testimg = ArrayImgs.doubles( data, bsd.xsize,bsd.ysize);
- uiService.show(testimg);
-
- displayProgressBar(false, null, null);
- } catch (Exception e) {
- // TODO Auto-generated catch block
-// e.printStackTrace();
- uiService.showDialog("theCacheKey,var,VCellHelper.VARTYPE_POSTPROC.NotPostProcess,time,0\n"+e.getMessage(), "getTimePoint(...) failed", MessageType.ERROR_MESSAGE);
- displayProgressBar(false, null, null);
-
- }
- startJProgressThread0("getTimePointData",null);
- }
-}
diff --git a/vcell-imagej-helper/src/main/java/org/vcell/imagej/plugin/ModelSearch.java b/vcell-imagej-helper/src/main/java/org/vcell/imagej/plugin/ModelSearch.java
deleted file mode 100644
index 20447dc502..0000000000
--- a/vcell-imagej-helper/src/main/java/org/vcell/imagej/plugin/ModelSearch.java
+++ /dev/null
@@ -1,627 +0,0 @@
-/*
- * 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.Dimension;
-import java.awt.FlowLayout;
-import java.awt.GridLayout;
-import java.awt.Rectangle;
-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.TreeSet;
-
-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.SwingUtilities;
-import javax.swing.plaf.basic.BasicComboBoxUI;
-import javax.swing.plaf.basic.BasicComboPopup;
-import javax.swing.plaf.basic.ComboPopup;
-
-import org.scijava.command.ContextCommand;
-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.Parameter;
-import org.scijava.plugin.Plugin;
-import org.scijava.ui.DialogPrompt.MessageType;
-import org.scijava.ui.UIService;
-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.IJVarInfos;
-import org.vcell.imagej.helper.VCellHelper.VCellModelSearchResults;
-
-import net.imagej.ImageJ;
-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;
-
-
-/**
- * This example illustrates how to create an ImageJ {@link ContextCommand} plugin that uses VCellHelper.
- *
- * You should replace the parameter fields with your own inputs and outputs,
- * and replace the {@link run} method implementation with your own logic.
- *
- *
- * 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.
- *
- *
- * 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.
- *
- *
- * When editing the original VCellHelper in another running Eclipse,
- * to make the changes show up in this project choose thisEclipse->Project->Clean...->clean.
- *
- */
-@Plugin(type = ContextCommand.class, menuPath = "Plugins>VCellPluginSearch")
-public class ModelSearch extends ContextCommand {
-
-
-
- public static class StyledComboBoxUI extends BasicComboBoxUI {
- protected ComboPopup createPopup() {
- 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;
- }
- }
-
- public static class StyledComboBox extends JComboBox {
- public StyledComboBox() {
- setUI(new StyledComboBoxUI());
- }
- public StyledComboBox(E[] items) {
- setUI(new StyledComboBoxUI());
- setModel(new DefaultComboBoxModel(items));
- }
- }
-
- public static class VCellSelection {
- public String theCacheKey;
- public String userid;
- public String modelName;
- public String appName;
- public String simname;
- public String varName;
- public int timePointIndex;
- public Exception exception;
- public VCellSelection(String theCacheKey, String userid,String modelName, String appName, String simname,String varName,int timePointIndex) {
- super();
- this.theCacheKey = theCacheKey;
- this.userid=userid;
- this.modelName = modelName;
- this.appName = appName;
- this.simname = simname;
- this.varName = varName;
- this.timePointIndex = timePointIndex;
- }
- 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;
-
-
- @Override
- public void process(Module module) {
- final ModuleItem vcellModelsInput = getvcellModelsInput(module);
- if (vcellModelsInput == null) {
- return;
- }
- Comparator comp = new Comparator() {
- @Override
- public int compare(String o1, String o2) {
- return o1.toLowerCase().compareTo(o2.toLowerCase());
- }};
- TreeSet useridSet = new TreeSet(comp);
- Hashtable> mapUseridToModelNameTime = new Hashtable>();
- Hashtable mapModelNameTimeToActualModelname = new Hashtable();
- Hashtable> mapModelToApps = new Hashtable>();
- Hashtable> mapAppsToSims = new Hashtable>();
-// VCellHelper.VCellModelSearch vcms = new VCellHelper.VCellModelSearch(VCellHelper.ModelType.bm,"tutorial","Tutorial_MultiApp","3D pde","Simulation4",null,null);
- displayProgressBar(true, "Searching Database...", "VCell Model Loader", 25,uiService);
- VCellHelper.VCellModelSearch vcms = new VCellHelper.VCellModelSearch(VCellHelper.ModelType.bm,null,null,null,null,null,null);
- displayProgressBar(true, "Creating GUI...", "VCell Model Loader", 100,uiService);
- try {
- final DateFormat dateTimeInstance = DateFormat.getDateTimeInstance();
- ArrayList vcmsr = vcellHelper.getSearchedModelSimCacheKey(false,vcms,null);
- final Iterator 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.getDate()==null?"unsaved":dateTimeInstance.format(new Date(next.getDate())));
- TreeSet modelsForUserid = mapUseridToModelNameTime.get(userid);
- if(modelsForUserid == null) {
- modelsForUserid = new TreeSet();
- mapUseridToModelNameTime.put(userid, modelsForUserid);
- }
- modelsForUserid.add(modelNameTime);
- mapModelNameTimeToActualModelname.put(modelNameTime, modelName);
- //System.out.println(modelName+" "+next.getApplicationName()+" "+next.getSimulationName());
- TreeSet appsForModel = mapModelToApps.get(modelNameTime);
- if(appsForModel == null) {
- appsForModel = new TreeSet();
- mapModelToApps.put(modelNameTime, appsForModel);
- }
- appsForModel.add(next.getApplicationName());
- String modelNameTimeApp = modelNameTime+" "+next.getApplicationName();
- TreeSet simsForApp = mapAppsToSims.get(modelNameTimeApp);
- if(simsForApp == null) {
- simsForApp = new TreeSet();
- 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);
- }
-
- JFrame applicationFrame = (JFrame)uiService.getDefaultUI().getApplicationFrame();
- final Dimension dim = new Dimension(300,120);
- JPanel jp = new JPanel() {
- @Override
- public Dimension getPreferredSize() {
- return dim;
- }
- };
- jp.setLayout(new GridLayout(7,2));
-
- jp.add(new JLabel("VCell Userid"));
- JComboBox jcbUserid = new StyledComboBox(useridSet.toArray(new String[0]));
- jp.add(jcbUserid);
-
- jp.add(new JLabel("Model Name"));
- JComboBox jcbModelNames = new StyledComboBox(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(mapUseridToModelNameTime.get(jcbUserid.getSelectedItem()).toArray(new String[0])));
- jcbModelNames.setSelectedIndex(0);
- }
- }});
- jp.add(jcbModelNames);
-
-
- jp.add(new JLabel("App Name"));
- JComboBox jcbAppNames = new StyledComboBox(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(mapModelToApps.get(jcbModelNames.getSelectedItem()).toArray(new String[0])));
- jcbAppNames.setSelectedIndex(0);
- }
- }});
- jp.add(jcbAppNames);
-
- final JComboBox jcbVars = new StyledComboBox();
- jcbVars.setEnabled(false);
-
- final JComboBox jcbTimes = new StyledComboBox();
- jcbTimes.setEnabled(false);
-
- jp.add(new JLabel("Sim Name"));
- JComboBox jcbSimNames = new StyledComboBox(mapAppsToSims.get(jcbModelNames.getSelectedItem()+" "+jcbAppNames.getSelectedItem()).toArray(new String[0]));
- 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(mapAppsToSims.get(jcbModelNames.getSelectedItem()+" "+jcbAppNames.getSelectedItem()).toArray(new String[0])));
- jcbSimNames.setSelectedIndex(0);
- }
- }});
- jp.add(jcbSimNames);
-
- 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];
-
- jp.add(new JLabel("Load Vars and Times"));
- JButton loadVarsAndTimesBtn = new JButton("Load...");
- loadVarsAndTimesBtn.addActionListener(new ActionListener() {
- @Override
- public void actionPerformed(ActionEvent e) {
- new Thread(new Runnable() {
- @Override
- public void run() {
- 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(VCellHelper.ModelType.bm,userid,modelName,appName,simName,null,null);
- try {
- ArrayList 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]);
-
- SwingUtilities.invokeAndWait(new Runnable() {
- @Override
- public void run() {
- try {
- displayProgressBar(true, "Setting Var Times GUI...", "VCell Model Loader", 100,uiService);
- jcbVars.setEnabled(true);
- ijVarInfosHolder[0] = vcellHelper.getVarInfos(cacheKeyHolder[0]);
- for(int i=0;i 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 inputs = module.getInputs();
-// for(String key:inputs.keySet()) {
-// System.out.println(" "+key+" "+inputs.get(key));
-// }
- }
-
- private ModuleItem getvcellModelsInput(final Module module) {
- ModuleItem 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 vcellSelect = (ModuleItem) input;
- result = vcellSelect;
- }
- return result;
- }
-
- private JPanel getLabeledJComboBox(String labelName,String[] items) {
- JPanel jp = new JPanel(new FlowLayout());
- jp.add(new JLabel(labelName));
- JComboBox jcbModelNames = new JComboBox(items);
- jp.add(jcbModelNames);
- return jp;
- }
-
- }
-
- @Parameter
- private UIService uiService;
-
- @Parameter
- private VCellHelper vcellHelper;
-
- @Parameter
- private VCellSelection vcellSelection = new VCellSelection("-1", "colreeze","Monkeyflower_pigmentation_v2", "Pattern_formation", "WT","A",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);
- 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) {
- JFrame applicationFrame = (JFrame)uiService.getDefaultUI().getApplicationFrame();
- progressDialog = new JDialog(applicationFrame,"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 threadHash = new Hashtable();
-// 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();
-// break;
-// }
-// }
-// }
-// if(newName == null) {
-// return;
-// }
-// final Thread progressThread = new Thread(new Runnable(){
-// @Override
-// public void run() {
-// final int[] progress = new int[] {1};
-// while(progressDialog.isVisible()) {
-// if(Thread.currentThread().isInterrupted()) {
-// break;
-// }
-// SwingUtilities.invokeLater(new Runnable() {
-// @Override
-// public void run() {
-// jProgressBar.setValue(progress[0]);
-// }});
-// progress[0]++;
-// try {
-// Thread.sleep(500);
-// } catch (InterruptedException e) {
-// break;
-// }
-// }
-// threadHash.remove(Thread.currentThread().getName());
-// }});
-// threadHash.put(newName, progressThread);
-// progressThread.setName(newName);
-// progressThread.setDaemon(true);//So not block JVM exit
-// progressThread.start();
-// }
-
- @Override
- public void run() {
- try {
- if(vcellSelection != null && vcellSelection.exception != null) {
- if(!vcellSelection.exception.getMessage().equals(MyPreProcessor.CANCELLED)) {
- uiService.showDialog("Model search failed\n"+vcellSelection.exception.getClass().getName()+"\n"+vcellSelection.exception.getMessage(), MessageType.ERROR_MESSAGE);
- }
- return;
- }
- if(vcellSelection == null || vcellSelection.theCacheKey==null) {
- return;
- }
- String var = vcellSelection.varName;
- int[] time = new int[] {vcellSelection.timePointIndex};
- displayProgressBar(true, "loading Image...", "VCell Model Loader", 50,uiService);
- IJDataList tpd = vcellHelper.getTimePointData(vcellSelection.theCacheKey,var,VCellHelper.VARTYPE_POSTPROC.NotPostProcess,time,0);
- displayProgressBar(true, "displaying Image...", "VCell Model Loader", 100,uiService);
- double[] data = tpd.ijData[0].getDoubleData();
- BasicStackDimensions bsd = tpd.ijData[0].stackInfo;
- System.out.println(bsd.xsize+" "+bsd.ysize);
- ArrayImg testimg = ArrayImgs.doubles( data, bsd.xsize,bsd.ysize,bsd.zsize);
- uiService.show(testimg);
- } catch (Exception e) {
- displayProgressBar(false, "displaying Image...", "VCell Model Loader", 100,uiService);
- uiService.showDialog("theCacheKey,var,VCellHelper.VARTYPE_POSTPROC.NotPostProcess,time,0\n"+e.getMessage(), "getTimePoint(...) failed", MessageType.ERROR_MESSAGE);
- }finally {
- displayProgressBar(false, "displaying Image...", "VCell Model Loader", 100,uiService);
- }
- }
-}
diff --git a/vcell-imagej-helper/src/main/java/org/vcell/imagej/plugin/NikitaTest.java b/vcell-imagej-helper/src/main/java/org/vcell/imagej/plugin/NikitaTest.java
deleted file mode 100644
index fa3aea0f7d..0000000000
--- a/vcell-imagej-helper/src/main/java/org/vcell/imagej/plugin/NikitaTest.java
+++ /dev/null
@@ -1,201 +0,0 @@
-package org.vcell.imagej.plugin;
-
-import java.util.ArrayList;
-
-import javax.swing.JFrame;
-
-import org.jfree.chart.ChartFactory;
-import org.jfree.chart.ChartPanel;
-import org.jfree.chart.JFreeChart;
-import org.jfree.chart.plot.PlotOrientation;
-import org.jfree.data.Range;
-import org.jfree.data.xy.DefaultXYDataset;
-import org.scijava.command.ContextCommand;
-import org.scijava.plugin.Parameter;
-import org.scijava.plugin.Plugin;
-import org.scijava.ui.DialogPrompt.MessageType;
-import org.scijava.ui.UIService;
-import org.vcell.imagej.helper.VCellHelper;
-import org.vcell.imagej.helper.VCellHelper.IJDataList;
-import org.vcell.imagej.helper.VCellHelper.IJTimeSeriesJobResults;
-import org.vcell.imagej.helper.VCellHelper.IJVarInfos;
-import org.vcell.imagej.helper.VCellHelper.VARTYPE_POSTPROC;
-import org.vcell.imagej.helper.VCellHelper.VCellModelSearchResults;
-
-import net.imagej.ImageJ;
-
-@Plugin(type = ContextCommand.class, menuPath = "Plugins>NikitaTest")
-public class NikitaTest extends ContextCommand{
-
- @Parameter
- private UIService uiService;
-
- @Parameter
- private VCellHelper vcellHelper;
-
- @Parameter (choices={"bm", "mm"}, style="listBox")
- private String modelType;
-
- @Parameter
- private String vCellUser = "colreeze";
-
- @Parameter
- private String vCellModel = "Monkeyflower_pigmentation_v2";
-
- @Parameter
- private String application = "Pattern_formation";
-
- @Parameter
- private String simulation = "WT";
-
- //String[] require more complicated programming
- //For now use just 1 string
- @Parameter
- private String variable = "A";
-
- @Parameter
- private int timePoint = 500;
-
- @Parameter
- private int startIndex = 1279;
-
- @Parameter
- private int endIndex = 1321;
-
- @Parameter
- private String imageName = "test";
-
- public static void main(String[] args) {
- // create the ImageJ application context with all available services
- final ImageJ ij = new ImageJ();
- ij.ui().showUI();
- }
-
- @Override
- public void run() {
-
- try {
- //Find the port that a separately running VCell client is listening on
- System.out.println("vcell service port="+vcellHelper.findVCellApiServerPort());
- } catch (Exception e) {
- uiService.showDialog("Activate VCell client ImageJ service\nTools->'Start Fiji (ImageJ) service'\n"+e.getMessage(), "Couldn't contact VCell client", MessageType.ERROR_MESSAGE);
- return;
- }
- String theCacheKey = null;
- VCellHelper.VCellModelSearch vcms = new VCellHelper.VCellModelSearch(VCellHelper.ModelType.valueOf(modelType),vCellUser,vCellModel,application,simulation,null,null);
- try {
- ArrayList 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);
- } catch (Exception e) {
- uiService.showDialog(modelType+", "+vCellUser+", "+vCellModel+", "+application+", "+simulation+", null, null\n"+e.getMessage(), "Search failed", MessageType.ERROR_MESSAGE);
- return;
- }
-
- IJDataList timePointData = null;
- int[] timePointIndexes = new int[1]; // there is 1 timePoint
- int theTimePointIndex = 0;
- timePointIndexes[theTimePointIndex] = timePoint;
- try {
- timePointData = vcellHelper.getTimePointData(theCacheKey, variable, VARTYPE_POSTPROC.NotPostProcess, timePointIndexes, 0);
- } catch (Exception e) {
- uiService.showDialog(modelType+", "+vCellUser+", "+vCellModel+", "+application+", "+simulation+", "+variable+", "+timePoint+"\n"+e.getMessage(), "Get Data failed", MessageType.ERROR_MESSAGE);
- return;
- }
- double[] theTimePointData = timePointData.ijData[theTimePointIndex].getDoubleData();
- Range xAxisRange = null;
- int[] dataIndexes = new int[endIndex-startIndex+1];
- double[] dataIndexesDouble = new double[dataIndexes.length];// This is just for JFreeChart
- for(int i=startIndex;i<=endIndex;i++) {
- dataIndexes[i-startIndex] = i;
- dataIndexesDouble[i-startIndex] = i;
- xAxisRange = Range.expandToInclude(xAxisRange, dataIndexesDouble[i-startIndex]);
- }
-
- Range yAxisRange = null;
- double[] chartTheseDataPoints = new double[dataIndexes.length];
- for(int i=0;i
- * You should replace the parameter fields with your own inputs and outputs,
- * and replace the {@link run} method implementation with your own logic.
- *
- *
- * 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.
- *
- *
- * 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.
- *
- *
- * When editing the original VCellHelper in another running Eclipse,
- * to make the changes show up in this project choose thisEclipse->Project->Clean...->clean.
- *
- */
-@Plugin(type = ContextCommand.class, menuPath = "Plugins>VCellPlugin")
-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 extends JComboBox {
- public StyledComboBox() {
- setUI(new StyledComboBoxUI());
- }
- public StyledComboBox(String[] items) {
- setUI(new StyledComboBoxUI());
- setModel(new DefaultComboBoxModel(items));
- }
- }
-
- 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 jcbModelType = new StyledComboBox(new String[] {ModelType.bm.name(),ModelType.mm.name(),ModelType.quick.name()});
- private JComboBox jcbUserid = new StyledComboBox();
- private JComboBox jcbModelNames = new StyledComboBox();
- private JComboBox jcbAppNames = new StyledComboBox();
- private JComboBox jcbSimNames = new StyledComboBox();
-
-
- private Comparator comp = new Comparator() {
- @Override
- public int compare(String o1, String o2) {
- return o1.toLowerCase().compareTo(o2.toLowerCase());
- }
- };
- private TreeSet useridSet = new TreeSet(comp);
- private Hashtable> mapUseridToModelNameTime = new Hashtable>();
- private Hashtable mapModelNameTimeToActualModelname = new Hashtable();
- private Hashtable> mapModelToApps = new Hashtable>();
- private Hashtable> mapAppsToSims = new Hashtable>();
-
- 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 vcmsr = vcellHelper.getSearchedModelSimCacheKey(false,vcms,null);
- useridSet = new TreeSet(comp);
- mapUseridToModelNameTime = new Hashtable>();
- mapModelNameTimeToActualModelname = new Hashtable();
- mapModelToApps = new Hashtable>();
- mapAppsToSims = new Hashtable>();
-
- final Iterator