diff --git a/Testing/Data/SystemTest/ISIS_Powder/input/GEM83605.nxs.md5 b/Testing/Data/SystemTest/ISIS_Powder/input/GEM83605.nxs.md5
new file mode 100644
index 0000000000000000000000000000000000000000..1788a579f1ee600d6d3aa0068f3671654dc1280e
--- /dev/null
+++ b/Testing/Data/SystemTest/ISIS_Powder/input/GEM83605.nxs.md5
@@ -0,0 +1 @@
+8fc5b99698df90d930eddcbca7d6767c
diff --git a/Testing/Data/SystemTest/ISIS_Powder/input/GEM83607.nxs.md5 b/Testing/Data/SystemTest/ISIS_Powder/input/GEM83607.nxs.md5
new file mode 100644
index 0000000000000000000000000000000000000000..403c02a66eb7b4b0f20f6181a7d1b9a08446bcc6
--- /dev/null
+++ b/Testing/Data/SystemTest/ISIS_Powder/input/GEM83607.nxs.md5
@@ -0,0 +1 @@
+4f441f16f4c07de67dfef295dacb790d
diff --git a/Testing/Data/SystemTest/ISIS_Powder/input/GEM83608.nxs.md5 b/Testing/Data/SystemTest/ISIS_Powder/input/GEM83608.nxs.md5
new file mode 100644
index 0000000000000000000000000000000000000000..7a3cf4f273b9ea82cf70c768727e259ccf63346d
--- /dev/null
+++ b/Testing/Data/SystemTest/ISIS_Powder/input/GEM83608.nxs.md5
@@ -0,0 +1 @@
+6eb5619f8eac2ac1a6ae0566b1a73c23
diff --git a/Testing/Data/SystemTest/ISIS_Powder/input/GEM83664.nxs.md5 b/Testing/Data/SystemTest/ISIS_Powder/input/GEM83664.nxs.md5
new file mode 100644
index 0000000000000000000000000000000000000000..356c19fa01673f8c92b71d4f66d6f0d9c3c3555f
--- /dev/null
+++ b/Testing/Data/SystemTest/ISIS_Powder/input/GEM83664.nxs.md5
@@ -0,0 +1 @@
+517ea9fd7b580bfd4c7cb9f4c9eb0072
diff --git a/Testing/Data/SystemTest/ISIS_Powder/input/GEM83665.nxs.md5 b/Testing/Data/SystemTest/ISIS_Powder/input/GEM83665.nxs.md5
new file mode 100644
index 0000000000000000000000000000000000000000..a3674973f0522112045898dc9e00a7462ca85c4c
--- /dev/null
+++ b/Testing/Data/SystemTest/ISIS_Powder/input/GEM83665.nxs.md5
@@ -0,0 +1 @@
+1a87419df68632fc25c1f24703c71ff6
diff --git a/Testing/Data/SystemTest/ISIS_Powder/input/GEM83666.nxs.md5 b/Testing/Data/SystemTest/ISIS_Powder/input/GEM83666.nxs.md5
new file mode 100644
index 0000000000000000000000000000000000000000..3533345ba3d5e84bcb52bfad65ea0672119dad6a
--- /dev/null
+++ b/Testing/Data/SystemTest/ISIS_Powder/input/GEM83666.nxs.md5
@@ -0,0 +1 @@
+233b2a1fa57ec4c9442c881b3c32f7b3
diff --git a/Testing/Data/SystemTest/ISIS_Powder/input/calibration/gem/17_1/offsets_2011_cycle111b.cal.md5 b/Testing/Data/SystemTest/ISIS_Powder/input/calibration/gem/17_1/offsets_2011_cycle111b.cal.md5
new file mode 100644
index 0000000000000000000000000000000000000000..612b94f4183ab640d69ff51558f226cc3a02607b
--- /dev/null
+++ b/Testing/Data/SystemTest/ISIS_Powder/input/calibration/gem/17_1/offsets_2011_cycle111b.cal.md5
@@ -0,0 +1 @@
+d59cb19944cf8a186b7124f4497f7e61
diff --git a/Testing/Data/SystemTest/ISIS_Powder/input/calibration/gem/GEM_Instrument_grouping.cal.md5 b/Testing/Data/SystemTest/ISIS_Powder/input/calibration/gem/GEM_Instrument_grouping.cal.md5
new file mode 100644
index 0000000000000000000000000000000000000000..34b033a2eea6de6fe6848dcc3de6c00c1d0c27f3
--- /dev/null
+++ b/Testing/Data/SystemTest/ISIS_Powder/input/calibration/gem/GEM_Instrument_grouping.cal.md5
@@ -0,0 +1 @@
+370c13263b4ccd6e22cc215e66cbc548
diff --git a/Testing/Data/SystemTest/ISIS_Powder/input/yaml_files/gem_system_test_mapping.yaml.md5 b/Testing/Data/SystemTest/ISIS_Powder/input/yaml_files/gem_system_test_mapping.yaml.md5
new file mode 100644
index 0000000000000000000000000000000000000000..8d10a7142d3d5011b6cf24b49cfe8fa42b3cae61
--- /dev/null
+++ b/Testing/Data/SystemTest/ISIS_Powder/input/yaml_files/gem_system_test_mapping.yaml.md5
@@ -0,0 +1 @@
+b63fb7eebb20e0279e7a165932eeb702
diff --git a/Testing/SystemTests/tests/analysis/ISIS_PowderGemTest.py b/Testing/SystemTests/tests/analysis/ISIS_PowderGemTest.py
new file mode 100644
index 0000000000000000000000000000000000000000..8b092426b595704a6e4ec346e482b646083d23b5
--- /dev/null
+++ b/Testing/SystemTests/tests/analysis/ISIS_PowderGemTest.py
@@ -0,0 +1,184 @@
+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)
diff --git a/Testing/SystemTests/tests/analysis/ISIS_PowderDiffraction.py b/Testing/SystemTests/tests/analysis/ISIS_PowderGeneric.py
similarity index 100%
rename from Testing/SystemTests/tests/analysis/ISIS_PowderDiffraction.py
rename to Testing/SystemTests/tests/analysis/ISIS_PowderGeneric.py
diff --git a/Testing/SystemTests/tests/analysis/ISIS_PowderPolarisTest.py b/Testing/SystemTests/tests/analysis/ISIS_PowderPolarisTest.py
index af7292d376e006d93ff44bfdbd4a88bdbb2f2e06..4e25f3a3ed8ca731e0d208c7bddde2e100870438 100644
--- a/Testing/SystemTests/tests/analysis/ISIS_PowderPolarisTest.py
+++ b/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()
diff --git a/Testing/SystemTests/tests/analysis/reference/ISIS_Powder-GEM-VanSplined_83608_offsets_2011_cycle111b.cal.nxs.md5 b/Testing/SystemTests/tests/analysis/reference/ISIS_Powder-GEM-VanSplined_83608_offsets_2011_cycle111b.cal.nxs.md5
new file mode 100644
index 0000000000000000000000000000000000000000..6beb21d836c02bd3b114893958a88a342d81fa9a
--- /dev/null
+++ b/Testing/SystemTests/tests/analysis/reference/ISIS_Powder-GEM-VanSplined_83608_offsets_2011_cycle111b.cal.nxs.md5
@@ -0,0 +1 @@
+ae7980d3a4879b3adaa4332da9e238e2
diff --git a/Testing/SystemTests/tests/analysis/reference/ISIS_PowderPEARL95634-95647_Van_Cal.nxs.md5 b/Testing/SystemTests/tests/analysis/reference/ISIS_PowderPEARL95634-95647_Van_Cal.nxs.md5
deleted file mode 100644
index f50b06c6be5eed2ad560e1b9fb2816ed38257c11..0000000000000000000000000000000000000000
--- a/Testing/SystemTests/tests/analysis/reference/ISIS_PowderPEARL95634-95647_Van_Cal.nxs.md5
+++ /dev/null
@@ -1 +0,0 @@
-35cbcc39432281c90c97e36bd6be7e1f
diff --git a/scripts/Diffraction/isis_powder/gem_routines/gem_algs.py b/scripts/Diffraction/isis_powder/gem_routines/gem_algs.py
index 3250f661ee24734733fda851be923f3df664369c..fbe4c9a9aea0004ed3035295caec570646782afe 100644
--- a/scripts/Diffraction/isis_powder/gem_routines/gem_algs.py
+++ b/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)
diff --git a/scripts/Diffraction/isis_powder/routines/common.py b/scripts/Diffraction/isis_powder/routines/common.py
index e567cbcbef047b32f2ef948642539fd765e680d0..3bdd9086d6e0fc3f1a330405a60383cf1c20d839 100644
--- a/scripts/Diffraction/isis_powder/routines/common.py
+++ b/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