Examples with SourceDataInfo cbit.image.SourceDataInfo used on opensource projects

Example 11 with SourceDataInfo

use of cbit.image.SourceDataInfo in project vcell by virtualcell.

the class KymographPanel method initStandAloneTimeSeries_private.

/**
 * Insert the method's description here.
 * Creation date: (12/14/2004 9:47:38 AM)
 * @param timeSeries double[][]
 * @param distances double[]
 */
private void initStandAloneTimeSeries_private(double[][] timeSeriesOrig, double[] accumDistancesOrig) throws DataAccessException {
    if (accumDistancesOrig.length != (timeSeriesOrig.length - 1)) {
        throw new IllegalArgumentException(this.getClass().getName() + " accumDistances.length != numSamplePoints");
    }
    timeSeriesDataOrig = timeSeriesOrig;
    accumDistancesDataOrig = accumDistancesOrig;
    currentTimes = timeSeriesDataOrig[0];
    // Resample for even distances
    RESAMP_SIZE = timeSeriesDataOrig.length - 1;
    int rvSize = (currentTimes.length) * RESAMP_SIZE;
    rawValues = new double[rvSize];
    double incr = accumDistancesDataOrig[accumDistancesDataOrig.length - 1] / (double) (RESAMP_SIZE - 1);
    currentDistances = new double[RESAMP_SIZE];
    for (int j = 0; j < currentTimes.length; j += 1) {
        int sourceIndex = 0;
        double currentDistance = 0;
        for (int k = 0; k < RESAMP_SIZE; k += 1) {
            while (currentDistance > accumDistancesDataOrig[sourceIndex + 1]) {
                sourceIndex += 1;
            }
            double subShort = currentDistance - accumDistancesDataOrig[sourceIndex];
            double subLong = accumDistancesDataOrig[sourceIndex + 1] - accumDistancesDataOrig[sourceIndex];
            double proportion = subShort / subLong;
            // System.out.println("prop="+proportion+" j="+j+" k="+k+" sourceIndex="+sourceIndex+"sourcedist="+accumDistancesDataOrig[sourceIndex]+" currentDistance="+currentDistance);
            double value = timeSeriesDataOrig[1 + sourceIndex + (proportion > .5 ? 1 : 0)][j];
            // double value = timeSeriesDataOrig[1+sourceIndex][j] + ((timeSeriesDataOrig[1+sourceIndex+1][j]-timeSeriesDataOrig[1+sourceIndex][j])*proportion);
            // if(k == (RESAMP_SIZE-1)){
            // value = timeSeriesDataOrig[timeSeriesDataOrig.length-1][j];
            // }
            rawValues[(j * RESAMP_SIZE) + (k)] = value;
            currentDistances[k] = currentDistance;
            currentDistance += incr;
            if (currentDistance > accumDistancesDataOrig[accumDistancesDataOrig.length - 1]) {
                currentDistance = accumDistancesDataOrig[accumDistancesDataOrig.length - 1];
            }
        }
    }
    Range minmaxRange = null;
    allDataMMMH = calcMMM(rawValues);
    if (allDataMMMH != null) {
        minmaxRange = allDataMMMH.getRange();
    }
    SourceDataInfo sdi = new SourceDataInfo(SourceDataInfo.RAW_VALUE_TYPE, rawValues, minmaxRange, 0, RESAMP_SIZE, 1, 0, accumDistancesDataOrig[accumDistancesDataOrig.length - 1], currentTimes.length, RESAMP_SIZE, currentTimes[0], currentTimes[currentTimes.length - 1] - currentTimes[0]);
    getImagePaneScroller1().getImagePaneModel().setSourceData(sdi);
    getImagePlaneManager1().setSourceDataInfo(sdi);
    if (isInit) {
        zoomUpJButton_ActionPerformed(null);
        zoomDownJButton_ActionPerformed(null);
    // getImagePaneScroller1().getImagePaneModel().changeZoomToFillViewport();
    }
    getDisplayJLabel().setText(NONE_MESSAGE);
    configurePlotData(currentSelectionImg.x, currentSelectionImg.y);
}

Example 12 with SourceDataInfo

use of cbit.image.SourceDataInfo in project vcell by virtualcell.

the class ImagePaneScroller method viewport1_Change.

/**
 * Comment
 */
private void viewport1_Change() {
    // 
    // -----Begin Fix for Jumping scroll bars
    // This CRRRAAAPPP!!!!!! is here because of an apparent bug in ScrollPaneLayout that
    // does not take into account the scrollbar sizes when calculating the size of the viewport
    java.awt.Rectangle availR = new java.awt.Rectangle(getJScrollPane1().getSize());
    java.awt.Insets insets = getJScrollPane1().getInsets();
    availR.x = insets.left;
    availR.y = insets.top;
    availR.width -= insets.left + insets.right;
    availR.height -= insets.top + insets.bottom;
    /* If there's a visible column header remove the space it 
	 * needs from the top of availR.  The column header is treated 
	 * as if it were fixed height, arbitrary width.
	 */
    java.awt.Rectangle colHeadR = new java.awt.Rectangle(0, availR.y, 0, 0);
    javax.swing.JViewport colHead = getJScrollPane1().getColumnHeader();
    if ((colHead != null) && (colHead.isVisible())) {
        int colHeadHeight = colHead.getPreferredSize().height;
        colHeadR.height = colHeadHeight;
        availR.y += colHeadHeight;
        availR.height -= colHeadHeight;
    }
    /* If there's a visible row header remove the space it needs
	 * from the left of availR.  The row header is treated 
	 * as if it were fixed width, arbitrary height.
	 */
    java.awt.Rectangle rowHeadR = new java.awt.Rectangle(availR.x, 0, 0, 0);
    javax.swing.JViewport rowHead = getJScrollPane1().getRowHeader();
    boolean leftToRight = true;
    if ((rowHead != null) && (rowHead.isVisible())) {
        int rowHeadWidth = rowHead.getPreferredSize().width;
        rowHeadR.width = rowHeadWidth;
        availR.width -= rowHeadWidth;
        if (leftToRight) {
            // ibm.597
            // ibm.597
            rowHeadR.x = availR.x;
            // ibm.597
            availR.x += rowHeadWidth;
        } else {
            // ibm.597
            // ibm.597
            rowHeadR.x = availR.x + availR.width;
        }
    // ibm.597
    }
    // System.out.println("availR="+availR);
    // System.out.println("viewportBounds="+getJScrollPane1().getViewport().getBounds());
    // System.out.println("hsb="+getJScrollPane1().getHorizontalScrollBar().getSize()+" "+getJScrollPane1().getHorizontalScrollBar().getInsets());
    // System.out.println("vsb="+getJScrollPane1().getVerticalScrollBar().getSize()+" "+getJScrollPane1().getVerticalScrollBar().getInsets());
    // System.out.println();
    getJScrollPane1().getViewport().reshape(availR.x, availR.y, (int) availR.getWidth() - (int) getJScrollPane1().getVerticalScrollBar().getSize().getWidth(), (int) availR.getHeight() - (int) getJScrollPane1().getHorizontalScrollBar().getSize().getHeight());
    // 
    if (getviewport1() != null && getJScrollPane1().getViewport() != null) {
        // System.out.println("ImagePaneScroller.viewport bounds=           "+getviewport1().getBounds());
        // System.out.println("ImagePaneScroller.viewport borderbounds *** ="+getJScrollPane1().getViewportBorderBounds());
        // System.out.println("ImagePaneScroller.viewport size=             "+getJScrollPane1().getViewport().getSize());
        // System.out.println("ImagePaneScroller.viewport viewpostion=      "+getJScrollPane1().getViewport().getViewPosition());
        // System.out.println("ImagePaneScroller.viewport viewsize=         "+getJScrollPane1().getViewport().getViewSize());
        // if(getviewport1().getBounds().equals(getJScrollPane1().getViewportBorderBounds())){
        java.awt.Point viewULC = getJScrollPane1().getViewport().getViewPosition();
        java.awt.Rectangle visibleArea = getJScrollPane1().getViewportBorderBounds();
        visibleArea.setLocation(getJScrollPane1().getViewport().getViewPosition());
        getImagePaneView().getImagePaneModel().setViewport(visibleArea);
        // 
        if (!hasUserSetZoom && getImagePaneModel() != null && getImagePaneModel().getSourceData() != null) {
            SourceDataInfo sdi = getImagePaneModel().getSourceData();
            int boundsXSize = (int) getJScrollPane1().getViewportBorderBounds().getWidth();
            int boundsYSize = (int) getJScrollPane1().getViewportBorderBounds().getHeight();
            int zoom = Math.min(boundsXSize / (sdi.getXSize() * 2), boundsYSize / (sdi.getYSize() * 2));
            zoom = (zoom < 1 ? 1 : zoom);
            getImagePaneModel().setZoom(zoom);
        }
        // 
        if (getImagePaneModel().getSourceData() != null) {
            // java.awt.Point vpPos = getJScrollPane1().getViewport().getViewPosition();
            // java.awt.Dimension vpDim = getJScrollPane1().getViewport().getSize();
            // java.awt.geom.Point2D.Double unitOrigin =
            // getImagePaneModel().calculateImagePointUnitized(
            // new java.awt.Point((int)vpPos.getX(),(int)vpPos.getY()));
            // java.awt.geom.Point2D.Double unitend =
            // getImagePaneModel().calculateImagePointUnitized(
            // new java.awt.Point((int)(vpPos.getX()+vpDim.getWidth()),(int)(vpPos.getY()+vpDim.getHeight())));
            // double worldExtent = getImagePaneModel().getSourceData().getExtent().getX()*(unitend.getX()-unitOrigin.getX());
            // double worldOrigin =
            // getImagePaneModel().getSourceData().getOrigin().getX()+
            // getImagePaneModel().getSourceData().getExtent().getX()*unitOrigin.getX();
            // ((ImagePaneRuler)getJScrollPane1().getColumnHeader().getView()).setWorldOrigin(worldOrigin);
            // ((ImagePaneRuler)getJScrollPane1().getColumnHeader().getView()).setWorldExtent(worldExtent);
            // 
            // 
            // 
            // double worldExtent = getImagePaneModel().getSourceData().getExtent().getX();
            // double worldOrigin = getImagePaneModel().getSourceData().getOrigin().getX();
            // ((ImagePaneRuler)getJScrollPane1().getColumnHeader().getView()).setWorldOrigin(worldOrigin);
            // ((ImagePaneRuler)getJScrollPane1().getColumnHeader().getView()).setWorldExtent(worldExtent);
            sizeHeaders();
        }
        getJScrollPane1().getColumnHeader().getView().repaint();
        getJScrollPane1().getRowHeader().getView().repaint();
    // getJScrollPane1().getColumnHeader().getView().invalidate();
    // revalidate();
    // }
    // System.out.println();
    }
}

Example 13 with SourceDataInfo

use of cbit.image.SourceDataInfo in project vcell by virtualcell.

the class ImagePaneScrollerTest method main.

/**
 * Starts the application.
 * @param args an array of command-line arguments
 */
public static void main(java.lang.String[] args) {
    // Insert code to start the application here.
    // Create default image
    int w = Integer.valueOf(args[2]).intValue();
    int h = Integer.valueOf(args[3]).intValue();
    String type = args[0];
    SourceDataInfo sdi = getExampleSDI(type, w, h);
    DisplayAdapterService das = null;
    if (type.equals("double")) {
        das = new DisplayAdapterService();
        das.setActiveScaleRange(new Range(0, 450));
        das.setValueDomain(new Range(-50, 550));
        das.addColorModelForValues(DisplayAdapterService.createGrayColorModel(), DisplayAdapterService.createGraySpecialColors(), DisplayAdapterService.GRAY);
        das.addColorModelForValues(DisplayAdapterService.createBlueRedColorModel(), DisplayAdapterService.createBlueRedSpecialColors(), DisplayAdapterService.BLUERED);
        das.setActiveColorModelID(DisplayAdapterService.GRAY);
    } else if (type.equals("index")) {
        das = new DisplayAdapterService();
        das.addColorModelForIndexes(DisplayAdapterService.createGrayColorModel(), DisplayAdapterService.GRAY);
        das.addColorModelForIndexes(DisplayAdapterService.createBlueRedColorModel(), DisplayAdapterService.BLUERED);
        das.setActiveColorModelID(DisplayAdapterService.GRAY);
    }
    try {
        javax.swing.JFrame frame = new javax.swing.JFrame();
        ImagePaneScroller aImagePaneScroller;
        aImagePaneScroller = new ImagePaneScroller();
        aImagePaneScroller.getImagePaneModel().setSourceData(sdi);
        aImagePaneScroller.getImagePaneModel().setDisplayAdapterService(das);
        // aImagePaneScroller.getImagePaneModel().setBackgroundColor(java.awt.Color.yellow);
        if (args[1].equals("true")) {
            aImagePaneScroller.getImagePaneModel().setMode(ImagePaneModel.MESH_MODE);
        }
        javax.swing.JPanel jp = new javax.swing.JPanel();
        jp.setLayout(new java.awt.BorderLayout());
        jp.add(aImagePaneScroller);
        frame.setContentPane(jp);
        frame.setSize(aImagePaneScroller.getSize());
        frame.addWindowListener(new java.awt.event.WindowAdapter() {

            public void windowClosing(java.awt.event.WindowEvent e) {
                System.exit(0);
            }
        });
        frame.show();
        java.awt.Insets insets = frame.getInsets();
        frame.setSize(frame.getWidth() + insets.left + insets.right, frame.getHeight() + insets.top + insets.bottom);
        frame.setVisible(true);
    } catch (Throwable exception) {
        System.err.println("Exception occurred in main() of javax.swing.JPanel");
        exception.printStackTrace(System.out);
    }
}

Example 14 with SourceDataInfo

use of cbit.image.SourceDataInfo in project vcell by virtualcell.

the class ImagePaneScrollerTest method getExampleSDI.

/**
 * Insert the method's description here.
 * Creation date: (10/12/00 2:08:24 PM)
 * @return cbit.image.SourceDataInfo
 */
public static final SourceDataInfo getExampleSDI(String type, int w, int h) {
    int numZ = 20;
    SourceDataInfo sdi = null;
    if (type.equals("rgb")) {
        int[] pixels = new int[w * h * numZ];
        for (int z = 0; z < numZ; z += 1) {
            for (int y = 0; y < h; y += 1) {
                for (int x = 0; x < w; x += 1) {
                    if (y % 2 == 0) {
                        if (x % 2 == 0) {
                            pixels[x + (y * w) + (z * w * h)] = 0x00ff0000;
                        }
                    } else {
                        if (x % 2 != 0) {
                            pixels[x + (y * w) + (z * w * h)] = 0x00ff0000;
                        }
                    }
                    if (x >= w / 3 && x < w / 2 && y >= h / 3 && y < h / 1.5) {
                        pixels[x + (y * w) + (z * w * h)] = 0xFF * z / numZ * 0xFFFF;
                    }
                }
            }
        }
        // 
        sdi = new SourceDataInfo(SourceDataInfo.INT_RGB_TYPE, pixels, new org.vcell.util.Extent(1, 2, 3), new org.vcell.util.Origin(0, -5, 10), null, 0, w, 1, h, w, numZ, h * w);
    } else if (type.equals("double")) {
        double[] pixels = new double[w * h * numZ];
        for (int z = 0; z < numZ; z += 1) {
            for (int y = 0; y < h; y += 1) {
                for (int x = 0; x < w; x += 1) {
                    pixels[x + (y * w) + (z * w * h)] = -150 + ((double) x / ((double) w - 1)) * (800);
                    if (y > h - (h / 4)) {
                        pixels[x + (y * w) + (z * w * h)] = Double.POSITIVE_INFINITY;
                    }
                    if (x >= w / 3 && x < w / 2 && y >= h / 3 && y < h / 1.5) {
                        pixels[x + (y * w) + (z * w * h)] = 300 * z / numZ;
                    }
                }
            }
        }
        sdi = new SourceDataInfo(SourceDataInfo.RAW_VALUE_TYPE, pixels, new org.vcell.util.Extent(1, 2, 3), new org.vcell.util.Origin(0, -5, 10), new Range(-150, 650), 0, w, 1, h, w, numZ, h * w);
    } else if (type.equals("index")) {
        byte[] pixels = new byte[w * h * numZ];
        for (int i = 0; i < pixels.length; i += 1) {
            pixels[i] = (byte) (i % 256);
        }
        sdi = new SourceDataInfo(SourceDataInfo.INDEX_TYPE, pixels, new org.vcell.util.Extent(1, 2, 3), new org.vcell.util.Origin(0, -5, 10), null, 0, w, 1, h, w, numZ, h * w);
    } else if (type.equals("facecube")) {
        numZ = 50;
        w = 50;
        h = 50;
        int[] pixels = new int[w * h * numZ];
        int[] facePixels = new int[w * h];
        java.awt.image.BufferedImage face = new java.awt.image.BufferedImage(w, h, java.awt.image.BufferedImage.TYPE_INT_RGB);
        java.awt.Graphics2D g2d = face.createGraphics();
        g2d.setRenderingHint(java.awt.RenderingHints.KEY_FRACTIONALMETRICS, java.awt.RenderingHints.VALUE_FRACTIONALMETRICS_ON);
        g2d.setRenderingHint(java.awt.RenderingHints.KEY_ANTIALIASING, java.awt.RenderingHints.VALUE_ANTIALIAS_ON);
        g2d.setFont(new java.awt.Font("SansSerif", java.awt.Font.PLAIN, 6));
        // g2d.scale(2,2);
        // java.awt.Font smallFont = g2d.getFont().deriveFont(10);
        // g2d.setFont(smallFont);
        int xStart = 0;
        int xEnd = 0;
        int xIncr = 0;
        int yStart = 0;
        int yEnd = 0;
        int yIncr = 0;
        int zStart = 0;
        int zEnd = 0;
        int zIncr = 0;
        for (int i = 0; i < 2; i += 1) {
            g2d.setColor(java.awt.Color.red);
            g2d.fillRect(0, 0, w, h);
            g2d.setColor(java.awt.Color.white);
            switch(i) {
                case 0:
                    xStart = 0;
                    xEnd = w;
                    xIncr = 1;
                    yStart = 0;
                    yEnd = w * h;
                    yIncr = w;
                    zStart = 0;
                    zEnd = w * h * numZ;
                    zIncr = w * h;
                    g2d.drawString("- FRNT(-) +", 0, 15);
                    g2d.drawString("- FRNT (+) +", 0, h - 2);
                    break;
                case 1:
                    xStart = 0;
                    xEnd = w;
                    xIncr = 1;
                    yStart = 0;
                    yEnd = w * h;
                    yIncr = w;
                    zStart = 0;
                    zEnd = w * h * numZ;
                    zIncr = w * h;
                    g2d.drawString("- BTM(-) +", 0, 15);
                    g2d.drawString("- BTM (+) +", 0, h - 2);
                    break;
                case 2:
                    break;
                case 3:
                    break;
                case 4:
                    break;
                case 5:
                    break;
                default:
            }
            face.getRGB(0, 0, w, h, facePixels, 0, w);
            for (int z = zStart; z != zEnd; z += zIncr * (zEnd - zStart < 0 ? -1 : 1)) {
                int index = 0;
                for (int y = yStart; y != yEnd; y += yIncr * (yEnd - yStart < 0 ? -1 : 1)) {
                    for (int x = xStart; x != xEnd; x += xIncr * (xEnd - xStart < 0 ? -1 : 1)) {
                        pixels[x + (y) + (z)] = facePixels[index];
                        index += 1;
                    }
                }
            }
        }
        sdi = new SourceDataInfo(SourceDataInfo.INT_RGB_TYPE, pixels, new org.vcell.util.Extent(1, 2, 3), new org.vcell.util.Origin(0, -5, 10), null, 0, w, 1, h, w, numZ, h * w);
    }
    // 
    return sdi;
}

Example 15 with SourceDataInfo

use of cbit.image.SourceDataInfo in project vcell by virtualcell.

the class ImagePlaneManagerPanel method setSourceDataInfo.

/**
 * Sets the sourceDataInfo property (cbit.image.SourceDataInfo) value.
 * @param sourceDataInfo The new value for the property.
 * @see #getSourceDataInfo
 */
public void setSourceDataInfo(SourceDataInfo sourceDataInfo) {
    SourceDataInfo oldValue = fieldSourceDataInfo;
    fieldSourceDataInfo = sourceDataInfo;
    firePropertyChange("sourceDataInfo", oldValue, sourceDataInfo);
    // 
    // Sometimes if a change of data timepoint,variable,paramscan takes a long time and the user moves the mouse
    // into the data display before the new data has fully updated the wrong value will be displayed
    // make sure the data value text display is always updated if the mouse is in the data display
    updateInfo(lastValidMouseEvent);
    if (lastValidMouseEvent != null) {
        // make sure the tooltip is updated if the mouse is in the data display
        ToolTipManager.sharedInstance().mouseMoved(lastValidMouseEvent);
    }
    // 
    getImagePaneScroller1().repaint();
}