// static
MultiGradient MultiGradient::getDefaultGradientLogarithmicIntensityMode()
{
MultiGradient mg;
mg.fromString("Linear|0,#EEEEEE;100,#000000");
return mg;
}
MultiGradient* d10_nullPointer = 0; START_SECTION((MultiGradient())) d10_ptr = new MultiGradient(); TEST_NOT_EQUAL(d10_ptr, d10_nullPointer) END_SECTION START_SECTION((~MultiGradient())) delete d10_ptr; END_SECTION START_SECTION((InterpolationMode getInterpolationMode() const)) TEST_EQUAL(MultiGradient().getInterpolationMode(),MultiGradient::IM_LINEAR) END_SECTION START_SECTION((void setInterpolationMode(InterpolationMode mode))) MultiGradient mg; mg.setInterpolationMode(MultiGradient::IM_STAIRS); TEST_EQUAL(mg.getInterpolationMode(),MultiGradient::IM_STAIRS) END_SECTION START_SECTION((Size size() const)) MultiGradient mg; TEST_EQUAL(mg.size(),2); END_SECTION START_SECTION((UInt position(UInt index))) MultiGradient mg; TEST_EQUAL(mg.position(0),0); TEST_EQUAL(mg.position(1),100); END_SECTION
// static
MultiGradient MultiGradient::getDefaultGradientLinearIntensityMode()
{
MultiGradient mg;
mg.fromString("Linear|0,#eeeeee;1,#ffea00;6,#ff0000;14,#aa00ff;23,#5500ff;100,#000000");
return mg;
}
ExitCodes main_(int, const char **)
{
//----------------------------------------------------------------
// load data
//----------------------------------------------------------------
String in = getStringOption_("in");
String in_featureXML = getStringOption_("in_featureXML");
String out = getStringOption_("out");
String format = getStringOption_("out_type");
if (format.trim() == "") // get from filename
{
try
{
format = out.suffix('.');
}
catch (Exception::ElementNotFound & /*e*/)
{
format = "nosuffix";
}
StringListUtils::toUpper(out_formats_);
if (!ListUtils::contains(out_formats_, format.toUpper()))
{
LOG_ERROR << "No explicit image output format was provided via 'out_type', and the suffix ('" << format << "') does not resemble a valid type. Please fix one of them." << std::endl;
return ILLEGAL_PARAMETERS;
}
}
MSExperiment<> exp;
MzMLFile f;
f.setLogType(log_type_);
f.load(in, exp);
exp.updateRanges(1);
SignedSize rows = getIntOption_("height");
if (rows == 0)
{
rows = exp.size();
}
if (rows <= 0)
{
writeLog_("Error: Zero rows is not possible.");
return ILLEGAL_PARAMETERS;
}
SignedSize cols = getIntOption_("width");
if (cols == 0)
{
cols = UInt(ceil(exp.getMaxMZ() - exp.getMinMZ()));
}
if (cols <= 0)
{
writeLog_("Error: Zero columns is not possible.");
return ILLEGAL_PARAMETERS;
}
//----------------------------------------------------------------
//Do the actual resampling
BilinearInterpolation<double, double> bilip;
bilip.getData().resize(rows, cols);
if (!getFlag_("transpose"))
{
// scans run bottom-up:
bilip.setMapping_0(0, exp.getMaxRT(), rows - 1, exp.getMinRT());
// peaks run left-right:
bilip.setMapping_1(0, exp.getMinMZ(), cols - 1, exp.getMaxMZ());
for (MSExperiment<>::Iterator spec_iter = exp.begin();
spec_iter != exp.end(); ++spec_iter)
{
if (spec_iter->getMSLevel() != 1) continue;
for (MSExperiment<>::SpectrumType::ConstIterator peak1_iter =
spec_iter->begin(); peak1_iter != spec_iter->end();
++peak1_iter)
{
bilip.addValue(spec_iter->getRT(), peak1_iter->getMZ(),
peak1_iter->getIntensity());
}
}
}
else // transpose
{
// spectra run bottom-up:
bilip.setMapping_0(0, exp.getMaxMZ(), rows - 1, exp.getMinMZ());
// scans run left-right:
bilip.setMapping_1(0, exp.getMinRT(), cols - 1, exp.getMaxRT());
for (MSExperiment<>::Iterator spec_iter = exp.begin();
spec_iter != exp.end(); ++spec_iter)
{
if (spec_iter->getMSLevel() != 1) continue;
for (MSExperiment<>::SpectrumType::ConstIterator peak1_iter =
spec_iter->begin(); peak1_iter != spec_iter->end();
++peak1_iter)
{
bilip.addValue(peak1_iter->getMZ(), spec_iter->getRT(),
peak1_iter->getIntensity());
}
}
}
//----------------------------------------------------------------
//create and store image
int scans = (int) bilip.getData().sizePair().first;
int peaks = (int) bilip.getData().sizePair().second;
MultiGradient gradient;
String gradient_str = getStringOption_("gradient");
if (gradient_str != "")
{
gradient.fromString(String("Linear|") + gradient_str);
}
else
{
gradient.fromString("Linear|0,#FFFFFF;2,#FFFF00;11,#FFAA00;32,#FF0000;55,#AA00FF;78,#5500FF;100,#000000");
}
bool use_log = getFlag_("log_intensity");
writeDebug_("log_intensity: " + String(use_log), 1);
QImage image(peaks, scans, QImage::Format_RGB32);
string s = getStringOption_("background_color");
QColor background_color(s.c_str());
string feature_color_string = getStringOption_("feature_color");
QColor feature_color(feature_color_string.c_str());
QPainter * painter = new QPainter(&image);
painter->setPen(background_color);
painter->fillRect(0, 0, peaks, scans, Qt::SolidPattern);
delete painter;
double factor = getDoubleOption_("max_intensity");
if (factor == 0)
{
factor = (*std::max_element(bilip.getData().begin(), bilip.getData().end()));
}
// logarithmize max. intensity as well:
if (use_log) factor = std::log(factor);
factor /= 100.0;
for (int i = 0; i < scans; ++i)
{
for (int j = 0; j < peaks; ++j)
{
double value = bilip.getData().getValue(i, j);
if (use_log) value = std::log(value);
if (value > 1e-4)
{
image.setPixel(j, i, gradient.interpolatedColorAt(value / factor).rgb());
}
else
{
image.setPixel(j, i, background_color.rgb());
}
}
}
if (getFlag_("precursors"))
{
markMS2Locations_(exp, image, getFlag_("transpose"),
getStringOption_("precursor_color").toQString(),
Size(getIntOption_("precursor_size")));
}
if (!in_featureXML.empty())
{
FeatureMap feature_map;
FeatureXMLFile ff;
ff.load(in_featureXML, feature_map);
markFeatureLocations_(feature_map, exp, image, getFlag_("transpose"), feature_color);
}
if (image.save(out.toQString(), format.c_str())) return EXECUTION_OK;
else return CANNOT_WRITE_OUTPUT_FILE;
}
