Merge remote-tracking branch 'origin/release-next'

Framework/PythonInterface/plugins/algorithms/SaveGEMMAUDParamFile.py

@@ -85,7 +85,12 @@ class SaveGEMMAUDParamFile(PythonAlgorithm):
         def create_empty_param_list(default_value="0"):
             return "\n".join(default_value for _ in range(num_banks))
 
-        with open(self.getProperty(self.PROP_TEMPLATE_FILE).value) as template_file:
+        template_file_path = self.getProperty(self.PROP_TEMPLATE_FILE).value
+        if len(template_file_path) == 0:
+            logger.error("Could not find default diffraction directory for .maud template file: "
+                         "you'll have to find it yourself")
+
+        with open(template_file_path) as template_file:
             template = template_file.read()
 
         output_params["function_types"] = create_empty_param_list("1")
@@ -136,8 +141,6 @@ class SaveGEMMAUDParamFile(PythonAlgorithm):
             if os.path.exists(path_to_test):
                 return path_to_test
 
-        logger.warning("Could not find default diffraction directory for .maud template file: "
-                       "you'll have to find it yourself")
         return ""
 
     def _format_param_list(self, param_list):

Framework/PythonInterface/plugins/algorithms/WorkflowAlgorithms/ISISIndirectEnergyTransfer.py

@@ -360,9 +360,6 @@ class ISISIndirectEnergyTransfer(DataProcessorAlgorithm):
 
         self._output_ws = self.getPropertyValue('OutputWorkspace')
 
-        if self._grouping_string is not None:
-            self._grouping_string = self._grouping_string.replace('-', ':')
-
         # Disable sum files if there is only one file
         if len(self._data_files) == 1:
             if self._sum_files:

Framework/PythonInterface/plugins/algorithms/WorkflowAlgorithms/SANS/SANSBeamCentreFinder.py

@@ -187,8 +187,8 @@ class SANSBeamCentreFinder(DataProcessorAlgorithm):
             residueTB.append(self._calculate_residuals(sample_quartiles[MaskingQuadrant.Top],
                                                        sample_quartiles[MaskingQuadrant.Bottom]))
             if(j == 0):
-                logger.notice("Itr " + str(j) + ": (" + str(self.scale_1 * centre1) + ", " + str(self.scale_2 * centre2) + ")  SX="
-                              + str(residueLR[j]) + "  SY=" + str(residueTB[j]))
+                logger.notice("Itr {0}: ( {1}, {2} )  SX={3:.5g}  SY={4:.5g}".
+                              format(j, self.scale_1 * centre1, self.scale_2 * centre2, residueLR[j], residueTB[j]))
                 if mantidplot:
                     self._plot_quartiles(output_workspaces, state.data.sample_scatter)
 
@@ -200,8 +200,8 @@ class SANSBeamCentreFinder(DataProcessorAlgorithm):
                 if residueTB[j] > residueTB[j-1]:
                     position_2_step = - position_2_step / 2
 
-                logger.notice("Itr " + str(j) + ": (" + str(self.scale_1 * centre1) + ", " + str(self.scale_2 * centre2) + ")  SX="
-                              + str(residueLR[j]) + "  SY=" + str(residueTB[j]))
+                logger.notice("Itr {0}: ( {1}, {2} )  SX={3:.5g}  SY={4:.5g}".
+                              format(j, self.scale_1 * centre1, self.scale_2 * centre2, residueLR[j], residueTB[j]))
 
                 if (residueLR[j]+residueTB[j]) < (residueLR[j-1]+residueTB[j-1]) or state.compatibility.use_compatibility_mode:
                     centre_1_hold = centre1

Framework/PythonInterface/plugins/algorithms/WorkflowAlgorithms/SANS/SANSSave.py

@@ -127,7 +127,7 @@ class SANSSave(DataProcessorAlgorithm):
 
         # SaveNXcanSAS clashes with SaveNexusProcessed
         self.add_file_format_with_appended_name_requirement(file_formats, SaveType.NXcanSAS, file_types,
-                                                            [SaveType.Nexus])
+                                                            [])
 
         # SaveNISTDAT clashes with SaveRKH, both can save to .dat
         self.add_file_format_with_appended_name_requirement(file_formats, SaveType.NistQxy, file_types, [SaveType.RKH])

Testing/SystemTests/tests/analysis/SANSSaveTest.py

@@ -80,7 +80,7 @@ class SANSSaveTest(unittest.TestCase):
 
         # Assert
         expected_files = ["sample_sans_save_file.xml", "sample_sans_save_file.txt", "sample_sans_save_file_nistqxy.dat",
-                          "sample_sans_save_file_nxcansas.nxs", "sample_sans_save_file.nxs",
+                          "sample_sans_save_file.h5", "sample_sans_save_file.nxs",
                           "sample_sans_save_file.csv"]
         expected_full_file_names = [os.path.join(mantid.config.getString('defaultsave.directory'), elem)
                                     for elem in expected_files]

docs/source/interfaces/Indirect Data Reduction.rst

@@ -136,7 +136,11 @@ Grouping
 The following options are available for grouping output data:
 
 Custom
-  A comma separated list can be entered to specify the groups, e.g. 1, 3-5, 6-8, 10.
+  Follows the same grouping patterns used in the :ref:`GroupDetectors <algm-GroupDetectors>` algorithm.
+  An example of the syntax is 1,2+3,4-6,7-10
+
+  This would produce spectra for: spectra 1, the sum of spectra 2 and 3, the sum of spectra 4-6 (4+5+6)
+  and individual spectra from 7 to 10 (7,8,9,10)
 
 Individual
   All detectors will remain on individual spectra.

docs/source/release/v3.13.0/reflectometry.rst

@@ -7,6 +7,9 @@ Reflectometry Changes
 
 ISIS Reflectometry Interface
 ----------------------------
+.. image::  ../../images/ISIS_reflectometry_release313.png
+   :align: right
+   :width: 800px
 
 New
 ###

docs/source/release/v3.13.0/sans.rst

@@ -9,6 +9,7 @@ ILL
 ---
 
 * :ref:`LoadILLSANS <algm-LoadILLSANS>` is upgraded to load the modern nexus files from instruments D11, D22 and D33 at the ILL.
+* :ref:`SANSMask <algm-SANSMask>` is extended to have a `MaskedWorkspace` property, to copy the mask from.
 
 SNS
 ---
@@ -17,10 +18,13 @@ SNS
 
 ISIS SANS Interface
 -------------------
+.. image::  ../../images/ISIS_SANS_release313.png
+   :align: right
+   :width: 800px
+
 New
 ###
 * A string of wavelength ranges can now be specified. A reduction is then done for each wavelength range.
-* :ref:`SANSMask <algm-SANSMask>` is extended to have a `MaskedWorkspace` property, to copy the mask from.
 
 Improvements
 ############
@@ -33,6 +37,7 @@ Improvements
 * Improved error messages in the new GUI to be more obvious and clearer.
 * Updated the naming of workspace groups in a sliced reduction.
 * Updated old backend to mask by detector ID rather than spectrum number, improving reliability.
+* NXcanSAS is now saved out with a .h5 extension so it can be read into SASView.
 
 Bugfixes
 ########
@@ -43,10 +48,12 @@ Bugfixes
 * Fixed a bug where save_format was not being specified if a user file was entered for a row.
 * Use gravity now defaulting to false. 
 * MASK/TIME and TIME/MASK now both work in new backend.
+* SET Centre/HAB command is now correctly parsed into a seperate variable to SET Centre. 
 
 Features Removed
 ################
 
 * Removed SaveNist as an option from both GUI's
+* The Q range option on the beam centre tab was producing erroneous results so has been removed until it can be improved and fixed.
 
 :ref:`Release 3.13.0 <v3.13.0>`

qt/scientific_interfaces/Indirect/ISISEnergyTransfer.cpp

@@ -48,7 +48,7 @@ ISISEnergyTransfer::ISISEnergyTransfer(IndirectDataReduction *idrUI,
   mappingOptionSelected(m_uiForm.cbGroupingOptions->currentText());
 
   // Add validation to custom detector grouping
-  QRegExp re("([0-9]+[-]?[0-9]*,[ ]?)*[0-9]+[-]?[0-9]*");
+  QRegExp re("([0-9]+[-:+]?[0-9]*,[ ]?)*[0-9]+[-:+]?[0-9]*");
   m_uiForm.leCustomGroups->setValidator(new QRegExpValidator(re, this));
 
   // Validate to remove invalid markers

qt/scientific_interfaces/Indirect/ISISEnergyTransfer.ui

@@ -313,6 +313,13 @@
             <property name="enabled">
              <bool>true</bool>
             </property>
+            <property name="toolTip">
+              <string>, allows you to specify additional indices. 1,2,4 will keep indices 1, 2 and 4 only.
+: indicates a continuous range of indices. For example, 1:5 is the same as 1,2,3,4,5.
++ sums two spectra together. 7+9 will produce a single spectra listing the sum of 7 and 9, ignoring any others.
+- sums a range of spectra together. For example, 3-8 is the same as 3+4+5+6+7+8.
+              </string>
+            </property>
             <property name="maximumSize">
              <size>
               <width>16777215</width>

qt/widgets/common/src/MWRunFiles.cpp

@@ -586,13 +586,11 @@ const QString MWRunFiles::findFilesGetSearchText(QString &searchText) {
 * @param searchText :: text to create search parameters from
 */
 void MWRunFiles::runFindFiles(const QString &searchText) {
-  if (!searchText.isEmpty()) {
-    emit findingFiles();
+  emit findingFiles();
 
-    const auto parameters =
-        createFindFilesSearchParameters(searchText.toStdString());
-    m_pool.createWorker(this, parameters);
-  }
+  const auto parameters =
+      createFindFilesSearchParameters(searchText.toStdString());
+  m_pool.createWorker(this, parameters);
 }
 
 /** Calls cancel on a running instance of MonitorLiveData.

scripts/ExternalInterfaces/CMakeLists.txt

@@ -6,7 +6,7 @@ set ( _mslice_external_root ${CMAKE_CURRENT_BINARY_DIR}/mslice )
 ExternalProject_Add ( mslice
   PREFIX ${_mslice_external_root}
   GIT_REPOSITORY "https://github.com/mantidproject/mslice.git"
-  GIT_TAG 3c6eadfe38ea9d57dcacf57f5df2c150639a2779
+  GIT_TAG 82c4fae1356f770d5f8ad59edea4bd5f58206190
   EXCLUDE_FROM_ALL 1
 
   CONFIGURE_COMMAND ""

scripts/Interface/reduction_gui/instruments/eqsans_interface_dev.py

@@ -31,7 +31,7 @@ class EQSANSInterface(InstrumentInterface):
     """
         Defines the widgets for EQSANS reduction
     """
-    data_type = "Data files *.nxs *.dat (*.nxs *.dat)"
+    data_type = "Data files *.nxs *.dat *.h5 (*.nxs *.dat *.h5)"
 
     def __init__(self, name, settings):
         super(EQSANSInterface, self).__init__(name, settings)

scripts/Interface/ui/sans_isis/beam_centre.py

@@ -38,6 +38,13 @@ class BeamCentre(QtGui.QWidget, ui_beam_centre.Ui_BeamCentre):
         # Attach validators
         self._attach_validators()
 
+        # This feature is currently broken and not strictly needed so I am hiding this part of the GUI.
+        self.Q_limits.hide()
+        self.Q_from.hide()
+        self.q_min_line_edit.hide()
+        self.q_max_line_edit.hide()
+        self.Q_to.hide()
+
     def _setup_log_widget(self):
         self.log_widget = MantidQt.MantidWidgets.MessageDisplay(self.groupBox_2)
         self.log_widget.setMinimumSize(QtCore.QSize(491, 371))

scripts/Interface/ui/sans_isis/beam_centre.ui

@@ -7,7 +7,7 @@
     <x>0</x>
     <y>0</y>
     <width>1015</width>
-    <height>649</height>
+    <height>709</height>
    </rect>
   </property>
   <property name="windowTitle">
@@ -130,7 +130,7 @@
           </widget>
          </item>
          <item row="5" column="3">
-          <widget class="QLabel" name="label">
+          <widget class="QLabel" name="Q_to">
            <property name="text">
             <string>to</string>
            </property>
@@ -151,7 +151,7 @@
           </widget>
          </item>
          <item row="5" column="0">
-          <widget class="QLabel" name="label_3">
+          <widget class="QLabel" name="Q_from">
            <property name="text">
             <string>from</string>
            </property>
@@ -161,7 +161,7 @@
           <widget class="QLineEdit" name="r_max_line_edit"/>
          </item>
          <item row="3" column="2">
-          <widget class="QLabel" name="label_2">
+          <widget class="QLabel" name="Q_limits">
            <property name="toolTip">
             <string>&lt;html&gt;&lt;head/&gt;&lt;body&gt;&lt;p&gt;The Q range which will be considered when finding the beam centre.&lt;/p&gt;&lt;/body&gt;&lt;/html&gt;</string>
            </property>
@@ -310,6 +310,26 @@
    </item>
   </layout>
  </widget>
+ <tabstops>
+  <tabstop>lab_pos_1_line_edit</tabstop>
+  <tabstop>lab_pos_2_line_edit</tabstop>
+  <tabstop>hab_pos_1_line_edit</tabstop>
+  <tabstop>hab_pos_2_line_edit</tabstop>
+  <tabstop>component_combo_box</tabstop>
+  <tabstop>update_lab_check_box</tabstop>
+  <tabstop>update_hab_check_box</tabstop>
+  <tabstop>r_min_line_edit</tabstop>
+  <tabstop>r_max_line_edit</tabstop>
+  <tabstop>q_min_line_edit</tabstop>
+  <tabstop>q_max_line_edit</tabstop>
+  <tabstop>max_iterations_line_edit</tabstop>
+  <tabstop>tolerance_line_edit</tabstop>
+  <tabstop>verbose_check_box</tabstop>
+  <tabstop>COM_check_box</tabstop>
+  <tabstop>left_right_check_box</tabstop>
+  <tabstop>up_down_check_box</tabstop>
+  <tabstop>run_button</tabstop>
+ </tabstops>
  <resources/>
  <connections/>
 </ui>

scripts/Interface/ui/sans_isis/diagnostics_page.ui

@@ -7,7 +7,7 @@
     <x>0</x>
     <y>0</y>
     <width>695</width>
-    <height>252</height>
+    <height>297</height>
    </rect>
   </property>
   <property name="windowTitle">
@@ -58,6 +58,9 @@
       </item>
       <item row="0" column="2">
        <widget class="QPushButton" name="browse_button">
+        <property name="focusPolicy">
+         <enum>Qt::StrongFocus</enum>
+        </property>
         <property name="text">
          <string>Browse</string>
         </property>
@@ -133,6 +136,9 @@
       </item>
       <item row="2" column="0">
        <widget class="QPushButton" name="time_button">
+        <property name="focusPolicy">
+         <enum>Qt::StrongFocus</enum>
+        </property>
         <property name="text">
          <string>Time Integral</string>
         </property>
@@ -146,6 +152,9 @@
       </item>
       <item row="0" column="0">
        <widget class="QPushButton" name="horizontal_button">
+        <property name="focusPolicy">
+         <enum>Qt::StrongFocus</enum>
+        </property>
         <property name="text">
          <string>Horizontal Integral</string>
         </property>
@@ -160,6 +169,9 @@
       </item>
       <item row="1" column="0">
        <widget class="QPushButton" name="vertical_button">
+        <property name="focusPolicy">
+         <enum>Qt::StrongFocus</enum>
+        </property>
         <property name="text">
          <string>Vertical Integral</string>
         </property>
@@ -239,6 +251,21 @@
    </item>
   </layout>
  </widget>
+ <tabstops>
+  <tabstop>run_input_line_edit</tabstop>
+  <tabstop>browse_button</tabstop>
+  <tabstop>detector_combo_box</tabstop>
+  <tabstop>period_line_edit</tabstop>
+  <tabstop>horizontal_button</tabstop>
+  <tabstop>horizontal_range_line_edit</tabstop>
+  <tabstop>horizontal_mask_check_box</tabstop>
+  <tabstop>vertical_button</tabstop>
+  <tabstop>vertical_range_line_edit</tabstop>
+  <tabstop>vertical_mask_check_box</tabstop>
+  <tabstop>time_button</tabstop>
+  <tabstop>time_range_line_edit</tabstop>
+  <tabstop>time_mask_checkbox</tabstop>
+ </tabstops>
  <resources/>
  <connections/>
 </ui>

scripts/SANS/sans/algorithm_detail/save_workspace.py

@@ -43,7 +43,7 @@ def get_save_strategy(file_format_bundle, file_name, save_options):
         file_name = get_file_name(file_format_bundle, file_name, "", ".xml")
         save_name = "SaveCanSAS1D"
     elif file_format is SaveType.NXcanSAS:
-        file_name = get_file_name(file_format_bundle, file_name, "_nxcansas", ".nxs")
+        file_name = get_file_name(file_format_bundle, file_name, "_nxcansas", ".h5")
         save_name = "SaveNXcanSAS"
     elif file_format is SaveType.NistQxy:
         file_name = get_file_name(file_format_bundle, file_name, "_nistqxy", ".dat")