Examples with DataProcessingInstructions cbit.vcell.solver.DataProcessingInstructions used on opensource projects

Example 1 with DataProcessingInstructions

use of cbit.vcell.solver.DataProcessingInstructions in project vcell by virtualcell.

the class SmoldynFileWriter method writeDataProcessor.

private void writeDataProcessor() throws DataAccessException, IOException, MathException, DivideByZeroException, ExpressionException {
    Simulation simulation = simTask.getSimulation();
    DataProcessingInstructions dpi = simulation.getDataProcessingInstructions();
    if (dpi == null) {
        printWriter.println(SmoldynVCellMapper.SmoldynKeyword.cmd + " " + SmoldynVCellMapper.SmoldynKeyword.B + " " + VCellSmoldynKeyword.vcellDataProcess + " begin " + DataProcessingInstructions.ROI_TIME_SERIES);
        printWriter.println(SmoldynVCellMapper.SmoldynKeyword.cmd + " " + SmoldynVCellMapper.SmoldynKeyword.B + " " + VCellSmoldynKeyword.vcellDataProcess + " end");
    } else {
        FieldDataIdentifierSpec fdis = dpi.getSampleImageFieldData(simulation.getVersion().getOwner());
        if (fdis == null) {
            throw new DataAccessException("Can't find sample image in data processing instructions");
        }
        File userDirectory = outputFile.getParentFile();
        String secondarySimDataDir = PropertyLoader.getProperty(PropertyLoader.secondarySimDataDirInternalProperty, null);
        DataSetControllerImpl dsci = new DataSetControllerImpl(null, userDirectory.getParentFile(), secondarySimDataDir == null ? null : new File(secondarySimDataDir));
        CartesianMesh origMesh = dsci.getMesh(fdis.getExternalDataIdentifier());
        SimDataBlock simDataBlock = dsci.getSimDataBlock(null, fdis.getExternalDataIdentifier(), fdis.getFieldFuncArgs().getVariableName(), fdis.getFieldFuncArgs().getTime().evaluateConstant());
        VariableType varType = fdis.getFieldFuncArgs().getVariableType();
        VariableType dataVarType = simDataBlock.getVariableType();
        if (!varType.equals(VariableType.UNKNOWN) && !varType.equals(dataVarType)) {
            throw new IllegalArgumentException("field function variable type (" + varType.getTypeName() + ") doesn't match real variable type (" + dataVarType.getTypeName() + ")");
        }
        double[] origData = simDataBlock.getData();
        String filename = SimulationJob.createSimulationJobID(Simulation.createSimulationID(simulation.getKey()), simTask.getSimulationJob().getJobIndex()) + SimulationData.getDefaultFieldDataFileNameForSimulation(fdis.getFieldFuncArgs());
        File fdatFile = new File(userDirectory, filename);
        DataSet.writeNew(fdatFile, new String[] { fdis.getFieldFuncArgs().getVariableName() }, new VariableType[] { simDataBlock.getVariableType() }, new ISize(origMesh.getSizeX(), origMesh.getSizeY(), origMesh.getSizeZ()), new double[][] { origData });
        printWriter.println(SmoldynVCellMapper.SmoldynKeyword.cmd + " " + SmoldynVCellMapper.SmoldynKeyword.B + " " + VCellSmoldynKeyword.vcellDataProcess + " begin " + dpi.getScriptName());
        StringTokenizer st = new StringTokenizer(dpi.getScriptInput(), "\n\r");
        while (st.hasMoreTokens()) {
            String str = st.nextToken();
            if (str.trim().length() > 0) {
                printWriter.println(SmoldynVCellMapper.SmoldynKeyword.cmd + " " + SmoldynVCellMapper.SmoldynKeyword.B + " " + VCellSmoldynKeyword.vcellDataProcess + " " + str);
            }
        }
        printWriter.println(SmoldynVCellMapper.SmoldynKeyword.cmd + " " + SmoldynVCellMapper.SmoldynKeyword.B + " " + VCellSmoldynKeyword.vcellDataProcess + " SampleImageFile " + fdis.getFieldFuncArgs().getVariableName() + " " + fdis.getFieldFuncArgs().getTime().infix() + " " + fdatFile);
        printWriter.println(SmoldynVCellMapper.SmoldynKeyword.cmd + " " + SmoldynVCellMapper.SmoldynKeyword.B + " " + VCellSmoldynKeyword.vcellDataProcess + " end");
    }
}

Example 2 with DataProcessingInstructions

use of cbit.vcell.solver.DataProcessingInstructions in project vcell by virtualcell.

the class XmlReader method getSimulation.

/**
 * This method returns a Simulation object from a XML element.
 * Creation date: (4/26/2001 12:14:30 PM)
 * @return cbit.vcell.solver.Simulation
 * @param param org.jdom.Element
 * @exception cbit.vcell.xml.XmlParseException The exception description.
 */
Simulation getSimulation(Element param, MathDescription mathDesc) throws XmlParseException {
    // retrive metadata (if any)
    SimulationVersion simulationVersion = getSimulationVersion(param.getChild(XMLTags.VersionTag, vcNamespace));
    // create new simulation
    Simulation simulation = null;
    if (simulationVersion != null) {
        simulation = new Simulation(simulationVersion, mathDesc);
    } else {
        simulation = new Simulation(mathDesc);
    }
    // set attributes
    String name = unMangle(param.getAttributeValue(XMLTags.NameAttrTag));
    try {
        simulation.setName(name);
        // String annotation = param.getAttributeValue(XMLTags.AnnotationAttrTag);
        // if (annotation!=null) {
        // simulation.setDescription(unMangle(annotation));
        // }
        // Add Annotation
        String annotationText = param.getChildText(XMLTags.AnnotationTag, vcNamespace);
        if (annotationText != null && annotationText.length() > 0) {
            simulation.setDescription(unMangle(annotationText));
        }
    } catch (java.beans.PropertyVetoException e) {
        throw new XmlParseException(e);
    }
    // Retrieve MathOverrides
    simulation.setMathOverrides(getMathOverrides(param.getChild(XMLTags.MathOverridesTag, vcNamespace), simulation));
    // Retrieve SolverTaskDescription
    try {
        simulation.setSolverTaskDescription(getSolverTaskDescription(param.getChild(XMLTags.SolverTaskDescriptionTag, vcNamespace), simulation));
    } catch (java.beans.PropertyVetoException e) {
        e.printStackTrace();
        throw new XmlParseException("A PropertyVetoException was fired when setting the SolverTaskDescroiption object to the Simulation object " + name, e);
    }
    Element dataProcessingInstructionsElement = param.getChild(XMLTags.DataProcessingInstructionsTag, vcNamespace);
    if (dataProcessingInstructionsElement != null) {
        String scriptName = dataProcessingInstructionsElement.getAttributeValue(XMLTags.DataProcessingScriptNameAttrTag);
        String scriptInput = dataProcessingInstructionsElement.getText();
        simulation.setDataProcessingInstructions(new DataProcessingInstructions(scriptName, scriptInput));
    }
    // Retrieve MeshEspecification (if any)
    Element tempElement = param.getChild(XMLTags.MeshSpecTag, vcNamespace);
    if (tempElement != null) {
        try {
            simulation.setMeshSpecification(getMeshSpecification(tempElement, mathDesc.getGeometry()));
        } catch (java.beans.PropertyVetoException e) {
            e.printStackTrace();
            throw new XmlParseException("A ProperyVetoException was fired when setting the MeshSpecification to a new Simulation!", e);
        }
    }
    return simulation;
}

Example 3 with DataProcessingInstructions

use of cbit.vcell.solver.DataProcessingInstructions in project vcell by virtualcell.

the class ClientSimManager method runQuickSimulation.

public void runQuickSimulation(final Simulation originalSimulation, ViewerType viewerType) {
    Collection<AsynchClientTask> taskList = new ArrayList<AsynchClientTask>();
    final SimulationOwner simulationOwner = simWorkspace.getSimulationOwner();
    // ----------- update math if it is from biomodel (simulationContext)
    if (simulationOwner instanceof SimulationContext) {
        Collection<AsynchClientTask> ut = ClientRequestManager.updateMath(documentWindowManager.getComponent(), ((SimulationContext) simulationOwner), false, NetworkGenerationRequirements.ComputeFullStandardTimeout);
        taskList.addAll(ut);
    }
    // Let user tell how many simultaneous processes to run if this is local paramscan
    final int[] simultaneousSimsSetting = new int[] { 1 };
    if (originalSimulation.getScanCount() > 1) {
        try {
            String simultaneousSims = DialogUtils.showInputDialog0(getDocumentWindowManager().getComponent(), "Local multi-scan simulation, enter maximum simulataneous sims to run at once", "1");
            simultaneousSimsSetting[0] = Integer.parseInt(simultaneousSims);
        } catch (UtilCancelException e) {
            return;
        }
    }
    // ----------- run simulation(s)
    final File localSimDataDir = ResourceUtil.getLocalSimDir(User.tempUser.getName());
    AsynchClientTask runSimTask = new AsynchClientTask("running simulation", AsynchClientTask.TASKTYPE_NONSWING_BLOCKING) {

        @Override
        public void run(Hashtable<String, Object> hashTable) throws Exception {
            Simulation simulation = new TempSimulation(originalSimulation, false);
            simulation.setSimulationOwner(originalSimulation.getSimulationOwner());
            SimulationTask simTask = new SimulationTask(new SimulationJob(simulation, 0, null), 0);
            Solver solver = createQuickRunSolver(localSimDataDir, simTask);
            if (solver == null) {
                throw new RuntimeException("null solver");
            }
            // check if spatial stochastic simulation (smoldyn solver) has data processing instructions with field data - need to access server for field data, so cannot do local simulation run.
            if (solver instanceof SmoldynSolver) {
                DataProcessingInstructions dpi = simulation.getDataProcessingInstructions();
                if (dpi != null) {
                    FieldDataIdentifierSpec fdis = dpi.getSampleImageFieldData(simulation.getVersion().getOwner());
                    if (fdis != null) {
                        throw new RuntimeException("Spatial Stochastic simulation '" + simulation.getName() + "' (Smoldyn solver) with field data (in data processing instructions) cannot be run locally at this time since field data needs to be retrieved from the VCell server.");
                    }
                }
            }
            solver.addSolverListener(new SolverListener() {

                public void solverStopped(SolverEvent event) {
                    getClientTaskStatusSupport().setMessage(event.getSimulationMessage().getDisplayMessage());
                }

                public void solverStarting(SolverEvent event) {
                    String displayMessage = event.getSimulationMessage().getDisplayMessage();
                    System.out.println(displayMessage);
                    getClientTaskStatusSupport().setMessage(displayMessage);
                    if (displayMessage.equals(SimulationMessage.MESSAGE_SOLVEREVENT_STARTING_INIT.getDisplayMessage())) {
                        getClientTaskStatusSupport().setProgress(75);
                    } else if (displayMessage.equals(SimulationMessage.MESSAGE_SOLVER_RUNNING_INPUT_FILE.getDisplayMessage())) {
                        getClientTaskStatusSupport().setProgress(90);
                    }
                }

                public void solverProgress(SolverEvent event) {
                    getClientTaskStatusSupport().setMessage("Running...");
                    int progress = (int) (event.getProgress() * 100);
                    getClientTaskStatusSupport().setProgress(progress);
                }

                public void solverPrinted(SolverEvent event) {
                    getClientTaskStatusSupport().setMessage("Running...");
                }

                public void solverFinished(SolverEvent event) {
                    getClientTaskStatusSupport().setMessage(event.getSimulationMessage().getDisplayMessage());
                }

                public void solverAborted(SolverEvent event) {
                    getClientTaskStatusSupport().setMessage(event.getSimulationMessage().getDisplayMessage());
                }
            });
            solver.startSolver();
            while (true) {
                try {
                    Thread.sleep(500);
                } catch (InterruptedException e) {
                }
                if (getClientTaskStatusSupport().isInterrupted()) {
                    solver.stopSolver();
                    throw UserCancelException.CANCEL_GENERIC;
                }
                SolverStatus solverStatus = solver.getSolverStatus();
                if (solverStatus != null) {
                    if (solverStatus.getStatus() == SolverStatus.SOLVER_ABORTED) {
                        String simulationMessage = solverStatus.getSimulationMessage().getDisplayMessage();
                        String translatedMessage = solver.translateSimulationMessage(simulationMessage);
                        if (translatedMessage.startsWith(BeanUtils.FD_EXP_MESSG)) {
                            throw new RuntimeException("Sims with FieldData can only be run remotely (cannot use QuickRun).\n" + translatedMessage);
                        } else {
                            throw new RuntimeException(translatedMessage);
                        }
                    }
                    if (solverStatus.getStatus() != SolverStatus.SOLVER_STARTING && solverStatus.getStatus() != SolverStatus.SOLVER_READY && solverStatus.getStatus() != SolverStatus.SOLVER_RUNNING) {
                        break;
                    }
                }
            }
            ArrayList<AnnotatedFunction> outputFunctionsList = getSimWorkspace().getSimulationOwner().getOutputFunctionContext().getOutputFunctionsList();
            OutputContext outputContext = new OutputContext(outputFunctionsList.toArray(new AnnotatedFunction[outputFunctionsList.size()]));
            Simulation[] simsArray = new Simulation[] { simulation };
            hashTable.put("outputContext", outputContext);
            hashTable.put("simsArray", simsArray);
        }
    };
    taskList.add(runSimTask);
    // --------- add tasks from showSimResults : retrieve data, display results
    AsynchClientTask[] showResultsTask = showSimulationResults0(true, viewerType);
    for (AsynchClientTask task : showResultsTask) {
        taskList.add(task);
    }
    AsynchClientTask runOthers = new AsynchClientTask("running scans", AsynchClientTask.TASKTYPE_NONSWING_BLOCKING) {

        @Override
        public void run(Hashtable<String, Object> hashTable) throws Exception {
            if (getClientTaskStatusSupport().isInterrupted()) {
                throw UserCancelException.CANCEL_GENERIC;
            }
            Simulation[] sims = (Simulation[]) hashTable.get("simsArray");
            Simulation simulation = sims[0];
            // Run param scans to generate data for scansnum > 0
            if (simulation.getScanCount() > 1) {
                // Start master thread so clientdispatcher modal dialog can end
                new Thread(new Runnable() {

                    @Override
                    public void run() {
                        // Flag (set by dataviewer being closed) so sim scan threads know if they should stop
                        final boolean[] bWinCloseHolder = new boolean[] { false };
                        // Add close listener to dataviewer to end all scans and exit
                        final SimulationWindow haveSimulationWindow = getDocumentWindowManager().haveSimulationWindow(simulation.getSimulationInfo().getAuthoritativeVCSimulationIdentifier());
                        final Window window = (Window) BeanUtils.findTypeParentOfComponent(haveSimulationWindow.getDataViewer(), Window.class);
                        window.addWindowListener(new WindowAdapter() {

                            @Override
                            public void windowClosing(WindowEvent e) {
                                // TODO Auto-generated method stub
                                super.windowClosing(e);
                                bWinCloseHolder[0] = true;
                            }
                        });
                        // First sim scan (0) is done already before viewer is shown
                        ((SimResultsViewer) haveSimulationWindow.getDataViewer()).setLocalScanProgress(1);
                        // Counter of how many simultaneous param scan threads are running (decremented when scan thread finishes)
                        final int[] currentlyRunningCountHolder = new int[] { 0 };
                        // Run other scans starting at 1 (scan 0 is already done if we got here)
                        for (int i = 1; i < simulation.getScanCount(); i++) {
                            // Check if we can start another new param scan thread
                            while (currentlyRunningCountHolder[0] >= simultaneousSimsSetting[0]) {
                                try {
                                    Thread.sleep(50);
                                    // Check if user closed the viewer window, no need to continue
                                    if (bWinCloseHolder[0]) {
                                        return;
                                    }
                                } catch (InterruptedException e) {
                                    e.printStackTrace();
                                }
                            }
                            final int scanNum = i;
                            // increment the concurrent running counter
                            currentlyRunningCountHolder[0] += 1;
                            // Start new param scan thread
                            new Thread(new Runnable() {

                                @Override
                                public void run() {
                                    try {
                                        SimulationTask simTask = new SimulationTask(new SimulationJob(simulation, scanNum, null), 0);
                                        Solver solver = createQuickRunSolver(localSimDataDir, simTask);
                                        solver.startSolver();
                                        while (true) {
                                            SolverStatus solverStatus = solver.getSolverStatus();
                                            // System.out.println("ScanNum="+scanNum+" "+solverStatus);
                                            try {
                                                Thread.sleep(100);
                                            } catch (InterruptedException e) {
                                            }
                                            // Stop if user closed the dataviewer window
                                            if (bWinCloseHolder[0]) {
                                                solver.stopSolver();
                                                break;
                                            }
                                            if (solverStatus != null) {
                                                if (solverStatus.getStatus() == SolverStatus.SOLVER_ABORTED) {
                                                    String simulationMessage = solverStatus.getSimulationMessage().getDisplayMessage();
                                                    String translatedMessage = solver.translateSimulationMessage(simulationMessage);
                                                    if (translatedMessage.startsWith(BeanUtils.FD_EXP_MESSG)) {
                                                        throw new RuntimeException("Sims with FieldData can only be run remotely (cannot use QuickRun).\n" + translatedMessage);
                                                    } else {
                                                        throw new RuntimeException(translatedMessage);
                                                    }
                                                }
                                                if (solverStatus.getStatus() != SolverStatus.SOLVER_STARTING && solverStatus.getStatus() != SolverStatus.SOLVER_READY && solverStatus.getStatus() != SolverStatus.SOLVER_RUNNING) {
                                                    break;
                                                }
                                            }
                                        }
                                    // SolverStatus solverStatus = solver.getSolverStatus();
                                    // System.out.println("ScanNum="+scanNum+" "+"FinalStatus="+solverStatus);
                                    } catch (Exception e) {
                                        e.printStackTrace();
                                    } finally {
                                        // decrement the concurrent running counter
                                        currentlyRunningCountHolder[0] -= 1;
                                        // Set progress on dataviewer
                                        if (((SimResultsViewer) haveSimulationWindow.getDataViewer()).getLocalScanProgress() < (scanNum + 1)) {
                                            ((SimResultsViewer) haveSimulationWindow.getDataViewer()).setLocalScanProgress(scanNum + 1);
                                        }
                                    }
                                }
                            }).start();
                        }
                    }
                }).start();
            }
        }
    };
    taskList.add(runOthers);
    // ------- dispatch
    AsynchClientTask[] taskArray = new AsynchClientTask[taskList.size()];
    taskList.toArray(taskArray);
    ClientTaskDispatcher.dispatch(documentWindowManager.getComponent(), new Hashtable<String, Object>(), taskArray, true, true, null);
}

Example 4 with DataProcessingInstructions

use of cbit.vcell.solver.DataProcessingInstructions in project vcell by virtualcell.

the class DataProcessingInstructionPanel method editDataProcessor.

/**
 * Method to handle events for the ActionListener interface.
 * @param e java.awt.event.ActionEvent
 */
private void editDataProcessor(boolean bEdit) {
    DataProcessingInstructions dpi = solverTaskDescription.getSimulation().getDataProcessingInstructions();
    JPanel mainPanel = new JPanel(new BorderLayout());
    JPanel panel = new JPanel(new FlowLayout(FlowLayout.LEFT));
    JLabel nameLabel = new JLabel("Name");
    panel.add(nameLabel);
    JComboBox nameComboBox = new JComboBox();
    nameComboBox.addItem(DataProcessingInstructions.ROI_TIME_SERIES);
    nameComboBox.addItem(DataProcessingInstructions.VFRAP);
    if (dpi != null) {
        nameComboBox.setSelectedItem(dpi.getScriptName());
    }
    panel.add(nameComboBox);
    mainPanel.add(panel, BorderLayout.NORTH);
    panel = new JPanel(new GridBagLayout());
    JLabel label = new JLabel("Text");
    GridBagConstraints cbc = new GridBagConstraints();
    cbc.gridx = 0;
    cbc.gridy = 0;
    cbc.insets = new Insets(4, 4, 4, 8);
    panel.add(label, cbc);
    JScrollPane sp = new JScrollPane();
    sp.setHorizontalScrollBarPolicy(JScrollPane.HORIZONTAL_SCROLLBAR_ALWAYS);
    sp.setVerticalScrollBarPolicy(JScrollPane.VERTICAL_SCROLLBAR_ALWAYS);
    JTextArea textArea = new JTextArea();
    if (dpi != null) {
        textArea.setText(dpi.getScriptInput());
    }
    textArea.setColumns(20);
    textArea.setRows(8);
    sp.setViewportView(textArea);
    cbc = new GridBagConstraints();
    cbc.gridx = 1;
    cbc.gridy = 0;
    cbc.weightx = 1;
    cbc.weighty = 1;
    cbc.fill = GridBagConstraints.BOTH;
    panel.add(sp, cbc);
    mainPanel.add(panel, BorderLayout.CENTER);
    int ok = DialogUtils.showComponentOKCancelDialog(this.getParent(), mainPanel, "Add Data Processor");
    if (ok == JOptionPane.OK_OPTION && textArea.getText().length() > 0) {
        String name = (String) nameComboBox.getSelectedItem();
        solverTaskDescription.getSimulation().setDataProcessingInstructions(new DataProcessingInstructions(name, textArea.getText()));
    } else {
        if (!bEdit) {
            solverTaskDescription.getSimulation().setDataProcessingInstructions(null);
        }
    }
}

Example 5 with DataProcessingInstructions

use of cbit.vcell.solver.DataProcessingInstructions in project vcell by virtualcell.

the class DataProcessingInstructionPanel method refresh.

private void refresh() {
    if (solverTaskDescription == null) {
        return;
    }
    SolverDescription solverDesc = solverTaskDescription.getSolverDescription();
    if (solverDesc.supports(SolverFeature.Feature_DataProcessingInstructions)) {
        setVisible(true);
        DataProcessingInstructions dpi = solverTaskDescription.getSimulation().getDataProcessingInstructions();
        if (dpi != null) {
            dataProcessorCheckBox.setSelected(true);
            editDataProcessorButton.setEnabled(true);
        } else {
            editDataProcessorButton.setEnabled(false);
        }
    } else {
        setVisible(false);
    }
}