Mercurial Hosting > traffic-intelligence
annotate scripts/process.py @ 1128:e5c43496d9d8 Etienne-Beauchamp/added-d-optional-argument-1581358671588
added -d optional argument
author | Etienne Beauchamp <etienne-2.beauchamp@polymtl.ca> |
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date | Mon, 10 Feb 2020 18:18:10 +0000 |
parents | 8734742c08c0 |
children | b968c33f8c2f |
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1 #! /usr/bin/env python3 |
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2 |
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3 import sys, argparse |
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4 from pathlib import Path |
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5 from multiprocessing.pool import Pool |
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6 |
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7 #import matplotlib |
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8 #atplotlib.use('Agg') |
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9 import matplotlib.pyplot as plt |
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10 import numpy as np |
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11 import pandas as pd |
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12 |
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13 from trafficintelligence import storage, events, prediction, cvutils, utils, moving, processing, ml |
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14 from trafficintelligence.metadata import * |
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16 parser = argparse.ArgumentParser(description='This program manages the processing of several files based on a description of the sites and video data in an SQLite database following the metadata module.') |
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17 # input |
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18 parser.add_argument('--db', dest = 'metadataFilename', help = 'name of the metadata file', required = True) |
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19 parser.add_argument('--videos', dest = 'videoIds', help = 'indices of the video sequences', nargs = '*') |
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20 parser.add_argument('--sites', dest = 'siteIds', help = 'indices of the video sequences', nargs = '*') |
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21 |
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22 # main function |
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23 parser.add_argument('--delete', dest = 'delete', help = 'data to delete', choices = ['feature', 'object', 'classification', 'interaction']) |
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24 parser.add_argument('--process', dest = 'process', help = 'data to process', choices = ['feature', 'object', 'classification', 'prototype', 'interaction']) |
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25 parser.add_argument('--display', dest = 'display', help = 'data to display (replay over video)', choices = ['feature', 'object', 'classification', 'interaction']) |
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26 parser.add_argument('--progress', dest = 'progress', help = 'information about the progress of processing', action = 'store_true') |
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27 parser.add_argument('--analyze', dest = 'analyze', help = 'data to analyze (results)', choices = ['feature', 'object', 'classification', 'interaction', 'event-speed', 'event-interaction']) |
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28 |
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29 # common options |
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30 parser.add_argument('--cfg', dest = 'configFilename', help = 'name of the configuration file') |
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31 parser.add_argument('-n', dest = 'nObjects', help = 'number of objects/interactions to process', type = int) |
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32 parser.add_argument('-t', dest = 'trajectoryType', help = 'type of trajectories', choices = ['feature', 'object'], default = 'feature') |
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33 parser.add_argument('--dry', dest = 'dryRun', help = 'dry run of processing', action = 'store_true') |
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34 parser.add_argument('--nthreads', dest = 'nProcesses', help = 'number of processes to run in parallel', type = int, default = 1) |
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35 parser.add_argument('--subsample', dest = 'positionSubsamplingRate', help = 'rate of position subsampling (1 every n positions)', type = int) |
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36 |
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37 ### process options |
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38 # motion pattern learning and assignment |
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39 parser.add_argument('--prototype-filename', dest = 'outputPrototypeDatabaseFilename', help = 'name of the Sqlite database file to save prototypes', default = 'prototypes.sqlite') |
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40 #parser.add_argument('-i', dest = 'inputPrototypeDatabaseFilename', help = 'name of the Sqlite database file for prototypes to start the algorithm with') |
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41 parser.add_argument('--nobjects-mp', dest = 'nMPObjects', help = 'number of objects/interactions to process', type = int) |
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42 parser.add_argument('--nfeatures-per-object', dest = 'nLongestFeaturesPerObject', help = 'maximum number of features per object to load', type = int) |
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43 parser.add_argument('--epsilon', dest = 'epsilon', help = 'distance for the similarity of trajectory points', type = float) |
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44 parser.add_argument('--metric', dest = 'metric', help = 'metric for the similarity of trajectory points', default = 'cityblock') # default is manhattan distance |
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45 parser.add_argument('--minsimil', dest = 'minSimilarity', help = 'minimum similarity to put a trajectory in a cluster', type = float) |
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46 parser.add_argument('--min-cluster-size', dest = 'minClusterSize', help = 'minimum cluster size', type = int, default = 0) |
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47 #parser.add_argument('--learn', dest = 'learn', help = 'learn', action = 'store_true') |
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48 parser.add_argument('--optimize', dest = 'optimizeCentroid', help = 'recompute centroid at each assignment', action = 'store_true') |
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49 parser.add_argument('--random', dest = 'randomInitialization', help = 'random initialization of clustering algorithm', action = 'store_true') |
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50 #parser.add_argument('--similarities-filename', dest = 'similaritiesFilename', help = 'filename of the similarities') |
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51 parser.add_argument('--save-similarities', dest = 'saveSimilarities', help = 'save computed similarities (in addition to prototypes)', action = 'store_true') |
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52 parser.add_argument('--save-assignments', dest = 'saveAssignments', help = 'saves the assignments of the objects to the prototypes', action = 'store_true') |
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53 parser.add_argument('--assign', dest = 'assign', help = 'assigns the objects to the prototypes and saves the assignments', action = 'store_true') |
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54 |
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55 # safety analysis |
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56 parser.add_argument('--prediction-method', dest = 'predictionMethod', help = 'prediction method (constant velocity (cvd: vector computation (approximate); cve: equation solving; cv: discrete time (approximate)), normal adaptation, point set prediction)', choices = ['cvd', 'cve', 'cv', 'na', 'ps', 'mp']) |
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57 parser.add_argument('--pet', dest = 'computePET', help = 'computes PET', action = 'store_true') |
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58 # override other tracking config, erase sqlite? |
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59 |
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60 |
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61 # analysis options |
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62 parser.add_argument('--output', dest = 'output', help = 'kind of output to produce (interval means)', choices = ['figure', 'interval', 'event']) |
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63 parser.add_argument('--min-duration', dest = 'minDuration', help = 'mininum duration we have to see the user or interaction to take into account in the analysis (s)', type = float) |
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64 parser.add_argument('--interval-duration', dest = 'intervalDuration', help = 'length of time interval to aggregate data (min)', type = int, default = 15) |
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65 parser.add_argument('--aggregation', dest = 'aggMethods', help = 'aggregation method per user/interaction and per interval', choices = ['mean', 'median', 'centile'], nargs = '*', default = ['median']) |
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66 parser.add_argument('--aggregation-centiles', dest = 'aggCentiles', help = 'centile(s) to compute from the observations', nargs = '*', type = int) |
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67 parser.add_argument('--event-thresholds', dest = 'eventThresholds', help = 'threshold to count severe situations', nargs = '*', type = float) |
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68 parser.add_argument('--event-filename', dest = 'eventFilename', help = 'filename of the event data') |
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69 dpi = 150 |
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70 # unit of analysis: site - camera-view |
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71 |
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72 # need way of selecting sites as similar as possible to sql alchemy syntax |
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73 # override tracking.cfg from db |
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74 # manage cfg files, overwrite them (or a subset of parameters) |
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75 # delete sqlite files |
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76 # info of metadata |
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77 |
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78 args = parser.parse_args() |
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79 |
1009 | 80 ################################# |
81 # Data preparation | |
82 ################################# | |
83 session = connectDatabase(args.metadataFilename) | |
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84 parentPath = Path(args.metadataFilename).parent # files are relative to metadata location |
1009 | 85 videoSequences = [] |
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86 sites = [] |
1009 | 87 if args.videoIds is not None: |
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88 for videoId in args.videoIds: |
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89 if '-' in videoId: |
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90 videoSequences.extend([session.query(VideoSequence).get(i) for i in moving.TimeInterval.parse(videoId)]) |
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91 else: |
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92 videoSequences.append(session.query(VideoSequence).get(int(videoId))) |
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93 videoSequences = [vs for vs in videoSequences if vs is not None] |
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94 sites = set([vs.cameraView.site for vs in videoSequences]) |
1009 | 95 elif args.siteIds is not None: |
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96 for siteId in args.siteIds: |
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97 if '-' in siteId: |
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98 sites.extend([session.query(Site).get(i) for i in moving.TimeInterval.parse(siteId)]) |
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99 else: |
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100 sites.append(session.query(Site).get(int(siteId))) |
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101 sites = [s for s in sites if s is not None] |
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102 for site in sites: |
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103 videoSequences.extend(getSiteVideoSequences(site)) |
1009 | 104 else: |
105 print('No video/site to process') | |
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106 |
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107 if args.nProcesses > 1: |
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108 pool = Pool(args.nProcesses) |
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109 |
1009 | 110 ################################# |
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111 # Report progress in the processing |
1009 | 112 ################################# |
1073 | 113 if args.progress: # TODO find video sequences that have null camera view, to work with them |
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114 print('Providing information on progress of data processing') |
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115 headers = ['site', 'vs', 'features', 'objects', 'interactions'] # todo add prototypes and object classification |
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116 data = [] |
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117 for site in sites: |
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118 unprocessedVideoSequences = [] |
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119 for vs in getSiteVideoSequences(site): |
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120 if (parentPath/vs.getDatabaseFilename()).is_file(): # TODO check time of file? |
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121 tableNames = storage.tableNames(str(parentPath.absolute()/vs.getDatabaseFilename())) |
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122 data.append([site.name, vs.idx, 'positions' in tableNames, 'objects' in tableNames, 'interactions' in tableNames]) |
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123 else: |
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124 unprocessedVideoSequences.append(vs) |
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125 data.append([site.name, vs.idx, False, False, False]) |
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126 #if len(unprocessedVideoSequences): |
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127 # print('Site {} ({}) has {} completely unprocessed video sequences'.format (site.name, site.idx, len(unprocessedVideoSequences))) |
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128 videoSequences = session.query(VideoSequence).filter(VideoSequence.cameraViewIdx.is_(None)).all() |
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129 data = pd.DataFrame(data, columns = headers) |
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130 print('-'*80) |
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131 print('\t'+' '.join(headers[2:])) |
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132 print('-'*80) |
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133 for name, group in data.groupby(['site']): #.agg({'vs': 'count'})) |
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134 n = group.vs.count() |
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135 print('{}: {} % / {} % / {} % ({})'.format(name, 100*group.features.sum()/float(n), 100*group.objects.sum()/float(n), 100*group.interactions.sum()/float(n), n)) |
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136 print('-'*80) |
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137 if len(videoSequences) > 0: |
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138 print('{} video sequences without a camera view:'.format(len(videoSequences))) |
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139 print([vs.idx for vs in videoSequences]) |
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140 print('-'*80) |
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141 print(data) |
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142 |
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143 ################################# |
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144 # Delete |
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145 ################################# |
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146 if args.delete is not None: |
1009 | 147 if args.delete == 'feature': |
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148 response = input('Are you sure you want to delete the tracking results (SQLite files) of all these sites (y/n)?') |
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149 if response == 'y': |
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150 for vs in videoSequences: |
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151 p = parentPath.absolute()/vs.getDatabaseFilename() |
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152 p.unlink() |
1009 | 153 elif args.delete in ['object', 'interaction']: |
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154 #parser.add_argument('-t', dest = 'dataType', help = 'type of the data to remove', required = True, choices = ['object','interaction', 'bb', 'pois', 'prototype']) |
1009 | 155 for vs in videoSequences: |
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156 storage.deleteFromSqlite(str(parentPath/vs.getDatabaseFilename()), args.delete) |
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157 |
1009 | 158 ################################# |
159 # Process | |
160 ################################# | |
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161 if args.process in ['feature', 'object']: # tracking |
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162 if args.nProcesses == 1: |
1009 | 163 for vs in videoSequences: |
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164 if not (parentPath/vs.getDatabaseFilename()).is_file() or args.process == 'object': |
1009 | 165 if args.configFilename is None: |
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166 configFilename = str(parentPath/vs.cameraView.getTrackingConfigurationFilename()) |
1009 | 167 else: |
168 configFilename = args.configFilename | |
169 if vs.cameraView.cameraType is None: | |
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170 cvutils.tracking(configFilename, args.process == 'object', str(parentPath.absolute()/vs.getVideoSequenceFilename()), str(parentPath.absolute()/vs.getDatabaseFilename()), str(parentPath.absolute()/vs.cameraView.getHomographyFilename()), str(parentPath.absolute()/vs.cameraView.getMaskFilename()), False, None, None, args.dryRun) |
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171 else: #caution: cameratype can be not none, but without parameters for undistortion |
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172 cvutils.tracking(configFilename, args.process == 'object', str(parentPath.absolute()/vs.getVideoSequenceFilename()), str(parentPath.absolute()/vs.getDatabaseFilename()), str(parentPath.absolute()/vs.cameraView.getHomographyFilename()), str(parentPath.absolute()/vs.cameraView.getMaskFilename()), True, vs.cameraView.cameraType.intrinsicCameraMatrix, vs.cameraView.cameraType.distortionCoefficients, args.dryRun) |
1009 | 173 else: |
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174 print('SQLite already exists: {}'.format(parentPath/vs.getDatabaseFilename())) |
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175 else: |
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176 for vs in videoSequences: |
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177 if not (parentPath/vs.getDatabaseFilename()).is_file() or args.process == 'object': |
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178 if args.configFilename is None: |
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179 configFilename = str(parentPath/vs.cameraView.getTrackingConfigurationFilename()) |
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180 else: |
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181 configFilename = args.configFilename |
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182 if vs.cameraView.cameraType is None: |
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183 pool.apply_async(cvutils.tracking, args = (configFilename, args.process == 'object', str(parentPath.absolute()/vs.getVideoSequenceFilename()), str(parentPath.absolute()/vs.getDatabaseFilename()), str(parentPath.absolute()/vs.cameraView.getHomographyFilename()), str(parentPath.absolute()/vs.cameraView.getMaskFilename()), False, None, None, args.dryRun)) |
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184 else: |
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185 pool.apply_async(cvutils.tracking, args = (configFilename, args.process == 'object', str(parentPath.absolute()/vs.getVideoSequenceFilename()), str(parentPath.absolute()/vs.getDatabaseFilename()), str(parentPath.absolute()/vs.cameraView.getHomographyFilename()), str(parentPath.absolute()/vs.cameraView.getMaskFilename()), True, vs.cameraView.cameraType.intrinsicCameraMatrix, vs.cameraView.cameraType.distortionCoefficients, args.dryRun)) |
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186 else: |
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187 print('SQLite already exists: {}'.format(parentPath/vs.getDatabaseFilename())) |
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188 pool.close() |
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189 pool.join() |
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190 |
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191 elif args.process == 'prototype': # motion pattern learning |
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192 # learn by site by default -> group videos by camera view TODO |
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193 # by default, load all objects, learn and then assign (BUT not save the assignments) |
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194 for site in sites: |
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195 print('Learning motion patterns for site {} ({})'.format(site.idx, site.name)) |
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196 objects = {} |
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197 object2VideoSequences = {} |
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198 for cv in site.cameraViews: |
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199 for vs in cv.videoSequences: |
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200 print('Loading '+vs.getDatabaseFilename()) |
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201 objects[vs.idx] = storage.loadTrajectoriesFromSqlite(str(parentPath/vs.getDatabaseFilename()), args.trajectoryType, args.nObjects, timeStep = args.positionSubsamplingRate, nLongestFeaturesPerObject = args.nLongestFeaturesPerObject) |
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202 if args.trajectoryType == 'object' and args.nLongestFeaturesPerObject is not None: |
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203 objectsWithFeatures = objects[vs.idx] |
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204 objects[vs.idx] = [f for o in objectsWithFeatures for f in o.getFeatures()] |
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205 prototypeType = 'feature' |
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206 else: |
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207 prototypeType = args.trajectoryType |
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208 for obj in objects[vs.idx]: |
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209 object2VideoSequences[obj] = vs |
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210 lcss = utils.LCSS(metric = args.metric, epsilon = args.epsilon) |
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211 similarityFunc = lambda x,y : lcss.computeNormalized(x, y) |
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212 trainingObjects = [o for tmpobjects in objects.values() for o in tmpobjects] |
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213 if args.nMPObjects is not None and args.nMPObjects < len(trainingObjects): |
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214 m = int(np.floor(float(len(trainingObjects))/args.nMPObjects)) |
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215 trainingObjects = trainingObjects[::m] |
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216 similarities = -np.ones((len(trainingObjects), len(trainingObjects))) |
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217 prototypeIndices, labels = processing.learnAssignMotionPatterns(True, True, trainingObjects, similarities, args.minSimilarity, similarityFunc, args.minClusterSize, args.optimizeCentroid, args.randomInitialization, True, []) |
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218 if args.outputPrototypeDatabaseFilename is None: |
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219 outputPrototypeDatabaseFilename = args.databaseFilename |
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220 else: |
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221 outputPrototypeDatabaseFilename = args.outputPrototypeDatabaseFilename |
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222 clusterSizes = ml.computeClusterSizes(labels, prototypeIndices, -1) |
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223 storage.savePrototypesToSqlite(str(parentPath/site.getPath()/outputPrototypeDatabaseFilename), [moving.Prototype(object2VideoSequences[trainingObjects[i]].getDatabaseFilename(False), trainingObjects[i].getNum(), prototypeType, clusterSizes[i]) for i in prototypeIndices]) |
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224 |
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225 elif args.process == 'interaction': |
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226 # safety analysis TODO make function in safety analysis script |
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227 if args.predictionMethod == 'cvd': |
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228 predictionParameters = prediction.CVDirectPredictionParameters() |
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229 elif args.predictionMethod == 'cve': |
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230 predictionParameters = prediction.CVExactPredictionParameters() |
1009 | 231 for vs in videoSequences: |
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232 print('Processing '+vs.getDatabaseFilename()) |
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233 if args.configFilename is None: |
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234 params = storage.ProcessParameters(str(parentPath/vs.cameraView.getTrackingConfigurationFilename())) |
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235 else: |
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236 params = storage.ProcessParameters(args.configFilename) |
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237 objects = storage.loadTrajectoriesFromSqlite(str(parentPath/vs.getDatabaseFilename()), 'object')#, args.nObjects, withFeatures = (params.useFeaturesForPrediction or predictionMethod == 'ps' or predictionMethod == 'mp')) |
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238 interactions = events.createInteractions(objects) |
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239 if args.nProcesses == 1: |
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240 #print(len(interactions), args.computePET, predictionParameters, params.collisionDistance, params.predictionTimeHorizon, params.crossingZones) |
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241 processed = events.computeIndicators(interactions, True, args.computePET, predictionParameters, params.collisionDistance, params.predictionTimeHorizon, False, False, None) # params.crossingZones |
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242 else: |
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243 #pool = Pool(processes = args.nProcesses) |
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244 nInteractionPerProcess = int(np.ceil(len(interactions)/float(args.nProcesses))) |
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245 jobs = [pool.apply_async(events.computeIndicators, args = (interactions[i*nInteractionPerProcess:(i+1)*nInteractionPerProcess], True, args.computePET, predictionParameters, params.collisionDistance, params.predictionTimeHorizon, False, False, None)) for i in range(args.nProcesses)] # params.crossingZones |
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246 processed = [] |
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247 for job in jobs: |
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248 processed += job.get() |
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249 #pool.close() |
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250 storage.saveIndicatorsToSqlite(str(parentPath/vs.getDatabaseFilename()), processed) |
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251 |
1009 | 252 ################################# |
253 # Analyze | |
254 ################################# | |
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255 if args.analyze == 'object': |
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256 # user speeds, accelerations |
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257 # aggregation per site |
1068 | 258 if args.eventFilename is None: |
259 print('Missing output filename (event-filename). Exiting') | |
260 sys.exit(0) | |
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261 data = [] # list of observation per site-user with time |
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262 headers = ['site', 'date', 'time', 'user_type'] |
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263 aggFunctions, tmpheaders = utils.aggregationMethods(args.aggMethods, args.aggCentiles) |
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264 headers.extend(tmpheaders) |
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265 if args.nProcesses == 1: |
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266 for vs in videoSequences: |
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267 data.extend(processing.extractVideoSequenceSpeeds(str(parentPath/vs.getDatabaseFilename()), vs.cameraView.site.name, args.nObjects, vs.startTime, vs.cameraView.cameraType.frameRate, vs.cameraView.cameraType.frameRate*args.minDuration, args.aggMethods, args.aggCentiles)) |
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268 else: |
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269 jobs = [pool.apply_async(processing.extractVideoSequenceSpeeds, args = (str(parentPath/vs.getDatabaseFilename()), vs.cameraView.site.name, args.nObjects, vs.startTime, vs.cameraView.cameraType.frameRate, vs.cameraView.cameraType.frameRate*args.minDuration, args.aggMethods, args.aggCentiles)) for vs in videoSequences] |
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270 for job in jobs: |
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271 data.extend(job.get()) |
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272 pool.close() |
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273 data = pd.DataFrame(data, columns = headers) |
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274 if args.output == 'figure': |
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275 for name in headers[4:]: |
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276 plt.ioff() |
1068 | 277 plt.figure() |
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278 plt.boxplot([data.loc[data['site']==site.name, name] for site in sites], labels = [site.name for site in sites]) |
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279 plt.ylabel(name+' Speeds (km/h)') |
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280 plt.savefig(name.lower()+'-speeds.png', dpi=dpi) |
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281 plt.close() |
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282 elif args.output == 'event': |
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283 data.to_csv(args.eventFilename, index = False) |
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284 |
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285 if args.analyze == 'interaction': # redo as for object, export in dataframe all interaction data |
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286 indicatorIds = [2,5,7,10] |
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287 conversionFactors = {2: 1., 5: 30.*3.6, 7:1./30, 10:1./30} |
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288 #maxIndicatorValue = {2: float('inf'), 5: float('inf'), 7:10., 10:10.} |
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289 data = [] # list of observation per site-user with time |
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290 headers = ['site', 'date', 'time', events.Interaction.indicatorNames[10].replace(' ','-')] # user types? |
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291 aggFunctions, tmpheaders = utils.aggregationMethods(args.aggMethods, args.aggCentiles) |
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292 for i in indicatorIds[:3]: |
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293 for h in tmpheaders: |
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294 headers.append(events.Interaction.indicatorNames[i].replace(' ','-')+'-'+h) |
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295 indicators = {} |
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296 interactions = {} |
1009 | 297 for vs in videoSequences: |
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298 print('Extracting SMoS from '+vs.getDatabaseFilename()) |
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299 interactions = storage.loadInteractionsFromSqlite(str(parentPath/vs.getDatabaseFilename())) |
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300 minDuration = vs.cameraView.cameraType.frameRate*args.minDuration |
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301 for inter in interactions: |
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302 if inter.length() > minDuration: |
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303 d = vs.startTime.date() |
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304 t = vs.startTime.time() |
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305 row = [vs.cameraView.site.name, d, utils.framesToTime(inter.getFirstInstant(), vs.cameraView.cameraType.frameRate, t)] |
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306 pet = inter.getIndicator('Post Encroachment Time') |
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307 if pet is None: |
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308 row.append(None) |
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309 else: |
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310 row.append(conversionFactors[10]*pet.getValues()[0]) |
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311 for i in indicatorIds[:3]: |
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312 indic = inter.getIndicator(events.Interaction.indicatorNames[i]) |
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313 if indic is not None: |
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314 #v = indic.getMostSevereValue()* |
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315 tmp = list(indic.values.values()) |
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316 for method,func in aggFunctions.items(): |
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317 agg = conversionFactors[i]*func(tmp) |
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318 if method == 'centile': |
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319 row.extend(agg.tolist()) |
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320 else: |
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321 row.append(agg) |
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322 else: |
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323 row.extend([None]*len(aggFunctions)) |
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324 data.append(row) |
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325 data = pd.DataFrame(data, columns = headers) |
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326 if args.output == 'figure': |
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327 for i in indicatorIds: |
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328 pass # tmp = [indicators[siteId][i] for siteId in indicators] |
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329 # plt.ioff() |
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330 # plt.figure() |
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331 # plt.boxplot(tmp, labels = [session.query(Site).get(siteId).name for siteId in indicators]) |
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332 # plt.ylabel(events.Interaction.indicatorNames[i]+' ('+events.Interaction.indicatorUnits[i]+')') |
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333 # plt.savefig(events.Interaction.indicatorNames[i]+'.png', dpi=150) |
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334 # plt.close() |
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335 elif args.output == 'event': |
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336 data.to_csv(args.eventFilename, index = False) |
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337 |
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338 if args.analyze == 'event-speed': # aggregate event data by 15 min interval (args.intervalDuration), count events with thresholds |
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339 data = pd.read_csv(args.eventFilename, parse_dates = [2]) |
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340 #data = pd.read_csv('./speeds.csv', converters = {'time': lambda s: datetime.datetime.strptime(s, "%H:%M:%S").time()}, nrows = 5000) |
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341 # create time for end of each 15 min, then group by, using the agg method for each data column |
1061 | 342 headers = ['site', 'date', 'intervalend15', 'duration', 'count'] |
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343 aggFunctions, tmpheaders = utils.aggregationMethods(args.aggMethods, args.aggCentiles) |
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344 dataColumns = list(data.columns[4:]) |
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345 print(dataColumns) |
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346 for h in dataColumns: |
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347 for h2 in tmpheaders: |
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348 headers.append(h+'-'+h2) |
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349 if args.eventThresholds is not None: |
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350 for h in dataColumns: |
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351 for t in args.eventThresholds: |
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352 headers.append('n-{}-{}'.format(h, t)) |
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353 data['intervalend15'] = data.time.apply(lambda t: (pd.Timestamp(year = t.year, month = t.month, day = t.day,hour = t.hour, minute = (t.minute // args.intervalDuration)*args.intervalDuration)+pd.Timedelta(minutes = 15)).time()) |
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354 outputData = [] |
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355 for name, group in data.groupby(['site', 'date', 'intervalend15']): |
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356 row = [] |
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357 row.extend(name) |
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358 groupStartTime = group.time.min() |
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359 groupEndTime = group.time.max() |
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360 row.append((groupEndTime.minute+1-groupStartTime.minute) % 60)#(name[2].minute*60+name[2].second-groupStartTime.minute*60+groupStartTime.second) % 3600) |
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361 row.append(len(group)) |
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362 for h in dataColumns: |
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363 for method,func in aggFunctions.items(): |
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364 aggregated = func(group[h]) |
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365 if method == 'centile': |
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366 row.extend(aggregated) |
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367 else: |
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368 row.append(aggregated) |
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369 if args.eventThresholds is not None: |
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370 for h in dataColumns: |
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371 for t in args.eventThresholds: |
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372 row.append((group[h] > t).sum()) |
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373 outputData.append(row) |
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374 pd.DataFrame(outputData, columns = headers).to_csv(utils.removeExtension(args.eventFilename)+'-aggregated.csv', index = False) |
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375 |
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376 elif args.analyze == 'event-interaction': # aggregate event data by 15 min interval (args.intervalDuration), count events with thresholds |
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377 data = pd.read_csv(args.eventFilename, parse_dates = [2]) |
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378 headers = ['site', 'date', 'intervalend15', 'duration', 'count'] |
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379 aggFunctions, tmpheaders = utils.aggregationMethods(args.aggMethods, args.aggCentiles) |
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380 dataColumns = list(data.columns[3:]) |
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381 for h in dataColumns: |
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382 if not 'speed' in h.lower(): # proximity indicators are reversed, taking 85th centile of this column will yield the 15th centile (which we have to take the opposite again) |
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383 data[h] = -data[h] |
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384 for h in dataColumns: |
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385 for h2 in tmpheaders: |
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386 headers.append(h+'-'+h2) |
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387 for h,t in zip(dataColumns, args.eventThresholds): # each threshold in this case applies to one indicator |
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388 headers.append('n-{}-{}'.format(h, t)) |
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389 data['intervalend15'] = data.time.apply(lambda t: (pd.Timestamp(year = t.year, month = t.month, day = t.day,hour = t.hour, minute = (t.minute // args.intervalDuration)*args.intervalDuration)+pd.Timedelta(minutes = 15)).time()) |
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390 outputData = [] |
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391 for name, group in data.groupby(['site', 'date', 'intervalend15']): |
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392 row = [] |
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393 row.extend(name) |
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394 groupStartTime = group.time.min() |
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395 groupEndTime = group.time.max() |
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396 row.append((groupEndTime.minute+1-groupStartTime.minute) % 60)#(name[2].minute*60+name[2].second-groupStartTime.minute*60+groupStartTime.second) % 3600) |
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397 row.append(len(group)) |
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398 for h in dataColumns: |
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399 for method,func in aggFunctions.items(): |
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400 tmp = group.loc[~group[h].isna(), h] |
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401 if len(tmp)>0: |
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402 aggregated = func(tmp) # todo invert if the resulting stat is negative |
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403 if method == 'centile': |
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404 row.extend(np.abs(aggregated)) |
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405 else: |
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406 row.append(np.abs(aggregated)) |
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407 else: |
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408 row.extend([None]*len(aggFunctions)) |
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409 for h,t in zip(dataColumns, args.eventThresholds): # each threshold in this case applies to one indicator |
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410 if 'speed' in h.lower(): |
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411 row.append((group[h] > t).sum()) |
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412 else: |
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413 row.append((group[h] > -t).sum()) # take larger than than negative threshold for proximity indicators |
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414 outputData.append(row) |
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415 pd.DataFrame(outputData, columns = headers).to_csv(utils.removeExtension(args.eventFilename)+'-aggregated.csv', index = False) |