Fixes multiphase fit and adds test

Author: AndrewSazonov

.github/workflows/testing-code.yaml

@@ -62,7 +62,7 @@ jobs:
 
       - name: Install Python dependencies
         shell: bash
-        run: python -m pip install -r requirements.txt
+        run: python -m pip install .
 
       - name: Run Python unit tests
         shell: bash

src/easydiffraction/analysis/calculators/calculator_cryspy.py

@@ -4,8 +4,7 @@
 from .calculator_base import CalculatorBase
 from easydiffraction.utils.formatting import warning
 
-from easydiffraction.sample_models.sample_models import SampleModels
-from easydiffraction.experiments.experiments import Experiments
+from easydiffraction.sample_models.sample_model import SampleModel
 from easydiffraction.experiments.experiment import Experiment
 
 try:
@@ -33,19 +32,21 @@ def __init__(self) -> None:
         super().__init__()
         self._cryspy_dicts: Dict[str, Dict[str, Any]] = {}
 
-    def calculate_structure_factors(self, sample_models: SampleModels, experiments: Experiments) -> None:
+    def calculate_structure_factors(self,
+                                    sample_model: SampleModel,
+                                    experiment: Experiment) -> None:
         """
         Raises a NotImplementedError as HKL calculation is not implemented.
 
         Args:
-            sample_models: The sample models to calculate structure factors for.
-            experiments: The experiments associated with the sample models.
+            sample_model: The sample model to calculate structure factors for.
+            experiment: The experiment associated with the sample models.
         """
         raise NotImplementedError("HKL calculation is not implemented for CryspyCalculator.")
 
     def _calculate_single_model_pattern(
         self,
-        sample_model: SampleModels,
+        sample_model: SampleModel,
         experiment: Experiment,
         called_by_minimizer: bool = False
     ) -> Union[np.ndarray, List[float]]:
@@ -65,8 +66,10 @@ def _calculate_single_model_pattern(
         Returns:
             The calculated diffraction pattern as a NumPy array or a list of floats.
         """
+        combined_name = f"{sample_model.name}_{experiment.name}"
+
         if called_by_minimizer:
-            if self._cryspy_dicts and experiment.name in self._cryspy_dicts:
+            if self._cryspy_dicts and combined_name in self._cryspy_dicts:
                 cryspy_dict = self._recreate_cryspy_dict(sample_model, experiment)
             else:
                 cryspy_obj = self._recreate_cryspy_obj(sample_model, experiment)
@@ -75,7 +78,7 @@ def _calculate_single_model_pattern(
             cryspy_obj = self._recreate_cryspy_obj(sample_model, experiment)
             cryspy_dict = cryspy_obj.get_dictionary()
 
-        self._cryspy_dicts[experiment.name] = copy.deepcopy(cryspy_dict)
+        self._cryspy_dicts[combined_name] = copy.deepcopy(cryspy_dict)
 
         cryspy_in_out_dict: Dict[str, Any] = {}
         rhochi_calc_chi_sq_by_dictionary(
@@ -99,14 +102,16 @@ def _calculate_single_model_pattern(
         try:
             signal_plus = cryspy_in_out_dict[cryspy_block_name]['signal_plus']
             signal_minus = cryspy_in_out_dict[cryspy_block_name]['signal_minus']
-            y_calc_total = signal_plus + signal_minus
+            y_calc = signal_plus + signal_minus
         except KeyError:
             print(f"[CryspyCalculator] Error: No calculated data for {cryspy_block_name}")
             return []
 
-        return y_calc_total
+        return y_calc
 
-    def _recreate_cryspy_dict(self, sample_model: SampleModels, experiment: Experiment) -> Dict[str, Any]:
+    def _recreate_cryspy_dict(self,
+                              sample_model: SampleModel,
+                              experiment: Experiment) -> Dict[str, Any]:
         """
         Recreates the Cryspy dictionary for the given sample model and experiment.
 
@@ -117,7 +122,8 @@ def _recreate_cryspy_dict(self, sample_model: SampleModels, experiment: Experime
         Returns:
             The updated Cryspy dictionary.
         """
-        cryspy_dict = copy.deepcopy(self._cryspy_dicts[experiment.name])
+        combined_name = f"{sample_model.name}_{experiment.name}"
+        cryspy_dict = copy.deepcopy(self._cryspy_dicts[combined_name])
 
         cryspy_model_id = f'crystal_{sample_model.name}'
         cryspy_model_dict = cryspy_dict[cryspy_model_id]
@@ -185,7 +191,9 @@ def _recreate_cryspy_dict(self, sample_model: SampleModels, experiment: Experime
 
         return cryspy_dict
 
-    def _recreate_cryspy_obj(self, sample_model: SampleModels, experiment: Experiment) -> Any:
+    def _recreate_cryspy_obj(self,
+                             sample_model: SampleModel,
+                             experiment: Experiment) -> Any:
         """
         Recreates the Cryspy object for the given sample model and experiment.
 
@@ -212,7 +220,8 @@ def _recreate_cryspy_obj(self, sample_model: SampleModels, experiment: Experimen
 
         return cryspy_obj
 
-    def _convert_sample_model_to_cryspy_cif(self, sample_model: SampleModels) -> str:
+    def _convert_sample_model_to_cryspy_cif(self,
+                                            sample_model: SampleModel) -> str:
         """
         Converts a sample model to a Cryspy CIF string.
 
@@ -224,7 +233,9 @@ def _convert_sample_model_to_cryspy_cif(self, sample_model: SampleModels) -> str
         """
         return sample_model.as_cif()
 
-    def _convert_experiment_to_cryspy_cif(self, experiment: Experiment, linked_phase: Any) -> str:
+    def _convert_experiment_to_cryspy_cif(self,
+                                          experiment: Experiment,
+                                          linked_phase: Any) -> str:
         """
         Converts an experiment to a Cryspy CIF string.
 

tests/functional_tests/fitting/test_powder-diffraction_multiphase.py

@@ -0,0 +1,92 @@
+import os
+import tempfile
+from numpy.testing import assert_almost_equal
+
+from easydiffraction import (
+    Project,
+    SampleModel,
+    Experiment,
+    download_from_repository
+)
+
+TEMP_DIR = tempfile.gettempdir()
+
+
+def test_single_fit_neutron_pd_tof_mcstas_lbco_si() -> None:
+    # Set sample models
+    model_1 = SampleModel('lbco')
+    model_1.space_group.name_h_m = 'P m -3 m'
+    model_1.space_group.it_coordinate_system_code = '1'
+    model_1.cell.length_a = 3.8909
+    model_1.atom_sites.add('La', 'La', 0, 0, 0, wyckoff_letter='a', b_iso=0.2, occupancy=0.5)
+    model_1.atom_sites.add('Ba', 'Ba', 0, 0, 0, wyckoff_letter='a', b_iso=0.2, occupancy=0.5)
+    model_1.atom_sites.add('Co', 'Co', 0.5, 0.5, 0.5, wyckoff_letter='b', b_iso=0.2567)
+    model_1.atom_sites.add('O', 'O', 0, 0.5, 0.5, wyckoff_letter='c', b_iso=1.4041)
+
+    model_2 = SampleModel('si')
+    model_2.space_group.name_h_m = 'F d -3 m'
+    model_2.space_group.it_coordinate_system_code = '2'
+    model_2.cell.length_a = 5.43146
+    model_2.atom_sites.add('Si', 'Si', 0.0, 0.0, 0.0, wyckoff_letter='a', b_iso=0.0)
+
+    # Set experiment
+    data_file = 'mcstas_lbco-si.xys'
+    download_from_repository(data_file, branch='fix-multiphase-fit', destination=TEMP_DIR)
+    expt = Experiment('mcstas', beam_mode='time-of-flight', data_path=os.path.join(TEMP_DIR, data_file))
+    expt.instrument.setup_twotheta_bank = 94.90931761529106
+    expt.instrument.calib_d_to_tof_offset = 0.0
+    expt.instrument.calib_d_to_tof_linear = 58724.76869981215
+    expt.instrument.calib_d_to_tof_quad = -0.00001
+    expt.peak_profile_type = 'pseudo-voigt * ikeda-carpenter'
+    expt.peak.broad_gauss_sigma_0 = 45137
+    expt.peak.broad_gauss_sigma_1 = -52394
+    expt.peak.broad_gauss_sigma_2 = 22998
+    expt.peak.broad_mix_beta_0 = 0.0055
+    expt.peak.broad_mix_beta_1 = 0.0041
+    expt.peak.asym_alpha_0 = 0.0
+    expt.peak.asym_alpha_1 = 0.0097
+    expt.linked_phases.add('lbco', scale=4.0)
+    expt.linked_phases.add('si', scale=0.2)
+    for x in range(45000, 115000, 5000):
+        expt.background.add(x=x, y=0.2)
+
+    # Create project
+    project = Project()
+    project.sample_models.add(model_1)
+    project.sample_models.add(model_2)
+    project.experiments.add(expt)
+
+    # Prepare for fitting
+    project.analysis.current_calculator = 'cryspy'
+    project.analysis.current_minimizer = 'lmfit (leastsq)'
+
+    # Select fitting parameters
+    model_1.cell.length_a.free = True
+    model_1.atom_sites['La'].b_iso.free = True
+    model_1.atom_sites['Ba'].b_iso.free = True
+    model_1.atom_sites['Co'].b_iso.free = True
+    model_1.atom_sites['O'].b_iso.free = True
+    model_2.cell.length_a.free = True
+    model_2.atom_sites['Si'].b_iso.free = True
+    expt.linked_phases['lbco'].scale.free = True
+    expt.linked_phases['si'].scale.free = True
+    expt.peak.broad_gauss_sigma_0.free = True
+    expt.peak.broad_gauss_sigma_1.free = True
+    expt.peak.broad_gauss_sigma_2.free = True
+    expt.peak.asym_alpha_1.free = True
+    expt.peak.broad_mix_beta_0.free = True
+    expt.peak.broad_mix_beta_1.free = True
+    for point in expt.background:
+        point.y.free = True
+
+    # Perform fit
+    project.analysis.fit()
+
+    # Compare fit quality
+    assert_almost_equal(project.analysis.fit_results.reduced_chi_square,
+                        desired=2.87,
+                        decimal=1)
+
+
+if __name__ == '__main__':
+    test_single_fit_neutron_pd_tof_mcstas_lbco_si()

tests/unit_tests/analysis/calculators/test_calculator_cryspy.py

@@ -68,7 +68,7 @@ def test_calculate_single_model_pattern(mock_rhochi_calc, mock_sample_model, moc
 def test_recreate_cryspy_dict(mock_sample_model, mock_experiment):
     calculator = CryspyCalculator()
     calculator._cryspy_dicts = {
-        "experiment1": {
+        "sample1_experiment1": {
             "pd_experiment1": {
                 "offset_ttheta": [0.1],
                 "wavelength": [1.54],