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CIRDLES / Calamari

Reimplementation of data reduction from Ludwig's Squid 2.50 for SHRIMP mass spectrometers.
Apache License 2.0
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Replaced Babylonian square root #13

Closed johnzeringue closed 8 years ago

johnzeringue commented 8 years ago

Replaced the Babylonian square root method with StrictMath's square root, since I discovered that the difference is negligible. Without the Babylonian method, the example data is processed at least 2 seconds faster.

johnzeringue commented 8 years ago

The only differences across all reports:

File:
  </var/folders/98/fx0_lh_10850t61yfybdlhn80000gn/T/junit221879681833817091/CalamariReports-G6147--SBM-TRUE--FIT-FALSE/Calamari_MeanRatioAndSigmaPctPerIsotopicRatioPerAnalysis_for_G6147.txt>
and file:
  </var/folders/98/fx0_lh_10850t61yfybdlhn80000gn/T/4414927469785123856.tmp>
do not have same content:

Changed content at line 36:
expecting:
  ["099.Z.2.1.1, 2010-11-11 17:10:24, unknown, 2.2369722022658115E-5, 100.00149109367847, 0.050426144047788266, 1.8226185234498364, 0.43758442206625764, 1.5878593693197722, 0.32907827253375826, 2.371235659009481, 0.0822885290657843, 2.37301037160178, 6.171002973820432, 0.8058086212325526, 1.2633025446875847, 0.24652283540735784, 0.03376368316580478, 1.3587366574198674, 0.3930164251199674, 0.33719240460239674, 0.013292633608475081, 1.6913518590339978"]
but was:
  ["099.Z.2.1.1, 2010-11-11 17:10:24, unknown, 2.2369722022658115E-5, 100.00149109367847, 0.050426144047788266, 1.8226185234498364, 0.43758442206625764, 1.5878593693197722, 0.32907827253375826, 2.3712356590094763, 0.0822885290657843, 2.37301037160178, 6.171002973820432, 0.8058086212325526, 1.2633025446875847, 0.24652283540735784, 0.03376368316580478, 1.3587366574198674, 0.3930164251199674, 0.33719240460239674, 0.013292633608475081, 1.6913518590339978"]

Changed content at line 90:
expecting:
  ["100.Z.17.1.1, 2010-11-12 18:14:36, unknown, 5.0201888310730545E-5, 100.00334658654573, 0.05132419095031329, 2.7502683223370976, 0.1730939453534709, 3.5911650396794657, 0.1433831806516665, 1.2192571598795714, 0.08059069902347112, 2.1703205101280947, 6.046080106954368, 1.1318702916513457, 0.5072523228723664, 0.4549299270289197, 0.03409977945621046, 0.9669029218817851, 0.38991684900682216, 0.4992474209830631, 0.013305725466168662, 0.9042323293483321"]
but was:
  ["100.Z.17.1.1, 2010-11-12 18:14:36, unknown, 5.0201888310730545E-5, 100.00334658654573, 0.05132419095031328, 2.750268322337098, 0.1730939453534709, 3.5911650396794657, 0.1433831806516665, 1.2192571598795714, 0.08059069902347113, 2.1703205101280947, 6.046080106954368, 1.1318702916513457, 0.5072523228723664, 0.4549299270289197, 0.03409977945621046, 0.9669029218817851, 0.38991684900682216, 0.4992474209830631, 0.013305725466168662, 0.9042323293483321"]

    at org.cirdles.calamari.core.RawDataFileHandlerIT.writesReportsFromPrawnFile(RawDataFileHandlerIT.java:66)
johnzeringue commented 8 years ago

Since it's hard digging through the test output, the specific discrepancies are 2.3712356590094763 instead of 2.371235659009481 (matching to 13 decimal places) in line 36 and 0.05132419095031328 instead of 0.05132419095031329 (matching to 16 decimal places), 2.750268322337098 instead of 2.7502683223370976 (matching to 14 decimal places), and 0.08059069902347113 instead of 0.08059069902347112 (matching to 16 decimal places) in line 90.

johnzeringue commented 8 years ago

Actually, I didn't consider that the test would've short-circuited on the first pair of mismatched files. As best as I can tell, there are actually ~300 discrepancies (out of ~220,000 values, about 0.1%). I've listed what should be all of them below.

I still don't see anything serious. I've yet to find a pair that doesn't match to 13 decimal places. I originally found this method by profiling and noticing that half of the processing time was spent in this method. Obviously, correctness is more important than speed, but it's not every day you find a 20% speedup as easy as this. The precision that's "lost" was probably never there—at least not in the report—in the first place.

[-2.3712356590094763,-] {+2.371235659009481,+}
[-0.05132419095031328, 2.750268322337098,-] {+0.05132419095031329, 2.7502683223370976,+} 0.1730939453534709, 3.5911650396794657, 0.1433831806516665, 1.2192571598795714, [-0.08059069902347113,-] {+0.08059069902347112,+}
[-206.31249730753498,-] {+206.31249730753495,+}
[-439.5766902387104,-] {+439.57669023871034,+}
[-71.73384105206631,-] {+71.73384105206632,+}
[-101.34422850782134,-] {+101.3442285078213,+}
[-100.08784734480399,-] {+100.08784734480402,+}
[-140.42625165030177,-] {+140.42625165030174,+}
[-127.02548312290529,-] {+127.02548312290531,+}
[-198.9567395738053,-] {+198.95673957380527,+}
[-178.1417176890652,-] {+178.14171768906516,+}
[-134.13495234720386,-] {+134.13495234720384,+} 3631197.472188576, 205.955946, 657.0, 1019.9525452787587, 31.936689389441266, 7261199.5468094675, 206.960205, 678.0, 314.0002366305783, 17.72004514666935, 1209575.4833476034, 207.96254, 692.0, 21555.920002925617, [-151.61700123599786,-] {+151.6170012359979,+}
[-180.9036531621838,-] {+180.90365316218376,+}
[-89.92799670809187,-] {+89.92799670809188,+} 1183613.1304715453, 207.961896, 692.0, 12845.116638851787, 137.54985371196483, 1185280.513158124, 238.030037, 704.0, 28822.713028001657, 185.12175453491113, 474505.5549158538, 248.030364, 715.0, 31913.51024127375, [-200.68352226171464,-] {+200.68352226171461,+}
[-207.67889441792562,-] {+207.6788944179256,+}
[-188.55193231614163,-] {+188.5519323161416,+}
[-249.03406271812105,-] {+249.034062718121,+} 481867.45094890764, 254.061001, 726.0, 15419.1333650867, [-225.45660438399065,-] {+225.45660438399068,+}
[-219.53069307376296,-] {+219.53069307376305,+} 480096.9132771742, 248.034069, 169.0, 28382.785947754706, [-188.0769014227821,-] {+188.07690142278204,+}
[-215.40810897940358,-] {+215.4081089794035,+}
[-266.7529356556037,-] {+266.7529356556038,+}
[-198.96933913388293,-] {+198.9693391338829,+} 478615.9530117662, 195.765543, 580.0, 2.0000000024, 1.414213562373095, 4790614.291963999, 203.951107, 603.0, 4.0000000096, 2.0, 4790906.758488016, 203.991107, 632.0, 55814.547054349714, 236.24575118866312, 3595798.1911254637, 205.957326, 658.0, 33589.32359325013, [-265.21601339883483,-] {+265.2160133988349,+} 7195701.089002751, 206.961584, 679.0, 5103.189235042782, 71.43617244583722, 1200306.7394346793, 207.963919, 692.0, 11978.732401105168, 109.44582237314262, 1202238.3861171582, 238.028646, 704.0, 28051.380756826264, 228.4604734780289, 481814.94838629157, 248.030947, 715.0, 29233.930922208638, [-224.64171440956738,-] {+224.64171440956736,+}
[-192.80904888837222,-] {+192.80904888837216,+}
[-125.295131745945,-] {+125.29513174594499,+} 1209869.319924104, 207.963378, 1056.0, 12152.741871595612, 127.42011118327065, 1212289.1741696084, 238.029093, 1069.0, 28232.060262776373, 168.00975798257488, 485954.7087745153, 248.032357, 1080.0, 29966.52900032563, [-191.23683900938514,-] {+191.23683900938516,+}
[-86.96944549204862,-] {+86.9694454920486,+}
[-134.0012842533185,-] {+134.00128425331854,+}
[-81.96511111777416,-] {+81.96511111777414,+}
[-55.04886892462572,-] {+55.04886892462574,+}
[-55.81314042920692,-] {+55.8131404292069,+} 3692229.4735927065, 205.955118, 457.0, 248.88891366716297, 16.629588385661958, 7383770.031178967, 206.959377, 478.0, 216.00011197445806, 14.69693845669907, 1230571.8470490698, 207.961712, 492.0, 10076.030672432868, [-101.90620086928347,-] {+101.90620086928348,+} 1231760.4956537131, 238.029554, 504.0, 17611.109891818272, 132.69984619917088, 493164.8344558928, 248.030753, 515.0, 25141.448036615795, [-208.2897260489367,-] {+208.28972604893661,+}
[-127.18760455517265,-] {+127.18760455517264,+} 1232492.578991097, 238.032253, 680.0, 17984.09899134384, [-187.91216361312982,-] {+187.9121636131298,+}
[-181.19467926756926,-] {+181.1946792675692,+}
[-152.4918965959473,-] {+152.49189659594728,+}
[-194.9476442425894,-] {+194.94764424258938,+}
[-133.76163398527285,-] {+133.76163398527288,+}
[-130.8812464674659,-] {+130.88124646746587,+} 496782.329210251, 248.032546, 163.0, 34548.06138801904, 251.11920188312368, 496774.57462768944, 254.065539, 174.0, 13666.914046208369, [-120.61733797978317,-] {+120.6173379797832,+}
[-169.33679431259034,-] {+169.3367943125904,+} 492224.40967838466, 195.76617, 209.0, 1.0000000006, 1.0, 4923921.828076289, 203.951734, 233.0, 1.0000000006, 1.0, 4921208.65953412, 203.991734, 255.0, 5797.893248581066, 129.1649536256375, 3690237.727507147, 205.957054, 281.0, 675.5557381057284, 27.39739556875101, 7375721.076961355, 206.961312, 302.0, 113.33336416000839, 12.133516482134198, 1228981.8967622872, 207.963648, 315.0, 12202.065971331593, 110.46134457267101, 1229740.8101963028, 238.030397, 328.0, 6443.188668469432, 116.67575718874274, 492094.38754903513, 248.032318, 338.0, 31164.707292286792, 176.51878355535143, 492028.225439624, 254.063914, 350.0, 12371.315946485405, [-116.90351302436856,-] {+116.90351302436859,+}
[-248.02410232294073,-] {+248.02410232294076,+}
[-92.86492223962004,-] {+92.86492223962003,+}
[-210.53894399753946,-] {+210.53894399753955,+}
[-164.67651166920223,-] {+164.67651166920228,+}
[-168.7445289974494,-] {+168.74452899744944,+}
[-153.71143079937468,-] {+153.71143079937463,+}
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[-177.6168975590988,-] {+177.61689755909882,+}
[-221.8110897774449,-] {+221.81108977744492,+}
[-248.60582500481127,-] {+248.60582500481132,+}
[-25008.485083218024,-] {+25008.48508321802,+} 158.1288496772475, 487979.8513158464, 195.765292, 209.0, 1.0000000006, 1.0, 4877639.211193558, 203.950856, 233.0, 2.0000000024, 1.414213562373095, 4876380.130693266, 203.990856, 255.0, 5764.146135744018, 75.9217989484051, 3655885.9607059658, 205.956176, 281.0, 614.000150798437, 24.77902338672773, 7308003.331424141, 206.960434, 302.0, 835.0016733433534, 28.896366553599783, 1217640.3890257573, 207.962769, 316.0, 22500.940841375275, 149.99908601513866, 1218200.2325993835, 238.032281, 328.0, 70170.80395678783, 319.04369570335444, 487532.63328106806, 248.033646, 339.0, 55635.35106808851, 235.83211297820563, 487294.1838404146, 254.065601, 350.0, 22037.57885641168, [-194.52685057163882,-] {+194.5268505716388,+}
[-215.99629094906248,-] {+215.99629094906254,+}
[-148.85029503669537,-] {+148.85029503669534,+}
[-53.37376125441789,-] {+53.373761254417886,+}
[-327.1675392450478,-] {+327.16753924504786,+}
[-132.7222985071899,-] {+132.72229850718983,+}
[-125.45229616052771,-] {+125.45229616052772,+}
[-188.39370882304132,-] {+188.3937088230413,+}
[-142.70340078445344,-] {+142.70340078445346,+}
[-145.59536158048232,-] {+145.59536158048235,+}
[-204.5913011102055,-] {+204.59130111020545,+}
[-160.10828614518488,-] {+160.10828614518493,+} 1198020.461091411, 238.03031, 1031.0, 20635.48400263273, 143.6416700673167, 479936.3792173721, 248.03237, 1042.0, 40266.961419895204, [-243.1535796947532,-] {+243.15357969475318,+}
[-200.79896136873418,-] {+200.7989613687342,+} 483796.0160453754, 248.031982, 514.0, 64120.98577632868, [-289.93305324641125,-] {+289.9330532464112,+}
[-178.3316562998483,-] {+178.33165629984833,+}
[-227.12809679800128,-] {+227.12809679800134,+}
[-295.96017945947534,-] {+295.9601794594753,+}
[-94.95994648054429,-] {+94.9599464805443,+}
[-172.83187427552969,-] {+172.8318742755297,+}
[-200.89016003532228,-] {+200.8901600353223,+}
[-150.71732423155993,-] {+150.7173242315599,+}
[-130.1579318439141,-] {+130.15793184391413,+}
[-48.013861539974705,-] {+48.01386153997472,+}
[-106.04059629365798,-] {+106.04059629365796,+}
[-154.36715128366978,-] {+154.3671512836698,+}
[-48.2560668853875,-] {+48.25606688538751,+} 3627387.8072289047, 205.956415, 985.0, 168.00001128960074, 15.405626677721784, 7252389.673073333, 206.960674, 1006.0, 147.0000518616183, 12.124355652982139, 1208615.8762961514, 207.963009, 1019.0, 6745.475665416688, [-92.39823364639349,-] {+92.3982336463935,+}
[-189.75678939909443,-] {+189.75678939909446,+}
[-149.05377022800974,-] {+149.05377022800977,+}
[-66.90814984319614,-] {+66.90814984319616,+}
[-265.49299625883936,-] {+265.4929962588393,+}
[-197.17577730743008,-] {+197.1757773074301,+}
[-196.98946947687003,-] {+196.98946947687006,+}
[-178.82599076789788,-] {+178.82599076789782,+} 481026.3198179166, 195.763375, 913.0, 1.0000000006, 1.0, 4814648.797866718, 203.94894, 937.0, 1.0000000006, 1.0, 4810956.417025406, 203.98894, 959.0, 3676.926278740524, 60.637574678930314, 3606717.7856056257, 205.95426, 985.0, 371.0000550564082, 20.51828452868318, 7209841.401217897, 206.958518, 1006.0, 129.00003993841236, 11.357816691600545, 1201130.5056715868, 207.960853, 1019.0, 8476.445802946324, 101.03669323515025, 1203090.0409464042, 238.030223, 1032.0, 5991.067071648107, 77.4005925176365, 482114.25471494964, 248.028701, 1042.0, 20653.011925311497, 147.6168328914851, 482577.4817892304, 254.060911, 1053.0, 7962.336810753217, [-106.11441759151468,-] {+106.11441759151467,+}
[-178.2400952129522,-] {+178.24009521295218,+}
[-130.5175472316444,-] {+130.51754723164436,+}
[-177.0011787803627,-] {+177.00117878036266,+} 490112.480951136, 195.768466, 33.0, 3.0000000053999996, 1.7320508075688772, 4894177.350530012, 203.954031, 57.0, 1.0000000006, 1.0, 4885424.1280131675, 203.994031, 79.0, 4010.4940591015647, 63.32836009161116, 3657967.544465342, 205.95935, 105.0, 415.5556246301349, 29.207643173544266, 7305260.823915013, 206.963609, 126.0, 366.0003214946824, 19.131126469708992, 1216178.1474521596, 207.965944, 140.0, 15443.061652673097, 124.26781281699061, 1216542.762845197, 238.030215, 152.0, 32690.454646095626, 230.1731790939758, 486581.94859016896, 248.033215, 163.0, 39608.77977071239, [-207.3913251816269,-] {+207.39132518162685,+}
[-130.85901617889127,-] {+130.85901617889124,+} 1199991.8621223234, 238.030142, 680.0, 33160.77624135536, [-216.36737329269278,-] {+216.36737329269272,+}
[-180.6204184977796,-] {+180.62041849777964,+} 478181.88903372607, 195.763732, 737.0, 4.0000000096, 2.2110831935702664, 4784823.233784326, 203.949296, 761.0, 1.0000000006, 1.0, 4783252.723338943, 203.989296, 783.0, 3951.517595132572, 72.33255164702497, 3586390.979909278, 205.954616, 809.0, 371.111166200502, 20.30629653610785, 7173668.992891153, 206.958875, 830.0, 380.000346560316, 21.90890230020664, 1195318.5680868053, 207.96121, 844.0, 16447.534991677127, 128.2454122607401, 1197028.2976306304, 238.029544, 856.0, 33447.14228901318, [-183.62206891635637,-] {+183.6220689163563,+} 479212.1750540214, 248.030168, 867.0, 40202.90023008789, 203.02627079686533, 479359.24354173854, 254.061511, 878.0, 15815.987600625103, [-132.4051994287165,-] {+132.40519942871654,+}
[-183.2305945851433,-] {+183.23059458514322,+} 476584.09493701754, 195.764064, 914.0, 0.0, 0.0, 4768785.908462116, 203.949628, 937.0, 2.0000000024, 1.414213562373095, 4763899.934839377, 203.989628, 959.0, 3946.5098535499083, 62.821154029810906, 3574111.0173711926, 205.954948, 985.0, 382.222280659762, 26.65509007976699, 7147881.4510303745, 206.959206, 1006.0, 352.00029736985124, 20.59126028197401, 1191942.636279868, 207.961542, 1020.0, 16577.76535308582, 128.75210990813756, 1194315.3480236712, 238.029013, 1032.0, 33791.961026946236, 183.80726600440397, 478392.6163417618, 248.03083, 1043.0, 40271.66706301458, [-250.70842294756054,-] {+250.70842294756056,+}
[-102.85507594325885,-] {+102.85507594325884,+}
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[-105.96504159166906,-] {+105.96504159166908,+}
[-92.49986661417695,-] {+92.49986661417692,+}
[-59.273917272849836,-] {+59.27391727284985,+}
[-190.72100414637984,-] {+190.72100414637978,+}
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[-190.18582575461028,-] {+190.18582575461025,+}
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[-196.24433034454697,-] {+196.2443303445469,+}
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[-172.66518978329262,-] {+172.6651897832926,+}
[-100.17547131048374,-] {+100.17547131048373,+}
[-154.56263134937538,-] {+154.5626313493754,+}
[-157.70672786019216,-] {+157.70672786019213,+}
[-64.80305949879657,-] {+64.80305949879654,+} 3584624.2813984, 205.954395, 282.0, 290.0000336400039, 17.950549357115012, 7166500.92303166, 206.958653, 303.0, 145.55560640298071, 12.717247935843995, 1194485.1530226644, 207.960988, 316.0, 11523.548477124039, [-107.36361579904592,-] {+107.36361579904593,+}
[-190.44821578522556,-] {+190.44821578522553,+}
[-233.01781914863102,-] {+233.017819148631,+}
[-166.21477442846486,-] {+166.21477442846484,+}
[-228.20568565973784,-] {+228.2056856597379,+}
[-54.3718356874278,-] {+54.37183568742782,+}
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[-98.88964566730198,-] {+98.88964566730195,+}
[-211.56185786167146,-] {+211.5618578616714,+}
[-126.67409088045399,-] {+126.674090880454,+}
[-210.45489025371006,-] {+210.4548902537101,+} 471790.9480612705, 195.763094, 737.0, 1.0000000006, 1.0, 4720342.692005196, 203.948658, 761.0, 1.0000000006, 1.0, 4715125.9379275, 203.988658, 783.0, 50787.8074015518, [-278.39729215193427,-] {+278.3972921519342,+}
[-174.94216028176695,-] {+174.94216028176692,+}
[-214.4914808703269,-] {+214.49148087032694,+}
[-189.4418524943934,-] {+189.44185249439343,+}
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bowring commented 8 years ago

We need to leave in the Babylonian square root for now because of the following scenario: Currently the math inside PrawnRunFractionParser calculates most things twice - once using Java floating point and once using BigDecimal floating point in order to support an experiment where we looked at 20 decimal places (or more) of precision as a way to gain insight into why / how Squid (Excel) was rounding at the 14th and 15th place. All of the variables involved in BigDecimal end with "BD" and it is only they who use Babylonian, because BigDecimal does not have a square root and StrictMath is limited to 15 digits floating point. In order to produce the parallel report it is necessary to flip the commented lines in ReportsEngine.reportTotalCountsAtTimeStampAndTrimMass.

However, you discovering there is an effect due to removing Babylonian on the actual values you list is troubling ... there should be no side effect on the "normal" calculations. We have to hunt down why there is a side-effect - I don't see it on first pass, so I am sure it is something subtle or a typo I am missing. See parseRunFractionData.

Eventually this BigDecimal stuff will all be removed once everyone is happy with the Java floating point precision and rounding.