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src/mvesuvio/config/analysis_inputs.py

@@ -17,33 +17,32 @@ class BackwardAnalysisInputs(SampleParameters):
     runs = "43066-43076"
     empty_runs = "41876-41923" 
     mode = "DoubleDifference"
-    ipfile = "ip2019.par"
-    firstSpec = 3  # 3
-    lastSpec = 134  # 134
-    maskedSpecAllNo = [18, 34, 42, 43, 59, 60, 62, 118, 119, 133]
-    tofBinning = "275.,1.,420"  # Binning of ToF spectra
-    maskTOFRange = None
-    subEmptyFromRaw = True  # Flag to control wether empty ws gets subtracted from raw
-    scaleEmpty = 1  # None or scaling factor
-    scaleRaw = 1
+    instrument_parameters_file = "ip2019.par"
+    detectors = "3-134"
+    mask_detectors = [18, 34, 42, 43, 59, 60, 62, 118, 119, 133]
+    time_of_flight_binning = "275.,1.,420"
+    mask_time_of_flight_range = None
+    subtract_empty_workspace_from_raw = True
+    scale_empty_workspace = 1  # None or scaling factor
+    scale_raw_workspace = 1
 
     masses = [12, 16, 27]
     # Intensities, NCP widths, NCP centers
-    initPars = [1, 12, 0.0, 1, 12, 0.0, 1, 12.5, 0.0]
-    bounds = [
+    initial_fitting_parameters = [1, 12, 0.0, 1, 12, 0.0, 1, 12.5, 0.0]
+    fitting_bounds = [
         [0, None], [8, 16], [-3, 1],
         [0, None], [8, 16], [-3, 1],
         [0, None], [11, 14], [-3, 1],
         ]
     constraints = ()
 
-    noOfMSIterations = 0  # 4
-    MSCorrectionFlag = True
-    HToMassIdxRatio = 19.0620008206  # Set to zero when H is not present
+    number_of_iterations_for_corrections = 0  # 4
+    do_multiple_scattering_correction = True
+    intensity_ratio_of_hydrogen_to_lowest_mass = 19.0620008206  # Set to zero to disable
     transmission_guess = 0.8537  # Experimental value from VesuvioTransmission
     multiple_scattering_order = 2
-    number_of_events = 1.0e5
-    GammaCorrectionFlag = False
+    multiple_scattering_number_of_events = 1.0e5
+    do_gamma_correction = False
 
 
 @dataclass
@@ -54,46 +53,57 @@ class ForwardAnalysisInputs(SampleParameters):
     runs = "43066-43076"
     empty_runs = "43868-43911"
     mode = "SingleDifference"
-    ipfile = "ip2018_3.par"
-    firstSpec = 144  # 144
-    lastSpec = 182  # 182
-    maskedSpecAllNo = [173, 174, 179]
-    tofBinning = "110,1,430"  # Binning of ToF spectra
-    maskTOFRange = None
-    subEmptyFromRaw = False  # Flag to control wether empty ws gets subtracted from raw
-    scaleEmpty = 1  # None or scaling factor
-    scaleRaw = 1
+    instrument_parameters_file = "ip2018_3.par"
+    detectors = '144-182'
+    mask_detectors = [173, 174, 179]
+    time_of_flight_binning = "110,1,430"
+    mask_time_of_flight_range = None
+    subtract_empty_workspace_from_raw = False
+    scale_empty_workspace = 1  # None or scaling factor
+    scale_raw_workspace = 1
 
     masses = 1.0079, 12, 16, 27
     # Intensities, NCP widths, NCP centers
-    initPars = [1, 4.7, 0, 1, 12.71, 0.0, 1, 8.76, 0.0, 1, 13.897, 0.0]
-    bounds = [
+    initial_fitting_parameters = [1, 4.7, 0, 1, 12.71, 0.0, 1, 8.76, 0.0, 1, 13.897, 0.0]
+    fitting_bounds = [
         [0, None], [3, 6], [-3, 1],
         [0, None], [12.71, 12.71], [-3, 1],
         [0, None], [8.76, 8.76], [-3, 1],
         [0, None], [13.897, 13.897], [-3, 1],
         ]
     constraints = ()
 
-    noOfMSIterations = 0  # 4
-    MSCorrectionFlag = True
+    number_of_iterations_for_corrections = 0  # 4
+    do_multiple_scattering_correction = True
     transmission_guess = 0.8537  # Experimental value from VesuvioTransmission
     multiple_scattering_order = 2
-    number_of_events = 1.0e5
-    GammaCorrectionFlag = True
+    multiple_scattering_number_of_events = 1.0e5
+    do_gamma_correction = True
 
 
 @dataclass
 class YSpaceFitInputs:
-    showPlots = True
-    symmetrisationFlag = False
-    subtractFSE = True
-    rebinParametersForYSpaceFit = "-25, 0.5, 25"  # Needs to be symetric
-    fitModel = "SINGLE_GAUSSIAN"  # Options: 'SINGLE_GAUSSIAN', 'GC_C4', 'GC_C6', 'GC_C4_C6', 'DOUBLE_WELL', 'ANSIO_GAUSSIAN', 'Gaussian3D'
-    runMinos = True
-    globalFit = True  # Performs global fit with Minuit by default
-    nGlobalFitGroups = 4  # Number or string "ALL"
-    maskTypeProcedure = "NAN"  # Options: 'NCP', 'NAN', None
+    show_plots = True
+    do_symmetrisation = False
+    subtract_calculated_fse_from_data = True
+    range_for_rebinning_in_y_space = "-25, 0.5, 25"  # Needs to be symetric
+    # Fitting model options
+    # 'gauss': Single Gaussian
+    # 'gcc4': Gram-Charlier with C4 parameter
+    # 'gcc6': Gram-Charlier with C6 parameter
+    # 'doublewell': Double Well function 
+    # 'gauss3D': 3-Dimensional Gaussian 
+    fitting_model = "gauss"
+    run_minos = True
+    do_global_fit = True   # Performs global fit with Minuit by default
+    # Number of groups of detectors to perform global (simultaneous) fit on
+    # Either an integer less than the number of detectors 
+    # or option 'all', which does not form groups and fits all spectra simultaneously and individualy 
+    number_of_global_fit_groups = 4
+    # Type of masking 
+    # 'nan': Zeros in workspace being fit are ignored
+    # 'ncp': Zeros in workspace being fit are replaced by the fitted neutron compton profile 
+    mask_zeros_with = "nan"   
 
 
 ########################

src/mvesuvio/main/run_routine.py

@@ -39,7 +39,7 @@ def setup(self):
         self.classes_to_fit_y_space = []
         for ai_cls in [self.bckwd_ai, self.fwd_ai]:
             if ai_cls.fit_in_y_space:
-                self.ws_to_fit_y_space.append(name_for_starting_ws(ai_cls) + '_' + str(ai_cls.noOfMSIterations))
+                self.ws_to_fit_y_space.append(name_for_starting_ws(ai_cls) + '_' + str(ai_cls.number_of_iterations_for_corrections))
                 self.classes_to_fit_y_space.append(ai_cls)
 
         self.analysis_result = None
@@ -49,7 +49,7 @@ def setup(self):
         inputs_script_path = Path(handle_config.read_config_var("caching.inputs"))
         script_name = handle_config.get_script_name()
         self.experiment_path = inputs_script_path.parent / script_name
-        self.input_ws_path =  self.experiment_path / "input_ws"
+        self.input_ws_path =  self.experiment_path / "input_workspaces"
         self.input_ws_path.mkdir(parents=True, exist_ok=True)
 
         # TODO: Output paths should probably not be set like this 
@@ -103,14 +103,14 @@ def runAnalysisRoutine(self):
 
         if self.bckwd_ai.run_this_scattering_type:
 
-            if is_hydrogen_present(self.fwd_ai.masses) & (self.bckwd_ai.HToMassIdxRatio==0):
+            if is_hydrogen_present(self.fwd_ai.masses) & (self.bckwd_ai.intensity_ratio_of_hydrogen_to_lowest_mass==0):
                 self.run_estimate_h_ratio()
                 return
 
             # TODO: make this automatic
             assert is_hydrogen_present(self.fwd_ai.masses) != (
-                self.bckwd_ai.HToMassIdxRatio==0 
-            ), "No Hydrogen detected, HToMassIdxRatio has to be set to 0"
+                self.bckwd_ai.intensity_ratio_of_hydrogen_to_lowest_mass==0 
+            ), "No Hydrogen detected, intensity_ratio_of_hydrogen_to_lowest_mass has to be set to 0"
 
         if self.bckwd_ai.run_this_scattering_type and self.fwd_ai.run_this_scattering_type:
             self.run_joint_analysis()
@@ -220,37 +220,38 @@ def _create_analysis_algorithm(self, ai):
         ws = loadRawAndEmptyWsFromUserPath(
             userWsRawPath=raw_path,
             userWsEmptyPath=empty_path,
-            tofBinning=ai.tofBinning,
+            tofBinning=ai.time_of_flight_binning,
             name=name_for_starting_ws(ai),
-            scaleRaw=ai.scaleRaw,
-            scaleEmpty=ai.scaleEmpty,
-            subEmptyFromRaw=ai.subEmptyFromRaw
+            scaleRaw=ai.scale_raw_workspace,
+            scaleEmpty=ai.scale_empty_workspace,
+            subEmptyFromRaw=ai.subtract_empty_workspace_from_raw
         )
+        first_detector, last_detector = [int(s) for s in ai.detectors.split('-')]
         cropedWs = cropAndMaskWorkspace(
             ws, 
-            firstSpec=ai.firstSpec,
-            lastSpec=ai.lastSpec,
-            maskedDetectors=ai.maskedSpecAllNo,
-            maskTOFRange=ai.maskTOFRange
+            firstSpec=first_detector,
+            lastSpec=last_detector,
+            maskedDetectors=ai.mask_detectors,
+            maskTOFRange=ai.mask_time_of_flight_range
         )
         profiles_table = create_profiles_table(cropedWs.name()+"_initial_parameters", ai)
         ipFilesPath = Path(handle_config.read_config_var("caching.ipfolder"))
         kwargs = {
             "InputWorkspace": cropedWs.name(),
             "InputProfiles": profiles_table.name(),
-            "InstrumentParametersFile": str(ipFilesPath / ai.ipfile),
-            "HRatioToLowestMass": ai.HToMassIdxRatio if hasattr(ai, 'HRatioToLowestMass') else 0,
-            "NumberOfIterations": int(ai.noOfMSIterations),
-            "InvalidDetectors": [int(det) for det in ai.maskedSpecAllNo],
-            "MultipleScatteringCorrection": ai.MSCorrectionFlag,
+            "InstrumentParametersFile": str(ipFilesPath / ai.instrument_parameters_file),
+            "HRatioToLowestMass": ai.intensity_ratio_of_hydrogen_to_lowest_mass if hasattr(ai, 'intensity_ratio_of_hydrogen_to_lowest_mass') else 0,
+            "NumberOfIterations": int(ai.number_of_iterations_for_corrections),
+            "InvalidDetectors": [int(det) for det in ai.mask_detectors],
+            "MultipleScatteringCorrection": ai.do_multiple_scattering_correction,
             "SampleVerticalWidth": ai.vertical_width, 
             "SampleHorizontalWidth": ai.horizontal_width, 
             "SampleThickness": ai.thickness,
-            "GammaCorrection": ai.GammaCorrectionFlag,
+            "GammaCorrection": ai.do_gamma_correction,
             "ModeRunning": scattering_type(ai),
             "TransmissionGuess": ai.transmission_guess,
             "MultipleScatteringOrder": int(ai.multiple_scattering_order),
-            "NumberOfEvents": int(ai.number_of_events),
+            "NumberOfEvents": int(ai.multiple_scattering_number_of_events),
             "Constraints": str(dill.dumps(ai.constraints)),
             "ResultsPath": str(self.results_save_path),
             "FiguresPath": str(self.fig_save_path),
@@ -271,8 +272,8 @@ def _create_analysis_algorithm(self, ai):
     def _make_neutron_profiles(cls, ai):
         profiles = []
         for mass, intensity, width, center, intensity_bound, width_bound, center_bound in zip(
-            ai.masses, ai.initPars[::3], ai.initPars[1::3], ai.initPars[2::3],
-            ai.bounds[::3], ai.bounds[1::3], ai.bounds[2::3]
+            ai.masses, ai.initial_fitting_parameters[::3], ai.initial_fitting_parameters[1::3], ai.initial_fitting_parameters[2::3],
+            ai.fitting_bounds[::3], ai.fitting_bounds[1::3], ai.fitting_bounds[2::3]
         ):
             profiles.append(NeutronComptonProfile(
                 label=str(float(mass)), mass=float(mass), intensity=float(intensity), width=float(width), center=float(center),
@@ -294,11 +295,11 @@ def _save_ws_if_not_on_path(self, load_ai):
 
         ipFilesPath = Path(handle_config.read_config_var("caching.ipfolder"))
 
-        if not ws_history_matches_inputs(load_ai.runs, load_ai.mode, load_ai.ipfile, rawPath):
-            save_ws_from_load_vesuvio(load_ai.runs, load_ai.mode, str(ipFilesPath/load_ai.ipfile), rawPath)
+        if not ws_history_matches_inputs(load_ai.runs, load_ai.mode, load_ai.instrument_parameters_file, rawPath):
+            save_ws_from_load_vesuvio(load_ai.runs, load_ai.mode, str(ipFilesPath/load_ai.instrument_parameters_file), rawPath)
 
-        if not ws_history_matches_inputs(load_ai.empty_runs, load_ai.mode, load_ai.ipfile, emptyPath):
-            save_ws_from_load_vesuvio(load_ai.empty_runs, load_ai.mode, str(ipFilesPath/load_ai.ipfile), emptyPath)
+        if not ws_history_matches_inputs(load_ai.empty_runs, load_ai.mode, load_ai.instrument_parameters_file, emptyPath):
+            save_ws_from_load_vesuvio(load_ai.empty_runs, load_ai.mode, str(ipFilesPath/load_ai.instrument_parameters_file), emptyPath)
         return rawPath, emptyPath
 
 
@@ -309,13 +310,13 @@ def _set_output_paths(self, ai):
 
         # Build Filename based on ic
         corr = ""
-        if ai.GammaCorrectionFlag & (ai.noOfMSIterations > 0):
+        if ai.do_gamma_correction & (ai.number_of_iterations_for_corrections > 0):
             corr += "_GC"
-        if ai.MSCorrectionFlag & (ai.noOfMSIterations > 0):
+        if ai.do_multiple_scattering_correction & (ai.number_of_iterations_for_corrections > 0):
             corr += "_MS"
 
         fileName = (
-            f"spec_{ai.firstSpec}-{ai.lastSpec}_iter_{ai.noOfMSIterations}{corr}" + ".npz"
+            f"spec_{ai.detectors.strip()}_iter_{ai.number_of_iterations_for_corrections}{corr}" + ".npz"
         )
         fileNameYSpace = fileName + "_ySpaceFit" + ".npz"
 

src/mvesuvio/util/analysis_helpers.py

@@ -23,8 +23,8 @@ def create_profiles_table(name, ai):
     table.addColumn(type="float", name="center")
     table.addColumn(type="str", name="center_bounds")
     for mass, intensity, width, center, intensity_bound, width_bound, center_bound in zip(
-        ai.masses, ai.initPars[::3], ai.initPars[1::3], ai.initPars[2::3],
-        ai.bounds[::3], ai.bounds[1::3], ai.bounds[2::3]
+        ai.masses, ai.initial_fitting_parameters[::3], ai.initial_fitting_parameters[1::3], ai.initial_fitting_parameters[2::3],
+        ai.fitting_bounds[::3], ai.fitting_bounds[1::3], ai.fitting_bounds[2::3]
     ):
         table.addRow(
             [str(float(mass)), float(mass), float(intensity), str(list(intensity_bound)),
@@ -203,13 +203,13 @@ def cropAndMaskWorkspace(ws, firstSpec, lastSpec, maskedDetectors, maskTOFRange)
         OutputWorkspace=newWsName,
     )
 
-    maskBinsWithZeros(wsCrop, maskTOFRange)  # Used to mask resonance peaks
+    mask_time_of_flight_bins_with_zeros(wsCrop, maskTOFRange)  # Used to mask resonance peaks
 
     MaskDetectors(Workspace=wsCrop, SpectraList=maskedDetectors)
     return wsCrop
 
 
-def maskBinsWithZeros(ws, maskTOFRange):
+def mask_time_of_flight_bins_with_zeros(ws, maskTOFRange):
     """
     Masks a given TOF range on ws with zeros on dataY.
     Leaves errors dataE unchanged, as they are used by later treatments.
@@ -220,7 +220,7 @@ def maskBinsWithZeros(ws, maskTOFRange):
         return
 
     dataX, dataY, dataE = extractWS(ws)
-    start, end = [int(s) for s in maskTOFRange.split(",")]
+    start, end = [float(s) for s in maskTOFRange.split("-")]
     assert (
         start <= end
     ), "Start value for masking needs to be smaller or equal than end."