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#include "MantidQtCustomInterfaces/ReflMainViewPresenter.h"
#include "MantidAPI/AlgorithmManager.h"
#include "MantidAPI/ITableWorkspace.h"
#include "MantidAPI/TableRow.h"
#include "MantidGeometry/Instrument/ParameterMap.h"
#include "MantidKernel/Strings.h"
#include "MantidKernel/TimeSeriesProperty.h"
#include "MantidKernel/Utils.h"
#include "MantidQtCustomInterfaces/ReflMainView.h"
using namespace Mantid::API;
using namespace Mantid::Geometry;
void checkValidModel(ITableWorkspace_sptr model)
if(model->columnCount() != 9)
throw std::runtime_error("Selected table has the incorrect number of columns (9) to be used as a reflectometry table.");
try
model->String(0,0);
model->String(0,1);
model->String(0,2);
model->String(0,3);
model->String(0,4);
model->String(0,5);
model->Double(0,6);
model->Int(0,7);
model->String(0,8);
catch(const std::runtime_error&)
{
throw std::runtime_error("Selected table does not meet the specifications to become a model for this interface.");
}
}
ITableWorkspace_sptr createWorkspace()
{
ITableWorkspace_sptr ws = WorkspaceFactory::Instance().createTable();
auto colRuns = ws->addColumn("str","Run(s)");
auto colTheta = ws->addColumn("str","ThetaIn");
auto colTrans = ws->addColumn("str","TransRun(s)");
auto colQmin = ws->addColumn("str","Qmin");
auto colQmax = ws->addColumn("str","Qmax");
auto colDqq = ws->addColumn("str","dq/q");
auto colScale = ws->addColumn("double","Scale");
auto colStitch = ws->addColumn("int","StitchGroup");
auto colOptions = ws->addColumn("str","Options");
colRuns->setPlotType(0);
colTheta->setPlotType(0);
colTrans->setPlotType(0);
colQmin->setPlotType(0);
colQmax->setPlotType(0);
colDqq->setPlotType(0);
colScale->setPlotType(0);
colStitch->setPlotType(0);
colOptions->setPlotType(0);
return ws;
}
}
namespace MantidQt
{
namespace CustomInterfaces
{
ReflMainViewPresenter::ReflMainViewPresenter(ReflMainView* view): m_view(view)
//Set up the instrument selectors
std::vector<std::string> instruments;
instruments.push_back("INTER");
instruments.push_back("SURF");
instruments.push_back("CRISP");
instruments.push_back("POLREF");
//If the user's configured default instrument is in this list, set it as the default, otherwise use INTER
const std::string defaultInst = Mantid::Kernel::ConfigService::Instance().getString("default.instrument");
if(std::find(instruments.begin(), instruments.end(), defaultInst) != instruments.end())
m_view->setInstrumentList(instruments, defaultInst);
else
m_view->setInstrumentList(instruments, "INTER");
ReflMainViewPresenter::~ReflMainViewPresenter()
{
/**
* Finds the first unused group id
*/
int ReflMainViewPresenter::getUnusedGroup(std::vector<size_t> ignoredRows) const
{
std::vector<int> usedGroups;
//Scan through all the rows, working out which group ids are used
for(size_t idx = 0; idx < m_model->rowCount(); ++idx)
{
if(std::find(ignoredRows.begin(), ignoredRows.end(), idx) != ignoredRows.end())
continue;
//This is an unselected row. Add it to the list of used group ids
usedGroups.push_back(m_model->Int(idx, COL_GROUP));
}
int groupId = 0;
//While the group id is one of the used ones, increment it by 1
while(std::find(usedGroups.begin(), usedGroups.end(), groupId) != usedGroups.end())
groupId++;
return groupId;
}
/**
Process selected rows
*/
void ReflMainViewPresenter::process()
{
if(m_model->rowCount() == 0)
{
m_view->giveUserWarning("Cannot process an empty Table","Warning");
return;
}
std::vector<size_t> rows = m_view->getSelectedRowIndexes();
//Does the user want to abort?
if(!m_view->askUserYesNo("This will process all rows in the table. Continue?","Process all rows?"))
return;
//They want to process all rows, so populate rows with every index in the model
for(size_t idx = 0; idx < m_model->rowCount(); ++idx)
rows.push_back(idx);
//Maps group numbers to the list of rows in that group we want to process
std::map<int,std::vector<size_t> > groups;
for(auto it = rows.begin(); it != rows.end(); ++it)
const int group = m_model->Int(*it, COL_GROUP);
groups[group].push_back(*it);
}
catch(std::exception& ex)
{
const std::string rowNo = Mantid::Kernel::Strings::toString<size_t>(*it + 1);
m_view->giveUserCritical("Error found in row " + rowNo + ":\n" + ex.what(), "Error");
return;
}
//Each group and each row within count as a progress step.
const int maxProgress = (int)(rows.size() + groups.size());
m_view->setProgressRange(progress, maxProgress);
m_view->setProgress(progress);
for(auto gIt = groups.begin(); gIt != groups.end(); ++gIt)
const std::vector<size_t> groupRows = gIt->second;
//Process each row individually
for(auto rIt = groupRows.begin(); rIt != groupRows.end(); ++rIt)
{
try
{
processRow(*rIt);
m_view->setProgress(++progress);
}
catch(std::exception& ex)
{
const std::string rowNo = Mantid::Kernel::Strings::toString<size_t>(*rIt + 1);
const std::string message = "Error encountered while processing row " + rowNo + ":\n";
m_view->giveUserCritical(message + ex.what(), "Error");
m_view->setProgress(0);
return;
}
}
stitchRows(groupRows);
m_view->setProgress(++progress);
}
catch(std::exception& ex)
{
const std::string groupNo = Mantid::Kernel::Strings::toString<int>(gIt->first);
const std::string message = "Error encountered while stitching group " + groupNo + ":\n";
m_view->giveUserCritical(message + ex.what(), "Error");
Validate a row.
If a row passes validation, it is ready to be autofilled, but
not necessarily ready for processing.
@param rowNo : The row in the model to validate
@throws std::invalid_argument if the row fails validation
*/
void ReflMainViewPresenter::validateRow(size_t rowNo) const
if(rowNo >= m_model->rowCount())
throw std::invalid_argument("Invalid row");
if(m_model->String(rowNo, COL_RUNS).empty())
throw std::invalid_argument("Run column may not be empty.");
}
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/**
Autofill a row
@param rowNo : The row in the model to autofill
@throws std::runtime_error if the row could not be auto-filled
*/
void ReflMainViewPresenter::autofillRow(size_t rowNo)
{
if(rowNo >= m_model->rowCount())
throw std::runtime_error("Invalid row");
const std::string runStr = m_model->String(rowNo, COL_RUNS);
MatrixWorkspace_sptr run = boost::dynamic_pointer_cast<MatrixWorkspace>(loadRun(runStr, m_view->getProcessInstrument()));
//Fetch two theta from the log if needed
if(m_model->String(rowNo, COL_ANGLE).empty())
{
Property* logData = NULL;
//First try TwoTheta
try
{
logData = run->mutableRun().getLogData("Theta");
}
catch(std::exception&)
{
throw std::runtime_error("Value for two theta could not be found in log.");
}
auto logPWV = dynamic_cast<const PropertyWithValue<double>*>(logData);
auto logTSP = dynamic_cast<const TimeSeriesProperty<double>*>(logData);
double thetaVal;
if(logPWV)
thetaVal = *logPWV;
else if(logTSP && logTSP->realSize() > 0)
thetaVal = logTSP->lastValue();
else
throw std::runtime_error("Value for two theta could not be found in log.");
//Update the model
m_model->String(rowNo, COL_ANGLE) = Strings::toString<double>(Utils::roundToDP(thetaVal, 3));
}
//If we need to calculate the resolution, do.
if(m_model->String(rowNo, COL_DQQ).empty())
{
IAlgorithm_sptr calcResAlg = AlgorithmManager::Instance().create("CalculateResolution");
calcResAlg->setProperty("Workspace", run);
calcResAlg->setProperty("TwoTheta", m_model->String(rowNo, COL_ANGLE));
calcResAlg->execute();
//Update the model
double dqqVal = calcResAlg->getProperty("Resolution");
m_model->String(rowNo, COL_DQQ) = Strings::toString<double>(dqqVal);
}
//Make sure the view updates
m_view->showTable(m_model);
}
/**
Extracts the run number of a workspace
@param ws : The workspace to fetch the run number from
@returns The run number of the workspace
*/
std::string ReflMainViewPresenter::getRunNumber(const Workspace_sptr& ws)
{
//If we can, use the run number from the workspace's sample log
MatrixWorkspace_sptr mws = boost::dynamic_pointer_cast<MatrixWorkspace>(ws);
if(mws)
{
try
{
const Property* runProperty = mws->mutableRun().getLogData("run_number");
auto runNumber = dynamic_cast<const PropertyWithValue<std::string>*>(runProperty);
if(runNumber)
return *runNumber;
}
catch(Mantid::Kernel::Exception::NotFoundError&)
{
//We'll just fall back to looking at the workspace's name
}
}
//Okay, let's see what we can get from the workspace's name
const std::string wsName = ws->name();
//Matches TOF_13460 -> 13460
boost::regex outputRegex("(TOF|IvsQ|IvsLam)_([0-9]+)");
//Matches INTER13460 -> 13460
boost::regex instrumentRegex("[a-zA-Z]{3,}([0-9]{3,})");
boost::smatch matches;
if(boost::regex_match(wsName, matches, outputRegex))
{
return matches[2].str();
}
else if(boost::regex_match(wsName, matches, instrumentRegex))
{
return matches[1].str();
}
//Resort to using the workspace name
return wsName;
}
Loads a run from disk or fetches it from the AnalysisDataService
@param run : The name of the run
@param instrument : The instrument the run belongs to
@throws std::runtime_error if the run could not be loaded
@returns a shared pointer to the workspace
*/
Workspace_sptr ReflMainViewPresenter::loadRun(const std::string& run, const std::string& instrument = "")
{
//First, let's see if the run given is the name of a workspace in the ADS
if(AnalysisDataService::Instance().doesExist(run))
return AnalysisDataService::Instance().retrieveWS<Workspace>(run);
//Is the run string is numeric
if(boost::regex_match(run, boost::regex("\\d+")))
{
std::string wsName;
//Look "TOF_<run_number>" in the ADS
wsName = "TOF_" + run;
if(AnalysisDataService::Instance().doesExist(wsName))
return AnalysisDataService::Instance().retrieveWS<Workspace>(wsName);
//Look for "<instrument><run_number>" in the ADS
wsName = instrument + run;
if(AnalysisDataService::Instance().doesExist(wsName))
return AnalysisDataService::Instance().retrieveWS<Workspace>(wsName);
}
//We'll just have to load it ourselves
const std::string filename = instrument + run;
IAlgorithm_sptr algLoadRun = AlgorithmManager::Instance().create("Load");
algLoadRun->initialize();
algLoadRun->setProperty("Filename", filename);
algLoadRun->setProperty("OutputWorkspace", "TOF_" + run);
algLoadRun->execute();
if(!algLoadRun->isExecuted())
throw std::runtime_error("Could not open " + filename);
return AnalysisDataService::Instance().retrieveWS<Workspace>("TOF_" + run);
@param rowNo : The row in the model to process
@throws std::runtime_error if processing fails
void ReflMainViewPresenter::processRow(size_t rowNo)
const std::string run = m_model->String(rowNo, COL_RUNS);
const std::string transStr = m_model->String(rowNo, COL_TRANSMISSION);
const std::string options = m_model->String(rowNo, COL_OPTIONS);
double theta = 0;
const bool thetaGiven = !m_model->String(rowNo, COL_ANGLE).empty();
if(thetaGiven)
Mantid::Kernel::Strings::convert<double>(m_model->String(rowNo, COL_ANGLE), theta);
Workspace_sptr runWS = loadRun(run, m_view->getProcessInstrument());
const std::string runNo = getRunNumber(runWS);
MatrixWorkspace_sptr transWS;
if(!transStr.empty())
transWS = makeTransWS(transStr);
IAlgorithm_sptr algReflOne = AlgorithmManager::Instance().create("ReflectometryReductionOneAuto");
algReflOne->initialize();
algReflOne->setProperty("InputWorkspace", runWS);
if(transWS)
algReflOne->setProperty("FirstTransmissionRun", transWS);
algReflOne->setProperty("OutputWorkspace", "IvsQ_" + runNo);
algReflOne->setProperty("OutputWorkspaceWaveLength", "IvsLam_" + runNo);
algReflOne->setProperty("ThetaIn", theta);
//Parse and set any user-specified options
auto optionsMap = Mantid::Kernel::Strings::splitToKeyValues(options);
for(auto kvp = optionsMap.begin(); kvp != optionsMap.end(); ++kvp)
{
try
{
algReflOne->setProperty(kvp->first, kvp->second);
}
catch(Mantid::Kernel::Exception::NotFoundError&)
{
throw std::runtime_error("Invalid property in options column: " + kvp->first);
}
}
algReflOne->execute();
if(!algReflOne->isExecuted())
throw std::runtime_error("Failed to run ReflectometryReductionOneAuto.");
const double scale = m_model->Double(rowNo, COL_SCALE);
if(scale != 1.0)
{
IAlgorithm_sptr algScale = AlgorithmManager::Instance().create("Scale");
algScale->initialize();
algScale->setProperty("InputWorkspace", "IvsQ_" + runNo);
algScale->setProperty("OutputWorkspace", "IvsQ_" + runNo);
algScale->setProperty("Factor", 1.0 / scale);
algScale->execute();
if(!algScale->isExecuted())
throw std::runtime_error("Failed to run Scale algorithm");
}
//Processing has completed. Put Qmin and Qmax into the table if needed, for stitching.
if(m_model->String(rowNo, COL_QMIN).empty() || m_model->String(rowNo, COL_QMAX).empty())
{
MatrixWorkspace_sptr ws = AnalysisDataService::Instance().retrieveWS<MatrixWorkspace>("IvsQ_" + runNo);
std::vector<double> qrange = calcQRange(ws, theta);
if(m_model->String(rowNo, COL_QMIN).empty())
m_model->String(rowNo, COL_QMIN) = Strings::toString<double>(qrange[0]);
if(m_model->String(rowNo, COL_QMAX).empty())
m_model->String(rowNo, COL_QMAX) = Strings::toString<double>(qrange[1]);
m_view->showTable(m_model);
}
}
/**
Calculates the minimum and maximum values for Q
@param ws : The workspace to fetch the instrument values from
@param theta : The value of two theta to use in calculations
*/
std::vector<double> ReflMainViewPresenter::calcQRange(MatrixWorkspace_sptr ws, double theta)
{
double lmin, lmax;
try
{
const Instrument_const_sptr instrument = ws->getInstrument();
lmin = instrument->getNumberParameter("LambdaMin")[0];
lmax = instrument->getNumberParameter("LambdaMax")[0];
}
catch(std::exception&)
{
throw std::runtime_error("LambdaMin/LambdaMax instrument parameters are required to calculate qmin/qmax");
}
double qmin = 4 * M_PI / lmax * sin(theta * M_PI / 180.0);
double qmax = 4 * M_PI / lmin * sin(theta * M_PI / 180.0);
qmin = Utils::roundToDP(qmin, 3);
qmax = Utils::roundToDP(qmax, 3);
std::vector<double> ret;
ret.push_back(qmin);
ret.push_back(qmax);
return ret;
/**
Stitches the workspaces created by the given rows together.
@param rows : the list of rows
*/
void ReflMainViewPresenter::stitchRows(std::vector<size_t> rows)
{
//If we can get away with doing nothing, do.
if(rows.size() < 2)
return;
//Ensure the rows are in order.
std::sort(rows.begin(), rows.end());
//Properties for Stitch1DMany
std::vector<std::string> workspaceNames;
std::vector<std::string> runs;
std::vector<double> params;
std::vector<double> startOverlaps;
std::vector<double> endOverlaps;
//Go through each row and prepare the properties
for(auto rowIt = rows.begin(); rowIt != rows.end(); ++rowIt)
{
const std::string runStr = m_model->String(*rowIt, COL_RUNS);
const std::string qMinStr = m_model->String(*rowIt, COL_QMIN);
const std::string qMaxStr = m_model->String(*rowIt, COL_QMAX);
double qmin, qmax;
Mantid::Kernel::Strings::convert<double>(qMinStr, qmin);
Mantid::Kernel::Strings::convert<double>(qMaxStr, qmax);
Workspace_sptr runWS = loadRun(runStr);
if(runWS)
{
const std::string runNo = getRunNumber(runWS);
if(AnalysisDataService::Instance().doesExist("IvsQ_" + runNo))
{
runs.push_back(runNo);
workspaceNames.push_back("IvsQ_" + runNo);
}
}
startOverlaps.push_back(qmin);
endOverlaps.push_back(qmax);
}
double dqq;
std::string dqqStr = m_model->String(rows.front(), COL_DQQ);
Mantid::Kernel::Strings::convert<double>(dqqStr, dqq);
//params are qmin, -dqq, qmax for the final output
params.push_back(*std::min_element(startOverlaps.begin(), startOverlaps.end()));
params.push_back(-dqq);
params.push_back(*std::max_element(endOverlaps.begin(), endOverlaps.end()));
//startOverlaps and endOverlaps need to be slightly offset from each other
//See usage examples of Stitch1DMany to see why we discard first qmin and last qmax
startOverlaps.erase(startOverlaps.begin());
endOverlaps.pop_back();
std::string outputWSName = "IvsQ_" + boost::algorithm::join(runs, "_");
IAlgorithm_sptr algStitch = AlgorithmManager::Instance().create("Stitch1DMany");
algStitch->initialize();
algStitch->setProperty("InputWorkspaces", workspaceNames);
algStitch->setProperty("OutputWorkspace", outputWSName);
algStitch->setProperty("Params", params);
algStitch->setProperty("StartOverlaps", startOverlaps);
algStitch->setProperty("EndOverlaps", endOverlaps);
algStitch->execute();
if(!algStitch->isExecuted())
throw std::runtime_error("Failed to run Stitch1DMany on IvsQ workspaces.");
@param transString : the numbers of the transmission runs to use
*/
MatrixWorkspace_sptr ReflMainViewPresenter::makeTransWS(const std::string& transString)
const size_t maxTransWS = 2;
std::vector<std::string> transVec;
//Take the first two run numbers
boost::split(transVec, transString, boost::is_any_of(","));
if(transVec.size() > maxTransWS)
transVec.resize(maxTransWS);
if(transVec.size() == 0)
throw std::runtime_error("Failed to parse the transmission run list.");
for(auto it = transVec.begin(); it != transVec.end(); ++it)
transWSVec.push_back(loadRun(*it, m_view->getProcessInstrument()));
//If the transmission workspace is already in the ADS, re-use it
std::string lastName = "TRANS_" + boost::algorithm::join(transVec, "_");
if(AnalysisDataService::Instance().doesExist(lastName))
return AnalysisDataService::Instance().retrieveWS<MatrixWorkspace>(lastName);
//We have the runs, so we can create a TransWS
IAlgorithm_sptr algCreateTrans = AlgorithmManager::Instance().create("CreateTransmissionWorkspaceAuto");
algCreateTrans->initialize();
algCreateTrans->setProperty("FirstTransmissionRun", transWSVec[0]->name());
if(transWSVec.size() > 1)
algCreateTrans->setProperty("SecondTransmissionRun", transWSVec[1]->name());
std::string wsName = "TRANS_" + getRunNumber(transWSVec[0]);
wsName += "_" + getRunNumber(transWSVec[1]);
algCreateTrans->setProperty("OutputWorkspace", wsName);
if(!algCreateTrans->isInitialized())
throw std::runtime_error("Could not initialize CreateTransmissionWorkspaceAuto");
algCreateTrans->execute();
if(!algCreateTrans->isExecuted())
throw std::runtime_error("CreateTransmissionWorkspaceAuto failed to execute");
return AnalysisDataService::Instance().retrieveWS<MatrixWorkspace>(wsName);
Inserts a new row in the specified location
@param before The index to insert the new row before
void ReflMainViewPresenter::insertRow(size_t before)
const int groupId = getUnusedGroup();
size_t row = m_model->insertRow(before);
//Set the default scale to 1.0
m_model->Double(row, COL_SCALE) = 1.0;
//Set the group id of the new row
m_model->Int(row, COL_GROUP) = groupId;
//Make sure the view updates
m_view->showTable(m_model);
}
/**
Add row(s) to the model
*/
void ReflMainViewPresenter::addRow()
{
std::vector<size_t> rows = m_view->getSelectedRowIndexes();
std::sort(rows.begin(), rows.end());
if(rows.size() == 0)
insertRow(m_model->rowCount());
else
insertRow(*rows.rbegin() + 1);
}
/**
Delete row(s) from the model
*/
void ReflMainViewPresenter::deleteRow()
{
std::vector<size_t> rows = m_view->getSelectedRowIndexes();
std::sort(rows.begin(), rows.end());
for(size_t idx = rows.size(); 0 < idx; --idx)
m_model->removeRow(rows.at(0));
/**
Group rows together
*/
void ReflMainViewPresenter::groupRows()
{
const std::vector<size_t> rows = m_view->getSelectedRowIndexes();
//Find the first unused group id, ignoring the selected rows
const int groupId = getUnusedGroup(rows);
//Now we just have to set the group id on the selected rows
for(auto it = rows.begin(); it != rows.end(); ++it)
m_model->Int(*it, COL_GROUP) = groupId;
/**
Used by the view to tell the presenter something has changed
*/
void ReflMainViewPresenter::notify(int flag)
case ReflMainView::SaveAsFlag: saveTableAs(); break;
case ReflMainView::SaveFlag: saveTable(); break;
case ReflMainView::AddRowFlag: addRow(); break;
case ReflMainView::DeleteRowFlag: deleteRow(); break;
case ReflMainView::ProcessFlag: process(); break;
case ReflMainView::GroupRowsFlag: groupRows(); break;
case ReflMainView::OpenTableFlag: openTable(); break;
case ReflMainView::NewTableFlag: newTable(); break;
case ReflMainView::NoFlags: return;
//Not having a 'default' case is deliberate. gcc issues a warning if there's a flag we aren't handling.
Press changes to the same item in the ADS
*/
void ReflMainViewPresenter::saveTable()
{
if(!m_wsName.empty())
AnalysisDataService::Instance().addOrReplace(m_wsName,boost::shared_ptr<ITableWorkspace>(m_model->clone()));
else
saveTableAs();
}
/**
Press changes to a new item in the ADS
void ReflMainViewPresenter::saveTableAs()
const std::string userString = m_view->askUserString("Save As", "Enter a workspace name:", "Workspace");
if(!userString.empty())
{
m_wsName = userString;
saveTable();
}
}
/**
Start a new, untitled table
*/
void ReflMainViewPresenter::newTable()
{
m_model = createWorkspace();
m_wsName.clear();
m_view->showTable(m_model);
}
/**
Open a table from the ADS
*/
void ReflMainViewPresenter::openTable()
{
auto& ads = AnalysisDataService::Instance();
const std::string toOpen = m_view->getWorkspaceToOpen();
if(toOpen.empty())
return;
if(!ads.isValid(toOpen).empty())
{
m_view->giveUserCritical("Could not open workspace: " + toOpen, "Error");
return;
}
ITableWorkspace_sptr newModel = AnalysisDataService::Instance().retrieveWS<ITableWorkspace>(toOpen);
try
{
checkValidModel(newModel);
}
catch(std::runtime_error& e)
{
m_view->giveUserCritical("Invalid workspace to open:\n" + std::string(e.what()), "Error");
return;
}
m_model = newModel;
m_wsName = toOpen;
m_view->showTable(m_model);