diff --git a/pom.xml b/pom.xml
index ccc76c79c834426b21a4cc030259812f2b78c86f..e68ef3989c3e7d4f3a9b531146363b6f86ebbc85 100644
--- a/pom.xml
+++ b/pom.xml
@@ -85,7 +85,7 @@
<groupId>cz.it4i</groupId>
<artifactId>QcmpCompression</artifactId>
- <version>0.5-SNAPSHOT</version>
+ <version>0.5.5-EXP-SNAPSHOT</version>
<build>
<plugins>
<plugin>
@@ -157,7 +157,7 @@
<dependency>
<groupId>org.junit.jupiter</groupId>
<artifactId>junit-jupiter</artifactId>
- <version>RELEASE</version>
+ <version>5.7.0</version>
<scope>test</scope>
</dependency>
</dependencies>
diff --git a/src/main/java/cz/it4i/qcmp/benchmark/SQBenchmark.java b/src/main/java/cz/it4i/qcmp/benchmark/SQBenchmark.java
index 5d99107ca84674d8bf564c85f938b06287cf58eb..00b69d86277656cead551f7b4fb691a0488d1119 100644
--- a/src/main/java/cz/it4i/qcmp/benchmark/SQBenchmark.java
+++ b/src/main/java/cz/it4i/qcmp/benchmark/SQBenchmark.java
@@ -37,6 +37,7 @@ public class SQBenchmark extends BenchmarkBase {
if (planes.length < 1) {
return;
}
+
final boolean dirCreated = new File(this.outputDirectory).mkdirs();
System.out.println(String.format("|CODEBOOK| = %d", codebookSize));
ScalarQuantizer quantizer = null;
diff --git a/src/main/java/cz/it4i/qcmp/data/HyperStackDimensions.java b/src/main/java/cz/it4i/qcmp/data/HyperStackDimensions.java
index 101a5f5d2099fdc3a62a00558f22d7be5127296c..258de2d57e5ff9496177f1a65abd9c7284b67ecd 100644
--- a/src/main/java/cz/it4i/qcmp/data/HyperStackDimensions.java
+++ b/src/main/java/cz/it4i/qcmp/data/HyperStackDimensions.java
@@ -1,5 +1,7 @@
package cz.it4i.qcmp.data;
+import cz.it4i.qcmp.utilities.Utils;
+
import java.util.Objects;
/**
@@ -11,6 +13,7 @@ public class HyperStackDimensions {
private final int height;
private final int planeCount;
private final int numberOfTimepoints;
+ private final int numberOfChannels;
/**
* Create HyperStackDimensions.
@@ -19,37 +22,34 @@ public class HyperStackDimensions {
* @param height Height of the plane.
* @param planeCount Plane count in the stack.
* @param numberOfTimepoints Number of stack timepoints.
+ * @param channelCount Number of image channels.
*/
- public HyperStackDimensions(final int width, final int height, final int planeCount, final int numberOfTimepoints) {
+ public HyperStackDimensions(final int width,
+ final int height,
+ final int planeCount,
+ final int numberOfTimepoints,
+ final int channelCount) {
+ assert (channelCount == 1) : "QcmpCompressionLibrary support only single channel datasets.";
this.width = width;
this.height = height;
this.planeCount = planeCount;
this.numberOfTimepoints = numberOfTimepoints;
+ this.numberOfChannels = channelCount;
}
/**
- * Get number of elements in hyperstack with dimensionality = dimension.
- * When calculating the element count, overflow is checked. This is because result of this
- * function is usually used in places where we want to allocate memory.
+ * Create HyperStackDimensions.
*
- * @param dimension Maximum dimension.
- * @return Number of elements.
+ * @param width Width of the plane.
+ * @param height Height of the plane.
+ * @param planeCount Plane count in the stack.
+ * @param numberOfTimepoints Number of stack timepoints.
*/
- @SuppressWarnings("DuplicateExpressions")
- public int getNumberOfElementsInDimension(final int dimension) {
- switch (dimension) {
- case 1:
- return width;
- case 2:
- return Math.multiplyExact(width, height);
- case 3:
- return Math.multiplyExact(planeCount, Math.multiplyExact(width, height));
- case 4:
- return Math.multiplyExact(numberOfTimepoints, Math.multiplyExact(planeCount, Math.multiplyExact(width, height)));
- default:
- assert (false) : "Wrong dimension in getNumberOfElementsInDimension";
- return -1;
- }
+ public HyperStackDimensions(final int width,
+ final int height,
+ final int planeCount,
+ final int numberOfTimepoints) {
+ this(width, height, planeCount, numberOfTimepoints, 1);
}
/**
@@ -60,7 +60,7 @@ public class HyperStackDimensions {
* @param planeCount Plane count in the stack.
*/
public HyperStackDimensions(final int width, final int height, final int planeCount) {
- this(width, height, planeCount, 1);
+ this(width, height, planeCount, 1, 1);
}
/**
@@ -70,7 +70,46 @@ public class HyperStackDimensions {
* @param height Height of the plane.
*/
public HyperStackDimensions(final int width, final int height) {
- this(width, height, 1, 1);
+ this(width, height, 1, 1, 1);
+ }
+
+ /**
+ * Create HyperStackDimensions from ij.ImagePlus dimensions array.
+ *
+ * @param imagePlusDimensions ImagePlus dimensions.
+ * @return Correct HyperStackDimensions.
+ */
+ public static HyperStackDimensions createFromImagePlusDimensions(final int[] imagePlusDimensions) {
+ // NOTE(Moravec): ij.ImagePlus dimensions array = (width, height, nChannels, nSlices, nFrames)
+ return new HyperStackDimensions(imagePlusDimensions[0],
+ imagePlusDimensions[1],
+ imagePlusDimensions[3],
+ imagePlusDimensions[4],
+ imagePlusDimensions[2]);
+ }
+
+ /**
+ * Get number of elements in hyperstack with dimensionality = dimension.
+ * When calculating the element count, overflow is checked. This is because result of this
+ * function is usually used in places where we want to allocate memory.
+ *
+ * @param dimension Maximum dimension.
+ * @return Number of elements.
+ */
+ public int getNumberOfElementsInDimension(final int dimension) {
+ switch (dimension) {
+ case 1:
+ return width;
+ case 2:
+ return Math.multiplyExact(width, height);
+ case 3:
+ return Utils.multiplyExact(width, height, planeCount);
+ case 4:
+ return Utils.multiplyExact(width, height, planeCount, numberOfChannels);
+ default:
+ assert (false) : "Wrong dimension in getNumberOfElementsInDimension";
+ return -1;
+ }
}
/**
@@ -109,6 +148,14 @@ public class HyperStackDimensions {
return new V2i(width, height);
}
+ /**
+ * Get number of channels in the dataset.
+ *
+ * @return Channel count.
+ */
+ public int getNumberOfChannels() {
+ return numberOfChannels;
+ }
/**
* Get number of timepoints of the stack.
diff --git a/src/main/java/cz/it4i/qcmp/utilities/Utils.java b/src/main/java/cz/it4i/qcmp/utilities/Utils.java
index 3730c98670b4c585dca700e70fa46de29b14bc87..6d71079b747518e5bbd098cb6d5f6ca55be7a1f9 100644
--- a/src/main/java/cz/it4i/qcmp/utilities/Utils.java
+++ b/src/main/java/cz/it4i/qcmp/utilities/Utils.java
@@ -160,4 +160,36 @@ public class Utils {
}
return Math.sqrt(sum);
}
+
+ /**
+ * Returns the product of the arguments,
+ * throwing an exception if the result overflows an {@code int}.
+ *
+ * @param numbers values to multiply
+ * @return the result
+ * @throws ArithmeticException if the result overflows an int
+ */
+ public static int multiplyExact(final int... numbers) throws ArithmeticException {
+ int result = numbers[0];
+ for (int i = 1; i < numbers.length; i++) {
+ result = Math.multiplyExact(result, numbers[i]);
+ }
+ return result;
+ }
+
+ /**
+ * Returns the product of the arguments,
+ * throwing an exception if the result overflows an {@code int}.
+ *
+ * @param numbers values to multiply
+ * @return the result
+ * @throws ArithmeticException if the result overflows an int
+ */
+ public static long multiplyExact(final long... numbers) throws ArithmeticException {
+ long result = numbers[0];
+ for (int i = 1; i < numbers.length; i++) {
+ result = Math.multiplyExact(result, numbers[i]);
+ }
+ return result;
+ }
}
\ No newline at end of file
diff --git a/src/test/java/cz/it4i/qcmp/utilities/UtilsTest.java b/src/test/java/cz/it4i/qcmp/utilities/UtilsTest.java
new file mode 100644
index 0000000000000000000000000000000000000000..6b6de6c0a15cbbf1858f76cd98d6f29ac800a2d1
--- /dev/null
+++ b/src/test/java/cz/it4i/qcmp/utilities/UtilsTest.java
@@ -0,0 +1,18 @@
+package cz.it4i.qcmp.utilities;
+
+import org.junit.jupiter.api.Assertions;
+import org.junit.jupiter.api.Test;
+
+class UtilsTest {
+
+ @Test
+ void multiplyExact() {
+ final int a = 200;
+ final int b = 54;
+ final int c = 783;
+
+ final int refResult = Math.multiplyExact(a, Math.multiplyExact(b, c));
+ final int result = Utils.multiplyExact(a, b, c);
+ Assertions.assertEquals(refResult, result);
+ }
+}
\ No newline at end of file