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I'm trying to calculate morfometrics index provided by SAGA using RQGIS 3 with QGIS 3.4 version.

I`ve followed tutorial examples, but i dont have been successful. The script run, but don't produce any results. Any suggestion?

Here my script:

find_algorithms(search_term = "slope",name_only = TRUE)

get_usage("saga:slopeaspectcurvature")

params2 = get_args_man(alg = "saga:slopeaspectcurvature")

wd = "E:/artigo_declividade/mdesrtm/saga" #workdirectory

params2$ELEVATION = RQGIS3::dem
params2$METHOD = 6
params2$UNIT_SLOPE = 1
params2$UNIT_ASPECT = 1
params2$SLOPE = file.path(wd, "slope.tif")
params2$ASPECT = file.path( wd, "aspect.tif")
params2$C_GENE = file.path( wd, "generalCurvature.tif")
params2$C_PLAN = file.path( wd, "planCurvature.tif")
params2$C_PROF = file.path( wd, "profCurvature.tif")
params2$C_TANG = file.path( wd, "tangencialCurvature.tif")
params2$C_LONG = file.path( wd, "longitudinalCurvature.tif")
params2$C_CROS = file.path( wd, "crossSectionalCurvature.tif")
params2$C_MINI = file.path( wd, "minimalCurvature.tif")
params2$C_MAXI = file.path( wd, "maximalCurvature.tif")
params2$C_TOTA = file.path( wd, "totalCurvature.tif")
params2$C_ROTO = file.path( wd, "flowLineCurvature.tif")


run_qgis(alg = "saga:slopeaspectcurvature",
         params = params2)

Results at Console:

$`ASPECT`
[1] "E:/artigo_declividade/mdesrtm/saga/aspect.tif"

$C_CROS
[1] "E:/artigo_declividade/mdesrtm/saga/crossSectionalCurvature.tif"

$C_GENE
[1] "E:/artigo_declividade/mdesrtm/saga/generalCurvature.tif"

$C_LONG
[1] "E:/artigo_declividade/mdesrtm/saga/longitudinalCurvature.tif"

$C_MAXI
[1] "E:/artigo_declividade/mdesrtm/saga/maximalCurvature.tif"

.
.
.

EDITED:

Im trying this. Its works until "Terrain Convexity". After that show the same behavior (morphometric functions run but with empty results).

devtools::install_github("jannes-m/RQGIS3")
require(devtools)
require(raster)
require(rgdal)
require(RQGIS3)


qgis_env <-set_env(root ='C:/Program Files/QGIS 3.4')
set_env()
open_app()


dem = RQGIS3::dem #file
wd = "E:/a" #output

morfometria = function(dem, wd){ #function that calculate many morfometric index

#aspect

  params2 = get_args_man(alg = "saga:slopeaspectcurvature")
  params2$ELEVATION = dem
  params2$METHOD = 6
  params2$UNIT_SLOPE = 1
  params2$UNIT_ASPECT = 1
  params2$SLOPE = file.path(wd, "slope.sdat")
  params2$ASPECT = file.path( wd, "aspect.sdat")
  params2$C_GENE = file.path( wd, "generalCurvature.sdat")
  params2$C_PLAN = file.path( wd, "planCurvature.sdat")
  params2$C_PROF = file.path( wd, "profCurvature.sdat")
  params2$C_TANG = file.path( wd, "tangencialCurvature.sdat")
  params2$C_LONG = file.path( wd, "longitudinalCurvature.sdat")
  params2$C_CROS = file.path( wd, "crossSectionalCurvature.sdat")
  params2$C_MINI = file.path( wd, "minimalCurvature.sdat")
  params2$C_MAXI = file.path( wd, "maximalCurvature.sdat")
  params2$C_TOTA = file.path( wd, "totalCurvature.sdat")
  params2$C_ROTO = file.path( wd, "flowLineCurvature.sdat")

  run_qgis(alg = "saga:slopeaspectcurvature",
           params = params2)


  # Valley and Ridge Detection

  paramValley = get_args_man(alg = "saga:valleyandridgedetectiontophatapproach")

  paramValley$DEM = dem
  paramValley$VALLEY = file.path( wd, "valleyDepth.sdat")
  paramValley$HILL = file.path( wd, "hillHeight.sdat")
  paramValley$VALLEY_IDX = file.path( wd, "valleyIDX.sdat")
  paramValley$HILL_IDX = file.path( wd, "hillIDX.sdat")
  paramValley$SLOPE_IDX = file.path( wd, "slopeIDX.sdat")

  run_qgis(alg = "saga:valleyandridgedetectiontophatapproach",
           params = paramValley)


  #Terrain Surface Convexity

  paramTerrainSurfaceConvexity = get_args_man(alg = "saga:terrainsurfaceconvexity")
  paramTerrainSurfaceConvexity$DEM = dem
  paramTerrainSurfaceConvexity$CONVEXITY = file.path( wd, "TSConvexity.sdat")
  paramTerrainSurfaceConvexity$METHOD = 1
  paramTerrainSurfaceConvexity$DW_WEIGHTING = 3


  run_qgis(alg = "saga:terrainsurfaceconvexity",
           params = paramTerrainSurfaceConvexity)  


  #Terrain Surface Texture

  paramTerrainSurfaceTexture = get_args_man(alg = "saga:terrainsurfacetexture")
  paramTerrainSurfaceTexture$DEM = dem
  paramTerrainSurfaceTexture$TEXTURE = file.path( wd, "TSTexture")
  paramTerrainSurfaceTexture$METHOD = 1
  paramTerrainSurfaceTexture$DW_WEIGHTING = 3


  run_qgis(alg = "saga:terrainsurfacetexture",
           params = paramTerrainSurfaceTexture)  


  #Terrain Surface Classification

  paramTSC = get_args_man(alg = "saga:terrainsurfaceclassificationiwahashiandpike")
  paramTSC$DEM = dem
  paramTSC$LANDFORMS = file.path(wd, "Landforms1.sdat")

  run_qgis(alg = "saga:terrainsurfaceclassificationiwahashiandpike",
           params = paramTSC)  

  #TPI Based Landform Classification 

  paramTPILand = get_args_man(alg = "saga:tpibasedlandformclassification")
  paramTPILand$DEM = dem
  paramTPILand$LANDFORMS = file.path( wd, "Landforms2.sdat")

  run_qgis(alg = "saga:tpibasedlandformclassification",
           params = paramTPILand) 

  # Topographic Position Index (TPI)

  paramTPI = get_args_man(alg = "saga:topographicpositionindextpi")
  paramTPI$DEM = dem
  paramTPI$TPI = file.path(wd, "TPI.sdat")

  run_qgis(alg = "saga:topographicpositionindextpi",
           params = paramTPI) 


  # Vector Ruggedness Index (VRI) 

  paramVector = get_args_man(alg = "saga:vectorruggednessmeasurevrm")
  paramVector$DEM = dem
  paramVector$VRM = file.path(wd, "vectorRuggednessIndex.sdat")

  run_qgis(alg = "saga:vectorruggednessmeasurevrm",
           params = paramVector)

  # Terrain Ruggedness Index (TRI)

  paramReggedness = get_args_man(alg = "saga:terrainruggednessindextri")

  paramReggedness$DEM = dem

  paramReggedness$TRI = file.path(wd, "terrainRuggednessIndex.sdat")

  run_qgis(alg = "saga:terrainruggednessindextri",
           params = paramReggedness)

  # Mass Balance Index

  paramMass = get_args_man(alg = "saga:massbalanceindex")
  paramMass$DEM = dem
  paramMass$MBI = file.path(wd, "massBalanceIndex.sdat")

  run_qgis(alg = "saga:massbalanceindex",
           params = paramMass)

  # Downslope Distance Gradient 

  paramGradient = get_args_man(alg = "saga:downslopedistancegradient")
  paramGradient$DEM = dem
  paramGradient$GRADIENT = file.path(wd, "gradient.sdat")
  paramGradient$DIFFERENCE = file.path(wd, "difference.sdat")

  run_qgis(alg = "saga:downslopedistancegradient",
           params = paramGradient)

  # Multiresolution Index of Valley Bottom Flatness (MRVBF)

  paramMultires = get_args_man(alg = "saga:multiresolutionindexofvalleybottomflatnessmrvbf")
  paramMultires$DEM = dem
  paramMultires$MRVBF = file.path(wd, "MRVBF.sdat")
  paramMultires$MRRTF = file.path(wd, "MRRTF.sdat")

  run_qgis(alg = "saga:multiresolutionindexofvalleybottomflatnessmrvbf",
           params = paramMultires)


  # Morphometric.Protection.Index

  paramMorphometric = get_args_man(alg = "saga:morphometricprotectionindex")
  paramMorphometric$DEM = dem
  paramMorphometric$RADIUS = 1000
  paramMorphometric$PROTECTION = file.path(wd, "morphoProtectionIndex.sdat")

  run_qgis(alg = "saga:morphometricprotectionindex",
           params = paramMorphometric)

  #Real Surface Area

  paramRealSA = get_args_man(alg = "saga:realsurfacearea")
  paramRealSA$DEM = dem
  paramRealSA$AREA = file.path(wd, "realSurfaceArea.sdat")

  run_qgis(alg = "saga:realsurfacearea",
           params = paramRealSA)


  #Curvature classification

  paramCurvature = get_args_man(alg = "saga:curvatureclassification")
  paramCurvature$DEM = dem
  paramCurvature$CLASS = file.path(wd, "curvatureClassification.sdat")

  run_qgis(alg = "saga:curvatureclassification",
           params = paramCurvature)

  #Surface.Specific.Points

  paramSSP = get_args_man(alg = "saga:surfacespecificpoints")
  paramSSP$ELEVATION = dem
  paramSSP$METHOD = 1
  paramSSP$RESULT = file.path(wd, "surfaceSpecificPoints.sdat")

  run_qgis(alg = "saga:surfacespecificpoints",
           params = paramSSP)

  # convergence index

  paramConvergence = get_args_man(alg = "saga:convergenceindex")
  paramConvergence$ELEVATION = dem
  paramConvergence$NEIGHBOURS = 1
  paramConvergence$RESULT = file.path(wd, "convergenceIndex.sdat") 

  run_qgis(alg = "saga:convergenceindex",
           params = paramConvergence)


  # wetness index

  paramWetness = get_args_man(alg = "saga:sagawetnessindex")
  paramWetness$DEM = dem
  paramWetness$TWI = file.path(wd, "topographicWetIndex.sdat") 
  paramWetness$AREA = file.path(wd, "AREAtopographicWetIndex.sdat") 
  paramWetness$SLOPE = file.path(wd, "SLOPEtopographicWetIndex.sdat") 
  paramWetness$AREA_MOD = file.path(wd, "AREAMODtopographicWetIndex.sdat") 

  run_qgis(alg = "saga:sagawetnessindex",
           params = paramWetness) 



}


morfometria(dem = dem, wd = wd)
  • Where are you installing RQGIS3 from - it doesn't appear to be on CRAN. – Spacedman Apr 2 at 21:48
  • link – Arthur Apr 3 at 11:42
1

For me, run_qgis creates a bundle of .sdat files in the working directory:

> list.files(wd,pattern="*.sdat$")
 [1] "aspect.sdat"                  "crossSectionalCurvature.sdat"
 [3] "flowLineCurvature.sdat"       "generalCurvature.sdat"       
 [5] "longitudinalCurvature.sdat"   "maximalCurvature.sdat"       
 [7] "minimalCurvature.sdat"        "planCurvature.sdat"          
 [9] "profCurvature.sdat"           "slope.sdat"                  
[11] "tangencialCurvature.sdat"     "totalCurvature.sdat"         

These can be read in using the raster package's raster function:

> aspect = raster(file.path(wd,"aspect.sdat"))
> slope = raster(file.path(wd,"slope.sdat"))
> plot(aspect)
> 

I don't know why you don't get tif files created or why run_qgis returns nothing and only prints the things it prints... I couldn't get the load_output option to work...

  • Worked perfectly! I advise you to convert .sdat files to .tif because it has a faster processing time, even after loading it in R. – Arthur Apr 3 at 11:40
1

The following code works including the load_output option. Just out of curiosity, are you running RQGIS3 from within RStudio? Because in my case running RQGIS3::open_app() crashes the RStudio R session. This was also confirmed by several other users (see the github issue tracker of RQGIS3). Since RQGIS3 works when run from the CLI, I am not really sure what to do about it... BTW running RQGIS3 in a rocker-docker container, i.e. in a docker container running RStudio, also works.

# attach libraries
library("RQGIS3")
#> Loading required package: reticulate
library("raster")
#> Loading required package: sp
# report QGIS3 session info
qgis_session_info()
#> Assuming that your root path is '/usr'!
#> $gdal
#> [1] "2.3.2"
#> 
#> $grass7
#> [1] "7.6.0"
#> 
#> $qgis_version
#> [1] "3.4.6-Madeira"
#> 
#> $saga
#> [1] "2.3.1"
# retrieve and specify parameters of a specific geoalgorithm
alg = "saga:slopeaspectcurvature"
params = get_args_man(alg)
#> Choosing default values for following parameters:
#> METHOD: 0
#> UNIT_SLOPE: 0
#> UNIT_ASPECT: 0
#> See get_options('saga:slopeaspectcurvature') for all available options.
params$ELEVATION = RQGIS3::dem
params$METHOD = 6
params$UNIT_SLOPE = 1
params$UNIT_ASPECT = 1
wd = tempdir()
params$SLOPE = file.path(wd, "slope.sdat")
params$ASPECT = file.path(wd, "aspect.sdat")
params$C_GENE = file.path(wd, "generalCurvature.sdat")
params$C_PLAN = file.path(wd, "planCurvature.sdat")
params$C_PROF = file.path(wd, "profCurvature.sdat")
params$C_TANG = file.path(wd, "tangencialCurvature.sdat")
params$C_LONG = file.path(wd, "longitudinalCurvature.sdat")
params$C_CROS = file.path(wd, "crossSectionalCurvature.sdat")
params$C_MINI = file.path(wd, "minimalCurvature.sdat")
params$C_MAXI = file.path(wd, "maximalCurvature.sdat")
params$C_TOTA = file.path(wd, "totalCurvature.sdat")
params$C_ROTO = file.path(wd, "flowLineCurvature.sdat")
out = run_qgis(alg, params = params, load_output = TRUE)
#> $ASPECT
#> [1] "/tmp/RtmpyQkN4o/aspect.sdat"
#> 
#> $C_CROS
#> [1] "/tmp/RtmpyQkN4o/crossSectionalCurvature.sdat"
#> 
#> $C_GENE
#> [1] "/tmp/RtmpyQkN4o/generalCurvature.sdat"
#> 
#> $C_LONG
#> [1] "/tmp/RtmpyQkN4o/longitudinalCurvature.sdat"
#> 
#> $C_MAXI
#> [1] "/tmp/RtmpyQkN4o/maximalCurvature.sdat"
#> 
#> $C_MINI
#> [1] "/tmp/RtmpyQkN4o/minimalCurvature.sdat"
#> 
#> $C_PLAN
#> [1] "/tmp/RtmpyQkN4o/planCurvature.sdat"
#> 
#> $C_PROF
#> [1] "/tmp/RtmpyQkN4o/profCurvature.sdat"
#> 
#> $C_ROTO
#> [1] "/tmp/RtmpyQkN4o/flowLineCurvature.sdat"
#> 
#> $C_TANG
#> [1] "/tmp/RtmpyQkN4o/tangencialCurvature.sdat"
#> 
#> $C_TOTA
#> [1] "/tmp/RtmpyQkN4o/totalCurvature.sdat"
#> 
#> $SLOPE
#> [1] "/tmp/RtmpyQkN4o/slope.sdat"
plot(stack(out))

  • Im using R-studio. I got some erros when loading RQGIS3, but nothing that crashes it. Another problem that im having is that im executing many morphometric index, one after other. After execute 5/6 indexs, happens what i said in the topic. Results doesnt appear. I tryed in RQGIS with QGIS 2.18, but looks the same. I tested it on CML too, but got the same problem. Any ideia? – Arthur Apr 4 at 1:56
  • 1
    I have edited my reply to include all morphometric indices and it works just fine. Yeah, my bad, you are under Windows, where RQGIS3 doesn't crash RStudio. – Jannes Apr 4 at 8:27
  • Dear Jannes, thanks for the anwser. I did it like you. But when i tryed many morfometric index, like edited question, it goes wrong. Can you run my edited question to check if im doing somethin wrong? Thank for the help. – Arthur Apr 15 at 14:11

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