HLoggerPtr LoggerUtil::getLogger(const char* id) {
#ifdef HAVE_LOG4CXX
return LoggerPtr(Logger::getLogger(id));
#else
return (HLoggerPtr)id;
#endif
}
int main( int argc, char ** argv )
{
//create qt application
Application a( argc,( char **) argv );
loadLocalizations( a, "src/lintouch-runtime/locale", "runtime_" );
a.connect( &a, SIGNAL( lastWindowClosed() ), SLOT( quit() ) );
printBanner( argv[0] );
if( lt_ui_initialize() == -1 ) {
qWarning( "Unable to initialize Lintouch Panel Library" );
return -1;
}
atexit( lt_ui_terminate );
if( lt_cp_initialize() == -1 ) {
qWarning( "Unable to initialize "
"Lintouch Communication Protocol Library" );
return -1;
}
atexit( lt_cp_terminate );
//parse commandline args and remember them so they can be later passed
// 0 - false, 1 - true, 2 - unspecified = project dependent
// host/port/project related
bool startServer = 1;
QString host_or_project;
int hostPortSelection = 2;
int projectSelection = 2;
// view/panel selection related
int viewSelection = 2;
int panelSelection = 2;
bool servicePanelShortcut = true;
// windows size related
bool fullscreen = true;
bool showFullScreenShortcut = true;
// view related
QString view;
// port related
int port = 5555;
bool portGiven = false;
// debug
QString debug_fn; // empty means no-debug
for( int i = 1; i < argc; i ++ ) {
if( ( QString( "-h" ) == argv[ i ] ) ||
( QString( "--help" ) == argv[ i ] ) ) {
printUsage( argv[0] );
exit( 1 );
}
if( ( QString( "-p" ) == argv[ i ] ) ||
( QString( "--port" ) == argv[ i ] ) ) {
if ( ++i >= argc ) {
qWarning ( "ERROR: No port specified" );
printUsage( argv[ 0 ] );
exit( 1 );
}
port = atoi( argv[ i ] );
portGiven = true;
continue;
}
if( ( QString( "-v" ) == argv[ i ] ) ||
( QString( "--view" ) == argv[ i ] ) ) {
if ( ++i >= argc ) {
qWarning ( "ERROR: No view specified" );
printUsage( argv[ 0 ] );
exit( 1 );
}
view = argv[ i ];
continue;
}
if( ( QString( "-f" ) == argv[ i ] ) ||
( QString( "--fullscreen" ) == argv[ i ] ) ) {
fullscreen = true;
continue;
}
if( ( QString( "-n" ) == argv[ i ] ) ||
( QString( "--normal" ) == argv[ i ] ) ) {
fullscreen = false;
continue;
}
if( QString( "--debug" ) == argv[ i ] ) {
if ( ++i >= argc ) {
qWarning ( "ERROR: No filename specified" );
printUsage( argv[ 0 ] );
exit( 1 );
}
debug_fn = argv[ i ];
continue;
}
if( ( QString( "--enable-host-port-selection" ) == argv[ i ] ) ) {
hostPortSelection = 1;
continue;
}
if( ( QString( "--disable-host-port-selection" ) == argv[ i ] ) ) {
hostPortSelection = 0;
continue;
}
if( ( QString( "--enable-project-selection" ) == argv[ i ] ) ) {
projectSelection = 1;
continue;
}
if( ( QString( "--disable-project-selection" ) == argv[ i ] ) ) {
projectSelection = 0;
continue;
}
if( ( QString( "--enable-view-switching" ) == argv[ i ] ) ) {
viewSelection = 1;
continue;
}
if( ( QString( "--disable-view-switching" ) == argv[ i ] ) ) {
viewSelection = 0;
continue;
}
if( ( QString( "--enable-panel-switching" ) == argv[ i ] ) ) {
panelSelection = 1;
continue;
}
if( ( QString( "--disable-panel-switching" ) == argv[ i ] ) ) {
panelSelection = 0;
continue;
}
if( ( QString( "--enable-service-panel-shortcut" ) == argv[ i ] ) ) {
servicePanelShortcut = true;
continue;
}
if( ( QString( "--disable-service-panel-shortcut" ) == argv[ i ] ) ) {
servicePanelShortcut = false;
continue;
}
if( ( QString( "--enable-fullscreen-shortcut" ) == argv[ i ] ) ) {
showFullScreenShortcut = true;
continue;
}
if( ( QString( "--disable-fullscreen-shortcut" ) == argv[ i ] ) ) {
showFullScreenShortcut = false;
continue;
}
if( QString( argv[ i ] ).startsWith( "-" ) ) {
qWarning( "ERROR: Invalid argument specified: %s",
argv[ i ] );
printUsage( argv[ 0 ] );
exit( 1 );
}
host_or_project = argv[ i ];
}
// validate commandline args
// problematic combinations
if( hostPortSelection == 1 && projectSelection == 1 ) {
qWarning( "ERROR: --enable-host-port-selection and "
"--enable-project-selection"
" can not be specified at the same time" );
printUsage( argv[ 0 ] );
exit( 1 );
}
if( hostPortSelection == 0 && projectSelection == 0 ) {
qWarning( "ERROR: --disable-host-port-selection and "
"--disable-project-selection"
" can not be specified at the same time" );
printUsage( argv[ 0 ] );
exit( 1 );
}
// no special --enable given, try to determine mode according to given
// host_or_project
if( hostPortSelection == 2 && projectSelection == 2 ) {
if( host_or_project.isEmpty() || QFile::exists( host_or_project ) ) {
projectSelection = 1;
} else {
hostPortSelection = 1;
}
}
// handle non-specified arguments and their defaults
if( hostPortSelection == 0 ) {
switch( projectSelection ) {
case 1:
case 2:
startServer = true;
projectSelection = 1;
break;
}
} else if( hostPortSelection == 1 ) {
switch( projectSelection ) {
case 0:
case 2:
startServer = false;
projectSelection = 0;
break;
}
} else if( hostPortSelection == 2 ) {
switch( projectSelection ) {
case 0:
startServer = false;
hostPortSelection = 1;
break;
case 1:
case 2:
startServer = true;
projectSelection = 1;
hostPortSelection = 0;
break;
}
}
// when no port has been specified and we are supposed to start local
// server, we'll use an unused port
// generated for us by ServerController
if( startServer && ! portGiven ) port = 0;
// print summary
if( !host_or_project.isEmpty() ) {
if( startServer ) {
host_or_project = QFileInfo( host_or_project ).absFilePath();
qWarning( QString( "Starting server %1:%2 with project %3" )
.arg( "localhost" ).arg( port ).arg( host_or_project ) );
} else {
qWarning( QString( "Using server %1:%2" )
.arg( host_or_project ).arg( port ) );
}
}
if( !view.isEmpty() ) {
qWarning( QString( "Using view %1" ).arg( view ) );
}
LoggerPtr l;
if( debug_fn.isEmpty() ) {
l = LoggerPtr( new lt::Logger );
} else {
l = LoggerPtr( new lt::FileLogger(debug_fn, "",
lt::FileLogger::LEVEL_DEBUG) );
}
// create main window
MainWindow mw( startServer, fullscreen, l, NULL );
// pass in commmand line defaults
if( startServer ) {
mw.setProjectNPort( host_or_project, port, host_or_project.isEmpty() );
} else {
mw.setHostNPort( host_or_project, port, host_or_project.isEmpty() );
}
mw.setViewSelectorEnabled( viewSelection );
mw.setPanelSelectorEnabled( panelSelection );
mw.setView( view );
mw.setServicePanelShortcutEnabled( servicePanelShortcut );
mw.setShowFullScreenEnabled( showFullScreenShortcut );
// and go ahead with startup
a.setMainWidget( &mw );
if( fullscreen ) {
mw.showFullScreen();
} else {
mw.show();
}
return a.exec();
}
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);
}
LoggerPtr Logger::getLogger(const std::string& name)
{
return LoggerPtr(name);
}
