[Camino-users] Gamma distributed cylinders used by datasynth

Wed Mar 25 04:38:48 PDT 2015

Dear all,

I'm having trouble reproducing the results of the "inflammation",
gamma-distributed cylinders substrate (
http://cmic.cs.ucl.ac.uk/camino//index.php?n=Tutorials.ActiveAx).

Although I specify 100 cylinders, the -substrateinfo switch of the
datasynth command outputs the info of more than 100 cylinders. As an
example, the following command

datasynth -walkers 5 -tmax 5 -geometry inflammation -numcylinders 100
-p 0.0 -initial uniform -voxels 1 \
-increments 1 -separateruns -latticesize 1.4E-5  -schemefile
${schemefile} -gamma 5.9242 1.065E-7  \
-diffusivity 6E-10  -substrateinfo > /tmp/test.Bfloat 2> LamD1a.txt

reports position and radius values for 118 cylinders (see below).

 I checked that only 84 of the 118 generated cylinders belong to the square
region [0,LATSIZE]x[0,LATSIZE], corresponding to an intracellullar volume
fraction of 0.563, although a value of 0.743 is reported on the tutorial
page for these parameters and the simulation outputs 0.714 (see below).

I would like to know if it is  possible to

-  know which cylinders are actually retained for the simulation
- force datasynth to use a specific substrate by providing the positions
and radii of the cylinders.

Thank you for all your hard work and help.

Best regards,
Gaëtan Rensonnet (Université Catholique de Louvain)

----------------------------------------------------------------------------------
[...]
INFO: cylinder 95 (95% complete)
[...]
INFO: dynamic cylinder placment finished
[...]
INFO: intracellular volume fraction 0.7141059134453311
[...]
INFO: cylinder positions and radii:
cylinder 0 pos = (6.65278756664775E-6, 1.8736510967768196E-6, 0.0)
radius = 1.8309144441424006E-6
cylinder 1 pos = (7.075179421691923E-6, 6.310782215503249E-6, 0.0)
radius = 1.3130486200693158E-6
cylinder 2 pos = (9.040679260286337E-7, 1.358410391168818E-5, 0.0)
radius = 1.2867878383211695E-6
cylinder 3 pos = (1.4904067926028634E-5, 1.358410391168818E-5, 0.0)
radius = 1.2867878383211695E-6
cylinder 4 pos = (9.040679260286337E-7, -4.15896088311819E-7, 0.0)
radius = 1.2867878383211695E-6
cylinder 5 pos = (1.4904067926028634E-5, -4.15896088311819E-7, 0.0)
radius = 1.2867878383211695E-6
cylinder 6 pos = (4.391993962910324E-6, 7.3503496846908985E-6, 0.0)
radius = 1.170539713300354E-6
cylinder 7 pos = (9.776132252482087E-6, 1.1165129374727735E-5, 0.0)
radius = 1.1024246032634817E-6
cylinder 8 pos = (9.854821502880044E-6, 2.4896525940959966E-6, 0.0)
radius = 1.0750480756080651E-6
cylinder 9 pos = (2.2709875877317475E-7, 2.8099470916851546E-6, 0.0)
radius = 1.0719291668660331E-6
cylinder 10 pos = (1.4227098758773174E-5, 2.8099470916851546E-6, 0.0)
radius = 1.0719291668660331E-6
cylinder 11 pos = (1.1537398151508934E-5, 3.565363278392075E-8, 0.0)
radius = 1.031191594706863E-6
cylinder 12 pos = (1.1537398151508934E-5, 1.403565363278392E-5, 0.0)
radius = 1.031191594706863E-6
cylinder 13 pos = (1.0340006460582223E-5, 6.451676513826287E-6, 0.0)
radius = 1.0124270292789868E-6
cylinder 14 pos = (2.2519641764756876E-6, 8.441594226432921E-6, 0.0)
radius = 1.0048425061319232E-6
cylinder 15 pos = (1.2722679772034706E-5, 6.974782651683031E-6, 0.0)
radius = 9.872316694172616E-7
cylinder 16 pos = (7.873932120318974E-7, 1.065154381095652E-5, 0.0)
radius = 9.078876730398304E-7
cylinder 17 pos = (1.4787393212031897E-5, 1.065154381095652E-5, 0.0)
radius = 9.078876730398304E-7
cylinder 18 pos = (3.8595492128658E-6, 1.1647417007333738E-5, 0.0)
radius = 9.062736934956832E-7
cylinder 19 pos = (3.3495290749725815E-6, 3.0571692943403056E-6, 0.0)
radius = 8.668738913127061E-7
cylinder 20 pos = (1.0685750207525376E-5, 8.881721760295971E-6, 0.0)
radius = 8.621126614092505E-7
cylinder 21 pos = (1.214903398868144E-5, 1.2059593433174175E-5, 0.0)
radius = 8.536515847753978E-7
cylinder 22 pos = (1.1697406815816152E-5, 4.049652849305582E-6, 0.0)
radius = 8.160904712487559E-7
cylinder 23 pos = (6.841939664747854E-6, 1.2823808368673251E-5, 0.0)
radius = 8.097652505766508E-7
cylinder 24 pos = (8.125191736069415E-6, 8.724791857973654E-6, 0.0)
radius = 7.859057590669876E-7
cylinder 25 pos = (3.226852744367267E-6, 5.29699565035402E-6, 0.0)
radius = 7.836857038677861E-7
cylinder 26 pos = (1.685137484248918E-6, 5.90728318100868E-6, 0.0)
radius = 7.765726575945123E-7
cylinder 27 pos = (4.472080444503521E-6, 9.927687962668107E-6, 0.0)
radius = 7.63724121772914E-7
cylinder 28 pos = (9.476544046632096E-6, 1.3678115396002353E-5, 0.0)
radius = 7.536846190481476E-7
cylinder 29 pos = (9.476544046632096E-6, -3.2188460399764683E-7, 0.0)
radius = 7.536846190481476E-7
cylinder 30 pos = (6.732265070800693E-6, 1.073136964187403E-5, 0.0)
radius = 7.536728605569323E-7
cylinder 31 pos = (1.3322436371829935E-5, 9.694092286472674E-6, 0.0)
radius = 7.48494084896715E-7
cylinder 32 pos = (-6.775636281700646E-7, 9.694092286472674E-6, 0.0)
radius = 7.48494084896715E-7
cylinder 33 pos = (6.401663606517542E-6, 8.591143502119861E-6, 0.0)
radius = 7.445473119338537E-7
cylinder 34 pos = (1.2181676383664622E-5, 1.7650069264010495E-6, 0.0)
radius = 7.342361764920267E-7
cylinder 35 pos = (3.0802507778048423E-6, 1.3685354227521925E-5, 0.0)
radius = 7.305388084993742E-7
cylinder 36 pos = (3.0802507778048423E-6, -3.1464577247807465E-7, 0.0)
radius = 7.305388084993742E-7
cylinder 37 pos = (1.5319494982698339E-6, 4.364372975768269E-6, 0.0)
radius = 7.268897230222544E-7
cylinder 38 pos = (1.353366577873182E-5, 1.0697418776705743E-6, 0.0)
radius = 7.01253812975066E-7
cylinder 39 pos = (-4.6633422126817956E-7, 1.0697418776705743E-6, 0.0)
radius = 7.01253812975066E-7
cylinder 40 pos = (1.28253563723869E-5, 5.101873119388538E-6, 0.0)
radius = 6.939503997667699E-7
cylinder 41 pos = (4.861593592953374E-6, 5.1397475489314535E-6, 0.0)
radius = 6.902909552399779E-7
cylinder 42 pos = (9.61070517996536E-6, 4.6625265755032885E-6, 0.0)
radius = 6.841392302291053E-7
cylinder 43 pos = (2.3637295267497987E-6, 1.5865094440852078E-6, 0.0)
radius = 6.83487118040518E-7
cylinder 44 pos = (2.6349281689752234E-7, 8.369426979631936E-6, 0.0)
radius = 6.824806312659665E-7
cylinder 45 pos = (1.4263492816897522E-5, 8.369426979631936E-6, 0.0)
radius = 6.824806312659665E-7
cylinder 46 pos = (8.135960076055787E-6, 4.266643876605137E-6, 0.0)
radius = 6.663563769613417E-7
cylinder 47 pos = (3.8106158297456182E-6, 1.4885088415747777E-6, 0.0)
radius = 6.611938571497645E-7
cylinder 48 pos = (2.604930052857489E-6, 1.03241213012474E-5, 0.0)
radius = 6.590803086284299E-7
cylinder 49 pos = (5.234213640959555E-6, 1.3590464661169439E-5, 0.0)
radius = 6.540939375066291E-7
cylinder 50 pos = (5.234213640959555E-6, -4.0953533883056083E-7, 0.0)
radius = 6.540939375066291E-7
cylinder 51 pos = (8.104247474772512E-6, 1.0367823864054893E-5, 0.0)
radius = 6.522307247915676E-7
cylinder 52 pos = (2.303222518050517E-6, 1.2054283375644193E-5, 0.0)
radius = 6.375606772298529E-7
cylinder 53 pos = (1.195913864591678E-5, 1.0018666734140369E-5, 0.0)
radius = 6.250017127604121E-7
cylinder 54 pos = (8.731872852239496E-6, 7.328496071869432E-6, 0.0)
radius = 6.233895250543902E-7
cylinder 55 pos = (5.43769967348012E-6, 1.2120144825722313E-5, 0.0)
radius = 6.184833221978085E-7
cylinder 56 pos = (1.0689306339141427E-5, 1.2617314717886405E-5, 0.0)
radius = 6.118541571544257E-7
cylinder 57 pos = (8.393711350345085E-7, 7.000726363329049E-6, 0.0)
radius = 6.041882587839234E-7
cylinder 58 pos = (1.3712530219733689E-5, 1.186346815204928E-5, 0.0)
radius = 6.039295025037359E-7
cylinder 59 pos = (-2.8746978026631083E-7, 1.186346815204928E-5, 0.0)
radius = 6.039295025037359E-7
cylinder 60 pos = (2.092599433155582E-7, 4.648793662888942E-6, 0.0)
radius = 5.97022365838571E-7
cylinder 61 pos = (1.4209259943315558E-5, 4.648793662888942E-6, 0.0)
radius = 5.97022365838571E-7
cylinder 62 pos = (9.015371714037986E-6, 9.955309026368793E-7, 0.0)
radius = 5.902473987168997E-7
cylinder 63 pos = (6.23294609082584E-6, 4.3812033423744895E-6, 0.0)
radius = 5.445044629884512E-7
cylinder 64 pos = (5.010149982455978E-6, 3.9008750225528885E-6, 0.0)
radius = 5.42632673166851E-7
cylinder 65 pos = (8.306221034093438E-6, 1.2683510363115873E-5, 0.0)
radius = 5.408415587263871E-7
cylinder 66 pos = (7.97081224933417E-6, 1.1644462105207594E-5, 0.0)
radius = 5.346549187153143E-7
cylinder 67 pos = (9.31937000838128E-6, 9.586002819675699E-6, 0.0)
radius = 5.321575247863868E-7
cylinder 68 pos = (1.1913621578454659E-7, 5.8630821368588705E-6, 0.0)
radius = 5.043869255959606E-7
cylinder 69 pos = (1.4119136215784547E-5, 5.8630821368588705E-6, 0.0)
radius = 5.043869255959606E-7
cylinder 70 pos = (8.22311606751533E-6, 3.1407774696126325E-8, 0.0)
radius = 4.981773743853883E-7
cylinder 71 pos = (8.22311606751533E-6, 1.4031407774696127E-5, 0.0)
radius = 4.981773743853883E-7
cylinder 72 pos = (1.2073021493898635E-5, 8.357959828117261E-6, 0.0)
radius = 4.965127404812847E-7
cylinder 73 pos = (4.281982901766791E-6, 2.671526702669944E-7, 0.0)
radius = 4.949500446654765E-7
cylinder 74 pos = (4.281982901766791E-6, 1.4267152670266995E-5, 0.0)
radius = 4.949500446654765E-7
cylinder 75 pos = (8.961490414177329E-6, 5.774769621275874E-6, 0.0)
radius = 4.936281583796397E-7
cylinder 76 pos = (1.2649354621794275E-5, 2.97022689076995E-6, 0.0)
radius = 4.889722437029032E-7
cylinder 77 pos = (2.005886640512281E-6, 2.8936902780054676E-6, 0.0)
radius = 4.830809542498509E-7
cylinder 78 pos = (1.0274125967407709E-5, 9.355670462072647E-7, 0.0)
radius = 4.789280972094244E-7
cylinder 79 pos = (5.752453399992135E-6, 9.635075633787422E-6, 0.0)
radius = 4.767711004522886E-7
cylinder 80 pos = (1.306211312779468E-5, 1.0973631562474445E-5, 0.0)
radius = 4.685377289574362E-7
cylinder 81 pos = (1.3129445396745599E-5, 1.3012091983133335E-5, 0.0)
radius = 4.6219390722824396E-7
cylinder 82 pos = (5.392088197635132E-6, 1.0742795622295795E-5, 0.0)
radius = 4.609495273344991E-7
cylinder 83 pos = (2.7093158473649967E-6, 6.813119835839052E-6, 0.0)
radius = 4.583801501491396E-7
cylinder 84 pos = (1.2961110314496492E-5, 3.885925837587764E-6, 0.0)
radius = 4.5477576694774526E-7
cylinder 85 pos = (1.0530494272909297E-6, 9.288484636693645E-6, 0.0)
radius = 4.5475905924365337E-7
cylinder 86 pos = (1.3072251844637978E-5, 4.824738083916369E-9, 0.0)
radius = 4.4902453388322985E-7
cylinder 87 pos = (1.3072251844637978E-5, 1.4004824738083916E-5, 0.0)
radius = 4.4902453388322985E-7
cylinder 88 pos = (1.3036959264937346E-5, 8.49671051413813E-6, 0.0)
radius = 4.43875976437138E-7
cylinder 89 pos = (3.381605615273224E-6, 9.378303652812466E-6, 0.0)
radius = 4.3161896586205746E-7
cylinder 90 pos = (4.1933236101362334E-6, 1.31807774117425E-5, 0.0)
radius = 4.2746675597628084E-7
cylinder 91 pos = (9.481842036772991E-6, 8.111612233493216E-6, 0.0)
radius = 4.254982466760184E-7
cylinder 92 pos = (1.1605898747266515E-5, 5.464234516820633E-6, 0.0)
radius = 4.2332356209864817E-7
cylinder 93 pos = (1.135293247067804E-5, 2.665497419530289E-6, 0.0)
radius = 4.206703274134296E-7
cylinder 94 pos = (8.46972800703016E-6, 3.1943051168448662E-6, 0.0)
radius = 4.14720968894025E-7
cylinder 95 pos = (5.247505425727153E-6, 8.85732101846264E-6, 0.0)
radius = 4.1417525920473954E-7
cylinder 96 pos = (4.060693906357917E-6, 4.307815700883465E-6, 0.0)
radius = 4.1126709949608657E-7
cylinder 97 pos = (7.285628358728024E-6, 9.594235375415075E-6, 0.0)
radius = 4.088011664583316E-7
cylinder 98 pos = (1.2617450508885802E-6, 1.5124721927125665E-6, 0.0)
radius = 4.0187028192289645E-7
cylinder 99 pos = (1.2170293332607849E-6, 1.1913749990226244E-5, 0.0)
radius = 3.9077912494418684E-7
cylinder 100 pos = (1.1298839061731403E-5, 1.1137793758009833E-5, 0.0)
radius = 3.8762597689055006E-7
cylinder 101 pos = (1.128523404774877E-5, 7.532984675931087E-6, 0.0)
radius = 3.840068078781612E-7
cylinder 102 pos = (1.10481742466428E-5, 1.62171948775399E-6, 0.0)
radius = 3.783443897651147E-7
cylinder 103 pos = (4.722982014704847E-6, 3.0135171498076217E-6, 0.0)
radius = 3.766381976772154E-7
cylinder 104 pos = (1.0712723575776512E-5, 4.857721767221852E-6, 0.0)
radius = 3.754596196078704E-7
cylinder 105 pos = (1.0511319150891607E-5, 3.98704722723136E-6, 0.0)
radius = 3.6339082364449434E-7
cylinder 106 pos = (5.293976438930132E-6, 6.103153756168652E-6, 0.0)
radius = 3.5269459740489675E-7
cylinder 107 pos = (9.238323606230268E-6, 1.257711211852192E-5, 0.0)
radius = 3.3810926396107214E-7
cylinder 108 pos = (1.9574481548292263E-6, 1.1121775260364214E-5, 0.0)
radius = 3.3047362623450117E-7
cylinder 109 pos = (1.0910674965275194E-5, 1.0116256228053546E-5, 0.0)
radius = 3.1948298628920646E-7
cylinder 110 pos = (3.8881430295923244E-6, 8.75116054169144E-6, 0.0)
radius = 3.1327405962693356E-7
cylinder 111 pos = (2.9461970712138414E-6, 4.233764523914158E-6, 0.0)
radius = 3.097532154464074E-7
cylinder 112 pos = (1.9549791979921866E-6, 6.989443691466957E-6, 0.0)
radius = 3.058428999347759E-7
cylinder 113 pos = (3.050833539534728E-6, 8.496926727291934E-7, 0.0)
radius = 2.786421087504928E-7
cylinder 114 pos = (7.263111644459846E-6, 8.085431709235085E-6, 0.0)
radius = 2.2098579788409588E-7
cylinder 115 pos = (5.581150621995247E-6, 8.067140703662396E-6, 0.0)
radius = 2.169764320782105E-7
cylinder 116 pos = (9.278209893610308E-6, 8.807336328089272E-6, 0.0)
radius = 1.8373966650957275E-7
cylinder 117 pos = (1.8201461532396626E-6, 1.0385934739124424E-5, 0.0)
radius = 1.0556656576034829E-7
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