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Hi,
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<div>If you run the following (from the tutorial page):</div>
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<pre class="escaped" style="margin-top: 0px; margin-bottom: 0px; color: rgb(80, 80, 80); background-color: rgb(255, 255, 255);">datasynth -walkers ${WALKERS} -tmax ${TIMESTEPS} -geometry inflammation -numcylinders 100 -p 0.0 -initial uniform -voxels 1 \
-increments 1 -separateruns -latticesize ${LATSIZE} -schemefile ${SCHEMEFILE} -gamma ${GAMA} ${GAMB} -diffusivity ${DIFF} \
> ${OUTPUTDIR}/${FNAME}</pre>
<div><br>
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<div>it will always produce the same set of cylinders with the same configuration, because the random seed is fixed. If you change "-voxels 1" to "-voxels 100" it will produce 100 copies each with the same set of cylinders.</div>
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<div>To get a different substrate, ie a different set of cylinders and configuration drawn from the same distribution, you need to run datasynth 10 times with a different random seed, which you can specify with "-seed <int>", where <int> is some integer. This
tutorial, <a href="http://cmic.cs.ucl.ac.uk/camino//index.php?n=Tutorials.MCSimulator">
http://cmic.cs.ucl.ac.uk/camino//index.php?n=Tutorials.MCSimulator</a>, and some of the man pages discuss best practice in using -seed.</div>
<div><br>
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<div>The other problem you had with this command:</div>
<div><br>
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<pre class="escaped" style="font-size: 16px;"><font style="font-size: 8pt;"><i>ParseSimOutput.pl LamD1a.txt</i></font></pre>
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<div>is because of a typo on the tutorial page, which I've now fixed. Specifically, this </div>
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<pre class="escaped" style="margin-top: 0px; margin-bottom: 0px; color: rgb(80, 80, 80); background-color: rgb(255, 255, 255); position: static; z-index: auto;">datasynth -walkers 5 -tmax 5 -geometry inflammation -numcylinders 100 -p 0.0 -initial uniform -voxels 1 \
-increments 1 -separateruns -latticesize ${LATSIZE} -schemefile ActiveAxG140_PM.scheme1 -gamma ${GAMA} ${GAMB} \
-diffusivity ${DIFF} -substrateinfo > /tmp/test.Bfloat 2> LamD1a.info</pre>
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<div><br>
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<div>should have "2> LamD1a.txt" at the end instead of "2> LamD1a.info".</div>
<div><br>
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<div>Danny</div>
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<div>On 30 May 2014, at 09:26, stefania oliviero <<a href="mailto:stefania.oliviero@hotmail.it">stefania.oliviero@hotmail.it</a>> wrote:</div>
<br class="Apple-interchange-newline">
<blockquote type="cite">
<div class="hmmessage" style="font-size: 12pt; font-family: Calibri; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;">
<div dir="ltr">Hi All,<br>
I am trying to generate a substrate of 100 voxels with cylinders distributed second a gamma function distribution , following the instructions of the tutorial Activeax.<span class="Apple-converted-space"> </span><br>
Due to the huge time required to generate 100 voxels I would like to generate 10 substrates each with 10 voxels.<br>
The questions are:<span class="Apple-converted-space"> </span><br>
<br>
- the spatial distribution of the cylinders in each voxel is fixed or not?<br>
<br>
- if not, is there a seed used to generate the different spatial distribution varying the voxel? How can I control it to avoid to use the same seed for each of the 10 substrates? In the worst case I will have only one substrate with 10 voxel and not 10 different
substrates with 10 voxels.<span class="Apple-converted-space"> </span><br>
<br>
I am trying to solve the problem but I don't find a solution:<br>
<br>
- at first I used the option -drawncrosssection of the command datasynth to view the spatial distribution of the voxels. For each different run (varying the number of voxel) I obtain alway the same image file debug_crossSec_113.gray (a fixed spatial distribution
of just one voxel)<br>
<br>
- at second I used the option -cylfile of the command datasynth to read the positions of all the cylinders: I obstained always the same file testcyls.csv with the same distribution<br>
<br>
- finally I generated the file *.info generated using the command suggested in the tutorial Activeax<span class="Apple-converted-space"> </span><br>
<br>
<font size="1" style="font-size: 8pt;">d</font><font size="1" style="font-size: 8pt;"><i>atasynth -walkers 5 -tmax 5 -geometry inflammation -numcylinders 100 -p 0.0 -initial uniform -voxels 1 \ -increments 1 -separateruns -latticesize ${LATSIZE} -schemefile
ActiveAxG140_PM.scheme1 -gamma ${GAMA} ${GAMB} \ -diffusivity ${DIFF} -substrateinfo > /tmp/test.Bfloat 2> LamD1a.info<br>
<br>
The file LamD1a.info contains the position and size of each cylinder:</i></font>
<pre class="escaped"><font size="1" style="font-size: 8pt;"><i>cylinder 0 pos = (6.65278756664775E-6, 1.8736510967768196E-6, 0.0) radius = 2.4836106445030362E-6
cylinder 1 pos = (7.075179421691923E-6, 6.310782215503249E-6, 0.0) radius = 1.2288218199625427E-6
cylinder 2 pos = (9.040679260286337E-7, 1.358410391168818E-5, 0.0) radius = 1.2057082606855263E-6
cylinder 3 pos = (4.391993962910324E-6, 7.3503496846908985E-6, 0.0) radius = 1.0606081830751333E-6
cylinder 4 pos = (9.776132252482087E-6, 1.1165129374727735E-5, 0.0) radius = 1.0479898302635493E-6
cylinder 5 pos = (2.2709875877317475E-7, 2.8099470916851546E-6, 0.0) radius = 1.0133293909377957E-6
cylinder 6 pos = (9.976382544843197E-6, 1.3158389965085646E-5, 0.0) radius = 9.45079565714962E-7
cylinder 7 pos = (1.01430033661826E-5, 2.5476110220568397E-6, 0.0) radius = 9.190732393643317E-7
cylinder 8 pos = (1.2759519960773037E-5, 1.3126264521291948E-5, 0.0) radius = 9.166534852189462E-7
:
:
</i></font></pre>
<font size="1" style="font-size: 8pt;"><i></i></font>
<div style="margin: 0px; padding: 0px;"><font size="1" style="font-size: 8pt;"><i>Here is a simple perl script to filter out just the list of cylinder radii:<span class="Apple-converted-space"> </span><a class="urllink" href="http://cmic.cs.ucl.ac.uk/camino//uploads/Tutorials/ParseSimOutput.pl" rel="nofollow">ParseSimOutput.pl</a>.
Thus,</i></font></div>
<font size="1" style="font-size: 8pt;"><i></i></font>
<pre class="escaped"><font size="1" style="font-size: 8pt;"><i>ParseSimOutput.pl LamD1a.txt
</i></font></pre>
<font size="1" style="font-size: 8pt;"><i></i></font>
<div style="margin: 0px; padding: 0px;"><font size="1" style="font-size: 8pt;"><i>Produces just the list:</i></font></div>
<font size="1" style="font-size: 8pt;"><i></i></font>
<pre class="escaped"><font size="2" style="font-size: 10pt;"><i><font size="1" style="font-size: 8pt;">2.4836106445030362E-6
1.2288218199625427E-6
1.2057082606855263E-6
1.0606081830751333E-6
1.0479898302635493E-6
1.0133293909377957E-6
9.45079565714962E-7
9.190732393643317E-7
9.166534852189462E-7
:
:</font>
</i></font></pre>
perl ParseSimOutput.pl LamD1a_test.txt<br>
output: Can't open LamD1a_test.txt: No such file or directory at ParseSimOutput.pl line 6.<br>
<br>
perl ParseSimOutput.pl LamD1a_test.info<br>
no output<br>
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<br>
Thanks a lot and sorry for the too long mail<br>
Cheers<br>
<br>
Stefania Oliviero<br>
Università degli Studi di Napoli Federico II<br>
ITAB, Università degli Studi G. d'Annunzio di Chieti<br>
<br>
<br>
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