From 840a891500eb923566be0b284193711c3c0d57bf Mon Sep 17 00:00:00 2001 From: "Documenter.jl" Date: Sat, 5 Oct 2024 23:56:58 +0000 Subject: [PATCH] build based on 2e5b172 --- dev/404.html | 4 +- dev/api.html | 39 +++++++++---------- ...{api.md.DehzNRDj.js => api.md.Dxqu1QHi.js} | 29 +++++++------- ...hzNRDj.lean.js => api.md.Dxqu1QHi.lean.js} | 29 +++++++------- .../{app.DWRAVX01.js => app.XWT9iCUG.js} | 2 +- .../chunks/@localSearchIndexroot.BIq-6JjD.js | 1 - .../chunks/@localSearchIndexroot.DkOCJlzL.js | 1 + ...9Crzas.js => VPLocalSearchBox.lx_FSht0.js} | 2 +- dev/assets/chunks/framework.BvdfcH24.js | 18 --------- dev/assets/chunks/framework.DT0TDSCa.js | 18 +++++++++ .../{theme._B5YJXUN.js => theme.Db56iT4S.js} | 4 +- ...r.md.CFpyQib2.js => docker.md.CeXB9QeU.js} | 2 +- ...ib2.lean.js => docker.md.CeXB9QeU.lean.js} | 2 +- ...PY1d.js => getting_started.md.ArdKq2gR.js} | 2 +- ...js => getting_started.md.ArdKq2gR.lean.js} | 2 +- ...ex.md.kAlQC9BQ.js => index.md.CBMAENFQ.js} | 2 +- ...C9BQ.lean.js => index.md.CBMAENFQ.lean.js} | 2 +- dev/docker.html | 10 ++--- dev/getting_started.html | 10 ++--- dev/hashmap.json | 2 +- dev/index.html | 10 ++--- 21 files changed, 94 insertions(+), 97 deletions(-) rename dev/assets/{api.md.DehzNRDj.js => api.md.Dxqu1QHi.js} (69%) rename dev/assets/{api.md.DehzNRDj.lean.js => api.md.Dxqu1QHi.lean.js} (69%) rename dev/assets/{app.DWRAVX01.js => app.XWT9iCUG.js} (90%) delete mode 100644 dev/assets/chunks/@localSearchIndexroot.BIq-6JjD.js create mode 100644 dev/assets/chunks/@localSearchIndexroot.DkOCJlzL.js rename dev/assets/chunks/{VPLocalSearchBox.BO9Crzas.js => VPLocalSearchBox.lx_FSht0.js} (99%) delete mode 100644 dev/assets/chunks/framework.BvdfcH24.js create mode 100644 dev/assets/chunks/framework.DT0TDSCa.js rename dev/assets/chunks/{theme._B5YJXUN.js => theme.Db56iT4S.js} (99%) rename dev/assets/{docker.md.CFpyQib2.js => docker.md.CeXB9QeU.js} (98%) rename dev/assets/{docker.md.CFpyQib2.lean.js => docker.md.CeXB9QeU.lean.js} (98%) rename dev/assets/{getting_started.md.DKqyPY1d.js => getting_started.md.ArdKq2gR.js} (99%) rename dev/assets/{getting_started.md.DKqyPY1d.lean.js => getting_started.md.ArdKq2gR.lean.js} (99%) rename dev/assets/{index.md.kAlQC9BQ.js => index.md.CBMAENFQ.js} (90%) rename dev/assets/{index.md.kAlQC9BQ.lean.js => index.md.CBMAENFQ.lean.js} (90%) diff --git a/dev/404.html b/dev/404.html index b6924e3..cb12e9e 100644 --- a/dev/404.html +++ b/dev/404.html @@ -8,14 +8,14 @@ - +
- + \ No newline at end of file diff --git a/dev/api.html b/dev/api.html index 2604fd6..575e3d2 100644 --- a/dev/api.html +++ b/dev/api.html @@ -8,18 +8,18 @@ - + - - - + + + -
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.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.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
 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 +28,20 @@
     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 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(
     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_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(
     df::DataFrame,
     search_pixels::DataFrame,
     res::Float64,
@@ -54,7 +54,7 @@
     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 : 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(
     rst_stack::RasterStack,
     search_pixels::DataFrame,
     gdf::DataFrame,
@@ -65,32 +65,31 @@
     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)
  • lats : Latitudinal extent (min and max)
Returns
True/false mask indicating locations within desired thresholds.
source
ReefGuideAPI.masked_nearest Method
julia
masked_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 prioritising performance over accuracy.
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 (lat, long). Note reversed order of coordinates.
Returns
Matrix with the resampled data.
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.nearest Method
julia
nearest(rst::Raster, tile_size::Tuple{Int, Int})::Matrix
Resample a raster to a tile size using nearest neighbor interpolation. This approach prioritising performance over accuracy.
Arguments
  • rst: The input raster to be resampled.
  • tile_size: The desired dimensions of the tile (lat, long).
Returns
Matrix with the resampled data.
Examples
julia
large_raster = Raster(rand(UInt8, 14756, 14838); dims=(X(1:1:14756), Y(1:1:14838)))
-small_matrix = nearest(large_raster, (256, 256))
source
ReefGuideAPI.output_geojson Method
julia
output_geojson(
+)::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(
+)::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(
     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.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.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.DehzNRDj.js b/dev/assets/api.md.Dxqu1QHi.js similarity index 69% rename from dev/assets/api.md.DehzNRDj.js rename to dev/assets/api.md.Dxqu1QHi.js index 96aaa0c..26203f3 100644 --- a/dev/assets/api.md.DehzNRDj.js +++ b/dev/assets/api.md.Dxqu1QHi.js @@ -1,6 +1,6 @@ -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.BvdfcH24.js";const ps=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:""},I={class:"jldocstring custom-block",open:""},R={class:"jldocstring custom-block",open:""},D={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:""},X={class:"jldocstring custom-block",open:""},Z={class:"jldocstring custom-block",open:""},Y={class:"jldocstring custom-block",open:""},K={class:"jldocstring custom-block",open:""};function ss(is,s,es,as,ts,ns){const a=r("Badge");return o(),p("div",null,[s[130]||(s[130]=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.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[13]||(s[13]=e()),t(a,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),s[14]||(s[14]=n(`
julia
apply_criteria_thresholds(criteria_stack::RasterStack, lookup::DataFrame, ruleset::Vector{CriteriaBounds{Function}})::Raster
+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
  • 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
',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
  • 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
`,7))]),i("details",y,[i("summary",null,[s[15]||(s[15]=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[16]||(s[16]=e()),t(a,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),s[17]||(s[17]=n(`
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
`,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,
@@ -9,20 +9,20 @@ import{_ as l,c as p,j as i,a as e,G as t,a5 as n,B as r,o}from"./chunks/framewo
     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
`,7))]),i("details",E,[i("summary",null,[s[18]||(s[18]=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[19]||(s[19]=e()),t(a,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),s[20]||(s[20]=n(`
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
`,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
  • 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
`,7))]),i("details",f,[i("summary",null,[s[21]||(s[21]=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[22]||(s[22]=e()),t(a,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),s[23]||(s[23]=n(`
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 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
`,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
  • 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
`,7))]),i("details",F,[i("summary",null,[s[24]||(s[24]=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[25]||(s[25]=e()),t(a,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),s[26]||(s[26]=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[27]||(s[27]=i("a",{id:"ReefGuideAPI.criteria_middleware-Tuple{Any}",href:"#ReefGuideAPI.criteria_middleware-Tuple{Any}"},[i("span",{class:"jlbinding"},"ReefGuideAPI.criteria_middleware")],-1)),s[28]||(s[28]=e()),t(a,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),s[29]||(s[29]=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",m,[i("summary",null,[s[30]||(s[30]=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[31]||(s[31]=e()),t(a,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),s[32]||(s[32]=n('
julia
degrees_to_meters(x, lat)
Convert degrees to meters at target latitude.
source
',3))]),i("details",C,[i("summary",null,[s[33]||(s[33]=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[34]||(s[34]=e()),t(a,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),s[35]||(s[35]=n(`
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
`,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
  • 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
`,8))]),i("details",A,[i("summary",null,[s[36]||(s[36]=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[37]||(s[37]=e()),t(a,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),s[38]||(s[38]=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",_,[i("summary",null,[s[39]||(s[39]=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[40]||(s[40]=e()),t(a,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),s[41]||(s[41]=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
  • 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
',7))]),i("details",j,[i("summary",null,[s[42]||(s[42]=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[43]||(s[43]=e()),t(a,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),s[44]||(s[44]=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",I,[i("summary",null,[s[45]||(s[45]=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[46]||(s[46]=e()),t(a,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),s[47]||(s[47]=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
  • v : Vector of point coordinates (Tuple{Float64, Float64}).
source
',5))]),i("details",R,[i("summary",null,[s[48]||(s[48]=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[49]||(s[49]=e()),t(a,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),s[50]||(s[50]=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
  • 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
',9))]),i("details",D,[i("summary",null,[s[51]||(s[51]=i("a",{id:"ReefGuideAPI.get_points-Tuple{Any}",href:"#ReefGuideAPI.get_points-Tuple{Any}"},[i("span",{class:"jlbinding"},"ReefGuideAPI.get_points")],-1)),s[52]||(s[52]=e()),t(a,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),s[53]||(s[53]=n('
julia
get_points(geom)
Helper method to retrieve points for a geometry.
source
',3))]),i("details",T,[i("summary",null,[s[54]||(s[54]=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[55]||(s[55]=e()),t(a,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),s[56]||(s[56]=n(`
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
`,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
  • 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
',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
  • v : Vector of point coordinates (Tuple{Float64, Float64}).
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
  • 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
',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,
@@ -35,7 +35,7 @@ import{_ as l,c as p,j as i,a as e,G as t,a5 as n,B as r,o}from"./chunks/framewo
     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
`,7))]),i("details",v,[i("summary",null,[s[57]||(s[57]=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[58]||(s[58]=e()),t(a,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),s[59]||(s[59]=n(`
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 : 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
`,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,
@@ -46,28 +46,27 @@ import{_ as l,c as p,j as i,a as e,G as t,a5 as n,B as r,o}from"./chunks/framewo
     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
`,7))]),i("details",B,[i("summary",null,[s[60]||(s[60]=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[61]||(s[61]=e()),t(a,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),s[62]||(s[62]=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
  • 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
',7))]),i("details",G,[i("summary",null,[s[63]||(s[63]=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[64]||(s[64]=e()),t(a,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),s[65]||(s[65]=n(`
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
`,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
  • 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
',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
  • (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
`,7))]),i("details",x,[i("summary",null,[s[66]||(s[66]=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[67]||(s[67]=e()),t(a,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),s[68]||(s[68]=n(`
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
`,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
  • 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
`,5))]),i("details",P,[i("summary",null,[s[69]||(s[69]=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[70]||(s[70]=e()),t(a,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),s[71]||(s[71]=n(`
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
`,9))]),i("details",M,[i("summary",null,[s[72]||(s[72]=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[73]||(s[73]=e()),t(a,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),s[74]||(s[74]=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
  • 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)
  • lats : Latitudinal extent (min and max)
Returns
True/false mask indicating locations within desired thresholds.
source
',9))]),i("details",S,[i("summary",null,[s[75]||(s[75]=i("a",{id:"ReefGuideAPI.masked_nearest-Tuple{Rasters.Raster, Int64, Int64, Int64, Tuple{Int64, Int64}}",href:"#ReefGuideAPI.masked_nearest-Tuple{Rasters.Raster, Int64, Int64, Int64, Tuple{Int64, Int64}}"},[i("span",{class:"jlbinding"},"ReefGuideAPI.masked_nearest")],-1)),s[76]||(s[76]=e()),t(a,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),s[77]||(s[77]=n('
julia
masked_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 prioritising performance over accuracy.
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 (lat, long). Note reversed order of coordinates.
Returns
Matrix with the resampled data.
source
',7))]),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
  • geom : geometry to move
  • new_centroid : Centroid given in (lon, lat).
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.nearest-Tuple{Rasters.Raster, Tuple{Int64, Int64}}",href:"#ReefGuideAPI.nearest-Tuple{Rasters.Raster, Tuple{Int64, Int64}}"},[i("span",{class:"jlbinding"},"ReefGuideAPI.nearest")],-1)),s[88]||(s[88]=e()),t(a,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),s[89]||(s[89]=n(`
julia
nearest(rst::Raster, tile_size::Tuple{Int, Int})::Matrix
Resample a raster to a tile size using nearest neighbor interpolation. This approach prioritising performance over accuracy.
Arguments
  • rst: The input raster to be resampled.
  • tile_size: The desired dimensions of the tile (lat, long).
Returns
Matrix with the resampled data.
Examples
julia
large_raster = Raster(rand(UInt8, 14756, 14838); dims=(X(1:1:14756), Y(1:1:14838)))
-small_matrix = nearest(large_raster, (256, 256))
source
`,9))]),i("details",U,[i("summary",null,[s[90]||(s[90]=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[91]||(s[91]=e()),t(a,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),s[92]||(s[92]=n(`
julia
output_geojson(
+)::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
`,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
  • 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
`,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
  • 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
',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
  • geom : geometry to move
  • new_centroid : Centroid given in (lon, lat).
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
  • df : DataFrame intended for writing to geojson file.
  • region : Region name for labelling output file.
  • output_dir : Directory to write geojson file to.
source
`,5))]),i("details",q,[i("summary",null,[s[93]||(s[93]=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[94]||(s[94]=e()),t(a,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),s[95]||(s[95]=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
  • qp : Parsed query string from request.
Returns
Tuple of criteria names, lower bounds, upper bounds
source
',8))]),i("details",z,[i("summary",null,[s[96]||(s[96]=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[97]||(s[97]=e()),t(a,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),s[98]||(s[98]=n(`
julia
polygon_to_lines(
+)::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
`,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
  • qp : Parsed query string from request.
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",W,[i("summary",null,[s[99]||(s[99]=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[100]||(s[100]=e()),t(a,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),s[101]||(s[101]=n('
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
',5))]),i("details",N,[i("summary",null,[s[102]||(s[102]=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[103]||(s[103]=e()),t(a,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),s[104]||(s[104]=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",H,[i("summary",null,[s[105]||(s[105]=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[106]||(s[106]=e()),t(a,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),s[107]||(s[107]=n(`
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
`,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
  • 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
',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",$,[i("summary",null,[s[108]||(s[108]=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[109]||(s[109]=e()),t(a,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),s[110]||(s[110]=i("p",null,"Rotate the polygon by the given angle about its center.",-1)),s[111]||(s[111]=i("p",null,[i("a",{href:"https://github.com/open-AIMS/ReefGuideAPI.jl/blob/aa4c0921565db4a6bfff4662e5b5e4220d4c4723/src/site_assessment/geom_ops.jl#L47",target:"_blank",rel:"noreferrer"},"source")],-1))]),i("details",J,[i("summary",null,[s[112]||(s[112]=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[113]||(s[113]=e()),t(a,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),s[114]||(s[114]=n('
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
',7))]),i("details",Q,[i("summary",null,[s[115]||(s[115]=i("a",{id:"ReefGuideAPI.tile_size-Tuple{Dict}",href:"#ReefGuideAPI.tile_size-Tuple{Dict}"},[i("span",{class:"jlbinding"},"ReefGuideAPI.tile_size")],-1)),s[116]||(s[116]=e()),t(a,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),s[117]||(s[117]=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",X,[i("summary",null,[s[118]||(s[118]=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[119]||(s[119]=e()),t(a,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),s[120]||(s[120]=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
  • data :
  • criteria :
  • lb :
  • ub :
Returns
Tuple{Vector{Int64}, Vector{Int64}}, of lon and lat indices.
source
',7))]),i("details",Z,[i("summary",null,[s[121]||(s[121]=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[122]||(s[122]=e()),t(a,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),s[123]||(s[123]=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
  • data :
  • criteria :
  • lb : lower bound
  • ub : upper bound
source
',6))]),i("details",Y,[i("summary",null,[s[124]||(s[124]=i("a",{id:"ReefGuideAPI.warmup_cache-Tuple{String}",href:"#ReefGuideAPI.warmup_cache-Tuple{String}"},[i("span",{class:"jlbinding"},"ReefGuideAPI.warmup_cache")],-1)),s[125]||(s[125]=e()),t(a,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),s[126]||(s[126]=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[127]||(s[127]=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[128]||(s[128]=e()),t(a,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),s[129]||(s[129]=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 rs=l(h,[["render",ss]]);export{ps as __pageData,rs as default};
+)

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.DehzNRDj.lean.js b/dev/assets/api.md.Dxqu1QHi.lean.js similarity index 69% rename from dev/assets/api.md.DehzNRDj.lean.js rename to dev/assets/api.md.Dxqu1QHi.lean.js index 96aaa0c..26203f3 100644 --- a/dev/assets/api.md.DehzNRDj.lean.js +++ b/dev/assets/api.md.Dxqu1QHi.lean.js @@ -1,6 +1,6 @@ -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.BvdfcH24.js";const ps=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:""},I={class:"jldocstring custom-block",open:""},R={class:"jldocstring custom-block",open:""},D={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:""},X={class:"jldocstring custom-block",open:""},Z={class:"jldocstring custom-block",open:""},Y={class:"jldocstring custom-block",open:""},K={class:"jldocstring custom-block",open:""};function ss(is,s,es,as,ts,ns){const a=r("Badge");return o(),p("div",null,[s[130]||(s[130]=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.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[13]||(s[13]=e()),t(a,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),s[14]||(s[14]=n(`
julia
apply_criteria_thresholds(criteria_stack::RasterStack, lookup::DataFrame, ruleset::Vector{CriteriaBounds{Function}})::Raster
+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
  • 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
',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
  • 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
`,7))]),i("details",y,[i("summary",null,[s[15]||(s[15]=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[16]||(s[16]=e()),t(a,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),s[17]||(s[17]=n(`
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
`,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,
@@ -9,20 +9,20 @@ import{_ as l,c as p,j as i,a as e,G as t,a5 as n,B as r,o}from"./chunks/framewo
     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
`,7))]),i("details",E,[i("summary",null,[s[18]||(s[18]=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[19]||(s[19]=e()),t(a,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),s[20]||(s[20]=n(`
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
`,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
  • 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
`,7))]),i("details",f,[i("summary",null,[s[21]||(s[21]=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[22]||(s[22]=e()),t(a,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),s[23]||(s[23]=n(`
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 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
`,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
  • 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
`,7))]),i("details",F,[i("summary",null,[s[24]||(s[24]=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[25]||(s[25]=e()),t(a,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),s[26]||(s[26]=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[27]||(s[27]=i("a",{id:"ReefGuideAPI.criteria_middleware-Tuple{Any}",href:"#ReefGuideAPI.criteria_middleware-Tuple{Any}"},[i("span",{class:"jlbinding"},"ReefGuideAPI.criteria_middleware")],-1)),s[28]||(s[28]=e()),t(a,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),s[29]||(s[29]=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",m,[i("summary",null,[s[30]||(s[30]=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[31]||(s[31]=e()),t(a,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),s[32]||(s[32]=n('
julia
degrees_to_meters(x, lat)
Convert degrees to meters at target latitude.
source
',3))]),i("details",C,[i("summary",null,[s[33]||(s[33]=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[34]||(s[34]=e()),t(a,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),s[35]||(s[35]=n(`
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
`,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
  • 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
`,8))]),i("details",A,[i("summary",null,[s[36]||(s[36]=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[37]||(s[37]=e()),t(a,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),s[38]||(s[38]=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",_,[i("summary",null,[s[39]||(s[39]=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[40]||(s[40]=e()),t(a,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),s[41]||(s[41]=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
  • 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
',7))]),i("details",j,[i("summary",null,[s[42]||(s[42]=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[43]||(s[43]=e()),t(a,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),s[44]||(s[44]=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",I,[i("summary",null,[s[45]||(s[45]=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[46]||(s[46]=e()),t(a,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),s[47]||(s[47]=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
  • v : Vector of point coordinates (Tuple{Float64, Float64}).
source
',5))]),i("details",R,[i("summary",null,[s[48]||(s[48]=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[49]||(s[49]=e()),t(a,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),s[50]||(s[50]=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
  • 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
',9))]),i("details",D,[i("summary",null,[s[51]||(s[51]=i("a",{id:"ReefGuideAPI.get_points-Tuple{Any}",href:"#ReefGuideAPI.get_points-Tuple{Any}"},[i("span",{class:"jlbinding"},"ReefGuideAPI.get_points")],-1)),s[52]||(s[52]=e()),t(a,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),s[53]||(s[53]=n('
julia
get_points(geom)
Helper method to retrieve points for a geometry.
source
',3))]),i("details",T,[i("summary",null,[s[54]||(s[54]=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[55]||(s[55]=e()),t(a,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),s[56]||(s[56]=n(`
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
`,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
  • 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
',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
  • v : Vector of point coordinates (Tuple{Float64, Float64}).
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
  • 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
',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,
@@ -35,7 +35,7 @@ import{_ as l,c as p,j as i,a as e,G as t,a5 as n,B as r,o}from"./chunks/framewo
     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
`,7))]),i("details",v,[i("summary",null,[s[57]||(s[57]=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[58]||(s[58]=e()),t(a,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),s[59]||(s[59]=n(`
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 : 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
`,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,
@@ -46,28 +46,27 @@ import{_ as l,c as p,j as i,a as e,G as t,a5 as n,B as r,o}from"./chunks/framewo
     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
`,7))]),i("details",B,[i("summary",null,[s[60]||(s[60]=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[61]||(s[61]=e()),t(a,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),s[62]||(s[62]=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
  • 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
',7))]),i("details",G,[i("summary",null,[s[63]||(s[63]=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[64]||(s[64]=e()),t(a,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),s[65]||(s[65]=n(`
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
`,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
  • 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
',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
  • (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
`,7))]),i("details",x,[i("summary",null,[s[66]||(s[66]=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[67]||(s[67]=e()),t(a,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),s[68]||(s[68]=n(`
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
`,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
  • 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
`,5))]),i("details",P,[i("summary",null,[s[69]||(s[69]=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[70]||(s[70]=e()),t(a,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),s[71]||(s[71]=n(`
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
`,9))]),i("details",M,[i("summary",null,[s[72]||(s[72]=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[73]||(s[73]=e()),t(a,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),s[74]||(s[74]=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
  • 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)
  • lats : Latitudinal extent (min and max)
Returns
True/false mask indicating locations within desired thresholds.
source
',9))]),i("details",S,[i("summary",null,[s[75]||(s[75]=i("a",{id:"ReefGuideAPI.masked_nearest-Tuple{Rasters.Raster, Int64, Int64, Int64, Tuple{Int64, Int64}}",href:"#ReefGuideAPI.masked_nearest-Tuple{Rasters.Raster, Int64, Int64, Int64, Tuple{Int64, Int64}}"},[i("span",{class:"jlbinding"},"ReefGuideAPI.masked_nearest")],-1)),s[76]||(s[76]=e()),t(a,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),s[77]||(s[77]=n('
julia
masked_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 prioritising performance over accuracy.
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 (lat, long). Note reversed order of coordinates.
Returns
Matrix with the resampled data.
source
',7))]),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
  • geom : geometry to move
  • new_centroid : Centroid given in (lon, lat).
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.nearest-Tuple{Rasters.Raster, Tuple{Int64, Int64}}",href:"#ReefGuideAPI.nearest-Tuple{Rasters.Raster, Tuple{Int64, Int64}}"},[i("span",{class:"jlbinding"},"ReefGuideAPI.nearest")],-1)),s[88]||(s[88]=e()),t(a,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),s[89]||(s[89]=n(`
julia
nearest(rst::Raster, tile_size::Tuple{Int, Int})::Matrix
Resample a raster to a tile size using nearest neighbor interpolation. This approach prioritising performance over accuracy.
Arguments
  • rst: The input raster to be resampled.
  • tile_size: The desired dimensions of the tile (lat, long).
Returns
Matrix with the resampled data.
Examples
julia
large_raster = Raster(rand(UInt8, 14756, 14838); dims=(X(1:1:14756), Y(1:1:14838)))
-small_matrix = nearest(large_raster, (256, 256))
source
`,9))]),i("details",U,[i("summary",null,[s[90]||(s[90]=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[91]||(s[91]=e()),t(a,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),s[92]||(s[92]=n(`
julia
output_geojson(
+)::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
`,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
  • 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
`,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
  • 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
',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
  • geom : geometry to move
  • new_centroid : Centroid given in (lon, lat).
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
  • df : DataFrame intended for writing to geojson file.
  • region : Region name for labelling output file.
  • output_dir : Directory to write geojson file to.
source
`,5))]),i("details",q,[i("summary",null,[s[93]||(s[93]=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[94]||(s[94]=e()),t(a,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),s[95]||(s[95]=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
  • qp : Parsed query string from request.
Returns
Tuple of criteria names, lower bounds, upper bounds
source
',8))]),i("details",z,[i("summary",null,[s[96]||(s[96]=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[97]||(s[97]=e()),t(a,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),s[98]||(s[98]=n(`
julia
polygon_to_lines(
+)::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
`,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
  • qp : Parsed query string from request.
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",W,[i("summary",null,[s[99]||(s[99]=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[100]||(s[100]=e()),t(a,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),s[101]||(s[101]=n('
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
',5))]),i("details",N,[i("summary",null,[s[102]||(s[102]=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[103]||(s[103]=e()),t(a,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),s[104]||(s[104]=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",H,[i("summary",null,[s[105]||(s[105]=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[106]||(s[106]=e()),t(a,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),s[107]||(s[107]=n(`
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
`,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
  • 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
',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",$,[i("summary",null,[s[108]||(s[108]=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[109]||(s[109]=e()),t(a,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),s[110]||(s[110]=i("p",null,"Rotate the polygon by the given angle about its center.",-1)),s[111]||(s[111]=i("p",null,[i("a",{href:"https://github.com/open-AIMS/ReefGuideAPI.jl/blob/aa4c0921565db4a6bfff4662e5b5e4220d4c4723/src/site_assessment/geom_ops.jl#L47",target:"_blank",rel:"noreferrer"},"source")],-1))]),i("details",J,[i("summary",null,[s[112]||(s[112]=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[113]||(s[113]=e()),t(a,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),s[114]||(s[114]=n('
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.
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tile_size(config::Dict)::Tuple
Retrieve the configured size of map tiles in pixels (width and height / lon and lat).
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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 :
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  • ub :
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Tuple{Vector{Int64}, Vector{Int64}}, of lon and lat indices.
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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
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',6))]),i("details",Y,[i("summary",null,[s[124]||(s[124]=i("a",{id:"ReefGuideAPI.warmup_cache-Tuple{String}",href:"#ReefGuideAPI.warmup_cache-Tuple{String}"},[i("span",{class:"jlbinding"},"ReefGuideAPI.warmup_cache")],-1)),s[125]||(s[125]=e()),t(a,{type:"info",class:"jlObjectType jlMethod",text:"Method"})]),s[126]||(s[126]=n('
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.
Notes
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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',5))])])}const rs=l(h,[["render",ss]]);export{ps as __pageData,rs as default};
+)

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

Returns

Rotated geometry.

source

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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

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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

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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.CFpyQib2.js b/dev/assets/docker.md.CeXB9QeU.js similarity index 98% rename from dev/assets/docker.md.CFpyQib2.js rename to dev/assets/docker.md.CeXB9QeU.js index 063ec24..33641f7 100644 --- a/dev/assets/docker.md.CFpyQib2.js +++ b/dev/assets/docker.md.CeXB9QeU.js @@ -1,2 +1,2 @@ -import{_ as e,c as s,a5 as a,o as t}from"./chunks/framework.BvdfcH24.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.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
 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.CFpyQib2.lean.js b/dev/assets/docker.md.CeXB9QeU.lean.js
similarity index 98%
rename from dev/assets/docker.md.CFpyQib2.lean.js
rename to dev/assets/docker.md.CeXB9QeU.lean.js
index 063ec24..33641f7 100644
--- a/dev/assets/docker.md.CFpyQib2.lean.js
+++ b/dev/assets/docker.md.CeXB9QeU.lean.js
@@ -1,2 +1,2 @@
-import{_ as e,c as s,a5 as a,o as t}from"./chunks/framework.BvdfcH24.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.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
 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.DKqyPY1d.js b/dev/assets/getting_started.md.ArdKq2gR.js
similarity index 99%
rename from dev/assets/getting_started.md.DKqyPY1d.js
rename to dev/assets/getting_started.md.ArdKq2gR.js
index d5b0c6a..d750b6d 100644
--- a/dev/assets/getting_started.md.DKqyPY1d.js
+++ b/dev/assets/getting_started.md.ArdKq2gR.js
@@ -1,4 +1,4 @@
-import{_ as e,c as i,a5 as a,o as t}from"./chunks/framework.BvdfcH24.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.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]
 PREPPED_DATA_DIR = "C:/some_path_to_data/MPA/"
 
 [server_config]
diff --git a/dev/assets/getting_started.md.DKqyPY1d.lean.js b/dev/assets/getting_started.md.ArdKq2gR.lean.js
similarity index 99%
rename from dev/assets/getting_started.md.DKqyPY1d.lean.js
rename to dev/assets/getting_started.md.ArdKq2gR.lean.js
index d5b0c6a..d750b6d 100644
--- a/dev/assets/getting_started.md.DKqyPY1d.lean.js
+++ b/dev/assets/getting_started.md.ArdKq2gR.lean.js
@@ -1,4 +1,4 @@
-import{_ as e,c as i,a5 as a,o as t}from"./chunks/framework.BvdfcH24.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.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]
 PREPPED_DATA_DIR = "C:/some_path_to_data/MPA/"
 
 [server_config]
diff --git a/dev/assets/index.md.kAlQC9BQ.js b/dev/assets/index.md.CBMAENFQ.js
similarity index 90%
rename from dev/assets/index.md.kAlQC9BQ.js
rename to dev/assets/index.md.CBMAENFQ.js
index 4d3fd0e..88e0294 100644
--- a/dev/assets/index.md.kAlQC9BQ.js
+++ b/dev/assets/index.md.CBMAENFQ.js
@@ -1 +1 @@
-import{_ as t,c as r,j as e,a as i,o as s}from"./chunks/framework.BvdfcH24.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.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};
diff --git a/dev/assets/index.md.kAlQC9BQ.lean.js b/dev/assets/index.md.CBMAENFQ.lean.js
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@@ -1 +1 @@
-import{_ as t,c as r,j as e,a as i,o as s}from"./chunks/framework.BvdfcH24.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.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};
diff --git a/dev/docker.html b/dev/docker.html
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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.start_server("/data/reefguide/config.toml")
bash
docker run --rm --interactive --entrypoint="julia" --tty -v ./data:/data/reefguide reefguide

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 (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).
- + \ No newline at end of file diff --git a/dev/hashmap.json b/dev/hashmap.json index b6abe4d..70f68fc 100644 --- a/dev/hashmap.json +++ b/dev/hashmap.json @@ -1 +1 @@ -{"api.md":"DehzNRDj","docker.md":"CFpyQib2","getting_started.md":"DKqyPY1d","index.md":"kAlQC9BQ"} +{"api.md":"Dxqu1QHi","docker.md":"CeXB9QeU","getting_started.md":"ArdKq2gR","index.md":"CBMAENFQ"} diff --git a/dev/index.html b/dev/index.html index 505630f..652cc7a 100644 --- a/dev/index.html +++ b/dev/index.html @@ -8,17 +8,17 @@ - + - - - + + +
ReefGuideAPI.jl

Appearance

ReefGuideAPI.jl ​

An API for supporting reef suitability assessments.

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