ZSwcTree* ZSwcGenerator::createRangeCompareSwc(
const ZFlyEmNeuronRange &range, const ZFlyEmNeuronRange &reference)
{
if (range.isEmpty()) {
return NULL;
}
double minZ = range.getMinZ();
double maxZ = range.getMaxZ();
double dz = (maxZ - minZ) / 50.0;
if (dz == 0.0) { //Avoid dead loop
dz = 1.0;
}
ZSwcTree *tree = createVirtualRootSwc();
double minReferenceZ = reference.getMinZ();
double maxReferenceZ = reference.getMaxZ();
for (double z = minReferenceZ; z < minZ; z += dz) {
ZSwcTree *subtree = createCircleSwc(0, 0, z, reference.getRadius(z));
subtree->setType(5);
tree->merge(subtree, true);
}
for (double z = maxZ + dz; z <= maxReferenceZ; z += dz) {
ZSwcTree *subtree = createCircleSwc(0, 0, z, reference.getRadius(z));
subtree->setType(5);
tree->merge(subtree, true);
}
for (double z = minZ; z <= maxZ; z += dz) {
double r = range.getRadius(z);
ZSwcTree *subtree = createCircleSwc(0, 0, z, r);
ZFlyEmNeuronRangeCompare comp;
ZFlyEmNeuronRangeCompare::EMatchStatus status =
comp.compare(range, reference, z);
switch (status) {
case ZFlyEmNeuronRangeCompare::MISSING_BRANCH:
subtree->setType(2);
break;
case ZFlyEmNeuronRangeCompare::EXTRA_BRANCH:
subtree->setType(3);
break;
case ZFlyEmNeuronRangeCompare::GOOD_MATCH:
subtree->setType(0);
break;
default:
subtree->setType(0);
}
tree->merge(subtree, true);
}
tree->resortId();
return tree;
}
ZSwcTree* ZSwcGenerator::createSwc(const ZFlyEmNeuronRange &range)
{
if (range.isEmpty()) {
return NULL;
}
double minZ = range.getMinZ();
double maxZ = range.getMaxZ();
double dz = (maxZ - minZ) / 50.0;
if (dz == 0.0) { //Avoid dead loop
dz = 1.0;
}
ZSwcTree *tree = createVirtualRootSwc();
for (double z = minZ; z <= maxZ; z += dz) {
double r = range.getRadius(z);
ZSwcTree *subtree = createCircleSwc(0, 0, z, r);
tree->merge(subtree, true);
}
tree->resortId();
return tree;
}
ZSwcTree* ZSwcGenerator::createSwc(
const ZObject3dScan &blockObj, int z, const ZDvidInfo &dvidInfo)
{
#ifdef _FLYEM_
ZObject3dScan slice = blockObj.getSlice(z);
size_t stripeNumber = slice.getStripeNumber();
ZSwcTree *tree = new ZSwcTree;
for (size_t s = 0; s < stripeNumber; ++s) {
const ZObject3dStripe &stripe = slice.getStripe(s);
int nseg = stripe.getSegmentNumber();
int y = stripe.getY();
int z = stripe.getZ();
for (int i = 0; i < nseg; ++i) {
int x0 = stripe.getSegmentStart(i);
int x1 = stripe.getSegmentEnd(i);
for (int x = x0; x <= x1; ++x) {
ZIntCuboid cuboid = dvidInfo.getBlockBox(x, y, z);
tree->merge(createBoxSwc(cuboid));
}
}
}
return tree;
#else
UNUSED_PARAMETER(&blockObj);
UNUSED_PARAMETER(z);
UNUSED_PARAMETER(&dvidInfo);
return NULL;
#endif
}
void FlyEm::ZSubstackRoi::exportSwc(const string &filePath)
{
if (!m_cuboidArray.empty()) {
ZSwcTree *tree = new ZSwcTree;
int index = 0;
for (ZIntCuboidArray::const_iterator iter = m_cuboidArray.begin();
iter != m_cuboidArray.end(); ++iter, ++index) {
ZCuboid cuboid;
cuboid.set(iter->cb[0], iter->cb[1], iter->cb[2], iter->ce[0], iter->ce[1],
iter->ce[2]);
ZSwcTree *subtree = ZSwcTree::CreateCuboidSwc(cuboid);
if (!m_idArray.empty()) {
subtree->setType(m_idArray[index]);
} else {
subtree->setType(index);
}
tree->merge(subtree, true);
}
tree->resortId();
tree->save(filePath);
delete tree;
}
}
ZSwcTree* ZSwcGenerator::createSwc(
const ZIntCuboidFaceArray &faceArray, double radius)
{
if (faceArray.empty()) {
return NULL;
}
ZSwcTree *tree = new ZSwcTree;
for (ZIntCuboidFaceArray::const_iterator iter = faceArray.begin();
iter != faceArray.end(); ++iter) {
ZSwcTree *subtree = createSwc(*iter, radius);
tree->merge(subtree, true);
}
return tree;
}
ZSwcTree* ZSwcGenerator::createSwc(
const ZFlyEmNeuronRange &range, const ZFlyEmNeuronAxis &axis)
{
double minZ = range.getMinZ();
double maxZ = range.getMaxZ();
double dz = (maxZ - minZ) / 50.0;
ZSwcTree *tree = createVirtualRootSwc();
for (double z = minZ; z <= maxZ; z += dz) {
double r = range.getRadius(z);
ZPoint pt = axis.getCenter(z);
ZSwcTree *subtree = createCircleSwc(pt.x(), pt.y(), z, r);
tree->merge(subtree, true);
}
tree->resortId();
return tree;
}
void ZIntCuboidArray::exportSwc(const string &filePath) const
{
if (!empty()) {
ZSwcTree *tree = new ZSwcTree;
int index = 0;
for (ZIntCuboidArray::const_iterator iter = begin(); iter != end();
++iter, ++index) {
ZCuboid cuboid;
cuboid.set(iter->cb[0], iter->cb[1], iter->cb[2], iter->ce[0], iter->ce[1],
iter->ce[2]);
ZSwcTree *subtree = ZSwcTree::CreateCuboidSwc(cuboid);
subtree->setType(index);
tree->merge(subtree, true);
}
tree->resortId();
tree->save(filePath);
delete tree;
}
}
ZSwcTree* ZIntCuboidArray::toSwc() const
{
ZSwcTree *tree = NULL;
if (!empty()) {
tree = new ZSwcTree;
int index = 0;
for (ZIntCuboidArray::const_iterator iter = begin(); iter != end();
++iter, ++index) {
ZCuboid cuboid;
cuboid.set(iter->cb[0], iter->cb[1], iter->cb[2], iter->ce[0], iter->ce[1],
iter->ce[2]);
ZSwcTree *subtree = ZSwcTree::CreateCuboidSwc(cuboid);
subtree->setType(index);
tree->merge(subtree, true);
}
tree->resortId();
}
return tree;
}
