Outputs Update #1- Gudrun Output File Organising

gudpy/core/gudrun_file.py

@@ -15,7 +15,8 @@
     firstNInts,
     nthfloat,
     nthint,
-    resolve
+    resolve,
+    uniquifyName
 )
 from core.instrument import Instrument
 from core.beam import Beam
@@ -145,6 +146,7 @@ def __init__(self, path=None, format=Format.YAML, config_=False):
         """
 
         self.path = path
+        self.filename = os.path.basename(path)
         self.yaml = YAML()
         self.format = format
 
@@ -856,8 +858,6 @@ def parseSample(self):
                 str(self.getNextToken()[:-2]).strip()
                 .replace("SAMPLE", "").strip()
             )
-            if not sample.name:
-                sample.name = "SAMPLE"
             self.consumeWhitespace()
             # The number of files and period number are both stored
             # on the same line.
@@ -1063,8 +1063,6 @@ def parseContainer(self):
                 str(self.getNextToken()[:-2]).strip()
                 .replace("CONTAINER", "").strip()
             )
-            if not container.name:
-                container.name = "CONTAINER"
             self.consumeWhitespace()
 
             # The number of files and period number are both stored
@@ -1275,10 +1273,25 @@ def sampleBackgroundHelper(self):
             elif "GO" in line:
                 self.getNextToken()
             elif "SAMPLE" in line and firstword(line) == "SAMPLE":
-                sampleBackground.samples.append(self.makeParse("SAMPLE"))
+                sample = self.makeParse("SAMPLE")
+                if not sample.name:
+                    sample.name = uniquifyName(
+                        "SAMPLE",
+                        [s.name for s in sampleBackground.samples],
+                        sep="",
+                        incFirst=True)
+                sampleBackground.samples.append(sample)
             elif "CONTAINER" in line and firstword(line) == "CONTAINER":
+                container = self.makeParse("CONTAINER")
+                if not container.name:
+                    container.name = uniquifyName(
+                        "CONTAINER",
+                        [c.name
+                         for c in sampleBackground.samples[-1].containers],
+                        sep="",
+                        incFirst=True)
                 sampleBackground.samples[-1].containers.append(
-                    self.makeParse("CONTAINER")
+                    container
                 )
             self.consumeWhitespace()
             line = self.peekNextToken()
@@ -1519,12 +1532,13 @@ def dcs(self, path='', headless=True, iterative=False):
 
         Parameters
         ----------
-        overwrite : bool, optional
-            Overwrite the initial file? (default is False).
         path : str, optional
             Path to parse from (default is empty, which indicates self.path).
-        purge : bool, optional
-            Should detectors be purged?
+        headless : bool, optional
+            Is this being run through CL or GUI?
+        iterative : bool, optional
+            Is Gudrun being iterated?
+
         Returns
         -------
         subprocess.CompletedProcess
@@ -1635,9 +1649,9 @@ def naiveOrganise(self):
         outputFileHandler = OutputFileHandler(self)
         outputFileHandler.naiveOrganise()
 
-    def iterativeOrganise(self, head):
+    def iterativeOrganise(self, nTotal, nCurrent, head):
         outputFileHandler = OutputFileHandler(self)
-        outputFileHandler.iterativeOrganise(head)
+        outputFileHandler.iterativeOrganise(nTotal, nCurrent, head)
 
     def determineError(self, sample):
         gudPath = sample.dataFiles[0].replace(

gudpy/core/composition_iterator.py → gudpy/core/iterators/composition_iterator.py

@@ -17,14 +17,14 @@ def gss(
 
     if (
         (abs(bounds[2] - bounds[0]) / min([abs(bounds[0]), abs(bounds[2])]))
-        < (rtol/100)**2
+        < (rtol / 100)**2
     ):
         if endIterFunc:
             endIterFunc(n)
         return (bounds[2] + bounds[1]) / 2
 
     # Calculate a potential centre = c + 2 - GR * (upper-c)
-    d = bounds[1] + (2 - (1 + math.sqrt(5))/2)*(bounds[2]-bounds[1])
+    d = bounds[1] + (2 - (1 + math.sqrt(5)) / 2) * (bounds[2] - bounds[1])
 
     # If the new centre evaluates to less than the current
     fd1 = f(d, *args)
@@ -43,7 +43,7 @@ def gss(
         if endIterFunc:
             endIterFunc(n)
         return gss(
-            f, bounds, n+1, maxN, rtol,
+            f, bounds, n + 1, maxN, rtol,
             args=args, startIterFunc=startIterFunc, endIterFunc=endIterFunc
         )
     # Otherwise, swap and reverse.
@@ -52,7 +52,7 @@ def gss(
         if endIterFunc:
             endIterFunc()
         return gss(
-            f, bounds, n+1, maxN, rtol,
+            f, bounds, n + 1, maxN, rtol,
             args=args, startIterFunc=startIterFunc, endIterFunc=endIterFunc
         )
 
@@ -103,6 +103,9 @@ class CompositionIterator():
     gss(f, bounds, n, args=())
         Performs n iterations using cost function f, args and bounds.
     """
+
+    name = "IterateByComposition"
+
     def __init__(self, gudrunFile):
         self.gudrunFile = gudrunFile
         self.components = []
@@ -118,6 +121,7 @@ def __init__(self, gudrunFile):
     ratio : int, optional
         Ratio of component.
     """
+
     def setComponent(self, component, ratio=1):
         self.components = [component]
         self.ratio = ratio
@@ -132,6 +136,7 @@ def setComponent(self, component, ratio=1):
     ratio : int, optional
         Ratio of component.
     """
+
     def setComponents(self, components, ratio=1):
         self.components = [c for c in components if c]
         self.ratio = ratio
@@ -146,6 +151,7 @@ def setComponents(self, components, ratio=1):
     sampleBackground : SampleBackground
         Target Sample Background.
     """
+
     def processSingleComponent(self, x, sampleBackground):
         self.gudrunFile.sampleBackgrounds = [sampleBackground]
 
@@ -165,9 +171,9 @@ def processSingleComponent(self, x, sampleBackground):
 
         time.sleep(1)
         gudPath = sampleBackground.samples[0].dataFiles[0].replace(
-                    self.gudrunFile.instrument.dataFileType,
-                    "gud"
-                )
+            self.gudrunFile.instrument.dataFileType,
+            "gud"
+        )
         gudFile = GudFile(
             os.path.join(
                 self.gudrunFile.instrument.GudrunInputFileDir, gudPath
@@ -177,7 +183,7 @@ def processSingleComponent(self, x, sampleBackground):
         if gudFile.averageLevelMergedDCS == gudFile.expectedDCS:
             return 0
         else:
-            return (gudFile.expectedDCS-gudFile.averageLevelMergedDCS)**2
+            return (gudFile.expectedDCS - gudFile.averageLevelMergedDCS)**2
 
     """
     Cost function for processing two components.
@@ -191,6 +197,7 @@ def processSingleComponent(self, x, sampleBackground):
     totalMolecules : float
         Sum of molecules of both components.
     """
+
     def processTwoComponents(self, x, sampleBackground, totalMolecules):
         self.gudrunFile.sampleBackgrounds = [sampleBackground]
         x = abs(x)
@@ -212,9 +219,9 @@ def processTwoComponents(self, x, sampleBackground, totalMolecules):
 
         time.sleep(1)
         gudPath = sampleBackground.samples[0].dataFiles[0].replace(
-                    self.gudrunFile.instrument.dataFileType,
-                    "gud"
-                )
+            self.gudrunFile.instrument.dataFileType,
+            "gud"
+        )
         gudFile = GudFile(
             os.path.join(
                 self.gudrunFile.instrument.GudrunInputFileDir, gudPath
@@ -244,6 +251,7 @@ def processTwoComponents(self, x, sampleBackground, totalMolecules):
     rtol : float
         Relative tolerance
     """
+
     def iterate(self, n=10, rtol=10.):
         if not self.components or not self.ratio:
             return None

gudpy/core/density_iterator.py → gudpy/core/iterators/density_iterator.py

@@ -1,4 +1,4 @@
-from core.single_param_iterator import SingleParamIterator
+from core.iterators.single_param_iterator import SingleParamIterator
 
 
 class DensityIterator(SingleParamIterator):
@@ -18,6 +18,8 @@ class DensityIterator(SingleParamIterator):
     organiseOutput
         Organises the output of the iteration.
     """
+    name = "IterateByDensity"
+
     def applyCoefficientToAttribute(self, object, coefficient):
         """
         Multiplies a sample's density by a given coefficient.
@@ -32,6 +34,3 @@ def applyCoefficientToAttribute(self, object, coefficient):
         """
         # Apply the coefficient to the density.
         object.density *= coefficient
-
-    def organiseOutput(self, n):
-        self.gudrunFile.iterativeOrganise(f"IterateByDensity_{n}")

gudpy/core/radius_iterator.py → gudpy/core/iterators/radius_iterator.py

@@ -1,4 +1,4 @@
-from core.single_param_iterator import SingleParamIterator
+from core.iterators.single_param_iterator import SingleParamIterator
 
 
 class RadiusIterator(SingleParamIterator):
@@ -21,6 +21,8 @@ class RadiusIterator(SingleParamIterator):
     organiseOutput
         Organises the output of the iteration.
     """
+    name = "IterateByRadius"
+
     def applyCoefficientToAttribute(self, object, coefficient):
         if self.targetRadius == "inner":
             object.innerRadius *= coefficient
@@ -29,6 +31,3 @@ def applyCoefficientToAttribute(self, object, coefficient):
 
     def setTargetRadius(self, targetRadius):
         self.targetRadius = targetRadius
-
-    def organiseOutput(self, n):
-        self.gudrunFile.iterativeOrganise(f"IterateByRadius_{n}")

gudpy/core/single_param_iterator.py → gudpy/core/iterators/single_param_iterator.py

@@ -29,6 +29,7 @@ class SingleParamIterator():
     organiseOutput
         To be overriden by sub-classes.
     """
+
     def __init__(self, gudrunFile):
         """
         Constructs all the necessary attributes for the
@@ -55,12 +56,12 @@ def performIteration(self, _n):
         for sampleBackground in self.gudrunFile.sampleBackgrounds:
             for sample in [
                 s for s in sampleBackground.samples
-                if s.runThisSample
+                if s.runThisSample and len(s.dataFiles)
             ]:
                 gudPath = sample.dataFiles[0].replace(
-                            self.gudrunFile.instrument.dataFileType,
-                            "gud"
-                        )
+                    self.gudrunFile.instrument.dataFileType,
+                    "gud"
+                )
                 gudFile = GudFile(
                     os.path.join(
                         self.gudrunFile.instrument.GudrunInputFileDir,
@@ -89,17 +90,19 @@ def applyCoefficientToAttribute(self, object, coefficient):
         """
         pass
 
-    def organiseOutput(self, n):
+    def organiseOutput(self, nTotal, nCurrent):
         """
-        Stub method to be overriden by sub-classes.
-        This method should organise the output of the iteration.
+        This should organises the output of the iteration.
 
         Parameters
         ----------
-        n : int
-            Iteration no.
+        nTotal : int
+            Total number of requested iterations
+        nCurrent : int
+            Current iteration
         """
-        pass
+        self.gudrunFile.iterativeOrganise(
+            nTotal, nCurrent, self.name)
 
     def iterate(self, n):
         """
@@ -118,4 +121,4 @@ def iterate(self, n):
             self.gudrunFile.process()
             time.sleep(1)
             self.performIteration(i)
-            self.organiseOutput(i)
+            self.organiseOutput(n, i)

gudpy/core/thickness_iterator.py → gudpy/core/iterators/thickness_iterator.py

@@ -1,4 +1,4 @@
-from core.single_param_iterator import SingleParamIterator
+from core.iterators.single_param_iterator import SingleParamIterator
 
 
 class ThicknessIterator(SingleParamIterator):
@@ -19,13 +19,13 @@ class ThicknessIterator(SingleParamIterator):
     organiseOutput
         Organises the output of the iteration.
     """
+
+    name = "IterateByThickness"
+
     def applyCoefficientToAttribute(self, object, coefficient):
         # Determine a new total thickness.
         totalThickness = object.upstreamThickness + object.downstreamThickness
         totalThickness *= coefficient
         # Assign the new thicknesses.
         object.downstreamThickness = totalThickness / 2
         object.upstreamThickness = totalThickness / 2
-
-    def organiseOutput(self, n):
-        self.gudrunFile.iterativeOrganise(f"IterateByThickness_{n}")

gudpy/core/tweak_factor_iterator.py → gudpy/core/iterators/tweak_factor_iterator.py

@@ -2,9 +2,10 @@
 import time
 
 from core.gud_file import GudFile
+from core.iterators.single_param_iterator import SingleParamIterator
 
 
-class TweakFactorIterator():
+class TweakFactorIterator(SingleParamIterator):
     """
     Class to represent a Tweak Factor Iterator.
     This class is used for iteratively tweaking by the tweak factor.
@@ -26,17 +27,8 @@ class TweakFactorIterator():
     iterate(n)
         Perform n iterations of iterating by tweak factor.
     """
-    def __init__(self, gudrunFile):
-        """
-        Constructs all the necessary attributes for the
-        TweakFactorIterator object.
 
-        Parameters
-        ----------
-        gudrunFile : GudrunFile
-            Input GudrunFile that we will be using for iterating.
-        """
-        self.gudrunFile = gudrunFile
+    name = "IterateByTweakFactor"
 
     def performIteration(self, _n):
         """
@@ -52,12 +44,12 @@ def performIteration(self, _n):
         for sampleBackground in self.gudrunFile.sampleBackgrounds:
             for sample in [
                 s for s in sampleBackground.samples
-                if s.runThisSample
+                if s.runThisSample and len(s.dataFiles)
             ]:
                 gudPath = sample.dataFiles[0].replace(
-                            self.gudrunFile.instrument.dataFileType,
-                            "gud"
-                        )
+                    self.gudrunFile.instrument.dataFileType,
+                    "gud"
+                )
                 gudFile = GudFile(
                     os.path.join(
                         self.gudrunFile.instrument.GudrunInputFileDir,
@@ -90,4 +82,4 @@ def iterate(self, n):
             self.gudrunFile.process(iterative=True)
             time.sleep(1)
             self.performIteration(i)
-            self.gudrunFile.iterativeOrganise(f"IterateByTweakFactor_{i+1}")
+            self.organiseOutput(n, i)