Cherry pick pull request #18888

Refs #18877 Add handling of missing file extension

(cherry picked from commit 6977e9e)

Refs #18877 Add correct workspace name for batch reduce

(cherry picked from commit 78de78b)

Refs #18877 Add metadata to saving

(cherry picked from commit c517eb0)

Refs #18877 Fix trailing white space

(cherry picked from commit d135f78)

Refs #188877 Grab geom info at right point

(cherry picked from commit bc7aed4)

Add patch release note

docs/source/release/v3.9.1/index.rst

@@ -30,6 +30,7 @@ Changes in this version
 * `18865 <https://www.github.com/mantidproject/mantid/pull/18865>`_ Fix bug in reflectometry GUI
 * `18875 <https://www.github.com/mantidproject/mantid/pull/18875>`_ U correction not correctly applied to viewport
 * `18884 <https://www.github.com/mantidproject/mantid/pull/18884>`_ Add support for NeXus files in LoadVesuvio
+* `18888 <https://www.github.com/mantidproject/mantid/pull/18888>`_ Fix LOQ Batch reduction issues
 * `18891 <https://www.github.com/mantidproject/mantid/pull/18891>`_ Fix bug in gd_prtn_chrg for chunked data
 * `18907 <https://www.github.com/mantidproject/mantid/pull/18907>`_ Fix zeropadding for IMAT in Facilities.XML
 * `18914 <https://www.github.com/mantidproject/mantid/pull/18914>`_ Fix mass ws deletion bug
@@ -57,6 +58,8 @@ Summary of impact
 +-------+-----------------------------------------------------------------------------------+---------------------------------------------+--------------+
 | 18884 | Allows Vesuvio to Load NeXus files from current cycle                             | Use Load not LoadRaw in algorithm           | **medium**   |
 +-------+-----------------------------------------------------------------------------------+---------------------------------------------+--------------+
+| 18888 | Fixes batch reduction for LOQ at ISIS                                             | Checks correctly for userfile in batch run  | **medium**   |
++-------+-----------------------------------------------------------------------------------+---------------------------------------------+--------------+
 | 18891 | Fixes bug in gd_prtn_chrg for chunked data                                        | Recalculate proton charge just prior to use | **low**      |
 +-------+-----------------------------------------------------------------------------------+---------------------------------------------+--------------+
 | 18907 | Allows IMAT to use general file finding mechanism                                 | Facilities file update                      | **low**      |

scripts/SANS/SANSBatchMode.py

@@ -140,6 +140,44 @@ def get_transmission_properties(workspace):
     return transmission_properties
 
 
+def get_geometry_properties(reducer):
+    """
+    This extracts geometry properties from the ReductionSingleton. They are saved in the CanSAS1D format.
+
+    @param reducer: a handle to the redcution singleton
+    @return: a dict with geometry properties
+    """
+    def _add_property(key, element, props):
+        if element is None:
+            raise RuntimeError("Could not extract value for {0}.".format(key))
+        props.update({key: element})
+
+    geometry_properties = {}
+    geometry = reducer.get_sample().geometry
+
+    # Get the shape
+    shape = geometry.shape
+    if shape == 'cylinder-axis-up':
+        shape_to_save = "Cylinder"
+    elif shape == 'cuboid':
+        shape_to_save = "Flat plate"
+    elif shape == 'cylinder-axis-along':
+        shape_to_save = 'Disc'
+    else:
+        raise RuntimeError("Unknown shape {0}. Cannot extract property".format(shape))
+    geometry_properties.update({"Geometry": shape_to_save})
+
+    # Get the Height
+    _add_property("SampleHeight", geometry.height, geometry_properties)
+
+    # Get the Width
+    _add_property("SampleWidth", geometry.width, geometry_properties)
+
+    # Get the thickness
+    _add_property("SampleThickness", geometry.thickness, geometry_properties)
+    return geometry_properties
+
+
 def BatchReduce(filename, format, plotresults=False, saveAlgs={'SaveRKH':'txt'},verbose=False,
                 centreit=False, reducer=None, combineDet=None, save_as_zero_error_free=False):
     """
@@ -197,14 +235,21 @@ def BatchReduce(filename, format, plotresults=False, saveAlgs={'SaveRKH':'txt'},
                                                        original_user_file=original_user_file,
                                                        original_settings = settings,
                                                        original_prop_man_settings = prop_man_settings)
-        except (RunTimeError, ValueError) as e:
+            # When we set a new user file, that means that the combineDet feature could be invalid,
+            # ie if the detector under investigation changed in the user file. We need to change this
+            # here too. But only if it is not None.
+            if combineDet is not None:
+                new_combineDet = ReductionSingleton().instrument.get_detector_selection()
+                combineDet = su.get_correct_combinDet_setting(ins_name, new_combineDet)
+        except (RuntimeError, ValueError) as e:
             sanslog.warning("Error in Batchmode user files: Could not reset the specified user file %s. More info: %s" %(
-                str(run['user_file']),str(e)))
+                str(run['user_file']), str(e)))
 
         local_settings = copy.deepcopy(ReductionSingleton().reference())
         local_prop_man_settings = ReductionSingleton().settings.clone("TEMP_SETTINGS")
 
         raw_workspaces = []
+        geometry_properties = {}
         try:
             # Load in the sample runs specified in the csv file
             raw_workspaces.append(read_run(run, 'sample_sans', format))
@@ -222,6 +267,12 @@ def BatchReduce(filename, format, plotresults=False, saveAlgs={'SaveRKH':'txt'},
                 if verbose == 1:
                     FindBeamCentre(50.,170.,12)
 
+            try:
+                geometry_properties = get_geometry_properties(ReductionSingleton())
+            except RuntimeError as e:
+                message = "Could not extract geometry properties from the reducer: {0}".format(str(e))
+                sanslog.warning(message)
+
             # WavRangeReduction runs the reduction for the specified
             # wavelength range where the final argument can either be
             # DefaultTrans or CalcTrans:
@@ -254,34 +305,42 @@ def BatchReduce(filename, format, plotresults=False, saveAlgs={'SaveRKH':'txt'},
         final_name = sanitize_name(final_name)
 
         #convert the names from the default one, to the agreement
+        # This caused a renaming with the following logic
+        # | combinDet      |    Name HAB    |   Name LAB   | Name Merged  |
+        # | rear           |    +_rear      |     -        |     -        |
+        # | front          |      -         |    +_front   |     -        |
+        # | both           |    +_rear      |    +_front   |     -        |
+        # | merged         |    +_rear      |    +_front   |     +_merged |
+        # This is not great since it uses SANS2D terminology for all instruments
+
         names = [final_name]
         if combineDet == 'rear':
-            names = [final_name+'_rear']
-            RenameWorkspace(InputWorkspace=reduced,OutputWorkspace= final_name+'_rear')
+            new_name = su.rename_workspace_correctly(ins_name, su.ReducedType.LAB, final_name, reduced)
+            names = [new_name]
         elif combineDet == 'front':
-            names = [final_name+'_front']
-            RenameWorkspace(InputWorkspace=reduced,OutputWorkspace= final_name+'_front')
+            new_name = su.rename_workspace_correctly(ins_name, su.ReducedType.HAB, final_name, reduced)
+            names = [new_name]
         elif combineDet == 'both':
-            names = [final_name+'_front', final_name+'_rear']
             if ins_name == 'SANS2D':
-                rear_reduced = reduced.replace('front','rear')
+                rear_reduced = reduced.replace('front', 'rear')
             else: #if ins_name == 'lOQ':
-                rear_reduced = reduced.replace('HAB','main')
-            RenameWorkspace(InputWorkspace=reduced,OutputWorkspace=final_name+'_front')
-            RenameWorkspace(InputWorkspace=rear_reduced,OutputWorkspace=final_name+'_rear')
+                rear_reduced = reduced.replace('HAB', 'main')
+            new_name_HAB = su.rename_workspace_correctly(ins_name, su.ReducedType.HAB, final_name, reduced)
+            new_name_LAB = su.rename_workspace_correctly(ins_name, su.ReducedType.LAB, final_name, rear_reduced)
+            names = [new_name_HAB, new_name_LAB]
         elif combineDet == 'merged':
-            names = [final_name + '_merged', final_name + '_rear',  final_name+'_front']
             if ins_name == 'SANS2D':
-                rear_reduced = reduced.replace('merged','rear')
-                front_reduced = reduced.replace('merged','front')
+                rear_reduced = reduced.replace('merged', 'rear')
+                front_reduced = reduced.replace('merged', 'front')
             else:
-                rear_reduced = reduced.replace('_merged','')
-                front_reduced = rear_reduced.replace('main','HAB')
-            RenameWorkspace(InputWorkspace=reduced,OutputWorkspace= final_name + '_merged')
-            RenameWorkspace(InputWorkspace=rear_reduced,OutputWorkspace= final_name + '_rear')
-            RenameWorkspace(InputWorkspace=front_reduced,OutputWorkspace= final_name+'_front')
+                rear_reduced = reduced.replace('_merged', '')
+                front_reduced = rear_reduced.replace('main', 'HAB')
+            new_name_Merged = su.rename_workspace_correctly(ins_name, su.ReducedType.Merged, final_name, reduced)
+            new_name_LAB = su.rename_workspace_correctly(ins_name, su.ReducedType.LAB, final_name, rear_reduced)
+            new_name_HAB = su.rename_workspace_correctly(ins_name, su.ReducedType.HAB, final_name, front_reduced)
+            names = [new_name_Merged, new_name_LAB, new_name_HAB]
         else:
-            RenameWorkspace(InputWorkspace=reduced,OutputWorkspace=final_name)
+            RenameWorkspace(InputWorkspace=reduced, OutputWorkspace=final_name)
 
         file = run['output_as']
         #saving if optional and doesn't happen if the result workspace is left blank. Is this feature used?
@@ -310,6 +369,11 @@ def BatchReduce(filename, format, plotresults=False, saveAlgs={'SaveRKH':'txt'},
                         # sample logs.
                         _ws = mtd[workspace_name]
                         transmission_properties = get_transmission_properties(_ws)
+
+                        # Add the geometry properties if they exist
+                        if geometry_properties:
+                            transmission_properties.update(geometry_properties)
+
                         # Call the SaveCanSAS1D with the Transmission and TransmissionCan if they are
                         # available
                         SaveCanSAS1D(save_names_dict[workspace_name], workspace_name+ext, DetectorNames=detnames,
@@ -496,7 +560,13 @@ def setUserFileInBatchMode(new_user_file, current_user_file, original_user_file,
 
     # Try to find the user file in the default paths
     if not os.path.isfile(new_user_file):
-        user_file = FileFinder.getFullPath(new_user_file)
+        # Find the user file in the Mantid path. we make sure that the user file has a txt extension.
+        user_file_names_with_extension = su.get_user_file_name_options_with_txt_extension(new_user_file)
+        for user_file_name_with_extension in user_file_names_with_extension:
+            user_file = FileFinder.getFullPath(user_file_name_with_extension)
+            if user_file:
+                break
+
         if not os.path.isfile(user_file):
             user_file_to_set = original_user_file
         else:

scripts/SANS/SANSUtility.py

@@ -1962,6 +1962,112 @@ def get_unfitted_transmission_workspace_name(workspace_name):
     return unfitted_workspace_name
 
 
+def get_user_file_name_options_with_txt_extension(user_file_name):
+    """
+    A user file is a .txt file. The user file can be specified without the .txt ending. Which will prevent the
+    FileFinder from picking it up.
+
+    @param user_file_name: the name of the user file
+    @return: either the original user file name or a list of user file names with .txt and .TXT extensions
+    """
+    capitalized_user_file = user_file_name.upper()
+    if capitalized_user_file.endswith('.TXT'):
+        user_file_with_extension = [user_file_name]
+    else:
+        user_file_with_extension = [user_file_name + ".txt", user_file_name + ".TXT"]
+    return user_file_with_extension
+
+
+def get_correct_combinDet_setting(instrument_name, detector_selection):
+    """
+    We want to get the correct combinDet variable for batch reductions from a new detector selection.
+
+    @param instrument_name: the name of the intrument
+    @param detector_selection: a detector selection comes directly from the reducer
+    @return: a combinedet option
+    """
+    if detector_selection is None:
+        return None
+
+    instrument_name = instrument_name.upper()
+    # If we are dealing with LARMOR, then the correct combineDet selection is None
+    if instrument_name == "LARMOR":
+        return None
+
+    detector_selection = detector_selection.upper()
+    # If we are dealing with LOQ, then the correct combineDet selection is
+    if instrument_name == "LOQ":
+        if detector_selection == "MAIN":
+            new_combine_detector_selection = 'rear'
+        elif detector_selection == "HAB":
+            new_combine_detector_selection = 'front'
+        elif detector_selection == "MERGED":
+            new_combine_detector_selection = 'merged'
+        elif detector_selection == "BOTH":
+            new_combine_detector_selection = 'both'
+        else:
+            raise RuntimeError("SANSBatchReduce: Unknown detector {0} for conversion "
+                               "to combineDet.".format(detector_selection))
+        return new_combine_detector_selection
+
+    # If we are dealing with SANS2D, then the correct combineDet selection is
+    if instrument_name == "SANS2D":
+        if detector_selection == "REAR":
+            new_combine_detector_selection = 'rear'
+        elif detector_selection == "FRONT":
+            new_combine_detector_selection = 'front'
+        elif detector_selection == "MERGED":
+            new_combine_detector_selection = 'merged'
+        elif detector_selection == "BOTH":
+            new_combine_detector_selection = 'both'
+        else:
+            raise RuntimeError("SANSBatchReduce: Unknown detector {0} for conversion "
+                               "to combineDet.".format(detector_selection))
+        return new_combine_detector_selection
+    raise RuntimeError("SANSBatchReduce: Unknown instrument {0}.".format(instrument_name))
+
+
+class ReducedType(object):
+    class LAB(object):
+        pass
+
+    class HAB(object):
+        pass
+
+    class Merged(object):
+        pass
+
+
+def rename_workspace_correctly(instrument_name, reduced_type, final_name, workspace):
+    def get_suffix(inst_name, red_type):
+        if inst_name == "SANS2D":
+            if red_type is ReducedType.LAB:
+                suffix = "_rear"
+            elif red_type is ReducedType.HAB:
+                suffix = "_front"
+            elif red_type is ReducedType.Merged:
+                suffix = "_merged"
+            else:
+                raise RuntimeError("Unknown reduction type {0}.".format(red_type))
+            return suffix
+        elif inst_name == "LOQ":
+            if red_type is ReducedType.LAB:
+                suffix = "_main"
+            elif red_type is ReducedType.HAB:
+                suffix = "_hab"
+            elif red_type is ReducedType.Merged:
+                suffix = "_merged"
+            else:
+                raise RuntimeError("Unknown reduction type {0}.".format(red_type))
+            return suffix
+        else:
+            return ""
+    final_suffix = get_suffix(instrument_name, reduced_type)
+    complete_name = final_name + final_suffix
+    RenameWorkspace(InputWorkspace=workspace, OutputWorkspace=complete_name)
+    return complete_name
+
+
 ###############################################################################
 ######################### Start of Deprecated Code ############################
 ###############################################################################

scripts/test/SANSBatchModeTest.py

@@ -142,5 +142,22 @@ def test_reducer_is_not_reset_if_file_to_set_is_original_and_current(self):
         # Clean up
         self._delete_minimal_user_files(user_files)
 
+
+class TestGeometrySettings(unittest.TestCase):
+    def test_that_can_get_geometry_properties(self):
+        LOQ()
+        reducer = ReductionSingleton()
+        geometry_settings = bm.get_geometry_properties(reducer)
+        self.assertTrue("Geometry" in geometry_settings)
+        self.assertTrue("SampleHeight" in geometry_settings)
+        self.assertTrue("SampleWidth" in geometry_settings)
+        self.assertTrue("SampleThickness" in geometry_settings)
+
+        self.assertTrue(geometry_settings["Geometry"] == "Disc")
+        self.assertTrue(geometry_settings["SampleHeight"] == 1.)
+        self.assertTrue(geometry_settings["SampleWidth"] == 1.)
+        self.assertTrue(geometry_settings["SampleThickness"] == 1.)
+
+
 if __name__ == "__main__":
     unittest.main()