Refactors ExperimentType initialization to use default values and updates experiment handling in factory methods

Author: AndrewSazonov

src/easydiffraction/experiments/categories/experiment_type.py

@@ -32,10 +32,10 @@ class ExperimentType(CategoryItem):
     def __init__(
         self,
         *,
-        sample_form: str,
-        beam_mode: str,
-        radiation_probe: str,
-        scattering_type: str,
+        sample_form=None,
+        beam_mode=None,
+        radiation_probe=None,
+        scattering_type=None,
     ):
         super().__init__()
 

src/easydiffraction/experiments/experiment/factory.py

@@ -50,6 +50,9 @@ def _make_experiment_type(cls, kwargs):
         """Helper to construct an ExperimentType from keyword arguments,
         using defaults as needed.
         """
+        # TODO: Defaults are already in the experiment type...
+        # TODO: Merging with experiment_type_from_block from
+        #  io.cif.parse
         return ExperimentType(
             sample_form=kwargs.get('sample_form', SampleFormEnum.default()),
             beam_mode=kwargs.get('beam_mode', BeamModeEnum.default()),
@@ -66,17 +69,20 @@ def _create_from_gemmi_block(
         """Build a model instance from a single CIF block."""
         name = 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)
+        # TODO: move to io.cif.parse?
+        expt_type = ExperimentType()
+        for param in expt_type.parameters:
+            param.from_cif(block)
 
         # Create experiment instance of appropriate class
+        # TODO: make helper method to create experiment from type
         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)
 
         # Read all categories from CIF block
+        # TODO: move to io.cif.parse?
         for category in expt_obj.categories:
             category.from_cif(block)
 

src/easydiffraction/io/cif/parse.py

@@ -23,3 +23,12 @@ def name_from_block(block: gemmi.cif.Block) -> str:
     """Extract a model name from the CIF block name."""
     # TODO: Need validator or normalization?
     return block.name
+
+
+# def experiment_type_from_block(
+#        exp_type: ExperimentType,
+#        block: gemmi.cif.Block,
+# ) -> dict:
+#    """Extract experiment type information from a CIF block."""
+#    for param in exp_type.parameters:
+#        param.from_cif(block)

src/easydiffraction/io/cif/serialize.py

@@ -316,6 +316,10 @@ def datastore_from_cif(
 ) -> None:
     """Populate a datastore from a CIF block."""
     # TODO: Make datastore category collection with cif names, etc.
+    #  We need multiple datastores for different experiment types.
+    #  Similar to e.g. background or instrument or peak categories.
+    #  Then, datastore will be automatically handled like other
+    #  categories and this method can be removed.
     x_name = '_pd_meas.2theta_scan'
     y_name = '_pd_meas.intensity_total'
     sy_name = '_pd_meas.intensity_total_su'

tmp/_read_cif.py

@@ -18,11 +18,6 @@
 
 # %% [markdown]
 # ## Import Library
-#
-# import gemmi
-# d = gemmi.cif.read_string("data_x\n_a 1\n")
-# b = d.sole_block()
-# do nothing else
 
 # %%
 import easydiffraction as ed
@@ -32,7 +27,6 @@
 Logger.configure(
     level=Logger.Level.INFO,
     mode=Logger.Mode.COMPACT,
-    #mode=Logger.Mode.VERBOSE,
     reaction=Logger.Reaction.WARN,
 )
 
@@ -52,10 +46,11 @@
 project.sample_models.show_names()
 
 # %%
-sample_model = project.sample_models['lbco']
+# Create an alias for easier access
+lbco = project.sample_models['lbco']
 
 # %%
-sample_model.show_as_cif()
+lbco.show_as_cif()
 
 # %% [markdown]
 # ## Step 3: Define Experiment
@@ -64,40 +59,47 @@
 project.experiments.add_from_cif_path("data/hrpt.cif")
 
 # %%
-experiment = project.experiments['hrpt']
+project.experiments.show_names()
 
 # %%
-project.experiments.show_names()
+# Create an alias for easier access
+hrpt = project.experiments['hrpt']
 
 # %%
-experiment.show_as_cif()
+hrpt.show_as_cif()
 
 # %% [markdown]
 # ## Step 4: Perform Analysis
 
 # %%
-sample_model.cell.length_a.free = True
+# Select sample model parameters to refine
+lbco.cell.length_a.free = True
 
-sample_model.atom_sites['La'].b_iso.free = True
-sample_model.atom_sites['Ba'].b_iso.free = True
-sample_model.atom_sites['Co'].b_iso.free = True
-sample_model.atom_sites['O'].b_iso.free = True
+#lbco.atom_sites['La'].b_iso.free = True
+#lbco.atom_sites['Ba'].b_iso.free = True
+#lbco.atom_sites['Co'].b_iso.free = True
+#lbco.atom_sites['O'].b_iso.free = True
+for atom_site in lbco.atom_sites:
+    atom_site.b_iso.free = True
 
 # %%
-experiment.instrument.calib_twotheta_offset.free = True
+# Select experiment parameters to refine
+hrpt.linked_phases['lbco'].scale.free = True
 
-experiment.peak.broad_gauss_u.free = True
-experiment.peak.broad_gauss_v.free = True
-experiment.peak.broad_gauss_w.free = True
-experiment.peak.broad_lorentz_y.free = True
+hrpt.instrument.calib_twotheta_offset.free = True
 
-#experiment.background['10'].y.free = True
-#experiment.background['30'].y.free = True
-#experiment.background['50'].y.free = True
-#experiment.background['110'].y.free = True
-#experiment.background['165'].y.free = True
+hrpt.peak.broad_gauss_u.free = True
+hrpt.peak.broad_gauss_v.free = True
+hrpt.peak.broad_gauss_w.free = True
+hrpt.peak.broad_lorentz_y.free = True
 
-experiment.linked_phases['lbco'].scale.free = True
+#hrpt.background['10'].y.free = True
+#hrpt.background['30'].y.free = True
+#hrpt.background['50'].y.free = True
+#hrpt.background['110'].y.free = True
+#hrpt.background['165'].y.free = True
+for line_segment in hrpt.background:
+    line_segment.y.free = True
 
 # %%
 project.analysis.fit()

tmp/data/hrpt.cif

@@ -15,25 +15,23 @@ _instr.wavelength 1.494
 _instr.2theta_offset 0.6
 
 loop_
-	_pd_phase_block.id
-	_pd_phase_block.scale
-	lbco 10.0
+_pd_phase_block.id
+_pd_phase_block.scale
+lbco 10.0
 
+loop_
+_pd_background_line_segment_X
+_pd_background_line_segment_intensity
+10 170
+30 170
+50 170
+110 170
+165 170
 
-
-	loop_
-	_pd_background.line_segment_X
-	_pd_background.line_segment_intensity
-	10 170
-	30 170
-	50 170
-	110 170
-	165 170
-
-	loop_
-	_pd_meas.2theta_scan
-	_pd_meas.intensity_total
-	_pd_meas.intensity_total_su
+loop_
+_pd_meas.2theta_scan
+_pd_meas.intensity_total
+_pd_meas.intensity_total_su
      10.00    167.00   12.60
      10.05    157.00   12.50
      10.10    187.00   13.30

tmp/data/lbco.cif

@@ -34,3 +34,4 @@
  10.15 197.0 14.0
  10.2 164.0 12.5
  10.25 171.0 13.0
+