Abstract out data interaction using setter and getter; allows to use …

…same methods for classes with hdf5 refs

src/nomad_measurements/utils.py

@@ -18,6 +18,7 @@
 import os.path
 from typing import (
     TYPE_CHECKING,
+    Any,
 )
 
 import numpy as np
@@ -151,3 +152,34 @@ def get_bounding_range_2d(ax1, ax2):
         ]
 
     return ax1_range, ax2_range
+
+
+def get_data(obj, key: str) -> Any:
+    """
+    Get the data for the quantity. If the quantity is a HDF5Reference, read the dataset
+    and corresponding units if available, and return a pint.Quantity.
+
+    Args:
+        obj (Any): The object to get the data from.
+        key (str): The key of the quantity.
+
+    Returns:
+        Any: The data for the quantity.
+    """
+    return getattr(obj, key, None)
+
+
+def set_data(obj, **kwargs):
+    """
+    Set the data for the quantity. If the quantity is a HDF5Reference, the new value is
+    set in the HDF5 file at the corresponding path.
+
+    Args:
+        obj (Any): The object to set the data for.
+    """
+    if not kwargs:
+        raise ValueError('At least one keyword argument must be provided.')
+
+    for key, value in kwargs.items():
+        if hasattr(obj, key):
+            setattr(obj, key, value)

src/nomad_measurements/xrd/schema.py

@@ -67,8 +67,12 @@
 from nomad_measurements.general import (
     NOMADMeasurementsCategory,
 )
-from nomad_measurements.utils import get_bounding_range_2d, merge_sections
-from nomad_measurements.xrd.nx import write_nx_section_and_create_file
+from nomad_measurements.utils import (
+    get_bounding_range_2d,
+    get_data,
+    merge_sections,
+    set_data,
+)
 
 if TYPE_CHECKING:
     import pint
@@ -358,12 +362,13 @@ def generate_plots(self, archive: 'EntryArchive', logger: 'BoundLogger'):
             (dict, dict): line_linear, line_log
         """
         plots = []
-        if self.two_theta is None or self.intensity is None:
+        two_theta = get_data(self, 'two_theta')
+        intensity = get_data(self, 'intensity')
+        if any([two_theta, intensity] == [None, None]):
             return plots
 
-        x = self.two_theta.to('degree').magnitude
-        y = self.intensity.magnitude
-
+        x = two_theta.to('degree').magnitude
+        y = intensity.magnitude
         fig_line_linear = px.line(
             x=x,
             y=y,
@@ -515,12 +520,15 @@ def normalize(self, archive: 'EntryArchive', logger: 'BoundLogger'):
                 self.name = f'{self.scan_axis} Scan Result'
             else:
                 self.name = 'XRD Scan Result'
+        q_norm = get_data(self, 'q_norm')
+        two_theta = get_data(self, 'two_theta')
         if self.source_peak_wavelength is not None:
-            self.q_norm, self.two_theta = calculate_two_theta_or_q(
+            q_norm, two_theta = calculate_two_theta_or_q(
                 wavelength=self.source_peak_wavelength,
-                two_theta=self.two_theta,
-                q=self.q_norm,
+                two_theta=two_theta,
+                q=q_norm,
             )
+            set_data(self, q_norm=q_norm, two_theta=two_theta)
 
 
 class XRDResultRSM(XRDResult):
@@ -561,14 +569,17 @@ def generate_plots(self, archive: 'EntryArchive', logger: 'BoundLogger'):
             (dict, dict): json_2theta_omega, json_q_vector
         """
         plots = []
-        if self.two_theta is None or self.intensity is None or self.omega is None:
+        two_theta = get_data(self, 'two_theta')
+        intensity = get_data(self, 'intensity')
+        omega = get_data(self, 'omega')
+        if two_theta is None or intensity is None or omega is None:
             return plots
 
         # Plot for 2theta-omega RSM
         # Zero values in intensity become -inf in log scale and are not plotted
-        x = self.omega.to('degree').magnitude
-        y = self.two_theta.to('degree').magnitude
-        z = self.intensity.magnitude
+        x = omega.to('degree').magnitude
+        y = two_theta.to('degree').magnitude
+        z = intensity.magnitude
         log_z = np.log10(z)
         x_range, y_range = get_bounding_range_2d(x, y)
 
@@ -637,8 +648,8 @@ def generate_plots(self, archive: 'EntryArchive', logger: 'BoundLogger'):
 
         # Plot for RSM in Q-vectors
         if self.q_parallel is not None and self.q_perpendicular is not None:
-            x = self.q_parallel.to('1/angstrom').magnitude.flatten()
-            y = self.q_perpendicular.to('1/angstrom').magnitude.flatten()
+            x = get_data(self, 'q_parallel').to('1/angstrom').magnitude.flatten()
+            y = get_data(self, 'q_perpendicular').to('1/angstrom').magnitude.flatten()
             # q_vectors lead to irregular grid
             # generate a regular grid using interpolation
             x_regular = np.linspace(x.min(), x.max(), z.shape[0])
@@ -721,19 +732,26 @@ def generate_plots(self, archive: 'EntryArchive', logger: 'BoundLogger'):
 
     def normalize(self, archive: 'EntryArchive', logger: 'BoundLogger'):
         super().normalize(archive, logger)
+
         if self.name is None:
             self.name = 'RSM Scan Result'
-        var_axis = 'omega'
+
         if self.source_peak_wavelength is not None:
             for var_axis in ['omega', 'chi', 'phi']:
+                var_axis_value = get_data(self, var_axis)
                 if (
-                    self[var_axis] is not None
-                    and len(np.unique(self[var_axis].magnitude)) > 1
+                    var_axis_value is not None
+                    and len(np.unique(var_axis_value.magnitude)) > 1
                 ):
-                    self.q_parallel, self.q_perpendicular = calculate_q_vectors_RSM(
+                    q_parallel, q_perpendicular = calculate_q_vectors_RSM(
                         wavelength=self.source_peak_wavelength,
                         two_theta=self.two_theta * np.ones_like(self.intensity),
-                        omega=self[var_axis],
+                        omega=var_axis_value,
+                    )
+                    set_data(
+                        self,
+                        q_parallel=q_parallel,
+                        q_perpendicular=q_perpendicular,
                     )
                     break