Enhances CIF parsing support in experiments: 1st step

Author: AndrewSazonov

src/easydiffraction/experiments/experiment/factory.py

@@ -1,11 +1,14 @@
 # SPDX-FileCopyrightText: 2021-2025 EasyDiffraction contributors <https://github.com/easyscience/diffraction>
 # SPDX-License-Identifier: BSD-3-Clause
 
+import gemmi
+
 from easydiffraction.core.factory import FactoryBase
 from easydiffraction.experiments.categories.experiment_type import ExperimentType
 from easydiffraction.experiments.experiment import BraggPdExperiment
 from easydiffraction.experiments.experiment import BraggScExperiment
 from easydiffraction.experiments.experiment import TotalPdExperiment
+from easydiffraction.experiments.experiment.base import ExperimentBase
 from easydiffraction.experiments.experiment.enums import BeamModeEnum
 from easydiffraction.experiments.experiment.enums import RadiationProbeEnum
 from easydiffraction.experiments.experiment.enums import SampleFormEnum
@@ -67,18 +70,75 @@ def create(cls, **kwargs):
         elif 'name' in kwargs:
             return cls._create_without_data(kwargs)
 
+    # -------------
+    # gemmi helpers
+    # -------------
+
+    # TODO: Move to a common CIF utility module? io.cif.parse?
+    @staticmethod
+    def _read_cif_document_from_path(path: str) -> gemmi.cif.Document:
+        """Read a CIF document from a file path."""
+        return gemmi.cif.read_file(path)
+
+    # TODO: Move to a common CIF utility module? io.cif.parse?
+    @staticmethod
+    def _read_cif_document_from_string(text: str) -> gemmi.cif.Document:
+        """Read a CIF document from a raw text string."""
+        return gemmi.cif.read_string(text)
+
+    # TODO: Move to a common CIF utility module? io.cif.parse?
+    @classmethod
+    def _pick_first_block(
+        cls,
+        doc: gemmi.cif.Document,
+    ) -> gemmi.cif.Block:
+        """Pick the first experimental block from a CIF document."""
+        try:
+            return doc.sole_block()
+        except Exception:
+            return doc[0]
+
+    # TODO: Move to a common CIF utility module? io.cif.parse?
+    @classmethod
+    def _extract_name_from_block(cls, block: gemmi.cif.Block) -> str:
+        """Extract a model name from the CIF block name."""
+        return block.name or 'model'
+
+    # TODO: Move to a common CIF utility module? io.cif.parse?
+    @classmethod
+    def _create_experiment_from_block(
+        cls,
+        block: gemmi.cif.Block,
+    ) -> ExperimentBase:
+        """Build a model instance from a single CIF block."""
+        name = cls._extract_name_from_block(block)
+
+        # TODO: experiment type need to be read from CIF block
+        kwargs = {'beam_mode': BeamModeEnum.CONSTANT_WAVELENGTH}
+        expt_type = cls._make_experiment_type(kwargs)
+
+        # Create experiment instance of appropriate class
+        scattering_type = expt_type.scattering_type.value
+        sample_form = expt_type.sample_form.value
+        expt_class = cls._SUPPORTED[scattering_type][sample_form]
+        expt_obj = expt_class(name=name, type=expt_type)
+
+        # TODO: Read all categories from CIF block into experiment
+
+        # TODO: Read data from CIF block into experiment datastore
+
+        return expt_obj
+
     # -------------------------------
     # Private creation helper methods
     # -------------------------------
 
-    @staticmethod
-    def _create_from_cif_path(cif_path):
-        """Create an experiment from a CIF file path.
-
-        Not yet implemented.
-        """
-        # TODO: Implement CIF file loading logic
-        raise NotImplementedError('CIF file loading not implemented yet.')
+    @classmethod
+    def _create_from_cif_path(cls, cif_path):
+        """Create an experiment from a CIF file path."""
+        doc = cls._read_cif_document_from_path(cif_path)
+        block = cls._pick_first_block(doc)
+        return cls._create_experiment_from_block(block)
 
     @staticmethod
     def _create_from_cif_str(cif_str):

src/easydiffraction/sample_models/sample_model/factory.py

@@ -59,7 +59,6 @@ def _create_from_cif_path(
         cif_path: str,
     ) -> SampleModelBase:
         """Create a model by reading and parsing a CIF file."""
-        # Parse CIF and build model
         doc = cls._read_cif_document_from_path(cif_path)
         block = cls._pick_first_structural_block(doc)
         return cls._create_model_from_block(block)
@@ -70,7 +69,6 @@ def _create_from_cif_str(
         cif_str: str,
     ) -> SampleModelBase:
         """Create a model by parsing a CIF string."""
-        # Parse CIF string and build model
         doc = cls._read_cif_document_from_string(cif_str)
         block = cls._pick_first_structural_block(doc)
         return cls._create_model_from_block(block)
@@ -81,16 +79,19 @@ def _create_from_cif_str(
     # gemmi helpers
     # -------------
 
+    # TODO: Move to a common CIF utility module? io.cif.parse?
     @staticmethod
     def _read_cif_document_from_path(path: str) -> gemmi.cif.Document:
         """Read a CIF document from a file path."""
         return gemmi.cif.read_file(path)
 
+    # TODO: Move to a common CIF utility module? io.cif.parse?
     @staticmethod
     def _read_cif_document_from_string(text: str) -> gemmi.cif.Document:
         """Read a CIF document from a raw text string."""
         return gemmi.cif.read_string(text)
 
+    # TODO: Move to a common CIF utility module? io.cif.parse?
     @staticmethod
     def _has_structural_content(block: gemmi.cif.Block) -> bool:
         """Return True if the CIF block contains structural content."""
@@ -108,6 +109,7 @@ def _has_structural_content(block: gemmi.cif.Block) -> bool:
         ]
         return all(block.find_value(tag) for tag in required_cell)
 
+    # TODO: Move to a common CIF utility module? io.cif.parse?
     @classmethod
     def _pick_first_structural_block(
         cls,
@@ -124,6 +126,7 @@ def _pick_first_structural_block(
         except Exception:
             return doc[0]
 
+    # TODO: Move to a common CIF utility module? io.cif.parse?
     @classmethod
     def _create_model_from_block(
         cls,
@@ -137,11 +140,13 @@ def _create_model_from_block(
         cls._set_atom_sites_from_cif_block(model, block)
         return model
 
+    # TODO: Move to a common CIF utility module? io.cif.parse?
     @classmethod
     def _extract_name_from_block(cls, block: gemmi.cif.Block) -> str:
         """Extract a model name from the CIF block name."""
         return block.name or 'model'
 
+    # TODO: Move to a common CIF utility module? io.cif.parse?
     @classmethod
     def _set_space_group_from_cif_block(
         cls,
@@ -151,6 +156,7 @@ def _set_space_group_from_cif_block(
         """Populate the model's space group from a CIF block."""
         model.space_group.from_cif(block)
 
+    # TODO: Move to a common CIF utility module? io.cif.parse?
     @classmethod
     def _set_cell_from_cif_block(
         cls,
@@ -160,6 +166,7 @@ def _set_cell_from_cif_block(
         """Populate the model's unit cell from a CIF block."""
         model.cell.from_cif(block)
 
+    # TODO: Move to a common CIF utility module? io.cif.parse?
     @classmethod
     def _set_atom_sites_from_cif_block(
         cls,
@@ -168,3 +175,7 @@ def _set_atom_sites_from_cif_block(
     ) -> None:
         """Populate the model's atom sites from a CIF block."""
         model.atom_sites.from_cif(block)
+
+    # TODO: How to automatically parce and populate all categories?
+    #  for category in model.categories:
+    #      cls._set_category_from_cif_block(category, block)

tmp/_read_cif.py

@@ -63,6 +63,9 @@
 # %%
 project.experiments.show_names()
 
+# %%
+experiment.show_as_cif()
+
 # %%
 experiment.instrument.setup_wavelength = 1.494
 experiment.instrument.calib_twotheta_offset = 0.6
@@ -90,6 +93,9 @@
 # %% [markdown]
 # ## Step 4: Perform Analysis
 
+# %%
+experiment.show_as_cif()
+
 # %%
 sample_model.cell.length_a.free = True