Merge pull request #51 from JuliaGeodynamics/bk-gmt-import

Import GeoTIFF
JuliaGeodynamics · Feb 21, 2024 · 83504cb · 83504cb
2 parents bde2a1d + 91ed562
commit 83504cb
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diff --git a/.github/dependabot.yml b/.github/dependabot.yml
@@ -4,4 +4,4 @@ updates:
   - package-ecosystem: "github-actions"
     directory: "/" # Location of package manifests
     schedule:
-      interval: "weekly"
+      interval: "monthly"
diff --git a/.github/workflows/blank.yml b/.github/workflows/blank.yml
@@ -14,9 +14,9 @@ jobs:
       fail-fast: false
       matrix:
         version:
-          - '1.8'
           - '1.9'
           - '1.10'
+          - 'nightly'
         os:
           - ubuntu-latest
           - macOS-latest

diff --git a/Project.toml b/Project.toml
@@ -1,7 +1,7 @@
 name = "GeophysicalModelGenerator"
 uuid = "3700c31b-fa53-48a6-808a-ef22d5a84742"
 authors = ["Boris Kaus", "Marcel Thielmann"]
-version = "0.5.8"
+version = "0.5.9"
 
 [deps]
 Colors = "5ae59095-9a9b-59fe-a467-6f913c188581"
@@ -20,15 +20,24 @@ MeshIO = "7269a6da-0436-5bbc-96c2-40638cbb6118"
 NearestNeighbors = "b8a86587-4115-5ab1-83bc-aa920d37bbce"
 Parameters = "d96e819e-fc66-5662-9728-84c9c7592b0a"
 Printf = "de0858da-6303-5e67-8744-51eddeeeb8d7"
-Requires = "ae029012-a4dd-5104-9daa-d747884805df"
 SpecialFunctions = "276daf66-3868-5448-9aa4-cd146d93841b"
 Statistics = "10745b16-79ce-11e8-11f9-7d13ad32a3b2"
+Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
 WriteVTK = "64499a7a-5c06-52f2-abe2-ccb03c286192"
 
+[weakdeps]
+GLMakie = "e9467ef8-e4e7-5192-8a1a-b1aee30e663a"
+GMT = "5752ebe1-31b9-557e-87aa-f909b540aa54"
+
+[extensions]
+GLMakie_Visualisation = "GLMakie"
+GMT_utils = "GMT"
+
 [compat]
 Colors = "0.9 - 0.12"
 Downloads = "1"
 FileIO = "1"
+GLMakie = "0.8, 0.9"
 GMT = "1"
 GeoParams = "0.2 - 0.5"
 Geodesy = "1"
@@ -40,15 +49,14 @@ JLD2 = "0.4"
 MeshIO = "0.1 - 0.4"
 NearestNeighbors = "0.2 - 0.4"
 Parameters = "0.9 - 0.12"
-Requires = "1.0, 2"
 SpecialFunctions = "1.0, 2"
 WriteVTK = "1"
-julia = "1.8"
+julia = "1.9"
 
 [extras]
 GLMakie = "e9467ef8-e4e7-5192-8a1a-b1aee30e663a"
 GMT = "5752ebe1-31b9-557e-87aa-f909b540aa54"
 Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
 
 [targets]
-test = ["Test"]
+test = ["Test","GMT"]
diff --git a/src/Visualisation.jl → ext/GLMakie_Visualisation.jl b/src/Visualisation.jl → ext/GLMakie_Visualisation.jl
@@ -1,8 +1,22 @@
+module GLMakie_Visualisation
 # This contains visualisation widgets which are optionally made available when GLMakie is loaded along with GMG
-using .GLMakie, Statistics
+
+using Statistics
+using GeophysicalModelGenerator: LonLatDepthGrid, GeoData, CartData, km
+
+# We do not check `isdefined(Base, :get_extension)` as recommended since
+# Julia v1.9.0 does not load package extensions when their dependency is
+# loaded from the main environment.
+if VERSION >= v"1.9.1"
+    using GLMakie
+else
+    using ..GLMakie
+end
 
 export Visualise
 
+println("Loading GLMakie extensions for GMG")
+
 """
     Visualise(DataSet; Topography=Topo_Data, Topo_range=nothing)
 
@@ -254,4 +268,7 @@ function Visualise(Data; Topography=nothing, Topo_range=nothing)
     display(fig)
 
     return nothing
+end
+
+
 end
diff --git a/src/GMT_utils.jl → ext/GMT_utils.jl b/src/GMT_utils.jl → ext/GMT_utils.jl
@@ -1,12 +1,26 @@
-# NOTE: these are useful routines that are only loaded when the GMT package is already loaded in the REPL
-using .GMT
+# NOTE: these are useful routines that are only made available when the GMT package is already loaded in the REPL
+module GMT_utils
+
+import GeophysicalModelGenerator: ImportTopo, ImportGeoTIFF
+
+# We do not check `isdefined(Base, :get_extension)` as recommended since
+# Julia v1.9.0 does not load package extensions when their dependency is
+# loaded from the main environment.
+if VERSION >= v"1.9.1"
+  using GMT
+else
+  using ..GMT
+end
+
+using GeophysicalModelGenerator: LonLatDepthGrid, GeoData, UTMData, km
+
+println("Loading GMT routines within GMG")
 
-export ImportTopo
 
 """
     Topo = ImportTopo(limits; file::String="@earth_relief_01m.grd") 
     
-Uses GMT to download the topography of a certain region, specified with limits=[lon_min, lon_max, lat_min, lat_max] 
+Uses `GMT` to download the topography of a certain region, specified with limits=[lon_min, lon_max, lat_min, lat_max] 
 
 Note: 
 ====
@@ -31,7 +45,7 @@ Note:
 | "@earth\\_relief\\_30m"	|  30 arc min	 | ETOPO1 after Gaussian spherical filtering (55 km fullwidth) |
 | "@earth\\_relief\\_60m"	|  60 arc min	 | ETOPO1 after Gaussian spherical filtering (111 km fullwidth)|
 
-*Note*: this routine is only available once the GMT.jl package is loaded on the REPL
+*Note*: this routine is only available once the GMT.jl package is loaded in the REPL
 
 # Example 
 ```julia-repl
@@ -90,3 +104,65 @@ julia> Topo = ImportTopo(lon=(-50, -40), lat=(-10,-5), file="@earth_relief_30s.g
 
 """
 ImportTopo(; lat=[37,49], lon=[4,20], file::String="@earth_relief_01m.grd") = ImportTopo([lon[1],lon[2], lat[1], lat[2]], file=file)
+
+
+"""
+  data_GMT = ImportGeoTIFF(fname::String; fieldname=:layer1, negative=false, iskm=true)
+
+This imports a GeoTIFF dataset (usually containing a surface of some sort) using GMT.
+The file should either have `UTM` coordinates of `longlat` coordinates. If it doesn't, you can 
+use QGIS to convert it to `longlat` coordinates.
+
+Optional keywords:
+- `fieldname` : name of the field (default=:layer1)
+- `negative`  : if true, the depth is multiplied by -1 (default=false)
+- `iskm`      : if true, the depth is multiplied by 1e-3 (default=true)
+- `NorthernHemisphere`: if true, the UTM zone is set to be in the northern hemisphere (default=true); only relevant if the data uses UTM projection
+"""
+function ImportGeoTIFF(fname::String; fieldname=:layer1, negative=false, iskm=true, NorthernHemisphere=true)
+  G = gmtread(fname);
+
+  # Transfer to GeoData
+  nx,ny = length(G.x)-1, length(G.y)-1
+  Lon,Lat,Depth   =   LonLatDepthGrid(G.x[1:nx],G.y[1:ny],0);
+  if  hasfield(typeof(G),:z)
+    Depth[:,:,1]    =   G.z';
+    if negative
+      Depth[:,:,1]  =   -G.z';
+    end
+    if iskm
+      Depth    *=   1e-3*km;
+    end
+  end
+
+  # Create GeoData structure
+  data = zero(Lon)
+  if hasfield(typeof(G),:z)
+    data = Depth
+
+  elseif hasfield(typeof(G),:image)
+    data[:,:,1] = G.image'
+
+  end
+  data_field  = NamedTuple{(fieldname,)}((data,));
+
+  if contains(G.proj4,"utm")
+    zone = parse(Int64,split.(split(G.proj4,"zone=")[2]," ")[1]); # retrieve UTM zone
+    data_GMT    = UTMData(Lon, Lat, Depth, zone, NorthernHemisphere, data_field)
+
+  elseif contains(G.proj4,"longlat") 
+    data_GMT    = GeoData(Lon, Lat, Depth, data_field)
+
+  else
+    error("I'm sorry, I don't know how to handle this projection yet: $(G.proj4)\n
+           We recommend that you transfer your GeoTIFF to longlat by using QGIS \n
+           Open the GeoTIFF there and Export -> Save As , while selecting \"EPSG:4326 - WGS 84\" projection.")
+  end
+
+
+
+  return data_GMT
+end
+
+
+end
diff --git a/src/GeophysicalModelGenerator.jl b/src/GeophysicalModelGenerator.jl
@@ -1,8 +1,6 @@
 module GeophysicalModelGenerator
 
 using Base: String, show_index, Tuple, FieldDescStorage
-using Requires
-
 
 # Load & export some useful commands/functions from GeoParams:
 import GeoParams
@@ -46,17 +44,24 @@ include("ProfileProcessing.jl")
 include("IO.jl")
 
 # Add optional routines (only activated when the packages are loaded)
-function __init__()
-        @require GMT = "5752ebe1-31b9-557e-87aa-f909b540aa54" begin
-                println("Loading GMT routines within GMG")
-                @eval include("./GMT_utils.jl")
-        end
-        @require GLMakie = "e9467ef8-e4e7-5192-8a1a-b1aee30e663a" begin
-                println("Loading GLMakie plotting routines within GMG")
-                @eval include("./Visualisation.jl")
-        end
-end
 
+# GMT routines
+
+"""
+Optional routine that imports topography. It requires you to load `GMT`
+"""
+function ImportTopo end
+function ImportGeoTIFF end
+export ImportTopo, ImportGeoTIFF
+
+# GLMakie routines
+
+"""
+Interactive widget that allows you to explore a 3D data set `DataSet` in an interactive manner.
+It requires you to load `GLMakie`
+"""
+function Visualise end        
+export Visualise
 
 
 end
diff --git a/src/data_types.jl b/src/data_types.jl
@@ -223,10 +223,26 @@ function Base.show(io::IO, d::GeoData)
     println(io,"  size      : $(size(d.lon))")
     println(io,"  lon       ϵ [ $(first(d.lon.val)) : $(last(d.lon.val))]")
     println(io,"  lat       ϵ [ $(first(d.lat.val)) : $(last(d.lat.val))]")
-    println(io,"  depth     ϵ [ $(first(d.depth.val)) : $(last(d.depth.val))]")
+    if  any(isnan.(NumValue(d.depth)))
+        z_vals = extrema(d.depth.val[isnan.(d.depth.val).==false])
+        println(io,"  depth     ϵ [ $(z_vals[1]) : $(z_vals[2])]; has NaN's")
+    else
+        z_vals = extrema(d.depth.val)
+        println(io,"  depth     ϵ [ $(z_vals[1]) : $(z_vals[2])]")
+    end
     println(io,"  fields    : $(keys(d.fields))")
+
+    # Only print attributes if we have non-default attributes
     if any( propertynames(d) .== :atts)
-        println(io,"  attributes: $(keys(d.atts))")
+        show_atts = true
+        if haskey(d.atts,"note") 
+            if d.atts["note"]=="No attributes were given to this dataset"
+                show_atts = false
+            end
+        end
+        if show_atts
+         println(io,"  attributes: $(keys(d.atts))")
+        end
     end
 end
 
@@ -256,8 +272,29 @@ function Base.show(io::IO, d::ParaviewData)
     println(io,"  size  : $(size(d.x))")
     println(io,"  x     ϵ [ $(first(d.x.val)) : $(last(d.x.val))]")
     println(io,"  y     ϵ [ $(first(d.y.val)) : $(last(d.y.val))]")
-    println(io,"  z     ϵ [ $(first(d.z.val)) : $(last(d.z.val))]")
+    if  any(isnan.(NumValue(d.z)))
+        z_vals = extrema(d.z.val[isnan.(d.z.val).==false])
+        println(io,"  z     ϵ [ $(z_vals[1]) : $(z_vals[2])]; has NaN's")
+    else
+        z_vals = extrema(d.z.val)
+        println(io,"  z     ϵ [ $(z_vals[1]) : $(z_vals[2])]")
+    end
+
     println(io,"  fields: $(keys(d.fields))")
+
+    # Only print attributes if we have non-default attributes
+    if any( propertynames(d) .== :atts)
+        show_atts = true
+        if haskey(d.atts,"note") 
+            if d.atts["note"]=="No attributes were given to this dataset"
+                show_atts = false
+            end
+        end
+        if show_atts
+         println(io,"  attributes: $(keys(d.atts))")
+        end
+    end
+
 end
 
 # conversion function from GeoData -> ParaviewData
@@ -439,10 +476,28 @@ function Base.show(io::IO, d::UTMData)
     println(io,"    size    : $(size(d.EW))")
     println(io,"    EW      ϵ [ $(first(d.EW.val)) : $(last(d.EW.val))]")
     println(io,"    NS      ϵ [ $(first(d.NS.val)) : $(last(d.NS.val))]")
-    println(io,"    depth   ϵ [ $(first(d.depth.val)) : $(last(d.depth.val))]")
+
+    if  any(isnan.(NumValue(d.depth)))
+        z_vals = extrema(d.depth.val[isnan.(d.depth.val).==false])
+        println(io,"  depth     ϵ [ $(z_vals[1]) : $(z_vals[2])]; has NaNs")
+    else
+        z_vals = extrema(d.depth.val)
+        println(io,"  depth     ϵ [ $(z_vals[1]) : $(z_vals[2])]")
+    end
+
     println(io,"    fields  : $(keys(d.fields))")
+
+    # Only print attributes if we have non-default attributes
     if any( propertynames(d) .== :atts)
-        println(io,"  attributes: $(keys(d.atts))")
+        show_atts = true
+        if haskey(d.atts,"note") 
+            if d.atts["note"]=="No attributes were given to this dataset"
+                show_atts = false
+            end
+        end
+        if show_atts
+         println(io,"  attributes: $(keys(d.atts))")
+        end
     end
 end
 
@@ -701,9 +756,29 @@ function Base.show(io::IO, d::CartData)
     println(io,"    x       ϵ [ $(minimum(d.x.val)) : $(maximum(d.x.val))]")
     println(io,"    y       ϵ [ $(minimum(d.y.val)) : $(maximum(d.y.val))]")
     println(io,"    z       ϵ [ $(minimum(d.z.val)) : $(maximum(d.z.val))]")
+
+    if  any(isnan.(NumValue(d.z)))
+        z_vals = extrema(d.z.val[isnan.(d.z.val).==false])
+        println(io,"    z       ϵ [ $(z_vals[1]) : $(z_vals[2])]; has NaN's")
+    else
+        z_vals = extrema(d.z.val)
+        println(io,"    z       ϵ [ $(z_vals[1]) : $(z_vals[2])]")
+    end
+
+
     println(io,"    fields  : $(keys(d.fields))")
+
+    # Only print attributes if we have non-default attributes
     if any( propertynames(d) .== :atts)
+        show_atts = true
+        if haskey(d.atts,"note") 
+            if d.atts["note"]=="No attributes were given to this dataset"
+                show_atts = false
+            end
+        end
+        if show_atts
         println(io,"  attributes: $(keys(d.atts))")
+        end
     end
 end
 

diff --git a/test/runtests.jl b/test/runtests.jl
@@ -40,6 +40,9 @@ end
     include("test_ProfileProcessing.jl")
 end
 
+@testset "GMT integration" begin
+    include("test_GMT.jl")
+end
 
 
 # Cleanup 

diff --git a/test/test_GMT.jl b/test/test_GMT.jl
@@ -0,0 +1,14 @@
+using Test
+using GeophysicalModelGenerator, GMT
+
+Topo = ImportTopo(lat=[30,31], lon=[50, 51] )
+@test sum(Topo.depth.val) ≈ 2773.3734999999997
+
+Topo = ImportTopo([50,51, 30,31]);
+@test sum(Topo.depth.val) ≈ 2773.3734999999997
+
+test_fwd =  ImportGeoTIFF("test_files/length_fwd.tif", fieldname=:forward)
+@test  maximum(test_fwd.fields.forward) ≈ 33.17775km
+
+test2 =  ImportGeoTIFF("test_files/UTM2GTIF.TIF")
+@test   test2.fields.layer1[20,20] == 105.0
diff --git a/test/test_files/UTM2GTIF.TIF b/test/test_files/UTM2GTIF.TIF
diff --git a/test/test_files/length_fwd.tif b/test/test_files/length_fwd.tif