diff --git a/.gitignore b/.gitignore new file mode 100644 index 0000000..9843059 --- /dev/null +++ b/.gitignore @@ -0,0 +1,6 @@ +venv_galomatch/ +share/ +bin/ +.bashrc +*.pyc +*/.ipynb_checkpoints/ diff --git a/data/descr.txt b/data/descr.txt new file mode 100644 index 0000000..e910cf5 --- /dev/null +++ b/data/descr.txt @@ -0,0 +1,37 @@ +Various column names + +Clump file columns: + "index", "lev", "parent", "ncell", "peak_x", "peak_y", "peak_z", "rho-", "rho+", "rho_av", "mass_cl", "relevance" + +Mergertree file columns: + "clump", "progenitor", "prog outputnr", "desc mass", "desc npart", "desc x", "desc y", "desc z", "desc vx", "desc vy", "desc vz" + + +%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% + + +The merger trees are stored in `output_XXXXX/mergertree_XXXXX.txtYYYYY` files. Each file contains 11 columns: + +* `clump`: clump ID of a clump at this output number +* `progenitor`: the progenitor clump ID in output number "prog_outputnr" +* `prog_outputnr`: the output number of when the progenitor was an alive clump +* `desc mass`: mass of the current clump. +* `desc npart`: number of particles of the current clump. +* `desc x,y,z`: x, y, z position of current clump. +* `desc vx, vy, vz`: x, y, z velocities of current clump. + +desc_mass and desc_npart will be either inclusive or exclusive, depending on how you set the `use_exclusive_mass` parameter. +(See below for details) + +**How to read the output:** + +* A clump > 0 has progenitor > 0: Standard case. A direct progenitor from the adjacent previous snapshot was identified for this clump. +* A clump > 0 has progenitor = 0: no progenitor could be established and the clump is treated as newly formed. +* A clump > 0 has progenitor < 0: it means that no direct progenitor could be found in the adjacent previous snapshot, but a progenitor was identified from an earlier, non-adjacent snapshot. +* A clump < 0 has progenitor > 0: this progenitor merged into this clump, but is not this clump's main progenitor. +* A clump < 0 has progenitor < 0: this shouldn't happen. + +### Visualisation + +`ramses/utils/py/mergertreeplot.py` is a python 2 script to plot the merger trees as found by this patch. + Details on options and usage are at the start of the script as a comment. \ No newline at end of file diff --git a/galomatch/__init__.py b/galomatch/__init__.py new file mode 100644 index 0000000..c62663c --- /dev/null +++ b/galomatch/__init__.py @@ -0,0 +1,16 @@ +# Copyright (C) 2022 Richard Stiskalek +# This program is free software; you can redistribute it and/or modify it +# under the terms of the GNU General Public License as published by the +# Free Software Foundation; either version 3 of the License, or (at your +# option) any later version. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General +# Public License for more details. +# +# You should have received a copy of the GNU General Public License along +# with this program; if not, write to the Free Software Foundation, Inc., +# 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA. + +from galomatch import io diff --git a/galomatch/io/__init__.py b/galomatch/io/__init__.py new file mode 100644 index 0000000..3d34c77 --- /dev/null +++ b/galomatch/io/__init__.py @@ -0,0 +1,18 @@ +# Copyright (C) 2022 Richard Stiskalek +# This program is free software; you can redistribute it and/or modify it +# under the terms of the GNU General Public License as published by the +# Free Software Foundation; either version 3 of the License, or (at your +# option) any later version. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General +# Public License for more details. +# +# You should have received a copy of the GNU General Public License along +# with this program; if not, write to the Free Software Foundation, Inc., +# 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA. + +from .readsim import (get_sim_path, open_particle, open_unbinding, + read_particle, read_clumpid, read_clumps, + convert_mass_cols, convert_position_cols) diff --git a/galomatch/io/readsim.py b/galomatch/io/readsim.py new file mode 100644 index 0000000..4852218 --- /dev/null +++ b/galomatch/io/readsim.py @@ -0,0 +1,365 @@ +# Copyright (C) 2022 Richard Stiskalek, Harry Desmond +# This program is free software; you can redistribute it and/or modify it +# under the terms of the GNU General Public License as published by the +# Free Software Foundation; either version 3 of the License, or (at your +# option) any later version. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General +# Public License for more details. +# +# You should have received a copy of the GNU General Public License along +# with this program; if not, write to the Free Software Foundation, Inc., +# 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA. + +"""Functions to read in the particle and clump files.""" + +import numpy +from scipy.io import FortranFile +from os import listdir +from os.path import (join, isfile) +from tqdm import tqdm + + +F16 = numpy.float16 +F32 = numpy.float32 +F64 = numpy.float64 +I32 = numpy.int32 +I64 = numpy.int64 +little_h = 0.705 +BOXSIZE = 677.7 / little_h # Mpc. Otherwise positions in [0, 1]. +BOXMASS = 3.749e19 # Msun + + +def get_sim_path(n, fname="ramses_out_{}", srcdir="/mnt/extraspace/hdesmond"): + """ + Get a path to a CSiBORG simulation. + + Parameters + ---------- + n : int + The index of the initial conditions (IC) realisation. + fname : str, optional + The file name. By default `ramses_out_{}`, where `n` is the IC index. + srcdir : str, optional + The file path to the folder where realisations of the ICs are stored. + + Returns + ------- + path : str + The complete path to the `n`th CSiBORG simulation. + """ + return join(srcdir, fname.format(n)) + + +def open_particle(n, simpath, verbose=True): + """ + Open particle files to a given CSiBORG simulation. + + Parameters + ---------- + n : int + The index of a redshift snapshot. + simpath : str + The complete path to the CSiBORG simulation. + verbose : bool, optional + Verbosity flag. + + Returns + ------- + nparts : 1-dimensional array + Number of parts assosiated with each CPU. + partfiles : list of `scipy.io.FortranFile` + Opened part files. + """ + # Zeros filled snapshot number and the snapshot path + nout = str(n).zfill(5) + snappath = join(simpath, "output_{}".format(nout)) + infopath = join(snappath, "info_{}.txt".format(nout)) + + with open(infopath, "r") as f: + ncpu = int(f.readline().split()[-1]) + if verbose: + print("Reading in output `{}` with ncpu = `{}`.".format(nout, ncpu)) + + # Check whether the unbinding file exists. + snapdirlist = listdir(snappath) + unbinding_file = "unbinding_{}.out00001".format(nout) + if unbinding_file not in snapdirlist: + raise FileNotFoundError( + "Couldn't find `{}` in `{}`. Use mergertreeplot.py -h or --help to " + "print help message.".format(unbinding_file, snappath)) + + # First read the headers. Reallocate arrays and fill them. + nparts = numpy.zeros(ncpu, dtype=int) + partfiles = [None] * ncpu + for cpu in range(ncpu): + cpu_str = str(cpu + 1).zfill(5) + fpath = join(snappath, "part_{}.out{}".format(nout, cpu_str)) + + f = FortranFile(fpath) + # Read in this order + ncpuloc = f.read_ints() + if ncpuloc != ncpu: + raise ValueError("`ncpu = {}` of `{}` disagrees with `ncpu = {}` " + "of `{}`.".format(ncpu, infopath, ncpuloc, fpath)) + ndim = f.read_ints() + nparts[cpu] = f.read_ints() + localseed = f.read_ints() + nstar_tot = f.read_ints() + mstar_tot = f.read_reals('d') + mstar_lost = f.read_reals('d') + nsink = f.read_ints() + + partfiles[cpu] = f + + return nparts, partfiles + + +def read_sp(dtype, partfile): + """ + Utility function to read a single particle file, depending on the dtype. + + Parameters + ---------- + dtype : str + The dtype of the part file to be read now. + partfile : `scipy.io.FortranFile` + Part file to read from. + + Returns + ------- + out : 1-dimensional array + The data read from the part file. + n : int + The index of the initial conditions (IC) realisation. + simpath : str + The complete path to the CSiBORG simulation. + """ + if dtype in [F16, F32, F64]: + return partfile.read_reals('d') + elif dtype in [I32]: + return partfile.read_ints() + else: + raise TypeError("Unexpected dtype `{}`.".format(dtype)) + + +def nparts_to_start_ind(nparts): + """ + Convert `nparts` array to starting indices in a pre-allocated array for looping over the CPU number. + + Parameters + ---------- + nparts : 1-dimensional array + Number of parts assosiated with each CPU. + + Returns + ------- + start_ind : 1-dimensional array + The starting indices calculated as a cumulative sum starting at 0. + """ + return numpy.hstack([[0], numpy.cumsum(nparts[:-1])]) + + +def read_particle(pars_extract, n, simpath, verbose=True): + """ + Read particle files of a simulation at a given snapshot and return + values of `pars_extract`. + + Parameters + ---------- + pars_extract : list of str + Parameters to be extacted. + n : int + The index of the redshift snapshot. + simpath : str + The complete path to the CSiBORG simulation. + verbose : bool, optional + Verbosity flag while for reading the CPU outputs. + + Returns + ------- + out : structured array + The data read from the particle file. + """ + # Open the particle files + nparts, partfiles = open_particle(n, simpath) + if verbose: + print("Opened {} particle files.".format(nparts.size)) + ncpu = nparts.size + # Order in which the particles are written in the FortranFile + forder = [("x", F16), ("y", F16), ("z", F16), + ("vx", F16), ("vy", F16), ("vz", F16), + ("M", F32), ("ID", I32), ("level", I32)] + fnames = [fp[0] for fp in forder] + fdtypes = [fp[1] for fp in forder] + # Check there are no strange parameters + for p in pars_extract: + if p not in fnames: + raise ValueError("Undefined parameter `{}`. Must be one of `{}`." + .format(p, fnames)) + + npart_tot = numpy.sum(nparts) + # A dummy array is necessary for reading the fortran files. + dum = numpy.full(npart_tot, numpy.nan, dtype=F16) + # These are the data we read along with types + dtype = {"names": pars_extract, + "formats": [forder[fnames.index(p)][1] for p in pars_extract]} + # Allocate the output structured array + out = numpy.full(npart_tot, numpy.nan, dtype) + start_ind = nparts_to_start_ind((nparts)) + iters = tqdm(range(ncpu)) if verbose else range(ncpu) + for cpu in iters: + i = start_ind[cpu] + j = nparts[cpu] + for (fname, fdtype) in zip(fnames, fdtypes): + if fname in pars_extract: + out[fname][i:i + j] = read_sp(fdtype, partfiles[cpu]) + else: + dum[i:i + j] = read_sp(fdtype, partfiles[cpu]) + + return out + + +def open_unbinding(cpu, n, simpath): + """ + Open particle files to a given CSiBORG simulation. Note that to be consistent CPU is incremented by 1. + + Parameters + ---------- + cpu : int + The CPU index. + n : int + The index of a redshift snapshot. + simpath : str + The complete path to the CSiBORG simulation. + + Returns + ------- + unbinding : `scipy.io.FortranFile` + The opened unbinding FortranFile. + """ + nout = str(n).zfill(5) + cpu = str(cpu + 1).zfill(5) + fpath = join(simpath, "output_{}".format(nout), + "unbinding_{}.out{}".format(nout, cpu)) + + return FortranFile(fpath) + + +def read_clumpid(n, simpath, verbose=True): + """ + Read clump IDs from unbinding files. + + Parameters + ---------- + n : int + The index of a redshift snapshot. + simpath : str + The complete path to the CSiBORG simulation. + verbose : bool, optional + Verbosity flag while for reading the CPU outputs. + + Returns + ------- + clumpid : 1-dimensional array + The array of clump IDs. + """ + nparts, __ = open_particle(n, simpath, verbose) + start_ind = nparts_to_start_ind(nparts) + ncpu = nparts.size + + clumpid = numpy.full(numpy.sum(nparts), numpy.nan) + iters = tqdm(range(ncpu)) if verbose else range(ncpu) + for cpu in iters: + i = start_ind[cpu] + j = nparts[cpu] + ff = open_unbinding(cpu, n, simpath) + clumpid[i:i + j] = ff.read_ints() + + return clumpid + + +def read_clumps(n, simpath): + """ + Read in a precomputed clump file `clump_N.dat`. + + Parameters + ---------- + n : int + The index of a redshift snapshot. + simpath : str + The complete path to the CSiBORG simulation. + + Returns + ------- + out : structured array + Structured array of the clumps. + """ + n = str(n).zfill(5) + fname = join(simpath, "output_{}".format(n), "clump_{}.dat".format(n)) + # Check the file exists. + if not isfile(fname): + raise FileExistsError("Clump file `{}` does not exist.".format(fname)) + + # Read in the clump array. This is how the columns must be written! + arr = numpy.genfromtxt(fname) + cols = [("index", I64), ("level", I64), ("parent", I64), ("ncell", F64), + ("peak_x", F64), ("peak_y", F64), ("peak_z", F64), + ("rho-", F64), ("rho+", F64), ("rho_av", F64), + ("mass_cl", F64), ("relevance", F64)] + # Write to a structured array + dtype = {"names": [col[0] for col in cols], + "formats": [col[1] for col in cols]} + out = numpy.full(arr.shape[0], numpy.nan, dtype=dtype) + for i, name in enumerate(dtype["names"]): + out[name] = arr[:, i] + return out + + +def convert_mass_cols(arr, cols): + """ + Convert mass columns from box units to :math:`M_{odot}`. `arr` is passed by + reference and is not explicitly returned back. + + Parameters + ---------- + arr : structured array + The array whose columns are to be converted. + cols : str or list of str + The mass columns to be converted. + + Returns + ------- + None + """ + cols = [cols] if isinstance(cols, str) else cols + for col in cols: + arr[col] *= BOXMASS + + +def convert_position_cols(arr, cols, zero_centered=False): + """ + Convert position columns from box units to :math:`\mathrm{Mpc}`. `arr` is + passed by reference and is not explicitly returned back. + + Parameters + ---------- + arr : structured array + The array whose columns are to be converted. + cols : str or list of str + The mass columns to be converted. + zero_centered : bool, optional + Whether to translate the well-resolved origin in the centre of the + simulation to the :math:`(0, 0 , 0)` point. + + Returns + ------- + None + """ + cols = [cols] if isinstance(cols, str) else cols + for col in cols: + arr[col] *= BOXSIZE + if zero_centered: + arr[col] -= BOXSIZE / 2 diff --git a/scripts/readsim.ipynb b/scripts/readsim.ipynb new file mode 100644 index 0000000..17d7eae --- /dev/null +++ b/scripts/readsim.ipynb @@ -0,0 +1,1125 @@ +{ + "cells": [ + { + "cell_type": "code", + "execution_count": 1, + "metadata": { + "ExecuteTime": { + "end_time": "2022-10-11T15:20:18.842852Z", + "start_time": "2022-10-11T15:20:18.056022Z" + } + }, + "outputs": [], + "source": [ + "import numpy as np\n", + "%matplotlib notebook\n", + "import matplotlib.pyplot as plt\n", + "# import fortranfile as ff\n", + "from os import listdir\n", + "\n", + "import sys\n", + "sys.path.append(\"../\")\n", + "\n", + "import galomatch\n", + "\n", + "%load_ext autoreload\n", + "%autoreload 2\n", + "\n", + "from copy import copy" + ] + }, + { + "cell_type": "code", + "execution_count": 2, + "metadata": { + "ExecuteTime": { + "end_time": "2022-10-11T15:20:18.862223Z", + "start_time": "2022-10-11T15:20:18.845901Z" + } + }, + "outputs": [], + "source": [ + "simpath = galomatch.io.get_sim_path(9844)" + ] + }, + { + "cell_type": "code", + "execution_count": 3, + "metadata": { + "ExecuteTime": { + "end_time": "2022-10-11T15:20:30.920275Z", + "start_time": "2022-10-11T15:20:18.863861Z" + } + }, + "outputs": [], + "source": [ + "arr = galomatch.io.read_clumps(1016, simpath)\n", + "galomatch.io.convert_mass_cols(arr, \"mass_cl\")\n", + "galomatch.io.convert_position_cols(arr, [\"peak_x\", \"peak_y\", \"peak_z\"])" + ] + }, + { + "cell_type": "code", + "execution_count": 12, + "metadata": { + "ExecuteTime": { + "end_time": "2022-10-11T15:21:10.493469Z", + "start_time": "2022-10-11T15:21:10.476059Z" + } + }, + "outputs": [ + { + "data": { + "text/plain": [ + "array([298.56982526, 330.92112924, 322.92393181, ..., 671.12820648,\n", + " 340.09090577, 354.01700821])" + ] + }, + "execution_count": 12, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "arr[\"peak_x\"]" + ] + }, + { + "cell_type": "code", + "execution_count": 20, + "metadata": { + "ExecuteTime": { + "end_time": "2022-10-11T15:22:18.132550Z", + "start_time": "2022-10-11T15:22:17.962004Z" + } + }, + "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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position: absolute; left: 0; top: 0; z-index: 1;'\n", + " );\n", + "\n", + " // Apply a ponyfill if ResizeObserver is not implemented by browser.\n", + " if (this.ResizeObserver === undefined) {\n", + " if (window.ResizeObserver !== undefined) {\n", + " this.ResizeObserver = window.ResizeObserver;\n", + " } else {\n", + " var obs = _JSXTOOLS_RESIZE_OBSERVER({});\n", + " this.ResizeObserver = obs.ResizeObserver;\n", + " }\n", + " }\n", + "\n", + " this.resizeObserverInstance = new this.ResizeObserver(function (entries) {\n", + " var nentries = entries.length;\n", + " for (var i = 0; i < nentries; i++) {\n", + " var entry = entries[i];\n", + " var width, height;\n", + " if (entry.contentBoxSize) {\n", + " if (entry.contentBoxSize instanceof Array) {\n", + " // Chrome 84 implements new version of spec.\n", + " width = entry.contentBoxSize[0].inlineSize;\n", + " height = entry.contentBoxSize[0].blockSize;\n", + " } else {\n", + " // Firefox implements old version of spec.\n", + " width = entry.contentBoxSize.inlineSize;\n", + " height = entry.contentBoxSize.blockSize;\n", + " }\n", + " } else {\n", + " // Chrome <84 implements even older version of spec.\n", + " width = entry.contentRect.width;\n", + " height = entry.contentRect.height;\n", + " }\n", + "\n", + " // Keep the size of the canvas and rubber band canvas in sync with\n", + " // the canvas container.\n", + " if (entry.devicePixelContentBoxSize) {\n", + " // Chrome 84 implements new version of spec.\n", + " canvas.setAttribute(\n", + " 'width',\n", + " entry.devicePixelContentBoxSize[0].inlineSize\n", + " );\n", + " canvas.setAttribute(\n", + " 'height',\n", + " entry.devicePixelContentBoxSize[0].blockSize\n", + " );\n", + " } else {\n", + " canvas.setAttribute('width', width * fig.ratio);\n", + " canvas.setAttribute('height', height * fig.ratio);\n", + " }\n", + " canvas.setAttribute(\n", + " 'style',\n", + " 'width: ' + width + 'px; height: ' + height + 'px;'\n", + " );\n", + "\n", + " rubberband_canvas.setAttribute('width', width);\n", + " rubberband_canvas.setAttribute('height', height);\n", + "\n", + " // And update the size in Python. We ignore the initial 0/0 size\n", + " // that occurs as the element is placed into the DOM, which should\n", + " // otherwise not happen due to the minimum size styling.\n", + " if (fig.ws.readyState == 1 && width != 0 && height != 0) {\n", + " fig.request_resize(width, height);\n", + " }\n", + " }\n", + " });\n", + " this.resizeObserverInstance.observe(canvas_div);\n", + "\n", + " function on_mouse_event_closure(name) {\n", + " return function (event) {\n", + " return fig.mouse_event(event, name);\n", + " };\n", + " }\n", + "\n", + " rubberband_canvas.addEventListener(\n", + " 'mousedown',\n", + " on_mouse_event_closure('button_press')\n", + " );\n", + " rubberband_canvas.addEventListener(\n", + " 'mouseup',\n", + " on_mouse_event_closure('button_release')\n", + " );\n", + " rubberband_canvas.addEventListener(\n", + " 'dblclick',\n", + " on_mouse_event_closure('dblclick')\n", + " );\n", + " // Throttle sequential mouse events to 1 every 20ms.\n", + " rubberband_canvas.addEventListener(\n", + " 'mousemove',\n", + " on_mouse_event_closure('motion_notify')\n", + " );\n", + "\n", + " rubberband_canvas.addEventListener(\n", + " 'mouseenter',\n", + " on_mouse_event_closure('figure_enter')\n", + " );\n", + " rubberband_canvas.addEventListener(\n", + " 'mouseleave',\n", + " on_mouse_event_closure('figure_leave')\n", + " );\n", + "\n", + " canvas_div.addEventListener('wheel', function (event) {\n", + " if (event.deltaY < 0) {\n", + " event.step = 1;\n", + " } else {\n", + " event.step = -1;\n", + " }\n", + " on_mouse_event_closure('scroll')(event);\n", + " });\n", + "\n", + " canvas_div.appendChild(canvas);\n", + " canvas_div.appendChild(rubberband_canvas);\n", + "\n", + " this.rubberband_context = rubberband_canvas.getContext('2d');\n", + " this.rubberband_context.strokeStyle = '#000000';\n", + "\n", + " this._resize_canvas = function (width, height, forward) {\n", + " if (forward) {\n", + " canvas_div.style.width = width + 'px';\n", + " canvas_div.style.height = height + 'px';\n", + " }\n", + " };\n", + "\n", + " // Disable right mouse context menu.\n", + " this.rubberband_canvas.addEventListener('contextmenu', function (_e) {\n", + " event.preventDefault();\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 toolbar = document.createElement('div');\n", + " toolbar.classList = 'mpl-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 = 'mpl-button-group';\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 = 'mpl-button-group';\n", + " continue;\n", + " }\n", + "\n", + " var button = (fig.buttons[name] = document.createElement('button'));\n", + " button.classList = 'mpl-widget';\n", + " button.setAttribute('role', 'button');\n", + " button.setAttribute('aria-disabled', 'false');\n", + " button.addEventListener('click', on_click_closure(method_name));\n", + " button.addEventListener('mouseover', on_mouseover_closure(tooltip));\n", + "\n", + " var icon_img = document.createElement('img');\n", + " icon_img.src = '_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", + " fig.rubberband_canvas.style.cursor = msg['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 https://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", + " * https://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\", \"home\"], [\"Back\", \"Back to previous view\", \"fa fa-arrow-left\", \"back\"], [\"Forward\", \"Forward to next view\", \"fa fa-arrow-right\", \"forward\"], [\"\", \"\", \"\", \"\"], [\"Pan\", \"Left button pans, Right button zooms\\nx/y fixes axis, CTRL fixes aspect\", \"fa fa-arrows\", \"pan\"], [\"Zoom\", \"Zoom to rectangle\\nx/y fixes axis\", \"fa fa-square-o\", \"zoom\"], [\"\", \"\", \"\", \"\"], [\"Download\", \"Download plot\", \"fa fa-floppy-o\", \"download\"]];\n", + "\n", + "mpl.extensions = [\"eps\", \"jpeg\", \"pgf\", \"pdf\", \"png\", \"ps\", \"raw\", \"svg\", \"tif\", \"webp\"];\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", + " // 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": [ + "plt.figure()\n", + "# plt.scatter(arr[\"peak_x\"], arr[\"peak_y\"], s=0.00001)\n", + "\n", + "plt.hist(np.log10(arr[\"mass_cl\"]), bins=\"auto\")\n", + "\n", + "plt.show()" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [] + } + ], + "metadata": { + "kernelspec": { + "display_name": "venv_galomatch", + "language": "python", + "name": "venv_galomatch" + }, + "language_info": { + "codemirror_mode": { + "name": "ipython", + "version": 3 + }, + "file_extension": ".py", + "mimetype": "text/x-python", + "name": "python", + "nbconvert_exporter": "python", + "pygments_lexer": "ipython3", + "version": "3.8.0" + }, + "vscode": { + "interpreter": { + "hash": "48b586a1ee27fc2e7b130d2436dca8c87c36333659e2ed3c8e31ccbf57230401" + } + } + }, + "nbformat": 4, + "nbformat_minor": 2 +} diff --git a/test.py b/test.py deleted file mode 100644 index e69de29..0000000