{ "cells": [ { "cell_type": "markdown", "metadata": {}, "source": [ "# Welcome to PyCO2SYS!\n", "\n", "***If you're totally new to PyCO2SYS, this is the right place to be!***\n", "\n", "If you're also new to Python, you should still be able to follow what's going on here and understand how to make some changes to the code - but this is not intended as a Python tutorial.\n", "\n", "We will work through a series of examples of PyCO2SYS calculations, starting with the most basic and gradually building up the complexity.\n", "\n", "> **How does this work?**\n", "> \n", "> This is a [Jupyter notebook](https://realpython.com/jupyter-notebook-introduction/). If you're viewing this [through Binder](https://mybinder.org/v2/gh/mvdh7/PyCO2SYS-examples/master), then Python is running live in your web browser!\n", ">\n", "> You can run the different sections of code below by clicking on them with your mouse. The selected code section gets outlined by a box with a thick green or blue bar down the left-hand side. Then either click the Run button at the top or press ctrl+enter on your keyboard to run the selected section.\n", ">\n", "> To the upper left of each code section you will see `In [ ]:`. An asterisk (`*`) appears between the brackets while the code is running, which changes to a number once each section of code has successfully run. Once it has been run (but not before!), the results calculated in one code section can be used in any other. **Some sections do rely on earlier ones having been run, so make sure you run them all in sequence!**\n", ">\n", "> You can edit the code freely and run it again to see what happens. Don't worry, your changes are only local, so they won't affect anyone else. If you close the notebook and start it up again it will all be reset (unless you've downloaded this and are running it on your own Jupyter server).\n", "\n", "## Import CO2SYS\n", "\n", "Before we can use any package like PyCO2SYS in Python we must import it. This is very simple to do, using the following convention. Not much appears to happen, but check that a number appears in the brackets at the top left (e.g. `In [1]:`):" ] }, { "cell_type": "code", "execution_count": 1, "metadata": {}, "outputs": [], "source": [ "import PyCO2SYS as pyco2" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "## Solve the marine carbonate system!\n", "\n", "Now that we've imported PyCO2SYS, we can define some seawater conditions and solve the marine carbonate system from them.\n", "\n", "Imagine we measured the pH and dissolved inorganic carbon (DIC) of a seawater sample in the lab at 25 °C. The sample was collected from a seawater pressure of 5 dbar (roughly 5 m depth - pressure excludes atmospheric pressure) and it had a temperature of 10 °C there. We want to know what the saturation state of aragonite was *in situ* when and where the sample was collected.\n", "\n", "The lab environment sets the \"input conditions\" for PyCO2SYS's arguments and results (i.e. temperature = 25 °C, pressure = 0), while the in situ environment sets the \"output conditions\" (i.e. temperature = 10 °C, pressure = 100 dbar).\n", "\n", "> For more information on the arguments and results below please consult the [online docs](https://pyco2sys.readthedocs.io/en/latest/co2sys_nd/).\n", ">\n", "> You can also find the [full citations](https://pyco2sys.readthedocs.io/en/latest/refs/) for the abbreviated references (e.g. `LDK00`) mentioned in the code." ] }, { "cell_type": "code", "execution_count": 2, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "The calculated result is: 3.23984172794113\n" ] } ], "source": [ "# Everything on a line after a # symbol is just a comment!\n", "\n", "# Set up a dict for the keyword arguments, for convenience\n", "pyco2_kws = {}\n", "\n", "# Define the known marine carbonate system parameters\n", "pyco2_kws[\"par1\"] = 8.05 # pH measured in the lab, Total scale\n", "pyco2_kws[\"par2\"] = 2050 # DIC measured in the lab in μmol/kg-sw\n", "pyco2_kws[\"par1_type\"] = 3 # tell PyCO2SYS: \"par1 is a pH value\"\n", "pyco2_kws[\"par2_type\"] = 2 # tell PyCO2SYS: \"par2 is a DIC value\"\n", "\n", "# Define the seawater conditions and add them to the dict\n", "pyco2_kws[\"salinity\"] = 35 # practical salinity\n", "pyco2_kws[\"temperature\"] = 25 # lab temperature (input conditions) in °C\n", "pyco2_kws[\"temperature_out\"] = 10 # in-situ temperature (output conditions) in °C\n", "pyco2_kws[\"pressure\"] = 0 # lab pressure (input conditions) in dbar, ignoring the atmosphere\n", "pyco2_kws[\"pressure_out\"] = 5 # in-situ pressure (output conditions) in dbar, ignoring the atmosphere\n", "pyco2_kws[\"total_silicate\"] = 8.2 # total silicate in μmol/kg-sw\n", "pyco2_kws[\"total_phosphate\"] = 0.3 # total phosphate in μmol/kg-sw\n", "pyco2_kws[\"total_ammonia\"] = 0.1 # total ammonia in μmol/kg-sw\n", "pyco2_kws[\"total_sulfide\"] = 0.2 # total sulfide in μmol/kg-sw\n", "\n", "# Define PyCO2SYS settings and add them to the dict\n", "pyco2_kws[\"opt_pH_scale\"] = 1 # tell PyCO2SYS: \"the pH input is on the Total scale\"\n", "pyco2_kws[\"opt_k_carbonic\"] = 10 # tell PyCO2SYS: \"use carbonate equilibrium constants of LDK00\"\n", "pyco2_kws[\"opt_k_bisulfate\"] = 1 # tell PyCO2SYS: \"use bisulfate dissociation constant of D90a\"\n", "pyco2_kws[\"opt_total_borate\"] = 1 # tell PyCO2SYS: \"use borate:salinity of LKB10\"\n", "\n", "# Now calculate everything with PyCO2SYS!\n", "results = pyco2.sys(**pyco2_kws)\n", "\n", "# `results` contains all the different calculated seawater properties as a dict.\n", "# Aragonite saturation state under the output conditions has the key \"saturation_aragonite_out\".\n", "# Here we extract that result only and store it as `omega_arag_insitu`:\n", "omega_arag_insitu = results[\"saturation_aragonite_out\"]\n", "\n", "# Now, tell us the answer!\n", "print(\"The calculated result is:\", omega_arag_insitu)" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "If all went well then you should see the aragonite saturation state (about 3.2 for the example values used) printed out directly above here.\n", "\n", "### Try changing the arguments\n", "\n", "You can edit the code above and then re-run it to see the effect on the result. Some things you might try:\n", "\n", " 1. Change the **seawater conditions** (any of `par1`, `par2`, `salinity`, `temperature`, `temperature_out`, `pressure`, `pressure_out`, `total_silicate`, `total_phosphate`, `total_ammonia` and `total_sulfide`).\n", " \n", " 2. Change the **equilibrium constants** used for the calculations (`opt_k_carbonic`, `opt_k_bisulfate` and `opt_total_borate`; see the [settings docs](https://pyco2sys.readthedocs.io/en/latest/co2sys_nd/#settings) for your options).\n", " \n", " 3. Change the **pH scale** that the input pH is declared as being on (`opt_pH_scale`; see the [settings docs](https://pyco2sys.readthedocs.io/en/latest/co2sys_nd/#settings)).\n", " \n", " 4. Change the input pair of **marine carbonate system parameters** (`par1` and `par1_type` and/or `par2` and `par2_type`; see the [carbonate system parameters docs](https://pyco2sys.readthedocs.io/en/latest/co2sys/#carbonate-system-parameters)).\n", " \n", " 5. Change the **results variable** that is printed out (change `\"saturation_aragonite_out\"` to something different; see the [results docs](https://pyco2sys.readthedocs.io/en/latest/co2sys_nd/#results))." ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "## Calculations with arrays\n", "\n", "PyCO2SYS doesn't have to process one calculation at a time - it is optimised to run calculations over many different solution compositions at the same time.\n", "\n", "> In the example below, only one of the arguments is an array, while the others are all single values.\n", ">\n", "> But every single input variable given to PyCO2SYS can be provided either as an array, or as a single value, in any combination - including those controlling the [settings](https://pyco2sys.readthedocs.io/en/latest/co2sys/#settings).\n", ">\n", "> Arrays should be [NumPy ndarrays](https://numpy.org/doc/stable/reference/generated/numpy.ndarray.html?highlight=ndarray#numpy.ndarray) but they can have as many dimensions as you like, in any combination that is compatible for NumPy broadcasting. Results that depend only on scalar arguments are also scalar. Results that depend on non-scalar arguments will all be in the shape of all arguments fully broadcasted together.\n", "\n", "### Effect of increasing pCO2\n", "\n", "Let's continue from the example above and see how increasing seawater pCO2 alone would change the saturation state of aragonite for that sample, assuming that total alkalinity remains constant.\n", "\n", "#### Get starting conditions\n", "\n", "We'll use the same seawater conditions and PyCO2SYS settings as we defined previously, so we don't need to write those out again. But we will redefine the marine carbonate system, starting from the total alkalinity and seawater pCO2 that we calculated above as part of `results`." ] }, { "cell_type": "code", "execution_count": 3, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "Total alkalinity is: 2358.7 μmol/kg-sw\n", "Initial seawater pCO2 is: 214.8 μatm\n" ] } ], "source": [ "# Get total alkalinity and initial seawater pCO2\n", "TAlk = results[\"alkalinity\"]\n", "pCO2_now = results[\"pCO2_out\"]\n", "\n", "# See what they are!\n", "print(\"Total alkalinity is: {:.1f} μmol/kg-sw\".format(TAlk))\n", "print(\"Initial seawater pCO2 is: {:.1f} μatm\".format(pCO2_now))" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "#### Generate array of increasing pCO2 values\n", "\n", "We can use a tool from the Python package [NumPy](https://numpy.org/doc/stable/) to conveniently generate an array of increasing seawater pCO2 values:" ] }, { "cell_type": "code", "execution_count": 4, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "Increasing pCO2 values in μatm:\n", "[ 214.79395387 256.12058788 297.44722189 338.77385589 380.1004899\n", " 421.42712391 462.75375791 504.08039192 545.40702593 586.73365993\n", " 628.06029394 669.38692795 710.71356195 752.04019596 793.36682997\n", " 834.69346397 876.02009798 917.34673199 958.67336599 1000. ]\n" ] } ], "source": [ "import numpy as np # now we have access to NumPy's tools\n", "\n", "pCO2_end = 1000 # maximum pCO2 value to go to in μatm\n", "n_steps = 20 # number of regularly-spaced values to make from `pCO2_now` to `pCO2_end`\n", "pCO2_increasing = np.linspace(pCO2_now, pCO2_end, n_steps) # generate the array of pCO2 values\n", "\n", "print(\"Increasing pCO2 values in μatm:\")\n", "print(pCO2_increasing)" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "#### Solve the marine carbonate system\n", "\n", "Now, we can simply pass in this array as one of the inputs to PyCO2SYS along with `TAlk` and the other values that we defined before. We also need to:\n", "\n", " * Update the `par1_type` and `par2_type` inputs to `1` for total alkalinity and `4` for seawater pCO2 (see the [input docs](https://pyco2sys.readthedocs.io/en/latest/co2sys_nd/#carbonate-system-parameters)).\n", " \n", " * Use `temperature_out` and `pressure_out` as the \\\"input\\\" conditions (i.e. `temperature` and `pressure`). This is because the pCO2 we're now using as our input was calculated at the \"output\" conditions of the original calculation (i.e. in situ). When we do calculations entirely using in situ values, then there's no distinction between \"input\" and \"output\" conditions.\n", "\n", "We access the calculated results in exactly the same way, but now they are all either scalar or arrays of the same size as `pCO2_increasing`:" ] }, { "cell_type": "code", "execution_count": 5, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "Aragonite saturation state response to increasing seawater pCO2:\n", "[3.23984173 2.89010613 2.61087189 2.38225023 2.1913333 2.02933287\n", " 1.89003607 1.76891481 1.66258458 1.56846121 1.48453529 1.40921945\n", " 1.34124222 1.2795726 1.22336541 1.17192096 1.12465488 1.08107516\n", " 1.04076449 1.00336659]\n" ] } ], "source": [ "# Copy original kwargs dict\n", "import copy\n", "pyco2_kws_response = copy.deepcopy(pyco2_kws)\n", "\n", "# Copy original output temperature and pressure as new input conditions\n", "pyco2_kws_response[\"temperature\"] = pyco2_kws[\"temperature_out\"]\n", "pyco2_kws_response[\"pressure\"] = pyco2_kws[\"pressure_out\"]\n", "\n", "# Remove now-unnecessary output conditions (optional)\n", "pyco2_kws_response.pop(\"temperature_out\")\n", "pyco2_kws_response.pop(\"pressure_out\")\n", "\n", "# Switch to the new known parameter values\n", "pyco2_kws_response[\"par1\"] = TAlk\n", "pyco2_kws_response[\"par2\"] = pCO2_increasing\n", "pyco2_kws_response[\"par1_type\"] = 1\n", "pyco2_kws_response[\"par2_type\"] = 4\n", "\n", "# Solve the marine carbonate system with increasing seawater pCO2\n", "results_response = pyco2.sys(**pyco2_kws_response)\n", "\n", "# See how aragonite saturation state changes\n", "omega_arag_response = results_response[\"saturation_aragonite\"]\n", "print(\"Aragonite saturation state response to increasing seawater pCO2:\")\n", "print(omega_arag_response)" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "#### Make a figure of the results\n", "\n", "The Python package [Matplotlib](https://matplotlib.org/) can help us visualise this result:" ] }, { "cell_type": "code", "execution_count": 6, "metadata": {}, "outputs": [ { "data": { "application/javascript": [ "/* Put everything inside the global mpl namespace */\n", "/* global mpl */\n", "window.mpl = {};\n", "\n", "mpl.get_websocket_type = function () {\n", " if (typeof WebSocket !== 'undefined') {\n", " return WebSocket;\n", " } else if (typeof MozWebSocket !== 'undefined') {\n", " return MozWebSocket;\n", " } else {\n", " alert(\n", " 'Your browser does not have WebSocket support. 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'_images/' + image + '.png';\n", " icon_img.srcset = '_images/' + image + '_large.png 2x';\n", " icon_img.alt = tooltip;\n", " button.appendChild(icon_img);\n", "\n", " buttonGroup.appendChild(button);\n", " }\n", "\n", " if (buttonGroup.hasChildNodes()) {\n", " toolbar.appendChild(buttonGroup);\n", " }\n", "\n", " var fmt_picker = document.createElement('select');\n", " fmt_picker.classList = 'mpl-widget';\n", " toolbar.appendChild(fmt_picker);\n", " this.format_dropdown = fmt_picker;\n", "\n", " for (var ind in mpl.extensions) {\n", " var fmt = mpl.extensions[ind];\n", " var option = document.createElement('option');\n", " option.selected = fmt === mpl.default_extension;\n", " option.innerHTML = fmt;\n", " fmt_picker.appendChild(option);\n", " }\n", "\n", " var status_bar = document.createElement('span');\n", " status_bar.classList = 'mpl-message';\n", " toolbar.appendChild(status_bar);\n", " this.message = status_bar;\n", "};\n", "\n", "mpl.figure.prototype.request_resize = function (x_pixels, y_pixels) {\n", " // Request matplotlib to resize the figure. Matplotlib will then trigger a resize in the client,\n", " // which will in turn request a refresh of the image.\n", " this.send_message('resize', { width: x_pixels, height: y_pixels });\n", "};\n", "\n", "mpl.figure.prototype.send_message = function (type, properties) {\n", " properties['type'] = type;\n", " properties['figure_id'] = this.id;\n", " this.ws.send(JSON.stringify(properties));\n", "};\n", "\n", "mpl.figure.prototype.send_draw_message = function () {\n", " if (!this.waiting) {\n", " this.waiting = true;\n", " this.ws.send(JSON.stringify({ type: 'draw', figure_id: this.id }));\n", " }\n", "};\n", "\n", "mpl.figure.prototype.handle_save = function (fig, _msg) {\n", " var format_dropdown = fig.format_dropdown;\n", " var format = format_dropdown.options[format_dropdown.selectedIndex].value;\n", " fig.ondownload(fig, format);\n", "};\n", "\n", "mpl.figure.prototype.handle_resize = function (fig, msg) {\n", " var size = msg['size'];\n", " if (size[0] !== fig.canvas.width || size[1] !== fig.canvas.height) {\n", " fig._resize_canvas(size[0], size[1], msg['forward']);\n", " fig.send_message('refresh', {});\n", " }\n", "};\n", "\n", "mpl.figure.prototype.handle_rubberband = function (fig, msg) {\n", " var x0 = msg['x0'] / fig.ratio;\n", " var y0 = (fig.canvas.height - msg['y0']) / fig.ratio;\n", " var x1 = msg['x1'] / fig.ratio;\n", " var y1 = (fig.canvas.height - msg['y1']) / fig.ratio;\n", " x0 = Math.floor(x0) + 0.5;\n", " y0 = Math.floor(y0) + 0.5;\n", " x1 = Math.floor(x1) + 0.5;\n", " y1 = Math.floor(y1) + 0.5;\n", " var min_x = Math.min(x0, x1);\n", " var min_y = Math.min(y0, y1);\n", " var width = Math.abs(x1 - x0);\n", " var height = Math.abs(y1 - y0);\n", "\n", " fig.rubberband_context.clearRect(\n", " 0,\n", " 0,\n", " fig.canvas.width / fig.ratio,\n", " fig.canvas.height / fig.ratio\n", " );\n", "\n", " fig.rubberband_context.strokeRect(min_x, min_y, width, height);\n", "};\n", "\n", "mpl.figure.prototype.handle_figure_label = function (fig, msg) {\n", " // Updates the figure title.\n", " fig.header.textContent = msg['label'];\n", "};\n", "\n", "mpl.figure.prototype.handle_cursor = function (fig, msg) {\n", " var cursor = msg['cursor'];\n", " switch (cursor) {\n", " case 0:\n", " cursor = 'pointer';\n", " break;\n", " case 1:\n", " cursor = 'default';\n", " break;\n", " case 2:\n", " cursor = 'crosshair';\n", " break;\n", " case 3:\n", " cursor = 'move';\n", " break;\n", " }\n", " fig.rubberband_canvas.style.cursor = cursor;\n", "};\n", "\n", "mpl.figure.prototype.handle_message = function (fig, msg) {\n", " fig.message.textContent = msg['message'];\n", "};\n", "\n", "mpl.figure.prototype.handle_draw = function (fig, _msg) {\n", " // Request the server to send over a new figure.\n", " fig.send_draw_message();\n", "};\n", "\n", "mpl.figure.prototype.handle_image_mode = function (fig, msg) {\n", " fig.image_mode = msg['mode'];\n", "};\n", "\n", "mpl.figure.prototype.handle_history_buttons = function (fig, msg) {\n", " for (var key in msg) {\n", " if (!(key in fig.buttons)) {\n", " continue;\n", " }\n", " fig.buttons[key].disabled = !msg[key];\n", " fig.buttons[key].setAttribute('aria-disabled', !msg[key]);\n", " }\n", "};\n", "\n", "mpl.figure.prototype.handle_navigate_mode = function (fig, msg) {\n", " if (msg['mode'] === 'PAN') {\n", " fig.buttons['Pan'].classList.add('active');\n", " fig.buttons['Zoom'].classList.remove('active');\n", " } else if (msg['mode'] === 'ZOOM') {\n", " fig.buttons['Pan'].classList.remove('active');\n", " fig.buttons['Zoom'].classList.add('active');\n", " } else {\n", " fig.buttons['Pan'].classList.remove('active');\n", " fig.buttons['Zoom'].classList.remove('active');\n", " }\n", "};\n", "\n", "mpl.figure.prototype.updated_canvas_event = function () {\n", " // Called whenever the canvas gets updated.\n", " this.send_message('ack', {});\n", "};\n", "\n", "// A function to construct a web socket function for onmessage handling.\n", "// Called in the figure constructor.\n", "mpl.figure.prototype._make_on_message_function = function (fig) {\n", " return function socket_on_message(evt) {\n", " if (evt.data instanceof Blob) {\n", " var img = evt.data;\n", " if (img.type !== 'image/png') {\n", " /* FIXME: We get \"Resource interpreted as Image but\n", " * transferred with MIME type text/plain:\" errors on\n", " * Chrome. But how to set the MIME type? It doesn't seem\n", " * to be part of the websocket stream */\n", " img.type = 'image/png';\n", " }\n", "\n", " /* Free the memory for the previous frames */\n", " if (fig.imageObj.src) {\n", " (window.URL || window.webkitURL).revokeObjectURL(\n", " fig.imageObj.src\n", " );\n", " }\n", "\n", " fig.imageObj.src = (window.URL || window.webkitURL).createObjectURL(\n", " img\n", " );\n", " fig.updated_canvas_event();\n", " fig.waiting = false;\n", " return;\n", " } else if (\n", " typeof evt.data === 'string' &&\n", " evt.data.slice(0, 21) === 'data:image/png;base64'\n", " ) {\n", " fig.imageObj.src = evt.data;\n", " fig.updated_canvas_event();\n", " fig.waiting = false;\n", " return;\n", " }\n", "\n", " var msg = JSON.parse(evt.data);\n", " var msg_type = msg['type'];\n", "\n", " // Call the \"handle_{type}\" callback, which takes\n", " // the figure and JSON message as its only arguments.\n", " try {\n", " var callback = fig['handle_' + msg_type];\n", " } catch (e) {\n", " console.log(\n", " \"No handler for the '\" + msg_type + \"' message type: \",\n", " msg\n", " );\n", " return;\n", " }\n", "\n", " if (callback) {\n", " try {\n", " // console.log(\"Handling '\" + msg_type + \"' message: \", msg);\n", " callback(fig, msg);\n", " } catch (e) {\n", " console.log(\n", " \"Exception inside the 'handler_\" + msg_type + \"' callback:\",\n", " e,\n", " e.stack,\n", " msg\n", " );\n", " }\n", " }\n", " };\n", "};\n", "\n", "// from http://stackoverflow.com/questions/1114465/getting-mouse-location-in-canvas\n", "mpl.findpos = function (e) {\n", " //this section is from http://www.quirksmode.org/js/events_properties.html\n", " var targ;\n", " if (!e) {\n", " e = window.event;\n", " }\n", " if (e.target) {\n", " targ = e.target;\n", " } else if (e.srcElement) {\n", " targ = e.srcElement;\n", " }\n", " if (targ.nodeType === 3) {\n", " // defeat Safari bug\n", " targ = targ.parentNode;\n", " }\n", "\n", " // pageX,Y are the mouse positions relative to the document\n", " var boundingRect = targ.getBoundingClientRect();\n", " var x = e.pageX - (boundingRect.left + document.body.scrollLeft);\n", " var y = e.pageY - (boundingRect.top + document.body.scrollTop);\n", "\n", " return { x: x, y: y };\n", "};\n", "\n", "/*\n", " * return a copy of an object with only non-object keys\n", " * we need this to avoid circular references\n", " * http://stackoverflow.com/a/24161582/3208463\n", " */\n", "function simpleKeys(original) {\n", " return Object.keys(original).reduce(function (obj, key) {\n", " if (typeof original[key] !== 'object') {\n", " obj[key] = original[key];\n", " }\n", " return obj;\n", " }, {});\n", "}\n", "\n", "mpl.figure.prototype.mouse_event = function (event, name) {\n", " var canvas_pos = mpl.findpos(event);\n", "\n", " if (name === 'button_press') {\n", " this.canvas.focus();\n", " this.canvas_div.focus();\n", " }\n", "\n", " var x = canvas_pos.x * this.ratio;\n", " var y = canvas_pos.y * this.ratio;\n", "\n", " this.send_message(name, {\n", " x: x,\n", " y: y,\n", " button: event.button,\n", " step: event.step,\n", " guiEvent: simpleKeys(event),\n", " });\n", "\n", " /* This prevents the web browser from automatically changing to\n", " * the text insertion cursor when the button is pressed. We want\n", " * to control all of the cursor setting manually through the\n", " * 'cursor' event from matplotlib */\n", " event.preventDefault();\n", " return false;\n", "};\n", "\n", "mpl.figure.prototype._key_event_extra = function (_event, _name) {\n", " // Handle any extra behaviour associated with a key event\n", "};\n", "\n", "mpl.figure.prototype.key_event = function (event, name) {\n", " // Prevent repeat events\n", " if (name === 'key_press') {\n", " if (event.key === this._key) {\n", " return;\n", " } else {\n", " this._key = event.key;\n", " }\n", " }\n", " if (name === 'key_release') {\n", " this._key = null;\n", " }\n", "\n", " var value = '';\n", " if (event.ctrlKey && event.key !== 'Control') {\n", " value += 'ctrl+';\n", " }\n", " else if (event.altKey && event.key !== 'Alt') {\n", " value += 'alt+';\n", " }\n", " else if (event.shiftKey && event.key !== 'Shift') {\n", " value += 'shift+';\n", " }\n", "\n", " value += 'k' + event.key;\n", "\n", " this._key_event_extra(event, name);\n", "\n", " this.send_message(name, { key: value, guiEvent: simpleKeys(event) });\n", " return false;\n", "};\n", "\n", "mpl.figure.prototype.toolbar_button_onclick = function (name) {\n", " if (name === 'download') {\n", " this.handle_save(this, null);\n", " } else {\n", " this.send_message('toolbar_button', { name: name });\n", " }\n", "};\n", "\n", "mpl.figure.prototype.toolbar_button_onmouseover = function (tooltip) {\n", " this.message.textContent = tooltip;\n", "};\n", "\n", "///////////////// REMAINING CONTENT GENERATED BY embed_js.py /////////////////\n", "// prettier-ignore\n", "var _JSXTOOLS_RESIZE_OBSERVER=function(A){var t,i=new WeakMap,n=new WeakMap,a=new WeakMap,r=new WeakMap,o=new Set;function s(e){if(!(this instanceof s))throw new TypeError(\"Constructor requires 'new' operator\");i.set(this,e)}function h(){throw new TypeError(\"Function is not a constructor\")}function c(e,t,i,n){e=0 in arguments?Number(arguments[0]):0,t=1 in arguments?Number(arguments[1]):0,i=2 in arguments?Number(arguments[2]):0,n=3 in arguments?Number(arguments[3]):0,this.right=(this.x=this.left=e)+(this.width=i),this.bottom=(this.y=this.top=t)+(this.height=n),Object.freeze(this)}function d(){t=requestAnimationFrame(d);var s=new WeakMap,p=new Set;o.forEach((function(t){r.get(t).forEach((function(i){var r=t instanceof window.SVGElement,o=a.get(t),d=r?0:parseFloat(o.paddingTop),f=r?0:parseFloat(o.paddingRight),l=r?0:parseFloat(o.paddingBottom),u=r?0:parseFloat(o.paddingLeft),g=r?0:parseFloat(o.borderTopWidth),m=r?0:parseFloat(o.borderRightWidth),w=r?0:parseFloat(o.borderBottomWidth),b=u+f,F=d+l,v=(r?0:parseFloat(o.borderLeftWidth))+m,W=g+w,y=r?0:t.offsetHeight-W-t.clientHeight,E=r?0:t.offsetWidth-v-t.clientWidth,R=b+v,z=F+W,M=r?t.width:parseFloat(o.width)-R-E,O=r?t.height:parseFloat(o.height)-z-y;if(n.has(t)){var k=n.get(t);if(k[0]===M&&k[1]===O)return}n.set(t,[M,O]);var S=Object.create(h.prototype);S.target=t,S.contentRect=new c(u,d,M,O),s.has(i)||(s.set(i,[]),p.add(i)),s.get(i).push(S)}))})),p.forEach((function(e){i.get(e).call(e,s.get(e),e)}))}return s.prototype.observe=function(i){if(i instanceof window.Element){r.has(i)||(r.set(i,new Set),o.add(i),a.set(i,window.getComputedStyle(i)));var n=r.get(i);n.has(this)||n.add(this),cancelAnimationFrame(t),t=requestAnimationFrame(d)}},s.prototype.unobserve=function(i){if(i instanceof window.Element&&r.has(i)){var n=r.get(i);n.has(this)&&(n.delete(this),n.size||(r.delete(i),o.delete(i))),n.size||r.delete(i),o.size||cancelAnimationFrame(t)}},A.DOMRectReadOnly=c,A.ResizeObserver=s,A.ResizeObserverEntry=h,A}; // eslint-disable-line\n", "mpl.toolbar_items = [[\"Home\", \"Reset original view\", \"fa fa-home icon-home\", \"home\"], [\"Back\", \"Back to previous view\", \"fa fa-arrow-left icon-arrow-left\", \"back\"], [\"Forward\", \"Forward to next view\", \"fa fa-arrow-right icon-arrow-right\", \"forward\"], [\"\", \"\", \"\", \"\"], [\"Pan\", \"Left button pans, Right button zooms\\nx/y fixes axis, CTRL fixes aspect\", \"fa fa-arrows icon-move\", \"pan\"], [\"Zoom\", \"Zoom to rectangle\\nx/y fixes axis, CTRL fixes aspect\", \"fa fa-square-o icon-check-empty\", \"zoom\"], [\"\", \"\", \"\", \"\"], [\"Download\", \"Download plot\", \"fa fa-floppy-o icon-save\", \"download\"]];\n", "\n", "mpl.extensions = [\"eps\", \"jpeg\", \"pgf\", \"pdf\", \"png\", \"ps\", \"raw\", \"svg\", \"tif\"];\n", "\n", "mpl.default_extension = \"png\";/* global mpl */\n", "\n", "var comm_websocket_adapter = function (comm) {\n", " // Create a \"websocket\"-like object which calls the given IPython comm\n", " // object with the appropriate methods. Currently this is a non binary\n", " // socket, so there is still some room for performance tuning.\n", " var ws = {};\n", "\n", " ws.binaryType = comm.kernel.ws.binaryType;\n", " ws.readyState = comm.kernel.ws.readyState;\n", " function updateReadyState(_event) {\n", " if (comm.kernel.ws) {\n", " ws.readyState = comm.kernel.ws.readyState;\n", " } else {\n", " ws.readyState = 3; // Closed state.\n", " }\n", " }\n", " comm.kernel.ws.addEventListener('open', updateReadyState);\n", " comm.kernel.ws.addEventListener('close', updateReadyState);\n", " comm.kernel.ws.addEventListener('error', updateReadyState);\n", "\n", " ws.close = function () {\n", " comm.close();\n", " };\n", " ws.send = function (m) {\n", " //console.log('sending', m);\n", " comm.send(m);\n", " };\n", " // Register the callback with on_msg.\n", " comm.on_msg(function (msg) {\n", " //console.log('receiving', msg['content']['data'], msg);\n", " var data = msg['content']['data'];\n", " if (data['blob'] !== undefined) {\n", " data = {\n", " data: new Blob(msg['buffers'], { type: data['blob'] }),\n", " };\n", " }\n", " // Pass the mpl event to the overridden (by mpl) onmessage function.\n", " ws.onmessage(data);\n", " });\n", " return ws;\n", "};\n", "\n", "mpl.mpl_figure_comm = function (comm, msg) {\n", " // This is the function which gets called when the mpl process\n", " // starts-up an IPython Comm through the \"matplotlib\" channel.\n", "\n", " var id = msg.content.data.id;\n", " // Get hold of the div created by the display call when the Comm\n", " // socket was opened in Python.\n", " var element = document.getElementById(id);\n", " var ws_proxy = comm_websocket_adapter(comm);\n", "\n", " function ondownload(figure, _format) {\n", " window.open(figure.canvas.toDataURL());\n", " }\n", "\n", " var fig = new mpl.figure(id, ws_proxy, ondownload, element);\n", "\n", " // Call onopen now - mpl needs it, as it is assuming we've passed it a real\n", " // web socket which is closed, not our websocket->open comm proxy.\n", " ws_proxy.onopen();\n", "\n", " fig.parent_element = element;\n", " fig.cell_info = mpl.find_output_cell(\"
\");\n", " if (!fig.cell_info) {\n", " console.error('Failed to find cell for figure', id, fig);\n", " return;\n", " }\n", " fig.cell_info[0].output_area.element.on(\n", " 'cleared',\n", " { fig: fig },\n", " fig._remove_fig_handler\n", " );\n", "};\n", "\n", "mpl.figure.prototype.handle_close = function (fig, msg) {\n", " var width = fig.canvas.width / fig.ratio;\n", " fig.cell_info[0].output_area.element.off(\n", " 'cleared',\n", " fig._remove_fig_handler\n", " );\n", " fig.resizeObserverInstance.unobserve(fig.canvas_div);\n", "\n", " // Update the output cell to use the data from the current canvas.\n", " fig.push_to_output();\n", " var dataURL = fig.canvas.toDataURL();\n", " // Re-enable the keyboard manager in IPython - without this line, in FF,\n", " // the notebook keyboard shortcuts fail.\n", " IPython.keyboard_manager.enable();\n", " fig.parent_element.innerHTML =\n", " '';\n", " fig.close_ws(fig, msg);\n", "};\n", "\n", "mpl.figure.prototype.close_ws = function (fig, msg) {\n", " fig.send_message('closing', msg);\n", " // fig.ws.close()\n", "};\n", "\n", "mpl.figure.prototype.push_to_output = function (_remove_interactive) {\n", " // Turn the data on the canvas into data in the output cell.\n", " var width = this.canvas.width / this.ratio;\n", " var dataURL = this.canvas.toDataURL();\n", " this.cell_info[1]['text/html'] =\n", " '';\n", "};\n", "\n", "mpl.figure.prototype.updated_canvas_event = function () {\n", " // Tell IPython that the notebook contents must change.\n", " IPython.notebook.set_dirty(true);\n", " this.send_message('ack', {});\n", " var fig = this;\n", " // Wait a second, then push the new image to the DOM so\n", " // that it is saved nicely (might be nice to debounce this).\n", " setTimeout(function () {\n", " fig.push_to_output();\n", " }, 1000);\n", "};\n", "\n", "mpl.figure.prototype._init_toolbar = function () {\n", " var fig = this;\n", "\n", " var toolbar = document.createElement('div');\n", " toolbar.classList = 'btn-toolbar';\n", " this.root.appendChild(toolbar);\n", "\n", " function on_click_closure(name) {\n", " return function (_event) {\n", " return fig.toolbar_button_onclick(name);\n", " };\n", " }\n", "\n", " function on_mouseover_closure(tooltip) {\n", " return function (event) {\n", " if (!event.currentTarget.disabled) {\n", " return fig.toolbar_button_onmouseover(tooltip);\n", " }\n", " };\n", " }\n", "\n", " fig.buttons = {};\n", " var buttonGroup = document.createElement('div');\n", " buttonGroup.classList = 'btn-group';\n", " var button;\n", " for (var toolbar_ind in mpl.toolbar_items) {\n", " var name = mpl.toolbar_items[toolbar_ind][0];\n", " var tooltip = mpl.toolbar_items[toolbar_ind][1];\n", " var image = mpl.toolbar_items[toolbar_ind][2];\n", " var method_name = mpl.toolbar_items[toolbar_ind][3];\n", "\n", " if (!name) {\n", " /* Instead of a spacer, we start a new button group. */\n", " if (buttonGroup.hasChildNodes()) {\n", " toolbar.appendChild(buttonGroup);\n", " }\n", " buttonGroup = document.createElement('div');\n", " buttonGroup.classList = 'btn-group';\n", " continue;\n", " }\n", "\n", " button = fig.buttons[name] = document.createElement('button');\n", " button.classList = 'btn btn-default';\n", " button.href = '#';\n", " button.title = name;\n", " button.innerHTML = '';\n", " button.addEventListener('click', on_click_closure(method_name));\n", " button.addEventListener('mouseover', on_mouseover_closure(tooltip));\n", " buttonGroup.appendChild(button);\n", " }\n", "\n", " if (buttonGroup.hasChildNodes()) {\n", " toolbar.appendChild(buttonGroup);\n", " }\n", "\n", " // Add the status bar.\n", " var status_bar = document.createElement('span');\n", " status_bar.classList = 'mpl-message pull-right';\n", " toolbar.appendChild(status_bar);\n", " this.message = status_bar;\n", "\n", " // Add the close button to the window.\n", " var buttongrp = document.createElement('div');\n", " buttongrp.classList = 'btn-group inline pull-right';\n", " button = document.createElement('button');\n", " button.classList = 'btn btn-mini btn-primary';\n", " button.href = '#';\n", " button.title = 'Stop Interaction';\n", " button.innerHTML = '';\n", " button.addEventListener('click', function (_evt) {\n", " fig.handle_close(fig, {});\n", " });\n", " button.addEventListener(\n", " 'mouseover',\n", " on_mouseover_closure('Stop Interaction')\n", " );\n", " buttongrp.appendChild(button);\n", " var titlebar = this.root.querySelector('.ui-dialog-titlebar');\n", " titlebar.insertBefore(buttongrp, titlebar.firstChild);\n", "};\n", "\n", "mpl.figure.prototype._remove_fig_handler = function (event) {\n", " var fig = event.data.fig;\n", " if (event.target !== this) {\n", " // Ignore bubbled events from children.\n", " return;\n", " }\n", " fig.close_ws(fig, {});\n", "};\n", "\n", "mpl.figure.prototype._root_extra_style = function (el) {\n", " el.style.boxSizing = 'content-box'; // override notebook setting of border-box.\n", "};\n", "\n", "mpl.figure.prototype._canvas_extra_style = function (el) {\n", " // this is important to make the div 'focusable\n", " el.setAttribute('tabindex', 0);\n", " // reach out to IPython and tell the keyboard manager to turn it's self\n", " // off when our div gets focus\n", "\n", " // location in version 3\n", " if (IPython.notebook.keyboard_manager) {\n", " IPython.notebook.keyboard_manager.register_events(el);\n", " } else {\n", " // location in version 2\n", " IPython.keyboard_manager.register_events(el);\n", " }\n", "};\n", "\n", "mpl.figure.prototype._key_event_extra = function (event, _name) {\n", " var manager = IPython.notebook.keyboard_manager;\n", " if (!manager) {\n", " manager = IPython.keyboard_manager;\n", " }\n", "\n", " // Check for shift+enter\n", " if (event.shiftKey && event.which === 13) {\n", " this.canvas_div.blur();\n", " // select the cell after this one\n", " var index = IPython.notebook.find_cell_index(this.cell_info[0]);\n", " IPython.notebook.select(index + 1);\n", " }\n", "};\n", "\n", "mpl.figure.prototype.handle_save = function (fig, _msg) {\n", " fig.ondownload(fig, null);\n", "};\n", "\n", "mpl.find_output_cell = function (html_output) {\n", " // Return the cell and output element which can be found *uniquely* in the notebook.\n", " // Note - this is a bit hacky, but it is done because the \"notebook_saving.Notebook\"\n", " // IPython event is triggered only after the cells have been serialised, which for\n", " // our purposes (turning an active figure into a static one), is too late.\n", " var cells = IPython.notebook.get_cells();\n", " var ncells = cells.length;\n", " for (var i = 0; i < ncells; i++) {\n", " var cell = cells[i];\n", " if (cell.cell_type === 'code') {\n", " for (var j = 0; j < cell.output_area.outputs.length; j++) {\n", " var data = cell.output_area.outputs[j];\n", " if (data.data) {\n", " // IPython >= 3 moved mimebundle to data attribute of output\n", " data = data.data;\n", " }\n", " if (data['text/html'] === html_output) {\n", " return [cell, data, j];\n", " }\n", " }\n", " }\n", " }\n", "};\n", "\n", "// Register the function which deals with the matplotlib target/channel.\n", "// The kernel may be null if the page has been refreshed.\n", "if (IPython.notebook.kernel !== null) {\n", " IPython.notebook.kernel.comm_manager.register_target(\n", " 'matplotlib',\n", " mpl.mpl_figure_comm\n", " );\n", "}\n" ], "text/plain": [ "" ] }, "metadata": {}, "output_type": "display_data" }, { "data": { "text/html": [ "" ], "text/plain": [ "" ] }, "metadata": {}, "output_type": "display_data" } ], "source": [ "from matplotlib import pyplot as plt # now we can use Matplotlib's plotting tools\n", "# Make the figures interactive:\n", "%matplotlib notebook\n", "\n", "# Draw a very basic plot\n", "fig, ax = plt.subplots()\n", "ax.scatter(pCO2_increasing, omega_arag_response)\n", "ax.set_xlabel('Seawater $p$CO$_2$ / μatm')\n", "ax.set_ylabel('Ω(aragonite)');" ] } ], "metadata": { "@webio": { "lastCommId": null, "lastKernelId": null }, "kernelspec": { "display_name": "Python 3", "language": "python", "name": "python3" }, "language_info": { "codemirror_mode": { "name": "ipython", "version": 3 }, "file_extension": ".py", "mimetype": "text/x-python", "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", "version": "3.9.4" } }, "nbformat": 4, "nbformat_minor": 4 }