Re: [fluka-discuss]: Post processing USRBIN file (*.bnn format)

From: Mohammad Islam <rafiqul.islam_at_okstate.edu>
Date: Fri, 24 Oct 2014 14:34:25 -0500

Dear mary,

Thanks for all your help. I will work on it as per suggestion. Thanks
again.

Rafiq
On Oct 24, 2014 1:29 PM, "me_at_marychin.org" <me_at_marychin.org> wrote:

> Dear Rafiq,
>
> I'm talking about your project file (bladeeblaa.flair), not Vasilis'
> system files, not the files under directory ".flair".
>
> You'll find:
> - some lines of headers
> - empty line
> - section beginning with a pound sign (#), terminated by an empty line
> - another section beginning with a pound sign (#), terminated by an empty
> line
> - many more similar sections, including some starting with, "# USRBIN
> plot" -- each of these corresponds to a plot you see on the left panel
> under your FLAIR plot tab.
>
> Choose the section most convenient in terms of similarities and
> systematic differences according to the many dat files you wish to
> generated. Cut out that section and use it as your template. Make the
> string(s) you need to replace unique i.e. if necessary change it to
> something unique eg. 'yahoo' instead of '1', which probably occurs more
> than once even in places you do not intend to replace. String-replace it
> with the parameter you wish to vary, eg
> for ((...))
> do
> sed .....
> done >> bladeeblaa.flair
> Just an example - there are of course dozens of different ways and
> scripting language to accomplish this.
> I think you'll need to reload bladeeblaa.flair under FLAIR.
> Understandably it is a good practice to first secure a duplicate of the
> original, eg bladeeblaa_orig.flair.
>
> :) mary
>
> > On 24 October 2014 at 06:39 Mohammad Islam <rafiqphy_at_gmail.com> wrote:
> >
> >
> > Dear Mary,
> > I found the flair templates which are basic input files as was stated
> > in the manual. I could not figure out how to change the template and
> > where to do that. For instance, if I have 5 bnn files and I want to
> > generate dat files from each of them what I need to change ? Do you
> > have any examples? Thank you very much.
> >
> > Rafiq
> >
> > On Thu, Oct 23, 2014 at 11:25 PM, me_at_marychin.org <me_at_marychin.org>
> wrote:
> > > Just to add/clarify: hundreds of dat files can be generated with no
> more
> > > than a few clicks from FLAIR > plot. .flair is ASCII. Just copy the
> relevant
> > > part for one dat file, use this as template, replace (sed) the
> necessary
> > > strings (eg. the fort unit and/or the detector name), loop through any
> > > number of dat you wish, append (cat >>) into .flair. Reopen .flair,
> under
> > > plot select all the plots, clicking 'Plot' once will generate all the
> dat
> > > files. Even if it's over a hundred dat files per simulation.
> > >
> > > :) mary
> > >
> > > On 23 October 2014 at 20:06 "me_at_marychin.org" <me_at_marychin.org>
> wrote:
> > >
> > > Dear Rafiq,
> > >
> > > No no no, please don't use FLAIR 50 times to generate 50 dat files.
> After
> > > the 50 runs complete, do FLAIR > Run > Data > Process. This will
> gather
> > > together all the *_fort.?? files and based on these, produce one
> merged bnn.
> > > Then go to plot, and plot this merge bnn. You will get a dat file
> which
> > > contains the merged results of your 50 runs.
> > >
> > > :) mary
> > >
> > > On 23 October 2014 at 18:52 Mohammad Islam <rafiqul.islam_at_okstate.edu>
>
> > > wrote:
> > >
> > > Dear mary,
> > >
> > > Thanks for your detail explanation. In my problem i run 50 input files
> > > using flair simultaneously. I would love to take the .dat file that
> comes
> > > from flair but in such case i have to use flair 50 times to generate
> 50 dat
> > > file. Right? Thats why i thought to use the available bnn files. Do
> you
> > > know any ways that will generate the dat files for all the bnn files
> at the
> > > same time using identical flair setup? Thanks for all your help.
> > >
> > > Rafiq
> > >
> > > On Oct 23, 2014 7:19 PM, " me_at_marychin.org" < me_at_marychin.org> wrote:
> > >
> > > Dear Rafiq,
> > >
> > > USRBIN scoring is 3D in general (unless eg you ask for nbin=1 for one
> of the
> > > dimensions). When we do a FLAIR plot for USRBIN it is typically 2D
> > > (colormap). dat is the output from FLAIR plot, so it is also typically
> 2D,
> > > unless you specifically ask for 1D projection (line plot). During
> FLAIR plot
> > > for USRBIN, windowing / averaging takes place when we *select* the
> ranges
> > > under 'Projection & Limits'. Note that this *select*ion takes place
> after
> > > the simulation, as opposed to the specification in the USRBIN card
> before
> > > the simulation. This windowing process makes dat a subset of bnn (tons
> of
> > > data, as you say). bnn contains what you asked for in the USRBIN card.
> dat
> > > contains what you ask for in FLAIR plot, and possibly some
> > > re-normalisations.
> > >
> > > If you want a file similar to dat, why don't you just take dat itself,
> as I
> > > mentioned earlier as one of the alternatives. Just make a duplicate of
> dat,
> > > throw off the header lines, then, in the case of 1D, in MATLAB:
> > > a = load('rafiqsfile.txt');
> > > stairs(a(:,1),a(;,3))
> > > --OR--
> > > errorbar((a(:,1)+a(:,2))/2,a(:,3),a(:,3).*a(:,4)/100)
> > > --OR--
> > > plot((a(:,1)+a(:,2))/2,a(:,3))
> > > --OR--
> > > whatever you prefer.
> > >
> > > In the case of more dimensions, you'd need a loop to rearrange 'a'
> into a
> > > matrix (in more general terms, 'array'). 2D matrix if 2D. 3D matrix if
> 3D.
> > > If 2D:
> > > imagesc(log10(b))
> > > If 3D:
> > > imagesc(log10(b(:,:,cut_rafiq_wants_to_see)))
> > >
> > > :) mary
> > >
> > >> On 23 October 2014 at 13:19 Mohammad Islam < rafiqphy_at_gmail.com>
> wrote:
> > >>
> > >>
> > >> Dear Mary,
> > >>
> > >> Thank you very much for your prompt answer. As your suggestion, I
> > >> converted using the approach => FLAIR>Run>Files>data then right-click
> > >> on the bnn file and select 'To ascii'. But now I see a tons of data
> > >> point (although most of them are zero), however if I plot the
> original
> > >> bnn file using flair it gives me a simple *dat file of the whatever
> > >> bin width that I had chosen in the input. Can you please tell me how
> > >> can I interpret this ascii file. I want a similar .dat file that
> flair
> > >> produces which is just a bragg curve in this case. Attached is one of
> > >> the converted ascii file for your comments. Thank you very much.
> > >>
> > >> On Thu, Oct 23, 2014 at 2:51 PM, me_at_marychin.org < me_at_marychin.org>
> wrote:
> > >> > Dear Rafiq,
> > >> >
> > >> > bnn is binary. If you'd like to do it the brute-force way, use
> MATLAB
> > >> > fread.
> > >> >
> > >> > The easy way is to convert bnn to ascii, under FLAIR>Run>Files>data
> then
> > >> > right-click on the bnn file and select 'To ascii'. Thereafter, use
> > >> > MATLAB
> > >> > fscanf, fgets, fgetl or ...
> > >> >
> > >> > An alternative to the 'To ascii' function would be just to take the
> dat
> > >> > file, assuming you plotted with FLAIR.
> > >> >
> > >> > The lazyman's way is: manually edit the ascii file by removing the
> > >> > header
> > >> > lines. Thereafter, use MATLAB load. This way, you won't even need
> to
> > >> > worry
> > >> > about bytes and fields. You won't even need to open and close the
> file.
> > >> >
> > >> > MATLAB or PYTHON or PERL the algorithm would be similar (with the
> > >> > exception
> > >> > that MATLAB's load condenses all the steps in to one):
> > >> > open the file
> > >> > read each line, split according to the spaces or fields or bytes
> > >> > arrange the numbers into an array
> > >> > close the file
> > >> >
> > >> > :) mary
> > >> >
> > >> >> On 23 October 2014 at 11:32 Mohammad Islam <
> rafiqul.islam_at_okstate.edu>
> > >> >> wrote:
> > >> >>
> > >> >>
> > >> >> Dear Users,
> > >> >>
> > >> >> Does anybody know how to read the *.bnn file that comes from
> USRBIN
> > >> >> using MATLAB or any other language. I tried to read it through
> MATLAB
> > >> >> but it did not give me the data I was looking for. I need to do
> some
> > >> >> post processing of the deposited energy which is in number of
> binary
> > >> >> files. FLAIR can read and plot it and also save it as *.dat file
> but I
> > >> >> have so many files that a little bit coding would be helpful. I
> > >> >> appreciate any help.
> > >> >>
> > >> >> Thanks
> > >> >> Rafiq
> > >> >>
> > >>
> > >>
> > >>
> > >> --
> > >> Mohammad Rafiqul Islam, PhD
> > >
> > >
> > >
> > >
> > >
> > >
> >
> >
> >
> > --
> > Mohammad Rafiqul Islam, PhD
> I think you'll need to reload bladeeblaa.flair under FLAIR.
>
Received on Fri Oct 24 2014 - 22:52:03 CEST

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