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1 parent b0aebae commit 44c4aebdcdce2527869cdd4750fb5da637cdc7d5 @zk committed Feb 13, 2009
Showing with 97 additions and 118 deletions.
  1. BIN .DS_Store
  2. +0 −1 .classpath
  3. BIN {src/main/resources → neuron_media_files}/10-PD-STN.wav
  4. BIN {src/main/resources → neuron_media_files}/15-PD-SNr.wav
  5. BIN {src/main/resources → neuron_media_files}/7-PD-gpi.wav
  6. +50 −64 neurons
  7. +1 −1 rundbssim.sh
  8. +0 −1 src/main/groovy/napplelabs/dbssim/NeuronPlayer.java
  9. +0 −3 src/main/groovy/napplelabs/dbssim/NeuronSignal.java
  10. +0 −2 src/main/groovy/napplelabs/dbssim/TracePanel.java
  11. +7 −4 src/main/groovy/napplelabs/dbssim/ui/CanvasPanel.java
  12. +37 −31 src/main/groovy/napplelabs/dbssim/ui/SimUI.groovy
  13. +2 −11 src/main/groovy/napplelabs/dbssim/ui/TabManager.groovy
  14. BIN src/main/resources/1-ET-thalamus-tremor.wav
  15. BIN src/main/resources/1-PD-gpe-pauser.wav
  16. BIN src/main/resources/1-dystonia-gpe.wav
  17. BIN src/main/resources/11-PD-STN-2unit.wav
  18. BIN src/main/resources/12-PD-STN.wav
  19. BIN src/main/resources/13-PD-STN.wav
  20. BIN src/main/resources/14-PD-STN.wav
  21. BIN src/main/resources/2-PD-GPe-burster.wav
  22. BIN src/main/resources/2-dystonia-gpe.wav
  23. BIN src/main/resources/3-dystonia-gpi.wav
  24. BIN src/main/resources/4-PD-border.wav
  25. BIN src/main/resources/4-dystonia-gpi.wav
  26. BIN src/main/resources/5-PD-gpi.wav
  27. BIN src/main/resources/5-dystonia-gpi.wav
  28. BIN src/main/resources/6-PD-gpi.wav
  29. BIN src/main/resources/8-PD-gpi-tremor.wav
  30. BIN src/main/resources/9-PD-optictract-multipleaxons.wav
  31. BIN src/main/resources/Rage Against The Machine - rage against the machine - 06 - Know Your Enemy.mp3
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BIN .DS_Store
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@@ -1,7 +1,6 @@
<?xml version="1.0" encoding="UTF-8"?>
<classpath>
<classpathentry kind="src" output="target/classes" path="src/main/java"/>
- <classpathentry excluding="**" kind="src" output="target/classes" path="src/main/resources"/>
<classpathentry kind="src" output="target/test-classes" path="src/test/java"/>
<classpathentry excluding="napplelabs/dbssim/ui/BirdsEyeViewExample.java" kind="src" path="src/main/groovy"/>
<classpathentry kind="con" path="org.eclipse.jdt.launching.JRE_CONTAINER/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/J2SE-1.5"/>
File renamed without changes.
File renamed without changes.
File renamed without changes.
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114 neurons
@@ -7,10 +7,10 @@
<blue>255</blue>
<alpha>255</alpha>
</color>
- <mediaFile>/Users/zkim/napplelabs/dbssim/src/main/resources/7-PD-gpi.wav</mediaFile>
+ <mediaFile>./neuron_media_files/7-PD-gpi.wav</mediaFile>
<location class="java.awt.geom.Point2D$Double">
- <x>149.156296559687</x>
- <y>-518.6706042430462</y>
+ <x>206.30288554458386</x>
+ <y>-863.7472844947131</y>
</location>
</napplelabs.dbssim.neuron.NeuronPathRep>
<napplelabs.dbssim.neuron.NeuronPathRep>
@@ -20,108 +20,94 @@
<blue>0</blue>
<alpha>255</alpha>
</color>
- <mediaFile>/Users/zkim/napplelabs/dbssim/src/main/resources/10-PD-STN.wav</mediaFile>
+ <mediaFile>./neuron_media_files/10-PD-STN.wav</mediaFile>
<location class="java.awt.geom.Point2D$Double">
- <x>48.440042696381255</x>
- <y>-274.1571471322358</y>
+ <x>129.95837579526884</x>
+ <y>-582.2385758007554</y>
</location>
</napplelabs.dbssim.neuron.NeuronPathRep>
<napplelabs.dbssim.neuron.NeuronPathRep>
<color>
<red>0</red>
- <green>255</green>
- <blue>0</blue>
+ <green>0</green>
+ <blue>255</blue>
<alpha>255</alpha>
</color>
- <mediaFile>/Users/zkim/napplelabs/dbssim/src/main/resources/15-PD-SNr.wav</mediaFile>
- <location class="java.awt.geom.Point2D$Double">
- <x>-44.27360294261013</x>
- <y>197.3131439735921</y>
- </location>
- </napplelabs.dbssim.neuron.NeuronPathRep>
- <napplelabs.dbssim.neuron.NeuronPathRep>
- <color reference="../../napplelabs.dbssim.neuron.NeuronPathRep/color"/>
- <mediaFile>/Users/zkim/napplelabs/dbssim/src/main/resources/7-PD-gpi.wav</mediaFile>
- <location class="java.awt.geom.Point2D$Double">
- <x>141.07125414265573</x>
- <y>-604.7039157066074</y>
- </location>
- </napplelabs.dbssim.neuron.NeuronPathRep>
- <napplelabs.dbssim.neuron.NeuronPathRep>
- <color reference="../../napplelabs.dbssim.neuron.NeuronPathRep/color"/>
- <mediaFile>/Users/zkim/napplelabs/dbssim/src/main/resources/7-PD-gpi.wav</mediaFile>
- <location class="java.awt.geom.Point2D$Double">
- <x>187.92401863138156</x>
- <y>-764.5665917980033</y>
- </location>
- </napplelabs.dbssim.neuron.NeuronPathRep>
- <napplelabs.dbssim.neuron.NeuronPathRep>
- <color reference="../../napplelabs.dbssim.neuron.NeuronPathRep[2]/color"/>
- <mediaFile>/Users/zkim/napplelabs/dbssim/src/main/resources/10-PD-STN.wav</mediaFile>
+ <mediaFile>./neuron_media_files/7-PD-gpi.wav</mediaFile>
<location class="java.awt.geom.Point2D$Double">
- <x>118.52850025973265</x>
- <y>-340.22120567130736</y>
+ <x>217.25986237762237</x>
+ <y>-753.4731707557885</y>
</location>
</napplelabs.dbssim.neuron.NeuronPathRep>
<napplelabs.dbssim.neuron.NeuronPathRep>
- <color reference="../../napplelabs.dbssim.neuron.NeuronPathRep[3]/color"/>
- <mediaFile>/Users/zkim/napplelabs/dbssim/src/main/resources/15-PD-SNr.wav</mediaFile>
+ <color>
+ <red>0</red>
+ <green>0</green>
+ <blue>255</blue>
+ <alpha>255</alpha>
+ </color>
+ <mediaFile>./neuron_media_files/7-PD-gpi.wav</mediaFile>
<location class="java.awt.geom.Point2D$Double">
- <x>-50.51388565140224</x>
- <y>136.1367638786892</y>
+ <x>268.0409325555711</x>
+ <y>-930.9906918563773</y>
</location>
</napplelabs.dbssim.neuron.NeuronPathRep>
<napplelabs.dbssim.neuron.NeuronPathRep>
- <color reference="../../napplelabs.dbssim.neuron.NeuronPathRep/color"/>
- <mediaFile>/Users/zkim/napplelabs/dbssim/src/main/resources/7-PD-gpi.wav</mediaFile>
+ <color>
+ <red>255</red>
+ <green>0</green>
+ <blue>0</blue>
+ <alpha>255</alpha>
+ </color>
+ <mediaFile>./neuron_media_files/10-PD-STN.wav</mediaFile>
<location class="java.awt.geom.Point2D$Double">
- <x>201.99041954260412</x>
- <y>-668.9987893152154</y>
+ <x>107.63154075080985</x>
+ <y>-469.4799166039502</y>
</location>
</napplelabs.dbssim.neuron.NeuronPathRep>
<napplelabs.dbssim.neuron.NeuronPathRep>
- <color reference="../../napplelabs.dbssim.neuron.NeuronPathRep[2]/color"/>
- <mediaFile>/Users/zkim/napplelabs/dbssim/src/main/resources/10-PD-STN.wav</mediaFile>
+ <color reference="../../napplelabs.dbssim.neuron.NeuronPathRep[5]/color"/>
+ <mediaFile>./neuron_media_files/10-PD-STN.wav</mediaFile>
<location class="java.awt.geom.Point2D$Double">
- <x>94.75919774223057</x>
- <y>-407.13689587633286</y>
+ <x>73.63154075080985</x>
+ <y>-385.4799166039502</y>
</location>
</napplelabs.dbssim.neuron.NeuronPathRep>
<napplelabs.dbssim.neuron.NeuronPathRep>
<color>
- <red>255</red>
- <green>0</green>
+ <red>0</red>
+ <green>255</green>
<blue>0</blue>
<alpha>255</alpha>
</color>
- <mediaFile>/Users/zkim/napplelabs/dbssim/src/main/resources/10-PD-STN.wav</mediaFile>
+ <mediaFile>./neuron_media_files/15-PD-SNr.wav</mediaFile>
<location class="java.awt.geom.Point2D$Double">
- <x>31.024171333051314</x>
- <y>-58.087158560243125</y>
+ <x>-12.705142441915882</x>
+ <y>194.37776133769628</y>
</location>
</napplelabs.dbssim.neuron.NeuronPathRep>
<napplelabs.dbssim.neuron.NeuronPathRep>
- <color reference="../../napplelabs.dbssim.neuron.NeuronPathRep[10]/color"/>
- <mediaFile>/Users/zkim/napplelabs/dbssim/src/main/resources/10-PD-STN.wav</mediaFile>
+ <color reference="../../napplelabs.dbssim.neuron.NeuronPathRep[7]/color"/>
+ <mediaFile>./neuron_media_files/15-PD-SNr.wav</mediaFile>
<location class="java.awt.geom.Point2D$Double">
- <x>18.30271291016822</x>
- <y>-143.45691658991515</y>
+ <x>-97.13996122278309</x>
+ <y>252.76589892433753</y>
</location>
</napplelabs.dbssim.neuron.NeuronPathRep>
<napplelabs.dbssim.neuron.NeuronPathRep>
- <color reference="../../napplelabs.dbssim.neuron.NeuronPathRep[10]/color"/>
- <mediaFile>/Users/zkim/napplelabs/dbssim/src/main/resources/10-PD-STN.wav</mediaFile>
+ <color reference="../../napplelabs.dbssim.neuron.NeuronPathRep[5]/color"/>
+ <mediaFile>./neuron_media_files/10-PD-STN.wav</mediaFile>
<location class="java.awt.geom.Point2D$Double">
- <x>85.3331976183333</x>
- <y>-184.81615183537872</y>
+ <x>81.34011368929743</x>
+ <y>-217.92442083050923</y>
</location>
</napplelabs.dbssim.neuron.NeuronPathRep>
<napplelabs.dbssim.neuron.NeuronPathRep>
- <color reference="../../napplelabs.dbssim.neuron.NeuronPathRep[10]/color"/>
- <mediaFile>/Users/zkim/napplelabs/dbssim/src/main/resources/10-PD-STN.wav</mediaFile>
+ <color reference="../../napplelabs.dbssim.neuron.NeuronPathRep[5]/color"/>
+ <mediaFile>./neuron_media_files/10-PD-STN.wav</mediaFile>
<location class="java.awt.geom.Point2D$Double">
- <x>-27.94880723462001</x>
- <y>23.002194025688002</y>
+ <x>-21.200152466514282</x>
+ <y>-49.8414780938283</y>
</location>
</napplelabs.dbssim.neuron.NeuronPathRep>
</list>
View
@@ -1,3 +1,3 @@
#!/bin/bash
-java -cp /Users/zkim/.m2/repository/com/explodingpixels/forms/1.2.1/forms-1.2.1.jar:/Users/zkim/.m2/repository/com/explodingpixels/macwidgets/1.0-SNAPSHOT/macwidgets-1.0-SNAPSHOT.jar:/Users/zkim/.m2/repository/com/google/code/guice/guice/1.0/guice-1.0.jar:/Users/zkim/.m2/repository/com/thoughtworks/qdox/qdox/1.6.3/qdox-1.6.3.jar:/Users/zkim/.m2/repository/com/thoughtworks/xstream/xstream/1.3.1/xstream-1.3.1.jar:/Users/zkim/.m2/repository/jline/jline/0.9.94/jline-0.9.94.jar:/Users/zkim/.m2/repository/junit/junit/4.5/junit-4.5.jar:/Users/zkim/.m2/repository/miglayout/miglayout/3.6.2/miglayout-3.6.2.jar:/Users/zkim/.m2/repository/minim/jl/1.0/jl-1.0.jar:/Users/zkim/.m2/repository/minim/jsminim/1.0/jsminim-1.0.jar:/Users/zkim/.m2/repository/minim/minim/1.0/minim-1.0.jar:/Users/zkim/.m2/repository/minim/minim-spi/1.0/minim-spi-1.0.jar:/Users/zkim/.m2/repository/minim/mp3spi/1.0/mp3spi-1.0.jar:/Users/zkim/.m2/repository/minim/tritonus_aos/1.0/tritonus_aos-1.0.jar:/Users/zkim/.m2/repository/minim/tritonus_share/1.0/tritonus_share-1.0.jar:/Users/zkim/.m2/repository/org/apache/ant/ant/1.7.1/ant-1.7.1.jar:/Users/zkim/.m2/repository/org/apache/ant/ant-launcher/1.7.1/ant-launcher-1.7.1.jar:/Users/zkim/.m2/repository/org/codehaus/groovy/groovy-all-minimal/1.5.6/groovy-all-minimal-1.5.6.jar:/Users/zkim/.m2/repository/org/codehaus/groovy/maven/gmaven-common/1.0-rc-3/gmaven-common-1.0-rc-3.jar:/Users/zkim/.m2/repository/org/codehaus/groovy/maven/feature/gmaven-feature-api/1.0-rc-3/gmaven-feature-api-1.0-rc-3.jar:/Users/zkim/.m2/repository/org/codehaus/groovy/maven/feature/gmaven-feature-support/1.0-rc-3/gmaven-feature-support-1.0-rc-3.jar:/Users/zkim/.m2/repository/org/codehaus/groovy/maven/runtime/gmaven-runtime-1.5/1.0-rc-3/gmaven-runtime-1.5-1.0-rc-3.jar:/Users/zkim/.m2/repository/org/codehaus/groovy/maven/runtime/gmaven-runtime-api/1.0-rc-3/gmaven-runtime-api-1.0-rc-3.jar:/Users/zkim/.m2/repository/org/codehaus/groovy/maven/runtime/gmaven-runtime-default/1.0-rc-3/gmaven-runtime-default-1.0-rc-3.jar:/Users/zkim/.m2/repository/org/codehaus/groovy/maven/runtime/gmaven-runtime-support/1.0-rc-3/gmaven-runtime-support-1.0-rc-3.jar:/Users/zkim/.m2/repository/org/codehaus/plexus/plexus-utils/1.5.5/plexus-utils-1.5.5.jar:/Users/zkim/.m2/repository/org/slf4j/slf4j-api/1.5.0/slf4j-api-1.5.0.jar:/Users/zkim/.m2/repository/piccolo/piccolo/1.2.1/piccolo-1.2.1.jar:/Users/zkim/.m2/repository/piccolo/piccolox/1.2.1/piccolox-1.2.1.jar:/Users/zkim/.m2/repository/processing/core/1.0/core-1.0.jar:/Users/zkim/.m2/repository/xpp3/xpp3_min/1.1.4c/xpp3_min-1.1.4c.jar:./target/dbssim-1.0-SNAPSHOT.jar napplelabs.dbssim.ui.SimUI
+java -Xmx256M -Xms256M -cp /Users/zkim/.m2/repository/com/explodingpixels/forms/1.2.1/forms-1.2.1.jar:/Users/zkim/.m2/repository/com/explodingpixels/macwidgets/1.0-SNAPSHOT/macwidgets-1.0-SNAPSHOT.jar:/Users/zkim/.m2/repository/com/google/code/guice/guice/1.0/guice-1.0.jar:/Users/zkim/.m2/repository/com/thoughtworks/qdox/qdox/1.6.3/qdox-1.6.3.jar:/Users/zkim/.m2/repository/com/thoughtworks/xstream/xstream/1.3.1/xstream-1.3.1.jar:/Users/zkim/.m2/repository/jline/jline/0.9.94/jline-0.9.94.jar:/Users/zkim/.m2/repository/junit/junit/4.5/junit-4.5.jar:/Users/zkim/.m2/repository/miglayout/miglayout/3.6.2/miglayout-3.6.2.jar:/Users/zkim/.m2/repository/minim/jl/1.0/jl-1.0.jar:/Users/zkim/.m2/repository/minim/jsminim/1.0/jsminim-1.0.jar:/Users/zkim/.m2/repository/minim/minim/1.0/minim-1.0.jar:/Users/zkim/.m2/repository/minim/minim-spi/1.0/minim-spi-1.0.jar:/Users/zkim/.m2/repository/minim/mp3spi/1.0/mp3spi-1.0.jar:/Users/zkim/.m2/repository/minim/tritonus_aos/1.0/tritonus_aos-1.0.jar:/Users/zkim/.m2/repository/minim/tritonus_share/1.0/tritonus_share-1.0.jar:/Users/zkim/.m2/repository/org/apache/ant/ant/1.7.1/ant-1.7.1.jar:/Users/zkim/.m2/repository/org/apache/ant/ant-launcher/1.7.1/ant-launcher-1.7.1.jar:/Users/zkim/.m2/repository/org/codehaus/groovy/groovy-all-minimal/1.5.6/groovy-all-minimal-1.5.6.jar:/Users/zkim/.m2/repository/org/codehaus/groovy/maven/gmaven-common/1.0-rc-3/gmaven-common-1.0-rc-3.jar:/Users/zkim/.m2/repository/org/codehaus/groovy/maven/feature/gmaven-feature-api/1.0-rc-3/gmaven-feature-api-1.0-rc-3.jar:/Users/zkim/.m2/repository/org/codehaus/groovy/maven/feature/gmaven-feature-support/1.0-rc-3/gmaven-feature-support-1.0-rc-3.jar:/Users/zkim/.m2/repository/org/codehaus/groovy/maven/runtime/gmaven-runtime-1.5/1.0-rc-3/gmaven-runtime-1.5-1.0-rc-3.jar:/Users/zkim/.m2/repository/org/codehaus/groovy/maven/runtime/gmaven-runtime-api/1.0-rc-3/gmaven-runtime-api-1.0-rc-3.jar:/Users/zkim/.m2/repository/org/codehaus/groovy/maven/runtime/gmaven-runtime-default/1.0-rc-3/gmaven-runtime-default-1.0-rc-3.jar:/Users/zkim/.m2/repository/org/codehaus/groovy/maven/runtime/gmaven-runtime-support/1.0-rc-3/gmaven-runtime-support-1.0-rc-3.jar:/Users/zkim/.m2/repository/org/codehaus/plexus/plexus-utils/1.5.5/plexus-utils-1.5.5.jar:/Users/zkim/.m2/repository/org/slf4j/slf4j-api/1.5.0/slf4j-api-1.5.0.jar:/Users/zkim/.m2/repository/piccolo/piccolo/1.2.1/piccolo-1.2.1.jar:/Users/zkim/.m2/repository/piccolo/piccolox/1.2.1/piccolox-1.2.1.jar:/Users/zkim/.m2/repository/processing/core/1.0/core-1.0.jar:/Users/zkim/.m2/repository/xpp3/xpp3_min/1.1.4c/xpp3_min-1.1.4c.jar:./target/dbssim-1.0-SNAPSHOT.jar napplelabs.dbssim.ui.SimUI
@@ -45,7 +45,6 @@ public NeuronPlayer() throws LineUnavailableException, InterruptedException {
File file = new File("/Users/zkim/Desktop/Rage Against The Machine - rage against the machine - 06 - Know Your Enemy.mp3");
- System.out.println("Exists: " + file.exists());
AudioPlayer player = minim.loadFile(file.getAbsolutePath());
player.play();
@@ -67,11 +67,8 @@ public float getNextValue() {
if(counter >= spike.length + space_len) {
counter = 0;
float diff = maxRate - minRate;
- //System.out.println(diff);
float rnd = (float) (Math.random() * diff + minRate);
space_len = (int) (44100 / rnd);
- //System.out.println(space_len);
- //System.out.println();
}
return next;
}
@@ -48,7 +48,6 @@ public void paint(Graphics _g) {
Graphics2D g = (Graphics2D) _g;
if(resizeFlag) {
- System.out.println("FILL BLACK");
g.setColor(Color.black);
g.fillRect(0, 0, getWidth(), getHeight());
resizeFlag = false;
@@ -71,7 +70,6 @@ public void paint(Graphics _g) {
counter++;
if(counter >= trace.length) {
- System.out.println("COUNTER = 0");
resizeFlag = true;
counter = 0;
}
@@ -15,6 +15,7 @@
import java.io.IOException;
import java.io.ObjectInputStream;
import java.io.ObjectOutputStream;
+import java.net.URL;
import java.text.DecimalFormat;
import java.util.ArrayList;
import java.util.List;
@@ -104,24 +105,23 @@ private Component createFeaturePanel() {
JButton thal = new JButton("Thalamus");
thal.addActionListener(new ActionListener() {
public void actionPerformed(ActionEvent e) {
- addNeuron(new NeuronPath(Color.blue, "/Users/zkim/napplelabs/dbssim/src/main/resources/7-PD-gpi.wav", minim));
+ addNeuron(new NeuronPath(Color.blue, "./neuron_media_files/7-PD-gpi.wav", minim));
}
});
panel.add(thal);
JButton stn = new JButton("STN");
stn.addActionListener(new ActionListener() {
public void actionPerformed(ActionEvent e) {
- addNeuron(new NeuronPath(Color.red, "/Users/zkim/napplelabs/dbssim/src/main/resources/10-PD-STN.wav", minim));
+ addNeuron(new NeuronPath(Color.red, "./neuron_media_files/10-PD-STN.wav", minim));
}
});
panel.add(stn);
JButton snr = new JButton("SNr");
snr.addActionListener(new ActionListener() {
-
public void actionPerformed(ActionEvent e) {
- addNeuron(new NeuronPath(Color.green, "/Users/zkim/napplelabs/dbssim/src/main/resources/15-PD-SNr.wav", minim));
+ addNeuron(new NeuronPath(Color.green, "./neuron_media_files/15-PD-SNr.wav", minim));
}
});
panel.add(snr);
@@ -216,6 +216,9 @@ public void load() {
XStream xs = new XStream();
//Write to a file in the file system
+
+ if(! new File("./neurons").exists()) return;
+
try {
ObjectInputStream is = xs.createObjectInputStream(new FileReader(new File("./neurons")));
List<NeuronPathRep> paths = (List<NeuronPathRep>) is.readObject();
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