pr_check_inputs: pr_check_inputs

In lbusett/prismaread: Import PRISMA L1/L2 hyperspectral data and convert them to a more user friendly format

Description

helper function used to check consistency of pr_convert arguments

Usage

pr_check_inputs(
  in_file,
  out_folder,
  out_filebase,
  out_format,
  base_georef,
  fill_gaps,
  VNIR,
  SWIR,
  FULL,
  source,
  join_priority,
  ATCOR,
  ATCOR_wls,
  PAN,
  CLOUD,
  LC,
  GLINT,
  ANGLES,
  LATLON,
  ERR_MATRIX,
  apply_errmatrix,
  overwrite,
  in_L2_file,
  selbands_vnir,
  selbands_swir,
  indexes,
  cust_indexes,
  keep_index_cube
)

Arguments

in_file	'character' full path of input HDF5 file
out_folder	'character' full path to output folder
out_filebase	'character' if "auto", output file names are based on filename of the input prisma file, with appropriate suffixes. If a different string is provided, it is used as prefix instead of the input file name, Default: "auto"
out_format	'character“ ["GTiff" | "ENVI"], Output format, Default: 'GTiff'
base_georef	'logical' if TRUE, apply base georeferencing on L1, L2B/C data, using the "Georeference from input GLT" procedure explained here: https://www.harrisgeospatial.com/docs/backgroundgltbowtiecorrection.html, Default: TRUE
fill_gaps	'logical' if TRUE, when georeferencing on L1, L2B/C data, substitute missing values with results of a 3x3 focal filter on the georeferenced data, Default: FALSE
VNIR	'logical' if TRUE, create the VNIR image, Default: FALSE
SWIR	'logical' if TRUE, create the SWIR image, Default: FALSE
FULL	'logical' if TRUE, create a single multispectral image from VNIR and SWIR, Default: FALSE
source	'character' ["HC0" | "HRC"], Considered Data Cub, Default: 'HCO'
join_priority	'character' ["VNIR" | "SWIR"], spectrometer to consider when join_spectra = TRUE, Default: SWIR - ignored if join_spectra is FALSE. Default: "SWIR"
ATCOR	logical' if TRUE, create the text files required to run ATCOR, Default: FALSE;
ATCOR_wls	NULL, or 'numeric' If NULL the only ATCOR wvl file created is the one containing Nominal wavelengths. If a numeric vector is provided, then one different wvl file is created for each selected COLUMN selected (e.g., if providing 'ATCOR_wls = c(200, 800)', then the wavelengths and FWHMs related to columns 200 and 800 are saved.)
PAN	'logical' if TRUE, also save PAN data, default: FALSE
CLOUD	'logical' if TRUE, also save CLOUD MASK mask data, Default: FALSE (Ignored for L2 data). It is coded as: 0 for not cloudy pixel 1 for cloudy pixel 10 = for not of all previous classification 255 = error
LC	'logical' if TRUE, also save the LAND COVER data, default: FALSE (Ignored for L2 data) It is coded as: 0 for water pixel 1 for snow pixel (and ice) 2 for not-vegetated land pixel :bare soil) 3 for crop and rangeland pixel 4 for forest pixel 5 for wetland pixel 6 for not-vegetated land pixel :urban component 10 for not of all previous classification 255 for error
GLINT	'logical' if TRUE, also save GLINT mask data, default: FALSE (Ignored for L2 data) It is coded as: 0 for not sun glint 1 for sun glint 10 for not of all previous classification 255 = error
ANGLES	if TRUE, also save the ACQUISITION ANGLES data. ANGLES data are saved as a 3-band raster. Band 1 contains "viewzen_ang", Band 2 contains "relaz_ang" and Band 3 contains "solzen_ang"), default: FALSE
LATLON	if TRUE, also save the LATITUDE and LONGITUDE data. LATLON data are saved as a 2-band raster. Band 1 contains "Lat", Band 2 contains "Lon", Default: FALSE
ERR_MATRIX	'logical' if TRUE, also save the SATURATION ERROR MATRIX Data, Default: FALSE SATURATION ERROR MATRIX is coded as: 0=pixel ok; 1=DEFECTIVE PIXEL from KDP 2= Pixel in saturation. 3= Pixel with lower radiometric accuracy, due to coregistration effects. 4= Pixel becomes NaN or Inf during processing.
apply_errmatrix	'logical' if TRUE, set pixels with values above 0 in the SATERR_MATRIX data cube (for L1) or ERRMATRIX cube (for L2) to NA, Default: FALSE
overwrite	'logical' if TRUE, existing files are overwritten, Default: FALSE
in_L2_file	'character' full path of an L2B/C file to be used to extract georeferencing info and angles for a corresponding L1 file. If not NULL, and 'in_file' is a L1 file, the LAT and LON fields used for bowtie georeferencing are taken from the L2 file instead than from the L1 file. The ANGLES data are also retrieved from the L2 file if requested.
selbands_vnir	'numeric array' containing wavelengths (in nanometers) of bands that should be extracted from the VNIR data cube. If not NULL, only the bands with wavelengths closest to these values are extracted, Default: NULL
selbands_swir	'numeric array' containing wavelengths (in nanometers) of bands that should be extracted from the SWIR data cube. If not NULL, only the bands with wavelengths closest to these values are extracted, Default: NULL
indexes	'character' array of names of indexes to be computed. You can see a list of available indexes using command 'pr_listindexes()', or see the corresponding table at: https://irea-cnr-mi.github.io/prismaread/articles/Computing-Spectral-Indexes.html, #nolint Default:NULL
cust_indexes	'character' named list containing names and formulas of custom indexes to be computed. The indexes formulas must be computable R formulas, where bands are referred to by the prefix "b", followed by the wavelength (e.g.,'cust_indexes = list(myindex1 = "R500 / R600", myindex2 = "(R800 - R680) / (R800 + R680)")', Default:NULL
keep_index_cube	'logical', if TRUE, and spectral indexes were computed, keep in the output folder the hyperspectral cube used to compute the indexes (containing only wavelengths required to compute the desired indexes). The file takes a "_INDEXES" suffix. If FALSE, put the file in tempdir so that it is deleted automatically afterwards. Default: FALSE

Value

Upon success of all checks, the input hdf file, opened using 'hdf5r::H5File'

lbusett/prismaread documentation built on Feb. 22, 2022, 7:33 p.m.