feat: expose NC options in peak reader (#234)

* feat: expose NC options in peak reader

* Update src/ess/diffraction/peaks.py

Co-authored-by: Jan-Lukas Wynen <jan-lukas.wynen@ess.eu>

* docs: add example

* fix

* fix

* fix

---------

Co-authored-by: Jan-Lukas Wynen <jan-lukas.wynen@ess.eu>

Author: jokasimr

src/ess/beer/peakfinding.py

@@ -1,9 +1,9 @@
-from ..diffraction.peaks import dspacing_peak_positions_from_cif
+from ..diffraction.peaks import dspacing_peaks_from_cif
 from .types import CIFIdentifierForPeakPositions, CIFPeaksMinIntensity, DHKLList
 
 
 def dhkl_peaks_from_cif(
     cif: CIFIdentifierForPeakPositions, intensity_threshold: CIFPeaksMinIntensity
 ) -> DHKLList:
     '''Gets the list of expected peak positions from a CIF file/identifier.'''
-    return dspacing_peak_positions_from_cif(cif, intensity_threshold)
+    return dspacing_peaks_from_cif(cif, intensity_threshold).coords['dspacing']

src/ess/diffraction/peaks.py

@@ -2,9 +2,9 @@
 import scipp as sc
 
 
-def dspacing_peak_positions_from_cif(cif, intensity_threshold=None) -> sc.Variable:
+def dspacing_peaks_from_cif(cif, intensity_threshold=None, **kwargs) -> sc.DataArray:
     """
-    Retrieves a list of the peak positions for the given material.
+    Retrieves a data array representing the bragg peaks of the given material.
 
     The material is represented by a cif file or a codid or similar.
     The number of peaks retrieved can be controlled by setting the intensity
@@ -27,20 +27,58 @@ def dspacing_peak_positions_from_cif(cif, intensity_threshold=None) -> sc.Variab
         times the multiplicity of the peak.
         The ``intensity_threshold`` must be convertible to unit ``barn``.
 
+    kwargs:
+        Can be anything that :py:`NCrystal.NCMATComposer.from_cif` supports.
+        For example: ``uiso_temperature`` or ``override_spacegroup``.
+
     Returns
     ------------
-        Array containing the peak positions in `dspacing`, with unit ``angstrom``.
-    """
-    info = NC.NCMATComposer.from_cif(cif).load('comp=bragg').info
+        Data array representing peak amplitudes and peak positions in ``dspacing``.
+        The full NCrystal information object is added as a coordinate with the name ``info``.
+        The input arguments are added as scalar coordinates.
+
+    Examples
+    --------
+    >>> from ess.diffraction.peaks import dspacing_peaks_from_cif
+    >>> dspacing_peaks_from_cif(
+    ...     'codid::9008460',
+    ...     uiso_temperature=400,
+    ...     override_spacegroup='F d -3 m:1',
+    ... )
+    <scipp.DataArray>
+    Dimensions: Sizes[peaks:162, ]
+    Coordinates:
+    * cif                        string        <no unit>  ()  "codid::9008460"
+    * dspacing                  float64             [Å]  (peaks)  [2.33803, 2.02479, ..., 0.243756, 0.243756]
+    * info                     PyObject        <no unit>  ()  <NCrystal.core.Info object at ...>
+    * override_spacegroup        string        <no unit>  ()  "F d -3 m:1"
+    * uiso_temperature            int64  [dimensionless]  ()  400
+    Data:
+                                float64           [barn]  (peaks)  [13.3631, 9.59562, ..., 0.000556426, 0.000556426]
+
+    """  # noqa: E501
+    info = NC.NCMATComposer.from_cif(cif, **kwargs).load('comp=bragg').info
     min_intensity = (
         intensity_threshold.to(unit='barn').value
         if intensity_threshold is not None
         else 0
     )
-    return sc.array(
-        dims=['peaks'],
-        values=[
-            hkl.d for hkl in info.hklObjects() if (hkl.f2 * hkl.mult) >= min_intensity
-        ],
+    dims = ['peaks']
+    peaks = [hkl for hkl in info.hklObjects() if (hkl.f2 * hkl.mult) >= min_intensity]
+    dspacing = sc.array(
+        dims=dims,
+        values=[hkl.d for hkl in peaks],
         unit='angstrom',
     )
+    out = sc.DataArray(
+        sc.array(dims=dims, values=[hkl.f2 * hkl.mult for hkl in peaks], unit='barn'),
+        coords={
+            'dspacing': dspacing,
+            'cif': sc.scalar(cif),
+            'info': sc.scalar(info),
+            **{name: sc.scalar(value) for name, value in kwargs.items()},
+        },
+    )
+    if intensity_threshold is not None:
+        out.coords['intensity_threshold'] = intensity_threshold
+    return out

tests/diffraction/test_peaks.py

@@ -1,25 +1,33 @@
 import scipp as sc
 
-from ess.diffraction.peaks import dspacing_peak_positions_from_cif
+from ess.diffraction.peaks import dspacing_peaks_from_cif
 
 
 def test_retreived_peak_list_has_expected_units():
-    d = dspacing_peak_positions_from_cif(
+    d = dspacing_peaks_from_cif(
         'codid::9011998',
         sc.scalar(50, unit='barn'),
     )
-    assert d.unit == 'angstrom'
+    assert d.coords['dspacing'].unit == 'angstrom'
+    assert d.unit == 'barn'
 
 
 def test_intensity_threshold_is_taken_into_account():
-    d = dspacing_peak_positions_from_cif(
+    d = dspacing_peaks_from_cif(
         'codid::9011998',
         sc.scalar(50, unit='barn'),
     )
     assert len(d) > 0
 
-    d = dspacing_peak_positions_from_cif(
+    d = dspacing_peaks_from_cif(
         'codid::9011998',
         sc.scalar(50, unit='Mbarn'),
     )
     assert len(d) == 0
+
+
+def test_retreived_peak_list_with_temperature_kwarg():
+    d = dspacing_peaks_from_cif(
+        'codid::9011998', sc.scalar(50, unit='barn'), uiso_temperature=300
+    )
+    assert d.coords['uiso_temperature'] == 300