Example 11 with RegionInfo
use of cbit.vcell.geometry.RegionImage.RegionInfo in project vcell by virtualcell.
the class ROIMultiPaintManager method getImportSTLtasks.
// private File lastImportDir;
private ArrayList<AsynchClientTask> getImportSTLtasks(File[] selectedFiles, Vect3d primarySampleSizes, Vect3d subSampleOffset) {
// try {
final RegionImage currRegionImage = regionImage;
final TreeMap<Integer, String> newROIindexes = new TreeMap<>();
final TreeMap<BoundingBox, Object[]> regionBounds = new TreeMap<>(new Comparator<BoundingBox>() {
@Override
public int compare(BoundingBox arg0, BoundingBox arg1) {
if (arg1 == arg0) {
return 0;
}
if (arg0.getLoX() == arg1.getLoX() && arg0.getLoY() == arg1.getLoY() && arg0.getLoZ() == arg1.getLoZ() && arg0.getHiX() == arg1.getHiX() && arg0.getHiY() == arg1.getHiY() && arg0.getHiZ() == arg1.getHiZ()) {
return 0;
}
return (arg0.getLoX() >= arg1.getLoX() && arg0.getLoY() >= arg1.getLoY() && arg0.getLoZ() >= arg1.getLoZ() && arg0.getHiX() <= arg1.getHiX() && arg0.getHiY() <= arg1.getHiY() && arg0.getHiZ() <= arg1.getHiZ() ? -1 : +1);
}
});
AsynchClientTask sampleSTLtask = new AsynchClientTask("importSTLtask", AsynchClientTask.TASKTYPE_NONSWING_BLOCKING) {
@Override
public void run(Hashtable<String, Object> hashTable) throws Exception {
StatsHelper statsHelper = calcMinMax(selectedFiles);
Vect3d worldOrigin = new Vect3d(statsHelper.xmin, statsHelper.ymin, statsHelper.zmin);
Vect3d worldCollapsedBoundingBox = new Vect3d(statsHelper.xmax - statsHelper.xmin, statsHelper.ymax - statsHelper.ymin, statsHelper.zmax - statsHelper.zmin);
Vect3d scale = new Vect3d(worldCollapsedBoundingBox.getX() / (2.0 * primarySampleSizes.getX()), worldCollapsedBoundingBox.getY() / (2.0 * primarySampleSizes.getY()), worldCollapsedBoundingBox.getZ() / (2.0 * primarySampleSizes.getZ()));
// }
if (scale.getX() != 0 && scale.getX() <= (scale.getY() == 0 ? scale.getX() : scale.getY()) && scale.getX() <= (scale.getZ() == 0 ? scale.getX() : scale.getZ())) {
scale = new Vect3d(scale.getX(), scale.getX(), scale.getX());
} else if (scale.getY() != 0 && scale.getY() <= (scale.getX() == 0 ? scale.getY() : scale.getX()) && scale.getY() <= (scale.getZ() == 0 ? scale.getY() : scale.getZ())) {
scale = new Vect3d(scale.getY(), scale.getY(), scale.getY());
} else if (scale.getZ() != 0 && scale.getZ() <= (scale.getY() == 0 ? scale.getZ() : scale.getY()) && scale.getZ() <= (scale.getX() == 0 ? scale.getZ() : scale.getX())) {
scale = new Vect3d(scale.getZ(), scale.getZ(), scale.getZ());
}
for (int j = 0; j < selectedFiles.length; j++) {
// ClientRequestManager.createSurfaceCollectionFromSurfaceFile(selectedFile);
SurfaceCollection surfaceCollection = statsHelper.recalSurfs.get(j);
for (int i = 0; i < surfaceCollection.getSurfaceCount(); i++) {
Surface surface = surfaceCollection.getSurfaces(i);
// System.out.println("surface "+i);
// Vect3d xyzLow = new Vect3d(surface.getPolygons(0).getNodes(0).getX(),surface.getPolygons(0).getNodes(1).getX(),surface.getPolygons(0).getNodes(2).getX());
// Vect3d xyzHigh = new Vect3d(xyzLow);
ComboboxROIName[] existingRoiNames = overlayEditorPanelJAI.getAllCompositeROINamesAndColors();
int newIndex = getUnusedROIColorIndex(existingRoiNames, newROIindexes.keySet());
newROIindexes.put(newIndex, selectedFiles[j].getName());
byte value = (byte) newIndex;
// overlayEditorPanelJAI.addROIName(roiName, true, roiName, true, value);
for (int k = 0; k < surface.getPolygonCount(); k++) {
Polygon polygon = surface.getPolygons(k);
// for (Node pnode:polygon.getNodes()) {
// xyzLow.set(Math.min(xyzLow.getX(), pnode.getX()),Math.min(xyzLow.getY(), pnode.getY()),Math.min(xyzLow.getZ(), pnode.getZ()));
// xyzHigh.set(Math.max(xyzHigh.getX(), pnode.getX()),Math.max(xyzHigh.getY(), pnode.getY()),Math.max(xyzHigh.getZ(), pnode.getZ()));
// }
// if(k%10000 == 0){
// System.out.println("progress= file "+(j+1)+" of "+selectedFiles.length+" "+((k*100)/surface.getPolygonCount())+"%");
// }
// System.out.println(" polygon "+j+" "+polygon.getNodes(0)+" "+polygon.getNodes(1)+" "+polygon.getNodes(2));
Vect3d line1 = new Vect3d(polygon.getNodes(0));
Vect3d end1 = new Vect3d(polygon.getNodes(2));
Vect3d incr1 = Vect3d.sub(end1, line1);
incr1.unit();
incr1.set(incr1.getX() * scale.getX(), incr1.getY() * scale.getY(), incr1.getZ() * scale.getZ());
Vect3d line2 = new Vect3d(line1);
Vect3d end2 = new Vect3d(polygon.getNodes(1));
Vect3d incr2 = Vect3d.sub(end2, line2);
incr2.unit();
incr2.set(incr2.getX() * scale.getX(), incr2.getY() * scale.getY(), incr2.getZ() * scale.getZ());
while (true) {
Vect3d line3 = new Vect3d(line1);
Vect3d end3 = new Vect3d(line2);
Vect3d incr3 = Vect3d.sub(end3, line3);
if (incr3.length() != 0) {
incr3.unit();
incr3.set(incr3.getX() * scale.getX(), incr3.getY() * scale.getY(), incr3.getZ() * scale.getZ());
}
while (true) {
calcXYZ(line3, worldOrigin, worldCollapsedBoundingBox, primarySampleSizes, subSampleOffset, value);
line3.add(incr3);
Vect3d check = Vect3d.sub(end3, line3);
if ((check.length() == 0) || Math.signum(check.getX()) != Math.signum(incr3.getX()) || Math.signum(check.getY()) != Math.signum(incr3.getY()) || Math.signum(check.getZ()) != Math.signum(incr3.getZ())) {
calcXYZ(end3, worldOrigin, worldCollapsedBoundingBox, primarySampleSizes, subSampleOffset, value);
break;
}
}
if (line1.equals(end1) && line2.equals(end2)) {
break;
}
line1.add(incr1);
Vect3d check = Vect3d.sub(end1, line1);
if (check.length() == 0 || Math.signum(check.getX()) != Math.signum(incr1.getX()) || Math.signum(check.getY()) != Math.signum(incr1.getY()) || Math.signum(check.getZ()) != Math.signum(incr1.getZ())) {
line1 = new Vect3d(end1);
}
line2.add(incr2);
check = Vect3d.sub(end2, line2);
if (check.length() == 0 || Math.signum(check.getX()) != Math.signum(incr2.getX()) || Math.signum(check.getY()) != Math.signum(incr2.getY()) || Math.signum(check.getZ()) != Math.signum(incr2.getZ())) {
line2 = new Vect3d(end2);
}
}
}
// regionBounds.put(new BoundingBox(xyzLow.getX(), xyzHigh.getX(),xyzLow.getY(), xyzHigh.getY(),xyzLow.getZ(), xyzHigh.getZ()),new Object[] {new int[] {j,i},roiName});
}
}
// for(BoundingBox bb:regionBounds.keySet()){
// System.out.println(((int[])regionBounds.get(bb)[0])[0]+","+((int[])regionBounds.get(bb)[0])[1]+" name="+((String)regionBounds.get(bb)[1])+" bound="+bb.getLoX()+","+bb.getHiX()+" "+bb.getLoY()+","+bb.getHiY()+" "+bb.getLoZ()+","+bb.getHiZ());
// }
updateAuxiliaryInfo(originalISize, getClientTaskStatusSupport());
// }
}
};
final int[] checkHolder = new int[1];
final String[] cleanupHolder = new String[1];
final String YES = "Yes";
final ComboboxROIName[] cbxHolder = new ComboboxROIName[1];
final String CHECK = "check";
AsynchClientTask addROInamesTask = new AsynchClientTask("Add new ROI names...", AsynchClientTask.TASKTYPE_SWING_BLOCKING) {
@Override
public void run(Hashtable<String, Object> hashTable) throws Exception {
int i = 0;
for (Integer newIndex : newROIindexes.keySet()) {
String roiName = FilenameUtils.getBaseName(newROIindexes.get(newIndex));
roiName = TokenMangler.fixTokenStrict(roiName, 6);
roiName += "_" + i++;
overlayEditorPanelJAI.addROIName(roiName, true, roiName, true, newIndex);
}
cleanupHolder[0] = DialogUtils.showWarningDialog(overlayEditorPanelJAI, "Cleanup imported geometry?", new String[] { YES, "No" }, YES);
if (!YES.equals(cleanupHolder[0])) {
return;
}
checkHolder[0] = getUnusedROIColorIndex(overlayEditorPanelJAI.getAllCompositeROINamesAndColors(), null);
overlayEditorPanelJAI.addROIName(CHECK, true, CHECK, true, checkHolder[0]);
ComboboxROIName[] temp = overlayEditorPanelJAI.getAllCompositeROINamesAndColors();
for (ComboboxROIName cbx : temp) {
if (cbx.getROIName().equals(CHECK)) {
cbxHolder[0] = cbx;
break;
}
}
}
};
// AsynchClientTask removeCheckROI = new AsynchClientTask("Remove check...",AsynchClientTask.TASKTYPE_SWING_BLOCKING) {
//
// @Override
// public void run(Hashtable<String, Object> hashTable) throws Exception {
// ComboboxROIName[] regNames = overlayEditorPanelJAI.getAllCompositeROINamesAndColors();
// for(ComboboxROIName cbx:regNames){
// if(cbx.get)
// }
// }
// };
final AsynchClientTask mergeBackgroundRegions = new AsynchClientTask("Merge background regions...", AsynchClientTask.TASKTYPE_NONSWING_BLOCKING) {
@Override
public void run(Hashtable<String, Object> hashTable) throws Exception {
if (!YES.equals(cleanupHolder[0])) {
return;
}
// long start = System.currentTimeMillis();
// while(currRegionImage == regionImage){
// int dur = (int)((System.currentTimeMillis()-start)/1000);
// if(dur > 10){
// return;
// }
// System.out.println("trying..."+dur);
// Thread.sleep(1000);
// }
final TreeMap<RegionInfo, Vect3d[]> regTobb = new TreeMap<>(new Comparator<RegionInfo>() {
@Override
public int compare(RegionInfo arg0, RegionInfo arg1) {
return arg0.getRegionIndex() - arg1.getRegionIndex();
}
});
Hashtable<String, Object> newRegionImgHolder = new Hashtable<>();
createRegionImageTask.run(newRegionImgHolder);
RegionImage newRegionImage = (RegionImage) newRegionImgHolder.get(LOCAL_REGION_IMAGE);
// ArrayList<RegionInfo> remainingRegionInfos = new ArrayList<>(Arrays.asList(newRegionImage.getRegionInfos()));
// BoundingBox bb = new BoundingBox(0, newRegionImage.getNumX()-1, 0, newRegionImage.getNumY()-1, 0, newRegionImage.getNumZ()-1);
// int currIndex = 0;
// for (int z = 0; z <= bb.getHiZ(); z++) {
// for (int y = 0; y <= bb.getHiY(); y++) {
// for (int x = 0; x <= bb.getHiX(); x++) {
// ArrayList<RegionInfo> tempRegionInfos = (ArrayList<RegionInfo>)remainingRegionInfos.clone();
// if(x==0 || x == bb.getHiX() || y==0 || y == bb.getHiY() || z==0 || z == bb.getHiZ()){
// for(RegionInfo reg:tempRegionInfos){
// if(reg.getPixelValue() == 0 && reg.isIndexInRegion(currIndex)){
// remainingRegionInfos.remove(reg);
// break;
// }
// }
// }else{
// for(RegionInfo reg:tempRegionInfos){
// if(reg.getPixelValue() == 0 && reg.isIndexInRegion(currIndex)){
// remainingRegionInfos.remove(reg);
// break;
// }
// }
// }
// currIndex++;
// }
// }
// }
// Remove unfilled regions (background) that touch the whole region border
int allPixCnt = 0;
ArrayList<RegionInfo> excluded = new ArrayList<>();
for (int z = 0; z < newRegionImage.getNumZ(); z++) {
for (int y = 0; y < newRegionImage.getNumY(); y++) {
for (int x = 0; x < newRegionImage.getNumX(); x++) {
RegionInfo regInfo = newRegionImage.getRegionInfoFromOffset(allPixCnt);
allPixCnt += 1;
if (excluded.contains(regInfo)) {
continue;
}
if (regInfo.getPixelValue() == 0 && (x == 0 || x == newRegionImage.getNumX() - 1 || y == 0 || y == newRegionImage.getNumY() - 1 || z == 0 || z == newRegionImage.getNumZ() - 1)) {
excluded.add(regInfo);
if (regTobb.containsKey(regInfo)) {
regTobb.remove(regInfo);
}
continue;
}
Vect3d[] bounds = regTobb.get(regInfo);
if (bounds == null) {
bounds = new Vect3d[] { new Vect3d(Double.POSITIVE_INFINITY, Double.POSITIVE_INFINITY, Double.POSITIVE_INFINITY), new Vect3d(Double.NEGATIVE_INFINITY, Double.NEGATIVE_INFINITY, Double.NEGATIVE_INFINITY) };
regTobb.put(regInfo, bounds);
}
bounds[0].set(Math.min(bounds[0].getX(), x), Math.min(bounds[0].getY(), y), Math.min(bounds[0].getZ(), z));
bounds[1].set(Math.max(bounds[1].getX(), x), Math.max(bounds[1].getY(), y), Math.max(bounds[1].getZ(), z));
}
}
}
// ArrayList<Object[]> tree = new ArrayList<>();//arraylist<object[]>,regionInfo
// ArrayList<RegionInfo> bucket = new ArrayList<>(regTobb.keySet());
// tree.add(new Object[] {null,regTobb.firstKey()});
// // ArrayList<Object[]> stack = new ArrayList<>();
// // stack.add(tree.get(0));
// while(bucket.size() > 0){
// // Object[] next = stack.remove(0);
// RegionInfo next = bucket.remove(0);
// Vect3d[] o2v = (Vect3d[])regTobb.get(regTobb.get(next));
// for(Object[] objArr:tree){
// // if(((RegionInfo)next[1]).getRegionIndex() != reg.getRegionIndex()){
// // for(RegionInfo bucketReg:bucket){
// Vect3d[] o1v = (Vect3d[])regTobb.get(objArr[1]);
// if( o1v[0].getX() >= o2v[0].getX() && o1v[0].getX() <= o2v[1].getX() &&
// o1v[0].getY() >= o2v[0].getY() && o1v[0].getY() <= o2v[1].getY() &&
// o1v[0].getZ() >= o2v[0].getZ() && o1v[0].getZ() <= o2v[1].getZ()
// ){
//
// }
// // }
// // }
// }
// }
// Sort filled/unfilled regions by boundingbox
ArrayList<RegionInfo> sortedRegionInfos = new ArrayList<>(Arrays.asList(regTobb.keySet().toArray(new RegionInfo[0])));
Collections.sort(sortedRegionInfos, new Comparator<RegionInfo>() {
@Override
public int compare(RegionInfo o1, RegionInfo o2) {
Vect3d[] o1v = (Vect3d[]) regTobb.get(o1);
Vect3d[] o2v = (Vect3d[]) regTobb.get(o2);
// }
if (o1v[0].getX() == o2v[0].getX() && o1v[1].getX() == o2v[1].getX() && o1v[0].getY() == o2v[0].getY() && o1v[1].getY() == o2v[1].getY() && o1v[0].getZ() >= o2v[0].getZ() && o1v[1].getZ() == o2v[1].getZ()) {
System.out.println(o1.getRegionIndex() + " == " + o2.getRegionIndex());
return 0;
} else if (o1v[0].getX() >= o2v[0].getX() && o1v[0].getX() <= o2v[1].getX() && // o1v[1].getX() >= o2v[0].getX() && o1v[1].getX() <= o2v[1].getX() &&
o1v[0].getY() >= o2v[0].getY() && o1v[0].getY() <= o2v[1].getY() && // o1v[1].getY() >= o2v[0].getY() && o1v[1].getY() <= o2v[1].getY() &&
o1v[0].getZ() >= o2v[0].getZ() && o1v[0].getZ() <= o2v[1].getZ()) // && o1v[1].getZ() >= o2v[0].getZ() && o1v[1].getZ() <= o2v[1].getZ()
{
System.out.println(o1.getRegionIndex() + " > " + o2.getRegionIndex());
return 1;
} else if (o1v[0].getX() <= o2v[0].getX() && o1v[1].getX() >= o2v[1].getX() && o1v[0].getY() <= o2v[0].getY() && o1v[1].getY() >= o2v[1].getY() && o1v[0].getZ() <= o2v[0].getZ() && o1v[1].getZ() >= o2v[1].getZ()) // (o1v[0].getX() < o2v[0].getX() && o1v[1].getX() < o2v[0].getX()) ||
// (o1v[0].getX() > o2v[1].getX() && o1v[1].getX() > o2v[1].getX()) ||
//
// (o1v[0].getY() < o2v[0].getY() && o1v[1].getY() < o2v[0].getY()) ||
// (o1v[0].getY() > o2v[1].getY() && o1v[1].getY() > o2v[1].getY()) ||
//
// (o1v[0].getZ() < o2v[0].getZ() && o1v[1].getZ() < o2v[0].getZ()) ||
// (o1v[0].getZ() > o2v[1].getZ() && o1v[1].getZ() > o2v[1].getZ())
//
// /* (o1v[0].getX() < o2v[0].getX() && o1v[0].getX() > o2v[1].getX() &&
// o1v[1].getX() < o2v[0].getX() && o1v[1].getX() > o2v[1].getX()) ||
// (o1v[0].getY() < o2v[0].getY() && o1v[0].getY() > o2v[1].getY() &&
// o1v[1].getY() < o2v[0].getY() && o1v[1].getY() > o2v[1].getY()) ||
// (o1v[0].getZ() < o2v[0].getZ() && o1v[0].getZ() > o2v[1].getZ() &&
// o1v[1].getZ() < o2v[0].getZ() && o1v[1].getZ() > o2v[1].getZ())*/
{
System.out.println(o1.getRegionIndex() + " <a " + o2.getRegionIndex());
return -1;
} else if ((o1v[0].getX() < o2v[0].getX() && o1v[1].getX() < o2v[0].getX()) || (o1v[0].getX() > o2v[1].getX() && o1v[1].getX() > o2v[1].getX()) || (o1v[0].getY() < o2v[0].getY() && o1v[1].getY() < o2v[0].getY()) || (o1v[0].getY() > o2v[1].getY() && o1v[1].getY() > o2v[1].getY()) || (o1v[0].getZ() < o2v[0].getZ() && o1v[1].getZ() < o2v[0].getZ()) || (o1v[0].getZ() > o2v[1].getZ() && o1v[1].getZ() > o2v[1].getZ())) {
System.out.println(o1.getRegionIndex() + " <b " + o2.getRegionIndex());
return -1;
}
System.out.println("inconclusive " + o1.getRegionIndex() + " == " + o2.getRegionIndex());
return 0;
// System.out.println("inconclusive "+o1.getRegionIndex()+" "+(o1.getNumPixels() - o2.getNumPixels()<0?"<":(o1.getNumPixels() - o2.getNumPixels()>0?">":"=="))+" "+o2.getRegionIndex());
// return o1.getNumPixels() - o2.getNumPixels();
// System.out.println("inconclusive "+o1.getRegionIndex()+" "+(o1.getRegionIndex()-o2.getRegionIndex()<0?"<":(o1.getRegionIndex()-o2.getRegionIndex()>0?">":"=="))+" "+o2.getRegionIndex());
// return o1.getRegionIndex()-o2.getRegionIndex();
// if(o1v[0].getZ() != o2v[0].getZ()){
// return (int)(o1v[0].getZ() - o2v[0].getZ());
// }else if(o1v[0].getY() != o2v[0].getY()){
// return (int)(o1v[0].getY() - o2v[0].getY());
// }else if(o1v[0].getX() != o2v[0].getX()){
// return (int)(o1v[0].getX() - o2v[0].getX());
// }else
// return 0;
}
});
// Convert unfilled regions into parent regions
int currColorIndex = -1;
// for (int i = sortedRegionInfos.size()-1; i >= 0; i--) {
for (int i = 0; i < sortedRegionInfos.size(); i++) {
RegionInfo regInfo = sortedRegionInfos.get(i);
Vect3d[] o1v = (Vect3d[]) regTobb.get(regInfo);
ComboboxROIName cbxroiName = overlayEditorPanelJAI.getComboboxROIName(regInfo);
// System.out.println(cbxroiName+" colorIndex="+regInfo.getPixelValue()+" regIndex="+regInfo.getRegionIndex()+" pixels="+regInfo.getNumPixels()+" "+o1v[0]+" "+o1v[1]);
if (cbxroiName != null) {
currColorIndex = cbxroiName.getContrastColorIndex();
continue;
}
allPixCnt = 0;
for (int z = 0; z < newRegionImage.getNumZ(); z++) {
for (int y = 0; y < newRegionImage.getNumY(); y++) {
for (int x = 0; x < newRegionImage.getNumX(); x++) {
if (regInfo.isIndexInRegion(allPixCnt)) {
BufferedImage plane = roiComposite[z];
byte[] data = ((DataBufferByte) plane.getRaster().getDataBuffer()).getData();
data[x + (plane.getWidth() * y)] = (byte) currColorIndex;
}
allPixCnt++;
}
}
}
}
// for(RegionInfo regInfo:regTobb.keySet()){
// Vect3d[] varr = regTobb.get(regInfo);
// ComboboxROIName cbxroiName = overlayEditorPanelJAI.getComboboxROIName(regInfo);
// regionBounds.put(new BoundingBox(varr[0].getX(), varr[1].getX(),varr[0].getY(), varr[1].getY(),varr[0].getZ(), varr[1].getZ()),new Object[] {cbxroiName});
// }
// for(BoundingBox bb:regionBounds.keySet()){
// ComboboxROIName cbxroiName = ((ComboboxROIName)regionBounds.get(bb)[0]);
// System.out.println(cbxroiName+" bound="+bb.getLoX()+","+bb.getHiX()+" "+bb.getLoY()+","+bb.getHiY()+" "+bb.getLoZ()+","+bb.getHiZ());
//
// }
// Make sure every pixel has only 1 kind of neighbor
// createRegionImageTask.run(newRegionImgHolder);
// newRegionImage = (RegionImage)newRegionImgHolder.get(LOCAL_REGION_IMAGE);
boolean bHasCheck = false;
VCImage checkImage = ROIMultiPaintManager.createVCImageFromBufferedImages(ROIMultiPaintManager.DEFAULT_EXTENT, roiComposite);
newRegionImage = new RegionImage(checkImage, 0, /*0 means generate no surfacecollection*/
checkImage.getExtent(), ROIMultiPaintManager.DEFAULT_ORIGIN, RegionImage.NO_SMOOTHING, null);
TreeSet<Integer> diffNeighbors = new TreeSet<>();
int[][] offsets = new int[][] { { -1, 0, 0 }, { 1, 0, 0 }, { 0, -1, 0 }, { 0, 1, 0 }, { 0, 0, -1 }, { 0, 0, 1 } };
for (int z = 0; z < newRegionImage.getNumZ(); z++) {
BufferedImage plane = roiComposite[z];
byte[] data = ((DataBufferByte) plane.getRaster().getDataBuffer()).getData();
allPixCnt = 0;
for (int y = 0; y < newRegionImage.getNumY(); y++) {
for (int x = 0; x < newRegionImage.getNumX(); x++) {
diffNeighbors.clear();
RegionInfo regInfo = newRegionImage.getRegionInfoFromOffset(allPixCnt);
if (regInfo.getPixelValue() == 0) {
allPixCnt++;
continue;
}
if (x == 19 && y == 15) {
System.out.println("here");
}
for (int i = 0; i < offsets.length; i++) {
int tmpx = offsets[i][0] + x;
if (tmpx < 0 || tmpx >= newRegionImage.getNumX()) {
continue;
}
int tmpy = offsets[i][1] + y;
if (tmpy < 0 || tmpy >= newRegionImage.getNumY()) {
continue;
}
int tmpz = offsets[i][2] + z;
if (tmpz < 0 || tmpz >= newRegionImage.getNumZ()) {
continue;
}
BufferedImage plane0 = roiComposite[tmpz];
byte[] data0 = ((DataBufferByte) plane.getRaster().getDataBuffer()).getData();
byte shiftb = data0[tmpx + (tmpy * newRegionImage.getNumX())];
if (shiftb != regInfo.getPixelValue()) {
diffNeighbors.add(0x000000FF & shiftb);
}
}
// for (int z0 = -1; z0 <= 1; z0+=2) {
// int tmpz = z+z0;
// if(tmpz < 0 || tmpz >= newRegionImage.getNumZ()){
// continue;
// }
// // tmpz = allPixCnt+(z0*newRegionImage.getNumXY());
// BufferedImage plane0 = roiComposite[z+z0];
// byte[] data0 = ((DataBufferByte)plane.getRaster().getDataBuffer()).getData();
// for (int y0 = -1; y0 <= 1; y0+=2) {
// int tmpy = y+y0;
// if(tmpy < 0 || tmpy >= newRegionImage.getNumY()){
// continue;
// }
// // tmpy = tmpz+(y0*newRegionImage.getNumX());
// for (int x0 = -1; x0 <= 1; x0+=2) {
// int tmpx = x+x0;
// if(tmpx < 0 || tmpx >= newRegionImage.getNumX()){
// continue;
// }
// // tmpx = tmpy+(x0);
// byte shiftb = data0[tmpx+(tmpy*newRegionImage.getNumX())];
// if(shiftb != regInfo.getPixelValue()){
// diffNeighbors.add(0x000000FF&shiftb);
// }
// }
// }
// }
allPixCnt++;
if (diffNeighbors.size() > 1) {
bHasCheck = true;
data[x + y * newRegionImage.getNumX()] = (byte) checkHolder[0];
}
}
}
}
if (!bHasCheck && cbxHolder[0] != null) {
SwingUtilities.invokeAndWait(new Runnable() {
@Override
public void run() {
overlayEditorPanelJAI.deleteROIName(cbxHolder[0]);
}
});
}
}
};
// }).start();
return new ArrayList<>(Arrays.asList(new AsynchClientTask[] { sampleSTLtask, addROInamesTask, mergeBackgroundRegions, getUpdateDisplayAfterCropTask() }));
// JFileChooser importJFC = new JFileChooser(ClientRequestManager.getPreferredPath(UserPreferences.getLastUserPreferences()));
// importJFC.setDialogTitle("Choose .stl file to import");
// importJFC.setMultiSelectionEnabled(true);
// int result = importJFC.showOpenDialog(overlayEditorPanelJAI);
// if(result == JFileChooser.APPROVE_OPTION){
// File[] selectedFiles = importJFC.getSelectedFiles();
// if(statsHelper == null){
// statsHelper = calcMinMax(selectedFiles);
// }
// ClientRequestManager.setPreferredPath(UserPreferences.getLastUserPreferences(), selectedFiles[0]);
//
// Vect3d worldOrigin = new Vect3d(statsHelper.xmin, statsHelper.ymin, statsHelper.zmin);
// Vect3d worldCollapsedBoundingBox = new Vect3d(statsHelper.xmax-statsHelper.xmin, statsHelper.ymax-statsHelper.ymin, statsHelper.zmax-statsHelper.zmin);
// Vect3d scale = new Vect3d(worldCollapsedBoundingBox.getX()/(2.0*primarySampleSizes.getX()), worldCollapsedBoundingBox.getY()/(2.0*primarySampleSizes.getY()), worldCollapsedBoundingBox.getZ()/(2.0*primarySampleSizes.getZ()));
// // if(scale.getX() !=0 && scale.getX() >= (scale.getY()==0?scale.getX():scale.getY()) && scale.getX() >= (scale.getZ()==0?scale.getX():scale.getZ())){
// // scale = new Vect3d(scale.getX(), scale.getX(), scale.getX());
// // }else if(scale.getY() !=0 && scale.getY() >= (scale.getX()==0?scale.getY():scale.getX()) && scale.getY() >= (scale.getZ()==0?scale.getY():scale.getZ())){
// // scale = new Vect3d(scale.getY(), scale.getY(), scale.getY());
// // }else if(scale.getZ() !=0 && scale.getZ() >= (scale.getY()==0?scale.getZ():scale.getY()) && scale.getZ() >= (scale.getX()==0?scale.getZ():scale.getX())){
// // scale = new Vect3d(scale.getZ(), scale.getZ(), scale.getZ());
// // }
// if(scale.getX() !=0 && scale.getX() <= (scale.getY()==0?scale.getX():scale.getY()) && scale.getX() <= (scale.getZ()==0?scale.getX():scale.getZ())){
// scale = new Vect3d(scale.getX(), scale.getX(), scale.getX());
// }else if(scale.getY() !=0 && scale.getY() <= (scale.getX()==0?scale.getY():scale.getX()) && scale.getY() <= (scale.getZ()==0?scale.getY():scale.getZ())){
// scale = new Vect3d(scale.getY(), scale.getY(), scale.getY());
// }else if(scale.getZ() !=0 && scale.getZ() <= (scale.getY()==0?scale.getZ():scale.getY()) && scale.getZ() <= (scale.getX()==0?scale.getZ():scale.getX())){
// scale = new Vect3d(scale.getZ(), scale.getZ(), scale.getZ());
// }
// TreeMap<BoundingBox,Object[]> regionBounds = new TreeMap<>(new Comparator<BoundingBox>() {
// @Override
// public int compare(BoundingBox arg0, BoundingBox arg1) {
// if(arg1 == arg0){
// return 0;
// }
// if(arg0.getLoX() == arg1.getLoX() &&
// arg0.getLoY() == arg1.getLoY() &&
// arg0.getLoZ() == arg1.getLoZ() &&
// arg0.getHiX() == arg1.getHiX() &&
// arg0.getHiY() == arg1.getHiY() &&
// arg0.getHiZ() == arg1.getHiZ()){
// return 0;
// }
// return (arg0.getLoX() >= arg1.getLoX() &&
// arg0.getLoY() >= arg1.getLoY() &&
// arg0.getLoZ() >= arg1.getLoZ() &&
// arg0.getHiX() <= arg1.getHiX() &&
// arg0.getHiY() <= arg1.getHiY() &&
// arg0.getHiZ() <= arg1.getHiZ()?-1:+1);
// }
// });
// for (int j = 0; j < selectedFiles.length; j++) {
// SurfaceCollection surfaceCollection = statsHelper.recalSurfs.get(j);//ClientRequestManager.createSurfaceCollectionFromSurfaceFile(selectedFile);
// for (int i = 0; i < surfaceCollection.getSurfaceCount(); i++) {
// Surface surface = surfaceCollection.getSurfaces(i);
// System.out.println("surface "+i);
// Vect3d xyzLow = new Vect3d(surface.getPolygons(0).getNodes(0).getX(),surface.getPolygons(0).getNodes(1).getX(),surface.getPolygons(0).getNodes(2).getX());
// Vect3d xyzHigh = new Vect3d(xyzLow);
// ComboboxROIName[] existingRoiNames = overlayEditorPanelJAI.getAllCompositeROINamesAndColors();
// byte value = (byte)getUnusedROIColorIndex(existingRoiNames);
// String roiName = FilenameUtils.getBaseName(selectedFiles[j].getName());
// roiName = TokenMangler.fixTokenStrict(roiName, 6);
// roiName+= "_"+i;
// overlayEditorPanelJAI.addROIName(roiName, true, roiName, true, value);
// for (int k = 0; k < surface.getPolygonCount(); k++){
// Polygon polygon = surface.getPolygons(k);
// // for (Node pnode:polygon.getNodes()) {
// // xyzLow.set(Math.min(xyzLow.getX(), pnode.getX()),Math.min(xyzLow.getY(), pnode.getY()),Math.min(xyzLow.getZ(), pnode.getZ()));
// // xyzHigh.set(Math.max(xyzHigh.getX(), pnode.getX()),Math.max(xyzHigh.getY(), pnode.getY()),Math.max(xyzHigh.getZ(), pnode.getZ()));
// // }
// if(k%10000 == 0){
// System.out.println("progress= file "+(j+1)+" of "+selectedFiles.length+" "+((k*100)/surface.getPolygonCount())+"%");
// }
// // System.out.println(" polygon "+j+" "+polygon.getNodes(0)+" "+polygon.getNodes(1)+" "+polygon.getNodes(2));
// Vect3d line1 = new Vect3d(polygon.getNodes(0));
// Vect3d end1 = new Vect3d(polygon.getNodes(2));
// Vect3d incr1 = Vect3d.sub(end1,line1);
// incr1.unit();
// incr1.set(incr1.getX()*scale.getX(), incr1.getY()*scale.getY(), incr1.getZ()*scale.getZ());
// Vect3d line2 = new Vect3d(line1);
// Vect3d end2 = new Vect3d(polygon.getNodes(1));
// Vect3d incr2 = Vect3d.sub(end2,line2);
// incr2.unit();
// incr2.set(incr2.getX()*scale.getX(), incr2.getY()*scale.getY(), incr2.getZ()*scale.getZ());
// while(true){
// Vect3d line3 = new Vect3d(line1);
// Vect3d end3 = new Vect3d(line2);
// Vect3d incr3 = Vect3d.sub(end3,line3);
// if(incr3.length() != 0){
// incr3.unit();
// incr3.set(incr3.getX()*scale.getX(), incr3.getY()*scale.getY(), incr3.getZ()*scale.getZ());
// }
// while(true){
// calcXYZ(line3, worldOrigin, worldCollapsedBoundingBox, primarySampleSizes,subSampleOffset,value);
// line3.add(incr3);
// Vect3d check = Vect3d.sub(end3, line3);
// if((check.length()==0) || Math.signum(check.getX()) != Math.signum(incr3.getX()) || Math.signum(check.getY()) != Math.signum(incr3.getY()) || Math.signum(check.getZ()) != Math.signum(incr3.getZ())){
// calcXYZ(end3, worldOrigin, worldCollapsedBoundingBox, primarySampleSizes,subSampleOffset,value);
// break;
// }
// }
// if(line1.equals(end1) && line2.equals(end2)){
// break;
// }
//
// line1.add(incr1);
// Vect3d check = Vect3d.sub(end1, line1);
// if(check.length()==0 || Math.signum(check.getX()) != Math.signum(incr1.getX()) || Math.signum(check.getY()) != Math.signum(incr1.getY()) || Math.signum(check.getZ()) != Math.signum(incr1.getZ())){
// line1 = new Vect3d(end1);
// }
// line2.add(incr2);
// check = Vect3d.sub(end2, line2);
// if(check.length()==0 || Math.signum(check.getX()) != Math.signum(incr2.getX()) || Math.signum(check.getY()) != Math.signum(incr2.getY()) || Math.signum(check.getZ()) != Math.signum(incr2.getZ())){
// line2 = new Vect3d(end2);
// }
// }
// }
// // regionBounds.put(new BoundingBox(xyzLow.getX(), xyzHigh.getX(),xyzLow.getY(), xyzHigh.getY(),xyzLow.getZ(), xyzHigh.getZ()),new Object[] {new int[] {j,i},roiName});
// }
// }
// // for(BoundingBox bb:regionBounds.keySet()){
// // System.out.println(((int[])regionBounds.get(bb)[0])[0]+","+((int[])regionBounds.get(bb)[0])[1]+" name="+((String)regionBounds.get(bb)[1])+" bound="+bb.getLoX()+","+bb.getHiX()+" "+bb.getLoY()+","+bb.getHiY()+" "+bb.getLoZ()+","+bb.getHiZ());
// // }
// updateAuxiliaryInfo(originalISize, null);
// getUpdateDisplayAfterCropTask().run(null);
//
// new Thread(new Runnable() {
// @Override
// public void run() {
// while(ClientTaskDispatcher.isBusy()){
// try {
// Thread.sleep(1000);
// } catch (InterruptedException e) {
// // TODO Auto-generated catch block
// e.printStackTrace();
// }
// }
// TreeMap<RegionInfo, Vect3d[]> regTobb = new TreeMap<>(new Comparator<RegionInfo>() {
// @Override
// public int compare(RegionInfo arg0, RegionInfo arg1) {
// return arg0.getRegionIndex()-arg1.getRegionIndex();
// }
// });
// int allPixCnt = regionImage.getNumX()*regionImage.getNumY()*regionImage.getNumZ();
// for (int z = 0; z < regionImage.getNumZ(); z++) {
// for (int y = 0; y < regionImage.getNumY(); y++) {
// for (int x = 0; x < regionImage.getNumX(); x++) {
// allPixCnt-=1;
// RegionInfo regInfo = regionImage.getRegionInfoFromOffset(allPixCnt);
// Vect3d[] bounds = regTobb.get(regInfo);
// if(bounds == null){
// bounds = new Vect3d[] {new Vect3d(),new Vect3d()};
// regTobb.put(regInfo, bounds);
// }
// bounds[0].set(Math.min(bounds[0].getX(), x),Math.min(bounds[0].getY(), y),Math.min(bounds[0].getZ(), z));
// bounds[1].set(Math.max(bounds[1].getX(), x),Math.max(bounds[1].getY(), y),Math.max(bounds[1].getZ(), z));
//
// }
// }
// }
// for(RegionInfo regInfo:regTobb.keySet()){
// Vect3d[] varr = regTobb.get(regInfo);
// ComboboxROIName cbxroiName = overlayEditorPanelJAI.getComboboxROIName(regInfo);
// regionBounds.put(new BoundingBox(varr[0].getX(), varr[1].getX(),varr[0].getY(), varr[1].getY(),varr[0].getZ(), varr[1].getZ()),new Object[] {cbxroiName});
// }
// for(BoundingBox bb:regionBounds.keySet()){
// ComboboxROIName cbxroiName = ((ComboboxROIName)regionBounds.get(bb)[0]);
// System.out.println(cbxroiName+" bound="+bb.getLoX()+","+bb.getHiX()+" "+bb.getLoY()+","+bb.getHiY()+" "+bb.getLoZ()+","+bb.getHiZ());
//
// }
// }
// }).start();
// }
// }catch (Exception e) {
// e.printStackTrace();
// DialogUtils.showErrorDialog(overlayEditorPanelJAI, e.getMessage());
// }
}
Also used :
AsynchClientTask(cbit.vcell.client.task.AsynchClientTask)
ArrayList(java.util.ArrayList)
RegionInfo(cbit.vcell.geometry.RegionImage.RegionInfo)
VCImage(cbit.image.VCImage)
DataBufferByte(java.awt.image.DataBufferByte)
BufferedImage(java.awt.image.BufferedImage)
Surface(cbit.vcell.geometry.surface.Surface)
OrigSurface(cbit.vcell.geometry.surface.OrigSurface)
TreeSet(java.util.TreeSet)
BoundingBox(cbit.vcell.geometry.surface.BoundingBox)
Polygon(cbit.vcell.geometry.surface.Polygon)
SurfaceCollection(cbit.vcell.geometry.surface.SurfaceCollection)
Hashtable(java.util.Hashtable)
TreeMap(java.util.TreeMap)
Point(java.awt.Point)
Vect3d(cbit.vcell.render.Vect3d)
RegionImage(cbit.vcell.geometry.RegionImage)
Example 12 with RegionInfo
use of cbit.vcell.geometry.RegionImage.RegionInfo in project vcell by virtualcell.
the class ROIMultiPaintManager method propertyChange.
public void propertyChange(PropertyChangeEvent evt) {
if (evt.getPropertyName().equals(OverlayEditorPanelJAI.FRAP_DATA_CROP_PROPERTY)) {
try {
overlayEditorPanelJAI.cropDrawAndConfirm((Rectangle) evt.getNewValue());
Rectangle rect2D = (Rectangle) evt.getNewValue();
ROIMultiPaintManager.Crop3D crop3D = new ROIMultiPaintManager.Crop3D();
crop3D.setBounds(rect2D.x, rect2D.y, 0, rect2D.width, rect2D.height, roiComposite.length);
cropROIData(crop3D);
} catch (UserCancelException e) {
updateUndoAfter(null);
}
} else if (evt.getPropertyName().equals(OverlayEditorPanelJAI.FRAP_DATA_CURRENTROI_PROPERTY)) {
} else if (evt.getPropertyName().equals(OverlayEditorPanelJAI.FRAP_DATA_DELETEROI_PROPERTY)) {
try {
deleteROI((ComboboxROIName) evt.getOldValue());
updateUndoAfter(false);
} catch (Exception e) {
updateUndoAfter(null);
}
} else if (evt.getPropertyName().equals(OverlayEditorPanelJAI.FRAP_DATA_ADDNEWROI_PROPERTY)) {
try {
addNewROI((ComboboxROIName[]) evt.getOldValue(), (String) evt.getNewValue());
updateUndoAfter(false);
} catch (UserCancelException e) {
updateUndoAfter(null);
} catch (Exception e) {
e.printStackTrace();
DialogUtils.showErrorDialog(overlayEditorPanelJAI, e.getMessage());
updateUndoAfter(null);
}
} else if (evt.getPropertyName().equals(OverlayEditorPanelJAI.FRAP_DATA_CLEARROI_PROPERTY)) {
try {
FLAG_CLEAR_ROI flag = askClearROI();
updateUndo(UNDO_INIT.ALLZ);
clearROI(flag, ((ComboboxROIName) evt.getOldValue()).getContrastColorIndex(), OverlayEditorPanelJAI.FRAP_DATA_CLEARROI_PROPERTY);
updateUndoAfter(true);
} catch (UserCancelException e) {
updateUndoAfter(null);
}
} else if (evt.getPropertyName().equals(OverlayEditorPanelJAI.FRAP_DATA_BLEND_PROPERTY)) {
overlayEditorPanelJAI.setBlendPercent((Integer) evt.getNewValue());
} else if (evt.getPropertyName().equals(OverlayEditorPanelJAI.FRAP_DATA_RESOLVEDHIGHLIGHT_PROPERTY)) {
highliteImageWithResolvedSelections((RegionInfo[]) evt.getNewValue());
} else if (evt.getPropertyName().equals(OverlayEditorPanelJAI.FRAP_DATA_RESOLVEDMERGE_PROPERTY)) {
try {
mergeResolvedSelections((RegionInfo[]) evt.getNewValue());
} catch (Exception e) {
e.printStackTrace();
DialogUtils.showErrorDialog(overlayEditorPanelJAI, "Merge failed\n" + e.getMessage());
}
} else if (evt.getPropertyName().equals(OverlayEditorPanelJAI.FRAP_DATA_AUTOCROP_PROPERTY)) {
try {
autoCropQuestion();
} catch (UserCancelException e) {
updateUndoAfter(null);
}
} else if (evt.getPropertyName().equals(OverlayEditorPanelJAI.FRAP_DATA_HISTOGRAM_PROPERTY)) {
overlayEditorPanelJAI.setHighliteInfo(null, OverlayEditorPanelJAI.FRAP_DATA_HISTOGRAM_PROPERTY);
calculateHistogram();
} else if (evt.getPropertyName().equals(OverlayEditorPanelJAI.FRAP_DATA_HISTOUPDATEHIGHLIGHT_PROPERTY)) {
highlightHistogramPixels((DefaultListSelectionModel) evt.getNewValue());
wantBlendSetToEnhance();
} else if (evt.getPropertyName().equals(OverlayEditorPanelJAI.FRAP_DATA_UPDATEROI_WITHHIGHLIGHT_PROPERTY)) {
try {
updateROIWithHighlight();
wantBlendSetToEnhance();
} catch (Exception e) {
updateUndoAfter(null);
}
} else if (evt.getPropertyName().equals(OverlayEditorPanelJAI.FRAP_DATA_UNDERLAY_SMOOTH_PROPERTY)) {
if (!overlayEditorPanelJAI.isHistogramSelectionEmpty()) {
overlayEditorPanelJAI.setHighliteInfo(null, OverlayEditorPanelJAI.FRAP_DATA_UNDERLAY_SMOOTH_PROPERTY);
}
enhanceImageAmount = (Integer) evt.getNewValue();
smoothUnderlay();
} else if (evt.getPropertyName().equals(OverlayEditorPanelJAI.FRAP_DATA_DISCARDHIGHLIGHT_PROPERTY)) {
overlayEditorPanelJAI.setHighliteInfo(null, OverlayEditorPanelJAI.FRAP_DATA_DISCARDHIGHLIGHT_PROPERTY);
} else if (evt.getPropertyName().equals(OverlayEditorPanelJAI.FRAP_DATA_ADDANALYTIC_PROPERTY)) {
updateUndo(UNDO_INIT.ALLZ);
sampleAnalyticIntoImage((OverlayEditorPanelJAI.ImgSubVolHelper) evt.getNewValue());
updateUndoAfter(true);
} else if (evt.getPropertyName().equals(OverlayEditorPanelJAI.FRAP_DATA_FILL_PROPERTY)) {
updateUndo(UNDO_INIT.ONEZ);
fillFromPoint((Point) evt.getNewValue());
updateUndoAfter(true);
} else if (evt.getPropertyName().equals(OverlayEditorPanelJAI.FRAP_DATA_CHANNEL_PROPERTY)) {
imageDatasetChannel = (Integer) evt.getNewValue();
if (!overlayEditorPanelJAI.isHistogramSelectionEmpty()) {
overlayEditorPanelJAI.setHighliteInfo(null, OverlayEditorPanelJAI.FRAP_DATA_CHANNEL_PROPERTY);
}
updateUnderlayHistogramDisplay();
} else // }
if (evt.getPropertyName().equals(OverlayEditorPanelJAI.FRAP_DATA_PAD_PROPERTY)) {
try {
padROIDataAsk();
} catch (Exception e) {
updateUndoAfter(null);
}
} else if (evt.getPropertyName().equals(OverlayEditorPanelJAI.FRAP_DATA_DUPLICATE_PROPERTY)) {
try {
duplicateROIDataAsk();
} catch (Exception e) {
updateUndoAfter(null);
}
} else if (evt.getPropertyName().equals(OverlayEditorPanelJAI.FRAP_DATA_PAINTERASE_PROPERTY)) {
wantBlendSetToEnhance();
updateUndo(UNDO_INIT.ONEZ);
updateUndoAfterPrivate(true, false);
} else if (evt.getPropertyName().equals(OverlayEditorPanelJAI.FRAP_DATA_UNDOROI_PROPERTY)) {
recoverUndo();
} else if (evt.getPropertyName().equals(OverlayEditorPanelJAI.FRAP_DATA_PAINTERASE_FINISH_PROPERTY)) {
refreshObjects();
} else if (evt.getPropertyName().equals(OverlayEditorPanelJAI.FRAP_DATA_FINDROI_PROPERTY)) {
findROI((RegionInfo) evt.getNewValue());
} else if (evt.getPropertyName().equals(OverlayEditorPanelJAI.FRAP_DATA_SELECTIMGROI_PROPERTY)) {
pickImgROI((SelectImgInfo) evt.getNewValue());
} else if (evt.getPropertyName().equals(OverlayEditorPanelJAI.FRAP_DATA_CONVERTDOMAIN_PROPERTY)) {
convertDomain((Integer) evt.getNewValue(), (RegionInfo[]) evt.getOldValue());
} else if (evt.getPropertyName().equals(OverlayEditorPanelJAI.FRAP_DATA_SEPARATE_PROPERTY)) {
updateUndo(UNDO_INIT.ALLZ);
separateDomains();
updateUndoAfter(true);
}
}
Also used :
Rectangle(java.awt.Rectangle)
UserCancelException(org.vcell.util.UserCancelException)
RegionInfo(cbit.vcell.geometry.RegionImage.RegionInfo)
Point(java.awt.Point)
UtilCancelException(org.vcell.util.UtilCancelException)
UserCancelException(org.vcell.util.UserCancelException)
Example 13 with RegionInfo
use of cbit.vcell.geometry.RegionImage.RegionInfo in project vcell by virtualcell.
the class ROIAssistPanel method pickKeepRegionInfoFromCurrentROI.
private RegionInfo[] pickKeepRegionInfoFromCurrentROI() throws Exception {
RegionInfo[] thresholdRegionInfos = calculateRegionInfos(dataToThreshold.getCurrentlyDisplayedROI().getPixelsXYZ());
Vector<RegionInfo> roiRegionInfoV = new Vector<RegionInfo>();
for (int i = 0; i < thresholdRegionInfos.length; i++) {
if (thresholdRegionInfos[i].getPixelValue() == 1) {
roiRegionInfoV.add(thresholdRegionInfos[i]);
}
}
if (roiRegionInfoV.size() == 0) {
DialogUtils.showInfoDialog(this, "There are no Regions Of Interest to resolve.");
return null;
}
// Present list to pick from
final RegionInfo[] regionInfoArr = roiRegionInfoV.toArray(new RegionInfo[0]);
Arrays.sort(regionInfoArr, new Comparator<RegionInfo>() {
public int compare(RegionInfo o1, RegionInfo o2) {
return o2.getNumPixels() - o1.getNumPixels();
}
});
final Object[][] rowData = new Object[regionInfoArr.length][1];
for (int i = 0; i < regionInfoArr.length; i++) {
rowData[i][0] = regionInfoArr[i].getNumPixels() + " pixels";
}
final ROI beforeROI = new ROI(dataToThreshold.getCurrentlyDisplayedROI());
int[] resultArr = null;
ListSelectionListener listSelectionListener = new ListSelectionListener() {
public void valueChanged(ListSelectionEvent e) {
if (!e.getValueIsAdjusting()) {
try {
DefaultListSelectionModel defaultListSelectionModel = (DefaultListSelectionModel) e.getSource();
Vector<Integer> pickedIndexes = new Vector<Integer>();
if (!defaultListSelectionModel.isSelectionEmpty()) {
for (int i = defaultListSelectionModel.getMinSelectionIndex(); i <= defaultListSelectionModel.getMaxSelectionIndex(); i++) {
if (defaultListSelectionModel.isSelectedIndex(i)) {
pickedIndexes.add(i);
}
}
}
// beforeROI.getPixelsXYZ();
short[] pickedPixels = new short[beforeROI.getISize().getXYZ()];
for (int i = 0; i < pickedPixels.length; i++) {
for (int j = 0; j < pickedIndexes.size(); j++) {
if (regionInfoArr[pickedIndexes.elementAt(j)].isIndexInRegion(i)) {
pickedPixels[i] = 1;
}
}
}
ROI newCellROI = null;
if (pickedIndexes.size() == 0) {
newCellROI = beforeROI;
} else {
UShortImage ushortImage = new UShortImage(pickedPixels, originalROI.getRoiImages()[0].getOrigin(), originalROI.getRoiImages()[0].getExtent(), originalROI.getISize().getX(), originalROI.getISize().getY(), originalROI.getISize().getZ());
newCellROI = new ROI(ushortImage, originalROI.getROIName());
}
dataToThreshold.addReplaceRoi(newCellROI);
} catch (Exception e2) {
e2.printStackTrace();
throw new RuntimeException("Error selecting resolved ROI", e2);
}
}
}
};
try {
resultArr = DialogUtils.showComponentOptionsTableList(this, "Select 1 or more pixel regions to keep in ROI", new String[] { "ROI Size (pixel count)" }, rowData, ListSelectionModel.MULTIPLE_INTERVAL_SELECTION, listSelectionListener, null, null, null).selectedTableRows;
} catch (UserCancelException e) {
resultArr = null;
}
if (resultArr != null && resultArr.length > 0) {
RegionInfo[] pickedRegions = new RegionInfo[resultArr.length];
for (int i = 0; i < resultArr.length; i++) {
pickedRegions[i] = regionInfoArr[resultArr[i]];
}
// (resultArr == null?null:regionInfoArr[resultArr]);
return pickedRegions;
} else {
dataToThreshold.addReplaceRoi(beforeROI);
}
return null;
}
Also used :
ListSelectionEvent(javax.swing.event.ListSelectionEvent)
UserCancelException(org.vcell.util.UserCancelException)
RegionInfo(cbit.vcell.geometry.RegionImage.RegionInfo)
DefaultListSelectionModel(javax.swing.DefaultListSelectionModel)
UShortImage(cbit.vcell.VirtualMicroscopy.UShortImage)
ROI(cbit.vcell.VirtualMicroscopy.ROI)
UserCancelException(org.vcell.util.UserCancelException)
ListSelectionListener(javax.swing.event.ListSelectionListener)
Vector(java.util.Vector)
Example 14 with RegionInfo
use of cbit.vcell.geometry.RegionImage.RegionInfo in project vcell by virtualcell.
the class ROIMultiPaintManager method fillVoids.
private boolean fillVoids(BufferedImage[] roiPixels, boolean bCheckOnly) throws Exception {
if (true) {
throw new IllegalArgumentException("Not yet implemented fully");
}
boolean bHadAnyInternalVoids = false;
int xSize = roiPixels[0].getWidth();
int ySize = roiPixels[0].getHeight();
int zSize = roiPixels.length;
int XYSIZE = xSize * ySize;
boolean bUseZ = roiPixels.length > 1;
VCImage checkImage = ROIMultiPaintManager.createVCImageFromBufferedImages(getImageDataSetChannel().getExtent(), roiComposite);
RegionImage regionImage = new RegionImage(checkImage, 0, /*0 means generate no surfacecollection*/
checkImage.getExtent(), getImageDataSetChannel().getAllImages()[0].getOrigin(), RegionImage.NO_SMOOTHING, progressWaitPopup);
RegionInfo[] newRegionInfos = regionImage.getRegionInfos();
for (int i = 0; i < newRegionInfos.length; i++) {
if (newRegionInfos[i].getPixelValue() == 0) {
boolean bInternalVoid = true;
for (int z = 0; z < zSize; z++) {
int zOffset = z * XYSIZE;
for (int y = 0; y < ySize; y++) {
int yoffset = y * xSize;
int zyOffset = zOffset + yoffset;
for (int x = 0; x < xSize; x++) {
if (newRegionInfos[i].isIndexInRegion(zyOffset + x)) {
if (x == 0 || y == 0 | (bUseZ && z == 0) | x == (xSize - 1) || y == (ySize - 1) || (bUseZ && z == (zSize - 1))) {
bInternalVoid = false;
break;
}
}
}
if (!bInternalVoid) {
break;
}
}
if (!bInternalVoid) {
break;
}
}
if (bInternalVoid) {
bHadAnyInternalVoids = true;
if (bCheckOnly) {
return bHadAnyInternalVoids;
}
for (int z = 0; z < zSize; z++) {
byte[] roiPixelsBytes = ((DataBufferByte) roiPixels[z].getRaster().getDataBuffer()).getData();
for (int xy = 0; xy < XYSIZE; xy++) {
// if(newRegionInfos[i].isIndexInRegion(j)){
// fillvoidPixels[j]|= 0xFFFF;
// }
}
}
}
}
}
return bHadAnyInternalVoids;
}
Also used :
RegionImage(cbit.vcell.geometry.RegionImage)
VCImage(cbit.image.VCImage)
RegionInfo(cbit.vcell.geometry.RegionImage.RegionInfo)
DataBufferByte(java.awt.image.DataBufferByte)
Point(java.awt.Point)
Example 15 with RegionInfo
use of cbit.vcell.geometry.RegionImage.RegionInfo in project vcell by virtualcell.
the class OverlayEditorPanelJAI method resolvedListSelection.
private void resolvedListSelection(boolean bMerge) {
RegionInfo[] selectedRegionInfos = Arrays.asList(resolvedList.getSelectedValues()).toArray(new RegionImage.RegionInfo[0]);
if (!bMerge) {
int numListItems = resolvedList.getModel().getSize();
boolean bEnableMerge = (numListItems > 1) && (selectedRegionInfos == null ? false : (selectedRegionInfos.length == 0 ? false : true));
bEnableMerge = bEnableMerge && (numListItems != selectedRegionInfos.length);
mergeButton.setEnabled(bEnableMerge);
firePropertyChange(FRAP_DATA_RESOLVEDHIGHLIGHT_PROPERTY, null, selectedRegionInfos);
} else {
firePropertyChange(FRAP_DATA_RESOLVEDMERGE_PROPERTY, null, selectedRegionInfos);
}
}
Also used :
RegionImage(cbit.vcell.geometry.RegionImage)
RegionInfo(cbit.vcell.geometry.RegionImage.RegionInfo)
Point(java.awt.Point)
Aggregations
RegionInfo (cbit.vcell.geometry.RegionImage.RegionInfo)18
Point (java.awt.Point)7
VCImage (cbit.image.VCImage)6
ISize (org.vcell.util.ISize)6
ROI (cbit.vcell.VirtualMicroscopy.ROI)5
RegionImage (cbit.vcell.geometry.RegionImage)5
SubVolume (cbit.vcell.geometry.SubVolume)5
GeometricRegion (cbit.vcell.geometry.surface.GeometricRegion)5
SurfaceGeometricRegion (cbit.vcell.geometry.surface.SurfaceGeometricRegion)5
VolumeGeometricRegion (cbit.vcell.geometry.surface.VolumeGeometricRegion)5
Vector (java.util.Vector)5
Origin (org.vcell.util.Origin)5
UShortImage (cbit.vcell.VirtualMicroscopy.UShortImage)4
AsynchClientTask (cbit.vcell.client.task.AsynchClientTask)4
Geometry (cbit.vcell.geometry.Geometry)4
SurfaceClass (cbit.vcell.geometry.SurfaceClass)4
GeometrySurfaceDescription (cbit.vcell.geometry.surface.GeometrySurfaceDescription)4
Hashtable (java.util.Hashtable)4
AnalyticSubVolume (cbit.vcell.geometry.AnalyticSubVolume)3
GeometryClass (cbit.vcell.geometry.GeometryClass)3
