Examples with DataIdentifier cbit.vcell.simdata.DataIdentifier used on opensource projects

Example 26 with DataIdentifier

use of cbit.vcell.simdata.DataIdentifier in project vcell by virtualcell.

the class KymographPanel method initDataManagerVariable.

/**
 * Insert the method's description here.
 * Creation date: (12/14/2004 9:47:38 AM)
 * @param timeSeries double[][]
 * @param distances double[]
 */
private void initDataManagerVariable() /*final DataIdentifier dataIdentifer,*/
/*boolean bFromGUI*/
{
    final DataIdentifier dataIdentifer = (DataIdentifier) getVarNamesJComboBox().getSelectedItem();
    // Thread.dumpStack();
    if ((initVariableTimer = ClientTaskDispatcher.getBlockingTimer(this, multiTimePlotHelper.getPdeDatacontext(), null, initVariableTimer, new ActionListener() {

        @Override
        public void actionPerformed(ActionEvent e) {
            initDataManagerVariable();
        }
    }, "KymographPanel get '" + dataIdentifer.getName() + "'")) != null) {
        return;
    }
    // Create SymbolTableEntry for Copy/Paste functionality
    currentSymbolTablEntry = (symbolTable != null ? symbolTable.getEntry(dataIdentifer.getName()) : null);
    String taskName = "Retrieving data for variable '" + dataIdentifer.getName() + "'";
    AsynchClientTask task1 = new AsynchClientTask(taskName, AsynchClientTask.TASKTYPE_NONSWING_BLOCKING) {

        public void run(final Hashtable<String, Object> hashTable) throws Exception {
            double[] timeValues = multiTimePlotHelper.getPdeDatacontext().getTimePoints();
            final TimeSeriesJobSpec timeSeriesJobSpec = new TimeSeriesJobSpec(new String[] { dataIdentifer.getName() }, new int[][] { dataManagerIndices }, (crossingMembraneIndices != null ? new int[][] { crossingMembraneIndices } : null), resampleStartTimeOrig, resampleStepOrig, timeValues[timeValues.length - 1], VCDataJobID.createVCDataJobID(multiTimePlotHelper.getUser(), true));
            hashTable.put(PDEDataViewer.StringKey_timeSeriesJobSpec, timeSeriesJobSpec);
        }
    };
    // new TimeSeriesDataRetrievalTask(title, PDEDataViewer.this, PDEDataViewer.this.getPdeDataContext());//timeSeriesDataRetrievalTask;
    AsynchClientTask task2 = new PDEDataViewer.TimeSeriesDataRetrievalTask("Retrieving Data", multiTimePlotHelper, multiTimePlotHelper.getPdeDatacontext());
    AsynchClientTask task3 = new AsynchClientTask("Showing kymograph", AsynchClientTask.TASKTYPE_SWING_BLOCKING, false, false) {

        public void run(Hashtable<String, Object> hashTable) throws Exception {
            Throwable timeSeriesJobFailed = (Throwable) hashTable.get(PDEDataViewer.StringKey_timeSeriesJobException);
            if (timeSeriesJobFailed == null) {
                timeSeriesJobFailed = (Throwable) hashTable.get(ClientTaskDispatcher.TASK_ABORTED_BY_USER);
            }
            if (failMethod(timeSeriesJobFailed, dataIdentifer)) {
                return;
            }
            TSJobResultsNoStats tsJobResultsNoStats = (TSJobResultsNoStats) hashTable.get(PDEDataViewer.StringKey_timeSeriesJobResults);
            currentDataIdentifier = dataIdentifer;
            final double[][] timeSeries = tsJobResultsNoStats.getTimesAndValuesForVariable(currentDataIdentifier.getName());
            try {
                initStandAloneTimeSeries_private(timeSeries, dataManagerAccumDistances);
            } catch (Exception e) {
                failMethod(e, dataIdentifer);
                throw e;
            }
            if (isInit) {
                // set crosshair to init time
                // resampleStartTimeOrig;
                double initTime = initialLineScanTime;
                isInit = false;
                int closestTimeIndex = 0;
                double closestDiff = Double.MAX_VALUE;
                for (int i = 0; i < currentTimes.length; i += 1) {
                    double diff = Math.abs(initTime - currentTimes[i]);
                    if (diff < closestDiff) {
                        closestTimeIndex = i;
                        closestDiff = diff;
                    }
                }
                currentSelectionImg = new Point(0, closestTimeIndex);
                currentSelectionUnit = new Point2D.Double(0, (double) closestTimeIndex / (double) (currentTimes.length - 1));
                configurePlotData((int) currentSelectionImg.getX(), (int) currentSelectionImg.getY());
            // ChildWindowManager childWindowManager = ChildWindowManager.findChildWindowManager(pdeDataViewer);
            // //				final ChildWindow childWindow = childWindowManager.addChildWindow(new javax.swing.JPanel(),this,title);
            // final ChildWindow childWindow = childWindowManager.addChildWindow(KymographPanel.this,KymographPanel.this,title);
            // childWindow.setIsCenteredOnParent();
            // childWindow.pack();
            // childWindow.show();
            // Timer timer = new Timer(1000,new ActionListener() {
            // 
            // @Override
            // public void actionPerformed(ActionEvent e) {
            // childWindow.toFront();
            // }
            // });
            // System.out.println("Kymograph panel ChildWindow requesting focus.  Answer is: "+childWindow.requestFocusInWindow());
            // zoomToFill();
            } else {
                getImagePaneScroller1().zooming(new ZoomEvent(getimagePaneView1(), 0, 0));
            }
        }
    };
    AsynchClientTask[] tasks = (task2 == null ? new AsynchClientTask[] { task1, task3 } : new AsynchClientTask[] { task1, task2, task3 });
    ClientTaskDispatcher.dispatch(KymographPanel.this, new Hashtable<String, Object>(), tasks, false, true, true, null, false);
// if(bFromGUI){
// ClientTaskDispatcher.dispatch(KymographPanel.this,  new Hashtable<String, Object>(), tasks, false, true, true, null, false);
// System.out.println("Waiting here");
// }else{
// multiTimePlotHelper.addExtraTasks(tasks);
// }
}

Example 27 with DataIdentifier

use of cbit.vcell.simdata.DataIdentifier in project vcell by virtualcell.

the class SimResultsViewer method updateScanParamChoices.

private void updateScanParamChoices(final String message, ListReset listReset) {
    if ((paramScanChoiceTimer = ClientTaskDispatcher.getBlockingTimer(this, null, null, paramScanChoiceTimer, new ActionListener() {

        @Override
        public void actionPerformed(ActionEvent e2) {
            updateScanParamChoices(message, listReset);
        }
    }, message)) != null) {
        return;
    }
    int selectedJobIndex = getSelectedParamScanJobIndex();
    // update viewer
    if (selectedJobIndex == -1) {
        if (isODEData) {
            if (listReset != null && odeDataViewer != null && odeDataViewer.getVcDataIdentifier() != null) {
                listReset.reset(odeDataViewer.getVcDataIdentifier());
            } else {
                odeDataViewer.setOdeSolverResultSet(null);
            }
        } else {
            if (listReset != null && pdeDataViewer != null && pdeDataViewer.getPdeDataContext() != null && pdeDataViewer.getPdeDataContext().getVCDataIdentifier() != null) {
                listReset.reset(pdeDataViewer.getPdeDataContext().getVCDataIdentifier());
            } else {
                pdeDataViewer.setPdeDataContext(null);
            }
        }
        return;
    }
    final VCSimulationDataIdentifier vcdid = new VCSimulationDataIdentifier(getSimulation().getSimulationInfo().getAuthoritativeVCSimulationIdentifier(), selectedJobIndex);
    if (isODEData) {
        AsynchClientTask task1 = new AsynchClientTask("get ode results", AsynchClientTask.TASKTYPE_NONSWING_BLOCKING) {

            @Override
            public void run(Hashtable<String, Object> hashTable) throws Exception {
                ODEDataManager odeDatamanager = ((ODEDataManager) dataManager).createNewODEDataManager(vcdid);
                hashTable.put("odeDatamanager", odeDatamanager);
            }
        };
        AsynchClientTask task2 = new AsynchClientTask("show results", AsynchClientTask.TASKTYPE_SWING_BLOCKING, false, false) {

            @Override
            public void run(Hashtable<String, Object> hashTable) throws Exception {
                if (hashTable.get(ClientTaskDispatcher.TASK_ABORTED_BY_ERROR) == null) {
                    ODEDataManager odeDatamanager = (ODEDataManager) hashTable.get("odeDatamanager");
                    odeDataViewer.setOdeSolverResultSet(odeDatamanager.getODESolverResultSet());
                    odeDataViewer.setVcDataIdentifier(vcdid);
                } else {
                    odeDataViewer.setOdeSolverResultSet(null);
                }
            }
        };
        ClientTaskDispatcher.dispatch(this, new Hashtable<String, Object>(), new AsynchClientTask[] { task1, task2 });
    } else {
        AsynchClientTask task1 = new AsynchClientTask("get pde results", AsynchClientTask.TASKTYPE_NONSWING_BLOCKING) {

            @Override
            public void run(Hashtable<String, Object> hashTable) throws Exception {
                PDEDataManager pdeDatamanager = ((PDEDataManager) dataManager).createNewPDEDataManager(vcdid, null);
                PDEDataContext newPDEDC = pdeDatamanager.getPDEDataContext();
                PDEDataContext oldPDEDC = pdeDataViewer.getPdeDataContext();
                hashTable.put("newPDEDC", newPDEDC);
                if (oldPDEDC != null && oldPDEDC.getTimePoints().length <= newPDEDC.getTimePoints().length) {
                    DataIdentifier setDid = (newPDEDC.getDataIdentifier() == null ? newPDEDC.getDataIdentifiers()[0] : newPDEDC.getDataIdentifier());
                    if (Arrays.asList(newPDEDC.getDataIdentifiers()).contains(oldPDEDC.getDataIdentifier())) {
                        setDid = oldPDEDC.getDataIdentifier();
                        newPDEDC.setVariableAndTime(setDid, newPDEDC.getTimePoints()[BeanUtils.firstIndexOf(oldPDEDC.getTimePoints(), oldPDEDC.getTimePoint())]);
                    }
                }
            }
        };
        AsynchClientTask task2 = new AsynchClientTask("show results", AsynchClientTask.TASKTYPE_SWING_BLOCKING, false, false) {

            @Override
            public void run(Hashtable<String, Object> hashTable) throws Exception {
                if (hashTable.get(ClientTaskDispatcher.TASK_ABORTED_BY_ERROR) == null) {
                    ClientPDEDataContext newPDEDC = (ClientPDEDataContext) hashTable.get("newPDEDC");
                    pdeDataViewer.setPdeDataContext(newPDEDC);
                    pdeDataViewer.setSimNameSimDataID(new ExportSpecs.SimNameSimDataID(getSimulation().getName(), getSimulation().getSimulationInfo().getAuthoritativeVCSimulationIdentifier(), SimResultsViewer.getParamScanInfo(getSimulation(), vcdid.getJobIndex())));
                } else {
                    if (listReset != null && pdeDataViewer != null && pdeDataViewer.getPdeDataContext() != null && pdeDataViewer.getPdeDataContext().getVCDataIdentifier() != null) {
                        listReset.reset(pdeDataViewer.getPdeDataContext().getVCDataIdentifier());
                    } else {
                        pdeDataViewer.setPdeDataContext(null);
                        pdeDataViewer.setSimNameSimDataID(null);
                    }
                }
            }
        };
        // AsynchClientTask refreshTask = new AsynchClientTask("",AsynchClientTask.TASKTYPE_NONSWING_BLOCKING) {
        // @Override
        // public void run(Hashtable<String, Object> hashTable) throws Exception {
        // ((ArrayList<AsynchClientTask>)hashTable.get(ClientTaskDispatcher.INTERMEDIATE_TASKS)).addAll(Arrays.asList(pdeDataViewer.getRefreshTasks()));
        // }
        // };
        ClientTaskDispatcher.dispatch(this, new Hashtable<String, Object>(), new AsynchClientTask[] { task1, task2 /*,refreshTask*/
        });
    }
}

Example 28 with DataIdentifier

use of cbit.vcell.simdata.DataIdentifier in project vcell by virtualcell.

the class MathTestingUtilities method comparePDEResults.

/**
 * Insert the method's description here.
 * Creation date: (8/20/2003 12:58:10 PM)
 */
public static SimulationComparisonSummary comparePDEResults(SimulationSymbolTable testSimSymbolTable, PDEDataManager testDataManager, SimulationSymbolTable refSimSymbolTable, PDEDataManager refDataManager, String[] varsToCompare, double absErrorThreshold, double relErrorThreshold, VCDocument refDocument, DataInfoProvider refDataInfoProvider, VCDocument testDocument, DataInfoProvider testDataInfoProvider) throws DataAccessException, ExpressionException {
    java.util.Hashtable<String, DataErrorSummary> tempVarHash = new java.util.Hashtable<String, DataErrorSummary>();
    boolean bTimesEqual = true;
    double[] testTimeArray = testDataManager.getDataSetTimes();
    double[] refTimeArray = refDataManager.getDataSetTimes();
    if (testTimeArray.length != refTimeArray.length) {
        bTimesEqual = false;
    // throw new RuntimeException("Data times for reference and test simulations don't match, cannot compare the two simulations!");
    } else {
        for (int i = 0; i < testTimeArray.length; i++) {
            if (testTimeArray[i] != refTimeArray[i]) {
                bTimesEqual = false;
            }
        }
    }
    // if (!checkSimVars(testSim, refSim)) {
    // //String errorS = "TestVars - ";
    // Variable[] testVars = testSim.getVariables();
    // //for(int i =0;i<vars.length;i+= 1){
    // //errorS+= vars[i].getName()+" ";
    // //}
    // //errorS+=" <<>> RefVars - ";
    // Variable[] refVars = refSim.getVariables();
    // //for(int i =0;i<vars.length;i+= 1){
    // //errorS+= vars[i].getName()+" ";
    // //}
    // throw new RuntimeException(
    // "VarNotMatch testLength="+(testVars != null?testVars.length+"":"null")+" refLength="+(refVars != null?refVars.length+"":"null"));
    // }
    CartesianMesh testMesh = testDataManager.getMesh();
    MathDescription testMathDesc = testSimSymbolTable.getSimulation().getMathDescription();
    // Variable[] refVars = refSim.getVariables();
    MathDescription refMathDesc = refSimSymbolTable.getSimulation().getMathDescription();
    CartesianMesh refMesh = refDataManager.getMesh();
    int[] membraneIndexMapping = null;
    // Get volumeSubdomains from mathDesc/mesh and store in lookupTable for testSimulation
    int testNumVol = testMesh.getSizeX() * testMesh.getSizeY() * testMesh.getSizeZ();
    CompartmentSubDomain[] testVolSubDomainLookup = new CompartmentSubDomain[testNumVol];
    for (int i = 0; i < testNumVol; i++) {
        int subVolumeIndex = testMesh.getSubVolumeFromVolumeIndex(i);
        SubVolume subVolume = testMathDesc.getGeometry().getGeometrySpec().getSubVolume(subVolumeIndex);
        CompartmentSubDomain compSubDomain = testMathDesc.getCompartmentSubDomain(subVolume.getName());
        testVolSubDomainLookup[i] = compSubDomain;
    }
    // Get membraneSubdomains from mathDesc/mesh and store in lookupTable for testSimulation
    int testNumMem = testMesh.getMembraneElements().length;
    MembraneSubDomain[] testMemSubDomainLookup = new MembraneSubDomain[testNumMem];
    for (int i = 0; i < testNumMem; i++) {
        int insideVolIndex = testMesh.getMembraneElements()[i].getInsideVolumeIndex();
        int outsideVolIndex = testMesh.getMembraneElements()[i].getOutsideVolumeIndex();
        MembraneSubDomain memSubDomain = testMathDesc.getMembraneSubDomain(testVolSubDomainLookup[insideVolIndex], testVolSubDomainLookup[outsideVolIndex]);
        testMemSubDomainLookup[i] = memSubDomain;
    }
    // Get volumeSubdomains from mathDesc/mesh and store in lookupTable for refSimulation
    int refNumVol = refMesh.getSizeX() * refMesh.getSizeY() * refMesh.getSizeZ();
    CompartmentSubDomain[] refVolSubDomainLookup = new CompartmentSubDomain[refNumVol];
    for (int i = 0; i < refNumVol; i++) {
        int subVolumeIndex = refMesh.getSubVolumeFromVolumeIndex(i);
        SubVolume subVolume = refMathDesc.getGeometry().getGeometrySpec().getSubVolume(subVolumeIndex);
        CompartmentSubDomain compSubDomain = refMathDesc.getCompartmentSubDomain(subVolume.getName());
        refVolSubDomainLookup[i] = compSubDomain;
    }
    // Get membraneSubdomains from mathDesc/mesh and store in lookupTable for refSimulation
    int refNumMem = refMesh.getMembraneElements().length;
    MembraneSubDomain[] refMemSubDomainLookup = new MembraneSubDomain[refNumMem];
    for (int i = 0; i < refNumMem; i++) {
        int insideVolIndex = refMesh.getMembraneElements()[i].getInsideVolumeIndex();
        int outsideVolIndex = refMesh.getMembraneElements()[i].getOutsideVolumeIndex();
        MembraneSubDomain memSubDomain = refMathDesc.getMembraneSubDomain(refVolSubDomainLookup[insideVolIndex], refVolSubDomainLookup[outsideVolIndex]);
        refMemSubDomainLookup[i] = memSubDomain;
    }
    SimulationComparisonSummary simComparisonSummary = new SimulationComparisonSummary();
    String hashKey = new String("");
    DataErrorSummary tempVar = null;
    DataIdentifier[] refDataIDs = refDataManager.getDataIdentifiers();
    // for each var, do the following :
    for (int i = 0; i < varsToCompare.length; i++) {
        DataIdentifier refDataID = null;
        for (int j = 0; j < refDataIDs.length; j++) {
            if (refDataIDs[j].getName().equals(varsToCompare[i])) {
                refDataID = refDataIDs[j];
                break;
            }
        }
        // 
        // Find REFERENCE variable
        // 
        Variable refVar = getSimVar(refSimSymbolTable, varsToCompare[i]);
        if (refVar == null) {
            // Should only happen if TEST sims were generated 'post-domains' and REFERENCE sims were generated 'pre-domains'
            if (refDataID != null) {
                throw new RuntimeException("Unexpected reference condition: '" + varsToCompare[i] + "' not found in symboltable but was found in dataidentifiers");
            }
            if (testDocument instanceof BioModel) {
                // Only BioModels need to be checked
                // Look in TEST for a speciescontext with matching species name
                System.out.println("ReferenceVariable: using alternate method to find '" + varsToCompare[i] + "'");
                BioModel refBioModel = (BioModel) refDocument;
                BioModel testBioModel = (BioModel) testDocument;
                SpeciesContext testSpeciesContext = testBioModel.getModel().getSpeciesContext(varsToCompare[i]);
                if (testSpeciesContext != null) {
                    refVar = refSimSymbolTable.getVariable(testSpeciesContext.getSpecies().getCommonName());
                    for (int j = 0; j < refDataIDs.length; j++) {
                        if (refDataIDs[j].getName().equals(testSpeciesContext.getSpecies().getCommonName())) {
                            refDataID = refDataIDs[j];
                            break;
                        }
                    }
                }
            }
            if (refVar == null || refDataID == null) {
                Simulation refSim = refSimSymbolTable.getSimulation();
                throw new RuntimeException("The variable " + varsToCompare[i] + " was not found in Simulation (" + refSim.getName() + " " + refSim.getVersion().getDate() + ")\n");
            }
        }
        // 
        // Find TEST variable (assumed to have sims generated with a software version later than REFERENCE)
        // 
        Variable testVar = getSimVar(testSimSymbolTable, varsToCompare[i]);
        if (testVar == null) {
            // Should only happen if TEST sims were generated 'post-domains' and REFERENCE sims were generated 'pre-domains'
            System.out.println("TestVariable: using alternate method to find '" + varsToCompare[i] + "'");
            BioModel testBioModel = (BioModel) testDocument;
            SpeciesContext[] speciesContexts = testBioModel.getModel().getSpeciesContexts();
            boolean bSkip = false;
            for (int j = 0; j < speciesContexts.length; j++) {
                if (speciesContexts[j].getSpecies().getCommonName().equals(varsToCompare[i])) {
                    testVar = testSimSymbolTable.getVariable(speciesContexts[j].getName());
                    if (testVar == null) {
                        throw new RuntimeException("Speciescontext name '" + speciesContexts[j].getName() + "' not found in testsimsymboltable");
                    }
                    // If we got here it means at least one matching speciescontext was found in TEST with
                    // a species name matching varsToCompare[i].  We can skip because the matching speciesconetext
                    // will be used to do a comparison at some point.
                    bSkip = true;
                    break;
                }
            }
            if (bSkip) {
                // these are tested already using full simcontext names
                System.out.println("Skipping '" + varsToCompare[i] + "' as lookup in testSimSymbolTable");
                continue;
            }
            Simulation refSim = refSimSymbolTable.getSimulation();
            throw new RuntimeException("The variable " + varsToCompare[i] + " was not found in Simulation (" + refSim.getName() + " " + refSim.getVersion().getDate() + ")\n");
        }
        // for each time in timeArray. ('t' is used to index the testTimeArray, for interpolation purposes.)
        int t = 0;
        for (int j = 0; j < refTimeArray.length; j++) {
            // get data block from varName, data from datablock
            SimDataBlock refSimDataBlock = refDataManager.getSimDataBlock(refVar.getName(), refTimeArray[j]);
            double[] refData = refSimDataBlock.getData();
            double[] resampledTestData = null;
            if (bTimesEqual) {
                // If time arrays for both sims are equal, no need to resample/interpolate, just obtain the datablock from dataManager
                SimDataBlock testSimDataBlock = testDataManager.getSimDataBlock(testVar.getName(), testTimeArray[j]);
                resampledTestData = testSimDataBlock.getData();
            } else {
                // Time resampling (interpolation) needed.
                while ((t < testTimeArray.length - 2) && (refTimeArray[j] >= testTimeArray[t + 1])) {
                    t++;
                }
                SimDataBlock testSimDataBlock_1 = testDataManager.getSimDataBlock(testVar.getName(), testTimeArray[t]);
                double[] testData_1 = testSimDataBlock_1.getData();
                SimDataBlock testSimDataBlock_2 = testDataManager.getSimDataBlock(testVar.getName(), testTimeArray[t + 1]);
                double[] testData_2 = testSimDataBlock_2.getData();
                resampledTestData = new double[testData_1.length];
                // 
                for (int m = 0; m < testData_1.length; m++) {
                    resampledTestData[m] = testData_1[m] + (testData_2[m] - testData_1[m]) * (refTimeArray[j] - testTimeArray[t]) / (testTimeArray[t + 1] - testTimeArray[t]);
                }
            }
            // Spatial resampling (interpolation) ...
            double[] spaceResampledData = new double[refData.length];
            if (!testMathDesc.getGeometry().getExtent().compareEqual(refMathDesc.getGeometry().getExtent()) || !testMathDesc.getGeometry().getOrigin().compareEqual(refMathDesc.getGeometry().getOrigin())) {
                throw new RuntimeException("Different origins and/or extents for the 2 geometries. Cannot compare the 2 simulations");
            }
            if (testMesh.getSizeX() != refMesh.getSizeX() || testMesh.getSizeY() != refMesh.getSizeY() || testMesh.getSizeZ() != refMesh.getSizeZ()) {
                if (testVar instanceof VolVariable) {
                    if (testMathDesc.getGeometry().getDimension() == 1 && refMathDesc.getGeometry().getDimension() == 1) {
                        spaceResampledData = resample1DSpatial(resampledTestData, testMesh, refMesh);
                    } else if (testMathDesc.getGeometry().getDimension() == 2 && refMathDesc.getGeometry().getDimension() == 2) {
                        spaceResampledData = resample2DSpatial(resampledTestData, testMesh, refMesh);
                    } else if (testMathDesc.getGeometry().getDimension() == 3 && refMathDesc.getGeometry().getDimension() == 3) {
                        spaceResampledData = resample3DSpatial(resampledTestData, testMesh, refMesh);
                    } else {
                        throw new RuntimeException("Comparison of 2 simulations with different geometry dimensions are not handled at this time!");
                    }
                } else {
                    throw new RuntimeException("spatial resampling for variable type: " + testVar.getClass().getName() + " not supported");
                }
            } else {
                // no space resampling required
                if (testVar instanceof MemVariable) {
                    // 
                    if (membraneIndexMapping == null) {
                        membraneIndexMapping = testMesh.getMembraneIndexMapping(refMesh);
                    }
                    spaceResampledData = new double[resampledTestData.length];
                    for (int k = 0; k < resampledTestData.length; k++) {
                        spaceResampledData[k] = resampledTestData[membraneIndexMapping[k]];
                    }
                } else {
                    // 
                    // no reordering needed for other variable types.
                    // 
                    spaceResampledData = resampledTestData;
                }
            }
            // for each point in data block ...
            testDataInfoProvider.getPDEDataContext().setVariableName(testVar.getName());
            for (int k = 0; k < refData.length; k++) {
                if (!testDataInfoProvider.isDefined(k)) {
                    continue;
                }
                // Determine maxRef, minRef, maxAbsErr for variable
                // SubDomain testSubDomain = null;
                String sn = null;
                VariableType refVarType = refDataID.getVariableType();
                if (refVarType.equals(VariableType.VOLUME)) {
                    // testSubDomain = refVolSubDomainLookup[k];
                    sn = refVolSubDomainLookup[k].getName();
                } else if (refVarType.equals(VariableType.MEMBRANE)) {
                    // testSubDomain = refMemSubDomainLookup[k];
                    sn = refMemSubDomainLookup[k].getName();
                } else if (refVarType.equals(VariableType.MEMBRANE_REGION)) {
                    sn = "MRV_" + i;
                } else if (refVarType.equals(VariableType.VOLUME_REGION)) {
                    sn = "VRV_" + i;
                } else {
                    throw new RuntimeException("Var " + refVar.getName() + " not supported yet!");
                }
                // hashKey = refVar.getName()+":"+testSubDomain.getName();
                hashKey = refVar.getName() + ":" + sn;
                tempVar = tempVarHash.get(hashKey);
                if (tempVar == null) {
                    tempVar = new DataErrorSummary(null);
                    tempVarHash.put(hashKey, tempVar);
                }
                tempVar.addDataValues(refData[k], spaceResampledData[k], refTimeArray[j], k, absErrorThreshold, relErrorThreshold);
            }
        // end for (k)
        }
    // end for (j)
    }
    // end for (i)
    Enumeration<String> enumKeys = tempVarHash.keys();
    while (enumKeys.hasMoreElements()) {
        String key = enumKeys.nextElement();
        DataErrorSummary tempVarSummary = tempVarHash.get(key);
        simComparisonSummary.addVariableComparisonSummary(new VariableComparisonSummary(key, tempVarSummary.getMinRef(), tempVarSummary.getMaxRef(), tempVarSummary.getMaxAbsoluteError(), tempVarSummary.getMaxRelativeError(), tempVarSummary.getL2Norm(), tempVarSummary.getTimeAtMaxAbsoluteError(), tempVarSummary.getIndexAtMaxAbsoluteError(), tempVarSummary.getTimeAtMaxRelativeError(), tempVarSummary.getIndexAtMaxRelativeError()));
    }
    return simComparisonSummary;
}

Example 29 with DataIdentifier

use of cbit.vcell.simdata.DataIdentifier in project vcell by virtualcell.

the class HybridSolverTester method makeAltCSV.

private static void makeAltCSV(AltArgsHelper altArgsHelper, FileWriter fw, int runIndex, File userSimDataDir) throws Exception {
    VCSimulationIdentifier vcSimID = new VCSimulationIdentifier(new KeyValue(altArgsHelper.simID), altArgsHelper.user);
    boolean bInit = runIndex == 0;
    ArrayList<Double> simTimes = new ArrayList<Double>();
    StringTokenizer st = null;
    if (altArgsHelper.times.equals("all")) {
    } else {
        st = new StringTokenizer(altArgsHelper.times, ":");
        while (st.hasMoreTokens()) {
            double timePoint = Double.parseDouble(st.nextToken());
            simTimes.add(timePoint);
        }
    }
    SimLocHelper simLocHelper0 = null;
    ArrayList<String> simVars = new ArrayList<String>();
    st = new StringTokenizer(altArgsHelper.varnames, ":");
    while (st.hasMoreTokens()) {
        String var = st.nextToken();
        simVars.add(var);
    }
    int jobCounter = 0;
    final int TIME_SPACE_EXTRA = 0;
    double[][][] trialData = null;
    while (true) {
        VCSimulationDataIdentifier vcSimulationDataIdentifier = new VCSimulationDataIdentifier(vcSimID, jobCounter);
        SimulationData simData = null;
        DataOperationResults.DataProcessingOutputInfo dataProcessingOutputInfo = null;
        try {
            simData = new SimulationData(vcSimulationDataIdentifier, userSimDataDir, null, null);
            dataProcessingOutputInfo = (DataOperationResults.DataProcessingOutputInfo) DataSetControllerImpl.getDataProcessingOutput(new DataOperation.DataProcessingOutputInfoOP(vcSimulationDataIdentifier, true, null), new File(userSimDataDir, SimulationData.createCanonicalPostProcessFileName(vcSimulationDataIdentifier)));
        } catch (FileNotFoundException e) {
            if (jobCounter == 0) {
                System.out.println("found no trials matching SimID=" + altArgsHelper.simID + " in user dir " + userSimDataDir.getAbsolutePath());
            } else {
                System.out.println("found " + jobCounter + " trials in dir " + userSimDataDir.getAbsolutePath() + " matching SimID=" + altArgsHelper.simID);
            }
            break;
        } catch (Exception e) {
            e.printStackTrace();
        }
        if (dataProcessingOutputInfo == null) {
            System.out.println("No postprocessing found for " + jobCounter + " trials in dir " + userSimDataDir.getAbsolutePath() + " matching SimID=" + altArgsHelper.simID);
            jobCounter++;
            continue;
        }
        if (simLocHelper0 == null && !altArgsHelper.dataIndexes.equals(POSTPROC)) {
            simLocHelper0 = calcSimLocs(altArgsHelper.dataIndexes, simData.getMesh());
        }
        if (jobCounter == 0) {
            double[] allDatasetTimes = simData.getDataTimes();
            if (altArgsHelper.times.equals("all")) {
                for (double thisTime : allDatasetTimes) {
                    simTimes.add(thisTime);
                }
            } else {
                // Convert user input times to actual data times
                for (int times = 0; times < simTimes.size(); times++) {
                    double masterDelta = Double.POSITIVE_INFINITY;
                    double timePoint = -1;
                    for (int j = 0; j < allDatasetTimes.length; j++) {
                        double tempDelta = Math.abs(simTimes.get(times) - allDatasetTimes[j]);
                        if (tempDelta < masterDelta) {
                            masterDelta = tempDelta;
                            timePoint = allDatasetTimes[j];
                            if (tempDelta == 0) {
                                break;
                            }
                        }
                    }
                    System.out.println("User time=" + simTimes.get(times) + " converted to dataset time=" + timePoint);
                    simTimes.set(times, timePoint);
                }
            }
            trialData = new double[simTimes.size()][(simLocHelper0 == null ? 1 : simLocHelper0.boxToLocs.size())][simVars.size()];
        }
        if (bInit && jobCounter == 0) {
            // print state vars
            DataIdentifier[] dataIdentifiers = simData.getVarAndFunctionDataIdentifiers(null);
            for (int j = 0; j < dataIdentifiers.length; j++) {
                System.out.println(dataIdentifiers[j]);
            }
            printheader(altArgsHelper, simTimes, simLocHelper0, simVars, fw, TIME_SPACE_EXTRA);
        }
        for (int times = 0; times < simTimes.size(); times++) {
            double timePoint = simTimes.get(times);
            for (int vars = 0; vars < simVars.size(); vars++) {
                double[] data = null;
                if (altArgsHelper.dataIndexes.equals(POSTPROC)) {
                    data = dataProcessingOutputInfo.getVariableStatValues().get(simVars.get(vars) + "_average");
                } else {
                    SimDataBlock simDataBlock = simData.getSimDataBlock(null, simVars.get(vars), timePoint);
                    data = simDataBlock.getData();
                }
                for (int locs = 0; locs < trialData[times].length; locs++) {
                    double val;
                    if (simLocHelper0 != null && simLocHelper0.boxToLocs.get(locs).size() == 1) {
                        // point
                        // System.out.println("pointIndex="+simLocHelper.boxToLocs.get(locs).get(0));
                        val = data[simLocHelper0.boxToLocs.get(locs).get(0)];
                    } else if (simLocHelper0 != null) {
                        // box, calculate the average, could be concentration or counts
                        double accum = 0;
                        for (Integer locIndex : simLocHelper0.boxToLocs.get(locs)) {
                            // System.out.println("boxIndex="+locIndex);
                            accum += data[locIndex];
                        }
                        val = accum / simLocHelper0.boxToLocs.get(locs).size();
                    } else {
                        // PostProcess
                        if (times < data.length) {
                            val = data[times];
                        } else {
                            val = Double.NaN;
                        }
                    }
                    trialData[times][locs][vars] = val;
                }
            }
        }
        fw.write("r=" + runIndex + " s=" + jobCounter + ",");
        for (int times = 0; times < simTimes.size(); times++) {
            for (int locs = 0; locs < trialData[times].length; locs++) {
                for (int vars = 0; vars < simVars.size(); vars++) {
                    // System.out.println("job="+jobCounter+" time="+simTimes.get(times)+" loc="+simLocHelper.boxToID.get(locs)+" var="+simVars.get(vars)+" data="+trialData[times][locs][vars]);
                    boolean isNan = Double.isNaN(trialData[times][locs][vars]);
                    fw.write((isNan ? "" : trialData[times][locs][vars]) + ",");
                }
                fw.write(",");
            }
            for (int timeSpace = 0; timeSpace < TIME_SPACE_EXTRA; timeSpace++) {
                fw.write(",");
            }
        }
        fw.write("\n");
        jobCounter++;
    }
    fw.flush();
}

Example 30 with DataIdentifier

use of cbit.vcell.simdata.DataIdentifier in project vcell by virtualcell.

the class FieldDataGUIPanel method copyMethod.

private void copyMethod(int copyMode) {
    String delimiter = "";
    if (copyMode == COPY_NL) {
        delimiter = "\n";
    } else if (copyMode == COPY_CRNL) {
        delimiter = "\r\n";
    } else if (copyMode == COPY_CSV) {
        delimiter = ",";
    } else if (copyMode == COPY_SPACE) {
        delimiter = " ";
    }
    String copyString = "";
    javax.swing.tree.TreePath selPath = getJTree1().getSelectionPath();
    if (selPath != null) {
        javax.swing.tree.DefaultMutableTreeNode lastPathComponent = (javax.swing.tree.DefaultMutableTreeNode) selPath.getLastPathComponent();
        if (lastPathComponent.equals(getJTree1().getModel().getRoot())) {
            int childCount = lastPathComponent.getChildCount();
            for (int i = 0; i < childCount; i += 1) {
                if (i != 0) {
                    copyString += delimiter;
                }
                copyString += ((FieldDataMainList) ((DefaultMutableTreeNode) lastPathComponent.getChildAt(i)).getUserObject()).externalDataIdentifier.getName();
            }
        } else if (lastPathComponent.getUserObject() instanceof FieldDataOriginList) {
            Origin origin = ((FieldDataOriginList) lastPathComponent.getUserObject()).origin;
            copyString = origin.getX() + delimiter + origin.getY() + delimiter + origin.getZ();
        } else if (lastPathComponent.getUserObject() instanceof FieldDataExtentList) {
            Extent extent = ((FieldDataExtentList) lastPathComponent.getUserObject()).extent;
            copyString = extent.getX() + delimiter + extent.getY() + delimiter + extent.getZ();
        } else if (lastPathComponent.getUserObject() instanceof FieldDataISizeList) {
            ISize isize = ((FieldDataISizeList) lastPathComponent.getUserObject()).isize;
            copyString = isize.getX() + delimiter + isize.getY() + delimiter + isize.getZ();
        } else if (lastPathComponent.getUserObject() instanceof FieldDataTimeList) {
            double[] times = ((FieldDataTimeList) lastPathComponent.getUserObject()).times;
            for (int i = 0; i < times.length; i += 1) {
                if (i != 0) {
                    copyString += delimiter;
                }
                copyString += times[i] + "";
            }
        } else if (lastPathComponent.getUserObject() instanceof FieldDataMainList) {
            ExternalDataIdentifier extDataID = ((FieldDataMainList) lastPathComponent.getUserObject()).externalDataIdentifier;
            copyString = extDataID.getName();
        } else if (lastPathComponent.getUserObject() instanceof FieldDataVarList) {
            DataIdentifier dataIdentifier = ((FieldDataVarList) lastPathComponent.getUserObject()).dataIdentifier;
            copyString = dataIdentifier.getName();
        } else if (lastPathComponent.getUserObject() instanceof FieldDataVarMainList) {
            int childCount = lastPathComponent.getChildCount();
            for (int i = 0; i < childCount; i += 1) {
                if (i != 0) {
                    copyString += delimiter;
                }
                copyString += ((FieldDataVarList) ((DefaultMutableTreeNode) lastPathComponent.getChildAt(i)).getUserObject()).dataIdentifier.getName();
            }
        }
        if (copyString.length() > 0) {
            VCellTransferable.sendToClipboard(copyString);
        }
    }
}