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Update bathymetry contours layer #586

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Update bathymetry contours layer #586

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8d7c906
Experiment with creating contours from GEBCO grid
trey-stafford Jun 26, 2023
418fd69
Update config lockfile
trey-stafford Jun 26, 2023
a26860b
CHANGELOG
trey-stafford Jun 26, 2023
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6 changes: 5 additions & 1 deletion CHANGELOG.md
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Expand Up @@ -43,7 +43,11 @@
grid. This update includes the most recent data and expands the spatial extent
of this layer to the QGreenland background boundary to make it consistent with
other ocenaography layers.

- Update "Oceanography/Bathymetry/Depth contours" layer to be derived from the
General Bathymetric Chart of the Oceans (GEBCO) Grid 2023, replacing the
contours obtained from the Geological map of the Arctic / Carte gologique de
l'Arctique (2011) dataset, which was based on the Bathymetric Chart of the
Arctic Ocean (IBCAO).

# v3.0.0alpha2 (2023-05-09)

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68 changes: 54 additions & 14 deletions qgreenland/config/cfg-lock.json
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Expand Up @@ -25204,7 +25204,7 @@
"children": [
{
"layer_cfg": {
"description": "Bathymetric elevation in meters.\n\nElevations can be assumed to be relative to mean sea level. However, in\nsome shallow water areas, the grids include data from sources having a\nvertical datum other than mean sea level. We are working to understand\nhow best to fully assimilate these data.",
"description": "Bathymetric elevation in meters.\n\nNegative values represent bathymetric depths and positive values are\ntopographic heights.\n\nElevations can be assumed to be relative to mean sea level. However, in\nsome shallow water areas, the grids include data from sources having a\nvertical datum other than mean sea level. We are working to understand\nhow best to fully assimilate these data.",
"id": "gebco_bathymetric_raster",
"in_package": true,
"input": {
Expand Down Expand Up @@ -25297,41 +25297,81 @@
},
{
"layer_cfg": {
"description": "This dataset includes linear features that represent\n bathymetric contours recorded in metres,\nderived from the International Bathymetric Chart of the Arctic Ocean.",
"id": "bathymetric_contours",
"description": "Bathymetric elevation contours in meters.\n\nContour interval is 100m and was derived from the \"Depth (400m)\" layer.\n\nElevations can be assumed to be relative to mean sea level. However, in\nsome shallow water areas, the grids include data from sources having a\nvertical datum other than mean sea level. We are working to understand\nhow best to fully assimilate these data.",
"id": "gebco_bathymetric_contours",
"in_package": true,
"input": {
"asset": {
"id": "only"
},
"dataset": {
"id": "geological_map"
"id": "gebco_bathymetric_chart"
}
},
"show": false,
"steps": [
{
"args": [
"unzip",
"{input_dir}/as_2159.zip",
"{input_dir}/gebco_2023.zip",
"-d",
"{output_dir}",
"data/shape/base/bathymetry.*"
""
],
"type": "command"
},
{
"args": [
"ogr2ogr",
"-lco",
"ENCODING=UTF-8",
"gdalwarp",
"-t_srs",
"EPSG:3413",
"-clipdst",
"-r",
"bilinear",
"-te",
"-5774572.727594967 -5774572.727594967 5774572.727594967 5774572.727594967",
"-tr",
"400",
"400",
"NETCDF:{input_dir}/GEBCO_2023.nc:elevation",
"{output_dir}/warped.tif"
],
"type": "command"
},
{
"args": [
"gdalwarp",
"-cutline",
"{assets_dir}/latitude_shape_40_degrees.geojson",
"-makevalid",
"{output_dir}/final.gpkg",
"{input_dir}/data/shape/base/bathymetry.shp"
"-crop_to_cutline",
"-co",
"COMPRESS=DEFLATE",
"{input_dir}/warped.tif",
"{output_dir}/bathymetric_chart.tif"
],
"type": "command"
},
{
"args": [
"gdal_calc.py",
"--calc=\"where(A < 0, absolute(A), nan)\"",
"--A_band=1",
"-A",
"{input_dir}/bathymetric_chart.tif",
"--outfile={output_dir}/positive_depths.tif"
],
"type": "command"
},
{
"args": [
"gdal_contour",
"-a",
"DEPTH",
"-i",
"500",
"-nln",
"bathymetry",
"{input_dir}/positive_depths.tif",
"{output_dir}/bathymetric_chart.gpkg"
],
"type": "command"
}
Expand All @@ -25340,7 +25380,7 @@
"tags": [],
"title": "Depth contours"
},
"name": "bathymetric_contours"
"name": "gebco_bathymetric_contours"
}
],
"name": "Bathymetry",
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75 changes: 59 additions & 16 deletions qgreenland/config/layers/Oceanography/Bathymetry/bathymetric_chart.py
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@@ -1,12 +1,12 @@
from qgreenland.config.datasets.bathymetric_chart import gebco_bathymetric_chart
from qgreenland.config.helpers.layers.geological_map import make_layer
from qgreenland.config.helpers.steps.compress_and_add_overviews import (
compress_and_add_overviews,
)
from qgreenland.config.helpers.steps.decompress import decompress_step
from qgreenland.config.helpers.steps.warp_and_cut import warp_and_cut
from qgreenland.config.project import project
from qgreenland.models.config.layer import Layer, LayerInput
from qgreenland.models.config.step import CommandStep

_background_boundary = project.boundaries["background"]
_background_bbox = _background_boundary.bbox
Expand All @@ -16,6 +16,9 @@
description=(
"""Bathymetric elevation in meters.

Negative values represent bathymetric depths and positive values are
topographic heights.

Elevations can be assumed to be relative to mean sea level. However, in
some shallow water areas, the grids include data from sources having a
vertical datum other than mean sea level. We are working to understand
Expand Down Expand Up @@ -49,21 +52,61 @@
],
)

gebco_bathymetric_contours = Layer(
id="gebco_bathymetric_contours",
title="Depth contours",
description=(
"""Bathymetric elevation contours in meters.

bathymetric_contours_params = {
"id": "bathymetric_contours",
"title": "Depth contours",
"description": (
"""This dataset includes linear features that represent
bathymetric contours recorded in metres,
derived from the International Bathymetric Chart of the Arctic Ocean."""
),
"style": "bathymetry",
"input_filepath": "data/shape/base/bathymetry",
"fn_mask": "bathymetry.*",
}
Contour interval is 100m and was derived from the "Depth (400m)" layer.

bathymetric_contours = make_layer(
layer_id=bathymetric_contours_params["id"],
layer_params=bathymetric_contours_params,
Elevations can be assumed to be relative to mean sea level. However, in
some shallow water areas, the grids include data from sources having a
vertical datum other than mean sea level. We are working to understand
how best to fully assimilate these data."""
),
tags=[],
style="bathymetry",
input=LayerInput(
dataset=gebco_bathymetric_chart,
asset=gebco_bathymetric_chart.assets["only"],
),
steps=[
decompress_step(input_file="{input_dir}/gebco_2023.zip"),
*warp_and_cut(
input_file="NETCDF:{input_dir}/GEBCO_2023.nc:elevation",
output_file="{output_dir}/bathymetric_chart.tif",
reproject_args=(
"-te",
f"{_background_bbox.min_x} {_background_bbox.min_y} {_background_bbox.max_x} {_background_bbox.max_y}",
"-tr",
"400",
"400",
),
cut_file=project.boundaries["background"].filepath,
),
CommandStep(
args=[
"gdal_calc.py",
'--calc="where(A < 0, absolute(A), nan)"',
"--A_band=1",
"-A",
"{input_dir}/bathymetric_chart.tif",
"--outfile={output_dir}/positive_depths.tif",
],
),
CommandStep(
args=[
"gdal_contour",
"-a",
"DEPTH",
"-i",
"500",
"-nln",
"bathymetry",
"{input_dir}/positive_depths.tif",
"{output_dir}/bathymetric_chart.gpkg",
],
),
],
)