---
title: "Optical Spectroscopy JSON-LD"
author: "Leean Jo, Laura S. Bruckman, Roger H. French"
date: "`r Sys.Date()`"
output: rmarkdown::html_vignette
vignette: >
  %\VignetteIndexEntry{Optical Spectroscopy JSON-LD}
  %\VignetteEngine{knitr::rmarkdown}
  %\VignetteEncoding{UTF-8}
---

Optical Spectroscopy JSON-LD Description
-----------------------------------
This json-ld template is used to store metadata information commonly used to describe optical spectroscopy measurements including FTIR, UV-vis, Raman, and Fluorescence spectroscopies. It includes some key meta information such as material type, wavelength, and intensity. More detailed structure is shown below.

Creating JSON-LD for Optical Spectroscopy in R
------------------------------------------
```{r, message=FALSE, eval=FALSE}
library(FAIRmaterials)

# An example data frame for Optical Spectroscopy
# FTIR spectroscopy example from PMMA samples

FTIR_example <- data.frame(
  'wavelength' = c('649.57', '2650.5'),
  'spc' = c('0.019966', '0.00315458'),
  'SampleMaterial' = c('UVT', 'FF1'),
  'SamplePhase' = c('solid', 'solid'),
  'sampleID' = c('sa17435', 'sa17559')
)

# This will generate JSON-LD file for the example data
output <- fairify_data(FTIR_example, domain = 'OpticalSpectroscopy', saveLocal = TRUE)
```

Creating JSON-LD for Optical Spectroscopy in Python
------------------------------------------
```{python, eval = FALSE, python.reticulate = FALSE}
from fairmaterials.fairify_data import *
import pandas as pd

# An example data frame for Optical Spectroscopy
# FTIR spectroscopy example from PMMA samples
FTIR_example = pd.DataFrame({
  'wavelength': ['649.57', '2650.5'],
  'spc': ['0.019966', '0.00315458'],
  'SampleMaterial': ['UVT', 'FF1'],
  'SamplePhase': ['solid', 'solid'],
  'sampleID': ['sa17435', 'sa17559']
})

# This will generate JSON-LD file for the example data
output <- fairify_data(FTIR_example, domain = 'OpticalSpectroscopy')
```

Optical Spectroscopy schema diagram
--------------------------

```{r, out.width="1200px", echo=FALSE, fig.cap="Optical Spectroscopy schema diagram"}
knitr::include_graphics("opticalSpectroscopy.png")
```

Acknowledgment
--------------------------
