Merge pull request #47 from PoisotLab/feature/geotiff-writer

Allow additional drivers to the geotiff writer

src/SpeciesDistributionToolkit.jl

@@ -21,6 +21,7 @@ using Reexport
 # Functions for IO
 include("io/geotiff.jl")
 include("io/ascii.jl")
+include("io/read_write.jl")
 
 # Integrate the datasets to the layers
 include("integrations/datasets_layers.jl")

src/integrations/datasets_layers.jl

@@ -6,7 +6,7 @@ function SimpleSDMLayers.SimpleSDMPredictor(data::R; kwargs...) where {R <: Rast
     filepath, filetype, bandnumber, crs = downloader(data; arguments...)
 
     if isequal(SimpleSDMDatasets._tiff)(filetype)
-        return geotiff(SimpleSDMPredictor, filepath, bandnumber; boundingbox...)
+        return SimpleSDMPredictor(filepath, "tiff"; bandnumber = bandnumber, boundingbox...)
     end
 
     return nothing
@@ -24,7 +24,7 @@ function SimpleSDMLayers.SimpleSDMPredictor(
     filepath, filetype, bandnumber, crs = downloader(data, future; arguments...)
 
     if isequal(SimpleSDMDatasets._tiff)(filetype)
-        return geotiff(SimpleSDMPredictor, filepath, bandnumber; boundingbox...)
+        return SimpleSDMPredictor(filepath, "tiff"; bandnumber = bandnumber, boundingbox...)
     end
 
     return nothing

src/io/geotiff.jl

@@ -21,7 +21,7 @@ function _find_span(n, m, M, pos, side)
 end
 
 """
-    geotiff(::Type{LT}, file, bandnumber::Integer=1; left=nothing, right=nothing, bottom=nothing, top=nothing) where {LT <: SimpleSDMLayer}
+    geotiff(file, ::Type{LT}; bandnumber::Integer=1, left=nothing, right=nothing, bottom=nothing, top=nothing) where {LT <: SimpleSDMLayer}
 
 The geotiff function reads a geotiff file, and returns it as a matrix of the
 correct type. The optional arguments `left`, `right`, `bottom`, and `left` are
@@ -30,16 +30,15 @@ you want to get a small subset from large files.
 
 The first argument is the type of the `SimpleSDMLayer` to be returned.
 """
-function geotiff(
-    ::Type{LT},
+function _read_geotiff(
     file::AbstractString,
-    bandnumber::Integer = 1;
+    ::Type{LT};
+    bandnumber::Integer = 1,
     left = -180.0,
     right = 180.0,
     bottom = -90.0,
     top = 90.0,
 ) where {LT <: SimpleSDMLayer}
-
     try
         ArchGDAL.read(file) do stuff
             wkt = ArchGDAL.importPROJ4(ArchGDAL.getproj(stuff))
@@ -135,7 +134,7 @@ end
 Write a single `layer` to a `file`, where the `nodata` field is set to an
 arbitrary value.
 """
-function geotiff(
+function _write_geotiff(
     file::AbstractString,
     layer::SimpleSDMPredictor{T};
     nodata::T = convert(T, -9999),
@@ -198,10 +197,11 @@ end
 Stores a series of `layers` in a `file`, where every layer in a band. See
 `geotiff` for other options.
 """
-function geotiff(
+function _write_geotiff(
     file::AbstractString,
     layers::Vector{SimpleSDMPredictor{T}};
     nodata::T = convert(T, -9999),
+    driver::String = "GTiff",
 ) where {T <: Number}
     bands = 1:length(layers)
     SimpleSDMLayers._layers_are_compatible(layers)
@@ -239,7 +239,7 @@ function geotiff(
         return ArchGDAL.write(
             dataset,
             file;
-            driver = ArchGDAL.getdriver("GTiff"),
+            driver = ArchGDAL.getdriver(driver),
             options = ["COMPRESS=LZW"],
         )
     end
@@ -251,23 +251,23 @@ end
 
 Write a single `SimpleSDMResponse` layer to a file.
 """
-function geotiff(
+function _write_geotiff(
     file::AbstractString,
     layer::SimpleSDMResponse{T};
-    nodata::T = convert(T, -9999),
+    kwargs...,
 ) where {T <: Number}
-    return geotiff(file, convert(SimpleSDMPredictor, layer); nodata = nodata)
+    return _write_geotiff(file, convert(SimpleSDMPredictor, layer); kwargs...)
 end
 
 """
     geotiff(file::AbstractString, layers::Vector{SimpleSDMResponse{T}}; nodata::T=convert(T, -9999)) where {T <: Number}
 
 Write a vector of `SimpleSDMResponse` layers to bands in a file.
 """
-function geotiff(
+function _write_geotiff(
     file::AbstractString,
     layers::Vector{SimpleSDMResponse{T}};
-    nodata::T = convert(T, -9999),
+    kwargs...,
 ) where {T <: Number}
-    return geotiff(file, convert.(SimpleSDMPredictor, layers); nodata = nodata)
+    return _write_geotiff(file, convert.(SimpleSDMPredictor, layers); kwargs...)
 end

src/io/read_write.jl

@@ -0,0 +1,45 @@
+for layertype in (:SimpleSDMResponse, :SimpleSDMPredictor)
+    eval(
+        quote
+            function SimpleSDMLayers.$layertype(
+                file::String,
+                format = "tiff";
+                bandnumber::Integer = 1,
+                left = nothing,
+                right = nothing,
+                bottom = nothing,
+                top = nothing,
+            )
+                @assert isfile(file)
+                if endswith(file, ".tif") | endswith(file, ".tiff") |
+                   (format in ["tiff", "tif"])
+                    return SpeciesDistributionToolkit._read_geotiff(
+                        file, $layertype; bandnumber = bandnumber, left = left,
+                        right = right, bottom = bottom, top = top,
+                    )
+                end
+                @error "Only tiff files are supported at the moment"
+            end
+
+            function save(
+                file::String,
+                layers::Vector{$layertype{T}};
+                kwargs...,
+            ) where {T <: Number}
+                if endswith(file, ".tif") | endswith(file, ".tiff")
+                    _write_geotiff(file, layers; kwargs...)
+                    return file
+                end
+                @error "Only tiff files are supported at the moment"
+            end
+
+            function save(
+                file::String,
+                layer::$layertype{T};
+                kwargs...,
+            ) where {T <: Number}
+                return SpeciesDistributionToolkit.save(file, [layer]; kwargs...)
+            end
+        end,
+    )
+end