Merge pull request #13142 from mganeva/corrections_to_LoadDNSLegacy

Corrections to LoadDNSLegacy

Code/Mantid/Framework/PythonInterface/plugins/algorithms/LoadDNSLegacy.py

@@ -12,11 +12,13 @@ from dnsdata import DNSdata
 sys.path.pop(0)
 
 POLARISATIONS = ['0', 'x', 'y', 'z', '-x', '-y', '-z']
+NORMALIZATIONS = ['duration', 'monitor']
 
 
 class LoadDNSLegacy(PythonAlgorithm):
     """
-    Load the DNS Legacy data file to the mantid workspace
+    Load the DNS Legacy data file to the matrix workspace
+    Monitor/duration data are loaded to the separate workspace
     """
     def category(self):
         """
@@ -42,98 +44,134 @@ class LoadDNSLegacy(PythonAlgorithm):
                              doc="Name of the workspace to store the experimental data.")
         self.declareProperty("Polarisation", "0",
                              StringListValidator(POLARISATIONS),
-                             doc="Type of polarisation. Valid values: %s" % str(POLARISATIONS))
+                             doc="Type of polarisation.")
+        self.declareProperty("Normalization", "duration",
+                             StringListValidator(NORMALIZATIONS),
+                             doc="Type of data for normalization.")
         return
 
     def PyExec(self):
         # Input
         filename = self.getPropertyValue("Filename")
-        outws = self.getPropertyValue("OutputWorkspace")
+        outws_name = self.getPropertyValue("OutputWorkspace")
+        monws_name = outws_name + '_NORM'
         pol = self.getPropertyValue("Polarisation")
+        norm = self.getPropertyValue("Normalization")
 
         # load data array from the given file
         data_array = np.loadtxt(filename)
+        if not data_array.size:
+            message = "File " + filename + " does not contain any data!"
+            self.log().error(message)
+            raise RuntimeError(message)
+
+        # load run information
+        metadata = DNSdata()
+        try:
+            metadata.read_legacy(filename)
+        except RuntimeError as err:
+            message = "Error of loading of file " + filename + ": " + err
+            self.log().error(message)
+            raise RuntimeError(message)
+
         ndet = 24
-        dataX = np.zeros(ndet)
+        # this needed to be able to use ConvertToMD
+        dataX = np.zeros(2*ndet)
+        dataX.fill(metadata.wavelength + 0.00001)
+        dataX[::2] -= 0.000002
         dataY = data_array[0:ndet, 1:]
         dataE = np.sqrt(dataY)
         # create workspace
-        __temporary_workspace__ = api.CreateWorkspace(DataX=dataX,
-                                                      DataY=dataY, DataE=dataE, NSpec=ndet, UnitX="Wavelength")
-        api.LoadInstrument(__temporary_workspace__, InstrumentName='DNS')
+        api.CreateWorkspace(OutputWorkspace=outws_name, DataX=dataX, DataY=dataY,
+                            DataE=dataE, NSpec=ndet, UnitX="Wavelength")
+        outws = api.mtd[outws_name]
+        api.LoadInstrument(outws, InstrumentName='DNS')
 
-        # load run information
-        metadata = DNSdata()
-        metadata.read_legacy(filename)
-        run = __temporary_workspace__.mutableRun()
+        run = outws.mutableRun()
         if metadata.start_time and metadata.end_time:
             run.setStartAndEndTime(DateAndTime(metadata.start_time),
                                    DateAndTime(metadata.end_time))
         # add name of file as a run title
         fname = os.path.splitext(os.path.split(filename)[1])[0]
         run.addProperty('run_title', fname, True)
-        # run.addProperty('dur_secs', str(metadata.duration), True)
 
         # rotate the detector bank to the proper position
-        api.RotateInstrumentComponent(__temporary_workspace__,
-                                      "bank0", X=0, Y=1, Z=0, Angle=metadata.deterota)
+        api.RotateInstrumentComponent(outws, "bank0", X=0, Y=1, Z=0, Angle=metadata.deterota)
         # add sample log Ei and wavelength
-        api.AddSampleLog(__temporary_workspace__,
-                         'Ei', LogText=str(metadata.incident_energy),
-                         LogType='Number')
-        api.AddSampleLog(__temporary_workspace__,
-                         'wavelength', LogText=str(metadata.wavelength),
-                         LogType='Number')
+        api.AddSampleLog(outws, LogName='Ei', LogText=str(metadata.incident_energy),
+                         LogType='Number', LogUnit='meV')
+        api.AddSampleLog(outws, LogName='wavelength', LogText=str(metadata.wavelength),
+                         LogType='Number', LogUnit='Angstrom')
         # add other sample logs
-        api.AddSampleLog(__temporary_workspace__, 'deterota',
-                         LogText=str(metadata.deterota), LogType='Number')
-        api.AddSampleLog(__temporary_workspace__, 'mon_sum',
-                         LogText=str(metadata.monitor_counts), LogType='Number')
-        api.AddSampleLog(__temporary_workspace__, 'duration',
-                         LogText=str(metadata.duration), LogType='Number')
-        api.AddSampleLog(__temporary_workspace__, 'huber',
-                         LogText=str(metadata.huber), LogType='Number')
-        api.AddSampleLog(__temporary_workspace__, 'T1',
-                         LogText=str(metadata.t1), LogType='Number')
-        api.AddSampleLog(__temporary_workspace__, 'T2',
-                         LogText=str(metadata.t2), LogType='Number')
-        api.AddSampleLog(__temporary_workspace__, 'Tsp',
-                         LogText=str(metadata.tsp), LogType='Number')
+        api.AddSampleLog(outws, LogName='deterota', LogText=str(metadata.deterota),
+                         LogType='Number', LogUnit='Degrees')
+        api.AddSampleLog(outws, 'mon_sum',
+                         LogText=str(float(metadata.monitor_counts)), LogType='Number')
+        api.AddSampleLog(outws, LogName='duration', LogText=str(metadata.duration),
+                         LogType='Number', LogUnit='Seconds')
+        api.AddSampleLog(outws, LogName='huber', LogText=str(metadata.huber),
+                         LogType='Number', LogUnit='Degrees')
+        api.AddSampleLog(outws, LogName='omega', LogText=str(metadata.huber - metadata.deterota),
+                         LogType='Number', LogUnit='Degrees')
+        api.AddSampleLog(outws, LogName='T1', LogText=str(metadata.t1),
+                         LogType='Number', LogUnit='K')
+        api.AddSampleLog(outws, LogName='T2', LogText=str(metadata.t2),
+                         LogType='Number', LogUnit='K')
+        api.AddSampleLog(outws, LogName='Tsp', LogText=str(metadata.tsp),
+                         LogType='Number', LogUnit='K')
         # flipper
-        api.AddSampleLog(__temporary_workspace__, 'flipper_precession',
-                         LogText=str(metadata.flipper_precession_current), LogType='Number')
-        api.AddSampleLog(__temporary_workspace__, 'flipper_z_compensation',
-                         LogText=str(metadata.flipper_z_compensation_current), LogType='Number')
-        flipper_status = 'OFF'
+        api.AddSampleLog(outws, LogName='flipper_precession',
+                         LogText=str(metadata.flipper_precession_current),
+                         LogType='Number', LogUnit='A')
+        api.AddSampleLog(outws, LogName='flipper_z_compensation',
+                         LogText=str(metadata.flipper_z_compensation_current),
+                         LogType='Number', LogUnit='A')
+        flipper_status = 'OFF'    # flipper OFF
         if abs(metadata.flipper_precession_current) > sys.float_info.epsilon:
-            flipper_status = 'ON'
-        api.AddSampleLog(__temporary_workspace__, 'flipper',
+            flipper_status = 'ON'    # flipper ON
+        api.AddSampleLog(outws, LogName='flipper',
                          LogText=flipper_status, LogType='String')
         # coil currents
-        api.AddSampleLog(__temporary_workspace__, 'C_a',
-                         LogText=str(metadata.a_coil_current), LogType='Number')
-        api.AddSampleLog(__temporary_workspace__, 'C_b',
-                         LogText=str(metadata.b_coil_current), LogType='Number')
-        api.AddSampleLog(__temporary_workspace__, 'C_c',
-                         LogText=str(metadata.c_coil_current), LogType='Number')
-        api.AddSampleLog(__temporary_workspace__, 'C_z',
-                         LogText=str(metadata.z_coil_current), LogType='Number')
+        api.AddSampleLog(outws, LogName='C_a', LogText=str(metadata.a_coil_current),
+                         LogType='Number', LogUnit='A')
+        api.AddSampleLog(outws, LogName='C_b', LogText=str(metadata.b_coil_current),
+                         LogType='Number', LogUnit='A')
+        api.AddSampleLog(outws, LogName='C_c', LogText=str(metadata.c_coil_current),
+                         LogType='Number', LogUnit='A')
+        api.AddSampleLog(outws, LogName='C_z', LogText=str(metadata.z_coil_current),
+                         LogType='Number', LogUnit='A')
         # type of polarisation
-        api.AddSampleLog(__temporary_workspace__, 'polarisation',
+        api.AddSampleLog(outws, 'polarisation',
                          LogText=pol, LogType='String')
         # slits
-        api.AddSampleLog(__temporary_workspace__, 'slit_i_upper_blade_position',
-                         LogText=str(metadata.slit_i_upper_blade_position), LogType='String')
-        api.AddSampleLog(__temporary_workspace__, 'slit_i_lower_blade_position',
-                         LogText=str(metadata.slit_i_lower_blade_position), LogType='String')
-        api.AddSampleLog(__temporary_workspace__, 'slit_i_left_blade_position',
-                         LogText=str(metadata.slit_i_left_blade_position), LogType='String')
-        api.AddSampleLog(__temporary_workspace__, 'slit_i_right_blade_position',
-                         LogText=str(metadata.slit_i_right_blade_position), LogType='String')
-
-        self.setProperty("OutputWorkspace", __temporary_workspace__)
-        self.log().debug('LoadDNSLegacy: data are loaded to the workspace ' + outws)
-        api.DeleteWorkspace(__temporary_workspace__)
+        api.AddSampleLog(outws, LogName='slit_i_upper_blade_position',
+                         LogText=str(metadata.slit_i_upper_blade_position),
+                         LogType='Number', LogUnit='mm')
+        api.AddSampleLog(outws, LogName='slit_i_lower_blade_position',
+                         LogText=str(metadata.slit_i_lower_blade_position),
+                         LogType='Number', LogUnit='mm')
+        api.AddSampleLog(outws, LogName='slit_i_left_blade_position',
+                         LogText=str(metadata.slit_i_left_blade_position),
+                         LogType='Number', LogUnit='mm')
+        api.AddSampleLog(outws, 'slit_i_right_blade_position',
+                         LogText=str(metadata.slit_i_right_blade_position),
+                         LogType='Number', LogUnit='mm')
+
+        # create workspace with normalization data (monitor or duration)
+        if norm == 'duration':
+            dataY.fill(metadata.duration)
+            dataE.fill(0.001)
+        else:
+            dataY.fill(metadata.monitor_counts)
+            dataE = np.sqrt(dataY)
+        api.CreateWorkspace(OutputWorkspace=monws_name, DataX=dataX, DataY=dataY,
+                            DataE=dataE, NSpec=ndet, UnitX="Wavelength")
+        monws = api.mtd[monws_name]
+        api.LoadInstrument(monws, InstrumentName='DNS')
+        api.CopyLogs(InputWorkspace=outws_name, OutputWorkspace=monws_name, MergeStrategy='MergeReplaceExisting')
+
+        self.setProperty("OutputWorkspace", outws)
+        self.log().debug('LoadDNSLegacy: data are loaded to the workspace ' + outws_name)
 
         return
 

Code/Mantid/Framework/PythonInterface/plugins/algorithms/dnsdata.py

@@ -69,6 +69,10 @@ class DNSdata(object):
             unparsed = fhandler.read()
             blocks = unparsed.split(splitsymbol)
 
+            # check whether the file is complete
+            if len(blocks) < 9:
+                raise RuntimeError("The file %s is not complete!" % filename)
+
             # parse each block
             # parse block 0 (header)
             res = parse_header(blocks[0])
@@ -79,7 +83,7 @@ class DNSdata(object):
                 self.sample_name = res['sample']
                 self.userid = res['userid']
             except:
-                raise ValueError("The file %s does not contain valid DNS data format." % filename)
+                raise RuntimeError("The file %s does not contain valid DNS data format." % filename)
             # parse block 1 (general information)
             b1splitted = [s.strip() for s in blocks[1].split('#')]
             b1rest = [el for el in b1splitted]

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

@@ -2,6 +2,8 @@ import unittest
 from testhelpers import run_algorithm
 from mantid.api import AnalysisDataService
 from math import pi
+import os
+from mantid.simpleapi import LoadDNSLegacy
 
 
 class LoadDNSLegacyTest(unittest.TestCase):
@@ -27,10 +29,31 @@ class LoadDNSLegacyTest(unittest.TestCase):
         self.assertEqual(8332872, run.getProperty('mon_sum').value)
         self.assertEqual('y', run.getProperty('polarisation').value)
         # check whether detector bank is rotated
-        det = ws.getDetector(1)
+        det = ws.getDetector(0)
         self.assertAlmostEqual(8.54, ws.detectorSignedTwoTheta(det)*180/pi)
         run_algorithm("DeleteWorkspace", Workspace=outputWorkspaceName)
         return
 
+    def _createIncompleteFile(self, filename):
+        """
+        creates an incomplete data file
+        """
+        with open(filename, "w") as f:
+            f.write("# DNS Data userid=sa,exp=961,file=988,sample=run2")
+            f.write("#--------------------------------------------------------------------------")
+            f.write("# 9")
+            f.write("# User: Some User")
+            f.close()
+        return
+
+    def test_LoadInvalidData(self):
+        outputWorkspaceName = "LoadDNSLegacyTest_Test2"
+        filename = "dns-incomplete.d_dat"
+        self._createIncompleteFile(filename)
+        self.assertRaises(RuntimeError, LoadDNSLegacy,  Filename=filename,
+                          OutputWorkspace=outputWorkspaceName, Polarisation='y')
+        os.remove(filename)
+
+
 if __name__ == '__main__':
     unittest.main()

Code/Mantid/docs/source/algorithms/LoadDNSLegacy-v1.rst

@@ -9,10 +9,17 @@
 Description
 -----------
 
-Loads a DNS legacy .d_dat data file into a :ref:`Workspace2D <Workspace2D>` with
-the given name. 
+.. warning::
 
-The loader rotates the detector bank in the position given in the data file.
+   This algorithm is being developed for a specific instrument. It might get changed or even 
+   removed without a notification, should instrument scientists decide to do so.
+
+This algorithm loads a DNS legacy data file into a :ref:`Workspace2D <Workspace2D>`. Two workspaces will be created: 
+
+-  raw data workspace with the given name. 
+-  workspace with normalization data (monitor counts or experiment duration by user's choice). The normalization workspace is named same as the data workspace, but has suffix "_NORM". 
+
+The loader rotates the detector bank in the position given in the data file. No operations on the neutron counts are performed. Sample logs are dublicated for both, data and normalization workspaces.
 
 This algorithm only supports DNS instrument in its configuration before major upgrade. 
 
@@ -27,10 +34,9 @@ Usage
    datafile = 'dn134011vana.d_dat'
 
    # Load dataset
-   ws = LoadDNSLegacy(datafile, Polarisation='x')
+   ws = LoadDNSLegacy(datafile, Polarisation='x', Normalization='monitor')
 
-   print "This workspace has", ws.getNumDims(), "dimensions and has", \
-        ws.getNumberHistograms(), "histograms."
+   print "This workspace has", ws.getNumDims(), "dimensions and has", ws.getNumberHistograms(), "histograms."
 
 Output:
 

Code/Mantid/instrument/DNS_Definition_PAonly.xml

@@ -22,13 +22,14 @@
   </component>
   <type name="moderator" is="Source"></type>
   <!-- monitor -->
-  <component type="monitor" idlist="monitor">
+  <!--<component type="monitor" idlist="monitor">
     <location z="-0.229" />
   </component>
   <type name="monitor" is="monitor"></type>
   <idlist idname="monitor">
     <id val="-1"/>
   </idlist>
+  -->
   <!-- Sample position -->
   <component type="sample-position">
     <location y="0.0" x="0.0" z="0.0" />