Fairmat 2024: proposal on optical spectroscopy

applications/NXraman.nxdl.xml

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+<?xml version='1.0' encoding='UTF-8'?>
+<?xml-stylesheet type="text/xsl" href="nxdlformat.xsl"?>
+<!--
+# NeXus - Neutron and X-ray Common Data Format
+#
+# Copyright (C) 2024-2025 NeXus International Advisory Committee (NIAC)
+#
+# This library is free software; you can redistribute it and/or
+# modify it under the terms of the GNU Lesser General Public
+# License as published by the Free Software Foundation; either
+# version 3 of the License, or (at your option) any later version.
+#
+# This library is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
+# Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this library; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA
+#
+# For further information, see http://www.nexusformat.org
+-->
+<!--
+N_incident_wavelengths: |
+ Number of the incident wavelen
+N_incident_beams: |
+ to be done....-->
+<!--
+04/2024
+A draft version of a NeXus application definition for Raman spectroscopy.-->
+<!--
+09/2024
+TODO (Workshop output):
+- Talk with VIBSO people - possible to syncrhonize raman_experiment_type with this ontology?
+- Similar to ellipsometry: Seperate in-situ from resonant/non-resonant stuff: OR maybe allow multiple selections?
+- Shorten raman_experiment_type by removal of Raman_spectroscopy, but as well fix the Raman Reader in the same run
+- Which for more dataconverters: Output from usualy Raman setups to neXus format?
+- Spot size description?
+- Descroption of defocusing / maybe as well as experiment_type?
+
+Wishes for NXraman or general next workshop:
+"convert excisting data to NeXus"
+"dictionary lookup keywords/fields in existing formats"(?)
+Template for specific experiments (i.e. too complex to get into NeXus/FAIRdata?) - unclear what to do.
+coorporation with VIBSO ontology?
+dataset examples (i.e. NXdata_raman)-->
+<definition xmlns="http://definition.nexusformat.org/nxdl/3.1" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" category="application" type="group" name="NXraman" extends="NXoptical_spectroscopy" xsi:schemaLocation="http://definition.nexusformat.org/nxdl/3.1 ../nxdl.xsd">
+    <symbols>
+        <doc>
+            Variables used throughout the document, e.g. dimensions or parameters.
+        </doc>
+        <symbol name="N_spectrum">
+            <doc>
+                Length of the spectrum array (e.g. wavelength or energy) of the measured
+                data.
+            </doc>
+        </symbol>
+        <symbol name="N_measurements">
+            <doc>
+                Number of measurements (1st dimension of measured_data array). This is
+                equal to the number of parameters scanned. For example, if the experiment
+                was performed at three different temperatures and two different pressures
+                N_measurements = 2*3 = 6.
+            </doc>
+        </symbol>
+        <symbol name="N_detection_angles">
+            <doc>
+                Number of detection angles of the beam reflected or scattered off the
+                sample.
+            </doc>
+        </symbol>
+        <symbol name="N_incident_angles">
+            <doc>
+                Number of angles of incidence of the incident beam.
+            </doc>
+        </symbol>
+        <symbol name="N_scattering_configurations">
+            <doc>
+                Number of scattering configurations used in the measurement.
+                It is 1 for only parallel polarization meausement, 2 for parallel and cross
+                polarization measurement or larger, if i.e. the incident and scattered photon
+                direction is varied.
+            </doc>
+        </symbol>
+    </symbols>
+    <doc>
+        An application definition for Raman spectrocopy experiments.
+
+        Such experiments may be as simple a single Raman spectrum from spontanous
+        Raman scattering and range to Raman imaging Raman spectrometer,
+        surface- and tip-enhanced Raman techniques, x-Ray Raman scattering, as well
+        as resonant Raman scattering phenomena or multidimenional Raman spectra (i.e.
+        varying temperature, pressure, electric field, ....)
+
+        The application definition contains two things:
+        1. The structures in the application definition of NXopt:
+        * Instrument and data calibrations
+        * Sensors for sample or beam conditions
+
+        AND
+
+        2. The strucutres specified and extended in NXraman:
+        * description of the experiment type
+        * descroption of the setup's meta data and optical elements (source, monochromator, detector, waveplate, lens, etc.)
+        * description of beam properties and their relations to the sample
+        * sample information
+
+        Information on Raman spectroscopy are provided in:
+
+        General
+
+        * Lewis, Ian R.; Edwards, Howell G. M.
+          Handbook of Raman Spectroscopy
+          ISBN 0-8247-0557-2
+
+        Raman scattering selection rules
+
+        * Dresselhaus, M. S.; Dresselhaus, G.; Jorio, A.
+          Group Theory - Application to the Physics ofCondensed Matter
+          ISBN 3540328971
+
+        Semiconductors
+
+        * Manuel Cardona
+          Light Scattering in Solids I
+          eBook ISBN: 978-3-540-37568-5
+          DOI: https://doi.org/10.1007/978-3-540-37568-5
+
+        * Manuel Cardona, Gernot Güntherodt
+          Light Scattering in Solids II
+          eBook ISBN:  978-3-540-39075-6
+          DOI: https://doi.org/10.1007/3-540-11380-0
+
+        * See as well other Books from the "Light Scattering in Solids" series:
+          III: Recent Results
+          IV: Electronic Scattering, Spin Effects, SERS, and Morphic Effects
+          V: Superlattices and Other Microstructures
+          VI: Recent Results, Including High-Tc Superconductivity
+          VII: Crystal-Field and Magnetic Excitations
+          VIII: Fullerenes, Semiconductor Surfaces, Coherent Phonons
+          IX: Novel Materials and Techniques
+
+        Glasses, Liquids, Gasses, ...
+
+        Review articles:
+        Stimulated Raman scattering, Coherent anti-Stokes Raman scattering,
+        Surface-enhanced Raman scattering, Tip-enhanced Raman scattering
+        * https://doi.org/10.1186/s11671-019-3039-2
+    </doc>
+    <group type="NXentry">
+        <field name="definition">
+            <doc>
+                An application definition for Raman spectrsocopy.
+            </doc>
+            <attribute name="version">
+                <doc>
+                    Version number to identify which definition of this application
+                    definition was used for this entry/data.
+                </doc>
+            </attribute>
+            <attribute name="URL">
+                <doc>
+                    URL where to find further material (documentation, examples) relevant
+                    to the application definition.
+                </doc>
+            </attribute>
+            <enumeration>
+                <item value="NXraman"/>
+            </enumeration>
+        </field>
+        <field name="title" recommended="true"/>
+        <field name="experiment_type">
+            <doc>
+                Specify the type of the optical experiment.
+
+                You may specify fundamental characteristics or properties in the experimental sub-type.
+            </doc>
+            <enumeration>
+                <item value="Raman spectroscopy"/>
+            </enumeration>
+        </field>
+        <field name="raman_experiment_type">
+            <doc>
+                Specify the type of Raman experiment.
+            </doc>
+            <enumeration open="true">
+                <item value="in situ Raman spectroscopy"/>
+                <item value="resonant Raman spectroscopy"/>
+                <item value="non-resonant Raman spectroscopy"/>
+                <item value="Raman imaging"/>
+                <item value="tip-enhanced Raman spectroscopy (TERS)"/>
+                <item value="surface-enhanced Raman spectroscopy (SERS)"/>
+                <item value="surface plasmon polariton enhanced Raman scattering (SPPERS)"/>
+                <item value="hyper Raman spectroscopy (HRS)"/>
+                <item value="stimulated Raman spectroscopy (SRS)"/>
+                <item value="inverse Raman spectroscopy (IRS)"/>
+                <item value="coherent anti-Stokes Raman spectroscopy (CARS)"/>
+            </enumeration>
+        </field>
+        <group type="NXinstrument">
+            <doc>
+                Metadata of the setup, its optical elements and physical properites which
+                defines the Raman measurement.
+            </doc>
+            <field name="scattering_configuration" type="NX_CHAR">
+                <doc>
+                    Scattering configuration as defined by the porto notation by three
+                    states, which are othogonal to each other. Example: z(xx)z for
+                    parallel polarized backscattering configuration.
+
+                    See:
+                    https://www.cryst.ehu.es/cgi-bin/cryst/programs/nph-doc-raman
+
+                    A(BC)D
+
+                    A = The propagation direction of the incident light (k_i)
+                    B = The polarization direction of the incident light (E_i)
+                    C = The polarization direction of the scattered light (E_s)
+                    D = The propagation direction of the scattered light (k_s)
+
+                    An orthogonal base is assumed.
+                    Linear polarized light is displayed by e.g. "x","y" or "z"
+                    Unpolarized light is displayed by "."
+                    For non-orthogonal vectors, use the attribute porto_notation_vectors.
+                </doc>
+                <attribute name="porto_notation_vectors" type="NX_NUMBER" recommended="true">
+                    <doc>
+                        Scattering configuration as defined by the porto notation given by
+                        respective vectors.
+
+                        Vectors in the porto notation are defined as for A, B, C, D above.
+                        Linear light polarization is assumed.
+                    </doc>
+                    <dimensions rank="3">
+                        <doc>
+                            3 x 4 Matrix, which lists the porto notation vectors A, B, C, D.
+                            A has to be perpendicular to B and C perpendicular to D.
+                        </doc>
+                        <dim index="1" value="4"/>
+                        <dim index="2" value="3"/>
+                        <dim index="3" value="N_scattering_configurations"/>
+                    </dimensions>
+                </attribute>
+            </field>
+            <group name="beam_incident" type="NXbeam">
+                <doc>
+                    Beam which is incident to the sample.
+                </doc>
+                <field name="wavelength" type="NX_NUMBER"/>
+            </group>
+        </group>
+    </group>
+</definition>

base_classes/NXbeam_transfer_matrix_table.nxdl.xml

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+<?xml version='1.0' encoding='UTF-8'?>
+<?xml-stylesheet type="text/xsl" href="nxdlformat.xsl"?>
+<!--
+# NeXus - Neutron and X-ray Common Data Format
+#
+# Copyright (C) 2024-2025 NeXus International Advisory Committee (NIAC)
+#
+# This library is free software; you can redistribute it and/or
+# modify it under the terms of the GNU Lesser General Public
+# License as published by the Free Software Foundation; either
+# version 3 of the License, or (at your option) any later version.
+#
+# This library is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
+# Lesser General Public License for more details.
+#
+# You should have received a copy of the GNU Lesser General Public
+# License along with this library; if not, write to the Free Software
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA
+#
+# For further information, see http://www.nexusformat.org
+-->
+<definition xmlns="http://definition.nexusformat.org/nxdl/3.1" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" category="base" type="group" name="NXbeam_transfer_matrix_table" extends="NXobject" xsi:schemaLocation="http://definition.nexusformat.org/nxdl/3.1 ../nxdl.xsd">
+    <symbols>
+        <doc>
+            Variables used throughout the document, e.g. dimensions or parameters.
+        </doc>
+        <symbol name="N_variables">
+            <doc>
+                Length of the array associated to the data type.
+            </doc>
+        </symbol>
+    </symbols>
+    <doc>
+        Contains datastructures of an experimental optical setup (i.e., multiple
+        transfermatrix tables).   These datastructures are used to relate physical
+        properties of two beams (NXbeam) which have one common optical element
+        (NXopt_element) (one specific transfermatrix).
+        One of these beams in an input beam and the other one is an output beam.
+
+        The data describes the change of beam properties, e.g. the intensity of a
+        beam is reduced because the transmission coefficient of the beam device is
+        lower than 1.
+    </doc>
+    <field name="datatype_N" nameType="partial">
+        <doc>
+            Select which type of data was recorded, for example aperture and
+            focal length.
+            It is possible to have multiple selections. This selection defines
+            how many columns (N_variables) are stored in the data array.
+            N in the name, is the index number in which order the given
+            property is listed.
+        </doc>
+        <enumeration>
+            <item value="aperture"/>
+            <item value="focallength"/>
+            <item value="orientation"/>
+            <item value="jones matrix"/>
+        </enumeration>
+    </field>
+    <field name="matrix_elements">
+        <doc>
+            Please list in this array the column and row names used in your actual data.
+            That is in the case of aperture ['diameter'] or focal length ['focal_length_value']
+            and for orientation matrix ['OM1', 'OM2', 'OM3'] or for jones matrix
+            ['JM1','JM2']
+        </doc>
+        <dimensions rank="1">
+            <dim index="1" value="N_variables"/>
+        </dimensions>
+    </field>
+    <field name="TRANSFER_MATRIX" type="NX_NUMBER" nameType="any">
+        <doc>
+            Contains the datastructure which relates beam properties of an
+            input and output beam as result of the input beam interaction
+            with the beam device.
+
+            Transfermatrix relationship between N input beams and M output beams.
+            It contains a table with the relevant matricis to be used for different
+            transmissitted properties (such as polarization, intensity, phase).
+
+            Data structure for all transfermatrices of an beam device in a setup.
+            For each combination of N input and M output beams and for L physical
+            concept (i.e. beam intensity), one matrix can be defined.
+
+            In this way, the transfermatrix table has the dimension NxM.
+
+            For each entry, in this transfermatrix, there are L formalisms.
+            Each formalism has the dimension math:`dim(L_i)xdim(L_i)`,
+            whereby math:`L_i` is the specific physical concept (Intensity, polarization, direction).
+
+            A beamsplitter with two input laser beams can have a total of
+            four transfermatrices (2 Input x 2 Output).
+
+            The dimension of the transfermatrix depends on the parameters.
+            Examples are:
+            1x1 for intensity/power
+            2x2 for jones formalism
+            3x3 for direction
+        </doc>
+        <dimensions rank="2">
+            <dim index="1" value="N_variables"/>
+            <dim index="2" value="N_variables"/>
+        </dimensions>
+        <attribute name="input">
+            <doc>
+                Specific name of input beam which the transfermatrix table is related to.
+            </doc>
+        </attribute>
+        <attribute name="output">
+            <doc>
+                Specific name of output beam which the transfermatrix table is related to.
+            </doc>
+        </attribute>
+    </field>
+</definition>