Merge pull request #20966 from mantidproject/19578_gsas_ii_integration

GSASIIRefineFitPeaks reintegrated with latest version of GSAS-II

Framework/PythonInterface/test/python/plugins/algorithms/GSASIIRefineFitPeaksTest.py

 from __future__ import (absolute_import, division, print_function)
 
+import os
+import tempfile
 import unittest
-from mantid.simpleapi import *
+import mantid.simpleapi as mantid
 from mantid.api import *
 
-class GSASIIRefineFitPeaksTest(unittest.TestCase):
+
+class _GSASFinder(object):
     """
-    Very limited test, as executing this algorithm requires a modified
-    version of GSASII. At least it does some check that the algorithm is
-    registered succesfully and basic sanity checks.
+    Helper class for unit test - the algorithm can't run without a version of GSAS-II that includes the module
+    GSASIIscriptable (added April 2017)
     """
+    @staticmethod
+    def _find_directory_by_name(cur_dir_name, cur_dir_path, name_to_find, level, max_level):
+        """
+        Perform a depth-limited depth-first search to try and find a directory with a given name
+        """
+        if level == max_level:
+            return None
+
+        if cur_dir_name == name_to_find:
+            return cur_dir_path
+
+        list_dir = os.listdir(cur_dir_path)
+        for child in list_dir:
+            child_path = os.path.join(cur_dir_path, child)
+            if os.path.isdir(child_path):
+                try:
+                    path = _GSASFinder._find_directory_by_name(cur_dir_name=child, cur_dir_path=child_path,
+                                                               level=level + 1, name_to_find=name_to_find,
+                                                               max_level=max_level)
+                except OSError:  # Probably "Permission denied". Either way, just ignore it
+                    pass
+                else:
+                    if path is not None:
+                        return path
 
-    def test_wrong_properties(self):
+    @staticmethod
+    def _path_to_g2conda():
         """
-        Handle in/out property issues appropriately.
+        Find the g2conda directory (where GSAS-II normally sits), as long as it exists less than 2 levels away from
+        the root directory
         """
-        ws_name = 'out_ws'
-        peak = "name=BackToBackExponential, I=5000,A=1, B=1., X0=10000, S=150"
-        sws = CreateSampleWorkspace(Function="User Defined", UserDefinedFunction=peak,
-                                    NumBanks=1, BankPixelWidth=1, XMin=5000, XMax=30000,
-                                    BinWidth=5, OutputWorkspace=ws_name)
-        instr_filename = 'inexistent_instr_par_file'
-
-        # No InputWorkspace property (required)
-        self.assertRaises(RuntimeError,
-                          GSASIIRefineFitPeaks,
-                          WorkspaceIndex=0, ExpectedPeaks='1.2, 3.1')
-
-        # Wrong WorkspaceIndex value
-        self.assertRaises(RuntimeError,
-                          GSASIIRefineFitPeaks,
-                          InputWorkspace=ws_name,
-                          WorkspaceIndex=-3)
-
-        # Wrong property
-        self.assertRaises(RuntimeError,
-                          GSASIIRefineFitPeaks,
-                          InputWorkspace=ws_name, BankPixelFoo=33,
-                          WorkspaceIndex=0)
-
-        # missing instrument file property
-        self.assertRaises(RuntimeError,
-                          GSASIIRefineFitPeaks,
-                          InputWorkspace=ws_name,
-                          WorkspaceIndex=0)
-
-        # Wrong InstrumentFile property name
-        self.assertRaises(ValueError,
-                          GSASIIRefineFitPeaks,
-                          InputWorkspace=ws_name,
-                          InstruMentFile=instr_filename,
-                          WorkspaceIndex=0, ExpectedPeaks='a')
-
-        # Missing file for InstrumentFile
-        self.assertRaises(ValueError,
-                          GSASIIRefineFitPeaks,
-                          InputWorkspace=ws_name,
-                          InstrumentFile=instr_filename,
-                          WorkspaceIndex=0, ExpectedPeaks='a')
-
-    def test_exec_import_fails(self):
-        pass
+        root_directory = os.path.abspath(os.sep)
+        return _GSASFinder._find_directory_by_name(cur_dir_path=root_directory, cur_dir_name=root_directory, level=0,
+                                                   name_to_find="g2conda", max_level=2)
+
+    @staticmethod
+    def GSASIIscriptable_location():
+        """
+        Find the path to GSASIIscriptable.py, if it exists and is less than 2 levels away from the root directory
+        """
+        path_to_g2conda = _GSASFinder._path_to_g2conda()
+        if path_to_g2conda is None:
+            return None
+
+        path_to_gsasii_scriptable = os.path.join(path_to_g2conda, "GSASII")
+        if os.path.isfile(os.path.join(path_to_gsasii_scriptable, "GSASIIscriptable.py")):
+            return path_to_gsasii_scriptable
+
+        return None
+
+
+class GSASIIRefineFitPeaksTest(unittest.TestCase):
+
+    _path_to_gsas = None
+    _gsas_proj = None
+    _input_ws = None
+    _phase_file = None
+    _inst_file = None
+
+    def setUp(self):
+        data_dir = mantid.config["datasearch.directories"].split(";")[0]
+        print(mantid.config["datasearch.directories"].split(";"))
+        
+        self._phase_file = os.path.join(data_dir, "FE_ALPHA.cif")
+        self._inst_file = os.path.join(data_dir, "template_ENGINX_241391_236516_North_bank.prm")
+
+        self._path_to_gsas = _GSASFinder.GSASIIscriptable_location()
+        if self._path_to_gsas is None:
+            self.skipTest("Could not find GSASIIscriptable.py")
+
+        temp_dir = tempfile.gettempdir()
+        self._gsas_proj = os.path.join(temp_dir, "GSASIIRefineFitPeaksTest.gpx")
+
+        spectrum_file = os.path.join(data_dir, "focused_bank1_ENGINX00256663.nxs")
+        self._input_ws = mantid.Load(Filename=spectrum_file, OutputWorkspace="input")
+
+    def tearDown(self):
+        if os.path.isfile(self._gsas_proj):
+            os.remove(self._gsas_proj)
+
+    def test_rietveld_refinement_with_default_params(self):
+        gof, rwp, lattice_table = mantid.GSASIIRefineFitPeaks(RefinementMethod="Rietveld refinement",
+                                                              InputWorkspace=self._input_ws,
+                                                              PhaseInfoFile=self._phase_file,
+                                                              InstrumentFile=self._inst_file,
+                                                              PathToGSASII=self._path_to_gsas,
+                                                              SaveGSASIIProjectFile=self._gsas_proj,
+                                                              MuteGSASII=True)
+
+        self.assertAlmostEqual(gof, 3.57776, delta=1e-6)
+        self.assertAlmostEquals(rwp, 77.75499, delta=1e6)
+        row = lattice_table.row(0)
+        self.assertAlmostEqual(row["a"], 2.8665)
+        self.assertAlmostEqual(row["b"], 2.8665)
+        self.assertAlmostEqual(row["c"], 2.8665)
+        self.assertAlmostEqual(row["alpha"], 90)
+        self.assertAlmostEqual(row["beta"], 90)
+        self.assertAlmostEqual(row["gamma"], 90)
+        self.assertAlmostEqual(row["volume"], 23.554, delta=1e4)
+
+    def test_pawley_refinement_with_default_params(self):
+        gof, rwp, lattice_table = mantid.GSASIIRefineFitPeaks(RefinementMethod="Pawley refinement",
+                                                              InputWorkspace=self._input_ws,
+                                                              PhaseInfoFile=self._phase_file,
+                                                              InstrumentFile=self._inst_file,
+                                                              PathToGSASII=self._path_to_gsas,
+                                                              SaveGSASIIProjectFile=self._gsas_proj,
+                                                              MuteGSASII=True)
 
+        self.assertAlmostEqual(gof, 3.57847, delta=1e-6)
+        self.assertAlmostEquals(rwp, 77.75515, delta=1e6)
+        row = lattice_table.row(0)
+        self.assertAlmostEqual(row["a"], 2.8665)
+        self.assertAlmostEqual(row["b"], 2.8665)
+        self.assertAlmostEqual(row["c"], 2.8665)
+        self.assertAlmostEqual(row["alpha"], 90)
+        self.assertAlmostEqual(row["beta"], 90)
+        self.assertAlmostEqual(row["gamma"], 90)
+        self.assertAlmostEqual(row["volume"], 23.554, delta=1e4)
 
 if __name__ == '__main__':
     unittest.main()

Testing/Data/SystemTest/FE_ALPHA.cif.md5

+b184c411cf657178803326c733b2a34c
\ No newline at end of file

Testing/Data/SystemTest/focused_bank1_ENGINX00256663.nxs.md5

+5e52c1fa6927d04649b6456e70a07999
\ No newline at end of file

Testing/Data/SystemTest/template_ENGINX_241391_236516_North_bank.prm.md5

+093020d8461c62709297603faf712449
\ No newline at end of file

docs/source/algorithms/GSASIIRefineFitPeaks-v1.rst

@@ -11,31 +11,19 @@ Description
 
 .. warning::
 
-   This algorithm is experimental and at the moment is being developed
-   for a specific technique. It might be changed, renamed or even
-   removed without a notification, should instrument scientists decide
-   to do so.
-
-.. warning::
-
-   This algorithm requires GSAS-II, with custom modifications to
-   enable it to be used from Mantid. Please contact the Mantid
-   developers for details. The GSAS-II installation instructions are
-   available from the `GSAS-II website
-   <https://subversion.xray.aps.anl.gov/trac/pyGSAS>`_.
+   This algorithm requires GSAS-II to be installed on your computer. A
+   version of GSAS-II containing the module GSASIIscriptable (added in
+   April 2017) is required.
 
 Uses `GSAS-II <https://subversion.xray.aps.anl.gov/trac/pyGSAS>`_
 [TobyVonDreele2013]_ as external software to fit peaks to a powder /
 engineering diffraction pattern. Here the process of peak fitting is
 in the context of Rietveld / Pawley / Le Bail analysis [LeBail2005]_
 
-The algorithm supports three refinement or fitting methods: Pawley
-refinement, Rietveld refinement, and single peak fitting (or "Peaks
-List" of GSAS-II). The first two methods of this algorithm implement
-whole diffraction pattern fitting whereas the third method fits peaks
-individually.  The use of this algorithm is very close to the examples
-described in these two GSAS-II tutorials: `Rietveld fitting / CW
-Neutron Powder fit for Yttrium-Iron Garnet
+The algorithm supports two refinement methods: Pawley refinement and
+Rietveld refinement. The use of this algorithm is very close to the
+examples described in these two GSAS-II tutorials: `Rietveld fitting /
+CW Neutron Powder fit for Yttrium-Iron Garnet
 <https://subversion.xray.aps.anl.gov/pyGSAS/Tutorials/CWNeutron/Neutron%20CW%20Powder%20Data.htm>`_,
 and `Getting started / Fitting individual peaks & autoindexing
 <https://subversion.xray.aps.anl.gov/pyGSAS/Tutorials/FitPeaks/Fit%20Peaks.htm>`_,
@@ -46,42 +34,28 @@ and the `structure routines
 <https://subversion.xray.aps.anl.gov/pyGSAS/sphinxdocs/build/html/GSASIIstruc.html>`_
 of GSAS-II.
 
-To run this algorithm GSAS-II must be installed and it must be
-available for importing from the Mantid Python interpreter. This
-algorithm requires a modified version of GSAS-II. Please contact the
-developers for details.
-
-The methods "Pawley refinement" and "Rietveld refinement" of this
-algorithm are equivalent to the function "Calculate / Refine" from the
-main menu of the GSAS-II GUI.  The method "Peak fitting" is equivalent
-to the "Peak Fitting / Peak fit" action of the "Peaks List" window
-menu of the GSAS-II GUI.
+The refinement methods of this algorithm are equivalent to the
+function "Calculate / Refine" from the main menu of the GSAS-II GUI.
 
 The main inputs required are histogram data, an instrument definition
-parameter (in GSAS format, readable by GSAS-II), and various
-parameters for the fitting/refinement process. Phase information is
-also required to use the Pawley and Rietveld refinement.
+parameter (in GSAS format, readable by GSAS-II), phase information and
+various parameters for the fitting/refinement process.
 
 The phase information must be provided in `CIF format
 (Crystallographic Information File)
 <https://en.wikipedia.org/wiki/Crystallographic_Information_File>`_.
-When phase information is available and the Rietveld/Pawley method is
-used the algorithm will output the lattice parameters in a table
-workspace. The values are given for the the full set of lattice
-parameters (three lattice constants, three angles, and volume in this
-sequence: a, b, c, alpha, beta, gamma, volume). The a,b, and c values
-are given in Angstroms (:math:`\mathrm{\AA{}}`). The angles are given
-in degrees, and the volume in :math:`\mathrm{\AA{}}^3`.
+When phase information is available the algorithm will output the
+lattice parameters in a table workspace. The values are given for the
+the full set of lattice parameters (three lattice constants, three
+angles, and volume in this sequence: a, b, c, alpha, beta, gamma,
+volume). The a,b, and c values are given in Angstroms
+(:math:`\mathrm{\AA{}}`). The angles are given in degrees, and the
+volume in :math:`\mathrm{\AA{}}^3`.
 
 The algorithm provides goodness-of-fit estimates in the outputs *GoF*
 and *Rwp* or weighted profile R-factor [Toby2008]_. The *Rwp* is given
 as a percentage value.
 
-Note that the option to save the GSAS-II project file
-(*SaveGSASIIProjectFile*) is mandatory. This is a requirement of
-GSAS-II. These project files can be opened in the GSAS-II GUI for
-further processing and analysis of the data.
-
 When Pawley refinement is selected as refinement method the flag for
 histogram scale factor refinement is disabled, as recommended in the
 `GSAS-II documentation
@@ -95,23 +69,6 @@ the same name as the output GSAS-II project file but with extension
 ".lst". This is noted in a log message that specifies where the file
 has been written (next to the output project file).
 
-When fitting individual peaks using the peak fitting method (not using
-Rietveld/Pawley refinement), the algorithm only supports peaks with
-shape of type back-to-back exponential convoluted with pseudo-voigt
-(BackToBackExponentialPV). It is possible to enable the refinement of
-the different function parameters via several properties (RefineAlpha,
-RefineSigma, etc.). The fitted peak parameters are given in an output
-table with as many rows as peaks have been found. The columns of the
-table give the parameters fitted, similarly to the information found
-in the "Peaks List" window of the GSAS-II GUI. These results are
-printed in the log messages as well.
-
-.. seealso:: For fitting single peaks, one at a time, :ref:`EnggFitPeaks
-             <algm-EnggFitPeaks>`. For other algorithms that implement different
-             variants of whole diffraction pattern refinement and fitting by
-             :ref:`PawleyFit <algm-PawleyFit>` and :ref:`LeBailFit <algm-LeBailFit>`.
-
-
 *References*:
 
 .. [LeBail2005] Le Bail, A (2005). "Whole Powder Pattern Decomposition Methods and
@@ -128,6 +85,13 @@ printed in the log messages as well.
 Usage
 -----
 
+.. warning::
+
+   Take these usage examples with a pinch of salt, as they are not
+   tested for correctness on our servers, due to the requirement to
+   have GSAS-II installed. Please contact the Mantid developers if
+   something is awry.
+   
 **Example - Pawley refinement of lattice parameters from a diffraction spectrum**
 
 .. code-block:: python
@@ -145,11 +109,11 @@ Usage
    #
    wks=Load('focused_bank1_ENGINX00256663.nxs')
    GoF, Rwp, lattice_tbl = GSASIIRefineFitPeaks(InputWorkspace=wks,
-                                                InstrumentFile='ENGINX_255924_254854_North_bank.par',
+                                                RefinementMethods="PawleyRefinement",
+                                                InstrumentFile='template_ENGINX_241391_236516_North_bank.prm',
                                                 PhaseInfoFile='FE_ALPHA.cif',
                                                 PathToGSASII='/home/user/gsas',
-                                                SaveGSASIIProjectFile='example_gsas2_project',
-                                                LatticeParameters='lattice_tbl')
+                                                SaveGSASIIProjectFile='example_gsas2_project')
    print "Goodness of fit coefficient: {0:.5f}".format(GoF)
    print "Weighted profile R-factor (Rwp): {0:.5f}".format(Rwp)
    print ("Lattice parameters, a: {a}, b: {b}, c: {c}, alpha: {alpha}, beta: {beta}, gamma: {gamma}, "
@@ -159,8 +123,8 @@ Output:
 
 .. code-block:: none
 
-    Goodness of fit coefficient: 3.63591
-    Weighted profile R-factor (Rwp): 77.27831
+    Goodness of fit coefficient: 3.57776
+    Weighted profile R-factor (Rwp): 77.75449
     Lattice parameters, a: 2.8665, b: 2.8665, c: 2.8665, alpha: 90.0, beta: 90.0, gamma: 90.0, Volume: 23.554
 
 **Example - Rietveld refinement of lattice parameters from a diffraction spectrum**
@@ -169,12 +133,11 @@ Output:
 
    wks=Load('focused_bank1_ENGINX00256663.nxs')
    GoF, Rwp, lattice_tbl = GSASIIRefineFitPeaks(InputWorkspace=wks,
-                                                Method='Rietveld refinement',
-                                                InstrumentFile='ENGINX_255924_254854_North_bank.par',
+                                                RefinementMethod='Rietveld refinement',
+                                                InstrumentFile='template_ENGINX_241391_236516_North_bank.prm',
                                                 PhaseInfoFile='FE_ALPHA.cif',
                                                 PathToGSASII='/home/user/gsas',
                                                 SaveGSASIIProjectFile='example_gsas2_project',
-                                                LatticeParameters='lattice_tbl')
    print "Goodness of fit coefficient: {0:.5f}".format(GoF)
    print "Weighted profile R-factor (Rwp): {0:.5f}".format(Rwp)
    print ("Lattice parameters, a: {a}, b: {b}, c: {c}, alpha: {alpha}, beta: {beta}, gamma: {gamma}, "
@@ -184,37 +147,10 @@ Output:
 
 .. code-block:: none
 
-    Goodness of fit coefficient: 3.62483
-    Weighted profile R-factor (Rwp): 77.03530
+    Goodness of fit coefficient: 3.57847
+    Weighted profile R-factor (Rwp): 77.75515
     Lattice parameters, a: 2.8665, b: 2.8665, c: 2.8665, alpha: 90.0, beta: 90.0, gamma: 90.0, Volume: 23.554
 
-**Example - Fit several peaks from a diffraction spectrum**
-
-.. code-block:: python
-
-   wks=Load('focused_bank1_ENGINX00256663.nxs')
-   params_tbl_name = 'tbl_fitted_params'
-   GoF, Rwp, lattice_tbl = GSASIIRefineFitPeaks(InputWorkspace=wks,
-                                                Method='Peak fitting',
-                                                FittedPeakParameters=params_tbl_name,
-                                                InstrumentFile='ENGINX_255924_254854_North_bank.par',
-                                                PhaseInfoFile='FE_ALPHA.cif',
-                                                PathToGSASII='/home/user/mantid-repos/gsas',
-                                                SaveGSASIIProjectFile='test_gsas2_project',
-                                                FittedPeakParameters=params_tbl_name)
-   tbl_fitted_params = mtd[params_tbl_name]
-   print "Fitted {0} peaks.".format(tbl_fitted_params.rowCount())
-   print ("Parameters of the first peak. Center: {Center:.6g}, intensity: {Intensity:.5f}, "
-          "alpha: {Alpha:.5f}, beta: {Beta:.5f}, sigma: {Sigma:.5f}, gamma: {Gamma:.5f}".
-          format(**tbl_fitted_params.row(0)))
-
-Output:
-
-.. code-block:: none
-
-    Fitted 18 peaks.
-    Parameters of the first peak. Center: 38563.8, intensity: 26.22137, alpha: 0.13125, beta: 0.01990, sigma: 125475.11036, gamma: -6681.38965
-
 .. categories::
 
 .. sourcelink::

docs/source/release/v3.12.0/diffraction.rst

@@ -22,6 +22,9 @@ Powder Diffraction
 Engineering Diffraction
 -----------------------
 
+- :ref:`algm-GSASIIRefineFitPeaks>` has been re-integrated with the
+  latest version of GSAS-II, allowing Rietveld and Pawley refinement
+  within Mantid.
 - Usability improvements in the GUI:
   - The "Invalid RB number" popup window in the GUI has been replaced with a more user-friendly message
   - Improved progress reporting for Calibration and Focus