Examples with Curve cbit.vcell.geometry.Curve used on opensource projects

Example 6 with Curve

use of cbit.vcell.geometry.Curve in project vcell by virtualcell.

the class PDEDataContextPanel method getInitalCurveSelection.

/**
 * Insert the method's description here.
 * Creation date: (7/4/2003 6:10:48 PM)
 */
public CurveSelectionInfo getInitalCurveSelection(int tool, Coordinate wc) {
    // 
    CurveSelectionInfo newCurveSelection = null;
    VariableType variableType = getPdeDataContext().getDataIdentifier().getVariableType();
    if (variableType.equals(VariableType.MEMBRANE) || variableType.equals(VariableType.MEMBRANE_REGION)) {
        if (getPdeDataContext().getCartesianMesh().isChomboMesh() && tool == CurveEditorTool.TOOL_POINT) {
            newCurveSelection = findChomboSinglePointSelectionInfoForPoint(wc);
        } else {
            CurveSelectionInfo[] closeCSI = getImagePlaneManagerPanel().getCurveRenderer().getCloseCurveSelectionInfos(wc);
            if (closeCSI != null) {
                for (int i = 0; i < closeCSI.length; i += 1) {
                    if (membranesAndIndexes != null && membranesAndIndexes.containsKey(closeCSI[i].getCurve())) {
                        if (tool == CurveEditorTool.TOOL_LINE) {
                            newCurveSelection = new CurveSelectionInfo(new CurveSelectionCurve((SampledCurve) (closeCSI[i].getCurve())));
                        } else if (tool == CurveEditorTool.TOOL_POINT) {
                            newCurveSelection = new CurveSelectionInfo(new CurveSelectionCurve((SampledCurve) (closeCSI[i].getCurve())));
                            double dist = closeCSI[i].getCurve().getDistanceTo(wc);
                            int segmentIndex = closeCSI[i].getCurve().pickSegment(wc, dist * 1.1);
                            Coordinate[] coordArr = closeCSI[i].getCurve().getSampledCurve().getControlPointsForSegment(segmentIndex);
                            Coordinate middleCoord = new Coordinate((coordArr[0].getX() + coordArr[1].getX()) / 2, (coordArr[0].getY() + coordArr[1].getY()) / 2, (coordArr[0].getZ() + coordArr[1].getZ()) / 2);
                            newCurveSelection = new CurveSelectionInfo(new SinglePoint(middleCoord));
                        }
                        break;
                    }
                }
            }
        }
    }
    if (newCurveSelection != null) {
        if (membraneSamplerCurves == null) {
            membraneSamplerCurves = new java.util.Vector<Curve>();
        }
        membraneSamplerCurves.add(newCurveSelection.getCurve());
    }
    return newCurveSelection;
}

Example 7 with Curve

use of cbit.vcell.geometry.Curve in project vcell by virtualcell.

the class GeometryFilamentCurvePanel method setCurve3.

/**
 * Set the Curve3 to a new value.
 * @param newValue cbit.vcell.geometry.Curve
 */
/* WARNING: THIS METHOD WILL BE REGENERATED. */
private void setCurve3(cbit.vcell.geometry.Curve newValue) {
    if (ivjCurve3 != newValue) {
        try {
            cbit.vcell.geometry.Curve oldValue = getCurve3();
            ivjCurve3 = newValue;
            connPtoP8SetSource();
            firePropertyChange("curve", 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
}

Example 8 with Curve

use of cbit.vcell.geometry.Curve in project vcell by virtualcell.

the class DisplayImageOp method displayImage.

public void displayImage(final Image image, String title, WindowListener listener) {
    final ImagePlaneManagerPanel imagePanel = new ImagePlaneManagerPanel();
    double[] doublePixels = image.getDoublePixels();
    double minPixel = Double.MAX_VALUE;
    double maxPixel = -Double.MAX_VALUE;
    for (int i = 0; i < doublePixels.length; i++) {
        double pixel = doublePixels[i];
        doublePixels[i] = pixel;
        minPixel = Math.min(minPixel, pixel);
        maxPixel = Math.max(maxPixel, pixel);
    }
    Range newRange = new Range(minPixel, maxPixel);
    SourceDataInfo source = new SourceDataInfo(SourceDataInfo.RAW_VALUE_TYPE, doublePixels, image.getExtent(), image.getOrigin(), newRange, 0, image.getNumX(), 1, image.getNumY(), image.getNumX(), image.getNumZ(), image.getNumX() * image.getNumY());
    imagePanel.setDisplayAdapterServicePanelVisible(true);
    imagePanel.setCurveValueProvider(new CurveValueProvider() {

        @Override
        public void curveAdded(Curve curve) {
            System.out.println("called curveAdded(" + curve + "), do nothing for now");
        }

        @Override
        public void curveRemoved(Curve curve) {
            System.out.println("called curveRemoved(" + curve + ")");
        }

        @Override
        public String getCurveValue(CurveSelectionInfo csi) {
            System.out.println("called getCurveValue(CurveSelectionInfo " + csi);
            return null;
        }

        @Override
        public CurveSelectionInfo getInitalCurveSelection(int tool, Coordinate wc) {
            System.out.println("called getInitialCurveSelection(tool=" + tool + ", coord=" + wc + ")");
            return null;
        }

        @Override
        public boolean isAddControlPointOK(int tool, Coordinate wc, Curve addedToThisCurve) {
            System.out.println("called isAddControlPointOK");
            return true;
        }

        @Override
        public boolean providesInitalCurve(int tool, Coordinate wc) {
            System.out.println("called providesInitialCurve(tool=" + tool + " (TOOL_LINE=" + CurveEditorTool.TOOL_LINE + "), coord=" + wc);
            return false;
        }

        @Override
        public void setDescription(Curve curve) {
            System.out.println("called setDescription(" + curve + ")");
            curve.setDescription(CurveValueProvider.DESCRIPTION_VOLUME);
        }

        @Override
        public CurveSelectionInfo findChomboCurveSelectionInfoForPoint(CoordinateIndex ci) {
            System.out.println("called find ChomboCurveSelectionInfoForPoint(coord=" + ci + ")");
            return null;
        }
    });
    DisplayAdapterService das = imagePanel.getDisplayAdapterServicePanel().getDisplayAdapterService();
    das.setValueDomain(null);
    das.addColorModelForValues(DisplayAdapterService.createGrayColorModel(), DisplayAdapterService.createGraySpecialColors(), DisplayAdapterService.GRAY);
    das.addColorModelForValues(DisplayAdapterService.createBlueRedColorModel(), DisplayAdapterService.createBlueRedSpecialColors(), DisplayAdapterService.BLUERED);
    das.setActiveColorModelID(DisplayAdapterService.BLUERED);
    final JFrame jframe = new JFrame();
    jframe.setTitle(title);
    JPanel panel = new JPanel();
    panel.setLayout(new GridBagLayout());
    GridBagConstraints imageConstraints = new GridBagConstraints();
    imageConstraints.gridx = 0;
    imageConstraints.gridy = 0;
    imageConstraints.weightx = 1.0;
    imageConstraints.weighty = 1.0;
    imageConstraints.fill = GridBagConstraints.BOTH;
    panel.add(imagePanel, imageConstraints);
    JButton plotButton = new JButton("plot");
    plotButton.addActionListener(new ActionListener() {

        @Override
        public void actionPerformed(ActionEvent e) {
            try {
                Curve curve = imagePanel.getCurveRenderer().getSelection().getCurve();
                VariableType variableType = VariableType.VOLUME;
                Curve samplerCurve = curve.getSampledCurve();
                samplerCurve.setDescription(curve.getDescription());
                VCImage vcImage = new VCImageUncompressed(null, new byte[image.getISize().getXYZ()], image.getExtent(), image.getISize().getX(), image.getISize().getY(), image.getISize().getZ());
                int dimension = 1 + (image.getISize().getY() > 0 ? 1 : 0) + (image.getISize().getZ() > 0 ? 1 : 0);
                RegionImage regionImage = new RegionImage(vcImage, dimension, image.getExtent(), image.getOrigin(), RegionImage.NO_SMOOTHING);
                CartesianMesh mesh = CartesianMesh.createSimpleCartesianMesh(image.getOrigin(), image.getExtent(), image.getISize(), regionImage);
                SpatialSelectionVolume ssVolume = new SpatialSelectionVolume(new CurveSelectionInfo(samplerCurve), variableType, mesh);
                String varName = "var";
                SymbolTableEntry[] symbolTableEntries = new SymbolTableEntry[] { new VolVariable(varName, null) };
                PlotData plotData = getLineScan(ssVolume, image, mesh);
                PlotPane plotPane = new PlotPane();
                DataSymbolMetadataResolver resolver = null;
                Plot2D plot2D = new Plot2D(symbolTableEntries, resolver, new String[] { varName }, new PlotData[] { plotData }, new String[] { "Values along curve", "Distance (\u00b5m)", "[" + varName + "]" });
                plotPane.setPlot2D(plot2D);
                DialogUtils.showComponentCloseDialog(jframe, plotPane, "plot");
            } catch (ImageException | IOException | DataAccessException | MathException e1) {
                e1.printStackTrace();
            }
        }
    });
    GridBagConstraints plotButtonConstraints = new GridBagConstraints();
    plotButtonConstraints.gridx = 0;
    plotButtonConstraints.gridy = 1;
    panel.add(plotButton, plotButtonConstraints);
    jframe.getContentPane().add(panel);
    jframe.setSize(500, 500);
    jframe.addWindowListener(listener);
    jframe.setVisible(true);
    imagePanel.setSourceDataInfo(source);
}

Example 9 with Curve

use of cbit.vcell.geometry.Curve in project vcell by virtualcell.

the class GeomDbDriver method getFilaments.

/**
 * Insert the method's description here.
 * Creation date: (7/29/00 2:10:42 PM)
 * @param con java.sql.Connection
 * @param geom cbit.vcell.geometry.Geometry
 */
private void getFilaments(Connection con, Geometry geom) throws SQLException, DataAccessException {
    String sql = null;
    sql = " SELECT " + filamentTable.filamentName.getQualifiedColName() + "," + curveTable.curveData.getQualifiedColName() + " FROM " + filamentTable.getTableName() + "," + curveTable.getTableName() + " WHERE " + filamentTable.geometryRef.getQualifiedColName() + " = " + geom.getVersion().getVersionKey() + " AND " + curveTable.filamentRef.getQualifiedColName() + " = " + filamentTable.id.getQualifiedColName();
    // System.out.println(sql);
    Statement stmt = con.createStatement();
    try {
        ResultSet rset = stmt.executeQuery(sql);
        while (rset.next()) {
            String filColName = filamentTable.filamentName.toString();
            String filamentType = rset.getString(filColName);
            Field curveCol = curveTable.curveData;
            // Curve curve = CurveTable.decodeCurve(new String(rset.getBytes(curveColName)));
            String curveString = (String) DbDriver.getLOB(rset, curveCol, dbSyntax);
            Curve curve = CurveTable.decodeCurve(curveString);
            // 
            geom.getGeometrySpec().getFilamentGroup().addCurve(filamentType, curve);
        }
    } catch (Exception e) {
        throw new DataAccessException(e.toString());
    } finally {
        // Release resources include resultset
        stmt.close();
    }
}

Example 10 with Curve

use of cbit.vcell.geometry.Curve in project vcell by virtualcell.

the class GeomDbDriver method insertFilamentsSQL.

/**
 * This method was created in VisualAge.
 * @param vcimage cbit.image.VCImage
 * @param userid java.lang.String
 * @exception java.rmi.RemoteException The exception description.
 */
private void insertFilamentsSQL(Connection con, Geometry geom, KeyValue geomKey) throws SQLException, DataAccessException {
    String sql;
    Filament[] filaments = geom.getGeometrySpec().getFilamentGroup().getFilaments();
    for (int i = 0; i < filaments.length; i++) {
        // Iterate through Filaments
        KeyValue newFilamentKey = keyFactory.getNewKey(con);
        // 
        // Insert Filament
        // 
        Filament currentFilament = filaments[i];
        sql = "INSERT INTO " + filamentTable.getTableName() + " " + filamentTable.getSQLColumnList() + " VALUES " + filamentTable.getSQLValueList(newFilamentKey, currentFilament.getName(), geomKey);
        updateCleanSQL(con, sql);
        // 
        // Insert all Curves for this filament
        // 
        Curve[] curves = currentFilament.getCurves();
        for (int j = 0; j < curves.length; j += 1) {
            KeyValue newCurveKey = keyFactory.getNewKey(con);
            sql = "INSERT INTO " + curveTable.getTableName() + " " + curveTable.getSQLColumnList() + " VALUES " + curveTable.getSQLValueList(newCurveKey, newFilamentKey, dbSyntax);
            // 
            switch(dbSyntax) {
                case ORACLE:
                    {
                        updateCleanSQL(con, sql);
                        updateCleanLOB(con, curveTable.id.toString(), newCurveKey, curveTable.tableName, curveTable.curveData, CurveTable.encodeCurve(curves[j]), dbSyntax);
                        break;
                    }
                case POSTGRES:
                    {
                        updatePreparedCleanSQL(con, sql, CurveTable.encodeCurve(curves[j]));
                        break;
                    }
                default:
                    {
                        throw new RuntimeException("unexpected DatabaseSyntax " + dbSyntax);
                    }
            }
        }
    }
}