Fixed issues in the LabView ETO class, separated out the ACT from the…

… ETO

pyproject.toml

@@ -111,9 +111,13 @@ package-dir = { "" = "src" }
 where = ["src"]
 
 [project.entry-points.'nomad.plugin']
-parser_entry_point_data = "cpfs_ppms.parsers:parser_entry_point_data"
+parser_entry_point_data_eto_default = "cpfs_ppms.parsers:parser_entry_point_data_eto_default"
+parser_entry_point_data_eto_labview = "cpfs_ppms.parsers:parser_entry_point_data_eto_labview"
+parser_entry_point_data_act_default = "cpfs_ppms.parsers:parser_entry_point_data_act_default"
 parser_entry_point_sqc = "cpfs_ppms.parsers:parser_entry_point_sqc"
 schema_entry_point_eto_default = "cpfs_ppms.schema_packages:schema_entry_point_eto_default"
+schema_entry_point_eto_labview = "cpfs_ppms.schema_packages:schema_entry_point_eto_labview"
+schema_entry_point_act_default = "cpfs_ppms.schema_packages:schema_entry_point_act_default"
 
 
 

src/cpfs_ppms/cpfsppmsdatastruct.py

@@ -346,36 +346,20 @@ def normalize(self, archive, logger: BoundLogger) -> None:  # noqa: PLR0912, PLR
         from plotly.subplots import make_subplots
 
         for data in self.data:
-            if self.software.startswith('ACTRANSPORT'):
-                if data.measurement_type == 'field':
-                    resistivity_ch1 = px.scatter(
-                        x=data.magnetic_field, y=data.channels[0].resistivity
-                    )
-                    resistivity_ch2 = px.scatter(
-                        x=data.magnetic_field, y=data.channels[1].resistivity
-                    )
-                if data.measurement_type == 'temperature':
-                    resistivity_ch1 = px.scatter(
-                        x=data.temperature, y=data.channels[0].resistivity
-                    )
-                    resistivity_ch2 = px.scatter(
-                        x=data.temperature, y=data.channels[1].resistivity
-                    )
-            if self.software.startswith('Electrical Transport Option'):
-                if data.measurement_type == 'field':
-                    resistivity_ch1 = px.scatter(
-                        x=data.magnetic_field, y=data.channels[0].resistance
-                    )
-                    resistivity_ch2 = px.scatter(
-                        x=data.magnetic_field, y=data.channels[1].resistance
-                    )
-                if data.measurement_type == 'temperature':
-                    resistivity_ch1 = px.scatter(
-                        x=data.temperature, y=data.channels[0].resistance
-                    )
-                    resistivity_ch2 = px.scatter(
-                        x=data.temperature, y=data.channels[1].resistance
-                    )
+            if data.measurement_type == 'field':
+                resistivity_ch1 = px.scatter(
+                    x=data.magnetic_field, y=data.channels[0].resistance
+                )
+                resistivity_ch2 = px.scatter(
+                    x=data.magnetic_field, y=data.channels[1].resistance
+                )
+            if data.measurement_type == 'temperature':
+                resistivity_ch1 = px.scatter(
+                    x=data.temperature, y=data.channels[0].resistance
+                )
+                resistivity_ch2 = px.scatter(
+                    x=data.temperature, y=data.channels[1].resistance
+                )
             figure1 = make_subplots(rows=2, cols=1, shared_xaxes=True)
             figure1.add_trace(resistivity_ch1.data[0], row=1, col=1)
             figure1.add_trace(resistivity_ch2.data[0], row=2, col=1)
@@ -385,17 +369,18 @@ def normalize(self, archive, logger: BoundLogger) -> None:  # noqa: PLR0912, PLR
             )
 
         # find measurement modes, for now coming from sample.comment
-        modelist = []
-        for channel in ['Ch1_', 'Ch2_']:
-            if channel + 'TMR' in self.samples[0].comment:
-                modelist.append('TMR')
-            elif channel + 'Hall' in self.samples[0].comment:
-                modelist.append('Hall')
-            else:
-                modelist.append('undefined')
-        self.channel_measurement_type = modelist
-
-        if self.software.startswith('Electrical Transport Option'):
+        if self.samples[0].comment:
+            modelist = []
+            for channel in ['Ch1_', 'Ch2_']:
+                if channel + 'TMR' in self.samples[0].comment:
+                    modelist.append('TMR')
+                elif channel + 'Hall' in self.samples[0].comment:
+                    modelist.append('Hall')
+                else:
+                    modelist.append('undefined')
+            self.channel_measurement_type = modelist
+
+        if 'Hall' in self.channel_measurement_type and 'TMR' in self.channel_measurement_type:
             # find biggest fitlength
             maxfield = 90000 * ureg('gauss')
             fitlength = 0
@@ -777,3 +762,58 @@ def normalize(self, archive, logger: BoundLogger) -> None:  # noqa: PLR0912, PLR
                 PlotlyFigure(label='AHC', figure=figure3.to_plotly_json())
             )
 
+class CPFSPPMSACTMeasurement(CPFSPPMSMeasurement, PlotSection, EntryData):
+
+    temperature_tolerance = Quantity(
+        type=float,
+        unit='kelvin',
+        a_eln=ELNAnnotation(
+            component='NumberEditQuantity', defaultDisplayUnit='kelvin'
+        ),
+    )
+
+    field_tolerance = Quantity(
+        type=float,
+        unit='gauss',
+        a_eln=ELNAnnotation(component='NumberEditQuantity', defaultDisplayUnit='gauss'),
+    )
+
+    def normalize(self, archive, logger: BoundLogger) -> None:  # noqa: PLR0912, PLR0915
+        super().normalize(archive, logger)
+
+        ### Start of the PPMSMeasurement normalizer
+
+        if archive.data.sequence_file:
+            logger.info('Parsing PPMS sequence file.')
+            with archive.m_context.raw_file(self.sequence_file, 'r') as file:
+                sequence = file.readlines()
+                self.steps = find_ppms_steps_from_sequence(sequence)
+
+
+
+        # Now create the according plots
+        import plotly.express as px
+        from plotly.subplots import make_subplots
+
+        for data in self.data:
+            if data.measurement_type == 'field':
+                resistivity_ch1 = px.scatter(
+                    x=data.magnetic_field, y=data.channels[0].resistivity
+                )
+                resistivity_ch2 = px.scatter(
+                    x=data.magnetic_field, y=data.channels[1].resistivity
+                )
+            if data.measurement_type == 'temperature':
+                resistivity_ch1 = px.scatter(
+                    x=data.temperature, y=data.channels[0].resistivity
+                )
+                resistivity_ch2 = px.scatter(
+                    x=data.temperature, y=data.channels[1].resistivity
+                )
+            figure1 = make_subplots(rows=2, cols=1, shared_xaxes=True)
+            figure1.add_trace(resistivity_ch1.data[0], row=1, col=1)
+            figure1.add_trace(resistivity_ch2.data[0], row=2, col=1)
+            figure1.update_layout(height=400, width=716, title_text=data.name)
+            self.figures.append(
+                PlotlyFigure(label=data.name, figure=figure1.to_plotly_json())
+            )

src/cpfs_ppms/parsers/__init__.py

@@ -2,22 +2,56 @@
 from pydantic import Field
 
 
-class DataParserEntryPoint(ParserEntryPoint):
+class DataParserEntryPointETODefault(ParserEntryPoint):
     parameter: int = Field(0, description='Custom configuration parameter')
 
     def load(self):
-        from cpfs_ppms.parsers.parser import CPFSPPMSParser
+        from cpfs_ppms.parsers.parser import CPFSPPMSETOParserDefault
 
-        return CPFSPPMSParser(**self.dict())
+        return CPFSPPMSETOParserDefault(**self.dict())
 
 
-parser_entry_point_data = DataParserEntryPoint(
+parser_entry_point_data_eto_default = DataParserEntryPointETODefault(
     name='DataParser',
     description='New parser entry point configuration.',
     mainfile_name_re='^.+\.dat$',
     mainfile_mime_re='application/x-wine-extension-ini',
+    mainfile_contents_re='BYAPP, Electrical Transport Option'
 )
 
+class DataParserEntryPointETOLabview(ParserEntryPoint):
+    parameter: int = Field(0, description='Custom configuration parameter')
+
+    def load(self):
+        from cpfs_ppms.parsers.parser import CPFSPPMSETOParserLabview
+
+        return CPFSPPMSETOParserLabview(**self.dict())
+
+
+parser_entry_point_data_eto_labview = DataParserEntryPointETOLabview(
+    name='DataParser',
+    description='New parser entry point configuration.',
+    #mainfile_name_re='^.+\.dat$',
+    mainfile_mime_re='text/plain',
+    mainfile_contents_re='; LABVIEW measurement file V2.6'
+)
+
+class DataParserEntryPointACTDefault(ParserEntryPoint):
+    parameter: int = Field(0, description='Custom configuration parameter')
+
+    def load(self):
+        from cpfs_ppms.parsers.parser import CPFSPPMSACTParserDefault
+
+        return CPFSPPMSACTParserDefault(**self.dict())
+
+
+parser_entry_point_data_act_default = DataParserEntryPointACTDefault(
+    name='DataParser',
+    description='New parser entry point configuration.',
+    mainfile_name_re='^.+\.dat$',
+    mainfile_mime_re='application/x-wine-extension-ini',
+    mainfile_contents_re='BYAPP,\s*ACTRANSPORT'
+)
 
 class SqcParserEntryPoint(ParserEntryPoint):
     parameter: int = Field(0, description='Custom configuration parameter')

src/cpfs_ppms/parsers/parser.py

@@ -33,7 +33,11 @@
 from nomad.search import search
 from nomad_material_processing.utils import create_archive
 
-from cpfs_ppms.schema_packages.schema_package import CPFSPPMSETOMeasurementDefault
+from cpfs_ppms.schema_packages.schema_package import (
+    CPFSPPMSETOMeasurementDefault,
+    CPFSPPMSETOMeasurementLabview,
+    CPFSPPMSACTMeasurementDefault,
+)
 
 if TYPE_CHECKING:
     from nomad.datamodel.datamodel import (
@@ -47,7 +51,13 @@
 )
 
 configuration = config.get_plugin_entry_point(
-    'cpfs_ppms.parsers:parser_entry_point_data'
+    'cpfs_ppms.parsers:parser_entry_point_data_eto_default'
+)
+configuration = config.get_plugin_entry_point(
+    'cpfs_ppms.parsers:parser_entry_point_data_eto_labview'
+)
+configuration = config.get_plugin_entry_point(
+    'cpfs_ppms.parsers:parser_entry_point_data_act_default'
 )
 configuration = config.get_plugin_entry_point(
     'cpfs_ppms.parsers:parser_entry_point_sqc'
@@ -63,14 +73,7 @@ class CPFSPPMSFile(EntryData):
     )
 
 
-class CPFSPPMSParser(MatchingParser):
-    # def __init__(self):
-    #    super().__init__(
-    #        name='NOMAD PPMS schema and parser plugin for the CPFS',
-    #        code_name='cpfs_ppms_data',
-    #        code_homepage='https://github.com/FAIRmat-NFDI/AreaA-data_modeling_and_schemas',
-    #        supported_compressions=['gz', 'bz2', 'xz'],
-    #    )
+class CPFSPPMSETOParserDefault(MatchingParser):
 
     def parse(self, mainfile: str, archive: EntryArchive, logger) -> None:
         timethreshold = 15
@@ -108,6 +111,58 @@ def parse(self, mainfile: str, archive: EntryArchive, logger) -> None:
         )
         archive.metadata.entry_name = data_file + ' measurement file'
 
+class CPFSPPMSETOParserLabview(MatchingParser):
+
+    def parse(self, mainfile: str, archive: EntryArchive, logger) -> None:
+        timethreshold = 15
+        data_file = mainfile.split('/')[-1]
+        data_file_with_path = mainfile.split('raw/')[-1]
+        entry = CPFSPPMSETOMeasurementLabview()
+        entry.data_file = data_file_with_path
+        file_name = f'{data_file[:-4]}.archive.json'
+        archive.data = CPFSPPMSFile(
+            measurement=create_archive(entry, archive, file_name)
+        )
+        archive.metadata.entry_name = data_file + ' measurement file'
+
+class CPFSPPMSACTParserDefault(MatchingParser):
+
+    def parse(self, mainfile: str, archive: EntryArchive, logger) -> None:
+        timethreshold = 15
+        data_file = mainfile.split('/')[-1]
+        data_file_with_path = mainfile.split('raw/')[-1]
+        entry = CPFSPPMSACTMeasurementDefault()
+        entry.data_file = data_file_with_path
+        file_name = f'{data_file[:-4]}.archive.json'
+        # entry.normalize(archive, logger)
+        tic = perf_counter()
+        while True:
+            search_result = search(
+                owner='user',
+                query={
+                    'results.eln.sections:any': ['CPFSPPMSSequenceFile'],
+                    'upload_id:any': [archive.m_context.upload_id],
+                },
+                user_id=archive.metadata.main_author.user_id,
+            )
+            if len(search_result.data) > 0:
+                for sequence in search_result.data:
+                    entry.sequence_file = sequence['search_quantities'][0]['str_value']
+                    logger.info(sequence['search_quantities'][0]['str_value'])
+                    break
+            sleep(0.1)
+            toc = perf_counter()
+            if toc - tic > timethreshold:
+                logger.warning(
+                    "The Sequence File entry/ies in the current upload \
+                               were not found and couldn't be referenced."
+                )
+                break
+        archive.data = CPFSPPMSFile(
+            measurement=create_archive(entry, archive, file_name)
+        )
+        archive.metadata.entry_name = data_file + ' measurement file'
+
 
 class CPFSPPMSSequenceFile(BaseSection, EntryData):
     file_path = Quantity(

src/cpfs_ppms/schema_packages/__init__.py

@@ -2,16 +2,41 @@
 from pydantic import Field
 
 
-class CPFSPPMSETOEntryPoint(SchemaPackageEntryPoint):
+class CPFSPPMSETOEntryPointDefault(SchemaPackageEntryPoint):
     parameter: int = Field(0, description='Custom configuration parameter')
 
     def load(self):
         from cpfs_ppms.schema_packages.schema_package import m_package_ppms_eto_default
 
         return m_package_ppms_eto_default
 
+class CPFSPPMSETOEntryPointLabview(SchemaPackageEntryPoint):
+    parameter: int = Field(0, description='Custom configuration parameter')
+
+    def load(self):
+        from cpfs_ppms.schema_packages.schema_package import m_package_ppms_eto_labview
+
+        return m_package_ppms_eto_labview
+
+class CPFSPPMSACTEntryPointDefault(SchemaPackageEntryPoint):
+    parameter: int = Field(0, description='Custom configuration parameter')
+
+    def load(self):
+        from cpfs_ppms.schema_packages.schema_package import m_package_ppms_act_default
 
-schema_entry_point_eto_default = CPFSPPMSETOEntryPoint(
+        return m_package_ppms_act_default
+
+schema_entry_point_eto_default = CPFSPPMSETOEntryPointDefault(
+    name='CPFSPPMSETOEntryPoint',
+    description='New schema package entry point configuration.',
+)
+
+schema_entry_point_eto_labview = CPFSPPMSETOEntryPointLabview(
     name='CPFSPPMSETOEntryPoint',
     description='New schema package entry point configuration.',
 )
+
+schema_entry_point_act_default = CPFSPPMSACTEntryPointDefault(
+    name='CPFSPPMSACTEntryPoint',
+    description='New schema package entry point configuration.',
+)