CODEWITHSUNDEEP
leafletr-markdownrasterqgis
GEX_HEX_420
GEX_HEX_420

Reputation: 105

Problem with colors when using R raster data generated from QGIS in leaflet in R markdown

I geo-referenced data from a picture in QGIS and tried exporting it as a R raster for use in a proyect (r markdown) like this:

r.raster<-raster("A:/Path/R-raster.gri", 
            varname = "r_raster_file")

leaflet(df) %>% addMarkers(popup = ~descr,label = ~Iden) %>% 
addRasterImage(r.raster)

the problem I have is that the colors of the image came all wrong. When I open the data in QGIS the colors seem fine, however, the raster layer read by leaflet has totally different colors:top is result, bottom is original

The original colors are at the bottom.

The object in the enviroment has an structure like this:

Formal class 'RasterLayer' [package "raster"] with 12 slots
  ..@ file    :Formal class '.RasterFile' [package "raster"] with 13 slots
  .. .. ..@ name        : chr "R-raster.grd"
  .. .. ..@ datanotation: chr "INT1U"
  .. .. ..@ byteorder   : Named chr "little"
  .. .. .. ..- attr(*, "names")= chr "value"
  .. .. ..@ nodatavalue : num -Inf
  .. .. ..@ NAchanged   : logi FALSE
  .. .. ..@ nbands      : int 3
  .. .. ..@ bandorder   : Named chr "BIL"
  .. .. .. ..- attr(*, "names")= chr "value"
  .. .. ..@ offset      : int 0
  .. .. ..@ toptobottom : logi TRUE
  .. .. ..@ blockrows   : int 0
  .. .. ..@ blockcols   : int 0
  .. .. ..@ driver      : chr "raster"
  .. .. ..@ open        : logi FALSE
  ..@ data    :Formal class '.SingleLayerData' [package "raster"] with 13 slots
  .. .. ..@ values    : logi(0) 
  .. .. ..@ offset    : num 0
  .. .. ..@ gain      : num 1
  .. .. ..@ inmemory  : logi FALSE
  .. .. ..@ fromdisk  : logi TRUE
  .. .. ..@ isfactor  : logi FALSE
  .. .. ..@ attributes: list()
  .. .. ..@ haveminmax: logi TRUE
  .. .. ..@ min       : num 0
  .. .. ..@ max       : num 255
  .. .. ..@ band      : int 1
  .. .. ..@ unit      : chr ""
  .. .. ..@ names     : chr "Someros.R.raster"
  ..@ legend  :Formal class '.RasterLegend' [package "raster"] with 5 slots
  .. .. ..@ type      : chr(0) 
  .. .. ..@ values    : logi(0) 
  .. .. ..@ color     : logi(0) 
  .. .. ..@ names     : logi(0) 
  .. .. ..@ colortable: logi(0) 
  ..@ title   : chr(0) 
  ..@ extent  :Formal class 'Extent' [package "raster"] with 4 slots
  .. .. ..@ xmin: num -9390940
  .. .. ..@ xmax: num -9327759
  .. .. ..@ ymin: num 1095039
  .. .. ..@ ymax: num 1127491
  ..@ rotated : logi FALSE
  ..@ rotation:Formal class '.Rotation' [package "raster"] with 2 slots
  .. .. ..@ geotrans: num(0) 
  .. .. ..@ transfun:function ()  
  ..@ ncols   : int 1246
  ..@ nrows   : int 640
  ..@ crs     :Formal class 'CRS' [package "sp"] with 1 slot
  .. .. ..@ projargs: chr "+proj=merc +a=6378137 +b=6378137 +lat_ts=0 +lon_0=0 +x_0=0 +y_0=0 +k=1 +units=m +nadgrids=@null +wktext +no_defs"
  .. .. ..$ comment: chr "PROJCRS[\"WGS 84 / Pseudo-Mercator\",\n    BASEGEOGCRS[\"WGS 84\",\n        DATUM[\"World Geodetic System 1984\"| __truncated__
  ..@ history : list()
  ..@ z       : list()

I searched the internet for hours and I am at a stall. The colors are significant since they represent data from geological studies. I've tried stuff like this:

pal <- colorNumeric(c("red","blue","green"), values(someros))
leaflet(df) %>% addMarkers(popup = ~descr,label = ~Iden) %>% 
addRasterImage(someros,color=pal)

but I don´t know what I'm doing enter image description here

Help appreciated.

Edit:here's the content of the grd file

[general]
[georeference]
nrows=640
ncols=1246
xmin=-9390939.65870000049
ymin=1095038.68050000002
xmax=-9327758.77869999968
ymax=1127491.1388999999
projection=+proj=merc +a=6378137 +b=6378137 +lat_ts=0 +lon_0=0 +x_0=0 +y_0=0 +k=1 +units=m +nadgrids=@null +wktext +no_defs
[data]
datatype=INT1U
byteorder=little
nbands=3
bandorder=BIL
minvalue=0:0:0
maxvalue=255:255:255
categorical=FALSE

Upvotes: 0

Views: 249

Answers (1)

Robert Hijmans
Robert Hijmans

Reputation: 47601

With this image

enter image description here

You can read it like this:

library(terra)
img <- rast("https://i.sstatic.net/ZyyaD.jpg")

And get the extent and crs from the other file (or set it directly)

#r <- rast("Someros-R-raster.grd")
#crs(img) <- crs(r)
#ext(img) <- ext(r)

crs(img) <- "+proj=merc +a=6378137 +b=6378137 +lat_ts=0 +lon_0=0 +x_0=0 +y_0=0 +k=1 +units=m"
ext(img) <- c(-9390939.6587, -9327758.7787, 1095038.6805, 1127491.1389)
plot(img)

Save to disk

writeRaster(img, "temp.tif")

This is a SpatRaster with three layers (red, green, blue) and you can reduce it to one layer (with a color-table) like this

img2 <- colorize(img, "col")
writeRaster(img2, "temp2.tif")

If you want to use the old raster objects, you can read the file like this

library(raster)
x <- raster("temp.tif")
plot(x)

Upvotes: 1

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