{ "cells": [ { "cell_type": "markdown", "metadata": {}, "source": [ "# HST WFC3 Chemically Consistent Transmission/Transit Tutorial \n", "\n", "Welcome to the transmission spectrum model/retrieval tutorial!\n", "\n", "For this particular setup, the atmosphere is parameterized within the \"chemically-consistent\" framework as described in Kreidberg et al. 2015. The atmospheric composition is parameterized with only a metalicity and carbon-to-oxygen ratio assumed to be in thermochemical equilibrium along the temperature-pressure profile. Originally this code would compute the gas and condensate phase mixing ratios by calling the NASA CEA routine. However, in order to remove fortran dependencies, a finely sampled pre-computed, interpolateable chemistry grid was instead produced with CEA as a function of temperature (T from 400K - 3400K in 100K increments), pressure ($log_{10}(P)$ from -7.0 (0.1$\\mu$bar) - 2.4 (316 bar) in 0.1 increments), metallicity ($[M/H]$ from -2.0 (0.01$\\times$) to 3.0 (1000$\\times$)), and C/O ($log_{10}(C/O)$ from -2.0 (0.01) to 0.3 (2) awkwardly spaced to better sample the transition about C/O=1). All elemental abundances are scaled with respect to the Lodders 2009 solar abundance pattern. A pseudo-hack rainout approximation is made to the gas phase abundances of TiO, VO, Na, K, and FeH. In this hack, these species are set to 0 abundance at levels above where they first fall below some critical value ($10^{-8}$). This is to mimic the loss of these species from the gas phase into the condensate phase. In no case are we accounting for the loss of elemental abundances.\n", "\n", "The 3-parameter temperature profile parameterization utilizes the Guillot 2010/Parmentier et al. 2014 analytic formulism (see Line et al. 2013a for implementation details). \n", "\n", "The transmission spectrum routine closely follows the equations (and figure) in Tinetti et al. 2012 (as described in the tutorial text). Instead of using line-by-line, or \"sampled\" cross-sections, this implementation uses the \"correlated-K\" method (see Lacis & Oinas 1990, or more recently Amundsen et al. 2017). Correlated-K is advantageous as it preserves the wavelength bin\"integrated\" precision as line-by-line but with far less demanding computation. We include as correlated-K line opacites H2O, CH4, CO, CO2, NH3, HCN, H2S, C2H2, Na, K, TiO, VO, FeH and as continuum gas opacities H2-H2, H2-He CIA, and the H- bound free and free free (e.g., Arcangeli et al. 2018). See the \"opacity\" tutorial for more details on correlated-K. \n", "\n", "To handle the effects of disequilibrium chemistry due to vertical mixing, we apply the \"quench-pressure\" approximation. We include a quench pressure parameter for the carbon-system and one for the nitrogen system (as in Morley et al. 2017 for GJ436b, and Kreidberg et al. 2018 for WASP-107b). The carbon quench pressure fixes the H2O, CO, and CH4 abundances above the quench pressure level to their abundances at the quench pressure level. Similarly, the nitrogen quench pressure fixes the N2, NH3, and HCN abundances above the quench pressure to their values at the quench pressure level. This is indeed a kludge, and a better implementation would be to use the timescale/eddy mixing prescription described in Zahnle & Marley 2015. Regardless, any non-full kinetics approach is a kludge anyway (not to mention the 1D nature of the problem...). \n", "\n", "There are two different cloud prescriptions built in. The first is the Ackerman & Marley 2001 \"eddy-sed\" approach that self-consistently computes the vertical particle size distribution given a sedimentation factor, $f_{sed}$ and an eddy mixing factor (K$_{zz}$) from some cloud base pressure and intrinsic condensate mixing ratio. The classic \"power-law haze\" and \"grey cloud\" prescripton is also included.\n", "\n", "Finally, if one doesn't like the \"chemically-consistent\" concept, they can use the \"gas_scale\" array to switch off or scale the abundances each opacity source. \n", "\n", "This specific notebook goes through the steps to generate the forward model, and illustrate how to actually perform the retrieval. However, the retrievals are bust run on a compute cluster or a node with more than 4 cores. We will use the \"benchmark\" system, WASP-43b as our example utilizing the HST WFC3 data presented in Kreidberg et al. 2014b.\n", "\n", "Note, this particular version does not include marginilzation over spots (e.g., Iyer & Line 2019). However, this can be trivially implemented in the fx_trans rouutine in fm.py. Simply add in the \"rackham\" formula along with a grid of stellar spectral models, say, drawn from pysynphot (or whatever your favorite stellar model generator is). Interpolate over this grid of stellar models using standard built in python linear interpolators.\n", "\n", "\n", "Software Requirements: This runs in the python 3 anaconda environment. It is also crucial that anaconda numba is installed as many of the routines are optimized using numba's \"@jit\" decorator (http://numba.pydata.org/). \n" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "## Import Routines\n", "\n", "This first segment loads in the routines from fm.py and the correlated-K coefficients. There are two sets of correlated-K coefficients (which I've called \"xsecs\" here). There are ones taylored for HST WFC3+STIS (xsects_HST function in fm.py) and JWST (xsects_JWST in fm.py). The WFC3+STIS correlated-K coefficients are generated at an R=200 longwards of 1 $\\mu$m (up to 5$\\mu$m and R=500 from 0.3 - 1 $\\mu$m. Note...these *are not sampled cross-sections* so each resolution element at that R is correctly computed and matches line-by-line when binned to that same R.\n", "\n", "Note that the \"core\" set of routines are all in fm.py. If you want to know more about what is in the sausage, look into fm.py. " ] }, { "cell_type": "code", "execution_count": 5, "metadata": {}, "outputs": [ { "name": "stderr", "output_type": "stream", "text": [ "/Users/michaelline/anaconda3/lib/python3.6/site-packages/numpy/core/fromnumeric.py:2957: RuntimeWarning: Mean of empty slice.\n", " out=out, **kwargs)\n", "/Users/michaelline/anaconda3/lib/python3.6/site-packages/numpy/core/_methods.py:80: RuntimeWarning: invalid value encountered in double_scalars\n", " ret = ret.dtype.type(ret / rcount)\n" ] }, { "name": "stdout", "output_type": "stream", "text": [ "Cross-sections Loaded\n" ] } ], "source": [ "#import all of the functions in fm, namely, the CK-coefficients (may take a minute)\n", "from chimera import *\n", "%matplotlib notebook\n" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "## Load Opacities, Make Star" ] }, { "cell_type": "code", "execution_count": null, "metadata": {}, "outputs": [], "source": [ "\n", "stellar_file = 'sum_star.h5'\n", "temp = 5000\n", "logmh = 0 \n", "logg = 4.0\n", "stellar_db = 'phoenix'\n", "make_stellar(temp,logmh,logg,stellar_db,stellar_file)\n", "\n", "#preload CK-coeffs--a giant array/variable to be passed--inputs are lower wavenumber, upper wavenumber\n", "#between 2000 and 30000 cm-1 for HST--R=200 > 1 um, then R=500 < 1 um \n", "#to convert between microns and wavenumbers-- wavelength [um] = 10,000/wavenumber [cm-1]\n", "#make sure xsec wavenumber/wavelength range is *larger* than data wavelength range\n", "\n", "wnomin = 2000\n", "wnomax = 25000\n", "observatory='HST'\n", "directory = os.path.join(os.getcwd(),'..','..','ABSCOEFF_CK')\n", "xsecs=xsects(wnomin, wnomax, observatory, directory,stellar_file=stellar_file)\n" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "## Setup Atmospheric Parameters to Generate a Spectrum\n", "\n", "This segement defines the various atmospheric quantities and assignes them values for the generation of a simple transmission spectrum. A description of each parameter along with a reasonable range of values is given as a comment following the assigned value. All of the parameters are then put into the parameter \"state-vector\" array, x." ] }, { "cell_type": "code", "execution_count": 6, "metadata": {}, "outputs": [], "source": [ "#setup \"input\" parameters. We are defining our 1D atmosphere with these\n", "#the parameters\n", "#planet/star system params--xRp is the \"Rp\" free parameter, M right now is fixed, but could be free param\n", "Rp=1.036 #Planet radius in Jupiter Radii--this will be forced to be 10 bar radius--arbitrary (scaling to this is free par)\n", "Rstar=0.667 # #Stellar Radius in Solar Radii\n", "M =2.034 #Mass in Jupiter Masses\n", "D=0.01526 #semimajor axis in AU\n", "\n", "#TP profile params (3--Guillot 2010, Parmentier & Guillot 2013--see Line et al. 2013a for implementation)\n", "Tirr=1400 #Irradiation temperature as defined in Guillot 2010\n", "logKir=-1.5 #TP profile IR opacity (log there-of) controlls the \"vertical\" location of the gradient\n", "logg1=-0.7 #single channel Vis/IR (log) opacity. Controls the delta T between deep T and TOA T\n", "Tint=200 #interior temperature...this would be the \"effective temperature\" if object were not irradiated\n", "\n", "#Composition parameters---assumes \"chemically consistent model\" described in Kreidberg et al. 2015\n", "logMet=0.0 #. #Metallicity relative to solar log--solar is 0, 10x=1, 0.1x = -1: valid range is -1.5 - 3.0\n", "logCtoO=-0.26 #log C-to-O ratio: log solar is -0.26: valid range is -1.0 - 0.3 \n", "logPQCarbon=-5.5 #CH4, CO, H2O Qunech pressure--forces CH4, CO, and H2O to constant value at quench pressure value: valid range -6.0 - 1.5\n", "logPQNitrogen=-5.5 #N2, NH3 Quench pressure--forces N2 and NH3 to \"\" \n", "\n", "#Ackerman & Marley 2001 Cloud parameters--physically motivated with Mie particles\n", "logKzz=7 #log Kzz (cm2/s)--valid range: 2 - 11 -- higher values make larger particles\n", "fsed=2.0 #sediminetation efficiency--valid range: 0.5 - 5--lower values make \"puffier\" more extended cloud \n", "logPbase=-1.0 #cloud base pressure--valid range: -6.0 - 1.5\n", "logCldVMR=-5.5 #cloud condensate base mixing ratio (e.g, see Fortney 2005)--valid range: -15 - -2.0\n", "\n", "#simple 'grey+rayleigh' parameters just in case you don't want to use a physically motivated cloud\n", "#(most are just made up anyway since we don't really understand all of the micro-physics.....)\n", "logKcld = -40 #uniform in altitude and in wavelength \"grey\" opacity (it's a cross-section)--valid range: -50 - -10 \n", "logRayAmp = -30 #power-law haze amplitude (log) as defined in des Etangs 2008 \"0\" would be like H2/He scat--valid range: -30 - 3 \n", "RaySlope = 0 #power law index 4 for Rayleigh, 0 for \"gray\". Valid range: 0 - 6\n", "\n", "#10 bar radiuss scaling param (only used in transmission)\n", "xRp=0.991\n", "\n", "#stuffing all variables into state vector array\n", "x=np.array([Tirr, logKir,logg1,Tint, logMet, logCtoO, logPQCarbon,logPQNitrogen, Rp*xRp, Rstar, M, logKzz, fsed,logPbase,logCldVMR, logKcld, logRayAmp, RaySlope])\n", "#gas scaling factors to mess with turning on various species\n", "#set to \"0\" to turn off a gas. Otherwise keep set at 1\n", "#thermochemical gas profile scaling factors\n", "# 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21\n", "#H2O CH4 CO CO2 NH3 N2 HCN H2S PH3 C2H2 C2H6 Na K TiO VO FeH H H2 He e- h- mmw\n", "gas_scale=np.array([1.,1.,1.,1.,1.,1.,1.,1.,1.,1.,1.,1.,1.,1.,1.,1.,1.,1.,1.,1., 1., 1.]) #can be made free params if desired (won't affect mmw)#can be made free params if desired (won't affect mmw)" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "## Load in Transmission Data Set \n", "\n" ] }, { "cell_type": "code", "execution_count": 7, "metadata": {}, "outputs": [], "source": [ "#WASP43b transmission spectrum from kreidberg et al. 2014...a 3 column ascii file\n", "wlgrid, y_meas, err=np.loadtxt('w43b_trans.txt').T\n" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "## Generate Model Atmosphere & Transmission Spectrum \n", "\n", "Here we call the forward model routine \"fx\" (think F(x)) from fm.py. fx controls the input values and calls the relevent functions to compute the transmission spectrum. The inputs into fx are the parameter state vector, \"x\", the data wavelength grid, \"wlgrid\", the gas scaling factors (for turning off particular gases), \"gas_scale\", and the correlated-K tables, \"xsects\". Fx then returns the simulated model spectrum ($(R_p/R_{\\star})^2$) at the native CK-table resolution, \"y_mod\", the native wavenumber grid, \"wno\", the data wavelength grid binned model spectrum, \"y_binned\". The \"atm\" array contains the generated temperature-pressure profile and gas mixing ratio profiles generated under the chemically consistent assumption. " ] }, { "cell_type": "code", "execution_count": 8, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "DONE\n" ] } ], "source": [ "#calling forward model, fx. This will produce the (Rp/Rstar)^2 spectrum....\n", "y_binned,y_mod,wno,atm=fx_trans(x,wlgrid,gas_scale, xsecs) #returns binned model spectrum, higher res model spectrum, wavenumber grid, and vertical abundance profiles from chemistry\n", "print('DONE')" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "## Plotting the Model Atmosphere & Transmission Spectrum \n", "\n", "Self-explanatory...\n", "\n", "## Plot Model Atmosphere \n", "\n", "Spaghetti plot of the model atmosphere." ] }, { "cell_type": "code", "execution_count": 11, "metadata": {}, "outputs": [ { "data": { "application/javascript": [ "/* Put everything inside the global mpl namespace */\n", "window.mpl = {};\n", "\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('Your browser does not have WebSocket support.' +\n", " 'Please try Chrome, Safari or Firefox ≥ 6. 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height: ' + height + 'px;');\n", "\n", " rubberband.attr('width', width);\n", " rubberband.attr('height', height);\n", " }\n", "\n", " // Set the figure to an initial 600x600px, this will subsequently be updated\n", " // upon first draw.\n", " this._resize_canvas(600, 600);\n", "\n", " // Disable right mouse context menu.\n", " $(this.rubberband_canvas).bind(\"contextmenu\",function(e){\n", " return false;\n", " });\n", "\n", " function set_focus () {\n", " canvas.focus();\n", " canvas_div.focus();\n", " }\n", "\n", " window.setTimeout(set_focus, 100);\n", "}\n", "\n", "mpl.figure.prototype._init_toolbar = function() {\n", " var fig = this;\n", "\n", " var nav_element = $('')\n", " nav_element.attr('style', 'width: 100%');\n", " this.root.append(nav_element);\n", "\n", " // Define a callback function for later on.\n", " function toolbar_event(event) {\n", " return fig.toolbar_button_onclick(event['data']);\n", " }\n", " function toolbar_mouse_event(event) {\n", " return fig.toolbar_button_onmouseover(event['data']);\n", " }\n", "\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", " // put a spacer in here.\n", " continue;\n", " }\n", " var button = $('');\n", " button.addClass('ui-button ui-widget ui-state-default ui-corner-all ' +\n", " 'ui-button-icon-only');\n", " button.attr('role', 'button');\n", " button.attr('aria-disabled', 'false');\n", " button.click(method_name, toolbar_event);\n", " button.mouseover(tooltip, toolbar_mouse_event);\n", "\n", " var icon_img = $('');\n", " icon_img.addClass('ui-button-icon-primary ui-icon');\n", " icon_img.addClass(image);\n", " icon_img.addClass('ui-corner-all');\n", "\n", " var tooltip_span = $('');\n", " tooltip_span.addClass('ui-button-text');\n", " tooltip_span.html(tooltip);\n", "\n", " button.append(icon_img);\n", " button.append(tooltip_span);\n", "\n", " nav_element.append(button);\n", " }\n", "\n", " var fmt_picker_span = $('');\n", "\n", " var fmt_picker = $('');\n", " fmt_picker.addClass('mpl-toolbar-option ui-widget ui-widget-content');\n", " fmt_picker_span.append(fmt_picker);\n", " nav_element.append(fmt_picker_span);\n", " this.format_dropdown = fmt_picker[0];\n", "\n", " for (var ind in mpl.extensions) {\n", " var fmt = mpl.extensions[ind];\n", " var option = $(\n", " '', {selected: fmt === mpl.default_extension}).html(fmt);\n", " fmt_picker.append(option)\n", " }\n", "\n", " // Add hover states to the ui-buttons\n", " $( \".ui-button\" ).hover(\n", " function() { $(this).addClass(\"ui-state-hover\");},\n", " function() { $(this).removeClass(\"ui-state-hover\");}\n", " );\n", "\n", " var status_bar = $('');\n", " nav_element.append(status_bar);\n", " this.message = status_bar[0];\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", "\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", "\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]);\n", " fig.send_message(\"refresh\", {});\n", " };\n", "}\n", "\n", "mpl.figure.prototype.handle_rubberband = function(fig, msg) {\n", " var x0 = msg['x0'] / mpl.ratio;\n", " var y0 = (fig.canvas.height - msg['y0']) / mpl.ratio;\n", " var x1 = msg['x1'] / mpl.ratio;\n", " var y1 = (fig.canvas.height - msg['y1']) / mpl.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, 0, fig.canvas.width, fig.canvas.height);\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", " {\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.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", " /* 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", " evt.data.type = \"image/png\";\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", " fig.imageObj.src = (window.URL || window.webkitURL).createObjectURL(\n", " evt.data);\n", " fig.updated_canvas_event();\n", " fig.waiting = false;\n", " return;\n", " }\n", " else if (typeof evt.data === 'string' && evt.data.slice(0, 21) == \"data:image/png;base64\") {\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(\"No handler for the '\" + msg_type + \"' message type: \", msg);\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(\"Exception inside the 'handler_\" + msg_type + \"' callback:\", e, e.stack, msg);\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", " if (e.target)\n", " targ = e.target;\n", " else if (e.srcElement)\n", " targ = e.srcElement;\n", " if (targ.nodeType == 3) // defeat Safari bug\n", " targ = targ.parentNode;\n", "\n", " // jQuery normalizes the pageX and pageY\n", " // pageX,Y are the mouse positions relative to the document\n", " // offset() returns the position of the element relative to the document\n", " var x = e.pageX - $(targ).offset().left;\n", " var y = e.pageY - $(targ).offset().top;\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", " 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", " {\n", " this.canvas.focus();\n", " this.canvas_div.focus();\n", " }\n", "\n", " var x = canvas_pos.x * mpl.ratio;\n", " var y = canvas_pos.y * mpl.ratio;\n", "\n", " this.send_message(name, {x: x, y: y, button: event.button,\n", " step: event.step,\n", " guiEvent: simpleKeys(event)});\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", "\n", " // Prevent repeat events\n", " if (name == 'key_press')\n", " {\n", " if (event.which === this._key)\n", " return;\n", " else\n", " this._key = event.which;\n", " }\n", " if (name == 'key_release')\n", " this._key = null;\n", "\n", " var value = '';\n", " if (event.ctrlKey && event.which != 17)\n", " value += \"ctrl+\";\n", " if (event.altKey && event.which != 18)\n", " value += \"alt+\";\n", " if (event.shiftKey && event.which != 16)\n", " value += \"shift+\";\n", "\n", " value += 'k';\n", " value += event.which.toString();\n", "\n", " this._key_event_extra(event, name);\n", "\n", " this.send_message(name, {key: value,\n", " 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", "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\", \"Pan axes with left mouse, zoom with right\", \"fa fa-arrows icon-move\", \"pan\"], [\"Zoom\", \"Zoom to rectangle\", \"fa fa-square-o icon-check-empty\", \"zoom\"], [\"\", \"\", \"\", \"\"], [\"Download\", \"Download plot\", \"fa fa-floppy-o icon-save\", \"download\"]];\n", "\n", "mpl.extensions = [\"eps\", \"jpeg\", \"pdf\", \"png\", \"ps\", \"raw\", \"svg\", \"tif\"];\n", "\n", "mpl.default_extension = \"png\";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.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", " // Pass the mpl event to the overriden (by mpl) onmessage function.\n", " ws.onmessage(msg['content']['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 = $(\"#\" + id);\n", " var ws_proxy = comm_websocket_adapter(comm)\n", "\n", " function ondownload(figure, format) {\n", " window.open(figure.imageObj.src);\n", " }\n", "\n", " var fig = new mpl.figure(id, ws_proxy,\n", " ondownload,\n", " element.get(0));\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.get(0);\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", "\n", " var output_index = fig.cell_info[2]\n", " var cell = fig.cell_info[0];\n", "\n", "};\n", "\n", "mpl.figure.prototype.handle_close = function(fig, msg) {\n", " var width = fig.canvas.width/mpl.ratio\n", " fig.root.unbind('remove')\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).html('');\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/mpl.ratio\n", " var dataURL = this.canvas.toDataURL();\n", " this.cell_info[1]['text/html'] = '';\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 () { fig.push_to_output() }, 1000);\n", "}\n", "\n", "mpl.figure.prototype._init_toolbar = function() {\n", " var fig = this;\n", "\n", " var nav_element = $('')\n", " nav_element.attr('style', 'width: 100%');\n", " this.root.append(nav_element);\n", "\n", " // Define a callback function for later on.\n", " function toolbar_event(event) {\n", " return fig.toolbar_button_onclick(event['data']);\n", " }\n", " function toolbar_mouse_event(event) {\n", " return fig.toolbar_button_onmouseover(event['data']);\n", " }\n", "\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) { continue; };\n", "\n", " var button = $('');\n", " button.click(method_name, toolbar_event);\n", " button.mouseover(tooltip, toolbar_mouse_event);\n", " nav_element.append(button);\n", " }\n", "\n", " // Add the status bar.\n", " var status_bar = $('');\n", " nav_element.append(status_bar);\n", " this.message = status_bar[0];\n", "\n", " // Add the close button to the window.\n", " var buttongrp = $('');\n", " var button = $('');\n", " button.click(function (evt) { fig.handle_close(fig, {}); } );\n", " button.mouseover('Stop Interaction', toolbar_mouse_event);\n", " buttongrp.append(button);\n", " var titlebar = this.root.find($('.ui-dialog-titlebar'));\n", " titlebar.prepend(buttongrp);\n", "}\n", "\n", "mpl.figure.prototype._root_extra_style = function(el){\n", " var fig = this\n", " el.on(\"remove\", function(){\n", "\tfig.close_ws(fig, {});\n", " });\n", "}\n", "\n", "mpl.figure.prototype._canvas_extra_style = function(el){\n", " // this is important to make the div 'focusable\n", " el.attr('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", " }\n", " else {\n", " // location in version 2\n", " IPython.keyboard_manager.register_events(el);\n", " }\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", " // Check for shift+enter\n", " if (event.shiftKey && event.which == 13) {\n", " this.canvas_div.blur();\n", " event.shiftKey = false;\n", " // Send a \"J\" for go to next cell\n", " event.which = 74;\n", " event.keyCode = 74;\n", " manager.command_mode();\n", " manager.handle_keydown(event);\n", " }\n", "}\n", "\n", "mpl.figure.prototype.handle_save = function(fig, msg) {\n", " fig.ondownload(fig, null);\n", "}\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