Updated for compatibility with MIA 0.12.0

Former-commit-id: b4379e9

.project

@@ -0,0 +1,17 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<projectDescription>
+	<name>VideoHandler</name>
+	<comment></comment>
+	<projects>
+	</projects>
+	<buildSpec>
+		<buildCommand>
+			<name>org.eclipse.m2e.core.maven2Builder</name>
+			<arguments>
+			</arguments>
+		</buildCommand>
+	</buildSpec>
+	<natures>
+		<nature>org.eclipse.m2e.core.maven2Nature</nature>
+	</natures>
+</projectDescription>

.settings/org.eclipse.core.resources.prefs

@@ -0,0 +1,2 @@
+eclipse.preferences.version=1
+encoding/<project>=UTF-8

.settings/org.eclipse.m2e.core.prefs

@@ -0,0 +1,4 @@
+activeProfiles=
+eclipse.preferences.version=1
+resolveWorkspaceProjects=true
+version=1

.vscode/settings.json

@@ -0,0 +1,3 @@
+{
+    "java.configuration.updateBuildConfiguration": "automatic"
+}

core/.classpath

@@ -0,0 +1,49 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<classpath>
+	<classpathentry kind="src" output="target/classes" path="src/main/java">
+		<attributes>
+			<attribute name="optional" value="true"/>
+			<attribute name="maven.pomderived" value="true"/>
+		</attributes>
+	</classpathentry>
+	<classpathentry excluding="**" kind="src" output="target/classes" path="src/main/resources">
+		<attributes>
+			<attribute name="maven.pomderived" value="true"/>
+		</attributes>
+	</classpathentry>
+	<classpathentry kind="src" output="target/test-classes" path="src/test/java">
+		<attributes>
+			<attribute name="optional" value="true"/>
+			<attribute name="maven.pomderived" value="true"/>
+			<attribute name="test" value="true"/>
+		</attributes>
+	</classpathentry>
+	<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-1.8">
+		<attributes>
+			<attribute name="maven.pomderived" value="true"/>
+		</attributes>
+	</classpathentry>
+	<classpathentry kind="con" path="org.eclipse.m2e.MAVEN2_CLASSPATH_CONTAINER">
+		<attributes>
+			<attribute name="maven.pomderived" value="true"/>
+		</attributes>
+	</classpathentry>
+	<classpathentry kind="src" path="target/generated-sources/annotations">
+		<attributes>
+			<attribute name="optional" value="true"/>
+			<attribute name="maven.pomderived" value="true"/>
+			<attribute name="ignore_optional_problems" value="true"/>
+			<attribute name="m2e-apt" value="true"/>
+		</attributes>
+	</classpathentry>
+	<classpathentry kind="src" output="target/test-classes" path="target/generated-test-sources/test-annotations">
+		<attributes>
+			<attribute name="optional" value="true"/>
+			<attribute name="maven.pomderived" value="true"/>
+			<attribute name="ignore_optional_problems" value="true"/>
+			<attribute name="m2e-apt" value="true"/>
+			<attribute name="test" value="true"/>
+		</attributes>
+	</classpathentry>
+	<classpathentry kind="output" path="target/classes"/>
+</classpath>

core/.project

@@ -0,0 +1,23 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<projectDescription>
+	<name>core</name>
+	<comment></comment>
+	<projects>
+	</projects>
+	<buildSpec>
+		<buildCommand>
+			<name>org.eclipse.jdt.core.javabuilder</name>
+			<arguments>
+			</arguments>
+		</buildCommand>
+		<buildCommand>
+			<name>org.eclipse.m2e.core.maven2Builder</name>
+			<arguments>
+			</arguments>
+		</buildCommand>
+	</buildSpec>
+	<natures>
+		<nature>org.eclipse.jdt.core.javanature</nature>
+		<nature>org.eclipse.m2e.core.maven2Nature</nature>
+	</natures>
+</projectDescription>

core/.settings/org.eclipse.core.resources.prefs

@@ -0,0 +1,4 @@
+eclipse.preferences.version=1
+encoding//src/main/java=UTF-8
+encoding//src/main/resources=UTF-8
+encoding/<project>=UTF-8

core/.settings/org.eclipse.jdt.apt.core.prefs

@@ -0,0 +1,4 @@
+eclipse.preferences.version=1
+org.eclipse.jdt.apt.aptEnabled=true
+org.eclipse.jdt.apt.genSrcDir=target\\generated-sources\\annotations
+org.eclipse.jdt.apt.genTestSrcDir=target\\generated-test-sources\\test-annotations

core/.settings/org.eclipse.jdt.core.prefs

@@ -0,0 +1,9 @@
+eclipse.preferences.version=1
+org.eclipse.jdt.core.compiler.codegen.targetPlatform=1.8
+org.eclipse.jdt.core.compiler.compliance=1.8
+org.eclipse.jdt.core.compiler.problem.enablePreviewFeatures=disabled
+org.eclipse.jdt.core.compiler.problem.forbiddenReference=warning
+org.eclipse.jdt.core.compiler.problem.reportPreviewFeatures=ignore
+org.eclipse.jdt.core.compiler.processAnnotations=enabled
+org.eclipse.jdt.core.compiler.release=disabled
+org.eclipse.jdt.core.compiler.source=1.8

core/.settings/org.eclipse.m2e.core.prefs

@@ -0,0 +1,4 @@
+activeProfiles=
+eclipse.preferences.version=1
+resolveWorkspaceProjects=true
+version=1

core/dependency-reduced-pom.xml

@@ -3,7 +3,7 @@
   <parent>
     <artifactId>VideoHandler</artifactId>
     <groupId>wbif.sjx</groupId>
-    <version>1.0.0</version>
+    <version>1.0.1</version>
   </parent>
   <modelVersion>4.0.0</modelVersion>
   <artifactId>core</artifactId>
@@ -25,7 +25,7 @@
     <dependency>
       <groupId>com.github.SJCross</groupId>
       <artifactId>ModularImageAnalysis</artifactId>
-      <version>0.11.15</version>
+      <version>0.12.0</version>
       <scope>provided</scope>
       <exclusions>
         <exclusion>
@@ -109,12 +109,8 @@
           <groupId>de.biomedical-imaging.imagej</groupId>
         </exclusion>
         <exclusion>
-          <artifactId>javacv-platform</artifactId>
-          <groupId>org.bytedeco</groupId>
-        </exclusion>
-        <exclusion>
-          <artifactId>reflections</artifactId>
-          <groupId>org.reflections</groupId>
+          <artifactId>classgraph</artifactId>
+          <groupId>io.github.classgraph</groupId>
         </exclusion>
         <exclusion>
           <artifactId>commonmark</artifactId>

core/pom.xml

@@ -5,7 +5,7 @@
     <parent>
         <artifactId>VideoHandler</artifactId>
         <groupId>wbif.sjx</groupId>
-        <version>1.0.0</version>
+        <version>1.0.1</version>
     </parent>
     <modelVersion>4.0.0</modelVersion>
 
@@ -49,7 +49,7 @@
         <dependency>
             <groupId>com.github.SJCross</groupId>
             <artifactId>ModularImageAnalysis</artifactId>
-            <version>0.11.15</version>
+            <version>0.12.0</version>
             <scope>${myscope}</scope>
         </dependency>
     </dependencies>

core/src/main/java/wbif/sjx/VideoHandler/VideoLoader.java

@@ -1,37 +1,34 @@
 package wbif.sjx.VideoHandler;
 
-import ij.IJ;
+import org.apache.commons.io.FilenameUtils;
+
 import ij.ImagePlus;
-import ij.ImageStack;
 import ij.measure.Calibration;
-import ij.plugin.ChannelSplitter;
-import ij.process.ImageProcessor;
-import org.apache.commons.io.FilenameUtils;
 import wbif.sjx.MIA.MIA;
-import wbif.sjx.MIA.Module.ImageProcessing.Stack.ConvertStackToTimeseries;
-import wbif.sjx.MIA.Module.InputOutput.ImageLoader;
 import wbif.sjx.MIA.Module.Module;
 import wbif.sjx.MIA.Module.ModuleCollection;
 import wbif.sjx.MIA.Module.PackageNames;
+import wbif.sjx.MIA.Module.InputOutput.ImageLoader;
 import wbif.sjx.MIA.Object.Image;
-import wbif.sjx.MIA.Object.Parameters.*;
+import wbif.sjx.MIA.Object.Units;
+import wbif.sjx.MIA.Object.Workspace;
+import wbif.sjx.MIA.Object.Parameters.BooleanP;
+import wbif.sjx.MIA.Object.Parameters.ChoiceP;
+import wbif.sjx.MIA.Object.Parameters.DoubleP;
+import wbif.sjx.MIA.Object.Parameters.FilePathP;
+import wbif.sjx.MIA.Object.Parameters.InputImageP;
+import wbif.sjx.MIA.Object.Parameters.IntegerP;
+import wbif.sjx.MIA.Object.Parameters.OutputImageP;
+import wbif.sjx.MIA.Object.Parameters.ParamSeparatorP;
+import wbif.sjx.MIA.Object.Parameters.ParameterCollection;
+import wbif.sjx.MIA.Object.Parameters.StringP;
+import wbif.sjx.MIA.Object.Parameters.TextAreaP;
 import wbif.sjx.MIA.Object.References.ImageMeasurementRefCollection;
 import wbif.sjx.MIA.Object.References.MetadataRefCollection;
 import wbif.sjx.MIA.Object.References.ObjMeasurementRefCollection;
 import wbif.sjx.MIA.Object.References.RelationshipRefCollection;
-import wbif.sjx.MIA.Object.Units;
-import wbif.sjx.MIA.Object.Workspace;
-import wbif.sjx.MIA.Process.CommaSeparatedStringInterpreter;
 import wbif.sjx.common.Object.Metadata;
 
-import javax.annotation.Nullable;
-import java.io.FileNotFoundException;
-import java.util.Arrays;
-import java.util.TreeSet;
-import java.util.stream.Collectors;
-
-import static wbif.sjx.MIA.Module.ImageProcessing.Stack.ExtractSubstack.extendRangeToEnd;
-
 public class VideoLoader extends Module {
     public static final String LOADER_SEPARATOR = "Core video loading controls";
     public static final String OUTPUT_IMAGE = "Output image";
@@ -103,14 +100,12 @@ public interface Measurements {
     public String getGenericName(Metadata metadata, String genericFormat) {
         String absolutePath = metadata.getFile().getAbsolutePath();
         String path = FilenameUtils.getFullPath(absolutePath);
-        String name = FilenameUtils.removeExtension(FilenameUtils.getName(absolutePath));
-        String comment = metadata.getComment();
         String filename = ImageLoader.compileGenericFilename(genericFormat, metadata);
         return path + filename;
 
     }
 
-    public String getPrefixName(Metadata metadata, int seriesNumber, boolean includeSeries, String ext) {
+    public String getPrefixName(Metadata metadata, boolean includeSeries, String ext) {
         String absolutePath = metadata.getFile().getAbsolutePath();
         String path = FilenameUtils.getFullPath(absolutePath);
         String name = FilenameUtils.removeExtension(FilenameUtils.getName(absolutePath));
@@ -121,7 +116,7 @@ public String getPrefixName(Metadata metadata, int seriesNumber, boolean include
 
     }
 
-    public String getSuffixName(Metadata metadata, int seriesNumber, boolean includeSeries, String ext ) {
+    public String getSuffixName(Metadata metadata, boolean includeSeries, String ext ) {
         String absolutePath = metadata.getFile().getAbsolutePath();
         String path = FilenameUtils.getFullPath(absolutePath);
         String name = FilenameUtils.removeExtension(FilenameUtils.getName(absolutePath));
@@ -168,9 +163,6 @@ public boolean process(Workspace workspace) {
         double xyCal = parameters.getValue(XY_CAL);
         double zCal = parameters.getValue(Z_CAL);
 
-        // Series number comes from the Workspace
-        int seriesNumber = workspace.getMetadata().getSeriesNumber();
-
         int[] crop = null;
         switch (cropMode) {
             case CropModes.FIXED:
@@ -199,13 +191,13 @@ public boolean process(Workspace workspace) {
                     case NameFormats.INPUT_FILE_PREFIX:
                         metadata = (Metadata) workspace.getMetadata().clone();
                         metadata.setComment(prefix);
-                        pathName = getPrefixName(metadata, seriesNumber,  includeSeriesNumber,ext);
+                        pathName = getPrefixName(metadata,  includeSeriesNumber,ext);
                         break;
 
                     case NameFormats.INPUT_FILE_SUFFIX:
                         metadata = (Metadata) workspace.getMetadata().clone();
                         metadata.setComment(suffix);
-                        pathName = getSuffixName(metadata, seriesNumber, includeSeriesNumber,ext);
+                        pathName = getSuffixName(metadata, includeSeriesNumber,ext);
                         break;
                 }
                 break;
@@ -217,7 +209,6 @@ public boolean process(Workspace workspace) {
 
         if (pathName == null) return false;
 
-        String extension = FilenameUtils.getExtension(pathName);
         Image outputImage = null;
         try {
             // First first, testing new loader
@@ -245,9 +236,6 @@ public boolean process(Workspace workspace) {
 
         }
 
-        // Converting RGB to 3-channel
-        ImagePlus outputImagePlus = outputImage.getImagePlus();
-
         // Adding image to workspace
         writeMessage("Adding image (" + outputImageName + ") to workspace");
         workspace.addImage(outputImage);
@@ -352,7 +340,7 @@ public ParameterCollection updateAndGetParameters() {
 
         returnedParameters.add(parameters.getParameter(CALIBRATION_SEPARATOR));
         returnedParameters.add(parameters.getParameter(SET_CAL));
-        if (parameters.getValue(SET_CAL)) {
+        if ((boolean) parameters.getValue(SET_CAL)) {
             returnedParameters.add(parameters.getParameter(XY_CAL));
             returnedParameters.add(parameters.getParameter(Z_CAL));
         }

core/src/main/java/wbif/sjx/VideoHandler/VideoLoaderCore.java

@@ -88,6 +88,9 @@ public static ImagePlus getVideo(String path, String frameRange, String channelR
             ipl.getCalibration().pixelDepth = 1;
         }
 
+        // Closing the loader
+        loader.close();
+
         return ipl;
 
     }
@@ -104,7 +107,7 @@ public static void convertToTimeseries(ImagePlus inputImagePlus) {
     }
 
     public static int[] extendRangeToEnd(int[] inputRange, int end) {
-        TreeSet<Integer> values = new TreeSet();
+        TreeSet<Integer> values = new TreeSet<>();
 
         int start;
         for(start = 0; start < inputRange.length - 3; ++start) {

core/src/main/java/wbif/sjx/VideoHandler/Video_Loader.java

@@ -1,12 +1,11 @@
 package wbif.sjx.VideoHandler;
 
-import ij.ImagePlus;
+import java.io.File;
+
 import ij.gui.GenericDialog;
 import ij.io.OpenDialog;
 import ij.plugin.PlugIn;
 
-import java.io.File;
-
 public class Video_Loader implements PlugIn {
     @Override
     public void run(String path) {

linux32/.classpath

@@ -0,0 +1,44 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<classpath>
+	<classpathentry kind="src" output="target/classes" path="src/main/java">
+		<attributes>
+			<attribute name="optional" value="true"/>
+			<attribute name="maven.pomderived" value="true"/>
+		</attributes>
+	</classpathentry>
+	<classpathentry kind="src" output="target/test-classes" path="src/test/java">
+		<attributes>
+			<attribute name="optional" value="true"/>
+			<attribute name="maven.pomderived" value="true"/>
+			<attribute name="test" value="true"/>
+		</attributes>
+	</classpathentry>
+	<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-1.8">
+		<attributes>
+			<attribute name="maven.pomderived" value="true"/>
+		</attributes>
+	</classpathentry>
+	<classpathentry kind="con" path="org.eclipse.m2e.MAVEN2_CLASSPATH_CONTAINER">
+		<attributes>
+			<attribute name="maven.pomderived" value="true"/>
+		</attributes>
+	</classpathentry>
+	<classpathentry kind="src" path="target/generated-sources/annotations">
+		<attributes>
+			<attribute name="optional" value="true"/>
+			<attribute name="maven.pomderived" value="true"/>
+			<attribute name="ignore_optional_problems" value="true"/>
+			<attribute name="m2e-apt" value="true"/>
+		</attributes>
+	</classpathentry>
+	<classpathentry kind="src" output="target/test-classes" path="target/generated-test-sources/test-annotations">
+		<attributes>
+			<attribute name="optional" value="true"/>
+			<attribute name="maven.pomderived" value="true"/>
+			<attribute name="ignore_optional_problems" value="true"/>
+			<attribute name="m2e-apt" value="true"/>
+			<attribute name="test" value="true"/>
+		</attributes>
+	</classpathentry>
+	<classpathentry kind="output" path="target/classes"/>
+</classpath>