{ "cells": [ { "cell_type": "code", "execution_count": 2, "metadata": {}, "outputs": [], "source": [ "import sys\n", "\n", "import glob\n", "import matplotlib.pyplot as plt\n", "import os\n", "import numpy as np\n", "import h5py\n", "import pandas as pd\n", "from functions import *\n", "from pathlib import Path\n", "\n", "plt.rcParams.update({'font.size': 9})\n", "%matplotlib notebook\n", "\n", "TUD_cyan = '#00a6d6ff'\n", "TUD_lightblue = '#6ebbd5ff'\n", "TUD_darkblue = '#1d1c73ff'\n", "TUD_orange = '#e64616ff'\n", "TUD_red = '#e21a1aff'\n", "TUD_yellow = '#ffd100ff'\n", "TUD_green = '#008891ff'\n", "TUD_lightgreen = '#a5ca1aff'\n", "TUD_purple = '#6d177fff'\n", "TUD_grey = '#6b8689ff'\n", "TUD_brown = '#a65628ff'\n", "TUD_pink = '#fb9a99'" ] }, { "cell_type": "code", "execution_count": 3, "metadata": {}, "outputs": [], "source": [ "plt.rcParams.update({'font.size': 9})" ] }, { "cell_type": "code", "execution_count": 5, "metadata": {}, "outputs": [], "source": [ "analyfolder = '/locatio/of/the/dna/files/with/results'\n", "analydir = 'location/of/the/analyses'\n", "\n", "stage = 'hsnr'\n", "\n", "reslist = glob.glob(analyfolder + 'Results/*_results.hdf5')\n", " \n", "respd = gen_respd(reslist, stage, analytype='DNA')" ] }, { "cell_type": "code", "execution_count": 6, "metadata": {}, "outputs": [ { "data": { "text/html": [ "
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chnl0 event_ratechnl1 event_ratechnl0 analytechnl1 analytechnl0 colorchnl1 colorchnl0 diff_coeffchnl1 diff_coeffchnl0 diff_coeff_errchnl1 diff_coeff_err...chnl0 rgyrchnl1 rgyrvoltagepore_diampore_areachnl0 rate_errchnl0 concentration unitchnl1 rate_errchnl1 concentration unitorder
fname
R9_1104/R9_1104_18/2020_05_11_R9_1104_18_short_DNA.sptw/Results/DA_1000bp_m50mV1_results.hdf50.0000000.046905None1 kbp DNA#a65628ff#6d177fffNoneNoneNoneNone...None60-50.059x47None0.00000000.0270805.013
R9_1104/R9_1104_18/2020_05_11_R9_1104_18_short_DNA.sptw/Results/DB_1000bp_0mV_1_results.hdf50.0000000.196576None1 kbp DNA#a65628ff#6d177fffNoneNoneNoneNone...None600.059x47None0.00000000.0545205.014
R9_1104/R9_1104_18/2020_05_11_R9_1104_18_short_DNA.sptw/Results/DC_1000bp_5mV_1_results.hdf50.0000000.042986None1 kbp DNA#a65628ff#6d177fffNoneNoneNoneNone...None605.059x47None0.00000000.0214935.015
R9_1104/R9_1104_18/2020_05_11_R9_1104_18_short_DNA.sptw/Results/DD_1000bp_10mV_1_results.hdf50.0000000.026475None1 kbp DNA#a65628ff#6d177fffNoneNoneNoneNone...None6010.059x47None0.00000000.0187215.016
R9_1104/R9_1104_18/2020_05_11_R9_1104_18_short_DNA.sptw/Results/DE_1000bp_20mV_1_results.hdf50.0270570.027056None1 kbp DNA#a65628ff#6d177fffNoneNoneNoneNone...None6020.059x47None0.01913200.0191325.017
R9_1104/R9_1104_18/2020_05_11_R9_1104_18_short_DNA.sptw/Results/DF_1000bp_40mV_1_results.hdf50.0133330.126667None1 kbp DNA#a65628ff#6d177fffNoneNoneNoneNone...None6040.059x47None0.00666700.0205485.018
R9_1104/R9_1104_18/2020_05_11_R9_1104_18_short_DNA.sptw/Results/DGA_1000bp_50mV_1_results.hdf50.0200000.873333None1 kbp DNA#a65628ff#6d177fffNoneNoneNoneNone...None6050.059x47None0.00816500.0539555.019
R9_1104/R9_1104_18/2020_05_11_R9_1104_18_short_DNA.sptw/Results/DGB_1000bp_30mV_1_results.hdf50.0000000.032958None1 kbp DNA#a65628ff#6d177fffNoneNoneNoneNone...None6030.059x47None0.00000000.0233055.020
R9_1104/R9_1104_18/2020_05_11_R9_1104_18_short_DNA.sptw/Results/DG_1000bp_60mV_1_results.hdf50.24333415.320043None1 kbp DNA#a65628ff#6d177fffNoneNoneNoneNone...None6060.059x47None0.02848000.2259805.021
R9_1104/R9_1104_18/2020_05_11_R9_1104_18_short_DNA.sptw/Results/DH_1000bp_70mV_1_results.hdf50.41359729.115503None1 kbp DNA#a65628ff#6d177fffNoneNoneNoneNone...None6070.059x47None0.05969800.5008765.022
R9_1104/R9_1104_18/2020_05_11_R9_1104_18_short_DNA.sptw/Results/DI_1000bp_80mV_1_results.hdf50.70749965.500158None1 kbp DNA#a65628ff#6d177fffNoneNoneNoneNone...None6080.059x47None0.08224500.7913445.023
R9_1104/R9_1104_18/2020_05_11_R9_1104_18_short_DNA.sptw/Results/DJ_1000bp_90mV_1_results.hdf51.37606099.320905None1 kbp DNA#a65628ff#6d177fffNoneNoneNoneNone...None6090.059x47None0.14504901.2323035.024
R9_1104/R9_1104_18/2020_05_11_R9_1104_18_short_DNA.sptw/Results/DK_1000bp_100mV_1_results.hdf51.761757141.342464None1 kbp DNA#a65628ff#6d177fffNoneNoneNoneNone...None60100.059x47None0.12274701.0994505.025
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None \n", "R9_1104/R9_1104_18/2020_05_11_R9_1104_18_short_... None \n", "R9_1104/R9_1104_18/2020_05_11_R9_1104_18_short_... None \n", "R9_1104/R9_1104_18/2020_05_11_R9_1104_18_short_... None \n", "R9_1104/R9_1104_18/2020_05_11_R9_1104_18_short_... None \n", "R9_1104/R9_1104_18/2020_05_11_R9_1104_18_short_... None \n", "R9_1104/R9_1104_18/2020_05_11_R9_1104_18_short_... None \n", "R9_1104/R9_1104_18/2020_05_11_R9_1104_18_short_... None \n", "R9_1104/R9_1104_18/2020_05_11_R9_1104_18_short_... None \n", "R9_1104/R9_1104_18/2020_05_11_R9_1104_18_short_... None \n", "R9_1104/R9_1104_18/2020_05_11_R9_1104_18_short_... None \n", "\n", " chnl0 diff_coeff_err \\\n", "fname \n", "R9_1104/R9_1104_18/2020_05_11_R9_1104_18_short_... None \n", "R9_1104/R9_1104_18/2020_05_11_R9_1104_18_short_... None \n", "R9_1104/R9_1104_18/2020_05_11_R9_1104_18_short_... None \n", "R9_1104/R9_1104_18/2020_05_11_R9_1104_18_short_... None \n", "R9_1104/R9_1104_18/2020_05_11_R9_1104_18_short_... None \n", "R9_1104/R9_1104_18/2020_05_11_R9_1104_18_short_... None \n", "R9_1104/R9_1104_18/2020_05_11_R9_1104_18_short_... None \n", "R9_1104/R9_1104_18/2020_05_11_R9_1104_18_short_... None \n", "R9_1104/R9_1104_18/2020_05_11_R9_1104_18_short_... None \n", "R9_1104/R9_1104_18/2020_05_11_R9_1104_18_short_... None \n", "R9_1104/R9_1104_18/2020_05_11_R9_1104_18_short_... None \n", "R9_1104/R9_1104_18/2020_05_11_R9_1104_18_short_... None \n", "R9_1104/R9_1104_18/2020_05_11_R9_1104_18_short_... None \n", "\n", " chnl1 diff_coeff_err ... \\\n", "fname ... \n", "R9_1104/R9_1104_18/2020_05_11_R9_1104_18_short_... None ... \n", "R9_1104/R9_1104_18/2020_05_11_R9_1104_18_short_... None ... \n", "R9_1104/R9_1104_18/2020_05_11_R9_1104_18_short_... None ... \n", "R9_1104/R9_1104_18/2020_05_11_R9_1104_18_short_... None ... \n", "R9_1104/R9_1104_18/2020_05_11_R9_1104_18_short_... None ... \n", "R9_1104/R9_1104_18/2020_05_11_R9_1104_18_short_... None ... \n", "R9_1104/R9_1104_18/2020_05_11_R9_1104_18_short_... None ... \n", "R9_1104/R9_1104_18/2020_05_11_R9_1104_18_short_... None ... \n", "R9_1104/R9_1104_18/2020_05_11_R9_1104_18_short_... None ... \n", "R9_1104/R9_1104_18/2020_05_11_R9_1104_18_short_... None ... \n", "R9_1104/R9_1104_18/2020_05_11_R9_1104_18_short_... None ... \n", "R9_1104/R9_1104_18/2020_05_11_R9_1104_18_short_... None ... \n", "R9_1104/R9_1104_18/2020_05_11_R9_1104_18_short_... None ... \n", "\n", " chnl0 rgyr chnl1 rgyr \\\n", "fname \n", "R9_1104/R9_1104_18/2020_05_11_R9_1104_18_short_... None 60 \n", "R9_1104/R9_1104_18/2020_05_11_R9_1104_18_short_... None 60 \n", "R9_1104/R9_1104_18/2020_05_11_R9_1104_18_short_... None 60 \n", "R9_1104/R9_1104_18/2020_05_11_R9_1104_18_short_... None 60 \n", "R9_1104/R9_1104_18/2020_05_11_R9_1104_18_short_... None 60 \n", "R9_1104/R9_1104_18/2020_05_11_R9_1104_18_short_... None 60 \n", "R9_1104/R9_1104_18/2020_05_11_R9_1104_18_short_... None 60 \n", "R9_1104/R9_1104_18/2020_05_11_R9_1104_18_short_... None 60 \n", "R9_1104/R9_1104_18/2020_05_11_R9_1104_18_short_... None 60 \n", "R9_1104/R9_1104_18/2020_05_11_R9_1104_18_short_... None 60 \n", "R9_1104/R9_1104_18/2020_05_11_R9_1104_18_short_... None 60 \n", "R9_1104/R9_1104_18/2020_05_11_R9_1104_18_short_... None 60 \n", "R9_1104/R9_1104_18/2020_05_11_R9_1104_18_short_... None 60 \n", "\n", " voltage pore_diam \\\n", "fname \n", "R9_1104/R9_1104_18/2020_05_11_R9_1104_18_short_... -50.0 59x47 \n", "R9_1104/R9_1104_18/2020_05_11_R9_1104_18_short_... 0.0 59x47 \n", "R9_1104/R9_1104_18/2020_05_11_R9_1104_18_short_... 5.0 59x47 \n", "R9_1104/R9_1104_18/2020_05_11_R9_1104_18_short_... 10.0 59x47 \n", "R9_1104/R9_1104_18/2020_05_11_R9_1104_18_short_... 20.0 59x47 \n", "R9_1104/R9_1104_18/2020_05_11_R9_1104_18_short_... 40.0 59x47 \n", "R9_1104/R9_1104_18/2020_05_11_R9_1104_18_short_... 50.0 59x47 \n", "R9_1104/R9_1104_18/2020_05_11_R9_1104_18_short_... 30.0 59x47 \n", "R9_1104/R9_1104_18/2020_05_11_R9_1104_18_short_... 60.0 59x47 \n", "R9_1104/R9_1104_18/2020_05_11_R9_1104_18_short_... 70.0 59x47 \n", "R9_1104/R9_1104_18/2020_05_11_R9_1104_18_short_... 80.0 59x47 \n", "R9_1104/R9_1104_18/2020_05_11_R9_1104_18_short_... 90.0 59x47 \n", "R9_1104/R9_1104_18/2020_05_11_R9_1104_18_short_... 100.0 59x47 \n", "\n", " pore_area chnl0 rate_err \\\n", "fname \n", "R9_1104/R9_1104_18/2020_05_11_R9_1104_18_short_... None 0.000000 \n", "R9_1104/R9_1104_18/2020_05_11_R9_1104_18_short_... None 0.000000 \n", "R9_1104/R9_1104_18/2020_05_11_R9_1104_18_short_... None 0.000000 \n", "R9_1104/R9_1104_18/2020_05_11_R9_1104_18_short_... None 0.000000 \n", "R9_1104/R9_1104_18/2020_05_11_R9_1104_18_short_... None 0.019132 \n", "R9_1104/R9_1104_18/2020_05_11_R9_1104_18_short_... None 0.006667 \n", "R9_1104/R9_1104_18/2020_05_11_R9_1104_18_short_... None 0.008165 \n", "R9_1104/R9_1104_18/2020_05_11_R9_1104_18_short_... None 0.000000 \n", "R9_1104/R9_1104_18/2020_05_11_R9_1104_18_short_... None 0.028480 \n", "R9_1104/R9_1104_18/2020_05_11_R9_1104_18_short_... None 0.059698 \n", "R9_1104/R9_1104_18/2020_05_11_R9_1104_18_short_... None 0.082245 \n", "R9_1104/R9_1104_18/2020_05_11_R9_1104_18_short_... None 0.145049 \n", "R9_1104/R9_1104_18/2020_05_11_R9_1104_18_short_... None 0.122747 \n", "\n", " chnl0 concentration unit \\\n", "fname \n", "R9_1104/R9_1104_18/2020_05_11_R9_1104_18_short_... 0 \n", "R9_1104/R9_1104_18/2020_05_11_R9_1104_18_short_... 0 \n", "R9_1104/R9_1104_18/2020_05_11_R9_1104_18_short_... 0 \n", "R9_1104/R9_1104_18/2020_05_11_R9_1104_18_short_... 0 \n", "R9_1104/R9_1104_18/2020_05_11_R9_1104_18_short_... 0 \n", "R9_1104/R9_1104_18/2020_05_11_R9_1104_18_short_... 0 \n", "R9_1104/R9_1104_18/2020_05_11_R9_1104_18_short_... 0 \n", "R9_1104/R9_1104_18/2020_05_11_R9_1104_18_short_... 0 \n", "R9_1104/R9_1104_18/2020_05_11_R9_1104_18_short_... 0 \n", "R9_1104/R9_1104_18/2020_05_11_R9_1104_18_short_... 0 \n", "R9_1104/R9_1104_18/2020_05_11_R9_1104_18_short_... 0 \n", "R9_1104/R9_1104_18/2020_05_11_R9_1104_18_short_... 0 \n", "R9_1104/R9_1104_18/2020_05_11_R9_1104_18_short_... 0 \n", "\n", " chnl1 rate_err \\\n", "fname \n", "R9_1104/R9_1104_18/2020_05_11_R9_1104_18_short_... 0.027080 \n", "R9_1104/R9_1104_18/2020_05_11_R9_1104_18_short_... 0.054520 \n", "R9_1104/R9_1104_18/2020_05_11_R9_1104_18_short_... 0.021493 \n", "R9_1104/R9_1104_18/2020_05_11_R9_1104_18_short_... 0.018721 \n", "R9_1104/R9_1104_18/2020_05_11_R9_1104_18_short_... 0.019132 \n", "R9_1104/R9_1104_18/2020_05_11_R9_1104_18_short_... 0.020548 \n", "R9_1104/R9_1104_18/2020_05_11_R9_1104_18_short_... 0.053955 \n", "R9_1104/R9_1104_18/2020_05_11_R9_1104_18_short_... 0.023305 \n", "R9_1104/R9_1104_18/2020_05_11_R9_1104_18_short_... 0.225980 \n", "R9_1104/R9_1104_18/2020_05_11_R9_1104_18_short_... 0.500876 \n", "R9_1104/R9_1104_18/2020_05_11_R9_1104_18_short_... 0.791344 \n", "R9_1104/R9_1104_18/2020_05_11_R9_1104_18_short_... 1.232303 \n", "R9_1104/R9_1104_18/2020_05_11_R9_1104_18_short_... 1.099450 \n", "\n", " chnl1 concentration unit \\\n", "fname \n", "R9_1104/R9_1104_18/2020_05_11_R9_1104_18_short_... 5.0 \n", "R9_1104/R9_1104_18/2020_05_11_R9_1104_18_short_... 5.0 \n", "R9_1104/R9_1104_18/2020_05_11_R9_1104_18_short_... 5.0 \n", "R9_1104/R9_1104_18/2020_05_11_R9_1104_18_short_... 5.0 \n", "R9_1104/R9_1104_18/2020_05_11_R9_1104_18_short_... 5.0 \n", "R9_1104/R9_1104_18/2020_05_11_R9_1104_18_short_... 5.0 \n", "R9_1104/R9_1104_18/2020_05_11_R9_1104_18_short_... 5.0 \n", "R9_1104/R9_1104_18/2020_05_11_R9_1104_18_short_... 5.0 \n", "R9_1104/R9_1104_18/2020_05_11_R9_1104_18_short_... 5.0 \n", "R9_1104/R9_1104_18/2020_05_11_R9_1104_18_short_... 5.0 \n", "R9_1104/R9_1104_18/2020_05_11_R9_1104_18_short_... 5.0 \n", "R9_1104/R9_1104_18/2020_05_11_R9_1104_18_short_... 5.0 \n", "R9_1104/R9_1104_18/2020_05_11_R9_1104_18_short_... 5.0 \n", "\n", " order \n", "fname \n", "R9_1104/R9_1104_18/2020_05_11_R9_1104_18_short_... 13 \n", "R9_1104/R9_1104_18/2020_05_11_R9_1104_18_short_... 14 \n", "R9_1104/R9_1104_18/2020_05_11_R9_1104_18_short_... 15 \n", "R9_1104/R9_1104_18/2020_05_11_R9_1104_18_short_... 16 \n", "R9_1104/R9_1104_18/2020_05_11_R9_1104_18_short_... 17 \n", "R9_1104/R9_1104_18/2020_05_11_R9_1104_18_short_... 18 \n", "R9_1104/R9_1104_18/2020_05_11_R9_1104_18_short_... 19 \n", "R9_1104/R9_1104_18/2020_05_11_R9_1104_18_short_... 20 \n", "R9_1104/R9_1104_18/2020_05_11_R9_1104_18_short_... 21 \n", "R9_1104/R9_1104_18/2020_05_11_R9_1104_18_short_... 22 \n", "R9_1104/R9_1104_18/2020_05_11_R9_1104_18_short_... 23 \n", "R9_1104/R9_1104_18/2020_05_11_R9_1104_18_short_... 24 \n", "R9_1104/R9_1104_18/2020_05_11_R9_1104_18_short_... 25 \n", "\n", "[13 rows x 24 columns]" ] }, "execution_count": 6, "metadata": {}, "output_type": "execute_result" } ], "source": [ "respd[respd['chnl1 analyte'] == '1 kbp DNA']\n" ] }, { "cell_type": "code", "execution_count": 10, "metadata": { "scrolled": false }, "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. ' +\n", " 'Firefox 4 and 5 are also supported but you ' +\n", " 'have to enable WebSockets in about:config.');\n", " };\n", "}\n", "\n", "mpl.figure = function(figure_id, websocket, ondownload, parent_element) {\n", " this.id = figure_id;\n", "\n", " this.ws = websocket;\n", "\n", " this.supports_binary = (this.ws.binaryType != undefined);\n", "\n", " if (!this.supports_binary) {\n", " var warnings = document.getElementById(\"mpl-warnings\");\n", " if (warnings) {\n", " warnings.style.display = 'block';\n", " warnings.textContent = (\n", " \"This browser does not support binary websocket messages. \" +\n", " \"Performance may be slow.\");\n", " }\n", " }\n", "\n", " this.imageObj = new Image();\n", "\n", " this.context = undefined;\n", " this.message = undefined;\n", " this.canvas = undefined;\n", " this.rubberband_canvas = undefined;\n", " this.rubberband_context = undefined;\n", " this.format_dropdown = undefined;\n", "\n", " this.image_mode = 'full';\n", "\n", " this.root = $('
');\n", " this._root_extra_style(this.root)\n", " this.root.attr('style', 'display: inline-block');\n", "\n", " $(parent_element).append(this.root);\n", "\n", " this._init_header(this);\n", " this._init_canvas(this);\n", " this._init_toolbar(this);\n", "\n", " var fig = this;\n", "\n", " this.waiting = false;\n", "\n", " this.ws.onopen = function () {\n", " fig.send_message(\"supports_binary\", {value: fig.supports_binary});\n", " fig.send_message(\"send_image_mode\", {});\n", " if (mpl.ratio != 1) {\n", " fig.send_message(\"set_dpi_ratio\", {'dpi_ratio': mpl.ratio});\n", " }\n", " fig.send_message(\"refresh\", {});\n", " }\n", "\n", " this.imageObj.onload = function() {\n", " if (fig.image_mode == 'full') {\n", " // Full images could contain transparency (where diff images\n", " // almost always do), so we need to clear the canvas so that\n", " // there is no ghosting.\n", " fig.context.clearRect(0, 0, fig.canvas.width, fig.canvas.height);\n", " }\n", " fig.context.drawImage(fig.imageObj, 0, 0);\n", " };\n", "\n", " this.imageObj.onunload = function() {\n", " fig.ws.close();\n", " }\n", "\n", " this.ws.onmessage = this._make_on_message_function(this);\n", "\n", " this.ondownload = ondownload;\n", "}\n", "\n", "mpl.figure.prototype._init_header = function() {\n", " var titlebar = $(\n", " '
');\n", " var titletext = $(\n", " '
');\n", " titlebar.append(titletext)\n", " this.root.append(titlebar);\n", " this.header = titletext[0];\n", "}\n", "\n", "\n", "\n", "mpl.figure.prototype._canvas_extra_style = function(canvas_div) {\n", "\n", "}\n", "\n", "\n", "mpl.figure.prototype._root_extra_style = function(canvas_div) {\n", "\n", "}\n", "\n", "mpl.figure.prototype._init_canvas = function() {\n", " var fig = this;\n", "\n", " var canvas_div = $('
');\n", "\n", " canvas_div.attr('style', 'position: relative; clear: both; outline: 0');\n", "\n", " function canvas_keyboard_event(event) {\n", " return fig.key_event(event, event['data']);\n", " }\n", "\n", " canvas_div.keydown('key_press', canvas_keyboard_event);\n", " canvas_div.keyup('key_release', canvas_keyboard_event);\n", " this.canvas_div = canvas_div\n", " this._canvas_extra_style(canvas_div)\n", " this.root.append(canvas_div);\n", "\n", " var canvas = $('');\n", " canvas.addClass('mpl-canvas');\n", " canvas.attr('style', \"left: 0; top: 0; z-index: 0; outline: 0\")\n", "\n", " this.canvas = canvas[0];\n", " this.context = canvas[0].getContext(\"2d\");\n", "\n", " var backingStore = this.context.backingStorePixelRatio ||\n", "\tthis.context.webkitBackingStorePixelRatio ||\n", "\tthis.context.mozBackingStorePixelRatio ||\n", "\tthis.context.msBackingStorePixelRatio ||\n", "\tthis.context.oBackingStorePixelRatio ||\n", "\tthis.context.backingStorePixelRatio || 1;\n", "\n", " mpl.ratio = (window.devicePixelRatio || 1) / backingStore;\n", "\n", " var rubberband = $('');\n", " rubberband.attr('style', \"position: absolute; left: 0; top: 0; z-index: 1;\")\n", "\n", " var pass_mouse_events = true;\n", "\n", " canvas_div.resizable({\n", " start: function(event, ui) {\n", " pass_mouse_events = false;\n", " },\n", " resize: function(event, ui) {\n", " fig.request_resize(ui.size.width, ui.size.height);\n", " },\n", " stop: function(event, ui) {\n", " pass_mouse_events = true;\n", " fig.request_resize(ui.size.width, ui.size.height);\n", " },\n", " });\n", "\n", " function mouse_event_fn(event) {\n", " if (pass_mouse_events)\n", " return fig.mouse_event(event, event['data']);\n", " }\n", "\n", " rubberband.mousedown('button_press', mouse_event_fn);\n", " rubberband.mouseup('button_release', mouse_event_fn);\n", " // Throttle sequential mouse events to 1 every 20ms.\n", " rubberband.mousemove('motion_notify', mouse_event_fn);\n", "\n", " rubberband.mouseenter('figure_enter', mouse_event_fn);\n", " rubberband.mouseleave('figure_leave', mouse_event_fn);\n", "\n", " canvas_div.on(\"wheel\", function (event) {\n", " event = event.originalEvent;\n", " event['data'] = 'scroll'\n", " if (event.deltaY < 0) {\n", " event.step = 1;\n", " } else {\n", " event.step = -1;\n", " }\n", " mouse_event_fn(event);\n", " });\n", "\n", " canvas_div.append(canvas);\n", " canvas_div.append(rubberband);\n", "\n", " this.rubberband = rubberband;\n", " this.rubberband_canvas = rubberband[0];\n", " this.rubberband_context = rubberband[0].getContext(\"2d\");\n", " this.rubberband_context.strokeStyle = \"#000000\";\n", "\n", " this._resize_canvas = function(width, height) {\n", " // Keep the size of the canvas, canvas container, and rubber band\n", " // canvas in synch.\n", " canvas_div.css('width', width)\n", " canvas_div.css('height', height)\n", "\n", " canvas.attr('width', width * mpl.ratio);\n", " canvas.attr('height', height * mpl.ratio);\n", " canvas.attr('style', 'width: ' + width + 'px; 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.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", " // 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", "\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= 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('matplotlib', mpl.mpl_figure_comm);\n", "}\n" ], "text/plain": [ "" ] }, "metadata": {}, "output_type": "display_data" }, { "data": { "text/html": [ "" ], "text/plain": [ "" ] }, "metadata": {}, "output_type": "display_data" }, { "name": "stdout", "output_type": "stream", "text": [ "2020-07-21 11:24:47.247307: Comment: Now plotting cp trace\n" ] } ], "source": [ "res_hdf_loc = analydir + respd.index[11]\n", "print(res_hdf_loc)\n", "\n", "fig, ax = plt.subplots(figsize = (3,2))\n", "tt_dict={'chnl':'chnl1', 'ax':ax, 'tt_binning':1e-4, 'stages':['hsnr', 'combined'], 'tt_start':0, 'tt_end':2, 'plt_cp':False}\n", "plotted = plot_cp_trace(res_hdf_loc, tt_dict)\n", "\n", "ax.set_title('')\n", "\n", "ax.set_ylim(bottom=-10, top=270)\n", "ln = ax.get_lines()\n", "plt.setp(ln, linewidth=1)\n", "fig.tight_layout()\n", "\n", "fig.savefig('fig_4_50bp_tt.png', dpi=600, transparent=True)" ] }, { "cell_type": "code", "execution_count": 7, "metadata": { "scrolled": false }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "/home/nils/Dokumente/Promotion/Inhaltliches/Analyses/R9_1104/R9_1104_18/2020_05_11_R9_1104_18_short_DNA.sptw/Results/BA_50bp_m50mV_1_results.hdf5\n" ] }, { "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. ' +\n", " 'Firefox 4 and 5 are also supported but you ' +\n", " 'have to enable WebSockets in about:config.');\n", " };\n", "}\n", "\n", "mpl.figure = function(figure_id, websocket, ondownload, parent_element) {\n", " this.id = figure_id;\n", "\n", " this.ws = websocket;\n", "\n", " this.supports_binary = (this.ws.binaryType != undefined);\n", "\n", " if (!this.supports_binary) {\n", " var warnings = document.getElementById(\"mpl-warnings\");\n", " if (warnings) {\n", " warnings.style.display = 'block';\n", " warnings.textContent = (\n", " \"This browser does not support binary websocket messages. \" +\n", " \"Performance may be slow.\");\n", " }\n", " }\n", "\n", " this.imageObj = new Image();\n", "\n", " this.context = undefined;\n", " this.message = undefined;\n", " this.canvas = undefined;\n", " this.rubberband_canvas = undefined;\n", " this.rubberband_context = undefined;\n", " this.format_dropdown = undefined;\n", "\n", " this.image_mode = 'full';\n", "\n", " this.root = $('
');\n", " this._root_extra_style(this.root)\n", " this.root.attr('style', 'display: inline-block');\n", "\n", " $(parent_element).append(this.root);\n", "\n", " this._init_header(this);\n", " this._init_canvas(this);\n", " this._init_toolbar(this);\n", "\n", " var fig = this;\n", "\n", " this.waiting = false;\n", "\n", " this.ws.onopen = function () {\n", " fig.send_message(\"supports_binary\", {value: fig.supports_binary});\n", " fig.send_message(\"send_image_mode\", {});\n", " if (mpl.ratio != 1) {\n", " fig.send_message(\"set_dpi_ratio\", {'dpi_ratio': mpl.ratio});\n", " }\n", " fig.send_message(\"refresh\", {});\n", " }\n", "\n", " this.imageObj.onload = function() {\n", " if (fig.image_mode == 'full') {\n", " // Full images could contain transparency (where diff images\n", " // almost always do), so we need to clear the canvas so that\n", " // there is no ghosting.\n", " fig.context.clearRect(0, 0, fig.canvas.width, fig.canvas.height);\n", " }\n", " fig.context.drawImage(fig.imageObj, 0, 0);\n", " };\n", "\n", " this.imageObj.onunload = function() {\n", " fig.ws.close();\n", " }\n", "\n", " this.ws.onmessage = this._make_on_message_function(this);\n", "\n", " this.ondownload = ondownload;\n", "}\n", "\n", "mpl.figure.prototype._init_header = function() {\n", " var titlebar = $(\n", " '
');\n", " var titletext = $(\n", " '
');\n", " titlebar.append(titletext)\n", " this.root.append(titlebar);\n", " this.header = titletext[0];\n", "}\n", "\n", "\n", "\n", "mpl.figure.prototype._canvas_extra_style = function(canvas_div) {\n", "\n", "}\n", "\n", "\n", "mpl.figure.prototype._root_extra_style = function(canvas_div) {\n", "\n", "}\n", "\n", "mpl.figure.prototype._init_canvas = function() {\n", " var fig = this;\n", "\n", " var canvas_div = $('
');\n", "\n", " canvas_div.attr('style', 'position: relative; clear: both; outline: 0');\n", "\n", " function canvas_keyboard_event(event) {\n", " return fig.key_event(event, event['data']);\n", " }\n", "\n", " canvas_div.keydown('key_press', canvas_keyboard_event);\n", " canvas_div.keyup('key_release', canvas_keyboard_event);\n", " this.canvas_div = canvas_div\n", " this._canvas_extra_style(canvas_div)\n", " this.root.append(canvas_div);\n", "\n", " var canvas = $('');\n", " canvas.addClass('mpl-canvas');\n", " canvas.attr('style', \"left: 0; top: 0; z-index: 0; outline: 0\")\n", "\n", " this.canvas = canvas[0];\n", " this.context = canvas[0].getContext(\"2d\");\n", "\n", " var backingStore = this.context.backingStorePixelRatio ||\n", "\tthis.context.webkitBackingStorePixelRatio ||\n", "\tthis.context.mozBackingStorePixelRatio ||\n", "\tthis.context.msBackingStorePixelRatio ||\n", "\tthis.context.oBackingStorePixelRatio ||\n", "\tthis.context.backingStorePixelRatio || 1;\n", "\n", " mpl.ratio = (window.devicePixelRatio || 1) / backingStore;\n", "\n", " var rubberband = $('');\n", " rubberband.attr('style', \"position: absolute; left: 0; top: 0; z-index: 1;\")\n", "\n", " var pass_mouse_events = true;\n", "\n", " canvas_div.resizable({\n", " start: function(event, ui) {\n", " pass_mouse_events = false;\n", " },\n", " resize: function(event, ui) {\n", " fig.request_resize(ui.size.width, ui.size.height);\n", " },\n", " stop: function(event, ui) {\n", " pass_mouse_events = true;\n", " fig.request_resize(ui.size.width, ui.size.height);\n", " },\n", " });\n", "\n", " function mouse_event_fn(event) {\n", " if (pass_mouse_events)\n", " return fig.mouse_event(event, event['data']);\n", " }\n", "\n", " rubberband.mousedown('button_press', mouse_event_fn);\n", " rubberband.mouseup('button_release', mouse_event_fn);\n", " // Throttle sequential mouse events to 1 every 20ms.\n", " rubberband.mousemove('motion_notify', mouse_event_fn);\n", "\n", " rubberband.mouseenter('figure_enter', mouse_event_fn);\n", " rubberband.mouseleave('figure_leave', mouse_event_fn);\n", "\n", " canvas_div.on(\"wheel\", function (event) {\n", " event = event.originalEvent;\n", " event['data'] = 'scroll'\n", " if (event.deltaY < 0) {\n", " event.step = 1;\n", " } else {\n", " event.step = -1;\n", " }\n", " mouse_event_fn(event);\n", " });\n", "\n", " canvas_div.append(canvas);\n", " canvas_div.append(rubberband);\n", "\n", " this.rubberband = rubberband;\n", " this.rubberband_canvas = rubberband[0];\n", " this.rubberband_context = rubberband[0].getContext(\"2d\");\n", " this.rubberband_context.strokeStyle = \"#000000\";\n", "\n", " this._resize_canvas = function(width, height) {\n", " // Keep the size of the canvas, canvas container, and rubber band\n", " // canvas in synch.\n", " canvas_div.css('width', width)\n", " canvas_div.css('height', height)\n", "\n", " canvas.attr('width', width * mpl.ratio);\n", " canvas.attr('height', height * mpl.ratio);\n", " canvas.attr('style', 'width: ' + width + 'px; 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.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", " // 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", "\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= 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('matplotlib', mpl.mpl_figure_comm);\n", "}\n" ], "text/plain": [ "" ] }, "metadata": {}, "output_type": "display_data" }, { "data": { "text/html": [ "" ], "text/plain": [ "" ] }, "metadata": {}, "output_type": "display_data" }, { "name": "stdout", "output_type": "stream", "text": [ "2020-08-28 13:20:49.824270: Comment: plotting event overlay of chnl1\n" ] } ], "source": [ "res_hdf_loc = analydir + respd.index[11]\n", "print(res_hdf_loc)\n", "\n", "\n", "fig, ax = plt.subplots(ncols = 1, nrows = 1, figsize = cmtoinch(5.0,6.0))\n", "ovdict = {'chnl':'chnl1', 'ax':ax, 't_before':0.001, 't_after':0.001,\n", " 'stage':'hsnr', 'binning':0.00001, 'amnt':2000, 'avcol':TUD_orange}\n", "plotted = plot_event_overlay(res_hdf_loc, ovdict)\n", "ax.set_xlim(left = -0.5, right=1)\n", "\n", "#ax.text(0.18, 1100, 'Individual Events', fontdict={'color':TUD_purple})\n", "#ax.text(0.18, 1000, 'Average')\n", "\n", "\n", "ax.set_ylim(bottom=0, top=1000)\n", "ax.set_title('')\n", "ax.get_legend().remove()\n", "ax.set_xticks([0, 0.5, 1])\n", "ax.set_yticks([0, 500, 1000])\n", "\n", "fig.tight_layout()\n", "#fig.savefig('fig_4_1kb_overlay.svg')\n", "fig.savefig('fig_4_50bp_overlay.png', dpi=600)" ] }, { "cell_type": "code", "execution_count": 25, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "/home/nils/Dokumente/Promotion/Inhaltliches/Analyses/R9_1104/R9_1104_18/2020_05_11_R9_1104_18_short_DNA.sptw/Results/DK_1000bp_100mV_1_results.hdf5\n" ] }, { "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. ' +\n", " 'Firefox 4 and 5 are also supported but you ' +\n", " 'have to enable WebSockets in about:config.');\n", " };\n", "}\n", "\n", "mpl.figure = function(figure_id, websocket, ondownload, parent_element) {\n", " this.id = figure_id;\n", "\n", " this.ws = websocket;\n", "\n", " this.supports_binary = (this.ws.binaryType != undefined);\n", "\n", " if (!this.supports_binary) {\n", " var warnings = document.getElementById(\"mpl-warnings\");\n", " if (warnings) {\n", " warnings.style.display = 'block';\n", " warnings.textContent = (\n", " \"This browser does not support binary websocket messages. \" +\n", " \"Performance may be slow.\");\n", " }\n", " }\n", "\n", " this.imageObj = new Image();\n", "\n", " this.context = undefined;\n", " this.message = undefined;\n", " this.canvas = undefined;\n", " this.rubberband_canvas = undefined;\n", " this.rubberband_context = undefined;\n", " this.format_dropdown = undefined;\n", "\n", " this.image_mode = 'full';\n", "\n", " this.root = $('
');\n", " this._root_extra_style(this.root)\n", " this.root.attr('style', 'display: inline-block');\n", "\n", " $(parent_element).append(this.root);\n", "\n", " this._init_header(this);\n", " this._init_canvas(this);\n", " this._init_toolbar(this);\n", "\n", " var fig = this;\n", "\n", " this.waiting = false;\n", "\n", " this.ws.onopen = function () {\n", " fig.send_message(\"supports_binary\", {value: fig.supports_binary});\n", " fig.send_message(\"send_image_mode\", {});\n", " if (mpl.ratio != 1) {\n", " fig.send_message(\"set_dpi_ratio\", {'dpi_ratio': mpl.ratio});\n", " }\n", " fig.send_message(\"refresh\", {});\n", " }\n", "\n", " this.imageObj.onload = function() {\n", " if (fig.image_mode == 'full') {\n", " // Full images could contain transparency (where diff images\n", " // almost always do), so we need to clear the canvas so that\n", " // there is no ghosting.\n", " fig.context.clearRect(0, 0, fig.canvas.width, fig.canvas.height);\n", " }\n", " fig.context.drawImage(fig.imageObj, 0, 0);\n", " };\n", "\n", " this.imageObj.onunload = function() {\n", " fig.ws.close();\n", " }\n", "\n", " this.ws.onmessage = this._make_on_message_function(this);\n", "\n", " this.ondownload = ondownload;\n", "}\n", "\n", "mpl.figure.prototype._init_header = function() {\n", " var titlebar = $(\n", " '
');\n", " var titletext = $(\n", " '
');\n", " titlebar.append(titletext)\n", " this.root.append(titlebar);\n", " this.header = titletext[0];\n", "}\n", "\n", "\n", "\n", "mpl.figure.prototype._canvas_extra_style = function(canvas_div) {\n", "\n", "}\n", "\n", "\n", "mpl.figure.prototype._root_extra_style = function(canvas_div) {\n", "\n", "}\n", "\n", "mpl.figure.prototype._init_canvas = function() {\n", " var fig = this;\n", "\n", " var canvas_div = $('
');\n", "\n", " canvas_div.attr('style', 'position: relative; clear: both; outline: 0');\n", "\n", " function canvas_keyboard_event(event) {\n", " return fig.key_event(event, event['data']);\n", " }\n", "\n", " canvas_div.keydown('key_press', canvas_keyboard_event);\n", " canvas_div.keyup('key_release', canvas_keyboard_event);\n", " this.canvas_div = canvas_div\n", " this._canvas_extra_style(canvas_div)\n", " this.root.append(canvas_div);\n", "\n", " var canvas = $('');\n", " canvas.addClass('mpl-canvas');\n", " canvas.attr('style', \"left: 0; top: 0; z-index: 0; outline: 0\")\n", "\n", " this.canvas = canvas[0];\n", " this.context = canvas[0].getContext(\"2d\");\n", "\n", " var backingStore = this.context.backingStorePixelRatio ||\n", "\tthis.context.webkitBackingStorePixelRatio ||\n", "\tthis.context.mozBackingStorePixelRatio ||\n", "\tthis.context.msBackingStorePixelRatio ||\n", "\tthis.context.oBackingStorePixelRatio ||\n", "\tthis.context.backingStorePixelRatio || 1;\n", "\n", " mpl.ratio = (window.devicePixelRatio || 1) / backingStore;\n", "\n", " var rubberband = $('');\n", " rubberband.attr('style', \"position: absolute; left: 0; top: 0; z-index: 1;\")\n", "\n", " var pass_mouse_events = true;\n", "\n", " canvas_div.resizable({\n", " start: function(event, ui) {\n", " pass_mouse_events = false;\n", " },\n", " resize: function(event, ui) {\n", " fig.request_resize(ui.size.width, ui.size.height);\n", " },\n", " stop: function(event, ui) {\n", " pass_mouse_events = true;\n", " fig.request_resize(ui.size.width, ui.size.height);\n", " },\n", " });\n", "\n", " function mouse_event_fn(event) {\n", " if (pass_mouse_events)\n", " return fig.mouse_event(event, event['data']);\n", " }\n", "\n", " rubberband.mousedown('button_press', mouse_event_fn);\n", " rubberband.mouseup('button_release', mouse_event_fn);\n", " // Throttle sequential mouse events to 1 every 20ms.\n", " rubberband.mousemove('motion_notify', mouse_event_fn);\n", "\n", " rubberband.mouseenter('figure_enter', mouse_event_fn);\n", " rubberband.mouseleave('figure_leave', mouse_event_fn);\n", "\n", " canvas_div.on(\"wheel\", function (event) {\n", " event = event.originalEvent;\n", " event['data'] = 'scroll'\n", " if (event.deltaY < 0) {\n", " event.step = 1;\n", " } else {\n", " event.step = -1;\n", " }\n", " mouse_event_fn(event);\n", " });\n", "\n", " canvas_div.append(canvas);\n", " canvas_div.append(rubberband);\n", "\n", " this.rubberband = rubberband;\n", " this.rubberband_canvas = rubberband[0];\n", " this.rubberband_context = rubberband[0].getContext(\"2d\");\n", " this.rubberband_context.strokeStyle = \"#000000\";\n", "\n", " this._resize_canvas = function(width, height) {\n", " // Keep the size of the canvas, canvas container, and rubber band\n", " // canvas in synch.\n", " canvas_div.css('width', width)\n", " canvas_div.css('height', height)\n", "\n", " canvas.attr('width', width * mpl.ratio);\n", " canvas.attr('height', height * mpl.ratio);\n", " canvas.attr('style', 'width: ' + width + 'px; 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.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", " // 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", "\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= 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('matplotlib', mpl.mpl_figure_comm);\n", "}\n" ], "text/plain": [ "" ] }, "metadata": {}, "output_type": "display_data" }, { "data": { "text/html": [ "" ], "text/plain": [ "" ] }, "metadata": {}, "output_type": "display_data" } ], "source": [ "fig, ax = plt.subplots(nrows = 1, figsize = cmtoinch((6,6)))\n", "\n", "evst_dict = {'chnl':'chnl1', 'stages':['hsnr'], 'ax':ax, 'what':'photon', 'fig':fig, 'threshold':True}\n", "chnl = evst_dict['chnl']\n", "stage = evst_dict['stages'][0]\n", "state = 2\n", "\n", "res_hdf_loc = analydir + respd.index[25]\n", "results_hdf = h5py.File(res_hdf_loc, \"a\")\n", "runstr = 'run_%s'%results_hdf['amnt_runs'][...]\n", "rungrp = results_hdf['run_%s'%results_hdf['amnt_runs'][...]]\n", "\n", "spkgrp = rungrp[chnl]['spikes']\n", "states = spkgrp['states_' + stage][()].astype(int)\n", "scatter_xs = spkgrp['eventdurations_' + stage][states[:,2] == state] * 1000\n", "plt_lengths = spkgrp['eventphots_' + stage][states[:,2] == state]\n", "ax.scatter(scatter_xs, plt_lengths, facecolors='none', alpha=0.1, edgecolors=TUD_grey, s=10)\n", "\n", "\n", "res_hdf_loc = analydir + respd.index[11]\n", "results_hdf = h5py.File(res_hdf_loc, \"a\")\n", "runstr = 'run_%s'%results_hdf['amnt_runs'][...]\n", "rungrp = results_hdf['run_%s'%results_hdf['amnt_runs'][...]]\n", "\n", "spkgrp = rungrp[chnl]['spikes']\n", "states = spkgrp['states_' + stage][()].astype(int)\n", "scatter_xs = spkgrp['eventdurations_' + stage][states[:,2] == state] * 1000\n", "plt_lengths = spkgrp['eventphots_' + stage][states[:,2] == state]\n", "ax.scatter(scatter_xs, plt_lengths, facecolors='none', alpha=0.1, edgecolors=TUD_purple, s=10)\n", "\n", "\n", "ax.set_ylabel('Number of photons')\n", "ax.set_xlabel('Duration (ms)')\n", "ax.tick_params(right=True, top=True, which='both', direction='in')\n", "x = np.linspace(0, 0.015, num=1000)\n", "ax.plot(x * 1000., sort_fct(x,rungrp[chnl]['background_rate']) , '--', c='k', lw=1)\n", "ax.set_ylim(0,2500)\n", "ax.set_xlim(0, 5)\n", "ax.set_xticks((0,2.5,5))\n", "ax.set_yticks([0, 1000, 2000])\n", "fig.tight_layout()\n", "fig.savefig('fig_4_scatter.png', dpi=600, transparent=True)" ] } ], "metadata": { "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": "3.7.3" } }, "nbformat": 4, "nbformat_minor": 4 }