Example foreign data files

Package 'ooacquire' includes example data files. Some of these files are in foreign formats, mostly variations of text file formats with raw-counts data obtained with the software from spectrometer manufacturer Ocean Optics.

Details

These files are used in the documentation and for testing file import functions. The files can be also useful when learning to use 'ooacquire'. The collection is incomplete as it covers only a few models of spectrometers. There is some variation in the file format used by Ocean Optics. Please share your files acquired with Ocean Optics spectrometers, especially examples of those that fail to be correctly imported, if you encounter them.

See also

Package photobiologyInOut supports the import of additional formats, including those acquired with other brands of spectrometers. However, the conversion of raw counts into physical quantities is not directly supported for these other spectrometers.

Examples

# find where the foreign files are installed as part of the package
path <- system.file("extdata", "foreign-files", package = "ooacquire")

# list the files in the folder
list.files(path)
#>  [1] "UVA365-dark-long.txt"       "UVA365-dark-short.txt"     
#>  [3] "UVA365-flt-long.txt"        "UVA365-flt-short.txt"      
#>  [5] "UVA365-light-long.txt"      "UVA365-light-short.txt"    
#>  [7] "calibration-2016"           "canopyb2normal.txt"        
#>  [9] "canopyb2normalPC.txt"       "canopyb2normaldark.txt"    
#> [11] "canopyb2normallong.txt"     "canopyb2normallongPC.txt"  
#> [13] "canopyb2normallongdark.txt" "dark-long-dot.txt"         
#> [15] "dark-long.txt"              "dark-short-dot.txt"        
#> [17] "dark-short.txt"             "dark_MAYP112785.txt"       
#> [19] "filter_MAYP112785.txt"      "flt-long-dot.txt"          
#> [21] "flt-long.txt"               "led-dark.txt"              
#> [23] "led-flt.txt"                "led-light.txt"             
#> [25] "light-long-dot.txt"         "light-long.txt"            
#> [27] "light-short-dot.txt"        "light-short.txt"           
#> [29] "light_MAYP112785.txt"      

# read the top 20 lines of an example file
readLines(paste(path, "led-light.txt", sep = "/"), n = 20)
#>  [1] "SpectraSuite Data File"                            
#>  [2] "++++++++++++++++++++++++++++++++++++"              
#>  [3] "Date: Thu Nov 10 13:58:36 EET 2016"                
#>  [4] "User: OO Maya"                                     
#>  [5] "Dark Spectrum Present: No"                         
#>  [6] "Reference Spectrum Present: No"                    
#>  [7] "Number of Sampled Component Spectra: 1"            
#>  [8] "Spectrometers: MAYP11278"                          
#>  [9] "Integration Time (usec): 2250000 (MAYP11278)"      
#> [10] "Spectra Averaged: 1 (MAYP11278)"                   
#> [11] "Boxcar Smoothing: 0 (MAYP11278)"                   
#> [12] "Correct for Electrical Dark: No (MAYP11278)"       
#> [13] "Strobe/Lamp Enabled: No (MAYP11278)"               
#> [14] "Correct for Detector Non-linearity: No (MAYP11278)"
#> [15] "Correct for Stray Light: No (MAYP11278)"           
#> [16] "Number of Pixels in Processed Spectrum: 2068"      
#> [17] ">>>>>Begin Processed Spectral Data<<<<<"           
#> [18] "187,82\t2283,00"                                   
#> [19] "188,30\t2205,00"                                   
#> [20] "188,78\t2177,00"