;
ChromosomeBand band = null;
int resolution = 0;
@@ -85,22 +85,22 @@ private void idiogramSheetParser(File file) {
// End debug
if (token.toLowerCase().equals("white")) {
- bandType = Type.WHITE;
+ bandType = BandType.WHITE;
bandLength = lineReader.nextInt();
band = new ChromosomeBand(bandType, bandLength);
newIdiogram.add(band);
} else if (token.toLowerCase().equals("black")) {
- bandType = Type.BLACK;
+ bandType = BandType.BLACK;
bandLength = lineReader.nextInt();
band = new ChromosomeBand(bandType, bandLength);
newIdiogram.add(band);
} else if (token.toLowerCase().equals("grey")) {
- bandType = Type.GREY;
+ bandType = BandType.GREY;
bandLength = lineReader.nextInt();
band = new ChromosomeBand(bandType, bandLength);
newIdiogram.add(band);
} else if (token.toLowerCase().equals("centromere")) {
- bandType = Type.CENTROMERE;
+ bandType = BandType.CENTROMERE;
bandLength = lineReader.nextInt();
band = new ChromosomeBand(bandType, bandLength);
newIdiogram.add(band);
@@ -123,7 +123,7 @@ private void idiogramSheetParser(File file) {
* Gets the chromosome number that the requested idiogram maps to. If the idiogram requested is
* not in the list of keys then null is returned.
*
- * @param i
+ * @param index
* Requested idiogram
* @return Chromosome number mapped to or null if the requested idiogram doesn't exist.
*/
diff --git a/test/basic_objects/AroundPixelTest.java b/test/basic_objects/AroundPixelTest.java
index 1e3fe48..1925697 100644
--- a/test/basic_objects/AroundPixelTest.java
+++ b/test/basic_objects/AroundPixelTest.java
@@ -1,16 +1,15 @@
package basic_objects;
import java.util.LinkedList;
+import org.junit.Test;
-import basic_objects.AroundPixel;
-import junit.framework.TestCase;
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertFalse;
+import static org.junit.Assert.assertTrue;
-public class AroundPixelTest extends TestCase {
- protected void setUp() throws Exception {
- super.setUp();
-
- }
+public class AroundPixelTest {
+ @Test
public void testGetPositionsBetweenNeg() {
LinkedList posList = AroundPixel.getPositionsBetweenNeg(0, 4);
assertEquals(posList.size(), 3);
@@ -24,7 +23,7 @@ public void testGetPositionsBetweenNeg() {
assertFalse(posList.contains(0));
}
-
+ @Test
public void testGetPositionsBetweenPlus() {
LinkedList posList = AroundPixel.getPositionsBetweenPlus(0, 4);
assertEquals(posList.size(), 3);
@@ -38,7 +37,7 @@ public void testGetPositionsBetweenPlus() {
assertFalse(posList.contains(0));
}
-
+ @Test
public void testGetOppisitPos() {
assertEquals(4, AroundPixel.getOppisitePos(0));
assertEquals(5, AroundPixel.getOppisitePos(1));
@@ -50,7 +49,7 @@ public void testGetOppisitPos() {
assertEquals(3, AroundPixel.getOppisitePos(7));
}
-
+ @Test
public void testHandleLoop() {
assertEquals(7, AroundPixel.handleLoop(-1));
assertEquals(6, AroundPixel.handleLoop(-2));
diff --git a/test/basic_objects/IdiogramMapTest.java b/test/basic_objects/IdiogramMapTest.java
index 6abd565..67dc0e0 100644
--- a/test/basic_objects/IdiogramMapTest.java
+++ b/test/basic_objects/IdiogramMapTest.java
@@ -4,44 +4,33 @@
package basic_objects;
import java.io.File;
-
-import characterization.ChromosomeBand;
import idiogram.IdiogramMap;
-import junit.framework.TestCase;
+import org.junit.Before;
+import org.junit.Test;
+
+import static org.junit.Assert.fail;
/**
* @author Robert
*
*/
-public class IdiogramMapTest extends TestCase {
+public class IdiogramMapTest {
private IdiogramMap map;
-
- /**
- * @param name
- */
- public IdiogramMapTest(String name) {
- super(name);
- map = new IdiogramMap(new File(".\\ChromosomeIdiogramSheet.csv"));
- }
/* (non-Javadoc)
* @see junit.framework.TestCase#setUp()
*/
- protected void setUp() throws Exception {
- super.setUp();
- }
+ @Before
+ public void setUp() throws Exception {
+ map = new IdiogramMap(new File(".\\ChromosomeIdiogramSheet.csv"));
- /* (non-Javadoc)
- * @see junit.framework.TestCase#tearDown()
- */
- protected void tearDown() throws Exception {
- super.tearDown();
}
/**
* Test method for {@link idiogram.IdiogramMap#get(Idiogram)}.
*/
+ @Test
public void testGet() {
// Chromosome chromosome = new Chromosome(10);
// chromosome.add(new ChromosomeBand(ChromosomeBand.Type.WHITE, 21));
diff --git a/test/basic_objects/PointListTest.java b/test/basic_objects/PointListTest.java
index ea88e2a..27f284b 100644
--- a/test/basic_objects/PointListTest.java
+++ b/test/basic_objects/PointListTest.java
@@ -1,17 +1,14 @@
package basic_objects;
import java.awt.Point;
+import org.junit.Test;
-import basic_objects.PointList;
-
-import junit.framework.TestCase;
-
-public class PointListTest extends TestCase {
-
- protected void setUp() throws Exception {
- super.setUp();
- }
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertFalse;
+import static org.junit.Assert.assertTrue;
+public class PointListTest{
+ @Test
public void testSetList() {
PointList tempList = new PointList(new Point(10, 2), 2);
tempList.addPoint(new Point(3, 2), 2);
@@ -27,7 +24,7 @@ public void testSetList() {
assertFalse(pointList.getList().contains(new Point(6, 10)));
}
-
+ @Test
public void testAddPoint() {
PointList tempList = new PointList(new Point(10, 2), 2);
assertTrue(tempList.addPoint(new Point(3, 2), 2));
diff --git a/test/basic_objects/RadialVectorsTest.java b/test/basic_objects/RadialVectorsTest.java
index c68126b..8c1b4d1 100644
--- a/test/basic_objects/RadialVectorsTest.java
+++ b/test/basic_objects/RadialVectorsTest.java
@@ -6,7 +6,9 @@
import java.awt.Point;
import java.util.ArrayList;
-import org.apache.commons.math3.analysis.function.Ceil;
+import org.junit.After;
+import org.junit.Before;
+import org.junit.Test;
import junit.framework.TestCase;
@@ -21,31 +23,15 @@ public class RadialVectorsTest extends TestCase {
private final int NUM_VECTORS = 8;
private final double DISTANCE = 10;
- /**
- * @param name
- */
- public RadialVectorsTest(String name) {
- super(name);
- }
-
- /* (non-Javadoc)
- * @see junit.framework.TestCase#setUp()
- */
- protected void setUp() throws Exception {
+ @Before
+ public void setUp() throws Exception {
radialVectors = new RadialVectors(CENTER_POINT, NUM_VECTORS, DISTANCE);
- super.setUp();
- }
-
- /* (non-Javadoc)
- * @see junit.framework.TestCase#tearDown()
- */
- protected void tearDown() throws Exception {
- super.tearDown();
}
/**
* Test method for {@link basic_objects.RadialVectors#getVectors()}.
*/
+ @Test
public void testGetVectors() {
ArrayList vectorList = radialVectors.getVectors();
@@ -81,6 +67,7 @@ public void testGetVectors() {
/**
* Test method for {@link basic_objects.RadialVectors#getTheta()}.
*/
+ @Test
public void testGetTheta() {
double expectedTheta = 2 * Math.PI / NUM_VECTORS;
assertEquals(expectedTheta, radialVectors.getTheta());
@@ -89,6 +76,7 @@ public void testGetTheta() {
/**
* Test method for {@link basic_objects.RadialVectors#getCenterPoint()}.
*/
+ @Test
public void testGetCenterPoint() {
assertEquals(CENTER_POINT, radialVectors.getCenterPoint());
}
@@ -96,6 +84,7 @@ public void testGetCenterPoint() {
/**
* Test method for {@link basic_objects.RadialVectors#getVectorsAsPointsOnImage()}.
*/
+ @Test
public void testGetVectorsAsPointsOnImage() {
ArrayList pointList = radialVectors.getVectorsAsPointsOnImage();
@@ -114,6 +103,7 @@ public void testGetVectorsAsPointsOnImage() {
/**
* Test method for {@link basic_objects.RadialVectors#getPointsInRange(java.awt.Point, double, int)}.
*/
+ @Test
public void testGetRange() {
ArrayList range = radialVectors.getPointsInRange(new Point(3,4), Math.PI/2, 5);
@@ -140,6 +130,7 @@ public void testGetRange() {
/**
* Test method for {@link basic_objects.RadialVectors#getOpposite(java.awt.Point)}.
*/
+ @Test
public void testGetOpposite() {
Point oppPoint = radialVectors.getOpposite(new Point(CENTER_POINT.x + 1, CENTER_POINT.y));
@@ -154,6 +145,7 @@ public void testGetOpposite() {
/**
* Test method for {@link basic_objects.RadialVectors#getPointAtIndex(int)}.
*/
+ @Test
public void testGetPointAtIndex() {
Point pointAtIndex = radialVectors.getPointAtIndex(2);
Point testPoint = new Point(CENTER_POINT.x, CENTER_POINT.y + 10);
@@ -164,11 +156,12 @@ public void testGetPointAtIndex() {
/**
* Test method for {@link basic_objects.RadialVectors#multiplyRadius(double)}.
*/
+ @Test
public void testMultiplyRadius() {
radialVectors.multiplyRadius(2);
assertEquals(20.0, radialVectors.getDistance());
}
-
+ @Test
public void testToString() {
radialVectors.normalize();
System.out.println(radialVectors.toString());
diff --git a/test/basic_objects/VectorTest.java b/test/basic_objects/VectorTest.java
index 920a3b7..1722a8b 100644
--- a/test/basic_objects/VectorTest.java
+++ b/test/basic_objects/VectorTest.java
@@ -3,58 +3,46 @@
*/
package basic_objects;
+import org.junit.Before;
+import org.junit.Test;
import java.awt.Point;
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertTrue;
-import junit.framework.TestCase;
/**
* @author Robert
*
*/
-public class VectorTest extends TestCase {
+public class VectorTest{
private Vector vector;
-
- /**
- * @param name
- */
- public VectorTest(String name) {
- super(name);
- }
-
/*
* (non-Javadoc)
*
* @see junit.framework.TestCase#setUp()
*/
- protected void setUp() throws Exception {
+ @Before
+ public void setUp()throws Exception {
vector = new Vector(1, 0);
- super.setUp();
- }
-
- /*
- * (non-Javadoc)
- *
- * @see junit.framework.TestCase#tearDown()
- */
- protected void tearDown() throws Exception {
- super.tearDown();
}
/**
* Test method for {@link basic_objects.Vector#Vector(double, double)}.
*/
+ @Test
public void testVector() {
double xComp = vector.x;
double yComp = vector.y;
- assertEquals(1.0, xComp);
- assertEquals(0.0, yComp);
+ assertEquals(1.0, xComp,.001);
+ assertEquals(0.0, yComp,.001);
}
/**
* Test method for {@link basic_objects.Vector#rotateVector(double)}.
*/
+ @Test
public void testRotateVectorDouble() {
vector.rotateVector(Math.PI / 4);
double testX = Math.sqrt(2) / 2;
@@ -72,6 +60,7 @@ public void testRotateVectorDouble() {
/**
* Test method for {@link basic_objects.Vector#rotateVector(basic_objects.Vector, double)}.
*/
+ @Test
public void testRotateVectorVectorDouble() {
Vector v1 = Vector.rotateVector(vector, Math.PI / 4);
long actualX = Math.round(v1.x * 100000);
@@ -86,19 +75,21 @@ public void testRotateVectorVectorDouble() {
/**
* Test method for {@link basic_objects.Vector#normalize(basic_objects.Vector)}.
*/
+ @Test
public void testNormalize() {
Vector testVector = new Vector(3, 3);
testVector = Vector.normalize(testVector);
double newX = Math.sqrt(2) / 2;
double newY = Math.sqrt(2) / 2;
- assertEquals(testVector.x, newX);
- assertEquals(testVector.y, newY);
+ assertEquals(testVector.x, newX,.001);
+ assertEquals(testVector.y, newY,.001);
}
/**
* Test method for {@link basic_objects.Vector#add(basic_objects.Vector, basic_objects.Vector)}.
*/
+ @Test
public void testAdd() {
Vector v1 = new Vector(2, 5);
Vector v2 = new Vector(-4, 9);
@@ -106,9 +97,10 @@ public void testAdd() {
double newX = 2 - 4;
double newY = 5 + 9;
- assertEquals(v1.x, newX);
- assertEquals(v1.y, newY);
+ assertEquals(v1.x, newX,.001);
+ assertEquals(v1.y, newY,.001);
}
+ @Test
public void testAngleBetween(){
Vector v1 = new Vector(3, 0);
Vector v2 = new Vector(0, 4);
@@ -143,26 +135,29 @@ public void testAngleBetween(){
/**
* Test method for {@link basic_objects.Vector#getVectorBetweenTwoPoints(Point, Point)}
*/
+ @Test
public void testMagnitude() {
Vector v1 = new Vector(1,0);
- assertEquals(1.0, Vector.magnitude(v1));
+ assertEquals(1.0, Vector.magnitude(v1),.001);
}
/**
* Test method for {@link basic_objects.Vector#dotProduct(Vector, Vector)
*/
+ @Test
public void testDotProduct() {
Vector v1 = new Vector(1,2);
Vector v2 = new Vector(3,2);
double testProduct = 7;
double actualProduct = Vector.dotProduct(v1, v2);
- assertEquals(testProduct, actualProduct);
+ assertEquals(testProduct, actualProduct,.001);
}
/**
* Test method for
* {@link basic_objects.Vector#getVectorBetweenTwoPoints(java.awt.Point, java.awt.Point)}.
*/
+ @Test
public void testGetVectorBetweenTwoPoints() {
Point p1 = new Point(1, 2);
Point p2 = new Point(3, 4);
@@ -175,6 +170,7 @@ public void testGetVectorBetweenTwoPoints() {
/**
* Test method for {@link basic_objects.Vector#getDirectionalAngle(Vector, Vector)}.
*/
+ @Test
public void testGetAngle() {
Vector v1 = new Vector(2, 1);
double testAngle = Math.PI / 4;
@@ -190,7 +186,7 @@ public void testGetAngle() {
testAngle = 5 * Math.PI / 4;
Vector v3 = Vector.rotateVector(v1, testAngle);
actualAngle = Vector.getDirectionalAngle(v1, v3);
- assertEquals(testAngle, actualAngle);
+ assertEquals(testAngle, actualAngle,.001);
}
diff --git a/test/basic_objects/VertexTest.java b/test/basic_objects/VertexTest.java
index 9e3732c..5d0acd4 100644
--- a/test/basic_objects/VertexTest.java
+++ b/test/basic_objects/VertexTest.java
@@ -5,46 +5,28 @@
import java.awt.Point;
import java.util.LinkedList;
-
import medial_axis.DistanceMap;
import medial_axis.MedialAxisGraph;
+import org.junit.Before;
+import org.junit.Test;
-import junit.framework.TestCase;
+import static org.junit.Assert.*;
/**
* @author Robert
*
*/
-public class VertexTest extends TestCase {
+public class VertexTest{
private Vertex vertex;
/** Points ordered in breadth-first ordering from vertex */
private LinkedList pointList;
-
- /**
- * @param name
- */
- public VertexTest(String name) {
- super(name);
-
- }
/* (non-Javadoc)
* @see junit.framework.TestCase#setUp()
*/
- protected void setUp() throws Exception {
- super.setUp();
- buildAxisGraph();
- }
-
- /* (non-Javadoc)
- * @see junit.framework.TestCase#tearDown()
- */
- protected void tearDown() throws Exception {
- super.tearDown();
- }
-
- private void buildAxisGraph() {
+ @Before
+ public void setUp()throws Exception {
buildPointList();
MedialAxisGraph graph = new MedialAxisGraph();
graph.buildGraph(pointList, new DistanceMap(100, 100));
@@ -70,6 +52,7 @@ private void buildPointList() {
/**
* Test method for {@link basic_objects.Vertex#calculateTangentLine(double, double)}.
*/
+ @Test
public void testCalculateTangentLine() {
double[] tangentLine = null;
try {
@@ -91,6 +74,7 @@ public void testCalculateTangentLine() {
/**
* Test method for {@link basic_objects.Vertex#calculateOrthogonalLine(double, double)}.
*/
+ @Test
public void testCalculateOrthogonalLine() {
double[] orthoLine = null;
try {
@@ -105,12 +89,13 @@ public void testCalculateOrthogonalLine() {
assertEquals(vertex.getPoint(), new Point(20,20));
assertTrue(slope == -1 * (19.0 - 20.0)/(17.0 - 20.0) || slope == -1 * (23.0 - 20.0)/(22.0 - 20.0));
- assertEquals(intercept, 20.0 - 20.0*slope);
+ assertEquals(intercept, 20.0 - 20.0*slope,.001);
}
/**
* Test method for {@link basic_objects.Vertex#hasBeenChecked()}.
*/
+ @Test
public void testHasBeenChecked() {
assertFalse(vertex.hasBeenChecked());
}
@@ -118,6 +103,7 @@ public void testHasBeenChecked() {
/**
* Test method for {@link basic_objects.Vertex#setHasBeenChecked(boolean)}.
*/
+ @Test
public void testSetHasBeenChecked() {
vertex.setHasBeenChecked(true);
assertTrue(vertex.hasBeenChecked());
@@ -126,6 +112,7 @@ public void testSetHasBeenChecked() {
/**
* Test method for {@link basic_objects.Vertex#tangentLine(int)}.
*/
+ @Test
public void testTangentLine() {
double[] tangent = null;
try {
@@ -157,6 +144,7 @@ public void testTangentLine() {
/**
* Test method for {@link basic_objects.Vertex#orthogonalLine(int)}.
*/
+ @Test
public void testOrthogonalLine() {
double[] orthogonal = null;
try {
diff --git a/src/testing/RegressionLibTest.java b/test/blackbox/RegressionLibTest.java
similarity index 77%
rename from src/testing/RegressionLibTest.java
rename to test/blackbox/RegressionLibTest.java
index b16aafb..566383a 100644
--- a/src/testing/RegressionLibTest.java
+++ b/test/blackbox/RegressionLibTest.java
@@ -1,17 +1,17 @@
-package testing;
+package blackbox;
import java.awt.Point;
import java.util.ArrayList;
import java.util.Arrays;
-
import medial_axis.RegressionLib;
-
import org.apache.commons.math3.analysis.DifferentiableUnivariateFunction;
+import org.junit.Test;
-import junit.framework.TestCase;
-
-public class RegressionLibTest extends TestCase {
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertTrue;
+public class RegressionLibTest {
+ @Test
public void testApproxByPolynomial() {
RegressionLib testObj = new RegressionLib();
double testVal = 0;
@@ -19,14 +19,14 @@ public void testApproxByPolynomial() {
ArrayList linearInput = new ArrayList(Arrays.asList(new Point(0, 0),
new Point(1, 1)));
DifferentiableUnivariateFunction linearFunc = testObj.approxByPolynomial(1, linearInput);
- assertEquals(2.0, linearFunc.value(2));
- assertEquals(0.0, testObj.getFitError());
+ assertEquals(2.0, linearFunc.value(2),.001);
+ assertEquals(0.0, testObj.getFitError(),.001);
ArrayList cubicInput = new ArrayList(Arrays.asList(new Point(-2, -8),
new Point(-1, -1), new Point(0, 0), new Point(2, 8)));
DifferentiableUnivariateFunction cubicFunc = testObj.approxByPolynomial(3, cubicInput);
- assertEquals(-27.0, cubicFunc.value(-3));
- assertEquals(0.0, testObj.getFitError());
+ assertEquals(-27.0, cubicFunc.value(-3),.001);
+ assertEquals(0.0, testObj.getFitError(),.001);
ArrayList dirtyInput = new ArrayList(Arrays.asList(new Point(-200, -10),
new Point(-1, -100), new Point(0, 30), new Point(10, 9)));
diff --git a/src/characterize/CharacterizerTest.java b/test/characterize/CharacterizerTest.java
similarity index 98%
rename from src/characterize/CharacterizerTest.java
rename to test/characterize/CharacterizerTest.java
index bef2191..e2fa7d5 100644
--- a/src/characterize/CharacterizerTest.java
+++ b/test/characterize/CharacterizerTest.java
@@ -1,7 +1,6 @@
package characterize;
import java.awt.Color;
-import java.awt.Graphics2D;
import java.awt.Point;
import java.awt.geom.Point2D;
import java.awt.image.BufferedImage;
@@ -9,15 +8,16 @@
import java.io.IOException;
import java.util.ArrayList;
import java.util.Arrays;
-
import javax.imageio.ImageIO;
-
-import junit.framework.TestCase;
import color.PixelColor;
+import org.junit.Test;
-public class CharacterizerTest extends TestCase {
- private final double fpThreshold = 0.0001;
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertTrue;
+public class CharacterizerTest {
+ private final double fpThreshold = 0.0001;
+ @Test
public void testPolygonalArea() {
ArrayList rightTriangle = new ArrayList(Arrays.asList(new Point(0, 0),
new Point(0, 2), new Point(2, 0)));
@@ -76,7 +76,7 @@ public void testPolygonalArea() {
pentagonExpected, pentagonArea), pentagonArea < pentagonExpected + fpThreshold
&& pentagonArea > pentagonExpected - fpThreshold);
}
-
+ @Test
public void testBuildSlopeBufferVertical() {
/******** Test a basic linear buffer vertically ************************************ */
@@ -134,7 +134,7 @@ public void testBuildSlopeBufferVertical() {
}
}
}
-
+ @Test
public void testBuildSlopeBufferHorizontal() {
/******** Test a basic linear buffer horizontally *********************************** */
@@ -194,7 +194,7 @@ public void testBuildSlopeBufferHorizontal() {
}
}
}
-
+ @Test
public void testLinearizeChromosome() throws IOException {
String currentPath = (new File(".")).getCanonicalPath();
String chromFile = currentPath + File.separator + "testData" + File.separator
@@ -272,7 +272,7 @@ public void testLinearizeChromosome() throws IOException {
}
}
}
-
+ @Test
public void testCalculateBandFunction() throws IOException {
String currentPath = (new File(".")).getCanonicalPath();
String linearChromFile = currentPath + File.separator + "testData" + File.separator
diff --git a/test/chromosome/GeneticSlideImageTest.java b/test/chromosome/GeneticSlideImageTest.java
index bb701f8..f1a2832 100644
--- a/test/chromosome/GeneticSlideImageTest.java
+++ b/test/chromosome/GeneticSlideImageTest.java
@@ -1,29 +1,29 @@
package chromosome;
+import org.junit.Before;
+import org.junit.Test;
import java.io.File;
import java.io.IOException;
-import chromosome.GeneticSlideImage;
+import static org.junit.Assert.assertEquals;
-import junit.framework.TestCase;
-
-public class GeneticSlideImageTest extends TestCase {
+public class GeneticSlideImageTest{
GeneticSlideImage slide;
- @Override
- protected void setUp() throws Exception {
+ @Before
+ public void setUp()throws Exception {
String currentPath = (new File(".")).getCanonicalPath();
String gradientImageFile = currentPath + File.separator + "testData" + File.separator
+ "GradientSwatch.png";
slide = new GeneticSlideImage(gradientImageFile);
}
-
+ @Test
public void testGetBackgroundThreshold() {
// Note that this test checks "proper behavior", however, it is very far from a "real world"
// test as we shouldn't see gradient images for slides.
assertEquals(139, slide.getBackgroundThreshold());
}
-
+ @Test
public void testComputeHistogram() throws IOException {
int[] expected = { 3, 3, 3, 1, 5, 5, 1, 7, 7, 1, 9, 9, 1, 11, 11, 3, 11, 13, 5, 11, 15, 7,
11, 17, 9, 11, 19, 11, 12, 20, 13, 14, 20, 15, 16, 20, 17, 18, 20, 19, 20, 21, 20,
diff --git a/test/color/PixelColorTest.java b/test/color/PixelColorTest.java
index fa75f3b..2cd385c 100644
--- a/test/color/PixelColorTest.java
+++ b/test/color/PixelColorTest.java
@@ -1,13 +1,14 @@
package color;
import java.awt.Color;
-
import color.PixelColor;
+import org.junit.Test;
-import junit.framework.TestCase;
-
-public class PixelColorTest extends TestCase {
+import static org.junit.Assert.assertFalse;
+import static org.junit.Assert.assertTrue;
+public class PixelColorTest {
+ @Test
public void testIsAboveThreshold() {
// Test for expected exception
boolean exceptionFlag = false;
diff --git a/test/extraction/ClusterSplitterTest.java b/test/extraction/ClusterSplitterTest.java
index d465887..8ac5007 100644
--- a/test/extraction/ClusterSplitterTest.java
+++ b/test/extraction/ClusterSplitterTest.java
@@ -2,24 +2,21 @@
import java.awt.Point;
import java.util.LinkedList;
-
import chromosome.ChromosomeCluster;
-import extraction.ClusterSplitter;
-
import basic_objects.PointList;
+import org.junit.Before;
+import org.junit.Test;
-import junit.framework.TestCase;
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertFalse;
+import static org.junit.Assert.assertTrue;
-public class ClusterSplitterTest extends TestCase {
+public class ClusterSplitterTest{
private ChromosomeCluster myCluster;
- protected void setUp() throws Exception {
- super.setUp();
+ @Before
+ public void setUp()throws Exception {
myCluster = new ChromosomeCluster(new Point(40, 40));
- initCluster();
- }
-
- public void initCluster() {
// create vertical chromosome
for (int i = 8; i < 16; i++) {
for (int j = 0; j < 28; j++) {
@@ -45,9 +42,9 @@ public void initCluster() {
myCluster.setPixel(new Point(19, 28), true);
myCluster.setPixel(new Point(18, 29), true);
myCluster.setSize(40, 40);
-
}
+ @Test
public void testGetCutPoints() {
int directions[] = { 3, 3, 3, 3, 6, 6, 6, 6 };
PointList tempList = ClusterSplitter.getCutPoints(new Point(14, 14), 1, 4, directions);
@@ -64,7 +61,7 @@ public void testGetCutPoints() {
assertTrue(tempList.getList().contains(new Point(14, 20)));
}
-
+ @Test
public void testGet4Lowest() {
int directions[] = { 3, 2, 10, 3, 9, 6, 9, 6 };
LinkedList tempList = ClusterSplitter.get4Lowest(directions);
@@ -75,7 +72,7 @@ public void testGet4Lowest() {
assertEquals(tempList.get(3).intValue(), 5);
}
-
+ @Test
public void testGetLowestOppisiteSide() {
int directions[] = { 3, 2, 10, 3, 9, 6, 9, 6 };
assertEquals(ClusterSplitter.getLowestOppisiteSide(0, directions), 3);
@@ -84,7 +81,7 @@ public void testGetLowestOppisiteSide() {
assertEquals(ClusterSplitter.getLowestOppisiteSide(7, directions), 3);
}
-
+ @Test
public void testIsCrossSectionPartOfCluster() {
int directions[] = { 3, 2, 10, 3, 9, 6, 9, 6 };
assertTrue(ClusterSplitter.isCrossSectionPartOfCluster(0, 3, directions, 5));
@@ -94,7 +91,7 @@ public void testIsCrossSectionPartOfCluster() {
assertFalse(ClusterSplitter.isCrossSectionPartOfCluster(0, 3, directions2, 5));
}
-
+ @Test
public void testGetQueenMoveLength() {
assertEquals(7, 12 - ClusterSplitter.getQueenMoveLength(myCluster, new Point(8, 27), 6, 12));
assertEquals(0, 12 - ClusterSplitter.getQueenMoveLength(myCluster, new Point(8, 27), 1, 12));
@@ -118,7 +115,7 @@ public void testGetQueenMoveLength() {
12 - ClusterSplitter.getQueenMoveLength(myCluster, new Point(8, 29), 0, 12));
}
-
+ @Test
public void testCheckForSplit() {
PointList tempList = ClusterSplitter.checkForSplit(myCluster, new Point(8, 29), 7);
assertEquals(tempList.getList().size(), 2);
diff --git a/test/extraction/ExtractorTest.java b/test/extraction/ExtractorTest.java
index 60793e9..ec1ac6e 100644
--- a/test/extraction/ExtractorTest.java
+++ b/test/extraction/ExtractorTest.java
@@ -6,23 +6,19 @@
import java.awt.image.BufferedImage;
import java.io.File;
import java.util.LinkedList;
-
import javax.imageio.ImageIO;
-import javax.imageio.ImageWriter;
-
import chromosome.ChromosomeCluster;
import chromosome.GeneticSlideImage;
+import basic_objects.SearchArea;
+import org.junit.Test;
-import extraction.Extractor;
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertFalse;
+import static org.junit.Assert.assertTrue;
-import basic_objects.SearchArea;
-import junit.framework.TestCase;
+public class ExtractorTest{
-public class ExtractorTest extends TestCase {
- protected void setUp() throws Exception {
- super.setUp();
- }
public SearchArea cutInHalf(SearchArea searchArea){
int middle=(int)Math.round(searchArea.getHeight()/2);
for(int i=0;i horizantolLine;
private LinkedList straightLine;
private DistanceMap distanceMap;
private DistanceMap distanceMapHorz;
private MedialAxisGraph testGraph;
private MirrorSplit mirror;
- protected void setUp() throws Exception {
- super.setUp();
+
+ @Before
+ public void setUp()throws Exception {
generateVertical();
generateHorizantal();
testGraph=new MedialAxisGraph();
@@ -53,6 +56,7 @@ protected void setUp() throws Exception {
horizantolLine.add(new Point(11, 7));
}
+
public void generateVertical(){
distanceMap = new DistanceMap(15, 15);
for (int i = 0; i < distanceMap.getWidth(); i++) {
@@ -78,6 +82,7 @@ public void generateHorizantal(){
}
}
+ @Test
public void testGetShortestDistance() {
MedialAxis tempAxis = new MedialAxis();
@@ -95,7 +100,7 @@ public void testGetShortestDistance() {
System.out.println(e);
}
- assertEquals(tempOrtho.getlength(), 8.0);
+ assertEquals(tempOrtho.getlength(), 8.0,.001);
assertEquals(tempOrtho.getUpperPoint(), new Point(3, 5));
assertEquals(tempOrtho.getLowerPoint(), new Point(11, 5));
@@ -116,7 +121,7 @@ public void testGetShortestDistance() {
System.out.println(e);
}
- assertEquals(tempOrtho.getlength(), 8.0);
+ assertEquals(tempOrtho.getlength(), 8.0,.001);
assertEquals(tempOrtho.getUpperPoint(), new Point(5, 3));
assertEquals(tempOrtho.getLowerPoint(), new Point(5, 11));
@@ -134,11 +139,12 @@ public void testGetShortestDistance() {
assertEquals(testGraph.getDistanceMap().getDistanceFromEdge(new Point(5, 3)), 0);
tempOrtho = mirror.getShortestDistance(bounds, new Point(-1, -1), new Point(5, 5),
testGraph.getChromoWidth(), distanceMapHorz);
- assertEquals(tempOrtho.getlength(), 8.0);
+ assertEquals(tempOrtho.getlength(), 8.0,.001);
assertEquals(tempOrtho.getUpperPoint(), new Point(5, 3));
assertEquals(tempOrtho.getLowerPoint(), new Point(5, 11));
}
+ @Test
public void testgetPathOrtho() {
MedialAxis tempAxis = new MedialAxis();
@@ -157,7 +163,7 @@ public void testgetPathOrtho() {
}
assertTrue(tempOrtho.isTwoLines());
- assertEquals(tempOrtho.getlength(), 8.0);
+ assertEquals(tempOrtho.getlength(), 8.0,.001);
assertEquals(tempOrtho.getUpperPoint(), new Point(3, 5));
assertEquals(tempOrtho.getLowerPoint(), new Point(11, 5));
@@ -280,7 +286,7 @@ public void testgetPathOrtho() {
assertEquals(tempOrtho.getLowerPoint(), new Point(5, 5));
- }
+ } @Test
public void testGetAllDistances() {
MedialAxis tempAxis = new MedialAxis();
tempAxis.setDistanceMap(distanceMap);
@@ -326,7 +332,7 @@ public void testGetAllDistances() {
- }
+ } @Test
public void testIsProjectionEnd(){
//test only one side oppisite previos touches distance map zero
generateHorizantal();
@@ -338,7 +344,7 @@ public void testIsProjectionEnd(){
assertTrue(mirror.isProjectionEnd(bounds, distanceMapHorz,new Vertex(new Point(5,7),5),new Vector(1,1)));
assertTrue(mirror.isProjectionEnd(bounds, distanceMapHorz,new Vertex(new Point(5,7),5),new Vector(-1,-1)));
- }
+ } @Test
public void testGetNextPoint(){
assertEquals(new Point(6,5), (mirror.getNextPoint(new Point(5,5), new Point(5,3), new Point(5,7), new Vector(1,0))).getPoint());
@@ -353,7 +359,7 @@ public void testGetNextPoint(){
assertEquals(new Point(6,8), (mirror.getNextPoint(new Point(5,8), new Point(5,4), new Point(5,10), new Vector(1,1))).getPoint());
assertEquals(new Point(7,9), (mirror.getNextPoint(new Point(5,8), new Point(5,4), new Point(5,10), new Vector(1,1))).getChildren().get(0).getPoint());
- }
+ } @Test
public void testGetNextVector(){
OrthogonalLine tempOrtho = new OrthogonalLine();
Vertex currPoint;
@@ -387,7 +393,7 @@ public void testGetNextVector(){
assertTrue(vect.x>-2&&vect.x<-1);
- }
+ } @Test
public void testRecenterForUpper(){
OrthogonalLine tempOrtho = new OrthogonalLine();
@@ -401,7 +407,7 @@ public void testRecenterForUpper(){
assertEquals(new Point(5,8),newPoint);
- }
+ } @Test
public void testRecenterForLower(){
OrthogonalLine tempOrtho = new OrthogonalLine();
Point newPoint;
@@ -413,7 +419,7 @@ public void testRecenterForLower(){
newPoint=mirror.recenterForLower(tempOrtho, 8);
assertEquals(new Point(9,1),newPoint);
- }
+ } @Test
public void testAngleBetween(){
OrthogonalLine tempOrtho = new OrthogonalLine();
diff --git a/test/medial_axis/MedialAxisGraphTest.java b/test/medial_axis/MedialAxisGraphTest.java
index a06512c..99a6fac 100644
--- a/test/medial_axis/MedialAxisGraphTest.java
+++ b/test/medial_axis/MedialAxisGraphTest.java
@@ -3,13 +3,15 @@
import java.awt.Point;
import java.util.ArrayList;
import java.util.LinkedList;
-
-import junit.framework.TestCase;
-import medial_axis.DistanceMap;
-import medial_axis.MedialAxisGraph;
import basic_objects.Vertex;
+import org.junit.Before;
+import org.junit.Test;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertFalse;
+import static org.junit.Assert.assertTrue;
-public class MedialAxisGraphTest extends TestCase {
+public class MedialAxisGraphTest{
private LinkedList straightLine;
private LinkedList diagonalLine;
private LinkedList curvedLine;
@@ -19,8 +21,8 @@ public class MedialAxisGraphTest extends TestCase {
private LinkedList chunk4TrimWith3brances;
private DistanceMap distanceMap;
- protected void setUp() throws Exception {
- super.setUp();
+ @Before
+ public void setUp()throws Exception {
distanceMap = new DistanceMap(15, 15);
for (int i = 0; i < distanceMap.getWidth(); i++) {
for (int j = 0; j < distanceMap.getHeight(); j++) {
@@ -167,7 +169,7 @@ protected void setUp() throws Exception {
this.chunk4TrimWith3brances.add(new Point(11, 12));
}
-
+ @Test
public void testBuildGraph() {
MedialAxisGraph testGraph = new MedialAxisGraph();
@@ -189,7 +191,7 @@ public void testBuildGraph() {
assertEquals(testGraph.getSegmentCount(), 3);
}
-
+ @Test
public void testRemoveSegments() {
LinkedList pointList;
@@ -205,7 +207,7 @@ public void testRemoveSegments() {
assertEquals(this.oneIntersection4branches.size() - 4, pointList.size());
}
-
+ @Test
public void testRemoveUnconnectedSegments() {
LinkedList pointList;
@@ -244,7 +246,7 @@ public void testRemoveUnconnectedSegments() {
.getMySegement(), 0);
}
-
+ @Test
public void testAddVertex() {
LinkedList pointList;
MedialAxisGraph testGraph = new MedialAxisGraph();
@@ -257,7 +259,7 @@ public void testAddVertex() {
assertEquals(testGraph.getSegmentCount(), 1);
assertEquals(testGraph.getIntersectionCount(testGraph.getAxisGraph()), 1);
- }
+ } @Test
public void testRemoveVertex(){
LinkedList pointList;
MedialAxisGraph testGraph = new MedialAxisGraph();
@@ -273,7 +275,7 @@ public void testRemoveVertex(){
}
-
+ @Test
public void testGetSegment() {
LinkedList pointList;
@@ -323,7 +325,7 @@ public void testGetSegment() {
assertEquals(orderedList.get(9).getPoint(), new Point(9,9));
assertEquals(orderedList.get(10).getPoint(), new Point(10,10));
}
-
+ @Test
public void testCheckTinyLoop() {
MedialAxisGraph testGraph = new MedialAxisGraph();
testGraph.buildGraph(this.oneIntersection4branches, distanceMap);
@@ -338,7 +340,7 @@ public void testCheckTinyLoop() {
assertEquals(new Point(4, 4), tempVertex.getPoint());
}
-
+ @Test
public void testFillInSkeleton() {
LinkedList pointList;
MedialAxisGraph testGraph = new MedialAxisGraph();
@@ -356,7 +358,7 @@ public void testFillInSkeleton() {
System.out.print(testGraph.getAxisGraph().get(i).getPoint().toString() + "--");
}
}
-
+ @Test
public void testGetBridgePoint() {
MedialAxisGraph testGraph = new MedialAxisGraph();
testGraph.buildGraph(this.threeSegmentGraph, distanceMap);
@@ -367,7 +369,7 @@ public void testGetBridgePoint() {
assertEquals(new Point(10, 11), testGraph.getBridgePoint(6, new Point(9, 11)));
assertEquals(new Point(10, 11), testGraph.getBridgePoint(6, new Point(9, 11)));
}
-
+ @Test
public void testCheckForMostNewConnection() {
MedialAxisGraph testGraph = new MedialAxisGraph();
testGraph.buildGraph(this.threeSegmentGraph, distanceMap);
@@ -378,7 +380,7 @@ public void testCheckForMostNewConnection() {
assertEquals(1, testGraph.checkForMostNewConnection(6, new Point(9, 11)));
assertEquals(1, testGraph.checkForMostNewConnection(6, new Point(9, 11)));
}
-
+ @Test
public void testSameSegment() {
LinkedList pointList;
MedialAxisGraph testGraph = new MedialAxisGraph();
@@ -391,7 +393,7 @@ public void testSameSegment() {
assertFalse(testGraph.sameSegment(new Point(9, 11), new Point(11, 11)));
}
-
+ @Test
public void testTrimGraph(){
LinkedList pointList;
MedialAxisGraph testGraph = new MedialAxisGraph();
@@ -409,7 +411,7 @@ public void testTrimGraph(){
assertFalse(pointList.contains(new Point(12, 11)));
assertTrue(pointList.contains(new Point(10, 10)));
- }
+ } @Test
public void testGetOrderedMedialAxis(){
MedialAxisGraph testGraph = new MedialAxisGraph();
diff --git a/test/medial_axis/MedialAxisTest.java b/test/medial_axis/MedialAxisTest.java
deleted file mode 100644
index 126def3..0000000
--- a/test/medial_axis/MedialAxisTest.java
+++ /dev/null
@@ -1,12 +0,0 @@
-package medial_axis;
-
-import junit.framework.TestCase;
-
-public class MedialAxisTest extends TestCase {
-
- protected void setUp() throws Exception {
- super.setUp();
-
- }
-
-}
diff --git a/test/medial_axis/SkeletonListTest.java b/test/medial_axis/SkeletonListTest.java
index 7e9d24f..09fdcb5 100644
--- a/test/medial_axis/SkeletonListTest.java
+++ b/test/medial_axis/SkeletonListTest.java
@@ -2,19 +2,20 @@
import java.awt.Point;
import java.util.LinkedList;
-
-import medial_axis.SkeletonList;
-
import basic_objects.PointList;
import basic_objects.Vertex;
+import org.junit.Before;
+import org.junit.Test;
-import junit.framework.TestCase;
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertFalse;
+import static org.junit.Assert.assertTrue;
-public class SkeletonListTest extends TestCase {
+public class SkeletonListTest{
private LinkedList vertList;
- protected void setUp() throws Exception {
- super.setUp();
+ @Before
+ public void setUp()throws Exception {
vertList = new LinkedList();
vertList.add(new Vertex(new Point(3, 1), 4));
vertList.add(new Vertex(new Point(2, 1), 5));
@@ -24,7 +25,7 @@ protected void setUp() throws Exception {
vertList.add(new Vertex(new Point(5, 1), 10));
}
-
+ @Test
public void testBuildFromVertexList() {
SkeletonList skelList = new SkeletonList();
@@ -41,7 +42,7 @@ public void testBuildFromVertexList() {
assertTrue(tempList2.getList().contains(new Point(5, 1)));
assertEquals(tempList2.getList().size(), 1);
}
-
+ @Test
public void testAdd() {
SkeletonList skelList = new SkeletonList();
skelList.add(new Point(4, 4), 6);
@@ -66,7 +67,7 @@ public void testAdd() {
assertEquals(skelList.getListAtDistance(6).getList().size(), 3);
}
-
+ @Test
public void testGetListAtDistance() {
SkeletonList skelList = new SkeletonList();
skelList.add(new Point(4, 4), 6);
@@ -82,7 +83,7 @@ public void testGetListAtDistance() {
assertTrue(tempList.getList().contains(new Point(7, 7)));
}
-
+ @Test
public void testGetOneList() {
SkeletonList skelList = new SkeletonList();
skelList.add(new Point(4, 4), 6);
diff --git a/test/symmetry/DetectSymmetryTest.java b/test/symmetry/DetectSymmetryTest.java
index 62a4cb3..c2991cf 100644
--- a/test/symmetry/DetectSymmetryTest.java
+++ b/test/symmetry/DetectSymmetryTest.java
@@ -5,37 +5,32 @@
import java.util.LinkedList;
+import org.junit.Before;
+import org.junit.Test;
import testing.TestShape;
import medial_axis.MedialAxisGraph;
import chromosome.ChromosomeCluster;
-import chromosome.ChromosomeList;
import chromosome.GeneticSlideImage;
-import junit.framework.TestCase;
+
+import static org.junit.Assert.fail;
/**
* @author Robert
*
*/
-public class DetectSymmetryTest extends TestCase {
+public class DetectSymmetryTest{
private GeneticSlideImage image;
private ChromosomeCluster cluster;
private MedialAxisGraph axisGraph;
- /**
- * @param name
- */
- public DetectSymmetryTest(String name) {
- super(name);
- }
-
/*
* (non-Javadoc)
*
* @see junit.framework.TestCase#setUp()
*/
- protected void setUp() throws Exception {
- super.setUp();
+ @Before
+ public void setUp()throws Exception {
String imagePath = ".\\testImages\\testImage1.png";
cluster = TestShape.getCluster(imagePath);
image = TestShape.getGeneticSlideImage();
@@ -44,20 +39,12 @@ protected void setUp() throws Exception {
axisGraph.generateOrthogonals(3, 5);
}
- /*
- * (non-Javadoc)
- *
- * @see junit.framework.TestCase#tearDown()
- */
- protected void tearDown() throws Exception {
- super.tearDown();
- }
-
/**
* Test method for
- * {@link symmetry.DetectSymmetryTest#detectWidthSymmetry(medial_axis.MedialAxisGraph, chromosome.GeneticSlideImage)}
+ * {@link symmetry.DetectSymmetryTest(medial_axis.MedialAxisGraph, chromosome.GeneticSlideImage)}
* .
*/
+ @Test
public void testDetectWidthSymmetry() {
DetectSymmetry.detectWidthSymmetry(axisGraph, image);
fail("Not yet implemented. DetectSymmetry may be obsolete (11/11/2012)");