Merge branch 'bugfix/10057_indirecttrans_python_algorithm' into develop

Conflicts:
	Code/Mantid/Framework/PythonInterface/test/python/plugins/algorithms/CMakeLists.txt
	Code/Mantid/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/IndirectDataReduction.ui

Refs #10057

Code/Mantid/Build/Jenkins/buildscript

@@ -13,6 +13,7 @@
 # Print out the versions of things we are using
 ###############################################################################
 cmake --version
+echo "SHA1=${sha1}"
 
 ###############################################################################
 # OS X setup steps

Code/Mantid/Framework/PythonInterface/plugins/algorithms/WorkflowAlgorithms/IndirectTransmissionReduction.py → Code/Mantid/Framework/PythonInterface/plugins/algorithms/WorkflowAlgorithms/IndirectTransmissionMonitor.py

@@ -7,7 +7,7 @@
 import os.path
 
 
-class IndirectTransmissionReduction(PythonAlgorithm):
+class IndirectTransmissionMonitor(PythonAlgorithm):
 
     def category(self):
         return "Workflow\\Inelastic;PythonAlgorithms;Inelastic"
@@ -16,82 +16,94 @@ def summary(self):
         return "Calculates the sample transmission using the raw data files of the sample and its background or container."
 
     def PyInit(self):
-        self.declareProperty(FileProperty('SampleFile', '', FileAction.Load, extensions=['raw']),
-                doc='Raw sample run file')
-        self.declareProperty(FileProperty('CanFile', '', FileAction.Load, extensions=['raw']),
-                doc='Raw background or can run file')
+        self.declareProperty(WorkspaceProperty('SampleWorkspace', '', direction=Direction.Input),
+                             doc='Sample workspace')
+
+        self.declareProperty(WorkspaceProperty('CanWorkspace', '', direction=Direction.Input),
+                             doc='Background/can workspace')
+
+        self.declareProperty(WorkspaceProperty('OutputWorkspace', '', direction=Direction.Output,
+                             optional=PropertyMode.Optional),
+                             doc='Output workspace group')
 
         self.declareProperty(name='Verbose', defaultValue=False, doc='Output more verbose message to log')
         self.declareProperty(name='Plot', defaultValue=False, doc='Plot result workspace')
         self.declareProperty(name='Save', defaultValue=False, doc='Save result workspace to nexus file in the default save directory')
 
     def PyExec(self):
         from IndirectCommon import StartTime, EndTime
-        StartTime('IndirectTransmissionReduction')
+        StartTime('IndirectTransmissionMonitor')
 
-        sample_filepath = self.getProperty("SampleFile").value
-        can_filepath = self.getProperty("CanFile").value
+        sample_ws_in = self.getPropertyValue("SampleWorkspace")
+        can_ws_in = self.getPropertyValue("CanWorkspace")
+        out_ws = self.getPropertyValue('OutputWorkspace')
         verbose = self.getProperty("Verbose").value
         plot = self.getProperty("Plot").value
         save = self.getProperty("Save").value
 
-        sample_filename = os.path.basename(sample_filepath)
-        ws_basename, _ = os.path.splitext(sample_filename)
+        ws_basename = str(sample_ws_in)
 
-        self.TransMon(ws_basename, 'Sam', sample_filepath, verbose)
-        self.TransMon(ws_basename, 'Can', can_filepath, verbose)
+        self._trans_mon(ws_basename, 'Sam', sample_ws_in)
+        self._trans_mon(ws_basename, 'Can', can_ws_in)
 
-        # Divide sample and can workspaces
+        # Generate workspace names
         sam_ws = ws_basename + '_Sam'
         can_ws = ws_basename + '_Can'
-        tr_ws = ws_basename + '_Trans'
-        Divide(LHSWorkspace=sam_ws, RHSWorkspace=can_ws, OutputWorkspace=tr_ws)
-        trans = numpy.average(mtd[tr_ws].readY(0))
+        trans_ws = ws_basename + '_Trans'
+
+        # Divide sample and can workspaces
+        Divide(LHSWorkspace=sam_ws, RHSWorkspace=can_ws, OutputWorkspace=trans_ws)
+        trans = numpy.average(mtd[trans_ws].readY(0))
+
+        AddSampleLog(Workspace=trans_ws, LogName='can_workspace', LogType='String', LogText=can_ws_in)
+
+        # Generate an output workspace name if none provided
+        if out_ws == '':
+            out_ws = ws_basename + '_Transmission'
 
         # Group workspaces
-        trans_ws = ws_basename + '_Transmission'
-        group = sam_ws + ',' + can_ws + ',' + tr_ws
-        GroupWorkspaces(InputWorkspaces=group, OutputWorkspace=trans_ws)
+        group = sam_ws + ',' + can_ws + ',' + trans_ws
+        GroupWorkspaces(InputWorkspaces=group, OutputWorkspace=out_ws)
+
+        self.setProperty('OutputWorkspace', out_ws)
 
         if verbose:
             logger.notice('Transmission : ' + str(trans))
 
         # Save the tranmissin workspace group to a nexus file
         if save:
             workdir = config['defaultsave.directory']
-            path = os.path.join(workdir, trans_ws + '.nxs')
-            SaveNexusProcessed(InputWorkspace=trans_ws, Filename=path)
+            path = os.path.join(workdir, out_ws + '.nxs')
+            SaveNexusProcessed(InputWorkspace=out_ws, Filename=path)
             if verbose:
                 logger.notice('Output file created : ' + path)
 
         # Plot spectra from transmission workspace
         if plot:
             mtd_plot = import_mantidplot()
-            mtd_plot.plotSpectrum(trans_ws, 0)
+            mtd_plot.plotSpectrum(out_ws, 0)
+
+        EndTime('IndirectTransmissionMonitor')
 
-        EndTime('IndirectTransmissionReduction')
+    def _unwrap_mon(self, input_ws):
+        out_ws = '_unwrap_mon_out'
 
-    def UnwrapMon(self, inWS):
         # Unwrap monitor - inWS contains M1,M2,S1 - outWS contains unwrapped Mon
         # Unwrap s1>2 to L of S2 (M2) ie 38.76  Ouput is in wavelength
-        out, join = UnwrapMonitor(InputWorkspace=inWS, LRef='37.86')
-        out_ws = 'out'
+        _, join = UnwrapMonitor(InputWorkspace=input_ws, OutputWorkspace=out_ws, LRef='37.86')
 
         # Fill bad (dip) in spectrum
-        RemoveBins(InputWorkspace=out_ws, OutputWorkspace=out_ws, Xmin=join-0.001, Xmax=join+0.001, Interpolation="Linear")
+        RemoveBins(InputWorkspace=out_ws, OutputWorkspace=out_ws, Xmin=join - 0.001, Xmax=join + 0.001, Interpolation="Linear")
         FFTSmooth(InputWorkspace=out_ws, OutputWorkspace=out_ws, WorkspaceIndex=0, IgnoreXBins=True)  # Smooth - FFT
 
-        DeleteWorkspace(inWS)  # delete monWS
+        DeleteWorkspace(input_ws)  # delete monWS
 
         return out_ws
 
-    def TransMon(self, ws_basename, file_type, filename, verbose):
-        if verbose:
-            logger.notice('Raw file : ' + file_type)
-
-        LoadRaw(Filename=filename, OutputWorkspace='__m1', SpectrumMin=1, SpectrumMax=1)
-        LoadRaw(Filename=filename, OutputWorkspace='__m2', SpectrumMin=2, SpectrumMax=2)
-        LoadRaw(Filename=filename, OutputWorkspace='__det', SpectrumMin=3, SpectrumMax=3)
+    def _trans_mon(self, ws_basename, file_type, input_ws):
+        CropWorkspace(InputWorkspace=input_ws, OutputWorkspace='__m1', StartWorkspaceIndex=0, EndWorkspaceIndex=0)
+        CropWorkspace(InputWorkspace=input_ws, OutputWorkspace='__m2', StartWorkspaceIndex=1, EndWorkspaceIndex=1)
+        CropWorkspace(InputWorkspace=input_ws, OutputWorkspace='__det', StartWorkspaceIndex=2, EndWorkspaceIndex=2)
 
         # Check for single or multiple time regimes
         mon_tcb_start = mtd['__m1'].readX(0)[0]
@@ -101,22 +113,21 @@ def TransMon(self, ws_basename, file_type, filename, verbose):
         mon_ws = '__Mon'
 
         if spec_tcb_start == mon_tcb_start:
-            mon_ws = self.UnwrapMon('__m1')  # unwrap the monitor spectrum and convert to wavelength
+            mon_ws = self._unwrap_mon('__m1')  # unwrap the monitor spectrum and convert to wavelength
             RenameWorkspace(InputWorkspace=mon_ws, OutputWorkspace='__Mon1')
         else:
             ConvertUnits(InputWorkspace='__m1', OutputWorkspace='__Mon1', Target="Wavelength")
 
-
         ConvertUnits(InputWorkspace='__m2', OutputWorkspace='__Mon2', Target="Wavelength")
 
         DeleteWorkspace('__m2')  # delete monWS
 
         x_in = mtd['__Mon1'].readX(0)
         xmin1 = mtd['__Mon1'].readX(0)[0]
-        xmax1 = mtd['__Mon1'].readX(0)[len(x_in)-1]
+        xmax1 = mtd['__Mon1'].readX(0)[len(x_in) - 1]
         x_in = mtd['__Mon2'].readX(0)
         xmin2 = mtd['__Mon2'].readX(0)[0]
-        xmax2 = mtd['__Mon2'].readX(0)[len(x_in)-1]
+        xmax2 = mtd['__Mon2'].readX(0)[len(x_in) - 1]
         wmin = max(xmin1, xmin2)
         wmax = min(xmax1, xmax2)
 
@@ -128,5 +139,6 @@ def TransMon(self, ws_basename, file_type, filename, verbose):
         DeleteWorkspace('__Mon1')  # delete monWS
         DeleteWorkspace('__Mon2')  # delete monWS
 
+
 # Register algorithm with Mantid
-AlgorithmFactory.subscribe(IndirectTransmissionReduction)
+AlgorithmFactory.subscribe(IndirectTransmissionMonitor)

Code/Mantid/Framework/PythonInterface/test/python/plugins/algorithms/CMakeLists.txt

@@ -15,8 +15,8 @@ set ( TEST_PY_FILES
   FindReflectometryLinesTest.py
   GetEiT0atSNSTest.py
   IndirectILLReductionTest.py
-  IndirectTransmissionReductionTest.py
   IndirectTransmissionTest.py
+  IndirectTransmissionMonitorTest.py
   LoadFullprofFileTest.py
   LoadLiveDataTest.py
   LoadLogPropertyTableTest.py

Code/Mantid/Framework/PythonInterface/test/python/plugins/algorithms/IndirectTransmissionMonitorTest.py

@@ -0,0 +1,48 @@
+import unittest, os
+import mantid
+from mantid.simpleapi import *
+
+class IndirectTransmissionMonitorTest(unittest.TestCase):
+
+    @classmethod
+    def setUpClass(cls):
+        ##TODO: Create sample workspaces
+        sample_workspace = Load('IRS26176.RAW')
+        can_workspace = Load('IRS26173.RAW')
+
+        cls._sample_workspace = sample_workspace
+        cls._can_workspace = can_workspace
+
+    def setUp(self):
+        self.kwargs = {}
+        self.kwargs['SampleWorkspace'] = self._sample_workspace
+        self.kwargs['CanWorkspace'] = self._can_workspace
+        self.kwargs['Verbose'] = True
+        self.kwargs['Plot'] = False
+
+    def tearDown(self):
+        # Clean up saved nexus files
+        path = os.path.join(config['defaultsave.directory'], 'IndirectTransmissionMonitorTest.nxs')
+        if os.path.isfile(path):
+            try:
+                os.remove(path)
+            except IOError, _:
+                pass
+
+    def test_basic(self):
+        trans_workspace = IndirectTransmissionMonitor(**self.kwargs)
+
+        self.assertTrue(isinstance(trans_workspace, mantid.api.WorkspaceGroup), msg='Result should be a workspace group')
+        self.assertEqual(trans_workspace.size(), 3, msg='Transmission workspace group should have 3 workspaces: sample, can and transfer')
+
+    def test_nexus_save(self):
+        self.kwargs['Save'] = True
+        self.kwargs['OutputWorkspace'] = 'IndirectTransmissionMonitorTest'
+
+        IndirectTransmissionMonitor(**self.kwargs)
+
+        path = os.path.join(config['defaultsave.directory'], 'IndirectTransmissionMonitorTest.nxs')
+        self.assertTrue(os.path.isfile(path), msg='Transmission workspace should be saved to default save directory')
+
+if __name__ == '__main__':
+    unittest.main()

Code/Mantid/MantidQt/CustomInterfaces/inc/MantidQtCustomInterfaces/IndirectDataReduction.ui

@@ -1613,40 +1613,70 @@ Later steps in the process (saving, renaming) will not be done.</string>
          </property>
          <layout class="QGridLayout" name="gridLayout_2">
           <item row="0" column="1">
-           <widget class="MantidQt::MantidWidgets::MWRunFiles" name="transInputFile" native="true">
-            <property name="label" stdset="0">
+           <widget class="MantidQt::MantidWidgets::DataSelector" name="trans_dsSampleInput" native="true">
+            <property name="sizePolicy">
+             <sizepolicy hsizetype="Minimum" vsizetype="Fixed">
+              <horstretch>0</horstretch>
+              <verstretch>0</verstretch>
+             </sizepolicy>
+            </property>
+            <property name="autoLoad" stdset="0">
+             <bool>true</bool>
+            </property>
+            <property name="loadLabelText" stdset="0">
              <string/>
             </property>
-            <property name="fileExtensions" stdset="0">
+            <property name="workspaceSuffixes" stdset="0">
+             <stringlist/>
+            </property>
+            <property name="fileBrowserSuffixes" stdset="0">
              <stringlist>
               <string>.raw</string>
              </stringlist>
             </property>
+            <property name="showLoad" stdset="0">
+             <bool>false</bool>
+            </property>
+           </widget>
+          </item>
+          <item row="0" column="0">
+           <widget class="QLabel" name="trans_lbSample">
+            <property name="text">
+             <string>Sample:</string>
+            </property>
            </widget>
           </item>
           <item row="1" column="1">
-           <widget class="MantidQt::MantidWidgets::MWRunFiles" name="transCanFile" native="true">
-            <property name="label" stdset="0">
+           <widget class="MantidQt::MantidWidgets::DataSelector" name="trans_dsCanInput" native="true">
+            <property name="sizePolicy">
+             <sizepolicy hsizetype="Minimum" vsizetype="Fixed">
+              <horstretch>0</horstretch>
+              <verstretch>0</verstretch>
+             </sizepolicy>
+            </property>
+            <property name="autoLoad" stdset="0">
+             <bool>true</bool>
+            </property>
+            <property name="loadLabelText" stdset="0">
              <string/>
             </property>
-            <property name="fileExtensions" stdset="0">
+            <property name="workspaceSuffixes" stdset="0">
+             <stringlist/>
+            </property>
+            <property name="fileBrowserSuffixes" stdset="0">
              <stringlist>
               <string>.raw</string>
              </stringlist>
             </property>
-           </widget>
-          </item>
-          <item row="0" column="0">
-           <widget class="QLabel" name="label_3">
-            <property name="text">
-             <string>Sample File: </string>
+            <property name="showLoad" stdset="0">
+             <bool>false</bool>
             </property>
            </widget>
           </item>
           <item row="1" column="0">
-           <widget class="QLabel" name="label_8">
+           <widget class="QLabel" name="trans_lbBackground">
             <property name="text">
-             <string>Can/Background File:</string>
+             <string>Background:</string>
             </property>
            </widget>
           </item>
@@ -2702,8 +2732,6 @@ Later steps in the process (saving, renaming) will not be done.</string>
   <tabstop>slice_ckVerbose</tabstop>
   <tabstop>slice_ckPlot</tabstop>
   <tabstop>slice_ckSave</tabstop>
-  <tabstop>transInputFile</tabstop>
-  <tabstop>transCanFile</tabstop>
   <tabstop>trans_ckVerbose</tabstop>
   <tabstop>trans_ckPlot</tabstop>
   <tabstop>trans_ckSave</tabstop>

Code/Mantid/MantidQt/CustomInterfaces/src/IndirectDataReduction.cpp

@@ -408,8 +408,6 @@ void IndirectDataReduction::loadSettings()
   m_uiForm.ind_mapFile->readSettings(settings.group());
   m_uiForm.slice_calibFile->readSettings(settings.group());
   m_uiForm.moment_dsInput->readSettings(settings.group());
-  m_uiForm.transInputFile->readSettings(settings.group());
-  m_uiForm.transCanFile->readSettings(settings.group());
   m_uiForm.sqw_dsSampleInput->readSettings(settings.group());
   settings.endGroup();
 }