Overview

soilspec.format is a package for extracting data frames and metadata lists from soil spectra of various formats, currently:

• Nicolet (.spa)
• Bruker Opus Binary (.0)
• Thermo (.spc)
• ASD (.asd)
• ASD SCO (.sco)
• Perkin Elmer (.sp) [PEPE and PE IR magic numbers]
• Hone Lab Red (.hlr)
• Hone Lab Red Reduced (.hlrr)
• Spectral Evolution (.sed)
• CSIRO SCANS (.scan)
• CSV (.csv)

The extracted data frames will always have the columns: "wavenumber" and "intensity".

Install

# need devtools and Rcpp packages
install.packages(c("devtools", "Rcpp"))
 
# need opusreader and opusreader2 packages
devtools::install_github("pierreroudier/opusreader")
devtools::install_github("spectral-cockpit/opusreader2")

# install package from GitHub
devtools::install_github("csiro/soilspec.format")

Under Windows, you will also need to install Rtools to match your R version.

Example Usage

> library(soilspec.format)

> path <- asd.binary.file.path()

> result <- read.soilspec(path)

> names(result)
 [1] "status"                  "mode"   "is.absorbance" "is.reflectance" "is.transmittance"       
 [6] "is.descending"           "origin" "type"          "data"           "standardised.metadata"  
[11] "all.instrument.metadata"   

> result$status
[1] 0

> result$is.descending
[1] FALSE

> result$is.reflectance
[1] TRUE

> result$mode
[1] "reflectance"

> head(result$data)
  wavenumber  intensity
1        350 0.05432920
2        351 0.04792801
3        352 0.05130503
4        353 0.05339854
5        354 0.04970677
6        355 0.05435767

> plot(result$data, type="l")

> result$standardised.metadata
$sample_id
[1] ""

$spectra_id
[1] ""

$spectra_source_file_name
[1] "example.asd"

$date_time
[1] "2017-06-21 10:33:49 ACST"

$response
[1] "reflectance"

$instrument_technology_type
[1] "visNIR"

$instrument_manufacturer
[1] "ASD"

$instrument
[1] "FieldSpec FR"

...

$bulb
[1] 0

$swir1_gain
[1] 569

$swir2_gain
[1] 1160

$swir1_offset
[1] 2180

$swir2_offset
[1] 2415

$splice1_wavelength
[1] 1000

$splice2_wavelength
[1] 1830

> result$all.instrument.metadata
$co
[1] "as7"

$comments
[1] ""

$when
[1] "2017-06-20 19:04:47 ACST"

$program_version
[1] "6.0"

$file_version
[1] "7.0"

$dc_corr
[1] TRUE
...

Developers

Install

Instead of using devtools::install_github() to install soilspec.format for development purposes, use this command to install the package:

devtools::install()

Test

To run unit tests use this command:

devtools::test()

Add Support for a New Format

• Create a sub-class of SpectrumFormat (see spectrum_format.R) in the R directory.

  • Look at R/*_format.R files for examples.

• Near the top of R/read_soilspec.R add a mapping from a file suffix to an instance of the new ``SpectrumFormat` sub-class, e.g.

  soilspec.readers[[".asd"]] <- ASDBinary$new()

• Create a format-specific reader function in R/read_soilspec.R by starting with an example, e.g. read.bruker.opus.binary

• Add an example file in a sub-directory under inst/extdata named to reflect the file format. The file should start with example and end in the suffix used for files of the format. In fact, it doesn't matter what the prefix of the file is but the suffix does matter (unlike the empty file referred to in a step below). Ensure there are no IP concerns with making the file available in the library.

• Create a file path function in R/file_paths.R to access this file. This function can be used for testing and by users of the library.

• Add an empty file in inst/extdata/Unknown that starts with example and ends in the suffix associated with the format. This will be used with common_read_test (see below).

• In tests/testthat/test_read_soilspec.R, add a test case for the new format above the lines:

     #######################################
     # Add tests for new formats above ^^^ #
     #######################################

• See examples above those lines for other format reader tests that call common_read_test.

• Add a unit test for the sub-class of SpectrumFormat in a new file under tests/testthat. Look at other format-specific test files there to get started, e.g. test_bruker_opus_binary.R or test_asd_sco_binary.R