Merge pull request #122 from albert-de-montserrat/adm/CI

Fix the download of topographyic data with GMT

Author: albert-de-montserrat

docs/src/man/Tutorial_AlpineData.md

@@ -29,7 +29,7 @@ using GeophysicalModelGenerator, GMT
 When loading both packages, several `GMT` routines within `GMG` will be loaded. One of these routines is the function `import_topo`, where one simply has to provide the region for which to download the topographic data and the data source.
 
 ```julia
-Topo = import_topo([4,20,37,50], file="@earth_relief_01m.grd")
+Topo = import_topo([4,20,37,50], file="@earth_relief_01m")
 ```
 
 The data is available in different resolutions; see [here](http://gmt.soest.hawaii.edu/doc/latest/grdimage.html) for an overview. Generally, it is advisable to not use the largest resolution if you have a large area, as the files become very large.

docs/src/man/Tutorial_Jura.md

@@ -18,7 +18,7 @@ using GeophysicalModelGenerator, GMT
 Download the topography with:
 
 ```julia
-Topo = import_topo(lat=[45.5,47.7], lon=[5, 8.1], file="@earth_relief_03s.grd")
+Topo = import_topo(lat=[45.5,47.7], lon=[5, 8.1], file="@earth_relief_03s")
 ```
 
 Next, we drape the geological map on top of the geological map.

docs/src/man/Tutorial_LaPalma.md

@@ -23,7 +23,7 @@ using GeophysicalModelGenerator, GMT, DelimitedFiles
 We will use GMT to download the topography with:
 
 ```julia
-Topo = import_topo(lon = [-18.2, -17.5], lat=[28.4, 29.0], file="@earth_relief_15s.grd")
+Topo = import_topo(lon = [-18.2, -17.5], lat=[28.4, 29.0], file="@earth_relief_15s")
 ```
 
 Next, lets load the seismicity. The earthquake data is available on [https://www.ign.es/web/ign/portal/vlc-catalogo](https://www.ign.es/web/ign/portal/vlc-catalogo).

docs/src/man/tutorial_GMT_Topography.md

@@ -15,7 +15,7 @@ The nice thing about GMT is that it automatically downloads data for you for a c
 
 ```julia
 julia> using GeophysicalModelGenerator, GMT
-julia> Topo = import_topo([4,20,37,49], file="@earth_relief_01m.grd")
+julia> Topo = import_topo([4,20,37,49], file="@earth_relief_01m")
 GeoData 
   size  : (960, 720, 1)
   lon   ϵ [ 4.0 : 19.983333333333334]

docs/src/man/tutorial_GMT_Topography_GeologicalMap.md

@@ -8,7 +8,7 @@ In many cases, we want to add topographic data as well a information about tecto
 
 #### 1. Download topographic data and tectonic maps of the Alpine region
 The ETOPO1 data file used in this example can be downloaded here:  
-[https://ngdc.noaa.gov/mgg/global/global.html](https://ngdc.noaa.gov/mgg/global/global.html). For this example, we downloaded `ETOPO1_Ice_g_gmt4.grd` and stored it directly in the folder where we will be working. For the geological map, we download the data from the [SPP 4DMB repository](http://www.spp-mountainbuilding.de/data/Maps.zip) and extract the zip file (to the current folder). In this data set, a `gmt` file with the data for different tectonic units is given in `./tectonic_maps_4dmb_2020_09_17/GMT_example/alcapadi_polygons.gmt`. 
+[https://ngdc.noaa.gov/mgg/global/global.html](https://ngdc.noaa.gov/mgg/global/global.html). For this example, we downloaded `ETOPO1_Ice_g_gmt4` and stored it directly in the folder where we will be working. For the geological map, we download the data from the [SPP 4DMB repository](http://www.spp-mountainbuilding.de/data/Maps.zip) and extract the zip file (to the current folder). In this data set, a `gmt` file with the data for different tectonic units is given in `./tectonic_maps_4dmb_2020_09_17/GMT_example/alcapadi_polygons.gmt`. 
 
 #### 2. Create a tectonic map with orthogonal projection 
 To create a png with an orthogonal map projection (which we need for the png import), we do the following in julia:  
@@ -28,7 +28,7 @@ julia> using GMT, NearestNeighbors, GeoParams, GeophysicalModelGenerator
 ```
 First, define the filenames of the files you want to import:  
 ```julia
-julia> filename_topo = "./ETOPO1/ETOPO1_Ice_g_gmt4.grd" 
+julia> filename_topo = "./ETOPO1/ETOPO1_Ice_g_gmt4" 
 julia> filename_geo  = "./tectonicmap_SPP.png"
 ```
 Next, define the region that you want to visualize (note that we use the same coordinates here as we used previously for the generation of the geological map):  

docs/src/man/tutorial_GPS.md

@@ -163,7 +163,7 @@ using GMT, Interpolations
 We use the `import_topo` function to read the topography from a file:
 
 ```julia
-Elevation   =   import_topo([3,17,42,50], file="@earth_relief_01m.grd");
+Elevation   =   import_topo([3,17,42,50], file="@earth_relief_01m");
 nothing #hide
 ```
 

ext/GMT_utils.jl

@@ -18,7 +18,7 @@ println("Loading GMT routines within GMG")
 
 
 """
-    Topo = import_topo(limits; file::String="@earth_relief_01m.grd", maxattempts=5) 
+    Topo = import_topo(limits; file::String="@earth_relief_01m", maxattempts=5) 
     
 Uses `GMT` to download the topography of a certain region, specified with limits=[lon_min, lon_max, lat_min, lat_max].
 Sometimes download fails because of the internet connection. We do `maxattempts` to download it.
@@ -65,45 +65,44 @@ julia> write_paraview(Topo,"Topo_Alps")
  "Topo_Alps.vts"
 ```
 """
-function import_topo(limits; file::String="@earth_relief_01m.grd", maxattempts=5)
+function import_topo(limits; file::String="@earth_relief_01m", maxattempts=5)
 
-    # Correct if negative values are given (longitude coordinates that are west)
-    ind = findall(limits[1:2] .< 0); 
+  # Correct if negative values are given (longitude coordinates that are west)
+  ind = limits[1:2] .< 0
 
-    if (limits[1] < 0) && (limits[2] < 0)
-      limits[ind] .= 360 .+ limits[ind]; 
-      limits[1:2] = sort(limits[1:2])   
-    end
+  if (limits[1] < 0) && (limits[2] < 0)
+      limits[ind] .= 360 .+ limits[ind]
+      limits[1:2]  = sort(limits[1:2])   
+  end
 
-    # Download topo file  - add a few attempts to do so
-    G = [];
-    attempt = 0
-    while attempt<maxattempts
-      try
-        G       =   gmtread(file, limits=limits, grid=true);
-        break
-      catch
-        @warn "Failed downloading GMT topography on attempt $attempt/$maxattempts"
-        sleep(5)  # wait a few sec
-      end
-      attempt += 1
-    end
-    if isempty(G)
-      error("Could not download GMT topography data")
+  # Download topo file  - add a few attempts to do so
+  local G
+  attempt = 0
+  while attempt < maxattempts
+    try
+      G = gmtread(file, limits=limits, grid=true);
+      break
+    catch
+      @warn "Failed downloading GMT topography on attempt $attempt/$maxattempts"
+      sleep(5)  # wait a few sec
     end
+    attempt += 1
+  end
+  if isempty(G)
+    error("Could not download GMT topography data")
+  end
 
-    # Transfer to GeoData
-    nx,ny           =   size(G.z,2), size(G.z,1)
-    Lon,Lat,Depth   =   lonlatdepth_grid(G.x[1:nx],G.y[1:ny],0);
-    Depth[:,:,1]    =   1e-3*G.z';
-    Topo            =   GeoData(Lon, Lat, Depth, (Topography=Depth*km,))
+  # Transfer to GeoData
+  nx, ny              = size(G.z,2), size(G.z,1)
+  Lon,Lat,Depth       = lonlatdepth_grid(G.x[1:nx],G.y[1:ny],0);
+  @views Depth[:,:,1] = 1e-3*G.z';
+  Topo                = GeoData(Lon, Lat, Depth, (Topography=Depth*km,))
 
-    return Topo
-
+  return Topo
 end
 
 """
-  import_topo(; lat::Vector{2}, lon::Vector{2}, file::String="@earth_relief_01m.grd", maxattempts=5)
+  import_topo(; lat::Vector{2}, lon::Vector{2}, file::String="@earth_relief_01m", maxattempts=5)
 
 Imports topography (using GMT), by specifying keywords for latitude and longitude ranges
 
@@ -114,11 +113,11 @@ julia> Topo = import_topo(lat=[30,40], lon=[30, 50] )
 ```
 The values can also be defined as tuples:
 ```julia
-julia> Topo = import_topo(lon=(-50, -40), lat=(-10,-5), file="@earth_relief_30s.grd")
+julia> Topo = import_topo(lon=(-50, -40), lat=(-10,-5), file="@earth_relief_30s")
 ```
 
 """
-import_topo(; lat=[37,49], lon=[4,20], file::String="@earth_relief_01m.grd", maxattempts=5) = import_topo([lon[1],lon[2], lat[1], lat[2]], file=file, maxattempts=maxattempts)
+import_topo(; lat=[37,49], lon=[4,20], file::String="@earth_relief_01m", maxattempts=5) = import_topo([lon[1],lon[2], lat[1], lat[2]], file=file, maxattempts=maxattempts)
 
 
 """