Examples with ExternalDataIdentifier org.vcell.util.document.ExternalDataIdentifier used on opensource projects

Example 26 with ExternalDataIdentifier

use of org.vcell.util.document.ExternalDataIdentifier in project vcell by virtualcell.

the class FRAPStudyPanel method showMovie.

private void showMovie() {
    AsynchClientTask createMovieTask = new AsynchClientTask("Buffering movie data...", AsynchClientTask.TASKTYPE_NONSWING_BLOCKING) {

        public void run(Hashtable<String, Object> hashTable) throws Exception {
            FRAPStudy fStudy = getFrapWorkspace().getWorkingFrapStudy();
            if (fStudy == null) {
                return;
            }
            if (fStudy.getMovieURLString() != null && fStudy.getMovieFileString() != null) {
                hashTable.put("FrapStudy", fStudy);
                return;
            }
            // create export specs
            Simulation sim = null;
            if (fStudy.getBioModel() == null || fStudy.getBioModel().getSimulations() == null || fStudy.getBioModel().getSimulations().length < 1) {
                return;
            } else {
                sim = fStudy.getBioModel().getSimulations()[0];
            }
            FieldFunctionArguments[] fieldFunctionArgs = FieldUtilities.getFieldFunctionArguments(sim.getMathDescription());
            FieldDataIdentifierSpec[] fieldDataIdentifierSpecs = new FieldDataIdentifierSpec[fieldFunctionArgs.length];
            for (int i = 0; i < fieldDataIdentifierSpecs.length; i++) {
                fieldDataIdentifierSpecs[i] = new FieldDataIdentifierSpec(fieldFunctionArgs[i], fStudy.getFrapDataExternalDataInfo().getExternalDataIdentifier());
            }
            ExternalDataIdentifier timeSeriesExtDataID = fStudy.getFrapDataExternalDataInfo().getExternalDataIdentifier();
            ExternalDataIdentifier maskExtDataID = fStudy.getRoiExternalDataInfo().getExternalDataIdentifier();
            // add sim
            int jobIndex = 0;
            SimulationJob simJob = new SimulationJob(sim, jobIndex, fieldDataIdentifierSpecs);
            VCDataIdentifier[] dataIDs = new VCDataIdentifier[] { timeSeriesExtDataID, maskExtDataID, simJob.getVCDataIdentifier() };
            VCDataIdentifier vcDataId = new MergedDataInfo(LocalWorkspace.getDefaultOwner(), dataIDs, FRAPStudy.VFRAP_DS_PREFIX);
            PDEDataManager dataManager = new PDEDataManager(null, getLocalWorkspace().getVCDataManager(), vcDataId);
            PDEDataContext pdeDataContext = new ClientPDEDataContext(dataManager);
            ExportFormat format = ExportFormat.QUICKTIME;
            String[] variableNames = new String[] { NORM_FLUOR_VAR, NORM_SIM_VAR };
            VariableSpecs variableSpecs = new VariableSpecs(variableNames, ExportConstants.VARIABLE_MULTI);
            // int endTimeIndex = (int)Math.round(sim.getSolverTaskDescription().getTimeBounds().getEndingTime()/((UniformOutputTimeSpec)sim.getSolverTaskDescription().getOutputTimeSpec()).getOutputTimeStep());
            int endTimeIndex = getFRAPSimDataViewerPanel().getOriginalDataViewer().getPdeDataContext().getTimePoints().length - 1;
            TimeSpecs timeSpecs = new TimeSpecs(0, endTimeIndex, pdeDataContext.getTimePoints(), ExportConstants.TIME_RANGE);
            int geoMode = ExportConstants.GEOMETRY_SLICE;
            GeometrySpecs geometrySpecs = new GeometrySpecs(null, Coordinate.Z_AXIS, 0, geoMode);
            // 10s
            double duration = 10000;
            DisplayPreferences pref1 = new DisplayPreferences("BlueRed", new Range(0.01, 1.1), DisplayAdapterService.createBlueRedSpecialColors());
            DisplayPreferences pref2 = new DisplayPreferences("BlueRed", new Range(0.01, 1.1), DisplayAdapterService.createBlueRedSpecialColors());
            DisplayPreferences[] displayPref = new DisplayPreferences[] { pref1, pref2 };
            int imageScale = 1;
            int membraneScale = 1;
            int scaleMode = ImagePaneModel.MESH_MODE;
            // the default setting in MediaSettingsPanel.
            int volVarMemOutlineThickness = 1;
            MovieSpecs mSpec = new MovieSpecs(duration, true, displayPref, ExportFormat.QUICKTIME, ExportConstants.NO_MIRRORING, volVarMemOutlineThickness, imageScale, membraneScale, scaleMode, FormatSpecificSpecs.CODEC_JPEG, 1.0f, /*lossless*/
            false, FormatSpecificSpecs.PARTICLE_NONE);
            // mSpec.setViewZoom(1);
            ExportSpecs exSpecs = new ExportSpecs(vcDataId, format, variableSpecs, timeSpecs, geometrySpecs, mSpec, fStudy.getName(), null);
            // pass the request
            ExportEvent exportEvt = ((VirtualFrapWindowManager) getFlourDataViewer().getDataViewerManager()).startExportMovie(exSpecs, outputContext, this.getClientTaskStatusSupport());
            hashTable.put("ExportEvt", exportEvt);
            hashTable.put("FrapStudy", fStudy);
        }
    };
    AsynchClientTask showMovieTask = new AsynchClientTask("Showing movie ...", AsynchClientTask.TASKTYPE_SWING_BLOCKING) {

        public void run(Hashtable<String, Object> hashTable) throws Exception {
            ExportEvent exportEvt = (ExportEvent) hashTable.get("ExportEvt");
            FRAPStudy fStudy = (FRAPStudy) hashTable.get("FrapStudy");
            // show movie if successfully exported
            if (exportEvt != null) {
                final String fileURLString = System.getProperty(PropertyLoader.exportBaseURLProperty) + exportEvt.getJobID() + ".mov";
                final String fileString = System.getProperty(PropertyLoader.exportBaseDirInternalProperty) + exportEvt.getJobID() + ".mov";
                fStudy.setMovieURLString(fileURLString);
                fStudy.setMovieFileString(fileString);
            }
            showMovieInDialog(fStudy.getMovieURLString(), fStudy.getMovieFileString());
        }
    };
    ClientTaskDispatcher.dispatch(this, new Hashtable<String, Object>(), new AsynchClientTask[] { createMovieTask, showMovieTask }, true, true, null, true);
}

Example 27 with ExternalDataIdentifier

use of org.vcell.util.document.ExternalDataIdentifier in project vcell by virtualcell.

the class DataSymbolsPanel method addVFrapDerivedImages.

private void addVFrapDerivedImages() {
    // add special (computed) images from vFrap
    AsynchClientTask[] taskArray = new AsynchClientTask[5];
    // select the desired vfrap file
    taskArray[0] = ChooseVFrapFile();
    // load the images from the vfrap file, compute derived images, store them all in memory
    taskArray[1] = new AsynchClientTask("Import images", AsynchClientTask.TASKTYPE_NONSWING_BLOCKING) {

        public void run(Hashtable<String, Object> hashTable) throws Exception {
            File vFrapFile = (File) hashTable.get("vFrapFile");
            Component requesterComponent = DataSymbolsPanel.this;
            DocumentWindow documentWindow = (DocumentWindow) BeanUtils.findTypeParentOfComponent(requesterComponent, DocumentWindow.class);
            DocumentManager documentManager = documentWindow.getTopLevelWindowManager().getRequestManager().getDocumentManager();
            if (documentManager == null) {
                throw new RuntimeException("Not connected to server.");
            }
            // ex  ccc8.vfrap
            String vFrapFileNameExtended = vFrapFile.getName();
            {
                // we want to make sure to reload these strings from the hash later on
                String initialFieldDataName = vFrapFileNameExtended.substring(0, vFrapFileNameExtended.indexOf(".vfrap"));
                // we'll save here the "special" vFrap images (prebleach_avg, ...)
                String mixedFieldDataName = initialFieldDataName + "Mx";
                hashTable.put("initialFieldDataName", initialFieldDataName);
                hashTable.put("mixedFieldDataName", mixedFieldDataName);
            }
            if (vFrapFileNameExtended.indexOf(".vfrap") <= -1) {
                throw new RuntimeException("File extension must be .vfrap");
            }
            // for derived images and ROIs
            checkNameAvailability(hashTable, true, documentManager, requesterComponent);
            // ----- read needed info from Virtual FRAP xml file
            System.out.println("Loading " + vFrapFileNameExtended + " ...");
            String xmlString = XmlUtil.getXMLString(vFrapFile.getAbsolutePath());
            MicroscopyXmlReader xmlReader = new MicroscopyXmlReader(true);
            Element vFrapRoot = XmlUtil.stringToXML(xmlString, null).getRootElement();
            // loading frap images and a ROIs subset for display purposes only (see next task)
            AnnotatedImageDataset annotatedImages = xmlReader.getAnnotatedImageDataset(vFrapRoot, null);
            hashTable.put("annotatedImages", annotatedImages);
            ROI[] rois = xmlReader.getPrimaryROIs(XmlUtil.stringToXML(xmlString, null).getRootElement(), null);
            LoadVFrapDisplayRoi(hashTable, annotatedImages, rois);
            // ------ locate the special images within the vFrap files and load them in memory
            if (!LoadVFrapSpecialImages(hashTable, vFrapRoot)) {
                throw new RuntimeException("Unable to recover derived images from vFrap.");
            }
        // int startingIndexRecovery = xmlReader.getStartindIndexForRecovery(XmlUtil.stringToXML(xmlString, null).getRootElement());
        // vFrapXmlHelper.LoadVFrapSpecialImages(annotatedImages, startingIndexRecovery);	// prebleach average and first postbleach
        // vFrapXmlHelper.LoadVFrapRoiCompositeImages(annotatedImages, rois);
        }
    };
    // show the images from the vfrap file in an OverlayEditorPanelJAI dialog
    taskArray[2] = new AsynchClientTask("Display images", AsynchClientTask.TASKTYPE_SWING_BLOCKING) {

        public void run(Hashtable<String, Object> hashTable) throws Exception {
            String mixedFieldDataName = (String) hashTable.get("mixedFieldDataName");
            if (mixedFieldDataName.equals("")) {
                JOptionPane.showMessageDialog(DataSymbolsPanel.this, "Field Data name " + mixedFieldDataName + " already in use.");
                // prevents the rest of tasks below from running
                throw UserCancelException.CANCEL_GENERIC;
            }
            AnnotatedImageDataset annotatedImages = (AnnotatedImageDataset) hashTable.get("annotatedImages");
            BufferedImage[] displayROI = (BufferedImage[]) hashTable.get("displayROI");
            if (annotatedImages == null || displayROI == null) {
                return;
            }
            // display the images
            OverlayEditorPanelJAI overlayPanel = new OverlayEditorPanelJAI();
            overlayPanel.setAllowAddROI(false);
            ImageDataset imageDataset = annotatedImages.getImageDataset();
            overlayPanel.setImages(imageDataset, 1, 0, new OverlayEditorPanelJAI.AllPixelValuesRange(1, 200));
            overlayPanel.setAllROICompositeImage(displayROI, OverlayEditorPanelJAI.FRAP_DATA_INIT_PROPERTY);
            int choice = DialogUtils.showComponentOKCancelDialog(DataSymbolsPanel.this, overlayPanel, "vFrap Field Data");
            if (choice != JOptionPane.OK_OPTION) {
                throw UserCancelException.CANCEL_GENERIC;
            }
        }
    };
    // save the ROIs, prebleach average and the first postbleach frame from memory to the database as field data
    taskArray[3] = new AsynchClientTask("Saving roi masks, pre-bleach average and first post-bleach", AsynchClientTask.TASKTYPE_NONSWING_BLOCKING) {

        public void run(Hashtable<String, Object> hashTable) throws Exception {
            Component requesterComponent = DataSymbolsPanel.this;
            DocumentWindow documentWindow = (DocumentWindow) BeanUtils.findTypeParentOfComponent(requesterComponent, DocumentWindow.class);
            DocumentManager documentManager = documentWindow.getTopLevelWindowManager().getRequestManager().getDocumentManager();
            if (documentManager == null) {
                throw new RuntimeException("Not connected to server.");
            }
            ExternalDataIdentifier derivedEDI = SaveVFrapSpecialImagesAsFieldData(hashTable, documentManager);
            hashTable.put("derivedEDI", derivedEDI);
        }
    };
    // create the data symbols for the images saved above and display them in the tree/table
    taskArray[4] = new AsynchClientTask("Display Data Symbols", AsynchClientTask.TASKTYPE_SWING_BLOCKING) {

        public void run(Hashtable<String, Object> hashTable) throws Exception {
            ExternalDataIdentifier derivedEDI = (ExternalDataIdentifier) hashTable.get("derivedEDI");
            BioModel bioModel = simulationContext.getBioModel();
            CreateSaveVFrapDataSymbols(hashTable, bioModel, derivedEDI);
        }
    };
    // save the ROIs, prebleach average and the first postbleach frame from memory to the database as field data
    // taskArray[4] = new AsynchClientTask("Saving roi masks, pre-bleach average and first post-bleach", AsynchClientTask.TASKTYPE_NONSWING_BLOCKING) {
    // public void run(Hashtable<String, Object> hashTable) throws Exception {
    // File vFrapFile = (File)hashTable.get("vFrapFile");
    // if(vFrapFile == null) {
    // return;
    // }
    // AnnotatedImageDataset annotatedImages = (AnnotatedImageDataset)hashTable.get("annotatedImages");
    // String initialFieldDataName = (String)hashTable.get("initialFieldDataName");
    // 
    // DocumentWindow documentWindow = (DocumentWindow)BeanUtils.findTypeParentOfComponent(DataSymbolsPanel.this, DocumentWindow.class);
    // DocumentManager dm = documentWindow.getTopLevelWindowManager().getRequestManager().getDocumentManager();
    // if(dm == null){
    // throw new RuntimeException("not connected to server");
    // }
    // 
    // // mesh
    // ImageDataset imageDataset = annotatedImages.getImageDataset();
    // Extent extent = imageDataset.getExtent();
    // ISize isize = imageDataset.getISize();
    // Origin origin = new Origin(0,0,0);
    // CartesianMesh cartesianMesh = CartesianMesh.createSimpleCartesianMesh(origin, extent,isize,
    // new RegionImage( new VCImageUncompressed(null, new byte[isize.getXYZ()], extent,
    // isize.getX(),isize.getY(),isize.getZ()),0,null,null,RegionImage.NO_SMOOTHING));
    // double[] firstPostBleach = (double[])hashTable.get("firstPostBleach");
    // double[] prebleachAvg = (double[])hashTable.get("prebleachAverage");
    // ROI[] rois = (ROI[])hashTable.get("rois");
    // 
    // int NumTimePoints = 1;
    // int NumChannels = 2+rois.length;  // prebleach, postbleach, roi1, roi2 ... roiN
    // String[] channelNames = new String[NumChannels];
    // VariableType[] channelTypes = new VariableType[NumChannels];
    // DataSymbolType[] channelVFrapImageType = new DataSymbolType[NumChannels];
    // double[][][] pixData = new double[NumTimePoints][NumChannels][];
    // pixData[0][0] = firstPostBleach;
    // channelNames[0] = "firstPostBleach";
    // channelTypes[0] = VariableType.VOLUME;
    // channelVFrapImageType[0] = DataSymbolType.VFRAP_FIRST_POSTBLEACH;
    // pixData[0][1] = prebleachAvg;
    // channelNames[1] = "prebleachAverage";
    // channelTypes[1] = VariableType.VOLUME;
    // channelVFrapImageType[1] = DataSymbolType.VFRAP_PREBLEACH_AVG;
    // int index = 0;
    // for (ROI roi : rois){
    // short[] ushortPixels = roi.getPixelsXYZ();
    // double[] doublePixels = new double[ushortPixels.length];
    // for (int i = 0; i < ushortPixels.length; i++) {
    // doublePixels[i] = ((int)ushortPixels[i])&0xffff;
    // }
    // pixData[0][index+2] = doublePixels;
    // channelNames[index+2] = "roi_"+index;
    // channelTypes[index+2] = VariableType.VOLUME;
    // channelVFrapImageType[index+2] = DataSymbolType.VFRAP_ROI;
    // index++;
    // }
    // double[] times = new double[] { 0.0 };
    // 
    // FieldDataFileOperationSpec vfrapMiscFieldDataOpSpec = new FieldDataFileOperationSpec();
    // vfrapMiscFieldDataOpSpec.opType = FieldDataFileOperationSpec.FDOS_ADD;
    // vfrapMiscFieldDataOpSpec.cartesianMesh = cartesianMesh;
    // vfrapMiscFieldDataOpSpec.doubleSpecData =  pixData;
    // vfrapMiscFieldDataOpSpec.specEDI = null;
    // vfrapMiscFieldDataOpSpec.varNames = channelNames;
    // vfrapMiscFieldDataOpSpec.owner = dm.getUser();
    // vfrapMiscFieldDataOpSpec.times = times;
    // vfrapMiscFieldDataOpSpec.variableTypes = channelTypes;
    // vfrapMiscFieldDataOpSpec.origin = origin;
    // vfrapMiscFieldDataOpSpec.extent = extent;
    // vfrapMiscFieldDataOpSpec.isize = isize;
    // //  localWorkspace.getDataSetControllerImpl().fieldDataFileOperation(fdos);
    // 
    // //			String formattedDate = (String)hashTable.get("formattedDate");
    // //			String fieldDataName = initialFieldDataName + "_vfrapMisc_" + formattedDate;
    // String mixedFieldDataName = (String)hashTable.get("mixedFieldDataName");
    // ExternalDataIdentifier vfrapMisc = dm.saveFieldData(vfrapMiscFieldDataOpSpec, mixedFieldDataName);
    // 
    // hashTable.put("channelNames", channelNames);
    // hashTable.put("channelVFrapImageType", channelVFrapImageType);
    // hashTable.put("vfrapMisc", vfrapMisc);
    // }
    // };
    // create the data symbols for the images saved above and display them in the tree/table
    // taskArray[5] = new AsynchClientTask("Display Data Symbols", AsynchClientTask.TASKTYPE_SWING_BLOCKING) {
    // public void run(Hashtable<String, Object> hashTable) throws Exception {
    // 
    // // --- create the data symbols associated with the time series
    // String initialFieldDataName = (String)hashTable.get("initialFieldDataName");
    // String mixedFieldDataName = (String)hashTable.get("mixedFieldDataName");
    // String formattedDate = (String)hashTable.get("formattedDate");
    // ImageDataset imageDataset = (ImageDataset)hashTable.get("imageDataset");
    // ExternalDataIdentifier timeSeriesEDI = (ExternalDataIdentifier)hashTable.get("timeSeriesEDI");
    // 
    // for (double time : imageDataset.getImageTimeStamps()){
    // //	   			String fluorName = TokenMangler.fixTokenStrict("fluor_"+time+"_");
    // //				while (simulationContext.getDataContext().getDataSymbol(fluorName)!=null){
    // //					fluorName = TokenMangler.getNextEnumeratedToken(fluorName);
    // //	   			}
    // DecimalFormat df = new  DecimalFormat("0.##");
    // //	   			String fluorName = "fluor_" + df.format(time) + "_" + formattedDate;
    // String fluorName = "fluor_" + df.format(time) + "_" + initialFieldDataName;
    // //				FieldFunctionArguments fluorFFArgs = new FieldFunctionArguments(timeSeriesEDI.getName(), fluorName, new Expression(time), VariableType.VOLUME);
    // DataSymbol fluorDataSymbol = new FieldDataSymbol( fluorName, DataSymbolType.VFRAP_TIMEPOINT,
    // simulationContext.getDataContext(), VCUnitDefinition.UNIT_TBD,
    // timeSeriesEDI, fluorName, VariableType.VOLUME.getTypeName(), time);
    // simulationContext.getDataContext().addDataSymbol(fluorDataSymbol);
    // }
    // // --- create the vFrap-specific symbols (ROIs, first postbleach, prebleach average)
    // String[] channelNames = (String[])hashTable.get("channelNames");
    // DataSymbolType[] channelVFrapImageType = (DataSymbolType[])hashTable.get("channelVFrapImageType");
    // ExternalDataIdentifier vfrapMisc = (ExternalDataIdentifier)hashTable.get("vfrapMisc");
    // 
    // for (int i=0; i<channelNames.length; i++) {
    // String dataSymbolID = channelNames[i] + "_" + mixedFieldDataName;
    // //				while (simulationContext.getDataContext().getDataSymbol(dataSymbolID)!=null){
    // //					dataSymbolID = TokenMangler.getNextEnumeratedToken(dataSymbolID);
    // //				}
    // //				FieldFunctionArguments prebleachFFArgs = new FieldFunctionArguments(vfrapMisc.getName(), channelNames[i], new Expression(0.0), VariableType.VOLUME);
    // //				DataSymbol dataSymbol = new FieldDataSymbol(channelNames[i], channelVFrapImageType[i],
    // //				DataSymbol dataSymbol = new FieldDataSymbol(dataSymbolID + "_" + formattedDate, channelVFrapImageType[i],
    // DataSymbol dataSymbol = new FieldDataSymbol(dataSymbolID, channelVFrapImageType[i],
    // simulationContext.getDataContext(), VCUnitDefinition.UNIT_TBD,
    // vfrapMisc, channelNames[i], VariableType.VOLUME.getTypeName(), 0D);
    // simulationContext.getDataContext().addDataSymbol(dataSymbol);
    // }
    // }
    // };
    Hashtable<String, Object> hash = new Hashtable<String, Object>();
    ClientTaskDispatcher.dispatch(this, hash, taskArray, false, true, null);
}

Example 28 with ExternalDataIdentifier

use of org.vcell.util.document.ExternalDataIdentifier in project vcell by virtualcell.

the class PDEDataViewer method setPdeDataContext.

public void setPdeDataContext(ClientPDEDataContext pdeDataContext) {
    if (pdeDataContext != null && pdeDataContext.getVCDataIdentifier() instanceof ExternalDataIdentifier) {
        // getJTabbedPane1().removeTabAt(getJTabbedPane1().indexOfTab(POST_PROCESS_IMAGE_TABNAME));
        // getJTabbedPane1().removeTabAt(getJTabbedPane1().indexOfTab(POST_PROCESS_STATS_TABNAME));
        getJTabbedPane1().setEnabledAt(getJTabbedPane1().indexOfTab(POST_PROCESS_IMAGE_TABNAME), false);
        getJTabbedPane1().setEnabledAt(getJTabbedPane1().indexOfTab(POST_PROCESS_STATS_TABNAME), false);
    }
    getPDEDataContextPanel1().getdisplayAdapterServicePanel1().enableAutoAllTimes(true && !(pdeDataContext instanceof PostProcessDataPDEDataContext));
    PDEDataContext oldValue = fieldPdeDataContext;
    String setVarName = null;
    Integer setTimePoint = null;
    if (oldValue != null) {
        setVarName = oldValue.getVariableName();
        setTimePoint = getPDEPlotControlPanel1().getTimeSliderValue();
        try {
            if (pdeDataContext != null) {
                pdeDataContext.setVariableNameAndTime(setVarName, pdeDataContext.getTimePoints()[setTimePoint]);
            }
        } catch (Exception e) {
            e.printStackTrace();
            setVarName = null;
            setTimePoint = null;
        }
        oldValue.removePropertyChangeListener(ivjEventHandler);
    }
    fieldPdeDataContext = pdeDataContext;
    if (getPdeDataContext() != null && (setVarName == null || setTimePoint == null)) {
        setVarName = getPdeDataContext().getVariableNames()[0];
        setTimePoint = 0;
        try {
            pdeDataContext.setVariableNameAndTime(setVarName, pdeDataContext.getTimePoints()[setTimePoint]);
        } catch (Exception e2) {
            e2.printStackTrace();
            DialogUtils.showErrorDialog(this, "Couldn't set time and variable on pdeDataContext");
            return;
        }
    }
    if (getPdeDataContext() != null) {
        getPdeDataContext().removePropertyChangeListener(ivjEventHandler);
        getPdeDataContext().addPropertyChangeListener(ivjEventHandler);
        try {
            getPDEPlotControlPanel1().removePropertyChangeListener(ivjEventHandler);
            try {
                getPDEPlotControlPanel1().setup(((ClientPDEDataContext) getPdeDataContext()).getDataManager().getOutputContext().getOutputFunctions(), getPdeDataContext().getDataIdentifiers(), getPdeDataContext().getTimePoints(), setVarName, setTimePoint);
            } catch (Exception e) {
                e.printStackTrace();
                DialogUtils.showErrorDialog(this, "Couldn't setup PDEPlotControlPanel, " + e.getMessage());
                return;
            }
        } finally {
            getPDEPlotControlPanel1().addPropertyChangeListener(ivjEventHandler);
        }
    }
    bSkipSurfaceCalc = true;
    firePropertyChange(PDEDataContext.PROP_PDE_DATA_CONTEXT, null, pdeDataContext);
    bSkipSurfaceCalc = false;
    if (ivjJTabbedPane1.getTitleAt(ivjJTabbedPane1.getSelectedIndex()).equals(POST_PROCESS_STATS_TABNAME)) {
        dataProcessingResultsPanel.update(getPdeDataContext());
    }
    postProcessPdeDataViewerPanel.setParentPDEDataContext((ClientPDEDataContext) getPdeDataContext());
    if (ivjJTabbedPane1.getTitleAt(ivjJTabbedPane1.getSelectedIndex()).equals(POST_PROCESS_IMAGE_TABNAME)) {
        postProcessPdeDataViewerPanel.update();
    }
}

Example 29 with ExternalDataIdentifier

use of org.vcell.util.document.ExternalDataIdentifier in project vcell by virtualcell.

the class PDEDataViewer method calcAutoAllTimes.

private void calcAutoAllTimes() throws Exception {
    HashSet<String> stateVarNames = null;
    Variable theVariable = null;
    boolean bStateVar = true;
    boolean isFieldData = getPdeDataContext().getVCDataIdentifier() instanceof ExternalDataIdentifier || getPdeDataContext().getVCDataIdentifier() instanceof MergedDataInfo;
    if (isFieldData) {
        // fielddata
        DataIdentifier[] dataids = getPdeDataContext().getDataIdentifiers();
        stateVarNames = new HashSet<>();
        for (int i = 0; i < dataids.length; i++) {
            if (!dataids[i].isFunction()) {
                stateVarNames.add(dataids[i].getName());
            }
        // System.out.println("name:'"+dataids[i].getName()+"' type:"+dataids[i].getVariableType()+" func:"+dataids[i].isFunction());
        }
        bStateVar = !getPdeDataContext().getDataIdentifier().isFunction();
        if (bStateVar) {
            theVariable = new VolVariable(getPdeDataContext().getDataIdentifier().getName(), getPdeDataContext().getDataIdentifier().getDomain());
        } else {
            AnnotatedFunction[] funcs = getPdeDataContext().getFunctions();
            for (int i = 0; i < funcs.length; i++) {
                if (funcs[i].getName().equals(getPdeDataContext().getDataIdentifier().getName())) {
                    theVariable = funcs[i];
                    break;
                }
            }
        }
    } else {
        stateVarNames = getSimulation().getMathDescription().getStateVariableNames();
        theVariable = getSimulation().getMathDescription().getVariable(getPdeDataContext().getVariableName());
        if (theVariable == null) {
            theVariable = ((ClientPDEDataContext) getPdeDataContext()).getDataManager().getOutputContext().getOutputFunction(getPdeDataContext().getVariableName());
        }
        if (theVariable == null) {
            DataProcessingOutputInfo dataProcessingOutputInfo = DataProcessingResultsPanel.getDataProcessingOutputInfo(getPdeDataContext());
            if (dataProcessingOutputInfo != null && Arrays.asList(dataProcessingOutputInfo.getVariableNames()).contains(getPdeDataContext().getVariableName())) {
                // PostProcess Variable
                return;
            }
        }
        bStateVar = stateVarNames.contains(getPdeDataContext().getVariableName());
    }
    if (theVariable == null) {
        throw new Exception("Unexpected Alltimes... selected variable '" + getPdeDataContext().getVariableName() + "' is not stateVariable or OutputFunction");
    }
    if (getPDEDataContextPanel1().getdisplayAdapterService1().getAllTimes()) {
        // min-max over all timepoints (allTimes)
        if (theVariable.isConstant()) {
            getPDEDataContextPanel1().getdisplayAdapterServicePanel1().changeAllTimesButtonText(DisplayAdapterServicePanel.ALL_TIMES__STATE_TEXT);
            double constVal = theVariable.getExpression().evaluateConstant();
            getPDEDataContextPanel1().setFunctionStatisticsRange(new Range(constVal, constVal));
        } else if (bStateVar) {
            getPDEDataContextPanel1().getdisplayAdapterServicePanel1().changeAllTimesButtonText(DisplayAdapterServicePanel.ALL_TIMES__STATE_TEXT);
            ArrayList<VarStatistics> varStatsArr = calcVarStat(getPdeDataContext(), new String[] { theVariable.getName() });
            if (errorAutoAllTimes(varStatsArr != null, (varStatsArr == null ? null : varStatsArr.size() > 0), isFieldData)) {
                // no postprocessinfo
                return;
            }
            FunctionStatistics functionStatistics = new FunctionStatistics(varStatsArr.get(0).minValuesOverTime, varStatsArr.get(0).maxValuesOverTime);
            getPDEDataContextPanel1().setFunctionStatisticsRange(new Range(functionStatistics.getMinOverTime(), functionStatistics.getMaxOverTime()));
        } else if (theVariable instanceof Function) {
            getPDEDataContextPanel1().getdisplayAdapterServicePanel1().changeAllTimesButtonText(DisplayAdapterServicePanel.ALL_TIMES__APPROX_TEXT);
            Function flattened = MathDescription.getFlattenedFunctions(SimulationSymbolTable.createMathSymbolTableFactory(), getSimulation().getMathDescription(), new String[] { theVariable.getName() })[0];
            if (flattened == null) {
                flattened = (Function) theVariable;
            }
            ArrayList<VarStatistics> varStatsArr = calcVarStat(getPdeDataContext(), stateVarNames.toArray(new String[0]));
            if (errorAutoAllTimes(varStatsArr != null, (varStatsArr == null ? null : varStatsArr.size() > 0), isFieldData)) {
                // check for no postprocessinfo
                return;
            }
            if (varStatsArr.size() == stateVarNames.size()) {
                if (getSimulation().getMeshSpecification().getGeometry().getGeometrySurfaceDescription().getRegionImage() == null) {
                    getSimulation().getMeshSpecification().getGeometry().getGeometrySurfaceDescription().updateAll();
                }
                FunctionStatistics functionStatistics = FunctionRangeGenerator.getFunctionStatistics(flattened.getExpression(), varStatsArr.toArray(new VarStatistics[0]), getPdeDataContext().getTimePoints(), getPdeDataContext().getCartesianMesh(), calcInDomainBitSet(), getPdeDataContext().getDataIdentifier().getVariableType());
                getPDEDataContextPanel1().setFunctionStatisticsRange(new Range(functionStatistics.getMinOverTime(), functionStatistics.getMaxOverTime()));
            } else {
                throw new Exception("Unexpectede AllTimes... calculated state var stats size != mathdescr state var size");
            }
        } else {
            throw new Exception("Unexpected AllTimes... not constant, stateVar or function");
        }
    } else {
        // min-max at each timepoint (currTime)
        if (!(theVariable instanceof Function)) {
            getPDEDataContextPanel1().getdisplayAdapterServicePanel1().changeAllTimesButtonText(DisplayAdapterServicePanel.ALL_TIMES__STATE_TEXT);
        } else {
            getPDEDataContextPanel1().getdisplayAdapterServicePanel1().changeAllTimesButtonText(DisplayAdapterServicePanel.ALL_TIMES__APPROX_TEXT);
        }
        getPDEDataContextPanel1().setFunctionStatisticsRange(null);
    }
}

Example 30 with ExternalDataIdentifier

use of org.vcell.util.document.ExternalDataIdentifier in project vcell by virtualcell.

the class Xmlproducer method getXML.

private Element getXML(FieldDataSymbol fds, ModelUnitSystem modelUnitSystem) {
    Element fieldDataSymbolElement = new Element(XMLTags.FieldDataSymbolTag);
    fieldDataSymbolElement.setAttribute(XMLTags.DataSymbolNameTag, fds.getName());
    fieldDataSymbolElement.setAttribute(XMLTags.DataSymbolTypeTag, fds.getDataSymbolType().getDatabaseName());
    // DataContext is runtime only
    fieldDataSymbolElement.setAttribute(XMLTags.VCUnitDefinitionAttrTag, fds.getUnitDefinition().getSymbol());
    Element dataSetIDElement = new Element(XMLTags.ExternalDataIdentifierTag);
    ExternalDataIdentifier edi = fds.getExternalDataIdentifier();
    dataSetIDElement.setAttribute(XMLTags.NameAttrTag, edi.getName());
    dataSetIDElement.setAttribute(XMLTags.KeyValueAttrTag, edi.getKey().toString());
    dataSetIDElement.setAttribute(XMLTags.OwnerNameAttrTag, edi.getOwner().getName());
    dataSetIDElement.setAttribute(XMLTags.OwnerKeyAttrTag, edi.getOwner().getID().toString());
    fieldDataSymbolElement.addContent(dataSetIDElement);
    fieldDataSymbolElement.setAttribute(XMLTags.FieldItemNameTag, fds.getFieldDataVarName());
    fieldDataSymbolElement.setAttribute(XMLTags.FieldItemTypeTag, fds.getFieldDataVarType());
    fieldDataSymbolElement.setAttribute(XMLTags.FieldItemTimeTag, Double.toString(fds.getFieldDataVarTime()));
    return fieldDataSymbolElement;
}