Re #19794 Added system test for create_vanadium method in ISIS_Powder

Testing/Data/SystemTest/ISIS_Powder/input/GEM83605.nxs.md5

+8fc5b99698df90d930eddcbca7d6767c

Testing/Data/SystemTest/ISIS_Powder/input/GEM83607.nxs.md5

+4f441f16f4c07de67dfef295dacb790d

Testing/Data/SystemTest/ISIS_Powder/input/GEM83608.nxs.md5

+6eb5619f8eac2ac1a6ae0566b1a73c23

Testing/Data/SystemTest/ISIS_Powder/input/GEM83664.nxs.md5

+517ea9fd7b580bfd4c7cb9f4c9eb0072

Testing/Data/SystemTest/ISIS_Powder/input/GEM83665.nxs.md5

+1a87419df68632fc25c1f24703c71ff6

Testing/Data/SystemTest/ISIS_Powder/input/GEM83666.nxs.md5

+233b2a1fa57ec4c9442c881b3c32f7b3

Testing/Data/SystemTest/ISIS_Powder/input/calibration/gem/17_1/offsets_2011_cycle111b.cal.md5

+d59cb19944cf8a186b7124f4497f7e61

Testing/Data/SystemTest/ISIS_Powder/input/calibration/gem/GEM_Instrument_grouping.cal.md5

+370c13263b4ccd6e22cc215e66cbc548

Testing/Data/SystemTest/ISIS_Powder/input/yaml_files/gem_system_test_mapping.yaml.md5

+b63fb7eebb20e0279e7a165932eeb702

Testing/SystemTests/tests/analysis/ISIS_PowderGemTest.py

+from __future__ import (absolute_import, division, print_function)
+
+import os
+import stresstesting
+import shutil
+
+import mantid.simpleapi as mantid
+from mantid import config
+
+from isis_powder import Gem
+
+DIRS = config['datasearch.directories'].split(';')
+
+# Setup various path details
+
+inst_name = "GEM"
+# Relative to system data folder
+working_folder_name = "ISIS_Powder"
+
+# Relative to working folder
+input_folder_name = "input"
+output_folder_name = "output"
+
+# Relative to input folder
+calibration_folder_name = os.path.join("calibration", inst_name.lower())
+calibration_map_rel_path = os.path.join("yaml_files", "gem_system_test_mapping.yaml")
+
+# Generate paths for the tests
+# This implies DIRS[0] is the system test data folder
+working_folder = os.path.join(DIRS[0], working_folder_name)
+
+input_folder = os.path.join(working_folder, input_folder_name)
+output_folder = os.path.join(working_folder, output_folder_name)
+
+calibration_map_path = os.path.join(input_folder, calibration_map_rel_path)
+calibration_folder = os.path.join(input_folder, calibration_folder_name)
+
+
+class VanadiumCalibrationTest(stresstesting.MantidStressTest):
+
+    calibration_results = None
+    existing_config = config['datasearch.directories']
+
+    def requiredFiles(self):
+        return _gen_required_files()
+
+    def runTest(self):
+        setup_mantid_paths()
+        self.calibration_results = _run_vanadium_calibration()
+
+    def validate(self):
+        return calibration_validator(self, self.calibration_results)
+
+    def cleanup(self):
+        clean_up()
+        config['datasearch.directories'] = self.existing_config
+
+
+class FocusTest(stresstesting.MantidStressTest):
+
+    focus_results = None
+    existing_config = config['datasearch.directories']
+
+    # TODO
+    # Test disabled whilst in development as we were having to update the reference file on a daily basis
+    def skipTests(self):
+        return True
+
+    def requiredFiles(self):
+        return _gen_required_files()
+
+    def runTest(self):
+        # Gen vanadium calibration first
+        _run_vanadium_calibration()
+        self.focus_results = _run_focus()
+
+    def validation(self):
+        return _focus_validation(self, self.focus_results)
+
+    def cleanup(self):
+        config['datasearch.directories'] = self.existing_config
+        # TODO
+
+
+def _gen_required_files():
+    required_run_numbers = ["83605", "83607", "83608",  # create_van : PDF mode
+                            "83664", "83665", "83666"]  # create_van : Rietveld mode
+
+    # Generate file names of form "INSTxxxxx.nxs"
+    input_files = [os.path.join(input_folder, (inst_name + number + ".nxs")) for number in required_run_numbers]
+    input_files.append(calibration_map_path)
+    return input_files
+
+
+def _run_vanadium_calibration():
+    vanadium_run = 83605  # Choose arbitrary run in the cycle 17_1
+
+    pdf_inst_obj = setup_inst_object(mode="PDF")
+    rietveld_inst_obj = setup_inst_object(mode="Rietveld")
+
+    # Run create vanadium twice to ensure we get two different output splines / files
+    pdf_inst_obj.create_vanadium(first_cycle_run_no=vanadium_run,
+                                 do_absorb_corrections=True, multiple_scattering=False)
+    rietveld_inst_obj.create_vanadium(first_cycle_run_no=vanadium_run,
+                                      do_absorb_corrections=True, multiple_scattering=False)
+
+    # Check the spline looks good
+    spline_path = os.path.join(calibration_folder, "17_1", "VanSplined_83608_offsets_2011_cycle111b.cal.nxs")
+    if not os.path.exists(spline_path):
+        raise RuntimeError("Could not find output spline at the following path: " + spline_path)
+    splined_ws = mantid.Load(Filename=spline_path)
+
+    return splined_ws
+
+
+def _run_focus():
+    run_number = 95599
+    polaris_obj = setup_inst_object()
+    return polaris_obj.focus(run_number=run_number, input_mode="Individual", do_van_normalisation=True)
+
+
+def calibration_validator(cls, results):
+    _validation_setup(cls)
+
+    # Get the name of the grouped workspace list
+    reference_file_name = "ISIS_Powder-GEM-VanSplined_83608_offsets_2011_cycle111b.cal.nxs"
+    ref_ws = mantid.Load(Filename=reference_file_name)
+
+    is_valid = True if len(results) > 0 else False
+
+    for ws, ref in zip(results, ref_ws):
+        if not (mantid.CompareWorkspaces(Workspace1=ws, Workspace2=ref)):
+            is_valid = False
+            print (ws.getName() + " was not equal to: " + ref.getName())
+
+    return is_valid
+
+
+def _focus_validation(cls, results):
+    _validation_setup(cls)
+
+    reference_file_name = "POLARIS_PowderFocus79514.nxs"
+    focus_output_name = "Focus_results"
+    mantid.GroupWorkspaces(InputWorkspaces=results, OutputWorkspace=focus_output_name)
+
+    return focus_output_name, reference_file_name
+
+
+def _validation_setup(cls):
+    cls.disableChecking.append('Instrument')
+    cls.disableChecking.append('Sample')
+    cls.disableChecking.append('SpectraMap')
+
+
+def clean_up():
+    mantid.mtd.clear()
+
+    spline_folder = os.path.join(calibration_folder, "17_1")
+    try:
+        shutil.rmtree(output_folder)
+    except OSError:
+        print("Could not delete output file at: ", output_folder)
+
+    _try_delete(os.path.join(spline_folder, "VanSplined_83608_offsets_2011_cycle111b.cal.nxs"))
+    _try_delete(os.path.join(spline_folder, "VanSplined_83664_offsets_2011_cycle111b.cal.nxs"))
+
+
+def setup_mantid_paths():
+    config['datasearch.directories'] += ";" + input_folder
+
+
+def setup_inst_object(mode):
+    user_name = "Test"
+
+    inst_obj = Gem(user_name=user_name, calibration_mapping_file=calibration_map_path,
+                   calibration_directory=calibration_folder, output_directory=output_folder, mode=mode)
+    return inst_obj
+
+
+def _try_delete(path):
+    try:
+        os.remove(path)
+    except OSError:
+        print ("Could not delete output file at: ", path)

Testing/SystemTests/tests/analysis/ISIS_PowderPolarisTest.py

@@ -16,11 +16,6 @@ class VanadiumCalibrationTest(stresstesting.MantidStressTest):
     calibration_results = None
     existing_config = config['datasearch.directories']
 
-    # TODO
-    # Test disabled whilst in development as we were having to update the reference file on a daily basis
-    def skipTests(self):
-        return True
-
     def requiredFiles(self):
         return _gen_required_files()
 
@@ -41,11 +36,6 @@ class FocusTest(stresstesting.MantidStressTest):
     focus_results = None
     existing_config = config['datasearch.directories']
 
-    # TODO
-    # Test disabled whilst in development as we were having to update the reference file on a daily basis
-    def skipTests(self):
-        return True
-
     def requiredFiles(self):
         return _gen_required_files()
 

Testing/SystemTests/tests/analysis/reference/ISIS_Powder-GEM-VanSplined_83608_offsets_2011_cycle111b.cal.nxs.md5

+ae7980d3a4879b3adaa4332da9e238e2

Testing/SystemTests/tests/analysis/reference/ISIS_PowderPEARL95634-95647_Van_Cal.nxs.md5

-35cbcc39432281c90c97e36bd6be7e1f

scripts/Diffraction/isis_powder/gem_routines/gem_algs.py

@@ -10,7 +10,7 @@ from isis_powder.gem_routines import gem_advanced_config
 
 def calculate_van_absorb_corrections(ws_to_correct, multiple_scattering):
     # First 100 detectors are monitors or not connected to DAE
-    mantid.MaskDetectors(ws_to_correct, SpectraList=list(range(0, 101)))
+    mantid.MaskDetectors(ws_to_correct, SpectraList=range(1, 100))
 
     absorb_dict = gem_advanced_config.absorption_correction_params
     sample_details_obj = absorb_corrections.create_vanadium_sample_details_obj(config_dict=absorb_dict)

scripts/Diffraction/isis_powder/routines/common.py

@@ -350,10 +350,7 @@ def spline_vanadium_workspaces(focused_vanadium_spectra, spline_coefficient):
     :param spline_coefficient: The coefficient to use when creating the splined vanadium workspaces
     :return: The splined vanadium workspace
     """
-    stripped_ws_list = _strip_vanadium_peaks(workspaces_to_strip=focused_vanadium_spectra)
-    splined_workspaces = spline_workspaces(stripped_ws_list, num_splines=spline_coefficient)
-
-    remove_intermediate_workspace(stripped_ws_list)
+    splined_workspaces = spline_workspaces(focused_vanadium_spectra, num_splines=spline_coefficient)
     return splined_workspaces
 
 
@@ -489,7 +486,7 @@ def _load_list_of_files(run_numbers_list, instrument, file_ext=None):
 def _strip_vanadium_peaks(workspaces_to_strip):
     out_list = []
     for i, ws in enumerate(workspaces_to_strip):
-        out_name = ws.getName() + "_splined-" + str(i+1)
+        out_name = ws.getName() + "_toSpline-" + str(i+1)
         out_list.append(mantid.StripVanadiumPeaks(InputWorkspace=ws, OutputWorkspace=out_name))
     return out_list