Issue #25 - Add code documentation

- Add docstrings and apply formatting to:
    - src/EndmemberLibrary.jl
    - src/Plotting.jl
    - src/Solvers.jl
    - src/Datasets.jl

src/Datasets.jl

@@ -17,7 +17,17 @@
 using ArchGDAL
 using GDAL
 
+"""
+    set_band_names(filename::String, band_names::Vector)
 
+Set the names of the bands in a raster dataset specified by the given filename.
+
+# Arguments
+- `filename::String`: Path to the raster file. The file must be in a format supported by
+GDAL. The data file is updated in place.
+- `band_names::Vector`: A vector of strings containing the new names for each band in the
+raster dataset. The length of this vector must match the number of bands in the raster.
+"""
 function set_band_names(filename::String, band_names::Vector)
     GC.gc()
     local_ods = GDAL.gdalopen(filename, GDAL.GA_Update)
@@ -27,45 +37,104 @@ function set_band_names(filename::String, band_names::Vector)
     local_ods = nothing
 end
 
-function initiate_output_datasets(output_files::Vector{String}, x_len::Int64, y_len::Int64, output_bands::Vector, reference_dataset::ArchGDAL.IDataset)
+"""
+    initiate_output_datasets(output_files::Vector{String}, x_len::Int64, y_len::Int64,
+                             output_bands::Vector, reference_dataset::ArchGDAL.IDataset)
+
+Initialize multiple output raster datasets in ENVI format with specified dimensions and
+band information using a reference dataset for projection and geotransformation.
+
+# Arguments
+- `output_files::Vector{String}`: File paths of the output datasets. Each entry corresponds
+to a separate output raster.
+- `x_len::Int64`: Width of the output datasets.
+- `y_len::Int64`: Height of the output datasets.
+- `output_bands::Vector`: Number of bands for each output dataset. The length of this
+vector must match the length of `output_files`.
+- `reference_dataset::ArchGDAL.IDataset`: Reference dataset object from which projection
+and geotransformation information will be copied.
+
+# Notes
+- All bands in the output datasets are initialized with the no-data value of `-9999`.
+"""
+function initiate_output_datasets(output_files::Vector{String}, x_len::Int64, y_len::Int64,
+    output_bands::Vector, reference_dataset::ArchGDAL.IDataset)
     GC.gc()
     for _o in 1:length(output_files)
-        outDataset = ArchGDAL.create(output_files[_o], driver=ArchGDAL.getdriver("ENVI"), width=x_len,
-                                     height=y_len, nbands=output_bands[_o], dtype=Float64)
+        outDataset = ArchGDAL.create(
+            output_files[_o], driver=ArchGDAL.getdriver("ENVI"), width=x_len,
+            height=y_len, nbands=output_bands[_o], dtype=Float64
+        )
         ArchGDAL.setproj!(outDataset, ArchGDAL.getproj(reference_dataset))
-        @info "Output Image Size (x,y,b): $x_len, $y_len, $output_bands.  Creating output fractional cover dataset."
+        @info "Output Image Size (x,y,b): $x_len, $y_len, $output_bands.
+        Creating output fractional cover dataset."
         try
-            ArchGDAL.setgeotransform!(outDataset, ArchGDAL.getgeotransform(reference_dataset))
+            ArchGDAL.setgeotransform!(
+                outDataset, ArchGDAL.getgeotransform(reference_dataset)
+            )
         catch e
-            println("No geotransorm avaialble, proceeding without")
+            println("No geotransorm available, proceeding without")
         end
 
         for _b in 1:length(output_bands)
-            ArchGDAL.setnodatavalue!(ArchGDAL.getband(outDataset,_b), -9999)
+            ArchGDAL.setnodatavalue!(ArchGDAL.getband(outDataset, _b), -9999)
         end
 
         output = zeros(x_len, y_len, output_bands[_o]) .- 9999
-        ArchGDAL.write!(outDataset, output, [1:size(output)[end];], 0, 0, size(output)[1], size(output)[2])
+        ArchGDAL.write!(
+            outDataset, output, [1:size(output)[end];], 0, 0, size(output)[1],
+            size(output)[2]
+        )
 
         outDataset = nothing
-
     end
 end
 
+"""
+    write_results(output_files::Vector{String}, output_bands::Vector, x_len::Int64,
+                  y_len::Int64, results, args)
+
+Write processed results to specified output ENVI raster files, including primary outputs,
+uncertainty estimates, and complete fractions, based on the provided parameters.
+
+# Arguments
+- `output_files::Vector{String}`: File paths of the output datasets to be created or
+updated. Each entry corresponds to a separate output raster.
+- `output_bands::Vector`: Number of bands for each output dataset. The length of this
+vector must match the number of output files.
+- `x_len::Int64`: Width of the output datasets.
+- `y_len::Int64`: Height of the output datasets.
+- `results`: A collection of results, where each result is expected to be a tuple or
+similar structure. Specific elements contain the data to be written to the output datasets.
+- `args`: An object or structure containing additional parameters that dictate the
+writing behavior. Available options are:
+    - `args.n_mc`: If greater than 1, an uncertainty output is also written to the second
+    output file.
+    - `args.write_complete_fractions`: If set to 1, write complete fractions to the
+    subsequent output file.
+
+# Notes
+- The primary output is initialized with a no-data value of `-9999` and written to the
+  first output file specified in `output_files`.
+- Each output array is permuted to match the desired dimensions before writing.
+"""
+function write_results(output_files::Vector{String}, output_bands::Vector, x_len::Int64,
+    y_len::Int64, results, args)
 
-function write_results(output_files::Vector{String}, output_bands::Vector, x_len::Int64, y_len::Int64, results, args)
     GC.gc()
 
     @info "Write primary output"
     output = zeros(y_len, x_len, output_bands[1]) .- 9999
     for res in results
         if isnothing(res[2]) == false
-            output[res[1],res[3], :] = res[2]
+            output[res[1], res[3], :] = res[2]
         end
     end
-    output = permutedims( output, (2,1,3))
-    outDataset = ArchGDAL.read(output_files[1], flags=1, alloweddrivers =["ENVI"])
-    ArchGDAL.write!(outDataset, output, [1:size(output)[end];], 0, 0, size(output)[1], size(output)[2])
+    output = permutedims(output, (2, 1, 3))
+    outDataset = ArchGDAL.read(output_files[1], flags=1, alloweddrivers=["ENVI"])
+    ArchGDAL.write!(
+        outDataset, output, [1:size(output)[end];], 0, 0, size(output)[1], size(output)[2]
+    )
     outDataset = nothing
 
     ods_idx = 2
@@ -74,13 +143,16 @@ function write_results(output_files::Vector{String}, output_bands::Vector, x_len
         output = zeros(y_len, x_len, output_bands[ods_idx]) .- 9999
         for res in results
             if isnothing(res[4]) == false
-                output[res[1],res[3], :] = res[4]
+                output[res[1], res[3], :] = res[4]
             end
         end
 
-        output = permutedims( output, (2,1,3))
-        outDataset = ArchGDAL.read(output_files[ods_idx], flags=1, alloweddrivers =["ENVI"])
-        ArchGDAL.write!(outDataset, output, [1:size(output)[end];], 0, 0, size(output)[1], size(output)[2])
+        output = permutedims(output, (2, 1, 3))
+        outDataset = ArchGDAL.read(output_files[ods_idx], flags=1, alloweddrivers=["ENVI"])
+        ArchGDAL.write!(
+            outDataset, output, [1:size(output)[end];], 0, 0, size(output)[1],
+            size(output)[2]
+        )
         outDataset = nothing
         ods_idx += 1
     end
@@ -90,29 +162,53 @@ function write_results(output_files::Vector{String}, output_bands::Vector, x_len
         output = zeros(y_len, x_len, output_bands[ods_idx]) .- 9999
         for res in results
             if isnothing(res[5]) == false
-                output[res[1],res[3], :] = res[5]
+                output[res[1], res[3], :] = res[5]
             end
         end
 
-        output = permutedims( output, (2,1,3))
-        outDataset = ArchGDAL.read(output_files[ods_idx], flags=1, alloweddrivers =["ENVI"])
-        ArchGDAL.write!(outDataset, output, [1:size(output)[end];], 0, 0, size(output)[1], size(output)[2])
+        output = permutedims(output, (2, 1, 3))
+        outDataset = ArchGDAL.read(output_files[ods_idx], flags=1, alloweddrivers=["ENVI"])
+        ArchGDAL.write!(
+            outDataset, output, [1:size(output)[end];], 0, 0, size(output)[1],
+            size(output)[2]
+        )
         outDataset = nothing
         ods_idx += 1
     end
-
 end
 
-function write_line_results(output_files::Vector{String}, results, n_mc::Int64, write_complete_fractions::Bool)
+"""
+    write_line_results(output_files::Vector{String}, results, n_mc::Int64,
+                       write_complete_fractions::Bool)
+
+Write line-based results to specified output ENVI raster files, including primary results,
+uncertainty estimates, and complete fractions based on provided parameters.
+
+# Arguments
+- `output_files::Vector{String}`: File paths of the output datasets to be created or
+updated. Each entry corresponds to a separate output raster.
+- `results`: A collection of results, where each entry is expected to be a tuple or
+similar structure. Specific elements contain the data to be written to the output datasets.
+- `n_mc::Int64`: If greater than one, uncertainty outputs will be written to the
+subsequent output file.
+- `write_complete_fractions::Bool`: Indicates whether to write complete fractions
+to the subsequent output file.
+"""
+function write_line_results(output_files::Vector{String}, results, n_mc::Int64,
+    write_complete_fractions::Bool)
+
     GC.gc()
-    
+
     if isnothing(results[2]) == false
-        
+
         output = zeros(size(results[3])[1], 1, size(results[2])[2]) .- 9999
         output[results[3], 1, :] = results[2]
 
-        outDataset = ArchGDAL.read(output_files[1], flags=1, alloweddrivers =["ENVI"])
-        ArchGDAL.write!(outDataset, output, [1:size(output)[end];], 0, results[1]-1, size(output)[1], 1)
+        outDataset = ArchGDAL.read(output_files[1], flags=1, alloweddrivers=["ENVI"])
+        ArchGDAL.write!(
+            outDataset, output, [1:size(output)[end];], 0, results[1] - 1,
+            size(output)[1], 1
+        )
         outDataset = nothing
     end
     ods_idx = 2
@@ -121,9 +217,14 @@ function write_line_results(output_files::Vector{String}, results, n_mc::Int64,
         if isnothing(results[4]) == false
             output = zeros(size(results[3])[1], 1, size(results[4])[2]) .- 9999
             output[results[3], 1, :] = results[4]
-
-            outDataset = ArchGDAL.read(output_files[ods_idx], flags=1, alloweddrivers =["ENVI"])
-            ArchGDAL.write!(outDataset, output, [1:size(output)[end];], 0, results[1]-1, size(output)[1], 1)
+
+            outDataset = ArchGDAL.read(
+                output_files[ods_idx], flags=1, alloweddrivers=["ENVI"]
+            )
+            ArchGDAL.write!(
+                outDataset, output, [1:size(output)[end];], 0, results[1] - 1,
+                size(output)[1], 1
+            )
             outDataset = nothing
         end
         ods_idx += 1
@@ -133,36 +234,72 @@ function write_line_results(output_files::Vector{String}, results, n_mc::Int64,
         if isnothing(results[5]) == false
             output = zeros(size(results[3])[1], 1, size(results[5])[2]) .- 9999
             output[results[3], 1, :] = results[5]
-
-            outDataset = ArchGDAL.read(output_files[ods_idx], flags=1, alloweddrivers =["ENVI"])
-            ArchGDAL.write!(outDataset, output, [1:size(output)[end];], 0, results[1]-1, size(output)[1], 1)
+
+            outDataset = ArchGDAL.read(
+                output_files[ods_idx], flags=1, alloweddrivers=["ENVI"]
+            )
+            ArchGDAL.write!(
+                outDataset, output, [1:size(output)[end];], 0, results[1] - 1,
+                size(output)[1], 1
+            )
             outDataset = nothing
         end
         ods_idx += 1
     end
-
 end
 
-function load_line(reflectance_file::String, reflectance_uncertainty_file::String, line::Int64,
-                       good_bands::Array{Bool}, refl_nodata::Float64)
-
-        reflectance_dataset = ArchGDAL.read(reflectance_file, alloweddrivers =["ENVI"])
-        img_dat = convert(Array{Float64},ArchGDAL.readraster(reflectance_file, alloweddrivers =["ENVI"])[:,line,:])
-        img_dat = img_dat[:, good_bands]
-        good_data = .!all(img_dat .== refl_nodata, dims=2)[:,1]
-        img_dat = img_dat[good_data,:]
-
-        if sum(good_data) >= 1
-            if reflectance_uncertainty_file != ""
-                unc_dat = convert(Array{Float64},ArchGDAL.readraster(reflectance_uncertainty_file, alloweddrivers =["ENVI"])[:,line,:])
-                unc_dat = unc_dat[:, good_bands]
-                unc_dat = unc_dat[good_data,:]
-            else
-                unc_dat = nothing
-            end
+"""
+    load_line(reflectance_file::String, reflectance_uncertainty_file::String,
+               line::Int64, good_bands::Array{Bool}, refl_nodata::Float64)
+
+Load a specific line (row) of reflectance data and its associated uncertainty from raster
+files, filtering based on specified good bands and no-data values.
+
+# Arguments
+- `reflectance_file::String`: Path to the ENVI reflectance raster file.
+- `reflectance_uncertainty_file::String`: Path to the uncertainty raster file corresponding
+to the reflectance data. An empty string indicates no uncertainty data.
+- `line::Int64`: Line (row) of the raster data to be loaded.
+- `good_bands::Array{Bool}`: Boolean array indicating which bands of the data to keep and
+process.
+- `refl_nodata::Float64`: The no-data value used in the reflectance data.
+
+# Returns
+- A tuple containing:
+  - `img_dat::Array{Float64}`: The filtered reflectance data for the specified line and
+  good bands. If no valid data exists, this will be `nothing`.
+  - `unc_dat::Array{Float64}`: The uncertainty data, filtered similarly. If no uncertainty
+  data is loaded or valid, this will be `nothing`.
+  - `good_data`: A boolean array indicating which pixels contain valid reflectance data.
+"""
+function load_line(reflectance_file::String, reflectance_uncertainty_file::String,
+    line::Int64, good_bands::Array{Bool}, refl_nodata::Float64)
+
+    reflectance_dataset = ArchGDAL.read(reflectance_file, alloweddrivers=["ENVI"])
+    img_dat = convert(
+        Array{Float64},
+        ArchGDAL.readraster(reflectance_file, alloweddrivers=["ENVI"])[:, line, :]
+    )
+    img_dat = img_dat[:, good_bands]
+    good_data = .!all(img_dat .== refl_nodata, dims=2)[:, 1]
+    img_dat = img_dat[good_data, :]
+
+    if sum(good_data) >= 1
+        if reflectance_uncertainty_file != ""
+            unc_dat = convert(
+                Array{Float64},
+                ArchGDAL.readraster(
+                    reflectance_uncertainty_file, alloweddrivers=["ENVI"]
+                )[:, line, :]
+            )
+            unc_dat = unc_dat[:, good_bands]
+            unc_dat = unc_dat[good_data, :]
         else
-            return nothing, nothing, good_data
+            unc_dat = nothing
         end
+    else
+        return nothing, nothing, good_data
+    end
 
-        return img_dat, unc_dat, good_data
+    return img_dat, unc_dat, good_data
 end