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

Example 86 with SimulationContext

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

the class ElectricalStimulusPanel method newStimulus.

/**
 * Comment
 */
private void newStimulus() {
    try {
        SimulationContext simContext = getSimulationContext();
        if (simContext == null) {
            return;
        }
        // 
        // When the voltage and current clamp radio buttons is deselected within the same simulation context (application),
        // display a warning saying that the present clamp settings will be lost (not applicable when the 'no clamp'
        // radiobutton is deselected.
        // 
        ElectricalStimulus currElectricalStimulus = null;
        if (simContext.getElectricalStimuli() != null && simContext.getElectricalStimuli().length > 0) {
            currElectricalStimulus = simContext.getElectricalStimuli()[0];
        }
        // 
        // ignore selection if already selected
        // warn upon deselect if about to loose edits
        // 
        Clamp selectedClamp = (Clamp) clampComboBox.getSelectedItem();
        if (currElectricalStimulus instanceof VoltageClampStimulus) {
            if (selectedClamp == Clamp.Voltage_Clamp) {
                return;
            }
            String response = PopupGenerator.showWarningDialog(this, "warning: the present voltage clamp settings will be lost", new String[] { UserMessage.OPTION_CONTINUE, UserMessage.OPTION_CANCEL }, UserMessage.OPTION_CONTINUE);
            if (response == null || response.equals(UserMessage.OPTION_CANCEL)) {
                // revert back to Voltage Clamp
                clampComboBox.setSelectedItem(Clamp.Voltage_Clamp);
                return;
            }
        }
        if (currElectricalStimulus instanceof TotalCurrentClampStimulus) {
            if (selectedClamp == Clamp.Total_Current_Clamp) {
                return;
            }
            String response = PopupGenerator.showWarningDialog(this, "warning: the present current clamp settings will be lost", new String[] { UserMessage.OPTION_CONTINUE, UserMessage.OPTION_CANCEL }, UserMessage.OPTION_CONTINUE);
            if (response == null || response.equals(UserMessage.OPTION_CANCEL)) {
                // revert back to Current Clamp
                clampComboBox.setSelectedItem(Clamp.Total_Current_Clamp);
                return;
            }
        }
        if (currElectricalStimulus instanceof CurrentDensityClampStimulus) {
            if (selectedClamp == Clamp.Current_Density_Clamp) {
                return;
            }
            String response = PopupGenerator.showWarningDialog(this, "warning: the present current clamp settings will be lost", new String[] { UserMessage.OPTION_CONTINUE, UserMessage.OPTION_CANCEL }, UserMessage.OPTION_CONTINUE);
            if (response == null || response.equals(UserMessage.OPTION_CANCEL)) {
                // revert back to Current Clamp
                clampComboBox.setSelectedItem(Clamp.Current_Density_Clamp);
                return;
            }
        }
        if (currElectricalStimulus == null && selectedClamp == Clamp.No_Clamp) {
            return;
        }
        StructureTopology structTopology = getSimulationContext().getModel().getStructureTopology();
        Structure[] structures = getSimulationContext().getModel().getStructures();
        ArrayList<Feature> features = new ArrayList<Feature>();
        for (Structure structure : structures) {
            if (structure instanceof Feature) {
                features.add((Feature) structure);
            }
        }
        if (features.size() < 2) {
            PopupGenerator.showErrorDialog(this, "error: electrodes must be placed in distinct volumetric structures, found " + features.size() + " volumetric structures in model");
            return;
        }
        Feature groundFeature = features.get(0);
        Feature clampedFeature = features.get(1);
        // 
        if (selectedClamp == Clamp.Total_Current_Clamp) {
            if (simContext.getElectricalStimuli().length == 0 || !(simContext.getElectricalStimuli()[0] instanceof TotalCurrentClampStimulus)) {
                Electrode probeElectrode = new Electrode(clampedFeature, new Coordinate(0, 0, 0));
                TotalCurrentClampStimulus ccStimulus = new TotalCurrentClampStimulus(probeElectrode, "ccElectrode", new Expression(0.0), simContext);
                System.out.println(" Geo's dim = " + simContext.getGeometry().getDimension());
                simContext.setElectricalStimuli(new ElectricalStimulus[] { ccStimulus });
                simContext.setGroundElectrode(new Electrode(groundFeature, new Coordinate(0, 0, 0)));
            }
        }
        // 
        if (selectedClamp == Clamp.Current_Density_Clamp) {
            if (simContext.getElectricalStimuli().length == 0 || !(simContext.getElectricalStimuli()[0] instanceof CurrentDensityClampStimulus)) {
                Electrode probeElectrode = new Electrode(clampedFeature, new Coordinate(0, 0, 0));
                CurrentDensityClampStimulus ccStimulus = new CurrentDensityClampStimulus(probeElectrode, "ccElectrode", new Expression(0.0), simContext);
                System.out.println(" Geo's dim = " + simContext.getGeometry().getDimension());
                simContext.setElectricalStimuli(new ElectricalStimulus[] { ccStimulus });
                simContext.setGroundElectrode(new Electrode(groundFeature, new Coordinate(0, 0, 0)));
            }
        }
        // 
        if (selectedClamp == Clamp.No_Clamp) {
            if (simContext.getElectricalStimuli().length > 0) {
                simContext.setElectricalStimuli(new ElectricalStimulus[0]);
            }
        }
        // 
        if (selectedClamp == Clamp.Voltage_Clamp) {
            if (simContext.getElectricalStimuli().length == 0 || !(simContext.getElectricalStimuli()[0] instanceof VoltageClampStimulus)) {
                Electrode probeElectrode = new Electrode(clampedFeature, new Coordinate(0, 0, 0));
                VoltageClampStimulus vcStimulus = new VoltageClampStimulus(probeElectrode, "vcElectrode", new Expression(0.0), simContext);
                System.out.println(" Geo's dim = " + simContext.getGeometry().getDimension());
                simContext.setElectricalStimuli(new ElectricalStimulus[] { vcStimulus });
                simContext.setGroundElectrode(new Electrode(groundFeature, new Coordinate(0, 0, 0)));
            }
        }
    } catch (java.beans.PropertyVetoException e) {
        PopupGenerator.showErrorDialog(this, "Error setting electrical stimulus: " + e.getMessage());
    }
}

Example 87 with SimulationContext

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

the class ModelProcessSpecsPanel method setSimulationContext.

/**
 * Sets the simulationContext property (cbit.vcell.mapping.SimulationContext) value.
 * @param simulationContext The new value for the property.
 * @see #getSimulationContext
 */
public void setSimulationContext(SimulationContext simulationContext) {
    SimulationContext oldValue = fieldSimulationContext;
    fieldSimulationContext = simulationContext;
    firePropertyChange("simulationContext", oldValue, simulationContext);
}

Example 88 with SimulationContext

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

the class SpeciesContextSpecParameterTableModel method propertyChange.

/**
 * This method gets called when a bound property is changed.
 * @param evt A PropertyChangeEvent object describing the event source
 *   and the property that has changed.
 */
public void propertyChange(java.beans.PropertyChangeEvent evt) {
    // 
    try {
        // 
        if (fieldSpeciesContextSpec != null && evt.getSource() == fieldSpeciesContextSpec.getSimulationContext().getGeometryContext() && evt.getPropertyName().equals("geometry")) {
            refreshData();
        }
        // 
        if (fieldSpeciesContextSpec != null && evt.getSource() == fieldSpeciesContextSpec.getSimulationContext().getGeometryContext() && evt.getPropertyName().equals("structureMappings")) {
            StructureMapping[] oldStructureMappings = (StructureMapping[]) evt.getOldValue();
            for (int i = 0; oldStructureMappings != null && i < oldStructureMappings.length; i++) {
                oldStructureMappings[i].removePropertyChangeListener(this);
            }
            StructureMapping[] newStructureMappings = (StructureMapping[]) evt.getNewValue();
            for (int i = 0; newStructureMappings != null && i < newStructureMappings.length; i++) {
                newStructureMappings[i].addPropertyChangeListener(this);
            }
            refreshData();
        }
        // 
        if (evt.getSource() instanceof StructureMapping) {
            refreshData();
        }
        if (evt.getSource() == this && evt.getPropertyName().equals("speciesContextSpec")) {
            SpeciesContextSpec oldValue = (SpeciesContextSpec) evt.getOldValue();
            if (oldValue != null) {
                oldValue.removePropertyChangeListener(this);
                Parameter[] oldParameters = oldValue.getParameters();
                if (oldParameters != null) {
                    for (int i = 0; i < oldParameters.length; i++) {
                        oldParameters[i].removePropertyChangeListener(this);
                    }
                }
                SimulationContext oldSimContext = oldValue.getSimulationContext();
                if (oldSimContext != null) {
                    oldSimContext.getGeometryContext().removePropertyChangeListener(this);
                    StructureMapping[] oldStructureMappings = oldSimContext.getGeometryContext().getStructureMappings();
                    if (oldStructureMappings != null) {
                        for (int i = 0; i < oldStructureMappings.length; i++) {
                            oldStructureMappings[i].removePropertyChangeListener(this);
                        }
                    }
                }
            }
            SpeciesContextSpec newValue = (SpeciesContextSpec) evt.getNewValue();
            if (newValue != null) {
                newValue.addPropertyChangeListener(this);
                Parameter[] newParameters = newValue.getParameters();
                if (newParameters != null) {
                    for (int i = 0; i < newParameters.length; i++) {
                        newParameters[i].addPropertyChangeListener(this);
                    }
                }
                SimulationContext newSimContext = newValue.getSimulationContext();
                if (newSimContext != null) {
                    newSimContext.getGeometryContext().addPropertyChangeListener(this);
                    StructureMapping[] newStructureMappings = newSimContext.getGeometryContext().getStructureMappings();
                    if (newStructureMappings != null) {
                        for (int i = 0; i < newStructureMappings.length; i++) {
                            newStructureMappings[i].addPropertyChangeListener(this);
                        }
                    }
                }
            }
            refreshData();
        }
        if (evt.getSource() instanceof SpeciesContextSpec) {
            // if parameters changed must update listeners
            if (evt.getPropertyName().equals("parameters")) {
                Parameter[] oldParameters = (Parameter[]) evt.getOldValue();
                if (oldParameters != null) {
                    for (int i = 0; i < oldParameters.length; i++) {
                        oldParameters[i].removePropertyChangeListener(this);
                    }
                }
                Parameter[] newParameters = (Parameter[]) evt.getNewValue();
                if (newParameters != null) {
                    for (int i = 0; i < newParameters.length; i++) {
                        newParameters[i].addPropertyChangeListener(this);
                    }
                }
            }
            if (!evt.getPropertyName().equals(SpeciesContextSpec.PARAMETER_NAME_PROXY_PARAMETERS)) {
                // for any change to the SpeciesContextSpec, want to update all.
                // proxy parameters don't affect table
                refreshData();
            }
        }
        if (evt.getSource() instanceof Parameter) {
            refreshData();
        }
    } catch (Exception e) {
        e.printStackTrace(System.out);
    }
}

Example 89 with SimulationContext

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

the class StructureMappingCartoonPanel method setSimulationContext.

/**
 * Sets the simulationContext property (cbit.vcell.mapping.SimulationContext) value.
 * @param simulationContext The new value for the property.
 * @see #getSimulationContext
 */
public void setSimulationContext(SimulationContext simulationContext) {
    SimulationContext oldValue = fieldSimulationContext;
    fieldSimulationContext = simulationContext;
    getMessageLabel().setVisible(this.hasMappableGeometry());
    getBoundaryMessageLabel().setVisible(this.hasMappableGeometry());
    firePropertyChange("simulationContext", oldValue, simulationContext);
}

Example 90 with SimulationContext

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

the class StructureMappingCartoonPanel method setsimulationContext1.

/**
 * Set the simulationContext1 to a new value.
 * @param newValue cbit.vcell.mapping.SimulationContext
 */
/* WARNING: THIS METHOD WILL BE REGENERATED. */
private void setsimulationContext1(SimulationContext newValue) {
    if (ivjsimulationContext1 != newValue) {
        try {
            SimulationContext oldValue = getsimulationContext1();
            /* Stop listening for events from the current object */
            if (ivjsimulationContext1 != null) {
                ivjsimulationContext1.removePropertyChangeListener(this);
            }
            ivjsimulationContext1 = newValue;
            /* Listen for events from the new object */
            if (ivjsimulationContext1 != null) {
                ivjsimulationContext1.addPropertyChangeListener(this);
            }
            connPtoP3SetSource();
            connEtoM15(ivjsimulationContext1);
            connEtoM3(ivjsimulationContext1);
            connEtoM10(ivjsimulationContext1);
            firePropertyChange("simulationContext", oldValue, newValue);
        // user code begin {1}
        // user code end
        } catch (java.lang.Throwable ivjExc) {
            // user code begin {2}
            // user code end
            handleException(ivjExc);
        }
    }
    ;
// user code begin {3}
// user code end
}