diff --git a/README.rst b/README.rst index 25c7dae..ab15cbb 100644 --- a/README.rst +++ b/README.rst @@ -18,7 +18,9 @@ OpenBadge Analysis :alt: Updates -Python libraries for analysing OpenBadge data +Python libraries for analysing OpenBadge data. See examples in the `examples repository`_ + +.. _examples repository: https://github.com/HumanDynamics/openbadge-analysis-examples * Free software: MIT license diff --git a/examples/misc/999.0-ol-check_gaps2-old.ipynb b/examples/misc/999.0-ol-check_gaps2-old.ipynb deleted file mode 100644 index fcf53e5..0000000 --- a/examples/misc/999.0-ol-check_gaps2-old.ipynb +++ /dev/null @@ -1,2590 +0,0 @@ -{ - "cells": [ - { - "cell_type": "code", - "execution_count": 1, - "metadata": { - "collapsed": false - }, - "outputs": [ - { - "data": { - "text/html": [ - "\n", - "
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i < inline_js.length; i++) {\n", - " inline_js[i](window.Bokeh);\n", - " }\n", - " }\n", - "\n", - " if (window._bokeh_is_loading === 0) {\n", - " console.log(\"Bokeh: BokehJS loaded, going straight to plotting\");\n", - " run_inline_js();\n", - " } else {\n", - " load_libs(js_urls, function() {\n", - " console.log(\"Bokeh: BokehJS plotting callback run at\", now());\n", - " run_inline_js();\n", - " });\n", - " }\n", - "}(this));" - ] - }, - "metadata": {}, - "output_type": "display_data" - } - ], - "source": [ - "from data_loader2 import *\n", - "from __future__ import division\n", - "from __future__ import print_function\n", - "import pandas as pd\n", - "import bokeh\n", - "import numpy as np\n", - "\n", - "import bokeh.plotting as bp\n", - "from bokeh.plotting import figure, output_file, show,gridplot\n", - "from bokeh.models.formatters import DatetimeTickFormatter\n", - "from bokeh.models.axes import DatetimeAxis\n", - "\n", - "from datetime import datetime\n", - "from datetime import timedelta\n", - "\n", - "import pandas as pd\n", - "\n", - "bp.output_notebook()" - ] - }, - { - "cell_type": "code", - "execution_count": 15, - "metadata": { - "collapsed": false - }, - "outputs": [], - "source": [ - "#data = DataLoader('bat_data/E6_AA_91_B9_BF_48.scn.3') #\n", - "data = DataLoader('bat_data/D2_3C_F6_B9_87_24.scn.3') #" - ] - }, - { - "cell_type": "code", - "execution_count": 16, - "metadata": { - "collapsed": false - }, - "outputs": [], - "source": [ - "freq = data.data[0]['Frequency'] #assuming same freq. for all samples" - ] - }, - { - "cell_type": "code", - "execution_count": 17, - "metadata": { - "collapsed": false - }, - "outputs": [], - "source": [ - "# take only samples\n", - "signals = map(lambda x: x['samples'], data.data)\n", - "\n", - "# convert \n", - "con_signals = [map(lambda x: {\"datetime\": x[\"time\"], \"signal\": x['signal']}, i) for i in signals]\n", - "#con_signals[0]\n", - "\n", - "# Append all samples into an array\n", - "singals_all = []\n", - "for s in con_signals:\n", - " if len(s) == 114: #only load full chunks\n", - " singals_all.extend(s)\n", - " \n", - "# sort\n", - "sdata = sorted(singals_all, key=lambda x: x['datetime'])" - ] - }, - { - "cell_type": "code", - "execution_count": 18, - "metadata": { - "collapsed": false - }, - "outputs": [], - "source": [ - "#signals[2]" - ] - }, - { - "cell_type": "markdown", - "metadata": {}, - "source": [ - "# Check for gaps in data (before loading into pandas. It's faster)" - ] - }, - { - "cell_type": "code", - "execution_count": 19, - "metadata": { - "collapsed": true - }, - "outputs": [], - "source": [ - "def check_raw_gaps(arr, max_delta_sec = 250):\n", - " #max_diff = np.timedelta64(max_delta_sec, 's')\n", - " max_diff = timedelta(milliseconds=max_delta_sec);\n", - " prev = None\n", - " for i in range (0,len(arr)): # iterate over all lines\n", - " #print df.iloc[i].datetime\n", - " curr = arr[i]['datetime']\n", - " if (prev):\n", - " diff = curr-prev\n", - " if diff > max_diff:\n", - " print (\"{},{},{}\".format(curr,prev,diff))\n", - " prev = curr\n" - ] - }, - { - "cell_type": "code", - "execution_count": 20, - "metadata": { - "collapsed": false - }, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "2016-06-02 20:34:52.943000,2016-06-02 20:34:52.828000,0:00:00.115000\n", - "2016-06-03 00:32:23.628000,2016-06-03 00:32:23.506000,0:00:00.122000\n", - "2016-06-03 01:27:12.685000,2016-06-03 01:27:12.570000,0:00:00.115000\n", - "2016-06-03 02:45:41.114000,2016-06-03 02:45:40.992000,0:00:00.122000\n", - "2016-06-03 03:01:04.559000,2016-06-03 03:01:04.440000,0:00:00.119000\n", - "2016-06-03 14:49:20.132000,2016-06-03 14:49:20.012000,0:00:00.120000\n", - "2016-06-03 14:52:45.341000,2016-06-03 14:52:45.220000,0:00:00.121000\n" - ] - } - ], - "source": [ - "check_raw_gaps(sdata,70)" - ] - }, - { - "cell_type": "markdown", - "metadata": {}, - "source": [ - "# look at chunk dates" - ] - }, - { - "cell_type": "code", - "execution_count": 21, - "metadata": { - "collapsed": false - }, - "outputs": [], - "source": [ - "#data.data[3]" - ] - }, - { - "cell_type": "code", - "execution_count": 22, - "metadata": { - "collapsed": false - }, - "outputs": [], - "source": [ - "# take only chunk dates\n", - "dates = map(lambda x: x['Intial_dtime'], data.data)\n", - "sdates = sorted(dates)" - ] - }, - { - "cell_type": "code", - "execution_count": 23, - "metadata": { - "collapsed": false - }, - "outputs": [ - { - "data": { - "text/plain": [ - "datetime.datetime(2016, 6, 2, 18, 45, 31, 920000)" - ] - }, - "execution_count": 23, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [ - "sdates[0]" - ] - }, - { - "cell_type": "code", - "execution_count": 24, - "metadata": { - "collapsed": false - }, - "outputs": [], - "source": [ - "def check_raw_gaps_chunks(arr, max_delta_sec = 250):\n", - " max_diff = timedelta(milliseconds=max_delta_sec);\n", - " prev = None\n", - " for i in range (0,len(arr)): # iterate over all lines\n", - " #print df.iloc[i].datetime\n", - " curr = arr[i]\n", - " if (prev):\n", - " diff = curr-prev\n", - " if diff > max_diff:\n", - " print (\"{},{},{}\".format(curr,prev,diff))\n", - " #break\n", - " prev = curr\n", - " \n" - ] - }, - { - "cell_type": "code", - "execution_count": 25, - "metadata": { - "collapsed": false - }, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "2016-06-02 18:45:54.728000,2016-06-02 18:45:49.020000,0:00:05.708000\n", - "2016-06-02 18:46:17.529000,2016-06-02 18:46:11.828000,0:00:05.701000\n", - 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"source": [ - "ms_between = 50*114\n", - "check_raw_gaps_chunks(sdates,ms_between)" - ] - }, - { - "cell_type": "code", - "execution_count": 26, - "metadata": { - "collapsed": false - }, - "outputs": [ - { - "data": { - "text/plain": [ - "datetime.timedelta(0, 5, 700000)" - ] - }, - "execution_count": 26, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [ - "timedelta(milliseconds=ms_between)" - ] - }, - { - "cell_type": "code", - "execution_count": null, - "metadata": { - "collapsed": true - }, - "outputs": [], - "source": [] - }, - { - "cell_type": "code", - "execution_count": null, - "metadata": { - "collapsed": true - }, - "outputs": [], - "source": [] - } - ], - "metadata": { - "kernelspec": { - "display_name": "Python 2", - "language": "python", - "name": "python2" - }, - "language_info": { - "codemirror_mode": { - "name": "ipython", - "version": 2 - }, - "file_extension": ".py", - "mimetype": "text/x-python", - "name": "python", - "nbconvert_exporter": "python", - "pygments_lexer": "ipython2", - "version": "2.7.6" - } - }, - "nbformat": 4, - "nbformat_minor": 0 -} diff --git a/examples/misc/show_sample_meeting.ipynb b/examples/misc/show_sample_meeting.ipynb deleted file mode 100644 index 0255337..0000000 --- a/examples/misc/show_sample_meeting.ipynb +++ /dev/null @@ -1,496 +0,0 @@ -{ - "cells": [ - { - "cell_type": "code", - "execution_count": 1, - "metadata": { - "collapsed": false - }, - "outputs": [], - "source": [ - "import os\n", - "import sys\n", - "import datetime\n", - "import ast\n", - "import pandas\n", - "\n", - "from bokeh.io import output_notebook\n", - "from bokeh.charts import show\n", - "\n", - "# add the 'src' directory as one where we can import modules\n", - "src_dir = os.path.join(os.getcwd(), os.pardir, os.pardir)\n", - "sys.path.append(src_dir)\n", - "\n", - "# import data analysis modules\n", - "import openbadge_analysis as ob\n", - "import openbadge_analysis.visualization.contribution as contribution\n", - "import openbadge_analysis.visualization.participation as participation\n", - "import openbadge_analysis.visualization.participation_interactive as participation_interactive" - ] - }, - { - "cell_type": "code", - "execution_count": 2, - "metadata": { - "collapsed": false - }, - "outputs": [ - { - "data": { - "text/html": [ - "\n", - " " - ] - }, - "metadata": {}, - "output_type": "display_data" - }, - { - "data": { - "application/javascript": [ - "\n", - "(function(global) {\n", - " function now() {\n", - " return new Date();\n", - " }\n", - "\n", - " var force = \"1\";\n", - "\n", - " if (typeof (window._bokeh_onload_callbacks) === \"undefined\" || force !== \"\") {\n", - " window._bokeh_onload_callbacks = [];\n", - " window._bokeh_is_loading = undefined;\n", - " }\n", - "\n", - " function run_callbacks() {\n", - " window._bokeh_onload_callbacks.forEach(function(callback) { callback() });\n", - " delete window._bokeh_onload_callbacks\n", - " console.info(\"Bokeh: all callbacks have finished\");\n", - " }\n", - "\n", - " function load_libs(js_urls, callback) {\n", - " window._bokeh_onload_callbacks.push(callback);\n", - " if (window._bokeh_is_loading > 0) {\n", - " console.log(\"Bokeh: BokehJS is being loaded, scheduling callback at\", now());\n", - " return null;\n", - " }\n", - " if (js_urls == null || js_urls.length === 0) {\n", - " run_callbacks();\n", - " return null;\n", - " }\n", - " console.log(\"Bokeh: BokehJS not loaded, scheduling load and callback at\", now());\n", - " window._bokeh_is_loading = js_urls.length;\n", - " for (var i = 0; i < js_urls.length; i++) {\n", - " var url = js_urls[i];\n", - " var s = document.createElement('script');\n", - " s.src = url;\n", - " s.async = false;\n", - " s.onreadystatechange = s.onload = function() {\n", - " window._bokeh_is_loading--;\n", - " if (window._bokeh_is_loading === 0) {\n", - " console.log(\"Bokeh: all BokehJS libraries loaded\");\n", - " run_callbacks()\n", - " }\n", - " };\n", - " s.onerror = function() {\n", - " console.warn(\"failed to load library \" + url);\n", - " };\n", - " console.log(\"Bokeh: injecting script tag for BokehJS library: \", url);\n", - " document.getElementsByTagName(\"head\")[0].appendChild(s);\n", - " }\n", - " };\n", - "\n", - " var js_urls = ['https://cdn.pydata.org/bokeh/release/bokeh-0.12.1.min.js', 'https://cdn.pydata.org/bokeh/release/bokeh-widgets-0.12.1.min.js', 'https://cdn.pydata.org/bokeh/release/bokeh-compiler-0.12.1.min.js'];\n", - "\n", - " var inline_js = [\n", - " function(Bokeh) {\n", - " Bokeh.set_log_level(\"info\");\n", - " },\n", - " \n", - " function(Bokeh) {\n", - " \n", - " Bokeh.$(\"#d6414074-739d-4172-8388-b5dffe2cd344\").text(\"BokehJS successfully loaded\");\n", - " var kernel = Jupyter.notebook.kernel\n", - " if (kernel.execute !== undefined) {\n", - " kernel.execute(\"import bokeh.io; bokeh.io._nb_loaded = True\");\n", - " }\n", - " },\n", - " function(Bokeh) {\n", - " console.log(\"Bokeh: injecting CSS: https://cdn.pydata.org/bokeh/release/bokeh-0.12.1.min.css\");\n", - " Bokeh.embed.inject_css(\"https://cdn.pydata.org/bokeh/release/bokeh-0.12.1.min.css\");\n", - " console.log(\"Bokeh: injecting CSS: https://cdn.pydata.org/bokeh/release/bokeh-widgets-0.12.1.min.css\");\n", - " Bokeh.embed.inject_css(\"https://cdn.pydata.org/bokeh/release/bokeh-widgets-0.12.1.min.css\");\n", - " }\n", - " ];\n", - "\n", - " function run_inline_js() {\n", - " for (var i = 0; i < inline_js.length; i++) {\n", - " inline_js[i](window.Bokeh);\n", - " }\n", - " }\n", - "\n", - " if (window._bokeh_is_loading === 0) {\n", - " console.log(\"Bokeh: BokehJS loaded, going straight to plotting\");\n", - " run_inline_js();\n", - " } else {\n", - " load_libs(js_urls, function() {\n", - " console.log(\"Bokeh: BokehJS plotting callback run at\", now());\n", - " run_inline_js();\n", - " });\n", - " }\n", - "}(this));" - ] - }, - "metadata": {}, - "output_type": "display_data" - } - ], - "source": [ - "output_notebook()" - ] - }, - { - "cell_type": "code", - "execution_count": 3, - "metadata": { - "collapsed": false - }, - "outputs": [], - "source": [ - "# Load the \"autoreload\" extension\n", - "%load_ext autoreload\n", - "# always reload modules marked with \"%aimport\"\n", - "%autoreload 1\n", - "# list of modules to autoload\n", - "%aimport openbadge_analysis\n", - "%aimport openbadge_analysis.visualization.contribution\n", - "%aimport openbadge_analysis.visualization.participation\n", - "%aimport openbadge_analysis.visualization.participation_interactive" - ] - }, - { - "cell_type": "code", - "execution_count": 4, - "metadata": { - "collapsed": true - }, - "outputs": [], - "source": [ - "log_file_path = '../sample_data/sample_meeting.txt'\n", - "member_names = {\n", - " 'B7H6NPMKQT': 'Brittany',\n", - " '8JB8GZYFVW': 'Shirley',\n", - " 'TYCN86EZ5F': 'Don',\n", - " 'TZPQ1AKVD2': 'Aaron',\n", - " '9LLE6DZUPU': 'Alexander',\n", - " 'QNT3BBQ0X1': 'Otto'\n", - "}\n", - "\n", - "meeting_name = \"Sample\"" - ] - }, - { - "cell_type": "code", - "execution_count": 9, - "metadata": { - "collapsed": false - }, - "outputs": [], - "source": [ - "# Read data\n", - "df_meeting = ob.sample2data(log_file_path)\n", - "\n", - "# Create speaking intervals\n", - "df_stitched = ob.make_df_stitched(df_meeting) # Data for speaking intervals" - ] - }, - { - "cell_type": "code", - "execution_count": 10, - "metadata": { - "collapsed": false - }, - "outputs": [ - { - "data": { - "text/html": [ - "\n", - "\n", - "<Bokeh Notebook handle for In[10]>
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2017-01-17 03:49:59-05:00 | \n", - "2017-01-17 03:49:59-05:00 | \n", - "C7:59:BE:8B:9C:E0 | \n", - "1.484643e+09 | \n", - "1.484643e+09 | \n", - "120.0 | \n", - "|
2017-01-17 03:52:59-05:00 | \n", - "2017-01-17 03:52:59-05:00 | \n", - "C7:59:BE:8B:9C:E0 | \n", - "1.484643e+09 | \n", - "1.484643e+09 | \n", - "120.0 | \n", - "|
2017-01-17 04:14:59-05:00 | \n", - "2017-01-17 04:14:59-05:00 | \n", - "C7:59:BE:8B:9C:E0 | \n", - "1.484644e+09 | \n", - "1.484643e+09 | \n", - "1320.0 | \n", - "|
2017-01-17 04:38:59-05:00 | \n", - "2017-01-17 04:38:59-05:00 | \n", - "C7:59:BE:8B:9C:E0 | \n", - "1.484646e+09 | \n", - "1.484644e+09 | \n", - "1440.0 | \n", - "|
2017-01-17 04:45:59-05:00 | \n", - "2017-01-17 04:45:59-05:00 | \n", - "C7:59:BE:8B:9C:E0 | \n", - "1.484646e+09 | \n", - "1.484646e+09 | \n", - "420.0 | \n", - "|
2017-01-17 04:55:59-05:00 | \n", - "2017-01-17 04:55:59-05:00 | \n", - "C7:59:BE:8B:9C:E0 | \n", - "1.484647e+09 | \n", - "1.484646e+09 | \n", - "540.0 | \n", - "|
C7:75:13:05:10:EE | \n", - "2017-01-15 22:12:54-05:00 | \n", - "2017-01-15 22:12:54-05:00 | \n", - "C7:75:13:05:10:EE | \n", - "1.484536e+09 | \n", - "1.484536e+09 | \n", - "120.0 | \n", - "
D8:A1:84:25:FF:B7 | \n", - "2017-01-17 00:05:11-05:00 | \n", - "2017-01-17 00:05:11-05:00 | \n", - "D8:A1:84:25:FF:B7 | \n", - "1.484630e+09 | \n", - "1.484629e+09 | \n", - "360.0 | \n", - "
2017-01-17 00:12:11-05:00 | \n", - "2017-01-17 00:12:11-05:00 | \n", - "D8:A1:84:25:FF:B7 | \n", - "1.484630e+09 | \n", - "1.484630e+09 | \n", - "300.0 | \n", - "|
2017-01-17 00:14:11-05:00 | \n", - "2017-01-17 00:14:11-05:00 | \n", - "D8:A1:84:25:FF:B7 | \n", - "1.484630e+09 | \n", - "1.484630e+09 | \n", - "120.0 | \n", - "|
2017-01-17 00:20:11-05:00 | \n", - "2017-01-17 00:20:11-05:00 | \n", - "D8:A1:84:25:FF:B7 | \n", - "1.484630e+09 | \n", - "1.484630e+09 | \n", - "300.0 | \n", - "|
2017-01-17 00:22:11-05:00 | \n", - "2017-01-17 00:22:11-05:00 | \n", - "D8:A1:84:25:FF:B7 | \n", - "1.484631e+09 | \n", - "1.484630e+09 | \n", - "120.0 | \n", - "|
2017-01-17 00:31:11-05:00 | \n", - "2017-01-17 00:31:11-05:00 | \n", - "D8:A1:84:25:FF:B7 | \n", - "1.484631e+09 | \n", - "1.484631e+09 | \n", - "480.0 | \n", - "|
2017-01-17 00:36:11-05:00 | \n", - "2017-01-17 00:36:11-05:00 | \n", - "D8:A1:84:25:FF:B7 | \n", - "1.484631e+09 | \n", - "1.484631e+09 | \n", - "300.0 | \n", - "|
2017-01-17 00:55:11-05:00 | \n", - "2017-01-17 00:55:11-05:00 | \n", - "D8:A1:84:25:FF:B7 | \n", - "1.484633e+09 | \n", - "1.484631e+09 | \n", - "1140.0 | \n", - "|
2017-01-17 01:10:11-05:00 | \n", - "2017-01-17 01:10:11-05:00 | \n", - "D8:A1:84:25:FF:B7 | \n", - "1.484633e+09 | \n", - "1.484633e+09 | \n", - "900.0 | \n", - "|
2017-01-17 01:13:11-05:00 | \n", - "2017-01-17 01:13:11-05:00 | \n", - "D8:A1:84:25:FF:B7 | \n", - "1.484634e+09 | \n", - "1.484633e+09 | \n", - "180.0 | \n", - "
\n", - " | badge_address | \n", - "first_datetime | \n", - "
---|---|---|
0 | \n", - "C7:59:BE:8B:9C:E0 | \n", - "2017-01-10 16:03:35-05:00 | \n", - "
1 | \n", - "C7:75:13:05:10:EE | \n", - "2017-01-10 16:03:35-05:00 | \n", - "
2 | \n", - "D4:E4:47:A5:F0:B3 | \n", - "2017-01-10 16:03:45-05:00 | \n", - "
3 | \n", - "D8:A1:84:25:FF:B7 | \n", - "2017-01-10 16:03:45-05:00 | \n", - "
4 | \n", - "F2:37:E3:BA:70:9D | \n", - "2017-01-10 16:03:40-05:00 | \n", - "
<Bokeh Notebook handle for In[10]>
<Bokeh Notebook handle for In[11]>