newcomb-d
commented
4 years ago Upon further investigation, it was noted that rgeos was not loaded,
Checking rgeos availability: FALSE
Note: when rgeos is not available, polygon geometry computations in maptools depend on gpclib,
which has a restricted licence. It is disabled by default;
to enable gpclib, type gpclibPermit()
and the reason that the raster module was failing was that the sp libary sp() was not being used.
When line 236 if the script was modified from :
libs = ['GWmodel', 'data.table', 'rgrass7', 'rgdal', 'raster']
to:
libs = ['GWmodel', 'data.table', 'sp', 'rgeos', 'rgrass7', 'rgdal', 'raster']
and the following line was added after line 248
r_file.write('use_sp()\n')
The script was then able to get past this error. However, in line 293
predict = g.read_command("g.tempfile", pid=os.getpid()).strip() + '.txt'
a temporary file is written to hold the results of the GWR analysis.
On windows, this leads to a filename like this:
D:\grass\lake\u18wgs84\bathy.tmp/unknown\13752.5.txt , which throws an escape character error in R on windows.
This was worked around by setting a static filename in the directory that the script is run from:
predict="tempgwr.txt"
While this works for a desktop user and makes things os-independent, it requires the user have write access to the directory the script is running in.
It might be better to set the filename with a suffix more dynamically from the os.getpid process for a result like tempgwr13725.txt in more dynamic settings.
neteler
tmszi
wenzeslaus
Describe the bug i.image.bathymetry can call the R GWModel program with three options, Adaptive Gaussian , Bisquare, and Fixed Gaussian. If there are issues running bisquare or adaptive, the script fails over to Fixed. With versions 3.5.3 and 3.6.3 of R, the current call to the R package raster fails and the script runs GWR in Fixed Gaussian mode , no matter what option is given in the command
To Reproduce Steps to reproduce the behavior:
Load multispectral imagery into GRASS ( Sentinel 2 bands 2,3,4,8, and 11) for an area of interest with a water body for which bathymetry is needed. Also load know depth points, tide level, and a polygon area of interest.
Set region to match Area of interest with resolution matching satellite imagery.
Run script from the command line. ( Example) i.image.bathymetry blue_band=T18STF_20191212T155641_B02_10m green_band=T18STF_20191212T155641_B03_10m red_band=T18STF_20191212T155641_B04_10m nir_band=T18STF_20191212T155641_B08_10m band_for_correction=T18STF_20191212T155641_B11_20m calibration_points=bathy_points calibration_column=depth depth_estimate=depth_out area_of_interest=lake_Shoreline_trim_buffer
See error Attaching package: 'raster'
The following object is masked from 'package:data.table':
Warning message: package 'raster' was built under R version 3.5.3 Error in .read_rast_non_plugin(vname = vname, NODATA = NODATA, driverFileExt = driverFileExt, : no stars import yet Calls: readRAST -> tryCatch -> tryCatchList -> .read_rast_non_plugin Execution halted Integer outflow... Running Fixed-GWR using gaussian kernel...
Expected behavior A clear and concise description of what you expected to happen. The default should use the Adaptive Guassian kernel
Calculating optimal bandwidth using gaussian kernel.. Adaptive bandwidth: 217 CV score: 1608.003 Adaptive bandwidth: 142 CV score: 1511.212 Adaptive bandwidth: 94 CV score: 1430.953 Adaptive bandwidth: 66 CV score: 1335.32 Adaptive bandwidth: 47 CV score: 1271.241 Adaptive bandwidth: 37 CV score: 1249.903 Adaptive bandwidth: 29 CV score: 1231.113 Adaptive bandwidth: 25 CV score: 1217.598 Adaptive bandwidth: 22 CV score: 1212.767 Adaptive bandwidth: 20 CV score: 1207.13 Adaptive bandwidth: 19 CV score: 1208.674 Adaptive bandwidth: 21 CV score: 1211.075 Adaptive bandwidth: 20 CV score: 1207.13
Calculating euclidean distance
Running A-GWR using gaussian kernel Reading input data... 100% 146789 points found in input file Writing to output raster map... 100%
Screenshots If applicable, add screenshots to help explain your problem.
System description (please complete the following information):
Additional context Add any other context about the problem here.