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
}
Stack *ZFlyEmNeuronImageFactory::createSurfaceImage(const ZObject3dScan &obj) const
{
Stack *stack = NULL;
if (!obj.isEmpty()) {
ZObject3dScan tmpObj = obj;
tmpObj.downsampleMax(m_downsampleInterval[0], m_downsampleInterval[1],
m_downsampleInterval[2]);
int offset[3] = { 0, 0, 0 };
tmpObj.switchYZ();
Stack *objStack = tmpObj.toStack(offset);
offset[1] -= 1500 / (m_downsampleInterval[2] + 1); //hard-coded calibration, need modification later
stack = misc::computeNormal(objStack, NeuTube::Z_AXIS);
C_Stack::kill(objStack);
int height= C_Stack::height(stack);
if (m_sizePolicy[2] == SIZE_SOURCE) {
height = m_sourceDimension[2];
if (m_downsampleInterval[2] > 0) {
height /= m_downsampleInterval[2] + 1;
height += 1;
}
}
if (height > C_Stack::height(stack)) {
Stack *out = C_Stack::crop(stack, 0, -offset[1], 0, C_Stack::width(stack),
height, 1, NULL);
C_Stack::kill(stack);
stack = out;
}
}
return stack;
}
Stack* ZFlyEmNeuronImageFactory::createImage(const ZObject3dScan &obj) const
{
Stack *stack = NULL;
if (!obj.isEmpty()) {
ZObject3dScan objProj = obj.makeYProjection();
objProj.downsampleMax(m_downsampleInterval[0], m_downsampleInterval[2], 0);
Cuboid_I boundBox;
objProj.getBoundBox(&boundBox);
int width = 0;
int height = 0;
//int depth = 0;
if (m_sizePolicy[0] == SIZE_SOURCE) {
width = m_sourceDimension[0] / (m_downsampleInterval[0] + 1) + 1;
}
if (m_sizePolicy[2] == SIZE_SOURCE) {
height = m_sourceDimension[2];
if (m_downsampleInterval[2] > 0) {
height /= m_downsampleInterval[2] + 1;
height += 1;
}
}
/*
if (m_sizePolicy[2] == SIZE_SOURCE) {
depth = m_sourceDimension[2];
}
*/
int offset[3] = { 0, 0, 0 };
if (width == 0) {
width = Cuboid_I_Width(&boundBox);
offset[0] = -boundBox.cb[0];
}
if (height == 0) {
height = Cuboid_I_Height(&boundBox);
offset[1] = -boundBox.cb[1];
}
/*
if (depth == 0) {
depth = Cuboid_I_Depth(&boundBox);
offset[2] = -boundBox.cb[2];
}
*/
if (width > 0 && height > 0/* && depth > 0*/) {
stack = C_Stack::make(GREY, width, height, 1);
C_Stack::setZero(stack);
objProj.drawStack(stack, 255, offset);
}
}
return stack;
}
ZObject3dScan ZDvidInfo::getBlockIndex(const ZIntCuboidArray &boxArray) const
{
ZObject3dScan obj;
for (ZIntCuboidArray::const_iterator iter = boxArray.begin();
iter != boxArray.end(); ++iter) {
const ZIntCuboid &box = *iter;
obj.unify(getBlockIndex(box));
}
return obj;
}
ZObject3dScan ZDvidInfo::getBlockIndex(const ZObject3dScan &obj) const
{
ZIntPoint gridSize = m_endBlockIndex - m_startBlockIndex + 1;
size_t area = ((size_t) gridSize.getX()) * gridSize.getY();
size_t blockNumber = area * gridSize.getZ();
std::vector<bool> isAdded(blockNumber, false);
//std::set<ZIntPoint> blockSet;
//ZIntPointArray blockArray;
ZObject3dScan blockObj;
for (size_t i = 0; i < obj.getStripeNumber(); ++i) {
#ifdef _DEBUG_2
if (i % 10000 == 0) {
std::cout << i << "/" << obj.getStripeNumber() << std::endl;
}
#endif
const ZObject3dStripe &stripe = obj.getStripe(i);
int y = stripe.getY();
int z = stripe.getZ();
if (y > 0 && z > 0 && y < m_startCoordinates[1] + m_stackSize[1] &&
z < m_startCoordinates[2] + m_stackSize[2]) {
for (int j = 0; j < stripe.getSegmentNumber(); ++j) {
int x0 = stripe.getSegmentStart(j);
int x1 = stripe.getSegmentEnd(j);
if (x0 < 0) {
x0 = 0;
} else if (x0 >= m_startCoordinates[0] + m_stackSize[0]) {
x0 = m_startCoordinates[0] + m_stackSize[0] - 1;
}
if (x1 < 0) {
x1 = 0;
} else if (x1 >= m_startCoordinates[0] + m_stackSize[0]) {
x1 = m_startCoordinates[0] + m_stackSize[0] - 1;
}
ZIntPoint block1 = getBlockIndex(x0, y, z);
size_t blockIndex1 = area * block1.getZ() +
gridSize.getY() * block1.getY() + block1.getX();
ZIntPoint block2 = getBlockIndex(x1, y, z);
size_t blockIndex2 = area * block2.getZ() +
gridSize.getY() * block2.getY() + block2.getX();
if (!isAdded[blockIndex1] || !isAdded[blockIndex2]) {
blockObj.addSegment(
block1.getZ(), block1.getY(), block1.getX(), block2.getX(), false);
isAdded[blockIndex1] = true;
isAdded[blockIndex2] = true;
}
}
}
}
//blockArray.append(blockSet.begin(), blockSet.end());
blockObj.canonize();
return blockObj;
}
void ZSparseObject::append(const ZObject3dScan &obj)
{
for (size_t i = 0; i < obj.getStripeNumber(); ++i) {
m_stripeArray.push_back(obj.getStripe(i));
}
}
QList<ZObject3dScan*> ZFlyEmBodyMergeDoc::extractAllObject()
{
QList<ZObject3dScan*> objList;
if (m_originalLabel == NULL) {
return objList;
}
if (m_originalLabel->isEmpty()) {
return objList;
}
ZFlyEmBodyMerger::TLabelMap finalMap = m_bodyMerger.getFinalMap();
std::map<uint64_t, ZObject3dScan*> bodySet;
uint64_t *array = m_originalLabel->getDataPointer<uint64_t>();
int width = m_originalLabel->getDim(0);
int height = m_originalLabel->getDim(1);
int depth = m_originalLabel->getDim(2);
int x0 = m_originalLabel->getStartCoordinate(0);
int y0 = m_originalLabel->getStartCoordinate(1);
int z0 = m_originalLabel->getStartCoordinate(2);
ZObject3dScan *obj = NULL;
for (int z = 0; z < depth; ++z) {
for (int y = 0; y < height; ++y) {
int x = 0;
while (x < width) {
uint64_t v = array[x];
if (finalMap.contains(v)) {
v = finalMap[v];
}
std::map<uint64_t, ZObject3dScan*>::iterator iter = bodySet.find(v);
if (iter == bodySet.end()) {
obj = new ZObject3dScan;
obj->setLabel(v);
//(*bodySet)[v] = obj;
bodySet.insert(std::map<uint64_t, ZObject3dScan*>::value_type(v, obj));
} else {
obj = iter->second;
}
int length = obj->scanArray(array, x, y + y0, z + z0, width, x0);
x += length;
}
array += width;
}
}
for (std::map<uint64_t, ZObject3dScan*>::iterator iter = bodySet.begin();
iter != bodySet.end(); ++iter) {
ZObject3dScan *obj = iter->second;
obj->setRole(ZStackObjectRole::ROLE_SEGMENTATION);
QColor color = m_objColorSheme.getColor(abs((int) obj->getLabel()));
color.setAlpha(64);
obj->setColor(color);
objList.append(obj);
}
return objList;
}
int main(int argc, char *argv[])
{
if (Show_Version(argc, argv, "0.1") == 1) {
return 0;
}
static char const *Spec[] = {
"<input:string> [-o <string>]",
"[--landmark <string>]", "[--intv <int> <int> <int>]",
"[--minloop <int(100)>]", "[--bound_adjust]",
NULL};
ZArgumentProcessor::processArguments(argc, argv, Spec);
const char *input =
ZArgumentProcessor::getStringArg(const_cast<char*>("input"));
cout << "Loading object ..." << endl;
ZObject3dScan obj;
if (ZFileType::fileType(input) == ZFileType::OBJECT_SCAN_FILE) {
obj.load(input);
} else if (ZFileType::fileType(input) == ZFileType::TIFF_FILE) {
ZStack stack;
stack.load(input);
if (stack.channelNumber() > 1) {
cout << " More than one channel found. Only the first channel will be loaded" << endl;
}
Stack_Binarize(stack.c_stack(0));
obj.loadStack(stack.c_stack(0));
} else {
cout << "Invalid input. Abort." << endl;
return 1;
}
if (!obj.isEmpty()) {
if (ZArgumentProcessor::isArgMatched("--landmark")) {
ZPointArray pts;
const char *landmark = ZArgumentProcessor::getStringArg("--landmark");
ZFlyEmBodyAnalyzer bodyAnalyzer;
int intv[3] = {0, 0, 0};
bool usingDefaultIntv = true;
if (ZArgumentProcessor::isArgMatched("--intv")) {
for (int i = 0; i < 3; ++i) {
intv[i] = ZArgumentProcessor::getIntArg("--intv", i + 1);
}
usingDefaultIntv = false;
}
if (eqstr(landmark, "hole")) {
if (usingDefaultIntv) {
intv[0] = 1;
intv[1] = 1;
intv[2] = 0;
}
bodyAnalyzer.setDownsampleInterval(intv[0], intv[1], intv[2]);
cout << "Examining holes ..." << endl;
pts = bodyAnalyzer.computeHoleCenter(obj);
} else if (eqstr(landmark, "terminal")) {
if (usingDefaultIntv) {
intv[0] = 1;
intv[1] = 1;
intv[2] = 1;
}
bodyAnalyzer.setDownsampleInterval(intv[0], intv[1], intv[2]);
cout << "Examining termini ..." << endl;
pts = bodyAnalyzer.computeTerminalPoint(obj);
} else if (eqstr(landmark, "loop")) {
if (usingDefaultIntv) {
intv[0] = 1;
intv[1] = 1;
intv[2] = 1;
}
bodyAnalyzer.setDownsampleInterval(intv[0], intv[1], intv[2]);
bodyAnalyzer.setMinLoopSize(ZArgumentProcessor::getIntArg("--minloop"));
pts = bodyAnalyzer.computeLoopCenter(obj);
} else {
cout << "Invalid landmark, which must be one one of the following:" << endl;
cout << " hole, terminal" << endl;
return 1;
}
if (!pts.empty()) {
cout << "Saving results ...";
if (ZArgumentProcessor::isArgMatched("--bound_adjust")) {
ZCuboid box = obj.getBoundBox();
ZPoint corner = box.firstCorner();
corner *= -1;
pts.translate(corner);
}
std::string output = ZArgumentProcessor::getStringArg("-o");
switch (ZFileType::fileType(output)) {
case ZFileType::SWC_FILE:
pts.exportSwcFile(output, 3.0);
break;
case ZFileType::JSON_FILE:
pts.exportJsonFile(output);
break;
default:
cout << "Unknown output format. Saved as csv file" << endl;
pts.exportCsvFile(output);
break;
}
cout << output << " saved." << endl;
} else {
cout << "No landmark found." << endl;
return 0;
}
}
} else {
cout << "Invalid or empty object. Abort." << endl;
return 1;
}
return 0;
}
