diff --git a/dev/404.html b/dev/404.html index cb12e9e..20ae255 100644 --- a/dev/404.html +++ b/dev/404.html @@ -5,17 +5,17 @@ 404 | ReefGuideAPI.jl - - + + - +
- + \ No newline at end of file diff --git a/dev/api.html b/dev/api.html index 575e3d2..ceebd63 100644 --- a/dev/api.html +++ b/dev/api.html @@ -5,21 +5,25 @@ API | ReefGuideAPI.jl - - + + - + - - - + + + -
ReefGuideAPI.jl

Appearance

API ​

ReefGuideAPI._cache_location Method
julia
_cache_location(config::Dict)::String

Retrieve cache location for geotiffs.

source

ReefGuideAPI._lon_lat_to_tile Method
julia
_lon_lat_to_tile(zoom, lon, lat)

Identify the corresponding tile coordinates for a given lon/lat.

Returns

x and y tile coordinates

source

ReefGuideAPI._tile_bounds Method
julia
_tile_bounds(z::T, x::T, y::T) where {T<:Int64}

Obtain lon/lat bounds of a requested tile.

Returns

West, East, North South (min lon, max lon, lat max, lat min)

source

ReefGuideAPI._tile_to_lon_lat Method
julia
_tile_to_lon_lat(z::T, x::T, y::T) where {T<:Int64}

Obtain lon/lat of top-left corner of a requested tile.

Returns

lon, lat

source

ReefGuideAPI.adjusted_nearest Method
julia
adjusted_nearest(rst::Raster, z::Int, x::Int, y::Int, tile_size::Tuple{Int,Int}, orig_rst_size::Tuple{Int,Int})::Matrix

Resample a raster using nearest neighbor interpolation when the tile includes area outside where data exists (e.g., viewing the globe where the data may appear in a small corner of the tile). This approach attempts to account for planetary curvature while still maintaining some performance.

Arguments

  • rst: The input raster to be resampled.

  • z: Tile zoom level requested.

  • x: x coordinate for requested tile.

  • y: y coordinate for the requested tile.

  • tile_size: The desired dimensions of the tile (long, lat).

Returns

Matrix with the resampled data.

source

ReefGuideAPI.apply_criteria_thresholds Method
julia
apply_criteria_thresholds(criteria_stack::RasterStack, lookup::DataFrame, ruleset::Vector{CriteriaBounds{Function}})::Raster
+    
ReefGuideAPI.jl
Appearance
API ​
ReefGuideAPI._cache_location Method
julia
_cache_location(config::Dict)::String
Retrieve cache location for geotiffs.
source
ReefGuideAPI._lon_lat_to_tile Method
julia
_lon_lat_to_tile(zoom, lon, lat)
Identify the corresponding tile coordinates for a given lon/lat.
Returns
x and y tile coordinates
source
ReefGuideAPI._tile_bounds Method
julia
_tile_bounds(z::T, x::T, y::T) where {T<:Int64}
Obtain lon/lat bounds of a requested tile.
Returns
West, East, North South (min lon, max lon, lat max, lat min)
source
ReefGuideAPI._tile_to_lon_lat Method
julia
_tile_to_lon_lat(z::T, x::T, y::T) where {T<:Int64}
Obtain lon/lat of top-left corner of a requested tile.
Returns
lon, lat
source
ReefGuideAPI._write_cog Method
julia
_write_cog(file_path::String, data::Raster, config::Dict)::Nothing
Write out a COG using common options.
Arguments
  • file_path : Path to write data out to
  • data : Raster data to write out
source
ReefGuideAPI.adjusted_nearest Method
julia
adjusted_nearest(rst::Raster, z::Int, x::Int, y::Int, tile_size::Tuple{Int,Int}, orig_rst_size::Tuple{Int,Int})::Matrix
Resample a raster using nearest neighbor interpolation when the tile includes area outside where data exists (e.g., viewing the globe where the data may appear in a small corner of the tile). This approach attempts to account for planetary curvature while still maintaining some performance.
Arguments
  • rst: The input raster to be resampled.
  • z: Tile zoom level requested.
  • x: x coordinate for requested tile.
  • y: y coordinate for the requested tile.
  • tile_size: The desired dimensions of the tile (long, lat).
Returns
Matrix with the resampled data.
source
ReefGuideAPI.apply_criteria_lookup Method
julia
apply_criteria_lookup(
+    reg_criteria,
+    rtype::Symbol,
+    ruleset::Vector{CriteriaBounds{Function}}
+)
Filter lookup table by applying user defined ruleset criteria.
Arguments
  • reg_criteria : RegionalCriteria containing valid_rtype lookup table for filtering.
  • rtype : Flats or slope category for assessment.
  • ruleset : User defined ruleset for upper and lower bounds.
Returns
Filtered lookup table containing points that meet all criteria in ruleset.
source
ReefGuideAPI.apply_criteria_thresholds Method
julia
apply_criteria_thresholds(criteria_stack::RasterStack, lookup::DataFrame, ruleset::Vector{CriteriaBounds{Function}})::Raster
 apply_criteria_thresholds(criteria_stack::RasterStack, lookup::DataFrame, ruleset::Dict)::Raster
-apply_criteria_thresholds(criteria_stack::RasterStack, lookup::DataFrame, ruleset::NamedTuple)::Raster
Apply thresholds for each criteria.
Arguments
  • criteria_stack : RasterStack of criteria data for a given region
  • lookup : Lookup dataframe for the region
  • ruleset : A set of CriteriaBounds, Dictionary or NamedTuple indicating a mapping of criteria names to their lower and upper thresholds.
Returns
BitMatrix indicating locations within desired thresholds
source
ReefGuideAPI.assess_reef_site Method
julia
assess_reef_site(
+apply_criteria_thresholds(criteria_stack::RasterStack, lookup::DataFrame, ruleset::NamedTuple)::Raster
Apply thresholds for each criteria.
Arguments
  • criteria_stack : RasterStack of criteria data for a given region
  • lookup : Lookup dataframe for the region
  • ruleset : A set of CriteriaBounds, Dictionary or NamedTuple indicating a mapping of criteria names to their lower and upper thresholds.
Returns
BitMatrix indicating locations within desired thresholds
source
ReefGuideAPI.assess_reef_site Method
julia
assess_reef_site(
     rel_pix::DataFrame,
     geom::GI.Wrappers.Polygon,
     max_count::Float64,
@@ -28,20 +32,35 @@
     start_rot::Float64=0.0,
     n_per_side::Int64=2,
     surr_threshold::Float64=0.33
-)::Tuple{Float64,Int64,GI.Wrappers.Polygon,Int64}
Assesses the rotations of a search box geom for their suitability score (calculated as the proportion of pixels that meet all specified criteria thresholds). Search box rotation steps are returned so that the start_rot angle is 0, rotations anti-clockwise are negative and rotations clockwise are positive.
Arguments
  • rel_pix : DataFrame containing the point data for pixels that are within maxmimum user search box dimensions from a pixel.
  • geom : Starting search box for assessment.
  • max_count : The maximum number of pixels that can intersect the search box (used to standardise scores between 0 and 1).
  • target_crs : Coordinate Reference System used for analysis vector and raster data.
  • degree_step : Step to vary the search box rotations.
  • start_rot : Starting angle rotation that aligns the box with the closest reef edge.
  • n_per_side : Number of rotations to perform around the starting search box angle.
  • surr_threshold : Suitability threshold, below which sites are excluded from result sets.
Returns
  • Highest score
  • Highest scoring rotation step
  • Highest scoring polygon
  • Quality control flag for site, indicating if surr_threshold was met in the highest scoring rotation.
source
ReefGuideAPI.assess_reef_site Method
julia
assess_reef_site(
+)::Tuple{Float64,Int64,GI.Wrappers.Polygon,Int64}
Assesses the rotations of a search box geom for their suitability score (calculated as the proportion of pixels that meet all specified criteria thresholds). Search box rotation steps are returned so that the start_rot angle is 0, rotations anti-clockwise are negative and rotations clockwise are positive.
Arguments
  • rel_pix : DataFrame containing the point data for pixels that are within maxmimum user search box dimensions from a pixel.
  • geom : Starting search box for assessment.
  • max_count : The maximum number of pixels that can intersect the search box (used to standardise scores between 0 and 1).
  • target_crs : Coordinate Reference System used for analysis vector and raster data.
  • degree_step : Step to vary the search box rotations.
  • start_rot : Starting angle rotation that aligns the box with the closest reef edge.
  • n_per_side : Number of rotations to perform around the starting search box angle.
  • surr_threshold : Suitability threshold, below which sites are excluded from result sets.
Returns
  • Highest score
  • Highest scoring rotation step
  • Highest scoring polygon
  • Quality control flag for site, indicating if surr_threshold was met in the highest scoring rotation.
source
ReefGuideAPI.assess_reef_site Method
julia
assess_reef_site(
     rst::Union{Raster,RasterStack},
     geom::GI.Wrappers.Polygon,
     ruleset::Dict{Symbol,Function};
     degree_step::Float64=15.0,
     start_rot::Float64=0.0,
     n_per_side::Int64=1
-)::Tuple{Float64,Int64,GI.Wrappers.Polygon}
Assess given reef site for it's suitability score at different specified rotations around the initial reef-edge rotation.
Arguments
  • rst : Raster or RasterStack object used to assess site suitability.
  • geom : Initial site polygon with no rotation applied.
  • ruleset : Criteria ruleset to apply to rst pixels when assessing which pixels are suitable.
  • degree_step : Degree value to vary each rotation by. Default = 15 degrees.
  • start_rot : Initial rotation used to align the site polygon with the nearest reef edge. Default = 0 degrees.
  • n_per_side : Number of times to rotate polygon on each side (clockwise and anticlockwise). Default = 2 rotations on each side.
Returns
  • Highest score identified with rotating polygons.
  • The index of the highest scoring rotation.
  • The polygon with the highest score out of the assessed rotated polygons.
source
ReefGuideAPI.closest_reef_edge Method
julia
closest_reef_edge(
+)::Tuple{Float64,Int64,GI.Wrappers.Polygon}
Assess given reef site for it's suitability score at different specified rotations around the initial reef-edge rotation.
Arguments
  • rst : Raster of suitability scores.
  • geom : Initial site polygon with no rotation applied.
  • ruleset : Criteria ruleset to apply to rst pixels when assessing which pixels are suitable.
  • degree_step : Degree value to vary each rotation by. Default = 15 degrees.
  • start_rot : Initial rotation used to align the site polygon with the nearest reef edge. Default = 0 degrees.
  • n_per_side : Number of times to rotate polygon on each side (clockwise and anticlockwise). Default = 2 rotations on each side.
Returns
  • Highest score identified with rotating polygons.
  • The index of the highest scoring rotation.
  • The polygon with the highest score out of the assessed rotated polygons.
source
ReefGuideAPI.assess_region Method
julia
assess_region(reg_assess_data, reg, qp, rtype)
Perform raster suitability assessment based on user defined criteria.
Arguments
  • reg_assess_data : Dictionary containing the regional data paths, reef outlines and full region names.
  • reg : Name of the region being assessed (format Cairns-Cooktown rather than Cairns/Cooktown Management Area).
  • qp : Dict containing bounds for each variable being filtered.
  • rtype : Type of zone to assess (flats or slopes).
Returns
GeoTiff file of surrounding hectare suitability (1-100%) based on the criteria bounds input by a user.
source
ReefGuideAPI.assess_sites Method
julia
assess_sites(
+    reg_assess_data::OrderedDict,
+    reg::String,
+    rtype::String,
+    pixel_criteria::Dict,
+    site_criteria::Dict,
+    assess_locs::Raster
+)
Arguments
  • reg_assess_data : Regional assessment data
  • reg : Short region name
  • rtype : Slopes or Flats assessment type
  • pixel_criteria : parameters to assess specific locations with
  • site_criteria : parameters to assess sites based on their polygonal representation
  • assess_locs : Raster of suitability scores for each valid pixel
Returns
GeoDataFrame of all potential sites
source
ReefGuideAPI.buffer_simplify Method
julia
buffer_simplify(
+    gdf::DataFrame;
+    number_verts::Int64=30,
+    buffer_dist_m::Int64=40
+)::Vector{GeoInterface.Wrappers.WrapperGeometry}
Simplify and buffer the polygons in a GeoDataFrame to account for uncertainty and inaccuracies in the reef outlines.
Arguments
  • gdf : GeoDataFrame containing the reef polygons in gdf.geometry.
  • number_verts : Number of vertices to simplify the reefs to. Default is 30 vertices.
  • buffer_dist_m : Buffering distance in meters to account for innacuracies in reef outlines. Default distance is 40m.
Returns
Vector containing buffered and simplified reef polygons
source
ReefGuideAPI.cache_filename Method
julia
cache_filename(qp::Dict, config::Dict, suffix::String, ext::String)
Generate a filename for a cache.
Arguments
  • qp : Query parameters to hash
  • config : app configuration (to extract cache parent directory from)
  • suffix : a suffix to use in the filename (pass "" if none required)
  • ext : file extension to use
source
ReefGuideAPI.closest_reef_edge Method
julia
closest_reef_edge(
     pixel::GeometryBasics.Point{2, Float64},
     reef_lines::Vector{GeometryBasics.Line{2, Float64}}
-)::Vector{Tuple{Float64, Float64}}
Find the nearest line in reef_lines to a point pixel.
Arguments
  • pixel : Target point geometry.
  • reef_lines : Vector containing lines for comparison.
Returns
Coordinates of the reef edge line that is closest to the target pixel. Returned in Tuples.
source
ReefGuideAPI.create_bbox Method
julia
create_bbox(xs::Tuple, ys::Tuple)::Vector{Tuple{Float64, Float64}}
Create bounding box from x and y coordinates
Returns
Bounding box coordinates in order of top left, top right, bottom right, bottom left, top left.
source
ReefGuideAPI.criteria_middleware Method
julia
criteria_middleware(handle)
Creates middleware that parses a criteria query before reaching an endpoint
Example
https://somewhere:8000/suitability/assess/region-name/reeftype?criteria_names=Depth,Slope&lb=-9.0,0.0&ub=-2.0,40
source
ReefGuideAPI.degrees_to_meters Method
julia
degrees_to_meters(x, lat)
Convert degrees to meters at target latitude.
source
ReefGuideAPI.filter_distances Method
julia
filter_distances(
+)::Vector{Tuple{Float64, Float64}}
Find the nearest line in reef_lines to a point pixel.
Arguments
  • pixel : Target point geometry.
  • reef_lines : Vector containing lines for comparison.
Returns
Coordinates of the reef edge line that is closest to the target pixel. Returned in Tuples.
source
ReefGuideAPI.create_bbox Method
julia
create_bbox(xs::Tuple, ys::Tuple)::Vector{Tuple{Float64, Float64}}
Create bounding box from x and y coordinates
Returns
Bounding box coordinates in order of top left, top right, bottom right, bottom left, top left.
source
ReefGuideAPI.criteria_middleware Method
julia
criteria_middleware(handle)
Creates middleware that parses a criteria query before reaching an endpoint
Example
https://somewhere:8000/suitability/assess/region-name/reeftype?criteria_names=Depth,Slope&lb=-9.0,0.0&ub=-2.0,40
source
ReefGuideAPI.degrees_to_meters Method
julia
degrees_to_meters(x, lat)
Convert degrees to meters at target latitude.
source
ReefGuideAPI.filter_distances Method
julia
filter_distances(
     target_rast::Raster,
     dist_buffer
-)::Raster
Apply a mask to exclude pixels that are outside the indicated distance buffer(s).
target_rast and the dist_buffer should be in the same CRS (e.g., EPSG:7844 / GDA2020).
Arguments
  • target_rast : Raster of suitable pixels (Bool) to filter pixels from.
  • dist_buffer : Buffer geometry to use as the mask.
Returns
  • Masked boolean raster indicating pixels that are within the target distance.
source
ReefGuideAPI.filter_far_polygons Method
julia
filter_far_polygons(gdf::DataFrame, pixel::GIWrap.Point, lat::Float64, dist::Union{Int64,Float64})::BitVector
Filter out reefs that are > dist (meters) from the target pixel (currently dist is hardcoded in initial_search_rotation()).
source
ReefGuideAPI.filter_sites Method
julia
filter_sites(res_df::DataFrame)::DataFrame
Filter out sites where the qc_flag indicates a suitabiltiy < surr_threshold in searching. Where site polygons are overlapping, keep only the highest scoring site polygon.
Arguments
  • res_df : Results DataFrame containing potential site polygons (output from identify_potential_sites() or identify_potential_sites_edges()).
Returns
DataFrame containing only the highest scoring sites where site polygons intersect, and containing only sites with scores greater than the surr_threshold specified in identify_potential_sites_edges() (default=0.33).
source
ReefGuideAPI.find_horizontal Method
julia
find_horizontal(geom::GI.Wrappers.Polygon)::Vector{Tuple{Float64,Float64}, Tuple{Float64,Float64}}
Find a horizontal line if one exists within a geometry.
Returns
Vector containing tuples of coordinates for a horizontal line found within geom.
source
ReefGuideAPI.from_zero Method
julia
from_zero(v::Vector{Tuple{Float64,Float64}})::Vector{Tuple{Float64, Float64}}
Translates Vector of points v to begin from (0, 0), retaining direction and length.
Argument
  • v : Vector of point coordinates (Tuple{Float64, Float64}).
source
ReefGuideAPI.generate_criteria_mask! Method
julia
generate_criteria_mask!(fn::String, rst_stack::RasterStack, lookup::DataFrame, ruleset::Vector{CriteriaBounds{Function}})
Generate mask file for a given region and reef type (slopes or flats) according to thresholds applied to a set of criteria.
Notes
  • Zeros indicate locations to mask out.
  • Ones indicate locations to keep.
Arguments
  • fn : File to write geotiff to
  • reg_criteria : RegionalCriteria to assess
  • rtype : reef type to assess (:slopes or :flats)
  • crit_map : List of criteria thresholds to apply (see apply_criteria_thresholds())
Returns
Nothing
source
ReefGuideAPI.get_points Method
julia
get_points(geom)
Helper method to retrieve points for a geometry.
source
ReefGuideAPI.identify_potential_sites_edges Method
julia
identify_potential_sites_edges(
+)::Raster
Apply a mask to exclude pixels that are outside the indicated distance buffer(s).
target_rast and the dist_buffer should be in the same CRS (e.g., EPSG:7844 / GDA2020).
Arguments
  • target_rast : Raster of suitable pixels (Bool) to filter pixels from.
  • dist_buffer : Buffer geometry to use as the mask.
Returns
  • Masked boolean raster indicating pixels that are within the target distance.
source
ReefGuideAPI.filter_distances Method
julia
filter_distances(
+    target_rast::Raster,
+    gdf::DataFrame,
+    dist_nm
+)::Raster
Exclude pixels in target_rast that are beyond dist_nm (nautical miles) from a geometry in gdf. target_rast and gdf should be in the same CRS (EPSG:7844 / GDA2020 for GBR-reef-guidance-assessment).
Arguments
  • target_rast : Boolean raster of suitable pixels to filter.
  • gdf : DataFrame with geometry column that contains vector objects of interest.
  • dist_nm : Filtering distance from geometry object in nautical miles.
Returns
  • tmp_areas : Raster of filtered pixels containing only pixels within target distance
from a geometry centroid.
source
ReefGuideAPI.filter_far_polygons Method
julia
filter_far_polygons(gdf::DataFrame, pixel::GIWrap.Point, lat::Float64, dist::Union{Int64,Float64})::BitVector
Filter out reefs that are > dist (meters) from the target pixel (currently dist is hardcoded in initial_search_rotation()).
source
ReefGuideAPI.filter_sites Method
julia
filter_sites(res_df::DataFrame)::DataFrame
Filter out sites where the qc_flag indicates a suitabiltiy < surr_threshold in searching. Where site polygons are overlapping, keep only the highest scoring site polygon.
Arguments
  • res_df : Results DataFrame containing potential site polygons (output from identify_potential_sites() or identify_edge_aligned_sites()).
Returns
DataFrame containing only the highest scoring sites where site polygons intersect, and containing only sites with scores greater than the surr_threshold specified in identify_edge_aligned_sites() (default=0.33).
source
ReefGuideAPI.find_horizontal Method
julia
find_horizontal(geom::GI.Wrappers.Polygon)::Vector{Tuple{Float64,Float64}, Tuple{Float64,Float64}}
Find a horizontal line if one exists within a geometry.
Returns
Vector containing tuples of coordinates for a horizontal line found within geom.
source
ReefGuideAPI.from_zero Method
julia
from_zero(v::Vector{Tuple{Float64,Float64}})::Vector{Tuple{Float64, Float64}}
Translates Vector of points v to begin from (0, 0), retaining direction and length.
Argument
  • v : Vector of point coordinates (Tuple{Float64, Float64}).
source
ReefGuideAPI.generate_criteria_mask! Method
julia
generate_criteria_mask!(fn::String, rst_stack::RasterStack, lookup::DataFrame, ruleset::Vector{CriteriaBounds{Function}})
Generate mask file for a given region and reef type (slopes or flats) according to thresholds applied to a set of criteria.
Notes
  • Zeros indicate locations to mask out.
  • Ones indicate locations to keep.
Arguments
  • fn : File to write geotiff to
  • reg_criteria : RegionalCriteria to assess
  • rtype : reef type to assess (:slopes or :flats)
  • crit_map : List of criteria thresholds to apply (see apply_criteria_thresholds())
Returns
Nothing
source
ReefGuideAPI.get_points Method
julia
get_points(geom)
Helper method to retrieve points for a geometry.
source
ReefGuideAPI.identify_edge_aligned_sites Method
julia
identify_edge_aligned_sites(
     df::DataFrame,
     search_pixels::DataFrame,
     res::Float64,
@@ -54,7 +73,7 @@
     degree_step::Float64=15.0,
     n_rot_p_side::Int64=2,
     surr_threshold::Float64=0.33
-)::DataFrame
Identify the most suitable site polygons for each pixel in the search_pixels DataFrame. x_dist and y_dist are x and y lengths of the search polygon in meters. A buffer of the raster files' resolution is applied to the search box. And angle from a pixel to a reef edge is identified and used for searching with custom rotation parameters. Method is currently opperating for CRS in degrees units.
Arguments
  • df : DataFrame containing environmental variables for assessment.
  • search_pixels : DataFrame containing lon and lat columns for each pixel that is intended for analysis.
  • res : Resolution of the original raster pixels. Can by found via abs(step(dims(raster, X))).
  • gdf : GeoDataFrame containing the reef outlines used to align the search box edge.
  • x_dist : Length of horizontal side of search box (in meters).
  • y_dist : Length of vertical side of search box (in meters).
  • target_crs : CRS of the input Rasters. Using GeoFormatTypes.EPSG().
  • reef_lines : Vector containing reef outline segments created from polygons in gdf.geometry (Must be separate object to gdf rather than column).
  • region : Management region name in GBRMPA format - e.g. "Mackay/Capricorn Management Area"
  • degree_step : Degree to perform rotations around identified edge angle.
  • n_rot_p_side : Number of rotations to perform clockwise and anticlockwise around the identified edge angle. Default 2 rotations.
  • surr_threshold : Theshold used to skip searching where the proportion of suitable pixels is too low.
Returns
DataFrame containing highest score, rotation and polygon for each assessment at pixels in indices.
source
ReefGuideAPI.identify_potential_sites_edges Method
julia
identify_potential_sites_edges(
+)::DataFrame
Identify the most suitable site polygons for each pixel in the search_pixels DataFrame. x_dist and y_dist are x and y lengths of the search polygon in meters. A buffer of the raster files' resolution is applied to the search box. And angle from a pixel to a reef edge is identified and used for searching with custom rotation parameters. Method is currently opperating for CRS in degrees units.
Arguments
  • df : DataFrame containing environmental variables for assessment.
  • search_pixels : DataFrame containing lon and lat columns for each pixel that is intended for analysis.
  • res : Resolution of the original raster pixels. Can by found via abs(step(dims(raster, X))).
  • gdf : GeoDataFrame containing the reef outlines used to align the search box edge.
  • x_dist : Length of horizontal side of search box (in meters).
  • y_dist : Length of vertical side of search box (in meters).
  • target_crs : CRS of the input Rasters. Using GeoFormatTypes.EPSG().
  • reef_lines : Vector containing reef outline segments created from polygons in gdf.geometry (Must be separate object to gdf rather than column).
  • region : Region name, e.g. "Cairns-Cooktown" or "FarNorthern".
  • degree_step : Degree to perform rotations around identified edge angle.
  • n_rot_p_side : Number of rotations to perform clockwise and anticlockwise around the identified edge angle. Default 2 rotations.
  • surr_threshold : Theshold used to skip searching where the proportion of suitable pixels is too low.
Returns
DataFrame containing highest score, rotation and polygon for each assessment at pixels in indices.
source
ReefGuideAPI.identify_edge_aligned_sites Method
julia
identify_edge_aligned_sites(
     rst_stack::RasterStack,
     search_pixels::DataFrame,
     gdf::DataFrame,
@@ -65,31 +84,27 @@
     reef_lines::Vector{Vector{GeometryBasics.Line{2,Float64}}};
     degree_step::Float64=15.0,
     n_rot_per_side::Int64=2
-)::DataFrame
Identify the most suitable site polygons for each pixel in the search_pixels DataFrame. x_dist and y_dist are x and y lengths of the search polygon. A buffer of rst_stack resolution is applied to the search box. And angle from a pixel to a reef edge is identified and used for searching with custom rotation parameters.
Arguments
  • rst_stack : RasterStack containing environmental variables for assessment.
  • search_pixels : DataFrame containing lon and lat values for each pixel intended for
  • gdf : GeoDataFrame containing the reef outlines used to align the search box edge.
  • x_dist : Length of horizontal side of search box.
  • y_dist : Length of vertical side of search box.
  • target_crs : CRS of the input Rasters. Using GeoFormatTypes.EPSG().
  • region : Management region name in GBRMPA format - e.g. "Mackay/Capricorn Management Area"
  • reef_lines : Vector containing reef outline segments for each reef in gdf.geometry (Must be separate object to gdf rather than a column).
  • degree_step : Degree to perform rotations around identified edge angle.
  • n_rot_per_side : Number of rotations to perform clockwise and anticlockwise around the identified edge angle. Default 2 rotations.
Returns
DataFrame containing highest score, rotation and polygon for each assessment at pixels in indices.
source
ReefGuideAPI.identify_search_pixels Method
julia
identify_search_pixels(input_raster::Raster, criteria_function)::DataFrame
Identifies all pixels in an input raster that return true for the function criteria_function.
Arguments
  • input_raster : Raster containing pixels for the target region.
  • criteria_function : Function that returns a boolean value for each pixel in input_raster. Pixels that return true will be targetted in analysis.
Returns
DataFrame containing indices, lon and lat for each pixel that is intended for further analysis.
source
ReefGuideAPI.initial_search_box Method
julia
initial_search_box(
+)::DataFrame
Identify the most suitable site polygons for each pixel in the search_pixels DataFrame. x_dist and y_dist are x and y lengths of the search polygon. A buffer of rst_stack resolution is applied to the search box. And angle from a pixel to a reef edge is identified and used for searching with custom rotation parameters.
Arguments
  • rst_stack : RasterStack containing environmental variables for assessment.
  • search_pixels : DataFrame containing lon and lat values for each pixel intended for
  • gdf : GeoDataFrame containing the reef outlines used to align the search box edge.
  • x_dist : Length of horizontal side of search box.
  • y_dist : Length of vertical side of search box.
  • target_crs : CRS of the input Rasters. Using GeoFormatTypes.EPSG().
  • region : Management region name in GBRMPA format - e.g. "Mackay/Capricorn Management Area"
  • reef_lines : Vector containing reef outline segments for each reef in gdf.geometry (Must be separate object to gdf rather than a column).
  • degree_step : Degree to perform rotations around identified edge angle.
  • n_rot_per_side : Number of rotations to perform clockwise and anticlockwise around the identified edge angle. Default 2 rotations.
Returns
DataFrame containing highest score, rotation and polygon for each assessment at pixels in indices.
source
ReefGuideAPI.identify_search_pixels Method
julia
identify_search_pixels(input_raster::Raster, criteria_function)::DataFrame
Identifies all pixels in an input raster that return true for the function criteria_function.
Arguments
  • input_raster : Raster containing pixels for the target region.
  • criteria_function : Function that returns a boolean value for each pixel in input_raster. Pixels that return true will be targetted in analysis.
Returns
DataFrame containing indices, lon and lat for each pixel that is intended for further analysis.
source
ReefGuideAPI.initial_search_box Method
julia
initial_search_box(
     (lon::Float64, lat::Float64),
     x_dist::Union{Int64, Float64},
     y_dist::Union{Int64, Float64},
     target_crs::GeoFormatTypes.CoordinateReferenceSystemFormat,
     res::Float64
-)::GI.Wrappers.Polygon
Create an initial search box that is centered around the point (lon, lat) in target_crs, and is buffered by res distance.
Arguments
  • (lon, lat) : Longitude and latitude coordinates of the center target pixel.
  • x_dist : x (longitude) dimension length of initial search box.
  • y_dist : y (latitude) dimension length of initial search box.
  • target_crs : Target CRS of box to match input data types.
  • res : Buffer distance (resolution of input raster search data).
Returns
Initial search box geometry.
source
ReefGuideAPI.initial_search_rotation Method
julia
initial_search_rotation(
+)::GI.Wrappers.Polygon
Create an initial search box that is centered around the point (lon, lat) in target_crs, and is buffered by res distance.
Arguments
  • (lon, lat) : Longitude and latitude coordinates of the center target pixel.
  • x_dist : x (longitude) dimension length of initial search box.
  • y_dist : y (latitude) dimension length of initial search box.
  • target_crs : Target CRS of box to match input data types.
  • res : Buffer distance (resolution of input raster search data).
Returns
Initial search box geometry.
source
ReefGuideAPI.initial_search_rotation Method
julia
initial_search_rotation(
     pixel::GeometryBasics.Point{2, Float64},
     geom_buff::GI.Wrappers.Polygon,
     gdf::DataFrame,
     reef_outlines::Vector{Vector{GeometryBasics.Line{2, Float64}}};
     search_buffer::Union{Int64,Float64}=20000.0
-)::Float64
Identifies the closest edge to the target pixel/'geom_buff and returns the initial rotation angle required to match the edge line.
Arguments
  • pixel : Target point at the center of the search polygon.
  • geom_buff : Initial search box with zero rotation.
  • gdf : GeoDataFrame containing a geometry column used for pixel masking.
  • reef_outlines : Line segments for the outlines of each reef in gdf.
  • search_buffer : Distance to search from pixel to find closest reef.
source
ReefGuideAPI.line_angle Method
julia
line_angle(a::T, b::T)::Float64 where {T <: Vector{Tuple{Float64,Float64}}}
Calculate the angle between two lines.
Arguments
  • a : Line between point coordinates.
  • b : Line between point coordinates.
Returns
Angle between the two lines.
Examples
julia
line_angle([(0.0,5.0), (0.0,0.0)], from_zero(edge_line))
-line_angle([(0.0,5.0), (0.0,0.0)], [(1.0, 4.0), (7.0, 8.0)])
source
ReefGuideAPI.make_threshold_mask Method
julia
make_threshold_mask(reg::String, rtype::Symbol, crit_map)
Generate mask for a given region and reef type (slopes or flats) according to thresholds applied to a set of criteria.
Notes
  • Zeros indicate locations to mask out.
  • Ones indicate locations to keep.
Arguments
  • reg_criteria : RegionalCriteria to assess
  • rtype : reef type to assess (:slopes or :flats)
  • crit_map : List of criteria thresholds to apply (see apply_criteria_thresholds())
  • lons : Longitudinal extent (min and max, required when generating masks for tiles)
  • lats : Latitudinal extent (min and max, required when generating masks for tiles)
Returns
True/false mask indicating locations within desired thresholds.
source
ReefGuideAPI.meters_to_degrees Method
julia
meters_to_degrees(x, lat)
Convert meters to degrees at target latitude.
source
ReefGuideAPI.move_geom Method
julia
move_geom(geom, new_centroid::Tuple)
Move a geom to a new centroid.
Arguments
  • geom : geometry to move
  • new_centroid : Centroid given in (lon, lat).
source
ReefGuideAPI.n_gdal_threads Method
julia
n_gdal_threads(config::Dict)::String
Retrieve the configured number of threads to use when writing COGs with GDAL.
source
ReefGuideAPI.output_geojson Method
julia
output_geojson(
-    df::DataFrame,
-    region::String,
-    output_dir::String
-)::Nothing
Writes out GeoJSON file to a target directory. Output file will be located at location: "output_dir/output_sites_region.geojson"
Arguments
  • df : DataFrame intended for writing to geojson file.
  • region : Region name for labelling output file.
  • output_dir : Directory to write geojson file to.
source
ReefGuideAPI.parse_criteria_query Method
julia
parse_criteria_query(qp)::Tuple
Parse criteria values from request query.
Queries should take the form of: Depth=-9.0:0.0&Slope=0.0:40.0&Rugosity=0.0:0.0
Arguments
  • qp : Parsed query string from request.
Returns
Tuple of criteria names, lower bounds, upper bounds
source
ReefGuideAPI.polygon_to_lines Method
julia
polygon_to_lines(
+)::Float64
Identifies the closest edge to the target pixel/'geom_buff and returns the initial rotation angle required to match the edge line.
Arguments
  • pixel : Target point at the center of the search polygon.
  • geom_buff : Initial search box with zero rotation.
  • gdf : GeoDataFrame containing a geometry column used for pixel masking.
  • reef_outlines : Line segments for the outlines of each reef in gdf.
  • search_buffer : Distance to search from pixel to find closest reef.
source
ReefGuideAPI.initialize_regional_data_cache Method
julia
initialize_regional_data_cache(reef_data_path::String, reg_cache_fn::String)
Create initial regional data store with data from reef_data_path, excluding geospatial data and save to reg_cache_fn path.
source
ReefGuideAPI.line_angle Method
julia
line_angle(a::T, b::T)::Float64 where {T <: Vector{Tuple{Float64,Float64}}}
Calculate the angle between two lines.
Arguments
  • a : Line between point coordinates.
  • b : Line between point coordinates.
Returns
Angle between the two lines.
Examples
julia
line_angle([(0.0,5.0), (0.0,0.0)], from_zero(edge_line))
+line_angle([(0.0,5.0), (0.0,0.0)], [(1.0, 4.0), (7.0, 8.0)])
source
ReefGuideAPI.mask_region Method
julia
mask_region(reg_assess_data, reg, qp, rtype)
Arguments
  • reg_assess_data : Regional assessment data
  • reg : The region name to assess
  • qp : query parameters
  • rtype : region type (one of :slopes or :flats)
Returns
Raster of region with locations that meet criteria masked.
source
ReefGuideAPI.meters_to_degrees Method
julia
meters_to_degrees(x, lat)
Convert meters to degrees at target latitude.
source
ReefGuideAPI.move_geom Method
julia
move_geom(geom, new_centroid::Tuple)
Move a geom to a new centroid.
Arguments
  • geom : geometry to move
  • new_centroid : Centroid given in (lon, lat).
source
ReefGuideAPI.n_gdal_threads Method
julia
n_gdal_threads(config::Dict)::String
Retrieve the configured number of threads to use when writing COGs with GDAL.
source
ReefGuideAPI.output_geojson Method
julia
output_geojson(destination_path::String, df::DataFrame)::Nothing
Writes out GeoJSON file to a target directory. Output file will be located at location: destination_path.
Arguments
  • destination_path : File path to write geojson file to.
  • df : DataFrame intended for writing to geojson file.
source
ReefGuideAPI.parse_criteria_query Method
julia
parse_criteria_query(qp)::Tuple
Parse criteria values from request query.
Queries should take the form of: Depth=-9.0:0.0&Slope=0.0:40.0&Rugosity=0.0:0.0
Arguments
  • qp : Parsed query string from request.
Returns
Tuple of criteria names, lower bounds, upper bounds
source
ReefGuideAPI.polygon_to_lines Method
julia
polygon_to_lines(
     polygon::Union{Vector{T},T,GIWrap.MultiPolygon}
-) where {T<:GIWrap.Polygon}
Extract the individual lines between vertices that make up the outline of a polygon.
Returns
Vector of GeometryBasics.Line{2, Float64} with one line for each adjacent vertex pair in polygon.
source
ReefGuideAPI.port_buffer_mask Method
julia
port_buffer_mask(gdf::DataFrame, dist::Float64; unit::String="NM")
Create a masking buffer around indicated port locations.
Arguments
  • gdf : GeoDataFrame of port locations (given as long/lat points)
  • dist : distance from port in degrees (deg), kilometers (km), or nautical miles (NM; default)
  • unit : unit dist is in
source
ReefGuideAPI.remove_rugosity Method
julia
remove_rugosity(reg, criteria, lbs, ubs)
Remove rugosity layer from consideration if region is not Townsville. Rugosity data currently only exists for the Townsville region.
source
ReefGuideAPI.rotate_geom Method
julia
rotate_geom(
+) where {T<:GIWrap.Polygon}
Extract the individual lines between vertices that make up the outline of a polygon.
Returns
Vector of GeometryBasics.Line{2, Float64} with one line for each adjacent vertex pair in polygon.
source
ReefGuideAPI.port_buffer_mask Method
julia
port_buffer_mask(gdf::DataFrame, dist::Float64; unit::String="NM")
Create a masking buffer around indicated port locations.
Arguments
  • gdf : GeoDataFrame of port locations (given as long/lat points)
  • dist : distance from port in degrees (deg), kilometers (km), or nautical miles (NM; default)
  • unit : unit dist is in
source
ReefGuideAPI.proportion_suitable Method
julia
proportion_suitable(subsection::BitMatrix, square_offset::Tuple=(-4,5))::Matrix{Int16}
Calculate the the proportion of the subsection that is suitable for deployments. The subsection is the surrounding a rough hectare area centred on each cell of a raster marked as being suitable according to user-selected criteria.
Cells on the edges of a raster object are assessed using a smaller surrounding area, rather than shifting the window inward. In usual applications, there will be no target pixel close to the edge due to the use of buffer areas.
Arguments
  • x : Matrix of boolean pixels after filtering with user criteria.
  • square_offset : The number of pixels +/- around a center "target" pixel to assess as the moving window. Defaults to (-4, 5). Assuming a 10m² pixel, the default square_offset resolves to a one hectare area.
Returns
Matrix of values 0 - 100 indicating the percentage of the area around the target pixel that meet suitability criteria.
source
ReefGuideAPI.remove_rugosity Method
julia
remove_rugosity(reg, criteria, lbs, ubs)
Remove rugosity layer from consideration if region is not Townsville. Rugosity data currently only exists for the Townsville region.
source
ReefGuideAPI.rotate_geom Method
julia
rotate_geom(
     geom,
     degrees::Float64,
     target_crs::GeoFormatTypes.CoordinateReferenceSystemFormat
-)
Rotate target geom by degrees rotation in clockwise direction. target_crs is applied to output geometry.
Returns
Rotated geometry.
source
ReefGuideAPI.rotate_polygon Method
Rotate the polygon by the given angle about its center.
source
ReefGuideAPI.setup_regional_data Method
julia
setup_regional_data(config::Dict)
Load regional data to act as an in-memory cache.
Arguments
  • config : Configuration settings, typically loaded from a TOML file.
  • reef_data_path : Path to pre-prepared reef data
Returns
OrderedDict of RegionalCriteria for each region.
source
ReefGuideAPI.tile_size Method
julia
tile_size(config::Dict)::Tuple
Retrieve the configured size of map tiles in pixels (width and height / lon and lat).
source
ReefGuideAPI.valid_lonlat_inds Method
julia
valid_lonlat_inds(data::DataFrame, criteria::Symbol, lb::T, ub::T) where {T}
Retrieve the indices of valid data for a region.
Arguments
  • data :
  • criteria :
  • lb :
  • ub :
Returns
Tuple{Vector{Int64}, Vector{Int64}}, of lon and lat indices.
source
ReefGuideAPI.valid_pixel_positions Method
julia
valid_pixel_positions(data::DataFrame, criteria::Symbol, lb::T, ub::T) where {T}
Obtain the pixel positions of valid data.
Intended for use in applications similar to ImageryLayer - client side pixel filter.
Arguments
  • data :
  • criteria :
  • lb : lower bound
  • ub : upper bound
source
ReefGuideAPI.warmup_cache Method
julia
warmup_cache(config_path::String)
Invokes warm up of regional data cache to reduce later spin up times.
source
ReefGuideAPI.within_thresholds Method
julia
within_thresholds(ctype::Val, data::Raster, lb::T, ub::T) where {T}
Apply in-bound constraints.
Notes
Why is this a simple one line function? Because we want to be able to cache results for each constraint type.
source

-    
+)

Rotate target geom by degrees rotation in clockwise direction. target_crs is applied to output geometry.

Returns

Rotated geometry.

source

ReefGuideAPI.rotate_polygon Method

Rotate the polygon by the given angle about its center.

source

ReefGuideAPI.setup_regional_data Method
julia
setup_regional_data(config::Dict)

Load regional data to act as an in-memory cache.

Arguments

  • config : Configuration settings, typically loaded from a TOML file.

  • reef_data_path : Path to pre-prepared reef data

Returns

OrderedDict of RegionalCriteria for each region.

source

ReefGuideAPI.threshold_mask Method
julia
threshold_mask(reg::String, rtype::Symbol, crit_map)

Generate mask for a given region and reef type (slopes or flats) according to thresholds applied to a set of criteria.

Notes

  • Zeros indicate locations to mask out.

  • Ones indicate locations to keep.

Arguments

  • reg_criteria : RegionalCriteria to assess

  • rtype : reef type to assess (:slopes or :flats)

  • crit_map : List of criteria thresholds to apply (see apply_criteria_thresholds())

  • lons : Longitudinal extent (min and max, required when generating masks for tiles)

  • lats : Latitudinal extent (min and max, required when generating masks for tiles)

Returns

True/false mask indicating locations within desired thresholds.

source

ReefGuideAPI.tile_size Method
julia
tile_size(config::Dict)::Tuple

Retrieve the configured size of map tiles in pixels (width and height / lon and lat).

source

ReefGuideAPI.valid_lonlat_inds Method
julia
valid_lonlat_inds(data::DataFrame, criteria::Symbol, lb::T, ub::T) where {T}

Retrieve the indices of valid data for a region.

Arguments

  • data :

  • criteria :

  • lb :

  • ub :

Returns

Tuple{Vector{Int64}, Vector{Int64}}, of lon and lat indices.

source

ReefGuideAPI.valid_pixel_positions Method
julia
valid_pixel_positions(data::DataFrame, criteria::Symbol, lb::T, ub::T) where {T}

Obtain the pixel positions of valid data.

Intended for use in applications similar to ImageryLayer - client side pixel filter.

Arguments

  • data :

  • criteria :

  • lb : lower bound

  • ub : upper bound

source

ReefGuideAPI.warmup_cache Method
julia
warmup_cache(config_path::String)

Invokes warm up of regional data cache to reduce later spin up times.

source

ReefGuideAPI.within_thresholds Method
julia
within_thresholds(ctype::Val, data::Raster, lb::T, ub::T) where {T}

Apply in-bound constraints.

Notes

Why is this a simple one line function? Because we want to be able to cache results for each constraint type.

source

+ \ No newline at end of file diff --git a/dev/assets/api.md.DYWJQ0KO.js b/dev/assets/api.md.DYWJQ0KO.js new file mode 100644 index 0000000..acd82d6 --- /dev/null +++ b/dev/assets/api.md.DYWJQ0KO.js @@ -0,0 +1,87 @@ +import{_ as l,c as p,j as i,a as e,G as t,a5 as n,B as r,o}from"./chunks/framework.CX_bWI7S.js";const ys=JSON.parse('{"title":"API","description":"","frontmatter":{},"headers":[],"relativePath":"api.md","filePath":"api.md","lastUpdated":null}'),h={name:"api.md"},d={class:"jldocstring custom-block",open:""},k={class:"jldocstring custom-block",open:""},g={class:"jldocstring custom-block",open:""},c={class:"jldocstring custom-block",open:""},u={class:"jldocstring custom-block",open:""},y={class:"jldocstring custom-block",open:""},E={class:"jldocstring custom-block",open:""},f={class:"jldocstring custom-block",open:""},F={class:"jldocstring custom-block",open:""},b={class:"jldocstring custom-block",open:""},m={class:"jldocstring custom-block",open:""},C={class:"jldocstring custom-block",open:""},A={class:"jldocstring custom-block",open:""},_={class:"jldocstring custom-block",open:""},j={class:"jldocstring custom-block",open:""},R={class:"jldocstring custom-block",open:""},I={class:"jldocstring custom-block",open:""},D={class:"jldocstring custom-block",open:""},v={class:"jldocstring custom-block",open:""},T={class:"jldocstring custom-block",open:""},B={class:"jldocstring custom-block",open:""},G={class:"jldocstring custom-block",open:""},x={class:"jldocstring custom-block",open:""},P={class:"jldocstring custom-block",open:""},M={class:"jldocstring custom-block",open:""},S={class:"jldocstring custom-block",open:""},L={class:"jldocstring custom-block",open:""},w={class:"jldocstring custom-block",open:""},O={class:"jldocstring custom-block",open:""},V={class:"jldocstring custom-block",open:""},q={class:"jldocstring custom-block",open:""},U={class:"jldocstring custom-block",open:""},z={class:"jldocstring custom-block",open:""},N={class:"jldocstring custom-block",open:""},W={class:"jldocstring custom-block",open:""},H={class:"jldocstring custom-block",open:""},$={class:"jldocstring custom-block",open:""},Q={class:"jldocstring custom-block",open:""},J={class:"jldocstring custom-block",open:""},Z={class:"jldocstring custom-block",open:""},X={class:"jldocstring custom-block",open:""},K={class:"jldocstring custom-block",open:""},Y={class:"jldocstring custom-block",open:""},ss={class:"jldocstring custom-block",open:""},is={class:"jldocstring custom-block",open:""},es={class:"jldocstring custom-block",open:""},as={class:"jldocstring custom-block",open:""},ts={class:"jldocstring custom-block",open:""},ns={class:"jldocstring custom-block",open:""},ls={class:"jldocstring custom-block",open:""},ps={class:"jldocstring custom-block",open:""},rs={class:"jldocstring custom-block",open:""};function os(hs,s,ds,ks,gs,cs){const a=r("Badge");return o(),p("div",null,[s[157]||(s[157]=i("h1",{id:"api",tabindex:"-1"},[e("API "),i("a",{class:"header-anchor",href:"#api","aria-label":'Permalink to "API"'},"​")],-1)),i("details",d,[i("summary",null,[s[0]||(s[0]=i("a",{id:"ReefGuideAPI._cache_location-Tuple{Dict}",href:"#ReefGuideAPI._cache_location-Tuple{Dict}"},[i("span",{class:"jlbinding"},"ReefGuideAPI._cache_location")],-1)),s[1]||(s[1]=e()),t(a,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),s[2]||(s[2]=n('
julia
_cache_location(config::Dict)::String

Retrieve cache location for geotiffs.

source

',3))]),i("details",k,[i("summary",null,[s[3]||(s[3]=i("a",{id:"ReefGuideAPI._lon_lat_to_tile-Tuple{Any, Any, Any}",href:"#ReefGuideAPI._lon_lat_to_tile-Tuple{Any, Any, Any}"},[i("span",{class:"jlbinding"},"ReefGuideAPI._lon_lat_to_tile")],-1)),s[4]||(s[4]=e()),t(a,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),s[5]||(s[5]=n('
julia
_lon_lat_to_tile(zoom, lon, lat)

Identify the corresponding tile coordinates for a given lon/lat.

Returns

x and y tile coordinates

source

',5))]),i("details",g,[i("summary",null,[s[6]||(s[6]=i("a",{id:"ReefGuideAPI._tile_bounds-Union{Tuple{T}, Tuple{T, T, T}} where T<:Int64",href:"#ReefGuideAPI._tile_bounds-Union{Tuple{T}, Tuple{T, T, T}} where T<:Int64"},[i("span",{class:"jlbinding"},"ReefGuideAPI._tile_bounds")],-1)),s[7]||(s[7]=e()),t(a,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),s[8]||(s[8]=n('
julia
_tile_bounds(z::T, x::T, y::T) where {T<:Int64}

Obtain lon/lat bounds of a requested tile.

Returns

West, East, North South (min lon, max lon, lat max, lat min)

source

',5))]),i("details",c,[i("summary",null,[s[9]||(s[9]=i("a",{id:"ReefGuideAPI._tile_to_lon_lat-Union{Tuple{T}, Tuple{T, T, T}} where T<:Int64",href:"#ReefGuideAPI._tile_to_lon_lat-Union{Tuple{T}, Tuple{T, T, T}} where T<:Int64"},[i("span",{class:"jlbinding"},"ReefGuideAPI._tile_to_lon_lat")],-1)),s[10]||(s[10]=e()),t(a,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),s[11]||(s[11]=n('
julia
_tile_to_lon_lat(z::T, x::T, y::T) where {T<:Int64}

Obtain lon/lat of top-left corner of a requested tile.

Returns

lon, lat

source

',5))]),i("details",u,[i("summary",null,[s[12]||(s[12]=i("a",{id:"ReefGuideAPI._write_cog-Tuple{String, Rasters.Raster, Dict}",href:"#ReefGuideAPI._write_cog-Tuple{String, Rasters.Raster, Dict}"},[i("span",{class:"jlbinding"},"ReefGuideAPI._write_cog")],-1)),s[13]||(s[13]=e()),t(a,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),s[14]||(s[14]=n('
julia
_write_cog(file_path::String, data::Raster, config::Dict)::Nothing

Write out a COG using common options.

Arguments

source

',5))]),i("details",y,[i("summary",null,[s[15]||(s[15]=i("a",{id:"ReefGuideAPI.adjusted_nearest-Tuple{Rasters.Raster, Int64, Int64, Int64, Tuple{Int64, Int64}}",href:"#ReefGuideAPI.adjusted_nearest-Tuple{Rasters.Raster, Int64, Int64, Int64, Tuple{Int64, Int64}}"},[i("span",{class:"jlbinding"},"ReefGuideAPI.adjusted_nearest")],-1)),s[16]||(s[16]=e()),t(a,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),s[17]||(s[17]=n('
julia
adjusted_nearest(rst::Raster, z::Int, x::Int, y::Int, tile_size::Tuple{Int,Int}, orig_rst_size::Tuple{Int,Int})::Matrix

Resample a raster using nearest neighbor interpolation when the tile includes area outside where data exists (e.g., viewing the globe where the data may appear in a small corner of the tile). This approach attempts to account for planetary curvature while still maintaining some performance.

Arguments

Returns

Matrix with the resampled data.

source

',7))]),i("details",E,[i("summary",null,[s[18]||(s[18]=i("a",{id:"ReefGuideAPI.apply_criteria_lookup-Tuple{RegionalCriteria, Symbol, Any}",href:"#ReefGuideAPI.apply_criteria_lookup-Tuple{RegionalCriteria, Symbol, Any}"},[i("span",{class:"jlbinding"},"ReefGuideAPI.apply_criteria_lookup")],-1)),s[19]||(s[19]=e()),t(a,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),s[20]||(s[20]=n(`
julia
apply_criteria_lookup(
+    reg_criteria,
+    rtype::Symbol,
+    ruleset::Vector{CriteriaBounds{Function}}
+)

Filter lookup table by applying user defined ruleset criteria.

Arguments

Returns

Filtered lookup table containing points that meet all criteria in ruleset.

source

`,7))]),i("details",f,[i("summary",null,[s[21]||(s[21]=i("a",{id:"ReefGuideAPI.apply_criteria_thresholds-Tuple{Rasters.RasterStack, DataFrames.DataFrame, Dict}",href:"#ReefGuideAPI.apply_criteria_thresholds-Tuple{Rasters.RasterStack, DataFrames.DataFrame, Dict}"},[i("span",{class:"jlbinding"},"ReefGuideAPI.apply_criteria_thresholds")],-1)),s[22]||(s[22]=e()),t(a,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),s[23]||(s[23]=n(`
julia
apply_criteria_thresholds(criteria_stack::RasterStack, lookup::DataFrame, ruleset::Vector{CriteriaBounds{Function}})::Raster
+apply_criteria_thresholds(criteria_stack::RasterStack, lookup::DataFrame, ruleset::Dict)::Raster
+apply_criteria_thresholds(criteria_stack::RasterStack, lookup::DataFrame, ruleset::NamedTuple)::Raster

Apply thresholds for each criteria.

Arguments

Returns

BitMatrix indicating locations within desired thresholds

source

`,7))]),i("details",F,[i("summary",null,[s[24]||(s[24]=i("a",{id:"ReefGuideAPI.assess_reef_site-Tuple{DataFrames.DataFrame, GeoInterface.Wrappers.Polygon, Float64, GeoFormatTypes.CoordinateReferenceSystemFormat}",href:"#ReefGuideAPI.assess_reef_site-Tuple{DataFrames.DataFrame, GeoInterface.Wrappers.Polygon, Float64, GeoFormatTypes.CoordinateReferenceSystemFormat}"},[i("span",{class:"jlbinding"},"ReefGuideAPI.assess_reef_site")],-1)),s[25]||(s[25]=e()),t(a,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),s[26]||(s[26]=n(`
julia
assess_reef_site(
+    rel_pix::DataFrame,
+    geom::GI.Wrappers.Polygon,
+    max_count::Float64,
+    target_crs::GeoFormatTypes.CoordinateReferenceSystemFormat;
+    degree_step::Float64=15.0,
+    start_rot::Float64=0.0,
+    n_per_side::Int64=2,
+    surr_threshold::Float64=0.33
+)::Tuple{Float64,Int64,GI.Wrappers.Polygon,Int64}

Assesses the rotations of a search box geom for their suitability score (calculated as the proportion of pixels that meet all specified criteria thresholds). Search box rotation steps are returned so that the start_rot angle is 0, rotations anti-clockwise are negative and rotations clockwise are positive.

Arguments

Returns

source

`,7))]),i("details",b,[i("summary",null,[s[27]||(s[27]=i("a",{id:"ReefGuideAPI.assess_reef_site-Tuple{Union{Rasters.Raster, Rasters.RasterStack}, GeoInterface.Wrappers.Polygon}",href:"#ReefGuideAPI.assess_reef_site-Tuple{Union{Rasters.Raster, Rasters.RasterStack}, GeoInterface.Wrappers.Polygon}"},[i("span",{class:"jlbinding"},"ReefGuideAPI.assess_reef_site")],-1)),s[28]||(s[28]=e()),t(a,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),s[29]||(s[29]=n(`
julia
assess_reef_site(
+    rst::Union{Raster,RasterStack},
+    geom::GI.Wrappers.Polygon,
+    ruleset::Dict{Symbol,Function};
+    degree_step::Float64=15.0,
+    start_rot::Float64=0.0,
+    n_per_side::Int64=1
+)::Tuple{Float64,Int64,GI.Wrappers.Polygon}

Assess given reef site for it's suitability score at different specified rotations around the initial reef-edge rotation.

Arguments

Returns

source

`,7))]),i("details",m,[i("summary",null,[s[30]||(s[30]=i("a",{id:"ReefGuideAPI.assess_region-NTuple{4, Any}",href:"#ReefGuideAPI.assess_region-NTuple{4, Any}"},[i("span",{class:"jlbinding"},"ReefGuideAPI.assess_region")],-1)),s[31]||(s[31]=e()),t(a,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),s[32]||(s[32]=n('
julia
assess_region(reg_assess_data, reg, qp, rtype)

Perform raster suitability assessment based on user defined criteria.

Arguments

Returns

GeoTiff file of surrounding hectare suitability (1-100%) based on the criteria bounds input by a user.

source

',7))]),i("details",C,[i("summary",null,[s[33]||(s[33]=i("a",{id:"ReefGuideAPI.assess_sites-Tuple{OrderedCollections.OrderedDict, String, String, Dict, Dict, Rasters.Raster}",href:"#ReefGuideAPI.assess_sites-Tuple{OrderedCollections.OrderedDict, String, String, Dict, Dict, Rasters.Raster}"},[i("span",{class:"jlbinding"},"ReefGuideAPI.assess_sites")],-1)),s[34]||(s[34]=e()),t(a,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),s[35]||(s[35]=n(`
julia
assess_sites(
+    reg_assess_data::OrderedDict,
+    reg::String,
+    rtype::String,
+    pixel_criteria::Dict,
+    site_criteria::Dict,
+    assess_locs::Raster
+)

Arguments

Returns

GeoDataFrame of all potential sites

source

`,6))]),i("details",A,[i("summary",null,[s[36]||(s[36]=i("a",{id:"ReefGuideAPI.buffer_simplify-Tuple{DataFrames.DataFrame}",href:"#ReefGuideAPI.buffer_simplify-Tuple{DataFrames.DataFrame}"},[i("span",{class:"jlbinding"},"ReefGuideAPI.buffer_simplify")],-1)),s[37]||(s[37]=e()),t(a,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),s[38]||(s[38]=n(`
julia
buffer_simplify(
+    gdf::DataFrame;
+    number_verts::Int64=30,
+    buffer_dist_m::Int64=40
+)::Vector{GeoInterface.Wrappers.WrapperGeometry}

Simplify and buffer the polygons in a GeoDataFrame to account for uncertainty and inaccuracies in the reef outlines.

Arguments

Returns

Vector containing buffered and simplified reef polygons

source

`,7))]),i("details",_,[i("summary",null,[s[39]||(s[39]=i("a",{id:"ReefGuideAPI.cache_filename-Tuple{Dict, Dict, String, String}",href:"#ReefGuideAPI.cache_filename-Tuple{Dict, Dict, String, String}"},[i("span",{class:"jlbinding"},"ReefGuideAPI.cache_filename")],-1)),s[40]||(s[40]=e()),t(a,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),s[41]||(s[41]=n('
julia
cache_filename(qp::Dict, config::Dict, suffix::String, ext::String)

Generate a filename for a cache.

Arguments

source

',5))]),i("details",j,[i("summary",null,[s[42]||(s[42]=i("a",{id:"ReefGuideAPI.closest_reef_edge-Tuple{GeometryBasics.Point{2, Float64}, Vector{GeometryBasics.Line{2, Float64}}}",href:"#ReefGuideAPI.closest_reef_edge-Tuple{GeometryBasics.Point{2, Float64}, Vector{GeometryBasics.Line{2, Float64}}}"},[i("span",{class:"jlbinding"},"ReefGuideAPI.closest_reef_edge")],-1)),s[43]||(s[43]=e()),t(a,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),s[44]||(s[44]=n(`
julia
closest_reef_edge(
+    pixel::GeometryBasics.Point{2, Float64},
+    reef_lines::Vector{GeometryBasics.Line{2, Float64}}
+)::Vector{Tuple{Float64, Float64}}

Find the nearest line in reef_lines to a point pixel.

Arguments

Returns

Coordinates of the reef edge line that is closest to the target pixel. Returned in Tuples.

source

`,7))]),i("details",R,[i("summary",null,[s[45]||(s[45]=i("a",{id:"ReefGuideAPI.create_bbox-Tuple{Tuple, Tuple}",href:"#ReefGuideAPI.create_bbox-Tuple{Tuple, Tuple}"},[i("span",{class:"jlbinding"},"ReefGuideAPI.create_bbox")],-1)),s[46]||(s[46]=e()),t(a,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),s[47]||(s[47]=n('
julia
create_bbox(xs::Tuple, ys::Tuple)::Vector{Tuple{Float64, Float64}}

Create bounding box from x and y coordinates

Returns

Bounding box coordinates in order of top left, top right, bottom right, bottom left, top left.

source

',5))]),i("details",I,[i("summary",null,[s[48]||(s[48]=i("a",{id:"ReefGuideAPI.criteria_middleware-Tuple{Any}",href:"#ReefGuideAPI.criteria_middleware-Tuple{Any}"},[i("span",{class:"jlbinding"},"ReefGuideAPI.criteria_middleware")],-1)),s[49]||(s[49]=e()),t(a,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),s[50]||(s[50]=n('
julia
criteria_middleware(handle)

Creates middleware that parses a criteria query before reaching an endpoint

Example

https://somewhere:8000/suitability/assess/region-name/reeftype?criteria_names=Depth,Slope&lb=-9.0,0.0&ub=-2.0,40

source

',5))]),i("details",D,[i("summary",null,[s[51]||(s[51]=i("a",{id:"ReefGuideAPI.degrees_to_meters-Tuple{Any, Any}",href:"#ReefGuideAPI.degrees_to_meters-Tuple{Any, Any}"},[i("span",{class:"jlbinding"},"ReefGuideAPI.degrees_to_meters")],-1)),s[52]||(s[52]=e()),t(a,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),s[53]||(s[53]=n('
julia
degrees_to_meters(x, lat)

Convert degrees to meters at target latitude.

source

',3))]),i("details",v,[i("summary",null,[s[54]||(s[54]=i("a",{id:"ReefGuideAPI.filter_distances-Tuple{Rasters.Raster, Any}",href:"#ReefGuideAPI.filter_distances-Tuple{Rasters.Raster, Any}"},[i("span",{class:"jlbinding"},"ReefGuideAPI.filter_distances")],-1)),s[55]||(s[55]=e()),t(a,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),s[56]||(s[56]=n(`
julia
filter_distances(
+    target_rast::Raster,
+    dist_buffer
+)::Raster

Apply a mask to exclude pixels that are outside the indicated distance buffer(s).

target_rast and the dist_buffer should be in the same CRS (e.g., EPSG:7844 / GDA2020).

Arguments

Returns

source

`,8))]),i("details",T,[i("summary",null,[s[57]||(s[57]=i("a",{id:"ReefGuideAPI.filter_distances-Tuple{Rasters.Raster, DataFrames.DataFrame, Any}",href:"#ReefGuideAPI.filter_distances-Tuple{Rasters.Raster, DataFrames.DataFrame, Any}"},[i("span",{class:"jlbinding"},"ReefGuideAPI.filter_distances")],-1)),s[58]||(s[58]=e()),t(a,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),s[59]||(s[59]=n(`
julia
filter_distances(
+    target_rast::Raster,
+    gdf::DataFrame,
+    dist_nm
+)::Raster

Exclude pixels in target_rast that are beyond dist_nm (nautical miles) from a geometry in gdf. target_rast and gdf should be in the same CRS (EPSG:7844 / GDA2020 for GBR-reef-guidance-assessment).

Arguments

Returns

from a geometry centroid.

source

`,8))]),i("details",B,[i("summary",null,[s[60]||(s[60]=i("a",{id:"ReefGuideAPI.filter_far_polygons-Tuple{Any, GeometryBasics.Point, Float64, Union{Float64, Int64}}",href:"#ReefGuideAPI.filter_far_polygons-Tuple{Any, GeometryBasics.Point, Float64, Union{Float64, Int64}}"},[i("span",{class:"jlbinding"},"ReefGuideAPI.filter_far_polygons")],-1)),s[61]||(s[61]=e()),t(a,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),s[62]||(s[62]=n('
julia
filter_far_polygons(gdf::DataFrame, pixel::GIWrap.Point, lat::Float64, dist::Union{Int64,Float64})::BitVector

Filter out reefs that are > dist (meters) from the target pixel (currently dist is hardcoded in initial_search_rotation()).

source

',3))]),i("details",G,[i("summary",null,[s[63]||(s[63]=i("a",{id:"ReefGuideAPI.filter_sites-Tuple{DataFrames.DataFrame}",href:"#ReefGuideAPI.filter_sites-Tuple{DataFrames.DataFrame}"},[i("span",{class:"jlbinding"},"ReefGuideAPI.filter_sites")],-1)),s[64]||(s[64]=e()),t(a,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),s[65]||(s[65]=n('
julia
filter_sites(res_df::DataFrame)::DataFrame

Filter out sites where the qc_flag indicates a suitabiltiy < surr_threshold in searching. Where site polygons are overlapping, keep only the highest scoring site polygon.

Arguments

Returns

DataFrame containing only the highest scoring sites where site polygons intersect, and containing only sites with scores greater than the surr_threshold specified in identify_edge_aligned_sites() (default=0.33).

source

',7))]),i("details",x,[i("summary",null,[s[66]||(s[66]=i("a",{id:"ReefGuideAPI.find_horizontal-Tuple{GeoInterface.Wrappers.Polygon}",href:"#ReefGuideAPI.find_horizontal-Tuple{GeoInterface.Wrappers.Polygon}"},[i("span",{class:"jlbinding"},"ReefGuideAPI.find_horizontal")],-1)),s[67]||(s[67]=e()),t(a,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),s[68]||(s[68]=n('
julia
find_horizontal(geom::GI.Wrappers.Polygon)::Vector{Tuple{Float64,Float64}, Tuple{Float64,Float64}}

Find a horizontal line if one exists within a geometry.

Returns

Vector containing tuples of coordinates for a horizontal line found within geom.

source

',5))]),i("details",P,[i("summary",null,[s[69]||(s[69]=i("a",{id:"ReefGuideAPI.from_zero-Tuple{Vector{Tuple{Float64, Float64}}}",href:"#ReefGuideAPI.from_zero-Tuple{Vector{Tuple{Float64, Float64}}}"},[i("span",{class:"jlbinding"},"ReefGuideAPI.from_zero")],-1)),s[70]||(s[70]=e()),t(a,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),s[71]||(s[71]=n('
julia
from_zero(v::Vector{Tuple{Float64,Float64}})::Vector{Tuple{Float64, Float64}}

Translates Vector of points v to begin from (0, 0), retaining direction and length.

Argument

source

',5))]),i("details",M,[i("summary",null,[s[72]||(s[72]=i("a",{id:"ReefGuideAPI.generate_criteria_mask!-Tuple{String, Rasters.RasterStack, DataFrames.DataFrame, Vector{ReefGuideAPI.CriteriaBounds{Function}}}",href:"#ReefGuideAPI.generate_criteria_mask!-Tuple{String, Rasters.RasterStack, DataFrames.DataFrame, Vector{ReefGuideAPI.CriteriaBounds{Function}}}"},[i("span",{class:"jlbinding"},"ReefGuideAPI.generate_criteria_mask!")],-1)),s[73]||(s[73]=e()),t(a,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),s[74]||(s[74]=n('
julia
generate_criteria_mask!(fn::String, rst_stack::RasterStack, lookup::DataFrame, ruleset::Vector{CriteriaBounds{Function}})

Generate mask file for a given region and reef type (slopes or flats) according to thresholds applied to a set of criteria.

Notes

Arguments

Returns

Nothing

source

',9))]),i("details",S,[i("summary",null,[s[75]||(s[75]=i("a",{id:"ReefGuideAPI.get_points-Tuple{Any}",href:"#ReefGuideAPI.get_points-Tuple{Any}"},[i("span",{class:"jlbinding"},"ReefGuideAPI.get_points")],-1)),s[76]||(s[76]=e()),t(a,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),s[77]||(s[77]=n('
julia
get_points(geom)

Helper method to retrieve points for a geometry.

source

',3))]),i("details",L,[i("summary",null,[s[78]||(s[78]=i("a",{id:"ReefGuideAPI.identify_edge_aligned_sites-Tuple{DataFrames.DataFrame, DataFrames.DataFrame, Float64, DataFrames.DataFrame, Union{Float64, Int64}, Union{Float64, Int64}, GeoFormatTypes.CoordinateReferenceSystemFormat, Vector{Vector{GeometryBasics.Line{2, Float64}}}, String}",href:"#ReefGuideAPI.identify_edge_aligned_sites-Tuple{DataFrames.DataFrame, DataFrames.DataFrame, Float64, DataFrames.DataFrame, Union{Float64, Int64}, Union{Float64, Int64}, GeoFormatTypes.CoordinateReferenceSystemFormat, Vector{Vector{GeometryBasics.Line{2, Float64}}}, String}"},[i("span",{class:"jlbinding"},"ReefGuideAPI.identify_edge_aligned_sites")],-1)),s[79]||(s[79]=e()),t(a,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),s[80]||(s[80]=n(`
julia
identify_edge_aligned_sites(
+    df::DataFrame,
+    search_pixels::DataFrame,
+    res::Float64,
+    gdf::DataFrame,
+    x_dist::Union{Int64,Float64},
+    y_dist::Union{Int64,Float64},
+    target_crs::GeoFormatTypes.CoordinateReferenceSystemFormat,
+    reef_lines::Vector{Vector{GeometryBasics.Line{2,Float64}}},
+    region::String;
+    degree_step::Float64=15.0,
+    n_rot_p_side::Int64=2,
+    surr_threshold::Float64=0.33
+)::DataFrame

Identify the most suitable site polygons for each pixel in the search_pixels DataFrame. x_dist and y_dist are x and y lengths of the search polygon in meters. A buffer of the raster files' resolution is applied to the search box. And angle from a pixel to a reef edge is identified and used for searching with custom rotation parameters. Method is currently opperating for CRS in degrees units.

Arguments

Returns

DataFrame containing highest score, rotation and polygon for each assessment at pixels in indices.

source

`,7))]),i("details",w,[i("summary",null,[s[81]||(s[81]=i("a",{id:"ReefGuideAPI.identify_edge_aligned_sites-Tuple{Rasters.RasterStack, DataFrames.DataFrame, DataFrames.DataFrame, Union{Float64, Int64}, Union{Float64, Int64}, GeoFormatTypes.CoordinateReferenceSystemFormat, String, Vector{Vector{GeometryBasics.Line{2, Float64}}}}",href:"#ReefGuideAPI.identify_edge_aligned_sites-Tuple{Rasters.RasterStack, DataFrames.DataFrame, DataFrames.DataFrame, Union{Float64, Int64}, Union{Float64, Int64}, GeoFormatTypes.CoordinateReferenceSystemFormat, String, Vector{Vector{GeometryBasics.Line{2, Float64}}}}"},[i("span",{class:"jlbinding"},"ReefGuideAPI.identify_edge_aligned_sites")],-1)),s[82]||(s[82]=e()),t(a,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),s[83]||(s[83]=n(`
julia
identify_edge_aligned_sites(
+    rst_stack::RasterStack,
+    search_pixels::DataFrame,
+    gdf::DataFrame,
+    x_dist::Union{Int64,Float64},
+    y_dist::Union{Int64,Float64},
+    target_crs::GeoFormatTypes.CoordinateReferenceSystemFormat,
+    region::String,
+    reef_lines::Vector{Vector{GeometryBasics.Line{2,Float64}}};
+    degree_step::Float64=15.0,
+    n_rot_per_side::Int64=2
+)::DataFrame

Identify the most suitable site polygons for each pixel in the search_pixels DataFrame. x_dist and y_dist are x and y lengths of the search polygon. A buffer of rst_stack resolution is applied to the search box. And angle from a pixel to a reef edge is identified and used for searching with custom rotation parameters.

Arguments

Returns

DataFrame containing highest score, rotation and polygon for each assessment at pixels in indices.

source

`,7))]),i("details",O,[i("summary",null,[s[84]||(s[84]=i("a",{id:"ReefGuideAPI.identify_search_pixels-Tuple{Rasters.Raster, Any}",href:"#ReefGuideAPI.identify_search_pixels-Tuple{Rasters.Raster, Any}"},[i("span",{class:"jlbinding"},"ReefGuideAPI.identify_search_pixels")],-1)),s[85]||(s[85]=e()),t(a,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),s[86]||(s[86]=n('
julia
identify_search_pixels(input_raster::Raster, criteria_function)::DataFrame

Identifies all pixels in an input raster that return true for the function criteria_function.

Arguments

Returns

DataFrame containing indices, lon and lat for each pixel that is intended for further analysis.

source

',7))]),i("details",V,[i("summary",null,[s[87]||(s[87]=i("a",{id:"ReefGuideAPI.initial_search_box-Tuple{Any, Union{Float64, Int64}, Union{Float64, Int64}, GeoFormatTypes.CoordinateReferenceSystemFormat, Float64}",href:"#ReefGuideAPI.initial_search_box-Tuple{Any, Union{Float64, Int64}, Union{Float64, Int64}, GeoFormatTypes.CoordinateReferenceSystemFormat, Float64}"},[i("span",{class:"jlbinding"},"ReefGuideAPI.initial_search_box")],-1)),s[88]||(s[88]=e()),t(a,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),s[89]||(s[89]=n(`
julia
initial_search_box(
+    (lon::Float64, lat::Float64),
+    x_dist::Union{Int64, Float64},
+    y_dist::Union{Int64, Float64},
+    target_crs::GeoFormatTypes.CoordinateReferenceSystemFormat,
+    res::Float64
+)::GI.Wrappers.Polygon

Create an initial search box that is centered around the point (lon, lat) in target_crs, and is buffered by res distance.

Arguments

Returns

Initial search box geometry.

source

`,7))]),i("details",q,[i("summary",null,[s[90]||(s[90]=i("a",{id:"ReefGuideAPI.initial_search_rotation-Tuple{GeometryBasics.Point{2, Float64}, GeoInterface.Wrappers.Polygon, DataFrames.DataFrame, Vector{Vector{GeometryBasics.Line{2, Float64}}}}",href:"#ReefGuideAPI.initial_search_rotation-Tuple{GeometryBasics.Point{2, Float64}, GeoInterface.Wrappers.Polygon, DataFrames.DataFrame, Vector{Vector{GeometryBasics.Line{2, Float64}}}}"},[i("span",{class:"jlbinding"},"ReefGuideAPI.initial_search_rotation")],-1)),s[91]||(s[91]=e()),t(a,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),s[92]||(s[92]=n(`
julia
initial_search_rotation(
+    pixel::GeometryBasics.Point{2, Float64},
+    geom_buff::GI.Wrappers.Polygon,
+    gdf::DataFrame,
+    reef_outlines::Vector{Vector{GeometryBasics.Line{2, Float64}}};
+    search_buffer::Union{Int64,Float64}=20000.0
+)::Float64

Identifies the closest edge to the target pixel/'geom_buff and returns the initial rotation angle required to match the edge line.

Arguments

source

`,5))]),i("details",U,[i("summary",null,[s[93]||(s[93]=i("a",{id:"ReefGuideAPI.initialize_regional_data_cache-Tuple{String, String}",href:"#ReefGuideAPI.initialize_regional_data_cache-Tuple{String, String}"},[i("span",{class:"jlbinding"},"ReefGuideAPI.initialize_regional_data_cache")],-1)),s[94]||(s[94]=e()),t(a,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),s[95]||(s[95]=n('
julia
initialize_regional_data_cache(reef_data_path::String, reg_cache_fn::String)

Create initial regional data store with data from reef_data_path, excluding geospatial data and save to reg_cache_fn path.

source

',3))]),i("details",z,[i("summary",null,[s[96]||(s[96]=i("a",{id:"ReefGuideAPI.line_angle-Union{Tuple{T}, Tuple{T, T}} where T<:Vector{Tuple{Float64, Float64}}",href:"#ReefGuideAPI.line_angle-Union{Tuple{T}, Tuple{T, T}} where T<:Vector{Tuple{Float64, Float64}}"},[i("span",{class:"jlbinding"},"ReefGuideAPI.line_angle")],-1)),s[97]||(s[97]=e()),t(a,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),s[98]||(s[98]=n(`
julia
line_angle(a::T, b::T)::Float64 where {T <: Vector{Tuple{Float64,Float64}}}

Calculate the angle between two lines.

Arguments

Returns

Angle between the two lines.

Examples

julia
line_angle([(0.0,5.0), (0.0,0.0)], from_zero(edge_line))
+line_angle([(0.0,5.0), (0.0,0.0)], [(1.0, 4.0), (7.0, 8.0)])

source

`,9))]),i("details",N,[i("summary",null,[s[99]||(s[99]=i("a",{id:"ReefGuideAPI.mask_region-NTuple{4, Any}",href:"#ReefGuideAPI.mask_region-NTuple{4, Any}"},[i("span",{class:"jlbinding"},"ReefGuideAPI.mask_region")],-1)),s[100]||(s[100]=e()),t(a,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),s[101]||(s[101]=n('
julia
mask_region(reg_assess_data, reg, qp, rtype)

Arguments

Returns

Raster of region with locations that meet criteria masked.

source

',6))]),i("details",W,[i("summary",null,[s[102]||(s[102]=i("a",{id:"ReefGuideAPI.meters_to_degrees-Tuple{Any, Any}",href:"#ReefGuideAPI.meters_to_degrees-Tuple{Any, Any}"},[i("span",{class:"jlbinding"},"ReefGuideAPI.meters_to_degrees")],-1)),s[103]||(s[103]=e()),t(a,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),s[104]||(s[104]=n('
julia
meters_to_degrees(x, lat)

Convert meters to degrees at target latitude.

source

',3))]),i("details",H,[i("summary",null,[s[105]||(s[105]=i("a",{id:"ReefGuideAPI.move_geom-Tuple{Any, Tuple}",href:"#ReefGuideAPI.move_geom-Tuple{Any, Tuple}"},[i("span",{class:"jlbinding"},"ReefGuideAPI.move_geom")],-1)),s[106]||(s[106]=e()),t(a,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),s[107]||(s[107]=n('
julia
move_geom(geom, new_centroid::Tuple)

Move a geom to a new centroid.

Arguments

source

',5))]),i("details",$,[i("summary",null,[s[108]||(s[108]=i("a",{id:"ReefGuideAPI.n_gdal_threads-Tuple{Dict}",href:"#ReefGuideAPI.n_gdal_threads-Tuple{Dict}"},[i("span",{class:"jlbinding"},"ReefGuideAPI.n_gdal_threads")],-1)),s[109]||(s[109]=e()),t(a,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),s[110]||(s[110]=n('
julia
n_gdal_threads(config::Dict)::String

Retrieve the configured number of threads to use when writing COGs with GDAL.

source

',3))]),i("details",Q,[i("summary",null,[s[111]||(s[111]=i("a",{id:"ReefGuideAPI.output_geojson-Tuple{String, DataFrames.DataFrame}",href:"#ReefGuideAPI.output_geojson-Tuple{String, DataFrames.DataFrame}"},[i("span",{class:"jlbinding"},"ReefGuideAPI.output_geojson")],-1)),s[112]||(s[112]=e()),t(a,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),s[113]||(s[113]=n('
julia
output_geojson(destination_path::String, df::DataFrame)::Nothing

Writes out GeoJSON file to a target directory. Output file will be located at location: destination_path.

Arguments

source

',5))]),i("details",J,[i("summary",null,[s[114]||(s[114]=i("a",{id:"ReefGuideAPI.parse_criteria_query-Tuple{Dict}",href:"#ReefGuideAPI.parse_criteria_query-Tuple{Dict}"},[i("span",{class:"jlbinding"},"ReefGuideAPI.parse_criteria_query")],-1)),s[115]||(s[115]=e()),t(a,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),s[116]||(s[116]=n('
julia
parse_criteria_query(qp)::Tuple

Parse criteria values from request query.

Queries should take the form of: Depth=-9.0:0.0&Slope=0.0:40.0&Rugosity=0.0:0.0

Arguments

Returns

Tuple of criteria names, lower bounds, upper bounds

source

',8))]),i("details",Z,[i("summary",null,[s[117]||(s[117]=i("a",{id:"ReefGuideAPI.polygon_to_lines-Union{Tuple{Union{GeoInterface.Wrappers.MultiPolygon, Vector{T}, T}}, Tuple{T}} where T<:GeoInterface.Wrappers.Polygon",href:"#ReefGuideAPI.polygon_to_lines-Union{Tuple{Union{GeoInterface.Wrappers.MultiPolygon, Vector{T}, T}}, Tuple{T}} where T<:GeoInterface.Wrappers.Polygon"},[i("span",{class:"jlbinding"},"ReefGuideAPI.polygon_to_lines")],-1)),s[118]||(s[118]=e()),t(a,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),s[119]||(s[119]=n(`
julia
polygon_to_lines(
+    polygon::Union{Vector{T},T,GIWrap.MultiPolygon}
+) where {T<:GIWrap.Polygon}

Extract the individual lines between vertices that make up the outline of a polygon.

Returns

Vector of GeometryBasics.Line{2, Float64} with one line for each adjacent vertex pair in polygon.

source

`,5))]),i("details",X,[i("summary",null,[s[120]||(s[120]=i("a",{id:"ReefGuideAPI.port_buffer_mask-Tuple{DataFrames.DataFrame, Float64}",href:"#ReefGuideAPI.port_buffer_mask-Tuple{DataFrames.DataFrame, Float64}"},[i("span",{class:"jlbinding"},"ReefGuideAPI.port_buffer_mask")],-1)),s[121]||(s[121]=e()),t(a,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),s[122]||(s[122]=n('
julia
port_buffer_mask(gdf::DataFrame, dist::Float64; unit::String="NM")

Create a masking buffer around indicated port locations.

Arguments

source

',5))]),i("details",K,[i("summary",null,[s[123]||(s[123]=i("a",{id:"ReefGuideAPI.proportion_suitable-Tuple{BitMatrix}",href:"#ReefGuideAPI.proportion_suitable-Tuple{BitMatrix}"},[i("span",{class:"jlbinding"},"ReefGuideAPI.proportion_suitable")],-1)),s[124]||(s[124]=e()),t(a,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),s[125]||(s[125]=n('
julia
proportion_suitable(subsection::BitMatrix, square_offset::Tuple=(-4,5))::Matrix{Int16}

Calculate the the proportion of the subsection that is suitable for deployments. The subsection is the surrounding a rough hectare area centred on each cell of a raster marked as being suitable according to user-selected criteria.

Cells on the edges of a raster object are assessed using a smaller surrounding area, rather than shifting the window inward. In usual applications, there will be no target pixel close to the edge due to the use of buffer areas.

Arguments

Returns

Matrix of values 0 - 100 indicating the percentage of the area around the target pixel that meet suitability criteria.

source

',8))]),i("details",Y,[i("summary",null,[s[126]||(s[126]=i("a",{id:"ReefGuideAPI.remove_rugosity-NTuple{4, Any}",href:"#ReefGuideAPI.remove_rugosity-NTuple{4, Any}"},[i("span",{class:"jlbinding"},"ReefGuideAPI.remove_rugosity")],-1)),s[127]||(s[127]=e()),t(a,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),s[128]||(s[128]=n('
julia
remove_rugosity(reg, criteria, lbs, ubs)

Remove rugosity layer from consideration if region is not Townsville. Rugosity data currently only exists for the Townsville region.

source

',3))]),i("details",ss,[i("summary",null,[s[129]||(s[129]=i("a",{id:"ReefGuideAPI.rotate_geom-Tuple{Any, Float64, GeoFormatTypes.CoordinateReferenceSystemFormat}",href:"#ReefGuideAPI.rotate_geom-Tuple{Any, Float64, GeoFormatTypes.CoordinateReferenceSystemFormat}"},[i("span",{class:"jlbinding"},"ReefGuideAPI.rotate_geom")],-1)),s[130]||(s[130]=e()),t(a,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),s[131]||(s[131]=n(`
julia
rotate_geom(
+    geom,
+    degrees::Float64,
+    target_crs::GeoFormatTypes.CoordinateReferenceSystemFormat
+)

Rotate target geom by degrees rotation in clockwise direction. target_crs is applied to output geometry.

Returns

Rotated geometry.

source

`,5))]),i("details",is,[i("summary",null,[s[132]||(s[132]=i("a",{id:"ReefGuideAPI.rotate_polygon-Tuple{Any, Any, Any}",href:"#ReefGuideAPI.rotate_polygon-Tuple{Any, Any, Any}"},[i("span",{class:"jlbinding"},"ReefGuideAPI.rotate_polygon")],-1)),s[133]||(s[133]=e()),t(a,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),s[134]||(s[134]=i("p",null,"Rotate the polygon by the given angle about its center.",-1)),s[135]||(s[135]=i("p",null,[i("a",{href:"https://github.com/open-AIMS/ReefGuideAPI.jl/blob/39637e8d1926c44317ec99036d199c22251bfb19/src/site_assessment/geom_ops.jl#L47",target:"_blank",rel:"noreferrer"},"source")],-1))]),i("details",es,[i("summary",null,[s[136]||(s[136]=i("a",{id:"ReefGuideAPI.setup_regional_data-Tuple{Dict}",href:"#ReefGuideAPI.setup_regional_data-Tuple{Dict}"},[i("span",{class:"jlbinding"},"ReefGuideAPI.setup_regional_data")],-1)),s[137]||(s[137]=e()),t(a,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),s[138]||(s[138]=n('
julia
setup_regional_data(config::Dict)

Load regional data to act as an in-memory cache.

Arguments

Returns

OrderedDict of RegionalCriteria for each region.

source

',7))]),i("details",as,[i("summary",null,[s[139]||(s[139]=i("a",{id:"ReefGuideAPI.threshold_mask-Tuple{Any, Symbol, Any}",href:"#ReefGuideAPI.threshold_mask-Tuple{Any, Symbol, Any}"},[i("span",{class:"jlbinding"},"ReefGuideAPI.threshold_mask")],-1)),s[140]||(s[140]=e()),t(a,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),s[141]||(s[141]=n('
julia
threshold_mask(reg::String, rtype::Symbol, crit_map)

Generate mask for a given region and reef type (slopes or flats) according to thresholds applied to a set of criteria.

Notes

Arguments

Returns

True/false mask indicating locations within desired thresholds.

source

',9))]),i("details",ts,[i("summary",null,[s[142]||(s[142]=i("a",{id:"ReefGuideAPI.tile_size-Tuple{Dict}",href:"#ReefGuideAPI.tile_size-Tuple{Dict}"},[i("span",{class:"jlbinding"},"ReefGuideAPI.tile_size")],-1)),s[143]||(s[143]=e()),t(a,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),s[144]||(s[144]=n('
julia
tile_size(config::Dict)::Tuple

Retrieve the configured size of map tiles in pixels (width and height / lon and lat).

source

',3))]),i("details",ns,[i("summary",null,[s[145]||(s[145]=i("a",{id:"ReefGuideAPI.valid_lonlat_inds-Union{Tuple{T}, Tuple{DataFrames.DataFrame, Symbol, T, T}} where T",href:"#ReefGuideAPI.valid_lonlat_inds-Union{Tuple{T}, Tuple{DataFrames.DataFrame, Symbol, T, T}} where T"},[i("span",{class:"jlbinding"},"ReefGuideAPI.valid_lonlat_inds")],-1)),s[146]||(s[146]=e()),t(a,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),s[147]||(s[147]=n('
julia
valid_lonlat_inds(data::DataFrame, criteria::Symbol, lb::T, ub::T) where {T}

Retrieve the indices of valid data for a region.

Arguments

Returns

Tuple{Vector{Int64}, Vector{Int64}}, of lon and lat indices.

source

',7))]),i("details",ls,[i("summary",null,[s[148]||(s[148]=i("a",{id:"ReefGuideAPI.valid_pixel_positions-Union{Tuple{T}, Tuple{DataFrames.DataFrame, Symbol, T, T}} where T",href:"#ReefGuideAPI.valid_pixel_positions-Union{Tuple{T}, Tuple{DataFrames.DataFrame, Symbol, T, T}} where T"},[i("span",{class:"jlbinding"},"ReefGuideAPI.valid_pixel_positions")],-1)),s[149]||(s[149]=e()),t(a,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),s[150]||(s[150]=n('
julia
valid_pixel_positions(data::DataFrame, criteria::Symbol, lb::T, ub::T) where {T}

Obtain the pixel positions of valid data.

Intended for use in applications similar to ImageryLayer - client side pixel filter.

Arguments

source

',6))]),i("details",ps,[i("summary",null,[s[151]||(s[151]=i("a",{id:"ReefGuideAPI.warmup_cache-Tuple{String}",href:"#ReefGuideAPI.warmup_cache-Tuple{String}"},[i("span",{class:"jlbinding"},"ReefGuideAPI.warmup_cache")],-1)),s[152]||(s[152]=e()),t(a,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),s[153]||(s[153]=n('
julia
warmup_cache(config_path::String)

Invokes warm up of regional data cache to reduce later spin up times.

source

',3))]),i("details",rs,[i("summary",null,[s[154]||(s[154]=i("a",{id:"ReefGuideAPI.within_thresholds-Union{Tuple{T}, Tuple{Val, Val, Rasters.Raster, T, T}} where T",href:"#ReefGuideAPI.within_thresholds-Union{Tuple{T}, Tuple{Val, Val, Rasters.Raster, T, T}} where T"},[i("span",{class:"jlbinding"},"ReefGuideAPI.within_thresholds")],-1)),s[155]||(s[155]=e()),t(a,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),s[156]||(s[156]=n('
julia
within_thresholds(ctype::Val, data::Raster, lb::T, ub::T) where {T}

Apply in-bound constraints.

Notes

Why is this a simple one line function? Because we want to be able to cache results for each constraint type.

source

',5))])])}const Es=l(h,[["render",os]]);export{ys as __pageData,Es as default}; diff --git a/dev/assets/api.md.DYWJQ0KO.lean.js b/dev/assets/api.md.DYWJQ0KO.lean.js new file mode 100644 index 0000000..acd82d6 --- /dev/null +++ b/dev/assets/api.md.DYWJQ0KO.lean.js @@ -0,0 +1,87 @@ +import{_ as l,c as p,j as i,a as e,G as t,a5 as n,B as r,o}from"./chunks/framework.CX_bWI7S.js";const ys=JSON.parse('{"title":"API","description":"","frontmatter":{},"headers":[],"relativePath":"api.md","filePath":"api.md","lastUpdated":null}'),h={name:"api.md"},d={class:"jldocstring custom-block",open:""},k={class:"jldocstring custom-block",open:""},g={class:"jldocstring custom-block",open:""},c={class:"jldocstring custom-block",open:""},u={class:"jldocstring custom-block",open:""},y={class:"jldocstring custom-block",open:""},E={class:"jldocstring custom-block",open:""},f={class:"jldocstring custom-block",open:""},F={class:"jldocstring custom-block",open:""},b={class:"jldocstring custom-block",open:""},m={class:"jldocstring custom-block",open:""},C={class:"jldocstring custom-block",open:""},A={class:"jldocstring custom-block",open:""},_={class:"jldocstring custom-block",open:""},j={class:"jldocstring custom-block",open:""},R={class:"jldocstring custom-block",open:""},I={class:"jldocstring custom-block",open:""},D={class:"jldocstring custom-block",open:""},v={class:"jldocstring custom-block",open:""},T={class:"jldocstring custom-block",open:""},B={class:"jldocstring custom-block",open:""},G={class:"jldocstring custom-block",open:""},x={class:"jldocstring custom-block",open:""},P={class:"jldocstring custom-block",open:""},M={class:"jldocstring custom-block",open:""},S={class:"jldocstring custom-block",open:""},L={class:"jldocstring custom-block",open:""},w={class:"jldocstring custom-block",open:""},O={class:"jldocstring custom-block",open:""},V={class:"jldocstring custom-block",open:""},q={class:"jldocstring custom-block",open:""},U={class:"jldocstring custom-block",open:""},z={class:"jldocstring custom-block",open:""},N={class:"jldocstring custom-block",open:""},W={class:"jldocstring custom-block",open:""},H={class:"jldocstring custom-block",open:""},$={class:"jldocstring custom-block",open:""},Q={class:"jldocstring custom-block",open:""},J={class:"jldocstring custom-block",open:""},Z={class:"jldocstring custom-block",open:""},X={class:"jldocstring custom-block",open:""},K={class:"jldocstring custom-block",open:""},Y={class:"jldocstring custom-block",open:""},ss={class:"jldocstring custom-block",open:""},is={class:"jldocstring custom-block",open:""},es={class:"jldocstring custom-block",open:""},as={class:"jldocstring custom-block",open:""},ts={class:"jldocstring custom-block",open:""},ns={class:"jldocstring custom-block",open:""},ls={class:"jldocstring custom-block",open:""},ps={class:"jldocstring custom-block",open:""},rs={class:"jldocstring custom-block",open:""};function os(hs,s,ds,ks,gs,cs){const a=r("Badge");return o(),p("div",null,[s[157]||(s[157]=i("h1",{id:"api",tabindex:"-1"},[e("API "),i("a",{class:"header-anchor",href:"#api","aria-label":'Permalink to "API"'},"​")],-1)),i("details",d,[i("summary",null,[s[0]||(s[0]=i("a",{id:"ReefGuideAPI._cache_location-Tuple{Dict}",href:"#ReefGuideAPI._cache_location-Tuple{Dict}"},[i("span",{class:"jlbinding"},"ReefGuideAPI._cache_location")],-1)),s[1]||(s[1]=e()),t(a,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),s[2]||(s[2]=n('
julia
_cache_location(config::Dict)::String

Retrieve cache location for geotiffs.

source

',3))]),i("details",k,[i("summary",null,[s[3]||(s[3]=i("a",{id:"ReefGuideAPI._lon_lat_to_tile-Tuple{Any, Any, Any}",href:"#ReefGuideAPI._lon_lat_to_tile-Tuple{Any, Any, Any}"},[i("span",{class:"jlbinding"},"ReefGuideAPI._lon_lat_to_tile")],-1)),s[4]||(s[4]=e()),t(a,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),s[5]||(s[5]=n('
julia
_lon_lat_to_tile(zoom, lon, lat)

Identify the corresponding tile coordinates for a given lon/lat.

Returns

x and y tile coordinates

source

',5))]),i("details",g,[i("summary",null,[s[6]||(s[6]=i("a",{id:"ReefGuideAPI._tile_bounds-Union{Tuple{T}, Tuple{T, T, T}} where T<:Int64",href:"#ReefGuideAPI._tile_bounds-Union{Tuple{T}, Tuple{T, T, T}} where T<:Int64"},[i("span",{class:"jlbinding"},"ReefGuideAPI._tile_bounds")],-1)),s[7]||(s[7]=e()),t(a,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),s[8]||(s[8]=n('
julia
_tile_bounds(z::T, x::T, y::T) where {T<:Int64}

Obtain lon/lat bounds of a requested tile.

Returns

West, East, North South (min lon, max lon, lat max, lat min)

source

',5))]),i("details",c,[i("summary",null,[s[9]||(s[9]=i("a",{id:"ReefGuideAPI._tile_to_lon_lat-Union{Tuple{T}, Tuple{T, T, T}} where T<:Int64",href:"#ReefGuideAPI._tile_to_lon_lat-Union{Tuple{T}, Tuple{T, T, T}} where T<:Int64"},[i("span",{class:"jlbinding"},"ReefGuideAPI._tile_to_lon_lat")],-1)),s[10]||(s[10]=e()),t(a,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),s[11]||(s[11]=n('
julia
_tile_to_lon_lat(z::T, x::T, y::T) where {T<:Int64}

Obtain lon/lat of top-left corner of a requested tile.

Returns

lon, lat

source

',5))]),i("details",u,[i("summary",null,[s[12]||(s[12]=i("a",{id:"ReefGuideAPI._write_cog-Tuple{String, Rasters.Raster, Dict}",href:"#ReefGuideAPI._write_cog-Tuple{String, Rasters.Raster, Dict}"},[i("span",{class:"jlbinding"},"ReefGuideAPI._write_cog")],-1)),s[13]||(s[13]=e()),t(a,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),s[14]||(s[14]=n('
julia
_write_cog(file_path::String, data::Raster, config::Dict)::Nothing

Write out a COG using common options.

Arguments

source

',5))]),i("details",y,[i("summary",null,[s[15]||(s[15]=i("a",{id:"ReefGuideAPI.adjusted_nearest-Tuple{Rasters.Raster, Int64, Int64, Int64, Tuple{Int64, Int64}}",href:"#ReefGuideAPI.adjusted_nearest-Tuple{Rasters.Raster, Int64, Int64, Int64, Tuple{Int64, Int64}}"},[i("span",{class:"jlbinding"},"ReefGuideAPI.adjusted_nearest")],-1)),s[16]||(s[16]=e()),t(a,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),s[17]||(s[17]=n('
julia
adjusted_nearest(rst::Raster, z::Int, x::Int, y::Int, tile_size::Tuple{Int,Int}, orig_rst_size::Tuple{Int,Int})::Matrix

Resample a raster using nearest neighbor interpolation when the tile includes area outside where data exists (e.g., viewing the globe where the data may appear in a small corner of the tile). This approach attempts to account for planetary curvature while still maintaining some performance.

Arguments

Returns

Matrix with the resampled data.

source

',7))]),i("details",E,[i("summary",null,[s[18]||(s[18]=i("a",{id:"ReefGuideAPI.apply_criteria_lookup-Tuple{RegionalCriteria, Symbol, Any}",href:"#ReefGuideAPI.apply_criteria_lookup-Tuple{RegionalCriteria, Symbol, Any}"},[i("span",{class:"jlbinding"},"ReefGuideAPI.apply_criteria_lookup")],-1)),s[19]||(s[19]=e()),t(a,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),s[20]||(s[20]=n(`
julia
apply_criteria_lookup(
+    reg_criteria,
+    rtype::Symbol,
+    ruleset::Vector{CriteriaBounds{Function}}
+)

Filter lookup table by applying user defined ruleset criteria.

Arguments

Returns

Filtered lookup table containing points that meet all criteria in ruleset.

source

`,7))]),i("details",f,[i("summary",null,[s[21]||(s[21]=i("a",{id:"ReefGuideAPI.apply_criteria_thresholds-Tuple{Rasters.RasterStack, DataFrames.DataFrame, Dict}",href:"#ReefGuideAPI.apply_criteria_thresholds-Tuple{Rasters.RasterStack, DataFrames.DataFrame, Dict}"},[i("span",{class:"jlbinding"},"ReefGuideAPI.apply_criteria_thresholds")],-1)),s[22]||(s[22]=e()),t(a,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),s[23]||(s[23]=n(`
julia
apply_criteria_thresholds(criteria_stack::RasterStack, lookup::DataFrame, ruleset::Vector{CriteriaBounds{Function}})::Raster
+apply_criteria_thresholds(criteria_stack::RasterStack, lookup::DataFrame, ruleset::Dict)::Raster
+apply_criteria_thresholds(criteria_stack::RasterStack, lookup::DataFrame, ruleset::NamedTuple)::Raster

Apply thresholds for each criteria.

Arguments

Returns

BitMatrix indicating locations within desired thresholds

source

`,7))]),i("details",F,[i("summary",null,[s[24]||(s[24]=i("a",{id:"ReefGuideAPI.assess_reef_site-Tuple{DataFrames.DataFrame, GeoInterface.Wrappers.Polygon, Float64, GeoFormatTypes.CoordinateReferenceSystemFormat}",href:"#ReefGuideAPI.assess_reef_site-Tuple{DataFrames.DataFrame, GeoInterface.Wrappers.Polygon, Float64, GeoFormatTypes.CoordinateReferenceSystemFormat}"},[i("span",{class:"jlbinding"},"ReefGuideAPI.assess_reef_site")],-1)),s[25]||(s[25]=e()),t(a,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),s[26]||(s[26]=n(`
julia
assess_reef_site(
+    rel_pix::DataFrame,
+    geom::GI.Wrappers.Polygon,
+    max_count::Float64,
+    target_crs::GeoFormatTypes.CoordinateReferenceSystemFormat;
+    degree_step::Float64=15.0,
+    start_rot::Float64=0.0,
+    n_per_side::Int64=2,
+    surr_threshold::Float64=0.33
+)::Tuple{Float64,Int64,GI.Wrappers.Polygon,Int64}

Assesses the rotations of a search box geom for their suitability score (calculated as the proportion of pixels that meet all specified criteria thresholds). Search box rotation steps are returned so that the start_rot angle is 0, rotations anti-clockwise are negative and rotations clockwise are positive.

Arguments

Returns

source

`,7))]),i("details",b,[i("summary",null,[s[27]||(s[27]=i("a",{id:"ReefGuideAPI.assess_reef_site-Tuple{Union{Rasters.Raster, Rasters.RasterStack}, GeoInterface.Wrappers.Polygon}",href:"#ReefGuideAPI.assess_reef_site-Tuple{Union{Rasters.Raster, Rasters.RasterStack}, GeoInterface.Wrappers.Polygon}"},[i("span",{class:"jlbinding"},"ReefGuideAPI.assess_reef_site")],-1)),s[28]||(s[28]=e()),t(a,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),s[29]||(s[29]=n(`
julia
assess_reef_site(
+    rst::Union{Raster,RasterStack},
+    geom::GI.Wrappers.Polygon,
+    ruleset::Dict{Symbol,Function};
+    degree_step::Float64=15.0,
+    start_rot::Float64=0.0,
+    n_per_side::Int64=1
+)::Tuple{Float64,Int64,GI.Wrappers.Polygon}

Assess given reef site for it's suitability score at different specified rotations around the initial reef-edge rotation.

Arguments

Returns

source

`,7))]),i("details",m,[i("summary",null,[s[30]||(s[30]=i("a",{id:"ReefGuideAPI.assess_region-NTuple{4, Any}",href:"#ReefGuideAPI.assess_region-NTuple{4, Any}"},[i("span",{class:"jlbinding"},"ReefGuideAPI.assess_region")],-1)),s[31]||(s[31]=e()),t(a,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),s[32]||(s[32]=n('
julia
assess_region(reg_assess_data, reg, qp, rtype)

Perform raster suitability assessment based on user defined criteria.

Arguments

Returns

GeoTiff file of surrounding hectare suitability (1-100%) based on the criteria bounds input by a user.

source

',7))]),i("details",C,[i("summary",null,[s[33]||(s[33]=i("a",{id:"ReefGuideAPI.assess_sites-Tuple{OrderedCollections.OrderedDict, String, String, Dict, Dict, Rasters.Raster}",href:"#ReefGuideAPI.assess_sites-Tuple{OrderedCollections.OrderedDict, String, String, Dict, Dict, Rasters.Raster}"},[i("span",{class:"jlbinding"},"ReefGuideAPI.assess_sites")],-1)),s[34]||(s[34]=e()),t(a,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),s[35]||(s[35]=n(`
julia
assess_sites(
+    reg_assess_data::OrderedDict,
+    reg::String,
+    rtype::String,
+    pixel_criteria::Dict,
+    site_criteria::Dict,
+    assess_locs::Raster
+)

Arguments

Returns

GeoDataFrame of all potential sites

source

`,6))]),i("details",A,[i("summary",null,[s[36]||(s[36]=i("a",{id:"ReefGuideAPI.buffer_simplify-Tuple{DataFrames.DataFrame}",href:"#ReefGuideAPI.buffer_simplify-Tuple{DataFrames.DataFrame}"},[i("span",{class:"jlbinding"},"ReefGuideAPI.buffer_simplify")],-1)),s[37]||(s[37]=e()),t(a,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),s[38]||(s[38]=n(`
julia
buffer_simplify(
+    gdf::DataFrame;
+    number_verts::Int64=30,
+    buffer_dist_m::Int64=40
+)::Vector{GeoInterface.Wrappers.WrapperGeometry}

Simplify and buffer the polygons in a GeoDataFrame to account for uncertainty and inaccuracies in the reef outlines.

Arguments

Returns

Vector containing buffered and simplified reef polygons

source

`,7))]),i("details",_,[i("summary",null,[s[39]||(s[39]=i("a",{id:"ReefGuideAPI.cache_filename-Tuple{Dict, Dict, String, String}",href:"#ReefGuideAPI.cache_filename-Tuple{Dict, Dict, String, String}"},[i("span",{class:"jlbinding"},"ReefGuideAPI.cache_filename")],-1)),s[40]||(s[40]=e()),t(a,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),s[41]||(s[41]=n('
julia
cache_filename(qp::Dict, config::Dict, suffix::String, ext::String)

Generate a filename for a cache.

Arguments

source

',5))]),i("details",j,[i("summary",null,[s[42]||(s[42]=i("a",{id:"ReefGuideAPI.closest_reef_edge-Tuple{GeometryBasics.Point{2, Float64}, Vector{GeometryBasics.Line{2, Float64}}}",href:"#ReefGuideAPI.closest_reef_edge-Tuple{GeometryBasics.Point{2, Float64}, Vector{GeometryBasics.Line{2, Float64}}}"},[i("span",{class:"jlbinding"},"ReefGuideAPI.closest_reef_edge")],-1)),s[43]||(s[43]=e()),t(a,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),s[44]||(s[44]=n(`
julia
closest_reef_edge(
+    pixel::GeometryBasics.Point{2, Float64},
+    reef_lines::Vector{GeometryBasics.Line{2, Float64}}
+)::Vector{Tuple{Float64, Float64}}

Find the nearest line in reef_lines to a point pixel.

Arguments

Returns

Coordinates of the reef edge line that is closest to the target pixel. Returned in Tuples.

source

`,7))]),i("details",R,[i("summary",null,[s[45]||(s[45]=i("a",{id:"ReefGuideAPI.create_bbox-Tuple{Tuple, Tuple}",href:"#ReefGuideAPI.create_bbox-Tuple{Tuple, Tuple}"},[i("span",{class:"jlbinding"},"ReefGuideAPI.create_bbox")],-1)),s[46]||(s[46]=e()),t(a,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),s[47]||(s[47]=n('
julia
create_bbox(xs::Tuple, ys::Tuple)::Vector{Tuple{Float64, Float64}}

Create bounding box from x and y coordinates

Returns

Bounding box coordinates in order of top left, top right, bottom right, bottom left, top left.

source

',5))]),i("details",I,[i("summary",null,[s[48]||(s[48]=i("a",{id:"ReefGuideAPI.criteria_middleware-Tuple{Any}",href:"#ReefGuideAPI.criteria_middleware-Tuple{Any}"},[i("span",{class:"jlbinding"},"ReefGuideAPI.criteria_middleware")],-1)),s[49]||(s[49]=e()),t(a,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),s[50]||(s[50]=n('
julia
criteria_middleware(handle)

Creates middleware that parses a criteria query before reaching an endpoint

Example

https://somewhere:8000/suitability/assess/region-name/reeftype?criteria_names=Depth,Slope&lb=-9.0,0.0&ub=-2.0,40

source

',5))]),i("details",D,[i("summary",null,[s[51]||(s[51]=i("a",{id:"ReefGuideAPI.degrees_to_meters-Tuple{Any, Any}",href:"#ReefGuideAPI.degrees_to_meters-Tuple{Any, Any}"},[i("span",{class:"jlbinding"},"ReefGuideAPI.degrees_to_meters")],-1)),s[52]||(s[52]=e()),t(a,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),s[53]||(s[53]=n('
julia
degrees_to_meters(x, lat)

Convert degrees to meters at target latitude.

source

',3))]),i("details",v,[i("summary",null,[s[54]||(s[54]=i("a",{id:"ReefGuideAPI.filter_distances-Tuple{Rasters.Raster, Any}",href:"#ReefGuideAPI.filter_distances-Tuple{Rasters.Raster, Any}"},[i("span",{class:"jlbinding"},"ReefGuideAPI.filter_distances")],-1)),s[55]||(s[55]=e()),t(a,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),s[56]||(s[56]=n(`
julia
filter_distances(
+    target_rast::Raster,
+    dist_buffer
+)::Raster

Apply a mask to exclude pixels that are outside the indicated distance buffer(s).

target_rast and the dist_buffer should be in the same CRS (e.g., EPSG:7844 / GDA2020).

Arguments

Returns

source

`,8))]),i("details",T,[i("summary",null,[s[57]||(s[57]=i("a",{id:"ReefGuideAPI.filter_distances-Tuple{Rasters.Raster, DataFrames.DataFrame, Any}",href:"#ReefGuideAPI.filter_distances-Tuple{Rasters.Raster, DataFrames.DataFrame, Any}"},[i("span",{class:"jlbinding"},"ReefGuideAPI.filter_distances")],-1)),s[58]||(s[58]=e()),t(a,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),s[59]||(s[59]=n(`
julia
filter_distances(
+    target_rast::Raster,
+    gdf::DataFrame,
+    dist_nm
+)::Raster

Exclude pixels in target_rast that are beyond dist_nm (nautical miles) from a geometry in gdf. target_rast and gdf should be in the same CRS (EPSG:7844 / GDA2020 for GBR-reef-guidance-assessment).

Arguments

Returns

from a geometry centroid.

source

`,8))]),i("details",B,[i("summary",null,[s[60]||(s[60]=i("a",{id:"ReefGuideAPI.filter_far_polygons-Tuple{Any, GeometryBasics.Point, Float64, Union{Float64, Int64}}",href:"#ReefGuideAPI.filter_far_polygons-Tuple{Any, GeometryBasics.Point, Float64, Union{Float64, Int64}}"},[i("span",{class:"jlbinding"},"ReefGuideAPI.filter_far_polygons")],-1)),s[61]||(s[61]=e()),t(a,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),s[62]||(s[62]=n('
julia
filter_far_polygons(gdf::DataFrame, pixel::GIWrap.Point, lat::Float64, dist::Union{Int64,Float64})::BitVector

Filter out reefs that are > dist (meters) from the target pixel (currently dist is hardcoded in initial_search_rotation()).

source

',3))]),i("details",G,[i("summary",null,[s[63]||(s[63]=i("a",{id:"ReefGuideAPI.filter_sites-Tuple{DataFrames.DataFrame}",href:"#ReefGuideAPI.filter_sites-Tuple{DataFrames.DataFrame}"},[i("span",{class:"jlbinding"},"ReefGuideAPI.filter_sites")],-1)),s[64]||(s[64]=e()),t(a,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),s[65]||(s[65]=n('
julia
filter_sites(res_df::DataFrame)::DataFrame

Filter out sites where the qc_flag indicates a suitabiltiy < surr_threshold in searching. Where site polygons are overlapping, keep only the highest scoring site polygon.

Arguments

Returns

DataFrame containing only the highest scoring sites where site polygons intersect, and containing only sites with scores greater than the surr_threshold specified in identify_edge_aligned_sites() (default=0.33).

source

',7))]),i("details",x,[i("summary",null,[s[66]||(s[66]=i("a",{id:"ReefGuideAPI.find_horizontal-Tuple{GeoInterface.Wrappers.Polygon}",href:"#ReefGuideAPI.find_horizontal-Tuple{GeoInterface.Wrappers.Polygon}"},[i("span",{class:"jlbinding"},"ReefGuideAPI.find_horizontal")],-1)),s[67]||(s[67]=e()),t(a,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),s[68]||(s[68]=n('
julia
find_horizontal(geom::GI.Wrappers.Polygon)::Vector{Tuple{Float64,Float64}, Tuple{Float64,Float64}}

Find a horizontal line if one exists within a geometry.

Returns

Vector containing tuples of coordinates for a horizontal line found within geom.

source

',5))]),i("details",P,[i("summary",null,[s[69]||(s[69]=i("a",{id:"ReefGuideAPI.from_zero-Tuple{Vector{Tuple{Float64, Float64}}}",href:"#ReefGuideAPI.from_zero-Tuple{Vector{Tuple{Float64, Float64}}}"},[i("span",{class:"jlbinding"},"ReefGuideAPI.from_zero")],-1)),s[70]||(s[70]=e()),t(a,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),s[71]||(s[71]=n('
julia
from_zero(v::Vector{Tuple{Float64,Float64}})::Vector{Tuple{Float64, Float64}}

Translates Vector of points v to begin from (0, 0), retaining direction and length.

Argument

source

',5))]),i("details",M,[i("summary",null,[s[72]||(s[72]=i("a",{id:"ReefGuideAPI.generate_criteria_mask!-Tuple{String, Rasters.RasterStack, DataFrames.DataFrame, Vector{ReefGuideAPI.CriteriaBounds{Function}}}",href:"#ReefGuideAPI.generate_criteria_mask!-Tuple{String, Rasters.RasterStack, DataFrames.DataFrame, Vector{ReefGuideAPI.CriteriaBounds{Function}}}"},[i("span",{class:"jlbinding"},"ReefGuideAPI.generate_criteria_mask!")],-1)),s[73]||(s[73]=e()),t(a,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),s[74]||(s[74]=n('
julia
generate_criteria_mask!(fn::String, rst_stack::RasterStack, lookup::DataFrame, ruleset::Vector{CriteriaBounds{Function}})

Generate mask file for a given region and reef type (slopes or flats) according to thresholds applied to a set of criteria.

Notes

Arguments

Returns

Nothing

source

',9))]),i("details",S,[i("summary",null,[s[75]||(s[75]=i("a",{id:"ReefGuideAPI.get_points-Tuple{Any}",href:"#ReefGuideAPI.get_points-Tuple{Any}"},[i("span",{class:"jlbinding"},"ReefGuideAPI.get_points")],-1)),s[76]||(s[76]=e()),t(a,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),s[77]||(s[77]=n('
julia
get_points(geom)

Helper method to retrieve points for a geometry.

source

',3))]),i("details",L,[i("summary",null,[s[78]||(s[78]=i("a",{id:"ReefGuideAPI.identify_edge_aligned_sites-Tuple{DataFrames.DataFrame, DataFrames.DataFrame, Float64, DataFrames.DataFrame, Union{Float64, Int64}, Union{Float64, Int64}, GeoFormatTypes.CoordinateReferenceSystemFormat, Vector{Vector{GeometryBasics.Line{2, Float64}}}, String}",href:"#ReefGuideAPI.identify_edge_aligned_sites-Tuple{DataFrames.DataFrame, DataFrames.DataFrame, Float64, DataFrames.DataFrame, Union{Float64, Int64}, Union{Float64, Int64}, GeoFormatTypes.CoordinateReferenceSystemFormat, Vector{Vector{GeometryBasics.Line{2, Float64}}}, String}"},[i("span",{class:"jlbinding"},"ReefGuideAPI.identify_edge_aligned_sites")],-1)),s[79]||(s[79]=e()),t(a,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),s[80]||(s[80]=n(`
julia
identify_edge_aligned_sites(
+    df::DataFrame,
+    search_pixels::DataFrame,
+    res::Float64,
+    gdf::DataFrame,
+    x_dist::Union{Int64,Float64},
+    y_dist::Union{Int64,Float64},
+    target_crs::GeoFormatTypes.CoordinateReferenceSystemFormat,
+    reef_lines::Vector{Vector{GeometryBasics.Line{2,Float64}}},
+    region::String;
+    degree_step::Float64=15.0,
+    n_rot_p_side::Int64=2,
+    surr_threshold::Float64=0.33
+)::DataFrame

Identify the most suitable site polygons for each pixel in the search_pixels DataFrame. x_dist and y_dist are x and y lengths of the search polygon in meters. A buffer of the raster files' resolution is applied to the search box. And angle from a pixel to a reef edge is identified and used for searching with custom rotation parameters. Method is currently opperating for CRS in degrees units.

Arguments

Returns

DataFrame containing highest score, rotation and polygon for each assessment at pixels in indices.

source

`,7))]),i("details",w,[i("summary",null,[s[81]||(s[81]=i("a",{id:"ReefGuideAPI.identify_edge_aligned_sites-Tuple{Rasters.RasterStack, DataFrames.DataFrame, DataFrames.DataFrame, Union{Float64, Int64}, Union{Float64, Int64}, GeoFormatTypes.CoordinateReferenceSystemFormat, String, Vector{Vector{GeometryBasics.Line{2, Float64}}}}",href:"#ReefGuideAPI.identify_edge_aligned_sites-Tuple{Rasters.RasterStack, DataFrames.DataFrame, DataFrames.DataFrame, Union{Float64, Int64}, Union{Float64, Int64}, GeoFormatTypes.CoordinateReferenceSystemFormat, String, Vector{Vector{GeometryBasics.Line{2, Float64}}}}"},[i("span",{class:"jlbinding"},"ReefGuideAPI.identify_edge_aligned_sites")],-1)),s[82]||(s[82]=e()),t(a,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),s[83]||(s[83]=n(`
julia
identify_edge_aligned_sites(
+    rst_stack::RasterStack,
+    search_pixels::DataFrame,
+    gdf::DataFrame,
+    x_dist::Union{Int64,Float64},
+    y_dist::Union{Int64,Float64},
+    target_crs::GeoFormatTypes.CoordinateReferenceSystemFormat,
+    region::String,
+    reef_lines::Vector{Vector{GeometryBasics.Line{2,Float64}}};
+    degree_step::Float64=15.0,
+    n_rot_per_side::Int64=2
+)::DataFrame

Identify the most suitable site polygons for each pixel in the search_pixels DataFrame. x_dist and y_dist are x and y lengths of the search polygon. A buffer of rst_stack resolution is applied to the search box. And angle from a pixel to a reef edge is identified and used for searching with custom rotation parameters.

Arguments

Returns

DataFrame containing highest score, rotation and polygon for each assessment at pixels in indices.

source

`,7))]),i("details",O,[i("summary",null,[s[84]||(s[84]=i("a",{id:"ReefGuideAPI.identify_search_pixels-Tuple{Rasters.Raster, Any}",href:"#ReefGuideAPI.identify_search_pixels-Tuple{Rasters.Raster, Any}"},[i("span",{class:"jlbinding"},"ReefGuideAPI.identify_search_pixels")],-1)),s[85]||(s[85]=e()),t(a,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),s[86]||(s[86]=n('
julia
identify_search_pixels(input_raster::Raster, criteria_function)::DataFrame

Identifies all pixels in an input raster that return true for the function criteria_function.

Arguments

Returns

DataFrame containing indices, lon and lat for each pixel that is intended for further analysis.

source

',7))]),i("details",V,[i("summary",null,[s[87]||(s[87]=i("a",{id:"ReefGuideAPI.initial_search_box-Tuple{Any, Union{Float64, Int64}, Union{Float64, Int64}, GeoFormatTypes.CoordinateReferenceSystemFormat, Float64}",href:"#ReefGuideAPI.initial_search_box-Tuple{Any, Union{Float64, Int64}, Union{Float64, Int64}, GeoFormatTypes.CoordinateReferenceSystemFormat, Float64}"},[i("span",{class:"jlbinding"},"ReefGuideAPI.initial_search_box")],-1)),s[88]||(s[88]=e()),t(a,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),s[89]||(s[89]=n(`
julia
initial_search_box(
+    (lon::Float64, lat::Float64),
+    x_dist::Union{Int64, Float64},
+    y_dist::Union{Int64, Float64},
+    target_crs::GeoFormatTypes.CoordinateReferenceSystemFormat,
+    res::Float64
+)::GI.Wrappers.Polygon

Create an initial search box that is centered around the point (lon, lat) in target_crs, and is buffered by res distance.

Arguments

Returns

Initial search box geometry.

source

`,7))]),i("details",q,[i("summary",null,[s[90]||(s[90]=i("a",{id:"ReefGuideAPI.initial_search_rotation-Tuple{GeometryBasics.Point{2, Float64}, GeoInterface.Wrappers.Polygon, DataFrames.DataFrame, Vector{Vector{GeometryBasics.Line{2, Float64}}}}",href:"#ReefGuideAPI.initial_search_rotation-Tuple{GeometryBasics.Point{2, Float64}, GeoInterface.Wrappers.Polygon, DataFrames.DataFrame, Vector{Vector{GeometryBasics.Line{2, Float64}}}}"},[i("span",{class:"jlbinding"},"ReefGuideAPI.initial_search_rotation")],-1)),s[91]||(s[91]=e()),t(a,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),s[92]||(s[92]=n(`
julia
initial_search_rotation(
+    pixel::GeometryBasics.Point{2, Float64},
+    geom_buff::GI.Wrappers.Polygon,
+    gdf::DataFrame,
+    reef_outlines::Vector{Vector{GeometryBasics.Line{2, Float64}}};
+    search_buffer::Union{Int64,Float64}=20000.0
+)::Float64

Identifies the closest edge to the target pixel/'geom_buff and returns the initial rotation angle required to match the edge line.

Arguments

source

`,5))]),i("details",U,[i("summary",null,[s[93]||(s[93]=i("a",{id:"ReefGuideAPI.initialize_regional_data_cache-Tuple{String, String}",href:"#ReefGuideAPI.initialize_regional_data_cache-Tuple{String, String}"},[i("span",{class:"jlbinding"},"ReefGuideAPI.initialize_regional_data_cache")],-1)),s[94]||(s[94]=e()),t(a,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),s[95]||(s[95]=n('
julia
initialize_regional_data_cache(reef_data_path::String, reg_cache_fn::String)

Create initial regional data store with data from reef_data_path, excluding geospatial data and save to reg_cache_fn path.

source

',3))]),i("details",z,[i("summary",null,[s[96]||(s[96]=i("a",{id:"ReefGuideAPI.line_angle-Union{Tuple{T}, Tuple{T, T}} where T<:Vector{Tuple{Float64, Float64}}",href:"#ReefGuideAPI.line_angle-Union{Tuple{T}, Tuple{T, T}} where T<:Vector{Tuple{Float64, Float64}}"},[i("span",{class:"jlbinding"},"ReefGuideAPI.line_angle")],-1)),s[97]||(s[97]=e()),t(a,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),s[98]||(s[98]=n(`
julia
line_angle(a::T, b::T)::Float64 where {T <: Vector{Tuple{Float64,Float64}}}

Calculate the angle between two lines.

Arguments

Returns

Angle between the two lines.

Examples

julia
line_angle([(0.0,5.0), (0.0,0.0)], from_zero(edge_line))
+line_angle([(0.0,5.0), (0.0,0.0)], [(1.0, 4.0), (7.0, 8.0)])

source

`,9))]),i("details",N,[i("summary",null,[s[99]||(s[99]=i("a",{id:"ReefGuideAPI.mask_region-NTuple{4, Any}",href:"#ReefGuideAPI.mask_region-NTuple{4, Any}"},[i("span",{class:"jlbinding"},"ReefGuideAPI.mask_region")],-1)),s[100]||(s[100]=e()),t(a,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),s[101]||(s[101]=n('
julia
mask_region(reg_assess_data, reg, qp, rtype)

Arguments

Returns

Raster of region with locations that meet criteria masked.

source

',6))]),i("details",W,[i("summary",null,[s[102]||(s[102]=i("a",{id:"ReefGuideAPI.meters_to_degrees-Tuple{Any, Any}",href:"#ReefGuideAPI.meters_to_degrees-Tuple{Any, Any}"},[i("span",{class:"jlbinding"},"ReefGuideAPI.meters_to_degrees")],-1)),s[103]||(s[103]=e()),t(a,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),s[104]||(s[104]=n('
julia
meters_to_degrees(x, lat)

Convert meters to degrees at target latitude.

source

',3))]),i("details",H,[i("summary",null,[s[105]||(s[105]=i("a",{id:"ReefGuideAPI.move_geom-Tuple{Any, Tuple}",href:"#ReefGuideAPI.move_geom-Tuple{Any, Tuple}"},[i("span",{class:"jlbinding"},"ReefGuideAPI.move_geom")],-1)),s[106]||(s[106]=e()),t(a,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),s[107]||(s[107]=n('
julia
move_geom(geom, new_centroid::Tuple)

Move a geom to a new centroid.

Arguments

source

',5))]),i("details",$,[i("summary",null,[s[108]||(s[108]=i("a",{id:"ReefGuideAPI.n_gdal_threads-Tuple{Dict}",href:"#ReefGuideAPI.n_gdal_threads-Tuple{Dict}"},[i("span",{class:"jlbinding"},"ReefGuideAPI.n_gdal_threads")],-1)),s[109]||(s[109]=e()),t(a,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),s[110]||(s[110]=n('
julia
n_gdal_threads(config::Dict)::String

Retrieve the configured number of threads to use when writing COGs with GDAL.

source

',3))]),i("details",Q,[i("summary",null,[s[111]||(s[111]=i("a",{id:"ReefGuideAPI.output_geojson-Tuple{String, DataFrames.DataFrame}",href:"#ReefGuideAPI.output_geojson-Tuple{String, DataFrames.DataFrame}"},[i("span",{class:"jlbinding"},"ReefGuideAPI.output_geojson")],-1)),s[112]||(s[112]=e()),t(a,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),s[113]||(s[113]=n('
julia
output_geojson(destination_path::String, df::DataFrame)::Nothing

Writes out GeoJSON file to a target directory. Output file will be located at location: destination_path.

Arguments

source

',5))]),i("details",J,[i("summary",null,[s[114]||(s[114]=i("a",{id:"ReefGuideAPI.parse_criteria_query-Tuple{Dict}",href:"#ReefGuideAPI.parse_criteria_query-Tuple{Dict}"},[i("span",{class:"jlbinding"},"ReefGuideAPI.parse_criteria_query")],-1)),s[115]||(s[115]=e()),t(a,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),s[116]||(s[116]=n('
julia
parse_criteria_query(qp)::Tuple

Parse criteria values from request query.

Queries should take the form of: Depth=-9.0:0.0&Slope=0.0:40.0&Rugosity=0.0:0.0

Arguments

Returns

Tuple of criteria names, lower bounds, upper bounds

source

',8))]),i("details",Z,[i("summary",null,[s[117]||(s[117]=i("a",{id:"ReefGuideAPI.polygon_to_lines-Union{Tuple{Union{GeoInterface.Wrappers.MultiPolygon, Vector{T}, T}}, Tuple{T}} where T<:GeoInterface.Wrappers.Polygon",href:"#ReefGuideAPI.polygon_to_lines-Union{Tuple{Union{GeoInterface.Wrappers.MultiPolygon, Vector{T}, T}}, Tuple{T}} where T<:GeoInterface.Wrappers.Polygon"},[i("span",{class:"jlbinding"},"ReefGuideAPI.polygon_to_lines")],-1)),s[118]||(s[118]=e()),t(a,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),s[119]||(s[119]=n(`
julia
polygon_to_lines(
+    polygon::Union{Vector{T},T,GIWrap.MultiPolygon}
+) where {T<:GIWrap.Polygon}

Extract the individual lines between vertices that make up the outline of a polygon.

Returns

Vector of GeometryBasics.Line{2, Float64} with one line for each adjacent vertex pair in polygon.

source

`,5))]),i("details",X,[i("summary",null,[s[120]||(s[120]=i("a",{id:"ReefGuideAPI.port_buffer_mask-Tuple{DataFrames.DataFrame, Float64}",href:"#ReefGuideAPI.port_buffer_mask-Tuple{DataFrames.DataFrame, Float64}"},[i("span",{class:"jlbinding"},"ReefGuideAPI.port_buffer_mask")],-1)),s[121]||(s[121]=e()),t(a,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),s[122]||(s[122]=n('
julia
port_buffer_mask(gdf::DataFrame, dist::Float64; unit::String="NM")

Create a masking buffer around indicated port locations.

Arguments

source

',5))]),i("details",K,[i("summary",null,[s[123]||(s[123]=i("a",{id:"ReefGuideAPI.proportion_suitable-Tuple{BitMatrix}",href:"#ReefGuideAPI.proportion_suitable-Tuple{BitMatrix}"},[i("span",{class:"jlbinding"},"ReefGuideAPI.proportion_suitable")],-1)),s[124]||(s[124]=e()),t(a,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),s[125]||(s[125]=n('
julia
proportion_suitable(subsection::BitMatrix, square_offset::Tuple=(-4,5))::Matrix{Int16}

Calculate the the proportion of the subsection that is suitable for deployments. The subsection is the surrounding a rough hectare area centred on each cell of a raster marked as being suitable according to user-selected criteria.

Cells on the edges of a raster object are assessed using a smaller surrounding area, rather than shifting the window inward. In usual applications, there will be no target pixel close to the edge due to the use of buffer areas.

Arguments

Returns

Matrix of values 0 - 100 indicating the percentage of the area around the target pixel that meet suitability criteria.

source

',8))]),i("details",Y,[i("summary",null,[s[126]||(s[126]=i("a",{id:"ReefGuideAPI.remove_rugosity-NTuple{4, Any}",href:"#ReefGuideAPI.remove_rugosity-NTuple{4, Any}"},[i("span",{class:"jlbinding"},"ReefGuideAPI.remove_rugosity")],-1)),s[127]||(s[127]=e()),t(a,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),s[128]||(s[128]=n('
julia
remove_rugosity(reg, criteria, lbs, ubs)

Remove rugosity layer from consideration if region is not Townsville. Rugosity data currently only exists for the Townsville region.

source

',3))]),i("details",ss,[i("summary",null,[s[129]||(s[129]=i("a",{id:"ReefGuideAPI.rotate_geom-Tuple{Any, Float64, GeoFormatTypes.CoordinateReferenceSystemFormat}",href:"#ReefGuideAPI.rotate_geom-Tuple{Any, Float64, GeoFormatTypes.CoordinateReferenceSystemFormat}"},[i("span",{class:"jlbinding"},"ReefGuideAPI.rotate_geom")],-1)),s[130]||(s[130]=e()),t(a,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),s[131]||(s[131]=n(`
julia
rotate_geom(
+    geom,
+    degrees::Float64,
+    target_crs::GeoFormatTypes.CoordinateReferenceSystemFormat
+)

Rotate target geom by degrees rotation in clockwise direction. target_crs is applied to output geometry.

Returns

Rotated geometry.

source

`,5))]),i("details",is,[i("summary",null,[s[132]||(s[132]=i("a",{id:"ReefGuideAPI.rotate_polygon-Tuple{Any, Any, Any}",href:"#ReefGuideAPI.rotate_polygon-Tuple{Any, Any, Any}"},[i("span",{class:"jlbinding"},"ReefGuideAPI.rotate_polygon")],-1)),s[133]||(s[133]=e()),t(a,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),s[134]||(s[134]=i("p",null,"Rotate the polygon by the given angle about its center.",-1)),s[135]||(s[135]=i("p",null,[i("a",{href:"https://github.com/open-AIMS/ReefGuideAPI.jl/blob/39637e8d1926c44317ec99036d199c22251bfb19/src/site_assessment/geom_ops.jl#L47",target:"_blank",rel:"noreferrer"},"source")],-1))]),i("details",es,[i("summary",null,[s[136]||(s[136]=i("a",{id:"ReefGuideAPI.setup_regional_data-Tuple{Dict}",href:"#ReefGuideAPI.setup_regional_data-Tuple{Dict}"},[i("span",{class:"jlbinding"},"ReefGuideAPI.setup_regional_data")],-1)),s[137]||(s[137]=e()),t(a,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),s[138]||(s[138]=n('
julia
setup_regional_data(config::Dict)

Load regional data to act as an in-memory cache.

Arguments

Returns

OrderedDict of RegionalCriteria for each region.

source

',7))]),i("details",as,[i("summary",null,[s[139]||(s[139]=i("a",{id:"ReefGuideAPI.threshold_mask-Tuple{Any, Symbol, Any}",href:"#ReefGuideAPI.threshold_mask-Tuple{Any, Symbol, Any}"},[i("span",{class:"jlbinding"},"ReefGuideAPI.threshold_mask")],-1)),s[140]||(s[140]=e()),t(a,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),s[141]||(s[141]=n('
julia
threshold_mask(reg::String, rtype::Symbol, crit_map)

Generate mask for a given region and reef type (slopes or flats) according to thresholds applied to a set of criteria.

Notes

Arguments

Returns

True/false mask indicating locations within desired thresholds.

source

',9))]),i("details",ts,[i("summary",null,[s[142]||(s[142]=i("a",{id:"ReefGuideAPI.tile_size-Tuple{Dict}",href:"#ReefGuideAPI.tile_size-Tuple{Dict}"},[i("span",{class:"jlbinding"},"ReefGuideAPI.tile_size")],-1)),s[143]||(s[143]=e()),t(a,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),s[144]||(s[144]=n('
julia
tile_size(config::Dict)::Tuple

Retrieve the configured size of map tiles in pixels (width and height / lon and lat).

source

',3))]),i("details",ns,[i("summary",null,[s[145]||(s[145]=i("a",{id:"ReefGuideAPI.valid_lonlat_inds-Union{Tuple{T}, Tuple{DataFrames.DataFrame, Symbol, T, T}} where T",href:"#ReefGuideAPI.valid_lonlat_inds-Union{Tuple{T}, Tuple{DataFrames.DataFrame, Symbol, T, T}} where T"},[i("span",{class:"jlbinding"},"ReefGuideAPI.valid_lonlat_inds")],-1)),s[146]||(s[146]=e()),t(a,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),s[147]||(s[147]=n('
julia
valid_lonlat_inds(data::DataFrame, criteria::Symbol, lb::T, ub::T) where {T}

Retrieve the indices of valid data for a region.

Arguments

Returns

Tuple{Vector{Int64}, Vector{Int64}}, of lon and lat indices.

source

',7))]),i("details",ls,[i("summary",null,[s[148]||(s[148]=i("a",{id:"ReefGuideAPI.valid_pixel_positions-Union{Tuple{T}, Tuple{DataFrames.DataFrame, Symbol, T, T}} where T",href:"#ReefGuideAPI.valid_pixel_positions-Union{Tuple{T}, Tuple{DataFrames.DataFrame, Symbol, T, T}} where T"},[i("span",{class:"jlbinding"},"ReefGuideAPI.valid_pixel_positions")],-1)),s[149]||(s[149]=e()),t(a,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),s[150]||(s[150]=n('
julia
valid_pixel_positions(data::DataFrame, criteria::Symbol, lb::T, ub::T) where {T}

Obtain the pixel positions of valid data.

Intended for use in applications similar to ImageryLayer - client side pixel filter.

Arguments

source

',6))]),i("details",ps,[i("summary",null,[s[151]||(s[151]=i("a",{id:"ReefGuideAPI.warmup_cache-Tuple{String}",href:"#ReefGuideAPI.warmup_cache-Tuple{String}"},[i("span",{class:"jlbinding"},"ReefGuideAPI.warmup_cache")],-1)),s[152]||(s[152]=e()),t(a,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),s[153]||(s[153]=n('
julia
warmup_cache(config_path::String)

Invokes warm up of regional data cache to reduce later spin up times.

source

',3))]),i("details",rs,[i("summary",null,[s[154]||(s[154]=i("a",{id:"ReefGuideAPI.within_thresholds-Union{Tuple{T}, Tuple{Val, Val, Rasters.Raster, T, T}} where T",href:"#ReefGuideAPI.within_thresholds-Union{Tuple{T}, Tuple{Val, Val, Rasters.Raster, T, T}} where T"},[i("span",{class:"jlbinding"},"ReefGuideAPI.within_thresholds")],-1)),s[155]||(s[155]=e()),t(a,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),s[156]||(s[156]=n('
julia
within_thresholds(ctype::Val, data::Raster, lb::T, ub::T) where {T}

Apply in-bound constraints.

Notes

Why is this a simple one line function? Because we want to be able to cache results for each constraint type.

source

',5))])])}const Es=l(h,[["render",os]]);export{ys as __pageData,Es as default}; diff --git a/dev/assets/api.md.Dxqu1QHi.js b/dev/assets/api.md.Dxqu1QHi.js deleted file mode 100644 index 26203f3..0000000 --- a/dev/assets/api.md.Dxqu1QHi.js +++ /dev/null @@ -1,72 +0,0 @@ -import{_ as l,c as p,j as i,a as e,G as t,a5 as n,B as r,o}from"./chunks/framework.DT0TDSCa.js";const ls=JSON.parse('{"title":"API","description":"","frontmatter":{},"headers":[],"relativePath":"api.md","filePath":"api.md","lastUpdated":null}'),h={name:"api.md"},d={class:"jldocstring custom-block",open:""},k={class:"jldocstring custom-block",open:""},g={class:"jldocstring custom-block",open:""},c={class:"jldocstring custom-block",open:""},u={class:"jldocstring custom-block",open:""},y={class:"jldocstring custom-block",open:""},E={class:"jldocstring custom-block",open:""},f={class:"jldocstring custom-block",open:""},F={class:"jldocstring custom-block",open:""},m={class:"jldocstring custom-block",open:""},b={class:"jldocstring custom-block",open:""},C={class:"jldocstring custom-block",open:""},A={class:"jldocstring custom-block",open:""},_={class:"jldocstring custom-block",open:""},j={class:"jldocstring custom-block",open:""},I={class:"jldocstring custom-block",open:""},D={class:"jldocstring custom-block",open:""},R={class:"jldocstring custom-block",open:""},T={class:"jldocstring custom-block",open:""},v={class:"jldocstring custom-block",open:""},B={class:"jldocstring custom-block",open:""},G={class:"jldocstring custom-block",open:""},x={class:"jldocstring custom-block",open:""},P={class:"jldocstring custom-block",open:""},M={class:"jldocstring custom-block",open:""},S={class:"jldocstring custom-block",open:""},L={class:"jldocstring custom-block",open:""},w={class:"jldocstring custom-block",open:""},V={class:"jldocstring custom-block",open:""},O={class:"jldocstring custom-block",open:""},U={class:"jldocstring custom-block",open:""},q={class:"jldocstring custom-block",open:""},z={class:"jldocstring custom-block",open:""},W={class:"jldocstring custom-block",open:""},N={class:"jldocstring custom-block",open:""},H={class:"jldocstring custom-block",open:""},$={class:"jldocstring custom-block",open:""},J={class:"jldocstring custom-block",open:""},Q={class:"jldocstring custom-block",open:""},Z={class:"jldocstring custom-block",open:""},X={class:"jldocstring custom-block",open:""},K={class:"jldocstring custom-block",open:""};function Y(ss,s,is,es,as,ts){const a=r("Badge");return o(),p("div",null,[s[127]||(s[127]=i("h1",{id:"api",tabindex:"-1"},[e("API "),i("a",{class:"header-anchor",href:"#api","aria-label":'Permalink to "API"'},"​")],-1)),i("details",d,[i("summary",null,[s[0]||(s[0]=i("a",{id:"ReefGuideAPI._cache_location-Tuple{Dict}",href:"#ReefGuideAPI._cache_location-Tuple{Dict}"},[i("span",{class:"jlbinding"},"ReefGuideAPI._cache_location")],-1)),s[1]||(s[1]=e()),t(a,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),s[2]||(s[2]=n('
julia
_cache_location(config::Dict)::String

Retrieve cache location for geotiffs.

source

',3))]),i("details",k,[i("summary",null,[s[3]||(s[3]=i("a",{id:"ReefGuideAPI._lon_lat_to_tile-Tuple{Any, Any, Any}",href:"#ReefGuideAPI._lon_lat_to_tile-Tuple{Any, Any, Any}"},[i("span",{class:"jlbinding"},"ReefGuideAPI._lon_lat_to_tile")],-1)),s[4]||(s[4]=e()),t(a,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),s[5]||(s[5]=n('
julia
_lon_lat_to_tile(zoom, lon, lat)

Identify the corresponding tile coordinates for a given lon/lat.

Returns

x and y tile coordinates

source

',5))]),i("details",g,[i("summary",null,[s[6]||(s[6]=i("a",{id:"ReefGuideAPI._tile_bounds-Union{Tuple{T}, Tuple{T, T, T}} where T<:Int64",href:"#ReefGuideAPI._tile_bounds-Union{Tuple{T}, Tuple{T, T, T}} where T<:Int64"},[i("span",{class:"jlbinding"},"ReefGuideAPI._tile_bounds")],-1)),s[7]||(s[7]=e()),t(a,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),s[8]||(s[8]=n('
julia
_tile_bounds(z::T, x::T, y::T) where {T<:Int64}

Obtain lon/lat bounds of a requested tile.

Returns

West, East, North South (min lon, max lon, lat max, lat min)

source

',5))]),i("details",c,[i("summary",null,[s[9]||(s[9]=i("a",{id:"ReefGuideAPI._tile_to_lon_lat-Union{Tuple{T}, Tuple{T, T, T}} where T<:Int64",href:"#ReefGuideAPI._tile_to_lon_lat-Union{Tuple{T}, Tuple{T, T, T}} where T<:Int64"},[i("span",{class:"jlbinding"},"ReefGuideAPI._tile_to_lon_lat")],-1)),s[10]||(s[10]=e()),t(a,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),s[11]||(s[11]=n('
julia
_tile_to_lon_lat(z::T, x::T, y::T) where {T<:Int64}

Obtain lon/lat of top-left corner of a requested tile.

Returns

lon, lat

source

',5))]),i("details",u,[i("summary",null,[s[12]||(s[12]=i("a",{id:"ReefGuideAPI.adjusted_nearest-Tuple{Rasters.Raster, Int64, Int64, Int64, Tuple{Int64, Int64}}",href:"#ReefGuideAPI.adjusted_nearest-Tuple{Rasters.Raster, Int64, Int64, Int64, Tuple{Int64, Int64}}"},[i("span",{class:"jlbinding"},"ReefGuideAPI.adjusted_nearest")],-1)),s[13]||(s[13]=e()),t(a,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),s[14]||(s[14]=n('
julia
adjusted_nearest(rst::Raster, z::Int, x::Int, y::Int, tile_size::Tuple{Int,Int}, orig_rst_size::Tuple{Int,Int})::Matrix

Resample a raster using nearest neighbor interpolation when the tile includes area outside where data exists (e.g., viewing the globe where the data may appear in a small corner of the tile). This approach attempts to account for planetary curvature while still maintaining some performance.

Arguments

Returns

Matrix with the resampled data.

source

',7))]),i("details",y,[i("summary",null,[s[15]||(s[15]=i("a",{id:"ReefGuideAPI.apply_criteria_thresholds-Tuple{Rasters.RasterStack, DataFrames.DataFrame, Dict}",href:"#ReefGuideAPI.apply_criteria_thresholds-Tuple{Rasters.RasterStack, DataFrames.DataFrame, Dict}"},[i("span",{class:"jlbinding"},"ReefGuideAPI.apply_criteria_thresholds")],-1)),s[16]||(s[16]=e()),t(a,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),s[17]||(s[17]=n(`
julia
apply_criteria_thresholds(criteria_stack::RasterStack, lookup::DataFrame, ruleset::Vector{CriteriaBounds{Function}})::Raster
-apply_criteria_thresholds(criteria_stack::RasterStack, lookup::DataFrame, ruleset::Dict)::Raster
-apply_criteria_thresholds(criteria_stack::RasterStack, lookup::DataFrame, ruleset::NamedTuple)::Raster

Apply thresholds for each criteria.

Arguments

Returns

BitMatrix indicating locations within desired thresholds

source

`,7))]),i("details",E,[i("summary",null,[s[18]||(s[18]=i("a",{id:"ReefGuideAPI.assess_reef_site-Tuple{DataFrames.DataFrame, GeoInterface.Wrappers.Polygon, Float64, GeoFormatTypes.CoordinateReferenceSystemFormat}",href:"#ReefGuideAPI.assess_reef_site-Tuple{DataFrames.DataFrame, GeoInterface.Wrappers.Polygon, Float64, GeoFormatTypes.CoordinateReferenceSystemFormat}"},[i("span",{class:"jlbinding"},"ReefGuideAPI.assess_reef_site")],-1)),s[19]||(s[19]=e()),t(a,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),s[20]||(s[20]=n(`
julia
assess_reef_site(
-    rel_pix::DataFrame,
-    geom::GI.Wrappers.Polygon,
-    max_count::Float64,
-    target_crs::GeoFormatTypes.CoordinateReferenceSystemFormat;
-    degree_step::Float64=15.0,
-    start_rot::Float64=0.0,
-    n_per_side::Int64=2,
-    surr_threshold::Float64=0.33
-)::Tuple{Float64,Int64,GI.Wrappers.Polygon,Int64}

Assesses the rotations of a search box geom for their suitability score (calculated as the proportion of pixels that meet all specified criteria thresholds). Search box rotation steps are returned so that the start_rot angle is 0, rotations anti-clockwise are negative and rotations clockwise are positive.

Arguments

Returns

source

`,7))]),i("details",f,[i("summary",null,[s[21]||(s[21]=i("a",{id:"ReefGuideAPI.assess_reef_site-Tuple{Union{Rasters.Raster, Rasters.RasterStack}, GeoInterface.Wrappers.Polygon, Dict{Symbol, Function}}",href:"#ReefGuideAPI.assess_reef_site-Tuple{Union{Rasters.Raster, Rasters.RasterStack}, GeoInterface.Wrappers.Polygon, Dict{Symbol, Function}}"},[i("span",{class:"jlbinding"},"ReefGuideAPI.assess_reef_site")],-1)),s[22]||(s[22]=e()),t(a,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),s[23]||(s[23]=n(`
julia
assess_reef_site(
-    rst::Union{Raster,RasterStack},
-    geom::GI.Wrappers.Polygon,
-    ruleset::Dict{Symbol,Function};
-    degree_step::Float64=15.0,
-    start_rot::Float64=0.0,
-    n_per_side::Int64=1
-)::Tuple{Float64,Int64,GI.Wrappers.Polygon}

Assess given reef site for it's suitability score at different specified rotations around the initial reef-edge rotation.

Arguments

Returns

source

`,7))]),i("details",F,[i("summary",null,[s[24]||(s[24]=i("a",{id:"ReefGuideAPI.closest_reef_edge-Tuple{GeometryBasics.Point{2, Float64}, Vector{GeometryBasics.Line{2, Float64}}}",href:"#ReefGuideAPI.closest_reef_edge-Tuple{GeometryBasics.Point{2, Float64}, Vector{GeometryBasics.Line{2, Float64}}}"},[i("span",{class:"jlbinding"},"ReefGuideAPI.closest_reef_edge")],-1)),s[25]||(s[25]=e()),t(a,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),s[26]||(s[26]=n(`
julia
closest_reef_edge(
-    pixel::GeometryBasics.Point{2, Float64},
-    reef_lines::Vector{GeometryBasics.Line{2, Float64}}
-)::Vector{Tuple{Float64, Float64}}

Find the nearest line in reef_lines to a point pixel.

Arguments

Returns

Coordinates of the reef edge line that is closest to the target pixel. Returned in Tuples.

source

`,7))]),i("details",m,[i("summary",null,[s[27]||(s[27]=i("a",{id:"ReefGuideAPI.create_bbox-Tuple{Tuple, Tuple}",href:"#ReefGuideAPI.create_bbox-Tuple{Tuple, Tuple}"},[i("span",{class:"jlbinding"},"ReefGuideAPI.create_bbox")],-1)),s[28]||(s[28]=e()),t(a,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),s[29]||(s[29]=n('
julia
create_bbox(xs::Tuple, ys::Tuple)::Vector{Tuple{Float64, Float64}}

Create bounding box from x and y coordinates

Returns

Bounding box coordinates in order of top left, top right, bottom right, bottom left, top left.

source

',5))]),i("details",b,[i("summary",null,[s[30]||(s[30]=i("a",{id:"ReefGuideAPI.criteria_middleware-Tuple{Any}",href:"#ReefGuideAPI.criteria_middleware-Tuple{Any}"},[i("span",{class:"jlbinding"},"ReefGuideAPI.criteria_middleware")],-1)),s[31]||(s[31]=e()),t(a,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),s[32]||(s[32]=n('
julia
criteria_middleware(handle)

Creates middleware that parses a criteria query before reaching an endpoint

Example

https://somewhere:8000/suitability/assess/region-name/reeftype?criteria_names=Depth,Slope&lb=-9.0,0.0&ub=-2.0,40

source

',5))]),i("details",C,[i("summary",null,[s[33]||(s[33]=i("a",{id:"ReefGuideAPI.degrees_to_meters-Tuple{Any, Any}",href:"#ReefGuideAPI.degrees_to_meters-Tuple{Any, Any}"},[i("span",{class:"jlbinding"},"ReefGuideAPI.degrees_to_meters")],-1)),s[34]||(s[34]=e()),t(a,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),s[35]||(s[35]=n('
julia
degrees_to_meters(x, lat)

Convert degrees to meters at target latitude.

source

',3))]),i("details",A,[i("summary",null,[s[36]||(s[36]=i("a",{id:"ReefGuideAPI.filter_distances-Tuple{Rasters.Raster, Any}",href:"#ReefGuideAPI.filter_distances-Tuple{Rasters.Raster, Any}"},[i("span",{class:"jlbinding"},"ReefGuideAPI.filter_distances")],-1)),s[37]||(s[37]=e()),t(a,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),s[38]||(s[38]=n(`
julia
filter_distances(
-    target_rast::Raster,
-    dist_buffer
-)::Raster

Apply a mask to exclude pixels that are outside the indicated distance buffer(s).

target_rast and the dist_buffer should be in the same CRS (e.g., EPSG:7844 / GDA2020).

Arguments

Returns

source

`,8))]),i("details",_,[i("summary",null,[s[39]||(s[39]=i("a",{id:"ReefGuideAPI.filter_far_polygons-Tuple{DataFrames.DataFrame, GeometryBasics.Point, Float64, Union{Float64, Int64}}",href:"#ReefGuideAPI.filter_far_polygons-Tuple{DataFrames.DataFrame, GeometryBasics.Point, Float64, Union{Float64, Int64}}"},[i("span",{class:"jlbinding"},"ReefGuideAPI.filter_far_polygons")],-1)),s[40]||(s[40]=e()),t(a,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),s[41]||(s[41]=n('
julia
filter_far_polygons(gdf::DataFrame, pixel::GIWrap.Point, lat::Float64, dist::Union{Int64,Float64})::BitVector

Filter out reefs that are > dist (meters) from the target pixel (currently dist is hardcoded in initial_search_rotation()).

source

',3))]),i("details",j,[i("summary",null,[s[42]||(s[42]=i("a",{id:"ReefGuideAPI.filter_sites-Tuple{DataFrames.DataFrame}",href:"#ReefGuideAPI.filter_sites-Tuple{DataFrames.DataFrame}"},[i("span",{class:"jlbinding"},"ReefGuideAPI.filter_sites")],-1)),s[43]||(s[43]=e()),t(a,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),s[44]||(s[44]=n('
julia
filter_sites(res_df::DataFrame)::DataFrame

Filter out sites where the qc_flag indicates a suitabiltiy < surr_threshold in searching. Where site polygons are overlapping, keep only the highest scoring site polygon.

Arguments

Returns

DataFrame containing only the highest scoring sites where site polygons intersect, and containing only sites with scores greater than the surr_threshold specified in identify_potential_sites_edges() (default=0.33).

source

',7))]),i("details",I,[i("summary",null,[s[45]||(s[45]=i("a",{id:"ReefGuideAPI.find_horizontal-Tuple{GeoInterface.Wrappers.Polygon}",href:"#ReefGuideAPI.find_horizontal-Tuple{GeoInterface.Wrappers.Polygon}"},[i("span",{class:"jlbinding"},"ReefGuideAPI.find_horizontal")],-1)),s[46]||(s[46]=e()),t(a,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),s[47]||(s[47]=n('
julia
find_horizontal(geom::GI.Wrappers.Polygon)::Vector{Tuple{Float64,Float64}, Tuple{Float64,Float64}}

Find a horizontal line if one exists within a geometry.

Returns

Vector containing tuples of coordinates for a horizontal line found within geom.

source

',5))]),i("details",D,[i("summary",null,[s[48]||(s[48]=i("a",{id:"ReefGuideAPI.from_zero-Tuple{Vector{Tuple{Float64, Float64}}}",href:"#ReefGuideAPI.from_zero-Tuple{Vector{Tuple{Float64, Float64}}}"},[i("span",{class:"jlbinding"},"ReefGuideAPI.from_zero")],-1)),s[49]||(s[49]=e()),t(a,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),s[50]||(s[50]=n('
julia
from_zero(v::Vector{Tuple{Float64,Float64}})::Vector{Tuple{Float64, Float64}}

Translates Vector of points v to begin from (0, 0), retaining direction and length.

Argument

source

',5))]),i("details",R,[i("summary",null,[s[51]||(s[51]=i("a",{id:"ReefGuideAPI.generate_criteria_mask!-Tuple{String, Rasters.RasterStack, DataFrames.DataFrame, Vector{ReefGuideAPI.CriteriaBounds{Function}}}",href:"#ReefGuideAPI.generate_criteria_mask!-Tuple{String, Rasters.RasterStack, DataFrames.DataFrame, Vector{ReefGuideAPI.CriteriaBounds{Function}}}"},[i("span",{class:"jlbinding"},"ReefGuideAPI.generate_criteria_mask!")],-1)),s[52]||(s[52]=e()),t(a,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),s[53]||(s[53]=n('
julia
generate_criteria_mask!(fn::String, rst_stack::RasterStack, lookup::DataFrame, ruleset::Vector{CriteriaBounds{Function}})

Generate mask file for a given region and reef type (slopes or flats) according to thresholds applied to a set of criteria.

Notes

Arguments

Returns

Nothing

source

',9))]),i("details",T,[i("summary",null,[s[54]||(s[54]=i("a",{id:"ReefGuideAPI.get_points-Tuple{Any}",href:"#ReefGuideAPI.get_points-Tuple{Any}"},[i("span",{class:"jlbinding"},"ReefGuideAPI.get_points")],-1)),s[55]||(s[55]=e()),t(a,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),s[56]||(s[56]=n('
julia
get_points(geom)

Helper method to retrieve points for a geometry.

source

',3))]),i("details",v,[i("summary",null,[s[57]||(s[57]=i("a",{id:"ReefGuideAPI.identify_potential_sites_edges-Tuple{DataFrames.DataFrame, DataFrames.DataFrame, Float64, DataFrames.DataFrame, Union{Float64, Int64}, Union{Float64, Int64}, GeoFormatTypes.CoordinateReferenceSystemFormat, Vector{Vector{GeometryBasics.Line{2, Float64}}}, String}",href:"#ReefGuideAPI.identify_potential_sites_edges-Tuple{DataFrames.DataFrame, DataFrames.DataFrame, Float64, DataFrames.DataFrame, Union{Float64, Int64}, Union{Float64, Int64}, GeoFormatTypes.CoordinateReferenceSystemFormat, Vector{Vector{GeometryBasics.Line{2, Float64}}}, String}"},[i("span",{class:"jlbinding"},"ReefGuideAPI.identify_potential_sites_edges")],-1)),s[58]||(s[58]=e()),t(a,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),s[59]||(s[59]=n(`
julia
identify_potential_sites_edges(
-    df::DataFrame,
-    search_pixels::DataFrame,
-    res::Float64,
-    gdf::DataFrame,
-    x_dist::Union{Int64,Float64},
-    y_dist::Union{Int64,Float64},
-    target_crs::GeoFormatTypes.CoordinateReferenceSystemFormat,
-    reef_lines::Vector{Vector{GeometryBasics.Line{2,Float64}}},
-    region::String;
-    degree_step::Float64=15.0,
-    n_rot_p_side::Int64=2,
-    surr_threshold::Float64=0.33
-)::DataFrame

Identify the most suitable site polygons for each pixel in the search_pixels DataFrame. x_dist and y_dist are x and y lengths of the search polygon in meters. A buffer of the raster files' resolution is applied to the search box. And angle from a pixel to a reef edge is identified and used for searching with custom rotation parameters. Method is currently opperating for CRS in degrees units.

Arguments

Returns

DataFrame containing highest score, rotation and polygon for each assessment at pixels in indices.

source

`,7))]),i("details",B,[i("summary",null,[s[60]||(s[60]=i("a",{id:"ReefGuideAPI.identify_potential_sites_edges-Tuple{Rasters.RasterStack, DataFrames.DataFrame, DataFrames.DataFrame, Union{Float64, Int64}, Union{Float64, Int64}, GeoFormatTypes.CoordinateReferenceSystemFormat, String, Vector{Vector{GeometryBasics.Line{2, Float64}}}}",href:"#ReefGuideAPI.identify_potential_sites_edges-Tuple{Rasters.RasterStack, DataFrames.DataFrame, DataFrames.DataFrame, Union{Float64, Int64}, Union{Float64, Int64}, GeoFormatTypes.CoordinateReferenceSystemFormat, String, Vector{Vector{GeometryBasics.Line{2, Float64}}}}"},[i("span",{class:"jlbinding"},"ReefGuideAPI.identify_potential_sites_edges")],-1)),s[61]||(s[61]=e()),t(a,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),s[62]||(s[62]=n(`
julia
identify_potential_sites_edges(
-    rst_stack::RasterStack,
-    search_pixels::DataFrame,
-    gdf::DataFrame,
-    x_dist::Union{Int64,Float64},
-    y_dist::Union{Int64,Float64},
-    target_crs::GeoFormatTypes.CoordinateReferenceSystemFormat,
-    region::String,
-    reef_lines::Vector{Vector{GeometryBasics.Line{2,Float64}}};
-    degree_step::Float64=15.0,
-    n_rot_per_side::Int64=2
-)::DataFrame

Identify the most suitable site polygons for each pixel in the search_pixels DataFrame. x_dist and y_dist are x and y lengths of the search polygon. A buffer of rst_stack resolution is applied to the search box. And angle from a pixel to a reef edge is identified and used for searching with custom rotation parameters.

Arguments

Returns

DataFrame containing highest score, rotation and polygon for each assessment at pixels in indices.

source

`,7))]),i("details",G,[i("summary",null,[s[63]||(s[63]=i("a",{id:"ReefGuideAPI.identify_search_pixels-Tuple{Rasters.Raster, Any}",href:"#ReefGuideAPI.identify_search_pixels-Tuple{Rasters.Raster, Any}"},[i("span",{class:"jlbinding"},"ReefGuideAPI.identify_search_pixels")],-1)),s[64]||(s[64]=e()),t(a,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),s[65]||(s[65]=n('
julia
identify_search_pixels(input_raster::Raster, criteria_function)::DataFrame

Identifies all pixels in an input raster that return true for the function criteria_function.

Arguments

Returns

DataFrame containing indices, lon and lat for each pixel that is intended for further analysis.

source

',7))]),i("details",x,[i("summary",null,[s[66]||(s[66]=i("a",{id:"ReefGuideAPI.initial_search_box-Tuple{Any, Union{Float64, Int64}, Union{Float64, Int64}, GeoFormatTypes.CoordinateReferenceSystemFormat, Float64}",href:"#ReefGuideAPI.initial_search_box-Tuple{Any, Union{Float64, Int64}, Union{Float64, Int64}, GeoFormatTypes.CoordinateReferenceSystemFormat, Float64}"},[i("span",{class:"jlbinding"},"ReefGuideAPI.initial_search_box")],-1)),s[67]||(s[67]=e()),t(a,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),s[68]||(s[68]=n(`
julia
initial_search_box(
-    (lon::Float64, lat::Float64),
-    x_dist::Union{Int64, Float64},
-    y_dist::Union{Int64, Float64},
-    target_crs::GeoFormatTypes.CoordinateReferenceSystemFormat,
-    res::Float64
-)::GI.Wrappers.Polygon

Create an initial search box that is centered around the point (lon, lat) in target_crs, and is buffered by res distance.

Arguments

Returns

Initial search box geometry.

source

`,7))]),i("details",P,[i("summary",null,[s[69]||(s[69]=i("a",{id:"ReefGuideAPI.initial_search_rotation-Tuple{GeometryBasics.Point{2, Float64}, GeoInterface.Wrappers.Polygon, DataFrames.DataFrame, Vector{Vector{GeometryBasics.Line{2, Float64}}}}",href:"#ReefGuideAPI.initial_search_rotation-Tuple{GeometryBasics.Point{2, Float64}, GeoInterface.Wrappers.Polygon, DataFrames.DataFrame, Vector{Vector{GeometryBasics.Line{2, Float64}}}}"},[i("span",{class:"jlbinding"},"ReefGuideAPI.initial_search_rotation")],-1)),s[70]||(s[70]=e()),t(a,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),s[71]||(s[71]=n(`
julia
initial_search_rotation(
-    pixel::GeometryBasics.Point{2, Float64},
-    geom_buff::GI.Wrappers.Polygon,
-    gdf::DataFrame,
-    reef_outlines::Vector{Vector{GeometryBasics.Line{2, Float64}}};
-    search_buffer::Union{Int64,Float64}=20000.0
-)::Float64

Identifies the closest edge to the target pixel/'geom_buff and returns the initial rotation angle required to match the edge line.

Arguments

source

`,5))]),i("details",M,[i("summary",null,[s[72]||(s[72]=i("a",{id:"ReefGuideAPI.line_angle-Union{Tuple{T}, Tuple{T, T}} where T<:Vector{Tuple{Float64, Float64}}",href:"#ReefGuideAPI.line_angle-Union{Tuple{T}, Tuple{T, T}} where T<:Vector{Tuple{Float64, Float64}}"},[i("span",{class:"jlbinding"},"ReefGuideAPI.line_angle")],-1)),s[73]||(s[73]=e()),t(a,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),s[74]||(s[74]=n(`
julia
line_angle(a::T, b::T)::Float64 where {T <: Vector{Tuple{Float64,Float64}}}

Calculate the angle between two lines.

Arguments

Returns

Angle between the two lines.

Examples

julia
line_angle([(0.0,5.0), (0.0,0.0)], from_zero(edge_line))
-line_angle([(0.0,5.0), (0.0,0.0)], [(1.0, 4.0), (7.0, 8.0)])

source

`,9))]),i("details",S,[i("summary",null,[s[75]||(s[75]=i("a",{id:"ReefGuideAPI.make_threshold_mask-Tuple{Any, Symbol, Any}",href:"#ReefGuideAPI.make_threshold_mask-Tuple{Any, Symbol, Any}"},[i("span",{class:"jlbinding"},"ReefGuideAPI.make_threshold_mask")],-1)),s[76]||(s[76]=e()),t(a,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),s[77]||(s[77]=n('
julia
make_threshold_mask(reg::String, rtype::Symbol, crit_map)

Generate mask for a given region and reef type (slopes or flats) according to thresholds applied to a set of criteria.

Notes

Arguments

Returns

True/false mask indicating locations within desired thresholds.

source

',9))]),i("details",L,[i("summary",null,[s[78]||(s[78]=i("a",{id:"ReefGuideAPI.meters_to_degrees-Tuple{Any, Any}",href:"#ReefGuideAPI.meters_to_degrees-Tuple{Any, Any}"},[i("span",{class:"jlbinding"},"ReefGuideAPI.meters_to_degrees")],-1)),s[79]||(s[79]=e()),t(a,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),s[80]||(s[80]=n('
julia
meters_to_degrees(x, lat)

Convert meters to degrees at target latitude.

source

',3))]),i("details",w,[i("summary",null,[s[81]||(s[81]=i("a",{id:"ReefGuideAPI.move_geom-Tuple{Any, Tuple}",href:"#ReefGuideAPI.move_geom-Tuple{Any, Tuple}"},[i("span",{class:"jlbinding"},"ReefGuideAPI.move_geom")],-1)),s[82]||(s[82]=e()),t(a,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),s[83]||(s[83]=n('
julia
move_geom(geom, new_centroid::Tuple)

Move a geom to a new centroid.

Arguments

source

',5))]),i("details",V,[i("summary",null,[s[84]||(s[84]=i("a",{id:"ReefGuideAPI.n_gdal_threads-Tuple{Dict}",href:"#ReefGuideAPI.n_gdal_threads-Tuple{Dict}"},[i("span",{class:"jlbinding"},"ReefGuideAPI.n_gdal_threads")],-1)),s[85]||(s[85]=e()),t(a,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),s[86]||(s[86]=n('
julia
n_gdal_threads(config::Dict)::String

Retrieve the configured number of threads to use when writing COGs with GDAL.

source

',3))]),i("details",O,[i("summary",null,[s[87]||(s[87]=i("a",{id:"ReefGuideAPI.output_geojson-Tuple{DataFrames.DataFrame, String, String}",href:"#ReefGuideAPI.output_geojson-Tuple{DataFrames.DataFrame, String, String}"},[i("span",{class:"jlbinding"},"ReefGuideAPI.output_geojson")],-1)),s[88]||(s[88]=e()),t(a,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),s[89]||(s[89]=n(`
julia
output_geojson(
-    df::DataFrame,
-    region::String,
-    output_dir::String
-)::Nothing

Writes out GeoJSON file to a target directory. Output file will be located at location: "output_dir/output_sites_region.geojson"

Arguments

source

`,5))]),i("details",U,[i("summary",null,[s[90]||(s[90]=i("a",{id:"ReefGuideAPI.parse_criteria_query-Tuple{Dict}",href:"#ReefGuideAPI.parse_criteria_query-Tuple{Dict}"},[i("span",{class:"jlbinding"},"ReefGuideAPI.parse_criteria_query")],-1)),s[91]||(s[91]=e()),t(a,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),s[92]||(s[92]=n('
julia
parse_criteria_query(qp)::Tuple

Parse criteria values from request query.

Queries should take the form of: Depth=-9.0:0.0&Slope=0.0:40.0&Rugosity=0.0:0.0

Arguments

Returns

Tuple of criteria names, lower bounds, upper bounds

source

',8))]),i("details",q,[i("summary",null,[s[93]||(s[93]=i("a",{id:"ReefGuideAPI.polygon_to_lines-Union{Tuple{Union{GeoInterface.Wrappers.MultiPolygon, Vector{T}, T}}, Tuple{T}} where T<:GeoInterface.Wrappers.Polygon",href:"#ReefGuideAPI.polygon_to_lines-Union{Tuple{Union{GeoInterface.Wrappers.MultiPolygon, Vector{T}, T}}, Tuple{T}} where T<:GeoInterface.Wrappers.Polygon"},[i("span",{class:"jlbinding"},"ReefGuideAPI.polygon_to_lines")],-1)),s[94]||(s[94]=e()),t(a,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),s[95]||(s[95]=n(`
julia
polygon_to_lines(
-    polygon::Union{Vector{T},T,GIWrap.MultiPolygon}
-) where {T<:GIWrap.Polygon}

Extract the individual lines between vertices that make up the outline of a polygon.

Returns

Vector of GeometryBasics.Line{2, Float64} with one line for each adjacent vertex pair in polygon.

source

`,5))]),i("details",z,[i("summary",null,[s[96]||(s[96]=i("a",{id:"ReefGuideAPI.port_buffer_mask-Tuple{DataFrames.DataFrame, Float64}",href:"#ReefGuideAPI.port_buffer_mask-Tuple{DataFrames.DataFrame, Float64}"},[i("span",{class:"jlbinding"},"ReefGuideAPI.port_buffer_mask")],-1)),s[97]||(s[97]=e()),t(a,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),s[98]||(s[98]=n('
julia
port_buffer_mask(gdf::DataFrame, dist::Float64; unit::String="NM")

Create a masking buffer around indicated port locations.

Arguments

source

',5))]),i("details",W,[i("summary",null,[s[99]||(s[99]=i("a",{id:"ReefGuideAPI.remove_rugosity-NTuple{4, Any}",href:"#ReefGuideAPI.remove_rugosity-NTuple{4, Any}"},[i("span",{class:"jlbinding"},"ReefGuideAPI.remove_rugosity")],-1)),s[100]||(s[100]=e()),t(a,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),s[101]||(s[101]=n('
julia
remove_rugosity(reg, criteria, lbs, ubs)

Remove rugosity layer from consideration if region is not Townsville. Rugosity data currently only exists for the Townsville region.

source

',3))]),i("details",N,[i("summary",null,[s[102]||(s[102]=i("a",{id:"ReefGuideAPI.rotate_geom-Tuple{Any, Float64, GeoFormatTypes.CoordinateReferenceSystemFormat}",href:"#ReefGuideAPI.rotate_geom-Tuple{Any, Float64, GeoFormatTypes.CoordinateReferenceSystemFormat}"},[i("span",{class:"jlbinding"},"ReefGuideAPI.rotate_geom")],-1)),s[103]||(s[103]=e()),t(a,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),s[104]||(s[104]=n(`
julia
rotate_geom(
-    geom,
-    degrees::Float64,
-    target_crs::GeoFormatTypes.CoordinateReferenceSystemFormat
-)

Rotate target geom by degrees rotation in clockwise direction. target_crs is applied to output geometry.

Returns

Rotated geometry.

source

`,5))]),i("details",H,[i("summary",null,[s[105]||(s[105]=i("a",{id:"ReefGuideAPI.rotate_polygon-Tuple{Any, Any, Any}",href:"#ReefGuideAPI.rotate_polygon-Tuple{Any, Any, Any}"},[i("span",{class:"jlbinding"},"ReefGuideAPI.rotate_polygon")],-1)),s[106]||(s[106]=e()),t(a,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),s[107]||(s[107]=i("p",null,"Rotate the polygon by the given angle about its center.",-1)),s[108]||(s[108]=i("p",null,[i("a",{href:"https://github.com/open-AIMS/ReefGuideAPI.jl/blob/2e5b172fc20425944a2795c3fe2676d47fecde65/src/site_assessment/geom_ops.jl#L47",target:"_blank",rel:"noreferrer"},"source")],-1))]),i("details",$,[i("summary",null,[s[109]||(s[109]=i("a",{id:"ReefGuideAPI.setup_regional_data-Tuple{Dict}",href:"#ReefGuideAPI.setup_regional_data-Tuple{Dict}"},[i("span",{class:"jlbinding"},"ReefGuideAPI.setup_regional_data")],-1)),s[110]||(s[110]=e()),t(a,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),s[111]||(s[111]=n('
julia
setup_regional_data(config::Dict)

Load regional data to act as an in-memory cache.

Arguments

Returns

OrderedDict of RegionalCriteria for each region.

source

',7))]),i("details",J,[i("summary",null,[s[112]||(s[112]=i("a",{id:"ReefGuideAPI.tile_size-Tuple{Dict}",href:"#ReefGuideAPI.tile_size-Tuple{Dict}"},[i("span",{class:"jlbinding"},"ReefGuideAPI.tile_size")],-1)),s[113]||(s[113]=e()),t(a,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),s[114]||(s[114]=n('
julia
tile_size(config::Dict)::Tuple

Retrieve the configured size of map tiles in pixels (width and height / lon and lat).

source

',3))]),i("details",Q,[i("summary",null,[s[115]||(s[115]=i("a",{id:"ReefGuideAPI.valid_lonlat_inds-Union{Tuple{T}, Tuple{DataFrames.DataFrame, Symbol, T, T}} where T",href:"#ReefGuideAPI.valid_lonlat_inds-Union{Tuple{T}, Tuple{DataFrames.DataFrame, Symbol, T, T}} where T"},[i("span",{class:"jlbinding"},"ReefGuideAPI.valid_lonlat_inds")],-1)),s[116]||(s[116]=e()),t(a,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),s[117]||(s[117]=n('
julia
valid_lonlat_inds(data::DataFrame, criteria::Symbol, lb::T, ub::T) where {T}

Retrieve the indices of valid data for a region.

Arguments

Returns

Tuple{Vector{Int64}, Vector{Int64}}, of lon and lat indices.

source

',7))]),i("details",Z,[i("summary",null,[s[118]||(s[118]=i("a",{id:"ReefGuideAPI.valid_pixel_positions-Union{Tuple{T}, Tuple{DataFrames.DataFrame, Symbol, T, T}} where T",href:"#ReefGuideAPI.valid_pixel_positions-Union{Tuple{T}, Tuple{DataFrames.DataFrame, Symbol, T, T}} where T"},[i("span",{class:"jlbinding"},"ReefGuideAPI.valid_pixel_positions")],-1)),s[119]||(s[119]=e()),t(a,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),s[120]||(s[120]=n('
julia
valid_pixel_positions(data::DataFrame, criteria::Symbol, lb::T, ub::T) where {T}

Obtain the pixel positions of valid data.

Intended for use in applications similar to ImageryLayer - client side pixel filter.

Arguments

source

',6))]),i("details",X,[i("summary",null,[s[121]||(s[121]=i("a",{id:"ReefGuideAPI.warmup_cache-Tuple{String}",href:"#ReefGuideAPI.warmup_cache-Tuple{String}"},[i("span",{class:"jlbinding"},"ReefGuideAPI.warmup_cache")],-1)),s[122]||(s[122]=e()),t(a,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),s[123]||(s[123]=n('
julia
warmup_cache(config_path::String)

Invokes warm up of regional data cache to reduce later spin up times.

source

',3))]),i("details",K,[i("summary",null,[s[124]||(s[124]=i("a",{id:"ReefGuideAPI.within_thresholds-Union{Tuple{T}, Tuple{Val, Val, Rasters.Raster, T, T}} where T",href:"#ReefGuideAPI.within_thresholds-Union{Tuple{T}, Tuple{Val, Val, Rasters.Raster, T, T}} where T"},[i("span",{class:"jlbinding"},"ReefGuideAPI.within_thresholds")],-1)),s[125]||(s[125]=e()),t(a,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),s[126]||(s[126]=n('
julia
within_thresholds(ctype::Val, data::Raster, lb::T, ub::T) where {T}

Apply in-bound constraints.

Notes

Why is this a simple one line function? Because we want to be able to cache results for each constraint type.

source

',5))])])}const ps=l(h,[["render",Y]]);export{ls as __pageData,ps as default}; diff --git a/dev/assets/api.md.Dxqu1QHi.lean.js b/dev/assets/api.md.Dxqu1QHi.lean.js deleted file mode 100644 index 26203f3..0000000 --- a/dev/assets/api.md.Dxqu1QHi.lean.js +++ /dev/null @@ -1,72 +0,0 @@ -import{_ as l,c as p,j as i,a as e,G as t,a5 as n,B as r,o}from"./chunks/framework.DT0TDSCa.js";const ls=JSON.parse('{"title":"API","description":"","frontmatter":{},"headers":[],"relativePath":"api.md","filePath":"api.md","lastUpdated":null}'),h={name:"api.md"},d={class:"jldocstring custom-block",open:""},k={class:"jldocstring custom-block",open:""},g={class:"jldocstring custom-block",open:""},c={class:"jldocstring custom-block",open:""},u={class:"jldocstring custom-block",open:""},y={class:"jldocstring custom-block",open:""},E={class:"jldocstring custom-block",open:""},f={class:"jldocstring custom-block",open:""},F={class:"jldocstring custom-block",open:""},m={class:"jldocstring custom-block",open:""},b={class:"jldocstring custom-block",open:""},C={class:"jldocstring custom-block",open:""},A={class:"jldocstring custom-block",open:""},_={class:"jldocstring custom-block",open:""},j={class:"jldocstring custom-block",open:""},I={class:"jldocstring custom-block",open:""},D={class:"jldocstring custom-block",open:""},R={class:"jldocstring custom-block",open:""},T={class:"jldocstring custom-block",open:""},v={class:"jldocstring custom-block",open:""},B={class:"jldocstring custom-block",open:""},G={class:"jldocstring custom-block",open:""},x={class:"jldocstring custom-block",open:""},P={class:"jldocstring custom-block",open:""},M={class:"jldocstring custom-block",open:""},S={class:"jldocstring custom-block",open:""},L={class:"jldocstring custom-block",open:""},w={class:"jldocstring custom-block",open:""},V={class:"jldocstring custom-block",open:""},O={class:"jldocstring custom-block",open:""},U={class:"jldocstring custom-block",open:""},q={class:"jldocstring custom-block",open:""},z={class:"jldocstring custom-block",open:""},W={class:"jldocstring custom-block",open:""},N={class:"jldocstring custom-block",open:""},H={class:"jldocstring custom-block",open:""},$={class:"jldocstring custom-block",open:""},J={class:"jldocstring custom-block",open:""},Q={class:"jldocstring custom-block",open:""},Z={class:"jldocstring custom-block",open:""},X={class:"jldocstring custom-block",open:""},K={class:"jldocstring custom-block",open:""};function Y(ss,s,is,es,as,ts){const a=r("Badge");return o(),p("div",null,[s[127]||(s[127]=i("h1",{id:"api",tabindex:"-1"},[e("API "),i("a",{class:"header-anchor",href:"#api","aria-label":'Permalink to "API"'},"​")],-1)),i("details",d,[i("summary",null,[s[0]||(s[0]=i("a",{id:"ReefGuideAPI._cache_location-Tuple{Dict}",href:"#ReefGuideAPI._cache_location-Tuple{Dict}"},[i("span",{class:"jlbinding"},"ReefGuideAPI._cache_location")],-1)),s[1]||(s[1]=e()),t(a,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),s[2]||(s[2]=n('
julia
_cache_location(config::Dict)::String

Retrieve cache location for geotiffs.

source

',3))]),i("details",k,[i("summary",null,[s[3]||(s[3]=i("a",{id:"ReefGuideAPI._lon_lat_to_tile-Tuple{Any, Any, Any}",href:"#ReefGuideAPI._lon_lat_to_tile-Tuple{Any, Any, Any}"},[i("span",{class:"jlbinding"},"ReefGuideAPI._lon_lat_to_tile")],-1)),s[4]||(s[4]=e()),t(a,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),s[5]||(s[5]=n('
julia
_lon_lat_to_tile(zoom, lon, lat)

Identify the corresponding tile coordinates for a given lon/lat.

Returns

x and y tile coordinates

source

',5))]),i("details",g,[i("summary",null,[s[6]||(s[6]=i("a",{id:"ReefGuideAPI._tile_bounds-Union{Tuple{T}, Tuple{T, T, T}} where T<:Int64",href:"#ReefGuideAPI._tile_bounds-Union{Tuple{T}, Tuple{T, T, T}} where T<:Int64"},[i("span",{class:"jlbinding"},"ReefGuideAPI._tile_bounds")],-1)),s[7]||(s[7]=e()),t(a,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),s[8]||(s[8]=n('
julia
_tile_bounds(z::T, x::T, y::T) where {T<:Int64}

Obtain lon/lat bounds of a requested tile.

Returns

West, East, North South (min lon, max lon, lat max, lat min)

source

',5))]),i("details",c,[i("summary",null,[s[9]||(s[9]=i("a",{id:"ReefGuideAPI._tile_to_lon_lat-Union{Tuple{T}, Tuple{T, T, T}} where T<:Int64",href:"#ReefGuideAPI._tile_to_lon_lat-Union{Tuple{T}, Tuple{T, T, T}} where T<:Int64"},[i("span",{class:"jlbinding"},"ReefGuideAPI._tile_to_lon_lat")],-1)),s[10]||(s[10]=e()),t(a,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),s[11]||(s[11]=n('
julia
_tile_to_lon_lat(z::T, x::T, y::T) where {T<:Int64}

Obtain lon/lat of top-left corner of a requested tile.

Returns

lon, lat

source

',5))]),i("details",u,[i("summary",null,[s[12]||(s[12]=i("a",{id:"ReefGuideAPI.adjusted_nearest-Tuple{Rasters.Raster, Int64, Int64, Int64, Tuple{Int64, Int64}}",href:"#ReefGuideAPI.adjusted_nearest-Tuple{Rasters.Raster, Int64, Int64, Int64, Tuple{Int64, Int64}}"},[i("span",{class:"jlbinding"},"ReefGuideAPI.adjusted_nearest")],-1)),s[13]||(s[13]=e()),t(a,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),s[14]||(s[14]=n('
julia
adjusted_nearest(rst::Raster, z::Int, x::Int, y::Int, tile_size::Tuple{Int,Int}, orig_rst_size::Tuple{Int,Int})::Matrix

Resample a raster using nearest neighbor interpolation when the tile includes area outside where data exists (e.g., viewing the globe where the data may appear in a small corner of the tile). This approach attempts to account for planetary curvature while still maintaining some performance.

Arguments

Returns

Matrix with the resampled data.

source

',7))]),i("details",y,[i("summary",null,[s[15]||(s[15]=i("a",{id:"ReefGuideAPI.apply_criteria_thresholds-Tuple{Rasters.RasterStack, DataFrames.DataFrame, Dict}",href:"#ReefGuideAPI.apply_criteria_thresholds-Tuple{Rasters.RasterStack, DataFrames.DataFrame, Dict}"},[i("span",{class:"jlbinding"},"ReefGuideAPI.apply_criteria_thresholds")],-1)),s[16]||(s[16]=e()),t(a,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),s[17]||(s[17]=n(`
julia
apply_criteria_thresholds(criteria_stack::RasterStack, lookup::DataFrame, ruleset::Vector{CriteriaBounds{Function}})::Raster
-apply_criteria_thresholds(criteria_stack::RasterStack, lookup::DataFrame, ruleset::Dict)::Raster
-apply_criteria_thresholds(criteria_stack::RasterStack, lookup::DataFrame, ruleset::NamedTuple)::Raster

Apply thresholds for each criteria.

Arguments

Returns

BitMatrix indicating locations within desired thresholds

source

`,7))]),i("details",E,[i("summary",null,[s[18]||(s[18]=i("a",{id:"ReefGuideAPI.assess_reef_site-Tuple{DataFrames.DataFrame, GeoInterface.Wrappers.Polygon, Float64, GeoFormatTypes.CoordinateReferenceSystemFormat}",href:"#ReefGuideAPI.assess_reef_site-Tuple{DataFrames.DataFrame, GeoInterface.Wrappers.Polygon, Float64, GeoFormatTypes.CoordinateReferenceSystemFormat}"},[i("span",{class:"jlbinding"},"ReefGuideAPI.assess_reef_site")],-1)),s[19]||(s[19]=e()),t(a,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),s[20]||(s[20]=n(`
julia
assess_reef_site(
-    rel_pix::DataFrame,
-    geom::GI.Wrappers.Polygon,
-    max_count::Float64,
-    target_crs::GeoFormatTypes.CoordinateReferenceSystemFormat;
-    degree_step::Float64=15.0,
-    start_rot::Float64=0.0,
-    n_per_side::Int64=2,
-    surr_threshold::Float64=0.33
-)::Tuple{Float64,Int64,GI.Wrappers.Polygon,Int64}

Assesses the rotations of a search box geom for their suitability score (calculated as the proportion of pixels that meet all specified criteria thresholds). Search box rotation steps are returned so that the start_rot angle is 0, rotations anti-clockwise are negative and rotations clockwise are positive.

Arguments

Returns

source

`,7))]),i("details",f,[i("summary",null,[s[21]||(s[21]=i("a",{id:"ReefGuideAPI.assess_reef_site-Tuple{Union{Rasters.Raster, Rasters.RasterStack}, GeoInterface.Wrappers.Polygon, Dict{Symbol, Function}}",href:"#ReefGuideAPI.assess_reef_site-Tuple{Union{Rasters.Raster, Rasters.RasterStack}, GeoInterface.Wrappers.Polygon, Dict{Symbol, Function}}"},[i("span",{class:"jlbinding"},"ReefGuideAPI.assess_reef_site")],-1)),s[22]||(s[22]=e()),t(a,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),s[23]||(s[23]=n(`
julia
assess_reef_site(
-    rst::Union{Raster,RasterStack},
-    geom::GI.Wrappers.Polygon,
-    ruleset::Dict{Symbol,Function};
-    degree_step::Float64=15.0,
-    start_rot::Float64=0.0,
-    n_per_side::Int64=1
-)::Tuple{Float64,Int64,GI.Wrappers.Polygon}

Assess given reef site for it's suitability score at different specified rotations around the initial reef-edge rotation.

Arguments

Returns

source

`,7))]),i("details",F,[i("summary",null,[s[24]||(s[24]=i("a",{id:"ReefGuideAPI.closest_reef_edge-Tuple{GeometryBasics.Point{2, Float64}, Vector{GeometryBasics.Line{2, Float64}}}",href:"#ReefGuideAPI.closest_reef_edge-Tuple{GeometryBasics.Point{2, Float64}, Vector{GeometryBasics.Line{2, Float64}}}"},[i("span",{class:"jlbinding"},"ReefGuideAPI.closest_reef_edge")],-1)),s[25]||(s[25]=e()),t(a,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),s[26]||(s[26]=n(`
julia
closest_reef_edge(
-    pixel::GeometryBasics.Point{2, Float64},
-    reef_lines::Vector{GeometryBasics.Line{2, Float64}}
-)::Vector{Tuple{Float64, Float64}}

Find the nearest line in reef_lines to a point pixel.

Arguments

Returns

Coordinates of the reef edge line that is closest to the target pixel. Returned in Tuples.

source

`,7))]),i("details",m,[i("summary",null,[s[27]||(s[27]=i("a",{id:"ReefGuideAPI.create_bbox-Tuple{Tuple, Tuple}",href:"#ReefGuideAPI.create_bbox-Tuple{Tuple, Tuple}"},[i("span",{class:"jlbinding"},"ReefGuideAPI.create_bbox")],-1)),s[28]||(s[28]=e()),t(a,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),s[29]||(s[29]=n('
julia
create_bbox(xs::Tuple, ys::Tuple)::Vector{Tuple{Float64, Float64}}

Create bounding box from x and y coordinates

Returns

Bounding box coordinates in order of top left, top right, bottom right, bottom left, top left.

source

',5))]),i("details",b,[i("summary",null,[s[30]||(s[30]=i("a",{id:"ReefGuideAPI.criteria_middleware-Tuple{Any}",href:"#ReefGuideAPI.criteria_middleware-Tuple{Any}"},[i("span",{class:"jlbinding"},"ReefGuideAPI.criteria_middleware")],-1)),s[31]||(s[31]=e()),t(a,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),s[32]||(s[32]=n('
julia
criteria_middleware(handle)

Creates middleware that parses a criteria query before reaching an endpoint

Example

https://somewhere:8000/suitability/assess/region-name/reeftype?criteria_names=Depth,Slope&lb=-9.0,0.0&ub=-2.0,40

source

',5))]),i("details",C,[i("summary",null,[s[33]||(s[33]=i("a",{id:"ReefGuideAPI.degrees_to_meters-Tuple{Any, Any}",href:"#ReefGuideAPI.degrees_to_meters-Tuple{Any, Any}"},[i("span",{class:"jlbinding"},"ReefGuideAPI.degrees_to_meters")],-1)),s[34]||(s[34]=e()),t(a,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),s[35]||(s[35]=n('
julia
degrees_to_meters(x, lat)

Convert degrees to meters at target latitude.

source

',3))]),i("details",A,[i("summary",null,[s[36]||(s[36]=i("a",{id:"ReefGuideAPI.filter_distances-Tuple{Rasters.Raster, Any}",href:"#ReefGuideAPI.filter_distances-Tuple{Rasters.Raster, Any}"},[i("span",{class:"jlbinding"},"ReefGuideAPI.filter_distances")],-1)),s[37]||(s[37]=e()),t(a,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),s[38]||(s[38]=n(`
julia
filter_distances(
-    target_rast::Raster,
-    dist_buffer
-)::Raster

Apply a mask to exclude pixels that are outside the indicated distance buffer(s).

target_rast and the dist_buffer should be in the same CRS (e.g., EPSG:7844 / GDA2020).

Arguments

Returns

source

`,8))]),i("details",_,[i("summary",null,[s[39]||(s[39]=i("a",{id:"ReefGuideAPI.filter_far_polygons-Tuple{DataFrames.DataFrame, GeometryBasics.Point, Float64, Union{Float64, Int64}}",href:"#ReefGuideAPI.filter_far_polygons-Tuple{DataFrames.DataFrame, GeometryBasics.Point, Float64, Union{Float64, Int64}}"},[i("span",{class:"jlbinding"},"ReefGuideAPI.filter_far_polygons")],-1)),s[40]||(s[40]=e()),t(a,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),s[41]||(s[41]=n('
julia
filter_far_polygons(gdf::DataFrame, pixel::GIWrap.Point, lat::Float64, dist::Union{Int64,Float64})::BitVector

Filter out reefs that are > dist (meters) from the target pixel (currently dist is hardcoded in initial_search_rotation()).

source

',3))]),i("details",j,[i("summary",null,[s[42]||(s[42]=i("a",{id:"ReefGuideAPI.filter_sites-Tuple{DataFrames.DataFrame}",href:"#ReefGuideAPI.filter_sites-Tuple{DataFrames.DataFrame}"},[i("span",{class:"jlbinding"},"ReefGuideAPI.filter_sites")],-1)),s[43]||(s[43]=e()),t(a,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),s[44]||(s[44]=n('
julia
filter_sites(res_df::DataFrame)::DataFrame

Filter out sites where the qc_flag indicates a suitabiltiy < surr_threshold in searching. Where site polygons are overlapping, keep only the highest scoring site polygon.

Arguments

Returns

DataFrame containing only the highest scoring sites where site polygons intersect, and containing only sites with scores greater than the surr_threshold specified in identify_potential_sites_edges() (default=0.33).

source

',7))]),i("details",I,[i("summary",null,[s[45]||(s[45]=i("a",{id:"ReefGuideAPI.find_horizontal-Tuple{GeoInterface.Wrappers.Polygon}",href:"#ReefGuideAPI.find_horizontal-Tuple{GeoInterface.Wrappers.Polygon}"},[i("span",{class:"jlbinding"},"ReefGuideAPI.find_horizontal")],-1)),s[46]||(s[46]=e()),t(a,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),s[47]||(s[47]=n('
julia
find_horizontal(geom::GI.Wrappers.Polygon)::Vector{Tuple{Float64,Float64}, Tuple{Float64,Float64}}

Find a horizontal line if one exists within a geometry.

Returns

Vector containing tuples of coordinates for a horizontal line found within geom.

source

',5))]),i("details",D,[i("summary",null,[s[48]||(s[48]=i("a",{id:"ReefGuideAPI.from_zero-Tuple{Vector{Tuple{Float64, Float64}}}",href:"#ReefGuideAPI.from_zero-Tuple{Vector{Tuple{Float64, Float64}}}"},[i("span",{class:"jlbinding"},"ReefGuideAPI.from_zero")],-1)),s[49]||(s[49]=e()),t(a,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),s[50]||(s[50]=n('
julia
from_zero(v::Vector{Tuple{Float64,Float64}})::Vector{Tuple{Float64, Float64}}

Translates Vector of points v to begin from (0, 0), retaining direction and length.

Argument

source

',5))]),i("details",R,[i("summary",null,[s[51]||(s[51]=i("a",{id:"ReefGuideAPI.generate_criteria_mask!-Tuple{String, Rasters.RasterStack, DataFrames.DataFrame, Vector{ReefGuideAPI.CriteriaBounds{Function}}}",href:"#ReefGuideAPI.generate_criteria_mask!-Tuple{String, Rasters.RasterStack, DataFrames.DataFrame, Vector{ReefGuideAPI.CriteriaBounds{Function}}}"},[i("span",{class:"jlbinding"},"ReefGuideAPI.generate_criteria_mask!")],-1)),s[52]||(s[52]=e()),t(a,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),s[53]||(s[53]=n('
julia
generate_criteria_mask!(fn::String, rst_stack::RasterStack, lookup::DataFrame, ruleset::Vector{CriteriaBounds{Function}})

Generate mask file for a given region and reef type (slopes or flats) according to thresholds applied to a set of criteria.

Notes

Arguments

Returns

Nothing

source

',9))]),i("details",T,[i("summary",null,[s[54]||(s[54]=i("a",{id:"ReefGuideAPI.get_points-Tuple{Any}",href:"#ReefGuideAPI.get_points-Tuple{Any}"},[i("span",{class:"jlbinding"},"ReefGuideAPI.get_points")],-1)),s[55]||(s[55]=e()),t(a,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),s[56]||(s[56]=n('
julia
get_points(geom)

Helper method to retrieve points for a geometry.

source

',3))]),i("details",v,[i("summary",null,[s[57]||(s[57]=i("a",{id:"ReefGuideAPI.identify_potential_sites_edges-Tuple{DataFrames.DataFrame, DataFrames.DataFrame, Float64, DataFrames.DataFrame, Union{Float64, Int64}, Union{Float64, Int64}, GeoFormatTypes.CoordinateReferenceSystemFormat, Vector{Vector{GeometryBasics.Line{2, Float64}}}, String}",href:"#ReefGuideAPI.identify_potential_sites_edges-Tuple{DataFrames.DataFrame, DataFrames.DataFrame, Float64, DataFrames.DataFrame, Union{Float64, Int64}, Union{Float64, Int64}, GeoFormatTypes.CoordinateReferenceSystemFormat, Vector{Vector{GeometryBasics.Line{2, Float64}}}, String}"},[i("span",{class:"jlbinding"},"ReefGuideAPI.identify_potential_sites_edges")],-1)),s[58]||(s[58]=e()),t(a,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),s[59]||(s[59]=n(`
julia
identify_potential_sites_edges(
-    df::DataFrame,
-    search_pixels::DataFrame,
-    res::Float64,
-    gdf::DataFrame,
-    x_dist::Union{Int64,Float64},
-    y_dist::Union{Int64,Float64},
-    target_crs::GeoFormatTypes.CoordinateReferenceSystemFormat,
-    reef_lines::Vector{Vector{GeometryBasics.Line{2,Float64}}},
-    region::String;
-    degree_step::Float64=15.0,
-    n_rot_p_side::Int64=2,
-    surr_threshold::Float64=0.33
-)::DataFrame

Identify the most suitable site polygons for each pixel in the search_pixels DataFrame. x_dist and y_dist are x and y lengths of the search polygon in meters. A buffer of the raster files' resolution is applied to the search box. And angle from a pixel to a reef edge is identified and used for searching with custom rotation parameters. Method is currently opperating for CRS in degrees units.

Arguments

Returns

DataFrame containing highest score, rotation and polygon for each assessment at pixels in indices.

source

`,7))]),i("details",B,[i("summary",null,[s[60]||(s[60]=i("a",{id:"ReefGuideAPI.identify_potential_sites_edges-Tuple{Rasters.RasterStack, DataFrames.DataFrame, DataFrames.DataFrame, Union{Float64, Int64}, Union{Float64, Int64}, GeoFormatTypes.CoordinateReferenceSystemFormat, String, Vector{Vector{GeometryBasics.Line{2, Float64}}}}",href:"#ReefGuideAPI.identify_potential_sites_edges-Tuple{Rasters.RasterStack, DataFrames.DataFrame, DataFrames.DataFrame, Union{Float64, Int64}, Union{Float64, Int64}, GeoFormatTypes.CoordinateReferenceSystemFormat, String, Vector{Vector{GeometryBasics.Line{2, Float64}}}}"},[i("span",{class:"jlbinding"},"ReefGuideAPI.identify_potential_sites_edges")],-1)),s[61]||(s[61]=e()),t(a,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),s[62]||(s[62]=n(`
julia
identify_potential_sites_edges(
-    rst_stack::RasterStack,
-    search_pixels::DataFrame,
-    gdf::DataFrame,
-    x_dist::Union{Int64,Float64},
-    y_dist::Union{Int64,Float64},
-    target_crs::GeoFormatTypes.CoordinateReferenceSystemFormat,
-    region::String,
-    reef_lines::Vector{Vector{GeometryBasics.Line{2,Float64}}};
-    degree_step::Float64=15.0,
-    n_rot_per_side::Int64=2
-)::DataFrame

Identify the most suitable site polygons for each pixel in the search_pixels DataFrame. x_dist and y_dist are x and y lengths of the search polygon. A buffer of rst_stack resolution is applied to the search box. And angle from a pixel to a reef edge is identified and used for searching with custom rotation parameters.

Arguments

Returns

DataFrame containing highest score, rotation and polygon for each assessment at pixels in indices.

source

`,7))]),i("details",G,[i("summary",null,[s[63]||(s[63]=i("a",{id:"ReefGuideAPI.identify_search_pixels-Tuple{Rasters.Raster, Any}",href:"#ReefGuideAPI.identify_search_pixels-Tuple{Rasters.Raster, Any}"},[i("span",{class:"jlbinding"},"ReefGuideAPI.identify_search_pixels")],-1)),s[64]||(s[64]=e()),t(a,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),s[65]||(s[65]=n('
julia
identify_search_pixels(input_raster::Raster, criteria_function)::DataFrame

Identifies all pixels in an input raster that return true for the function criteria_function.

Arguments

Returns

DataFrame containing indices, lon and lat for each pixel that is intended for further analysis.

source

',7))]),i("details",x,[i("summary",null,[s[66]||(s[66]=i("a",{id:"ReefGuideAPI.initial_search_box-Tuple{Any, Union{Float64, Int64}, Union{Float64, Int64}, GeoFormatTypes.CoordinateReferenceSystemFormat, Float64}",href:"#ReefGuideAPI.initial_search_box-Tuple{Any, Union{Float64, Int64}, Union{Float64, Int64}, GeoFormatTypes.CoordinateReferenceSystemFormat, Float64}"},[i("span",{class:"jlbinding"},"ReefGuideAPI.initial_search_box")],-1)),s[67]||(s[67]=e()),t(a,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),s[68]||(s[68]=n(`
julia
initial_search_box(
-    (lon::Float64, lat::Float64),
-    x_dist::Union{Int64, Float64},
-    y_dist::Union{Int64, Float64},
-    target_crs::GeoFormatTypes.CoordinateReferenceSystemFormat,
-    res::Float64
-)::GI.Wrappers.Polygon

Create an initial search box that is centered around the point (lon, lat) in target_crs, and is buffered by res distance.

Arguments

Returns

Initial search box geometry.

source

`,7))]),i("details",P,[i("summary",null,[s[69]||(s[69]=i("a",{id:"ReefGuideAPI.initial_search_rotation-Tuple{GeometryBasics.Point{2, Float64}, GeoInterface.Wrappers.Polygon, DataFrames.DataFrame, Vector{Vector{GeometryBasics.Line{2, Float64}}}}",href:"#ReefGuideAPI.initial_search_rotation-Tuple{GeometryBasics.Point{2, Float64}, GeoInterface.Wrappers.Polygon, DataFrames.DataFrame, Vector{Vector{GeometryBasics.Line{2, Float64}}}}"},[i("span",{class:"jlbinding"},"ReefGuideAPI.initial_search_rotation")],-1)),s[70]||(s[70]=e()),t(a,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),s[71]||(s[71]=n(`
julia
initial_search_rotation(
-    pixel::GeometryBasics.Point{2, Float64},
-    geom_buff::GI.Wrappers.Polygon,
-    gdf::DataFrame,
-    reef_outlines::Vector{Vector{GeometryBasics.Line{2, Float64}}};
-    search_buffer::Union{Int64,Float64}=20000.0
-)::Float64

Identifies the closest edge to the target pixel/'geom_buff and returns the initial rotation angle required to match the edge line.

Arguments

source

`,5))]),i("details",M,[i("summary",null,[s[72]||(s[72]=i("a",{id:"ReefGuideAPI.line_angle-Union{Tuple{T}, Tuple{T, T}} where T<:Vector{Tuple{Float64, Float64}}",href:"#ReefGuideAPI.line_angle-Union{Tuple{T}, Tuple{T, T}} where T<:Vector{Tuple{Float64, Float64}}"},[i("span",{class:"jlbinding"},"ReefGuideAPI.line_angle")],-1)),s[73]||(s[73]=e()),t(a,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),s[74]||(s[74]=n(`
julia
line_angle(a::T, b::T)::Float64 where {T <: Vector{Tuple{Float64,Float64}}}

Calculate the angle between two lines.

Arguments

Returns

Angle between the two lines.

Examples

julia
line_angle([(0.0,5.0), (0.0,0.0)], from_zero(edge_line))
-line_angle([(0.0,5.0), (0.0,0.0)], [(1.0, 4.0), (7.0, 8.0)])

source

`,9))]),i("details",S,[i("summary",null,[s[75]||(s[75]=i("a",{id:"ReefGuideAPI.make_threshold_mask-Tuple{Any, Symbol, Any}",href:"#ReefGuideAPI.make_threshold_mask-Tuple{Any, Symbol, Any}"},[i("span",{class:"jlbinding"},"ReefGuideAPI.make_threshold_mask")],-1)),s[76]||(s[76]=e()),t(a,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),s[77]||(s[77]=n('
julia
make_threshold_mask(reg::String, rtype::Symbol, crit_map)

Generate mask for a given region and reef type (slopes or flats) according to thresholds applied to a set of criteria.

Notes

Arguments

Returns

True/false mask indicating locations within desired thresholds.

source

',9))]),i("details",L,[i("summary",null,[s[78]||(s[78]=i("a",{id:"ReefGuideAPI.meters_to_degrees-Tuple{Any, Any}",href:"#ReefGuideAPI.meters_to_degrees-Tuple{Any, Any}"},[i("span",{class:"jlbinding"},"ReefGuideAPI.meters_to_degrees")],-1)),s[79]||(s[79]=e()),t(a,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),s[80]||(s[80]=n('
julia
meters_to_degrees(x, lat)

Convert meters to degrees at target latitude.

source

',3))]),i("details",w,[i("summary",null,[s[81]||(s[81]=i("a",{id:"ReefGuideAPI.move_geom-Tuple{Any, Tuple}",href:"#ReefGuideAPI.move_geom-Tuple{Any, Tuple}"},[i("span",{class:"jlbinding"},"ReefGuideAPI.move_geom")],-1)),s[82]||(s[82]=e()),t(a,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),s[83]||(s[83]=n('
julia
move_geom(geom, new_centroid::Tuple)

Move a geom to a new centroid.

Arguments

source

',5))]),i("details",V,[i("summary",null,[s[84]||(s[84]=i("a",{id:"ReefGuideAPI.n_gdal_threads-Tuple{Dict}",href:"#ReefGuideAPI.n_gdal_threads-Tuple{Dict}"},[i("span",{class:"jlbinding"},"ReefGuideAPI.n_gdal_threads")],-1)),s[85]||(s[85]=e()),t(a,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),s[86]||(s[86]=n('
julia
n_gdal_threads(config::Dict)::String

Retrieve the configured number of threads to use when writing COGs with GDAL.

source

',3))]),i("details",O,[i("summary",null,[s[87]||(s[87]=i("a",{id:"ReefGuideAPI.output_geojson-Tuple{DataFrames.DataFrame, String, String}",href:"#ReefGuideAPI.output_geojson-Tuple{DataFrames.DataFrame, String, String}"},[i("span",{class:"jlbinding"},"ReefGuideAPI.output_geojson")],-1)),s[88]||(s[88]=e()),t(a,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),s[89]||(s[89]=n(`
julia
output_geojson(
-    df::DataFrame,
-    region::String,
-    output_dir::String
-)::Nothing

Writes out GeoJSON file to a target directory. Output file will be located at location: "output_dir/output_sites_region.geojson"

Arguments

source

`,5))]),i("details",U,[i("summary",null,[s[90]||(s[90]=i("a",{id:"ReefGuideAPI.parse_criteria_query-Tuple{Dict}",href:"#ReefGuideAPI.parse_criteria_query-Tuple{Dict}"},[i("span",{class:"jlbinding"},"ReefGuideAPI.parse_criteria_query")],-1)),s[91]||(s[91]=e()),t(a,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),s[92]||(s[92]=n('
julia
parse_criteria_query(qp)::Tuple

Parse criteria values from request query.

Queries should take the form of: Depth=-9.0:0.0&Slope=0.0:40.0&Rugosity=0.0:0.0

Arguments

Returns

Tuple of criteria names, lower bounds, upper bounds

source

',8))]),i("details",q,[i("summary",null,[s[93]||(s[93]=i("a",{id:"ReefGuideAPI.polygon_to_lines-Union{Tuple{Union{GeoInterface.Wrappers.MultiPolygon, Vector{T}, T}}, Tuple{T}} where T<:GeoInterface.Wrappers.Polygon",href:"#ReefGuideAPI.polygon_to_lines-Union{Tuple{Union{GeoInterface.Wrappers.MultiPolygon, Vector{T}, T}}, Tuple{T}} where T<:GeoInterface.Wrappers.Polygon"},[i("span",{class:"jlbinding"},"ReefGuideAPI.polygon_to_lines")],-1)),s[94]||(s[94]=e()),t(a,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),s[95]||(s[95]=n(`
julia
polygon_to_lines(
-    polygon::Union{Vector{T},T,GIWrap.MultiPolygon}
-) where {T<:GIWrap.Polygon}

Extract the individual lines between vertices that make up the outline of a polygon.

Returns

Vector of GeometryBasics.Line{2, Float64} with one line for each adjacent vertex pair in polygon.

source

`,5))]),i("details",z,[i("summary",null,[s[96]||(s[96]=i("a",{id:"ReefGuideAPI.port_buffer_mask-Tuple{DataFrames.DataFrame, Float64}",href:"#ReefGuideAPI.port_buffer_mask-Tuple{DataFrames.DataFrame, Float64}"},[i("span",{class:"jlbinding"},"ReefGuideAPI.port_buffer_mask")],-1)),s[97]||(s[97]=e()),t(a,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),s[98]||(s[98]=n('
julia
port_buffer_mask(gdf::DataFrame, dist::Float64; unit::String="NM")

Create a masking buffer around indicated port locations.

Arguments

source

',5))]),i("details",W,[i("summary",null,[s[99]||(s[99]=i("a",{id:"ReefGuideAPI.remove_rugosity-NTuple{4, Any}",href:"#ReefGuideAPI.remove_rugosity-NTuple{4, Any}"},[i("span",{class:"jlbinding"},"ReefGuideAPI.remove_rugosity")],-1)),s[100]||(s[100]=e()),t(a,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),s[101]||(s[101]=n('
julia
remove_rugosity(reg, criteria, lbs, ubs)

Remove rugosity layer from consideration if region is not Townsville. Rugosity data currently only exists for the Townsville region.

source

',3))]),i("details",N,[i("summary",null,[s[102]||(s[102]=i("a",{id:"ReefGuideAPI.rotate_geom-Tuple{Any, Float64, GeoFormatTypes.CoordinateReferenceSystemFormat}",href:"#ReefGuideAPI.rotate_geom-Tuple{Any, Float64, GeoFormatTypes.CoordinateReferenceSystemFormat}"},[i("span",{class:"jlbinding"},"ReefGuideAPI.rotate_geom")],-1)),s[103]||(s[103]=e()),t(a,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),s[104]||(s[104]=n(`
julia
rotate_geom(
-    geom,
-    degrees::Float64,
-    target_crs::GeoFormatTypes.CoordinateReferenceSystemFormat
-)

Rotate target geom by degrees rotation in clockwise direction. target_crs is applied to output geometry.

Returns

Rotated geometry.

source

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Load regional data to act as an in-memory cache.

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OrderedDict of RegionalCriteria for each region.

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Retrieve the configured size of map tiles in pixels (width and height / lon and lat).

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Retrieve the indices of valid data for a region.

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valid_pixel_positions(data::DataFrame, criteria::Symbol, lb::T, ub::T) where {T}

Obtain the pixel positions of valid data.

Intended for use in applications similar to ImageryLayer - client side pixel filter.

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julia
warmup_cache(config_path::String)

Invokes warm up of regional data cache to reduce later spin up times.

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julia
within_thresholds(ctype::Val, data::Raster, lb::T, ub::T) where {T}

Apply in-bound constraints.

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Why is this a simple one line function? Because we want to be able to cache results for each constraint type.

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nt(Pe.Layout,null,{})},enhanceApp({app:o,router:e,siteData:t}){Ya(o)}};export{Qa as R,bo as c,L as u}; diff --git a/dev/assets/docker.md.CeXB9QeU.js b/dev/assets/docker.md.DslhilOy.js similarity index 98% rename from dev/assets/docker.md.CeXB9QeU.js rename to dev/assets/docker.md.DslhilOy.js index 33641f7..e8227ac 100644 --- a/dev/assets/docker.md.CeXB9QeU.js +++ b/dev/assets/docker.md.DslhilOy.js @@ -1,2 +1,2 @@ -import{_ as e,c as s,a5 as a,o as t}from"./chunks/framework.DT0TDSCa.js";const k=JSON.parse('{"title":"Docker build and run","description":"","frontmatter":{},"headers":[],"relativePath":"docker.md","filePath":"docker.md","lastUpdated":null}'),n={name:"docker.md"};function l(r,i,o,h,d,p){return t(),s("div",null,i[0]||(i[0]=[a(`

Docker build and run ​

The ReefGuideAPI.jl package has an associated Dockerfile and build/publish process. This means you can run an instance of the ReefGuideAPI.jl package without needing to compile/build it with a local Julia installation. You will be able to view the latest published versions of the Docker image on the repository packages page.

Mounting files and required data ​

As mentioned in Getting Started, the ReefGuideAPI.jl package currently requires

  • a config.toml file and

  • a set of input data files

Please include these in a folder called data in your working directory.

When running the below commands, it is assumed you have data available locally with the required files.

Note: Due to how Docker excludes . files, we have named the config file config.toml in the data folder. This is required to launch the server.

To build from src files using Docker ​

bash
docker build . --target reefguide-src -t reefguide

To build from src files using Docker Compose ​

bash
docker compose up --build reefguide-src

To run with mounted files (launch server) using Docker ​

bash
docker run -p 8000:8000 -v ./data:/data/reefguide reefguide

To run with mounted files (launch server) using Docker Compose ​

bash
docker compose up reefguide-src

To run with mounted files (interactive shell) using Docker ​

This will start a Julia shell where ReefGuideAPI is compiled and ready for use e.g.

julia
using ReefGuideAPI
+import{_ as e,c as s,a5 as a,o as t}from"./chunks/framework.CX_bWI7S.js";const k=JSON.parse('{"title":"Docker build and run","description":"","frontmatter":{},"headers":[],"relativePath":"docker.md","filePath":"docker.md","lastUpdated":null}'),n={name:"docker.md"};function l(r,i,o,h,d,p){return t(),s("div",null,i[0]||(i[0]=[a(`
Docker build and run ​
The ReefGuideAPI.jl package has an associated Dockerfile and build/publish process. This means you can run an instance of the ReefGuideAPI.jl package without needing to compile/build it with a local Julia installation. You will be able to view the latest published versions of the Docker image on the repository packages page.
Mounting files and required data ​
As mentioned in Getting Started, the ReefGuideAPI.jl package currently requires
  • a config.toml file and
  • a set of input data files
Please include these in a folder called data in your working directory.
When running the below commands, it is assumed you have data available locally with the required files.
Note: Due to how Docker excludes . files, we have named the config file config.toml in the data folder. This is required to launch the server.
To build from src files using Docker ​
bash
docker build . --target reefguide-src -t reefguide
To build from src files using Docker Compose ​
bash
docker compose up --build reefguide-src
To run with mounted files (launch server) using Docker ​
bash
docker run -p 8000:8000 -v ./data:/data/reefguide reefguide
To run with mounted files (launch server) using Docker Compose ​
bash
docker compose up reefguide-src
To run with mounted files (interactive shell) using Docker ​
This will start a Julia shell where ReefGuideAPI is compiled and ready for use e.g.
julia
using ReefGuideAPI
 ReefGuideAPI.start_server("/data/reefguide/config.toml")
bash
docker run --rm --interactive --entrypoint="julia" --tty -v ./data:/data/reefguide reefguide
`,20)]))}const c=e(n,[["render",l]]);export{k as __pageData,c as default};
diff --git a/dev/assets/docker.md.CeXB9QeU.lean.js b/dev/assets/docker.md.DslhilOy.lean.js
similarity index 98%
rename from dev/assets/docker.md.CeXB9QeU.lean.js
rename to dev/assets/docker.md.DslhilOy.lean.js
index 33641f7..e8227ac 100644
--- a/dev/assets/docker.md.CeXB9QeU.lean.js
+++ b/dev/assets/docker.md.DslhilOy.lean.js
@@ -1,2 +1,2 @@
-import{_ as e,c as s,a5 as a,o as t}from"./chunks/framework.DT0TDSCa.js";const k=JSON.parse('{"title":"Docker build and run","description":"","frontmatter":{},"headers":[],"relativePath":"docker.md","filePath":"docker.md","lastUpdated":null}'),n={name:"docker.md"};function l(r,i,o,h,d,p){return t(),s("div",null,i[0]||(i[0]=[a(`
Docker build and run ​
The ReefGuideAPI.jl package has an associated Dockerfile and build/publish process. This means you can run an instance of the ReefGuideAPI.jl package without needing to compile/build it with a local Julia installation. You will be able to view the latest published versions of the Docker image on the repository packages page.
Mounting files and required data ​
As mentioned in Getting Started, the ReefGuideAPI.jl package currently requires
  • a config.toml file and
  • a set of input data files
Please include these in a folder called data in your working directory.
When running the below commands, it is assumed you have data available locally with the required files.
Note: Due to how Docker excludes . files, we have named the config file config.toml in the data folder. This is required to launch the server.
To build from src files using Docker ​
bash
docker build . --target reefguide-src -t reefguide
To build from src files using Docker Compose ​
bash
docker compose up --build reefguide-src
To run with mounted files (launch server) using Docker ​
bash
docker run -p 8000:8000 -v ./data:/data/reefguide reefguide
To run with mounted files (launch server) using Docker Compose ​
bash
docker compose up reefguide-src
To run with mounted files (interactive shell) using Docker ​
This will start a Julia shell where ReefGuideAPI is compiled and ready for use e.g.
julia
using ReefGuideAPI
+import{_ as e,c as s,a5 as a,o as t}from"./chunks/framework.CX_bWI7S.js";const k=JSON.parse('{"title":"Docker build and run","description":"","frontmatter":{},"headers":[],"relativePath":"docker.md","filePath":"docker.md","lastUpdated":null}'),n={name:"docker.md"};function l(r,i,o,h,d,p){return t(),s("div",null,i[0]||(i[0]=[a(`
Docker build and run ​
The ReefGuideAPI.jl package has an associated Dockerfile and build/publish process. This means you can run an instance of the ReefGuideAPI.jl package without needing to compile/build it with a local Julia installation. You will be able to view the latest published versions of the Docker image on the repository packages page.
Mounting files and required data ​
As mentioned in Getting Started, the ReefGuideAPI.jl package currently requires
  • a config.toml file and
  • a set of input data files
Please include these in a folder called data in your working directory.
When running the below commands, it is assumed you have data available locally with the required files.
Note: Due to how Docker excludes . files, we have named the config file config.toml in the data folder. This is required to launch the server.
To build from src files using Docker ​
bash
docker build . --target reefguide-src -t reefguide
To build from src files using Docker Compose ​
bash
docker compose up --build reefguide-src
To run with mounted files (launch server) using Docker ​
bash
docker run -p 8000:8000 -v ./data:/data/reefguide reefguide
To run with mounted files (launch server) using Docker Compose ​
bash
docker compose up reefguide-src
To run with mounted files (interactive shell) using Docker ​
This will start a Julia shell where ReefGuideAPI is compiled and ready for use e.g.
julia
using ReefGuideAPI
 ReefGuideAPI.start_server("/data/reefguide/config.toml")
bash
docker run --rm --interactive --entrypoint="julia" --tty -v ./data:/data/reefguide reefguide
`,20)]))}const c=e(n,[["render",l]]);export{k as __pageData,c as default};
diff --git a/dev/assets/getting_started.md.ArdKq2gR.js b/dev/assets/getting_started.md.CWSKhprt.js
similarity index 86%
rename from dev/assets/getting_started.md.ArdKq2gR.js
rename to dev/assets/getting_started.md.CWSKhprt.js
index d750b6d..a4e34e7 100644
--- a/dev/assets/getting_started.md.ArdKq2gR.js
+++ b/dev/assets/getting_started.md.CWSKhprt.js
@@ -1,4 +1,4 @@
-import{_ as e,c as i,a5 as a,o as t}from"./chunks/framework.DT0TDSCa.js";const k=JSON.parse('{"title":"Getting Started","description":"","frontmatter":{},"headers":[],"relativePath":"getting_started.md","filePath":"getting_started.md","lastUpdated":null}'),n={name:"getting_started.md"};function l(p,s,o,h,d,r){return t(),i("div",null,s[0]||(s[0]=[a(`
Getting Started ​
Setup ​
Initialize the project the usual way:
julia
]instantiate
A TOML file should be defined indicating location of the MPA dataset. These are currently the files/data created in Step/Script 1a in https://github.com/open-AIMS/GBR-reef-guidance-assessment
toml
[prepped_data]
+import{_ as e,c as i,a5 as a,o as t}from"./chunks/framework.CX_bWI7S.js";const k=JSON.parse('{"title":"Getting Started","description":"","frontmatter":{},"headers":[],"relativePath":"getting_started.md","filePath":"getting_started.md","lastUpdated":null}'),n={name:"getting_started.md"};function l(p,s,h,o,d,r){return t(),i("div",null,s[0]||(s[0]=[a(`
Getting Started ​
Setup ​
Initialize the project the usual way:
julia
]instantiate
A TOML file should be defined indicating location of the MPA dataset. These are currently the files/data created in Step/Script 1a in https://github.com/open-AIMS/GBR-reef-guidance-assessment
toml
[prepped_data]
 PREPPED_DATA_DIR = "C:/some_path_to_data/MPA/"
 
 [server_config]
@@ -23,4 +23,4 @@ import{_ as e,c as i,a5 as a,o as t}from"./chunks/framework.DT0TDSCa.js";const k
 $ julia --project=.
 (sandbox) julia> ]add Revise Infiltrator Chairmarks
 (sandbox) julia> ]dev ..
Copy the quickstart to a file (e.g., dev_server.jl).
Create the .config.toml file and save to the sandbox directory.
Assuming VS Code is configured to default to the sandbox environment and start the Julia REPL at project root:
julia
;cd sandbox
-include("dev_server.jl")
Note that the server now caches the initially loaded spatial data in between server launches to reduce downtime. It will be necessary to restart the Julia session to reload spatial data.
Performance notes ​
The config setting COG_THREADS controls how many threads should be requested when writing out COGs. Ideally this will be set to at least 2 (preferably 4). Higher values do seem to reduce write times but with diminishing returns (tested up to 8). Locally, write times with four threads configured range from 10 to 15 seconds.
Reef edge alignment for site searching ​
identify_potential_sites_edges() can be used to identify potential sites that only align with the nearest reef edge (or specified rotations away from this angle). This method works by identifying the closest edge of reef polygon geometries that have been converted into lines.
The following processing is required before use:
  • Reef polygons should be simplified (GO.simplify()) and buffered to avoid matching possibly inaccurate reef edges.
  • Simplified reef polygons should be provided as vertex-vertex lines with polygon_to_lines().
  • Require raster of target pixels to search, and their indices (currently a vector of CartesianIndices for identifying search pixels). Use findall(bool_search_raster) to return pixel indices.
  • Raster of search pixels should be masked by reef polygons or simplified reef polygons.
  • The target region name should be specified in GBRMPA format.
    • E.g. "Townsville/Whitsunday Management Area" rather than "Townsville-Whitsunday".
Parquet assessment additional setup ​
  • A parquet GeoDataFrame must be loaded and filtered for unsuitable pixels based on user criteria thresholds using a Dict and within_thresholds().
  • lon and lat columns (FLoat64) must be added to the GeoDataFrame.
    • E.g. valid_pixels.lon = first.(GI.coordinates.(valid_pixels.geometry))
    The column used for masking should be the same as the column specified as geometry_col in identify_potential_sites_edges(default =:geometry).
`,42)]))}const u=e(n,[["render",l]]);export{k as __pageData,u as default};
+include("dev_server.jl")
Note that the server now caches the initially loaded spatial data in between server launches to reduce downtime. It will be necessary to restart the Julia session to reload spatial data.
Performance notes ​
The config setting COG_THREADS controls how many threads should be requested when writing out COGs. Ideally this will be set to at least 2 (preferably 4). Higher values do seem to reduce write times but with diminishing returns (tested up to 8). Locally, write times with four threads configured range from 10 to 15 seconds.
Reef edge alignment for site searching ​
identify_edge_aligned_sites() can be used to identify potential sites that only align with the nearest reef edge (or specified rotations away from this angle). This method works by identifying the closest edge of reef polygon geometries that have been converted into lines.
The following processing is required before use:
  • Reef polygons should be simplified (GO.simplify()) and buffered to avoid matching possibly inaccurate reef edges.
  • Simplified reef polygons should be provided as vertex-vertex lines with polygon_to_lines().
  • Require raster of target pixels to search, and their indices (currently a vector of CartesianIndices for identifying search pixels). Use findall(bool_search_raster) to return pixel indices.
  • Raster of search pixels should be masked by reef polygons or simplified reef polygons.
  • The target region name should be specified in GBRMPA format.
    • E.g. "Townsville/Whitsunday Management Area" rather than "Townsville-Whitsunday".
Parquet assessment additional setup ​
  • A parquet GeoDataFrame must be loaded and filtered for unsuitable pixels based on user criteria thresholds using a Dict and within_thresholds().
  • lon and lat columns (FLoat64) must be added to the GeoDataFrame.
    • E.g. valid_pixels.lon = first.(GI.coordinates.(valid_pixels.geometry))
    The column used for masking should be the same as the column specified as geometry_col in identify_edge_aligned_sites(default =:geometry).
`,42)]))}const u=e(n,[["render",l]]);export{k as __pageData,u as default};
diff --git a/dev/assets/getting_started.md.ArdKq2gR.lean.js b/dev/assets/getting_started.md.CWSKhprt.lean.js
similarity index 86%
rename from dev/assets/getting_started.md.ArdKq2gR.lean.js
rename to dev/assets/getting_started.md.CWSKhprt.lean.js
index d750b6d..a4e34e7 100644
--- a/dev/assets/getting_started.md.ArdKq2gR.lean.js
+++ b/dev/assets/getting_started.md.CWSKhprt.lean.js
@@ -1,4 +1,4 @@
-import{_ as e,c as i,a5 as a,o as t}from"./chunks/framework.DT0TDSCa.js";const k=JSON.parse('{"title":"Getting Started","description":"","frontmatter":{},"headers":[],"relativePath":"getting_started.md","filePath":"getting_started.md","lastUpdated":null}'),n={name:"getting_started.md"};function l(p,s,o,h,d,r){return t(),i("div",null,s[0]||(s[0]=[a(`
Getting Started ​
Setup ​
Initialize the project the usual way:
julia
]instantiate
A TOML file should be defined indicating location of the MPA dataset. These are currently the files/data created in Step/Script 1a in https://github.com/open-AIMS/GBR-reef-guidance-assessment
toml
[prepped_data]
+import{_ as e,c as i,a5 as a,o as t}from"./chunks/framework.CX_bWI7S.js";const k=JSON.parse('{"title":"Getting Started","description":"","frontmatter":{},"headers":[],"relativePath":"getting_started.md","filePath":"getting_started.md","lastUpdated":null}'),n={name:"getting_started.md"};function l(p,s,h,o,d,r){return t(),i("div",null,s[0]||(s[0]=[a(`
Getting Started ​
Setup ​
Initialize the project the usual way:
julia
]instantiate
A TOML file should be defined indicating location of the MPA dataset. These are currently the files/data created in Step/Script 1a in https://github.com/open-AIMS/GBR-reef-guidance-assessment
toml
[prepped_data]
 PREPPED_DATA_DIR = "C:/some_path_to_data/MPA/"
 
 [server_config]
@@ -23,4 +23,4 @@ import{_ as e,c as i,a5 as a,o as t}from"./chunks/framework.DT0TDSCa.js";const k
 $ julia --project=.
 (sandbox) julia> ]add Revise Infiltrator Chairmarks
 (sandbox) julia> ]dev ..
Copy the quickstart to a file (e.g., dev_server.jl).
Create the .config.toml file and save to the sandbox directory.
Assuming VS Code is configured to default to the sandbox environment and start the Julia REPL at project root:
julia
;cd sandbox
-include("dev_server.jl")
Note that the server now caches the initially loaded spatial data in between server launches to reduce downtime. It will be necessary to restart the Julia session to reload spatial data.
Performance notes ​
The config setting COG_THREADS controls how many threads should be requested when writing out COGs. Ideally this will be set to at least 2 (preferably 4). Higher values do seem to reduce write times but with diminishing returns (tested up to 8). Locally, write times with four threads configured range from 10 to 15 seconds.
Reef edge alignment for site searching ​
identify_potential_sites_edges() can be used to identify potential sites that only align with the nearest reef edge (or specified rotations away from this angle). This method works by identifying the closest edge of reef polygon geometries that have been converted into lines.
The following processing is required before use:
  • Reef polygons should be simplified (GO.simplify()) and buffered to avoid matching possibly inaccurate reef edges.
  • Simplified reef polygons should be provided as vertex-vertex lines with polygon_to_lines().
  • Require raster of target pixels to search, and their indices (currently a vector of CartesianIndices for identifying search pixels). Use findall(bool_search_raster) to return pixel indices.
  • Raster of search pixels should be masked by reef polygons or simplified reef polygons.
  • The target region name should be specified in GBRMPA format.
    • E.g. "Townsville/Whitsunday Management Area" rather than "Townsville-Whitsunday".
Parquet assessment additional setup ​
  • A parquet GeoDataFrame must be loaded and filtered for unsuitable pixels based on user criteria thresholds using a Dict and within_thresholds().
  • lon and lat columns (FLoat64) must be added to the GeoDataFrame.
    • E.g. valid_pixels.lon = first.(GI.coordinates.(valid_pixels.geometry))
    The column used for masking should be the same as the column specified as geometry_col in identify_potential_sites_edges(default =:geometry).
`,42)]))}const u=e(n,[["render",l]]);export{k as __pageData,u as default};
+include("dev_server.jl")
Note that the server now caches the initially loaded spatial data in between server launches to reduce downtime. It will be necessary to restart the Julia session to reload spatial data.
Performance notes ​
The config setting COG_THREADS controls how many threads should be requested when writing out COGs. Ideally this will be set to at least 2 (preferably 4). Higher values do seem to reduce write times but with diminishing returns (tested up to 8). Locally, write times with four threads configured range from 10 to 15 seconds.
Reef edge alignment for site searching ​
identify_edge_aligned_sites() can be used to identify potential sites that only align with the nearest reef edge (or specified rotations away from this angle). This method works by identifying the closest edge of reef polygon geometries that have been converted into lines.
The following processing is required before use:
  • Reef polygons should be simplified (GO.simplify()) and buffered to avoid matching possibly inaccurate reef edges.
  • Simplified reef polygons should be provided as vertex-vertex lines with polygon_to_lines().
  • Require raster of target pixels to search, and their indices (currently a vector of CartesianIndices for identifying search pixels). Use findall(bool_search_raster) to return pixel indices.
  • Raster of search pixels should be masked by reef polygons or simplified reef polygons.
  • The target region name should be specified in GBRMPA format.
    • E.g. "Townsville/Whitsunday Management Area" rather than "Townsville-Whitsunday".
Parquet assessment additional setup ​
  • A parquet GeoDataFrame must be loaded and filtered for unsuitable pixels based on user criteria thresholds using a Dict and within_thresholds().
  • lon and lat columns (FLoat64) must be added to the GeoDataFrame.
    • E.g. valid_pixels.lon = first.(GI.coordinates.(valid_pixels.geometry))
    The column used for masking should be the same as the column specified as geometry_col in identify_edge_aligned_sites(default =:geometry).
`,42)]))}const u=e(n,[["render",l]]);export{k as __pageData,u as default};
diff --git a/dev/assets/index.md.CBMAENFQ.js b/dev/assets/index.md.BF5iuP_Y.js
similarity index 90%
rename from dev/assets/index.md.CBMAENFQ.js
rename to dev/assets/index.md.BF5iuP_Y.js
index 88e0294..6bb79ae 100644
--- a/dev/assets/index.md.CBMAENFQ.js
+++ b/dev/assets/index.md.BF5iuP_Y.js
@@ -1 +1 @@
-import{_ as t,c as r,j as e,a as i,o as s}from"./chunks/framework.DT0TDSCa.js";const m=JSON.parse('{"title":"ReefGuideAPI.jl","description":"","frontmatter":{},"headers":[],"relativePath":"index.md","filePath":"index.md","lastUpdated":null}'),n={name:"index.md"};function d(l,a,o,p,f,c){return s(),r("div",null,a[0]||(a[0]=[e("h1",{id:"reefguideapi-jl",tabindex:"-1"},[i("ReefGuideAPI.jl "),e("a",{class:"header-anchor",href:"#reefguideapi-jl","aria-label":'Permalink to "ReefGuideAPI.jl"'},"​")],-1),e("p",null,"An API for supporting reef suitability assessments.",-1)]))}const x=t(n,[["render",d]]);export{m as __pageData,x as default};
+import{_ as t,c as r,j as e,a as i,o as s}from"./chunks/framework.CX_bWI7S.js";const m=JSON.parse('{"title":"ReefGuideAPI.jl","description":"","frontmatter":{},"headers":[],"relativePath":"index.md","filePath":"index.md","lastUpdated":null}'),n={name:"index.md"};function d(l,a,o,p,f,c){return s(),r("div",null,a[0]||(a[0]=[e("h1",{id:"reefguideapi-jl",tabindex:"-1"},[i("ReefGuideAPI.jl "),e("a",{class:"header-anchor",href:"#reefguideapi-jl","aria-label":'Permalink to "ReefGuideAPI.jl"'},"​")],-1),e("p",null,"An API for supporting reef suitability assessments.",-1)]))}const x=t(n,[["render",d]]);export{m as __pageData,x as default};
diff --git a/dev/assets/index.md.CBMAENFQ.lean.js b/dev/assets/index.md.BF5iuP_Y.lean.js
similarity index 90%
rename from dev/assets/index.md.CBMAENFQ.lean.js
rename to dev/assets/index.md.BF5iuP_Y.lean.js
index 88e0294..6bb79ae 100644
--- a/dev/assets/index.md.CBMAENFQ.lean.js
+++ b/dev/assets/index.md.BF5iuP_Y.lean.js
@@ -1 +1 @@
-import{_ as t,c as r,j as e,a as i,o as s}from"./chunks/framework.DT0TDSCa.js";const m=JSON.parse('{"title":"ReefGuideAPI.jl","description":"","frontmatter":{},"headers":[],"relativePath":"index.md","filePath":"index.md","lastUpdated":null}'),n={name:"index.md"};function d(l,a,o,p,f,c){return s(),r("div",null,a[0]||(a[0]=[e("h1",{id:"reefguideapi-jl",tabindex:"-1"},[i("ReefGuideAPI.jl "),e("a",{class:"header-anchor",href:"#reefguideapi-jl","aria-label":'Permalink to "ReefGuideAPI.jl"'},"​")],-1),e("p",null,"An API for supporting reef suitability assessments.",-1)]))}const x=t(n,[["render",d]]);export{m as __pageData,x as default};
+import{_ as t,c as r,j as e,a as i,o as s}from"./chunks/framework.CX_bWI7S.js";const m=JSON.parse('{"title":"ReefGuideAPI.jl","description":"","frontmatter":{},"headers":[],"relativePath":"index.md","filePath":"index.md","lastUpdated":null}'),n={name:"index.md"};function d(l,a,o,p,f,c){return s(),r("div",null,a[0]||(a[0]=[e("h1",{id:"reefguideapi-jl",tabindex:"-1"},[i("ReefGuideAPI.jl "),e("a",{class:"header-anchor",href:"#reefguideapi-jl","aria-label":'Permalink to "ReefGuideAPI.jl"'},"​")],-1),e("p",null,"An API for supporting reef suitability assessments.",-1)]))}const x=t(n,[["render",d]]);export{m as __pageData,x as default};
diff --git a/dev/assets/style.Bh_rbBNd.css b/dev/assets/style.CuQhdqpM.css
similarity index 98%
rename from dev/assets/style.Bh_rbBNd.css
rename to dev/assets/style.CuQhdqpM.css
index 562a676..2b8b196 100644
--- a/dev/assets/style.Bh_rbBNd.css
+++ b/dev/assets/style.CuQhdqpM.css
@@ -1 +1 @@
-@import"https://fonts.googleapis.com/css?family=Space+Mono:regular,italic,700,700italic";@import"https://fonts.googleapis.com/css?family=Space+Grotesk:regular,italic,700,700italic";@font-face{font-family:Inter;font-style:normal;font-weight:100 900;font-display:swap;src:url(/ReefGuideAPI.jl/dev/assets/inter-roman-cyrillic-ext.BBPuwvHQ.woff2) format("woff2");unicode-range:U+0460-052F,U+1C80-1C88,U+20B4,U+2DE0-2DFF,U+A640-A69F,U+FE2E-FE2F}@font-face{font-family:Inter;font-style:normal;font-weight:100 900;font-display:swap;src:url(/ReefGuideAPI.jl/dev/assets/inter-roman-cyrillic.C5lxZ8CY.woff2) format("woff2");unicode-range:U+0301,U+0400-045F,U+0490-0491,U+04B0-04B1,U+2116}@font-face{font-family:Inter;font-style:normal;font-weight:100 900;font-display:swap;src:url(/ReefGuideAPI.jl/dev/assets/inter-roman-greek-ext.CqjqNYQ-.woff2) format("woff2");unicode-range:U+1F00-1FFF}@font-face{font-family:Inter;font-style:normal;font-weight:100 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var(--c-black-lighter);--vp-c-bg-mute: var(--c-black-light);--vp-c-bg-soft-mute: var(--c-black-lighter);--vp-c-bg-alt: #0d121b;--vp-c-bg-elv: var(--vp-c-bg-soft);--vp-c-bg-elv-mute: var(--vp-c-bg-soft-mute);--vp-c-mute: var(--vp-c-bg-mute);--vp-c-mute-dark: var(--c-black-lighter);--vp-c-mute-darker: var(--c-black-darker);--vp-home-hero-name-background: -webkit-linear-gradient(78deg, var(--c-yellow-2) 30%, var(--c-green-3))}html.dark .DocSearch{--docsearch-hit-active-color: var(--c-text-light-1)}:root{--vp-button-brand-border: var(--c-yellow-soft-1);--vp-button-brand-text: var(--c-black);--vp-button-brand-bg: var(--c-yellow-1);--vp-button-brand-hover-border: var(--c-yellow-2);--vp-button-brand-hover-text: var(--c-black-darker);--vp-button-brand-hover-bg: var(--c-yellow-2);--vp-button-brand-active-border: var(--c-yellow-soft-1);--vp-button-brand-active-text: var(--c-black-darker);--vp-button-brand-active-bg: var(--vp-button-brand-bg)}:root{--vp-home-hero-name-color: transparent;--vp-home-hero-name-background: linear-gradient(292deg, var(--c-text-light-2) 50%, var(--c-green-2));--vp-home-hero-image-background-image: linear-gradient(15deg, var(--c-yellow-2) 35%, var(--c-text-light-2) 15%);--vp-home-hero-image-filter: blur(40px)}.VPHero .VPImage.image-src{max-height:192px}@media (min-width: 640px){:root{--vp-home-hero-image-filter: blur(56px)}.VPHero .VPImage.image-src{max-height:256px}}@media (min-width: 960px){:root{--vp-home-hero-image-filter: blur(72px)}.VPHero .VPImage.image-src{max-height:320px}}.become-sponsor{font-size:.9em;font-weight:700;width:auto;text-align:center;background-color:transparent;padding:.75em 2em;border-radius:2em;transition:all .15s ease;box-sizing:border-box;border:2px solid var(--c-yellow-2)}.become-sponsor:hover{background-color:var(--c-yellow-1);text-decoration:none;border-color:var(--c-yellow-1);color:var(--c-text-light-1)}.vp-doc a{text-decoration:none}.vp-doc a:hover{text-decoration:underline}.sponsors-top .become-sponsor{font-size:.75em;padding:.2em;width:auto;max-width:150px}kbd{display:inline-block;padding:3px 5px;font-size:.65em;color:var(--vp-c-text-1);vertical-align:middle;background-color:var(--vp-c-bg-mute);border:solid 1px var(--vp-c-bg-soft-mute);border-radius:6px;box-shadow:inset 0 -1px 0 var(--vp-c-bg-soft-mute);line-height:.95em}.VPLocalSearchBox[data-v-5b749456]{position:fixed;z-index:100;top:0;right:0;bottom:0;left:0;display:flex}.backdrop[data-v-5b749456]{position:absolute;top:0;right:0;bottom:0;left:0;background:var(--vp-backdrop-bg-color);transition:opacity .5s}.shell[data-v-5b749456]{position:relative;padding:12px;margin:64px auto;display:flex;flex-direction:column;gap:16px;background:var(--vp-local-search-bg);width:min(100vw - 60px,900px);height:min-content;max-height:min(100vh - 128px,900px);border-radius:6px}@media (max-width: 767px){.shell[data-v-5b749456]{margin:0;width:100vw;height:100vh;max-height:none;border-radius:0}}.search-bar[data-v-5b749456]{border:1px solid var(--vp-c-divider);border-radius:4px;display:flex;align-items:center;padding:0 12px;cursor:text}@media (max-width: 767px){.search-bar[data-v-5b749456]{padding:0 8px}}.search-bar[data-v-5b749456]:focus-within{border-color:var(--vp-c-brand-1)}.local-search-icon[data-v-5b749456]{display:block;font-size:18px}.navigate-icon[data-v-5b749456]{display:block;font-size:14px}.search-icon[data-v-5b749456]{margin:8px}@media (max-width: 767px){.search-icon[data-v-5b749456]{display:none}}.search-input[data-v-5b749456]{padding:6px 12px;font-size:inherit;width:100%}@media (max-width: 767px){.search-input[data-v-5b749456]{padding:6px 4px}}.search-actions[data-v-5b749456]{display:flex;gap:4px}@media (any-pointer: coarse){.search-actions[data-v-5b749456]{gap:8px}}@media (min-width: 769px){.search-actions.before[data-v-5b749456]{display:none}}.search-actions button[data-v-5b749456]{padding:8px}.search-actions 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diff --git a/dev/docker.html b/dev/docker.html
index 72d191f..23e7f4d 100644
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@@ -5,21 +5,21 @@
     
     Docker build and run | ReefGuideAPI.jl
     
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ReefGuideAPI.jl
Appearance
Docker build and run ​
The ReefGuideAPI.jl package has an associated Dockerfile and build/publish process. This means you can run an instance of the ReefGuideAPI.jl package without needing to compile/build it with a local Julia installation. You will be able to view the latest published versions of the Docker image on the repository packages page.
Mounting files and required data ​
As mentioned in Getting Started, the ReefGuideAPI.jl package currently requires
  • a config.toml file and
  • a set of input data files
Please include these in a folder called data in your working directory.
When running the below commands, it is assumed you have data available locally with the required files.
Note: Due to how Docker excludes . files, we have named the config file config.toml in the data folder. This is required to launch the server.
To build from src files using Docker ​
bash
docker build . --target reefguide-src -t reefguide
To build from src files using Docker Compose ​
bash
docker compose up --build reefguide-src
To run with mounted files (launch server) using Docker ​
bash
docker run -p 8000:8000 -v ./data:/data/reefguide reefguide
To run with mounted files (launch server) using Docker Compose ​
bash
docker compose up reefguide-src
To run with mounted files (interactive shell) using Docker ​
This will start a Julia shell where ReefGuideAPI is compiled and ready for use e.g.
julia
using ReefGuideAPI
+    
ReefGuideAPI.jl
Appearance
Docker build and run ​
The ReefGuideAPI.jl package has an associated Dockerfile and build/publish process. This means you can run an instance of the ReefGuideAPI.jl package without needing to compile/build it with a local Julia installation. You will be able to view the latest published versions of the Docker image on the repository packages page.
Mounting files and required data ​
As mentioned in Getting Started, the ReefGuideAPI.jl package currently requires
  • a config.toml file and
  • a set of input data files
Please include these in a folder called data in your working directory.
When running the below commands, it is assumed you have data available locally with the required files.
Note: Due to how Docker excludes . files, we have named the config file config.toml in the data folder. This is required to launch the server.
To build from src files using Docker ​
bash
docker build . --target reefguide-src -t reefguide
To build from src files using Docker Compose ​
bash
docker compose up --build reefguide-src
To run with mounted files (launch server) using Docker ​
bash
docker run -p 8000:8000 -v ./data:/data/reefguide reefguide
To run with mounted files (launch server) using Docker Compose ​
bash
docker compose up reefguide-src
To run with mounted files (interactive shell) using Docker ​
This will start a Julia shell where ReefGuideAPI is compiled and ready for use e.g.
julia
using ReefGuideAPI
 ReefGuideAPI.start_server("/data/reefguide/config.toml")
bash
docker run --rm --interactive --entrypoint="julia" --tty -v ./data:/data/reefguide reefguide

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diff --git a/dev/getting_started.html b/dev/getting_started.html
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     Getting Started | ReefGuideAPI.jl
     
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ReefGuideAPI.jl
Appearance
Getting Started ​
Setup ​
Initialize the project the usual way:
julia
]instantiate
A TOML file should be defined indicating location of the MPA dataset. These are currently the files/data created in Step/Script 1a in https://github.com/open-AIMS/GBR-reef-guidance-assessment
toml
[prepped_data]
+    
ReefGuideAPI.jl
Appearance
Getting Started ​
Setup ​
Initialize the project the usual way:
julia
]instantiate
A TOML file should be defined indicating location of the MPA dataset. These are currently the files/data created in Step/Script 1a in https://github.com/open-AIMS/GBR-reef-guidance-assessment
toml
[prepped_data]
 PREPPED_DATA_DIR = "C:/some_path_to_data/MPA/"
 
 [server_config]
@@ -42,8 +42,8 @@
 $ julia --project=.
 (sandbox) julia> ]add Revise Infiltrator Chairmarks
 (sandbox) julia> ]dev ..
Copy the quickstart to a file (e.g., dev_server.jl).
Create the .config.toml file and save to the sandbox directory.
Assuming VS Code is configured to default to the sandbox environment and start the Julia REPL at project root:
julia
;cd sandbox
-include("dev_server.jl")
Note that the server now caches the initially loaded spatial data in between server launches to reduce downtime. It will be necessary to restart the Julia session to reload spatial data.
Performance notes ​
The config setting COG_THREADS controls how many threads should be requested when writing out COGs. Ideally this will be set to at least 2 (preferably 4). Higher values do seem to reduce write times but with diminishing returns (tested up to 8). Locally, write times with four threads configured range from 10 to 15 seconds.
Reef edge alignment for site searching ​
identify_potential_sites_edges() can be used to identify potential sites that only align with the nearest reef edge (or specified rotations away from this angle). This method works by identifying the closest edge of reef polygon geometries that have been converted into lines.
The following processing is required before use:
  • Reef polygons should be simplified (GO.simplify()) and buffered to avoid matching possibly inaccurate reef edges.
  • Simplified reef polygons should be provided as vertex-vertex lines with polygon_to_lines().
  • Require raster of target pixels to search, and their indices (currently a vector of CartesianIndices for identifying search pixels). Use findall(bool_search_raster) to return pixel indices.
  • Raster of search pixels should be masked by reef polygons or simplified reef polygons.
  • The target region name should be specified in GBRMPA format.
    • E.g. "Townsville/Whitsunday Management Area" rather than "Townsville-Whitsunday".
Parquet assessment additional setup ​
  • A parquet GeoDataFrame must be loaded and filtered for unsuitable pixels based on user criteria thresholds using a Dict and within_thresholds().
  • lon and lat columns (FLoat64) must be added to the GeoDataFrame.
    • E.g. valid_pixels.lon = first.(GI.coordinates.(valid_pixels.geometry))
    The column used for masking should be the same as the column specified as geometry_col in identify_potential_sites_edges(default =:geometry).

-    
+include("dev_server.jl")
Note that the server now caches the initially loaded spatial data in between server launches to reduce downtime. It will be necessary to restart the Julia session to reload spatial data.
Performance notes ​
The config setting COG_THREADS controls how many threads should be requested when writing out COGs. Ideally this will be set to at least 2 (preferably 4). Higher values do seem to reduce write times but with diminishing returns (tested up to 8). Locally, write times with four threads configured range from 10 to 15 seconds.
Reef edge alignment for site searching ​
identify_edge_aligned_sites() can be used to identify potential sites that only align with the nearest reef edge (or specified rotations away from this angle). This method works by identifying the closest edge of reef polygon geometries that have been converted into lines.
The following processing is required before use:
  • Reef polygons should be simplified (GO.simplify()) and buffered to avoid matching possibly inaccurate reef edges.
  • Simplified reef polygons should be provided as vertex-vertex lines with polygon_to_lines().
  • Require raster of target pixels to search, and their indices (currently a vector of CartesianIndices for identifying search pixels). Use findall(bool_search_raster) to return pixel indices.
  • Raster of search pixels should be masked by reef polygons or simplified reef polygons.
  • The target region name should be specified in GBRMPA format.
    • E.g. "Townsville/Whitsunday Management Area" rather than "Townsville-Whitsunday".
Parquet assessment additional setup ​
  • A parquet GeoDataFrame must be loaded and filtered for unsuitable pixels based on user criteria thresholds using a Dict and within_thresholds().
  • lon and lat columns (FLoat64) must be added to the GeoDataFrame.
    • E.g. valid_pixels.lon = first.(GI.coordinates.(valid_pixels.geometry))
    The column used for masking should be the same as the column specified as geometry_col in identify_edge_aligned_sites(default =:geometry).

+    
     
   
 
\ No newline at end of file
diff --git a/dev/hashmap.json b/dev/hashmap.json
index 70f68fc..193cf83 100644
--- a/dev/hashmap.json
+++ b/dev/hashmap.json
@@ -1 +1 @@
-{"api.md":"Dxqu1QHi","docker.md":"CeXB9QeU","getting_started.md":"ArdKq2gR","index.md":"CBMAENFQ"}
+{"api.md":"DYWJQ0KO","docker.md":"DslhilOy","getting_started.md":"CWSKhprt","index.md":"BF5iuP_Y"}
diff --git a/dev/index.html b/dev/index.html
index 652cc7a..47e534a 100644
--- a/dev/index.html
+++ b/dev/index.html
@@ -5,20 +5,20 @@
     
     ReefGuideAPI.jl
     
-    
-    
+    
+    
     
-    
+    
     
-    
-    
-    
+    
+    
+    
     
     
   
   
-    
ReefGuideAPI.jl
Appearance
ReefGuideAPI.jl ​
An API for supporting reef suitability assessments.

-    
+    
ReefGuideAPI.jl
Appearance
ReefGuideAPI.jl ​
An API for supporting reef suitability assessments.

+    
     
   
 
\ No newline at end of file