Merge branch 'dev'

vignettes/biodivMapR.Rmd

@@ -61,10 +61,10 @@ The output directory defined with `Output_Dir` will contain all the results. For
 library(biodivMapR)
 Input_Image_File  = system.file('extdata', 'RASTER', 'S2A_T33NUD_20180104_Subset', package = 'biodivMapR')
 
+# please visit this webpage if you need to convert your raster image file using raster2BIL
+# https://jbferet.github.io/biodivMapR/articles/biodivMapR_1.html
 # Input_Image_File  = raster2BIL(Raster_Path = Input_Image_File,
-#                                        Sensor = 'SENTINEL_2A',
-#                                        Convert_Integer = TRUE,
-#                                        Output_Dir = '~/test')
+#                                        Sensor = 'SENTINEL_2A')
 
 Input_Mask_File   = FALSE
 
@@ -115,6 +115,7 @@ nbclusters    = 50
 
 ```{r Mask non vegetated / shaded / cloudy pixels}
 NDVI_Thresh = 0.5
+# these values are relevant only if reflectance is coded as integer values between 0 and 10000. 
 Blue_Thresh = 500
 NIR_Thresh  = 1500
 print("PERFORM RADIOMETRIC FILTERING")

vignettes/biodivMapR_1.Rmd

@@ -36,12 +36,26 @@ A function is dedicated to conversion of a raster file into appropriate image fo
 
 ```{r raster2BIL}
 library(biodivMapR)
+# define input variables for raster2BIL:
+# full path or relative path for the raster file to convert
+Path_Raster_File <- 'Where/is/your/raster/file/?'
+# you also need to define a template for the .hdr file corresponding to your sensor. 
+# locate the install directory for biodivMapR
+# system.file(package = "biodivMapR")`
+# and write a file with description corresponding to your image (in terms of spectral bands, band name, etc)
+Name_Template_HDR <- 'Name_of_hdr_template'
+# you may want to convert reflectance from [0-1] real32 values to [0-10000] integer16
+# see explanation below
+Convert_Integer <- TRUE
+Multiplying_Factor <- 10000
+Multiplying_Factor_Last <- 1.0
 
 Input_Image_File  = raster2BIL(Raster_Path = Path_Raster_File,
-                                       Sensor = Path_Template_HDR,
-                                       Convert_Integer = TRUE,
-                                       Output_Dir = Path_Output_Directory)
-
+                               Sensor = Name_Template_HDR,
+                               Output_Dir = Path_Output_Directory,
+                               Convert_Integer = Convert_Integer,
+                               Multiplying_Factor = Multiplying_Factor,
+                               Multiplying_Factor_Last=Multiplying_Factor_Last)
 ```
 
 ## Input variables
@@ -50,10 +64,10 @@ The following information is expected 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.
-* `Output_Dir` [optional]: a string defining the path for the output directory where converted file will be stored.
-* `Multiplying_Factor_Last` [optional]: a multiplying factor for last band. This option is useful 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. 
+* `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__.
 
 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.
@@ -66,3 +80,5 @@ iii) `Convert_Integer=TRUE` saves 50% space if original image is stored in real
 ## output variable
 
 `raster2BIL` returns a string containing the full path for the raster once converted.
+
+You can directly use this output variable as input for the next steps of the process.