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;
}
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;
}