[MINC-users] median filter

[francois hebert]

Hello Mishkin,

I want to filter the data not the histogram of the data.
Maybe I miss something...
I thank you for the script.

2011/1/28 Mishkin Derakhshan <mishkind at gmail.com>

> Alternatively, here is a perl script that does the filtering on the
> histogram of the data, and not the data itself.
>
>
> #! /usr/bin/perl
>
> my $default = 5;
> if (scalar(@ARGV) < 1) {
>    usage(1);
>    exit(1);
> }
>
>
> my $cnt=0;
> my ($i, $j, $p);
> my @pts;
> my @arr;
> my @bins;
> my $median_samples=$ARGV[1];
>
>
> if(!defined($median_samples)){
>    $median_sample=$default;
>    print "Using default window size of: $default\n";
> }
>
> open(FIN,"$ARGV[0]");
> while(<FIN>){
>    $i="";
>    chomp;
>    ($j, $i, $p)=split(/ +/,$_);
>    #  print "[$j] [$i] [$p]\n";
>    if($j !~ m/\#/){
>        if("$i" ne ""){
>            push @pts, $p;
>            push @bins, $i;
>            $cnt++;
>        }
>    }
> }
>
> my $hmedian= int($median_samples/2);
> for ($i=0; $i<=$cnt-$median_samples; $i++){
>    my @arr;
>    for ($j=0; $j<=$median_samples; $j++){
>        $arr[$j]= $pts[$i+$j]
>    }
>    my @sorted= sort {$a <=> $b} @arr;
>    push @filtered, $sorted[$hmedian];
> }
>
> for ($i=0; $i< $hmedian; $i++){
>    unshift @filtered, $filtered[0];
>    push @filtered, $filtered[$#filtered];
> }
>
> # print map "$_\n", @filtered;
> for ($i=0; $i< $cnt; $i++){
>    print " $bins[$i] $filtered[$i]\n";
> }
>
> sub usage{
>    @params = @_;
>    @array = split(/\//,$0);
>    $me = $array[$#array];
>    if($params[0]==1){
>        print "\nDoes a median filter on histogram data. The input
> file is the output from mincstats\n";
>        #print "\tOptions:\n";
>        print "\n[window_size] is the number of bins to include when
> calculating the median (default: ${default})\n";
>        print "\n";
>    }
>    print "\nUsage:";
>    print "\t$me <histfile.txt> [window_size]\n";
>    #print "\t$me -help\n";
> }
>
>
> On Fri, Jan 28, 2011 at 12:28 PM, francois hebert
> <francois.hebert007 at gmail.com> wrote:
> > Thanks a lot.
> >
> > Francois
> >
> > 2011/1/28 Vladimir S. FONOV <vladimir.fonov at gmail.com>
> >
> >> Hello,
> >>
> >> looks like mailing list removes attachments. Here it is:
> >> http://www.bic.mni.mcgill.ca/~vfonov/software/itk_g_morph.cpp<http://www.bic.mni.mcgill.ca/%7Evfonov/software/itk_g_morph.cpp>
> <http://www.bic.mni.mcgill.ca/%7Evfonov/software/itk_g_morph.cpp>
> >>
> >>
> >> francois hebert wrote:
> >>
> >>> Hello,
> >>>
> >>> Not sure but I think you forgot to attach the file.
> >>>
> >>> 2011/1/28 Vladimir FONOV <vladimir.fonov at gmail.com>
> >>>
> >>>  Hello,
> >>>>
> >>>> see attached file for my grayscale morphology program.
> >>>>
> >>>>
> >>>> francois hebert wrote:
> >>>>
> >>>>  Thanks for the tip I will have a look on it.
> >>>>>
> >>>>> Francois
> >>>>>
> >>>>> 2011/1/28 Vladimir FONOV <vladimir.fonov at gmail.com>
> >>>>>
> >>>>>  Hello,
> >>>>>
> >>>>>>
> >>>>>> I use morphology filters from ITK, using ezminc to interface it with
> >>>>>> MINC:
> >>>>>>
> >>>>>> http://en.wikibooks.org/wiki/MINC/EZMINC
> >>>>>>
> >>>>>>
> >>>>>>
> >>>>>> francois hebert wrote:
> >>>>>>
> >>>>>>  I wuld like to know if there is a median filter in the minc tool or
> if
> >>>>>>
> >>>>>>> somebody have it?
> >>>>>>> I know that we can specified kernel with mincmoprh but i'm not sure
> I
> >>>>>>> can
> >>>>>>> use mincmorph to perform the median filtering.
> >>>>>>>
> >>>>>>>  --
> >>>> Best regards,
> >>>>  Vladimir S. FONOV ~ v.s.fonov  <at> ilmarin.info
> >>>>
> >>>> _______________________________________________
> >>>> MINC-users at bic.mni.mcgill.ca
> >>>> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
> >>>>
> >>>>
> >>>>  _______________________________________________
> >>> MINC-users at bic.mni.mcgill.ca
> >>> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
> >>>
> >>
> >>
> >> --
> >> Best regards,
> >>  Vladimir S. FONOV ~ v.s.fonov  <at> ilmarin.info
> >> _______________________________________________
> >> MINC-users at bic.mni.mcgill.ca
> >> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
> >>
> > _______________________________________________
> > MINC-users at bic.mni.mcgill.ca
> > http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
> >
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>