/
VCellPlugin.java
1419 lines (1319 loc) · 55.2 KB
/
VCellPlugin.java
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/*
* To the extent possible under law, the ImageJ developers have waived
* all copyright and related or neighboring rights to this tutorial code.
*
* See the CC0 1.0 Universal license for details:
* http://creativecommons.org/publicdomain/zero/1.0/
*/
package org.vcell.imagej.plugin;
import java.awt.Component;
import java.awt.Container;
import java.awt.Dimension;
import java.awt.Frame;
import java.awt.GridLayout;
import java.awt.Rectangle;
import java.awt.Window;
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
import java.awt.event.WindowAdapter;
import java.awt.event.WindowEvent;
import java.text.DateFormat;
import java.util.ArrayList;
import java.util.Comparator;
import java.util.Date;
import java.util.Hashtable;
import java.util.Iterator;
import java.util.List;
import java.util.TreeSet;
import javax.swing.BoxLayout;
import javax.swing.DefaultComboBoxModel;
import javax.swing.JButton;
import javax.swing.JComboBox;
import javax.swing.JDialog;
import javax.swing.JFrame;
import javax.swing.JLabel;
import javax.swing.JOptionPane;
import javax.swing.JPanel;
import javax.swing.JProgressBar;
import javax.swing.JScrollPane;
import javax.swing.JSlider;
import javax.swing.JTable;
import javax.swing.SwingUtilities;
import javax.swing.event.ChangeEvent;
import javax.swing.event.ChangeListener;
import javax.swing.plaf.basic.BasicComboBoxUI;
import javax.swing.plaf.basic.BasicComboPopup;
import javax.swing.plaf.basic.ComboPopup;
import javax.swing.table.DefaultTableModel;
import org.scijava.command.Command;
import org.scijava.command.ContextCommand;
import org.scijava.display.Display;
import org.scijava.display.DisplayService;
import org.scijava.display.event.DisplayUpdatedEvent;
import org.scijava.event.EventService;
import org.scijava.io.RecentFileService;
import org.scijava.menu.MenuConstants;
import org.scijava.module.Module;
import org.scijava.module.ModuleItem;
import org.scijava.module.process.AbstractPreprocessorPlugin;
import org.scijava.module.process.PreprocessorPlugin;
import org.scijava.plugin.Attr;
import org.scijava.plugin.Menu;
import org.scijava.plugin.Parameter;
import org.scijava.plugin.Plugin;
import org.scijava.plugin.PluginInfo;
import org.scijava.run.RunService;
import org.scijava.ui.DialogPrompt.MessageType;
import org.scijava.ui.UIService;
import org.scijava.widget.UIComponent;
import org.vcell.imagej.helper.VCellHelper;
import org.vcell.imagej.helper.VCellHelper.BasicStackDimensions;
import org.vcell.imagej.helper.VCellHelper.IJDataList;
import org.vcell.imagej.helper.VCellHelper.IJVarInfo;
import org.vcell.imagej.helper.VCellHelper.IJVarInfos;
import org.vcell.imagej.helper.VCellHelper.ModelType;
import org.vcell.imagej.helper.VCellHelper.VCellModelSearchResults;
import ij.IJ;
import ij.ImagePlus;
import ij.ImageStack;
import ij.WindowManager;
import ij.gui.NewImage;
import net.imagej.ImageJ;
import net.imagej.ImgPlus;
import net.imagej.axis.Axes;
import net.imagej.axis.AxisType;
import net.imagej.axis.CalibratedAxis;
import net.imagej.axis.DefaultAxisType;
import net.imagej.axis.DefaultLinearAxis;
import net.imagej.display.DefaultDatasetView;
import net.imagej.display.DefaultImageDisplay;
import net.imagej.display.ImageDisplay;
import net.imagej.display.ImageDisplayService;
import net.imagej.display.WindowService;
import net.imagej.display.ZoomService;
import net.imagej.display.event.PanZoomEvent;
import net.imagej.ops.Op;
import net.imagej.ops.OpService;
import net.imagej.ops.Ops.Map;
import net.imglib2.img.array.ArrayImg;
import net.imglib2.img.array.ArrayImgs;
import net.imglib2.img.basictypeaccess.array.DoubleArray;
import net.imglib2.type.numeric.real.DoubleType;
import net.imglib2.util.Pair;
/**
* This example illustrates how to create an ImageJ {@link ContextCommand} plugin that uses VCellHelper.
* <p>
* You should replace the parameter fields with your own inputs and outputs,
* and replace the {@link run} method implementation with your own logic.
* </p>
* <p>
* To add VCellHelper to this project,
* rt-click on topmost tree element
* "imagej-plugin2"->Properties->Libraries tab->Add External Jars...->
* File Dialog->{EclipseVCellWorkspaceRootDir}/vcell/vcell-imagej-helper/target/vcell-imagej-helper-0.0.1-SNAPSHOT.jar.
* </p>
* <p>
* Once vcell-imagej-helper-0.0.1-SNAPSHOT.jar has been added to the Libraries tab open
* the small arrow to the left and select "Source Attachment"->Add/Edit->External Location->
* External File Dialog->{EclipseVCellWorkspaceRootDir}/vcell/vcell-imagej-helper/target/vcell-imagej-helper-0.0.1-SNAPSHOT-sources.jar.
* </p>
* <p>
* When editing the original VCellHelper in another running Eclipse,
* to make the changes show up in this project choose thisEclipse->Project->Clean...->clean.
* </p>
*/
@Plugin(type = Command.class, label = "VCell Model Search", iconPath="search_icon.gif",menu = {
@Menu(label = MenuConstants.PLUGINS_LABEL, weight = MenuConstants.FILE_WEIGHT,
mnemonic = MenuConstants.FILE_MNEMONIC),
@Menu(label = "VCell Plugins", weight = 4, mnemonic = 'V'),
@Menu(label = "VCell Model Search", weight = RecentFileService.MAX_FILES_SHOWN + 10,
mnemonic = 'm',accelerator = "^M") }, attrs = { @Attr(name = "no-legacy") })
public class VCellPlugin extends ContextCommand {
// final UIService service = getContext().getService(UIService.class);
// System.out.println(service.getDefaultUI().getApplicationFrame().getClass().getName()+" "+(service.getDefaultUI().getApplicationFrame() instanceof Frame));
private static Frame mainApplicationFrame;
public static class StyledComboBoxUI extends BasicComboBoxUI {
protected ComboPopup createPopup() {
@SuppressWarnings("serial")
BasicComboPopup popup = new BasicComboPopup(comboBox) {
@Override
protected Rectangle computePopupBounds(int px,int py,int pw,int ph) {
return super.computePopupBounds(
px,py,Math.max(comboBox.getPreferredSize().width,pw),ph
);
}
};
popup.getAccessibleContext().setAccessibleParent(comboBox);
return popup;
}
}
@SuppressWarnings("serial")
public static class StyledComboBox<E> extends JComboBox<String> {
public StyledComboBox() {
setUI(new StyledComboBoxUI());
}
public StyledComboBox(String[] items) {
setUI(new StyledComboBoxUI());
setModel(new DefaultComboBoxModel<String>(items));
}
}
@SuppressWarnings("unused")
private void handleException(Throwable exception) {
System.out.println("--------- UNCAUGHT EXCEPTION ---------");
exception.printStackTrace(System.out);
}
public static class VCellSelection {
public String theCacheKey;
public VCellHelper.ModelType modelType;
public String userid;
public String modelName;
public String appName;
public String simname;
public String[] varName;
public int[] timePointIndexes;
public Exception exception;
public VCellSelection(String theCacheKey, VCellHelper.ModelType modelType,String userid,String modelName, String appName, String simname,String[] varName,int[] timePointIndexes) {
super();
this.theCacheKey = theCacheKey;
this.modelType = modelType;
this.userid=userid;
this.modelName = modelName;
this.appName = appName;
this.simname = simname;
this.varName = varName;
this.timePointIndexes = timePointIndexes;
}
public VCellSelection(Exception exception) {
this.exception = exception;
}
}
@Plugin(type = PreprocessorPlugin.class)
public static class MyPreProcessor extends AbstractPreprocessorPlugin {
public static final String CANCELLED = "cancelled";
@Parameter
private UIService uiService;
@Parameter(required = true)
private VCellHelper vcellHelper;
private JComboBox<String> jcbModelType = new StyledComboBox<String>(new String[] {ModelType.bm.name(),ModelType.mm.name(),ModelType.quick.name()});
private JComboBox<String> jcbUserid = new StyledComboBox<String>();
private JComboBox<String> jcbModelNames = new StyledComboBox<String>();
private JComboBox<String> jcbAppNames = new StyledComboBox<String>();
private JComboBox<String> jcbSimNames = new StyledComboBox<String>();
private Comparator<String> comp = new Comparator<String>() {
@Override
public int compare(String o1, String o2) {
return o1.toLowerCase().compareTo(o2.toLowerCase());
}
};
private TreeSet<String> useridSet = new TreeSet<String>(comp);
private Hashtable<String,TreeSet<String>> mapUseridToModelNameTime = new Hashtable<String, TreeSet<String>>();
private Hashtable<String,String> mapModelNameTimeToActualModelname = new Hashtable<String, String>();
private Hashtable<String,TreeSet<String>> mapModelToApps = new Hashtable<String, TreeSet<String>>();
private Hashtable<String,TreeSet<String>> mapAppsToSims = new Hashtable<String, TreeSet<String>>();
public MyPreProcessor() {
// jcbModelType.addActionListener(new ActionListener() {
// @Override
// public void actionPerformed(ActionEvent e) {
// try {
// searchVCell();
// } catch (Exception e1) {
//// // TODO Auto-generated catch block
//// e1.printStackTrace();
// }
// }});
// jcbModelType.setSelectedIndex(0);
}
private String createMapAppToSimsKeyName(String modelName,String appName) {
//return jcbModelNames.getSelectedItem()+" "+jcbAppNames.getSelectedItem();
return modelName+" "+(appName==null?modelName:appName);
}
private void searchVCell() throws Exception{
final UIService service = getContext().getService(UIService.class);
Object obj = service.getDefaultUI().getApplicationFrame();
if(obj instanceof UIComponent && ((UIComponent)obj).getComponent() instanceof Frame) {
mainApplicationFrame = (Frame)((UIComponent)obj).getComponent();
}else if(obj instanceof Frame) {
mainApplicationFrame = (Frame)obj;
}
//System.out.println(service.getDefaultUI().getApplicationFrame().getClass().getName()+" "+(service.getDefaultUI().getApplicationFrame() instanceof Frame));
displayProgressBar(true, "Searching Database...", "VCell Model Loader", 25,uiService);
VCellHelper.VCellModelSearch vcms = new VCellHelper.VCellModelSearch(ModelType.valueOf(jcbModelType.getSelectedItem().toString()),null,null,null,null,null,null);
displayProgressBar(true, "Creating GUI...", "VCell Model Loader", 100,uiService);
try {
final DateFormat dateTimeInstance = DateFormat.getDateTimeInstance();
ArrayList<VCellModelSearchResults> vcmsr = vcellHelper.getSearchedModelSimCacheKey(false,vcms,null);
useridSet = new TreeSet<String>(comp);
mapUseridToModelNameTime = new Hashtable<String, TreeSet<String>>();
mapModelNameTimeToActualModelname = new Hashtable<String, String>();
mapModelToApps = new Hashtable<String, TreeSet<String>>();
mapAppsToSims = new Hashtable<String, TreeSet<String>>();
final Iterator<VCellModelSearchResults> iterator = vcmsr.iterator();
while(iterator.hasNext()) {
final VCellModelSearchResults next = iterator.next();
String userid = next.getUserId();
useridSet.add(userid);
final String modelName = next.getModelName();
final String modelNameTime = modelName+" ("+next.getModelType().name()+")"+" - "+(next.getDate()==null?"unsaved":dateTimeInstance.format(new Date(next.getDate())));
TreeSet<String> modelsForUserid = mapUseridToModelNameTime.get(userid);
if(modelsForUserid == null) {
modelsForUserid = new TreeSet<String>();
mapUseridToModelNameTime.put(userid, modelsForUserid);
}
modelsForUserid.add(modelNameTime);
mapModelNameTimeToActualModelname.put(modelNameTime, modelName);
//System.out.println(modelName+" "+next.getApplicationName()+" "+next.getSimulationName());
TreeSet<String> appsForModel = mapModelToApps.get(modelNameTime);
if(appsForModel == null) {
appsForModel = new TreeSet<String>();
mapModelToApps.put(modelNameTime, appsForModel);
}
appsForModel.add((next.getModelType()==ModelType.mm?modelNameTime:next.getApplicationName()));
String modelNameTimeApp = createMapAppToSimsKeyName(modelNameTime,(next.getModelType()==ModelType.mm?null:next.getApplicationName()));//modelNameTime+(next.getModelType()==ModelType.mm?"":" "+next.getApplicationName());
TreeSet<String> simsForApp = mapAppsToSims.get(modelNameTimeApp);
if(simsForApp == null) {
simsForApp = new TreeSet<String>();
mapAppsToSims.put(modelNameTimeApp, simsForApp);
}
simsForApp.add(next.getSimulationName());
}
// DefaultComboBoxModel a= null;
// ((DefaultComboBoxModel)jcbUserid.getModel()).
} catch (Exception e) {
throw e;
// //e.printStackTrace();
// displayProgressBar(false, "Creating GUI...", "VCell Model Loader", 100,uiService);
// vcellModelsInput.setValue(module, new VCellSelection(e));//return empty VCellSelection
// module.resolveInput(vcellModelsInput.getName());
// return;
}finally {
displayProgressBar(false, "Creating GUI...", "VCell Model Loader", 100,uiService);
}
}
@Override
public void process(Module module) {
final ModuleItem<VCellSelection> vcellModelsInput = getvcellModelsInput(module);
if (vcellModelsInput == null) {
return;
}
// try {
// searchVCell();
// } catch (Exception e) {
// vcellModelsInput.setValue(module, new VCellSelection(e));//return empty VCellSelection
// module.resolveInput(vcellModelsInput.getName());
// return;
// }
// displayProgressBar(true, "Searching Database...", "VCell Model Loader", 25,uiService);
// VCellHelper.VCellModelSearch vcms = new VCellHelper.VCellModelSearch(ModelType.valueOf(jcbModelType.getSelectedItem().toString()),null,null,null,null,null,null);
// displayProgressBar(true, "Creating GUI...", "VCell Model Loader", 100,uiService);
// try {
// final DateFormat dateTimeInstance = DateFormat.getDateTimeInstance();
// ArrayList<VCellModelSearchResults> vcmsr = vcellHelper.getSearchedModelSimCacheKey(false,vcms,null);
// final Iterator<VCellModelSearchResults> iterator = vcmsr.iterator();
// while(iterator.hasNext()) {
// final VCellModelSearchResults next = iterator.next();
// String userid = next.getUserId();
// useridSet.add(userid);
// final String modelName = next.getModelName();
// final String modelNameTime = modelName+" ("+next.getModelType().name()+")"+" - "+(next.getDate()==null?"unsaved":dateTimeInstance.format(new Date(next.getDate())));
// TreeSet<String> modelsForUserid = mapUseridToModelNameTime.get(userid);
// if(modelsForUserid == null) {
// modelsForUserid = new TreeSet<String>();
// mapUseridToModelNameTime.put(userid, modelsForUserid);
// }
// modelsForUserid.add(modelNameTime);
// mapModelNameTimeToActualModelname.put(modelNameTime, modelName);
// //System.out.println(modelName+" "+next.getApplicationName()+" "+next.getSimulationName());
// TreeSet<String> appsForModel = mapModelToApps.get(modelNameTime);
// if(appsForModel == null) {
// appsForModel = new TreeSet<String>();
// mapModelToApps.put(modelNameTime, appsForModel);
// }
// appsForModel.add(next.getApplicationName());
// String modelNameTimeApp = modelNameTime+" "+next.getApplicationName();
// TreeSet<String> simsForApp = mapAppsToSims.get(modelNameTimeApp);
// if(simsForApp == null) {
// simsForApp = new TreeSet<String>();
// mapAppsToSims.put(modelNameTimeApp, simsForApp);
// }
// simsForApp.add(next.getSimulationName());
// }
// } catch (Exception e) {
// //e.printStackTrace();
// displayProgressBar(false, "Creating GUI...", "VCell Model Loader", 100,uiService);
// vcellModelsInput.setValue(module, new VCellSelection(e));//return empty VCellSelection
// module.resolveInput(vcellModelsInput.getName());
// return;
// }finally {
// displayProgressBar(false, "Creating GUI...", "VCell Model Loader", 100,uiService);
// }
//ApplicationFrame applicationFrame = uiService.getDefaultUI().getApplicationFrame();
final Dimension dim = new Dimension(300,120);
@SuppressWarnings("serial")
final JPanel jp = new JPanel() {
@Override
public Dimension getPreferredSize() {
return dim;
}
};
jp.setLayout(new GridLayout(8,2));
final boolean[] bUseVCellSelectionHolder = new boolean[] {false};
//jcbModelType
// jp.add(new JLabel("Model Type"));
// jp.add(jcbModelType);
jp.add(new JLabel("VCell Userid"));
// JComboBox<String> jcbUserid = new StyledComboBox<String>(useridSet.toArray(new String[0]));
jcbModelType.addActionListener(new ActionListener() {
@Override
public void actionPerformed(ActionEvent e) {
new Thread(new Runnable() {
@Override
public void run() {
try {
searchVCell();
} catch (Exception e1) {
uiService.showDialog("Activate VCell Client ImageJ service\\nTools->'Start Fiji (ImageJ) service'\n\n\""+e1.getClass().getName()+"\n"+e1.getMessage());//
JFrame topFrame = (JFrame) SwingUtilities.getWindowAncestor(jp);
topFrame.dispose();
return;
}
SwingUtilities.invokeLater(new Runnable() {
@Override
public void run() {
if(vcellModelsInput.getDefaultValue() != null && vcellModelsInput.getDefaultValue().modelType.name().equals(jcbModelType.getSelectedItem().toString())) {
bUseVCellSelectionHolder[0] = true;
}
jcbUserid.removeAllItems();
jcbUserid.setModel(new DefaultComboBoxModel<String>(useridSet.toArray(new String[0])));
if(jcbUserid.getItemCount()==0) {
jcbUserid.addItem("Nothing Found");
uiService.showDialog("Check connectivity. Login with your userId or as a guest.");
}else if(bUseVCellSelectionHolder[0]) {
jcbUserid.setSelectedItem(vcellModelsInput.getDefaultValue().userid);
}else {
jcbUserid.setSelectedIndex(0);
}
bUseVCellSelectionHolder[0] = false;
}});
}}).start();
}});
jp.add(jcbUserid);
jp.add(new JLabel("Model Name"));
// JComboBox<String> jcbModelNames = new StyledComboBox<String>(mapUseridToModelNameTime.get(jcbUserid.getSelectedItem()).toArray(new String[0]));
jcbUserid.addActionListener(new ActionListener() {
@Override
public void actionPerformed(ActionEvent e) {
jcbModelNames.removeAllItems();
if(jcbUserid.getSelectedItem() != null && mapUseridToModelNameTime.get(jcbUserid.getSelectedItem()) != null) {
jcbModelNames.setModel(new DefaultComboBoxModel<String>(mapUseridToModelNameTime.get(jcbUserid.getSelectedItem()).toArray(new String[0])));
if(bUseVCellSelectionHolder[0]) {
for(int i=0;i<jcbModelNames.getModel().getSize();i++) {
//Do this because the model names are annotated with their date in this combobox
if(jcbModelNames.getModel().getElementAt(i).toString().startsWith(vcellModelsInput.getDefaultValue().modelName)) {
jcbModelNames.setSelectedIndex(i);
break;
}
}
}else {
jcbModelNames.setSelectedIndex(0);
}
}
}});
jp.add(jcbModelNames);
jp.add(new JLabel("App Name"));
// JComboBox<String> jcbAppNames = new StyledComboBox<String>(mapModelToApps.get(jcbModelNames.getSelectedItem()).toArray(new String[0]));
jcbModelNames.addActionListener(new ActionListener() {
@Override
public void actionPerformed(ActionEvent e) {
jcbAppNames.removeAllItems();
if(jcbModelNames.getSelectedItem() != null && mapModelToApps.get(jcbModelNames.getSelectedItem()) != null) {
jcbAppNames.setModel(new DefaultComboBoxModel<String>(mapModelToApps.get(jcbModelNames.getSelectedItem()).toArray(new String[0])));
if(bUseVCellSelectionHolder[0]) {
jcbAppNames.setSelectedItem(vcellModelsInput.getDefaultValue().appName);
}else {
jcbAppNames.setSelectedIndex(0);
}
}
}});
jp.add(jcbAppNames);
//final JComboBox<String> jcbVars = new StyledComboBox<String>();
//jcbVars.setEnabled(false);
// JComboBox<String> jcbTimes = new StyledComboBox<String>();
//jcbTimes.setEnabled(false);
jp.add(new JLabel("Sim Name"));
jcbAppNames.addActionListener(new ActionListener() {
@Override
public void actionPerformed(ActionEvent e) {
// jcbVars.removeAllItems();
// jcbTimes.removeAllItems();
jcbSimNames.removeAllItems();
if(jcbAppNames.getSelectedItem() != null && mapAppsToSims.get(jcbModelNames.getSelectedItem()+" "+jcbAppNames.getSelectedItem()) != null) {
jcbSimNames.setModel(new DefaultComboBoxModel<String>(mapAppsToSims.get(jcbModelNames.getSelectedItem()+" "+jcbAppNames.getSelectedItem()).toArray(new String[0])));
if(bUseVCellSelectionHolder[0]) {
jcbSimNames.setSelectedItem(vcellModelsInput.getDefaultValue().simname);
}else {
jcbSimNames.setSelectedIndex(0);
}
}
}});
jp.add(jcbSimNames);
// if(vcellModelsInput.getDefaultValue() != null) {//If user provided an inital value for VCellSelection var in VCellPlugin
// final VCellSelection defaultValue = vcellModelsInput.getDefaultValue();
// jcbUserid.setSelectedItem(defaultValue.userid);
// System.out.println(jcbUserid.getSelectedItem());
// for(int i=0;i<jcbModelNames.getModel().getSize();i++) {
// //Do this because the model names are annotated with their date in this combobox
// if(jcbModelNames.getModel().getElementAt(i).toString().startsWith(defaultValue.modelName)) {
// jcbModelNames.setSelectedIndex(i);
// break;
// }
// }
// System.out.println(jcbModelNames.getSelectedItem());
// jcbAppNames.setSelectedItem(defaultValue.appName);
// System.out.println(jcbAppNames.getSelectedItem());
// jcbSimNames.setSelectedItem(defaultValue.simname);
// System.out.println(jcbSimNames.getSelectedItem());
// }
// jp.add(new JLabel("Variables"));
// jp.add(jcbVars);
// jp.add(new JLabel("Times"));
// jp.add(jcbTimes);
final String[] cacheKeyHolder = new String[1];
final IJVarInfos[] ijVarInfosHolder = new IJVarInfos[1];
// final int[] ijVarInfoSelectionIndexesVars;
// final int[] ijVarInfoSelectionIndexesTimes;
// jp.add(new JLabel("Show Vars and Times"));
// final JButton loadVarsAndTimesBtn = new JButton("Show...");
// loadVarsAndTimesBtn.addActionListener(new ActionListener() {
// @Override
// public void actionPerformed(ActionEvent e) {
// new Thread(new Runnable() {
// @Override
// public void run() {
// populateVarAndTimes(vcellModelsInput.getDefaultValue(), jcbVars, jcbTimes, cacheKeyHolder, ijVarInfosHolder);
// }
// }).start();
// }
// });
// jp.add(loadVarsAndTimesBtn);
JTable jtVars = new JTable();
JSlider minTimeJSlider1 = new javax.swing.JSlider();
JSlider maxTimeJSlider1 = new javax.swing.JSlider();
jp.add(new JLabel("Vars and Times"));
JButton selectMultipleVarsAndTimesBtn = new JButton("Select...");
selectMultipleVarsAndTimesBtn.addActionListener(new ActionListener() {
@Override
public void actionPerformed(ActionEvent e) {
new Thread(new Runnable() {
@Override
public void run() {
ijVarInfosHolder[0] = null;
populateVarAndTimes(cacheKeyHolder, ijVarInfosHolder/*
* vcellModelsInput.getDefaultValue(), jcbVars, jcbTimes,
* cacheKeyHolder, ijVarInfosHolder
*/);
while(ijVarInfosHolder[0] == null) {
try {
Thread.sleep(0);
} catch (InterruptedException e) {
// TODO Auto-generated catch block
e.printStackTrace();
}
}
if(ijVarInfosHolder[0].getSimname() == null) {//nothing found or error
return;
}
SwingUtilities.invokeLater(new Runnable() {
@Override
public void run() {
JPanel selectJPanel = new JPanel();
//GridLayout selectGridLayout = new GridLayout(5,1);
BoxLayout boxLayout = new BoxLayout(selectJPanel,BoxLayout.Y_AXIS);
selectJPanel.setLayout(boxLayout);
//Variables
// for(int i=0;i<ijVarInfosHolder[0].getIjVarInfo().size();i++) {
// jcbVars.insertItemAt(""+ijVarInfosHolder[0].getIjVarInfo().get(i).getName()+":"+ijVarInfosHolder[0].getIjVarInfo().get(i).getDomain()+" ("+ijVarInfosHolder[0].getIjVarInfo().get(i).getVariableType()+")", i);
// }
Object[][] dataVars = new Object[ijVarInfosHolder[0].getIjVarInfo().size()][3];
for(int i=0;i<ijVarInfosHolder[0].getIjVarInfo().size();i++) {
dataVars[i][0] = ijVarInfosHolder[0].getIjVarInfo().get(i).getName();
dataVars[i][1] = ijVarInfosHolder[0].getIjVarInfo().get(i).getDomain();
dataVars[i][2] = ijVarInfosHolder[0].getIjVarInfo().get(i).getVariableType();
}
// JTable jtVars = new JTable(dataVars,new String[] {"Variables"});
jtVars.setModel(new DefaultTableModel(dataVars,new String[] {"Variable","Domain","Type"}));
//jtVars.setBounds(0, 0, 300,300);
//jtVars.setAutoResizeMode(JTable.AUTO_RESIZE_OFF);
//jtVars.setPreferredSize(new Dimension(200,200));
JScrollPane jspVars = new JScrollPane(jtVars);
//Times
// for(int i=0;i<ijVarInfosHolder[0].getTimes().length;i++) {
// jcbTimes.insertItemAt(""+ijVarInfosHolder[0].getTimes()[i], i);
// }
final String MINTIMESTR = "Min Time ";
final String MAXTIMESTR = "Max Time ";
final JLabel minTimeJLabel = new JLabel(MINTIMESTR+ijVarInfosHolder[0].getTimes()[0]);
final JLabel maxTimeJLabel = new JLabel(MAXTIMESTR+ijVarInfosHolder[0].getTimes()[ijVarInfosHolder[0].getTimes().length-1]);
// JSlider minTimeJSlider1 = new javax.swing.JSlider();
// JSlider maxTimeJSlider1 = new javax.swing.JSlider();
ChangeListener changeListener = new ChangeListener() {
@Override
public void stateChanged(ChangeEvent ce) {
if(ce.getSource()==minTimeJSlider1 && minTimeJSlider1.getValue() > maxTimeJSlider1.getValue()){
maxTimeJSlider1.setValue(minTimeJSlider1.getValue());
return;
}else if(ce.getSource()==maxTimeJSlider1 && maxTimeJSlider1.getValue() < minTimeJSlider1.getValue()){
minTimeJSlider1.setValue(maxTimeJSlider1.getValue());
return;
}
minTimeJLabel.setText(MINTIMESTR+ijVarInfosHolder[0].getTimes()[minTimeJSlider1.getValue()]);
maxTimeJLabel.setText(MAXTIMESTR+ijVarInfosHolder[0].getTimes()[maxTimeJSlider1.getValue()]);
}};
minTimeJSlider1.setName("minTime");
minTimeJSlider1.setPaintTicks(true);
minTimeJSlider1.setMajorTickSpacing(10);
minTimeJSlider1.setSnapToTicks(true);
minTimeJSlider1.setMinorTickSpacing(1);
minTimeJSlider1.setMaximum(ijVarInfosHolder[0].getTimes().length - 1);
minTimeJSlider1.setValue(0);
minTimeJSlider1.addChangeListener(changeListener);
maxTimeJSlider1.setName("maxTime");
maxTimeJSlider1.setPaintTicks(true);
maxTimeJSlider1.setMajorTickSpacing(10);
maxTimeJSlider1.setSnapToTicks(true);
maxTimeJSlider1.setMinorTickSpacing(1);
maxTimeJSlider1.setMaximum(ijVarInfosHolder[0].getTimes().length - 1);
maxTimeJSlider1.setValue(ijVarInfosHolder[0].getTimes().length - 1);
maxTimeJSlider1.addChangeListener(changeListener);
// Object[][] dataVars = new Object[jcbVars.getModel().getSize()][1];
// for(int i=0;i<jcbVars.getModel().getSize();i++) {
// dataVars[i][0] = jcbVars.getModel().getElementAt(i);
// }
// JTable jtVars = new JTable(dataVars,new String[] {"Variables"});
// jtVars.setBounds(0, 0, 300,300);
// JScrollPane jspVars = new JScrollPane(jtVars);
//jtVars.setPreferredScrollableViewportSize(jtVars.getPreferredSize());
selectJPanel.add(jspVars);
selectJPanel.add(minTimeJLabel);
selectJPanel.add(minTimeJSlider1);
selectJPanel.add(maxTimeJLabel);
selectJPanel.add(maxTimeJSlider1);
//jp.setSize(325, 450);
int response = JOptionPane.showConfirmDialog(jp, selectJPanel,"Select Vars and Times",JOptionPane.OK_CANCEL_OPTION);
if(response != JOptionPane.OK_OPTION) {
return;
}
ArrayList<Container> compList = new ArrayList<Container>();
compList.add(SwingUtilities.getAncestorOfClass(Window.class, selectMultipleVarsAndTimesBtn));
while(compList.size() > 0) {
Container container = compList.remove(0);
for(int i=0;i<container.getComponentCount();i++) {
Component comp = container.getComponent(i);
if(comp instanceof JButton && ((JButton)comp).getText().equals("OK")) {
((JButton)comp).doClick();
return;
}else if(comp instanceof Container) {
compList.add((Container)comp);
}
}
}
}
});
}}).start();
}});
jp.add(selectMultipleVarsAndTimesBtn);
jcbModelType.setSelectedIndex(0);
// if(vcellModelsInput.getDefaultValue() != null) {//If user provided an inital value for VCellSelection var in VCellPlugin
// final VCellSelection defaultValue = vcellModelsInput.getDefaultValue();
// jcbUserid.setSelectedItem(defaultValue.userid);
// System.out.println(jcbUserid.getSelectedItem());
// for(int i=0;i<jcbModelNames.getModel().getSize();i++) {
// //Do this because the model names are annotated with their date in this combobox
// if(jcbModelNames.getModel().getElementAt(i).toString().startsWith(defaultValue.modelName)) {
// jcbModelNames.setSelectedIndex(i);
// break;
// }
// }
// System.out.println(jcbModelNames.getSelectedItem());
// jcbAppNames.setSelectedItem(defaultValue.appName);
// System.out.println(jcbAppNames.getSelectedItem());
// jcbSimNames.setSelectedItem(defaultValue.simname);
// System.out.println(jcbSimNames.getSelectedItem());
// }
displayProgressBar(false, "Creating GUI...", "VCell Model Loader", 100,uiService);
int response = JOptionPane.showConfirmDialog(VCellPlugin.mainApplicationFrame
/* (Component)IJ.getInstance() *//* uiService.getDefaultUI().getApplicationFrame() */, jp,"Select User Model App Sim",JOptionPane.OK_CANCEL_OPTION);
if(response != JOptionPane.OK_OPTION) {
vcellModelsInput.setValue(module, new VCellSelection(new Exception(CANCELLED)));//return VCellSelection with 'cancel' exception
module.resolveInput(vcellModelsInput.getName());
return;
}
ModelType modelType = ModelType.valueOf((String)jcbModelType.getSelectedItem());
String userid = jcbUserid.getSelectedItem().toString();
String modelName = (jcbModelNames.getSelectedItem()==null?null:mapModelNameTimeToActualModelname.get(jcbModelNames.getSelectedItem()).toString());
String appName = (jcbModelNames.getSelectedItem()==null?null:jcbAppNames.getSelectedItem().toString());
String simName = (jcbModelNames.getSelectedItem()==null?null:jcbSimNames.getSelectedItem().toString());
String[] selectedVarNames = new String[jtVars.getSelectedRows().length];
for(int i=0;i<jtVars.getSelectedRows().length;i++) {
selectedVarNames[i] = ijVarInfosHolder[0].getIjVarInfo().get(jtVars.getSelectedRows()[i]).getName();
}
int[] selectedTimeIndexes = new int[maxTimeJSlider1.getValue()-minTimeJSlider1.getValue()+1];
for(int i=minTimeJSlider1.getValue();i<=maxTimeJSlider1.getValue();i++) {
selectedTimeIndexes[i-minTimeJSlider1.getValue()] = i;
}
VCellSelection result = new VCellSelection(cacheKeyHolder[0], modelType, userid,modelName, appName, simName,selectedVarNames,selectedTimeIndexes);
vcellModelsInput.setValue(module, result);
module.resolveInput(vcellModelsInput.getName());
// String userid = jcbUserid.getSelectedItem().toString();
// String modelName = (jcbModelNames.getSelectedItem()==null?null:mapModelNameTimeToActualModelname.get(jcbModelNames.getSelectedItem()).toString());
// String appName = (jcbModelNames.getSelectedItem()==null?null:jcbAppNames.getSelectedItem().toString());
// String simName = (jcbModelNames.getSelectedItem()==null?null:jcbSimNames.getSelectedItem().toString());
// vcms = new VCellHelper.VCellModelSearch(VCellHelper.ModelType.bm,userid,modelName,appName,simName,null,null);
// String theCacheKey = null;
// try {
// ArrayList<VCellModelSearchResults> vcmsr = vcellHelper.getSearchedModelSimCacheKey(false,vcms,null);
// if(vcmsr.size() == 0) {
// throw new Exception("No Results for search found");
// }
// theCacheKey = vcmsr.get(0).getCacheKey();
// System.out.println("theCacheKey="+theCacheKey);
//
// jcbTimes.setEnabled(true);
// IJVarInfos ijVarInfos = vcellHelper.getVarInfos(theCacheKey);
// for(int i=0;i<ijVarInfos.getTimes().length;i++) {
// jcbTimes.insertItemAt(""+ijVarInfos.getTimes()[i], i);
// }
//
// //displayProgressBar(false, null, null);
// } catch (Exception e) {
// //e.printStackTrace();
// uiService.showDialog("VCellHelper.ModelType.bm,\"tutorial\",\""+modelName+"\",\""+appName+"\",\""+simName+"\",null,null\n"+e.getMessage(), "Search failed", MessageType.ERROR_MESSAGE);
// //displayProgressBar(false, null, null);
// }
//
// VCellSelection result = new VCellSelection(theCacheKey, userid,modelName, appName, simName);
// vcellModelsInput.setValue(module, result);
// module.resolveInput(vcellModelsInput.getName());
// System.out.println(module);
// final Map<String, Object> inputs = module.getInputs();
// for(String key:inputs.keySet()) {
// System.out.println(" "+key+" "+inputs.get(key));
// }
}
private void populateVarAndTimes(final String[] cacheKeyHolder,IJVarInfos[] ijVarInfosHolder
/*
* final VCellSelection vcellSelection, final JComboBox<String> jcbVars,
* final JComboBox<String> jcbTimes, final String[] cacheKeyHolder, final
* IJVarInfos[] ijVarInfosHolder
*/){
displayProgressBar(true, "Getting Vars and Times...", "VCell Model Loader", 25,uiService);
String userid = jcbUserid.getSelectedItem().toString();
String modelName = (jcbModelNames.getSelectedItem()==null?null:mapModelNameTimeToActualModelname.get(jcbModelNames.getSelectedItem()).toString());
String appName = (jcbModelNames.getSelectedItem()==null?null:jcbAppNames.getSelectedItem().toString());
String simName = (jcbModelNames.getSelectedItem()==null?null:jcbSimNames.getSelectedItem().toString());
VCellHelper.VCellModelSearch vcms = new VCellHelper.VCellModelSearch(ModelType.valueOf(jcbModelType.getSelectedItem().toString()),userid,modelName,appName,simName,null,null);
try {
// jcbVars.removeAllItems();
// jcbTimes.removeAllItems();
ArrayList<VCellModelSearchResults> vcmsr = vcellHelper.getSearchedModelSimCacheKey(false,vcms,null);
if(vcmsr.size() == 0) {
throw new Exception("No Results for search found");
}
cacheKeyHolder[0] = vcmsr.get(0).getCacheKey();
System.out.println("theCacheKey="+cacheKeyHolder[0]);
ijVarInfosHolder[0] = vcellHelper.getVarInfos(cacheKeyHolder[0]);
ijVarInfosHolder[0].getIjVarInfo().sort(new Comparator<IJVarInfo>() {
@Override
public int compare(IJVarInfo o1, IJVarInfo o2) {
return o1.getName().compareToIgnoreCase(o2.getName());
}});
// SwingUtilities.invokeAndWait(new Runnable() {
// @Override
// public void run() {
// try {
// displayProgressBar(true, "Getting Var Times GUI...", "VCell Model Loader", 100,uiService);
// jcbVars.setEnabled(true);
// ijVarInfosHolder[0] = vcellHelper.getVarInfos(cacheKeyHolder[0]);
// for(int i=0;i<ijVarInfosHolder[0].getIjVarInfo().size();i++) {
// jcbVars.insertItemAt(""+ijVarInfosHolder[0].getIjVarInfo().get(i).getName()+":"+ijVarInfosHolder[0].getIjVarInfo().get(i).getDomain()+" ("+ijVarInfosHolder[0].getIjVarInfo().get(i).getVariableType()+")", i);
// }
//
// jcbTimes.setEnabled(true);
// for(int i=0;i<ijVarInfosHolder[0].getTimes().length;i++) {
// jcbTimes.insertItemAt(""+ijVarInfosHolder[0].getTimes()[i], i);
// }
//
// if(vcellSelection != null) {//If user provided an inital value for VCellSelection var in VCellPlugin
// final VCellSelection defaultValue = vcellSelection;
// jcbVars.setSelectedIndex(0);
// for(int i=0;i<jcbVars.getModel().getSize();i++) {
// if(jcbVars.getModel().getElementAt(i).startsWith(defaultValue.varName+":")) {
// jcbVars.setSelectedIndex(i);
// break;
// }
// }
//
// jcbTimes.setSelectedIndex(0);
// if(defaultValue.timePointIndex < jcbTimes.getModel().getSize()) {
// jcbTimes.setSelectedIndex(defaultValue.timePointIndex);
// }
// }
// } catch (Exception e) {
// //e.printStackTrace();
// ijVarInfosHolder[0] = new IJVarInfos();// set empty
// if(e.getMessage().contains(".log not exist")) {
// uiService.showDialog("VCellHelper.ModelType.bm,\""+userid+"\",\""+modelName+"\",\""+appName+"\",\""+simName+"\",null,null\n"+"Data Not Found.", "GUI setupfailed", MessageType.ERROR_MESSAGE);
// }else {
// uiService.showDialog("VCellHelper.ModelType.bm,\""+userid+"\",\""+modelName+"\",\""+appName+"\",\""+simName+"\",null,null\n"+e.getMessage(), "GUI setupfailed", MessageType.ERROR_MESSAGE);
// }
//
// }finally {
// displayProgressBar(false, "Getting Var Times GUI...", "VCell Model Loader", 25,uiService);
// }
//
// }});
} catch (Exception e2) {
displayProgressBar(false, "Error", "VCell Model Loader", 100,uiService);
//e.printStackTrace();
if(e2.getMessage().contains(".log not exist")) {
uiService.showDialog("VCellHelper.ModelType.bm,\""+userid+"\",\""+modelName+"\",\""+appName+"\",\""+simName+"\",null,null\n"+"Data Not Found.", "populateVarAndTimes failed", MessageType.ERROR_MESSAGE);
}else {
uiService.showDialog("VCellHelper.ModelType.bm,\""+userid+"\",\""+modelName+"\",\""+appName+"\",\""+simName+"\",null,null\n"+e2.getMessage(), "populateVarAndTimes failed", MessageType.ERROR_MESSAGE);
}
}finally {
displayProgressBar(false, "Done", "VCell Model Loader", 100,uiService);
}
}
private ModuleItem<VCellSelection> getvcellModelsInput(final Module module) {
ModuleItem<VCellSelection> result = null;
for (final ModuleItem<?> input : module.getInfo().inputs()) {
if (module.isInputResolved(input.getName())) continue;
final Class<?> type = input.getType();
if (!VCellSelection.class.isAssignableFrom(type)) {
// not a VCellSelection parameter; abort
return null;
}
if (result != null) {
// second VCellSelection parameter; abort
return null;
}
@SuppressWarnings("unchecked")
final ModuleItem<VCellSelection> vcellSelect = (ModuleItem<VCellSelection>) input;
result = vcellSelect;
}
return result;
}
// private JPanel getLabeledJComboBox(String labelName,String[] items) {
// JPanel jp = new JPanel(new FlowLayout());
// jp.add(new JLabel(labelName));
// JComboBox<String> jcbModelNames = new JComboBox<String>(items);
// jp.add(jcbModelNames);
// return jp;
// }
}
@Parameter
private UIService uiService;
@Parameter
private DisplayService displayService;
@Parameter
EventService eventService;
@Parameter
ZoomService zoomService;
@Parameter
private VCellHelper vcellHelper;
@Parameter
private VCellSelection vcellSelection = new VCellSelection("-1",ModelType.bm, "tutorial","Tutorial_MultiApp", "3D pde", "Simulation4",new String[] {"C_cyt"},new int[] {50});
//private VCellSelection vcellSelection;
/**
* This main function serves for development purposes.
* It allows you to run the plugin immediately out of
* your integrated development environment (IDE).
*
* @param args whatever, it's ignored
* @throws Exception
*/
public static void main(final String... args) throws Exception {
// create the ImageJ application context with all available services
final ImageJ ij = new ImageJ();
ij.ui().showUI();
}
private static JDialog progressDialog = null;
private static final Dimension dim = new Dimension(200,30);
@SuppressWarnings("serial")
private static final JProgressBar jProgressBar = new JProgressBar(0,100) {
@Override
public Dimension getPreferredSize() {
return dim;
}
@Override
public Dimension getSize(Dimension rv) {
return dim;
}
};
private static void displayProgressBar(boolean bShow,String message,String title,int progress,UIService uiService) {
if(progressDialog == null) {
//Frame applicationFrame = VCellPlugin.mainApplicationFrame;//IJ.getInstance();//(Frame)uiService.getDefaultUI().getApplicationFrame();
progressDialog = new JDialog(VCellPlugin.mainApplicationFrame,"Checking for VCell Client",false);
progressDialog.addWindowListener(new WindowAdapter() {
@Override
public void windowClosing(WindowEvent e) {
super.windowClosing(e);
progressDialog.dispose();
progressDialog = null;
}});
progressDialog.getContentPane().add(jProgressBar);
jProgressBar.setStringPainted(true);
jProgressBar.setString("setting up...");
progressDialog.pack();
}
if(SwingUtilities.isEventDispatchThread()) {
if(progressDialog ==null) {
return;
}
if(!bShow) {
progressDialog.dispose();
progressDialog = null;
return;
}
progressDialog.setVisible(true);
jProgressBar.setValue(progress);
progressDialog.setTitle(title);
jProgressBar.setString(message);
jProgressBar.invalidate();
progressDialog.revalidate();
}else {
SwingUtilities.invokeLater(new Runnable() {
@Override
public void run() {
if(progressDialog ==null) {
return;
}
if(!bShow) {
progressDialog.dispose();
progressDialog = null;
return;
}
progressDialog.setVisible(true);
jProgressBar.setValue(progress);
progressDialog.setTitle(title);
jProgressBar.setString(message);
jProgressBar.invalidate();
progressDialog.revalidate();
}
});
}
}
// private Hashtable<String,Thread> threadHash = new Hashtable<String,Thread>();
// private void startJProgressThread0(String lastName,String newName) {
// if(lastName != null && threadHash.get(lastName) != null) {
// threadHash.get(lastName).interrupt();
// while(threadHash.get(lastName) != null) {
// try {
// Thread.sleep(50);
// } catch (InterruptedException e) {
// e.printStackTrace();