API Documentation

INI method:

run_omniscape(path::String)

In-memory method:

run_omniscape(
    cfg::Dict{String, String}
    resistance::MissingArray{Number, 2};
    reclass_table = MissingArray{Float64, 2}(undef, 1, 2),
    source_strength = source_from_resistance(resistance, cfg, reclass_table),
    condition1 = MissingArray{Float64, 2}(undef, 1, 1),
    condition2 = MissingArray{Float64, 2}(undef, 1, 1),
    condition1_future = MissingArray{Float64, 2}(undef, 1, 1),
    condition2_future = MissingArray{Float64, 2}(undef, 1, 1),
    wkt = "",
    geotransform = [0.0, 1.0, 0.0, 0.0, 0.0, -1.0],
    write_outputs = false
)

Compute omnidirectional current flow. All array inputs for the in-memory method should be of type MissingArray{T, 2}, which is just an alias for Array{Union{Missing, T}, 2}. missing entries correspond to NoData pixels. If you are starting with an array with a numeric NoData value, use missingarray to convert it to a MissingArray.

Parameters

path: The path to an INI file containing run parameters. See the Settings and Options section of the User Guide for descriptions of the run parameters.

cfg: A dictionary of Omniscape run parameters. See the Settings and Options section of the User Guide for descriptions of the run parameters and their default values. The in-memory method of run_omniscape ignores the following keys: resistance_file, source_file, reclass_table, condition1_file, condition2_file, condition1_future_file, and condition2_future_file. These all specify file paths, so they do not apply to the in-memory method of run_omniscape.

resistance: A 2D, north-oriented array of resistance values. Use missing for NoData (infinite resistance). resistance cannot contain zeros or negative values.

Keyword Arguments

reclass_table: A two column array. The first column contains the original resistance values in the resistance surface, and the second column specifies what those values should be changed to. You can reclassify values to missing to replace them with infinite resistance (NoData).

source_strength: A 2D, north-oriented array (with size equal to size(resistance)) of source strength values. source_strength is only required if source_from_resistance in cfg is set to "false" (the default value).

condition1: Optional. Required if conditional incfg is set to "true". A 2D, north-oriented array (with size equal to size(resistance)). See Climate Connectivity and Conditional Connectivity Options for more information.

condition2: Optional. Required if conditional incfg is set to "true" and n_conditions in cfg is set to "2". A 2D, north-oriented array (with size equal to size(resistance)). See Climate Connectivity and Conditional Connectivity Options for more information.

condition1_future: Optional. Required if conditional in cfg is set to "true" and compare_to_future in cfg is set to "1" or "both". A 2D, north-oriented array (with size equal to size(resistance)). See Climate Connectivity and Conditional Connectivity Options for more information.

condition2_future: Optional. A 2D, north-oriented array (with size equal to size(resistance)). See Climate Connectivity and Conditional Connectivity Options for more information. Required if conditional incfg is set to "true", n_conditions in cfg is set to "2", and compare_to_future in cfg is set to "2" or "both".

wkt: Optionally specify a Well Known Text representation of the projection used for your spatial data inputs. Only used if Omniscape writes raster outputs to disk.

geotransform: In addition to wkt, optionally specify a geotransform. The geotransform is a 6-element vector with elements as follows for a north up oriented image: [<x coord of upper left orner>, <pixel width>, <row rotation (typically 0)>, <y coord of upper left corner>, <column rotation (typically 0)>, <pixel height (negative number)>]. Only used when writing raster outputs to disk.

write_outputs: Boolean specifying if outputs should be written to disk. Defaults to false. If true, cfg must contain a value for the project_name key.

missingarray(A::Array{T, N}, T::DataType, nodata::Number)

This function converts an array to a MissingArray and replaces nodata values with missing in the output. MissingArray{T, N} is an alias for Array{Union{T, Missing}, N}. This function can be used to prepare inputs for run_omniscape.

Parameters

A: The array to convert.

T: The data type for the output (e.g. Float64 or Float32).

nodata: The numeric value to be replaced by missing in the result.

missing_array_to_array(A::MissingArray{T, N}, nodata::Number)

This function converts an array of type MissingArray to a numeric array and replaces missing entries with nodata. MissingArray{T, N} is an alias for Array{Union{T, Missing}, N}.

Parameters

A: The array to convert.

nodata: The numeric value with which missing values will be replaced in the result.