Examples with SimulationContext cbit.vcell.mapping.SimulationContext used on opensource projects

Example 11 with SimulationContext

use of cbit.vcell.mapping.SimulationContext in project vcell by virtualcell.

the class SimulationListPanel method quickRun.

/*
	private void particleView() {
		int row = getScrollPaneTable().getSelectedRow();
		if (row < 0) {
			return;
		}
		Simulation selectedSim = getSimulationListTableModel1().getValueAt(row);
		getSimulationWorkspace().getClientSimManager().runSmoldynParticleView(selectedSim);
	}
	*/
private void quickRun(ViewerType viewerType) {
    int row = getScrollPaneTable().getSelectedRow();
    if (row < 0) {
        return;
    }
    activateConsole();
    Simulation selectedSim = getSimulationListTableModel1().getValueAt(row);
    SolverDescription solverDescription = selectedSim.getSolverTaskDescription().getSolverDescription();
    if (solverDescription.equals(SolverDescription.FiniteVolume)) {
        if (getSimulationWorkspace().getSimulationOwner() instanceof SimulationContext) {
            String option = DialogUtils.showOKCancelWarningDialog(SimulationListPanel.this, "Deprecated Solver", VCellErrorMessages.getSemiFVSolverCompiledSolverDeprecated(selectedSim));
            if (option.equals(SimpleUserMessage.OPTION_CANCEL)) {
                return;
            }
            try {
                selectedSim.getSolverTaskDescription().setSolverDescription(SolverDescription.FiniteVolumeStandalone);
                selectedSim.setIsDirty(true);
            } catch (PropertyVetoException e) {
                e.printStackTrace();
            }
        }
    }
    getSimulationWorkspace().getClientSimManager().runQuickSimulation(selectedSim, viewerType);
}

Example 12 with SimulationContext

use of cbit.vcell.mapping.SimulationContext in project vcell by virtualcell.

the class SimulationListPanel method newSimulation.

/**
 * Comment
 */
private void newSimulation(final NetworkGenerationRequirements networkGenerationRequirements) {
    AsynchClientTask task1 = new AsynchClientTask("new simulation", AsynchClientTask.TASKTYPE_NONSWING_BLOCKING) {

        @Override
        public void run(Hashtable<String, Object> hashTable) throws Exception {
            MathMappingCallback mathMappingCallback = new MathMappingCallbackTaskAdapter(getClientTaskStatusSupport());
            if (getSimulationWorkspace().getSimulationOwner() instanceof SimulationContext) {
                SimulationContext simulationContext = (SimulationContext) getSimulationWorkspace().getSimulationOwner();
                simulationContext.refreshMathDescription(mathMappingCallback, networkGenerationRequirements);
            }
        }
    };
    AsynchClientTask task2 = new AsynchClientTask("new simulation", AsynchClientTask.TASKTYPE_SWING_BLOCKING) {

        @Override
        public void run(Hashtable<String, Object> hashTable) throws Exception {
            MathMappingCallback mathMappingCallback = new MathMappingCallbackTaskAdapter(getClientTaskStatusSupport());
            int newSimIndex = getSimulationWorkspace().newSimulation(SimulationListPanel.this, mathMappingCallback, networkGenerationRequirements);
            getScrollPaneTable().getSelectionModel().setSelectionInterval(newSimIndex, newSimIndex);
            getScrollPaneTable().scrollRectToVisible(getScrollPaneTable().getCellRect(newSimIndex, 0, true));
        }
    };
    ClientTaskDispatcher.dispatch(this, new Hashtable<String, Object>(), new AsynchClientTask[] { task1, task2 });
}

Example 13 with SimulationContext

use of cbit.vcell.mapping.SimulationContext in project vcell by virtualcell.

the class SimulationListPanel method massConservationButtonAdjust.

private void massConservationButtonAdjust() {
    if (fieldSimulationWorkspace != null && fieldSimulationWorkspace.getSimulationOwner() instanceof SimulationContext) {
        SimulationContext simContext = (SimulationContext) fieldSimulationWorkspace.getSimulationOwner();
        if (simContext.getGeometry().getDimension() == 0 && simContext.getApplicationType() == SimulationContext.Application.NETWORK_DETERMINISTIC) {
            getMassConservationModelReductionCheckBox().setVisible(true);
            getMassConservationModelReductionCheckBox().setEnabled(true);
            getMassConservationModelReductionCheckBox().setSelected(simContext.isUsingMassConservationModelReduction());
            getMassConservationModelReductionHelpButton().setVisible(true);
            getMassConservationModelReductionHelpButton().setEnabled(true);
        } else {
            getMassConservationModelReductionCheckBox().setVisible(false);
            getMassConservationModelReductionHelpButton().setVisible(false);
        }
    } else {
        getMassConservationModelReductionCheckBox().setVisible(false);
        getMassConservationModelReductionHelpButton().setVisible(false);
    }
}

Example 14 with SimulationContext

use of cbit.vcell.mapping.SimulationContext in project vcell by virtualcell.

the class SimulationListPanel method runSimulations.

/**
 * Comment
 */
private void runSimulations() {
    if (User.isGuest(getSimulationWorkspace().getLoggedInUser().getName())) {
        DialogUtils.showErrorDialog(this, User.createGuestErrorMessage("runVCellServerSimulations"));
        return;
    }
    final ArrayList<Simulation> simList = new ArrayList<Simulation>();
    int[] selections = getScrollPaneTable().getSelectedRows();
    for (int i = 0; i < selections.length; i++) {
        Simulation sim = (Simulation) (ivjSimulationListTableModel1.getValueAt(selections[i]));
        if (sim.getSolverTaskDescription().getSolverDescription().equals(SolverDescription.FiniteVolume)) {
            if (getSimulationWorkspace().getSimulationOwner() instanceof SimulationContext) {
                String option = DialogUtils.showOKCancelWarningDialog(SimulationListPanel.this, "Deprecated Solver", VCellErrorMessages.getSemiFVSolverCompiledSolverDeprecated(sim));
                if (option.equals(SimpleUserMessage.OPTION_CANCEL)) {
                    return;
                }
                try {
                    sim.getSolverTaskDescription().setSolverDescription(SolverDescription.FiniteVolumeStandalone);
                    sim.setIsDirty(true);
                } catch (PropertyVetoException e) {
                    e.printStackTrace();
                }
            }
        }
        simList.add(sim);
    }
    if (simList.size() > 0) {
        activateConsole();
        Simulation[] toRun = simList.toArray(new Simulation[0]);
        try {
            getSimulationWorkspace().runSimulations(toRun, this);
        } catch (Exception e) {
            // TODO Auto-generated catch block
            e.printStackTrace();
            DialogUtils.showErrorDialog(this, e.getMessage());
        }
    }
}

Example 15 with SimulationContext

use of cbit.vcell.mapping.SimulationContext in project vcell by virtualcell.

the class ImageJHelper method populateDesktopIJModelInfos.

private static void populateDesktopIJModelInfos(IJDocType docType, ArrayList<KeyValue> openVCDocumentVersionKeys, ArrayList<IJModelInfo> modelInfos) {
    if (VCellClientTest.getVCellClient() == null) {
        return;
    }
    Collection<TopLevelWindowManager> windowManagers = VCellClientTest.getVCellClient().getMdiManager().getWindowManagers();
    for (TopLevelWindowManager topLevelWindowManager : windowManagers) {
        if (topLevelWindowManager instanceof DocumentWindowManager) {
            DocumentWindowManager documentWindowManager = (DocumentWindowManager) topLevelWindowManager;
            VCDocument.VCDocumentType currDocType = documentWindowManager.getVCDocument().getDocumentType();
            if (currDocType == docType.getVCDocType()) {
                if (documentWindowManager.getVCDocument().getVersion() != null && documentWindowManager.getVCDocument().getVersion().getVersionKey() != null) {
                    openVCDocumentVersionKeys.add(documentWindowManager.getVCDocument().getVersion().getVersionKey());
                } else {
                    ArrayList<IJContextInfo> ijContextInfos = new ArrayList<>();
                    if (documentWindowManager instanceof BioModelWindowManager) {
                        for (SimulationContext simulationContext : ((BioModelWindowManager) documentWindowManager).getBioModel().getSimulationContexts()) {
                            addSimToIJContextInfo(ijContextInfos, simulationContext.getName(), simulationContext.getMathType(), simulationContext.getGeometryContext().getGeometry().getDimension(), simulationContext.getGeometry().getName(), simulationContext.getSimulations());
                        }
                        modelInfos.add(new IJModelInfo(documentWindowManager.getVCDocument().getName(), null, IJDocType.bm, true, (documentWindowManager.getUser() == null ? null : documentWindowManager.getUser().getName()), null, ijContextInfos));
                    } else if (documentWindowManager instanceof MathModelWindowManager) {
                        MathModel mathModel = ((MathModelWindowManager) documentWindowManager).getMathModel();
                        addSimToIJContextInfo(ijContextInfos, null, mathModel.getMathDescription().getMathType(), mathModel.getGeometry().getDimension(), mathModel.getGeometry().getName(), ((MathModelWindowManager) documentWindowManager).getSimulationWorkspace().getSimulations());
                        modelInfos.add(new IJModelInfo(documentWindowManager.getVCDocument().getName(), null, IJDocType.mm, true, (documentWindowManager.getUser() == null ? null : documentWindowManager.getUser().getName()), null, ijContextInfos));
                    }
                }
            }
        }
    }
}