bool ThresholdWholeSlideFilter::process() {
std::vector<unsigned long long> dims = this->_input->getLevelDimensions(this->_processedLevel);
double downsample = this->_input->getLevelDownsample(this->_processedLevel);
MultiResolutionImageWriter writer;
unsigned int outSamplesPerPixel = _input->getSamplesPerPixel();
unsigned int inSamplesPerPixel = _input->getSamplesPerPixel();
if (_component >= inSamplesPerPixel) {
std::cerr << "ERROR: Selected component is larger than number of input components, fallback to all components" << std::endl;
_component = -1;
}
if (_component >= 0 || _input->getSamplesPerPixel() == 1) {
writer.setColorType(pathology::ColorType::Monochrome);
outSamplesPerPixel = 1;
} else {
writer.setColorType(pathology::ColorType::Indexed);
writer.setNumberOfIndexedColors(_input->getSamplesPerPixel());
}
writer.setCompression(pathology::Compression::LZW);
writer.setDataType(pathology::DataType::UChar);
writer.setInterpolation(pathology::Interpolation::NearestNeighbor);
writer.setTileSize(512);
std::vector<double> spacing = _input->getSpacing();
if (!spacing.empty()) {
spacing[0] *= downsample;
spacing[1] *= downsample;
writer.setSpacing(spacing);
}
if (writer.openFile(_outPath) != 0) {
std::cerr << "ERROR: Could not open file for writing" << std::endl;
return false;
}
writer.setProgressMonitor(_monitor);
writer.writeImageInformation(dims[0], dims[1]);
float* tile = new float[512 * 512 * _input->getSamplesPerPixel()];
unsigned char* out_tile = new unsigned char[512 * 512 * outSamplesPerPixel];
for (unsigned long long t_y = 0; t_y < dims[1]; t_y += 512) {
for (unsigned long long t_x = 0; t_x < dims[0]; t_x += 512) {
this->_input->getRawRegion<float>(static_cast<unsigned long long>(t_x*downsample), static_cast<unsigned long long>(t_y*downsample), 512, 512, this->_processedLevel, tile);
for (unsigned int y = 0; y < 512; ++y) {
for (unsigned int x = 0; x < 512; ++x) {
for (unsigned int c = 0; c < _input->getSamplesPerPixel(); ++c) {
if (c == _component) {
float curVal = tile[y * 512 * inSamplesPerPixel + x * inSamplesPerPixel + c];
if (curVal >= _lowerThreshold && curVal < _upperThreshold) {
out_tile[y * 512 + x] = 1;
}
else {
out_tile[y * 512 + x] = 0;
}
}
else if (_component < 0) {
float curVal = tile[y * 512 * inSamplesPerPixel + x * inSamplesPerPixel + c];
if (curVal >= _lowerThreshold && curVal < _upperThreshold) {
out_tile[y * 512 * inSamplesPerPixel + x * inSamplesPerPixel + c] = 1;
}
else {
out_tile[y * 512 * inSamplesPerPixel + x * inSamplesPerPixel + c] = 0;
}
}
}
}
}
writer.writeBaseImagePart(reinterpret_cast<void*>(out_tile));
}
}
writer.finishImage();
delete[] tile;
delete[] out_tile;
return true;
}
