Add gudpy inelasticity optimiser

gudpy/core/gudpy.py

@@ -591,56 +591,6 @@ def iterate(self, purge) -> typ.Tuple[int, str]:
         return self.exitcode
 
 
-class InelasiticityIterator(GudrunIterator):
-    def __init__(
-        self,
-        gudrunFile: GudrunFile,
-        iterator: iterators.Iterator,
-    ):
-
-        super().__init__(
-            gudrunFile=gudrunFile,
-            iterator=iterator
-        )
-
-    def singleIteration(
-        self,
-        gudrunFile: GudrunFile,
-        gudrun: Gudrun,
-        purge: Purge,
-    ) -> typ.Tuple[int, str]:  # (exitcode, error)
-        modGfFile = self.iterator.performIteration(gudrunFile)
-        exitcode = gudrun.gudrun(modGfFile, purge, self.iterator)
-        if exitcode:
-            return exitcode
-        return 0
-
-    def iterate(self, purge) -> typ.Tuple[int, str]:
-        # If the iterator requires a prelimenary run
-        if self.iterator.requireDefault:
-            exitcode = self.gudrunObjects[0].gudrun(
-                self.gudrunFile, purge, self.iterator)
-            if exitcode:  # An exit code != 0 indicates failure
-                self.exitcode = (exitcode, self.gudrunObjects[0].error)
-                return self.exitcode
-
-        # Iterate through gudrun objects
-        for gudrun in self.gudrunObjects:
-            if gudrun.output:
-                # If object has already been run, skip
-                continue
-            exitcode = self.singleIteration(
-                self.gudrunFile, gudrun, purge)
-            if exitcode:  # An exit code != 0 indicates failure
-                self.exitcode = (exitcode, gudrun.error)
-                return self.exitcode
-
-        self.result = self.iterator.result
-
-        self.exitcode = (0, "")
-        return self.exitcode
-
-
 class CompositionIterator:
     def __init__(
         self,

gudpy/core/iterators.py

@@ -568,7 +568,7 @@ def performIteration(self, gudrunFile):
             self.iterationCount += 1
         else:
             self.QIteration(gudrunFile)
-            self.nCurrent += 1
+        self.nCurrent += 1
         return gudrunFile
 
     def organiseOutput(self, gudrunFile, exclude=[]):

gudpy/core/optimise.py

@@ -1,7 +1,9 @@
 import skopt
 import os
 import tempfile
+import copy
 from scipy.optimize import minimize
+import shutil
 
 import gudpy_cli as cli
 from core import data
@@ -12,9 +14,55 @@
 from core.sample import Sample
 
 
-class ParameterOptimisation:
-    def __init__(self):
-        pass
+class InelasticityOptimisation:
+    def __init__(
+        self,
+        gudrunFile: GudrunFile,
+    ):
+        self.originalGudrunFile = copy.deepcopy(gudrunFile)
+        self.gudrunIterators = gudpy.GudrunIterator(
+            gudrunFile, iterators.InelasticitySubtraction(3))
+        self.samples = {}
+        self.results = {}
+
+        for sample in gudrunFile.runSamples():
+            if not sample.mse:
+                continue
+
+            self.mse[sample.name]["initial"] = copy.deepcopy(sample)
+
+    def optimise(self, purge: gudpy.Purge):
+        for i, gudrun in enumerate(self.gudrunIterators.gudrunObjects):
+            exitcode = self.gudrunIterators.singleIteration(
+                self.gudrunIterators.gudrunFile, gudrun, purge)
+            if exitcode:  # An exit code != 0 indicates failure
+                self.exitcode = (exitcode, gudrun.error)
+                return self.exitcode
+            if self.gudrunIterators.iterator.iterationType == "QIteration":
+                for sample in self.gudrunIterators.gudrunFile.runSamples():
+                    self.mse[sample.name][i] = copy.deepcopy(sample)
+
+        for sample in self.originalGudrunFile.runSamples():
+            self.results[sample.name]["bestSample"] = (
+                self.mse[sample.name]["initial"]
+            )
+            self.results[sample.name]["bestIt"] = "initial"
+            for iteration, sample in self.mse[sample.name]:
+                if sample.mse < self.results[sample.name]["bestSample"]:
+                    self.results[sample.name]["bestSample"] = sample
+                    self.results[sample.name]["bestIt"] = iteration
+
+        return self.results
+
+    def exportResults(self, path):
+        utils.makeDir(path)
+        for sample in self.originalGudrunFile.runSamples():
+            bestMint = (
+                self.results[sample.name]["bestSample"].dataFiles[0].mintFile
+            )
+            shutil.copyfile(bestMint, os.path.join(
+                path, f"{sample.name}.mint01"
+            ))
 
 
 class BayesianOptimisation:

gudpy/core/sample.py

@@ -7,6 +7,7 @@
 )
 from core import utils
 from core import config
+from core import data
 
 
 class Sample:
@@ -145,17 +146,40 @@ def __init__(self):
         self.containers = []
 
         self.yamlignore = {
-            "yamlignore"
+            "yamlignore",
         }
 
         self.outputFolder = ""
         self.sampleFile = ""
         self.selfScatteringFilePath = ""
 
+        self._referenceDataFile = ""
+
     @property
     def gudFile(self):
         return self.dataFiles[0].gudFile
 
+    @property
+    def referenceDataFile(self):
+        return self._referenceDataFile
+
+    @referenceDataFile.setter
+    def referenceDataFile(self, path):
+        self._referenceDataFile = path
+        self.referenceData = data.NpDataSet(path)
+
+    @property
+    def referenceData(self):
+        return data.NpDataSet(self._referenceDataFile)
+
+    @property
+    def mse(self):
+        if not self.dataFiles[0].mintFile or self.referenceData:
+            return None
+        expData = data.NpDataSet(self.dataFiles[0].mintFile)
+        mse = data.meanSquaredError(self.referenceData, expData)
+        return mse
+
     def pathName(self):
         return utils.replace_unwanted_chars(self.name).translate(
             {ord(x): '' for x in r'/\!*~,&|[]'}

gudpy/test/TestData/NIMROD-water/good_water/good_water.yaml

@@ -236,6 +236,7 @@ sampleBackgrounds:
     outputFolder: ''
     sampleFile: ''
     selfScatteringFilePath: ''
+    _referenceDataFile: "",
   - name: D2O,_Can_N10
     periodNumber: 1
     dataFiles:
@@ -344,6 +345,7 @@ sampleBackgrounds:
     outputFolder: ''
     sampleFile: ''
     selfScatteringFilePath: ''
+    _referenceDataFile: "",
   - name: HDO,_Can_N6
     periodNumber: 1
     dataFiles:
@@ -441,6 +443,7 @@ sampleBackgrounds:
     outputFolder: ''
     sampleFile: ''
     selfScatteringFilePath: ''
+    _referenceDataFile: "",
   - name: Null_Water,_Can_N8
     periodNumber: 1
     dataFiles:
@@ -538,5 +541,6 @@ sampleBackgrounds:
     outputFolder: ''
     sampleFile: ''
     selfScatteringFilePath: ''
+    _referenceDataFile: "",
   outputFolder: ''
 GUI: {useComponents: false}

gudpy/test/test_gudpy_io.py

@@ -466,6 +466,7 @@ def setUp(self) -> None:
             "outputFolder": '',
             "sampleFile": '',
             "selfScatteringFilePath": '',
+            "_referenceDataFile": "",
             "yamlignore": {
                 "yamlignore",
             }
@@ -524,6 +525,7 @@ def setUp(self) -> None:
             "outputFolder": '',
             "sampleFile": '',
             "selfScatteringFilePath": '',
+            "_referenceDataFile": "",
             "yamlignore": {
                 "yamlignore"
             }
@@ -582,6 +584,7 @@ def setUp(self) -> None:
             "outputFolder": '',
             "sampleFile": '',
             "selfScatteringFilePath": '',
+            "_referenceDataFile": "",
             "yamlignore": {
                 "yamlignore"
             }
@@ -641,6 +644,7 @@ def setUp(self) -> None:
             "outputFolder": '',
             "sampleFile": '',
             "selfScatteringFilePath": '',
+            "_referenceDataFile": "",
             "yamlignore": {
                 "yamlignore"
             }
@@ -1312,6 +1316,8 @@ def testLoadMissingSampleAttributesSeq(self):
         expectedSampleA.pop("outputFolder", None)
         expectedSampleA.pop("sampleFile", None)
         expectedSampleA.pop("selfScatteringFilePath", None)
+        expectedSampleA.pop("_referenceDataFile", None)
+
         expectedSampleA.pop("yamlignore", None)
 
         self.goodSampleBackground.samples[0].dataFiles = DataFiles([], "")
@@ -1366,6 +1372,7 @@ def testLoadMissingSampleAttributesRand(self):
         expectedSampleA.pop("outputFolder", None)
         expectedSampleA.pop("sampleFile", None)
         expectedSampleA.pop("selfScatteringFilePath", None)
+        expectedSampleA.pop("_referenceDataFile", None)
         expectedSampleA.pop("yamlignore", None)
 
         self.goodSampleBackground.samples[0].dataFiles = DataFiles([], "")