update tutorial for Friday

OceanParcels · Feb 19, 2025 · 788e3f8 · 788e3f8
1 parent 0d4466a
commit 788e3f8
Showing 1 changed file with 56 additions and 10 deletions.
diff --git a/docs/user-guide/tutorials/Sail_the_ship.ipynb b/docs/user-guide/tutorials/Sail_the_ship.ipynb
@@ -4,7 +4,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "### Time has come to start your expedition!\n",
+    "### Start your expedition!\n",
     "\n",
     "https://www.youtube.com/watch?v=G82kIgc1imk\n",
     "\n",
@@ -15,7 +15,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "Create a folder for your expedition where the results will be saved. Initialize the virtualship using a `!` to use the tool directly from this notebook or copy the commands (without the `!`) directly into your terminal\n",
+    "On your (virtual) machine change directory into the folder where your expedition will be run. Initialize the virtualship by copying the commands directly into a terminal.\n",
     "```\n",
     "Usage: virtualship init [OPTIONS] PATH\n",
     "\n",
@@ -30,7 +30,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "!virtualship init EXPEDITION_NAME"
+    "virtualship init EXPEDITION_NAME"
    ]
   },
   {
@@ -39,11 +39,48 @@
    "source": [
     "This will create a folder `EXPEDITION_NAME` with two files: `schedule.yaml` and\t`ship_config.yaml`.\n",
     "\n",
-    "Populate the `schedule.yaml` file manually with each sampling CTD station and drifer/argo float deployment position. The route between points will be sailed as the shortest great-cirlce distance.  \n",
-    "[TODO: or initialize from a MFP csv file and correct where needed]\n",
+    "You can populate the `schedule.yaml` file manually with each sampling CTD station and XBT/DRIFTER/ARGO_FLOAT deployment position. Or use the exported cruise coordinates from MFP. In that case, add an extra column to the .xlsx file called `Instrument` and on each line write which instruments you want to use or deploy there. Multiple instrument are allowed, e.g. `DRIFTER, CTD` or `DRIFTER, ARGO_FLOAT`. If you want to use your MFP export, make sure your directory is clean and run:"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "virtualship init EXPEDITION_NAME --from-mfp CoordinatesExport.xlsx"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "\n",
+    "Mind that the route between points will be sailed as the shortest great-cirlce distance.  \n",
+    "\n",
+    "Instrument configurations can be provided in `ship_config`. \n",
     "\n",
-    "When you have finished your schedule, run the fetch command to download input data for the virtual ship from the Copernicus marine data store. \n",
-    "You will need to register via: https://data.marine.copernicus.eu/register and provide your username and password as command line arguments:\n",
+    "Under `adcp_config` provide the configuration of your ADCP, so either \n",
+    ">  max_depth_meter: -1000.0\n",
+    "\n",
+    "if you want to use the OceanObserver \n",
+    "\n",
+    "OR\n",
+    "\n",
+    "> max_depth_meter: -150.0 \n",
+    "\n",
+    "if you want to use the SeaSeven. \n",
+    "If you don't need the ADCP to measure, remove the `adcp_config` and underlying lines from the configuration file. \n",
+    "\n",
+    "If you do not want to collect underway data, remove `ship_underwater_st_config` from the configuration file.\n",
+    "\n",
+    "Change the xbt, drifter and argo_float configurations if you want.\n",
+    "\n",
+    "For the CTD, provide the maximum depth you will want to measure at. All other CTD casts will be done to approximately 20 meter of the ocean floor. \n",
+    "\n",
+    "When you have finished your schedule and config, run the fetch command to download input data for the virtual ship from the Copernicus marine data store. \n",
+    "You will need to register via: https://data.marine.copernicus.eu/register \n",
+    "You can provide your username and password as command line arguments. If you don't you will be prompted for your credentials.\n",
     "```\n",
     "Usage: virtualship fetch [OPTIONS] PATH\n",
     "\n",
@@ -57,14 +94,23 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "!virtualship fetch EXPEDITION_NAME --username <USERNAME> --password <PASSWORD>"
+    "virtualship fetch EXPEDITION_NAME --username <USERNAME> --password <PASSWORD>"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "virtualship fetch EXPEDITION_NAME"
    ]
   },
   {
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "After your input data has been downloaded you can begin your expedition:\n",
+    "After your input data has been downloaded you can do your expedition:\n",
     "```\n",
     "Usage: virtualship run [OPTIONS] PATH\n",
     "\n",
@@ -78,7 +124,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "!virtualship run EXPEDITION_NAME"
+    "virtualship run EXPEDITION_NAME"
    ]
   },
   {