Test iterators (#332)

* tests: iterate by thickness.

* tests: test composition iterator.

src/gudrun_classes/composition_iterator.py

@@ -90,7 +90,7 @@ class CompositionIterator():
         Performs n iterations using cost function f, args and bounds.
     """
     def __init__(self, gudrunFile):
-        self.gudrunFile = deepcopy(gudrunFile)
+        self.gudrunFile = gudrunFile
         self.components = []
         self.ratio = 0
 
@@ -133,8 +133,7 @@ def setComponents(self, components, ratio=1):
         Target Sample Background.
     """
     def processSingleComponent(self, x, sampleBackground):
-        gudrunFile = deepcopy(self.gudrunFile)
-        gudrunFile.sampleBackgrounds = [sampleBackground]
+        self.gudrunFile.sampleBackgrounds = [sampleBackground]
 
         x = abs(x)
         weightedComponents = [
@@ -148,16 +147,16 @@ def processSingleComponent(self, x, sampleBackground):
             component.ratio = x
 
         sampleBackground.samples[0].composition.translate()
-        gudrunFile.process()
+        self.gudrunFile.process()
 
         time.sleep(1)
         gudPath = sampleBackground.samples[0].dataFiles.dataFiles[0].replace(
-                    gudrunFile.instrument.dataFileType,
+                    self.gudrunFile.instrument.dataFileType,
                     "gud"
                 )
         gudFile = GudFile(
             os.path.join(
-                gudrunFile.instrument.GudrunInputFileDir, gudPath
+                self.gudrunFile.instrument.GudrunInputFileDir, gudPath
             )
         )
 
@@ -179,8 +178,7 @@ def processSingleComponent(self, x, sampleBackground):
         Sum of molecules of both components.
     """
     def processTwoComponents(self, x, sampleBackground, totalMolecules):
-        gudrunFile = deepcopy(self.gudrunFile)
-        gudrunFile.sampleBackgrounds = [sampleBackground]
+        self.gudrunFile.sampleBackgrounds = [sampleBackground]
         x = abs(x)
         wcA = wcB = None
         for weightedComponent in (
@@ -196,16 +194,16 @@ def processTwoComponents(self, x, sampleBackground, totalMolecules):
             wcB.ratio = abs(totalMolecules - x)
 
         sampleBackground.samples[0].composition.translate()
-        gudrunFile.process()
+        self.gudrunFile.process()
 
         time.sleep(1)
         gudPath = sampleBackground.samples[0].dataFiles.dataFiles[0].replace(
-                    gudrunFile.instrument.dataFileType,
+                    self.gudrunFile.instrument.dataFileType,
                     "gud"
                 )
         gudFile = GudFile(
             os.path.join(
-                gudrunFile.instrument.GudrunInputFileDir, gudPath
+                self.gudrunFile.instrument.GudrunInputFileDir, gudPath
             )
         )
 
@@ -232,7 +230,7 @@ def processTwoComponents(self, x, sampleBackground, totalMolecules):
     rtol : float
         Relative tolerance
     """
-    def iterate(self, n=10, rtol=10):
+    def iterate(self, n=10, rtol=10.):
         if not self.components or not self.ratio:
             return None
         # Only include samples that are marked for analysis.

tests/test_gudpy_workflows.py

@@ -1,13 +1,15 @@
+from copy import deepcopy
 import os
 from shutil import copyfile
 from unittest import TestCase
 import re
 import math
-
+from src.gudrun_classes.composition import Composition, Component
 from src.gudrun_classes.gudrun_file import GudrunFile
 from src.gudrun_classes.thickness_iterator import ThicknessIterator
 from src.gudrun_classes.density_iterator import DensityIterator
 from src.gudrun_classes.tweak_factor_iterator import TweakFactorIterator
+from src.gudrun_classes.composition_iterator import CompositionIterator
 from src.gudrun_classes.gud_file import GudFile
 from src.gudrun_classes.wavelength_subtraction_iterator import (
     WavelengthSubtractionIterator
@@ -281,6 +283,89 @@ def testGudPyIterateByDensity(self):
         dcsLevelPercentage = float(dcsLevelPercentage.replace('%', ''))
         self.assertAlmostEqual(dcsLevelPercentage, 100.0, 0)
 
+    def testIterateByThickness(self):
+
+        self.g.purge()
+        thicknessIterator = ThicknessIterator(self.g)
+        thicknessIterator.iterate(5)
+
+        gfPath = self.g.sampleBackgrounds[0].samples[0].dataFiles.dataFiles[0]
+        gfPath = gfPath.replace(self.g.instrument.dataFileType, 'gud')
+        gf1 = GudFile(
+            os.path.join(
+                self.g.instrument.GudrunInputFileDir, gfPath
+            )
+        )
+        dcsLevelPercentage = re.findall(r'\d*[.]?\d*%', gf1.result)[0]
+        dcsLevelPercentage = float(dcsLevelPercentage.replace('%', ''))
+        self.assertAlmostEqual(dcsLevelPercentage, 100.0, 0)
+
+        gfPath = self.g.sampleBackgrounds[0].samples[1].dataFiles.dataFiles[0]
+        gfPath = gfPath.replace(self.g.instrument.dataFileType, 'gud')
+        gf2 = GudFile(
+            os.path.join(
+                self.g.instrument.GudrunInputFileDir, gfPath
+            )
+        )
+        dcsLevelPercentage = re.findall(r'\d*[.]?\d*%', gf2.result)[0]
+        dcsLevelPercentage = float(dcsLevelPercentage.replace('%', ''))
+        self.assertAlmostEqual(dcsLevelPercentage, 100.0, 0)
+
+        gfPath = self.g.sampleBackgrounds[0].samples[2].dataFiles.dataFiles[0]
+        gfPath = gfPath.replace(self.g.instrument.dataFileType, 'gud')
+        gf3 = GudFile(
+            os.path.join(
+                self.g.instrument.GudrunInputFileDir, gfPath
+            )
+        )
+        dcsLevelPercentage = re.findall(r'\d*[.]?\d*%', gf3.result)[0]
+        dcsLevelPercentage = float(dcsLevelPercentage.replace('%', ''))
+        self.assertAlmostEqual(dcsLevelPercentage, 100.0, 0)
+
+        gfPath = self.g.sampleBackgrounds[0].samples[3].dataFiles.dataFiles[0]
+        gfPath = gfPath.replace(self.g.instrument.dataFileType, 'gud')
+        gf4 = GudFile(
+            os.path.join(
+                self.g.instrument.GudrunInputFileDir, gfPath
+            )
+        )
+        dcsLevelPercentage = re.findall(r'\d*[.]?\d*%', gf4.result)[0]
+        dcsLevelPercentage = float(dcsLevelPercentage.replace('%', ''))
+        self.assertAlmostEqual(dcsLevelPercentage, 100.0, 0)
+
+    def testIterateByComposition(self):
+
+        g = deepcopy(self.g)
+        g.purge()
+
+        g.sampleBackgrounds[0].samples[0].runThisSample = False
+        g.sampleBackgrounds[0].samples[2].runThisSample = False
+        g.sampleBackgrounds[0].samples[3].runThisSample = False
+        sample = g.sampleBackgrounds[0].samples[1]
+
+        composition = Composition("Sample")
+
+        h2 = Component("H[2]")
+        h2.parse()
+        o = Component("O")
+        o.parse()
+
+        composition.addComponent(h2, 1)
+        composition.addComponent(o, 1)
+
+        sample.composition = composition
+
+        compositionIterator = CompositionIterator(g)
+        compositionIterator.setComponent(h2, 1)
+        compositionIterator.iterate(10, 3)
+        self.assertAlmostEqual(
+            sample.composition.weightedComponents[0].ratio, 2, 1
+        )
+
+        self.assertEqual(
+            sample.composition.weightedComponents[1].ratio, 1
+        )
+
     def testGudPyIterateBySubtractingWavelength(self):
 
         for i in range(1, 4):