Reflection/Transmission (RT) Measurements

These schemas support high-throughput optical measurements from the Agilent Cary 7000 UMS + UMA autosampler workflow.

Overview

This schema package defines two complementary entry types:

• DtuAutosamplerMeasurement: experiment container that ingests the autosampler data files and creates per-sample measurement archives.
• RTMeasurement: measurement archive containing position-resolved reflection and transmission spectra.

The data model is designed for combinatorial mapping and keeps full provenance between raw files, grid mapping, and generated RT results.

Input Files

The autosampler workflow uses three file types:

• Data file (.csv): exported spectra and metadata from Agilent software.
• Grid/config file (*_grid.csv): maps autosampler positions to sample names and sample coordinates.
• Raw batch file (.bsw): native instrument batch file for traceability and provenance.

Typical Workflow

1. Generate a measurement map with the grid-generator notebook.
2. Use the generated *_polar.csv in the autosampler software to run the measurement.
3. Export measurement data as .csv from Agilent software.
4. Upload the .csv data file and the matching *_grid.csv into DtuAutosamplerMeasurement.
5. Let normalization generate one or more RTMeasurement entries automatically.

What RT Captures

• Reflection and transmission spectra per position.
• Measurement geometry (sample angle, detector angle, polarization).
• Spatially resolved maps through x/y coordinates from the grid file.
• Derived visualization (stacked spectra and configuration-specific maps).

Related Schemas

• Samples and libraries: Samples
• Shared measurement base: Base Measurement Infrastructure
• Other optical methods: PL, Ellipsometry, Raman
• Analysis workflows: Jupyter Analysis

How-To Guide

For a complete upload procedure, see Add Autosampler Reflection/Transmission Measurements.

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Schema Documentation

RTSpectrum

description: Single R or T spectrum with measurement geometry information.

inherits from: nomad.datamodel.data.ArchiveSection

properties:

name	type
spectrum_type	['Reflection', 'Transmission']	Type of spectrum: Reflection (R) or Transmission (T).
wavelength	float64	Wavelength array in nanometers. shape=['*'], unit=nanometer
intensity	float64	Intensity values (R or T as fraction 0-1). shape=['*']
detector_angle	float64	Detector angle in degrees, the angle between the beam and the detector. 180° means is in the direction of the transmitted beam (typically for transmission measurements), while small angles means it is in the direction of the reflected beam (typically for reflection measurements). Angles constrained between 12 and 180° (if the beam is detector is on the left side of the optical path) and -12 and -179° (if the detector is on the right side of the optical path) based on typical Agilent Cary 7000 UMS configurations. unit=degree
sample_angle	float64	Sample angle in degrees, the angle between the beam and the sample surface. 0° means the beam is normal to the sample surface, while larger angles mean the beam is more grazing. Angles are typically between 0 and 85° based on typical Agilent Cary 7000 UMS configurations. unit=degree
polarization	['p', 's', 'unpolarized(p-biased)']	Polarisation of the light if the polarizer element was used during the measurement. 's (angle 0°)' means the electric field is perpendicular to the plane of incidence, 'p (angle 90°)' means the electric field is parallel to the plane of incidence, and 'unpolarized (p-biased)' means the polarizer was set to unpolarized mode to increase measurement throughput, which typically results in a p-polarized bias in the transmitted beam.

normalization:

The normalizer for the RTSpectrum class.

RTResult

description: Results from a single spatial position containing multiple R/T spectra.

inherits from: nomad_measurements.mapping.schema.MappingResult

properties:

name	type
spectra	RTSpectrum	List of Reflection and/or Transmission spectra measured at this position. sub-section, repeats

normalization:

Normalizes the results data for the RT measurement.

DtuAutosamplerMeasurement

description: Experiment container for autosampler R/T measurements

inherits from: nomad.datamodel.metainfo.basesections.v1.Experiment, nomad.datamodel.metainfo.plot.PlotSection, nomad.datamodel.data.EntryData

properties:

name	type
data_file	str	CSV file containing all R and T spectra recorded by the Agilent Cary 7000 UMS autosampler. This file contains the raw spectral data along with metadata and needs to be parsed together with the config file to extract individual spectra and associate them with the correct sample/library and position.
config_file	str	CSV file containing the grid/position metadata mapping. This file maps each position on each library to the corresponding recorded spectra in the data file, (Ex: the first recorded spectrum of the data_file has been recorded at position X=5mm, Y=10mm on library "eugbe_0025_Zr_FL")
raw_file	str	Raw binary file from the Agilent Cary 7000 UMS instrument (for bookkeeping and data provenance). File extension is typically .bsw.
vertical_back_slit	float64	Vertical back slit setting in degrees. unit=degree, default=1.0
vertical_front_slit	float64	Vertical front slit setting in degrees. unit=degree, default=1.0
horizontal_slit	float64	Horizontal slit setting in degrees. unit=degree, default=3.0

normalization:

The normalizer for the DtuAutosamplerMeasurement class.

This method: 1. Parses the data and config files using autosampler_reader 2. Groups data by sample/library 3. Creates separate RTMeasurement archives for each library 4. Adds them as steps to this experiment

RTMeasurement

inherits from: nomad_dtu_nanolab_plugin.schema_packages.basesections.DtuNanolabMeasurement, nomad.datamodel.metainfo.plot.PlotSection, nomad.datamodel.data.EntryData

properties:

name	type
accessory	['DRA', 'None', 'UMA']	Instrument accessory used for the measurement.DRA is the integrating sphere accessory whileUMA is the universal measurement accessory(variable incidence, detector and polarization). default=None
vertical_back_slit	float64	Vertical back slit setting in degrees (V_back slot). unit=degree
vertical_front_slit	float64	Vertical front slit setting in degrees (V_front slot). unit=degree
horizontal_slit	float64	Horizontal slit setting in degrees (H slot). unit=degree
data_file	str	CSV file(s) for single-point R/T measurement. Can include R, T, or both spectra in one or multiple files. Only used when uploading single-point measurements directly; NOT used for autosampler batch experiments. shape=['*']
raw_file	str	Optional raw .bsw batch file for single-point measurements (provenance). Only used when uploading single-point measurements directly; NOT used for autosampler batch experiments. shape=['*']
results	RTResult	The result of the measurement. sub-section, repeats
sample_alignment	nomad_measurements.mapping.schema.RectangularSampleAlignment	The alignment of the sample. sub-section

normalization:

The normalizer for the RTMeasurement class.