Ad IR schema and test

src/nomad_unisyscat/schema_packages/mypackage.py

@@ -39,14 +39,14 @@ class NRVSResult(MeasurementResult):
         type=np.float64,
         shape=['*'],
         unit='dimensionless',
-        description='The count at each wavenumber value, dimensionless',
+        description='The 57Fe PVDOS count at each wavenumber value, dimensionless',
         a_plot={'x': 'array_index', 'y': 'intensity'},
     )
     wavenumber = Quantity(
         type=np.float64,
         shape=['*'],
         unit='1/cm',
-        description='The wavenumber range of the sprectrum',
+        description='The wavenumber range of the spectrum',
         a_eln=ELNAnnotation(defaultDisplayUnit='1/cm'),
         a_plot={'x': 'array_index', 'y': 'wavenumber'},
     )
@@ -116,10 +116,100 @@ def normalize(self, archive, logger):
 
         self.figures = []
 
-        fig = px.line(x=data['wavenumber, cm-1'], y=data['57Fe PVDOS'])
+        fig = px.line(x=self.results.wavenumber, y=self.results.intensity)
         fig.update_xaxes(title_text=col_names[0])
         fig.update_yaxes(title_text=col_names[1])
         self.figures.append(PlotlyFigure(label='NRVS', figure=fig.to_plotly_json()))
 
 
+class IRResult(MeasurementResult):
+    m_def = Section()
+
+    array_index = Quantity(
+        type=np.float64,
+        shape=['*'],
+        description=(
+            'A placeholder for the indices of vectorial quantities. '
+            'Used as x-axis for plots within quantities.'
+        ),
+        a_display={'visible': False},
+    )
+    intensity = Quantity(
+        type=np.float64,
+        shape=['*'],
+        unit='dimensionless',
+        description='The absorbance at each wavenumber value, dimensionless',
+        a_plot={'x': 'array_index', 'y': 'intensity'},
+    )
+    wavenumber = Quantity(
+        type=np.float64,
+        shape=['*'],
+        unit='1/cm',
+        description='The wavenumber range of the spectrum',
+        a_eln=ELNAnnotation(defaultDisplayUnit='1/cm'),
+        a_plot={'x': 'array_index', 'y': 'wavenumber'},
+    )
+
+
+class IRSpectroscopy(Measurement, PlotSection, Schema):
+    data_file = Quantity(
+        type=str,
+        description="""
+            csv data file ending .dat
+            """,
+        a_eln=ELNAnnotation(component='FileEditQuantity'),
+        a_browser=dict(adaptor='RawFileAdaptor'),
+    )
+
+    method = Quantity(
+        type=str,
+        description="""
+            name of the method
+            """,
+        a_eln=ELNAnnotation(
+            component='StringEditQuantity',
+            default='infra red vibrational spectroscopy',
+            props=dict(
+                suggestions=[
+                    'experimental IR vibrational spectroscopy',
+                    'simulated IR vibrational spectroscopy',
+                ]
+            ),
+        ),
+    )
+
+    results = Measurement.results.m_copy()
+    results.section_def = IRResult
+
+    def normalize(self, archive, logger):
+        super().normalize(archive, logger)
+        if self.data_file is None:
+            return
+
+        if (self.data_file is not None) and (
+            os.path.splitext(self.data_file)[-1] != '.dat'
+        ):
+            raise ValueError('Unsupported file format. Only .dat file')
+
+        if self.data_file.endswith('.dat'):
+            with archive.m_context.raw_file(self.data_file) as f:
+                import pandas as pd
+
+                col_names = ['wavenumber, cm-1', 'Absorbance']
+                data = pd.read_csv(f.name, header=None, names=col_names)
+        result = IRResult()
+        result.wavenumber = data['wavenumber, cm-1']
+        result.intensity = data['Absorbance']
+        results = []
+        results.append(result)
+        self.results = results
+
+        self.figures = []
+
+        fig = px.line(x=data['wavenumber, cm-1'], y=data['57Fe PVDOS'])
+        fig.update_xaxes(title_text=col_names[0])
+        fig.update_yaxes(title_text=col_names[1])
+        self.figures.append(PlotlyFigure(label='IR', figure=fig.to_plotly_json()))
+
+
 m_package.__init_metainfo__()

tests/data/ir_test.archive.yaml

@@ -0,0 +1,3 @@
+data:
+  m_def: nomad_unisyscat.schema_packages.mypackage.IRSpectroscopy
+  measurement_data_file: ReRH_Nia-C_H_IR_exp.dat