Hi Guillermo, Very glad to hear you got it working!
Scripts are clearly being checked differently, with the code-execution the OS security layer limits being only machine-code stuff. It would be legitimate to have a different check that prevented any script at all, but that's not true here. Best regards, Ed ________________________________ From: Guillermo P. Ortiz <gor...@exa.unne.edu.ar> Sent: 28 October 2024 3:13 PM To: Ed . <ej...@hotmail.com>; pdl-devel@lists.sourceforge.net <pdl-devel@lists.sourceforge.net> Cc: perldl <pdl-gene...@lists.sourceforge.net> Subject: Re: [Pdl-devel] project ordered sequence image Hello Ed, yes you are right. Changing to real /home directory I can run the script with inlinePdlpp. Curiously no problem with running other perl codes I did not have there. Also, I can check the David solution against your firstnonzeroover solution, both works fine for me given the same results. But, your version is almost double quicker ! Thanks you all developers, David, Ingo and for your work and helps Regards El dom, 27 oct 2024 a las 22:42, Ed . (<ej...@hotmail.com<mailto:ej...@hotmail.com>>) escribió: Hi Guillermo, This may be very similar to the problem in https://stackoverflow.com/questions/13502156/what-are-possible-causes-of-failed-to-map-segment-from-shared-object-operation, and also actually faced by Ingo not so long ago. I suspect it's because the directory you're using doesn't allow code execution from files there. If that's right, you'd need to instead run the script (with the compiling and especially the dynaloading) in a place where you can execute code from. The alternative here is to install the very latest "git master" version of PDL, doing effectively the "git clone ..." from Q4.9 of https://metacpan.org/pod/PDL::FAQ, then "cd pdl; perl Makefile.PL; make install". Alternatively you can use cpanm: "cpanm https://github.com/PDLPorters/pdl/tarball/master";. [https://metacpan.org/static/images/dots.png]<https://metacpan.org/pod/PDL::FAQ> PDL::FAQ<https://metacpan.org/pod/PDL::FAQ> Frequently asked questions about PDL metacpan.org<http://metacpan.org> Best regards, Ed ________________________________ From: Guillermo P. Ortiz <gor...@exa.unne.edu.ar<mailto:gor...@exa.unne.edu.ar>> Sent: 28 October 2024 1:24 AM To: Ed . <ej...@hotmail.com<mailto:ej...@hotmail.com>> Cc: perldl <pdl-gene...@lists.sourceforge.net<mailto:pdl-gene...@lists.sourceforge.net>> Subject: Re: [Pdl-devel] project ordered sequence image Hello Ed, My PDL version is 2.084 Here the output after to add to end of the line: use inline ...build_noisy=>1, force_build=>1 ===================================== validate Stage get_maps Stage Starting "perl Makefile.PL" Stage Generating a Unix-style Makefile Writing Makefile for pru_fnzo_pl_5262 Writing MYMETA.yml and MYMETA.json Finished "perl Makefile.PL" Stage Starting "make" Stage Running Mkbootstrap for pru_fnzo_pl_5262 () chmod 644 "pru_fnzo_pl_5262.bs<http://pru_fnzo_pl_5262.bs>" "/opt/perl5/perls/perl-5.36.0/bin/perl" -MExtUtils::Command::MM -e 'cp_nonempty' -- pru_fnzo_pl_5262.bs<http://pru_fnzo_pl_5262.bs> blib/arch/auto/pru_fnzo_pl_5262/pru_fnzo_pl_5262.bs<http://pru_fnzo_pl_5262.bs> 644 "/opt/perl5/perls/perl-5.36.0/bin/perl" "-I/opt/perl5/perls/perl-5.36.0/lib/site_perl/5.36.0/x86_64-linux" "-MPDL::PP=pru_fnzo_pl_5262 ,pru_fnzo_pl_5262,pru_fnzo_pl_5262,," pru_fnzo_pl_5262.pd touch pru_fnzo_pl_5262.pm<http://pru_fnzo_pl_5262.pm> "/opt/perl5/perls/perl-5.36.0/bin/perl" "/opt/perl5/perls/perl-5.36.0/lib/5.36.0/ExtUtils/xsubpp" -typemap '/opt/perl5/perls/perl-5.3 6.0/lib/5.36.0/ExtUtils/typemap' -typemap '/opt/perl5/perls/perl-5.36.0/lib/5.36.0/ExtUtils/typemap' -typemap '/opt/perl5/perls/perl-5 .36.0/lib/site_perl/5.36.0/x86_64-linux/PDL/Core/typemap' pru_fnzo_pl_5262.xs > pru_fnzo_pl_5262.xsc mv pru_fnzo_pl_5262.xsc pru_fnzo_pl_5262.c cc -c "-I/opt/perl5/perls/perl-5.36.0/lib/site_perl/5.36.0/x86_64-linux/PDL/Core" -fwrapv -fno-strict-aliasing -pipe -fstack-protector-strong -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_FORTIFY_SOURCE=2 -O2 -DVERSION=\"0.00\" -DXS_VERSION=\"0 .00\" -fPIC "-I/opt/perl5/perls/perl-5.36.0/lib/5.36.0/x86_64-linux/CORE" pru_fnzo_pl_5262.c rm -f blib/arch/auto/pru_fnzo_pl_5262/pru_fnzo_pl_5262.so cc -shared -O2 -L/usr/local/lib -fstack-protector-strong pru_fnzo_pl_5262.o -o blib/arch/auto/pru_fnzo_pl_5262/pru_fnzo_pl_5262.so \ \ chmod 755 blib/arch/auto/pru_fnzo_pl_5262/pru_fnzo_pl_5262.so Finished "make" Stage Starting "make install" Stage "/opt/perl5/perls/perl-5.36.0/bin/perl" -MExtUtils::Command::MM -e 'cp_nonempty' -- pru_fnzo_pl_5262.bs<http://pru_fnzo_pl_5262.bs> blib/arch/auto/pru_fnzo_pl_5262/pru_fnzo_pl_5262.bs<http://pru_fnzo_pl_5262.bs> 644 Files found in blib/arch: installing files in blib/lib into architecture dependent library tree Finished "make install" Stage Starting Cleaning Up Stage Finished Cleaning Up Stage Had problems bootstrapping Inline module 'pru_fnzo_pl_5262' Can't load '/mnt/diskHD/home/gortiz/Proyectos/Clasifica/_Inline/lib/auto/pru_fnzo_pl_5262/pru_fnzo_pl_5262.so' for module pru_fnzo_pl_5262: /mnt/diskHD/home/gortiz/Proyectos/Clasifica/_Inline/lib/auto/pru_fnzo_pl_5262/pru_fnzo_pl_5262.so: failed to map segment from shared object at /opt/perl5/perls/perl-5.36.0/lib/5.36.0/x86_64-linux/DynaLoader.pm line 206. at /opt/perl5/perls/perl-5.36.0/lib/site_perl/5.36.0/Inline.pm line 541. at codes/pru_fnzo.pl<http://pru_fnzo.pl> line 0. INIT failed--call queue aborted. ============================ Seems that the lib generated was installed in blib/lib, but after that I can load the code Maybe I need to rebuild my tree structure, I did not remember how to do that if it is the case. Regards, G. El dom., 27 de octubre de 2024 21:44, Ed . <ej...@hotmail.com<mailto:ej...@hotmail.com>> escribió: Hi Guillermo, Please keep at least the pdl-general mailing list on Cc, since this discussion might help someone in the future googling with similar problems. Could you try changing the "use Inline" line to read: use Inline Pdlpp => 'DATA', build_noisy => 1, force_build => 1; Then re-run it and send the output? You don't need to read the PP doc, that is for writing/updating the code, not running it. If you want more directly-useful info, you might do "perldoc Inline" and/or "perldoc Inline::Pdlpp". I'm using 5.32 here, it shouldn't make any difference what Perl version you have so long as it's >= 5.10.1. It will be helpful if you can include what version of PDL you have: perl -MPDL -E 'say $PDL::VERSION' Best regards, Ed ________________________________ From: Guillermo P. Ortiz <gor...@exa.unne.edu.ar<mailto:gor...@exa.unne.edu.ar>> Sent: 28 October 2024 12:32 AM To: Ed . <ej...@hotmail.com<mailto:ej...@hotmail.com>> Subject: Re: [Pdl-devel] project ordered sequence image Hello Ed, before to check the reference for PP and from my impatients I try to run a code that I named pru_fnzo.pl<http://pru_fnzo.pl> with the lines from your message from : use strict ... to the end and with a bangshe #!/usr/bin/env perl and the result was ========= perl codes/pru_fnzo.pl<http://pru_fnzo.pl> Had problems bootstrapping Inline module 'pru_fnzo_pl_5262' Can't load '/mnt/diskHD/home/gortiz/Proyectos/Clasifica/_Inline/lib/auto/pru_fnzo_pl_5262/pru_fnzo_pl_5262.so' for module pru_fnzo_pl_5262: /mnt/diskHD/home/gortiz/Proyectos/Clasifica/_Inline/lib/auto/pru_fnzo_pl_5262/pru_fnzo_pl_5262.so: failed to map segment from shared object at /opt/perl5/perls/perl-5.36.0/lib/5.36.0/x86_64-linux/DynaLoader.pm line 206. at /opt/perl5/perls/perl-5.36.0/lib/site_perl/5.36.0/Inline.pm line 541. at codes/pru_fnzo.pl<http://pru_fnzo.pl> line 0. INIT failed--call queue aborted. ========================== Seems like I need to read first PP, is not it? I am using perlbrew maybe with an older perl version (5.36.0) than you are expecting? Regards El dom., 27 de octubre de 2024 15:47, Ed . <ej...@hotmail.com<mailto:ej...@hotmail.com>> escribió: Hi Guillermo, I've just added to PDL::Ufunc "firstnonzeroover", and the script below produces this output to demo it works: in= [ [0 0 3 4] [0 5 0 1] ] out=[3 5] If you don't want to install the very latest PDL from git "master", see below for a slightly cut-down Inline::Pdlpp so you can try it. Based on previous discussion, you probably want this code: $final_image = $imn->mv(-1,0)->slice('-1:0')->firstnonzeroover; You're exactly right that "pp_def" sets up all the broadcasting stuff, see https://metacpan.org/pod/PDL::PP for a guide. The "leftzero" stuff is a term from R.S Bird's paper at https://academic.oup.com/comjnl/article-pdf/32/2/122/1445670/320122.pdf, it just means no further computation will make a difference as of that point, so the loop can conclude there. The script you could modify to have that, or a more correct version: use strict; use warnings; use PDL; use Inline Pdlpp => 'DATA';#, clean_after_build => 0; my $in = pdl '0 0 3 4; 0 5 0 1'; print "in=$in\nout=", $in->firstnonzeroover, "\n"; __DATA__ __Pdlpp__ use PDL::Types qw(ppdefs_all); %over = ( firstnonzeroover => { def=>'$GENERIC() tmp', txt => 'first non-zero value', init => '0', otype => '', op => 'tmp = $a();', leftzero => 'tmp' }, ); my $func = 'firstnonzeroover'; my $def = $over{$func}{def}; my $txt = $over{$func}{txt}; my $init = $over{$func}{init}; my $otype = $over{$func}{otype}; my $op = $over{$func}{op}; my $leftzero = $over{$func}{leftzero}; pp_def( $func, HandleBad => 1, Pars => 'a(n); ' . $otype . ' [o]b();', GenericTypes => [ppdefs_all], Code => <<EOF, $def = $init; int flag = 0; loop(n) %{ PDL_IF_BAD(if ( \$ISBAD(a()) ) continue; flag = 1;,) $op if ( $leftzero ) break; %} PDL_IF_BAD(if (!flag) { \$SETBAD(b()); \$PDLSTATESETBAD(b); } else,) \$b() = tmp; EOF ); Best regards, Ed ________________________________ From: Guillermo P. Ortiz <gor...@exa.unne.edu.ar<mailto:gor...@exa.unne.edu.ar>> Sent: 25 October 2024 11:49 PM To: Ed . <ej...@hotmail.com<mailto:ej...@hotmail.com>> Subject: Re: [Pdl-devel] project ordered sequence image Hello Ed, I'm not sure what help could be useful for you from my curiosity rather than developers capabilities that I have. It is interesting that PP_def is the master part for broadcasting from loop(n) I suppose but not sure. the hash of hash %over have the key zcover for the hash { def=>'char tmp', txt => '== 0', init => 1, alltypes => 1, otype => 'int+', op => 'tmp &= ($a() == 0);', leftzero => '!tmp' }, and it seems that op is the key for the $op variable that is used inside loop(n) for performing zcover I guess. I did not understand the trick for $leftzero, they reach a 'break' for what? Lines belows appear pp_def for diffover, or diff2 seems to be more friendly for a type of CODE like the suggested by David could be placed for a firstnonzeroover implementation task But do not worry about explaining to me. As you can see I have not expertise with pp_def nomenclature Regards El vie, 25 oct 2024 a las 17:06, Ed . (<ej...@hotmail.com<mailto:ej...@hotmail.com>>) escribió: Hi Guillermo, Glad that helps a bit. Look in Basic/Ufunc/ufunc.pd, and I'd start from "zc" (which is generated from a hash). Note especially the "leftzero" mechanism, which is the shortcut. Best regards, Ed ________________________________ From: Guillermo P. Ortiz <gor...@exa.unne.edu.ar<mailto:gor...@exa.unne.edu.ar>> Sent: 25 October 2024 9:03 PM To: Ed . <ej...@hotmail.com<mailto:ej...@hotmail.com>> Cc: pdl-devel@lists.sourceforge.net<mailto:pdl-devel@lists.sourceforge.net> <pdl-devel@lists.sourceforge.net<mailto:pdl-devel@lists.sourceforge.net>>; pdl-gene...@lists.sourceforge.net<mailto:pdl-gene...@lists.sourceforge.net> <pdl-gene...@lists.sourceforge.net<mailto:pdl-gene...@lists.sourceforge.net>> Subject: Re: [Pdl-devel] project ordered sequence image Thanks Ed, using $inds runs quicker (a little), maybe. I believe that you are right a 'firstnonzeroover' could be a such operation that I need. From where I can learn how to do xfor for Ufunc ? Regards El vie, 25 oct 2024 a las 14:38, Ed . (<ej...@hotmail.com<mailto:ej...@hotmail.com>>) escribió: Hi Guillermo, Glad you have progress! A quick change that will compute a bit less is to change: $image->where($sub_image > 0) .= $sub_image->where($sub_image > 0); to: my $inds = $sub_image > 0; $image->where($inds) .= $sub_image->where($inds); The algorithm you're using looks like it takes, for each pixel channel, the last (highest-n) non-zero pixel channel value. There isn't a "first non-zero" (which you could use with a slice("-1:0")) operation that I know of, but if there were, it would operate over the whole image-stack in one go, which would probably be optimally quick, especially since it would shortcut. Also with the miracle of auto-pthreading and broadcasting, it could use POSIX threads. Any volunteers to write a "firstnonzeroover" xform for Ufunc? Best regards, Ed ________________________________ From: Guillermo P. Ortiz <gor...@exa.unne.edu.ar<mailto:gor...@exa.unne.edu.ar>> Sent: 25 October 2024 5:29 PM To: Ed . <ej...@hotmail.com<mailto:ej...@hotmail.com>> Cc: David Mertens <dcmertens.p...@gmail.com<mailto:dcmertens.p...@gmail.com>>; pdl-devel@lists.sourceforge.net<mailto:pdl-devel@lists.sourceforge.net> <pdl-devel@lists.sourceforge.net<mailto:pdl-devel@lists.sourceforge.net>>; pdl-gene...@lists.sourceforge.net<mailto:pdl-gene...@lists.sourceforge.net> <pdl-gene...@lists.sourceforge.net<mailto:pdl-gene...@lists.sourceforge.net>> Subject: Re: [Pdl-devel] project ordered sequence image Thanks to Ingo, David, Ed, After some minor modification to the David help, and using: use PDL::NiceSlice; my $image = $imn(,,,(0)); for my $layer (1 .. $imn->dim(3)-1) { my $sub_image = $imn(,,,($layer)); $image->where($sub_image > 0) .= $sub_image->where($sub_image > 0); } works fine to solve my problem, but yes it is some slow thinking in hundreds of these operations. Nevertheless, it does not impact the overall computation cost. The change I made is $image->dim(3) => $imn->dim(3)-1, because $image is (3,x,y) and the number of layer is in $imn->dim(3) Regards El vie, 25 oct 2024 a las 9:42, Ed . (<ej...@hotmail.com<mailto:ej...@hotmail.com>>) escribió: A thing I didn't think of before: to add to David's thought, you might consider adding a fourth value to make your images RGBA, where the A is "alpha", i.e. opacity. Then you would only add each pixel (or channel value) to the final image where its numerical value * the alpha value was >0 (or, if you're doing addition or "or"-ing, just add/or the value * the alpha, which if 0 does nothing). Best regards, Ed ________________________________ From: David Mertens <dcmertens.p...@gmail.com<mailto:dcmertens.p...@gmail.com>> Sent: 25 October 2024 11:10 AM To: Ed . <ej...@hotmail.com<mailto:ej...@hotmail.com>> Cc: Guillermo P. Ortiz <gor...@exa.unne.edu.ar<mailto:gor...@exa.unne.edu.ar>>; pdl-devel@lists.sourceforge.net<mailto:pdl-devel@lists.sourceforge.net> <pdl-devel@lists.sourceforge.net<mailto:pdl-devel@lists.sourceforge.net>>; pdl-gene...@lists.sourceforge.net<mailto:pdl-gene...@lists.sourceforge.net> <pdl-gene...@lists.sourceforge.net<mailto:pdl-gene...@lists.sourceforge.net>> Subject: Re: [Pdl-devel] project ordered sequence image Hello Guillermo, You said something interesting. You discussed a sub-image with "a red circle" and another with "a blue rectangle". But what you have are full images: an image with a red circle is an image with a red circle and a black background. It sounds like you want to treat that background color as transparent, then "layer" the images by overwriting the non-transparent pixels. If I had to do this myself, I can only think of a way to do this using a Perl loop. If you find that this loop is too slow, then think of ways to rewrite using a PDL expression, but only if you actually deem it to be too slow. It would go something like this: use PDL::NiceSlice; my $image = $imn(,,,(0)); for my $layer (1 .. $image->dim(3)) { my $sub_image = $imn(,,,($layer)); $image->where($sub_image > 0) .= $sub_image->where($sub_image > 0); } This isn't perfect: if you have a pixel in your sub-image that is pure red, it'll copy the red channel to the final image, but not the green or blue. That's as much as I can put into it for now, thouogh, and hopefully it's enough to get you started. David On Thu, Oct 24, 2024 at 3:30 PM Ed . <ej...@hotmail.com<mailto:ej...@hotmail.com>> wrote: Hi Guillermo, That will depend on how you want to combine each pixel. If you can deal independently with each R/G/B value, then to just add the values together, you'd do: $im = $imn->mv(-1,0)->sumover; Otherwise you'll have to spell out a bit more what you mean by sorting. Another operation that might be useful is "borover" (bitwise or, on each R/G/B value along the sequence of images). Best regards, Ed ________________________________ From: Guillermo P. Ortiz <gor...@exa.unne.edu.ar<mailto:gor...@exa.unne.edu.ar>> Sent: 24 October 2024 4:52 PM To: Ed . <ej...@hotmail.com<mailto:ej...@hotmail.com>> Cc: pdl-devel@lists.sourceforge.net<mailto:pdl-devel@lists.sourceforge.net> <pdl-devel@lists.sourceforge.net<mailto:pdl-devel@lists.sourceforge.net>>; pdl-gene...@lists.sourceforge.net<mailto:pdl-gene...@lists.sourceforge.net> <pdl-gene...@lists.sourceforge.net<mailto:pdl-gene...@lists.sourceforge.net>> Subject: Re: [Pdl-devel] project ordered sequence image Hello again, thanks to Ed for show me a typo error in my example. Where I wrote $im=$imn->reduce('op',2); it must say $im=$imn->reduce('op',3); But, the question remain in how to do an 'op' that result in a sorted overlapping between all the sub images In other words. Suppose you have n=0 sub image with a red circle and in n=1 a sub image with a blue rectangle. Some pixeles of both images are in common. Then, what I want is to get a composed image that shows the red circle overlapping the blue rectangle. The same idea for many subimages with sorted overlapping. Regards, El jue, 24 oct 2024 a las 9:57, Guillermo P. Ortiz (<gor...@exa.unne.edu.ar<mailto:gor...@exa.unne.edu.ar>>) escribió: Hello Ed, thanks for your reply. That I trying to mean with 'reduce' is some of projection operation (op) like in PDL::Reduce module that performs "(op)over" to reduce to N-1 dimension after some operation over the set of (3,x,y, n) to (3,x,y) rgb images. I mean a composed rgb image from a set of (layer) n rgb images. For example: $imn-> info : pdl D [3,nx,ny,n] $im=$imn->reduce('op',2); $im-> info : pdl D [3,nx,ny] Then, maybe I need to introduce some "sort" operation in order that when I reduce to one composed $im image each layer in $imn overlap the following layer. But, I did not realize how to do that using some pdl trick. Thanks a lot for your help Regards El jue, 24 oct 2024 a las 9:12, Ed . (<ej...@hotmail.com<mailto:ej...@hotmail.com>>) escribió: Hi Guillermo, I believe the situation you're describing is you have effectively a series of (3,x,y) images. You mention "reducing", but you haven't said what you mean by that - would it turn that series of images into one image? wpic is intended to write out a single image, so an ndarray with multiple images won't work with that. To write out a series of images as a movie you could use wmpeg, or just to store the data you could use https://metacpan.org/pod/PDL::IO::FastRaw and specifically writefraw. Otherwise to write each image in its own file you could use something like: $_->wpic(sprintf "img%03d.png", $count++) for $pdl->dog; Does that help? Best regards, Ed ________________________________ From: Guillermo P. Ortiz <gor...@exa.unne.edu.ar<mailto:gor...@exa.unne.edu.ar>> Sent: 23 October 2024 4:42 PM To: pdl-devel@lists.sourceforge.net<mailto:pdl-devel@lists.sourceforge.net> <pdl-devel@lists.sourceforge.net<mailto:pdl-devel@lists.sourceforge.net>>; pdl-gene...@lists.sourceforge.net<mailto:pdl-gene...@lists.sourceforge.net> <pdl-gene...@lists.sourceforge.net<mailto:pdl-gene...@lists.sourceforge.net>> Subject: [Pdl-devel] project ordered sequence image Hello everyone, I have created a pdl with structure (3,size_x,size_y,np) in order to manage different layer features to compose an rgb image. The idea that I can not connect yet is how to "reduce" over dim 3 to project to 3 X s_x X s_y rgb image in ordered fashion sequence. For example, suppose that for np=0, 1 and 2, in the resulting image is only view of 2 that is allowed by 1 and 0 layers, in that order. I am trying to use wpic command from PDL::IO::Pic module to convert via for example pnmtopng using options for it. There are hashes like {FLAGS => options} used for options {CONVERTER => 'pnmtopng'} indicating which conversor to use. But is seems to be intended of rgb 3(4) X s_x X s_y Thanks for your attention in advance Regards -- Dr. Guillermo P. Ortiz Electromagnetismo Aplicado Dto. Física, Facultad de Ciencias Exactas Universidad Nacional del Nordeste Avda Libertad 5460<https://www.google.com/maps/search/Avda+Libertad+5460?entry=gmail&source=g>, Campus UNNE. W3404AAS Corrientes, Argentina. (+54) 379-4424678 interno 4613 gortiz at unne edu ar _______________________________________________ pdl-devel mailing list pdl-devel@lists.sourceforge.net<mailto:pdl-devel@lists.sourceforge.net> https://lists.sourceforge.net/lists/listinfo/pdl-devel -- "Debugging is twice as hard as writing the code in the first place. Therefore, if you write the code as cleverly as possible, you are, by definition, not smart enough to debug it." -- Brian Kernighan
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