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Updates for latest sciview #6

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Updates for latest sciview #6

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b5a69bd
Updates for latest sciview
kephale Jul 21, 2023
1417aba
Update to get RandomBranchingDemo working
kephale Mar 27, 2024
7cdd350
Cleaning up ImgNeuriteChemoAttraction demo
kephale Apr 1, 2024
35cd22f
More reasonable behavior, not ideal though
kephale Apr 1, 2024
077e9ef
Sleep during simulation update, fix random branching demo
kephale Apr 3, 2024
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48 changes: 33 additions & 15 deletions pom.xml
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Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -5,14 +5,14 @@
<parent>
<groupId>org.scijava</groupId>
<artifactId>pom-scijava</artifactId>
<version>29.0.0-beta-2</version>
<version>37.0.0</version>
<relativePath />
</parent>


<groupId>org.morphonets</groupId>
<artifactId>cx3d</artifactId>
<version>0.0.4-SNAPSHOT</version>
<version>0.1.0-SNAPSHOT</version>
<packaging>jar</packaging>

<name>cx3d</name>
Expand Down Expand Up @@ -102,25 +102,19 @@
<!-- NB: Deploy releases to the SciJava Maven repository. -->
<releaseProfiles>deploy-to-scijava</releaseProfiles>

<bigdataviewer-core.version>7.0.0</bigdataviewer-core.version>
<scenery.version>0.10.1</scenery.version>
<sciview.version>0.3.0</sciview.version>
<snt.version>4.2.2-SNAPSHOT</snt.version>

<sciview.version>9a71de9</sciview.version>
<scenery.version>f55e46b</scenery.version>
<snt.version>2d8af5b6a0</snt.version>
<flatlaf.version>3.1.1</flatlaf.version>
<flatlaf-jide-oss.version>${flatlaf.version}</flatlaf-jide-oss.version>

<joml.version>1.9.22</joml.version>
<kotlin.version>1.4-M1</kotlin.version>
<jogl.version>2.4.0</jogl.version>

<grneat.version>a322110ac4</grneat.version>
<cleargl.version>2.2.10</cleargl.version>
<lwjgl.version>3.2.3</lwjgl.version>
</properties>

<repositories>
<repository>
<id>jitpack.io</id>
<url>https://jitpack.io</url>
</repository>
<repository>
<id>scijava.public</id>
<url>https://maven.scijava.org/content/groups/public</url>
Expand All @@ -133,6 +127,10 @@
<artifactId>grneat</artifactId>
<version>${grneat.version}</version>
</dependency>
<dependency>
<groupId>com.formdev</groupId>
<artifactId>flatlaf</artifactId>
</dependency>
<dependency>
<groupId>sc.iview</groupId>
<artifactId>sciview</artifactId>
Expand All @@ -142,7 +140,27 @@
<groupId>ch.qos.logback</groupId>
<artifactId>logback-classic</artifactId>
</exclusion>
</exclusions>
<exclusion>
<groupId>org.apache.logging.log4j</groupId>
<artifactId>log4j-1.2-api</artifactId>
</exclusion>
<exclusion>
<groupId>org.biojava</groupId>
<artifactId>biojava-core</artifactId>
</exclusion>
<exclusion>
<groupId>org.biojava</groupId>
<artifactId>biojava-structure</artifactId>
</exclusion>
<exclusion>
<groupId>org.biojava</groupId>
<artifactId>biojava-modfinder</artifactId>
</exclusion>
<exclusion>
<groupId>org.jetbrains.kotlin</groupId>
<artifactId>kotlin-stdlib</artifactId>
</exclusion>
</exclusions>
</dependency>
<dependency>
<groupId>org.morphonets</groupId>
Expand Down
34 changes: 22 additions & 12 deletions src/main/java/sc/iview/cx3d/SciViewCX3D.java
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Original file line number Diff line number Diff line change
@@ -1,9 +1,15 @@
package sc.iview.cx3d;

import graphics.scenery.*;
import graphics.scenery.DefaultNode;
import graphics.scenery.Group;
import graphics.scenery.Node;
import graphics.scenery.Sphere;
import graphics.scenery.Icosphere;
import graphics.scenery.attribute.material.DefaultMaterial;
import graphics.scenery.attribute.material.Material;
import graphics.scenery.primitives.Cylinder;
import org.joml.Vector3f;
import org.scijava.Context;
import org.scijava.ui.UIService;
import sc.iview.SciView;
import sc.iview.cx3d.physics.IntracellularSubstance;
import sc.iview.cx3d.physics.PhysicalCylinder;
Expand All @@ -28,7 +34,6 @@ public SciView getSciView() {
}

private Context context;
private UIService ui;
private SciView sciView;
private ECM ecm;

Expand All @@ -45,9 +50,8 @@ public Node getCx3dGroup() {
private HashMap<Integer, Node> scNodes;
private HashMap<Substance, Node> volumes;

public SciViewCX3D(Context context, UIService ui, SciView sciView, ECM ecm) {
public SciViewCX3D(Context context, SciView sciView, ECM ecm) {
this.context = context;
this.ui = ui;
this.sciView = sciView;
this.ecm = ecm;

Expand All @@ -72,7 +76,7 @@ public void clear() {
}

public void addNewChemical(Substance substance) {
chemicals.put(substance, new Node());
chemicals.put(substance, new DefaultNode());
}


Expand All @@ -86,7 +90,13 @@ public void syncCX3D() {
// Loop through all Cylinders
paintPhysicalCylinders();

// Loop through all PhysicalNodes FIXME currently this is done externally
try {
Thread.sleep(10);
} catch (InterruptedException e) {
throw new RuntimeException(e);
}

// Loop through all PhysicalNodes FIXME currently this is done externally
//paintPhysicalNodes();
}

Expand Down Expand Up @@ -154,7 +164,7 @@ private void paintPhysicalCylinders() {
svCylinder.orientBetweenPoints(myNeuriteDistalEnd, myNeuriteProximalEnd, true, true);
} else {
svCylinder = Cylinder.betweenPoints(myNeuriteDistalEnd, myNeuriteProximalEnd, (float)aCylinder.getDiameter() * scaleFactor, 1f, 12);
Material mat = new Material();
Material mat = new DefaultMaterial();
Vector3f col = new Vector3f(c.getRed() / 255.0f, c.getGreen() / 255.0f, c.getBlue() / 255.0f);
// mat.setAmbient(new GLVector(0.1f, 0f, 0f));
// mat.setDiffuse(new GLVector(0.8f, 0.7f, 0.7f));
Expand All @@ -178,8 +188,8 @@ private void paintPhysicalCylinders() {
svSphere.setVisible(true);
svSphere.setPosition(myNeuriteProximalEnd);
} else {
svSphere = new Sphere((float)aCylinder.getDiameter() * scaleFactor, 12);
Material mat = new Material();
svSphere = new Sphere((float)aCylinder.getDiameter() * scaleFactor, 12, false);
Material mat = new DefaultMaterial();
Vector3f col = new Vector3f(c.getRed() / 255.0f, c.getGreen() / 255.0f, c.getBlue() / 255.0f);
// mat.setAmbient(new GLVector(0.1f, 0f, 0f));
// mat.setDiffuse(new GLVector(0.8f, 0.7f, 0.7f));
Expand Down Expand Up @@ -258,9 +268,9 @@ private void paintPhysicalSpheres() {
svSphere.setVisible(true);
svSphere.setPosition(mySomaMassLocation);
} else {
svSphere = new Icosphere(sphereRadius, 2);
svSphere = new Icosphere(sphereRadius, 2, false);
svSphere.setVisible(false);
Material mat = new Material();
Material mat = new DefaultMaterial();
Vector3f col = new Vector3f(c.getRed() / 255.0f, c.getGreen() / 255.0f, c.getBlue() / 255.0f);
mat.setAmbient(col);
mat.setDiffuse(col);
Expand Down
6 changes: 3 additions & 3 deletions src/main/java/sc/iview/cx3d/commands/DendriteShaftWithSpines.java
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Original file line number Diff line number Diff line change
Expand Up @@ -58,7 +58,7 @@
import sc.iview.cx3d.utilities.ConvertUtils;

import static sc.iview.commands.MenuWeights.DEMO;
import static sc.iview.commands.MenuWeights.DEMO_LINES;
import static sc.iview.commands.MenuWeights.DEMO_BASIC_LINES;
import static sc.iview.cx3d.utilities.Matrix.randomNoise;

/**
Expand All @@ -69,7 +69,7 @@
@Plugin(type = Command.class, label = "Random Branching", menuRoot = "SciView", //
menu = { @Menu(label = "Demo", weight = DEMO), //
@Menu(label = "Cx3D", weight = DEMO), //
@Menu(label = "Random Branching", weight = DEMO_LINES) })
@Menu(label = "Random Branching", weight = DEMO_BASIC_LINES) })
public class DendriteShaftWithSpines implements Command {

@Parameter
Expand Down Expand Up @@ -139,7 +139,7 @@ public void run() {
public static void main( String... args ) {
SciView sciView = null;
try {
sciView = SciView.createSciView();
sciView = SciView.create();
} catch (Exception e) {
e.printStackTrace();
}
Expand Down
6 changes: 3 additions & 3 deletions src/main/java/sc/iview/cx3d/commands/GRNBranchingSWC.java
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Original file line number Diff line number Diff line change
Expand Up @@ -67,7 +67,7 @@
import java.util.function.Predicate;

import static sc.iview.commands.MenuWeights.DEMO;
import static sc.iview.commands.MenuWeights.DEMO_LINES;
import static sc.iview.commands.MenuWeights.DEMO_BASIC_LINES;
import static sc.iview.cx3d.utilities.Matrix.randomNoise;

/**
Expand All @@ -78,7 +78,7 @@
@Plugin(type = Command.class, label = "Genetically-regulated Branching (SWC output)", menuRoot = "SciView", //
menu = { @Menu(label = "Demo", weight = DEMO), //
@Menu(label = "Cx3D", weight = DEMO), //
@Menu(label = "Genetically-regulated Branching (SWC output)", weight = DEMO_LINES) })
@Menu(label = "Genetically-regulated Branching (SWC output)", weight = DEMO_BASIC_LINES) })
public class GRNBranchingSWC implements Command {

@Parameter
Expand Down Expand Up @@ -266,7 +266,7 @@ public static void main( String... args ) {
if( useSciview ) {
SciView sciView = null;
try {
sciView = SciView.createSciView();
sciView = SciView.create();
} catch (Exception e) {
e.printStackTrace();
}
Expand Down
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