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numTrials and randomSeed: editing, persistence. SolverTaskDescription…
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…: copy constructor, compareEqual fixes
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@danv61
danv61 committed Dec 18, 2024
1 parent 7a79c1b commit c52182e
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Showing 8 changed files with 146 additions and 119 deletions.
164 changes: 107 additions & 57 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
@@ -1,11 +1,13 @@
package cbit.vcell.solver.ode.gui;

import java.awt.*;
import java.math.BigInteger;

import javax.swing.*;
import javax.swing.border.Border;

import cbit.vcell.solver.NFsimSimulationOptions;
import org.vcell.solver.nfsim.gui.NFSimSimulationOptionsPanel;
import org.vcell.util.gui.CollapsiblePanel;

import cbit.vcell.client.PopupGenerator;
Expand Down Expand Up @@ -68,16 +70,25 @@ public void actionPerformed(java.awt.event.ActionEvent e) {
if (e.getSource() == getTrajectoryButton()) {
getJTextFieldNumOfTrials().setEnabled(false);
getJTextFieldNumOfParallelLocalRuns().setEnabled(false);
setNewOptions();
getJTextFieldNumOfParallelLocalRuns().setText("");
solverTaskDescription.setNumTrials(1);
getJTextFieldNumOfTrials().setText("");
} else if (e.getSource() == getMultiRunButton()) {
getJTextFieldNumOfTrials().setEnabled(true);
getJTextFieldNumOfParallelLocalRuns().setEnabled(true);
setNewOptions();
getJTextFieldNumOfParallelLocalRuns().setEnabled(false);
getJTextFieldNumOfParallelLocalRuns().setText(solverTaskDescription.getLangevinSimulationOptions().getNumOfParallelLocalRuns()+"");
int numTrials = solverTaskDescription.getNumTrials();
if(numTrials > 1) { // a multi-trial number is already set
getJTextFieldNumOfTrials().setText(numTrials+"");
} else {
solverTaskDescription.setNumTrials(SolverTaskDescription.DefaultNumTrials);
getJTextFieldNumOfTrials().setText(SolverTaskDescription.DefaultNumTrials+"");
}
} else if(e.getSource() == randomSeedCheckBox) {
randomSeedTextField.setEditable(randomSeedCheckBox.isSelected());
if(randomSeedCheckBox.isSelected()) {

Integer rs = solverTaskDescription.getLangevinSimulationOptions().getRandomSeed();
BigInteger rs = solverTaskDescription.getLangevinSimulationOptions().getRandomSeed();
if(rs == null) {
rs = LangevinSimulationOptions.DefaultRandomSeed;
solverTaskDescription.getLangevinSimulationOptions().setRandomSeed(rs);
Expand All @@ -87,7 +98,11 @@ public void actionPerformed(java.awt.event.ActionEvent e) {
solverTaskDescription.getLangevinSimulationOptions().setRandomSeed(null);
randomSeedTextField.setText("");
}

} else if(e.getSource() == randomSeedHelpButton) {
DialogUtils.showInfoDialogAndResize(LangevinOptionsPanel.this, "Set specific seed",
"<html>Provide a seed to the Langevin solver's random number generator so exact "
+ "trajectories can be reproduced. If this value is not entered, the solver will "
+ "generate different sequences for each run.</html>");
}
}

Expand All @@ -98,14 +113,29 @@ public void focusLost(java.awt.event.FocusEvent e) {
if (e.isTemporary()) {
return;
}
if (e.getSource() == getJTextFieldNumOfTrials() ||
e.getSource() == getJTextFieldNumOfParallelLocalRuns() ||
if (e.getSource() == getJTextFieldNumOfParallelLocalRuns() ||
e.getSource() == getJTextFieldIntervalImage() ||
e.getSource() == getJTextFieldIntervalSpring() ||
e.getSource() == getNumPartitionsXTextField() ||
e.getSource() == getNumPartitionsYTextField() ||
e.getSource() == getNumPartitionsXTextField()) {
e.getSource() == getNumPartitionsXTextField() ||
e.getSource() == getRandomSeedTextField() ) {
setNewOptions();
} else if(e.getSource() == getJTextFieldNumOfTrials()) {
int numTrials;
try {
numTrials = Integer.parseInt(getJTextFieldNumOfTrials().getText());
if(numTrials < 2) {
numTrials = SolverTaskDescription.DefaultNumTrials;
}
} catch(NumberFormatException ex) {
numTrials = solverTaskDescription.getNumTrials();
if(numTrials < 2) {
numTrials = SolverTaskDescription.DefaultNumTrials;
}
}
solverTaskDescription.setNumTrials(numTrials);
getJTextFieldNumOfTrials().setText(numTrials+"");
}
}
}
Expand All @@ -127,6 +157,8 @@ private void initialize() {
centerPanel.setLayout(new GridBagLayout());
JPanel rightPanel = new JPanel(new GridBagLayout()); // fake panel, for looks
rightPanel.setLayout(new GridBagLayout());
JPanel bottomPanel = new JPanel(new GridBagLayout());
bottomPanel.setLayout(new GridBagLayout());

GridBagConstraints gbc = new GridBagConstraints();
gbc.gridx = 0;
Expand Down Expand Up @@ -155,6 +187,16 @@ private void initialize() {
gbc.insets = new Insets(1,1,1,1);
getContentPanel().add(rightPanel, gbc);

gbc = new GridBagConstraints();
gbc.gridx = 0;
gbc.gridy = 1;
gbc.fill = GridBagConstraints.HORIZONTAL;
gbc.gridwidth = 3;
// gbc.weightx = 1.0;
// gbc.weighty = 1.0;
gbc.insets = new Insets(1,1,1,1);
getContentPanel().add(bottomPanel, gbc);

// ----- trialPanel --------------------------------------------------------------
gbc = new GridBagConstraints();
gbc.gridx = 0;
Expand Down Expand Up @@ -261,15 +303,6 @@ private void initialize() {
gbc.insets = new Insets(0,5,3,1);
trialPanel.add(getNumPartitionsZTextField(), gbc);

gbc = new GridBagConstraints();
gbc.gridx = 0;
gbc.gridy = 6;
gbc.anchor = GridBagConstraints.WEST;
gbc.fill = GridBagConstraints.HORIZONTAL;
gbc.insets = new Insets(5,5,3,1);
trialPanel.add(getRandomSeedCheckBox(), gbc);


// gbc = new GridBagConstraints(); // --- empty panel (filler)
// gbc.gridx = 3;
// gbc.gridy = 1;
Expand Down Expand Up @@ -334,34 +367,42 @@ private void initialize() {
gbc.weighty = 1.0;
centerPanel.add(new JLabel(""), gbc);

// ----- rightPanel ----------------------------------------------------
gbc = new GridBagConstraints();
gbc.gridx = 3;
gbc.gridy = 0;
gbc.anchor = GridBagConstraints.WEST;
gbc.fill = GridBagConstraints.BOTH;
gbc.weightx = 1.0;
gbc.weighty = 1.0;
gbc.insets = new Insets(0,22,1,6);
rightPanel.add(new JLabel(""), gbc); // fake, just for looks

// ----- bottomPanel ------------------------------------------------------
gbc = new GridBagConstraints();
gbc.gridx = 0;
gbc.gridy = 3;
gbc.gridy = 0;
gbc.anchor = GridBagConstraints.WEST;
gbc.fill = GridBagConstraints.HORIZONTAL;
gbc.insets = new Insets(5,2,6,5);
bottomPanel.add(getRandomSeedCheckBox(), gbc);

gbc = new GridBagConstraints();
gbc.gridx = 1;
gbc.gridy = 0;
gbc.weightx = 1;
gbc.gridwidth = 2;
gbc.insets = new Insets(0, 0, 6, 6);
gbc.insets = new Insets(2, 2, 6, 6);
gbc.fill = GridBagConstraints.HORIZONTAL;
gbc.anchor = GridBagConstraints.LINE_START;
centerPanel.add(getRandomSeedTextField(), gbc);
bottomPanel.add(getRandomSeedTextField(), gbc);

gbc = new GridBagConstraints();
gbc.gridx = 2;
gbc.gridy = 3;
gbc.anchor = GridBagConstraints.LINE_END;
gbc.insets = new Insets(0, 0, 6, 6);
centerPanel.add(getRandomSeedHelpButton(), gbc);


// ----- rightPanel ----------------------------------------------------
gbc = new GridBagConstraints();
gbc.gridx = 3;
gbc.gridy = 0;
gbc.anchor = GridBagConstraints.WEST;
gbc.fill = GridBagConstraints.BOTH;
gbc.weightx = 1.0;
gbc.weighty = 1.0;
gbc.insets = new Insets(0,22,1,6);
rightPanel.add(new JLabel(""), gbc); // fake, just for looks
gbc.insets = new Insets(2, 2, 6, 6);
bottomPanel.add(getRandomSeedHelpButton(), gbc);

// ----------------------------------------------------------------------
getButtonGroupTrials().add(getTrajectoryButton());
Expand Down Expand Up @@ -420,7 +461,7 @@ private javax.swing.JTextField getJTextFieldNumOfTrials() {
ivjJTextFieldNumOfTrials = new javax.swing.JTextField();
ivjJTextFieldNumOfTrials.setName("JTextFieldNumOfTrials");
ivjJTextFieldNumOfTrials.setColumns(9);
ivjJTextFieldNumOfTrials.setText("100");
ivjJTextFieldNumOfTrials.setText("");
} catch (java.lang.Throwable ivjExc) {
handleException(ivjExc);
}
Expand Down Expand Up @@ -451,7 +492,6 @@ private JTextField getRandomSeedTextField() {
if(randomSeedTextField == null) {
randomSeedTextField = new JTextField();
randomSeedTextField.setName("RandomSeedTextField");
randomSeedTextField.setText("");
}
return randomSeedTextField;
}
Expand All @@ -463,7 +503,7 @@ private JButton getRandomSeedHelpButton() {
randomSeedHelpButton.setName("RandomSeedHelpButton");
randomSeedHelpButton.setBorder(border);
randomSeedHelpButton.setFont(font);
randomSeedHelpButton.setText(" ? ");
randomSeedHelpButton.setText("<html><b>&nbsp;&nbsp;?&nbsp;&nbsp;</b></html>");
}
return randomSeedHelpButton;
}
Expand Down Expand Up @@ -563,7 +603,7 @@ private javax.swing.JTextField getJTextFieldNumOfParallelLocalRuns() {
ivjJTextFieldNumOfParallelLocalRuns = new javax.swing.JTextField();
ivjJTextFieldNumOfParallelLocalRuns.setName("JTextFieldNumOfParallelLocalRuns");
ivjJTextFieldNumOfParallelLocalRuns.setColumns(3);
ivjJTextFieldNumOfParallelLocalRuns.setText("1");
ivjJTextFieldNumOfParallelLocalRuns.setText("");
} catch (java.lang.Throwable ivjExc) {
handleException(ivjExc);
}
Expand Down Expand Up @@ -638,14 +678,17 @@ public final void setSolverTaskDescription(SolverTaskDescription newValue) {
private void initConnections() {
getTrajectoryButton().addActionListener(ivjEventHandler);
getMultiRunButton().addActionListener(ivjEventHandler);

getRandomSeedCheckBox().addActionListener(ivjEventHandler);
getRandomSeedHelpButton().addActionListener(ivjEventHandler);

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

private void refresh() {
Expand All @@ -657,19 +700,23 @@ private void refresh() {
return;
}
setVisible(true);


getMultiRunButton().setEnabled(true);

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

Expand All @@ -680,14 +727,16 @@ private void refresh() {
getJTextFieldIntervalImage().setText(lso.getIntervalImage()+"");
getJTextFieldIntervalSpring().setText(lso.getIntervalSpring()+"");

// TODO: temporarily disable the button
// UNDO THIS WHEN DEVELOPMENT IS COMPLETE
if(solverTaskDescription.getSolverDescription().isLangevinSolver()) {
getMultiRunButton().setEnabled(false);
return;
BigInteger randomSeed = lso.getRandomSeed();
if (randomSeed == null) {
randomSeedTextField.setEditable(false);
randomSeedCheckBox.setSelected(false);
randomSeedTextField.setText("");
} else {
randomSeedTextField.setEditable(true);
randomSeedCheckBox.setSelected(true);
randomSeedTextField.setText(randomSeed.toString());
}


}

private void setNewOptions() {
Expand All @@ -696,27 +745,29 @@ 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());
numOfParallelLocalRuns = Integer.parseInt(getJTextFieldNumOfParallelLocalRuns().getText());
if(getMultiRunButton().isSelected()) { // we can get here only on FocusLost event in the numOfTrials text field
try {
numOfParallelLocalRuns = Integer.parseInt(getJTextFieldNumOfParallelLocalRuns().getText());
} catch (NumberFormatException ex) {
numOfParallelLocalRuns = sso.getNumOfParallelLocalRuns();
}
}

Integer randomSeed = null;
BigInteger randomSeed = null;
if (randomSeedCheckBox.isSelected()) {
try {
randomSeed = Integer.valueOf(randomSeedTextField.getText());
randomSeed = new BigInteger(randomSeedTextField.getText());
} catch (NumberFormatException ex) {
randomSeed = solverTaskDescription.getLangevinSimulationOptions().getRandomSeed();
if(randomSeed == null) {
randomSeed = LangevinSimulationOptions.DefaultRandomSeed;
}
randomSeedTextField.setText(randomSeed.toString());
// randomSeedTextField.setText(randomSeed.toString());
}
}

Expand All @@ -729,7 +780,6 @@ private void setNewOptions() {

// make a copy
LangevinSimulationOptions lso = new LangevinSimulationOptions(sso);
lso.setNumTrials(numTrials);
lso.setNumOfParallelLocalRuns(numOfParallelLocalRuns);
lso.setRandomSeed(randomSeed);
lso.setIntervalImage(intervalImage);
Expand Down
3 changes: 1 addition & 2 deletions vcell-core/src/main/java/cbit/vcell/math/VCML.java
View file
Original file line number Diff line number Diff line change
Expand Up @@ -244,8 +244,7 @@ public class VCML {
public final static String VolumeParticleSpeciesPatterns = "VolumeParticleSpeciesPatterns";

public final static String LangevinSimulationOptions = "LangevinSimulationOptions";
public final static String LangevinSimulationOptions_numOfTrials = "NumOfTrials";
public final static String LangevinSimulationOptions_runIndex = "RunIndex";
public final static String LangevinSimulationOptions_randomSeed = "RandomSeed";
public final static String LangevinSimulationOptions_intervalSpring = "IntervalSpring";
public final static String LangevinSimulationOptions_intervalImage = "IntervalImage";
public final static String LangevinSimulationOptions_Partition_Nx = "PartitionNx";
Expand Down
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