\n",
@@ -55,13 +60,12 @@
},
{
"cell_type": "code",
- "execution_count": 2,
+ "execution_count": 7,
"id": "0cb630f6",
"metadata": {},
"outputs": [],
"source": [
- "data_dir = \"/path/to/EXPEDITION/results/\" # set this to be where your expedition output data is located on your (virtual) machine\n",
- "data_dir = \"/Users/Atkin004/Documents/test_expeditions/sept_course/NORTH/results/\""
+ "data_dir = \"/path/to/EXPEDITION/results/\" # set this to be where your expedition output data is located on your (virtual) machine"
]
},
{
@@ -148,6 +152,7 @@
"id": "88062e97",
"metadata": {},
"source": [
+ "\n",
"Now we will execute the various post-processing calculations, plus define some extra useful arrays to be used for the plotting..."
]
},
@@ -287,7 +292,7 @@
"id": "f2ada2b1",
"metadata": {},
"source": [
- "The resultant figure shows three components of velocity recorded by the ADCP instrument.\n",
+ "The resultant figure shows various components of the velocity field, derived from ADCP data.\n",
"\n",
"1) Absolute velocity\n",
"2) Along-track velocity (where positive values indicate flow in the direction of the ship's track across the the transect)\n",
diff --git a/docs/user-guide/tutorials/CTD_transects.ipynb b/docs/user-guide/tutorials/CTD_transects.ipynb
index 1f168e78..57748382 100644
--- a/docs/user-guide/tutorials/CTD_transects.ipynb
+++ b/docs/user-guide/tutorials/CTD_transects.ipynb
@@ -14,7 +14,7 @@
"The plot(s) we will produce are simple plots which follow the trajectory of the expedition as a function of distance from the first waypoint, and are intended to be a starting point for your analysis. \n",
"\n",
"
"
]
},
@@ -25,6 +25,8 @@
"source": [
"## Set up\n",
"\n",
+ "#### Imports\n",
+ "\n",
"The first step is to import the Python packages required for post-processing the data and plotting. "
]
},
@@ -48,6 +50,9 @@
"id": "4f387780",
"metadata": {},
"source": [
+ "\n",
+ "#### Data directory\n",
+ "\n",
"Next, you should set `data_dir` to be the path to your expedition results in the code block below. You should replace `\"/path/to/EXPEDITION/results/\"` with the path for your machine.\n",
"\n",
"
\n",
@@ -70,6 +75,8 @@
"id": "a499ebe2",
"metadata": {},
"source": [
+ "#### Variable choice\n",
+ "\n",
"You should now consider which variable from your CTD casts you would like to plot. Which ones are available to you will depend on whether you have used the `CTD` (physical variables) or `CTD_BGC` (biogeochemical) instrument, or both. Below is a list of all valid variable choices for both instruments...\n",
"\n",
"`CTD` (physical):\n",
@@ -104,7 +111,8 @@
"id": "a05fad14",
"metadata": {},
"source": [
- "We also define the `VARIABLES` dictionary here, which we use to store some parameters for the plots (e.g. variable labels, what units each is in, and which colour map we should use for the plots).\n",
+ "\n",
+ "We also define the `VARIABLES` dictionary here, which we use to store some parameters for the plots related to each variable choice (e.g. labels, what units each is in, and which colour map we should use for the plots).\n",
"\n",
"
\n",
"
Tip: You don't need to change anything here, but should you wish to change the colour scheme (`cmap`) for any CTD variable you can do so. At the moment it's set to use relevant cmaps from the cmocean Python package, which has developed specialist colour schemes for oceanographic data applications.\n",
@@ -306,6 +314,7 @@
"id": "2bdf98e6",
"metadata": {},
"source": [
+ "\n",
"Now we will execute the utility functions, plus define some extra useful arrays to be used for the plotting..."
]
},
@@ -409,7 +418,7 @@
"We can also also plot a 'filled' version without the distance bins, to give an alternative view of the evolution across the transect which is not dominated by gaps and white space. This time we will also add a 'sea bed' to the plot.\n",
"\n",
"
\n",
- "NOTE: It is important to always remember that the gaps do actually exist in reality and this is a caveat which must be considered when interpreting the transect derived from CTD casts. Indeed, if you look at the x-axis of the plot below you will see that the deployments are not necessarily regularly spaced and some gaps are larger than others.\n",
+ "Note: It is important to remember that the gaps do actually exist in reality and this is a caveat which must be considered when interpreting the transect derived from CTD casts. Indeed, if you look at the x-axis of the plot below you will see that the deployments are not necessarily regularly spaced and some gaps are larger than others.\n",
"
"
]
},
@@ -460,14 +469,6 @@
"plt.colorbar(mesh, ax=ax, label=VARIABLES[plot_variable][\"label\"])\n",
"plt.tight_layout()"
]
- },
- {
- "cell_type": "code",
- "execution_count": null,
- "id": "97e62cec",
- "metadata": {},
- "outputs": [],
- "source": []
}
],
"metadata": {
From 91e8f59fe23bf3f09870f37b81ed8cfdf1e15e1c Mon Sep 17 00:00:00 2001
From: j-atkins <106238905+j-atkins@users.noreply.github.com>
Date: Tue, 2 Sep 2025 10:03:45 +0200
Subject: [PATCH 5/9] more proof reading
---
.../user-guide/tutorials/ADCP_transects.ipynb | 7 +++---
docs/user-guide/tutorials/CTD_transects.ipynb | 24 +++++++++----------
2 files changed, 16 insertions(+), 15 deletions(-)
diff --git a/docs/user-guide/tutorials/ADCP_transects.ipynb b/docs/user-guide/tutorials/ADCP_transects.ipynb
index b0cf4d08..35faa881 100644
--- a/docs/user-guide/tutorials/ADCP_transects.ipynb
+++ b/docs/user-guide/tutorials/ADCP_transects.ipynb
@@ -12,7 +12,7 @@
"The plot(s) we will produce are simple plots which follow the trajectory of the expedition as a function of distance from the start, and are intended to be a starting point for your analysis. Because the `ADCP` instrument is an underway/onboard instrument, this means we benefit from continuous recordings across the length of the ship's track (unlike overboard instruments such as CTDs which have to deployed at individual sampling sites).\n",
"\n",
"
\n",
- "NOTE: This notebook assumes that each point along the expedition track is further from the start than the previous point. The code will still work if not, but the resultant plots might not be very intuitive.\n",
+ "Note: This notebook assumes that each point along the expedition track is further from the start than the previous point. The code will still work if not, but the resultant plots might not be very intuitive.\n",
"
"
]
},
@@ -55,12 +55,13 @@
"\n",
"
\n",
"Tip: You can get the path to your expedition results by navigating to to the folder in Terminal (using `cd`) and then using the `pwd` command. This will print your working directory which you can copy to the `data_dir` variable in this notebook. Don't forget to keep it as a string (in \"quotation\" marks)!\n",
- "
"
+ "
\n",
+ "\n"
]
},
{
"cell_type": "code",
- "execution_count": 7,
+ "execution_count": 2,
"id": "0cb630f6",
"metadata": {},
"outputs": [],
diff --git a/docs/user-guide/tutorials/CTD_transects.ipynb b/docs/user-guide/tutorials/CTD_transects.ipynb
index 57748382..61a109a1 100644
--- a/docs/user-guide/tutorials/CTD_transects.ipynb
+++ b/docs/user-guide/tutorials/CTD_transects.ipynb
@@ -98,7 +98,7 @@
},
{
"cell_type": "code",
- "execution_count": 46,
+ "execution_count": 74,
"id": "8de8b4ae",
"metadata": {},
"outputs": [],
@@ -121,7 +121,7 @@
},
{
"cell_type": "code",
- "execution_count": 47,
+ "execution_count": 75,
"id": "b32d2730",
"metadata": {},
"outputs": [],
@@ -139,17 +139,17 @@
" },\n",
" \"oxygen\": {\n",
" \"cmap\": cmo.oxy,\n",
- " \"label\": \"Dissolved oxygen (mmol m-3)\",\n",
+ " \"label\": r\"Dissolved oxygen (mmol m$^{-3}$)\",\n",
" \"ds_name\": \"o2\",\n",
" },\n",
" \"nitrate\": {\n",
" \"cmap\": cmo.matter,\n",
- " \"label\": \"Nitrate (mmol m-3)\",\n",
+ " \"label\": r\"Nitrate (mmol m$^{-3}$)\",\n",
" \"ds_name\": \"no3\",\n",
" },\n",
" \"phosphate\": {\n",
" \"cmap\": cmo.matter,\n",
- " \"label\": \"Phosphate (mmol m-3)\",\n",
+ " \"label\": r\"Phosphate (mmol m$^{-3}$)\",\n",
" \"ds_name\": \"po4\",\n",
" },\n",
" \"ph\": {\n",
@@ -159,22 +159,22 @@
" },\n",
" \"zooplankton\": {\n",
" \"cmap\": cmo.algae,\n",
- " \"label\": \"Total zooplankton (mmol m-3)\",\n",
+ " \"label\": r\"Total zooplankton (mmol m$^{-3}$)\",\n",
" \"ds_name\": \"zooc\",\n",
" },\n",
" \"phytoplankton\": {\n",
" \"cmap\": cmo.algae,\n",
- " \"label\": \"Total phytoplankton (mmol m-3)\",\n",
+ " \"label\": r\"Total phytoplankton (mmol m$^{-3}$)\",\n",
" \"ds_name\": \"phyc\",\n",
" },\n",
" \"primary_production\": {\n",
" \"cmap\": cmo.matter,\n",
- " \"label\": \"Total primary production of phytoplankton (mg m-3 day-1)\",\n",
+ " \"label\": r\"Total primary production of phytoplankton (mg m$^{-3}$ day$^{-1}$)\",\n",
" \"ds_name\": \"nppv\",\n",
" },\n",
" \"chlorophyll\": {\n",
" \"cmap\": cmo.algae,\n",
- " \"label\": \"Chlorophyll (mg m-3)\",\n",
+ " \"label\": r\"Chlorophyll (mg m$^{-3}$)\",\n",
" \"ds_name\": \"chl\",\n",
" },\n",
"}"
@@ -192,7 +192,7 @@
},
{
"cell_type": "code",
- "execution_count": 48,
+ "execution_count": 76,
"id": "13f4664b",
"metadata": {},
"outputs": [],
@@ -218,7 +218,7 @@
},
{
"cell_type": "code",
- "execution_count": 49,
+ "execution_count": 77,
"id": "785b2b35",
"metadata": {},
"outputs": [],
@@ -320,7 +320,7 @@
},
{
"cell_type": "code",
- "execution_count": 50,
+ "execution_count": 78,
"id": "f59824a1",
"metadata": {},
"outputs": [],
From d5b0a40e8ef3c978f380c875c44d9069ded37abb Mon Sep 17 00:00:00 2001
From: j-atkins <106238905+j-atkins@users.noreply.github.com>
Date: Tue, 2 Sep 2025 12:14:54 +0200
Subject: [PATCH 6/9] retry docs build
From c7ff4059d3b87b6769552348753f4aae41f76821 Mon Sep 17 00:00:00 2001
From: j-atkins <106238905+j-atkins@users.noreply.github.com>
Date: Tue, 2 Sep 2025 15:40:04 +0200
Subject: [PATCH 7/9] small edits to suit different setups
---
docs/user-guide/tutorials/ADCP_transects.ipynb | 16 ++++++++--------
docs/user-guide/tutorials/CTD_transects.ipynb | 17 +++++++++--------
2 files changed, 17 insertions(+), 16 deletions(-)
diff --git a/docs/user-guide/tutorials/ADCP_transects.ipynb b/docs/user-guide/tutorials/ADCP_transects.ipynb
index 35faa881..3fbb0a46 100644
--- a/docs/user-guide/tutorials/ADCP_transects.ipynb
+++ b/docs/user-guide/tutorials/ADCP_transects.ipynb
@@ -25,7 +25,11 @@
"\n",
"#### Imports\n",
"\n",
- "The first step is to import the Python packages required for post-processing the data and plotting. "
+ "The first step is to import the Python packages required for post-processing the data and plotting. \n",
+ "\n",
+ "
\n",
+ "Tip: You may need to set the Kernel to the relevant (Conda) environment in the top right of this notebook to access the required packages! \n",
+ "
\n"
]
},
{
@@ -54,7 +58,7 @@
"Next, you should set `data_dir` to be the path to your expedition results in the code block below. You should replace `\"/path/to/EXPEDITION/results/\"` with the path for your machine.\n",
"\n",
"
\n",
- "Tip: You can get the path to your expedition results by navigating to to the folder in Terminal (using `cd`) and then using the `pwd` command. This will print your working directory which you can copy to the `data_dir` variable in this notebook. Don't forget to keep it as a string (in \"quotation\" marks)!\n",
+ "Tip: You can get the path to your expedition results by navigating to the `results` folder in Terminal (using `cd`) and then using the `pwd` command. This will print your working directory which you can copy to the `data_dir` variable in this notebook. Don't forget to keep it as a string (in \"quotation\" marks)!\n",
"
\n",
"\n"
]
@@ -104,7 +108,7 @@
},
{
"cell_type": "code",
- "execution_count": 4,
+ "execution_count": null,
"id": "0aa1f8f4",
"metadata": {},
"outputs": [],
@@ -185,11 +189,7 @@
"
Note: The plots produced next are a starting point for your analysis. You are encouraged to make adjustments, for example axis limits and scaling if the defaults not best suited to your specific data. Use your preferred AI coding assistant for help!\n",
"
\n",
"\n",
- "We are now ready to plot our transect data. We will use distance from the start of the transect/expedition for the x-axis, and water column depth for the y-axis. The ADCP data will then be plotted according to the colour map for diagnostic. The profiles across the transect are likely to be different depths because some parts of the ocean are of course shallower than others.\n",
- "\n",
- "
"
+ "We are now ready to plot our transect data. We will use distance from the start of the transect/expedition for the x-axis, and water column depth for the y-axis. The ADCP data will then be plotted according to the colour map for diagnostic. The profiles across the transect are likely to be different depths because some parts of the ocean are of course shallower than others."
]
},
{
diff --git a/docs/user-guide/tutorials/CTD_transects.ipynb b/docs/user-guide/tutorials/CTD_transects.ipynb
index 61a109a1..63d8ad00 100644
--- a/docs/user-guide/tutorials/CTD_transects.ipynb
+++ b/docs/user-guide/tutorials/CTD_transects.ipynb
@@ -27,7 +27,11 @@
"\n",
"#### Imports\n",
"\n",
- "The first step is to import the Python packages required for post-processing the data and plotting. "
+ "The first step is to import the Python packages required for post-processing the data and plotting. \n",
+ "\n",
+ "
"
]
},
{
@@ -56,8 +60,9 @@
"Next, you should set `data_dir` to be the path to your expedition results in the code block below. You should replace `\"/path/to/EXPEDITION/results/\"` with the path for your machine.\n",
"\n",
"
You can get the path to your expedition results by navigating to the `results` folder in Terminal (using `cd`) and then using the `pwd` command. This will print your working directory which you can copy to the `data_dir` variable in this notebook. Don't forget to keep it as a string (in \"quotation\" marks)!\n",
+ "