Merge pull request #18884 from mantidproject/18843_loadvesuvio_nexus_…

…files

Add support for NeXus files in LoadVesuvio

Framework/PythonInterface/plugins/algorithms/LoadVesuvio.py

@@ -7,6 +7,9 @@
 
 import copy
 import numpy as np
+import os
+import re
+import six
 
 RUN_PROP = "Filename"
 WKSP_PROP = "OutputWorkspace"
@@ -18,6 +21,8 @@
 LOAD_MON = "LoadMonitors"
 WKSP_PROP_LOAD_MON= "OutputMonitorWorkspace"
 
+FILENAME_RE = re.compile(r'^([0-9]+)(\.[a-zA-z]+)?$')
+
 # Raw workspace names which are necessary at the moment
 SUMMED_WS = "__loadraw_evs"
 # Enumerate the indexes for the different foil state sums
@@ -37,7 +42,6 @@ class LoadVesuvio(LoadEmptyVesuvio):
     _ws_index = None
     _spectrum_no = None
     foil_map = None
-    _inst_prefix = None
     _back_scattering = None
     _load_common_called = False
     _load_monitors = False
@@ -154,7 +158,9 @@ def validateInputs(self):
         issues = {}
 
         # Validate run number ranges
-        run_str = self.getProperty(RUN_PROP).value
+        user_input = self.getProperty(RUN_PROP).value
+        run_str = os.path.basename(user_input)
+        # String could be a full file path
         if "-" in run_str:
             lower, upper = run_str.split("-")
             issues = self._validate_range_formatting(lower, upper, RUN_PROP, issues)
@@ -316,25 +322,13 @@ def _exec_single_foil_state_mode(self):
         """
 
         runs = self._get_runs()
-
         all_spectra = [item for sublist in self._spectra for item in sublist]
 
         if len(runs) > 1:
             self._set_spectra_type(all_spectra[0])
             self._setup_raw(all_spectra)
         else:
-            isis = config.getFacility("ISIS")
-            inst_prefix = isis.instrument("VESUVIO").shortName()
-
-            try:
-                run_str = inst_prefix + runs[0] +'.raw'
-            except ValueError:
-                run_str = runs[0]
-
-            self._raise_error_period_scatter(run_str, self._back_scattering)
-            all_spectra = [item for sublist in self._spectra for item in sublist]
-
-            self._load_single_run_spec_and_mon(all_spectra, run_str)
+            self._load_single_run_spec_and_mon(all_spectra, self._get_filename(runs[0]))
 
         raw_group = mtd[SUMMED_WS]
         self._nperiods = raw_group.size()
@@ -406,13 +400,33 @@ def _exec_single_foil_state_mode(self):
         if self._sumspectra:
             self._sum_all_spectra()
 
-        ms.DeleteWorkspace(Workspace=SUMMED_WS)
+        ms.DeleteWorkspace(Workspace=SUMMED_WS, EnableLogging=_LOGGING_)
         self._store_results()
         self._cleanup_raw()
 
 #----------------------------------------------------------------------------------------
 
+    def _get_filename(self, run_or_filename):
+        """Given a string containing either a filename/partial filename or run number find the correct
+        file prefix"""
+        isis = config.getFacility("ISIS")
+        vesuvio = isis.instrument("VESUVIO")
+        if isinstance(run_or_filename, six.integer_types):
+            run_no = run_or_filename
+            return vesuvio.filePrefix(int(run_no)) + str(run_or_filename)
+        else:
+            match = FILENAME_RE.match(run_or_filename)
+            if match:
+                run_no = match.group(1)
+                return vesuvio.filePrefix(int(run_no)) + str(run_or_filename)
+            else:
+                # Assume file is okay and give it a go with Load
+                return run_or_filename
+
+    #----------------------------------------------------------------------------------------
+
     def _load_single_run_spec_and_mon(self, all_spectra, run_str):
+        self._raise_error_period_scatter(run_str, self._back_scattering)
         # check if the monitor spectra are already in the spectra list
         filtered_spectra = sorted([i for i in all_spectra if i <= self._mon_spectra[-1]])
         mons_in_ws = False
@@ -423,13 +437,13 @@ def _load_single_run_spec_and_mon(self, all_spectra, run_str):
             logger.warning("LoadMonitors is true while monitor spectra are defined in the spectra list.")
             logger.warning("Monitors have been loaded into the data workspace not separately.")
         if mons_in_ws:
-            ms.LoadRaw(Filename=run_str, OutputWorkspace=SUMMED_WS, SpectrumList=all_spectra,
-                       EnableLogging=_LOGGING_)
+            ms.Load(Filename=run_str, OutputWorkspace=SUMMED_WS, SpectrumList=all_spectra,
+                    EnableLogging=_LOGGING_)
         else:
             all_spec_inc_mon = self._mon_spectra
             all_spec_inc_mon.extend(all_spectra)
-            ms.LoadRaw(Filename=run_str, OutputWorkspace=SUMMED_WS, SpectrumList=all_spec_inc_mon,
-                       LoadMonitors='Separate', EnableLogging=_LOGGING_)
+            ms.Load(Filename=run_str, OutputWorkspace=SUMMED_WS, SpectrumList=all_spec_inc_mon,
+                    LoadMonitors='Separate', EnableLogging=_LOGGING_)
             if self._load_monitors:
                 monitor_group = mtd[SUMMED_WS +'_monitors']
                 mon_out_name = self.getPropertyValue(WKSP_PROP) + "_monitors"
@@ -441,6 +455,7 @@ def _load_single_run_spec_and_mon(self, all_spectra, run_str):
                 self._load_monitors_workspace = self._sum_monitors_in_group(monitor_group,
                                                                             self._load_monitors_workspace)
             self._raw_monitors = mtd[SUMMED_WS +'_monitors']
+
 #----------------------------------------------------------------------------------------
 
     def _load_common_inst_parameters(self):
@@ -451,7 +466,6 @@ def _load_common_inst_parameters(self):
         if self._load_common_called:
             return
 
-        isis = config.getFacility("ISIS")
         empty_vesuvio_ws = self._load_empty_evs()
         empty_vesuvio = empty_vesuvio_ws.getInstrument()
 
@@ -461,7 +475,6 @@ def to_int_list(str_param):
             return list(range(int(elements[0]),int(elements[1]) + 1)) # range goes x_l,x_h-1
 
         # Attach parameters as attributes
-        self._inst_prefix = isis.instrument("VESUVIO").shortName()
         parnames = empty_vesuvio.getParameterNames(False)
         for name in parnames:
             # Irritating parameter access doesn't let you query the type
@@ -584,29 +597,25 @@ def _load_and_sum_runs(self, spectra):
             @param spectra :: The list of spectra to load
             @returns a tuple of length 2 containing (main_detector_ws, monitor_ws)
         """
-        isis = config.getFacility("ISIS")
-        inst_prefix = isis.instrument("VESUVIO").shortName()
-
         runs = self._get_runs()
 
         self.summed_ws, self.summed_mon = "__loadraw_evs", "__loadraw_evs_monitors"
         spec_inc_mon = self._mon_spectra
         spec_inc_mon.extend(spectra)
         for index, run in enumerate(runs):
-            run = inst_prefix + str(run)
-            self._raise_error_period_scatter(run, self._back_scattering)
+            filename = self._get_filename(run)
+            self._raise_error_period_scatter(filename, self._back_scattering)
             if index == 0:
                 out_name, out_mon = SUMMED_WS, SUMMED_WS + '_monitors'
             else:
                 out_name, out_mon = SUMMED_WS + 'tmp', SUMMED_WS + 'tmp_monitors'
 
             # Load data
-            raw_filepath = FileFinder.findRuns(run)[0]
-            ms.LoadRaw(Filename=raw_filepath,
-                       SpectrumList=spec_inc_mon,
-                       OutputWorkspace=out_name,
-                       LoadMonitors='Separate',
-                       EnableLogging=_LOGGING_)
+            ms.Load(Filename=filename,
+                    SpectrumList=spec_inc_mon,
+                    OutputWorkspace=out_name,
+                    LoadMonitors='Separate',
+                    EnableLogging=_LOGGING_)
 
             # Sum
             if index > 0:
@@ -677,17 +686,19 @@ def _get_runs(self):
         """
         Returns the runs as a list of strings
         """
-        run_str = self.getProperty(RUN_PROP).value
+        # String could be a full file path
+        user_input = self.getProperty(RUN_PROP).value
+        run_str = os.path.basename(user_input)
         # Load is not doing the right thing when summing. The numbers don't look correct
         if "-" in run_str:
             lower, upper = run_str.split("-")
             # Range goes lower to up-1 but we want to include the last number
             runs = list(range(int(lower), int(upper)+1))
-
         elif "," in run_str:
-            runs =  run_str.split(",")
+            runs = run_str.split(",")
         else:
-            runs = [run_str]
+            # Leave it as it is
+            runs = [user_input]
 
         return runs
 

Testing/SystemTests/tests/analysis/LoadVesuvioTest.py

@@ -1,7 +1,7 @@
 #pylint: disable=invalid-name,no-init,too-many-public-methods,too-many-arguments
 import stresstesting
 
-from mantid.api import MatrixWorkspace, mtd
+from mantid.api import FileFinder, MatrixWorkspace, mtd
 import mantid.simpleapi as ms
 
 import math
@@ -46,6 +46,25 @@ def test_spectrum_list_comma_separated_ranges(self):
 
     #================== Success cases ================================
 
+    def test_filename_accepts_full_filepath(self):
+        diff_mode = "FoilOut"
+        rawfile = FileFinder.getFullPath("EVS14188.raw")
+        self._run_load(rawfile, "3", diff_mode)
+        self.assertTrue(mtd.doesExist('evs_raw'))
+        self.assertEquals(mtd['evs_raw'].getNumberHistograms(), 1)
+
+    def test_filename_accepts_filename_no_path(self):
+        diff_mode = "FoilOut"
+        self._run_load("EVS14188.raw", "3", diff_mode)
+        self.assertTrue(mtd.doesExist('evs_raw'))
+        self.assertEquals(mtd['evs_raw'].getNumberHistograms(), 1)
+
+    def test_filename_accepts_run_and_ext(self):
+        diff_mode = "FoilOut"
+        self._run_load("14188.raw", "3", diff_mode)
+        self.assertTrue(mtd.doesExist('evs_raw'))
+        self.assertEquals(mtd['evs_raw'].getNumberHistograms(), 1)
+
     def test_load_with_back_scattering_spectra_produces_correct_workspace_using_double_difference(self):
         diff_mode = "DoubleDifference"
         self._run_load("14188", "3-134", diff_mode)

docs/conf.py.in

@@ -92,7 +92,9 @@ except NameError:
 # Run this after each test group has executed
 doctest_global_cleanup = """
 from mantid.api import FrameworkManager
+from mantid.kernel import ConfigService
 FrameworkManager.Instance().clear()
+ConfigService.Instance().reset()
 """
 
 # -- Options for pngmath --------------------------------------------------

docs/source/release/v3.10.0/indirect_inelastic.rst

@@ -12,6 +12,7 @@ Algorithms
 ##########
 
 - A new input property *RebinCanToSample* was added to :ref:`ApplyPaalmanPingsCorrection <algm-ApplyPaalmanPingsCorrection>` which enables or disables the rebinning of the empty container workspace.
+- :ref:`LoadVesuvio <algm-LoadVesuvio> can now load NeXus files as well as raw files
 
 Data Analysis
 #############

scripts/Inelastic/IndirectReductionCommon.py

@@ -37,8 +37,8 @@ def load_files(data_files, ipf_filename, spec_min, spec_max, sum_files=False, lo
         logger.debug('Loading file %s as workspace %s' % (filename, ws_name))
 
         if 'VESUVIO' in ipf_filename:
-            evs_filename = os.path.basename(str(filename)).replace('EVS', '')
-            LoadVesuvio(Filename=evs_filename,
+            # Load all spectra. They are cropped later
+            LoadVesuvio(Filename=str(filename),
                         OutputWorkspace=ws_name,
                         SpectrumList='1-198',
                         **load_opts)