Merge branch 'develop' into 30-refactor-default-constants

Author: AndrewSazonov

pixi.lock

@@ -57,7 +57,7 @@ def calculate_pattern(
         Returns:
             The calculated diffraction pattern as a NumPy array.
         """
-        x_data = experiment.datastore.pattern.x
+        x_data = experiment.datastore.x
         y_calc_zeros = np.zeros_like(x_data)
 
         valid_linked_phases = self._get_valid_linked_phases(sample_models, experiment)
@@ -92,11 +92,11 @@ def calculate_pattern(
         y_bkg = np.zeros_like(x_data)
         if hasattr(experiment, 'background'):
             y_bkg = experiment.background.calculate(x_data)
-        experiment.datastore.pattern.bkg = y_bkg
+        experiment.datastore.bkg = y_bkg
 
         # Calculate total pattern
         y_calc_total = y_calc_scaled + y_bkg
-        experiment.datastore.pattern.calc = y_calc_total
+        experiment.datastore.calc = y_calc_total
 
         return y_calc_total
 

src/easydiffraction/analysis/calculators/calculator_base.py

@@ -71,7 +71,7 @@ def _calculate_single_model_pattern(
         crysfml_dict = self._crysfml_dict(sample_model, experiment)
         try:
             _, y = cfml_py_utilities.cw_powder_pattern_from_dict(crysfml_dict)
-            y = self._adjust_pattern_length(y, len(experiment.datastore.pattern.x))
+            y = self._adjust_pattern_length(y, len(experiment.datastore.x))
         except KeyError:
             print('[CrysfmlCalculator] Error: No calculated data')
             y = []
@@ -177,7 +177,7 @@ def _convert_experiment_to_dict(
         instrument = getattr(experiment, 'instrument', None)
         peak = getattr(experiment, 'peak', None)
 
-        x_data = experiment.datastore.pattern.x
+        x_data = experiment.datastore.x
         twotheta_min = float(x_data.min())
         twotheta_max = float(x_data.max())
 

src/easydiffraction/analysis/calculators/calculator_crysfml.py

@@ -332,7 +332,7 @@ def _convert_experiment_to_cryspy_cif(
                     attr_value = getattr(peak, local_attr_name).value
                     cif_lines.append(f'{engine_key_name} {attr_value}')
 
-        x_data = experiment.datastore.pattern.x
+        x_data = experiment.datastore.x
         twotheta_min = float(x_data.min())
         twotheta_max = float(x_data.max())
         cif_lines.append('')
@@ -377,8 +377,8 @@ def _convert_experiment_to_cryspy_cif(
             cif_lines.append('_tof_meas_intensity')
             cif_lines.append('_tof_meas_intensity_sigma')
 
-        y_data = experiment.datastore.pattern.meas
-        sy_data = experiment.datastore.pattern.meas_su
+        y_data = experiment.datastore.meas
+        sy_data = experiment.datastore.meas_su
         for x_val, y_val, sy_val in zip(x_data, y_data, sy_data):
             cif_lines.append(f'  {x_val:.5f}   {y_val:.5f}   {sy_val:.5f}')
 

src/easydiffraction/analysis/calculators/calculator_cryspy.py

@@ -81,9 +81,8 @@ def _calculate_single_model_pattern(
         calculator.setvar('spdiameter', experiment.peak.damp_particle_diameter.value)
 
         # Data
-        pattern = experiment.datastore.pattern
-        x = list(pattern.x)
-        y_noise = list(np.zeros_like(pattern.x))
+        x = list(experiment.datastore.x)
+        y_noise = list(np.zeros_like(x))
 
         # Assign the data to the PDFfit calculator
         calculator.read_data_lists(

src/easydiffraction/analysis/calculators/calculator_pdffit.py

@@ -176,8 +176,8 @@ def _residual_function(
                 experiment,
                 called_by_minimizer=True,
             )
-            y_meas: np.ndarray = experiment.datastore.pattern.meas
-            y_meas_su: np.ndarray = experiment.datastore.pattern.meas_su
+            y_meas: np.ndarray = experiment.datastore.meas
+            y_meas_su: np.ndarray = experiment.datastore.meas_su
             diff = (y_meas - y_calc) / y_meas_su
 
             # Residuals are squared before going into reduced chi-squared

src/easydiffraction/analysis/minimization.py

@@ -143,8 +143,8 @@ def get_reliability_inputs(
     y_err_all = []
     for expt_name, experiment in experiments._items.items():
         y_calc = calculator.calculate_pattern(sample_models, experiment)
-        y_meas = experiment.datastore.pattern.meas
-        y_meas_su = experiment.datastore.pattern.meas_su
+        y_meas = experiment.datastore.meas
+        y_meas_su = experiment.datastore.meas_su
 
         if y_meas is not None and y_calc is not None:
             # If standard uncertainty is not provided, use ones

src/easydiffraction/analysis/reliability_factors.py

@@ -61,19 +61,18 @@ def on_item_added(self, item: ExcludedRegion) -> None:
         """
         Mark excluded points in the experiment pattern when a new region is added.
         """
-        experiment = self._parent
-        pattern = experiment.datastore.pattern
+        datastore = self._parent.datastore
 
         # Boolean mask for points within the new excluded region
-        in_region = (pattern.full_x >= item.start.value) & (pattern.full_x <= item.end.value)
+        in_region = (datastore.full_x >= item.start.value) & (datastore.full_x <= item.end.value)
 
         # Update the exclusion mask
-        pattern.excluded[in_region] = True
+        datastore.excluded[in_region] = True
 
         # Update the excluded points in the datastore
-        pattern.x = pattern.full_x[~pattern.excluded]
-        pattern.meas = pattern.full_meas[~pattern.excluded]
-        pattern.meas_su = pattern.full_meas_su[~pattern.excluded]
+        datastore.x = datastore.full_x[~datastore.excluded]
+        datastore.meas = datastore.full_meas[~datastore.excluded]
+        datastore.meas_su = datastore.full_meas_su[~datastore.excluded]
 
     def show(self) -> None:
         # TODO: Consider moving this to the base class