indexCrystals Namespace Reference

Functions
def	str2bool
def	checkJobExit
def	getMyChunkSize
def	writeStatus
def	getIndexedPeaks
Variables
tuple	parser = argparse.ArgumentParser()
tuple	args = parser.parse_args()
tuple	experimentName = args.expRun.split('exp=')
tuple	runNumber = int(args.expRun.split('run=')[-1])
	experimentName = args.exp
tuple	runNumber = int(args.run)
	detInfo = args.det
	geom = args.geom
	peakMethod = args.peakMethod
	integrationRadius = args.integrationRadius
	pdb = args.pdb
	indexingMethod = args.indexingMethod
	minPeaks = args.minPeaks
	maxPeaks = args.maxPeaks
	minRes = args.minRes
	tolerance = args.tolerance
	extra = args.extra
	outDir = args.outDir
	sample = args.sample
	tag = args.tag
	queue = args.queue
	chunkSize = args.chunkSize
	noe = args.noe
	instrument = args.instrument
	pixelSize = args.pixelSize
	coffset = args.coffset
	clenEpics = args.clenEpics
	logger = args.logger
	hitParam_threshold = args.hitParam_threshold
int	keepData = 2
string	runDir = "/r"
string	peakFile = '/'
string	indexingFile = '/.'
string	fnameIndex = "/status_index.txt"
int	f = 5
string	hasData = '/entry_1/instrument_1/detector_1/data'
list	minPeaksUsed = f["entry_1/result_1/nPeaks"]
list	maxPeaksUsed = f["entry_1/result_1/nPeaks"]
list	minResUsed = f["entry_1/result_1/nPeaks"]
dictionary	d = {"message": "#StartIndexing"}
int	f = 5
list	eventList = f['/LCLS/eventNumber']
tuple	numEvents = len(eventList)
tuple	numWorkers = int(np.ceil(numEvents*1./chunkSize))
list	myLogList = []
list	myJobList = []
list	myStreamList = []
tuple	myJobs = getMyChunkSize(numEvents, numWorkers, chunkSize, rank)
string	jobName = "_"
string	jobName = "_"
string	myList = "/temp_"
string	myStream = "/temp_"
string	cmd = "bsub -q "
tuple	process = subprocess.Popen(cmd, stdout=subprocess.PIPE, stderr=subprocess.PIPE, shell=True)
tuple	jobID = out.split("<")
string	myLog = "/."
string	myKeyString = "The output (if any) is above this job summary."
string	mySuccessString = "Successfully completed."
int	Done = 0
tuple	haveFinished = np.zeros((numWorkers,))
int	f = 5
list	hitEvents = f['/entry_1/result_1/nPeaksAll']
tuple	numHits = len(np.where(hitEvents >= hitParam_threshold)[0])
string	fname = '/status_peaks.txt'
tuple	d = json.load(infile)
tuple	numEvents = int(d['numHits'])
tuple	p = subprocess.Popen(["grep", myKeyString, myLog], stdout=subprocess.PIPE)
tuple	output = p.communicate()
tuple	p = subprocess.Popen(["grep", mySuccessString, myLog], stdout=subprocess.PIPE)
tuple	output = p.communicate()
int	Done = 1
int	Done = 1
	indexedPeaks = None
tuple	numIndexedNow = len(np.where(indexedPeaks > 0)[0])
int	indexRate = 0
int	indexRate = 100
int	fracDone = 100
dictionary	d = {"numIndexed": numIndexedNow, "indexRate": indexRate, "fracDone": fracDone}
tuple	nodeFailed = checkJobExit(myJobList[i])
tuple	numIndexedNow = len(np.where(indexedPeaks > 0)[0])
int	indexRate = 0
int	indexRate = 100
int	fracDone = 100
dictionary	d = {"numIndexed": numIndexedNow, "indexRate": indexRate, "fracDone": fracDone}
string	totalStream = "/"
string	totalStream = "/"
tuple	numIndexed = len(np.where(indexedPeaks > 0)[0])
int	f = 5

---

Function Documentation

def indexCrystals::str2bool

(

v

)

Definition at line 38 of file indexCrystals.py.

def indexCrystals::checkJobExit

(

jobID

)

Definition at line 72 of file indexCrystals.py.

def indexCrystals::getMyChunkSize	(		numJobs,
			numWorkers,
			chunkSize,
			rank
	)

Returns number of events assigned to the slave calling this function.

Definition at line 82 of file indexCrystals.py.

def indexCrystals::writeStatus	(		fname,
			d
	)

Definition at line 93 of file indexCrystals.py.

def indexCrystals::getIndexedPeaks

(

)

Definition at line 96 of file indexCrystals.py.

---

Variable Documentation

tuple indexCrystals::parser = argparse.ArgumentParser() [static]

Definition at line 7 of file indexCrystals.py.

tuple indexCrystals::args = parser.parse_args() [static]

Definition at line 36 of file indexCrystals.py.

tuple indexCrystals::experimentName = args.expRun.split('exp=') [static]

Definition at line 42 of file indexCrystals.py.

tuple indexCrystals::runNumber = int(args.expRun.split('run=')[-1]) [static]

Definition at line 43 of file indexCrystals.py.

Referenced by CalibFileFinder::findCalibFile(), main(), test01(), test02(), test03(), and test04().

indexCrystals::experimentName = args.exp [static]

Definition at line 45 of file indexCrystals.py.

tuple indexCrystals::runNumber = int(args.run) [static]

Definition at line 46 of file indexCrystals.py.

indexCrystals::detInfo = args.det [static]

Definition at line 47 of file indexCrystals.py.

indexCrystals::geom = args.geom [static]

Definition at line 48 of file indexCrystals.py.

indexCrystals::peakMethod = args.peakMethod [static]

Definition at line 49 of file indexCrystals.py.

indexCrystals::integrationRadius = args.integrationRadius [static]

Definition at line 50 of file indexCrystals.py.

indexCrystals::pdb = args.pdb [static]

Definition at line 51 of file indexCrystals.py.

indexCrystals::indexingMethod = args.indexingMethod [static]

Definition at line 52 of file indexCrystals.py.

indexCrystals::minPeaks = args.minPeaks [static]

Definition at line 53 of file indexCrystals.py.

indexCrystals::maxPeaks = args.maxPeaks [static]

Definition at line 54 of file indexCrystals.py.

indexCrystals::minRes = args.minRes [static]

Definition at line 55 of file indexCrystals.py.

indexCrystals::tolerance = args.tolerance [static]

Definition at line 56 of file indexCrystals.py.

Referenced by Eigen::internal::solve_retval< LDLT< _MatrixType, _UpLo >, Rhs >::evalTo().

indexCrystals::extra = args.extra [static]

Definition at line 57 of file indexCrystals.py.

Referenced by psddl_hdf2psana::Epics::dataset_epics_ctrl< DBR >::native_type(), and psddl_hdf2psana::Epics::dataset_epics_time< DBR >::native_type().

indexCrystals::outDir = args.outDir [static]

Definition at line 58 of file indexCrystals.py.

indexCrystals::sample = args.sample [static]

Definition at line 59 of file indexCrystals.py.

Referenced by createCXISkeleton().

indexCrystals::tag = args.tag [static]

Definition at line 60 of file indexCrystals.py.

indexCrystals::queue = args.queue [static]

Definition at line 61 of file indexCrystals.py.

indexCrystals::chunkSize = args.chunkSize [static]

Definition at line 62 of file indexCrystals.py.

Referenced by createDatasetAccessList(), createPropertyList(), and CXI::Node::createStack().

indexCrystals::noe = args.noe [static]

Definition at line 63 of file indexCrystals.py.

indexCrystals::instrument = args.instrument [static]

Definition at line 64 of file indexCrystals.py.

Referenced by LogBook::ConnectionImpl::allocateRunNumber(), LogBook::ConnectionImpl::beginRun(), createCXISkeleton(), LogBook::ConnectionImpl::createRun(), LogBook::ConnectionImpl::createRunAttr(), LogBook::ConnectionImpl::createRunParam(), LogBook::ConnectionImpl::endRun(), LogBook::ConnectionImpl::getAttrClasses(), LogBook::ConnectionImpl::getAttrInfo(), LogBook::ConnectionImpl::getAttrVal(), LogBook::ConnectionImpl::getCurrentExperiment(), LogBook::ConnectionImpl::getExperiments(), LogBook::ConnectionImpl::getOneExperiment(), LogBook::ConnectionImpl::getParamInfo(), LogBook::ConnectionImpl::getParamsInfo(), LogBook::ConnectionImpl::getRunParam(), parseExpName(), LogBook::ConnectionImpl::saveFiles(), and LogBook::ConnectionImpl::setRunParam().

indexCrystals::pixelSize = args.pixelSize [static]

Definition at line 65 of file indexCrystals.py.

Referenced by applyPolarizationCorrection(), applySolidAngleCorrection(), cGlobal::writeConfigurationLog(), and writeCXI().

indexCrystals::coffset = args.coffset [static]

Definition at line 66 of file indexCrystals.py.

indexCrystals::clenEpics = args.clenEpics [static]

Definition at line 67 of file indexCrystals.py.

indexCrystals::logger = args.logger [static]

Definition at line 68 of file indexCrystals.py.

indexCrystals::hitParam_threshold = args.hitParam_threshold [static]

Definition at line 69 of file indexCrystals.py.

int indexCrystals::keepData = 2 [static]

Definition at line 70 of file indexCrystals.py.

string indexCrystals::runDir = "/r" [static]

Definition at line 149 of file indexCrystals.py.

string indexCrystals::peakFile = '/' [static]

Definition at line 150 of file indexCrystals.py.

string indexCrystals::indexingFile = '/.' [static]

Definition at line 151 of file indexCrystals.py.

string indexCrystals::fnameIndex = "/status_index.txt" [static]

Definition at line 152 of file indexCrystals.py.

int indexCrystals::f = 5 [static]

Definition at line 155 of file indexCrystals.py.

string indexCrystals::hasData = '/entry_1/instrument_1/detector_1/data' [static]

Definition at line 156 of file indexCrystals.py.

list indexCrystals::minPeaksUsed = f["entry_1/result_1/nPeaks"] [static]

Definition at line 157 of file indexCrystals.py.

list indexCrystals::maxPeaksUsed = f["entry_1/result_1/nPeaks"] [static]

Definition at line 158 of file indexCrystals.py.

list indexCrystals::minResUsed = f["entry_1/result_1/nPeaks"] [static]

Definition at line 159 of file indexCrystals.py.

dictionary indexCrystals::d = {"message": "#StartIndexing"} [static]

Definition at line 171 of file indexCrystals.py.

int indexCrystals::f = 5 [static]

Definition at line 177 of file indexCrystals.py.

list indexCrystals::eventList = f['/LCLS/eventNumber'] [static]

Definition at line 178 of file indexCrystals.py.

tuple indexCrystals::numEvents = len(eventList) [static]

Definition at line 179 of file indexCrystals.py.

tuple indexCrystals::numWorkers = int(np.ceil(numEvents*1./chunkSize)) [static]

Definition at line 186 of file indexCrystals.py.

list indexCrystals::myLogList = [] [static]

Definition at line 188 of file indexCrystals.py.

list indexCrystals::myJobList = [] [static]

Definition at line 189 of file indexCrystals.py.

list indexCrystals::myStreamList = [] [static]

Definition at line 190 of file indexCrystals.py.

tuple indexCrystals::myJobs = getMyChunkSize(numEvents, numWorkers, chunkSize, rank) [static]

Definition at line 192 of file indexCrystals.py.

string indexCrystals::jobName = "_" [static]

Definition at line 194 of file indexCrystals.py.

Referenced by psana::PSAna::dataSource().

string indexCrystals::jobName = "_" [static]

Definition at line 196 of file indexCrystals.py.

string indexCrystals::myList = "/temp_" [static]

Definition at line 197 of file indexCrystals.py.

string indexCrystals::myStream = "/temp_" [static]

Definition at line 198 of file indexCrystals.py.

string indexCrystals::cmd = "bsub -q " [static]

Definition at line 206 of file indexCrystals.py.

tuple indexCrystals::process = subprocess.Popen(cmd, stdout=subprocess.PIPE, stderr=subprocess.PIPE, shell=True) [static]

Definition at line 218 of file indexCrystals.py.

Referenced by BOOST_PYTHON_MODULE().

tuple indexCrystals::jobID = out.split("<") [static]

Definition at line 220 of file indexCrystals.py.

string indexCrystals::myLog = "/." [static]

Definition at line 221 of file indexCrystals.py.

string indexCrystals::myKeyString = "The output (if any) is above this job summary." [static]

Definition at line 226 of file indexCrystals.py.

string indexCrystals::mySuccessString = "Successfully completed." [static]

Definition at line 227 of file indexCrystals.py.

int indexCrystals::Done = 0 [static]

Definition at line 228 of file indexCrystals.py.

tuple indexCrystals::haveFinished = np.zeros((numWorkers,)) [static]

Definition at line 229 of file indexCrystals.py.

int indexCrystals::f = 5 [static]

Definition at line 231 of file indexCrystals.py.

list indexCrystals::hitEvents = f['/entry_1/result_1/nPeaksAll'] [static]

Definition at line 232 of file indexCrystals.py.

tuple indexCrystals::numHits = len(np.where(hitEvents >= hitParam_threshold)[0]) [static]

Definition at line 233 of file indexCrystals.py.

string indexCrystals::fname = '/status_peaks.txt' [static]

Definition at line 237 of file indexCrystals.py.

tuple indexCrystals::d = json.load(infile) [static]

Definition at line 240 of file indexCrystals.py.

tuple indexCrystals::numEvents = int(d['numHits']) [static]

Definition at line 241 of file indexCrystals.py.

tuple indexCrystals::p = subprocess.Popen(["grep", myKeyString, myLog], stdout=subprocess.PIPE) [static]

Definition at line 247 of file indexCrystals.py.

Referenced by Eigen::Hyperplane< _Scalar, _AmbientDim, _Options >::absDistance(), pytools::EnumType::addEnum(), Eigen::AlignedBox< _Scalar, _AmbientDim >::AlignedBox(), ImgAlgos::applyCModeUnbond(), pypsalg::AreaDetHist::AreaDetHist(), hdf5pp::Group::basename(), Eigen::internal::bicgstab(), calculate_logic(), Eigen::SparseMatrix< _Scalar, _Options, _Index >::coeffRef(), Detector::DetectorAccess::common_mode(), Eigen::JacobiSVD< _MatrixType, QRPreconditioner >::compute(), Eigen::GeneralizedEigenSolver< _MatrixType >::compute(), Eigen::EigenSolver< _MatrixType >::compute(), Eigen::SVD< MatrixType >::compute(), psana::Configurable::Configurable(), Eigen::internal::conjugate_gradient(), RdbMySQL::Conn::Conn(), Eigen::AlignedBox< _Scalar, _AmbientDim >::contains(), Translator::TestModuleNDArrayString::createAndFillNDarrayThenPutInEvent(), Eigen::internal::cs_tdfs(), cspadSubtractBehindWires(), IData::Dataset::Dataset(), Eigen::ParametrizedLine< _Scalar, _AmbientDim, _Options >::distance(), pytools::EnumType::EnumType(), XtcInput::SharedFile::eof(), psana_test::epics2Str(), Eigen::internal::etree_find(), Eigen::internal::image_retval< FullPivLU< _MatrixType > >::evalTo(), Eigen::internal::kernel_retval< FullPivLU< _MatrixType > >::evalTo(), TimeTool::Check::event(), ImgAlgos::ImgPeakFinderAB::eventSelector(), ImgAlgos::CSPadArrPeakFinder::eventSelector(), H5DataTypes::EvrEventCodeV5::EvrEventCodeV5(), H5DataTypes::EvrEventCodeV6::EvrEventCodeV6(), H5DataTypes::EvrIOChannel::EvrIOChannel(), H5DataTypes::EvrSrcEventCode::EvrSrcEventCode(), Eigen::AlignedBox< _Scalar, _AmbientDim >::extend(), Eigen::AlignedBox< _Scalar, _AmbientDim >::exteriorDistance(), Eigen::SparseQR< _MatrixType, _OrderingType >::factorize(), Eigen::SimplicialCholeskyBase< Derived >::factorize_preordered(), Translator::Calib::CsPadPixelGainV1::fillHdf5WriteBuffer(), Translator::Calib::CsPad2x2PixelGainV1::fillHdf5WriteBuffer(), Translator::Calib::CsPad2x2PixelStatusV1::fillHdf5WriteBuffer(), Translator::Calib::CsPad2x2PedestalsV1::fillHdf5WriteBuffer(), Translator::Calib::CsPadPixelStatusV1::fillHdf5WriteBuffer(), Translator::Calib::CsPadPedestalsV1::fillHdf5WriteBuffer(), Translator::Calib::CsPadFilterV1::fillHdf5WriteBuffer(), Translator::Calib::CsPadCommonModeSubV1::fillHdf5WriteBuffer(), ImgAlgos::findCommonMode(), pdscalibdata::CsPadCommonModeSubV1::findCommonMode(), pdscalibdata::findCommonMode(), MsgLogger::MsgFormatter::format(), PSTime::TimeFormat::format(), getEventKey(), hdf5pp::Group::getSoftLink(), gsub(), hdf5pp::Group::hasChild(), PSQt::HSV2RGBA(), PSShmemInput::DgramSourceShmem::init(), internal::init_rows_cols(), Eigen::internal::gebp_traits< std::complex< RealScalar >, std::complex< RealScalar >, _ConjLhs, _ConjRhs >::initAcc(), Eigen::SparseVector< _Scalar, _Options, _Index >::insert(), Eigen::SparseMatrix< _Scalar, _Options, _Index >::insertBackByOuterInner(), Eigen::SparseMatrix< _Scalar, _Options, _Index >::insertBackByOuterInnerUnordered(), Eigen::SparseMatrix< _Scalar, _Options, _Index >::insertBackUncompressed(), Eigen::SparseMatrix< _Scalar, _Options, _Index >::insertCompressed(), Eigen::SparseMatrix< _Scalar, _Options, _Index >::insertUncompressed(), isCtrlEpics(), pypsalg::isIsolated(), killNearbyPeaks(), main(), ImgAlgos::CSPadArrPeakFinder::makeUnitedPeakVector(), ImgAlgos::medianEpix100V1(), Eigen::internal::minimum_degree_ordering(), PSQt::WdgImage::mousePressEvent(), XtcInput::XtcChunkDgIter::nextAtOffset(), CXI::Node::Node(), Eigen::internal::scalar_hypot_op< Scalar >::operator()(), LogBook::operator<<(), ImgAlgos::operator<<(), H5DataTypes::EvrIOChannel::operator=(), H5DataTypes::EvrSrcEventCode::operator=(), H5DataTypes::EvrEventCodeV6::operator=(), H5DataTypes::EvrEventCodeV5::operator=(), Eigen::BlockImpl< SparseMatrix< _Scalar, _Options, _Index >, BlockRows, BlockCols, true, Sparse >::operator=(), packArgs(), PSQt::CustomButton::paintEvent(), hdf5pp::Group::parent(), parseExpName(), IData::Dataset::parseHdfFileName(), parseRuns(), parseStreams(), IData::Dataset::parseXtcFileName(), peakfinder3(), peakfinder6(), peakfinder8(), peakfinder8old(), Detector::DetectorAccess::pedestals(), Detector::DetectorAccess::pixel_bkgd(), Detector::DetectorAccess::pixel_gain(), Detector::DetectorAccess::pixel_mask(), SegGeometryCspad2x1V1::pixel_mask_array(), Detector::DetectorAccess::pixel_rms(), Detector::DetectorAccess::pixel_status(), H5DataTypes::PnCCDConfigV2::PnCCDConfigV2(), XtcInput::DgramQueue::pop(), psana_test::printDgramHeaderHex(), ImgAlgos::CSPadMaskV1::printMaskStatistics(), ImgAlgos::ImgPeakFinderAB::printVectorOfPeaks(), ImgAlgos::CSPadArrPeakFinder::printVectorOfPeaks(), Eigen::ParametrizedLine< _Scalar, _AmbientDim, _Options >::projection(), Eigen::Hyperplane< _Scalar, _AmbientDim, _Options >::projection(), psana::PSAna::PSAna(), psddl_pds2psana::SmallDataProxy::readBlockFromLargeFile(), psana::PSAnaApp::run(), Eigen::internal::lpNorm_selector< Derived, p >::run(), Eigen::internal::hypot_impl< Scalar >::run(), psana::PSAnaApp::setConfigFileAndOptions(), ImgAlgos::AlgArrProc::setWindows(), Eigen::Hyperplane< _Scalar, _AmbientDim, _Options >::signedDistance(), Eigen::SVD< MatrixType >::sort(), split2(), Eigen::ParametrizedLine< _Scalar, _AmbientDim, _Options >::squaredDistance(), Eigen::AlignedBox< _Scalar, _AmbientDim >::squaredExteriorDistance(), Translator::TestModuleReadNDArrayString::testNDarrayInEvent(), and psddl_hdf2psana::HdfConverter::typeName().

tuple indexCrystals::output = p.communicate() [static]

Definition at line 248 of file indexCrystals.py.

Referenced by ImgAlgos::count_excess(), count_excess_1(), count_excess_2(), ImgAlgos::count_hits(), count_hits_1(), count_hits_2(), cspad_mod::DataProxyT< DataType, ElemType >::getTypedImpl(), cspad_mod::DataProxy2x2::getTypedImpl(), psddl_hdf2psana::EvrData::ns_IOChannelV2_v0_dataset_data_native_type(), psddl_hdf2psana::EvrData::ns_IOChannelV2_v0_dataset_data_stored_type(), ImgAlgos::sum_excess(), sum_excess_1(), sum_excess_2(), ImgAlgos::sum_hits(), sum_hits_1(), and sum_hits_2().

tuple indexCrystals::p = subprocess.Popen(["grep", mySuccessString, myLog], stdout=subprocess.PIPE) [static]

Definition at line 252 of file indexCrystals.py.

tuple indexCrystals::output = p.communicate() [static]

Definition at line 253 of file indexCrystals.py.

int indexCrystals::Done = 1 [static]

Definition at line 260 of file indexCrystals.py.

int indexCrystals::Done = 1 [static]

Definition at line 266 of file indexCrystals.py.

indexCrystals::indexedPeaks = None [static]

Definition at line 269 of file indexCrystals.py.

tuple indexCrystals::numIndexedNow = len(np.where(indexedPeaks > 0)[0]) [static]

Definition at line 272 of file indexCrystals.py.

int indexCrystals::indexRate = 0 [static]

Definition at line 274 of file indexCrystals.py.

int indexCrystals::indexRate = 100 [static]

Definition at line 276 of file indexCrystals.py.

int indexCrystals::fracDone = 100 [static]

Definition at line 277 of file indexCrystals.py.

dictionary indexCrystals::d = {"numIndexed": numIndexedNow, "indexRate": indexRate, "fracDone": fracDone} [static]

Definition at line 281 of file indexCrystals.py.

tuple indexCrystals::nodeFailed = checkJobExit(myJobList[i]) [static]

Definition at line 291 of file indexCrystals.py.

tuple indexCrystals::numIndexedNow = len(np.where(indexedPeaks > 0)[0]) [static]

Definition at line 300 of file indexCrystals.py.

int indexCrystals::indexRate = 0 [static]

Definition at line 302 of file indexCrystals.py.

int indexCrystals::indexRate = 100 [static]

Definition at line 304 of file indexCrystals.py.

int indexCrystals::fracDone = 100 [static]

Definition at line 305 of file indexCrystals.py.

dictionary indexCrystals::d = {"numIndexed": numIndexedNow, "indexRate": indexRate, "fracDone": fracDone} [static]

Definition at line 309 of file indexCrystals.py.

string indexCrystals::totalStream = "/" [static]

Definition at line 317 of file indexCrystals.py.

string indexCrystals::totalStream = "/" [static]

Definition at line 319 of file indexCrystals.py.

tuple indexCrystals::numIndexed = len(np.where(indexedPeaks > 0)[0]) [static]

Definition at line 326 of file indexCrystals.py.

int indexCrystals::f = 5 [static]

Definition at line 330 of file indexCrystals.py.

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