{ "cells": [ { "cell_type": "code", "execution_count": 1, "metadata": { "collapsed": true }, "outputs": [], "source": [ "import h2o\n", "import numpy as np\n", "import matplotlib.patches as mpatches\n", "import matplotlib.pyplot as plt\n", "from h2o.estimators.glrm import H2OGeneralizedLowRankEstimator" ] }, { "cell_type": "code", "execution_count": 2, "metadata": { "collapsed": false }, "outputs": [ { "data": { "text/html": [ "
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H2O cluster uptime: 7 seconds 288 milliseconds
H2O cluster version: 3.7.0.99999
H2O cluster name: spIdea
H2O cluster total nodes: 1
H2O cluster total free memory: 12.44 GB
H2O cluster total cores: 8
H2O cluster allowed cores: 8
H2O cluster healthy: True
H2O Connection ip: 127.0.0.1
H2O Connection port: 54321
H2O Connection proxy: None
Python Version: 3.5.0
" ], "text/plain": [ "------------------------------ --------------------------\n", "H2O cluster uptime: 7 seconds 288 milliseconds\n", "H2O cluster version: 3.7.0.99999\n", "H2O cluster name: spIdea\n", "H2O cluster total nodes: 1\n", "H2O cluster total free memory: 12.44 GB\n", "H2O cluster total cores: 8\n", "H2O cluster allowed cores: 8\n", "H2O cluster healthy: True\n", "H2O Connection ip: 127.0.0.1\n", "H2O Connection port: 54321\n", "H2O Connection proxy:\n", "Python Version: 3.5.0\n", "------------------------------ --------------------------" ] }, "metadata": {}, "output_type": "display_data" } ], "source": [ "h2o.init()" ] }, { "cell_type": "code", "execution_count": 3, "metadata": { "collapsed": false }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "\n", "Parse Progress: [##################################################] 100%\n", "Rows:151 Cols:124\n", "\n", "Chunk compression summary: \n" ] }, { "data": { "text/html": [ "
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chunk_typechunk_namecountcount_percentagesizesize_percentage
C2S2-Byte Fractions10.8064516 386 B0.4540642
C4S4-Byte Fractions12399.19355 82.6 KB99.54594
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sizenumber_of_rowsnumber_of_chunks_per_columnnumber_of_chunks
172.16.2.84:54321 83.0 KB151.01.0124.0
mean 83.0 KB151.01.0124.0
min 83.0 KB151.01.0124.0
max 83.0 KB151.01.0124.0
stddev 0 B0.00.00.0
total 83.0 KB151.01.0124.0
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Time R.ASIS.X R.ASIS.Y R.ASIS.Z L.ASIS.X L.ASIS.Y L.ASIS.Z V.Sacral.X V.Sacral.Y V.Sacral.Z R.Thigh.Upper.X R.Thigh.Upper.Y R.Thigh.Upper.Z R.Thigh.Front.X R.Thigh.Front.Y R.Thigh.Front.Z R.Thigh.Rear.X R.Thigh.Rear.Y R.Thigh.Rear.Z L.Thigh.Upper.X L.Thigh.Upper.Y L.Thigh.Upper.Z L.Thigh.Front.X L.Thigh.Front.Y L.Thigh.Front.Z L.Thigh.Rear.X L.Thigh.Rear.Y L.Thigh.Rear.Z R.Shank.Upper.X R.Shank.Upper.Y R.Shank.Upper.Z R.Shank.Front.X R.Shank.Front.Y R.Shank.Front.Z R.Shank.Rear.X R.Shank.Rear.Y R.Shank.Rear.Z L.Shank.Upper.X L.Shank.Upper.Y L.Shank.Upper.Z L.Shank.Front.X L.Shank.Front.Y L.Shank.Front.Z L.Shank.Rear.X L.Shank.Rear.Y L.Shank.Rear.Z R.Heel.X R.Heel.Y R.Heel.Z R.Midfoot.Sup.X R.Midfoot.Sup.Y R.Midfoot.Sup.Z R.Midfoot.Lat.X R.Midfoot.Lat.Y R.Midfoot.Lat.Z R.Toe.Tip.X R.Toe.Tip.Y R.Toe.Tip.Z L.Heel.X L.Heel.Y L.Heel.Z L.Midfoot.Sup.X L.Midfoot.Sup.Y L.Midfoot.Sup.Z L.Midfoot.Lat.X L.Midfoot.Lat.Y L.Midfoot.Lat.Z L.Toe.Tip.X L.Toe.Tip.Y L.Toe.Tip.Z Sternum.X Sternum.Y Sternum.Z R.Acromium.X R.Acromium.Y R.Acromium.Z L.Acromium.X L.Acromium.Y L.Acromium.Z R.Bicep.X R.Bicep.Y R.Bicep.Z L.Bicep.X L.Bicep.Y L.Bicep.Z R.Elbow.X R.Elbow.Y R.Elbow.Z L.Elbow.X L.Elbow.Y L.Elbow.Z R.Wrist.Med.X R.Wrist.Med.Y R.Wrist.Med.Z R.Wrist.Lat.X R.Wrist.Lat.Y R.Wrist.Lat.Z L.Wrist.Med.X L.Wrist.Med.Y L.Wrist.Med.Z L.Wrist.Lat.X L.Wrist.Lat.Y L.Wrist.Lat.Z R.Toe.Lat.X R.Toe.Lat.Y R.Toe.Lat.Z R.Toe.Med.X R.Toe.Med.Y R.Toe.Med.Z L.Toe.Lat.X L.Toe.Lat.Y L.Toe.Lat.Z L.Toe.Med.X L.Toe.Med.Y L.Toe.Med.Z R.Temple.X R.Temple.Y R.Temple.Z L.Temple.X L.Temple.Y L.Temple.Z Top.Head.X Top.Head.Y Top.Head.Z
type real real real real real real real real real real real real real real real real real real real real real real real real real real real real real real real real real real real real real real real real real real real real real real real real real real real real real real real real real real real real real real real real real real real real real real real real real real real real real real real real real real real real real real real real real real real real real real real real real real real real real real real real real real real real real real real real real real real real real real real real real real real real
mins 0.0 588.9071700000001 1042.5732400000002107.79163000000001600.01556 1028.7249800000002-152.53879 399.400090000000031034.9012500000001-21.440830000000002481.83603000000005732.70135 169.71159 535.63422 657.21033 74.20708 443.03299000000004613.54547 168.15961000000001468.19415000000004737.7208300000001 -194.25998 550.69415 684.75494 -133.58800000000002435.01773000000003627.4998800000001 -170.86086 319.34705 444.43289000000004157.69023 376.44724 403.25574000000006102.54192 293.89526 368.28577 165.6133 341.20230000000004438.80435000000006-172.96315 365.72482 375.95242 -120.97533000000001304.46347000000003393.67728000000005-173.38676 68.60076000000001 56.43383000000001 59.94800000000001 190.9884500000000376.90237 57.86759000000001157.3250300000000362.790000000000006159.97461 242.9085800000000333.52863 102.0894000000000176.37951000000001 58.7473 -74.0361 211.8596800000000369.02702000000001 -69.30095 185.39088 48.22646 -140.09074 254.42706 36.65646 -88.18266000000001 627.3817700000001 1342.8541300000002-35.207950000000004511.800320000000061427.4450700000002164.48206000000002551.72424 1453.5893600000002-249.89265000000003485.945590000000041227.90454 216.05853000000002531.12134 1217.6442900000002-266.60974000000004424.32767 1129.09949 242.29697000000002460.03223 1123.8029800000002-304.79358 535.8743900000001889.81964 262.1105 486.99316000000005876.5388200000001 304.71069 554.3527200000001895.9242600000001 -240.59163 502.82971000000003886.58942 -300.87775000000005179.7708 33.33099 181.24631000000002218.04131 36.96362000000000671.79319000000001 199.8069300000000236.02512 -153.13719 228.0489800000000342.970600000000005-54.889030000000005675.97009 1562.28418 44.154320000000006683.5089700000001 1567.2720900000002-94.07465 614.13971 1740.3891600000002-19.488380000000003
mean 1.2499999999999993613.8130531125828 1066.0396608609274147.31687456953645621.7555214569537 1053.9635696688736-113.08985682119204419.6205819205298 1059.090068145695321.623491456953648 604.8936437086089 752.1138705960262198.39496721854303673.9218970198674697.9239713907289 108.98507715231787611.8222588741723 633.8688175496687 191.19985695364238585.4907751655632 756.9971207947021 -165.26850715231774678.6867554966889728.6994552980129 -105.36090649006627595.9400021854307 651.7901406622518 -150.84564834437083546.5949239735097 475.6042311258279 178.1610840397351 612.0710297350994 427.5346344370859 128.65022192052976542.2670986754965 394.8237276821193 183.7567350993378 576.5967016556297 453.5735939735099 -145.61844165562923613.3957888079467 399.52025900662267-93.8556917880795 549.8781823841059 417.99366589403985-150.9459415231788 416.54885291390724129.3223385430464 90.8570246357616 548.3382341059602 111.6107755629138769.80901602649006529.6942462913908 98.34065304635762 174.1893321854304 666.8872204635761 65.94589735099338 120.55406225165562434.3669011920529 129.88390841059598-51.12726761589405 586.8231564900668 102.77086682119207-29.910332119205307567.242079536424196.33869509933773 -123.75095503311258681.115977880795 67.45840384105965 -57.79152264900662 644.3542851655633 1368.87501569536457.558123708609271 541.6915377483443 1458.7166388741728215.4138978807946 579.5313996026489 1480.7170782781461-200.59946940397344546.9539041721856 1259.3373474172188262.77322251655636596.1424768874172 1244.4854017218543-229.89472728476827504.19518139072851157.8487022516563292.1369874172185 548.27397735099361148.8425164238413-267.9194196688743 659.5054600662249943.7589347682123 282.792095960265 620.8649145695368 926.0463686754969 331.2522522516555 672.8674744370859938.0977625827818 -214.62415662251658631.5193429801323 921.9683218543047-274.01243317880784601.509835033112 61.89592642384106 194.6828558278145 619.8241700000001 68.4889279470199 86.61932410596025 618.3381468874173 65.92961562913905 -132.6487337748344 638.6451865562915 72.31719158940398 -31.812834701986745705.7277435761589 1598.039739867549394.05463324503312 718.7310321854308 1603.0323291390728-44.31930543046361 698.879092384106 1772.968212715232333.555429536423844
maxs 2.5 641.12048 1091.43665 180.07411000000002661.46918 1078.02356 -80.37424 451.5914 1077.82214 55.369930000000004 692.8951400000001 788.1136500000001217.07512000000003766.4453100000001750.7237500000001 136.25021 728.6724200000001 672.4224200000001 209.89946 674.53168 783.71576 -138.11635 773.9770500000001780.8144500000001 -66.30186 713.1610700000001 681.3862300000001 -123.18440000000001719.6970200000001 531.05676 200.56787000000003799.4701500000001 457.5513 154.56749000000002751.88885 458.64368 202.59061000000003764.30676 494.35605000000004-116.46951000000001821.6690100000001 425.57733 -63.516540000000006750.77588 473.02411000000006-124.50978 812.50183 320.70309000000003108.16100000000002935.61414 198.72064 86.30818000000001934.44775 211.37376 188.70589 1073.86951 179.28133000000003153.59363000000002821.7641000000001 321.80249000000003-34.92287 971.3176300000001 178.00603 -6.83138 955.7309600000001184.36398000000003-104.369800000000011082.51477 168.64880000000002-32.923210000000005673.89301 1393.888060000000243.751630000000006 573.6866500000001 1486.25891 262.06827000000004609.36566 1507.8101800000002-155.85466000000002593.64148 1288.58093 305.86801 643.91699 1271.7580600000001-196.56128 567.0025 1193.1440400000001339.82635000000005608.93268 1186.43945 -230.94901000000002772.61859 1003.0836800000001312.96448000000004751.62823 969.89471 362.03549000000004793.86859 998.83923 -188.33229000000003768.9158900000001 958.34167 -249.44443 1026.04944 136.89597 218.5173 1029.85803 153.3546 113.458900000000011024.0694600000002133.35187000000002-111.9407 1039.3868400000001146.49858 -9.441730000000002 740.63611 1640.0118400000001139.15808 754.6250600000001 1647.88391000000020.84904 752.89178 1809.149170000000185.29955000000001
sigma 0.728898255359873414.83995076415540414.30999526022579224.58383356023821 15.36779707811817114.02824535117059824.36427629012695 14.11243340170483 12.72414224314130823.931459574007416 67.02559441274039 14.4107151097476215.39848037495838976.6538306984108925.89650810587095717.97515171372145295.48294582943252 14.78340533539433512.67824081840557167.41798576873889 11.61026832927846417.763934708282942 73.0400331790454 26.21598677528543721.086473319381238 94.2449453288559 12.02320533963250213.804606160830287 134.9306120750535225.34986136205870410.794140358502371144.4989096511651816.47320774925503 12.011691455844378154.7774818646732 28.8364017246436938.399348444790137 142.9552469284849417.08281431209836814.879732446303096 154.9678895207592315.56002914124156414.911113572072345 151.594655659586 25.43502334344941213.275024941597394 237.4394420683093586.80343780253493 9.298073657103735 244.6407179572301 37.91043095679009 7.582862433872318251.0617538001127 44.41348608713427 6.393457760711201 267.4568938007459 36.23264239834704 13.613927648644092241.4994311068455883.28595104733681 9.622767350801517 252.6048859908782730.58190374407016412.50947521438336 255.374252039527636.29889281644612 9.253300952802068 271.4140524732357634.54637819120151 13.739176761986469 12.05756057046047214.74892026278064226.994429532604197 15.75877414903572 16.42509134119633 32.91664846673709 16.79559392531295715.43515813813026 31.807591147525685 32.68904808090951 16.85736603754852329.30191109925967 36.88818830203117515.24989444434202723.3207475248551 45.8558828835191118.35603820658157331.26746201441802250.6461886974073417.77634010039676 23.133037855069336 78.9687004520418 29.96213905357626 13.83968993914519288.31690351648665 24.84494486077593215.14984406347646779.9007206581816 27.51330232259274313.241126271876562 87.46500707322576 19.7761164082213713.554557493572418 267.8100374532013 31.2500342954966728.970180907322444 262.6042744555324531.35616964752636810.501730117970036269.2384196846214 30.69936556645051310.984343378703137 265.8516459251092 28.94356408596296511.776048533486595 19.02066688488165319.82496193721016231.94191643469688620.33298199992822220.85224012111768 31.71496888604484 43.7364675180223417.68386421119634 34.45203578396963
zeros 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
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0 0.0 617.2476200000001 1055.27502 170.78198 639.6063800000001 1044.2584200000001-88.90979 430.86984 1051.26465 29.96675 517.3327 741.0960100000001212.08337000000003570.2014800000001666.7055700000001 123.68554 480.06427 626.5148300000001 199.55385 659.57892 745.05798 -145.97218 750.4809 735.8501000000001 -73.48505 697.4296300000001 642.68182 -137.36960000000002360.9039 474.04004000000003186.84929000000002420.86743 412.36603 134.71933 343.73737000000006388.03668000000005189.83162000000002750.32623 446.17697000000004-128.52777 819.76385 415.13217000000003-81.7 750.0458400000001 397.94098 -138.88400000000001156.44276000000002113.07307000000002104.00257 297.18088 88.12213000000001 67.0685 288.24664 73.76623000000001 176.63014 429.0928600000000343.0861 110.59769000000001815.7641600000001 63.39788000000001 -51.75869 967.9899300000001 122.58054000000001-32.7704 943.78925 105.33720000000001-122.344420000000011078.70935 143.54796000000002-60.93587000000001 660.8267800000001 1353.77527 20.198390000000003 566.59839 1449.57959 229.99652000000003596.4238300000001 1468.9681400000002-186.70021000000003593.64148 1249.1079100000002279.7764 580.73468 1233.74133 -222.92732 567.0025 1143.1092500000002315.56631000000004518.10278 1146.32483 -260.95828 771.56329 973.7791100000001 273.7876 746.2069700000001 944.3781100000001 327.45282000000003619.82306 916.1698000000001 -218.32727000000003574.16254 905.87732 -276.12146 366.1229600000000335.908210000000004193.14078 375.8658400000000539.8688 81.17185 1022.03961 113.13824000000001-136.45811 1034.97046 125.07877 -34.938210000000005736.5223400000001 1571.5815400000001106.42087000000001748.2420000000001 1574.9641100000001-31.667230000000004749.33246000000011747.60767 46.741460000000004
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" ] }, "metadata": {}, "output_type": "display_data" } ], "source": [ "from h2o.utils.shared_utils import _locate # private function. used to find files within h2o git project directory.\n", "\n", "# Import walking gait data\n", "gait = h2o.upload_file(path=_locate(\"smalldata/glrm_test/subject01_walk1.csv\"))\n", "gait.describe()" ] }, { "cell_type": "code", "execution_count": 5, "metadata": { "collapsed": false }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "\n", "glrm Model Build Progress: [##################################################] 100%\n", "Model Details\n", "=============\n", "H2OGeneralizedLowRankEstimator : Beta - Generalized Low Rank Model\n", "Model Key: GLRM_model_python_1449616108681_4\n", "\n", "Model Summary: \n" ] }, { "data": { "text/html": [ "
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number_of_iterationsfinal_step_sizefinal_objective_value
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" ], "text/plain": [ " number_of_iterations final_step_size final_objective_value\n", "-- ---------------------- ----------------- -----------------------\n", " 15 3.36077e-05 348858" ] }, "metadata": {}, "output_type": "display_data" }, { "name": "stdout", "output_type": "stream", "text": [ "\n", "\n", "ModelMetricsGLRM: glrm\n", "** Reported on train data. **\n", "\n", "MSE: NaN\n", "Sum of Squared Error (Numeric): 348858.1373928058\n", "Misclassification Error (Categorical): 0.0\n", "\n", "Scoring History: \n" ] }, { "data": { "text/html": [ "
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2015-12-08 15:08:53 0.870 sec13.00.0001680348858.1320175
2015-12-08 15:08:53 0.883 sec14.00.0000336348858.1320175
" ], "text/plain": [ " timestamp duration iteration step_size objective\n", "-- ------------------- ---------- ----------- ----------- -----------\n", " 2015-12-08 15:08:53 0.567 sec 0 1.05 355953\n", " 2015-12-08 15:08:53 0.654 sec 1 0.7 355953\n", " 2015-12-08 15:08:53 0.696 sec 2 0.466667 355953\n", " 2015-12-08 15:08:53 0.738 sec 3 0.311111 355953\n", " 2015-12-08 15:08:53 0.751 sec 4 0.155556 355953\n", " 2015-12-08 15:08:53 0.764 sec 5 0.0518519 355953\n", " 2015-12-08 15:08:53 0.777 sec 6 0.012963 355953\n", " 2015-12-08 15:08:53 0.790 sec 7 0.0136111 348858\n", " 2015-12-08 15:08:53 0.804 sec 8 0.00907407 348858\n", " 2015-12-08 15:08:53 0.819 sec 9 0.00604938 348858\n", " 2015-12-08 15:08:53 0.832 sec 10 0.00403292 348858\n", " 2015-12-08 15:08:53 0.845 sec 11 0.00201646 348858\n", " 2015-12-08 15:08:53 0.857 sec 12 0.000672154 348858\n", " 2015-12-08 15:08:53 0.870 sec 13 0.000168038 348858\n", " 2015-12-08 15:08:53 0.883 sec 14 3.36077e-05 348858" ] }, "metadata": {}, "output_type": "display_data" } ], "source": [ "# Basic GLRM using quadratic loss and no regularization (PCA)\n", "model = H2OGeneralizedLowRankEstimator(k=10, loss=\"Quadratic\", regularization_x=\"None\", regularization_y=\"None\", max_iterations=1000)\n", "model.train(x=list(range(1,gait.ncol)), training_frame=gait)\n", "model.show()" ] }, { "cell_type": "code", "execution_count": 6, "metadata": { "collapsed": false }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ " timestamp duration iteration step_size objective\n", "0 2015-12-08 15:08:53 0.567 sec 0 1.050000 355953.049522\n", "1 2015-12-08 15:08:53 0.654 sec 1 0.700000 355953.049522\n", "2 2015-12-08 15:08:53 0.696 sec 2 0.466667 355953.049522\n", "3 2015-12-08 15:08:53 0.738 sec 3 0.311111 355953.049522\n", "4 2015-12-08 15:08:53 0.751 sec 4 0.155556 355953.049522\n", "5 2015-12-08 15:08:53 0.764 sec 5 0.051852 355953.049522\n", "6 2015-12-08 15:08:53 0.777 sec 6 0.012963 355953.049522\n", "7 2015-12-08 15:08:53 0.790 sec 7 0.013611 348858.132018\n", "8 2015-12-08 15:08:53 0.804 sec 8 0.009074 348858.132018\n", "9 2015-12-08 15:08:53 0.819 sec 9 0.006049 348858.132018\n", "10 2015-12-08 15:08:53 0.832 sec 10 0.004033 348858.132018\n", "11 2015-12-08 15:08:53 0.845 sec 11 0.002016 348858.132018\n", "12 2015-12-08 15:08:53 0.857 sec 12 0.000672 348858.132018\n", "13 2015-12-08 15:08:53 0.870 sec 13 0.000168 348858.132018\n", "14 2015-12-08 15:08:53 0.883 sec 14 0.000034 348858.132018\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "/Library/Frameworks/Python.framework/Versions/3.5/lib/python3.5/site-packages/pandas/__init__.py:7: DeprecationWarning: bad escape \\s\n", " from pandas import hashtable, tslib, lib\n" ] } ], "source": [ "# Plot objective function value each iteration\n", "model_score = model.score_history()\n", "plt.xlabel(\"Iteration\")\n", "plt.ylabel(\"Objective\")\n", "plt.title(\"Objective Function Value per Iteration\")\n", "print(model_score)\n", "plt.plot(model_score[\"iteration\"], model_score[\"objective\"])\n", "plt.show()" ] }, { "cell_type": "code", "execution_count": 7, "metadata": { "collapsed": false }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "\n", "Archetypes: \n" ] }, { "data": { "text/html": [ "
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Arch4600.95940271057.7990932118.1058774605.33391651042.2068270-142.4636631405.39322911052.4555789-2.4098461647.4189804750.1105988174.2624235721.1601710708.432863979.1556549683.5102025633.9423045172.1508775481.2664588757.1188042-185.6352465564.0463207700.0051080-125.1630820452.6043856651.6132001-164.1249200681.8117427456.0963981162.3541268770.5018587448.3466124117.6853928723.1357129380.6554155174.5053708375.0848534445.8035254-153.7986203412.9171897386.6951114-102.7748625344.4331708409.3052480-158.6521281769.158518162.227350695.5941002899.4541724124.693835579.8744025889.9804230100.8377357183.68754391037.1292155149.4638459135.9538853199.381895392.4269904-53.8801098368.879347376.6879428-33.8535905352.342305166.0845674-123.5875318475.817514746.2186211-54.1968137634.89866121357.2063145-16.6710540523.98360111450.0565995185.5827328583.72503991470.7048475-227.1329363499.66269321254.0460960232.3542530628.48934831237.8459620-251.9294998438.26433631159.4956991256.3333075600.93711751132.7358762-293.0281225557.8786562917.7756397268.8450987509.9673425907.1905807312.6486220787.5745297983.9596069-205.3076461759.9164126946.1289960-264.7758445979.0691087109.5955275207.2209488992.0034563129.142863899.4579938409.222033239.0135908-131.2702147428.092274348.6543012-30.1699637700.41154291585.039250669.8483815717.57660351590.6042601-67.9432586697.90192731761.35830099.8290693
Arch5612.05586881067.6274113145.2645257633.12852081061.1246054-114.3924546423.67080731059.40460168.5125347579.7560686745.1525038205.7238263657.6489893681.7305181131.5338894577.9958696624.5273094206.8049977630.3653943755.7622130-162.5766154723.7054588738.6956878-95.8144508651.5139791650.3337009-143.5309175472.8939467502.1601092194.4571509505.8995569417.1731723151.2023278419.0118501433.6938975197.9140158670.2843224439.5041432-134.6750454716.7711785393.0040550-76.6976937651.8995109395.8185841-141.8222862158.1670484288.322730589.4387317249.9863550173.335218378.5476333211.1734880173.8813158178.1043399296.263748249.6394098132.2695853589.250774174.2557095-42.1712996757.094580876.0357577-11.2090608743.867041769.1300749-108.8661799870.655789754.6958381-38.8626583641.64752761371.2305177-11.5831722536.40731651468.3057319191.4537569578.12004921471.9758001-225.7652360545.74728091270.4406118247.7316136597.74705821232.6703870-245.2282013503.85427501169.2446667282.7663918549.28055461136.4143127-279.7150751648.8491945942.0633273287.3337626608.7628186930.1361040338.2976184651.5150281908.3090137-228.9626614607.2658598898.2079885-288.9091899233.695975188.3943274200.5556129269.583986782.454481096.0622232806.948834044.7398774-115.7886542820.343196453.4904394-13.6862102703.84369031595.598549868.5518637719.47504301597.3926888-69.6845632712.40278941772.99228954.2459793
Arch6596.92807201068.1999102179.3913745607.41314371063.0127648-81.9867437403.45986101069.369177149.4930995521.7369015748.8442395215.7914006577.0360129681.3541114122.9888758497.2985440629.5759420201.9741641635.3188706766.9933849-141.8694915731.0292483760.9645448-76.9107933675.3046699665.0577434-134.3635381398.5647680465.2073121184.1062834469.3783969416.5999611132.4518558395.3125353377.7384969187.0950989711.1729771467.5845879-129.0558624770.6533018424.4422887-84.7022772694.7567015422.5424043-135.0339470262.886362379.578386891.0453647408.136193879.191691565.0839989394.879537565.2042666171.6201171548.952444045.4831998114.5052980691.962427385.7475149-40.6094711857.6303764112.5363379-37.3191724831.1999594104.0932497-130.8071256965.7770341106.8871553-80.0208940634.14127751375.932537937.4279446544.46521341464.0062923252.6852154554.17328231490.7869711-165.3759646577.10797651263.1924487299.4031852534.86467141256.1256619-203.4569272553.95371331156.1984573334.1033874466.73344201170.4955606-238.0359556762.4997332993.7290417287.0150230739.2635894962.9993826339.9692293567.3886134937.9058127-203.7570781516.6694494929.1235177-259.0472101479.980077137.9926658191.2204495491.675635543.627215782.2930902894.780973689.3715874-147.6578933921.888913197.9719761-48.5811334697.12946491608.1981399126.2225890705.03883221613.9960282-12.7587010681.17413421781.122742366.6517677
Arch7633.55069251081.0029707122.2919535650.13406821067.2734656-137.5873055443.73886131070.5992233-9.9635859644.8843318761.2285818188.3046283728.6625879708.7071096110.9048041661.8617108640.6371215189.7119717617.2613686762.3967952-183.8518317707.6250007733.1359196-117.6743817623.6859361654.0748040-163.9239643574.4552022519.0006635176.7541510609.1740659435.0213249134.7022759522.3844279449.5399319180.5721434620.0965933441.2243109-155.0480936664.8246032391.6623765-98.6874173598.5231764398.3904748-160.9867504267.3321352298.551360070.0051270362.8562877186.697534365.6315493324.1057257192.5927327164.2704133414.337485262.0532586127.0075965518.183450177.1059709-59.3632314688.424701176.7470696-28.4987345672.725266469.1373539-126.5023826800.238541451.1538216-58.1569799665.71496971382.0530775-30.4903831557.51047561481.1869938170.8242786608.02201781484.4734625-245.5341945554.38475631282.6227030224.9531514637.64374361244.5483944-261.1803517504.48708531184.1079627255.9699930594.33892461144.8878957-295.3740076629.0489267944.7414981269.9058262583.8918461935.5446399316.9192180711.6889669925.2018431-238.5165701668.8072734910.6968110-298.8913369350.7195106108.6251060190.4268820386.110690299.361832287.9851981735.565312942.8873398-134.0914765750.311113552.2629130-32.4959455730.57040361604.788601247.0021690745.74029361605.2923007-91.3282526740.03692731779.3820981-17.7940820
Arch8627.82228531055.8696242154.9743032650.73612981048.4046456-105.2306011440.81294871053.286983713.5710207537.9151826740.2244790204.0480227598.7795704664.7330315122.3976568508.1639774622.8395425197.4379109665.9398463748.6279076-157.4759173762.6125520740.6189277-91.1481668700.8799209646.1558178-142.2581797385.4431002483.2066003187.2127885432.0225682409.8823726138.0401505349.2592729404.6825701191.4213588745.4047589442.7090846-135.9730966801.8029885402.5426933-81.8172714734.0389096397.0547184-144.6488665117.7318986187.3152548101.6681663239.9328180119.168710072.8554150218.9391314105.3287289177.8965683334.417682939.1937120114.1180733726.678716870.7788058-52.8348666891.244957089.7334878-25.8363192877.144139381.8214760-122.35187061004.313807483.6834831-54.1974259667.56755961357.1225155-3.2467666571.33580821455.7829805203.9436193600.74119291465.1510301-214.0527878590.18600281256.5515610256.1717284595.05691181227.2589665-241.6618259556.47307501152.3790141292.5515044535.29765261136.3001233-276.0605937734.3634677953.3360007270.2471526703.3478313931.9927679323.6573253636.7290320905.8273848-231.4733080587.8766402895.5135382-288.2740464273.109904542.5434668194.4393038293.244075446.719641583.7429432941.930280265.5984737-130.9488409955.867816175.3804224-29.0303593740.88616391574.658472779.3309282754.19369861576.2404381-59.0664394759.76455011751.047665017.3802296
Arch9633.12525071067.3805142154.9123525623.33794101050.9882546-105.0278463431.00421841055.160119144.2471095660.5834017752.1603608204.7280426729.3004805707.6518424108.5242166681.7111387632.3270962192.8883962573.3213422748.1157918-166.8228703674.7325806712.7890973-123.2748814579.9445434639.1262960-160.1750222647.7587082457.2279862180.0257662721.9192547422.9996539122.6784157662.5721033371.1956235184.6972994509.7593433465.4313549-165.4279270505.6867923394.2412621-113.4254765462.2109942453.6737498-166.7543930579.218363870.253336095.2982785724.000899178.952541767.1710863712.658019564.1532517173.9951418866.536118150.8161915114.6423817178.5865074304.0856727-57.1864435270.0452765153.8046935-41.6603586239.4426665163.7435381-132.8002904301.464980755.7393915-68.0081168650.21647981369.445651835.6481340549.95323681447.4416331249.5125975583.19136721491.6765549-165.5061589553.65323711244.9031728288.2394683603.71670951254.7281287-204.2410885509.10821221141.4283075311.8787361556.28205991160.8872010-247.2341551656.2002597915.2766524304.9937660612.6332028898.0372366351.3154095657.6457522929.1769727-211.0505758616.6545914924.0798200-274.1841429799.814608940.5199502190.7176040811.158798848.430903981.6528528254.0959961100.5478718-141.8880420280.310381995.0801262-41.9476683710.09520331594.9198593131.4439267721.90385171603.6732747-6.5177796703.94605711771.836227376.2633474
Arch10608.20135461085.8013949116.4198743618.61118401063.4379926-143.4721423414.44087131071.5402852-8.1174399667.2975322781.5744807185.3741252752.9110124743.1109874100.1055224706.5266357665.5626996185.2017125540.3928455763.1608472-184.1777111628.3088730720.8094601-118.2282760530.2149688654.0645272-161.1165638653.4750476514.1412056172.6658681718.4417579453.7627998131.1174154637.3456190431.1420627180.7623767494.3794579440.5141437-149.1108978537.8895407388.5757874-94.6942494470.6163481399.2326565-154.4257263476.1777329176.699944080.6064944611.4726730134.792540475.5890414579.5793930121.7153985175.5716844720.937650760.0739552137.4081291370.650974979.4749664-50.7524998537.752405674.5019814-26.0313634525.159469563.3884851-118.1176265649.455151047.4266524-48.8902521639.24423831383.2628106-25.5174758524.87455191478.5627288173.9827704587.41913281490.4469319-239.8097346506.59169701282.2741687226.0017674633.34274811254.7386370-257.1330176448.77468481186.9247805252.7774664602.31321121150.1572030-295.2345935565.5432261944.2790059271.8645987517.1708213935.6101795315.7561557761.4457789967.6713723-218.0948446727.8694088939.7565385-279.0703260645.567954967.2023572203.2929667677.596852575.321709998.5962080585.153566840.4237777-125.6992695599.432909349.2400454-24.1058127700.83430171610.395455555.4276538717.90463071613.7742882-82.5784158701.78542651786.6759211-7.4517057
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rwristmedy rwristmedz rwristlatx rwristlaty rwristlatz lwristmedx lwristmedy lwristmedz lwristlatx lwristlaty lwristlatz rtoelatx rtoelaty rtoelatz rtoemedx rtoemedy rtoemedz ltoelatx ltoelaty ltoelatz ltoemedx ltoemedy ltoemedz rtemplex rtempley rtemplez ltemplex ltempley ltemplez topheadx topheady topheadz\n", "------ -------- -------- -------- -------- -------- -------- ---------- ---------- ---------- -------------- -------------- -------------- -------------- -------------- -------------- ------------- ------------- ------------- -------------- -------------- -------------- -------------- -------------- -------------- ------------- ------------- ------------- -------------- -------------- -------------- -------------- -------------- -------------- ------------- ------------- ------------- -------------- -------------- -------------- -------------- -------------- -------------- ------------- ------------- ------------- -------- -------- -------- -------------- -------------- -------------- -------------- -------------- -------------- ---------- ---------- ---------- -------- -------- -------- -------------- -------------- -------------- -------------- -------------- -------------- ---------- ---------- ---------- ---------- ---------- ---------- ------------ ------------ ------------ ------------ ------------ ------------ --------- --------- --------- --------- --------- --------- --------- --------- --------- --------- --------- --------- ------------ ------------ ------------ ------------ ------------ ------------ ------------ ------------ ------------ ------------ ------------ ------------ ---------- ---------- ---------- ---------- ---------- ---------- ---------- ---------- ---------- ---------- ---------- ---------- ---------- ---------- ---------- ---------- ---------- ---------- ---------- ---------- ----------\n", "Arch1 621.671 1048.26 133.49 615.507 1033.06 -127.325 422.301 1039.33 23.9917 677.908 745.236 183.617 751.541 708.819 85.867 714.92 628.892 172.979 491.697 748.035 -176.544 577.983 688.207 -125.974 464.633 642.609 -161.512 708.918 452.21 164.236 790.166 432.403 107.517 740.105 371.032 171.619 367.879 449.554 -160.247 384.74 380.219 -109.988 327.525 423.91 -164.945 719.5 63.5178 91.9593 860.179 90.8702 64.3472 851.403 74.1125 170.556 1003.89 86.4455 110.638 93.6832 172.137 -65.822 238.634 96.1832 -39.226 216.062 83.0191 -130.864 314.103 40.2095 -54.8557 645.174 1349.68 14.1055 533.603 1431.48 221.303 588.113 1467.9 -192.046 518.21 1232.2 261.147 624.508 1233.56 -225.29 462.786 1133.38 281.924 589.27 1132.83 -269.517 593.691 897.827 286.096 546.616 883.689 329.446 743.915 941.881 -206.018 709.139 917.879 -267.862 939.93 61.4481 188.345 950.664 73.2871 78.9473 250.926 40.5593 -133.043 277.984 47.1457 -32.3848 702.583 1581.78 104.877 716.731 1588.8 -33.1485 689.107 1756.99 46.0475\n", "Arch2 619.784 1078.3 174.125 619.069 1071.16 -86.6595 420.594 1071.66 52.4755 592.49 753.81 214.314 653.36 695.774 118.672 587.954 631.417 201.193 642.412 772.389 -152.787 747.397 763.997 -102.508 680.342 668.832 -146.943 520.718 458.258 184.251 593.773 418.505 129.472 527.479 371.572 187.481 659.162 487.294 -148.018 674.489 418.629 -97.9493 617.499 463.716 -151.134 424.361 71.1734 93.91 568.534 78.1706 64.1312 558.024 62.8729 171.055 710.991 49.014 109.731 394.774 235.102 -44.7555 527.725 138.518 -33.5789 500.267 142.279 -128.208 596.726 57.178 -70.2208 644.046 1387.92 40.4364 549.917 1469.25 257.098 563.644 1504.44 -161.692 575.146 1265.64 298.982 562.771 1266.95 -201.682 543.894 1158.89 328.55 502.934 1177.65 -239.571 724.389 961.085 301.72 690.063 937.026 352.171 598.064 942.144 -207.663 551.032 936.841 -266.305 645.773 38.7053 187.629 655.032 46.55 77.5652 533.394 86.2905 -140.898 561.78 84.4505 -41.3702 696.344 1625.06 134.132 705.109 1633.79 -4.88141 666.305 1798.12 76.871\n", "Arch3 595.978 1049.92 174.106 617.563 1041.74 -86.3426 408.197 1047.83 33.9567 493.869 736.255 212.8 546.559 661.055 125.836 456.728 620.946 200.769 637.241 741.886 -139.026 731.359 734.769 -69.6277 674.919 640.189 -127.125 335.764 470.835 185.446 394.622 408.922 134.217 315.612 387.062 188.626 732.033 443.055 -120.483 794.377 412.085 -69.6143 726.536 396.316 -128.467 128.466 119.658 95.4913 268.861 91.7201 65.2862 253.091 76.0728 173.038 392.561 43.4195 109.67 780.118 67.1312 -44.2806 935.928 120.336 -15.2861 922.159 108.667 -112.352 1048.06 135.285 -45.9135 635.081 1354.67 21.0897 539.725 1447.32 230.873 562.245 1462.13 -187.47 571.816 1247.81 281.655 550.691 1225.83 -219.09 547.527 1141.54 318.31 486.893 1137.25 -253.805 750.839 971.376 276.296 726.96 943.857 331.295 586.29 905.01 -212.894 537.718 895.925 -270.128 327.438 35.4986 190.979 341.773 39.8148 79.7959 988.581 105.629 -121.616 1002.48 117.297 -19.9811 692.219 1594.04 103.708 701.94 1597.52 -35.3287 668.647 1764.85 40.5665\n", "Arch4 600.959 1057.8 118.106 605.334 1042.21 -142.464 405.393 1052.46 -2.40985 647.419 750.111 174.262 721.16 708.433 79.1557 683.51 633.942 172.151 481.266 757.119 -185.635 564.046 700.005 -125.163 452.604 651.613 -164.125 681.812 456.096 162.354 770.502 448.347 117.685 723.136 380.655 174.505 375.085 445.804 -153.799 412.917 386.695 -102.775 344.433 409.305 -158.652 769.159 62.2274 95.5941 899.454 124.694 79.8744 889.98 100.838 183.688 1037.13 149.464 135.954 199.382 92.427 -53.8801 368.879 76.6879 -33.8536 352.342 66.0846 -123.588 475.818 46.2186 -54.1968 634.899 1357.21 -16.6711 523.984 1450.06 185.583 583.725 1470.7 -227.133 499.663 1254.05 232.354 628.489 1237.85 -251.929 438.264 1159.5 256.333 600.937 1132.74 -293.028 557.879 917.776 268.845 509.967 907.191 312.649 787.575 983.96 -205.308 759.916 946.129 -264.776 979.069 109.596 207.221 992.003 129.143 99.458 409.222 39.0136 -131.27 428.092 48.6543 -30.17 700.412 1585.04 69.8484 717.577 1590.6 -67.9433 697.902 1761.36 9.82907\n", "Arch5 612.056 1067.63 145.265 633.129 1061.12 -114.392 423.671 1059.4 8.51253 579.756 745.153 205.724 657.649 681.731 131.534 577.996 624.527 206.805 630.365 755.762 -162.577 723.705 738.696 -95.8145 651.514 650.334 -143.531 472.894 502.16 194.457 505.9 417.173 151.202 419.012 433.694 197.914 670.284 439.504 -134.675 716.771 393.004 -76.6977 651.9 395.819 -141.822 158.167 288.323 89.4387 249.986 173.335 78.5476 211.173 173.881 178.104 296.264 49.6394 132.27 589.251 74.2557 -42.1713 757.095 76.0358 -11.2091 743.867 69.1301 -108.866 870.656 54.6958 -38.8627 641.648 1371.23 -11.5832 536.407 1468.31 191.454 578.12 1471.98 -225.765 545.747 1270.44 247.732 597.747 1232.67 -245.228 503.854 1169.24 282.766 549.281 1136.41 -279.715 648.849 942.063 287.334 608.763 930.136 338.298 651.515 908.309 -228.963 607.266 898.208 -288.909 233.696 88.3943 200.556 269.584 82.4545 96.0622 806.949 44.7399 -115.789 820.343 53.4904 -13.6862 703.844 1595.6 68.5519 719.475 1597.39 -69.6846 712.403 1772.99 4.24598\n", "Arch6 596.928 1068.2 179.391 607.413 1063.01 -81.9867 403.46 1069.37 49.4931 521.737 748.844 215.791 577.036 681.354 122.989 497.299 629.576 201.974 635.319 766.993 -141.869 731.029 760.965 -76.9108 675.305 665.058 -134.364 398.565 465.207 184.106 469.378 416.6 132.452 395.313 377.738 187.095 711.173 467.585 -129.056 770.653 424.442 -84.7023 694.757 422.542 -135.034 262.886 79.5784 91.0454 408.136 79.1917 65.084 394.88 65.2043 171.62 548.952 45.4832 114.505 691.962 85.7475 -40.6095 857.63 112.536 -37.3192 831.2 104.093 -130.807 965.777 106.887 -80.0209 634.141 1375.93 37.4279 544.465 1464.01 252.685 554.173 1490.79 -165.376 577.108 1263.19 299.403 534.865 1256.13 -203.457 553.954 1156.2 334.103 466.733 1170.5 -238.036 762.5 993.729 287.015 739.264 962.999 339.969 567.389 937.906 -203.757 516.669 929.124 -259.047 479.98 37.9927 191.22 491.676 43.6272 82.2931 894.781 89.3716 -147.658 921.889 97.972 -48.5811 697.129 1608.2 126.223 705.039 1614 -12.7587 681.174 1781.12 66.6518\n", "Arch7 633.551 1081 122.292 650.134 1067.27 -137.587 443.739 1070.6 -9.96359 644.884 761.229 188.305 728.663 708.707 110.905 661.862 640.637 189.712 617.261 762.397 -183.852 707.625 733.136 -117.674 623.686 654.075 -163.924 574.455 519.001 176.754 609.174 435.021 134.702 522.384 449.54 180.572 620.097 441.224 -155.048 664.825 391.662 -98.6874 598.523 398.39 -160.987 267.332 298.551 70.0051 362.856 186.698 65.6315 324.106 192.593 164.27 414.337 62.0533 127.008 518.183 77.106 -59.3632 688.425 76.7471 -28.4987 672.725 69.1374 -126.502 800.239 51.1538 -58.157 665.715 1382.05 -30.4904 557.51 1481.19 170.824 608.022 1484.47 -245.534 554.385 1282.62 224.953 637.644 1244.55 -261.18 504.487 1184.11 255.97 594.339 1144.89 -295.374 629.049 944.741 269.906 583.892 935.545 316.919 711.689 925.202 -238.517 668.807 910.697 -298.891 350.72 108.625 190.427 386.111 99.3618 87.9852 735.565 42.8873 -134.091 750.311 52.2629 -32.4959 730.57 1604.79 47.0022 745.74 1605.29 -91.3283 740.037 1779.38 -17.7941\n", "Arch8 627.822 1055.87 154.974 650.736 1048.4 -105.231 440.813 1053.29 13.571 537.915 740.224 204.048 598.78 664.733 122.398 508.164 622.84 197.438 665.94 748.628 -157.476 762.613 740.619 -91.1482 700.88 646.156 -142.258 385.443 483.207 187.213 432.023 409.882 138.04 349.259 404.683 191.421 745.405 442.709 -135.973 801.803 402.543 -81.8173 734.039 397.055 -144.649 117.732 187.315 101.668 239.933 119.169 72.8554 218.939 105.329 177.897 334.418 39.1937 114.118 726.679 70.7788 -52.8349 891.245 89.7335 -25.8363 877.144 81.8215 -122.352 1004.31 83.6835 -54.1974 667.568 1357.12 -3.24677 571.336 1455.78 203.944 600.741 1465.15 -214.053 590.186 1256.55 256.172 595.057 1227.26 -241.662 556.473 1152.38 292.552 535.298 1136.3 -276.061 734.363 953.336 270.247 703.348 931.993 323.657 636.729 905.827 -231.473 587.877 895.514 -288.274 273.11 42.5435 194.439 293.244 46.7196 83.7429 941.93 65.5985 -130.949 955.868 75.3804 -29.0304 740.886 1574.66 79.3309 754.194 1576.24 -59.0664 759.765 1751.05 17.3802\n", "Arch9 633.125 1067.38 154.912 623.338 1050.99 -105.028 431.004 1055.16 44.2471 660.583 752.16 204.728 729.3 707.652 108.524 681.711 632.327 192.888 573.321 748.116 -166.823 674.733 712.789 -123.275 579.945 639.126 -160.175 647.759 457.228 180.026 721.919 423 122.678 662.572 371.196 184.697 509.759 465.431 -165.428 505.687 394.241 -113.425 462.211 453.674 -166.754 579.218 70.2533 95.2983 724.001 78.9525 67.1711 712.658 64.1533 173.995 866.536 50.8162 114.642 178.587 304.086 -57.1864 270.045 153.805 -41.6604 239.443 163.744 -132.8 301.465 55.7394 -68.0081 650.216 1369.45 35.6481 549.953 1447.44 249.513 583.191 1491.68 -165.506 553.653 1244.9 288.239 603.717 1254.73 -204.241 509.108 1141.43 311.879 556.282 1160.89 -247.234 656.2 915.277 304.994 612.633 898.037 351.315 657.646 929.177 -211.051 616.655 924.08 -274.184 799.815 40.52 190.718 811.159 48.4309 81.6529 254.096 100.548 -141.888 280.31 95.0801 -41.9477 710.095 1594.92 131.444 721.904 1603.67 -6.51778 703.946 1771.84 76.2633\n", "Arch10 608.201 1085.8 116.42 618.611 1063.44 -143.472 414.441 1071.54 -8.11744 667.298 781.574 185.374 752.911 743.111 100.106 706.527 665.563 185.202 540.393 763.161 -184.178 628.309 720.809 -118.228 530.215 654.065 -161.117 653.475 514.141 172.666 718.442 453.763 131.117 637.346 431.142 180.762 494.379 440.514 -149.111 537.89 388.576 -94.6942 470.616 399.233 -154.426 476.178 176.7 80.6065 611.473 134.793 75.589 579.579 121.715 175.572 720.938 60.074 137.408 370.651 79.475 -50.7525 537.752 74.502 -26.0314 525.159 63.3885 -118.118 649.455 47.4267 -48.8903 639.244 1383.26 -25.5175 524.875 1478.56 173.983 587.419 1490.45 -239.81 506.592 1282.27 226.002 633.343 1254.74 -257.133 448.775 1186.92 252.777 602.313 1150.16 -295.235 565.543 944.279 271.865 517.171 935.61 315.756 761.446 967.671 -218.095 727.869 939.757 -279.07 645.568 67.2024 203.293 677.597 75.3217 98.5962 585.154 40.4238 -125.699 599.433 49.24 -24.1058 700.834 1610.4 55.4277 717.905 1613.77 -82.5784 701.785 1786.68 -7.45171" ] }, "metadata": {}, "output_type": "display_data" }, { "name": "stdout", "output_type": "stream", "text": [ "\n" ] } ], "source": [ "# Archetype to feature mapping (Y)\n", "gait_y = model._model_json[\"output\"][\"archetypes\"]\n", "print(gait_y)\n", "\n", "gait_y_np = np.array(model.archetypes())\n", "x_coords = range(0, gait_y_np.shape[1], 3)\n", "y_coords = range(1, gait_y_np.shape[1], 3)\n", "\n", "# Plot archetypes on x- vs. y-coordinate features\n", "for k in range(gait_y_np.shape[0]):\n", " x_pts = gait_y_np[k, x_coords]\n", " y_pts = gait_y_np[k, y_coords]\n", " plt.plot(x_pts, y_pts, 'bo')\n", "\n", " # Add feature labels to each point\n", " feat_names = [nam[:-1] for nam in gait_y.col_header[1::3]]\n", " for i in range(len(feat_names)):\n", " plt.annotate(feat_names[i], xy = [x_pts[i], y_pts[i]])\n", " plt.title(\"Feature Weights of Archetype \" + str(k+1))\n", " plt.xlabel(\"X-Coordinate Weight\")\n", " plt.ylabel(\"Y-Coordinate Weight\")\n", " plt.show()" ] }, { "cell_type": "code", "execution_count": 8, "metadata": { "collapsed": false }, "outputs": [ { "data": { "text/html": [ "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "
Arch1 Arch2 Arch3 Arch4 Arch5 Arch6 Arch7 Arch8 Arch9 Arch10
-0.362422 -0.570615 0.366496 0.160492 -0.496611 0.545266 0.150324 0.685559 0.492391 0.0320439
-0.268436 -0.375445 0.323127 0.129955 -0.391362 0.353488 0.04921670.8056 0.332023 0.0441441
-0.157574 -0.19305 0.264606 0.088763 -0.273069 0.173273 -0.06318780.929926 0.169373 0.0625199
-0.0566838-0.0254627 0.206427 0.0448357 -0.171361 0.0163901-0.139129 1.02823 0.0227587 0.0743581
0.0149536 0.126614 0.143023 0.00511055-0.0848319 -0.120307 -0.188121 1.1071 -0.0968295 0.0928464
0.0835833 0.21865 0.0791339 -0.0338994 0.00405319-0.207306 -0.202243 1.1465 -0.177828 0.0886814
0.12449 0.296898 0.00377988-0.0662024 0.0645689 -0.258014 -0.1609 1.15533 -0.235635 0.0740767
0.139783 0.322037 -0.0557214 -0.0879325 0.11846 -0.275535 -0.08369941.11837 -0.249453 0.0517003
0.129183 0.297413 -0.109574 -0.0887692 0.176341 -0.255597 0.01551581.04285 -0.226476 0.0170711
0.115742 0.232302 -0.144512 -0.0850974 0.224998 -0.202661 0.153602 0.919357-0.181238 -0.0343747
" ] }, "metadata": {}, "output_type": "display_data" } ], "source": [ "# Projection into archetype space (X)\n", "x_key = model._model_json[\"output\"][\"representation_name\"]\n", "gait_x = h2o.get_frame(x_key)\n", "gait_x.show()\n", "\n", "time_np = np.array(h2o.as_list(gait[\"Time\"]))\n", "gait_x_np = np.array(h2o.as_list(gait_x))\n", "\n", "# Plot archetypes over time\n", "lines = []\n", "for i in range(gait_x_np.shape[1]):\n", " lines += plt.plot(time_np, gait_x_np[:,i], '-')\n", "plt.title(\"Archetypes over Time\")\n", "plt.xlabel(\"Time\")\n", "plt.ylabel(\"Archetypal Projection\")\n", "plt.legend(lines, gait_x.col_names)\n", "plt.show()" ] }, { "cell_type": "code", "execution_count": 9, "metadata": { "collapsed": false }, "outputs": [ { "data": { "text/html": [ "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "
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" ] }, "metadata": {}, "output_type": "display_data" }, { "data": { "text/plain": [] }, "execution_count": 9, "metadata": {}, "output_type": "execute_result" } ], "source": [ "# Reconstruct data from X and Y\n", "pred = model.predict(gait)\n", "pred.head()" ] }, { "cell_type": "code", "execution_count": 10, "metadata": { "collapsed": false }, "outputs": [], "source": [ "# Plot original and reconstructed L.Acromium.X over time\n", "lacro_np = np.array(h2o.as_list(gait[\"L.Acromium.X\"]))\n", "lacro_pred_np = np.array(h2o.as_list(pred[\"reconstr_L.Acromium.X\"]))\n", "line_orig = plt.plot(time_np, lacro_np, '-')\n", "line_imp = plt.plot(time_np, lacro_pred_np, '-')\n", "\n", "plt.title(\"Position of Left Acromium over Time\")\n", "plt.xlabel(\"Time\")\n", "plt.ylabel(\"X-Coordinate of Left Acromium\")\n", "blue_patch = mpatches.Patch(color = 'blue', label = 'Original')\n", "green_patch = mpatches.Patch(color = 'green', label='Imputed')\n", "plt.legend([blue_patch, green_patch], [\"Original\", \"Imputed\"])\n", "plt.show()" ] }, { "cell_type": "code", "execution_count": 11, "metadata": { "collapsed": false }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "\n", "Parse Progress: [##################################################] 100%\n", "Rows:151 Cols:124\n", "\n", "Chunk compression summary: \n" ] }, { "data": { "text/html": [ "
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Time R.ASIS.X R.ASIS.Y R.ASIS.Z L.ASIS.X L.ASIS.Y L.ASIS.Z V.Sacral.X V.Sacral.Y V.Sacral.Z R.Thigh.Upper.X R.Thigh.Upper.Y R.Thigh.Upper.Z R.Thigh.Front.X R.Thigh.Front.Y R.Thigh.Front.Z R.Thigh.Rear.X R.Thigh.Rear.Y R.Thigh.Rear.Z L.Thigh.Upper.X L.Thigh.Upper.Y L.Thigh.Upper.Z L.Thigh.Front.X L.Thigh.Front.Y L.Thigh.Front.Z L.Thigh.Rear.X L.Thigh.Rear.Y L.Thigh.Rear.Z R.Shank.Upper.X R.Shank.Upper.Y R.Shank.Upper.Z R.Shank.Front.X R.Shank.Front.Y R.Shank.Front.Z R.Shank.Rear.X R.Shank.Rear.Y R.Shank.Rear.Z L.Shank.Upper.X L.Shank.Upper.Y L.Shank.Upper.Z L.Shank.Front.X L.Shank.Front.Y L.Shank.Front.Z L.Shank.Rear.X L.Shank.Rear.Y L.Shank.Rear.Z R.Heel.X R.Heel.Y R.Heel.Z R.Midfoot.Sup.X R.Midfoot.Sup.Y R.Midfoot.Sup.Z R.Midfoot.Lat.X R.Midfoot.Lat.Y R.Midfoot.Lat.Z R.Toe.Tip.X R.Toe.Tip.Y R.Toe.Tip.Z L.Heel.X L.Heel.Y L.Heel.Z L.Midfoot.Sup.X L.Midfoot.Sup.Y L.Midfoot.Sup.Z L.Midfoot.Lat.X L.Midfoot.Lat.Y L.Midfoot.Lat.Z L.Toe.Tip.X L.Toe.Tip.Y L.Toe.Tip.Z Sternum.X Sternum.Y Sternum.Z R.Acromium.X R.Acromium.Y R.Acromium.Z L.Acromium.X L.Acromium.Y L.Acromium.Z R.Bicep.X R.Bicep.Y R.Bicep.Z L.Bicep.X L.Bicep.Y L.Bicep.Z R.Elbow.X R.Elbow.Y R.Elbow.Z L.Elbow.X L.Elbow.Y L.Elbow.Z R.Wrist.Med.X R.Wrist.Med.Y R.Wrist.Med.Z R.Wrist.Lat.X R.Wrist.Lat.Y R.Wrist.Lat.Z L.Wrist.Med.X L.Wrist.Med.Y L.Wrist.Med.Z L.Wrist.Lat.X L.Wrist.Lat.Y L.Wrist.Lat.Z R.Toe.Lat.X R.Toe.Lat.Y R.Toe.Lat.Z R.Toe.Med.X R.Toe.Med.Y R.Toe.Med.Z L.Toe.Lat.X L.Toe.Lat.Y L.Toe.Lat.Z L.Toe.Med.X L.Toe.Med.Y L.Toe.Med.Z R.Temple.X R.Temple.Y R.Temple.Z L.Temple.X L.Temple.Y L.Temple.Z Top.Head.X Top.Head.Y Top.Head.Z
type real real real real real real real real real real real real real real real real real real real real real real real real real real real real real real real real real real real real real real real real real real real real real real real real real real real real real real real real real real real real real real real real real real real real real real real real real real real real real real real real real real real real real real real real real real real real real real real real real real real real real real real real real real real real real real real real real real real real real real real real real real real real
mins 0.0 588.90717000000011042.5732400000002107.79163000000001600.01556 1029.2542700000001-152.53879 399.400090000000031034.9012500000001-21.440830000000002481.83603000000005732.70135 169.71159 535.63422 657.21033 74.20708 443.03299000000004613.54547 168.15961000000001468.19415000000004737.7208300000001 -194.25998 550.69415 684.75494 -133.58800000000002435.01773000000003627.4998800000001 -170.86086 319.34705 445.08429 157.69023 376.44724 403.25574000000006102.54192 295.04089000000005368.36661000000004165.6133 341.20230000000004438.80435000000006-172.96315 365.72482 375.95242 -120.97533000000001304.46347000000003393.67728000000005-173.38676 68.60076000000001 56.43383000000001 59.94800000000001 190.9884500000000376.90237 57.86759000000001157.3250300000000362.790000000000006159.97461 242.9085800000000333.52863 102.0894000000000176.37951000000001 60.01719000000001 -74.0361 211.8596800000000370.39124000000001 -69.30095 185.39088 48.22646 -140.09074 254.42706 36.65646 -88.18266000000001 627.3817700000001 1342.8541300000002-35.207950000000004511.800320000000061427.4450700000002164.48206000000002551.72424 1453.5893600000002-249.89265000000003485.945590000000041227.90454 216.05853000000002531.12134 1217.6442900000002-266.60974000000004424.32767 1129.49243 242.44150000000002460.207030000000031123.8029800000002-304.79358 535.8743900000001889.81964 262.1105 486.99316000000005876.5388200000001 304.71069 554.3527200000001895.9242600000001 -240.59163 503.10611000000006886.58942 -300.87775000000005179.7708 33.33099 181.24631000000002218.04131 36.96362000000000671.79319000000001 202.7406600000000236.02512 -153.13719 228.0489800000000342.970600000000005-54.889030000000005675.97009 1562.28418 44.154320000000006683.5089700000001 1567.2720900000002-94.07465 614.13971 1740.3891600000002-19.488380000000003
mean 1.2499999999999993614.52193738095261065.674211068702 147.70381085937498621.4685777519381 1053.8870899173553-113.1220462992126 419.961478582089571058.939616585365721.11738235294117 602.0237726515152 751.7273182677166 198.12656452380958676.998435725191 698.1164752554741 107.98844620155043607.4938511450381 634.0988691911766191.19427805084752589.7071056000001 756.6348315748031 -164.43936330769233676.351652421875 728.9683143750003-105.68779928571426598.0017102419358 651.4269711450382 -150.98209781250003543.6514965891474 476.8315416923078 177.90240643939393612.2485662962965 427.1291536065575 128.55800023437493550.9574812499998 395.28342082644616183.20065491803282578.969913643411 453.85756544776143-144.9175518897638 613.9014913636362 398.72314492063515-94.28277031496066 548.7100873076923 418.68888263157896-151.06090469696966418.61944007633605121.1801637007873590.99763584615388 545.7749826356588 110.4112203076923269.78039318518516524.5631150406504 93.92404014814814 173.7732026190476 654.1564922222226 66.88846407692313 120.13476531249998431.8754314285713 129.84234287878792-51.27995097560977 574.9778156249997 103.83877976377953-30.091574341085284566.1202526984124 96.79594126050421 -123.58381375939845678.8507586466168 66.44135443548387 -58.160875600000004643.7707248799999 1367.91781435114567.475559302325582 541.6002414960632 1458.3426990551186215.23162066176474578.89798065040631481.9918678571426-202.49140905511805547.4777600000001 1259.51176984252 262.38946829457376596.56774721804541244.4882707758622-229.6007026016261 503.46534892561981157.8093834848485293.64344187499995545.9599920634921 1147.6621124390247-268.3959422608696 657.2295957692305944.0677635200004 282.97286181818214617.1352212213739 928.3252148031497 331.3479852307692 673.9732800735296938.227669083969 -215.0208914173229 628.2167179365077 921.9658151162794-273.3403533333336 592.7331266917291 61.25295527131784 194.7007793939394 616.1231278030305 67.72312863999998 86.20805892561982 610.7499204098361 64.80942227642278 -131.93505530769218652.8815048837212 74.28172511811024 -32.449527720588215708.096513 1597.334039224806592.79476772727277 718.288894140625 1603.7745607031247-44.273716842105294698.76248312977121773.215342047244334.894787603305765
maxs 2.5 641.12048 1091.26807 180.07411000000002661.46918 1078.02356 -80.82956 451.5914 1077.77014 55.297180000000004 692.8951400000001 788.1136500000001 216.86717000000002766.4453100000001750.7237500000001 136.25021 726.57483 672.4224200000001209.89946 674.53168 781.90839 -138.11635 772.35175 780.8144500000001-66.30186 713.1610700000001 681.3862300000001 -123.18440000000001719.6970200000001 531.05676 200.56787000000003799.4701500000001 457.5513 154.56749000000002751.88885 458.64368 202.59061000000003764.30676 494.35605000000004-116.46951000000001821.6690100000001 425.57733 -63.825 750.77588 472.92294000000004-125.02680000000001812.50183 320.70309000000003108.16100000000002935.61414 197.97754 85.62352000000001934.44775 209.43217 188.70589 1071.77734 179.28133000000003153.59363000000002821.7641000000001 321.80249000000003-34.92287 971.3176300000001 178.00603 -6.83138 955.7309600000001 184.36398000000003-104.369800000000011082.51477 168.64880000000002-33.049710000000005673.89301 1393.888060000000243.520900000000005 573.64575 1485.37354 262.06827000000004609.36566 1507.8101800000002-156.17076 593.2045300000001 1288.58093 305.86801 643.91699 1271.7580600000001-196.56128 567.0025 1193.1440400000001339.82635000000005608.93268 1186.43945 -230.94901000000002771.56329 1003.0836800000001312.96448000000004750.302 969.89471 362.03549000000004793.86859 998.83923 -188.33229000000003768.9158900000001 958.34167 -249.44443 1022.3231800000001136.89597 218.5173 1029.85803 153.3546 113.458900000000011024.0694600000002132.61819 -111.9407 1039.3868400000001146.49858 -9.441730000000002 740.63611 1640.0118400000001139.15808 754.6250600000001 1647.88391000000020.84904 752.89178 1809.149170000000185.29955000000001
sigma 0.728898255359873414.9221530809129514.11188006049316425.43206689862728715.19850873128531414.16278869406504124.242934872860133 14.43471020752160612.10066654207011 24.0349655412507 67.10426858935227 14.20552272425050315.68790279071079874.6813145799344826.38901655534752818.4568665408435 96.42257330093962 15.0677784034913712.50842640879327366.34624439841295 11.26495807955522117.842421998298626 72.2174940572667526.1430363886991521.33082154502956 92.84194258669261 11.52326168054009213.95274158238682 134.8087650473843325.74387248724348611.136201948564182143.9726247367157 16.49871099843055711.671072512430744155.3766756069692628.5870499369530978.389006495328955 142.3712674424119817.23679898685475814.953128359661894 154.9570288398792615.24132966982570814.46404818246618 153.0523155406795625.82216949530055313.234972938997545 235.0416459510220881.84095704372828 9.390160712419974 245.1195505128138237.54678625858125 7.476463884374892257.1734347799746 40.7808770022412266.549059025113661 267.399230376123 38.05615841994596 13.748346965816776239.5998602037453581.74529874523965 9.376881326791628 253.0168588782225631.47339734876065 12.801449790647666 253.6938702864405336.85986071114475 9.416340833135983 273.1693534247587533.86869293420603 13.517431154052675 11.80534244021612414.88064978865375726.898774609851976 15.43030348440637816.66321328170864332.42123754088741 17.6393779516561315.67820042211684531.95813676896881 32.63858211452952 17.44753651421529 30.30168032369350336.8734670195072115.48244260091915923.64517489301381 46.3187852448647218.21399860672408331.11008071053091 51.04516428828603 17.46343027211013823.384008331138357 77.4533320458878830.17776134834941 13.76707658352512687.64627791278302 24.20759436497231614.87046798271282679.3083042867900927.59204311662796613.309301929402775 88.53358834622038 19.9890315752119413.58585077736218 271.4194425242253630.6521406139185448.95312719362286 264.732789740173 31.22227492622508310.605269876515221276.4313012373432330.67110657565838510.985169830234527 266.6254450613424 30.09569239846098711.659088133346604 18.8715775105807220.34374165547289732.18617612378534 20.59130858917457421.26650762370407231.616000370689523 42.8306035845672516.86155383968351634.73233463633775
zeros 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
missing0 25 20 23 22 30 24 17 28 15 19 24 25 20 14 22 20 15 33 26 24 21 23 23 25 27 20 23 22 21 19 16 29 23 23 30 29 22 17 24 19 25 24 21 18 19 20 24 21 22 21 16 28 16 25 25 21 23 25 19 28 23 24 22 25 32 18 18 27 26 26 20 22 24 24 15 28 25 24 18 24 22 18 35 28 30 19 23 25 28 36 21 26 19 20 24 21 15 20 24 25 22 25 18 22 19 19 26 30 29 28 21 22 24 15 31 22 19 23 23 18 20 24 30
0 0.0 nan 1055.27502 170.78198 639.6063800000001 1044.2584200000001-88.90979 430.86984 1051.26465 nan 517.3327 741.0960100000001 212.08337000000003570.2014800000001nan 123.68554 480.06427 626.5148300000001199.55385 659.57892 745.05798 -145.97218 nan 735.8501000000001-73.48505 697.4296300000001 642.68182 -137.36960000000002360.9039 474.04004000000003186.84929000000002420.86743 412.36603 134.71933 343.73737000000006388.03668000000005189.83162000000002750.32623 nan nan 819.76385 415.13217000000003-81.7 750.0458400000001 397.94098 -138.88400000000001156.44276000000002113.07307000000002104.00257 297.18088 88.12213000000001 67.0685 nan 73.76623000000001 nan 429.0928600000000343.0861 110.59769000000001nan nan -51.75869 967.9899300000001 nan -32.7704 943.78925 105.33720000000001-122.344420000000011078.70935 143.54796000000002-60.93587000000001 660.8267800000001 1353.77527 20.198390000000003 566.59839 1449.57959 229.99652000000003596.42383000000011468.9681400000002-186.70021000000003nan 1249.1079100000002279.7764 580.73468 nan -222.92732 567.0025 1143.1092500000002315.56631000000004518.10278 1146.32483 -260.95828 771.56329 973.7791100000001 nan 746.2069700000001 944.3781100000001 327.45282000000003619.82306 nan -218.32727000000003574.16254 905.87732 -276.12146 366.1229600000000335.908210000000004193.14078 375.8658400000000539.8688 81.17185 1022.03961 113.13824000000001-136.45811 1034.97046 125.07877 -34.938210000000005736.52234000000011571.5815400000001106.42087000000001nan nan -31.667230000000004nan 1747.60767 nan
1 0.017 617.99811 1053.2175300000001168.51317 641.23621 nan nan 432.34061 1050.237430000000126.846790000000002 516.61377 740.4259000000001 211.21942 570.5189200000001664.1987300000001 nan 479.64038000000005625.65308 199.31528000000003661.6131 743.5673200000001 -146.43872000000002nan 736.42303 -77.16084000000001 700.7197900000001 641.4929800000001 nan 357.69406000000004474.35721000000007187.04623 nan 411.81808 134.78728 336.91132000000005390.05734 190.88017000000002nan 443.93143000000003-128.7347 nan nan -79.03171 750.5651200000001 396.96808000000004nan 141.98363 121.29087000000001105.0378 281.9787300000000491.63458000000001 68.46623000000001271.8073100000000375.74918000000001 nan 409.8836100000000343.13917 110.56359 799.8198900000001 65.80063000000001 -49.9463 957.4516600000001 113.74644 -27.677100000000003nan nan -122.344420000000011069.2766100000001nan -56.2015 nan 1352.708250000000117.243570000000002 566.9248 1448.94153 226.13284000000002596.42023000000011466.4149200000002nan 593.2045300000001 nan 276.04364000000004582.39642 1230.6384300000002-225.94514 566.13733 1142.56213 312.59055 519.93042 1142.1728500000002-262.84161 nan nan 272.55261 nan 941.0106200000001 325.92441 623.0548100000001nan -220.41856 576.28583 902.63904 -278.4635 346.2450300000000435.811 193.41495 358.94989000000004nan nan 1011.0821500000001101.08356 -132.52734 1024.0022000000001111.6144 -30.679700000000004736.04187 1570.83057 101.78574 748.4116200000001 1574.0415 nan 750.67981000000011746.670410000000241.16423
2 0.033 nan 1051.77124 165.85938000000002643.5969200000001 1041.06079 -94.30722 434.099430000000041049.341430000000223.819360000000003 517.7789300000001 nan 209.92978000000002570.4550800000001663.09094 123.09371000000002479.47061 nan nan 663.7771600000001 742.55939 -147.20686 760.8386200000001nan -80.50614 702.586 640.56848 -134.51134000000002355.96603000000005476.07431 187.72906 411.18945 410.48535000000004135.65497000000002nan 392.03955 191.39008 755.7663600000001 441.96497000000005-126.80373000000002821.31488 407.06613000000004nan 750.77588 396.23285000000004-136.23216000000002128.05836000000002nan 106.09202 267.07681 95.34116 69.87910000000001255.8057700000000278.12271000000001 178.35294000000002390.7675200000000543.101560000000006110.35046000000001784.39679 68.05878 -48.83653 nan nan -23.485970000000002932.77124 97.33627000000001 -120.643270000000021059.0639600000002113.93506000000001nan 663.19812 1351.7868700000001nan 567.5697 1448.2222900000002221.82841000000002596.46210000000011463.91785 -196.01938 593.00885 1248.7484100000001272.54794000000004585.18445000000011227.7260700000002-228.90501000000003564.97345000000011142.9399400000002308.37927 523.07452 1139.1127900000001-266.43765 762.1574700000001964.9895000000001 271.42297 nan 937.31622 324.73819000000003626.50507 nan nan 579.6622900000001 899.1212200000001-281.07309000000004328.9225800000000434.77872 193.96858 341.7568700000000539.43059 80.78735 999.3184200000001 89.32551000000001 -129.324200000000021012.50629 98.88281 -27.288000000000004736.57086 1570.5422400000002nan 748.85468 1571.8595 -41.940810000000006751.0396700000001nan 36.05921
3 0.05 nan 1050.55212 163.53250000000003nan 1040.35681 -96.86188000000001 436.27994 1048.707150000000220.95202 519.19745 739.32581 208.32521000000003571.93127 661.63751 123.22423 481.81918 624.2301600000001nan 666.23505 nan -148.4931 763.56763 737.9541600000001-84.02015 703.2188100000001 nan -133.90343000000001356.08667 476.89316 187.23071000000002409.44373 410.43378 135.6963 329.61075000000005nan 191.91527000000002758.6344600000001 441.58249000000006nan 821.6690100000001 nan -75.78609 750.51422 395.89566 -136.16490000000002115.33288 141.10814000000002107.07024000000001252.83902000000003nan 71.28898000000001240.5090500000000381.28846 179.09006000000002371.8350200000000442.88871 109.90253000000001769.4459800000001 70.03754 -48.76834 934.0969200000001 nan -20.897740000000002920.9379900000001 90.00697000000001 nan 1047.43127 100.48981 nan nan 1351.30505000000029.24379 568.00946 1448.12561 216.41084 599.00385 1461.8778100000002-201.06389000000001592.6820700000001 nan 268.26801 587.1785900000001nan -232.17101000000002nan 1143.3822 304.28061 nan 1135.98755 -268.87439 756.53687 nan 270.02432000000005729.9737500000001 933.6328100000001 323.82111000000003629.7023300000001906.3137200000001 -225.57834000000003581.9775400000001 895.94104 nan 310.6837500000000334.73133 194.06519000000003324.2789600000000438.87956000000000580.76440000000001 986.2498200000001 78.36720000000001 -127.32961000000002999.9459200000001 nan -25.276780000000002736.53625000000011571.2082500000001nan 749.98224 1572.0024400000002nan 751.06842000000011747.012820000000130.698870000000003
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" ] }, "metadata": {}, "output_type": "display_data" } ], "source": [ "# Import walking gait data with missing values\n", "gait_miss = h2o.upload_file(_locate(\"smalldata/glrm_test/subject01_walk1_miss15.csv\"))\n", "gait_miss.describe()" ] }, { "cell_type": "code", "execution_count": 13, "metadata": { "collapsed": false }, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "\n", "glrm Model Build Progress: [##################################################] 100%\n", "Model Details\n", "=============\n", "H2OGeneralizedLowRankEstimator : Beta - Generalized Low Rank Model\n", "Model Key: GLRM_model_python_1449616108681_9\n", "\n", "Model Summary: \n" ] }, { "data": { "text/html": [ "
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number_of_iterationsfinal_step_sizefinal_objective_value
1000.00.0013404417370.6542389
" ], "text/plain": [ " number_of_iterations final_step_size final_objective_value\n", "-- ---------------------- ----------------- -----------------------\n", " 1000 0.00134035 417371" ] }, "metadata": {}, "output_type": "display_data" }, { "name": "stdout", "output_type": "stream", "text": [ "\n", "\n", "ModelMetricsGLRM: glrm\n", "** Reported on train data. **\n", "\n", "MSE: NaN\n", "Sum of Squared Error (Numeric): 417370.65961611824\n", "Misclassification Error (Categorical): 0.0\n", "\n", "ModelMetricsGLRM: glrm\n", "** Reported on validation data. **\n", "\n", "MSE: NaN\n", "Sum of Squared Error (Numeric): 860945.6344740451\n", "Misclassification Error (Categorical): 0.0\n", "\n", "Scoring History: \n" ] }, { "data": { "text/html": [ "
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timestampdurationiterationstep_sizeobjective
2015-12-08 15:09:34 0.724 sec0.00.66666674709528.8513359
2015-12-08 15:09:34 0.734 sec1.00.44444444709528.8513359
2015-12-08 15:09:34 0.744 sec2.00.22222224709528.8513359
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2015-12-08 15:09:34 0.764 sec4.00.01851854709528.8513359
------------------
2015-12-08 15:09:4814.574 sec995.00.0017368418507.6754296
2015-12-08 15:09:4814.592 sec996.00.0018236417934.4281432
2015-12-08 15:09:4814.612 sec997.00.0019148417473.7912993
2015-12-08 15:09:4814.630 sec998.00.0020105417370.6542389
2015-12-08 15:09:4814.649 sec999.00.0013404417370.6542389
" ], "text/plain": [ " timestamp duration iteration step_size objective\n", "--- ------------------- ---------- ----------- --------------------- ------------------\n", " 2015-12-08 15:09:34 0.724 sec 0.0 0.6666666666666666 4709528.851335923\n", " 2015-12-08 15:09:34 0.734 sec 1.0 0.4444444444444444 4709528.851335923\n", " 2015-12-08 15:09:34 0.744 sec 2.0 0.2222222222222222 4709528.851335923\n", " 2015-12-08 15:09:34 0.754 sec 3.0 0.07407407407407407 4709528.851335923\n", " 2015-12-08 15:09:34 0.764 sec 4.0 0.018518518518518517 4709528.851335923\n", "--- --- --- --- --- ---\n", " 2015-12-08 15:09:48 14.574 sec 995.0 0.0017367689153081505 418507.67542961944\n", " 2015-12-08 15:09:48 14.592 sec 996.0 0.001823607361073558 417934.42814320076\n", " 2015-12-08 15:09:48 14.612 sec 997.0 0.001914787729127236 417473.79129934387\n", " 2015-12-08 15:09:48 14.630 sec 998.0 0.002010527115583598 417370.6542389112\n", " 2015-12-08 15:09:48 14.649 sec 999.0 0.0013403514103890654 417370.6542389112" ] }, "metadata": {}, "output_type": "display_data" } ], "source": [ "# Basic GLRM using quadratic loss and no regularization\n", "\n", "model2 = H2OGeneralizedLowRankEstimator(k=10, init=\"SVD\", svd_method = \"GramSVD\", loss=\"Quadratic\", regularization_x=\"None\", regularization_y=\"None\", max_iterations=2000, min_step_size=1e-6)\n", "model2.train(x=list(range(1,gait_miss.ncol)), training_frame=gait_miss, validation_frame=gait)\n", "model2.show()" ] }, { "cell_type": "code", "execution_count": 14, "metadata": { "collapsed": true }, "outputs": [], "source": [ "# Plot objective function value each iteration\n", "model2_score = model2.score_history()\n", "plt.xlabel(\"Iteration\")\n", "plt.ylabel(\"Objective\")\n", "plt.title(\"Objective Function Value per Iteration\")\n", "plt.plot(model2_score[\"iteration\"], model2_score[\"objective\"])\n", "plt.show()" ] }, { "cell_type": "code", "execution_count": 15, "metadata": { "collapsed": false }, "outputs": [ { "data": { "text/html": [ "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "
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621.968 1051.51 161.288 644.432 1044.82 -99.4408 435.265 1051.14 18.3324 517.778 737.629 204.746 573.515 659.737 119.764 479.669 620.612 194.433 662.796 748.397 -153.294 757.27 740.683 -86.5735 700.385 647.023 -139.967 356.172 473.72 182.912 410.289 407.518 132.598 330.534 390.805 187.372 751.86 445.722 -135.138 813.116 409.489 -84.6309 743.492 398.791 -143.541 124.611 145.061 99.2328 256.621 98.8707 67.2945 238.766 82.2159 173.348 367.499 37.6717 109.25 763.38 64.99 -55.8715 931.636 98.3185 -30.9051 929.013 90.278 -126.767 1044.14 105.246 -62.0991 663.789 1353.88 3.21573 571.523 1451.5 213.274 595.388 1462.52 -206.377 597.105 1252.41 264.705 580.198 1225.47 -236.365 569.251 1146.74 301.66 514.408 1136.31 -269.938 763.79 967.124 267.583 738.354 938.406 322.154 617.453 903.068 -230.713 564.57 893.571 -286.423 305.094 31.247 190.557 320.972 37.0906 80.0161 990.786 79.9036 -135.731 1000.01 90.2548 -34.8167 736.544 1575.1 85.0311 747.543 1577.88 -52.8016 744.812 1749.3 23.874
622.111 1050.3 159.175 644.55 1044.11 -100.599 436.068 1049.45 16.6962 522.243 736.647 203.96 579.825 659.467 120.473 486.146 619.454 194.571 666.23 748.52 -154.39 761.449 742.01 -88.5712 704.716 647.524 -140.553 362.351 475.371 183.115 413.816 406.237 133.549 332.73 393.424 187.439 754.204 445.868 -135.647 813.537 407.333 -84.8786 743.683 399.496 -144.061 115.908 159.363 98.1248 244.303 103.864 67.5568 224.36 88.1556 172.553 348.82 34.6052 109.7 746.814 67.3683 -55.0607 917.537 93.1141 -30.2677 921.157 85.6225 -126.095 1030.34 94.6808 -61.5975 663.116 1351.83 0.876821 570.624 1449.39 209.838 594.829 1459.43 -208.229 595.378 1250.93 261.588 580.797 1222.8 -237.534 566.837 1145.94 298.51 515.763 1133.62 -270.691 756.982 962.257 267.746 730.357 934.969 321.866 616.896 900.004 -231.742 564.093 890.825 -287.379 286.397 32.3673 190.012 303.984 37.3061 80.0287 972.593 71.9331 -135.037 982.593 81.8547 -34.1431 735.719 1571.2 82.2085 746.997 1573.65 -54.9462 746.778 1745.05 21.1888
624.841 1051.43 156.764 647.685 1045.55 -103.196 438.819 1050.09 14.0989 528.897 736.473 203.229 588.483 659.61 121.004 494.842 618.768 194.952 667.114 749.149 -156.445 762.297 741.617 -90.77 703.943 647.783 -141.863 371.656 478.011 183.997 419.903 406.448 134.766 338.262 397.958 188.227 750.665 444.954 -136.844 808.628 405.349 -85.1711 739.292 398.862 -145.325 113.17 177.755 97.65 236.042 113.224 68.2548 214.294 99.1359 172.779 332.062 36.8681 110.709 733.86 67.8694 -55.4051 904.764 89.8697 -28.9355 910.628 82.3937 -125.284 1017.68 88.6806 -59.5434 665.146 1353.31 -2.4333 571.285 1451.46 206.028 597.56 1460.08 -212.391 594.463 1252.82 258.353 586.405 1222.7 -240.542 564.328 1148.18 295.143 522.797 1132.75 -273.631 749.295 958.648 268.373 721.209 932.959 322.361 623.414 898.884 -233.844 571.181 889.612 -289.927 270.82 39.1103 190.369 289.874 42.713 80.6396 956.314 67.3024 -133.688 969.797 77.1494 -32.441 737.426 1572.53 78.4398 749.247 1574.61 -58.8066 750.245 1746.76 16.8909
628.708 1052.29 154.515 652.158 1046.73 -105.558 442.902 1050.17 11.5271 536.184 736.63 202.429 597.639 659.947 121.351 503.624 618.455 194.952 671.61 750.11 -158.3 767.619 742.564 -93.0836 708.114 648.749 -142.816 380.163 480.515 184.564 424.961 405.973 135.369 342.584 401.724 188.646 752.614 444.67 -137.835 809.068 403.165 -85.2165 739.501 398.948 -146.57 105.626 194.903 97.5663 224.057 119.899 68.2116 200.741 106.76 172.413 312.806 35.5188 109.897 718.824 68.633 -55.9269 892.614 84.8522 -27.6775 912.487 76.794 -124.349 1006.38 79.2012 -57.1989 668.326 1354.87 -5.82511 572.562 1453.37 202.022 601.068 1460.35 -216.625 594.714 1254.43 254.845 592.635 1222.16 -243.897 563.31 1150.18 291.433 530.27 1131.39 -276.902 743.388 954.533 268.566 713.815 930.462 322.187 630.663 897.009 -236.313 578.456 887.617 -292.652 252.397 41.5592 189.669 272.704 44.1503 79.7287 940.435 59.2992 -132.132 953.203 69.338 -30.2605 738.799 1575.16 74.2595 751.044 1577.01 -62.8588 751.039 1749.32 12.336
629.66 1054.18 151.52 652.419 1048.14 -107.89 443.812 1051.25 9.37437 545.266 737.565 201.858 609.06 662.461 122.379 516.499 618.97 195.843 671.681 750.244 -160.732 767.504 742.147 -96.2162 707.123 648.133 -145.203 393.919 484.71 185.369 436.086 406.782 137.221 351.775 407.196 189.359 748.179 444.341 -140.281 801.596 401.626 -87.0782 733.961 399.76 -148.543 104.44 212.581 95.3332 218.513 128.452 69.1832 192.369 117.451 172.126 299.493 34.9597 112.99 702.883 77.585 -55.7632 872.07 85.2997 -27.5806 878.389 79.7422 -124.78 982.814 74.8541 -57.8961 667.965 1355.43 -8.40202 572.552 1454.2 198.55 601.654 1460.76 -219.035 592.725 1255.7 251.651 595.579 1222.68 -245.011 559.876 1151.96 288.266 534.425 1131.76 -277.787 734.064 951.557 269.634 702.929 928.916 323.001 631.582 895.768 -238.016 580.031 887.22 -294.835 238.793 47.4399 190.435 261.496 48.4732 81.837 922.559 59.4147 -132.728 935.42 67.7954 -31.142 740.317 1572.32 71.6171 752.971 1573.72 -65.4065 757.96 1746.91 9.68498
632.887 1056.96 147.665 655.762 1050.67 -111.877 446.888 1053.17 5.60209 556.364 739.168 200.613 622.967 665.292 122.623 531.43 620.024 196.11 671.388 751.576 -164.025 767.076 741.89 -99.7132 704.421 648.756 -147.617 410.24 489.399 186.058 449.196 408.311 138.624 363.599 413.566 190.07 741.25 443.535 -142.481 792.781 399.458 -88.2712 725.893 399.394 -150.671 106.096 233.285 94.0924 214.846 138.836 70.1094 186.129 129.627 172.277 286.915 36.4198 115.077 684.146 79.5919 -56.3313 852.654 81.8992 -26.6655 858.034 76.8904 -124.494 963.129 67.779 -56.4657 670.302 1358.16 -12.9493 573.444 1457.72 193.24 605.234 1462.77 -224.564 590.928 1259.09 246.969 603.09 1223.96 -248.945 555.795 1155.95 283.403 543.926 1131.99 -281.67 722.998 948.25 270.14 689.788 927.59 323.176 641.112 896.109 -240.681 590.363 887.314 -298.081 226.683 54.419 191.207 251.602 54.0922 83.1826 902.502 54.6889 -131.954 917.624 62.5262 -30.0411 743.047 1574.02 66.5511 756.373 1574.97 -70.581 763.961 1749.2 4.133
636.729 1063.8 145.457 659.754 1056.98 -115.186 449.774 1058.73 3.25221 568.597 743.134 200.711 637.709 670.543 123.433 547.561 623.012 197.489 671.77 754.938 -166.764 767.495 743.481 -101.967 702.372 650.905 -149.668 428.337 495.202 187.617 464.454 411.606 140.419 377.854 421.003 191.455 735.764 444.037 -144.251 785.574 399.119 -88.5592 719.708 400.205 -152.243 112.901 252.845 92.9059 216.56 150.167 70.768 185.852 143.172 172.756 280.731 40.2268 117.035 670.584 82.5269 -56.3484 837.97 81.9302 -24.7279 841.261 77.231 -123.592 948.139 64.6959 -54.1548 672.992 1366.69 -15.997 573.535 1466.79 190.117 608.491 1470.52 -229.469 589.191 1267.15 244.561 611.505 1230.06 -252.28 551.978 1164.06 280.738 554.467 1136.61 -285.165 713.049 949.295 272.15 677.827 930.481 324.889 652.427 900.473 -242.45 602.644 891.34 -300.757 221.212 63.9514 192.229 247.901 62.0311 84.3735 888.914 53.7524 -130.764 902.444 61.3355 -28.202 743.58 1585.41 63.153 757.383 1586.24 -74.8574 761.444 1761.16 -0.187107
" ] }, "metadata": {}, "output_type": "display_data" }, { "data": { "text/plain": [] }, "execution_count": 15, "metadata": {}, "output_type": "execute_result" } ], "source": [ "# Impute missing data from X and Y\n", "pred2 = model2.predict(gait_miss)\n", "pred2.head()" ] }, { "cell_type": "code", "execution_count": 16, "metadata": { "collapsed": false }, "outputs": [], "source": [ "# Plot original and imputed L.Acromium.X over time\n", "lacro_pred_np2 = np.array(h2o.as_list(pred2[\"reconstr_L.Acromium.X\"]))\n", "plt.plot(time_np, lacro_np, 'b-')\n", "plt.plot(time_np, lacro_pred_np2, 'g-')\n", "\n", "# Mark points where training data contains missing values\n", "idx_miss = list(zip(*gait_miss[\"L.Acromium.X\"].isna().which().as_data_frame(True).values.tolist()))\n", "plt.plot(time_np[idx_miss], lacro_np[idx_miss], \"o\", marker = \"x\", ms = 8, mew = 1.5, mec = \"r\")\n", "\n", "plt.title(\"Position of Left Acromium over Time\")\n", "plt.xlabel(\"Time\")\n", "plt.ylabel(\"X-Coordinate of Left Acromium\")\n", "blue_patch = mpatches.Patch(color = 'blue', label = 'Original')\n", "green_patch = mpatches.Patch(color = 'green', label = 'Imputed')\n", "red_patch = mpatches.Patch(color = 'red', label = \"Missing\")\n", "plt.legend([blue_patch, green_patch, red_patch], [\"Original\", \"Imputed\", \"Missing\"])\n", "plt.show()" ] } ], "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": "3.5.0" } }, "nbformat": 4, "nbformat_minor": 0 }