tests/testthat/test_pr_convert.R
In lbusett/prismaread: Import PRISMA L1/L2 hyperspectral data and convert them to a more user friendly format
# Tests on l2d -----
context("Access L2D data")
test_that(
"Tests on L2D", {
skip_on_cran()
skip_on_travis()
testfile <- file.path(
system.file("testdata/", package = "prismaread"),
"PRS_L2D_STD_20200524103704_20200524103708_0001.he5")
# Download and unzip using piggyback if necessary
if (!file.exists(testfile)){
message("Downloading test data - This may need a long time!")
piggyback::pb_download(
"PRS_L2D_STD_20200524103704_20200524103708_0001.zip",
repo = "irea-cnr-mi/prismaread",
dest = file.path(
system.file("",
package = "prismaread"), "/testdata"))
piggyback::pb_track(
glob = "inst/testdata/*.zip, inst/testdata/*.he5")
zipfile <- file.path(
system.file("testdata/", package = "prismaread"),
"PRS_L2D_STD_20200524103704_20200524103708_0001.zip")
unzip(zipfile, exdir = dirname(testfile))
unlink(zipfile)
}
out_folder_L2D <- file.path(tempdir(), "prismaread/L2D")
dir.create(out_folder_L2D, recursive = TRUE)
# launch pr_convert to creat VNIR (FULL), SWIR (FULL), FULL,
# ANGLES, LATLON, PAN - save to tiff
pr_convert(in_file = testfile, out_folder = out_folder_L2D,
out_filebase = "testL2D_1", out_format = "GTiff",
VNIR = TRUE,
SWIR = TRUE, FULL = FALSE, ANGLES = FALSE, PAN = FALSE,
LATLON = FALSE, ERR_MATRIX = FALSE, apply_errmatrix = TRUE,
overwrite = TRUE)
vnir <- raster::brick(file.path(out_folder_L2D,
"testL2D_1_HCO_VNIR.tif"))
testthat::expect_equal(dim(vnir), c(1236,1290,63))
swir <- raster::brick(file.path(out_folder_L2D,
"testL2D_1_HCO_SWIR.tif"))
testthat::expect_equal(dim(swir), c(1236,1290,171))
# launch pr_convert to creat VNIR (6 bands), SWIR (3 bands), FULL,
# ANGLES, LATLON, PAN - save to tiff
pr_convert(in_file = testfile, out_folder = out_folder_L2D,
out_filebase = "testL2D_1", out_format = "GTiff",
VNIR = TRUE, selbands_vnir = c(450, 550, 650, 750, 850, 950),
selbands_swir = c(1000, 1500 ,2300),
SWIR = TRUE, FULL = TRUE, ANGLES = TRUE, PAN = TRUE,
LATLON = TRUE, ERR_MATRIX = TRUE, apply_errmatrix = FALSE,
overwrite = TRUE)
# All files created
flist <- list.files(out_folder_L2D, pattern = "testL2D_1")
testthat::expect_equal(length(flist), 12)
vnir <- raster::brick(file.path(out_folder_L2D,
"testL2D_1_HCO_VNIR.tif"))
means_vnir <- as.numeric(raster::cellStats(vnir, "mean", na.rm = TRUE))
testthat::expect_equal(means_vnir,
c(0.022935, 0.05126269, 0.05515500,
0.12456146, 0.14181177, 0.14477050))
swir <- raster::brick(file.path(out_folder_L2D,
"testL2D_1_HCO_SWIR.tif"))
means_swir <- as.numeric(raster::cellStats(swir, "mean", na.rm = TRUE))
testthat::expect_equal(means_swir,
c(0.13954069, 0.10219114, 0.08076247))
full <- raster::brick(file.path(out_folder_L2D,
"testL2D_1_HCO_FULL.tif"))
means_full <- as.numeric(raster::cellStats(full, "mean", na.rm = TRUE))
testthat::expect_equal(means_full,
c(0.022935, 0.05126269, 0.05515500,
0.12456146, 0.14181177, 0.14477050,
0.13954069, 0.10219114, 0.08076247))
testthat::expect_true(raster::projection(vnir) %in% c(
"+proj=longlat +datum=WGS84 +no_defs",
"+proj=utm +zone=32 +datum=WGS84 +units=m +no_defs"))
# wavelengths in wvl files are correct
wvls_vnir <- read.table(file.path(out_folder_L2D,
"testL2D_1_HCO_VNIR.wvl"),
header = TRUE)
wvls_swir <- read.table(file.path(out_folder_L2D,
"testL2D_1_HCO_SWIR.wvl"),
header = TRUE)
wvls_full <- read.table(file.path(out_folder_L2D,
"testL2D_1_HCO_FULL.wvl"),
header = TRUE)
testthat::expect_equal(wvls_full$wl, c(wvls_vnir$wl, wvls_swir$wl))
# extent is correct
ext <- raster::extent(vnir)
testthat::expect_equal(ext[c(1,3)], c(443902.5 - 15, 5006667.5 -15))
pan <- raster::brick(file.path(out_folder_L2D, "testL2D_1_HCO_PAN.tif"))
rastres <- raster::res(pan)
testthat::expect_equal(rastres, c(5, 5))
# launch pr_convert to creat VNIR (3 bands), SWIR (3 bands), FULL,
# - save to envi
pr_convert(in_file = testfile, out_folder = out_folder_L2D,
out_filebase = "testL2D_2", out_format = "ENVI",
VNIR = TRUE, selbands_vnir = c(450, 650, 850),
selbands_swir = c(1500),
SWIR = TRUE, FULL = TRUE, ANGLES = FALSE,
LATLON = FALSE, ERR_MATRIX = TRUE, apply_errmatrix = FALSE,
overwrite = TRUE)
flist <- list.files(out_folder_L2D, pattern = "testL2D_2")
testthat::expect_equal(length(flist), 19)
vnir <- raster::brick(file.path(out_folder_L2D,
"testL2D_2_HCO_VNIR.envi"))
means_vnir <- as.numeric(raster::cellStats(vnir, "mean", na.rm = TRUE))
testthat::expect_equal(means_vnir, c(0.022935, 0.05515500, 0.14181177))
swir <- raster::brick(file.path(out_folder_L2D,
"testL2D_2_HCO_SWIR.envi"))
means_swir <- as.numeric(raster::cellStats(swir, "mean", na.rm = TRUE))
testthat::expect_equal(means_swir, c(0.10219114))
# see that apply_errmatrix does something
pr_convert(in_file = testfile, out_folder = out_folder_L2D,
out_filebase = "testL2D_3", out_format = "GTiff",
VNIR = TRUE, selbands_vnir = c(450, 650),
SWIR = FALSE, FULL = FALSE, ANGLES = FALSE,
LATLON = FALSE, ERR_MATRIX = FALSE, apply_errmatrix = TRUE,
overwrite = TRUE)
vnir <- raster::brick(file.path(out_folder_L2D,
"testL2D_3_HCO_VNIR.tif"))
means_vnir <- as.numeric(raster::cellStats(vnir, "mean", na.rm = TRUE))
testthat::expect_equal(means_vnir, c(0.02349694, 0.05520516))
# wavelengths in wvl files are correct
wvls_vnir <- read.table(file.path(out_folder_L2D,
"testL2D_1_HCO_VNIR.wvl"),
header = TRUE)
wvls_swir <- read.table(file.path(out_folder_L2D,
"testL2D_1_HCO_SWIR.wvl"),
header = TRUE)
wvls_full <- read.table(file.path(out_folder_L2D,
"testL2D_1_HCO_FULL.wvl"),
header = TRUE)
testthat::expect_equal(wvls_full$wl, c(wvls_vnir$wl, wvls_swir$wl))
})
# Tests on l2c -----
context("Access L2C data")
test_that(
"Tests on L2C", {
skip_on_cran()
skip_on_travis()
testfile <- file.path(
system.file("/testdata", package = "prismaread"),
"/PRS_L2C_STD_20200524103704_20200524103708_0001.he5")
# Download and unzip using piggyback if necessary
if (!file.exists(testfile)){
message("Downloading test data - This may need a long time!")
piggyback::pb_download(
"PRS_L2C_STD_20200524103704_20200524103708_0001.zip",
repo = "irea-cnr-mi/prismaread",
dest = file.path(
system.file("", package = "prismaread"), "/testdata"))
piggyback::pb_track(
glob = "inst/testdata/*.zip, inst/testdata/*.he5")
zipfile <- file.path(
system.file("/testdata", package = "prismaread"),
"/PRS_L2C_STD_20200524103704_20200524103708_0001.zip")
unzip(zipfile, exdir = dirname(testfile))
unlink(zipfile)
}
out_folder_L2C <- file.path(tempdir(), "prismaread/L2C")
dir.create(out_folder_L2C, recursive = TRUE)
# launch pr_convert to creat VNIR (6 bands), SWIR (3 bands), FULL,
# ANGLES, LATLON, PAN - save to tiff - with georef and gaps filling
pr_convert(in_file = testfile, out_folder = out_folder_L2C,
out_filebase = "testL2C_1", out_format = "GTiff",
VNIR = TRUE, selbands_vnir = c(450, 550, 650, 750, 850, 950),
selbands_swir = c(1000, 1500 ,2300),
SWIR = TRUE, FULL = TRUE, ANGLES = TRUE, PAN = TRUE,
LATLON = TRUE, ERR_MATRIX = TRUE, apply_errmatrix = FALSE,
overwrite = TRUE)
# All files created
flist <- list.files(out_folder_L2C, pattern = "testL2C_1")
testthat::expect_equal(length(flist), 12)
vnir <- raster::brick(
file.path(out_folder_L2C, "testL2C_1_HCO_VNIR.tif"))
means_vnir <- as.numeric(raster::cellStats(vnir, "mean", na.rm = TRUE))
testthat::expect_equal(means_vnir,
c(0.03527613 , 0.07889447 , 0.08488756 ,
0.19185325 , 0.21844948 , 0.22302736),
tolerance = 0.001)
swir <- raster::brick(
file.path(out_folder_L2C, "testL2C_1_HCO_SWIR.tif"))
means_swir <- as.numeric(raster::cellStats(swir, "mean", na.rm = TRUE))
testthat::expect_equal(means_swir,
c(0.2149935 , 0.1573347 , 0.1243109),
tolerance = 0.001)
full <- raster::brick(
file.path(out_folder_L2C, "testL2C_1_HCO_FULL.tif"))
means_full <- as.numeric(raster::cellStats(full, "mean", na.rm = TRUE))
testthat::expect_equal(means_full, c(0.03527613, 0.07889447, 0.08488756,
0.19185325, 0.21844948, 0.22302736,
0.2149935, 0.1573347, 0.1243109),
tolerance = 0.001)
angs <- raster::brick(
file.path(out_folder_L2C, "testL2C_1_HCO_ANG.tif"))
means_angs <- as.numeric(raster::cellStats(angs, "mean", na.rm = TRUE))
testthat::expect_equal(means_angs, c(11.73522, 129.13642, 26.24126),
tolerance = 0.001)
llon <- raster::brick(
file.path(out_folder_L2C, "testL2C_1_HCO_LATLON.tif"))
means_latlon <- as.numeric(
raster::cellStats(llon, "mean", na.rm = TRUE))
testthat::expect_equal(means_latlon, c(45.379759, 8.529825),
tolerance = 0.001)
# wavelengths in wvl files are correct
wvls_vnir <- read.table(
file.path(out_folder_L2C, "testL2C_1_HCO_VNIR.wvl"),
header = TRUE)
wvls_swir <- read.table(
file.path(out_folder_L2C, "testL2C_1_HCO_SWIR.wvl"),
header = TRUE)
wvls_full <- read.table(
file.path(out_folder_L2C, "testL2C_1_HCO_FULL.wvl"),
header = TRUE)
testthat::expect_equal(wvls_full$wl, c(wvls_vnir$wl, wvls_swir$wl))
# extent is correct: check left and top and not corner due to rotation
# introduced by GLT
ext <- raster::extent(vnir)
testthat::expect_equal(ext[c(1,4)], c(8.2876167, 45.544937),
tolerance = 0.00001)
# launch pr_convert to creat VNIR (3 bands), SWIR (3 bands), FULL,
# - save to GTiff - no fill gaps
pr_convert(in_file = testfile, out_folder = out_folder_L2C,
out_filebase = "testL2C_2", out_format = "GTiff",
fill_gaps = FALSE,
VNIR = TRUE, selbands_vnir = c(450, 650, 850),
selbands_swir = c(1500),
SWIR = TRUE, FULL = TRUE, ANGLES = FALSE,
LATLON = FALSE, ERR_MATRIX = FALSE, apply_errmatrix = FALSE,
overwrite = TRUE)
flist <- list.files(out_folder_L2C, pattern = "testL2C_2")
testthat::expect_equal(length(flist), 7)
vnir <- raster::brick(
file.path(out_folder_L2C, "testL2C_2_HCO_VNIR.tif"))
means_vnir <- as.numeric(raster::cellStats(vnir, "mean", na.rm = TRUE))
testthat::expect_equal(means_vnir,
c(0.03529589 , 0.08492260 , 0.21841796),
tolerance = 0.001)
swir <- raster::brick(
file.path(out_folder_L2C, "testL2C_2_HCO_SWIR.tif"))
means_swir <- as.numeric(raster::cellStats(swir, "mean", na.rm = TRUE))
testthat::expect_equal(means_swir, c(0.1573508), tolerance = 0.001)
full <- raster::brick(
file.path(out_folder_L2C, "testL2C_2_HCO_FULL.tif"))
means_full <- as.numeric(raster::cellStats(full, "mean", na.rm = TRUE))
testthat::expect_equal(means_full, c(0.03529589, 0.08492260, 0.21841796,
0.1573508), tolerance = 0.001)
testthat::expect_equal(raster::projection(vnir),
"+proj=longlat +datum=WGS84 +no_defs")
# launch pr_convert to creat VNIR (3 bands), SWIR (3 bands), FULL,
# - save to GTiff - no georef
testthat::expect_warning(
pr_convert(in_file = testfile, out_folder = out_folder_L2C,
out_filebase = "testL2C_3", out_format = "GTiff",
fill_gaps = FALSE, base_georef = FALSE,
VNIR = TRUE, selbands_vnir = c(450, 650, 850),
selbands_swir = c(1500),
SWIR = TRUE, FULL = TRUE, ANGLES = TRUE,
LATLON = TRUE, ERR_MATRIX = TRUE,
apply_errmatrix = FALSE,
overwrite = TRUE))
flist <- list.files(out_folder_L2C, pattern = "testL2C_3")
testthat::expect_equal(length(flist), 11)
vnir <- raster::brick(
file.path(out_folder_L2C, "testL2C_3_HCO_VNIR.tif"))
testthat::expect_error(projection(vnir))
testthat::expect_equal(dim(vnir), c(1000,1000,3))
})
context("Access L1 data")
# Tests on l1 -----
test_that(
"Tests on L1", {
skip_on_cran()
skip_on_travis()
testfile <- file.path(
system.file("testdata/", package = "prismaread"),
"PRS_L1_STD_OFFL_20200524103704_20200524103708_0001.he5")
# Download and unzip using piggyback if necessary
if (!file.exists(testfile)){
message("Downloading test data - This may need a long time!")
piggyback::pb_download(
"PRS_L1_STD_OFFL_20200524103704_20200524103708_0001.zip",
repo = "irea-cnr-mi/prismaread",
dest = file.path(
system.file("", package = "prismaread"), "/testdata"))
piggyback::pb_track(
glob = "inst/testdata/*.zip, inst/testdata/*.he5")
zipfile <- file.path(
system.file("testdata/", package = "prismaread"),
"PRS_L1_STD_OFFL_20200524103704_20200524103708_0001.zip")
unzip(zipfile, exdir = dirname(testfile))
unlink(zipfile)
}
out_folder_L1 <- file.path(tempdir(), "prismaread/L1")
dir.create(out_folder_L1, recursive = TRUE)
# launch pr_convert to creat VNIR (3 bands), SWIR (1 bands), FULL,
# ANGLES, LATLON, PAN - save to tiff
pr_convert(in_file = testfile, out_folder = out_folder_L1,
out_filebase = "testL1_1", out_format = "GTiff",
VNIR = TRUE, selbands_vnir = c(450, 650, 850),
selbands_swir = c(1500), ATCOR = TRUE,
SWIR = TRUE, FULL = TRUE, ANGLES = TRUE, PAN = TRUE,
CLOUD = TRUE, GLINT = TRUE, LC = TRUE,
LATLON = TRUE, ERR_MATRIX = TRUE, apply_errmatrix = FALSE,
overwrite = TRUE)
# All files created
flist <- list.files(out_folder_L1, pattern = "testL1_1")
testthat::expect_equal(length(flist), 14)
vnir <- raster::brick(
file.path(out_folder_L1, "testL1_1_HCO_VNIR.tif"))
means_vnir <- as.numeric(raster::cellStats(vnir, "mean", na.rm = TRUE))
testthat::expect_equal(means_vnir, c(71.74590 , 45.75219 , 58.21456),
tolerance = 0.0001)
swir <- raster::brick(
file.path(out_folder_L1, "testL1_1_HCO_SWIR.tif"))
means_swir <- as.numeric(raster::cellStats(swir, "mean", na.rm = TRUE))
testthat::expect_equal(means_swir, c(8.926156), tolerance = 0.0001)
full <- raster::brick(
file.path(out_folder_L1, "testL1_1_HCO_FULL.tif"))
means_full <- as.numeric(raster::cellStats(full, "mean", na.rm = TRUE))
testthat::expect_equal(means_full, c(71.74590, 45.75219, 58.21456,
8.926156), tolerance = 0.0001)
# Use L2file to georeference ----
in_L2_file <- file.path(
system.file("testdata/", package = "prismaread"),
"PRS_L2C_STD_20200524103704_20200524103708_0001.he5")
pr_convert(in_file = testfile, out_folder = out_folder_L1,
out_filebase = "testL1_2", out_format = "GTiff",
in_L2_file = in_L2_file,
VNIR = TRUE, selbands_vnir = c(450, 650, 850),
selbands_swir = c(1500),
SWIR = TRUE, FULL = TRUE, ANGLES = TRUE, PAN = TRUE,
CLOUD = TRUE, GLINT = TRUE, LC = TRUE,
LATLON = TRUE, ERR_MATRIX = TRUE, apply_errmatrix = FALSE,
overwrite = TRUE)
angs <- raster::brick(file.path(out_folder_L1, "testL1_2_HCO_ANG.tif"))
means_angs <- as.numeric(raster::cellStats(angs, "mean", na.rm = TRUE))
# angles retrieved by overwriting with L2 are equal to those of L2
testthat::expect_equal(means_angs, c(11.73522, 129.13642, 26.24126),
tolerance = 0.001)
# do not georeference ----
testthat::expect_warning(
pr_convert(in_file = testfile, out_folder = out_folder_L1,
out_filebase = "testL1_3", out_format = "GTiff",
base_georef = FALSE,
VNIR = TRUE, selbands_vnir = c(450, 650, 850),
SWIR = FALSE, FULL = FALSE, ANGLES = FALSE, PAN = FALSE,
CLOUD = FALSE, GLINT = FALSE, LC = FALSE,
LATLON = FALSE, ERR_MATRIX = FALSE,
apply_errmatrix = FALSE,
overwrite = FALSE))
vnir <- raster::brick(
file.path(out_folder_L1, "testL1_3_HCO_VNIR.tif"))
# angles retrieved by overwriting with L2 are equal to those of L2
testthat::expect_equal(dim(vnir), c(1000, 1000, 3),
tolerance = 0.001)
# get HRC and complex ATCOR
# launch pr_convert to creat VNIR (3 bands), SWIR (1 bands), FULL,
# ANGLES, LATLON, PAN - save to tiff
pr_convert(in_file = testfile, out_folder = out_folder_L1,
out_filebase = "testL1_1", out_format = "GTiff",
VNIR = TRUE, selbands_vnir = c(450),
selbands_swir = c(1500), ATCOR = TRUE,
ATCOR_wls = c(200,800),
SWIR = TRUE, FULL = TRUE, ANGLES = TRUE, PAN = TRUE,
CLOUD = TRUE, GLINT = TRUE, LC = TRUE,
LATLON = TRUE, ERR_MATRIX = TRUE, apply_errmatrix = FALSE,
overwrite = TRUE, source = "HRC")
})
lbusett/prismaread documentation built on Feb. 22, 2022, 7:33 p.m.
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# Tests on l2d -----
context("Access L2D data")
test_that(
"Tests on L2D", {
skip_on_cran()
skip_on_travis()
testfile <- file.path(
system.file("testdata/", package = "prismaread"),
"PRS_L2D_STD_20200524103704_20200524103708_0001.he5")
# Download and unzip using piggyback if necessary
if (!file.exists(testfile)){
message("Downloading test data - This may need a long time!")
piggyback::pb_download(
"PRS_L2D_STD_20200524103704_20200524103708_0001.zip",
repo = "irea-cnr-mi/prismaread",
dest = file.path(
system.file("",
package = "prismaread"), "/testdata"))
piggyback::pb_track(
glob = "inst/testdata/*.zip, inst/testdata/*.he5")
zipfile <- file.path(
system.file("testdata/", package = "prismaread"),
"PRS_L2D_STD_20200524103704_20200524103708_0001.zip")
unzip(zipfile, exdir = dirname(testfile))
unlink(zipfile)
}
out_folder_L2D <- file.path(tempdir(), "prismaread/L2D")
dir.create(out_folder_L2D, recursive = TRUE)
# launch pr_convert to creat VNIR (FULL), SWIR (FULL), FULL,
# ANGLES, LATLON, PAN - save to tiff
pr_convert(in_file = testfile, out_folder = out_folder_L2D,
out_filebase = "testL2D_1", out_format = "GTiff",
VNIR = TRUE,
SWIR = TRUE, FULL = FALSE, ANGLES = FALSE, PAN = FALSE,
LATLON = FALSE, ERR_MATRIX = FALSE, apply_errmatrix = TRUE,
overwrite = TRUE)
vnir <- raster::brick(file.path(out_folder_L2D,
"testL2D_1_HCO_VNIR.tif"))
testthat::expect_equal(dim(vnir), c(1236,1290,63))
swir <- raster::brick(file.path(out_folder_L2D,
"testL2D_1_HCO_SWIR.tif"))
testthat::expect_equal(dim(swir), c(1236,1290,171))
# launch pr_convert to creat VNIR (6 bands), SWIR (3 bands), FULL,
# ANGLES, LATLON, PAN - save to tiff
pr_convert(in_file = testfile, out_folder = out_folder_L2D,
out_filebase = "testL2D_1", out_format = "GTiff",
VNIR = TRUE, selbands_vnir = c(450, 550, 650, 750, 850, 950),
selbands_swir = c(1000, 1500 ,2300),
SWIR = TRUE, FULL = TRUE, ANGLES = TRUE, PAN = TRUE,
LATLON = TRUE, ERR_MATRIX = TRUE, apply_errmatrix = FALSE,
overwrite = TRUE)
# All files created
flist <- list.files(out_folder_L2D, pattern = "testL2D_1")
testthat::expect_equal(length(flist), 12)
vnir <- raster::brick(file.path(out_folder_L2D,
"testL2D_1_HCO_VNIR.tif"))
means_vnir <- as.numeric(raster::cellStats(vnir, "mean", na.rm = TRUE))
testthat::expect_equal(means_vnir,
c(0.022935, 0.05126269, 0.05515500,
0.12456146, 0.14181177, 0.14477050))
swir <- raster::brick(file.path(out_folder_L2D,
"testL2D_1_HCO_SWIR.tif"))
means_swir <- as.numeric(raster::cellStats(swir, "mean", na.rm = TRUE))
testthat::expect_equal(means_swir,
c(0.13954069, 0.10219114, 0.08076247))
full <- raster::brick(file.path(out_folder_L2D,
"testL2D_1_HCO_FULL.tif"))
means_full <- as.numeric(raster::cellStats(full, "mean", na.rm = TRUE))
testthat::expect_equal(means_full,
c(0.022935, 0.05126269, 0.05515500,
0.12456146, 0.14181177, 0.14477050,
0.13954069, 0.10219114, 0.08076247))
testthat::expect_true(raster::projection(vnir) %in% c(
"+proj=longlat +datum=WGS84 +no_defs",
"+proj=utm +zone=32 +datum=WGS84 +units=m +no_defs"))
# wavelengths in wvl files are correct
wvls_vnir <- read.table(file.path(out_folder_L2D,
"testL2D_1_HCO_VNIR.wvl"),
header = TRUE)
wvls_swir <- read.table(file.path(out_folder_L2D,
"testL2D_1_HCO_SWIR.wvl"),
header = TRUE)
wvls_full <- read.table(file.path(out_folder_L2D,
"testL2D_1_HCO_FULL.wvl"),
header = TRUE)
testthat::expect_equal(wvls_full$wl, c(wvls_vnir$wl, wvls_swir$wl))
# extent is correct
ext <- raster::extent(vnir)
testthat::expect_equal(ext[c(1,3)], c(443902.5 - 15, 5006667.5 -15))
pan <- raster::brick(file.path(out_folder_L2D, "testL2D_1_HCO_PAN.tif"))
rastres <- raster::res(pan)
testthat::expect_equal(rastres, c(5, 5))
# launch pr_convert to creat VNIR (3 bands), SWIR (3 bands), FULL,
# - save to envi
pr_convert(in_file = testfile, out_folder = out_folder_L2D,
out_filebase = "testL2D_2", out_format = "ENVI",
VNIR = TRUE, selbands_vnir = c(450, 650, 850),
selbands_swir = c(1500),
SWIR = TRUE, FULL = TRUE, ANGLES = FALSE,
LATLON = FALSE, ERR_MATRIX = TRUE, apply_errmatrix = FALSE,
overwrite = TRUE)
flist <- list.files(out_folder_L2D, pattern = "testL2D_2")
testthat::expect_equal(length(flist), 19)
vnir <- raster::brick(file.path(out_folder_L2D,
"testL2D_2_HCO_VNIR.envi"))
means_vnir <- as.numeric(raster::cellStats(vnir, "mean", na.rm = TRUE))
testthat::expect_equal(means_vnir, c(0.022935, 0.05515500, 0.14181177))
swir <- raster::brick(file.path(out_folder_L2D,
"testL2D_2_HCO_SWIR.envi"))
means_swir <- as.numeric(raster::cellStats(swir, "mean", na.rm = TRUE))
testthat::expect_equal(means_swir, c(0.10219114))
# see that apply_errmatrix does something
pr_convert(in_file = testfile, out_folder = out_folder_L2D,
out_filebase = "testL2D_3", out_format = "GTiff",
VNIR = TRUE, selbands_vnir = c(450, 650),
SWIR = FALSE, FULL = FALSE, ANGLES = FALSE,
LATLON = FALSE, ERR_MATRIX = FALSE, apply_errmatrix = TRUE,
overwrite = TRUE)
vnir <- raster::brick(file.path(out_folder_L2D,
"testL2D_3_HCO_VNIR.tif"))
means_vnir <- as.numeric(raster::cellStats(vnir, "mean", na.rm = TRUE))
testthat::expect_equal(means_vnir, c(0.02349694, 0.05520516))
# wavelengths in wvl files are correct
wvls_vnir <- read.table(file.path(out_folder_L2D,
"testL2D_1_HCO_VNIR.wvl"),
header = TRUE)
wvls_swir <- read.table(file.path(out_folder_L2D,
"testL2D_1_HCO_SWIR.wvl"),
header = TRUE)
wvls_full <- read.table(file.path(out_folder_L2D,
"testL2D_1_HCO_FULL.wvl"),
header = TRUE)
testthat::expect_equal(wvls_full$wl, c(wvls_vnir$wl, wvls_swir$wl))
})
# Tests on l2c -----
context("Access L2C data")
test_that(
"Tests on L2C", {
skip_on_cran()
skip_on_travis()
testfile <- file.path(
system.file("/testdata", package = "prismaread"),
"/PRS_L2C_STD_20200524103704_20200524103708_0001.he5")
# Download and unzip using piggyback if necessary
if (!file.exists(testfile)){
message("Downloading test data - This may need a long time!")
piggyback::pb_download(
"PRS_L2C_STD_20200524103704_20200524103708_0001.zip",
repo = "irea-cnr-mi/prismaread",
dest = file.path(
system.file("", package = "prismaread"), "/testdata"))
piggyback::pb_track(
glob = "inst/testdata/*.zip, inst/testdata/*.he5")
zipfile <- file.path(
system.file("/testdata", package = "prismaread"),
"/PRS_L2C_STD_20200524103704_20200524103708_0001.zip")
unzip(zipfile, exdir = dirname(testfile))
unlink(zipfile)
}
out_folder_L2C <- file.path(tempdir(), "prismaread/L2C")
dir.create(out_folder_L2C, recursive = TRUE)
# launch pr_convert to creat VNIR (6 bands), SWIR (3 bands), FULL,
# ANGLES, LATLON, PAN - save to tiff - with georef and gaps filling
pr_convert(in_file = testfile, out_folder = out_folder_L2C,
out_filebase = "testL2C_1", out_format = "GTiff",
VNIR = TRUE, selbands_vnir = c(450, 550, 650, 750, 850, 950),
selbands_swir = c(1000, 1500 ,2300),
SWIR = TRUE, FULL = TRUE, ANGLES = TRUE, PAN = TRUE,
LATLON = TRUE, ERR_MATRIX = TRUE, apply_errmatrix = FALSE,
overwrite = TRUE)
# All files created
flist <- list.files(out_folder_L2C, pattern = "testL2C_1")
testthat::expect_equal(length(flist), 12)
vnir <- raster::brick(
file.path(out_folder_L2C, "testL2C_1_HCO_VNIR.tif"))
means_vnir <- as.numeric(raster::cellStats(vnir, "mean", na.rm = TRUE))
testthat::expect_equal(means_vnir,
c(0.03527613 , 0.07889447 , 0.08488756 ,
0.19185325 , 0.21844948 , 0.22302736),
tolerance = 0.001)
swir <- raster::brick(
file.path(out_folder_L2C, "testL2C_1_HCO_SWIR.tif"))
means_swir <- as.numeric(raster::cellStats(swir, "mean", na.rm = TRUE))
testthat::expect_equal(means_swir,
c(0.2149935 , 0.1573347 , 0.1243109),
tolerance = 0.001)
full <- raster::brick(
file.path(out_folder_L2C, "testL2C_1_HCO_FULL.tif"))
means_full <- as.numeric(raster::cellStats(full, "mean", na.rm = TRUE))
testthat::expect_equal(means_full, c(0.03527613, 0.07889447, 0.08488756,
0.19185325, 0.21844948, 0.22302736,
0.2149935, 0.1573347, 0.1243109),
tolerance = 0.001)
angs <- raster::brick(
file.path(out_folder_L2C, "testL2C_1_HCO_ANG.tif"))
means_angs <- as.numeric(raster::cellStats(angs, "mean", na.rm = TRUE))
testthat::expect_equal(means_angs, c(11.73522, 129.13642, 26.24126),
tolerance = 0.001)
llon <- raster::brick(
file.path(out_folder_L2C, "testL2C_1_HCO_LATLON.tif"))
means_latlon <- as.numeric(
raster::cellStats(llon, "mean", na.rm = TRUE))
testthat::expect_equal(means_latlon, c(45.379759, 8.529825),
tolerance = 0.001)
# wavelengths in wvl files are correct
wvls_vnir <- read.table(
file.path(out_folder_L2C, "testL2C_1_HCO_VNIR.wvl"),
header = TRUE)
wvls_swir <- read.table(
file.path(out_folder_L2C, "testL2C_1_HCO_SWIR.wvl"),
header = TRUE)
wvls_full <- read.table(
file.path(out_folder_L2C, "testL2C_1_HCO_FULL.wvl"),
header = TRUE)
testthat::expect_equal(wvls_full$wl, c(wvls_vnir$wl, wvls_swir$wl))
# extent is correct: check left and top and not corner due to rotation
# introduced by GLT
ext <- raster::extent(vnir)
testthat::expect_equal(ext[c(1,4)], c(8.2876167, 45.544937),
tolerance = 0.00001)
# launch pr_convert to creat VNIR (3 bands), SWIR (3 bands), FULL,
# - save to GTiff - no fill gaps
pr_convert(in_file = testfile, out_folder = out_folder_L2C,
out_filebase = "testL2C_2", out_format = "GTiff",
fill_gaps = FALSE,
VNIR = TRUE, selbands_vnir = c(450, 650, 850),
selbands_swir = c(1500),
SWIR = TRUE, FULL = TRUE, ANGLES = FALSE,
LATLON = FALSE, ERR_MATRIX = FALSE, apply_errmatrix = FALSE,
overwrite = TRUE)
flist <- list.files(out_folder_L2C, pattern = "testL2C_2")
testthat::expect_equal(length(flist), 7)
vnir <- raster::brick(
file.path(out_folder_L2C, "testL2C_2_HCO_VNIR.tif"))
means_vnir <- as.numeric(raster::cellStats(vnir, "mean", na.rm = TRUE))
testthat::expect_equal(means_vnir,
c(0.03529589 , 0.08492260 , 0.21841796),
tolerance = 0.001)
swir <- raster::brick(
file.path(out_folder_L2C, "testL2C_2_HCO_SWIR.tif"))
means_swir <- as.numeric(raster::cellStats(swir, "mean", na.rm = TRUE))
testthat::expect_equal(means_swir, c(0.1573508), tolerance = 0.001)
full <- raster::brick(
file.path(out_folder_L2C, "testL2C_2_HCO_FULL.tif"))
means_full <- as.numeric(raster::cellStats(full, "mean", na.rm = TRUE))
testthat::expect_equal(means_full, c(0.03529589, 0.08492260, 0.21841796,
0.1573508), tolerance = 0.001)
testthat::expect_equal(raster::projection(vnir),
"+proj=longlat +datum=WGS84 +no_defs")
# launch pr_convert to creat VNIR (3 bands), SWIR (3 bands), FULL,
# - save to GTiff - no georef
testthat::expect_warning(
pr_convert(in_file = testfile, out_folder = out_folder_L2C,
out_filebase = "testL2C_3", out_format = "GTiff",
fill_gaps = FALSE, base_georef = FALSE,
VNIR = TRUE, selbands_vnir = c(450, 650, 850),
selbands_swir = c(1500),
SWIR = TRUE, FULL = TRUE, ANGLES = TRUE,
LATLON = TRUE, ERR_MATRIX = TRUE,
apply_errmatrix = FALSE,
overwrite = TRUE))
flist <- list.files(out_folder_L2C, pattern = "testL2C_3")
testthat::expect_equal(length(flist), 11)
vnir <- raster::brick(
file.path(out_folder_L2C, "testL2C_3_HCO_VNIR.tif"))
testthat::expect_error(projection(vnir))
testthat::expect_equal(dim(vnir), c(1000,1000,3))
})
context("Access L1 data")
# Tests on l1 -----
test_that(
"Tests on L1", {
skip_on_cran()
skip_on_travis()
testfile <- file.path(
system.file("testdata/", package = "prismaread"),
"PRS_L1_STD_OFFL_20200524103704_20200524103708_0001.he5")
# Download and unzip using piggyback if necessary
if (!file.exists(testfile)){
message("Downloading test data - This may need a long time!")
piggyback::pb_download(
"PRS_L1_STD_OFFL_20200524103704_20200524103708_0001.zip",
repo = "irea-cnr-mi/prismaread",
dest = file.path(
system.file("", package = "prismaread"), "/testdata"))
piggyback::pb_track(
glob = "inst/testdata/*.zip, inst/testdata/*.he5")
zipfile <- file.path(
system.file("testdata/", package = "prismaread"),
"PRS_L1_STD_OFFL_20200524103704_20200524103708_0001.zip")
unzip(zipfile, exdir = dirname(testfile))
unlink(zipfile)
}
out_folder_L1 <- file.path(tempdir(), "prismaread/L1")
dir.create(out_folder_L1, recursive = TRUE)
# launch pr_convert to creat VNIR (3 bands), SWIR (1 bands), FULL,
# ANGLES, LATLON, PAN - save to tiff
pr_convert(in_file = testfile, out_folder = out_folder_L1,
out_filebase = "testL1_1", out_format = "GTiff",
VNIR = TRUE, selbands_vnir = c(450, 650, 850),
selbands_swir = c(1500), ATCOR = TRUE,
SWIR = TRUE, FULL = TRUE, ANGLES = TRUE, PAN = TRUE,
CLOUD = TRUE, GLINT = TRUE, LC = TRUE,
LATLON = TRUE, ERR_MATRIX = TRUE, apply_errmatrix = FALSE,
overwrite = TRUE)
# All files created
flist <- list.files(out_folder_L1, pattern = "testL1_1")
testthat::expect_equal(length(flist), 14)
vnir <- raster::brick(
file.path(out_folder_L1, "testL1_1_HCO_VNIR.tif"))
means_vnir <- as.numeric(raster::cellStats(vnir, "mean", na.rm = TRUE))
testthat::expect_equal(means_vnir, c(71.74590 , 45.75219 , 58.21456),
tolerance = 0.0001)
swir <- raster::brick(
file.path(out_folder_L1, "testL1_1_HCO_SWIR.tif"))
means_swir <- as.numeric(raster::cellStats(swir, "mean", na.rm = TRUE))
testthat::expect_equal(means_swir, c(8.926156), tolerance = 0.0001)
full <- raster::brick(
file.path(out_folder_L1, "testL1_1_HCO_FULL.tif"))
means_full <- as.numeric(raster::cellStats(full, "mean", na.rm = TRUE))
testthat::expect_equal(means_full, c(71.74590, 45.75219, 58.21456,
8.926156), tolerance = 0.0001)
# Use L2file to georeference ----
in_L2_file <- file.path(
system.file("testdata/", package = "prismaread"),
"PRS_L2C_STD_20200524103704_20200524103708_0001.he5")
pr_convert(in_file = testfile, out_folder = out_folder_L1,
out_filebase = "testL1_2", out_format = "GTiff",
in_L2_file = in_L2_file,
VNIR = TRUE, selbands_vnir = c(450, 650, 850),
selbands_swir = c(1500),
SWIR = TRUE, FULL = TRUE, ANGLES = TRUE, PAN = TRUE,
CLOUD = TRUE, GLINT = TRUE, LC = TRUE,
LATLON = TRUE, ERR_MATRIX = TRUE, apply_errmatrix = FALSE,
overwrite = TRUE)
angs <- raster::brick(file.path(out_folder_L1, "testL1_2_HCO_ANG.tif"))
means_angs <- as.numeric(raster::cellStats(angs, "mean", na.rm = TRUE))
# angles retrieved by overwriting with L2 are equal to those of L2
testthat::expect_equal(means_angs, c(11.73522, 129.13642, 26.24126),
tolerance = 0.001)
# do not georeference ----
testthat::expect_warning(
pr_convert(in_file = testfile, out_folder = out_folder_L1,
out_filebase = "testL1_3", out_format = "GTiff",
base_georef = FALSE,
VNIR = TRUE, selbands_vnir = c(450, 650, 850),
SWIR = FALSE, FULL = FALSE, ANGLES = FALSE, PAN = FALSE,
CLOUD = FALSE, GLINT = FALSE, LC = FALSE,
LATLON = FALSE, ERR_MATRIX = FALSE,
apply_errmatrix = FALSE,
overwrite = FALSE))
vnir <- raster::brick(
file.path(out_folder_L1, "testL1_3_HCO_VNIR.tif"))
# angles retrieved by overwriting with L2 are equal to those of L2
testthat::expect_equal(dim(vnir), c(1000, 1000, 3),
tolerance = 0.001)
# get HRC and complex ATCOR
# launch pr_convert to creat VNIR (3 bands), SWIR (1 bands), FULL,
# ANGLES, LATLON, PAN - save to tiff
pr_convert(in_file = testfile, out_folder = out_folder_L1,
out_filebase = "testL1_1", out_format = "GTiff",
VNIR = TRUE, selbands_vnir = c(450),
selbands_swir = c(1500), ATCOR = TRUE,
ATCOR_wls = c(200,800),
SWIR = TRUE, FULL = TRUE, ANGLES = TRUE, PAN = TRUE,
CLOUD = TRUE, GLINT = TRUE, LC = TRUE,
LATLON = TRUE, ERR_MATRIX = TRUE, apply_errmatrix = FALSE,
overwrite = TRUE, source = "HRC")
})
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