move from GeoData to Rasters

Author: Vincent Landau

Project.toml

@@ -4,13 +4,13 @@ authors = ["Vincent A. Landau <[email protected]>"]
 version = "0.0.1"
 
 [deps]
-GeoData = "9b6fcbb8-86d6-11e9-1ce7-23a6bb139a78"
 Graphs = "86223c79-3864-5bf0-83f7-82e725a168b6"
+Rasters = "a3a2b9e3-a471-40c9-b274-f788e487c689"
 SimpleWeightedGraphs = "47aef6b3-ad0c-573a-a1e2-d07658019622"
 SparseArrays = "2f01184e-e22b-5df5-ae63-d93ebab69eaf"
 Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
 
 [compat]
-GeoData = "0.5"
 Graphs = "1.4"
+Rasters = "0.1"
 julia = "1.6"

README.md

@@ -12,5 +12,5 @@ out of the box.
 `AbstractSpatialGraph`s themselves contain an `AbstractGraph` in addition to 
 metadata that details the spatial location of each vertex in the
 graph. At this time, only raster-based graph types have been developed (and 
-vertex locations are stored in a `GeoData.GeoArray`), but there are plans to 
+vertex locations are stored in a `Rasters.Raster`), but there are plans to 
 implement graph types for vector data as well.

docs/src/graphtypes.md

@@ -1,7 +1,7 @@
 # [Graph Types in SpatialGraphs.jl](@id graph_types)
 
 At this time, only raster-based graph types have been developed (and 
-vertex locations are stored in a `GeoData.GeoArray`), but there are plans to 
+vertex locations are stored in a `Rasters.Raster`), but there are plans to 
 eventually implement graph types for vector data as well.
 
 ## Abstract Types
@@ -14,7 +14,7 @@ AbstractSpatialGraph
 
 The `AbstractRasterGraph` type is a subtype of `AbstractSpatialGraph`. All
 `AbstractRasterGraph` subtypes contain a field called `vertex_raster`, which is 
-a `GeoData.GeoArray` that describes the spatial locations for the vertices in 
+a `Rasters.Raster` that describes the spatial locations for the vertices in 
 the graph. If your graph has 10 vertices, then the corresponding `vertex_raster` 
 must have 10 unique values, starting at 1 (which corresponds to the first vertex
 in the graph) and going up to 10 (which corresponds to the tenth vertex in the 

src/SpatialGraphs.jl

@@ -1,6 +1,6 @@
 module SpatialGraphs
 
-using Graphs, SimpleWeightedGraphs, SparseArrays, GeoData
+using Graphs, SimpleWeightedGraphs, SparseArrays, Rasters
 
 include("structs.jl")
 include("graph_interface.jl")

src/rastergraphs.jl

@@ -1,35 +1,35 @@
 """
-    make_vertex_raster(A::GeoArray)
+    make_vertex_raster(A::Raster)
 
 Constuct a vertex raster (a raster where the value of each pixel corresponds
-to its ID in a graph, and 0s correspond to NoData). Returns a GeoArray. This 
+to its ID in a graph, and 0s correspond to NoData). Returns a Raster. This 
 function is recommended for internal use only.
 
 ## Parameters
-`A`: The GeoArray from which a graph will be built, which is used as the
+`A`: The Raster from which a graph will be built, which is used as the
 reference for building the vertex raster. Pixels with NoData (`A.missingval`)
 are skipped (no vertex is assigned). Pixels with NoData will get a value of 0 in
 the vertex raster.
 """
-function make_vertex_raster(A::GeoData.GeoArray)
+function make_vertex_raster(A::Raster)
     # Make an array of unique node identifiers
     nodemap = zeros(Int64, size(A.data))
     is_node = (A.data .!= A.missingval) .&
         ((!).(isnan.(A.data)))
 
     nodemap[is_node] = 1:sum(is_node)
 
-    nodemap = GeoData.GeoArray(nodemap, dims(A))
+    nodemap = Raster(nodemap, dims(A))
 
     nodemap
 end
 
 
 """
     weightedrastergraph(
-        weight_raster::GeoArray;
+        weight_raster::Raster;
         directed::Bool = false,
-        condition_raster::GeoArray = weight_raster,
+        condition_raster::Raster = weight_raster,
         condition::Function = is_data,
         cardinal_neighbors_only::Bool = false,
         connect_using_avg_weights::Bool = true
@@ -42,7 +42,7 @@ on vertices, edge weights are calculated as the average of the weights for each
 vertex.
 
 ## Parameters
-`weight_raster`: A GeoData.GeoArray contained values that, where applicable 
+`weight_raster`: A Rasters.Raster contained values that, where applicable 
 based on other arguments, determines which pixels to connect and the edge 
 weights between pixels. Any pixel in `weight_raster` with a value not equal to 
 `weight_raster.missingval` will be assigned a vertex in the graph (corresponding
@@ -90,9 +90,9 @@ neighbors) of the weights  in `weight_raster` is used.
 
 """
 function weightedrastergraph(
-        weight_raster::GeoArray;
+        weight_raster::Raster;
         directed::Bool = false,
-        condition_raster::GeoArray = weight_raster,
+        condition_raster::Raster = weight_raster,
         condition::Function = is_data,
         cardinal_neighbors_only::Bool = false,
         connect_using_avg_weights::Bool = true
@@ -120,7 +120,7 @@ end
 
 """
     RasterGraph(
-        raster::GeoArray;
+        raster::Raster;
         directed::Bool = true,
         condition::Function = is_data,
         cardinal_neighbors_only::Bool = false
@@ -130,7 +130,7 @@ Construct a `RasterGraph` or `RasterDiGraph` (if
 `directed = true`) from a raster dataset.
 
 ## Parameters
-`raster`: A GeoData.GeoArray on which to base the graph. Any pixel in `raster` 
+`raster`: A Rasters.Raster on which to base the graph. Any pixel in `raster` 
 with a value not equal to `raster.missingval` will be assigned a vertex
 in the graph (corresponding to its centroid). The values in the raster can also
 be used to determine which vertices to connect. See `condition` below for more
@@ -162,7 +162,7 @@ increased distance between them (as compared to the distance between cardinal
 neighbors) is accounted for.
 """
 function rastergraph(
-        raster::GeoArray;
+        raster::Raster;
         condition::Function = is_data,
         directed::Bool = true,
         cardinal_neighbors_only::Bool = false,
@@ -187,10 +187,10 @@ end
 
 """
     make_weighted_raster_graph(
-        weight_raster::GeoArray,
-        vertex_raster::GeoArray;
+        weight_raster::Raster,
+        vertex_raster::Raster;
         directed::Bool = false,
-        condition_raster::GeoArray = weight_raster,
+        condition_raster::Raster = weight_raster,
         condition::Function = is_data,
         cardinal_neighbors_only::Bool = false,
         connect_using_avg_weights::Bool = true,
@@ -206,13 +206,13 @@ vertex. Since edges are between rather than on vertices, edge weights are
 calculated as the average of the weights for each vertex being connected.
 
 ## Parameters
-`weight_raster`: A `GeoData.GeoArray` containing values that, where applicable 
+`weight_raster`: A `Rasters.Raster` containing values that, where applicable 
 based on other arguments, determine which pixels to connect and the edge 
 weights between pixels. Any pixel in `weight_raster` with a value not equal to 
 `weight_raster.missingval` will be assigned a vertex in the graph (corresponding
 to its centroid). 
 
-`vertex_raster`: A `GeoData.GeoArray` with integer values ranging from 1:n, 
+`vertex_raster`: A `Rasters.Raster` with integer values ranging from 1:n, 
 where n is the number of unique vertices in the graph. 
 
 ## Arguments
@@ -256,10 +256,10 @@ of vertices, how should the weight be chosen? Defaults to `min`. See the docs
 for `SparseArrays.sparse()` for more information.
 """
 function make_weighted_raster_graph(
-        weight_raster::GeoArray,
-        vertex_raster::GeoArray;
+        weight_raster::Raster,
+        vertex_raster::Raster;
         directed::Bool = false,
-        condition_raster::GeoArray = weight_raster,
+        condition_raster::Raster = weight_raster,
         condition::Function = is_data,
         cardinal_neighbors_only::Bool = false,
         connect_using_avg_weights::Bool = true,
@@ -289,8 +289,8 @@ end
 
 """
     make_simple_raster_graph(
-        raster::GeoArray,
-        vertex_raster::GeoArray;
+        raster::Raster,
+        vertex_raster::Raster;
         directed::Bool = false,
         condition::Function = is_data,
         cardinal_neighbors_only::Bool = false,
@@ -305,13 +305,13 @@ in the graph, and `raster` is used to construct the graph and determine which
 vertices to connect.
 
 ## Parameters
-`raster`: A GeoData.GeoArray on which to base the graph. Any pixel in `raster` 
+`raster`: A Rasters.Raster on which to base the graph. Any pixel in `raster` 
 with a value not equal to `raster.missingval` will be assigned a vertex
 in the graph (corresponding to its centroid). The values in the raster can also
 be used to determine which vertices to connect. See `condition` below for more
 information.
 
-`vertex_raster`: A `GeoData.GeoArray` with integer values ranging from 1:n, 
+`vertex_raster`: A `Rasters.Raster` with integer values ranging from 1:n, 
 where n is the number of unique vertices in the graph. 
 
 ## Arguments
@@ -355,8 +355,8 @@ of vertices, how should the weight be chosen? Defaults to `min`. See the docs
 for `SparseArrays.sparse()` for more information.
 """
 function make_simple_raster_graph(
-        raster::GeoArray,
-        vertex_raster::GeoArray;
+        raster::Raster,
+        vertex_raster::Raster;
         directed::Bool = false,
         condition::Function = is_data,
         cardinal_neighbors_only::Bool = false,
@@ -378,11 +378,11 @@ end
 
 
 function make_raster_graph(
-        raster::GeoArray,
-        vertex_raster::GeoArray;
+        raster::Raster,
+        vertex_raster::Raster;
         directed::Bool = false,
         weighted::Bool = true,
-        condition_raster::GeoArray = raster,
+        condition_raster::Raster = raster,
         condition::Function = is_data,
         cardinal_neighbors_only::Bool = false,
         connect_using_avg_weights::Bool = true,
@@ -410,7 +410,7 @@ function make_raster_graph(
     # Add the edges
     # Only need to do neighbors down or to the right for undirected graphs
     # because edge additions will be redundant.
-    # Cardinal directions are in quotes since sometimes GeoArray are permuted
+    # Cardinal directions are in quotes since sometimes Raster are permuted
     # such that the top row doesn't necessarily correspond to the northern-most
     # pixels
     for row in 1:dims[1]

src/show.jl

@@ -12,8 +12,8 @@ function show(io::IO, g::AbstractRasterGraph)
     )
     printstyled(" with dimensions:\n", color=:light_black)
 
-    x_dim = dims(g.vertex_raster, XDim)
-    y_dim = dims(g.vertex_raster, YDim)
+    x_dim = dims(g.vertex_raster, X)
+    y_dim = dims(g.vertex_raster, Y)
     printstyled("    X", color=:cyan)
     print(
         ": range($(minimum(x_dim)), $(maximum(x_dim)), step=$(x_dim.val[2] - x_dim.val[1]))\n"

src/structs.jl

@@ -18,7 +18,7 @@ An abstract type representing a spatially referenced graph, with graph vertices
 An AbstractRasterGraph must contain the following fields:
 
 - `graph::AbstractGraph`
-- `vertex_raster::GeoArray`
+- `vertex_raster::Raster`
 """
 abstract type AbstractRasterGraph{T} <: AbstractSpatialGraph{T} end
 
@@ -29,7 +29,7 @@ A composite type for a spatially referenced weighted graph. Vertices are spatial
 """
 mutable struct WeightedRasterGraph{T<:Integer, U<:Real} <: AbstractRasterGraph{T}
     graph::SimpleWeightedGraph{T, U} # a SimpleWeightedGraph with edge weights
-    vertex_raster::GeoArray # A GeoArray raster, where a pixel's value denotes its vertex ID in the graph
+    vertex_raster::Raster # A Raster raster, where a pixel's value denotes its vertex ID in the graph
 end
 """
     WeightedRasterDiGraph{T}
@@ -38,7 +38,7 @@ A composite type for a spatially referenced, weighted, directed graph. Vertices
 """
 mutable struct WeightedRasterDiGraph{T<:Integer, U<:Real} <: AbstractRasterGraph{T}
     graph::SimpleWeightedDiGraph{T, U} # a SimpleWeightedDiGraph with edge weights
-    vertex_raster::GeoArray # A GeoArray raster, where a pixel's value denotes its vertex ID in the graph
+    vertex_raster::Raster # A Raster raster, where a pixel's value denotes its vertex ID in the graph
 end
 
 """
@@ -48,7 +48,7 @@ A composite type for a spatially referenced graph. Vertices are spatially refere
 """
 mutable struct RasterGraph{T<:Integer} <: AbstractRasterGraph{T}
     graph::Graph{T} # A Graph
-    vertex_raster::GeoArray # A GeoArray raster, where a pixel's value denotes its vertex ID in the graph
+    vertex_raster::Raster # A Raster raster, where a pixel's value denotes its vertex ID in the graph
 end
 
 """
@@ -58,5 +58,5 @@ A composite type for a spatially referenced directed graph. Vertices are spatial
 """
 mutable struct RasterDiGraph{T<:Integer} <: AbstractRasterGraph{T}
     graph::DiGraph{T} # A DiGraph
-    vertex_raster::GeoArray # A GeoArray raster, where a pixel's value denotes its vertex ID in the graph
+    vertex_raster::Raster # A Raster raster, where a pixel's value denotes its vertex ID in the graph
 end

src/utils.jl

@@ -3,7 +3,7 @@
     is_data(a::Number, b::Number)
 
 This function is the default used for deciding whether to connect two neighbors
-in a GeoArray when constructing a graph. It always returns `true`, so all
+in a Raster when constructing a graph. It always returns `true`, so all
 neighbors will be connected
 
 Returns `true`
@@ -22,7 +22,7 @@ res_cardinal_avg(x, y) = (x + y) / 2
 res_diagonal_avg(x, y) = ((x + y) * √2) / 2
 
 
-# function get_dims(A::GeoData.GeoArray)
+# function get_dims(A::Rasters.Raster)
 #     y_first = dims(mytif)[1] isa XDim
 #     first_dim_type = y_first ? YDim : XDim
 #     second_dim_type = y_first ? XDim : YDim

test/lg_interface.jl renamed to test/graph_interface.jl

@@ -1,4 +1,4 @@
-using SpatialGraphs, Test, GeoData, Graphs, SimpleWeightedGraphs
+using SpatialGraphs, Test, Rasters, Graphs, SimpleWeightedGraphs
 ## This script tests methods for the LightGraph interface that aren't already 
 ## used in other tests
 
@@ -8,7 +8,7 @@ x = X(1:4)
 y = Y(1:3)
 band = Band(1:1)
 
-weight_raster = GeoArray(A_array, (y, x, band), missingval = -9999)
+weight_raster = Raster(A_array, (y, x, band), missingval = -9999)
 rasgraph = weightedrastergraph(weight_raster)
 
 @test nv(rasgraph) == maximum(rasgraph.vertex_raster)

test/rasterdigraphs.jl

@@ -1,4 +1,4 @@
-using GeoData, Graphs, SimpleWeightedGraphs, SpatialGraphs, Test
+using Rasters, Graphs, SimpleWeightedGraphs, SpatialGraphs, Test
 
 condition_array = Array{Float64}(undef, (3, 4, 1))
 condition_array[:,:,:] = [1, 0.5, 5, 2, 4, 8, 5, -9999, 2, 3, 6, 7]
@@ -7,7 +7,7 @@ x = X(1:4)
 y = Y(1:3)
 band = Band(1:1)
 
-condition_raster = GeoArray(condition_array, (y, x, band), missingval = -9999)
+condition_raster = Raster(condition_array, (y, x, band), missingval = -9999)
 
 compare = <
 rasgraph = rastergraph(