Add theta filter for issues with parts of incoming divergence

eos/__init__.py

@@ -2,5 +2,5 @@
 Package to handle data redction at AMOR instrument to be used by __main__.py script.
 """
 
-__version__ = '3.0.1'
+__version__ = '3.0.2'
 __date__    = '2025-10-10'

eos/file_reader.py

@@ -41,6 +41,7 @@ class AmorHeader:
 
     def __init__(self, fileName:Union[str, h5py.File, BinaryIO]):
         if type(fileName) is str:
+            logging.debug(f'    opening file {fileName}')
             self.hdf = h5py.File(fileName, 'r', swmr=True)
         elif type(fileName) is h5py.File:
             self.hdf = fileName
@@ -222,6 +223,7 @@ class AmorEventData(AmorHeader):
 
     def __init__(self, fileName:Union[str, h5py.File, BinaryIO], first_index:int=0, max_events:int=100_000_000):
         if type(fileName) is str:
+            logging.debug(f'    opening file {fileName}')
             self.file_list = [fileName]
             hdf = h5py.File(fileName, 'r', swmr=True)
         elif type(fileName) is h5py.File:

eos/options.py

@@ -91,10 +91,12 @@ class ArgParsable:
             if get_origin(typ) is list:
                 args['nargs'] = '+'
                 typ = get_args(typ)[0]
+                if get_origin(typ) is tuple:
+                    # tuple of items are put together during evaluation
+                    typ = get_args(typ)[0]
             elif get_origin(typ) is tuple:
                 args['nargs'] = len(get_args(typ))
                 typ = get_args(typ)[0]
-
             if issubclass(typ, StrEnum):
                 args['choices'] = [ci.value for ci in typ]
                 if field.default is not MISSING:
@@ -149,7 +151,12 @@ class ArgParsable:
             if get_origin(field.type) is Union and type(None) in get_args(field.type):
                 # optional argument
                 typ = get_args(field.type)[0]
-
+            if get_origin(typ) is list:
+                item_typ = get_args(typ)[0]
+                if get_origin(item_typ) is tuple:
+                    # tuple of items are put together during evaluation
+                    tuple_length = len(get_args(item_typ))
+                    value = [tuple(value[i*tuple_length+j] for j in range(tuple_length)) for i in range(len(value)//tuple_length)]
             if isinstance(typ, type) and issubclass(typ, StrEnum):
                 # convert str to enum
                 try:
@@ -359,6 +366,14 @@ class ReflectivityReductionConfig(ArgParsable):
                 'help': 'theta region of interest w.r.t. beam center',
                 },
             )
+    thetaFilters: List[Tuple[float, float]] = field(
+            default_factory=lambda: [],
+            metadata={
+                'short': 'TF',
+                'group': 'region of interest',
+                'help': 'add one or more theta ranges that will be filtered in reduction',
+                },
+            )
     normalisationMethod: NormalisationMethod = field(
             default=NormalisationMethod.over_illuminated,
             metadata={
@@ -701,6 +716,15 @@ class E2HReductionConfig(ArgParsable):
                 },
             )
 
+    thetaFilters: List[Tuple[float, float]] = field(
+            default_factory=lambda: [],
+            metadata={
+                'short': 'TF',
+                'group': 'region of interest',
+                'help': 'add one or more theta ranges that will be filtered in reduction',
+                },
+            )
+
     fontsize: float = field(
             default=8.,
             metadata={

eos/projection.py

@@ -760,7 +760,7 @@ class TProjection(ProjectionInterface):
 
         plt.xlabel('Reflection Angle / °')
         plt.ylabel('I / cpm')
-        plt.xlim(self.theta[0], self.theta[-1])
+        plt.xlim(self.theta[-1], self.theta[0])
         plt.title('Theta')
 
     def update_plot(self):

eos/reduction_e2h.py

@@ -37,6 +37,8 @@ class E2HReduction:
 
         self.header = Header()
 
+        self.fig = plt.figure()
+        self.register_colormap()
         self.prepare_actions()
 
     def prepare_actions(self):
@@ -47,7 +49,6 @@ class E2HReduction:
         self.file_list = self.path_resolver.resolve(self.config.reduction.fileIdentifier)
         self.file_index = 0
         self.plot_kwds = {}
-        self.fig = plt.figure()
         plt.rcParams.update({'font.size': self.config.reduction.fontsize})
 
         if self.config.reduction.update:
@@ -102,8 +103,6 @@ class E2HReduction:
             if self.config.reduction.plotArgs==E2HPlotArguments.Linear:
                 self.plot_kwds['norm'] = None
 
-        self.register_colormap()
-
     def reduce(self):
         if self.config.reduction.plot in [E2HPlotSelection.All, E2HPlotSelection.LT, E2HPlotSelection.Q]:
             if self.config.reduction.normalizationModel:
@@ -133,7 +132,7 @@ class E2HReduction:
             plt.show()
 
     def register_colormap(self):
-        cmap = plt.colormaps['gnuplot'](np.arange(256))
+        cmap = plt.colormaps['turbo'](np.arange(256))
         cmap[:1, :] = np.array([256/256, 255/256, 236/256, 1])
         cmap = ListedColormap(cmap, name='jochen_deluxe', N=cmap.shape[0])
         #cmap.set_bad((1.,1.,0.9))
@@ -155,6 +154,8 @@ class E2HReduction:
                 self.projection.correct_gravity(last_file_header.geometry.detectorDistance)
             self.projection.apply_lamda_mask(self.config.experiment.lambdaRange)
             self.projection.apply_theta_mask(thetaRange)
+            for thi in self.config.reduction.thetaFilters:
+                self.projection.apply_theta_filter((thi[0]+tthh, thi[1]+tthh))
             self.projection.apply_norm_mask(self.norm)
 
         if self.config.reduction.plot==E2HPlotSelection.Q:
@@ -164,6 +165,8 @@ class E2HReduction:
             plz.calculate_q()
             plz.apply_lamda_mask(self.config.experiment.lambdaRange)
             plz.apply_theta_mask(thetaRange)
+            for thi in self.config.reduction.thetaFilters:
+                self.projection.apply_theta_filter((thi[0]+tthh, thi[1]+tthh))
             plz.apply_norm_mask(self.norm)
             self.projection = ReflectivityProjector(plz, self.norm)
 
@@ -192,6 +195,8 @@ class E2HReduction:
             plz.calculate_q()
             plz.apply_lamda_mask(self.config.experiment.lambdaRange)
             plz.apply_theta_mask(thetaRange)
+            for thi in self.config.reduction.thetaFilters:
+                plz.apply_theta_filter((thi[0]+tthh, thi[1]+tthh))
             plz.apply_norm_mask(self.norm)
             pr = ReflectivityProjector(plz, self.norm)
             pyz = YZProjection()
@@ -227,7 +232,7 @@ class E2HReduction:
             self.projection.normalize_over_illuminated(self.norm)
 
     def create_file_output(self):
-        ...
+        raise NotImplementedError("Export to text output not yet implemented")
 
     def create_title(self):
         output = "Events to Histogram - "
@@ -247,14 +252,23 @@ class E2HReduction:
         new_files = self.path_resolver.resolve(f'{latest}')
         if not os.path.exists(new_files[-1]):
             return
+        try:
+            # check that events exist in the new file
+            AmorEventData(new_files[-1], 0, max_events=1000)
+        except Exception:
+            logging.debug("Problem when trying to load new dataset", exc_info=True)
+            return
+
         logging.warning(f"Preceding to next file {latest}")
         self.file_list = new_files
         self.file_index = 0
+        self.prepare_actions()
+        self.prepare_graphs()
         self.read_data()
-        self.projection.clear()
         self.add_data()
         self.fig.clear()
         self.create_graph()
+        plt.draw()
 
     def update(self):
         logging.debug("    check for update")

eos/reduction_reflectivity.py

@@ -373,8 +373,8 @@ class ReflectivityReduction:
         proj = LZProjection.from_dataset(dataset, self.grid,
                                          has_offspecular=(self.config.experiment.incidentAngle!=IncidentAngle.alphaF))
 
+        t0 = dataset.geometry.nu-dataset.geometry.mu
         if not self.config.reduction.is_default('thetaRangeR'):
-            t0 = dataset.geometry.nu - dataset.geometry.mu
             # adjust range based on detector center
             thetaRange = [ti+t0 for ti in self.config.reduction.thetaRangeR]
             proj.apply_theta_mask(thetaRange)
@@ -384,6 +384,9 @@ class ReflectivityReduction:
             thetaRange = [dataset.geometry.nu - dataset.geometry.mu - dataset.geometry.div/2,
                                               dataset.geometry.nu - dataset.geometry.mu + dataset.geometry.div/2]
             proj.apply_theta_mask(thetaRange)
+        for thi in self.config.reduction.thetaFilters:
+            # apply theta filters relative to angle on detector (issues with parts of the incoming divergence)
+            proj.apply_theta_filter((thi[0]+t0, thi[1]+t0))
 
         proj.apply_lamda_mask(self.config.experiment.lambdaRange)