Merge pull request #72 from kmdouglass/ADD_Image_Abstraction

Add image abstraction

CHANGELOG.md

@@ -6,6 +6,8 @@ All notable changes to this project will be documented in this file.
 ### Added
 - An RPC server was created that allows for remote control of the
   simulation over the network.
+- A new image abstraction layer called **ImageS** that separates image
+  data logic and display from the SASS core code.
 
 ### Changed
 - The package layout was restructured and simplified to make it easier

build.xml

@@ -3,7 +3,7 @@
 <project name="SASS" default="default" basedir=".">
     <description>Builds, tests, and runs the project SASS.</description>
     <import file="nbproject/build-impl.xml"/>
-    <property name="pluginsDir"  location="/home/douglass/apps/Fiji.app/plugins" />
+    <property name="pluginsDir"  location="/home/kmdouglass/apps/Fiji.app/plugins" />
     <property name="store.jar.name" value="SASS_0.6.1.jar"/>
     <property name="store.dir" value="store"/>
     <property name="store.jar" value="${store.dir}/${store.jar.name}"/>

nbproject/build-impl.xml

@@ -19,7 +19,7 @@ is divided into following sections:
   - cleanup
 
         -->
-<project xmlns:j2seproject1="http://www.netbeans.org/ns/j2se-project/1" xmlns:j2seproject3="http://www.netbeans.org/ns/j2se-project/3" xmlns:jaxrpc="http://www.netbeans.org/ns/j2se-project/jax-rpc" basedir=".." default="default" name="SASS-dev-impl">
+<project xmlns:j2seproject1="http://www.netbeans.org/ns/j2se-project/1" xmlns:j2seproject3="http://www.netbeans.org/ns/j2se-project/3" xmlns:jaxrpc="http://www.netbeans.org/ns/j2se-project/jax-rpc" basedir=".." default="default" name="SASS-impl">
     <fail message="Please build using Ant 1.8.0 or higher.">
         <condition>
             <not>
@@ -46,8 +46,8 @@ is divided into following sections:
         <property file="${user.properties.file}"/>
         <!-- The two properties below are usually overridden -->
         <!-- by the active platform. Just a fallback. -->
-        <property name="default.javac.source" value="1.6"/>
-        <property name="default.javac.target" value="1.6"/>
+        <property name="default.javac.source" value="1.4"/>
+        <property name="default.javac.target" value="1.4"/>
     </target>
     <target depends="-pre-init,-init-private,-init-user" name="-init-project">
         <property file="nbproject/configs/${config}.properties"/>
@@ -76,7 +76,7 @@ is divided into following sections:
             <and>
                 <isset property="javac.profile"/>
                 <length length="0" string="${javac.profile}" when="greater"/>
-                <matches pattern="((1\.[89])|9)(\..*)?" string="${javac.source}"/>
+                <matches pattern="1\.[89](\..*)?" string="${javac.source}"/>
             </and>
         </condition>
         <condition property="do.archive">
@@ -156,7 +156,6 @@ is divided into following sections:
         <property name="application.args" value=""/>
         <property name="source.encoding" value="${file.encoding}"/>
         <property name="runtime.encoding" value="${source.encoding}"/>
-        <property name="manifest.encoding" value="${source.encoding}"/>
         <condition property="javadoc.encoding.used" value="${javadoc.encoding}">
             <and>
                 <isset property="javadoc.encoding"/>
@@ -450,7 +449,7 @@ is divided into following sections:
                     </fileset>
                 </union>
                 <taskdef classname="org.testng.TestNGAntTask" classpath="${run.test.classpath}" name="testng"/>
-                <testng classfilesetref="test.set" failureProperty="tests.failed" listeners="org.testng.reporters.VerboseReporter" methods="${testng.methods.arg}" mode="${testng.mode}" outputdir="${build.test.results.dir}" suitename="SASS-dev" testname="TestNG tests" workingDir="${work.dir}">
+                <testng classfilesetref="test.set" failureProperty="tests.failed" listeners="org.testng.reporters.VerboseReporter" methods="${testng.methods.arg}" mode="${testng.mode}" outputdir="${build.test.results.dir}" suitename="SASS" testname="TestNG tests" workingDir="${work.dir}">
                     <xmlfileset dir="${build.test.classes.dir}" includes="@{testincludes}"/>
                     <propertyset>
                         <propertyref prefix="test-sys-prop."/>
@@ -601,7 +600,7 @@ is divided into following sections:
                 <condition else="-testclass @{testClass}" property="test.class.or.method" value="-methods @{testClass}.@{testMethod}">
                     <isset property="test.method"/>
                 </condition>
-                <condition else="-suitename SASS-dev -testname @{testClass} ${test.class.or.method}" property="testng.cmd.args" value="@{testClass}">
+                <condition else="-suitename SASS -testname @{testClass} ${test.class.or.method}" property="testng.cmd.args" value="@{testClass}">
                     <matches pattern=".*\.xml" string="@{testClass}"/>
                 </condition>
                 <delete dir="${build.test.results.dir}" quiet="true"/>
@@ -841,7 +840,7 @@ is divided into following sections:
                     </chainedmapper>
                 </pathconvert>
                 <taskdef classname="org.netbeans.modules.java.j2seproject.copylibstask.CopyLibs" classpath="${libs.CopyLibs.classpath}" name="copylibs"/>
-                <copylibs compress="${jar.compress}" excludeFromCopy="${copylibs.excludes}" index="${jar.index}" indexMetaInf="${jar.index.metainf}" jarfile="${dist.jar}" manifest="@{manifest}" manifestencoding="UTF-8" rebase="${copylibs.rebase}" runtimeclasspath="${run.classpath.without.build.classes.dir}">
+                <copylibs compress="${jar.compress}" excludeFromCopy="${copylibs.excludes}" index="${jar.index}" indexMetaInf="${jar.index.metainf}" jarfile="${dist.jar}" manifest="@{manifest}" rebase="${copylibs.rebase}" runtimeclasspath="${run.classpath.without.build.classes.dir}">
                     <fileset dir="${build.classes.dir}" excludes="${dist.archive.excludes}"/>
                     <manifest>
                         <attribute name="Class-Path" value="${jar.classpath}"/>
@@ -853,7 +852,7 @@ is divided into following sections:
     </target>
     <target name="-init-presetdef-jar">
         <presetdef name="jar" uri="http://www.netbeans.org/ns/j2se-project/1">
-            <jar compress="${jar.compress}" index="${jar.index}" jarfile="${dist.jar}" manifestencoding="UTF-8">
+            <jar compress="${jar.compress}" index="${jar.index}" jarfile="${dist.jar}">
                 <j2seproject1:fileset dir="${build.classes.dir}" excludes="${dist.archive.excludes}"/>
             </jar>
         </presetdef>
@@ -893,7 +892,7 @@ is divided into following sections:
         <delete file="${built-jar.properties}" quiet="true"/>
     </target>
     <target if="already.built.jar.${basedir}" name="-warn-already-built-jar">
-        <echo level="warn" message="Cycle detected: SASS-dev was already built"/>
+        <echo level="warn" message="Cycle detected: SASS was already built"/>
     </target>
     <target depends="init,-deps-jar-init" name="deps-jar" unless="no.deps">
         <mkdir dir="${build.dir}"/>
@@ -976,23 +975,23 @@ is divided into following sections:
     </target>
     <target depends="init" if="do.archive+manifest.available" name="-do-jar-copy-manifest">
         <tempfile deleteonexit="true" destdir="${build.dir}" property="tmp.manifest.file"/>
-        <copy encoding="${manifest.encoding}" file="${manifest.file}" outputencoding="UTF-8" tofile="${tmp.manifest.file}"/>
+        <copy file="${manifest.file}" tofile="${tmp.manifest.file}"/>
     </target>
     <target depends="init,-do-jar-create-manifest,-do-jar-copy-manifest" if="do.archive+main.class.available" name="-do-jar-set-mainclass">
-        <manifest encoding="UTF-8" file="${tmp.manifest.file}" mode="update">
+        <manifest file="${tmp.manifest.file}" mode="update">
             <attribute name="Main-Class" value="${main.class}"/>
         </manifest>
     </target>
     <target depends="init,-do-jar-create-manifest,-do-jar-copy-manifest" if="do.archive+profile.available" name="-do-jar-set-profile">
-        <manifest encoding="UTF-8" file="${tmp.manifest.file}" mode="update">
+        <manifest file="${tmp.manifest.file}" mode="update">
             <attribute name="Profile" value="${javac.profile}"/>
         </manifest>
     </target>
     <target depends="init,-do-jar-create-manifest,-do-jar-copy-manifest" if="do.archive+splashscreen.available" name="-do-jar-set-splashscreen">
         <basename file="${application.splash}" property="splashscreen.basename"/>
         <mkdir dir="${build.classes.dir}/META-INF"/>
         <copy failonerror="false" file="${application.splash}" todir="${build.classes.dir}/META-INF"/>
-        <manifest encoding="UTF-8" file="${tmp.manifest.file}" mode="update">
+        <manifest file="${tmp.manifest.file}" mode="update">
             <attribute name="SplashScreen-Image" value="META-INF/${splashscreen.basename}"/>
         </manifest>
     </target>
@@ -1187,7 +1186,7 @@ is divided into following sections:
     <target depends="-profile-check" description="Profile a selected class in the IDE." if="profiler.configured" name="profile-test-with-main">
         <fail unless="run.class">Must select one file in the IDE or set run.class</fail>
         <startprofiler/>
-        <antcall target="run-test-with-main"/>
+        <antcal target="run-test-with-main"/>
     </target>
     <target depends="-profile-check,-profile-applet-pre72" if="profiler.configured" name="profile-applet" unless="profiler.info.jvmargs.agent">
         <fail unless="applet.url">Must select one file in the IDE or set applet.url</fail>
@@ -1378,7 +1377,7 @@ is divided into following sections:
         <delete file="${built-clean.properties}" quiet="true"/>
     </target>
     <target if="already.built.clean.${basedir}" name="-warn-already-built-clean">
-        <echo level="warn" message="Cycle detected: SASS-dev was already built"/>
+        <echo level="warn" message="Cycle detected: SASS was already built"/>
     </target>
     <target depends="init,-deps-clean-init" name="deps-clean" unless="no.deps">
         <mkdir dir="${build.dir}"/>

nbproject/genfiles.properties

@@ -3,7 +3,7 @@ build.xml.script.CRC32=1c9a5f06
 build.xml.stylesheet.CRC32=[email protected]
 # This file is used by a NetBeans-based IDE to track changes in generated files such as build-impl.xml.
 # Do not edit this file. You may delete it but then the IDE will never regenerate such files for you.
-nbproject/build-impl.xml.data.CRC32=e8261fd9
-nbproject/build-impl.xml.script.CRC32=a5d77285
-nbproject/build-impl.xml.stylesheet.CRC32=830a3534@1.80.1.48
+nbproject/build-impl.xml.data.CRC32=dd76ab7f
+nbproject/build-impl.xml.script.CRC32=ca3d274f
+nbproject/build-impl.xml.stylesheet.CRC32=05530350@1.79.1.48
 

nbproject/project.properties

@@ -92,6 +92,7 @@ javadoc.nonavbar=false
 javadoc.notree=false
 javadoc.private=false
 javadoc.reference.gson-2.8.2.jar=src/lib/javadocs/gson-2.8.2-javadoc.jar
+javadoc.reference.ij-1.50e.jar=/home/kmdouglass/apps/Fiji.app/javadocs/ij
 javadoc.reference.jfreechart-1.0.19.jar=/home/douglass/src/jfreechart-1.0.19/javadoc
 javadoc.reference.libthrift-0.11.0.jar=src/lib/libthrift-0.11.0-javadoc.jar
 javadoc.splitindex=true

nbproject/project.xml

@@ -3,7 +3,7 @@
     <type>org.netbeans.modules.java.j2seproject</type>
     <configuration>
         <data xmlns="http://www.netbeans.org/ns/j2se-project/3">
-            <name>SASS-dev</name>
+            <name>SASS</name>
             <source-roots>
                 <root id="src.dir"/>
             </source-roots>
@@ -13,4 +13,3 @@
         </data>
     </configuration>
 </project>
-

scripts/example_Gibson_Lanni_PSF.bsh

@@ -152,12 +152,7 @@ for (i=0;i<1000;i++) {
 
 // save and show; uncomment these lines to save and display stack
 //generator.saveStack(new File("generated_stack.tif"));
-//import ij.ImagePlus;
-//ImagePlus ip = new ImagePlus("Simulation output", generator.getStack());
-//ip.show();
-//ip.updateAndRepaintWindow();
 
-//System.exit(0); // uncomment if you want termination immediately
 
 
 

scripts/example_dSTORM.bsh

@@ -115,12 +115,5 @@ for (i=0;i<100;i++) {
 
 // save and show; uncomment these lines to save and display stack
 //generator.saveStack(new File("generated_stack.tif"));
-//import ij.ImagePlus;
-//ImagePlus ip = new ImagePlus("Simulation output", generator.getStack());
-//ip.show();
-//ip.updateAndRepaintWindow();
-
-//System.exit(0); // uncomment if you want termination immediately
-
 
 

scripts/example_grid_2d_fluorophores.bsh

@@ -17,6 +17,7 @@ import ch.epfl.leb.sass.models.components.*;
 import ch.epfl.leb.sass.models.psfs.internal.Gaussian2D;
 import ch.epfl.leb.sass.models.fluorophores.internal.commands.GenerateFluorophoresGrid2D;
 import ch.epfl.leb.sass.utils.RNG;
+import ch.epfl.leb.sass.utils.images.ImageS;
 
 // The seed determines the outputs of the random number generator.
 RNG.setSeed(42);
@@ -114,9 +115,4 @@ for (i=0;i<10000;i++) {
 
 // save and show; uncomment these lines to save and display stack
 //generator.saveStack(new File("generated_stack.tif"));
-//import ij.ImagePlus;
-//ImagePlus ip = new ImagePlus("Simulation output", generator.getStack());
-//ip.show();
-//ip.updateAndRepaintWindow();
 
-//System.exit(0); // uncomment if you want termination immediately

scripts/example_grid_3d_fluorophores.bsh

@@ -128,10 +128,3 @@ for (i=0;i<10000;i++) {
 
 // save and show; uncomment these lines to save and display stack
 //generator.saveStack(new File("generated_stack.tif"));
-//import ij.ImagePlus;
-//ImagePlus ip = new ImagePlus("Simulation output", generator.getStack());
-//ip.show();
-//ip.updateAndRepaintWindow();
-
-//System.exit(0); // uncomment if you want termination immediately
-

scripts/example_loggers.bsh

@@ -122,13 +122,13 @@ for (i=0;i<10000;i++) {
 }
 
 // Save the stack
-generator.saveStack(new File("generated_stack.tif"));
+//generator.saveStack(new File("generated_stack.tif"));
 
 // Save the fluorophore positions.
-positionLogger.setFilename("fluorophore_positions.csv");
-positionLogger.saveLogFile();
+//positionLogger.setFilename("fluorophore_positions.csv");
+//positionLogger.saveLogFile();
 
 // Save the state transitions
-stateLogger.setFilename("state_transitions.csv");
-stateLogger.saveLogFile();
+//stateLogger.setFilename("state_transitions.csv");
+//stateLogger.saveLogFile();
 

scripts/example_random_2d_fluorophores.bsh

@@ -116,12 +116,3 @@ for (i=0;i<10000;i++) {
 
 // save and show; uncomment these lines to save and display stack
 //generator.saveStack(new File("generated_stack.tif"));
-//import ij.ImagePlus;
-//ImagePlus ip = new ImagePlus("Simulation output", generator.getStack());
-//ip.show();
-//ip.updateAndRepaintWindow();
-
-//System.exit(0); // uncomment if you want termination immediately
-
-
-

scripts/example_random_3d_fluorophores.bsh

@@ -127,12 +127,6 @@ for (i=0;i<10000;i++) {
 
 // save and show; uncomment these lines to save and display stack
 //generator.saveStack(new File("generated_stack.tif"));
-//import ij.ImagePlus;
-//ImagePlus ip = new ImagePlus("Simulation output", generator.getStack());
-//ip.show();
-//ip.updateAndRepaintWindow();
-
-//System.exit(0); // uncomment if you want termination immediately
 
 
 

scripts/example_run_generator_moving.bsh

@@ -83,12 +83,7 @@ for (i=0;i<10000;i++) {
 
 // save and show; uncomment these lines to save and display stack
 //generator.saveStack(new File("generated_stack.tif"));
-//import ij.ImagePlus;
-//ImagePlus ip = new ImagePlus("Simulation output", generator.getStack());
-//ip.show();
-//ip.updateAndRepaintWindow();
 
-//System.exit(0); // uncomment if you want termination immediately