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Merge pull request #1354 from virtualcell/dan-ss-partitions
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Dan ss partitions
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@danv61
danv61 authored Sep 18, 2024
2 parents c8358e6 + 710dfab commit a231a5d
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Showing 12 changed files with 388 additions and 28 deletions.
5 changes: 5 additions & 0 deletions vcell-client/src/main/java/cbit/vcell/client/desktop/simulation/SimulationEditor.java
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Original file line number Diff line number Diff line change
Expand Up @@ -18,6 +18,7 @@
import javax.swing.JPanel;
import javax.swing.JTabbedPane;

import cbit.vcell.mapping.SimulationContext;
import org.vcell.util.BeanUtils;

import cbit.vcell.geometry.ChomboInvalidGeometryException;
Expand Down Expand Up @@ -276,6 +277,10 @@ public void prepareToEdit(Simulation simulation, Component parent) throws Chombo
meshSpec.getGeometry().getDimension() > 0){
shouldMeshBeEnabled = true;
}
SimulationOwner so = simulation.getSimulationOwner();
if(so instanceof SimulationContext && ((SimulationContext)so).getApplicationType() == SimulationContext.Application.SPRINGSALAD) {
shouldMeshBeEnabled = false;
}
if (!shouldMeshBeEnabled) {
getJTabbedPane1().remove(getMeshTabPanel());
}
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260 changes: 252 additions & 8 deletions vcell-client/src/main/java/cbit/vcell/solver/ode/gui/LangevinOptionsPanel.java
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Original file line number Diff line number Diff line change
Expand Up @@ -28,7 +28,19 @@ public class LangevinOptionsPanel extends CollapsiblePanel {

private JLabel numOfTrialsLabel = null;
private JTextField ivjJTextFieldNumOfTrials = null;

private JLabel numOfParallelLocalRuns = null;
private JTextField ivjJTextFieldNumOfParallelLocalRuns = null;

private JTextField numPartitionsXTextField = null;
private JTextField numPartitionsYTextField = null;
private JTextField numPartitionsZTextField = null;
private JLabel numPartitionsXLabel = null;
private JLabel numPartitionsYLabel = null;
private JLabel numPartitionsZLabel = null;
private JLabel numPartitionsLabel = null;

// private int[] npart = {LangevinSimulationOptions.DefaultNPart[0], LangevinSimulationOptions.DefaultNPart[1], LangevinSimulationOptions.DefaultNPart[2]}; // number of partitions on each axis

private JTextField intervalImageTextField = null;
private JTextField intervalSpringTextField = null;

Expand All @@ -54,9 +66,11 @@ public void actionPerformed(java.awt.event.ActionEvent e) {
// }
if (e.getSource() == getTrajectoryButton()) {
getJTextFieldNumOfTrials().setEnabled(false);
getJTextFieldNumOfParallelLocalRuns().setEnabled(false);
setNewOptions();
} else if (e.getSource() == getMultiRunButton()) {
getJTextFieldNumOfTrials().setEnabled(true);
getJTextFieldNumOfParallelLocalRuns().setEnabled(true);
setNewOptions();
}
}
Expand All @@ -69,8 +83,12 @@ public void focusLost(java.awt.event.FocusEvent e) {
return;
}
if (e.getSource() == getJTextFieldNumOfTrials() ||
e.getSource() == getJTextFieldNumOfParallelLocalRuns() ||
e.getSource() == getJTextFieldIntervalImage() ||
e.getSource() == getJTextFieldIntervalSpring()) {
e.getSource() == getJTextFieldIntervalSpring() ||
e.getSource() == getNumPartitionsXTextField() ||
e.getSource() == getNumPartitionsYTextField() ||
e.getSource() == getNumPartitionsXTextField()) {
setNewOptions();
}
}
Expand Down Expand Up @@ -156,12 +174,86 @@ private void initialize() {
trialPanel.add(getJTextFieldNumOfTrials(), gbc);

gbc = new GridBagConstraints();
gbc.gridx = 3;
gbc.gridy = 1;
gbc.anchor = GridBagConstraints.EAST;
gbc.gridx = 1;
gbc.gridy = 2;
gbc.anchor = GridBagConstraints.WEST;
gbc.fill = GridBagConstraints.HORIZONTAL;
gbc.weightx = 1.0;
trialPanel.add(new JLabel(""), gbc);
gbc.insets = new Insets(0,22,1,6);
trialPanel.add(getNumOfParallelLocalRunsLabel(), gbc);

gbc = new GridBagConstraints();
gbc.gridx = 2;
gbc.gridy = 2;
gbc.anchor = GridBagConstraints.WEST;
gbc.fill = GridBagConstraints.HORIZONTAL;
gbc.insets = new Insets(0,5,3,1);
trialPanel.add(getJTextFieldNumOfParallelLocalRuns(), gbc);

// ----- aici
gbc = new GridBagConstraints();
gbc.gridx = 0;
gbc.gridy = 3;
gbc.anchor = GridBagConstraints.WEST;
gbc.fill = GridBagConstraints.HORIZONTAL;
gbc.insets = new Insets(5,5,1,1);
trialPanel.add(getNumPartitionsLabel(), gbc);

gbc = new GridBagConstraints();
gbc.gridx = 1;
gbc.gridy = 3;
gbc.anchor = GridBagConstraints.WEST;
gbc.fill = GridBagConstraints.HORIZONTAL;
gbc.insets = new Insets(5,22,1,6);
trialPanel.add(getNumPartitionsXLabel(), gbc);

gbc = new GridBagConstraints();
gbc.gridx = 2;
gbc.gridy = 3;
gbc.anchor = GridBagConstraints.WEST;
gbc.fill = GridBagConstraints.HORIZONTAL;
gbc.insets = new Insets(5,5,3,1);
trialPanel.add(getNumPartitionsXTextField(), gbc);

gbc = new GridBagConstraints();
gbc.gridx = 1;
gbc.gridy = 4;
gbc.anchor = GridBagConstraints.WEST;
gbc.fill = GridBagConstraints.HORIZONTAL;
gbc.insets = new Insets(0,22,1,6);
trialPanel.add(getNumPartitionsYLabel(), gbc);

gbc = new GridBagConstraints();
gbc.gridx = 2;
gbc.gridy = 4;
gbc.anchor = GridBagConstraints.WEST;
gbc.fill = GridBagConstraints.HORIZONTAL;
gbc.insets = new Insets(0,5,3,1);
trialPanel.add(getNumPartitionsYTextField(), gbc);

gbc = new GridBagConstraints();
gbc.gridx = 1;
gbc.gridy = 5;
gbc.anchor = GridBagConstraints.WEST;
gbc.fill = GridBagConstraints.HORIZONTAL;
gbc.insets = new Insets(0,22,1,6);
trialPanel.add(getNumPartitionsZLabel(), gbc);

gbc = new GridBagConstraints();
gbc.gridx = 2;
gbc.gridy = 5;
gbc.anchor = GridBagConstraints.WEST;
gbc.fill = GridBagConstraints.HORIZONTAL;
gbc.insets = new Insets(0,5,3,1);
trialPanel.add(getNumPartitionsZTextField(), gbc);


// gbc = new GridBagConstraints(); // --- empty panel (filler)
// gbc.gridx = 3;
// gbc.gridy = 1;
// gbc.anchor = GridBagConstraints.EAST;
// gbc.fill = GridBagConstraints.HORIZONTAL;
// gbc.weightx = 1.0;
// trialPanel.add(new JLabel(""), gbc);

// ----- centerPanel -----------------------------------------------------
gbc = new GridBagConstraints();
Expand Down Expand Up @@ -210,6 +302,15 @@ private void initialize() {
gbc.insets = new Insets(0,6,1,22);
centerPanel.add(new JLabel("s"), gbc);

gbc = new GridBagConstraints(); // --- empty panel (filler)
gbc.gridx = 0;
gbc.gridy = 2;
gbc.anchor = GridBagConstraints.EAST;
gbc.fill = GridBagConstraints.VERTICAL;
gbc.weightx = 1.0;
gbc.weighty = 1.0;
centerPanel.add(new JLabel(""), gbc);

// ----- rightPanel ----------------------------------------------------
gbc = new GridBagConstraints();
gbc.gridx = 3;
Expand All @@ -227,6 +328,11 @@ private void initialize() {
getButtonGroupTrials().setSelected(getTrajectoryButton().getModel(), true);

getJTextFieldNumOfTrials().setEnabled(false);
getJTextFieldNumOfParallelLocalRuns().setEnabled(false);

getNumPartitionsXTextField().setEnabled(true);
getNumPartitionsYTextField().setEnabled(true);
getNumPartitionsZTextField().setEnabled(true);

} catch (java.lang.Throwable ivjExc) {
handleException(ivjExc);
Expand Down Expand Up @@ -292,6 +398,122 @@ private javax.swing.JLabel getNumOfTrialsLabel() {
}
return numOfTrialsLabel;
}

// ======================================================================= Number of Partitions
private javax.swing.JTextField getNumPartitionsXTextField() {
if (numPartitionsXTextField == null) {
try {
numPartitionsXTextField = new javax.swing.JTextField();
numPartitionsXTextField.setName("NumPartitionsXTextField");
// numPartitionsXTextField.setColumns(3);
numPartitionsXTextField.setText(LangevinSimulationOptions.DefaultNPart[0]+"");
} catch (java.lang.Throwable ivjExc) {
handleException(ivjExc);
}
}
return numPartitionsXTextField;
}
private javax.swing.JLabel getNumPartitionsXLabel() {
if (numPartitionsXLabel == null) {
try {
numPartitionsXLabel = new javax.swing.JLabel();
numPartitionsXLabel.setName("NumPartitionsXLabel");
numPartitionsXLabel.setText("X-axis");
} catch (java.lang.Throwable ivjExc) {
handleException(ivjExc);
}
}
return numPartitionsXLabel;
}
private javax.swing.JTextField getNumPartitionsYTextField() {
if (numPartitionsYTextField == null) {
try {
numPartitionsYTextField = new javax.swing.JTextField();
numPartitionsYTextField.setName("NumPartitionsYTextField");
// numPartitionsYTextField.setColumns(3);
numPartitionsYTextField.setText(LangevinSimulationOptions.DefaultNPart[1]+"");
} catch (java.lang.Throwable ivjExc) {
handleException(ivjExc);
}
}
return numPartitionsYTextField;
}
private javax.swing.JLabel getNumPartitionsYLabel() {
if (numPartitionsYLabel == null) {
try {
numPartitionsYLabel = new javax.swing.JLabel();
numPartitionsYLabel.setName("NumPartitionsYLabel");
numPartitionsYLabel.setText("Y-axis");
} catch (java.lang.Throwable ivjExc) {
handleException(ivjExc);
}
}
return numPartitionsYLabel;
}
private javax.swing.JTextField getNumPartitionsZTextField() {
if (numPartitionsZTextField == null) {
try {
numPartitionsZTextField = new javax.swing.JTextField();
numPartitionsZTextField.setName("NumPartitionsZTextField");
// numPartitionsZTextField.setColumns(3);
numPartitionsZTextField.setText(LangevinSimulationOptions.DefaultNPart[2]+"");
} catch (java.lang.Throwable ivjExc) {
handleException(ivjExc);
}
}
return numPartitionsZTextField;
}
private javax.swing.JLabel getNumPartitionsZLabel() {
if (numPartitionsZLabel == null) {
try {
numPartitionsZLabel = new javax.swing.JLabel();
numPartitionsZLabel.setName("NumPartitionsZLabel");
numPartitionsZLabel.setText("Z-axis");
} catch (java.lang.Throwable ivjExc) {
handleException(ivjExc);
}
}
return numPartitionsZLabel;
}
private javax.swing.JLabel getNumPartitionsLabel() {
if (numPartitionsLabel == null) {
try {
numPartitionsLabel = new javax.swing.JLabel();
numPartitionsLabel.setName("NumPartitionsLabel");
numPartitionsLabel.setText("Partitions number");
} catch (java.lang.Throwable ivjExc) {
handleException(ivjExc);
}
}
return numPartitionsLabel;
}

private javax.swing.JTextField getJTextFieldNumOfParallelLocalRuns() {
if (ivjJTextFieldNumOfParallelLocalRuns == null) {
try {
ivjJTextFieldNumOfParallelLocalRuns = new javax.swing.JTextField();
ivjJTextFieldNumOfParallelLocalRuns.setName("JTextFieldNumOfParallelLocalRuns");
ivjJTextFieldNumOfParallelLocalRuns.setColumns(3);
ivjJTextFieldNumOfParallelLocalRuns.setText("1");
} catch (java.lang.Throwable ivjExc) {
handleException(ivjExc);
}
}
return ivjJTextFieldNumOfParallelLocalRuns;
}
private javax.swing.JLabel getNumOfParallelLocalRunsLabel() {
if (numOfParallelLocalRuns == null) {
try {
numOfParallelLocalRuns = new javax.swing.JLabel();
numOfParallelLocalRuns.setName("NumOfParallelLocalRuns");
numOfParallelLocalRuns.setText("Parallel Local Runs");
} catch (java.lang.Throwable ivjExc) {
handleException(ivjExc);
}
}
return numOfParallelLocalRuns;
}

private JTextField getJTextFieldIntervalImage() {
if (intervalImageTextField == null) {
try {
Expand Down Expand Up @@ -349,8 +571,12 @@ private void initConnections() {
getMultiRunButton().addActionListener(ivjEventHandler);

getJTextFieldNumOfTrials().addFocusListener(ivjEventHandler);
getJTextFieldNumOfParallelLocalRuns().addFocusListener(ivjEventHandler);
getJTextFieldIntervalImage().addFocusListener(ivjEventHandler);
getJTextFieldIntervalSpring().addFocusListener(ivjEventHandler);
getNumPartitionsXTextField().addFocusListener(ivjEventHandler);
getNumPartitionsYTextField().addFocusListener(ivjEventHandler);
getNumPartitionsZTextField().addFocusListener(ivjEventHandler);
}

private void refresh() {
Expand All @@ -365,14 +591,23 @@ private void refresh() {

LangevinSimulationOptions lso = solverTaskDescription.getLangevinSimulationOptions();
int numTrials = lso.getNumOfTrials();
int numOfParallelLocalRuns = lso.getNumOfParallelLocalRuns();
if(numTrials == 1) {
getTrajectoryButton().setSelected(true);
getJTextFieldNumOfTrials().setEnabled(false);
getJTextFieldNumOfParallelLocalRuns().setEnabled(false);
} else {
getMultiRunButton().setSelected(true);
getJTextFieldNumOfTrials().setEnabled(true);
getJTextFieldNumOfTrials().setText(numTrials+"");
getJTextFieldNumOfParallelLocalRuns().setEnabled(true);
getJTextFieldNumOfParallelLocalRuns().setText(numOfParallelLocalRuns + "");
}

getNumPartitionsXTextField().setText(lso.getNPart(0) + "");
getNumPartitionsYTextField().setText(lso.getNPart(1) + "");
getNumPartitionsZTextField().setText(lso.getNPart(2) + "");

getJTextFieldIntervalImage().setText(lso.getIntervalImage()+"");
getJTextFieldIntervalSpring().setText(lso.getIntervalSpring()+"");

Expand All @@ -393,21 +628,30 @@ private void setNewOptions() {
try {
LangevinSimulationOptions sso = solverTaskDescription.getLangevinSimulationOptions();
int numTrials = 1;
int numOfParallelLocalRuns = 1;
double intervalImage = solverTaskDescription.getLangevinSimulationOptions().getIntervalImage();
double intervalSpring = solverTaskDescription.getLangevinSimulationOptions().getIntervalSpring();
int[] npart = solverTaskDescription.getLangevinSimulationOptions().getNPart();

if(getMultiRunButton().isSelected()) {
numTrials = Integer.parseInt(getJTextFieldNumOfTrials().getText());
sso.setNumOfTrials(numTrials);
numOfParallelLocalRuns = Integer.parseInt(getJTextFieldNumOfParallelLocalRuns().getText());
sso.setNumOfParallelLocalRuns(numOfParallelLocalRuns);
}

intervalImage = Double.parseDouble(getJTextFieldIntervalImage().getText());
intervalSpring = Double.parseDouble(getJTextFieldIntervalSpring().getText());


npart[0] = Integer.parseInt(getNumPartitionsXTextField().getText());
npart[1] = Integer.parseInt(getNumPartitionsYTextField().getText());
npart[2] = Integer.parseInt(getNumPartitionsZTextField().getText());

// make a copy
LangevinSimulationOptions lso = new LangevinSimulationOptions(sso);
lso.setIntervalImage(intervalImage);
lso.setIntervalSpring(intervalSpring);
lso.setNPart(npart);
solverTaskDescription.setLangevinSimulationOptions(lso);

} catch(Exception e) {
Expand Down
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