Merge branch 'dev'

jbferet · May 13, 2020 · 07a5f04 · 07a5f04
2 parents 0507848 + 594e8e5
commit 07a5f04
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: biodivMapR
-Title: biodivMapR: an R package for α- and β-diversity mapping using remotely-sensed images
-Version: 1.2.0
+Title: biodivMapR: an R package for a- and ß-diversity mapping using remotely-sensed images
+Version: 1.2.1
 Authors@R: c(person(given = "Jean-Baptiste", 
 					family = "Feret", 
 					email = "jb.feret@teledetection.fr", 
@@ -36,7 +36,7 @@ Imports:
     tools,
     vegan,
     zip
-RoxygenNote: 6.1.1
+RoxygenNote: 7.1.0
 Suggests: knitr,
     rmarkdown
 VignetteBuilder: knitr

diff --git a/NEWS.md b/NEWS.md
@@ -1,3 +1,8 @@
+# biodivMapR v1.2.1
+
+## Changes
+- added option to convert the mask file into proper format with raster2BIL
+
 # biodivMapR v1.2.0
 
 ## Fixes

diff --git a/R/Lib_CheckConvertData.R b/R/Lib_CheckConvertData.R
@@ -10,20 +10,22 @@
 # if not, can convert the raster into BIL format expected for diversity mapping
 # ==============================================================================
 
-#' converts a raster into BIL format as expected by DivMapping codes
+#' converts a raster into BIL format as expected by biodivMapR codes
 #'
 #' @param Raster_Path character. Full path for the raster to be converted
 #' @param Sensor character. Name of the sensor. a .hdr template for the sensor should be provided in extdata/HDR
 #' @param Convert_Integer boolean. Should data be converted into integer ?
 #' @param Multiplying_Factor numeric. Multiplying factor (eg convert real reflectance values between 0 and 1 into integer between 0 and 10000).
 #' @param Output_Dir character. Path to output directory.
 #' @param Multiplying_Factor_Last numeric. Multiplying factor for last band.
+#' @param Mask boolean is the file a mask file with 0s and 1s only?
 #'
 #' @return Output_Path path for the image converted into ENVI BIL format
 #' @import raster
 #' @import tools
 #' @export
-raster2BIL <- function(Raster_Path, Sensor = "unknown", Output_Dir = FALSE, Convert_Integer = TRUE, Multiplying_Factor = 1, Multiplying_Factor_Last = 1) {
+raster2BIL <- function(Raster_Path, Sensor = "unknown", Output_Dir = FALSE, Convert_Integer = TRUE,
+                       Multiplying_Factor = 1, Multiplying_Factor_Last = 1, Mask = FALSE) {
 
   # get directory and file name of original image
   Input_File <- basename(Raster_Path)
@@ -46,15 +48,17 @@ raster2BIL <- function(Raster_Path, Sensor = "unknown", Output_Dir = FALSE, Conv
   Last_Band_Name <- Output_Img@data@names[length(Output_Img@data@names)]
   Output_Img[[Last_Band_Name]] <- Multiplying_Factor_Last * Output_Img[[Last_Band_Name]]
 
-  # convert into integer
-  if (Convert_Integer == TRUE) {
+  # convert into integer if requested or if is Mask
+  if (Convert_Integer == TRUE | Mask == TRUE) {
     Output_Img <- round(Output_Img)
   }
 
   # write raster
   message("writing converted file")
-  if (Convert_Integer == TRUE) {
+  if (Convert_Integer == TRUE & Mask == FALSE) {
     r <- writeRaster(Output_Img, filename = Output_Path, format = "EHdr", overwrite = TRUE, datatype = "INT2S")
+  } else if (Convert_Integer == TRUE & Mask == TRUE) {
+    r <- writeRaster(Output_Img, filename = Output_Path, format = "EHdr", overwrite = TRUE, datatype = "INT1U")
   } else {
     r <- writeRaster(Output_Img, filename = Output_Path, format = "EHdr", overwrite = TRUE)
   }

diff --git a/man/map_alpha_div.Rd b/man/map_alpha_div.Rd
diff --git a/man/map_beta_div.Rd b/man/map_beta_div.Rd
diff --git a/man/map_spectral_species.Rd b/man/map_spectral_species.Rd
diff --git a/man/perform_PCA.Rd b/man/perform_PCA.Rd
diff --git a/man/perform_radiometric_filtering.Rd b/man/perform_radiometric_filtering.Rd
diff --git a/man/raster2BIL.Rd b/man/raster2BIL.Rd
diff --git a/man/select_PCA_components.Rd b/man/select_PCA_components.Rd
diff --git a/vignettes/biodivMapR_1.Rmd b/vignettes/biodivMapR_1.Rmd
@@ -55,27 +55,30 @@ Input_Image_File  = raster2BIL(Raster_Path = Path_Raster_File,
                                Output_Dir = Path_Output_Directory,
                                Convert_Integer = Convert_Integer,
                                Multiplying_Factor = Multiplying_Factor,
-                               Multiplying_Factor_Last=Multiplying_Factor_Last)
+                               Multiplying_Factor_Last=Multiplying_Factor_Last,
+                               Mask = FALSE)
 ```
 
 ## Input variables
 
-The following information is expected as input information:  
+The following information is accepted as input information:  
 
 * `Raster_Path`: a string containing the full path for the raster to be converted.
 * `Sensor`: a string containing the name of the sensor, which should actually be linked to a template for the corresponding header file. 
 * `Output_Dir` [optional]: a string defining the path for the output directory where converted file will be stored.
 * `Convert_Integer` [optional]: a boolean stating if the raster data should be converted into integer
 * `Multiplying_Factor` [optional]:  a multiplying factor for the raster data. This is useful when converting real reflectance values between 0 and 1 into integer between 0 and 10000. Set `Multiplying_Factor =10000` in this case.
 * `Multiplying_Factor_Last` [optional]: a multiplying factor for last band. This option is useful only if working with dry vegetation acquired with Sentinel-2 images, in order to artifically increase the reflectance of the B12 band (SWIR 2, centered at 2200 nm), so that SWIR 1 band remains below the convex hull defined during Continuum removal. __You do not need to use this option most of the time, unless you want to enhance teh sensitivity to different types of dry vegetation__.
+* `Mask` [optional]: a boolean stating if the raster data corresponds to a mask (TRUE) or not (FALSE). If it is a mask, masked pixels should have a value of `0`, and pixels to keep for the analysis should have a value of `1`. raster2BIL converts image information into unsigned 8 bits integer.
+
 
 Please note that 
 i) the coordinate system and minimal metadata (spatial resolution, geographic information...) are expected to be provided in the original image or image + header defined in `Raster_Path` if user want them to be included in the final image products.
 
 ii) `Sensor` should refer to the name of a `.hdr` file stored in the installation directory of `biodivMapR`
 Please type `system.file(package = "biodivMapR")` in order to get the location of the install directory and create a proper `.hdr` file to be stored in `extdata/HDR/`, containing proper spectral bands __defined in nanometers__ if using optical data and using `perform_radiometric_filtering` and/or `Continuum_Removal = TRUE` in your process. Make sure that the __spectral bands in the binary file are stored with wavelengths following ascending order__. 
 
-iii) `Convert_Integer=TRUE` saves 50% space if original image is stored in real values (32bits per value). However, user need to make sure hat their original data are compatible with conversion: if reflectance values are stored as  real value between 0 and 1, the final image file will be unusable, unless proper multiplying factor is applied to the full image data (for example `Multiplying_Factor =10000`). Sentinel-2 reflectance data downloaded from ESA hub are stored as integer (16 bits) values between 0 and 10 000 instead of real (32 bits) values between 0 and 1, so integer conversion is unnecessary.
+iii) `Convert_Integer=TRUE` saves 50% space if original image is stored in real values (32 bits per value). However, user need to make sure hat their original data are compatible with conversion: if reflectance values are stored as  real value between 0 and 1, the final image file will be unusable, unless proper multiplying factor is applied to the full image data (for example `Multiplying_Factor =10000`). Sentinel-2 reflectance data downloaded from ESA hub are stored as integer (16 bits) values between 0 and 10 000 instead of real (32 bits) values between 0 and 1, so integer conversion is unnecessary.
 
 ## output variable