FAIRmat-NFDI · RonHildebrandt · Nov 21, 2024 · Nov 19, 2024 · Nov 19, 2024 · Nov 19, 2024
diff --git a/pyproject.toml b/pyproject.toml
@@ -27,6 +27,8 @@ dependencies = [
 
 [project.entry-points."pynxtools.reader"]
 raman = "pynxtools_raman.reader:RamanReader"
+raman_multi = "pynxtools_raman_multiformat.reader:RamanReaderMulti"
+
 
 [project.urls]
 "Homepage" = "https://github.com/FAIRmat-NFDI/pynxtools-raman"

diff --git a/src/pynxtools_raman_multiformat/README.md b/src/pynxtools_raman_multiformat/README.md
@@ -0,0 +1,5 @@
+## Multiformat data reader for Raman spectroscopy data
+This is example data for writing a new data reader based on the [`MultiFormatReader`](https://github.com/FAIRmat-NFDI/pynxtools/blob/master/src/pynxtools/dataconverter/readers/multi/reader.py) from scratch. A how-to guide to implement this reader is available [here](https://fairmat-nfdi.github.io/pynxtools/how-tos/use-multi-format-reader.html)
+
+## This file types are currently supported:
+- Witec Alpha Raman microscope - via ELN file (.yaml)
diff --git a/src/pynxtools_raman_multiformat/config_file.json b/src/pynxtools_raman_multiformat/config_file.json
@@ -0,0 +1,63 @@
+{
+  "/ENTRY[entry]/INSTRUMENT[instrument]/scattering_configuration": "@eln",
+  "/ENTRY[entry]/INSTRUMENT[instrument]/beam_incident/wavelength": "@eln",
+  "/ENTRY[entry]/INSTRUMENT[instrument]/beam_incident/wavelength/@units": "@eln",
+  "/ENTRY[entry]/INSTRUMENT[instrument]/beam_incident/parameter_reliability": "@eln",
+  "/ENTRY[entry]/INSTRUMENT[instrument]/beam_incident/average_power": "@eln",
+  "/ENTRY[entry]/INSTRUMENT[instrument]/beam_incident/average_power/@units": "@eln",
+  "/ENTRY[entry]/INSTRUMENT[instrument]/beam_incident/associated_source": "@eln",
+  "/ENTRY[entry]/INSTRUMENT[instrument]/detector_TYPE[detector_ccd]/detector_channel_type": "@eln",
+  "/ENTRY[entry]/INSTRUMENT[instrument]/detector_TYPE[detector_ccd]/count_time/@units": "@eln",
+  "/ENTRY[entry]/INSTRUMENT[instrument]/detector_TYPE[detector_ccd]/count_time": "@eln",
+  "/ENTRY[entry]/INSTRUMENT[instrument]/detector_TYPE[detector_ccd]/number_of_cycles": "@eln",
+  "/ENTRY[entry]/INSTRUMENT[instrument]/detector_TYPE[detector_ccd]/number_of_cycles/@units": "@eln",
+  "/ENTRY[entry]/INSTRUMENT[instrument]/detector_TYPE[detector_ccd]/detector_type": "@eln",
+  "/ENTRY[entry]/INSTRUMENT[instrument]/detector_TYPE[detector_ccd]/FABRICATION[device_information]/model": "@eln",
+  "/ENTRY[entry]/INSTRUMENT[instrument]/detector_TYPE[detector_ccd]/FABRICATION[device_information]/serial_number": "@eln",
+  "/ENTRY[entry]/INSTRUMENT[instrument]/detector_TYPE[detector_ccd]/detector_number": "@eln",
+  "/ENTRY[entry]/INSTRUMENT[instrument]/detector_TYPE[detector_ccd]/gain_setting": "@eln",
+  "/ENTRY[entry]/INSTRUMENT[instrument]/SOURCE[source_532nmlaser]/type": "@eln",
+  "/ENTRY[entry]/INSTRUMENT[instrument]/SOURCE[source_532nmlaser]/power": "@eln",
+  "/ENTRY[entry]/INSTRUMENT[instrument]/SOURCE[source_532nmlaser]/power/@units": "@eln",
+  "/ENTRY[entry]/INSTRUMENT[instrument]/FABRICATION[device_information]/vendor": "@eln",
+  "/ENTRY[entry]/INSTRUMENT[instrument]/FABRICATION[device_information]/model": "@eln",
+  "/ENTRY[entry]/INSTRUMENT[instrument]/LENS_OPT[objective_lens]/type": "@eln",
+  "/ENTRY[entry]/INSTRUMENT[instrument]/LENS_OPT[objective_lens]/FABRICATION[device_information]/vendor": "@eln",
+  "/ENTRY[entry]/INSTRUMENT[instrument]/LENS_OPT[objective_lens]/FABRICATION[device_information]/model": "@eln",
+  "/ENTRY[entry]/INSTRUMENT[instrument]/LENS_OPT[objective_lens]/magnification": "@eln",
+  "/ENTRY[entry]/INSTRUMENT[instrument]/LENS_OPT[objective_lens]/numerical_aperture": "@eln",
+  "/ENTRY[entry]/INSTRUMENT[instrument]/MONOCHROMATOR[monochromator]/device_information/model": "@eln",
+  "/ENTRY[entry]/INSTRUMENT[instrument]/MONOCHROMATOR[monochromator]/grating/period": "@eln",
+  "/ENTRY[entry]/INSTRUMENT[instrument]/MONOCHROMATOR[monochromator]/grating/period/@units": "@eln",
+  "/ENTRY[entry]/INSTRUMENT[instrument]/MONOCHROMATOR[monochromator]/wavelength": "@eln",
+  "/ENTRY[entry]/INSTRUMENT[instrument]/MONOCHROMATOR[monochromator]/wavelength/@units": "@eln",
+  "/ENTRY[entry]/INSTRUMENT[instrument]/SENSOR[temperature_sensor]/attached_to": "@eln",
+  "/ENTRY[entry]/INSTRUMENT[instrument]/SENSOR[temperature_sensor]/measurement": "@eln",
+  "/ENTRY[entry]/INSTRUMENT[instrument]/SENSOR[temperature_sensor]/value": "@eln",
+  "/ENTRY[entry]/INSTRUMENT[instrument]/SENSOR[temperature_sensor]/value/@units": "@eln",
+  "/ENTRY[entry]/SAMPLE[sample]/name": "@eln",
+  "/ENTRY[entry]/SAMPLE[sample]/atom_types": "@eln",
+  "/ENTRY[entry]/USER[user]/address": "@eln",
+  "/ENTRY[entry]/USER[user]/affiliation": "@eln",
+  "/ENTRY[entry]/USER[user]/email": "@eln",
+  "/ENTRY[entry]/USER[user]/name": "@eln",
+  "/ENTRY[entry]/experiment_description": "@eln",
+  "/ENTRY[entry]/experiment_type": "@eln",
+  "/ENTRY[entry]/raman_experiment_type": "@eln",
+  "/ENTRY[entry]/title": "@eln",
+  "/ENTRY[entry]/start_time": "@eln",
+  "/ENTRY[entry]/definition": "@eln",
+  "/ENTRY[entry]/@default": "data",
+  "/ENTRY[entry]/DATA[data]/@signal": "y_values",
+  "/ENTRY[entry]/DATA[data]/y_values": "@data:y_values",
+  "/ENTRY[entry]/DATA[data]/x_values": "@data:x_values",
+  "/ENTRY[entry]/DATA[data]/y_values/@unit": "@attrs:/ENTRY[entry]/data/unit_y",
+  "/ENTRY[entry]/DATA[data]/x_values/@unit": "@attrs:/ENTRY[entry]/data/unit_x",
+  "/ENTRY[entry]/DATA[data]/y_values/@long_name": "@attrs:/ENTRY[entry]/data/longname_y",
+  "/ENTRY[entry]/DATA[data]/x_values/@long_name": "@attrs:/ENTRY[entry]/data/longname_x",
+  "/ENTRY[entry]/DATA[data]/@axes":"x_values_raman",
+  "/ENTRY[entry]/DATA[data]/x_values_raman/@long_name": "@attrs:/ENTRY[entry]/data/longname_x_raman",
+  "/ENTRY[entry]/DATA[data]/x_values_raman": "@data:x_values_raman",
+  "/ENTRY[entry]/DATA[data]/x_values_raman/@unit": "1/cm"
+  }
+
diff --git a/src/pynxtools_raman_multiformat/eln_data.yaml b/src/pynxtools_raman_multiformat/eln_data.yaml
@@ -0,0 +1,122 @@
+# Original meta_data_1.txt file below
+#Spectrum--000
+#
+#General:
+# System ID: 100-1100-292
+# Start Time: 2:04:54 PM
+# Start Date: Friday, June 21, 2024
+# Duration: 0h 0m 21s
+# User Name: Witec
+# Sample Name: 
+# Configuration: Raman CCD1
+# 
+# UHTS300M:
+# Excitation Wavelength [nm]: 532.100
+# Grating: G1: 600 g/mm BLZ=500nm
+# Center Wavelength [nm]: 596.989
+# Spectral Center [rel. 1/cm]: 2042.739
+# 
+# DU970_BV:
+# Serial Number: 6358
+# Readout Mode: FVB (1-200)
+# Output Amplifier: Conventional
+# Vertical Shift Speed [µs]: 9.75
+# Horizontal Shift Speed [MHz]: 0.050
+# Preamplifier Gain: 1.00
+# Cycle Time [sec]: 1.00002
+# Sensor Temperature [°C]: -56
+# 
+# Number Of Accumulations: 20
+# Integration Time [s]: 1.00000
+# 
+# Objective:
+# Objective Name: Nikon 20x 20x / 0.4
+# Objective Magnification: 20.0
+# 
+# Sample Location (global position):
+# Position X [µm]: 0.000
+# Position Y [µm]: 0.000
+# Position Z [µm]: 0.000
+
+data:
+  unit_x: nm
+  unit_y: counts
+  longname_x: Wavelength
+  longname_y: Raman Intensity
+instrument:
+  scattering_configuration: z(xx)-z
+  beam_incident:
+    wavelength:
+      value: 532.1
+      unit: nm
+    average_power:
+      value: 60
+      unit: mW
+    parameter_reliability: nominal
+    associated_source: entry/instrument/source_532nmlaser
+  detector_ccd:
+    detector_channel_type: multichannel
+    count_time:
+      value: 1.0
+      unit: s
+    number_of_cycles:
+      value: 20
+      unit: counts
+    detector_type: CCD
+    device_information:
+      model: DU970_BV
+      serial_number: "6358"
+    detector_number:
+      - 1600
+      - 200
+    gain_setting: 1.0
+  temperature_sensor:
+    attached_to: CCD
+    measurement: temperature
+    value:
+      value: -56
+      unit: celsius
+  source_532nmlaser:
+    source_type: laser #DPSS
+    power:
+      value: 80
+      unit: mW
+  device_information:
+    vendor: Witec
+    model: Alpha Raman
+  objective_lens:
+    type: objective
+    device_information:
+      vendor: Nikon
+      model: "Nikon 20x"
+    magnification: 20
+    numerical_aperture: 0.4
+  monochromator:
+    device_information:
+      model: UHTS300M
+    grating:
+      period:
+        value: 600
+        unit: counts / mm
+    wavelength: 
+      value: 596.989 ##Spectral Center [rel. 1/cm]: 2042.739
+      unit: nm
+sample:
+  name: Silicon Wafer
+  atom_types: Si
+user:
+  address: Lennestr. 5, 04318 Leipzig
+  affiliation: Universität Leipzig
+  email: [email protected]
+  name: Hildebrandt, Ron
+experiment_description: Raman spectrum of commercial silicon wafer
+experiment_type: Raman spectroscopy
+raman_experiment_type: non-resonant Raman spectroscopy
+title: Si-Wafer
+start_time: '2024-06-21T14:04:54+02:00'
+definition: NXraman
+measurement_file_meta_data:
+  delimiter: ","
+  skip_lines: 17
+
+