Refactoring on plugin to add x, y and c projections

- git ignoring settings.xml and workspace folder
- Updated pom to 1.8.0 snapshot
- Updated pom parten to 1.0.4 to use Icy 2.1.3
- Implemented ProjectionCalculator to separate logic from plugin
- Updated Projection plugin to use ProjectionCalculator

.gitignore

-/target
+target/
+workspace/
+.settings/
+setting.xml
 .project
 .classpath
 *.prefs
 *.jardesc
-*.jar
-.settings/
+*.jar
\ No newline at end of file
\ No newline at end of file

pom.xml

@@ -8,12 +8,12 @@
     <parent>
         <groupId>org.bioimageanalysis.icy</groupId>
         <artifactId>parent-pom-plugin</artifactId>
-        <version>1.0.1</version>
+        <version>1.0.4</version>
     </parent>
 
     <!-- Project Information -->
     <artifactId>intensity-projection</artifactId>
-    <version>1.7.0-SNAPSHOT</version>
+    <version>1.8.0-SNAPSHOT</version>
     
     <packaging>jar</packaging>
 
@@ -77,7 +77,6 @@
         <dependency>
             <groupId>org.bioimageanalysis.icy</groupId>
             <artifactId>protocols</artifactId>
-            <version>${protocols.version}</version>
         </dependency>
     </dependencies>
 

src/main/java/org/bioimageanalysis/icy/image/projection/ProjectionAxis.java

+package org.bioimageanalysis.icy.image.projection;
+
+/**
+ * Indicates the direction on which the projection should be performed.
+ * 
+ * @author Daniel Felipe Gonzalez Obando
+ */
+public enum ProjectionAxis
+{
+    X("x"), Y("y"), Z("z"), T("t"), C("c");
+
+    private String name;
+
+    ProjectionAxis(String name)
+    {
+        this.name = name;
+    }
+
+    @Override
+    public String toString()
+    {
+        return name;
+    }
+}

src/main/java/org/bioimageanalysis/icy/image/projection/ProjectionOperationType.java

+/**
+ * 
+ */
+package org.bioimageanalysis.icy.image.projection;
+
+/**
+ * Represents the operation to be applied when performing an intensity projection on a sequence.
+ * 
+ * @author Daniel Felipe Gonzalez Obando
+ */
+public enum ProjectionOperationType
+{
+    MAX("Maximum"), MEAN("Average"), MED("Median"), MIN("Minimum"), STD("Standard Deviation"), SATSUM("Saturated Sum");
+
+    private final String description;
+
+    ProjectionOperationType(String description)
+    {
+        this.description = description;
+    }
+
+    @Override
+    public String toString()
+    {
+        return description;
+    }
+}

src/main/java/org/bioimageanalysis/icy/image/projection/util/MessageProgressListener.java

+/**
+ * 
+ */
+package org.bioimageanalysis.icy.image.projection.util;
+
+/**
+ * A Progress event listener that handles events associating a value and a message to them.
+ * 
+ * @author Daniel Felipe Gonzalez Obando
+ */
+public interface MessageProgressListener
+{
+    /**
+     * A method handling progress events with a value and a message.
+     * 
+     * @param progress
+     *        The progress value from 0.0 to 1.0. {@link Double#NaN} value should be taken as no change and -1.0 as indeterminate progress.
+     * @param message
+     *        The event message. A null value should be taken as no change on the message.
+     */
+    void onProgress(double progress, String message);
+}

src/main/java/org/bioimageanalysis/icy/image/projection/util/SequenceCursor.java

+package org.bioimageanalysis.icy.image.projection.util;
+
+import java.util.concurrent.atomic.AtomicBoolean;
+
+import icy.sequence.Sequence;
+
+/**
+ * This class allows to optimally access randomly around a {@link Sequence}. Instances of this class can perform reading and writing operations on
+ * non-contiguous positions of the sequence without incurring in important performance issues. When a set of modifications to pixel data is performed a call to
+ * {@link #commitChanges()} must be made in order to make this changes permanent of the image and let other resources using the image be aware of to these
+ * changes.
+ * 
+ * @author Daniel Felipe Gonzalez Obando
+ */
+public class SequenceCursor
+{
+    private Sequence seq;
+    private VolumetricImageCursor[] volumeCursors;
+    private AtomicBoolean sequenceChanged;
+
+    /**
+     * Creates a cursor for the given sequence {@code seq}.
+     */
+    public SequenceCursor(Sequence seq)
+    {
+        this.seq = seq;
+        this.volumeCursors = new VolumetricImageCursor[seq.getSizeT()];
+        this.sequenceChanged = new AtomicBoolean();
+        this.currentT = -1;
+    }
+
+    /**
+     * Retrieves the intensity of the channel {@code c} of the pixel located at position ({@code x}, {@code y}, {@code z}) at time {@code t}.
+     * 
+     * @param x
+     *        Position in the X-axis.
+     * @param y
+     *        Position in the Y-axis.
+     * @param z
+     *        Position in the Z-axis.
+     * @param t
+     *        Time point index.
+     * @param c
+     *        Channel index.
+     * @return Intensity value at specified position.
+     * @throws IndexOutOfBoundsException
+     *         If the position is not in the image.
+     * @throws RuntimeException
+     *         If the data type is not a valid format.
+     */
+    public double get(int x, int y, int z, int t, int c) throws IndexOutOfBoundsException, RuntimeException
+    {
+        return getVolumeCursor(t).get(x, y, z, c);
+    }
+
+    /**
+     * Sets the intensity of the channel {@code c} of the pixel located at position ({@code x}, {@code y}, {@code z}) at time {@code t}.
+     * 
+     * @param x
+     *        Position in the X-axis.
+     * @param y
+     *        Position in the Y-axis.
+     * @param z
+     *        Position in the Z-axis.
+     * @param t
+     *        Time point index.
+     * @param c
+     *        Channel index.
+     * @param val
+     *        Intensity value to set.
+     * @throws IndexOutOfBoundsException
+     *         If the position is not in the image.
+     * @throws RuntimeException
+     *         If the data type is not a valid format.
+     */
+    public synchronized void set(int x, int y, int z, int t, int c, double val)
+            throws IndexOutOfBoundsException, RuntimeException
+    {
+        getVolumeCursor(t).set(x, y, z, c, val);
+        sequenceChanged.set(true);
+    }
+
+    /**
+     * Sets the intensity of the channel {@code c} of the pixel located at position ({@code x}, {@code y}, {@code z}) at time {@code t}. This method limits the
+     * value of the intensity according to the image data type value range.
+     * 
+     * @param x
+     *        Position in the X-axis.
+     * @param y
+     *        Position in the Y-axis.
+     * @param z
+     *        Position in the Z-axis.
+     * @param t
+     *        Time point index.
+     * @param c
+     *        Channel index.
+     * @param val
+     *        Intensity value to set.
+     * @throws IndexOutOfBoundsException
+     *         If the position is not in the image.
+     * @throws RuntimeException
+     *         If the data type is not a valid format.
+     */
+    public synchronized void setSafe(int x, int y, int z, int t, int c, double val)
+            throws IndexOutOfBoundsException, RuntimeException
+    {
+        getVolumeCursor(t).setSafe(x, y, z, c, val);
+        sequenceChanged.set(true);
+    }
+
+    private int currentT;
+    private VolumetricImageCursor currentCursor;
+
+    private synchronized VolumetricImageCursor getVolumeCursor(int t) throws IndexOutOfBoundsException
+    {
+        if (currentT != t)
+        {
+            if (volumeCursors[t] == null)
+            {
+                volumeCursors[t] = new VolumetricImageCursor(seq, t);
+            }
+            currentCursor = volumeCursors[t];
+            currentT = t;
+        }
+        return currentCursor;
+    }
+
+    /**
+     * This method should be called after a set of intensity changes have been made to the target sequence. This methods allows other resources using the target
+     * sequence to be informed about the changes made to it.
+     */
+    public synchronized void commitChanges()
+    {
+        if (sequenceChanged.get())
+        {
+            for (int i = 0; i < volumeCursors.length; i++)
+            {
+                if (volumeCursors[i] != null)
+                    volumeCursors[i].commitChanges();
+            }
+            sequenceChanged.set(false);
+        }
+    }
+
+    @Override
+    public String toString()
+    {
+        return "last T=" + currentT + " " + currentCursor != null ? currentCursor.toString() : "";
+    }
+}

src/main/java/org/bioimageanalysis/icy/image/projection/util/VolumetricImageCursor.java

+package org.bioimageanalysis.icy.image.projection.util;
+
+import java.util.concurrent.atomic.AtomicBoolean;
+
+import icy.image.IcyBufferedImageCursor;
+import icy.sequence.Sequence;
+import icy.sequence.VolumetricImage;
+
+/**
+ * This class allows to optimally access randomly around an {@link VolumetricImage}. Instances of this class can perform reading and writing operations on
+ * non-contiguous positions of the volume without incurring in important performance issues. When a set of modifications to pixel data is performed a call to
+ * {@link #commitChanges()} must be made in order to make this changes permanent of the image and let other resources using the image be aware of to these
+ * changes.
+ * 
+ * @author Daniel Felipe Gonzalez Obando
+ */
+public class VolumetricImageCursor
+{
+    private VolumetricImage vol;
+
+    private AtomicBoolean volumeChanged;
+
+    private IcyBufferedImageCursor[] planeCursors;
+
+    /**
+     * Creates a cursor on the given volume {@code vol}.
+     * 
+     * @param vol
+     *        Target volume.
+     */
+    public VolumetricImageCursor(VolumetricImage vol)
+    {
+        this.vol = vol;
+        planeCursors = new IcyBufferedImageCursor[vol.getSize()];
+        volumeChanged = new AtomicBoolean(false);
+        currentZ = -1;
+    }
+
+    /**
+     * Creates a cursor on the volume at time position {@code t} in the given sequence {@code seq}.
+     * 
+     * @param seq
+     *        Target sequence.
+     * @param t
+     *        Time position where the volume is located in {@code seq}.
+     */
+    public VolumetricImageCursor(Sequence seq, int t)
+    {
+        this(seq.getVolumetricImage(t));
+    }
+
+    /**
+     * Retrieves the intensity of the channel {@code c} of the pixel located at position ({@code x}, {@code y}, {@code z}).
+     * 
+     * @param x
+     *        Position in the X-axis.
+     * @param y
+     *        Position in the Y-axis.
+     * @param z
+     *        Position in the Z-axis.
+     * @param c
+     *        Channel index.
+     * @return Intensity value at specified position.
+     * @throws IndexOutOfBoundsException
+     *         If the position is not in the image.
+     * @throws RuntimeException
+     *         If the data type is not a valid format.
+     */
+    public double get(int x, int y, int z, int c) throws IndexOutOfBoundsException, RuntimeException
+    {
+        return getPlaneCursor(z).get(x, y, c);
+
+    }
+
+    /**
+     * Sets the intensity of the channel {@code c} of the pixel located at position ({@code x}, {@code y}, {@code z}).
+     * 
+     * @param x
+     *        Position in the X-axis.
+     * @param y
+     *        Position in the Y-axis.
+     * @param z
+     *        Position in the Z-axis.
+     * @param c
+     *        Channel index.
+     * @param val
+     *        Intensity value to set.
+     * @throws IndexOutOfBoundsException
+     *         If the position is not in the image.
+     * @throws RuntimeException
+     *         If the data type is not a valid format.
+     */
+    public synchronized void set(int x, int y, int z, int c, double val)
+            throws IndexOutOfBoundsException, RuntimeException
+    {
+        getPlaneCursor(z).set(x, y, c, val);
+        volumeChanged.set(true);
+    }
+
+    /**
+     * Sets the intensity of the channel {@code c} of the pixel located at position ({@code x}, {@code y}, {@code z}). This method limits the
+     * value of the intensity according to the image data type value range.
+     * 
+     * @param x
+     *        Position in the X-axis.
+     * @param y
+     *        Position in the Y-axis.
+     * @param z
+     *        Position in the Z-axis.
+     * @param c
+     *        Channel index.
+     * @param val
+     *        Intensity value to set.
+     * @throws IndexOutOfBoundsException
+     *         If the position is not in the image.
+     * @throws RuntimeException
+     *         If the data type is not a valid format.
+     */
+    public synchronized void setSafe(int x, int y, int z, int c, double val)
+            throws IndexOutOfBoundsException, RuntimeException
+    {
+        getPlaneCursor(z).setSafe(x, y, c, val);
+        volumeChanged.set(true);
+    }
+
+    private IcyBufferedImageCursor currentCursor;
+    private int currentZ;
+
+    private synchronized IcyBufferedImageCursor getPlaneCursor(int z) throws IndexOutOfBoundsException
+    {
+        if (currentZ != z)
+        {
+            if (planeCursors[z] == null)
+            {
+                planeCursors[z] = new IcyBufferedImageCursor(vol.getImage(z));
+            }
+            currentCursor = planeCursors[z];
+            currentZ = z;
+        }
+        return currentCursor;
+    }
+
+    /**
+     * This method should be called after a set of intensity changes have been made to the target volume. This methods allows other resources using the target
+     * volume to be informed about the changes made to it.
+     */
+    public synchronized void commitChanges()
+    {
+        if (volumeChanged.get())
+        {
+            for (int i = 0; i < planeCursors.length; i++)
+            {
+                if (planeCursors[i] != null)
+                    planeCursors[i].commitChanges();
+            }
+            volumeChanged.set(false);
+        }
+    }
+
+    @Override
+    public String toString()
+    {
+        return "last Z=" + currentZ + " " + currentCursor != null ? currentCursor.toString() : "";
+    }
+}