Cif anal

cx_asap/overall_pipelines/variable_position_pipeline.py

@@ -23,7 +23,7 @@
 from data_refinement.pipelines.refine_pipeline import Refinement_Pipeline
 from cif_validation.pipelines.cif_pipeline import CIF_Compile_Pipeline
 from post_refinement_analysis.pipelines.rotation_pipeline import Rotation_Pipeline
-from post_refinement_analysis.pipelines.centroids_pipeline import Centroids_Pipeline
+from post_refinement_analysis.pipelines.points_pipeline import PointsPipeline
 from post_refinement_analysis.pipelines.variable_position_analysis import (
     VP_Analysis_Pipeline,
 )
@@ -102,6 +102,7 @@ def setup(
         MPLA_atoms: str,
         instrument_cif_path: str,
         total_angle: int,
+        minimum_fraction_of_indexed_spots: float,
     ) -> None:
         """Organises the directory tree for this experiment
 
@@ -128,6 +129,7 @@ def setup(
             MPLA_atoms (str): Atoms for mean plane analysis
             instrument_cif_path (str): full path to the instrument CIF
             total_angle (int): total wedge angle per experiment
+            minimum_fraction_of_indexed_spots (float): minimum fraction of indexed spots threshold for XDS indexing
 
         """
 
@@ -139,7 +141,12 @@ def setup(
             background_reference, instrument_parameters_path, instrument_cif_path
         )
         configure.flexible_setup(
-            max_processors, neggia_library, space_group_number, MPLA_atoms, total_angle
+            max_processors,
+            neggia_library,
+            space_group_number,
+            MPLA_atoms,
+            total_angle,
+            minimum_fraction_of_indexed_spots,
         )
         self.cfg, self.sys = self.config.yaml_reload()
 
@@ -523,14 +530,14 @@ def process(
         )
         rotation = Rotation_Pipeline()
         rotation.analysis(location, reference_plane, graph_output_location)
-        centroids = Centroids_Pipeline()
-        centroids.centroid_distance_analysis(
+        centroids = PointsPipeline()
+        centroids.point_group_distance_analysis(
             location,
-            self.cfg["centroid_1_atoms"],
-            self.cfg["centroid_2_atoms"],
+            self.cfg["point_group_1_atoms"],
+            self.cfg["point_group_2_atoms"],
             graph_output_location,
-            symmetry_1=self.cfg.get("centroid_1_symmetry"),
-            symmetry_2=self.cfg.get("centroid_2_symmetry"),
+            symmetry_1=self.cfg.get("point_group_1_symmetry"),
+            symmetry_2=self.cfg.get("point_group_2_symmetry"),
         )
         cif = CIF_Compile_Pipeline()
         cif.configure(

cx_asap/overall_pipelines/variable_temperature_pipeline.py

@@ -18,7 +18,7 @@
     VT_Analysis_Pipeline,
 )
 from post_refinement_analysis.pipelines.rotation_pipeline import Rotation_Pipeline
-from post_refinement_analysis.pipelines.centroids_pipeline import Centroids_Pipeline
+from post_refinement_analysis.pipelines.points_pipeline import PointsPipeline
 import yaml
 import os
 import logging
@@ -142,14 +142,14 @@ def process(
         )
         rotation = Rotation_Pipeline()
         rotation.analysis(location, reference_plane, graph_output_location)
-        centroids = Centroids_Pipeline()
-        centroids.centroid_distance_analysis(
+        centroids = PointsPipeline()
+        centroids.point_group_distance_analysis(
             location,
-            self.cfg["centroid_1_atoms"],
-            self.cfg["centroid_2_atoms"],
+            self.cfg["point_group_1_atoms"],
+            self.cfg["point_group_2_atoms"],
             graph_output_location,
-            symmetry_1=self.cfg.get("centroid_1_symmetry"),
-            symmetry_2=self.cfg.get("centroid_2_symmetry"),
+            symmetry_1=self.cfg.get("point_group_1_symmetry"),
+            symmetry_2=self.cfg.get("point_group_2_symmetry"),
         )
 
     def analyse(

cx_asap/post_refinement_analysis/modules/ADP_analysis.py

@@ -211,48 +211,14 @@ def analyse_data(self, csv_file: str, cell_data: str) -> None:
 
                 values_unsorted, vectors = np.linalg.eig(BG)
 
-                test = values_unsorted.tolist()
-
-                values = sorted(test)
-
-                values.reverse()
-
-                positions = {}
-
-                for i_1, i in enumerate(values_unsorted):
-                    for i_2, j in enumerate(values):
-                        if i == j:
-                            positions[i_1] = i_2
-
-                vector_1 = np.array(
-                    [
-                        [
-                            vectors[0][positions[0]],
-                            vectors[1][positions[0]],
-                            vectors[2][positions[0]],
-                        ]
-                    ]
-                )
-
-                vector_2 = np.array(
-                    [
-                        [
-                            vectors[0][positions[1]],
-                            vectors[1][positions[1]],
-                            vectors[2][positions[1]],
-                        ]
-                    ]
-                )
-
-                vector_3 = np.array(
-                    [
-                        [
-                            vectors[0][positions[2]],
-                            vectors[1][positions[2]],
-                            vectors[2][positions[2]],
-                        ]
-                    ]
-                )
+                # Numerical noise can produce tiny imaginary components.
+                # Sort by real part and coerce near-real values back to float.
+                order = np.argsort(np.real(values_unsorted))[::-1]
+                values = [float(np.real(values_unsorted[i])) for i in order]
+
+                vector_1 = np.array([np.real_if_close(vectors[:, order[0]]).astype(float)])
+                vector_2 = np.array([np.real_if_close(vectors[:, order[1]]).astype(float)])
+                vector_3 = np.array([np.real_if_close(vectors[:, order[2]]).astype(float)])
 
                 try:
                     principle_A.append(math.sqrt(values[0] / (2 * (math.pi**2))))

cx_asap/post_refinement_analysis/modules/centroids.py

@@ -109,6 +109,7 @@ def _extract_positions(
         """Gets transformed fractional coordinates for each requested atom."""
 
         atom_names = self._normalise_atom_names(atom_names)
+        symmetry = self._normalise_symmetry(symmetry)
         R, t = parse_symm_op(symmetry) if symmetry else (None, None)
 
         positions = []
@@ -126,6 +127,24 @@ def _extract_positions(
 
         return positions
 
+    @staticmethod
+    def _normalise_symmetry(symmetry: "str | list | None") -> "str | None":
+        """Converts placeholder symmetry values to None and normalises strings."""
+
+        if isinstance(symmetry, list):
+            if len(symmetry) == 0:
+                return None
+            symmetry = symmetry[0]
+
+        if symmetry is None:
+            return None
+
+        value = str(symmetry).strip()
+        if value in ["", "0", ".", "?"]:
+            return None
+
+        return value
+
     def calculate_centroid(
         self,
         coords: dict,
@@ -304,9 +323,13 @@ def point_torsion(
             logging.warning(__name__ + f" : {error}")
             return 0.0
 
-        has_symmetry = any(
-            item is not None for item in [symmetry_1, symmetry_2, symmetry_3, symmetry_4]
-        )
+        symmetry_values = [
+            self._normalise_symmetry(symmetry_1),
+            self._normalise_symmetry(symmetry_2),
+            self._normalise_symmetry(symmetry_3),
+            self._normalise_symmetry(symmetry_4),
+        ]
+        has_symmetry = any(item is not None for item in symmetry_values)
         has_centroid_point = any(
             len(item) > 1
             for item in [point_1_list, point_2_list, point_3_list, point_4_list]