ZVoxelArray ZSpGrowParser::extractPath(ssize_t index)
{
ZVoxelArray path;
int width = m_workspace->width;
int height = m_workspace->height;
if (m_workspace != NULL) {
while (index >= 0) {
ZVoxel voxel;
voxel.setFromIndex(index, width, height);
path.append(voxel);
if (m_pathMask != NULL) {
if (m_pathMask->array[index] == 1) {
break;
}
}
assert(index != m_workspace->path[index]);
index = m_workspace->path[index];
}
}
return path;
}
Swc_Tree* ZNeuronTracer::trace(double x1, double y1, double z1, double r1,
double x2, double y2, double z2, double r2)
{
if (x1 < 0 || y1 < 0 || z1 < 0 || x1 >= C_Stack::width(m_stack) ||
y1 >= C_Stack::height(m_stack) || z1 >= C_Stack::depth(m_stack)) {
return NULL;
}
if (ZPoint(x1, y1, z1).distanceTo(x2, y2, z2) > MAX_P2P_TRACE_DISTANCE) {
return NULL;
}
/*
int start[3];
int end[3];
start[0] = iround(x1);
start[1] = iround(y1);
start[2] = iround(z1);
end[0] = iround(x2);
end[1] = iround(y2);
end[2] = iround(z2);
*/
ZStackGraph stackGraph;
stackGraph.setResolution(m_resolution);
if (m_backgroundType == NeuTube::IMAGE_BACKGROUND_BRIGHT) {
stackGraph.setWeightFunction(Stack_Voxel_Weight);
} else {
stackGraph.setWeightFunction(Stack_Voxel_Weight_S);
}
stackGraph.inferWeightParameter(m_stack);
int startIndex = C_Stack::indexFromCoord(x1, y1, z1, C_Stack::width(m_stack),
C_Stack::height(m_stack),
C_Stack::depth(m_stack));
int endIndex = C_Stack::indexFromCoord(x2, y2, z2, C_Stack::width(m_stack),
C_Stack::height(m_stack),
C_Stack::depth(m_stack));
std::vector<int> path =
stackGraph.computeShortestPath(m_stack, startIndex, endIndex);
ZVoxelArray voxelArray;
for (size_t i = path.size(); i > 0; --i) {
int x, y, z;
C_Stack::indexToCoord(path[i - 1], C_Stack::width(m_stack),
C_Stack::height(m_stack), &x, &y, &z);
voxelArray.append(ZVoxel(x, y, z));
}
double length = voxelArray.getCurveLength();
double dist = 0.0;
for (size_t i = 0; i < path.size(); ++i) {
double ratio = dist / length;
double r = r1 * ratio + r2 * (1 - ratio);
voxelArray.setValue(i, r);
if (i < path.size() - 1) {
dist += voxelArray[i].distanceTo(voxelArray[i+1]);
}
}
return voxelArray.toSwcTree();
}
vector<ZVoxelArray> ZSpGrowParser::extractAllPath(double lengthThreshold,
Stack *ballStack)
{
bool isPathAvailable = true;
const double maskExpansionRadius = 2.0;
const double skeletonRadius = 3.0;
//Calibrate
lengthThreshold -= maskExpansionRadius;
vector<ZVoxelArray> pathArray;
//While any long path is available
while (isPathAvailable) {
//Extract the longest path
double length = 0.0;
ZVoxelArray path = extractLongestPath(&length);
cout << "Path length: " << length << endl;
cout << "Path size: " << path.size() << endl;
if (path.size() == 1) {
cout << "Debug here." << endl;
}
if (length < lengthThreshold) {
isPathAvailable = false;
} else {
pathArray.push_back(path);
//Update checkedMask
if (m_checkedMask == NULL) {
m_checkedMask = Make_Stack(GREY, m_workspace->width,
m_workspace->height, m_workspace->depth);
Zero_Stack(m_checkedMask);
}
if (m_pathMask == NULL) {
m_pathMask = Make_Stack(GREY, m_workspace->width,
m_workspace->height, m_workspace->depth);
Zero_Stack(m_pathMask);
}
if (ballStack != NULL) { //Extract distance field values
path.sample(ballStack, DistanceWeight);
path.addValue(1.0);
path.minimizeValue(skeletonRadius);
} else {
path.addValue(skeletonRadius);
}
path.labelStackWithBall(m_pathMask, 1); //Label skeletons with a certain width
if (ballStack != NULL) {
path.sample(ballStack, DistanceWeight);
path.addValue(maskExpansionRadius);
}
path.labelStackWithBall(m_checkedMask, 1); //Label mask
}
}
return pathArray;
}
Swc_Tree* ZNeuronTracer::trace(double x1, double y1, double z1, double r1,
double x2, double y2, double z2, double r2)
{
setTraceScoreThreshold(TRACING_INTERACTIVE);
ZIntPoint stackOffset = getStack()->getOffset();
ZPoint targetPos(x2, y2, z2);
x1 = iround(x1);
y1 = iround(y1);
z1 = iround(z1);
x2 = iround(x2);
y2 = iround(y2);
z2 = iround(z2);
x1 -= stackOffset.getX();
y1 -= stackOffset.getY();
z1 -= stackOffset.getZ();
x2 -= stackOffset.getX();
y2 -= stackOffset.getY();
z2 -= stackOffset.getZ();
if (x1 < 0 || y1 < 0 || z1 < 0 || x1 >= getStack()->width() ||
y1 >= getStack()->height() || z1 >= getStack()->depth()) {
return NULL;
}
ZStackGraph stackGraph;
if (m_resolution[2] / m_resolution[0] > 3.0) {
stackGraph.setZMargin(2);
}
stackGraph.updateRange(
x1, y1, z1, x2, y2, z2,
getStack()->width(), getStack()->height(), getStack()->depth());
if (stackGraph.getRoiVolume() > MAX_P2P_TRACE_VOLUME) {
return NULL;
}
stackGraph.setResolution(m_resolution);
if (m_vertexOption == ZStackGraph::VO_SURFACE) {
stackGraph.setWeightFunction(Stack_Voxel_Weight_I);
} else {
if (m_usingEdgePath) {
stackGraph.setWeightFunction(Stack_Voxel_Weight_S);
} else {
if (m_backgroundType == NeuTube::IMAGE_BACKGROUND_BRIGHT) {
stackGraph.setWeightFunction(Stack_Voxel_Weight_Sr);
} else {
stackGraph.setWeightFunction(Stack_Voxel_Weight_S);
}
}
}
ZIntCuboid box = stackGraph.getRange();
// if (m_usingEdgePath) {
// box.setFirstCorner(imin2(x1, x2), imin2(y1, y2), imin2(z1, z2));
// box.setLastCorner(imax2(x1, x2), imax2(y1, y2), imax2(z1, z2));
// }
Stack *partial = C_Stack::crop(
getIntensityData(), box.getFirstCorner().getX(), box.getFirstCorner().getY(),
box.getFirstCorner().getZ(), box.getWidth(), box.getHeight(),
box.getDepth(), NULL);
/*
if (m_bcAdjust) {
Stack_Scale(partial, 0, m_greyFactor, m_greyOffset);
}
*/
if (m_usingEdgePath) {
Stack *partialEdge = C_Stack::computeGradient(partial);
C_Stack::kill(partial);
partial = partialEdge;
#ifdef _DEBUG_2
C_Stack::write(GET_TEST_DATA_DIR + "/test.tif", partial);
#endif
}
stackGraph.inferWeightParameter(partial);
ZVoxelArray voxelArray;
std::vector<int> path;
if (m_usingEdgePath) {
int x0 = box.getFirstCorner().getX();
int y0 = box.getFirstCorner().getY();
int z0 = box.getFirstCorner().getZ();
int startIndex = C_Stack::indexFromCoord(
x1 - x0, y1 - y0 , z1 - z0, C_Stack::width(partial),
C_Stack::height(partial),
C_Stack::depth(partial));
int endIndex = C_Stack::indexFromCoord(
x2 - x0, y2 - y0, z2 - z0, C_Stack::width(partial),
C_Stack::height(partial),
C_Stack::depth(partial));
stackGraph.setRange(0, 0, 0, C_Stack::width(partial) - 1,
C_Stack::height(partial) - 1,
C_Stack::depth(partial) - 1);
path = stackGraph.computeShortestPath(
partial, startIndex, endIndex, m_vertexOption);
for (size_t i = path.size(); i > 0; --i) {
int x, y, z;
C_Stack::indexToCoord(path[i - 1], C_Stack::width(partial),
C_Stack::height(partial), &x, &y, &z);
voxelArray.append(ZVoxel(x + x0, y + y0, z + z0));
}
} else {
int width = getStack()->width();
int height = getStack()->height();
int depth = getStack()->depth();
int startIndex = C_Stack::indexFromCoord(
x1, y1, z1, width, height, depth);
int endIndex = C_Stack::indexFromCoord(
x2, y2, z2, width, height, depth);
path = stackGraph.computeShortestPath(
getIntensityData(), startIndex, endIndex, m_vertexOption);
// C_Stack::kill(stackField);
for (size_t i = path.size(); i > 0; --i) {
int x, y, z;
C_Stack::indexToCoord(path[i - 1], width, height, &x, &y, &z);
voxelArray.append(ZVoxel(x, y, z));
}
}
C_Stack::kill(partial);
double length = voxelArray.getCurveLength();
double dist = 0.0;
const std::vector<ZVoxel> &voxelData = voxelArray.getInternalData();
for (size_t i = 0; i < path.size(); ++i) {
double ratio = dist / length;
double r = r1 * ratio + r2 * (1 - ratio);
voxelArray.setValue(i, r);
if (i < path.size() - 1) {
dist += voxelData[i].distanceTo(voxelData[i+1]);
}
}
Swc_Tree *tree = voxelArray.toSwcTree();
if (tree != NULL) {
Swc_Tree_Translate(
tree, stackOffset.getX(), stackOffset.getY(), stackOffset.getZ());
ZSwcSignalFitter fitter;
fitter.setBackground(m_backgroundType);
fitter.setFixingTerminal(true);
fitter.fitSignal(tree, getStack(), getSignalChannel());
Swc_Tree_Node *leaf = tree->root;
while (SwcTreeNode::firstChild(leaf) != NULL) {
leaf = SwcTreeNode::firstChild(leaf);
}
SwcTreeNode::setPos(leaf, targetPos);
}
return tree;
}