Merge remote-tracking branch 'origin/master' into 11187_threadsanitizer

Code/Mantid/Framework/DataHandling/src/DownloadFile.cpp

@@ -56,8 +56,7 @@ const std::string DownloadFile::summary() const {
 void DownloadFile::init() {
   declareProperty("Address", "",
                   boost::make_shared<MandatoryValidator<std::string>>(),
-                  "The address of the network resource to download. This "
-                  "should start http:// or https:// .",
+                  "The address of the network resource to download.",
                   Direction::InOut);
   declareProperty(new FileProperty("Filename", "", FileProperty::Save),
                   "The filename to save the download to.");
@@ -83,4 +82,4 @@ void DownloadFile::exec() {
 }
 
 } // namespace DataHandling
-} // namespace Mantid
+} // namespace Mantid

Code/Mantid/Framework/Properties/Mantid.properties.template

@@ -16,7 +16,8 @@ default.facility = ISIS
 default.instrument =
 
 # Set of PyQt interfaces to add to the Interfaces menu, separated by a space.  Interfaces are seperated from their respective categories by a "/".
-mantidqt.python_interfaces = Direct/DGS_Reduction.py Direct/DGSPlanner.py SANS/ORNL_SANS.py Reflectometry/REFL_Reduction.py Reflectometry/REFL_SF_Calculator.py Reflectometry/REFM_Reduction.py Utility/TofConverter.py Reflectometry/ISIS_Reflectometry.py Diffraction/Powder_Diffraction_Reduction.py Utility/FilterEvents.py
+mantidqt.python_interfaces = Direct/DGS_Reduction.py Direct/DGSPlanner.py SANS/ORNL_SANS.py Reflectometry/REFL_Reduction.py Reflectometry/REFL_SF_Calculator.py Reflectometry/REFM_Reduction.py Utility/TofConverter.py Reflectometry/ISIS_Reflectometry.py Diffraction/Powder_Diffraction_Reduction.py Utility/FilterEvents.py Diffraction/HFIR_Powder_Diffraction_Reduction.py
+
 mantidqt.python_interfaces_directory = @MANTID_ROOT@/scripts
 
 # Where to find mantid plugin libraries

Code/Mantid/MantidPlot/ipython_widget/mantid_ipython_widget.py

@@ -1,5 +1,6 @@
 import threading
 import types
+import inspect
 
 from PyQt4 import QtGui
 
@@ -14,7 +15,7 @@
 from IPython.qt.inprocess import QtInProcessKernelManager
 
 
-def our_run_code(self, code_obj):
+def our_run_code(self, code_obj, result=None):
     """ Method with which we replace the run_code method of IPython's InteractiveShell class.
         It calls the original method (renamed to ipython_run_code) on a separate thread
         so that we can avoid locking up the whole of MantidPlot while a command runs.
@@ -23,12 +24,20 @@ def our_run_code(self, code_obj):
         ----------
         code_obj : code object
           A compiled code object, to be executed
-
+        result : ExecutionResult, optional
+          An object to store exceptions that occur during execution.
         Returns
         -------
         False : Always, as it doesn't seem to matter.
     """
-    t = threading.Thread(target=self.ipython_run_code, args=[code_obj])
+
+    t = threading.Thread()
+    #ipython 3.0 introduces a third argument named result
+    nargs = len(inspect.getargspec(self.ipython_run_code).args)
+    if (nargs == 3):
+        t = threading.Thread(target=self.ipython_run_code, args=[code_obj,result])
+    else:
+        t = threading.Thread(target=self.ipython_run_code, args=[code_obj])
     t.start()
     while t.is_alive():
         QtGui.QApplication.processEvents()

Code/Mantid/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/TomoReconstruction/TomoToolConfigDialog.h

@@ -88,7 +88,7 @@ private slots:
 private:
   QLabel *labelRun, *labelOpt;
   QLineEdit *editRun, *editOpt;
-  QHBoxLayout *hRun, *hOpt;
+  QHBoxLayout *hRun, *hOpt, *hBut;
   QGridLayout *layout;
   QPushButton *okButton, *cancelButton;
 };

Code/Mantid/MantidQt/CustomInterfaces/src/Indirect/CalcCorr.cpp

@@ -295,19 +295,26 @@ namespace IDA
       return;
     }
 
-    std::string paramName = "Workflow.beam-width";
     auto instrument = ws->getInstrument();
 
-    if(instrument->hasParameter(paramName))
+    const std::string beamWidthParamName = "Workflow.beam-width";
+    if(instrument->hasParameter(beamWidthParamName))
     {
-      QString beamWidth = QString::fromStdString(instrument->getStringParameter(paramName)[0]);
+      QString beamWidth = QString::fromStdString(instrument->getStringParameter(beamWidthParamName)[0]);
       double beamWidthValue = beamWidth.toDouble();
 
       m_uiForm.spCylBeamWidth->setValue(beamWidthValue);
-      m_uiForm.spCylBeamHeight->setValue(beamWidthValue);
-
       m_uiForm.spAnnBeamWidth->setValue(beamWidthValue);
-      m_uiForm.spAnnBeamHeight->setValue(beamWidthValue);
+    }
+
+    const std::string beamHeightParamName = "Workflow.beam-height";
+    if(instrument->hasParameter(beamHeightParamName))
+    {
+      QString beamHeight = QString::fromStdString(instrument->getStringParameter(beamHeightParamName)[0]);
+      double beamHeightValue = beamHeight.toDouble();
+
+      m_uiForm.spCylBeamHeight->setValue(beamHeightValue);
+      m_uiForm.spAnnBeamHeight->setValue(beamHeightValue);
     }
   }
 

Code/Mantid/MantidQt/CustomInterfaces/src/TomoReconstruction/SavuConfigDialog.cpp

@@ -137,32 +137,34 @@ class OwnTreeWidgetItem : public QTreeWidgetItem {
 void TomoReconstruction::paramValModified(QTreeWidgetItem *item,
                                           int /*column*/) {
   OwnTreeWidgetItem *ownItem = dynamic_cast<OwnTreeWidgetItem *>(item);
-  int topLevelIndex = -1;
+  if (!ownItem)
+    return;
 
+  int topLevelIndex = -1;
   if (ownItem->getRootParent() != NULL) {
     topLevelIndex = m_uiSavu.treeCurrentPlugins->indexOfTopLevelItem(
         ownItem->getRootParent());
   }
+  if (-1 == topLevelIndex)
+    return;
 
-  if (topLevelIndex != -1) {
-    // Recreate the json string from the nodes and write back
-    std::string json = m_currPlugins->cell<std::string>(topLevelIndex, 1);
-    // potential new line out, and trim spaces
-    json.erase(std::remove(json.begin(), json.end(), '\n'), json.end());
-    json.erase(std::remove(json.begin(), json.end(), '\r'), json.end());
-    json = Poco::trimInPlace(json);
-
-    ::Json::Reader r;
-    ::Json::Value root;
-    if (r.parse(json, root)) {
-      // Look for the key and replace it
-      root[ownItem->getKey()] = ownItem->text(0).toStdString();
-    }
+  // Recreate the json string from the nodes and write back
+  std::string json = m_currPlugins->cell<std::string>(topLevelIndex, 1);
+  // potential new line out, and trim spaces
+  json.erase(std::remove(json.begin(), json.end(), '\n'), json.end());
+  json.erase(std::remove(json.begin(), json.end(), '\r'), json.end());
+  json = Poco::trimInPlace(json);
 
-    m_currPlugins->cell<std::string>(topLevelIndex, 1) =
-        ::Json::FastWriter().write(root);
-    currentPluginSelected();
+  ::Json::Reader r;
+  ::Json::Value root;
+  if (r.parse(json, root)) {
+    // Look for the key and replace it
+    root[ownItem->getKey()] = ownItem->text(0).toStdString();
   }
+
+  m_currPlugins->cell<std::string>(topLevelIndex, 1) =
+      ::Json::FastWriter().write(root);
+  currentPluginSelected();
 }
 
 // When a top level item is expanded, also expand its child items - if tree
@@ -178,88 +180,93 @@ void TomoReconstruction::expandedItem(QTreeWidgetItem *item) {
 // Adds one plugin from the available plugins list into the list of
 // current plugins
 void TomoReconstruction::transferClicked() {
-  if (m_uiSavu.listAvailablePlugins->selectedItems().count() != 0) {
-    int idx = m_uiSavu.listAvailablePlugins->currentIndex().row();
-    Mantid::API::TableRow row = m_currPlugins->appendRow();
-    for (size_t j = 0; j < m_currPlugins->columnCount(); ++j) {
-      row << m_availPlugins->cell<std::string>(idx, j);
-    }
-    createPluginTreeEntry(row);
+  if (0 == m_uiSavu.listAvailablePlugins->selectedItems().count())
+    return;
+
+  int idx = m_uiSavu.listAvailablePlugins->currentIndex().row();
+  Mantid::API::TableRow row = m_currPlugins->appendRow();
+  for (size_t j = 0; j < m_currPlugins->columnCount(); ++j) {
+    row << m_availPlugins->cell<std::string>(idx, j);
   }
+  createPluginTreeEntry(row);
 }
 
 void TomoReconstruction::moveUpClicked() {
-  if (m_uiSavu.treeCurrentPlugins->selectedItems().count() != 0) {
-    size_t idx =
-        static_cast<size_t>(m_uiSavu.treeCurrentPlugins->currentIndex().row());
-    if (idx > 0 && idx < m_currPlugins->rowCount()) {
-      // swap row, all columns
-      for (size_t j = 0; j < m_currPlugins->columnCount(); ++j) {
-        std::string swap = m_currPlugins->cell<std::string>(idx, j);
-        m_currPlugins->cell<std::string>(idx, j) =
-            m_currPlugins->cell<std::string>(idx - 1, j);
-        m_currPlugins->cell<std::string>(idx - 1, j) = swap;
-      }
-      refreshCurrentPluginListUI();
+  if (0 == m_uiSavu.treeCurrentPlugins->selectedItems().count())
+    return;
+
+  size_t idx =
+      static_cast<size_t>(m_uiSavu.treeCurrentPlugins->currentIndex().row());
+  if (idx > 0 && idx < m_currPlugins->rowCount()) {
+    // swap row, all columns
+    for (size_t j = 0; j < m_currPlugins->columnCount(); ++j) {
+      std::string swap = m_currPlugins->cell<std::string>(idx, j);
+      m_currPlugins->cell<std::string>(idx, j) =
+          m_currPlugins->cell<std::string>(idx - 1, j);
+      m_currPlugins->cell<std::string>(idx - 1, j) = swap;
     }
+    refreshCurrentPluginListUI();
   }
 }
 
 void TomoReconstruction::moveDownClicked() {
   // TODO: this can be done with the same function as above...
-  if (m_uiSavu.treeCurrentPlugins->selectedItems().count() != 0) {
-    size_t idx =
-        static_cast<size_t>(m_uiSavu.treeCurrentPlugins->currentIndex().row());
-    if (idx < m_currPlugins->rowCount() - 1) {
-      // swap all columns
-      for (size_t j = 0; j < m_currPlugins->columnCount(); ++j) {
-        std::string swap = m_currPlugins->cell<std::string>(idx, j);
-        m_currPlugins->cell<std::string>(idx, j) =
-            m_currPlugins->cell<std::string>(idx + 1, j);
-        m_currPlugins->cell<std::string>(idx + 1, j) = swap;
-      }
-      refreshCurrentPluginListUI();
+  if (0 == m_uiSavu.treeCurrentPlugins->selectedItems().count())
+    return;
+
+  size_t idx =
+      static_cast<size_t>(m_uiSavu.treeCurrentPlugins->currentIndex().row());
+  if (idx < m_currPlugins->rowCount() - 1) {
+    // swap all columns
+    for (size_t j = 0; j < m_currPlugins->columnCount(); ++j) {
+      std::string swap = m_currPlugins->cell<std::string>(idx, j);
+      m_currPlugins->cell<std::string>(idx, j) =
+          m_currPlugins->cell<std::string>(idx + 1, j);
+      m_currPlugins->cell<std::string>(idx + 1, j) = swap;
     }
+    refreshCurrentPluginListUI();
   }
 }
 
 void TomoReconstruction::removeClicked() {
   // Also clear ADS entries
-  if (m_uiSavu.treeCurrentPlugins->selectedItems().count() != 0) {
-    int idx = m_uiSavu.treeCurrentPlugins->currentIndex().row();
-    m_currPlugins->removeRow(idx);
+  if (0 == m_uiSavu.treeCurrentPlugins->selectedItems().count())
+    return;
 
-    refreshCurrentPluginListUI();
-  }
+  int idx = m_uiSavu.treeCurrentPlugins->currentIndex().row();
+  m_currPlugins->removeRow(idx);
+
+  refreshCurrentPluginListUI();
 }
 
 void TomoReconstruction::menuOpenClicked() {
   QString s =
       QFileDialog::getOpenFileName(0, "Open file", QDir::currentPath(),
                                    "NeXus files (*.nxs);;All files (*.*)",
                                    new QString("NeXus files (*.nxs)"));
-  std::string returned = s.toStdString();
-  if (returned != "") {
-    bool opening = true;
-
-    if (m_currPlugins->rowCount() > 0) {
-      QMessageBox::StandardButton reply = QMessageBox::question(
-          this, "Open file confirmation",
-          "Opening the configuration file will clear the current list."
-          "\nWould you like to continue?",
-          QMessageBox::Yes | QMessageBox::No);
-      if (reply == QMessageBox::No) {
-        opening = false;
-      }
-    }
+  std::string name = s.toStdString();
 
-    if (opening) {
-      loadSavuTomoConfig(returned, m_currPlugins);
+  if ("" == name)
+    return;
 
-      m_currentParamPath = returned;
-      refreshCurrentPluginListUI();
+  bool opening = true;
+  if (m_currPlugins->rowCount() > 0) {
+    QMessageBox::StandardButton reply = QMessageBox::question(
+        this, "Open file confirmation",
+        "Opening the configuration file will clear the current list."
+        "\nWould you like to continue?",
+        QMessageBox::Yes | QMessageBox::No);
+    if (reply == QMessageBox::No) {
+      opening = false;
     }
   }
+
+  if (opening) {
+    loadSavuTomoConfig(name, m_currPlugins);
+
+    m_currentParamPath = name;
+    refreshCurrentPluginListUI();
+  }
 }
 
 void TomoReconstruction::menuSaveClicked() {
@@ -268,7 +275,12 @@ void TomoReconstruction::menuSaveClicked() {
     return;
   }
 
-  if (m_currPlugins->rowCount() != 0) {
+  if (0 == m_currPlugins->rowCount()) {
+    // Alert that the plugin list is empty
+    QMessageBox::information(this, tr("Unable to save file"),
+                             "The current plugin list is empty, please add one "
+                             "or more to the list.");
+  } else {
     AnalysisDataService::Instance().add(createUniqueNameHidden(),
                                         m_currPlugins);
     std::string csvWorkspaceNames = m_currPlugins->name();
@@ -282,11 +294,6 @@ void TomoReconstruction::menuSaveClicked() {
     if (!alg->isExecuted()) {
       throw std::runtime_error("Error when trying to save config file");
     }
-  } else {
-    // Alert that the plugin list is empty
-    QMessageBox::information(this, tr("Unable to save file"),
-                             "The current plugin list is empty, please add one "
-                             "or more to the list.");
   }
 }
 
@@ -295,11 +302,12 @@ void TomoReconstruction::menuSaveAsClicked() {
       QFileDialog::getSaveFileName(0, "Save file", QDir::currentPath(),
                                    "NeXus files (*.nxs);;All files (*.*)",
                                    new QString("NeXus files (*.nxs)"));
-  std::string returned = s.toStdString();
-  if (returned != "") {
-    m_currentParamPath = returned;
-    menuSaveClicked();
-  }
+  std::string name = s.toStdString();
+  if ("" == name)
+    return;
+
+  m_currentParamPath = name;
+  menuSaveClicked();
 }
 
 QString TomoReconstruction::tableWSRowToString(ITableWorkspace_sptr table,

Code/Mantid/MantidQt/CustomInterfaces/src/TomoReconstruction/TomoReconstruction.cpp

@@ -1285,18 +1285,25 @@ std::string TomoReconstruction::getPassword() {
  */
 void TomoReconstruction::drawImage(const MatrixWorkspace_sptr &ws) {
   // From logs we expect a name "run_title", width "Axis1" and height "Axis2"
-  size_t width, height;
+  const size_t MAXDIM = 2048 * 16;
+  size_t width;
   try {
     width = boost::lexical_cast<size_t>(ws->run().getLogData("Axis1")->value());
+    // TODO: add a settings option for this (like max mem allocation for images)?
+    if (width >= MAXDIM)
+      width = MAXDIM;
   } catch (std::exception &e) {
     userError("Cannot load image", "There was a problem while trying to "
                                    "find the width of the image: " +
                                        std::string(e.what()));
     return;
   }
+  size_t height;
   try {
     height =
         boost::lexical_cast<size_t>(ws->run().getLogData("Axis2")->value());
+    if (height >= MAXDIM)
+      height = MAXDIM;
   } catch (std::exception &e) {
     userError("Cannot load image", "There was a problem while trying to "
                                    "find the height of the image: " +

Code/Mantid/MantidQt/CustomInterfaces/src/TomoReconstruction/TomoToolConfigDialog.cpp

@@ -24,9 +24,17 @@ TomoToolConfigDialog::TomoToolConfigDialog(QWidget *parent) : QDialog(parent) {
   hOpt->addWidget(labelOpt);
   hOpt->addWidget(editOpt);
 
+  okButton = new QPushButton("Ok");
+  cancelButton = new QPushButton("Cancel");
+  hBut = new QHBoxLayout();
+  hBut->insertStretch(0,1);
+  hBut->addWidget(okButton);
+  hBut->addWidget(cancelButton);
+
   layout = new QGridLayout();
   layout->addLayout(hRun, 0, 0);
   layout->addLayout(hOpt, 1, 0);
+  layout->addLayout(hOpt, 2, 0);
 
   connect(okButton, SIGNAL(clicked()), this, SLOT(okClicked()));
   connect(cancelButton, SIGNAL(clicked()), this, SLOT(cancelClicked()));