Examples with ISize org.vcell.util.ISize used on opensource projects

Example 31 with ISize

use of org.vcell.util.ISize in project vcell by virtualcell.

the class MeshSpecification method getVCML.

/**
 * This method was created by a SmartGuide.
 * @return java.lang.String
 */
public String getVCML() {
    StringBuffer buffer = new StringBuffer();
    buffer.append(VCML.MeshSpecification + " {\n");
    ISize size = getSamplingSize();
    buffer.append("\t" + VCML.Size + " " + size.getX() + " " + size.getY() + " " + size.getZ() + "\n");
    buffer.append("}\n");
    return buffer.toString();
}

Example 32 with ISize

use of org.vcell.util.ISize in project vcell by virtualcell.

the class GeometryGuiTest method main.

public static void main(java.lang.String[] args) {
    try {
        javax.swing.JFrame frame = new javax.swing.JFrame();
        GeometryViewer aGeometryViewer;
        aGeometryViewer = new GeometryViewer();
        frame.setContentPane(aGeometryViewer);
        frame.setSize(aGeometryViewer.getSize());
        frame.addWindowListener(new java.awt.event.WindowAdapter() {

            public void windowClosing(java.awt.event.WindowEvent e) {
                System.exit(0);
            }
        });
        Geometry csGeometry = getExampleGeometryCSG();
        // try to convert this CSG geometry to image
        ISize imageSize = csGeometry.getGeometrySpec().getDefaultSampledImageSize();
        Geometry imageGeometry = RayCaster.resampleGeometry(new GeometryThumbnailImageFactoryAWT(), csGeometry, imageSize);
        // aGeometryViewer.setGeometry(csGeometry);
        aGeometryViewer.setGeometry(imageGeometry);
        frame.setSize(600, 600);
        frame.setVisible(true);
    } catch (Throwable exception) {
        System.err.println("Exception occurred in main() of javax.swing.JPanel");
        exception.printStackTrace(System.out);
    }
}

Example 33 with ISize

use of org.vcell.util.ISize in project vcell by virtualcell.

the class OverlayEditorPanelJAI method getImagePane.

/**
 * Method getImagePane.
 * @return OverlayImageDisplayJAI
 */
private OverlayImageDisplayJAI getImagePane() {
    if (imagePane == null) {
        imagePane = new OverlayImageDisplayJAI();
        // imagePane = new ZoomableOverlayImagePane();
        imagePane.addMouseListener(new java.awt.event.MouseAdapter() {

            public void mouseExited(MouseEvent e) {
                imagePane.setCursor(Cursor.getDefaultCursor());
                imagePane.setBrush(null);
                imagePane.refreshImage();
                updateLabel(-1, -1);
                if (histogramPanel.isVisible()) {
                    histogramPanel.setSpecialValue(null);
                }
            }

            public void mousePressed(MouseEvent e) {
                if (!bAllowAddROI) {
                    return;
                }
                updateLabel(e.getX(), e.getY());
                lastMousePoint = e.getPoint();
                if (showConvertPopup(e, true) == SHOWCONVERT.HANDLED) {
                    return;
                } else if (SwingUtilities.isLeftMouseButton(e) && (paintButton.isSelected() || eraseButton.isSelected()) && !brushToolHelper.isBrushSizeClickDragMode()) {
                    if (roiComboBox.getItemCount() == 0) {
                        giveROIRequiredWarning("paint or erase");
                        return;
                    }
                    firePropertyChange(FRAP_DATA_PAINTERASE_PROPERTY, null, null);
                    getImagePane().setBrush(null);
                    drawHighlight(e.getX(), e.getY(), brushToolHelper.getBrushSize(getImagePane().getZoom()), eraseButton.isSelected());
                } else if (SwingUtilities.isLeftMouseButton(e) && (paintButton.isSelected() || eraseButton.isSelected()) && brushToolHelper.isBrushSizeClickDragMode()) {
                    brushToolHelper.startBrushSizeClickDragMode(e);
                }
            }

            public void mouseReleased(MouseEvent e) {
                if (!bAllowAddROI) {
                    return;
                }
                if (showConvertPopup(e, true) == SHOWCONVERT.HANDLED) {
                    return;
                } else if (SwingUtilities.isLeftMouseButton(e) && (paintButton.isSelected() || eraseButton.isSelected()) && !brushToolHelper.isBrushSizeClickDragMode()) {
                    getImagePane().setBrush(brushToolHelper.getBrushShape(e));
                    firePropertyChange(FRAP_DATA_PAINTERASE_FINISH_PROPERTY, null, e);
                } else if (SwingUtilities.isLeftMouseButton(e) && cropButton.isSelected()) {
                    ISize iSize = getISizeDataset();
                    if (iSize == null || imagePane.getCrop() == null) {
                        imagePane.setCrop(null, null);
                        return;
                    }
                    // Copy crop from mousedragged rectangle
                    Rectangle cropRect = (Rectangle) imagePane.getCrop().clone();
                    // Check crop within bounds of dataset
                    cropRect.x = (int) (cropRect.x / imagePane.getZoom());
                    cropRect.y = (int) (cropRect.y / imagePane.getZoom());
                    cropRect.width = (int) (cropRect.width / imagePane.getZoom());
                    cropRect.height = (int) (cropRect.height / imagePane.getZoom());
                    if (cropRect.x < 0) {
                        cropRect.x = 0;
                    }
                    if (cropRect.y < 0) {
                        cropRect.y = 0;
                    }
                    if (cropRect.x >= iSize.getX() || cropRect.y >= iSize.getY()) {
                        imagePane.setCrop(null, null);
                        return;
                    }
                    if (cropRect.x + cropRect.width >= iSize.getX()) {
                        cropRect.width = iSize.getX() - cropRect.x;
                    }
                    if (cropRect.y + cropRect.height >= iSize.getY()) {
                        cropRect.height = iSize.getY() - cropRect.y;
                    }
                    if (cropRect.width <= 0) {
                        cropRect.width = 1;
                    }
                    if (cropRect.height <= 0) {
                        cropRect.height = 1;
                    }
                    // tell manager about crop
                    firePropertyChange(FRAP_DATA_CROP_PROPERTY, null, cropRect);
                } else if (SwingUtilities.isLeftMouseButton(e) && (paintButton.isSelected() || eraseButton.isSelected()) && brushToolHelper.isBrushSizeClickDragMode()) {
                    brushToolHelper.stopBrushSizeClickDragMode(e, imagePane);
                }
            }

            @Override
            public void mouseClicked(MouseEvent e) {
                if (!bAllowAddROI) {
                    return;
                }
                if (showConvertPopup(e, true) == SHOWCONVERT.HANDLED) {
                    return;
                } else if (SwingUtilities.isLeftMouseButton(e) && fillButton.isSelected()) {
                    if (roiComboBox.getItemCount() == 0) {
                        giveROIRequiredWarning("fill");
                        return;
                    }
                    firePropertyChange(FRAP_DATA_FILL_PROPERTY, null, new Point((int) (e.getPoint().getX() / imagePane.getZoom()), (int) (e.getPoint().getY() / imagePane.getZoom())));
                } else if (SwingUtilities.isLeftMouseButton(e) && selectButton.isSelected()) {
                    Object[] selectedResolvedObjects = resolvedList.getSelectedValues();
                    if (selectedResolvedObjects != null && selectedResolvedObjects.length > 0) {
                        if (selectedResolvedObjects[0] instanceof String) {
                            return;
                        }
                    }
                    fireSelectFromImage(e, false);
                }
            }

            @Override
            public void mouseEntered(MouseEvent e) {
                // Set cursor
                changeCursor();
                if (!paintButton.isSelected() && !eraseButton.isSelected()) {
                    getImagePane().setBrush(null);
                }
            }
        });
        imagePane.addMouseMotionListener(new java.awt.event.MouseMotionAdapter() {

            @Override
            public void mouseDragged(java.awt.event.MouseEvent e) {
                updateLabel(e.getX(), e.getY());
                if (!bAllowAddROI) {
                    return;
                }
                if (SwingUtilities.isLeftMouseButton(e) && (paintButton.isSelected() || eraseButton.isSelected()) && !brushToolHelper.isBrushSizeClickDragMode()) {
                    drawHighlight(e.getX(), e.getY(), brushToolHelper.getBrushSize(getImagePane().getZoom()), eraseButton.isSelected());
                    lastMousePoint = e.getPoint();
                } else if (SwingUtilities.isLeftMouseButton(e) && cropButton.isSelected()) {
                    imagePane.setCrop(lastMousePoint, e.getPoint());
                } else if (SwingUtilities.isLeftMouseButton(e) && (paintButton.isSelected() || eraseButton.isSelected()) && brushToolHelper.isBrushSizeClickDragMode()) {
                    brushToolHelper.dragBrushSizeClickDragMode(e, imagePane);
                }
            }

            @Override
            public void mouseMoved(java.awt.event.MouseEvent e) {
                updateLabel(e.getX(), e.getY());
                if (!brushToolHelper.isBrushSizeClickDragMode() && (paintButton.isSelected() || eraseButton.isSelected())) {
                    getImagePane().setBrush(brushToolHelper.getBrushShape(e));
                    getImagePane().refreshImage();
                }
            }
        });
    }
    return imagePane;
}

Example 34 with ISize

use of org.vcell.util.ISize in project vcell by virtualcell.

the class ROIMultiPaintManager method generateHighlightROIInfo.

private static HighlightROIInfo generateHighlightROIInfo(byte debugValue, BufferedImage[] roiArr, RegionImage regionImage, RegionAction regionAction, ClientTaskStatusSupport clientTaskStatusSupport) throws Exception {
    HighlightROIInfo highlightROIInfo = new HighlightROIInfo();
    // Create lookup map to speedup highlighting operation for large dataset
    RegionImage.RegionInfo[] selectedRegionMap = new RegionImage.RegionInfo[regionAction.getAllRegionInfos().length];
    Iterator<RegionImage.RegionInfo> selectedIter = regionAction.getSelectedRegionInfos().iterator();
    while (selectedIter.hasNext()) {
        RegionImage.RegionInfo nextRegion = selectedIter.next();
        selectedRegionMap[nextRegion.getRegionIndex()] = nextRegion;
    }
    byte[] shortEncodedRegionIndexes = regionImage.getShortEncodedRegionIndexImage();
    final int XSIZE = roiArr[0].getWidth();
    if (regionAction.getAction() == RegionAction.REGION_ACTION_HIGHLIGHT) {
        highlightROIInfo.highlightROI = createEmptyROI(new ISize(roiArr[0].getWidth(), roiArr[0].getHeight(), roiArr.length));
    }
    int allIndex = 0;
    final int ZMAX = roiArr.length - 1;
    final int XMAX = roiArr[0].getWidth() - 1;
    final int YMAX = roiArr[0].getHeight() - 1;
    for (int z = 0; z < roiArr.length; z++) {
        if (clientTaskStatusSupport != null && clientTaskStatusSupport.isInterrupted()) {
            return null;
        }
        int index = 0;
        byte[] zSlice = ((DataBufferByte) roiArr[z].getRaster().getDataBuffer()).getData();
        for (int y = 0; y < roiArr[0].getHeight(); y++) {
            for (int x = 0; x < XSIZE; x++) {
                int regionIndex = (shortEncodedRegionIndexes[allIndex] & 0x000000FF) | (shortEncodedRegionIndexes[allIndex + 1] & 0x000000FF) << 8;
                if (selectedRegionMap[regionIndex] != null) {
                    RegionInfo currentRegionInfo = selectedRegionMap[regionIndex];
                    if (regionAction.getAction() == RegionAction.REGION_ACTION_CHECKNEIGHBORSONLY) {
                        // Find neighbors
                        int[] neighbors = new int[6];
                        Arrays.fill(neighbors, -1);
                        if (z > 0) {
                            // top neighbor
                            neighbors[0] = 0x000000FF & ((DataBufferByte) roiArr[z - 1].getRaster().getDataBuffer()).getData()[index];
                        }
                        if (z < ZMAX) {
                            // bottom neighbor
                            neighbors[1] = 0x000000FF & ((DataBufferByte) roiArr[z + 1].getRaster().getDataBuffer()).getData()[index];
                        }
                        if (x > 0) {
                            // left neighbor
                            neighbors[2] = 0x000000FF & ((DataBufferByte) roiArr[z].getRaster().getDataBuffer()).getData()[index - 1];
                        }
                        if (x < XMAX) {
                            // right neighbor
                            neighbors[3] = 0x000000FF & ((DataBufferByte) roiArr[z].getRaster().getDataBuffer()).getData()[index + 1];
                        }
                        if (y > 0) {
                            // front neighbor
                            neighbors[4] = 0x000000FF & ((DataBufferByte) roiArr[z].getRaster().getDataBuffer()).getData()[index - XSIZE];
                        }
                        if (y < YMAX) {
                            // back neighbor
                            neighbors[5] = 0x000000FF & ((DataBufferByte) roiArr[z].getRaster().getDataBuffer()).getData()[index + XSIZE];
                        }
                        if (!highlightROIInfo.neighborsForRegionsMap.containsKey(currentRegionInfo)) {
                            highlightROIInfo.neighborsForRegionsMap.put(currentRegionInfo, new TreeSet<Integer>());
                        }
                        TreeSet<Integer> neighborTreeSet = highlightROIInfo.neighborsForRegionsMap.get(currentRegionInfo);
                        for (int i = 0; i < neighbors.length; i++) {
                            if (neighbors[i] != -1 && neighbors[i] != currentRegionInfo.getPixelValue()) {
                                neighborTreeSet.add(neighbors[i]);
                            }
                        }
                        if (!highlightROIInfo.coordIndexForRegionsMap.containsKey(currentRegionInfo)) {
                            highlightROIInfo.coordIndexForRegionsMap.put(currentRegionInfo, new CoordinateIndex(x, y, z));
                        }
                    } else if (regionAction.getAction() == RegionAction.REGION_ACTION_HIGHLIGHT) {
                        highlightROIInfo.highlightROI.getRoiImages()[z].getPixels()[index] = 1;
                    } else if (regionAction.getAction() == RegionAction.REGION_ACTION_MERGESELECTEDWITHNEIGHBORS) {
                        int numNeighbors = regionAction.getNeighborsForRegionMap().get(currentRegionInfo).size();
                        if (/*!regionAction.bLeaveMultiNeighborUnchanged || */
                        numNeighbors == 1) {
                            zSlice[index] = (byte) regionAction.getNeighborsForRegionMap().get(currentRegionInfo).first().intValue();
                        } else {
                            boolean hasBG = false;
                            Integer randomNeighbor = null;
                            Iterator<Integer> pixelValIter = regionAction.getNeighborsForRegionMap().get(currentRegionInfo).iterator();
                            while (pixelValIter.hasNext()) {
                                Integer pixelValue = pixelValIter.next();
                                if (pixelValue == 0) {
                                    hasBG = true;
                                    break;
                                } else {
                                    randomNeighbor = pixelValue;
                                }
                            }
                            if (hasBG) {
                                // merge with background
                                zSlice[index] = 0;
                            } else {
                                // merge with random
                                zSlice[index] = randomNeighbor.byteValue();
                            }
                        }
                    }
                }
                index++;
                allIndex += 2;
            }
        }
    }
    return highlightROIInfo;
}

Example 35 with ISize

use of org.vcell.util.ISize in project vcell by virtualcell.

the class ROIMultiPaintManager method createVCImageFromBufferedImages.

public static VCImage createVCImageFromBufferedImages(Extent extent, BufferedImage[] bufferedImages) throws Exception {
    // collect z-sections into 1 array for VCImage
    ISize isize = new ISize(bufferedImages[0].getWidth(), bufferedImages[0].getHeight(), bufferedImages.length);
    int sizeXY = isize.getX() * isize.getY();
    byte[] segmentedData = new byte[isize.getXYZ()];
    int index = 0;
    for (int i = 0; i < bufferedImages.length; i++) {
        System.arraycopy(((DataBufferByte) bufferedImages[i].getRaster().getDataBuffer()).getData(), 0, segmentedData, index, sizeXY);
        index += sizeXY;
    }
    return new VCImageUncompressed(null, segmentedData, extent, isize.getX(), isize.getY(), isize.getZ());
}