JOSS manuscript

.gitignore

@@ -179,3 +179,7 @@ src/virtualship/_version_setup.py
 
 .vscode/
 .DS_Store
+
+
+# some files created during paper (JOSS) writing
+docs/paper/**/*.txt

docs/conf.py

@@ -78,6 +78,8 @@
     "user-guide/assignments/Sail_the_ship": "user-guide/_images/freepik_research_vessel.jpg",
     "user-guide/assignments/Code_of_conduct": "user-guide/_images/freepik_code_of_conduct.jpg",
     "user-guide/teacher-content/ILOs": "user-guide/_images/ILOs.jpg",
+    "user-guide/teacher-content/UU-ocean-of-future/Tutorial1": "user-guide/_images/freepik_assignment.png",
+    "user-guide/teacher-content/UU-ocean-of-future/Tutorial2": "user-guide/_images/freepik_assignment.png",
 }
 
 sphinx_gallery_conf = {"default_thumb_file": "_static/virtual_ship_logo.png"}

docs/paper/figure1.py

@@ -0,0 +1,112 @@
+# %%
+
+import cartopy.crs as ccrs
+import matplotlib.gridspec as gridspec
+import matplotlib.image as mpimg
+import matplotlib.pyplot as plt
+import numpy as np
+import xarray as xr
+from plotting_functions import (
+    _ctd_distance_along_expedition,
+    plot_adcp,
+    plot_ctd,
+    plot_drifters,
+)
+
+SAMPLE_DIR = "sample_expedition/"
+CONFIG = "expedition.yaml"
+EXPEDITION = "MY_EXPEDITION"
+
+# %%
+
+# VirtualShip output
+ctd_ds = xr.open_dataset(f"{SAMPLE_DIR}{EXPEDITION}/results/ctd.zarr")
+ctd_bgc_ds = xr.open_dataset(f"{SAMPLE_DIR}{EXPEDITION}/results/ctd_bgc.zarr")
+drifter_ds = xr.open_dataset(f"{SAMPLE_DIR}{EXPEDITION}/results/drifter.zarr")
+adcp_ds = xr.open_dataset(f"{SAMPLE_DIR}{EXPEDITION}/results/adcp.zarr")
+
+
+# %%
+
+# plot
+
+PROJ = ccrs.PlateCarree()
+
+waypoint_distances = np.unique(_ctd_distance_along_expedition(ctd_ds)["distance"])
+
+
+def add_waypoint_markers(ax, distances, offset=15, marker_size=70):
+    ax.scatter(
+        (distances / 1000),
+        np.zeros_like(distances) - offset,
+        marker="v",
+        color="black",
+        edgecolors="white",
+        s=marker_size,
+        clip_on=False,
+    )
+
+
+# fig
+fig = plt.figure(figsize=(12, 13), dpi=300)
+
+# custom layout
+gs = gridspec.GridSpec(3, 2, height_ratios=[1.5, 1, 1])
+ax0 = fig.add_subplot(gs[0, :])
+ax1 = fig.add_subplot(gs[1, 0])
+ax2 = fig.add_subplot(gs[1, 1], projection=PROJ)
+ax3 = fig.add_subplot(gs[2, 0])
+ax4 = fig.add_subplot(gs[2, 1])
+
+# overview image
+ax0.set_title(r"$\bf{a}$" + ") MFP expedition overview", loc="left")
+img = mpimg.imread(f"{SAMPLE_DIR}expedition_overview.png")
+ax0.imshow(img)
+ax0.axis("off")
+
+# adcp
+ax1.set_title(r"$\bf{b}$" + ") ADCP (flow speed)", loc="left")
+ax1.set_ylabel("Depth (m)")
+ax1.set_xlabel("Distance (km)")
+plot_adcp(adcp_ds, ax1)
+add_waypoint_markers(ax1, waypoint_distances)
+
+# drifters
+ax2.set_title(r"$\bf{c}$" + ") Surface drifters", loc="left")
+plot_drifters(
+    drifter_ds,
+    ax2,
+    vmin=drifter_ds.temperature.min(),
+    vmax=drifter_ds.temperature.max(),
+)
+
+# CTD (temperature)
+ax3.set_title(r"$\bf{d}$" + ") CTD (temperature)", loc="left")
+ax3.set_ylabel("Depth (m)")
+ax3.set_xlabel("Distance (km)")
+_, _distances_regular, _var_masked = plot_ctd(
+    ctd_ds,
+    ax3,
+    plot_variable="temperature",
+    vmin=ctd_ds.temperature.min(),
+    vmax=ctd_ds.temperature.max(),
+)
+
+ctd_wp_distances = _distances_regular[np.nansum(_var_masked, axis=1) > 0]
+add_waypoint_markers(ax3, ctd_wp_distances, offset=45, marker_size=60)
+
+# CTD (oxygen)
+ax4.set_title(r"$\bf{e}$" + ") CTD (oxygen)", loc="left")
+ax4.set_xlabel("Distance (km)")
+plot_ctd(
+    ctd_bgc_ds, ax4, plot_variable="oxygen", vmin=0, vmax=ctd_bgc_ds.o2.max()
+)  # vmin tailored to mark red as approximate oxygen minimum zone (~ 45 mmol/m-3)
+add_waypoint_markers(ax4, ctd_wp_distances, offset=45, marker_size=60)
+
+
+plt.tight_layout()
+plt.show()
+
+fig.savefig("figure1.png", dpi=300)
+
+# %%