125 merge substrate classes from pld and movpe and place it under ikz category

IKZ_plugin/nomad.yaml

@@ -11,7 +11,9 @@ plugins:
     - 'parsers/hall_lakeshore_measurement'
     - 'parsers/hall_lakeshore_instrument'
     - 'parsers/laytec_epitt'
-    - 'schemas/basesections'
+    - 'schemas/basesections_IKZ'
+    - 'schemas/characterization_IKZ'
+    - 'schemas/substrate_IKZ'
     - 'parsers/czochralski'
     - 'parsers/movpe_2'
     - 'parsers/movpe_1_deposition_control'
@@ -33,8 +35,12 @@ plugins:
       python_package: hall.instrument_parser
     parsers/laytec_epitt:
       python_package: laytec_epitt
-    schemas/basesections:
+    schemas/basesections_IKZ:
       python_package: basesections
+    schemas/characterization_IKZ:
+      python_package: characterization
+    schemas/substrate_IKZ:
+      python_package: substrate
     parsers/czochralski:
       python_package: czochralski
     parsers/movpe_2:

IKZ_plugin/src/basesections/__init__.py → IKZ_plugin/src/ikz_plugin/__init__.py

@@ -1,12 +1,14 @@
-import json
-
-from nomad.metainfo import (
-    Package, Quantity, SubSection, Section, Category)
 from nomad.datamodel.data import EntryData, EntryDataCategory
-#from nomad.datamodel.metainfo.workflow import Link
-from nomad.datamodel.metainfo.eln import Entity, Activity, SampleID
-from nomad.datamodel.util import parse_path
+import numpy as np
+from nomad.datamodel.metainfo.basesections import (
+    CompositeSystem,
+    Activity,
+    Process,
+    CompositeSystemReference,
+)
 
+from nomad.metainfo import Package, Quantity, SubSection, Datetime, Section, Category
+from nomad.datamodel.data import EntryData
 
 m_package = Package(name='basesections_IKZ')
 
@@ -34,6 +36,82 @@ class IKZHallCategory(EntryDataCategory):
     m_def = Category(label='Hall', categories=[EntryDataCategory, IKZCategory])
 
 
+class SubstratePreparationStep(Activity):
+    """
+    A section used for referencing Activities performed on Substrate.
+    """
+
+    m_def = Section()
+
+
+class Etching(Process, SubstratePreparationStep, EntryData):
+    """
+    Class autogenerated from yaml schema.
+    """
+
+    m_def = Section(
+        a_eln=None,
+        categories=[IKZCategory],
+    )
+    method = Quantity(
+        type=str,
+        default="Etching (MOVPE IKZ)",
+    )
+    datetime = Quantity(
+        type=Datetime,
+        description="FILL",
+        a_eln={"component": "DateTimeEditQuantity", "label": "deposition_date"},
+    )
+    temperature = Quantity(
+        type=np.float64,
+        description="FILL THE DESCRIPTION",
+        a_eln={"component": "NumberEditQuantity", "defaultDisplayUnit": "celsius"},
+        unit="celsius",
+    )
+    elapsed_time = Quantity(
+        type=np.float64,
+        description="Past time since process started (minutes)",
+        a_eln={"component": "NumberEditQuantity", "defaultDisplayUnit": "minute"},
+        unit="minute",
+    )
+    etching_reagents = SubSection(section_def=CompositeSystem, repeats=True)
+
+
+class Annealing(Process, SubstratePreparationStep, EntryData):
+    """
+    Class autogenerated from yaml schema.
+    """
+
+    m_def = Section(
+        a_eln=None,
+        categories=[IKZCategory],
+    )
+    method = Quantity(
+        type=str,
+        default="Annealing (MOVPE IKZ)",
+    )
+    datetime = Quantity(
+        type=Datetime,
+        description="FILL",
+        a_eln={"component": "DateTimeEditQuantity", "label": "deposition_date"},
+    )
+    temperature = Quantity(
+        type=np.float64,
+        description="FILL THE DESCRIPTION",
+        a_eln={"component": "NumberEditQuantity", "defaultDisplayUnit": "celsius"},
+        unit="celsius",
+    )
+    elapsed_time = Quantity(
+        type=np.float64,
+        description="Past time since process started (minutes)",
+        a_eln={"component": "NumberEditQuantity", "defaultDisplayUnit": "minute"},
+        unit="minute",
+    )
+    anealing_reagents = SubSection(
+        section_def=CompositeSystemReference,
+    )
+
+
 # class CollectionOfSystems(Entity, EntryData):
 #     '''
 #     A base class for a batch of materials. Each component of the batch is

IKZ_plugin/src/ikz_plugin/characterization/schema.py

@@ -0,0 +1,127 @@
+import numpy as np
+from nomad.datamodel.metainfo.basesections import (
+    Measurement,
+    MeasurementResult,
+)
+from nomad.metainfo import Package, Quantity, SubSection, MEnum, Datetime, Section
+from nomad.datamodel.data import EntryData
+
+from ikz_plugin import (
+    IKZCategory,
+    SubstratePreparationStep,
+)
+
+m_package = Package(name="characterization_IKZ")
+
+
+class AFMresults(MeasurementResult):
+    """
+    The results of an AFM measurement
+    """
+
+    roughness = Quantity(
+        type=np.float64,
+        description="RMS roughness value obtained by AFM",
+        a_eln={"component": "NumberEditQuantity", "defaultDisplayUnit": "picometer"},
+        unit="picometer",
+    )
+    surface_features = Quantity(
+        type=MEnum(["Step Flow", "Step Bunching", "2D Island"]),
+        a_eln={"component": "EnumEditQuantity"},
+    )
+    scale = Quantity(
+        type=np.float64,
+        description="scale of the image, to be multiplied by 5 to know the image size",
+        a_eln={"component": "NumberEditQuantity", "defaultDisplayUnit": "nanometer"},
+        unit="nanometer",
+    )
+    image = Quantity(
+        type=str,
+        description="image showing the thickness measurement points",
+        a_browser={"adaptor": "RawFileAdaptor"},
+        a_eln={"component": "FileEditQuantity"},
+    )
+    crop_image = Quantity(
+        type=str,
+        description="crop image ready to be used for AI-based analysis",
+        a_browser={"adaptor": "RawFileAdaptor"},
+        a_eln={"component": "FileEditQuantity"},
+    )
+
+
+class AFMmeasurement(Measurement, SubstratePreparationStep, EntryData):
+    """
+    Class autogenerated from yaml schema.
+    """
+
+    m_def = Section(
+        a_eln={"hide": ["steps"]},
+        categories=[IKZCategory],
+        label="AFM",
+    )
+
+    method = Quantity(
+        type=str,
+        default="AFM (IKZ MOVPE)",
+    )
+    description = Quantity(
+        type=str,
+        a_eln={"component": "StringEditQuantity"},
+    )
+    datetime = Quantity(
+        type=Datetime,
+        a_eln={"component": "DateTimeEditQuantity"},
+    )
+    results = SubSection(
+        section_def=AFMresults,
+        repeats=True,
+    )
+
+
+class LiMiresults(MeasurementResult):
+    """
+    The results of a Light Microscope measurement
+    """
+
+    image = Quantity(
+        type=str,
+        description="image showing the thickness measurement points",
+        a_browser={"adaptor": "RawFileAdaptor"},
+        a_eln={"component": "FileEditQuantity"},
+    )
+    crop_image = Quantity(
+        type=str,
+        description="crop image ready to be used for AI-based analysis",
+        a_browser={"adaptor": "RawFileAdaptor"},
+        a_eln={"component": "FileEditQuantity"},
+    )
+    scale = Quantity(
+        type=np.float64,
+        description="scale of the image",
+        a_eln={"component": "NumberEditQuantity", "defaultDisplayUnit": "micrometer"},
+        unit="micrometer",
+    )
+
+
+class LightMicroscope(Measurement, SubstratePreparationStep, EntryData):
+    """
+    Class autogenerated from yaml schema.
+    """
+
+    m_def = Section(
+        a_eln={"hide": ["steps"]},
+        categories=[IKZCategory],
+        label="Light Microscope",
+    )
+    method = Quantity(
+        type=str,
+        default="Light Microscope (MOVPE IKZ)",
+    )
+    datetime = Quantity(
+        type=Datetime,
+        a_eln={"component": "DateTimeEditQuantity"},
+    )
+    results = SubSection(
+        section_def=LiMiresults,
+        repeats=True,
+    )

IKZ_plugin/src/directional_solidification/schema.py → IKZ_plugin/src/ikz_plugin/directional_solidification/schema.py

@@ -64,7 +64,7 @@
 )
 from nomad.datamodel.metainfo.plot import PlotSection, PlotlyFigure
 
-from basesections import IKZDSCategory
+from ikz_plugin import IKZDSCategory
 
 m_package = Package(name='Directional Solidification Experiment')
 

IKZ_plugin/src/ikz_plugin/mbe/__init__.py

@@ -0,0 +1,2 @@
+from .schema import *
+from ikz_plugin import *

IKZ_plugin/src/mbe/schema.py → IKZ_plugin/src/ikz_plugin/mbe/schema.py

@@ -11,7 +11,7 @@
 from nomad.datamodel.metainfo.eln import PublicationReference
 from nomad.datamodel.metainfo.eln import Entity, Activity, SampleID
 from nomad.datamodel.util import parse_path
-from basesections import SampleCut
+from ikz_plugin import SampleCut
 
 m_package = Package(name='mbe_IKZ')
 

IKZ_plugin/src/ikz_plugin/movpe/__init__.py

@@ -0,0 +1,18 @@
+# Copyright The NOMAD Authors.
+#
+# This file is part of NOMAD. See https://nomad-lab.eu for further info.
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+#
+
+from .schema import *

IKZ_plugin/src/movpe/movpe1_growth_parser/constant_parameters/parser.py → IKZ_plugin/src/ikz_plugin/movpe/movpe1_growth_parser/constant_parameters/parser.py

@@ -37,7 +37,7 @@
 )
 from nomad.search import search
 from nomad_material_processing.utils import create_archive as create_archive_ref
-from movpe import (
+from ikz_plugin.movpe import (
     ExperimentMovpe1IKZ,
     GrowthMovpe1IKZConstantParameters,
     ThinFilmStackMovpe
@@ -46,7 +46,7 @@
 from nomad.parsing.tabular import create_archive
 from nomad.utils import hash
 
-from basesections import IKZMOVPE1Category
+from ikz_plugin import IKZMOVPE1Category
 
 class RawFileConstantParameters(EntryData):
     m_def = Section(

IKZ_plugin/src/movpe/movpe1_growth_parser/deposition_control/parser.py → IKZ_plugin/src/ikz_plugin/movpe/movpe1_growth_parser/deposition_control/parser.py

@@ -39,7 +39,7 @@
 from nomad.app.v1.models.models import User
 from nomad.datamodel.data import EntryData, ArchiveSection
 from nomad.search import search, MetadataPagination
-from movpe import (
+from ikz_plugin.movpe import (
     ExperimentMovpe1IKZ,
     GrowthMovpe1IKZConstantParametersReference,
     GrowthMovpe1IKZDepositionControl,
@@ -64,7 +64,7 @@
 # from nomad.parsing.tabular import create_archive
 from nomad.utils import hash
 
-from basesections import IKZMOVPE1Category
+from ikz_plugin import IKZMOVPE1Category
 
 
 def create_archive(

IKZ_plugin/src/movpe/movpe2_growth_parser/parser.py → IKZ_plugin/src/ikz_plugin/movpe/movpe2_growth_parser/parser.py

@@ -39,15 +39,15 @@
     PubChemPureSubstanceSection,
 )
 
-from basesections import IKZMOVPE2Category
+from ikz_plugin import IKZMOVPE2Category
 from nomad.search import search
 
 # from nomad_material_processing.utils import create_archive as create_archive_ref
 from nomad_material_processing import (
     SubstrateReference,
     ThinFilmReference,
 )
-from movpe import (
+from ikz_plugin.movpe import (
     ExperimentMovpe2IKZ,
     GrowthStepMovpe2IKZ,
     GrowthMovpe2IKZ,