fix bug if index uses only one band

+ small improvements
IREA-CNR-MI · Sep 17, 2020 · a0692a0 · a0692a0
1 parent d073c5f
commit a0692a0
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -7,11 +7,14 @@ Authors@R:
     comment = c(ORCID = '0000-0001-9634-6038')), 
     person("Luigi", "Ranghetti", email = "[email protected]", role = c("aut"), 
     comment = c(ORCID = '0000-0001-6207-5188')))
-Description: `prismaread` allows easily importing PRISMA hyperspectral data (http://www.prisma-i.it/index.php/it/) 
- from the original data provided by ASI in HDF format, and convert them to a easier to use format (ENVI or GeoTiff). 
- It also provides functionality for automatically computing Spectral Indexes from either the original HDF data
- or from hyperspectral data already converted using function `pr_convert`, and for easily and quickly extracting 
- data and computing statistics for the different bands over areas of interest.
+Description: `prismaread` allows easily importing PRISMA (http://www.prisma-i.it/index.php/it/) 
+ satellite hyperspectral data cubes and ancillary information from the original
+ data provided by ASI in HDF format, and convert them to a easier to use format 
+ (ENVI or GeoTiff). 
+ It also provides functionality for automatically computing Spectral Indexes from
+ either the original HDF data or from hyperspectral data already converted using 
+ function `pr_convert`, and for easily and quickly extracting data and computing
+ statistics for the different bands over areas of interest.
 License: GPL-3
 Encoding: UTF-8
 LazyData: true

diff --git a/R/pr_compute_indexes.R b/R/pr_compute_indexes.R
@@ -142,7 +142,11 @@ pr_compute_indexes <- function(in_file,
                         message("Writing Block: ", i, " of: ", bs$n)
                         x <- raster::getValues(in_rast_comp, row = bs$row[i],
                                                nrows = bs$nrows[i])
-                        x <- eval(parse(text = indform))
+                        if (inherits(x, "numeric")) {
+                            x <- x
+                        } else {
+                            x <- eval(parse(text = indform))
+                        }
                         out <- raster::writeValues(out, x, bs$row[i])
                     }
                     out <- raster::writeStop(out)

diff --git a/R/pr_convert.R b/R/pr_convert.R
@@ -465,10 +465,6 @@ pr_convert <- function(in_file,
       wl_swir   <- wl_swir[seqbands_swir]
       fwhm_swir <- fwhm_swir[seqbands_swir]
     }
-    # be sure to remove zeroes also if swir already present to avoid  ----
-    # errors on creation of FULL if recycling an existing cube from file
-    # fwhm_swir <- fwhm_swir[wl_swir != 0]
-    # wl_swir   <- wl_swir[wl_swir != 0]
 
     # create FULL data cube and convert to raster ----
     if (FULL & is.null(indexes)) {
@@ -494,6 +490,7 @@ pr_convert <- function(in_file,
       }
     }
 
+    # Create and write the FULL hyperspectral cube if needed ----
     if (FULL) {
       if (file.exists(out_file_full) & !overwrite) {
         message("FULL file already exists - use overwrite = TRUE or change
@@ -556,7 +553,7 @@ pr_convert <- function(in_file,
           }
         }
 
-
+        # Write ENVI header if needed ----
         if (out_format == "ENVI") {
           cat("band names = {", paste(names(rast_tot),collapse=","), "}", "\n",
               file=raster::extension(out_file_full, "hdr"), append = TRUE)
@@ -606,12 +603,6 @@ pr_convert <- function(in_file,
                            overwrite = overwrite)
       }
 
-      # if (CONTREM) {
-      #
-      #   # TODO: Add functionality for continuum removal computatation ?
-      #
-      # }
-
     }
 
     # Save PAN if requested ----
@@ -789,7 +780,7 @@ pr_convert <- function(in_file,
 
   # second run: create indexes -----
   # in this way we can use the same function,
-  # and when creating indexes create a temporary full raster, containgn only
+  # and when creating indexes create a temporary full raster, containing  only
   # bands required for the selected indexes
 
   if (!is.null(indexes)) {

diff --git a/R/pr_create_vnir.R b/R/pr_create_vnir.R
@@ -177,8 +177,6 @@ pr_create_vnir <- function(f,
         fwhm_sub <- fwhm_vnir[seqbands]
     }
 
-    # wl_vnir   <- wl_vnir[wl_vnir != 0]
-    # fwhm_vnir <- fwhm_vnir[fwhm_vnir != 0]
     rm(vnir_cube)
     rm(band)
     gc()

diff --git a/inst/extdata/indexes_list.txt b/inst/extdata/indexes_list.txt
@@ -129,3 +129,5 @@
 "128"	"ZTM"	"Zarco-Tejada & Miller"	"R750 / R710"	"Chlorophyll"	"Zarco-Tejada et al. (2001)"
 "129"	"myindex"	"My custom Index"	"R600 / R700"	NA	"Me (2020)"
 "130"	"009066L"	"My custom Index"	"R600 / R700"	NA	"Me (2020)"
+"131"	"009449D"	"My custom Index"	"R600 / R700"	NA	"Me (2020)"
+"132"	"008530N"	"My custom Index"	"R600 / R700"	NA	"Me (2020)"
diff --git a/tests/testthat/test_pr_convert.R b/tests/testthat/test_pr_convert.R
@@ -356,19 +356,19 @@ test_that(
         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(71.72868  , 45.73275  , 58.20885),
+        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(8.921804), tolerance = 0.0001)
+        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(71.72868, 45.73275, 58.20885,
-                                             8.921804), tolerance = 0.0001)
+        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(

diff --git a/vignettes/Importing-Level-1-Data.Rmd b/vignettes/Importing-Level-1-Data.Rmd
@@ -154,7 +154,8 @@ raster::plotRGB(r, 4,3,2, stretch = "lin")
 
 DT::datatable(read.table(file.path(
   out_folder, 
-  "PRS_L1_STD_OFFL_20200524103704_20200524103708_0001_HCO_VNIR.wvl")))
+  "PRS_L1_STD_OFFL_20200524103704_20200524103708_0001_HCO_VNIR.wvl")), 
+  header = TRUE)
 ```
 
 

diff --git a/vignettes/Importing-Level-2-Data.Rmd b/vignettes/Importing-Level-2-Data.Rmd
@@ -79,7 +79,8 @@ The function also saves ancillary data related to wavelengths and fwhms of the d
 ```{r echo=TRUE, message=FALSE, warning=FALSE}
 wvls <- read.table(file.path(
   out_folder_L2D, 
-  "PRS_L2D_STD_20200524103704_20200524103708_0001_HCO_VNIR.wvl"))
+  "PRS_L2D_STD_20200524103704_20200524103708_0001_HCO_VNIR.wvl"), 
+  header = TRUE)
 DT::datatable(wvls)
 ```
 

diff --git a/vignettes/prismaread.Rmd → vignettes/prismaread_vignette.Rmd b/vignettes/prismaread.Rmd → vignettes/prismaread_vignette.Rmd