- Fixed loading of Simulation Files and introduced chaeck for sanity…

… of lower and upper channel bounds - Added "Move Up" / "Move Down" buttons to layer list in target configurator - Changed precision of charge and detector calibration inputs to 4 in main window - Changed precision of areal density inputs in target configurator to 4 - introduced option "open [simulation_file]" to be passed as argument for console operation
DrReneHeller · May 16, 2023 · e9be40c · e9be40c
1 parent 9f8bb6e
commit e9be40c
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Showing 8 changed files with 178 additions and 78 deletions.
diff --git a/ChangeLog b/ChangeLog
@@ -116,3 +116,12 @@
     - Reduced console output during DE optimization
     - Bugfix: Re-binning to "1" after DE optimization and update of simulation
     - Bugfix: Impact angle correction for BS yield
+
+
+2023_05_16 - V7.7.1
+
+    - Fixed loading of Simulation Files and introduced chaeck for sanity of lower and upper channel bounds
+    - Added "Move Up" / "Move Down" buttons to layer list in target configurator
+    - Changed precision of charge and detector calibration inputs to 4 in main window
+    - Changed precision of areal density inputs in target configurator to 4
+    - introduced option "open [simulation_file]" to be passed as argument for console operation
diff --git a/dependency-reduced-pom.xml b/dependency-reduced-pom.xml
@@ -3,7 +3,7 @@
   <modelVersion>4.0.0</modelVersion>
   <groupId>com.ruthelde</groupId>
   <artifactId>ruthelde</artifactId>
-  <version>7.7.0</version>
+  <version>7.7.1</version>
   <build>
     <plugins>
       <plugin>

diff --git a/pom.xml b/pom.xml
@@ -6,7 +6,7 @@
 
     <groupId>com.ruthelde</groupId>
     <artifactId>ruthelde</artifactId>
-    <version>7.7.0</version>
+    <version>7.7.1</version>
     <dependencies>
         <dependency>
             <groupId>com.google.code.gson</groupId>

diff --git a/src/main/java/com/ruthelde/GA/GAEngine.java b/src/main/java/com/ruthelde/GA/GAEngine.java
@@ -86,8 +86,6 @@ public boolean evolve(PlotWindow spectraPlotWindow, PlotWindow fitnessPlotWindow
 
         boolean plotRefresh = false;
 
-        //TODO: Reduce the console output to just the gneration numer and make line break only ech 10 generations
-
         //System.out.println("Starting calculation of new generation [" + generationCounter + "]");
         System.out.print(generationCounter + "");
 

diff --git a/src/main/java/com/ruthelde/IBA/Simulator/SpectrumSimulator.java b/src/main/java/com/ruthelde/IBA/Simulator/SpectrumSimulator.java
@@ -635,7 +635,8 @@ private double calFitness(){
         }
 
         //sigma2 = 100.0f / (Math.log(sigma2) - Math.log(LFF));
-        sigma2 = LFF / sigma2 * 100.0f;
+        //sigma2 = LFF / sigma2 * 100.0f;
+        sigma2 = Math.log(LFF) / Math.log(sigma2) * 100.0f;
         return sigma2;
     }
 

diff --git a/src/main/java/com/ruthelde/Main/MainWindow.java b/src/main/java/com/ruthelde/Main/MainWindow.java
@@ -137,21 +137,22 @@ public MainWindow(String args[]) {
 
         if (args.length == 0) {
 
-            System.out.println("Usage: java -jar IBA.jar {help|run_de|simulate} [...]");
+            System.out.println("Usage: java -jar IBA.jar {help|run_de|simulate|open} [...]");
             return;
         }
 
         if (args[0].equals("help")) {
 
-            System.out.println("Usage: java -jar IBA.jar {help|run_de|simulate} [...]");
+            System.out.println("Usage: java -jar IBA.jar {help|run_de|simulate|open} [...]");
             System.out.println("help ");
             System.out.println("run_de   [input] [fileType] [spectrum_1 ... spectrum_N]  runs differential evolution");
             System.out.println("         [input] (absolute) path to IBA simulation file which is used to extract");
             System.out.println("                 input parameters like target model and experimental constrains from.");
             System.out.println("         [fileType] specifies the tye of following iba spectra. Allowed values:");
             System.out.println("                    ASCII_ONE, ASCII_TWO, IBC_RBS, IBC_3MV_SINGLE, IBC_3MV_MULTI, IMEC, IBA_SIM");
             System.out.println("         [spectrum_1 ... spectrum_N] (absolute) file paths to spectra files");
-            System.out.println("simulate [input-file] [output-file] Generate data from simulation");
+            System.out.println("simulate [input-file] [output-file] Generate data automatically from simulation");
+            System.out.println("open [input-file] Opens Ruthelde with specified simulation file");
             System.exit(0);
         }
 
@@ -167,6 +168,12 @@ public MainWindow(String args[]) {
             System.exit(0);
         }
 
+        if (args[0].equals("open")) {
+
+            System.out.println("Starting Ruthelde with specified simulation file");
+            loadSimulation(args[1]);
+        }
+
         if (args[0].equals("run_de")) {
 
             System.out.println("Importing parameters from simulation file.");
@@ -644,10 +651,33 @@ private boolean loadSimulation(String fileName) {
 
                             deParameter = df.deParameter;
 
+                            if (deParameter.startCH >= df.experimentalSpectrum.length - 1) {
+
+                                deParameter.startCH = df.experimentalSpectrum.length - 2;
+                                System.out.print("Parameter *Start_Channel to high. Changed to ");
+                                System.out.println("" + deParameter.startCH);
+                            }
+
+                            if (deParameter.endCH >= df.experimentalSpectrum.length - 1) {
+
+                                deParameter.endCH = df.experimentalSpectrum.length - 2;
+                                System.out.print("Parameter *End_Channel to high. Changed to ");
+                                System.out.println("" + deParameter.endCH);
+                            }
+
+                            if (deParameter.startCH >= deParameter.endCH) {
+
+                                deParameter.startCH = deParameter.endCH - 2;
+                                System.out.print("Parameter *Start_Channel to high. Changed to ");
+                                System.out.println("" + deParameter.startCH);
+                            }
+
                             spectrumSimulator.setStartChannel(deParameter.startCH);
                             spectrumSimulator.setStopChannel(deParameter.endCH);
-                            tf_ch_min.setText("" + (int) df.deParameter.startCH);
-                            tf_ch_max.setText("" + (int) df.deParameter.endCH);
+                            //tf_ch_min.setText("" + (int) df.deParameter.startCH);
+                            //tf_ch_max.setText("" + (int) df.deParameter.endCH);
+                            tf_ch_min.setText("" + (int) deParameter.startCH);
+                            tf_ch_max.setText("" + (int) deParameter.endCH);
                             spectrumSimulator.setExperimentalSpectrum(df.experimentalSpectrum);
                             spectrumSimulator.applyStoppingCorrection();
 
@@ -723,7 +753,7 @@ private boolean loadSimulation(String fileName) {
 
         } catch (Exception ex) {
             result = false;
-            ex.toString();
+            ex.printStackTrace();
         }
 
         if (!result) System.out.println("Error loading simulation file.");
@@ -954,9 +984,9 @@ private void updateChargeValues() {
         double minCharge = experimentalSetup.getMinCharge();
         double maxCharge = experimentalSetup.getMaxCharge();
 
-        tfExpCharge.setText(Helper.dblToDecStr(charge, 2));
-        tfExpChargeMin.setText(Helper.dblToDecStr(minCharge, 2));
-        tfExpChargeMax.setText(Helper.dblToDecStr(maxCharge, 2));
+        tfExpCharge.setText(Helper.dblToDecStr(charge, 3));
+        tfExpChargeMin.setText(Helper.dblToDecStr(minCharge, 3));
+        tfExpChargeMax.setText(Helper.dblToDecStr(maxCharge, 3));
     }
 
     private void setExpCharge() {
@@ -1040,9 +1070,9 @@ private void updateDetDE() {
         double minRes = detectorSetup.getMinRes();
         double maxRes = detectorSetup.getMaxRes();
 
-        tfDetDE.setText(Helper.dblToDecStr(res, 2));
-        tfDetDEMin.setText(Helper.dblToDecStr(minRes, 2));
-        tfDetDEMax.setText(Helper.dblToDecStr(maxRes, 2));
+        tfDetDE.setText(Helper.dblToDecStr(res, 4));
+        tfDetDEMin.setText(Helper.dblToDecStr(minRes, 4));
+        tfDetDEMax.setText(Helper.dblToDecStr(maxRes, 4));
     }
 
     private void updateCalibration() {
@@ -1054,9 +1084,9 @@ private void updateCalibration() {
         double offsetMin = detectorSetup.getCalibration().getOffsetMin();
         double offsetMax = detectorSetup.getCalibration().getOffsetMax();
 
-        tfDetCalFactor.setText(Helper.dblToDecStr(factor, 2));
-        tfDetCalFactorMin.setText(Helper.dblToDecStr(factorMin, 2));
-        tfDetCalFactorMax.setText(Helper.dblToDecStr(factorMax, 2));
+        tfDetCalFactor.setText(Helper.dblToDecStr(factor, 4));
+        tfDetCalFactorMin.setText(Helper.dblToDecStr(factorMin, 4));
+        tfDetCalFactorMax.setText(Helper.dblToDecStr(factorMax, 4));
         tfDetCalOffset.setText(Helper.dblToDecStr(offset, 2));
         tfDetCalOffsetMin.setText(Helper.dblToDecStr(offsetMin, 2));
         tfDetCalOffsetMax.setText(Helper.dblToDecStr(offsetMax, 2));
@@ -1437,8 +1467,8 @@ private void copyBestCandidate() {
 
         tfDetCalFactor.setText(Helper.dblToDecStr(individual.getCalibrationFactor() / deParameter.numBins, 4));
         tfDetCalOffset.setText(Helper.dblToDecStr(individual.getCalibrationOffset(), 2));
-        tfExpCharge.setText(Helper.dblToDecStr(individual.getCharge(), 2));
-        tfDetDE.setText(Helper.dblToDecStr(individual.getResolution(), 2));
+        tfExpCharge.setText(Helper.dblToDecStr(individual.getCharge(), 4));
+        tfDetDE.setText(Helper.dblToDecStr(individual.getResolution(), 4));
 
         setExpCharge();
         blockEvents = false;
@@ -1454,7 +1484,7 @@ private void makeGACsFromCurrentSetting() {
 
     private void initComponents() {
 
-        this.setTitle("Ruthelde V7.7.0 - 2023_01_19 (C) R. Heller");
+        this.setTitle("Ruthelde V7.7.1 - 2023_05_16 (C) R. Heller");
         this.setDefaultCloseOperation(WindowConstants.EXIT_ON_CLOSE);
         setContentPane(rootPanel);
         pack();
@@ -1632,21 +1662,15 @@ public void focusLost(FocusEvent e) {
             blockEvents = false;
         });
 
-        tfExpChargeMin.addActionListener(new ActionListener() {
-            @Override
-            public void actionPerformed(ActionEvent e) {
-                if (!blockEvents) {
-                    setExpMinCharge();
-                }
+        tfExpChargeMin.addActionListener(e -> {
+            if (!blockEvents) {
+                setExpMinCharge();
             }
         });
 
-        tfExpChargeMax.addActionListener(new ActionListener() {
-            @Override
-            public void actionPerformed(ActionEvent e) {
-                if (!blockEvents) {
-                    setExpMaxCharge();
-                }
+        tfExpChargeMax.addActionListener(e -> {
+            if (!blockEvents) {
+                setExpMaxCharge();
             }
         });
 

diff --git a/src/main/java/com/ruthelde/Target/TargetView.form b/src/main/java/com/ruthelde/Target/TargetView.form
@@ -1,9 +1,9 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <form xmlns="http://www.intellij.com/uidesigner/form/" version="1" bind-to-class="com.ruthelde.Target.TargetView">
-  <grid id="27dc6" binding="rootPanel" layout-manager="GridLayoutManager" row-count="5" column-count="6" same-size-horizontally="false" same-size-vertically="false" hgap="-1" vgap="-1">
+  <grid id="27dc6" binding="rootPanel" layout-manager="GridLayoutManager" row-count="6" column-count="6" same-size-horizontally="false" same-size-vertically="false" hgap="-1" vgap="-1">
     <margin top="5" left="5" bottom="5" right="5"/>
     <constraints>
-      <xy x="20" y="20" width="954" height="457"/>
+      <xy x="20" y="20" width="954" height="485"/>
     </constraints>
     <properties/>
     <border type="none"/>
@@ -118,14 +118,6 @@
           <text value="Remove"/>
         </properties>
       </component>
-      <component id="c3a5a" class="javax.swing.JButton" binding="btnNormalizeElements">
-        <constraints>
-          <grid row="4" column="2" row-span="1" col-span="2" vsize-policy="0" hsize-policy="3" anchor="0" fill="1" indent="0" use-parent-layout="false"/>
-        </constraints>
-        <properties>
-          <text value="Normalize"/>
-        </properties>
-      </component>
       <component id="5bdcc" class="javax.swing.JButton" binding="btnAddIsotope">
         <constraints>
           <grid row="3" column="4" row-span="1" col-span="1" vsize-policy="0" hsize-policy="3" anchor="0" fill="1" indent="0" use-parent-layout="false"/>
@@ -142,22 +134,6 @@
           <text value="Remove"/>
         </properties>
       </component>
-      <component id="2c12f" class="javax.swing.JButton" binding="btnNormalizeIsotopes">
-        <constraints>
-          <grid row="4" column="4" row-span="1" col-span="1" vsize-policy="0" hsize-policy="3" anchor="0" fill="1" indent="0" use-parent-layout="false"/>
-        </constraints>
-        <properties>
-          <text value="Normalize"/>
-        </properties>
-      </component>
-      <component id="fd361" class="javax.swing.JButton" binding="btnNaturalizeIsotopes">
-        <constraints>
-          <grid row="4" column="5" row-span="1" col-span="1" vsize-policy="0" hsize-policy="3" anchor="0" fill="1" indent="0" use-parent-layout="false"/>
-        </constraints>
-        <properties>
-          <text value="Naturalize"/>
-        </properties>
-      </component>
       <grid id="3013a" layout-manager="GridLayoutManager" row-count="6" column-count="2" same-size-horizontally="false" same-size-vertically="false" hgap="-1" vgap="-1">
         <margin top="5" left="5" bottom="5" right="5"/>
         <constraints>
@@ -444,7 +420,7 @@
       </grid>
       <component id="a205f" class="javax.swing.JLabel" binding="lblErrorMsg">
         <constraints>
-          <grid row="4" column="0" row-span="1" col-span="2" vsize-policy="0" hsize-policy="0" anchor="8" fill="0" indent="0" use-parent-layout="false"/>
+          <grid row="5" column="0" row-span="1" col-span="2" vsize-policy="0" hsize-policy="0" anchor="8" fill="0" indent="0" use-parent-layout="false"/>
         </constraints>
         <properties>
           <text value=""/>
@@ -455,6 +431,46 @@
           <grid row="2" column="0" row-span="1" col-span="1" vsize-policy="6" hsize-policy="1" anchor="0" fill="2" indent="0" use-parent-layout="false"/>
         </constraints>
       </vspacer>
+      <component id="58b8f" class="javax.swing.JButton" binding="btnLayerUp">
+        <constraints>
+          <grid row="4" column="0" row-span="1" col-span="1" vsize-policy="0" hsize-policy="3" anchor="0" fill="1" indent="0" use-parent-layout="false"/>
+        </constraints>
+        <properties>
+          <text value="Up"/>
+        </properties>
+      </component>
+      <component id="c3a5a" class="javax.swing.JButton" binding="btnNormalizeElements">
+        <constraints>
+          <grid row="4" column="2" row-span="1" col-span="2" vsize-policy="0" hsize-policy="3" anchor="0" fill="1" indent="0" use-parent-layout="false"/>
+        </constraints>
+        <properties>
+          <text value="Normalize"/>
+        </properties>
+      </component>
+      <component id="2c12f" class="javax.swing.JButton" binding="btnNormalizeIsotopes">
+        <constraints>
+          <grid row="4" column="4" row-span="1" col-span="1" vsize-policy="0" hsize-policy="3" anchor="0" fill="1" indent="0" use-parent-layout="false"/>
+        </constraints>
+        <properties>
+          <text value="Normalize"/>
+        </properties>
+      </component>
+      <component id="fd361" class="javax.swing.JButton" binding="btnNaturalizeIsotopes">
+        <constraints>
+          <grid row="4" column="5" row-span="1" col-span="1" vsize-policy="0" hsize-policy="3" anchor="0" fill="1" indent="0" use-parent-layout="false"/>
+        </constraints>
+        <properties>
+          <text value="Naturalize"/>
+        </properties>
+      </component>
+      <component id="a4883" class="javax.swing.JButton" binding="btnLayerDown">
+        <constraints>
+          <grid row="4" column="1" row-span="1" col-span="1" vsize-policy="0" hsize-policy="3" anchor="0" fill="1" indent="0" use-parent-layout="false"/>
+        </constraints>
+        <properties>
+          <text value="Down"/>
+        </properties>
+      </component>
     </children>
   </grid>
 </form>