Implement passing constraints as arg

Previously the constraints argument was disabled because
I did not find a way to pass Python objects (tuple of dictionaries) into
the mantid algorithm.

This workaround converts the tuple of dictionaries into a byte string
using the dill library which can then be converted to a normal string and
passed into the mantid algorithm as an argument.
When the algorithm executes, the string is converted into byte string again
though eval() and then into the tuple of dicts of lambdas by the dill library.

A better solution might be implemented in the future but this will suffice for now.

environment.yml

@@ -18,3 +18,4 @@ dependencies:
   - pytest
   - jacobi==0.4.2 #pinned until newer versions functionality confirmed
   - coverage
+  - dill

pyproject.toml

@@ -26,6 +26,7 @@ dependencies = [
     "iminuit",
     "h5py",
     "jacobi==0.4.2",
+    "dill",
 ]
 
 [project.optional-dependencies]

src/mvesuvio/analysis_reduction.py

@@ -1,6 +1,7 @@
 import numpy as np 
 import matplotlib.pyplot as plt
 import scipy
+import dill      # Only for converting constraints from string
 from mantid.kernel import StringListValidator, Direction, IntArrayBoundedValidator, IntArrayProperty,\
      IntBoundedValidator, FloatBoundedValidator
 from mantid.api import FileProperty, FileAction, PythonAlgorithm, MatrixWorkspaceProperty
@@ -11,7 +12,7 @@
                             VesuvioThickness, Integration, Divide, Multiply, DeleteWorkspaces, \
                             CreateWorkspace, CreateSampleWorkspace
 
-from mvesuvio.util.analysis_helpers import loadConstants, numericalThirdDerivative
+from mvesuvio.util.analysis_helpers import deserialize_lambdas, loadConstants, numericalThirdDerivative
 
 
 
@@ -37,7 +38,7 @@ def PyInit(self):
             name="InputProfiles",
             defaultValue="",
             direction=Direction.Input),
-            doc="Table workspace containing starting parameters for profiles"
+            doc="Table workspace containing starting parameters for profiles."
         )
         self.declareProperty(FileProperty(
             name='InstrumentParametersFile', 
@@ -61,17 +62,17 @@ def PyInit(self):
             name="InvalidDetectors",
             validator=IntArrayBoundedValidator(lower=3, upper=198),
             direction=Direction.Input),
-            doc="List of invalid detectors whithin range 3-198"
+            doc="List of invalid detectors whithin range 3-198."
         )
         self.declareProperty(
             name="MultipleScatteringCorrection", 
             defaultValue=False, 
-            doc="Whether to run multiple scattering correction"
+            doc="Whether to run multiple scattering correction."
         )
         self.declareProperty(
             name="GammaCorrection", 
             defaultValue=False, 
-            doc="Whether to run gamma correction"
+            doc="Whether to run gamma correction."
         )
         self.declareProperty(
             name="SampleVerticalWidth",
@@ -99,11 +100,11 @@ def PyInit(self):
             defaultValue="",
             doc="Directory where to save analysis results."
         )
-        # self.declareProperty(
-        #     name="Constraints",
-        #     defaultValue=(),
-        #     doc="Constraints to use during fitting profiles."
-        # )
+        self.declareProperty(
+            name="Constraints",
+            defaultValue="",
+            doc="Constraints to use during fitting profiles."
+        )
         self.declareProperty(
             name="TransmissionGuess",
             defaultValue=-1.0,
@@ -122,12 +123,12 @@ def PyInit(self):
         self.declareProperty(
             name="ResultsPath",
             defaultValue="",
-            doc="Directory to store results, to be deleted later"
+            doc="Directory to store results, to be deleted later."
         )
         self.declareProperty(
             name="FiguresPath",
             defaultValue="",
-            doc="Directory to store figures, to be deleted later"
+            doc="Directory to store figures, to be deleted later."
         )
         # Outputs
         self.declareProperty(TableWorkspaceProperty(
@@ -158,7 +159,7 @@ def _setup(self):
         self._save_results_path = self.getProperty("ResultsPath").value
         self._save_figures_path = self.getProperty("FiguresPath").value 
         self._h_ratio = self.getProperty("HRatioToLowestMass").value 
-        self._constraints = () #self.getProperty("Constraints").value 
+        self._constraints = dill.loads(eval(self.getProperty("Constraints").value))
 
         self._profiles_table = self.getProperty("InputProfiles").value
 

src/mvesuvio/analysis_routines.py

@@ -3,10 +3,11 @@
 from mantid.simpleapi import CreateEmptyTableWorkspace, mtd, RenameWorkspace
 from mantid.api import AlgorithmFactory, AlgorithmManager
 import numpy as np
+import dill         # To convert constraints to string
 
 from mvesuvio.util.analysis_helpers import fix_profile_parameters,  \
                             loadRawAndEmptyWsFromUserPath, cropAndMaskWorkspace, \
-                            NeutronComptonProfile, calculate_h_ratio
+                            NeutronComptonProfile, calculate_h_ratio, serialize_lambdas
 from mvesuvio.analysis_reduction import AnalysisRoutine
 from tests.testhelpers.calibration.algorithms import create_algorithm
 
@@ -56,7 +57,7 @@ def _create_analysis_object_from_current_interface(IC, running_tests=False):
         "TransmissionGuess": IC.transmission_guess,
         "MultipleScatteringOrder": int(IC.multiple_scattering_order),
         "NumberOfEvents": int(IC.number_of_events),
-        # Constraints"": IC.constraints,
+        "Constraints": str(dill.dumps(IC.constraints)),
         "ResultsPath": str(IC.resultsSavePath),
         "FiguresPath": str(IC.figSavePath),
         "OutputMeansTable":" Final_Means"

tests/unit/analysis/test_analysis_helpers.py

@@ -1,5 +1,6 @@
 import unittest
 import numpy as np
+import dill
 import numpy.testing as nptest
 from mock import MagicMock
 from mvesuvio.util.analysis_helpers import extractWS, _convert_dict_to_table,  \
@@ -109,10 +110,19 @@ def test_fix_profile_parameters_without_H(self):
 
     def test_calculate_h_ratio(self):
         means_table_mock = MagicMock()
-        means_table_mock.column.side_effect = lambda x: [16, 1, 12] if x is "mass" else [0.1, 0.85, 0.05]
+        means_table_mock.column.side_effect = lambda x: [16, 1, 12] if x=="mass" else [0.1, 0.85, 0.05]
         h_ratio = calculate_h_ratio(means_table_mock)
         self.assertEqual(h_ratio, 0.85 / 0.05)
 
 
+    def test_conversion_of_constraints(self):
+        constraints = ({'type': 'eq', 'fun': lambda par:  par[0] - 2.7527*par[3] },{'type': 'eq', 'fun': lambda par:  par[3] - 0.7234*par[6] })
+        string_constraints = str(dill.dumps(constraints))
+        self.assertIsInstance(string_constraints, str)
+        converted_constraints = dill.loads(eval(string_constraints))
+        self.assertEqual(converted_constraints[0]['fun']([3, 0, 0, 1]), 3-2.7527)
+        self.assertEqual(converted_constraints[1]['fun']([0, 0, 0, 2, 0, 0, 1]), 2-0.7234)
+
+
 if __name__ == "__main__":
     unittest.main()

tests/unit/analysis/test_analysis_reduction.py

@@ -4,33 +4,25 @@
 from mock import MagicMock
 from mvesuvio.analysis_reduction import AnalysisRoutine 
 from mantid.simpleapi import CreateWorkspace, DeleteWorkspace
+import inspect
 
 
 class TestAnalysisFunctions(unittest.TestCase):
     def setUp(self):
         pass
 
-    def test_calculate_h_ratio_masses_ordered(self):
+    def test_constraints_are_passed_correctly(self):
         alg = AnalysisRoutine()
-        alg._mean_intensity_ratios = np.array([0.91175, 0.06286, 0.00732, 0.01806])
-        alg._masses = np.array([1.0079, 12.0, 16.0, 27.0])
-        h_ratio = alg.calculate_h_ratio()
-        self.assertAlmostEqual(14.504454343, h_ratio)
-
-    def test_calculate_h_ratio_masses_unordered(self):
-        alg = AnalysisRoutine()
-        alg._mean_intensity_ratios = np.array([0.00732, 0.06286, 0.01806, 0.91175])
-        alg._masses = np.array([16.0, 12.0, 27.0, 1.0079])
-        h_ratio = alg.calculate_h_ratio()
-        self.assertAlmostEqual(14.504454343, h_ratio)
-
-    def test_calculate_h_ratio_hydrogen_missing(self):
-        alg = AnalysisRoutine()
-        alg._mean_intensity_ratios = np.array([0.00732, 0.06286, 0.01806])
-        alg._masses = np.array([16.0, 12.0, 27.0])
-        h_ratio = alg.calculate_h_ratio()
-        self.assertAlmostEqual(None, h_ratio)
-
+        alg.initialize()
+        constraints = (
+            {'type': 'eq', 'fun': lambda par:  par[0] - 2.7527*par[3] }, {'type': 'eq', 'fun': lambda par:  par[3] - 0.7234*par[6] })
+        for c in constraints:
+            print(inspect.getsourcelines(c['fun'])[0])
+        # alg.setProperty("Constraints", str(constraints))
+        # print(str(constraints))
+        # print(alg.getPropertyValue("Constraints"))
+        # alg_constraints = eval(alg.getPropertyValue("Constraints"))
+        # self.assertEqual(constraints, alg_constraints)
 
 if __name__ == "__main__":
     unittest.main()