Examples with ProgressDialogListener org.vcell.util.ProgressDialogListener used on opensource projects

Example 11 with ProgressDialogListener

use of org.vcell.util.ProgressDialogListener in project vcell by virtualcell.

the class NetworkConstraintsPanel method runBioNetGen.

private void runBioNetGen() {
    EditConstraintsPanel panel = new EditConstraintsPanel(this);
    ChildWindowManager childWindowManager = ChildWindowManager.findChildWindowManager(this);
    ChildWindow childWindow = childWindowManager.addChildWindow(panel, panel, "Edit / Test Constraints");
    Dimension dim = new Dimension(360, 160);
    childWindow.pack();
    panel.setChildWindow(childWindow);
    childWindow.setPreferredSize(dim);
    childWindow.showModal();
    int maxIterations;
    int maxMolecules;
    if (panel.getButtonPushed() == ActionButtons.Run) {
        maxIterations = new Integer(panel.maxIterationTextField.getText());
        maxMolecules = new Integer(panel.maxMolTextField.getText());
        fieldSimulationContext.getNetworkConstraints().setTestConstraints(maxIterations, maxMolecules);
    } else if (panel.getButtonPushed() == ActionButtons.Apply) {
        activateConsole();
        maxIterations = new Integer(panel.maxIterationTextField.getText());
        maxMolecules = new Integer(panel.maxMolTextField.getText());
        fieldSimulationContext.getNetworkConstraints().setTestConstraints(maxIterations, maxMolecules);
        fieldSimulationContext.getNetworkConstraints().updateConstraintsFromTest();
        // apply will invalidate everything: generated species, reactions, console, cache, etc
        updateBioNetGenOutput(null);
        refreshInterface();
        TaskCallbackMessage tcm = new TaskCallbackMessage(TaskCallbackStatus.Clean, "");
        fieldSimulationContext.appendToConsole(tcm);
        String message = "Warning: The current Constraints are not tested / validated.";
        tcm = new TaskCallbackMessage(TaskCallbackStatus.Warning, message);
        fieldSimulationContext.appendToConsole(tcm);
        message = "The Network generation may take a very long time or the generated network may be incomplete. " + "We recommend testing this set of constraints.";
        tcm = new TaskCallbackMessage(TaskCallbackStatus.Notification, message);
        fieldSimulationContext.appendToConsole(tcm);
        return;
    } else {
        return;
    }
    // TODO: do not delete the commented code below
    // uncomment the next 6 lines to keep the data in the dialogs synchronized with the most recent reaction network
    // if(viewSpeciesDialog != null) {
    // viewSpeciesDialog.dispose();
    // }
    // if(viewReactionsDialog != null) {
    // viewReactionsDialog.dispose();
    // }
    activateConsole();
    // previousIterationSpecies = 0;
    synchronized (this) {
        fieldSimulationContext.setMd5hash(null);
        fieldSimulationContext.setMostRecentlyCreatedOutputSpec(null);
    }
    refreshInterface();
    if (!checkBnglRequirements()) {
        return;
    }
    NetworkTransformer transformer = new NetworkTransformer();
    MathMappingCallback dummyCallback = new MathMappingCallback() {

        public void setProgressFraction(float percentDone) {
        }

        public void setMessage(String message) {
        }

        public boolean isInterrupted() {
            return false;
        }
    };
    // we alter the input string to use the test values for max iterations and max molecules per species
    String input = transformer.convertToBngl(fieldSimulationContext, true, dummyCallback, NetworkGenerationRequirements.ComputeFullNoTimeout);
    // get rid of the default generate network command...
    input = input.substring(0, input.indexOf("generate_network({"));
    // ... and replace it with the "fake" one
    StringWriter bnglStringWriter = new StringWriter();
    PrintWriter pw = new PrintWriter(bnglStringWriter);
    RbmNetworkGenerator.generateNetworkEx(maxIterations, maxMolecules, pw, fieldSimulationContext.getModel().getRbmModelContainer(), fieldSimulationContext, NetworkGenerationRequirements.ComputeFullNoTimeout);
    String genNetStr = bnglStringWriter.toString();
    pw.close();
    input += genNetStr;
    BNGInput bngInput = new BNGInput(input);
    final BNGExecutorService bngService = BNGExecutorService.getInstance(bngInput, NetworkGenerationRequirements.NoTimeoutMS);
    bngService.registerBngUpdaterCallback(this);
    Hashtable<String, Object> hash = new Hashtable<String, Object>();
    AsynchClientTask[] tasksArray = new AsynchClientTask[3];
    TaskCallbackMessage message = new TaskCallbackMessage(TaskCallbackStatus.Clean, "");
    fieldSimulationContext.appendToConsole(message);
    tasksArray[0] = new RunBioNetGen(bngService);
    tasksArray[1] = new CreateBNGOutputSpec(bngService);
    tasksArray[2] = new ReturnBNGOutput(bngService, fieldSimulationContext, this);
    ClientTaskDispatcher.dispatch(this, hash, tasksArray, false, true, new ProgressDialogListener() {

        @Override
        public void cancelButton_actionPerformed(EventObject newEvent) {
            try {
                bngService.stopBNG();
                String s = "...user cancelled.";
                TaskCallbackMessage tcm = new TaskCallbackMessage(TaskCallbackStatus.TaskStopped, s);
                // message will be processed in TaskCallbackProcessor::case TaskStopped
                setNewCallbackMessage(tcm);
            } catch (Exception e) {
                e.printStackTrace();
            }
        }
    });
}

Example 12 with ProgressDialogListener

use of org.vcell.util.ProgressDialogListener in project vcell by virtualcell.

the class ViewJobsPanel method refreshInterface.

private void refreshInterface() {
    Hashtable<String, Object> hash = new Hashtable<String, Object>();
    AsynchClientTask[] tasksArray = new AsynchClientTask[2];
    tasksArray[0] = new RunQuery();
    tasksArray[1] = new DisplayResults();
    ClientTaskDispatcher.dispatch(this, hash, tasksArray, false, true, new ProgressDialogListener() {

        @Override
        public void cancelButton_actionPerformed(EventObject newEvent) {
            try {
                System.out.println("...user cancelled.");
            } catch (Exception e) {
                e.printStackTrace();
            }
        }
    });
}

Example 13 with ProgressDialogListener

use of org.vcell.util.ProgressDialogListener in project vcell by virtualcell.

the class FRAPOptData method main.

public static void main(String[] args) {
    String workingDir = "C:\\";
    LocalWorkspace localWorkspace = new LocalWorkspace(new File(workingDir));
    String xmlString;
    try {
        // read original data from file
        System.out.println("start loading original data....");
        String expFileName = "C:/VirtualMicroscopy/testFastD_4_fastFrac_0p5_slowD_1_slowFrac_0p3_ImmobileFrac_0p2_mwb_0p0015_new.vfrap";
        xmlString = XmlUtil.getXMLString(expFileName);
        MicroscopyXmlReader xmlReader = new MicroscopyXmlReader(true);
        FRAPStudy expFrapStudy = xmlReader.getFrapStudy(XmlUtil.stringToXML(xmlString, null).getRootElement(), null);
        expFrapStudy.setXmlFilename(expFileName);
        System.out.println("experimental data time points" + expFrapStudy.getFrapData().getImageDataset().getSizeT());
        System.out.println("finish loading original data....");
        // create reference data
        System.out.println("creating rederence data....");
        FRAPOptData optData = new FRAPOptData(expFrapStudy, 5, localWorkspace, new ClientTaskStatusSupport() {

            public void setProgress(int progress) {
            // TODO Auto-generated method stub
            }

            public void setMessage(String message) {
            // TODO Auto-generated method stub
            }

            public boolean isInterrupted() {
                // TODO Auto-generated method stub
                return false;
            }

            public int getProgress() {
                // TODO Auto-generated method stub
                return 0;
            }

            public void addProgressDialogListener(ProgressDialogListener progressDialogListener) {
                throw new RuntimeException("not yet implemented");
            }
        });
        // trying 3 parameters
        // Parameter diff = new cbit.vcell.opt.Parameter(FRAPOptData.PARAMETER_NAMES[FRAPOptData.DIFFUSION_RATE_INDEX], 0, 100, 1.0, Double.parseDouble(expFrapStudy.getFrapModelParameters().diffusionRate));
        // Parameter mobileFrac = new cbit.vcell.opt.Parameter(FRAPOptData.PARAMETER_NAMES[FRAPOptData.MOBILE_FRACTION_INDEX], 0, 1, 1.0, 1/*Double.parseDouble(expFrapStudy.getFrapModelParameters().mobileFraction)*/);
        // Parameter bleachWhileMonitoringRate = new cbit.vcell.opt.Parameter(FRAPOptData.PARAMETER_NAMES[FRAPOptData.BLEACH_WHILE_MONITOR_INDEX], 0, 10, 1.0,  0/*Double.parseDouble(expFrapStudy.getFrapModelParameters().monitorBleachRate)*/);
        // trying 5 parameters
        Parameter diffFastOffset = new cbit.vcell.opt.Parameter("fastDiffOffset", 0, 50, 1.0, 10);
        Parameter mFracFast = new cbit.vcell.opt.Parameter("fastMobileFrac", 0, 1, 1.0, 0.5);
        Parameter diffSlow = new cbit.vcell.opt.Parameter("slowDiffRate", 0, 10, 1.0, 0.1);
        Parameter mFracSlow = new cbit.vcell.opt.Parameter("slowMobileFrac", 0, 1, 1.0, 0.5);
        Parameter bleachWhileMonitoringRate = new cbit.vcell.opt.Parameter("bleachWhileMonitoringRate", 0, 20, 1.0, 0.1);
        Parameter[] inParams = new Parameter[] { diffFastOffset, mFracFast, diffSlow, mFracSlow, bleachWhileMonitoringRate };
        // Parameter diffFast = new cbit.vcell.opt.Parameter("fast_diff_rate", 0, 100, 1.0, 5);
        // Parameter mFracFast = new cbit.vcell.opt.Parameter("fast_mobile_fraction", 0, 1, 1.0, 0.5);
        // Parameter diffSlowFactor = new cbit.vcell.opt.Parameter("slow_diff_factor", 0, 1, 1.0, 0.2);
        // Parameter mFracSlow = new cbit.vcell.opt.Parameter("slow_mobile_fraction", 0, 1, 1.0, 0.5);
        // Parameter bleachWhileMonitoringRate = new cbit.vcell.opt.Parameter("bleach_while_monitoring_rate", 0, 1, 1.0,  0.1);
        // Parameter[] inParams = new Parameter[]{diffFast, mFracFast, diffSlowFactor, mFracSlow, bleachWhileMonitoringRate};
        // add some constraints, like fast mobile fraction + slow mobile fraction should smaller than 1.
        // slower rate should be 5 times smaller than fast rate.....??? 5*slowDiffRate < fastDiffRate
        // Expression exp1 = new Expression("("+mFracFast.getName()+" + "+mFracSlow.getName()+" - 1)");
        // Constraint con1 = new Constraint(ConstraintType.LinearInequality, exp1);
        // Expression exp2 = new Expression("( 4 * "+diffSlow.getName()+" - "+ diffFastOffset.getName() +")");
        // Constraint con2 = new Constraint(ConstraintType.LinearInequality, exp2);
        // Constraint[] cons = new Constraint[2];
        // cons[0] = con1;
        // cons[1] = con2;
        ROI[] rois = expFrapStudy.getFrapData().getRois();
        boolean[] errorOfInterest = new boolean[rois.length];
        for (int i = 0; i < rois.length; i++) {
            if (/*!rois[i].getROIType().equals(RoiType.ROI_BLEACHED)*/
            rois[i].getROIName().equals(FRAPData.VFRAP_ROI_ENUM.ROI_BACKGROUND.name()) || rois[i].getROIName().equals(FRAPData.VFRAP_ROI_ENUM.ROI_CELL.name())) {
                errorOfInterest[i] = false;
            } else {
                errorOfInterest[i] = true;
            }
        }
        optData.getBestParamters(inParams, errorOfInterest);
    // double[][] result = optData.getFitData(inParams, errorOfInterest); // double[roiLen][timePoints]
    // int indexROI = -1;
    // for(int j = 0; j < expFrapStudy.getFrapData().getRois().length; j++)
    // {
    // if(expFrapStudy.getFrapData().getRois()[j].getROIType().equals(RoiType.ROI_BLEACHED))
    // {
    // indexROI = j;
    // break;
    // }
    // }
    // int index = Integer.parseInt(expFrapStudy.getFrapModelParameters().startIndexForRecovery);
    // for(int i = 0; i < (expFrapStudy.getFrapData().getImageDataset().getImageTimeStamps().length - index); i++)
    // {
    // System.out.println(expFrapStudy.getFrapData().getImageDataset().getImageTimeStamps()[i+index]+"\t"+result[indexROI][i]);
    // }
    } catch (Exception e) {
        // TODO Auto-generated catch block
        e.printStackTrace();
    }
}

Example 14 with ProgressDialogListener

use of org.vcell.util.ProgressDialogListener in project vcell by virtualcell.

the class FRAPParamTest method runProfileLikelihood.

public void runProfileLikelihood() {
    String errorMsg = checkFrapStudyValidity();
    if (!errorMsg.equals("")) {
        System.out.println("Application terminated due to " + errorMsg);
        System.exit(1);
    } else {
        try {
            ClientTaskStatusSupport ctss = new ClientTaskStatusSupport() {

                public void setProgress(int progress) {
                    System.out.println(progress);
                }

                public void setMessage(String message) {
                    System.out.println(message);
                }

                public boolean isInterrupted() {
                    // TODO Auto-generated method stub
                    return false;
                }

                public int getProgress() {
                    // TODO Auto-generated method stub
                    return 0;
                }

                public void addProgressDialogListener(ProgressDialogListener progressDialogListener) {
                    throw new RuntimeException("not yet implemented");
                }
            };
            // get startign index
            if (frapStudy.getStartingIndexForRecovery() == null) {
                int index = FRAPDataAnalysis.calculateRecoveryIndex(frapStudy.getFrapData());
                frapStudy.setStartingIndexForRecovery(index);
            }
            // get dependent rois
            if (frapStudy.getFrapData().getRois().length < 4) {
                frapStudy.refreshDependentROIs();
            }
            // get selected ROIs
            if (frapStudy.getSelectedROIsForErrorCalculation() == null) {
                boolean[] selectedROIs = new boolean[FRAPData.VFRAP_ROI_ENUM.values().length];
                int counter = 0;
                for (FRAPData.VFRAP_ROI_ENUM roiEnum : FRAPData.VFRAP_ROI_ENUM.values()) {
                    if (roiEnum.name().equals(FRAPData.VFRAP_ROI_ENUM.ROI_CELL.name()) || roiEnum.name().equals(FRAPData.VFRAP_ROI_ENUM.ROI_BACKGROUND.name())) {
                        counter++;
                        continue;
                    }
                    if (frapStudy.getFrapData().getRoi(roiEnum.name()).getNonzeroPixelsCount() > 0) {
                        selectedROIs[counter] = true;
                        counter++;
                    }
                }
                frapStudy.setSelectedROIsForErrorCalculation(selectedROIs);
            }
            // get frap opt data
            if (frapStudy.getFrapOptData() == null) {
                if (!FRAPWorkspace.areExternalDataOK(getLocalWorkspace(), frapStudy.getFrapDataExternalDataInfo(), frapStudy.getRoiExternalDataInfo())) {
                    // if external files are missing/currupt or ROIs are changed, create keys and save them
                    frapStudy.setFrapDataExternalDataInfo(FRAPStudy.createNewExternalDataInfo(localWorkspace, FRAPStudy.IMAGE_EXTDATA_NAME));
                    frapStudy.setRoiExternalDataInfo(FRAPStudy.createNewExternalDataInfo(localWorkspace, FRAPStudy.ROI_EXTDATA_NAME));
                    frapStudy.saveROIsAsExternalData(localWorkspace, frapStudy.getRoiExternalDataInfo().getExternalDataIdentifier(), frapStudy.getStartingIndexForRecovery());
                    frapStudy.saveImageDatasetAsExternalData(localWorkspace, frapStudy.getFrapDataExternalDataInfo().getExternalDataIdentifier(), frapStudy.getStartingIndexForRecovery());
                }
                // run ref sim
                frapStudy.setFrapOptData(new FRAPOptData(frapStudy, FRAPModel.NUM_MODEL_PARAMETERS_ONE_DIFF, localWorkspace, ctss));
            }
            FRAPOptData optData = frapStudy.getFrapOptData();
            // create frapModels
            if (frapStudy.getModels()[FRAPModel.IDX_MODEL_DIFF_ONE_COMPONENT] == null) {
                frapStudy.getModels()[FRAPModel.IDX_MODEL_DIFF_ONE_COMPONENT] = new FRAPModel(FRAPModel.MODEL_TYPE_ARRAY[FRAPModel.IDX_MODEL_DIFF_ONE_COMPONENT], null, null, null);
                if (frapStudy.getModels()[FRAPModel.IDX_MODEL_DIFF_ONE_COMPONENT].getModelParameters() == null) {
                    frapStudy.getFrapOptData().setNumEstimatedParams(FRAPModel.NUM_MODEL_PARAMETERS_ONE_DIFF);
                    Parameter[] initialParams = FRAPModel.getInitialParameters(frapStudy.getFrapData(), FRAPModel.MODEL_TYPE_ARRAY[FRAPModel.IDX_MODEL_DIFF_ONE_COMPONENT], frapStudy.getStartingIndexForRecovery());
                    Parameter[] bestParameters = frapStudy.getFrapOptData().getBestParamters(initialParams, frapStudy.getSelectedROIsForErrorCalculation());
                    frapStudy.getModels()[FRAPModel.IDX_MODEL_DIFF_ONE_COMPONENT].setModelParameters(bestParameters);
                }
            }
            if (frapStudy.getModels()[FRAPModel.IDX_MODEL_DIFF_TWO_COMPONENTS] == null) {
                frapStudy.getModels()[FRAPModel.IDX_MODEL_DIFF_TWO_COMPONENTS] = new FRAPModel(FRAPModel.MODEL_TYPE_ARRAY[FRAPModel.IDX_MODEL_DIFF_TWO_COMPONENTS], null, null, null);
                if (frapStudy.getModels()[FRAPModel.IDX_MODEL_DIFF_TWO_COMPONENTS].getModelParameters() == null) {
                    frapStudy.getFrapOptData().setNumEstimatedParams(FRAPModel.NUM_MODEL_PARAMETERS_TWO_DIFF);
                    Parameter[] initialParams = FRAPModel.getInitialParameters(frapStudy.getFrapData(), FRAPModel.MODEL_TYPE_ARRAY[FRAPModel.IDX_MODEL_DIFF_TWO_COMPONENTS], frapStudy.getStartingIndexForRecovery());
                    Parameter[] bestParameters = frapStudy.getFrapOptData().getBestParamters(initialParams, frapStudy.getSelectedROIsForErrorCalculation());
                    frapStudy.getModels()[FRAPModel.IDX_MODEL_DIFF_TWO_COMPONENTS].setModelParameters(bestParameters);
                }
            }
            // try diffusion with one diffusing component model
            System.out.println("Evaluating parameters in diffusion with one diffusing compoent model...");
            Parameter[] bestParameters = frapStudy.getModels()[FRAPModel.IDX_MODEL_DIFF_ONE_COMPONENT].getModelParameters();
            ProfileData[] profileData = optData.evaluateParameters(bestParameters, ctss);
            // output profile likelihood
            File outputDir_oneComponent = new File(getLocalWorkspace().getDefaultWorkspaceDirectory() + SUB_DIRECTORY + "OneComponent_SAVED_AT_" + BeanUtils.generateDateTimeString() + System.getProperty("file.separator"));
            if (!outputDir_oneComponent.exists()) {
                outputDir_oneComponent.mkdirs();
            }
            for (int i = 0; i < profileData.length; i++) {
                ProfileDataElement profileDataElement = profileData[i].getProfileDataElements().get(0);
                outputProfileLikelihood(profileData[i].getProfileDataElements(), profileDataElement.getParamName(), outputDir_oneComponent);
            }
            // try diffusion with two diffusing components model
            System.out.println("Evaluating parameters in diffusion with two diffusing compoents model...");
            bestParameters = frapStudy.getModels()[FRAPModel.IDX_MODEL_DIFF_TWO_COMPONENTS].getModelParameters();
            profileData = optData.evaluateParameters(bestParameters, ctss);
            // output profile likelihood
            File outputDir_twoComponents = new File(getLocalWorkspace().getDefaultWorkspaceDirectory() + SUB_DIRECTORY + "TwoComponents_SAVED_AT_" + BeanUtils.generateDateTimeString() + System.getProperty("file.separator"));
            if (!outputDir_twoComponents.exists()) {
                outputDir_twoComponents.mkdirs();
            }
            for (int i = 0; i < profileData.length; i++) {
                ProfileDataElement profileDataElement = profileData[i].getProfileDataElements().get(0);
                outputProfileLikelihood(profileData[i].getProfileDataElements(), profileDataElement.getParamName(), outputDir_twoComponents);
            }
        } catch (Exception e) {
            e.printStackTrace(System.out);
            System.exit(1);
        }
    }
}

Example 15 with ProgressDialogListener

use of org.vcell.util.ProgressDialogListener in project vcell by virtualcell.

the class KenworthyWorkflowTest method main.

public static void main(String[] args) {
    try {
        File baseDir = new File(".");
        // File baseDir = new File("/Users/schaff/Documents/workspace/VCell_5.4");
        // initialize computing environment
        // 
        File workingDirectory = new File(baseDir, "workingDir");
        LocalWorkspace localWorkspace = new LocalWorkspace(workingDirectory);
        // 
        // import raw image time series data from VFRAP file format (can have noise, background, etc ... can be actual microscopy data)
        // 
        ClientTaskStatusSupport progressListener = new ClientTaskStatusSupport() {

            String message = "";

            int progress = 0;

            @Override
            public void setProgress(int progress) {
                this.progress = progress;
            }

            @Override
            public void setMessage(String message) {
                this.message = message;
            }

            @Override
            public boolean isInterrupted() {
                return false;
            }

            @Override
            public int getProgress() {
                return progress;
            }

            @Override
            public void addProgressDialogListener(ProgressDialogListener progressDialogListener) {
            }
        };
        // 
        // generate fake data (and save?)
        // 
        // ImageTimeSeries<UShortImage> simulatedFluorescence = generateFakeData(localWorkspace, progressListener);
        // new ExportRawTimeSeriesToVFrapOp().exportToVFRAP(vfrapFile, simulatedFluorescence, null);
        // 
        // analyze raw data (from file?) using Keyworthy method.
        // 
        File vfrapFile = new File(baseDir, "vfrapPaper/rawData/sim3/workflow.txt.save");
        // File vfrapFile = new File(baseDir, "tryit.vfrap");
        ImageTimeSeries<UShortImage> fluorTimeSeriesImages = new ImportRawTimeSeriesFromVFrapOp().importRawTimeSeriesFromVFrap(vfrapFile);
        analyzeKeyworthy(fluorTimeSeriesImages, localWorkspace);
    } catch (Exception e) {
        e.printStackTrace(System.out);
    }
}