void ColorDeconvolutionFilterPlugin::updateSettingsPanelFromFilter() {
ColorDeconvolutionFilter<double>* filter = dynamic_cast<ColorDeconvolutionFilter<double>* >(_filter.get());
if (_settingsPanel && filter) {
_mutex.lock();
QDoubleSpinBox* stain1R = _settingsPanel->findChild<QDoubleSpinBox*>("Stain1RSpinBox");
QDoubleSpinBox* stain1G = _settingsPanel->findChild<QDoubleSpinBox*>("Stain1GSpinBox");
QDoubleSpinBox* stain1B = _settingsPanel->findChild<QDoubleSpinBox*>("Stain1BSpinBox");
QDoubleSpinBox* stain2R = _settingsPanel->findChild<QDoubleSpinBox*>("Stain2RSpinBox");
QDoubleSpinBox* stain2G = _settingsPanel->findChild<QDoubleSpinBox*>("Stain2GSpinBox");
QDoubleSpinBox* stain2B = _settingsPanel->findChild<QDoubleSpinBox*>("Stain2BSpinBox");
QDoubleSpinBox* stain3R = _settingsPanel->findChild<QDoubleSpinBox*>("Stain3RSpinBox");
QDoubleSpinBox* stain3G = _settingsPanel->findChild<QDoubleSpinBox*>("Stain3GSpinBox");
QDoubleSpinBox* stain3B = _settingsPanel->findChild<QDoubleSpinBox*>("Stain3BSpinBox");
QDoubleSpinBox* rThreshold = _settingsPanel->findChild<QDoubleSpinBox*>("RThreshold");
QDoubleSpinBox* gThreshold = _settingsPanel->findChild<QDoubleSpinBox*>("GThreshold");
QDoubleSpinBox* bThreshold = _settingsPanel->findChild<QDoubleSpinBox*>("BThreshold");
QDoubleSpinBox* globalThreshold = _settingsPanel->findChild<QDoubleSpinBox*>("GlobalThreshold");
QComboBox* outputStain = _settingsPanel->findChild<QComboBox*>("OutputStainComboBox");
std::vector<std::vector<double> > stains = filter->getStain();
std::vector<double> rgbThresholds = filter->getRGBDensityThresholds();
double gbThreshold = filter->getGlobalDensityThreshold();
unsigned int outStain = filter->getOutputStain();
QList<QWidget*> boxes = _settingsPanel->findChildren<QWidget*>();
foreach(QWidget* sb, boxes) {
sb->blockSignals(true);
}
void ColorDeconvolutionFilterPlugin::revertStainToDefault() {
if (_filter) {
ColorDeconvolutionFilter<double>* filter = dynamic_cast<ColorDeconvolutionFilter<double>* >(_filter.get());
if (filter) {
filter->revertToDefaultStain();
updateSettingsPanelFromFilter();
emit filterParametersChanged();
}
}
}
void ColorDeconvolutionFilterPlugin::filter(const Patch<double> &input, QVariant &output) {
Patch<double>* outImg = new Patch<double>();
ColorDeconvolutionFilter<double>* filter = dynamic_cast<ColorDeconvolutionFilter<double>* >(_filter.get());
if (filter) {
if (filter->filter(input, *outImg)) {
output = QVariant::fromValue<Patch<double>*>(outImg);
}
else {
delete outImg;
}
}
}
void ColorDeconvolutionFilterPlugin::updateFilterFromSettingsPanel() {
ColorDeconvolutionFilter<double>* filter = dynamic_cast<ColorDeconvolutionFilter<double>* >(_filter.get());
if (_settingsPanel && filter) {
QDoubleSpinBox* stain1R = _settingsPanel->findChild<QDoubleSpinBox*>("Stain1RSpinBox");
QDoubleSpinBox* stain1G = _settingsPanel->findChild<QDoubleSpinBox*>("Stain1GSpinBox");
QDoubleSpinBox* stain1B = _settingsPanel->findChild<QDoubleSpinBox*>("Stain1BSpinBox");
QDoubleSpinBox* stain2R = _settingsPanel->findChild<QDoubleSpinBox*>("Stain2RSpinBox");
QDoubleSpinBox* stain2G = _settingsPanel->findChild<QDoubleSpinBox*>("Stain2GSpinBox");
QDoubleSpinBox* stain2B = _settingsPanel->findChild<QDoubleSpinBox*>("Stain2BSpinBox");
QDoubleSpinBox* stain3R = _settingsPanel->findChild<QDoubleSpinBox*>("Stain3RSpinBox");
QDoubleSpinBox* stain3G = _settingsPanel->findChild<QDoubleSpinBox*>("Stain3GSpinBox");
QDoubleSpinBox* stain3B = _settingsPanel->findChild<QDoubleSpinBox*>("Stain3BSpinBox");
QDoubleSpinBox* rThreshold = _settingsPanel->findChild<QDoubleSpinBox*>("RThreshold");
QDoubleSpinBox* gThreshold = _settingsPanel->findChild<QDoubleSpinBox*>("GThreshold");
QDoubleSpinBox* bThreshold = _settingsPanel->findChild<QDoubleSpinBox*>("BThreshold");
QDoubleSpinBox* globalThreshold = _settingsPanel->findChild<QDoubleSpinBox*>("GlobalThreshold");
QComboBox* outputStain = _settingsPanel->findChild<QComboBox*>("OutputStainComboBox");
filter->setGlobalDensityThreshold(globalThreshold->value());
std::vector<double> rgbThresholds;
rgbThresholds.push_back(rThreshold->value());
rgbThresholds.push_back(gThreshold->value());
rgbThresholds.push_back(bThreshold->value());
filter->setRGBDensityThresholds(rgbThresholds);
std::vector<std::vector<double> > stains(3, std::vector<double>(3, 0));
stains[0][0] = stain1R->value();
stains[0][1] = stain1G->value();
stains[0][2] = stain1B->value();
stains[1][0] = stain2R->value();
stains[1][1] = stain2G->value();
stains[1][2] = stain2B->value();
stains[2][0] = stain3R->value();
stains[2][1] = stain3G->value();
stains[2][2] = stain3B->value();
filter->setStain(stains[0], stains[1], stains[2]);
filter->setOutputStain(outputStain->currentIndex());
emit filterParametersChanged();
}
}
int main(int argc, char *argv[]) {
try {
std::string inputPth;
po::options_description desc("Options");
desc.add_options()
("help,h", "Displays this message")
;
po::positional_options_description positionalOptions;
positionalOptions.add("input", 1);
po::options_description posDesc("Positional descriptions");
posDesc.add_options()
("input", po::value<std::string>(&inputPth)->required(), "Path to input")
;
po::options_description descAndPos("All options");
descAndPos.add(desc).add(posDesc);
po::variables_map vm;
try {
po::store(po::command_line_parser(argc, argv).options(descAndPos)
.positional(positionalOptions).run(),
vm);
if (!vm.count("input")) {
cout << "Camelyon v1.0" << endl;
cout << "Usage: Camelyon.exe input [options]" << endl;
}
if (vm.count("help")) {
std::cout << desc << std::endl;
return 0;
}
po::notify(vm);
}
catch (boost::program_options::required_option& e) {
std::cerr << "ERROR: " << e.what() << std::endl << std::endl;
std::cerr << "Use -h or --help for usage information" << std::endl;
return 1;
}
MultiResolutionImageReader reader;
MultiResolutionImage* input = reader.open(inputPth);
CmdLineProgressMonitor monitor;
if (input) {
// Assume input has a lvl 8
int lowResLvl = 8;
vector<unsigned long long, allocator<unsigned long long>> lowResDim = input->getLevelDimensions(8);
Patch<uchar> lowResPatch = input->getPatch<uchar>(0, 0, lowResDim[0], lowResDim[1], lowResLvl);
Mat lowResMat = patchToMat(lowResPatch);
cvtColor(lowResMat, lowResMat, COLOR_BGR2HSV);
imshow("HSV", lowResMat);
// Convert level 8 image to HSD color model
ColorDeconvolutionFilter<uchar> *filter = new ColorDeconvolutionFilter<uchar>();
Patch<double> cxPatch, cyPatch, dPatch;
filter->filter(lowResPatch, cxPatch);
filter->setOutputStain(1);
filter->filter(lowResPatch, cyPatch);
filter->setOutputStain(2);
filter->filter(lowResPatch, dPatch);
Mat cX = patchToMat(cxPatch);
Mat cY = patchToMat(cyPatch);
Mat d = patchToMat(dPatch);
// (temporary check)
imshow("cX", cX);
imshow("cY", cY);
imshow("D", d);
waitKey(0);
// Assume 512 always fits integrally
int tileWidth = 512;
int tileHeight = 512;
int lowResTileWidth = tileWidth / pow(2, lowResLvl);
int lowResTileHeight = tileHeight / pow(2, lowResLvl);
vector<unsigned long long, allocator<unsigned long long>> dim = input->getLevelDimensions(0);
int numTilesX = dim[0] / tileWidth;
int numTilesY = dim[1] / tileHeight;
// Iterate over foreground tiles
for (int y = 0; y < numTilesY; y++) {
for (int x = 0; x < numTilesX; x++) {
Rect r(x * lowResTileWidth, y * lowResTileHeight, lowResTileWidth, lowResTileHeight);
if (isForeground(&d, r, 0.2, 0.1)) {
// Get level 0 for tile
Patch<uchar> p = input->getPatch<uchar>(x * tileWidth, y * tileHeight, tileWidth, tileHeight, 0);
Mat m = patchToMat(p);
// TODO Convert to HSD
// Create histogram
Mat rgbHist;
int histSize = 256;
int channels[] = { 0, 1, 2 };
float range[] = { 0, 256 };
const float* ranges[] = { range };
calcHist(&m, 1, channels, Mat(), rgbHist, 1, &histSize, ranges, true, false);
cout << "Histo Created for (" << x << "," << y << ")\n";
// TODO Get avg, median, mode, min, max, variance, stddev, etc..
}
}
}
delete filter;
// TODO Output results to csv
// TODO Train/Test model
// TODO Evaluate results
delete input;
}
else {
std::cerr << "ERROR: Invalid input image" << std::endl;
}
}
catch (std::exception& e) {
std::cerr << "Unhandled exception: "
<< e.what() << ", application will now exit" << std::endl;
return 2;
}
return 0;
}
