void Deconvoluter::process()
{
std::string file = FileParser::getKey("TWINNED_MTZ", std::string(""));
wangEnvName = FileParser::getKey("WANG_ENVELOPE_OUTPUT", std::string("wang.env"));
molUnitName = FileParser::getKey("MOL_UNIT_ENVELOPE_OUTPUT", std::string("mol_unit.env"));
tempFftMapName = FileParser::getKey("TEMP_FFT_MAP", std::string("temp_fft.map"));
tempAveMapName = FileParser::getKey("TEMP_AVERAGE_MAP", std::string("temp_ave.map"));
tempMtzName = FileParser::getKey("TEMP_AVERAGE_MTZ", std::string("temp_ave.mtz"));
tempSortedMtzName = FileParser::getKey("TEMP_AVERAGE_SORTED_MTZ", std::string("temp_sorted_ave.mtz"));
cadMtzName = FileParser::getKey("TEMP_CAD_MTZ", std::string("temp_cad.mtz"));
fsmeltMtzName = FileParser::getKey("TEMP_FSMELT_MTZ", std::string("temp_fsmelt.mtz"));
std::string fObsLab = FileParser::getKey("LABIN_AMPLITUDES", std::string("F"));
std::string fCalcLab = FileParser::getKey("LABOUT_CALC_AMPLITUDES", std::string("FC"));
std::string ncsDefs = FileParser::getKey("NCS_DEFINITIONS_FILE", std::string(""));
std::vector<double> ccAll, ccSinglets, rAll, rSinglets;
if (ncsDefs.length() == 0)
{
std::cout << "Warning! NCS definitions file missing. Please specify file in GAP format using keyword NCS_DEFINITIONS_FILE" << std::endl;
exit(1);
}
int bins = 20;
int maxCycles = FileParser::getKey("MAXIMUM_CYCLES", 10);
if (file == "")
{
std::cout << "Twinned MTZ has not been provided, please provide file path under keyword TWINNED_MTZ" << std::endl;
exit(1);
}
// loading original, twinned MTZ into memory.
originalMtz = MtzPtr(new MtzManager(file));
originalMtz->loadReflections(false);
MtzManager::setReference(&*originalMtz);
spaceGroup = FileParser::getKey("SPACE_GROUP", originalMtz->getLowGroup()->spg_num);
std::cout << "Loaded original MTZ file " << file << std::endl;
bool skipFirst = FileParser::getKey("SKIP_FIRST_CYCLE", false);
int beginning = FileParser::getKey("RESUME_FROM_CYCLE", 0);
if (beginning > 0) skipFirst = true;
for (int i = beginning; i < maxCycles; i++)
{
if (i > beginning || (i == beginning && !skipFirst))
{
fastFourierTransform(file, tempFftMapName, (i > 0));
gapEnvelope(tempFftMapName);
gapAverage(tempFftMapName, wangEnvName, molUnitName);
map_to_sf(tempAveMapName, tempMtzName);
sort_mtz(tempMtzName, tempSortedMtzName);
cad(tempSortedMtzName, cadMtzName);
fsmelt(file, cadMtzName, fsmeltMtzName);
}
MtzPtr nextMtz = MtzPtr(new MtzManager(fsmeltMtzName));
nextMtz->loadReflections(true); // fc in "intensity" and f in "fc"...
nextMtz->applyScaleFactorsForBins(bins);
nextMtz->individualDetwinningScales((i == maxCycles - 1));
nextMtz->copyOtherAmplitudesFromReference();
file = "detwinned_cycle_" + i_to_str(i) + ".mtz";
nextMtz->writeToFile(file);
std::cout << "******************************" << std::endl;
std::cout << "** CORRELATION (ALL) **" << std::endl;
std::cout << "******************************" << std::endl;
std::cout << std::endl << "Correlation between all scaled data and original twinned data" << std::endl;
std::cout << std::endl << std::setw(15) << "Low res " << std::setw(15) << "High res " << std::setw(15) << "Correl" << std::setw(15) << "Num refl" << std::endl;
ccAll.push_back(nextMtz->correlationWithManager(&*originalMtz, false, false, 0, 0, bins, NULL, false));
std::cout << "*******************************" << std::endl;
std::cout << "** CORRELATION (SINGLETS) **" << std::endl;
std::cout << "*******************************" << std::endl;
std::cout << std::endl << "Correlation between singlet scaled data and original twinned data" << std::endl;
std::cout << std::endl << std::setw(15) << "Low res " << std::setw(15) << "High res " << std::setw(15) << "Correl" << std::setw(15) << "Num refl" << std::endl;
ccSinglets.push_back(nextMtz->correlationWithManager(&*originalMtz, false, false, 0, 0, bins, NULL, true));
std::cout << "******************************" << std::endl;
std::cout << "** R FACTOR (ALL) **" << std::endl;
std::cout << "******************************" << std::endl;
std::cout << std::endl << "R factor between all scaled data and original twinned data" << std::endl;
std::cout << std::endl << std::setw(15) << "Low res " << std::setw(15) << "High res " << std::setw(15) << "Correl" << std::setw(15) << "Num refl" << std::endl;
rAll.push_back(nextMtz->rSplitWithManager(&*originalMtz, false, false, 0, 0, bins, NULL, false));
std::cout << "*******************************" << std::endl;
std::cout << "** R FACTOR (SINGLETS) **" << std::endl;
std::cout << "*******************************" << std::endl;
std::cout << std::endl << "R factor between singlet scaled data and original twinned data" << std::endl;
std::cout << std::endl << std::setw(15) << "Low res " << std::setw(15) << "High res " << std::setw(15) << "Correl" << std::setw(15) << "Num refl" << std::endl;
rSinglets.push_back(nextMtz->rSplitWithManager(&*originalMtz, false, false, 0, 0, bins, NULL, true));
}
std::cout << "*******************************" << std::endl;
std::cout << "** END OF DECONVOLUTION **" << std::endl;
std::cout << "*******************************" << std::endl;
std::cout << std::endl << "Summary of deconvolution:" << std::endl << std::endl;
std::cout << "Cycle\tCCall\tCCsinglets\tRall\tRsinglets" << std::endl;
for (int i = 0; i < ccAll.size(); i++)
{
std::cout << i << "\t" << ccAll[i] << "\t" << ccSinglets[i] << "\t" << rAll[i] << "\t" << rSinglets[i] << std::endl;
}
}
void new_main(int argc, char *argv[])
{
time_t startcputime;
time(&startcputime);
if (argc == 1)
{
std::cout << "Welcome to cppxfel version 1.1.1!" << std::endl;
std::cout << "Please refer to & cite paper in Journal of Applied Crystallography (unpublished)" << std::endl << std::endl;
std::cout << "Command order for regular structure solution:" << std::endl;
std::cout << "\tcppxfel.run_dials shot*.pickle" << std::endl;
std::cout << "\tcppxfel.input_gen" << std::endl;
std::cout << "\tcppxfel.run -i integrate.txt" << std::endl;
std::cout << "\tcppxfel.run -i refine.txt" << std::endl;
std::cout << "\tcppxfel.run -i merge.txt" << std::endl << std::endl;;
std::cout << "Other functions for assessing data quality:" << std::endl << std::endl;
std::cout << "Correlation between two MTZ files:" << std::endl << std::endl;
std::cout << "\tcppxfel.run -cc firstFile.mtz secondFile.mtz [ambiguity] [lowRes] [highRes] [bins]" << std::endl << std::endl;
std::cout << "ambiguity: 0, 1, 2 or 3 - will compare different indexing solutions where the Bravais lattice symmetry is higher than that of the point group for certain space groups. Default 0" << std::endl;
std::cout << "lowRes and highRes: set to resolution in Angstroms to bound the results, or set to 0 to take lowest/highest resolution data. Default 0, 0" << std::endl;
std::cout << "bins: number of bins to report correlation statistics. Default 20." << std::endl << std::endl;
std::cout << "Partiality CSV files:" << std::endl << std::endl;
std::cout << "\tcppxfel.run -partiality reference.mtz ref-img-shot-number.mtz [highRes]" << std::endl << std::endl;
std::cout << "highRes: 0, 1, 2 or 3 - highest resolution reflection to report results on. Default 1.4" << std::endl;
std::cout << "This outputs partiality_[m].csv where m is bin number, which can be imported into other graphing softwares such as R." << std::endl << std::endl;;
std::cout << "Merging statistics:" << std::endl << std::endl;
std::cout << "\tcppxfel.run -rpim unmerged_file.mtz [lowRes] [highRes] [bins]" << std::endl;
std::cout << "\tcppxfel.run -rmeas unmerged_file.mtz [lowRes] [highRes] [bins]" << std::endl;
std::cout << "\tcppxfel.run -rmerge unmerged_file.mtz [lowRes] [highRes] [bins]" << std::endl << std::endl;
std::cout << "lowRes and highRes: set to resolution in Angstroms to bound the results, or set to 0 to take lowest/highest resolution data. Default 0, 0" << std::endl;
std::cout << "bins: number of bins to report correlation statistics. Default 20." << std::endl << std::endl;
exit(1);
}
if (strcmp(argv[1], "-wiki") == 0)
{
if (argc <= 2)
{
std::cout << "arguments: -wiki <logfile>" << std::endl;
exit(1);
}
Wiki wiki = Wiki(std::string(argv[2]));
wiki.process();
exit(1);
}
std::cout << "Welcome to cppxfel!" << std::endl;
if (strcmp(argv[1], "-i") == 0 || strcmp(argv[1], "-dry") == 0)
{
bool dry = (strcmp(argv[1], "-dry") == 0);
if (argc < 3)
{
std::cout << "arguments: -i <input_script>" << std::endl;
exit(1);
}
std::vector<std::string> extras;
for (int i = 3; i < argc; i++)
{
extras.push_back(std::string(argv[i]));
}
InputFileParser *parser = new InputFileParser(std::string(argv[2]), extras);
parser->setDry(dry);
parser->parse(false);
delete parser;
}
else
{
Logger::mainLogger = LoggerPtr(new Logger());
boost::thread thr = boost::thread(Logger::awaitPrintingWrapper, Logger::mainLogger);
}
if (strcmp(argv[1], "-b") == 0)
{
float bFactor = atof(argv[2]);
MtzManager *mtz1 = new MtzManager();
mtz1->setFilename(std::string(argv[3]));
mtz1->loadReflections(0);
mtz1->applyBFactor(bFactor);
mtz1->writeToFile("b-" + std::string(argv[3]));
}
if (strcmp(argv[1], "-rmerge") == 0 || strcmp(argv[1], "-rpim") == 0
|| strcmp(argv[1], "-rmeas") == 0)
{
if (argc < 3)
{
std::cout << "arguments: -r{merge} <file1> [lowRes] [highRes] [bins]."
<< std::endl;
exit(1);
}
RFactorType rFactor = RFactorTypeMerge;
if (strcmp(argv[1], "-rpim") == 0)
{
rFactor = RFactorTypePim;
}
else if (strcmp(argv[1], "-rmeas") == 0)
{
rFactor = RFactorTypeMeas;
}
double highRes = 0;
double lowRes = 0;
int bins = 20;
if (argc > 5)
{
lowRes = atof(argv[4]);
highRes = atof(argv[5]);
}
if (argc > 6)
{
bins = atoi(argv[6]);
}
MtzManager *mtz = new MtzManager();
mtz->setFilename(std::string(argv[2]));
mtz->loadReflections(1);
mtz->rFactorWithManager(rFactor, false, false, lowRes, highRes, bins);
}
if (strcmp(argv[1], "-cc") == 0 || strcmp(argv[1], "-rsplit") == 0)
{
if (argc < 4)
{
std::cout
<< "arguments: -cc <file1> <file2> (0 / 1) [lowRes] [highRes] [bins]."
<< std::endl;
exit(1);
}
bool rsplit = (strcmp(argv[1], "-rsplit") == 0);
int inverted = 0;
double highRes = 0;
double lowRes = 0;
int bins = 20;
if (argc > 4)
{
inverted = atoi(argv[4]);
}
if (argc > 6)
{
lowRes = atof(argv[5]);
highRes = atof(argv[6]);
}
if (argc > 7)
{
bins = atoi(argv[7]);
}
MtzManager *mtz1 = new MtzManager();
mtz1->setFilename(std::string(argv[2]));
mtz1->loadReflections(1);
MtzManager *mtz2 = new MtzManager();
mtz2->setFilename(std::string(argv[3]));
mtz2->loadReflections(PartialityModelScaled, true);
if (inverted)
mtz1->setActiveAmbiguity(1);
if (rsplit)
{
mtz1->rSplitWithManager(mtz2, 1, 0, lowRes, highRes, bins);
}
else
{
mtz1->correlationWithManager(mtz2, 1, 0, lowRes, highRes, bins, NULL, true);
}
delete mtz1;
delete mtz2;
exit(1);
}
if (strcmp(argv[1], "-gradscaling") == 0)
{
if (argc <= 3)
{
std::cout << "arguments: -gradscaling <ref> <file2> ... <filen>."
<< std::endl;
exit(1);
}
MtzManager *reference = new MtzManager();
reference->setFilename(argv[2]);
reference->loadReflections(1);
for (int i = 3; i < argc; i++)
{
MtzManager *image = new MtzManager();
image->setFilename(argv[i]);
image->loadReflections(1);
double gradientOld = image->gradientAgainstManager(reference);
double gradientBefore = image->minimizeRFactor(reference);
std::cout << image->getFilename() << "\t" << gradientOld << "\t"
<< gradientBefore << std::endl;
}
}
if (strcmp(argv[1], "-inv") == 0)
{
if (argc <= 2)
{
std::cout << "arguments: -inv <file>." << std::endl;
exit(1);
}
MtzManager *mtz = new MtzManager();
mtz->setFilename(std::string(argv[2]));
mtz->loadReflections(1);
mtz->setActiveAmbiguity(1);
mtz->writeToFile(std::string("inv-") + argv[2], false, false, true);
}
if (strcmp(argv[1], "-stats") == 0)
{
if (argc < 3)
{
std::cout << "arguments: -stats <filein> <threshold>." << std::endl;
exit(1);
}
if (argc >= 3)
{
StatisticsManager stats;
stats.loadFiles(&argv[2], 1, 0);
double threshold = -100;
int h = 0; int k = 0; int l = 0;
if (argc >= 3)
{
threshold = atof(argv[3]);
std::cout << "Threshold set to " << threshold << std::endl;
}
if (argc >= 6)
{
h = atoi(argv[4]);
k = atoi(argv[5]);
l = atoi(argv[6]);
std::cout << "Searching for " << h << " " << k << " " << l << std::endl;
}
GraphDrawer drawer = GraphDrawer(&*stats.mtzs[0]);
drawer.plotPartialityStats(h, k, l);
}
}
if (strcmp(argv[1], "-intensities") == 0)
{
if (argc <= 5)
{
std::cout << "arguments: -intensities h k l <file1> {<file2> ...}." << std::endl;
exit(1);
}
int h = atoi(argv[2]);
int k = atoi(argv[3]);
int l = atoi(argv[4]);
if (h == 0 && k == 0 && l == 0)
{
h = (double)(rand() / RAND_MAX) * 40;
k = (double)rand() / RAND_MAX * (40 - h) + h;
l = (double)rand() / RAND_MAX * (40 - k) + k;
}
std::cout << "Plotting intensities for (" << h << ", " << k << ", " << l << ")" << std::endl;
std::vector<MtzPtr> mtzs;
for (int i = 5; i < argc; i++)
{
MtzPtr mtz = MtzPtr(new MtzManager());
mtz->setFilename(argv[i]);
mtz->loadReflections(1);
mtzs.push_back(mtz);
}
GraphDrawer drawer = GraphDrawer(&*mtzs[0]);
drawer.plotReflectionFromMtzs(mtzs, h, k, l);
}
#ifdef MAC
if (strcmp(argv[1], "-partiality") == 0)
{
if (argc <= 3)
{
std::cout << "arguments: -partiality <ref> <filein> {<maxres>}." << std::endl;
exit(1);
}
MtzManager *reference = new MtzManager();
reference->setFilename(argv[2]);
reference->loadReflections(1);
MtzManager::setReference(reference);
double maxRes = 1.6;
if (argc > 4)
{
maxRes = atof(argv[4]);
}
MtzManager *mtz = new MtzManager();
mtz->setFilename(argv[3]);
std::cout << "Partiality plot for " << argv[3] << std::endl;
mtz->loadReflections(PartialityModelNone, true);
vector<Reflection *>refReflections, imageReflections;
GraphDrawer graph = GraphDrawer(mtz);
graph.partialityPlot("partiality", GraphMap(), maxRes);
delete mtz;
delete reference;
}
if (strcmp(argv[1], "-scale") == 0)
{
if (argc <= 3)
{
std::cout << "arguments: -scale <ref> <file1>." << std::endl;
exit(1);
}
MtzManager *reference = new MtzManager();
reference->setFilename(argv[2]);
reference->loadReflections(1);
MtzManager::setReference(reference);
MtzManager *mtz = new MtzManager();
mtz->setFilename(argv[3]);
mtz->loadReflections(1);
mtz->applyScaleFactorsForBins(50);
mtz->writeToFile("scaled-" + std::string(argv[3]));
}
if (strcmp(argv[1], "-bfac") == 0)
{
MtzManager *reference = new MtzManager();
reference->setFilename(argv[2]);
reference->loadReflections(1);
double bFactor = atof(argv[3]);
reference->applyBFactor(bFactor);
reference->writeToFile("bfac-" + reference->getFilename(), true);
}
if (strcmp(argv[1], "-bfactor") == 0)
{
if (argc <= 2)
{
std::cout << "arguments: -bfactor <ref> <file1> {<file2> ...}." << std::endl;
exit(1);
}
vector<MtzManager *> managers = vector<MtzManager *>();
MtzManager *reference = new MtzManager();
reference->setFilename(argv[2]);
reference->loadReflections(1);
MtzManager::setReference(reference);
FileParser::setKey("REFINE_B_FACTOR", true);
for (int i = 3; i < argc; i++)
{
MtzManager *mtz = new MtzManager();
mtz->setFilename(argv[i]);
mtz->loadReflections(1);
managers.push_back(mtz);
}
GraphDrawer graph = GraphDrawer(reference);
graph.resolutionStatsPlot(managers, "intensity_bins", GraphMap(), true,
false);
graph.resolutionStatsPlot(managers, "intensity_bins_2", GraphMap(),
true, true);
graph.resolutionStatsPlot(managers);
graph.bFactorPlot(managers);
for (int i = 0; i < managers.size(); i++)
delete managers[i];
}
if (strcmp(argv[1], "-ccplot") == 0)
{
MtzManager *reference = new MtzManager();
reference->setFilename(argv[2]);
reference->loadReflections(1);
MtzManager::setReference(reference);
for (int i = 3; i < argc; i++)
{
MtzManager *image = new MtzManager();
image->setFilename(argv[i]);
image->loadReflections(1);
GraphDrawer graph = GraphDrawer(image);
graph.correlationPlot("correl");
delete image;
}
delete reference;
}
#endif
time_t endcputime;
time(&endcputime);
clock_t difference = endcputime - startcputime;
double seconds = difference;
int finalSeconds = (int) seconds % 60;
int minutes = seconds / 60;
std::ostringstream logged;
logged << "N: Total time: " << minutes << " minutes, "
<< finalSeconds << " seconds (" << seconds << " seconds)." << std::endl;
logged << "Done" << std::endl;
Logger::mainLogger->addStream(&logged);
if (strcmp(argv[1], "-i") == 0)
finishJobNotification(argc, argv, minutes);
sleep(2);
}