NA-Bug?

[raff-k]

Dear RQGIS team,
since the QGIS processing toolbox is working on my machine, I could further invesitage the issue with NA-values. I discovered, that it seems to be a more general RQGIS (to QGIS) issue. I tested different ways of writing out a raster containing NA values and then computed slope manually in QGIS (I tried SAGA and GRASS GIS version). I discovered that generally tiff-files written out using rgdal::writeGDAL(…) worked in QGIS. Tiffs written with raster::writeRaster(…) only worked in QGIS if I have set a NA-flag. Perhaps QGIS cannot deal with or pass a correct no data value to SAGA or GRASS when its no data value is -3.39e^38?

Can you repdoruce the issue? – If yes, maybe an alternative can be to set a default NA-value (i.e. -99999) or switching the write function to rgdal.

I used QGIS 2.18.15, and RQGIS_1.0.2.

# set environment and variables
setwd("d:/Users/Desktop/NA-Test")

library("RQGIS", "raster", "rgdal")

dem <- RQGIS::dem

RQGIS:::set_env(new = TRUE, dev = TRUE)
RQGIS::open_app()
RQGIS::qgis_session_info()

# create dem with NA values
dem.NA <- raster::calc(dem, fun = function(x){(ifelse(x > 500, NA, x))})
raster::plot(dem.NA)



# write data with different functions and with/without NAflag
raster::writeRaster(dem.NA, "dem_writRast_NAFlag.tif", NAflag = -99999, overwrite = TRUE) # 1
raster::writeRaster(dem.NA, "dem_writRast.tif", overwrite = TRUE) # 2

rgdal::writeGDAL(as(dem.NA, "SpatialGridDataFrame"), "dem_writGDAL_NAFlag.tif", mvFlag = -99999) # 3
rgdal::writeGDAL(as(dem.NA, "SpatialGridDataFrame"), "dem_writGDAL.tif") # 4

# ... then I tested manually in QGIS if the alogithm
# r.slope.aspect can deal with the NA value

# Result:
# 1. worked in QGIS
# 2. DID NOT WORK, NoData values are somehow included in output
# 3. worked in QGIS
# 4. worked in QGIS


# try: process slope in RQGIS that worked in QGIS
dem.WritRast.NAFlag <- raster::raster("dem_writRast_NAFlag.tif") # one with flag
dem.WritGDAL <- raster::raster(rgdal::readGDAL("dem_writRast_NAFlag.tif")) # one without flag



# calculate slope based on the different files
slope.WritRast.NAFlag <- RQGIS::run_qgis("grass:r.slope.aspect", elevation = dem.WritRast.NAFlag, 
                         slope = file.path(getwd(), "slope_WRNA.tif"), load_output = TRUE)
summary(raster::values(slope.WritRast.NAFlag)) # max = 90?!


slope.WritGDAL <- RQGIS::run_qgis("grass:r.slope.aspect", elevation = dem.WritGDAL, 
                                              slope = file.path(getwd(), "slope_WGDAL.tif"), 
                                               load_output = TRUE)
summary(raster::values(slope.WritGDAL)) # max = 90?!

[jannes-m]

Thanks @raff-k, will have a look at it the next days. If it the solution is as simple as specifying NA values, give it a try yourself, here is where we write out rasters:
https://github.com/jannes-m/RQGIS/blob/f413ee940c14062f9e3d0a55ddef61f2773467ad/R/helper_funs.R#L481-L494

Then you can issue a PR. In any case thanks for your valuable input!

[raff-k]

The NA issue is solved on my fork when I added NAflag = NaN as function parameter to save_spatial_objects <- function(params, type_name, NAflag = NaN) and of course to the writeRast-functions.

try(writeRaster(
            params[[i]], filename = fname, format = "GTiff",
            prj = TRUE, overwrite = TRUE, NAflag = NAflag
          ), silent = TRUE)
      )
      if (inherits(test, "try-error")) {
        while (tolower(basename(fname)) %in% tolower(dir(tempdir()))) {
          fname <- paste0(gsub(".tif", "", fname), 1, ".tif")
        }
        writeRaster(
          params[[i]], filename = fname, format = "GTiff",
          prj = TRUE, overwrite = TRUE, NAflag = NAflag
        )

Maybe you could think about to add NAflag as "flag"-parameter to RQGIS::run_qgis so that the user can specify themselves an appropriate no data value. I am not sure if NaN here is the best option - maybe -99999 is a better default value. When I open this NaN-written raster in ArcGIS, NoData values are -1,#IND - also a bit awful :-/

[jannes-m]

Commit 9e74a4a should address your issue, pls check and if solved, close the issue.

[raff-k]

thank you for implementation, @jannes-m. Issue is solved :-)