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Release zones #127

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merged 22 commits into from
Nov 22, 2023
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Release zones #127

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bfd26be
Shorten lines
jimc101 Nov 10, 2023
6dc34b2
Tidy module
jimc101 Nov 17, 2023
f3151d1
Make target length argument optional
jimc101 Nov 17, 2023
d3e9221
Remove redundant function
jimc101 Nov 17, 2023
2c89c39
Update cookbook
jimc101 Nov 17, 2023
048090f
Remove old reference shapefile data
jimc101 Nov 17, 2023
5d43679
Release zone class
jimc101 Nov 20, 2023
4b24e51
Add PyLagAttributeError exception
jimc101 Nov 21, 2023
346e730
Switch to using properties
jimc101 Nov 21, 2023
224261b
Shorten line
jimc101 Nov 21, 2023
69c8975
Expand ReleaseZone's interface
jimc101 Nov 21, 2023
8b0f50b
Release zone creation
jimc101 Nov 21, 2023
a2c8a2c
Release zones
jimc101 Nov 21, 2023
a6c7001
Align input module with new changes
jimc101 Nov 21, 2023
6659d5a
Initial positions documentation examples
jimc101 Nov 21, 2023
03316d1
Return copies of mutable objects
jimc101 Nov 21, 2023
f6937c3
Sync more notebooks
jimc101 Nov 21, 2023
9ba6e8c
Sync global example notebook
jimc101 Nov 21, 2023
032236f
Sync the final set of doc examples
jimc101 Nov 21, 2023
d339d1f
Sync release zone unit tests
jimc101 Nov 22, 2023
ce0aeb5
Print PyLag git commit in pylag-package-conda-linux.yml
jimc101 Nov 22, 2023
72af0eb
Update pylag-package-conda-linux.yml
jimc101 Nov 22, 2023
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5 changes: 5 additions & 0 deletions .github/workflows/pylag-package-conda-linux.yml
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Expand Up @@ -27,6 +27,11 @@ jobs:
run: |
conda info
conda list
- name: Install local changes
shell: bash -l {0}
run: |
pip install .
python -c "import pylag; print(f'PyLag Git commit: {pylag.version.git_revision}')"
# - name: Lint
# shell: bash -l {0}
# run: |
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221 changes: 155 additions & 66 deletions doc/source/documentation/cookbook/initial_positions.ipynb
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36 changes: 16 additions & 20 deletions doc/source/examples/arakawa_a_forward_tracking.ipynb
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Expand Up @@ -66,10 +66,6 @@
"lat = 50.32\n",
"lon = -4.17\n",
"\n",
"# Convert to UTM coordinates\n",
"epsg_code = '32630'\n",
"easting, northing, _ = utm_from_lonlat([lon], [lat], epsg_code=epsg_code)\n",
"\n",
"# Release zone radius (m)\n",
"radius = 200.0\n",
"\n",
Expand All @@ -84,31 +80,27 @@
"# Create the release zone\n",
"surface_release_zone = create_release_zone(group_id = group_id,\n",
" radius = radius,\n",
" centre = [easting, northing],\n",
" centre = [lon, lat],\n",
" coordinate_system = 'geographic',\n",
" n_particles = n_particles_target,\n",
" depth = depth_below_surface,\n",
" random = False)\n",
"\n",
"# Get the actual number of particles\n",
"n_particles = surface_release_zone.get_number_of_particles()\n",
"\n",
"# Convert to lat/lon coordinates\n",
"lons, lats = lonlat_from_utm(surface_release_zone.get_eastings(),\n",
" surface_release_zone.get_northings(),\n",
" epsg_code=epsg_code)\n",
"\n",
"# Get depths\n",
"depths = surface_release_zone.get_depths()\n",
"# Get coordinates\n",
"lons, lats, depths = surface_release_zone.get_coordinates()\n",
"\n",
"# Create input sub-directory\n",
"input_dir = '{}/input'.format(simulation_dir)\n",
"input_dir = f'{simulation_dir}/input'\n",
"try:\n",
" os.makedirs(input_dir)\n",
"except FileExistsError:\n",
" pass\n",
"\n",
"# Output filename\n",
"file_name = '{}/initial_positions.dat'.format(input_dir)\n",
"file_name = f'{input_dir}/initial_positions.dat'\n",
"\n",
"# Write data to file\n",
"create_initial_positions_file_single_group(file_name,\n",
Expand Down Expand Up @@ -246,7 +238,8 @@
"# Create figure\n",
"font_size = 15\n",
"cmap = colourmap('h_r')\n",
"fig, ax = create_figure(figure_size=(26., 26.), projection=ccrs.PlateCarree(), font_size=font_size, bg_color='gray')\n",
"fig, ax = create_figure(figure_size=(26., 26.), projection=ccrs.PlateCarree(),\n",
" font_size=font_size, bg_color='gray')\n",
"\n",
"# Configure plotter\n",
"plotter = ArakawaAPlotter(grid_metrics_file_name,\n",
Expand All @@ -261,8 +254,9 @@
"plotter.scatter(ax, [-4.17], [50.25], marker='o', c='r')\n",
"x, y = ax.projection.transform_point(-4.17, 50.25, src_crs=ccrs.PlateCarree())\n",
"ax.annotate('L4', xy=(x, y), xytext=(0.2, 0.35), textcoords='axes fraction',\n",
" arrowprops=dict(facecolor='red', edgecolor='red', width=1, headwidth=10, headlength=20, shrink=0.05),\n",
" fontsize=font_size, color='red')\n",
" arrowprops=dict(facecolor='red', edgecolor='red', width=1, headwidth=10,\n",
" headlength=20, shrink=0.05),\n",
" fontsize=font_size, color='red')\n",
"plotter.set_title(ax, 'Full grid (without grid lines)')\n",
"\n",
"# Grid subset (centered on Rame Head)\n",
Expand All @@ -271,7 +265,8 @@
"# Create figure\n",
"font_size = 15\n",
"cmap = colourmap('h_r')\n",
"fig, ax = create_figure(figure_size=(26., 26.), projection=ccrs.PlateCarree(), font_size=font_size, bg_color='gray')\n",
"fig, ax = create_figure(figure_size=(26., 26.), projection=ccrs.PlateCarree(),\n",
" font_size=font_size, bg_color='gray')\n",
"\n",
"# Configure plotter\n",
"plotter = ArakawaAPlotter(grid_metrics_file_name,\n",
Expand Down Expand Up @@ -496,7 +491,8 @@
"# Plot extents\n",
"extents = np.array([-4.3, -4.05, 50.25, 50.4], dtype=float)\n",
"\n",
"fig, ax = create_figure(figure_size=(26., 26.), projection=ccrs.PlateCarree(), font_size=font_size, bg_color='gray')\n",
"fig, ax = create_figure(figure_size=(26., 26.), projection=ccrs.PlateCarree(),\n",
" font_size=font_size, bg_color='gray')\n",
"\n",
"# Create plot of release \n",
"plotter = ArakawaAPlotter(grid_metrics_file_name,\n",
Expand Down Expand Up @@ -549,7 +545,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.9.15"
"version": "3.11.4"
}
},
"nbformat": 4,
Expand Down
53 changes: 29 additions & 24 deletions doc/source/examples/fvcom_backward_tracking.ipynb
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Expand Up @@ -65,10 +65,6 @@
"lat = 50.32\n",
"lon = -4.17\n",
"\n",
"# Convert to UTM coordinates\n",
"epsg_code = get_epsg_code(lon, lat)\n",
"easting, northing, _ = utm_from_lonlat([lon], [lat], epsg_code=epsg_code)\n",
"\n",
"# Release zone radius (m)\n",
"radius = 200.0\n",
"\n",
Expand All @@ -83,14 +79,22 @@
"# Create the release zone\n",
"surface_release_zone = create_release_zone(group_id = group_id,\n",
" radius = radius,\n",
" centre = [easting, northing],\n",
" centre = [lon, lat],\n",
" coordinate_system = 'geographic',\n",
" n_particles = n_particles_target,\n",
" depth = depth_below_surface,\n",
" random = False)\n",
"\n",
"# Get the actual number of particles\n",
"n_particles = surface_release_zone.get_number_of_particles()\n",
"\n",
"# Get coordinates of the particles. NB - we're going to run\n",
"# the model in cartesian coordinates. Objects of type\n",
"# ReleaseZone have a method that allows one to transform\n",
"# geographic coordinates into UTM coordinates with units\n",
"# of m. We use this here.\n",
"eastings, northings, depths, epsg_code = surface_release_zone.get_utm_coordinates()\n",
"\n",
"# Create input sub-directory\n",
"input_dir = f\"{simulation_dir}/input\"\n",
"try:\n",
Expand All @@ -105,9 +109,9 @@
"create_initial_positions_file_single_group(file_name,\n",
" n_particles,\n",
" group_id,\n",
" surface_release_zone.get_eastings(),\n",
" surface_release_zone.get_northings(),\n",
" surface_release_zone.get_depths())"
" eastings,\n",
" northings,\n",
" depths)"
]
},
{
Expand All @@ -123,18 +127,7 @@
"cell_type": "code",
"execution_count": 3,
"metadata": {},
"outputs": [
{
"data": {
"text/plain": [
"'/home/jcl/code/git/PyLag/PyLag/doc/source/examples/simulations/fvcom_backward/input/grid_metrics.nc'"
]
},
"execution_count": 3,
"metadata": {},
"output_type": "execute_result"
}
],
"outputs": [],
"source": [
"from shutil import copyfile\n",
"\n",
Expand Down Expand Up @@ -210,7 +203,18 @@
"cell_type": "code",
"execution_count": 5,
"metadata": {},
"outputs": [],
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"\n",
"Starting ensemble member 1 ...\n",
"Progress:\n",
"100% |###########################################|\n"
]
}
],
"source": [
"# Change to the run directory\n",
"os.chdir(f\"{simulation_dir}\")\n",
Expand Down Expand Up @@ -282,7 +286,8 @@
"# Plot extents\n",
"extents = np.array([-4.3, -4.05, 50.25, 50.4], dtype=float)\n",
"\n",
"fig, ax = create_figure(figure_size=(26., 26.), projection=ccrs.PlateCarree(), font_size=font_size, bg_color='gray')\n",
"fig, ax = create_figure(figure_size=(26., 26.), projection=ccrs.PlateCarree(),\n",
" font_size=font_size, bg_color='gray')\n",
"\n",
"# Configure plotter\n",
"plotter = FVCOMPlotter(grid_metrics_file_name,\n",
Expand Down Expand Up @@ -329,7 +334,7 @@
],
"metadata": {
"kernelspec": {
"display_name": "Python 3",
"display_name": "Python 3 (ipykernel)",
"language": "python",
"name": "python3"
},
Expand All @@ -343,7 +348,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.8.5"
"version": "3.11.4"
}
},
"nbformat": 4,
Expand Down
38 changes: 20 additions & 18 deletions doc/source/examples/fvcom_forward_tracking.ipynb
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Expand Up @@ -157,10 +157,6 @@
"lat = 50.32\n",
"lon = -4.17\n",
"\n",
"# Convert to UTM coordinates\n",
"epsg_code = get_epsg_code(lon, lat)\n",
"easting, northing, _ = utm_from_lonlat([lon], [lat], epsg_code=epsg_code)\n",
"\n",
"# Release zone radius (m)\n",
"radius = 200.0\n",
"\n",
Expand All @@ -175,14 +171,22 @@
"# Create the release zone\n",
"surface_release_zone = create_release_zone(group_id = group_id,\n",
" radius = radius,\n",
" centre = [easting, northing],\n",
" centre = [lon, lat],\n",
" coordinate_system = 'geographic',\n",
" n_particles = n_particles_target,\n",
" depth = depth_below_surface,\n",
" random = False)\n",
"\n",
"# Get the actual number of particles\n",
"n_particles = surface_release_zone.get_number_of_particles()\n",
"\n",
"# Get coordinates of the particles. NB - we're going to run\n",
"# the model in cartesian coordinates. Objects of type\n",
"# ReleaseZone have a method that allows one to transform\n",
"# geographic coordinates into UTM coordinates with units\n",
"# of m. We use this here.\n",
"eastings, northings, depths, epsg_code = surface_release_zone.get_utm_coordinates() \n",
"\n",
"# Create input sub-directory\n",
"input_dir = f\"{simulation_dir}/input\"\n",
"try:\n",
Expand All @@ -197,9 +201,9 @@
"create_initial_positions_file_single_group(file_name,\n",
" n_particles,\n",
" group_id,\n",
" surface_release_zone.get_eastings(),\n",
" surface_release_zone.get_northings(),\n",
" surface_release_zone.get_depths())\n"
" eastings,\n",
" northings,\n",
" depths)"
]
},
{
Expand All @@ -226,10 +230,8 @@
}
],
"source": [
"# Convert utm coords to degrees\n",
"lons, lats = lonlat_from_utm(surface_release_zone.get_eastings(),\n",
" surface_release_zone.get_northings(),\n",
" epsg_code=epsg_code)\n",
"# Get lon/lat coordinates\n",
"lons, lats, _ = surface_release_zone.get_coordinates()\n",
"\n",
"# Create figure\n",
"font_size = 15\n",
Expand All @@ -244,8 +246,8 @@
"\n",
"# Plot bathymetry\n",
"extents = np.array([-4.21, -4.15, 50.30, 50.33], dtype=float)\n",
"ax, plot = plotter.plot_field(ax, bathy, extents=extents, add_colour_bar=True, cb_label='Depth (m)',\n",
" vmin=-60., vmax=0., cmap=cmap)\n",
"ax, plot = plotter.plot_field(ax, bathy, extents=extents, add_colour_bar=True,\n",
" cb_label='Depth (m)', vmin=-60., vmax=0., cmap=cmap)\n",
"\n",
"# Overlay grid\n",
"plotter.draw_grid(ax, linewidth=1.0)\n",
Expand Down Expand Up @@ -377,7 +379,7 @@
},
{
"cell_type": "code",
"execution_count": null,
"execution_count": 7,
"metadata": {},
"outputs": [],
"source": [
Expand Down Expand Up @@ -473,8 +475,8 @@
" font_size=font_size)\n",
"\n",
"# Plot the bathymetry again. We'll overlay pathlines on top of this.\n",
"plotter.plot_field(ax, bathy, extents=extents, add_colour_bar=True, cb_label='Depth (m)',\n",
" vmin=-60., vmax=0., cmap=cmap)\n",
"plotter.plot_field(ax, bathy, extents=extents, add_colour_bar=True,\n",
" cb_label='Depth (m)', vmin=-60., vmax=0., cmap=cmap)\n",
"\n",
"# Dataset holding particle positions\n",
"viewer = Viewer(file_name, time_rounding=900)\n",
Expand Down Expand Up @@ -537,7 +539,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.9.15"
"version": "3.11.4"
}
},
"nbformat": 4,
Expand Down
21 changes: 6 additions & 15 deletions doc/source/examples/global_arakawa_a_forward_tracking.ipynb
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Expand Up @@ -74,11 +74,6 @@
"lat = 28.5\n",
"lon = -78.7\n",
"\n",
"# Convert to UTM coordinates\n",
"easting, northing, epsg_code = utm_from_lonlat([lon], [lat])\n",
"easting = easting[0]\n",
"northing = northing[0]\n",
"\n",
"# Release zone radius (m)\n",
"radius = 10000.0\n",
"\n",
Expand All @@ -91,7 +86,8 @@
"# Create the release zone\n",
"surface_release_zone = create_release_zone(group_id = group_id,\n",
" radius = radius,\n",
" centre = [easting, northing],\n",
" centre = [lon, lat],\n",
" coordinate_system = 'geographic',\n",
" n_particles = n_particles_target,\n",
" depth = depth_below_surface,\n",
" random = True)\n",
Expand All @@ -100,12 +96,7 @@
"n_particles = surface_release_zone.get_number_of_particles()\n",
"\n",
"# Convert to lat/lon coordinates\n",
"lons, lats = lonlat_from_utm(surface_release_zone.get_eastings(),\n",
" surface_release_zone.get_northings(),\n",
" epsg_code)\n",
"\n",
"# Get depths\n",
"depths = surface_release_zone.get_depths()\n",
"lons, lats, depths = surface_release_zone.get_coordinates()\n",
"\n",
"# Output filename\n",
"file_name = '{}/initial_positions.dat'.format(input_dir)\n",
Expand Down Expand Up @@ -412,14 +403,14 @@
"extents = np.array([-90, -30, 20, 50], dtype=float)\n",
"\n",
"# Projection\n",
"#projection = ccrs.NearsidePerspective(central_longitude=-60.0, central_latitude=35.0, satellite_height=35785800)\n",
"projection = ccrs.PlateCarree()\n",
"\n",
"# Plot positions after 180 and 360 days\n",
"for tof in [180, 360]:\n",
"\n",
" # Create figure\n",
" fig, ax1 = create_figure(figure_size=(26., 26.), projection=projection, font_size=font_size, bg_color='white')\n",
" fig, ax1 = create_figure(figure_size=(26., 26.), projection=projection,\n",
" font_size=font_size, bg_color='white')\n",
"\n",
" # Create plotter \n",
" plotter = ArakawaAPlotter(grid_metrics_file_name,\n",
Expand Down Expand Up @@ -469,7 +460,7 @@
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.9.7"
"version": "3.11.4"
}
},
"nbformat": 4,
Expand Down
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