added LR

src/pdi_nomad_plugin/characterization/schema.py

@@ -194,71 +194,20 @@ class PyrometerTemperature(TimeSeries):
     )
 
 
-class LaserReflectanceCurrent(TimeSeries):
+class LaserReflectanceIntensity(TimeSeries):
     """
     The current measured during the pyrometry experiment.
     """
 
-    m_def = Section(
-        a_plot=[
-            {
-                'label': 'measured current',
-                'x': 'time',
-                'y': ['value'],
-            },
-        ],
-        a_eln={
-            'hide': [
-                'set_value',
-                'set_time',
-            ]
-        },
-    )
+    m_def = Section(a_h5web=H5WebAnnotation(axes='time', signal='value'))
     value = Quantity(
-        type=float,
-        unit='ampere',
-        shape=['*'],
+        type=HDF5Dataset,
+        shape=[],
     )
     time = Quantity(
-        type=Datetime,
+        type=HDF5Dataset,
         description='The process time when each of the values were recorded.',
-        shape=['*'],
-    )
-
-
-class CurrentVsTime(ArchiveSection):
-    """
-    The current vs time data.
-    """
-
-    m_def = Section()
-
-    wavelength = Quantity(
-        type=float,
-        unit='meter',
-        description="""
-        Wavelength of the light used for the pyrometry measurement.
-        """,
-        a_eln=ELNAnnotation(
-            component=ELNComponentEnum.NumberEditQuantity,
-            defaultDisplayUnit='nanometer',
-        ),
-    )
-
-    incidence_angle = Quantity(
-        type=float,
-        unit='degree',
-        description="""
-        The angle of incidence of the light used for the pyrometry measurement.
-        """,
-        a_eln=ELNAnnotation(
-            component=ELNComponentEnum.NumberEditQuantity,
-            defaultDisplayUnit='degree',
-        ),
-    )
-
-    current = SubSection(
-        section_def=LaserReflectanceCurrent,
+        shape=[],
     )
 
 
@@ -322,7 +271,28 @@ class LaserReflectance(Measurement, EntryData):
         type=str,
         a_eln={'component': 'StringEditQuantity'},
     )
-    current_curves = SubSection(
-        section_def=CurrentVsTime,
-        repeats=True,
+    wavelength = Quantity(
+        type=float,
+        unit='meter',
+        description="""
+        Wavelength of the light used for the pyrometry measurement.
+        """,
+        a_eln=ELNAnnotation(
+            component=ELNComponentEnum.NumberEditQuantity,
+            defaultDisplayUnit='nanometer',
+        ),
+    )
+    incidence_angle = Quantity(
+        type=float,
+        unit='degree',
+        description="""
+        The angle of incidence of the light used for the pyrometry measurement.
+        """,
+        a_eln=ELNAnnotation(
+            component=ELNComponentEnum.NumberEditQuantity,
+            defaultDisplayUnit='degree',
+        ),
+    )
+    laser_reflectance_intensity = SubSection(
+        section_def=LaserReflectanceIntensity,
     )

src/pdi_nomad_plugin/mbe/epic_parser/__init__.py

@@ -32,7 +32,7 @@ def load(self):
     mainfile_mime_re='application/vnd.openxmlformats-officedocument.spreadsheetml.sheet',
     mainfile_contents_dict={
         'MBE sources': {'__has_all_keys': ['source_type', 'EPIC_loop']},
-        '__has_symbol': '#',
+        '__has_comment': '#',
     },
     # 'MBE gas mixing': {'__has_all_keys': ['mfc1_EPIC_name']},
 )

src/pdi_nomad_plugin/mbe/epic_parser/parser.py

@@ -36,6 +36,8 @@
 from pdi_nomad_plugin.characterization.schema import (
     PyrometerTemperature,
     Pyrometry,
+    LaserReflectance,
+    LaserReflectanceIntensity,
 )
 from pdi_nomad_plugin.mbe.instrument import (
     ColdLipEffusionCell,
@@ -154,6 +156,14 @@ def parse(
         )
         pyrometry_sheet.columns = pyrometry_sheet.columns.str.strip()
 
+        # "laser reflectance settings" sheet
+        lr_sheet = pd.read_excel(
+            xlsx,
+            'LR settings',
+            comment='#',
+        )
+        lr_sheet.columns = lr_sheet.columns.str.strip()
+
         # reading Messages.txt
         growth_starttime = None
         growth_id = None
@@ -216,39 +226,66 @@ def parse(
         child_archives['instrument'].data.name = f'{data_file} instrument'
         child_archives['instrument'].data.port_list = []
 
-        # read raw files
-        epiclog_value, epiclog_time = epiclog_parse_timeseries(
-            timezone,
-            growth_starttime,
-            folder_path,
-            pyrometry_sheet,
-            'temperature',
-            'temperature_unit',
-        )
         # instantiate objects
         child_archives['process'].data = GrowthMbePDI()
         child_archives['process'].data.steps = [GrowthStepMbePDI()]
         child_archives['process'].data.steps[0].sources = []
+
+        child_archives['process'].data.name = f'{exp_string} process'
+
+        # in situ characterization
         child_archives['process'].data.steps[
             0
         ].in_situ_characterization = InSituCharacterizationMbePDI()
+        # # pyrometry
         child_archives['process'].data.steps[0].in_situ_characterization.pyrometry = [
             Pyrometry()
         ]
         child_archives['process'].data.steps[0].in_situ_characterization.pyrometry[
             0
         ].pyrometer_temperature = PyrometerTemperature()
-
-        # fill in quantities
-        child_archives['process'].data.name = f'{exp_string} process'
         pyro_archive = (
             child_archives['process']
             .data.steps[0]
             .in_situ_characterization.pyrometry[0]
         )
         pyro_archive.name = f'{exp_string} pyrometry'
+        # # # read pyrometry raw files
+        epiclog_value, epiclog_time = epiclog_parse_timeseries(
+            timezone,
+            growth_starttime,
+            folder_path,
+            pyrometry_sheet,
+            'temperature',
+            'temperature_unit',
+        )
         pyro_archive.pyrometer_temperature.value = epiclog_value
         pyro_archive.pyrometer_temperature.time = epiclog_time
+        # # laser reflectance
+        child_archives['process'].data.steps[
+            0
+        ].in_situ_characterization.laser_reflectance = [LaserReflectance()]
+        child_archives['process'].data.steps[
+            0
+        ].in_situ_characterization.laser_reflectance[
+            0
+        ].laser_reflectance_intensity = LaserReflectanceIntensity()
+        lr_archive = (
+            child_archives['process']
+            .data.steps[0]
+            .in_situ_characterization.laser_reflectance[0]
+        )
+        lr_archive.name = f'{exp_string} laser reflectance'
+        # # # read laser reflectance raw files
+        epiclog_value, epiclog_time = epiclog_parse_timeseries(
+            timezone,
+            growth_starttime,
+            folder_path,
+            lr_sheet,
+            'intensity',
+        )
+        lr_archive.laser_reflectance_intensity.value = epiclog_value
+        lr_archive.laser_reflectance_intensity.time = epiclog_time
 
         # filling in the sources objects list
         for sources_index, sources_row in sources_sheet.iterrows():
@@ -445,7 +482,11 @@ def parse(
                             float(t0_param), ureg('°C')
                         )
                         source_object.impinging_flux[0].a_parameter = float(a_param)
-                        source_object.impinging_flux[0].value = impinging_flux
+                        source_object.impinging_flux[
+                            0
+                        ].value = (
+                            impinging_flux  # TODO this value is in nm -> convert to m
+                        )
                         source_object.impinging_flux[
                             0
                         ].time = epiclog_time  # TODO insert hdf5 link

src/pdi_nomad_plugin/mbe/instrument.py

@@ -336,7 +336,7 @@ class ImpingingFluxPDI(ImpingingFlux):
     bep_to_flux = Quantity(
         type=float,
         description='The conversion factor from Beam Equivalent Pressure (BEP) to the flux.',
-        unit='mol **-1 * meter ** -2 * second * pascal ** -1',
+        unit='meter ** -2 * second * pascal ** -1',
     )
     t_0_parameter = Quantity(
         type=float,
@@ -347,7 +347,7 @@ class ImpingingFluxPDI(ImpingingFlux):
     )
     value = Quantity(
         type=HDF5Dataset,
-        unit='mol/meter ** 2/second',
+        unit='1/meter ** 2/second',
         shape=[],
     )
     time = Quantity(

src/pdi_nomad_plugin/mbe/processes.py

@@ -420,12 +420,15 @@ class InSituCharacterizationMbePDI(ArchiveSection):
     )
     laser_reflectance = SubSection(
         section_def=LaserReflectanceReference,
+        repeats=True,
     )
     mass_spectrometry = SubSection(
         section_def=MassSpectrometryReference,
+        repeats=True,
     )
     rheed = SubSection(
         section_def=RHEEDReference,
+        repeats=True,
     )