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

Example 6 with ClientTaskStatusSupport

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

the class WorkflowJGraphProxy method workflowRun.

public void workflowRun() throws Exception {
    ClientTaskStatusSupport progress = 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) {
        }
    };
    context.getWorkflow().compute(context, progress);
}

Example 7 with ClientTaskStatusSupport

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

the class ImportRawTimeSeriesFromExperimentImageOp method importRawTimeSeries.

public ImageTimeSeries<UShortImage> importRawTimeSeries(File expTimeSeriesFile) throws Exception {
    ClientTaskStatusSupport clientTaskStatusSupport = null;
    ImageDataset rawTimeData = ImageDatasetReaderService.getInstance().getImageDatasetReader().readImageDataset(expTimeSeriesFile.getAbsolutePath(), clientTaskStatusSupport);
    ImageTimeSeries<UShortImage> imageTimeSeries = new ImageTimeSeries<UShortImage>(UShortImage.class, rawTimeData.getAllImages(), rawTimeData.getImageTimeStamps(), 1);
    return imageTimeSeries;
}

Example 8 with ClientTaskStatusSupport

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

the class BioModelsNetJPanel method searchImport.

private void searchImport() {
    AsynchClientTask searchTask = new AsynchClientTask("Search BioModels", AsynchClientTask.TASKTYPE_NONSWING_BLOCKING) {

        @Override
        public void run(Hashtable<String, Object> hashTable) throws Exception {
            Hashtable<String, String> vcellCompatibleBioModels_ID_Name_Hash = readVCellCompatibleBioModels_ID_Name_Hash();
            ClientTaskStatusSupport clientTaskStatusSupport = getClientTaskStatusSupport();
            // clientTaskStatusSupport.setProgress(0);
            clientTaskStatusSupport.setMessage("Initializing BioModels Search...");
            BioModelsWebServicesServiceLocator bioModelsWebServicesServiceLocator = new BioModelsWebServicesServiceLocator();
            BioModelsWebServices bioModelsWebServices = bioModelsWebServicesServiceLocator.getBioModelsWebServices();
            // clientTaskStatusSupport.setProgress(10);
            clientTaskStatusSupport.setMessage("Executing BioModels Search...");
            TreeSet<String> modelIDsMergedSearch = new TreeSet<String>();
            boolean bHasModelEntryID = modelEntryIDTextField.getText() != null && modelEntryIDTextField.getText().length() > 0;
            if (bHasModelEntryID) {
                clientTaskStatusSupport.setMessage("Executing BioModels Search (Model ID matches)...");
                // String[] modelIDsAll = bioModelsWebServices.getAllModelsId();
                String[] modelIDsAll = vcellCompatibleBioModels_ID_Name_Hash.keySet().toArray(new String[0]);
                for (int i = 0; i < modelIDsAll.length; i++) {
                    if (modelIDsAll[i].toUpperCase().indexOf(modelEntryIDTextField.getText().toUpperCase()) != -1) {
                        modelIDsMergedSearch.add(modelIDsAll[i]);
                    }
                }
            }
            boolean bHasModelName = modelNameTextField.getText() != null && modelNameTextField.getText().length() > 0;
            if (bHasModelName) {
                clientTaskStatusSupport.setMessage("Executing BioModels Search (Model Name matches)...");
                TreeSet<String> modelIDsByNameSet = new TreeSet<String>();
                // String[] modelIDsByName = bioModelsWebServices.getModelsIdByName(modelNameTextField.getText());
                String[] modelIDsAll = vcellCompatibleBioModels_ID_Name_Hash.keySet().toArray(new String[0]);
                for (int i = 0; i < modelIDsAll.length; i++) {
                    if (vcellCompatibleBioModels_ID_Name_Hash.get(modelIDsAll[i]).toUpperCase().indexOf(modelNameTextField.getText().toUpperCase()) != -1) {
                        modelIDsByNameSet.add(modelIDsAll[i]);
                    }
                }
                // }
                if (bHasModelEntryID) {
                    // intersection
                    modelIDsMergedSearch.retainAll(modelIDsByNameSet);
                } else {
                    modelIDsMergedSearch = modelIDsByNameSet;
                }
            }
            boolean bHasModelPublication = publicationTextField.getText() != null && publicationTextField.getText().length() > 0;
            if (bHasModelPublication) {
                clientTaskStatusSupport.setMessage("Executing BioModels Search (Publication matches)...");
                TreeSet<String> modelIDsByPublicationSet = new TreeSet<String>();
                String[] modelIDsbyPublication = bioModelsWebServices.getModelsIdByPublication(publicationTextField.getText());
                for (int i = 0; i < modelIDsbyPublication.length; i++) {
                    modelIDsByPublicationSet.add(modelIDsbyPublication[i]);
                }
                if (bHasModelEntryID || bHasModelName) {
                    // intersection
                    modelIDsMergedSearch.retainAll(modelIDsByPublicationSet);
                } else {
                    modelIDsMergedSearch = modelIDsByPublicationSet;
                }
            }
            if (!(bHasModelEntryID || bHasModelName || bHasModelPublication)) {
                // Get all models
                // modelIDsMergedSearch.addAll(Arrays.asList(bioModelsWebServices.getAllModelsId()));
                modelIDsMergedSearch.addAll(Arrays.asList(vcellCompatibleBioModels_ID_Name_Hash.keySet().toArray(new String[0])));
            }
            // clientTaskStatusSupport.setProgress(COLLECTION_PROGRESS);
            if (modelIDsMergedSearch.size() > 0) {
                // Intersect with supported BioModel IDs
                modelIDsMergedSearch.retainAll(Arrays.asList(vcellCompatibleBioModels_ID_Name_Hash.keySet().toArray(new String[0])));
                clientTaskStatusSupport.setMessage("Found " + modelIDsMergedSearch.size() + " VCell compatible BioModels");
                String[] modelIDMergedSearchArr = modelIDsMergedSearch.toArray(new String[0]);
                TreeMap<String, String> model_ID_Name_Map = new TreeMap<String, String>();
                String nameNotfound = "NameNotFound_0";
                for (int i = 0; i < modelIDMergedSearchArr.length; i++) {
                    if (clientTaskStatusSupport.isInterrupted()) {
                        // DialogUtils.showWarningDialog(BioModelsNetJPanel.this, "Search Cancelled");
                        throw UserCancelException.CANCEL_GENERIC;
                    }
                    try {
                        // clientTaskStatusSupport.setMessage("Retrieving "+modelIDMergedSearchArr[i]+" "+(i+1)+" of "+modelIDMergedSearchArr.length);
                        // String modelName = bioModelsWebServices.getModelNameById(modelIDMergedSearchArr[i]);
                        String modelName = vcellCompatibleBioModels_ID_Name_Hash.get(modelIDMergedSearchArr[i]);
                        // Assume model names are unique
                        model_ID_Name_Map.put(modelName, modelIDMergedSearchArr[i]);
                    } catch (Exception e) {
                        // For some reason Web Service API sometimes throws java.util.NoSuchElementException
                        // if id exists but name can't be found.
                        e.printStackTrace();
                        model_ID_Name_Map.put(nameNotfound, modelIDMergedSearchArr[i]);
                        nameNotfound = TokenMangler.getNextEnumeratedToken(nameNotfound);
                    }
                }
                // Make name,id rowdata for tablelist to allow user selection
                String[] sortedModelNames = model_ID_Name_Map.keySet().toArray(new String[0]);
                final String[][] rowData = new String[sortedModelNames.length][2];
                for (int i = 0; i < sortedModelNames.length; i++) {
                    rowData[i][0] = sortedModelNames[i];
                    rowData[i][1] = model_ID_Name_Map.get(sortedModelNames[i]);
                }
                // Allow user to select model for opening
                final String importNow = "Import";
                final String cancel = "Cancel";
                DialogUtils.TableListResult result = DialogUtils.showComponentOptionsTableList(BioModelsNetJPanel.this, "Select a BioModel to import", new String[] { "Model Names", "BioModels Entry ID" }, rowData, ListSelectionModel.SINGLE_SELECTION, null, new String[] { importNow, cancel }, importNow, new Comparator<Object>() {

                    public int compare(Object o1, Object o2) {
                        if (o1 instanceof String && o2 instanceof String) {
                            return ((String) o1).compareTo((String) o2);
                        }
                        throw new RuntimeException("row data should only be String");
                    }
                });
                if (result.selectedOption != null && result.selectedOption.equals(importNow)) {
                    // Close Dialog showing "this" panel so ProgressPopup not obscured during openDocument
                    SwingUtilities.invokeAndWait(new Runnable() {

                        public void run() {
                            disposeParentDialog();
                        }
                    });
                    closeClientTaskStatusSupport(clientTaskStatusSupport);
                    // Download and open (in new window) SBML document selected by user
                    String bioModelSBML = bioModelsWebServices.getModelSBMLById(rowData[result.selectedTableRows[0]][1]);
                    final ExternalDocInfo externalDocInfo = new ExternalDocInfo(bioModelSBML, sortedModelNames[result.selectedTableRows[0]]);
                    new Thread(new Runnable() {

                        public void run() {
                            documentWindow.getTopLevelWindowManager().getRequestManager().openDocument(externalDocInfo, documentWindow.getTopLevelWindowManager(), true);
                        }
                    }).start();
                }
            } else {
                closeClientTaskStatusSupport(clientTaskStatusSupport);
                DialogUtils.showWarningDialog(BioModelsNetJPanel.this, "No BioModels found matching current search criteria.");
                throw UserCancelException.CANCEL_GENERIC;
            }
        }
    };
    ClientTaskDispatcher.dispatch(BioModelsNetJPanel.this, new Hashtable<String, Object>(), new AsynchClientTask[] { searchTask }, true, true, null, true);
}

Example 9 with ClientTaskStatusSupport

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

the class ROIMultiPaintManager method smoothUnderlay.

private void smoothUnderlay() {
    AsynchClientTask smoothTask = new AsynchClientTask("Processing Image...", AsynchClientTask.TASKTYPE_NONSWING_BLOCKING) {

        @Override
        public void run(Hashtable<String, Object> hashTable) throws Exception {
            ClientTaskStatusSupport localClientTaskStatusSupport = new ClientTaskStatusSupport() {

                public void setProgress(int progress) {
                    if (getClientTaskStatusSupport() != null) {
                        getClientTaskStatusSupport().setProgress((int) (.9 * progress));
                    }
                }

                public void setMessage(String message) {
                }

                public boolean isInterrupted() {
                    return (getClientTaskStatusSupport() == null ? false : getClientTaskStatusSupport().isInterrupted());
                }

                public int getProgress() {
                    return 0;
                }

                public void addProgressDialogListener(ProgressDialogListener progressDialogListener) {
                    throw new RuntimeException("not yet implemented");
                }
            };
            enhancedImageDatasetChannels = smoothImageDataset(initImageDataSetChannels, enhanceImageAmount, localClientTaskStatusSupport);
            if (localClientTaskStatusSupport.isInterrupted()) {
                throw UserCancelException.CANCEL_GENERIC;
            }
            localClientTaskStatusSupport.setMessage("Calculating histogram...");
            condensedBinsMapChannels = calculateCondensedBinsChannels0(getImageDataset());
            allPixelValuesRangeChannels = calculateAllPixelValuesRangeChannels0(getImageDataset());
        }
    };
    AsynchClientTask updateDisplayTask = new AsynchClientTask("Updating display...", AsynchClientTask.TASKTYPE_SWING_BLOCKING) {

        @Override
        public void run(Hashtable<String, Object> hashTable) throws Exception {
            if (getClientTaskStatusSupport() != null) {
                getClientTaskStatusSupport().setProgress(100);
            }
            updateUnderlayHistogramDisplay();
        }
    };
    if (calculateCurrentSize() > 2000000) {
        // show update progress only if large
        ClientTaskDispatcher.dispatch(overlayEditorPanelJAI, new Hashtable<String, Object>(), new AsynchClientTask[] { smoothTask, updateDisplayTask }, true, true, null, true);
    } else {
        ClientTaskDispatcher.dispatch(overlayEditorPanelJAI, new Hashtable<String, Object>(), new AsynchClientTask[] { smoothTask, updateDisplayTask });
    }
}

Example 10 with ClientTaskStatusSupport

use of org.vcell.util.ClientTaskStatusSupport 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();
    }
}