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backend.pl
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use lib qw{/Users/Shared/bin /Users/Shared/bin/Cellfinder2 /srv/www/Cellfinder2/ /HHB/bin/Cellfinder/ /Users/boehringer/src/daboe01_Cellfinder/Cellfinder/ /Users/daboe01/src/daboe01_Cellfinder/Cellfinder /Users/boehringer/src/privatePerl /Users/daboe01/src/privatePerl};
use Mojolicious::Lite;
use Mojolicious::Plugin::Database;
use cellfinder_image;
use SQL::Abstract;
use Apache::Session::File;
use Data::Dumper;
use Mojo::UserAgent;
use POSIX;
use Try::Tiny;
use URI::Encode qw(uri_decode);
use Archive::Zip;
use Mojo::JSON qw(decode_json encode_json);
# enable receiving uploads up to 1GB
$ENV{MOJO_MAX_MESSAGE_SIZE} = 1_073_741_824;
plugin 'database', {
dsn => 'dbi:Pg:dbname=cellfinder;user=root;host=auginfo',
username => 'root',
password => 'root',
options => { 'pg_enable_utf8' => 1, AutoCommit => 1 },
helper => 'db'
};
# turn cache off
hook after_dispatch => sub {
my $tx = shift;
my $e = Mojo::Date->new(time-100);
$tx->res->headers->header(Expires => $e);
};
# <!> fixme: implement https://blog.darkpan.com/article/6/Perl-and-Google-Authenticator.html here
any '/DB/session_key/:key'=> [key =>qr/[-\da-z_]+/i] => sub {
my $self = shift;
my $key = $self->param('key');
my $sessionid = '';
# detect internet access
my $is_external = $self->req->headers->header('X-Forwarded-For')? 1:0;
my %session;
tie %session, 'Apache::Session::File', undef , {Transaction => 0};
$sessionid = $session{_session_id};
$session{is_external} = $is_external;
$self->render(text => $sessionid );
};
###########################################
# dbi part
# fetch all entities
get '/DB/:table'=> sub
{ my $self = shift;
my $sql = SQL::Abstract->new;
my $table = $self->param('table');
my $sessionid = $self->param('session');
my %session;
tie %session, 'Apache::Session::File', $sessionid , {Transaction => 0};
my($stmt, @bind) = $sql->select($table);
my $sth = $self->db->prepare($stmt);
$sth->execute(@bind);
app->log->debug( '**************************'.$session{is_external} );
$self->render( json=> $sth->fetchall_arrayref({}) );
};
# fetch entities by (foreign) key
get '/DB/:table/:col/:pk' => [col=>qr/.+/, pk=>qr/.+/] => sub
{ my $self = shift;
my $sql = SQL::Abstract->new;
my $table = $self->param('table');
my $pk = uri_decode( $self->param('pk'));
my $col = uri_decode( $self->param('col'));
warn $pk;
my($stmt, @bind) = $sql->select($table, undef, {$col=> $pk} );
my $sth = $self->db->prepare($stmt);
$sth->execute(@bind);
$self->render( json=> $sth->fetchall_arrayref({}) );
};
helper getTypeHashForTable => sub { my ($self, $table)=@_;
my $sth = $self->db->column_info('','',$table,'');
my $info = $sth->fetchall_arrayref({});
my $ret={};
foreach (@$info)
{ $ret->{$_->{COLUMN_NAME}}=$_->{TYPE_NAME};
}
return $ret;
};
# update
put '/DB/:table/:pk/:key'=> [key=>qr/\d+/] => sub
{ my $self = shift;
my $table = $self->param('table');
my $pk = uri_decode($self->param('pk'));
my $key = uri_decode($self->param('key'));
my $sql = SQL::Abstract->new;
my $jsonR = decode_json( $self->req->body );
my $types = $self->getTypeHashForTable($table);
for (keys %$jsonR) ## support for nullifying dates and integers with empty string or special string NULL
{
$jsonR->{$_}= ($jsonR->{$_} =~/(^NULL$)|(^\s*$)/o && $types->{$_} !~/text|varchar/o )? undef : $jsonR->{$_} ;
}
app->log->debug($self->req->body);
my($stmt, @bind) = $sql->update($table, $jsonR, {$pk=>$key});
my $sth = $self->db->prepare($stmt);
$sth->execute(@bind);
app->log->debug("err: ".$DBI::errstr ) if $DBI::errstr;
$self->render( json=> {err=> $DBI::errstr} );
};
# insert
post '/DB/:table/:pk'=> sub
{ my $self = shift;
my $table = $self->param('table');
my $pk = $self->param('pk');
my $sql = SQL::Abstract->new;
my $jsonR = decode_json( $self->req->body||'{"name":"New"}' );
my($stmt, @bind) = $sql->insert($table, $jsonR);
my $sth = $self->db->prepare($stmt);
$sth->execute(@bind);
app->log->debug("err: ".$DBI::errstr ) if $DBI::errstr;
my $valpk= $self->db->last_insert_id(undef, undef, $table, $pk);
$self->render( json=>{err=> $DBI::errstr, pk => $valpk} );
};
# delete
del '/DB/:table/:pk/:key'=> [key=>qr/\d+/] => sub
{ my $self = shift;
my $table = $self->param('table');
my $pk = $self->param('pk');
my $key = $self->param('key');
my $sql = SQL::Abstract->new;
my($stmt, @bind) = $sql->delete($table, {$pk=>$key});
my $sth = $self->db->prepare($stmt);
$sth->execute(@bind);
app->log->debug("err: ".$DBI::errstr ) if $DBI::errstr;
$self->render( json=>{err=> $DBI::errstr} );
};
#<!> experimental
# fuzzy-fetch entities by (foreign) key
get '/DB/:table/:col/like/:pk' => [pk=>qr/.+/] => sub
{ my $self = shift;
my $sql = SQL::Abstract->new;
my $table = $self->param('table');
my $pk = $self->param('pk');
my $col = $self->param('col');
app->log->debug( $pk );
app->log->debug( $col );
$self->db->quote_identifier($table);
my $sth = $self->db->prepare(qq/select * from /.$table.qq/ where /.$col.qq/~*?/);
$sth->execute(($pk));
my @a;
my $i=0;
while(my $c=$sth->fetchrow_hashref())
{ push @a,$c;
$i++;
}
warn $i;
# app->log->debug(Dumper \@a);
$self->render(json => \@a);
};
###################################################################
# cellfinder specific part
get '/IMG/:idimage'=> [idimage =>qr/\d+/] => sub
{ my $self= shift;
my $spc= $self->param("spc");
my $width= $self->param("width");
my $idimage= $self->param('idimage');
my $idanalysis= $self->param('idanalysis');
my $preload= $self->param('preload');
my $afterload= $self->param('afterload');
my $idcomposition= $self->param('cmp');
my $csize= $self->param('csize');
my $affine= $self->param('affine');
my $idstack= $self->param('idstack');
my $rnd= $self->param('rnd');
my $exif= $self->param('exif');
my $cc= $self->param('cc');
my $nocache=0;
$nocache= 1 if $width; # ignore cache
$nocache=-1 if $cc; # delete cache
$spc="" unless $spc;
my $f= cellfinder_image::readImageFunctionForIDAndWidth($self->db, $idimage, $width, $nocache, $csize, $affine, $idstack);
my $p= $f->(0);
if($exif)
{
my @exif = split(/[\r\n]/, $p->Get('format', '%[EXIF:*]'));
$self->render(json=>\@exif, format =>'json' );
return;
}
if($idstack && $idcomposition && !$idanalysis)
{ my $compo=cellfinder_image::getObjectFromDBHandID($self->db, 'patch_compositions', $idcomposition);
if($compo->{type} == 5 && !$idanalysis) #clusterstacks
{
$idanalysis=cellfinder_image::insertObjectIntoTable($self->db, 'analyses', 'id', { idstack=> $idstack } );
}
}
$p= cellfinder_image::imageForComposition($self->db, $preload,$f,$p) if($preload); # unused?
if($idanalysis){
my $tmpf=$f;
my $ana=cellfinder_image::getObjectFromDBHandID($self->db, 'analyses', $idanalysis);
if($ana->{ordering}){
my $sql=qq{select id, ordering, idcomposition_for_editing from analyses where idimage=? and ordering is not null and ordering < ? and idcomposition_for_editing is not null order by 2};
my $sth = $self->db->prepare( $sql );
$sth->execute(($idimage, $ana->{ordering}));
while ( my $base_ana=$sth->fetchrow_hashref())
{
$p= cellfinder_image::imageForComposition($self->db, $base_ana->{idcomposition_for_editing}, $tmpf, $p, 1, $base_ana->{id});
$tmpf= cellfinder_image::readImageFunctionForIDAndWidth($self->db, $idimage, $width, 1, $csize, $affine, $idstack, undef, undef, $p);
}
}
}
$p= cellfinder_image::imageForComposition($self->db, $idcomposition, $f, $p, 1, $idanalysis, $idstack) if($idcomposition);
$p= cellfinder_image::imageForComposition($self->db, $afterload, $f, $p, 1, $idanalysis, $idstack) if($afterload);
warn $afterload;
if($csize && !$idstack)
{ $p->Extent(geometry=>$csize, gravity=>'NorthWest', background=>'graya(0%, 0)');
}
if(ref $p eq 'Image::Magick')
{ if($spc eq 'geom') # geom-query
{ $self->render(text => join ' ', $p->Get('width', 'height') );
} elsif ($spc eq 'pixels')
{
my $geom=$self->param('geom');
$geom=~s/ /+/ogs;
warn $geom;
$p->Channel($self->param('channel')) if $self->param('channel');
$p->Crop(geometry=>$geom) if $geom;
my ($width, $height)= $p->Get('width', 'height');
my @h=$p->GetPixels(map=> ($self->param('map') || 'I' ), width=>$width, height=>$height, normalize=> ( $self->param('normalize') || '0' ) );
$self->render(json => \@h );
}
elsif(length $spc)
{ $self->render(text=> $p->Get($spc) );
}
else
{ my $outformat=$self->param('outformat') || 'jpg';
my $blob= ($p->ImageToBlob(magick=>$outformat))[0];
if($blob)
{ $self->render(data => $blob, format =>$outformat);
} else
{
app->log->debug("error: image is empty");
$self->render(data => 'error', format =>'text' );
}
}
} elsif($p)
{ if(ref $p eq 'ARRAY')
{ my $insertagg= $self->param('insertagg');
if($insertagg)
{ cellfinder_image::insertAggregation($self->db, $idanalysis, $p);
} else{
$self->render(json=>$p, format =>'json' );
}
} else
{ $self->render(text => $p);
}
}
};
get '/LASTIMGNAMEID/:imagename/:idtrial'=> [ imagename => qr/[a-z\d_]+/, idtrial => qr/\d+/ ] => sub
{ my $self= shift;
my $imagename= $self->param("imagename");
my $idtrial= $self->param("idtrial");
my $dbh= $self->db;
my $sql=qq{SELECT idimage, image_name, last_image.folder_name from (select max(name) as image_name, linkname, folder_name from folder_content group by folder_name, linkname) last_image
join folders on folders.linkname=last_image.linkname
join folder_content on folder_content.name=last_image.image_name
where idtrial=? and last_image.folder_name=?;
};
my $sth = $dbh->prepare( $sql );
$sth->execute(($idtrial, $imagename));
my $curr=$sth->fetchrow_arrayref();
$self->render(text => $curr->[0]);
};
get '/IMG/make_tags'=> sub
{ my $self=shift;
my $sql='INSERT INTO tags (idimage, idtag) (select images.id as idimage, tag_repository.id as idtag from images join tag_repository on images.idtrial=tag_repository.idtrial left join tags on idimage=images.id and tags.idtag=tag_repository.id where tags.id is null)';
my $sth = $self->db->prepare($sql);
$sth->execute();
$self->render(text=>'OK');
};
post '/IMG/reaggregate_all/:idtrial'=> [idtrial =>qr/\d+/] => sub
{ my $self=shift;
my $idtrial= $self->param("idtrial");
my $dbh=$self->db;
my $trial = cellfinder_image::getObjectFromDBHandID($dbh, 'trials', $idtrial);
$dbh->{AutoCommit}=0;
my $sql=qq{delete from aggregations using analyses, images where analyses.idimage=images.id and aggregations.idanalysis=analyses.id and idtrial=?};
my $sth = $dbh->prepare( $sql );
$sth->execute(($idtrial));
$sql=qq{select distinct analyses.id, idimage from analyses left join aggregations on aggregations.idanalysis=analyses.id join images on analyses.idimage=images.id join number_points on number_points.idanalysis=analyses.id where aggregations.idanalysis is null and idtrial=? order by 2};
$sth = $dbh->prepare( $sql );
$sth->execute(($idtrial));
while(my $curr=$sth->fetchrow_arrayref())
{ my ($idanalysis,$idimage)=($curr->[0],$curr->[1]);
my $f= cellfinder_image::readImageFunctionForIDAndWidth($dbh, $idimage);
my $p= $f->(0);
eval {
$p= cellfinder_image::imageForComposition($self->db, $trial->{composition_for_aggregation},$f,$p, 1, $idanalysis);
}
}
$dbh->{AutoCommit}=1;
$self->render(text => 'OK');
};
post '/IMG/reaggregate_folder/:idtrial/:folder_name'=> [idtrial=>qr/[0-9]+/, folder_name =>qr/.+/] => sub
{ my $self=shift;
my $idtrial= $self->param("idtrial");
my $folder_name = $self->param("folder_name");
my $linkname= $idtrial.$folder_name;
my $dbh=$self->db;
my $trial = cellfinder_image::getObjectFromDBHandID($dbh, 'trials', $idtrial);
$dbh->{AutoCommit}=0;
my $sql=qq{ select distinct analyses.id, analyses.idimage from analyses left join aggregations on aggregations.idanalysis=analyses.id join images on analyses.idimage=images.id join number_points on number_points.idanalysis=analyses.id
join folder_content on folder_content.idimage=analyses.idimage
where aggregations.idanalysis is null and idtrial=? and linkname=?};
my $sth = $dbh->prepare( $sql );
$sth->execute(($idtrial, $linkname));
my $dsth = $dbh->prepare( qq{delete from aggregations where aggregations.idanalysis=?} );
while(my $curr=$sth->fetchrow_arrayref())
{ my ($idanalysis,$idimage)=($curr->[0], $curr->[1]);
my $f= cellfinder_image::readImageFunctionForIDAndWidth($dbh, $idimage);
my $p= $f->(0);
eval {
$dsth->execute(($idanalysis));
$p= cellfinder_image::imageForComposition($self->db, $trial->{composition_for_aggregation},$f,$p, 1, $idanalysis);
}
}
$dbh->{AutoCommit}=1;
$self->render(text => 'OK');
};
get '/IMG/input_results/:idto/:results'=> [idto =>qr/\d+/,results =>qr/.+/] => sub
{ my $self=shift;
my $results = $self->param("results");
my $idanalysis = $self->param("idto");
my $dbh=$self->db;
$dbh->{AutoCommit}=0;
my $sql = 'delete from results where idanalysis = ?';
my $sth = $dbh->prepare($sql);
$sth->execute(($idanalysis));
$sql = 'insert into results (idanalysis, row, col, tag) values (?, ?, ?, ?)';
$sth = $dbh->prepare($sql);
my @result_arr=split/\s+/o, $results;
my ($x,$y);
while(($x,$y)= splice @result_arr,0,2)
{ my $tag;
$tag=$1 if $y=~s/\(([0-9]+)\)//ogs;
($x,$y)=(floor ($x), floor ($y));
$sth->execute(($idanalysis, $x, $y, $tag));
}
$dbh->commit;
$dbh->{AutoCommit}=1;
$self->render(text=> 'OK');
};
get '/IMG/delete_all_results/:idto'=> [idto =>qr/\d+/] => sub
{ my $self=shift;
my $idanalysis = $self->param("idto");
my $dbh=$self->db;
my $sql = 'delete from results where idanalysis = ?';
my $sth = $dbh->prepare($sql);
$sth->execute(($idanalysis));
$self->render(text=> 'OK');
};
get '/IMG/copy_results/:idfrom/:idto'=> [idfrom =>qr/\d+/,idto =>qr/\d+/] => sub
{ my $self=shift;
my $idfrom= $self->param("idfrom");
my $idto = $self->param("idto");
my $dbh=$self->db;
my $sql=qq{insert into results (row,col,tag,idanalysis) (select row,col,tag, ? as idanalysis from results where idanalysis=? order by id)};
my $sth = $dbh->prepare( $sql );
$sth->execute(($idto,$idfrom));
$self->render(text =>'OK');
};
get '/IMG/delete_images_in_folder/:idtrial/:folder_name'=> [idtrial =>qr/\d+/, folder_name =>qr/.+/] => sub
{ my $self=shift;
my $idtrial = $self->param("idtrial");
my $folder_name = $self->param("folder_name");
my $linkname= $idtrial.$folder_name;
my $dbh=$self->db;
my $sql=qq{select idimage from folder_content where linkname=?};
my $sth = $dbh->prepare( $sql );
$sth->execute(($linkname));
while(my $curr=$sth->fetchrow_arrayref())
{ my $idimage=$curr->[0];
cellfinder_image::deleteImage($dbh, $idimage);
}
$self->render(text =>'OK');
};
post '/IMG/batch_delete_images'=> sub
{ my $self = shift;
my $dbh = $self->db;
my @ids = split /,/, $self->req->body;
foreach my $idimage (@ids) # delete every single image
{
cellfinder_image::deleteImage($dbh, $idimage);
}
$self->render(text =>'OK');
};
get '/ANA/results/:idanalysis'=> [idanalysis =>qr/\d+/] => sub
{ my $self=shift;
my $idanalysis= $self->param("idanalysis");
my $dbh=$self->db;
my $sql=qq{select id, row,col,coalesce(tag,0) as tag,idanalysis from results where idanalysis=? order by 1};
my $sth = $dbh->prepare( $sql );
$sth->execute(($idanalysis));
my $result= join("\t", qw/id row col tag idanalysis/)."\n";
while(my $curr=$sth->fetchrow_arrayref())
{ $result.=join("\t", (@$curr));
$result.="\n";
}
$self->render(text=> $result);
};
get '/ANA/stackresults/:idstack'=> [idstack =>qr/\d+/] => sub
{ my $self=shift;
my $idstack= $self->param("idstack");
my $dbh=$self->db;
my $sql=qq{select results.id, row,col,coalesce(tag,0) as tag,montage_images.idanalysis from montages join montage_images on montages.id=idmontage join analyses on analyses.id=montage_images.idanalysis join results on results.idanalysis=montage_images.idanalysis where montages.id=? order by 1};
my $sth = $dbh->prepare( $sql );
$sth->execute(($idstack));
my $result= join("\t", qw/id row col tag idanalysis/)."\n";
while(my $curr=$sth->fetchrow_arrayref())
{ $result.=join("\t", (@$curr));
$result.="\n";
}
$self->render(text=> $result);
};
get '/ANA/clusterstackresults/:idstack'=> [idstack =>qr/\d+/] => sub
{ my $self=shift;
my $idstack= $self->param("idstack");
my $dbh=$self->db;
my $sql=qq{select results.id, row,col,coalesce(tag,0) as tag, montage_images.idimage, images.name, parameter from montages join montage_images on montages.id=idmontage join analyses on analyses.idstack=montages.id join results on results.idanalysis=analyses.id join images on images.id=montage_images.idimage where montages.id=? order by 1};
my $sth = $dbh->prepare( $sql );
$sth->execute(($idstack));
my $result= join("\t", qw/id row col tag idimage name parameter/)."\n";
while(my $curr=$sth->fetchrow_arrayref())
{ $result.=join("\t", (@$curr));
$result.="\n";
}
$self->render(text=> $result);
};
get '/ANA/aggregations/:idtrial'=> [idtrial =>qr/\d+/] => sub
{ my $self=shift;
my $idtrial= $self->param("idtrial");
my $dbh=$self->db;
my $sql=qq{SELECT distinct aggregations.name FROM aggregations join analyses on idanalysis =analyses.id join images on idimage=images.id where idtrial=? order by 1};
my $sth = $dbh->prepare( $sql );
$sth->execute(($idtrial));
my $a=$sth->fetchall_arrayref();
my @colnames=map {'"'.$_->[0].'"' } @$a;
my $colnames= join " text,",@colnames;
$sql="SELECT * FROM crosstab( 'select idanalysis, images.id as idimage, images.name as image_name, uploadtime, aggregations.name as cat, value from aggregations join analyses on idanalysis=analyses.id join images on idimage=images.id where idtrial=$idtrial order by 1,2', 'SELECT distinct aggregations.name FROM aggregations join analyses on idanalysis =analyses.id join images on idimage=images.id where idtrial=$idtrial order by 1') AS ct(idanalysis integer, idimage integer, image_name text, uploadtime date, $colnames text)";
$sth = $dbh->prepare( $sql );
$sth->execute();
my $result= "idanalysis\tidimage\timage_name\tuploadtime\t".join("\t", @colnames)."\n";
while(my $curr=$sth->fetchrow_arrayref())
{ $result.=join("\t", (@$curr));
$result.="\n";
}
$self->render(text=>$result);
};
get '/ANA/clusteraggregations/:idtrial'=> [idtrial =>qr/\d+/] => sub
{ my $self=shift;
my $idtrial= $self->param("idtrial");
my $dbh=$self->db;
my $sql=qq{SELECT distinct aggregations.name from montages join analyses on analyses.idstack=montages.id join aggregations on aggregations.idanalysis=analyses.id where idtrial=? order by 1};
my $sth = $dbh->prepare( $sql );
$sth->execute(($idtrial));
my $a=$sth->fetchall_arrayref();
my @colnames=map {'"'.$_->[0].'"' } @$a;
my $colnames= join " text,",@colnames;
$sql="SELECT * FROM crosstab( 'select idanalysis, montages.name as stack_name, aggregations.name as cat, value from aggregations join analyses on aggregations.idanalysis=analyses.id join montages on idstack=montages.id where idtrial=$idtrial order by 1,2', 'SELECT distinct aggregations.name FROM aggregations join analyses on aggregations.idanalysis=analyses.id join montages on idstack=montages.id where idtrial=$idtrial order by 1') AS ct(idanalysis integer, stack_name text, $colnames text)";
$sth = $dbh->prepare( $sql );
$sth->execute();
my $result= "idanalysis\tstack_name\t".join("\t", @colnames)."\n";
while(my $curr=$sth->fetchrow_arrayref())
{ $result.=join("\t", (@$curr));
$result.="\n";
}
$self->render(text=>$result);
};
get '/ANA/tags_image/:idimage'=> [idimage =>qr/\d+/] => sub
{ my $self=shift;
my $idimage= $self->param("idimage");
my $dbh=$self->db;
my $sql="SELECT * FROM tags where idimage=?";
my $sth = $dbh->prepare( $sql );
$sth->execute(($idimage));
my $res = $sth->fetchall_arrayref();
my $colnames = $sth->{NAME};
my $result= join("\t", @$colnames)."\n";
for my $curr (@$res)
{ $result.=join("\t", (@$curr));
$result.="\n";
}
warn $result;
$self->render(text=> $result);
};
get '/ANA/:table/:idtrial'=> [table=>qr/[^"]+/, idtrial =>qr/\d+/] => sub
{ my $self=shift;
my $idtrial= $self->param("idtrial");
my $table= $self->param("table");
my $dbh=$self->db;
my $sql="SELECT * FROM \"$table\" where idtrial=?";
my $sth = $dbh->prepare( $sql );
$sth->execute(($idtrial));
my $res = $sth->fetchall_arrayref();
my $colnames = $sth->{NAME};
my $result= join("\t", @$colnames)."\n";
for my $curr (@$res)
{ $result.=join("\t", (@$curr));
$result.="\n";
}
$self->render(text=> $result);
};
get '/IMG/STACK/:idstack'=> [idstack =>qr/\d+/] => sub
{ my $self=shift;
my $spc= $self->param("spc");
my $idstack= $self->param("idstack");
my $ransac= $self->param("ransac");
my $idcomposition= $self->param('cmp');
if($spc eq 'affine')
{ my $sql = SQL::Abstract->new;
my($stmt, @bind) = $sql->select('montage_images',undef, {idmontage => $idstack} );
my $sth = $self->db->prepare($stmt);
$sth->execute(@bind);
while ( my $curr = $sth->fetchrow_hashref() )
{
next unless $curr->{idanalysis_reference};
next if $curr->{id} == $curr->{idanalysis_reference};
my $par;
if($ransac)
{ my $params=$self->getRANSACParams($ransac);
$par= cellfinder_image::runRANSACRegistrationRCode($curr->{idanalysis_reference}, $curr->{idanalysis}, $params->{thresh}, $params->{identityradius}, $params->{iterations}, $params->{aiterations}, $params->{cfunc});
eval{
$par= cellfinder_image::reverseAffineMatrix(cellfinder_image::runRANSACRegistrationRCode($curr->{idanalysis}, $curr->{idanalysis_reference}, $params->{thresh}, $params->{identityradius}, $params->{iterations}, $params->{aiterations}, $params->{cfunc})) unless $par; # try reversed RANSAC
}
} else
{ $par=cellfinder_image::runSimpleRegistrationRCode($curr->{idanalysis_reference}, $curr->{idanalysis});
}
my $sql=SQL::Abstract->new();
my($stmt, @bind) = $sql->update('montage_images', {parameter=> $par}, {id=> $curr->{id} } );
my $sth = $self->db->prepare($stmt);
$sth->execute(@bind);
}
$self->render(text => $idstack);
} elsif($spc eq 'gif')
{ my $f= cellfinder_image::readImageFunctionForIDAndWidth($self->db, 0, undef, undef, undef, undef, $idstack, $idcomposition);
my $p= $f->(0);
$_->Set(delay=>15) for @$p; # <!> fixme: make configurable
my $tempfilename=cellfinder_image::tempFileName('/tmp/cellf');
$p->Write($tempfilename.'.gif');
$self->render(data=>cellfinder_image::readFile($tempfilename.'.gif'), format=>'gif');
} elsif($spc eq 'zip')
{ my $f= cellfinder_image::readImageFunctionForIDAndWidth($self->db, 0, undef, undef, undef, undef, $idstack, $idcomposition);
my $p= $f->(0);
my $zip = Archive::Zip->new();
my $i=1;
my $tempfilename=cellfinder_image::tempFileName('/tmp/cellf');
for(@$p)
{ my $fname=$tempfilename.sprintf('%04d', $i++).'.jpg';
$_->Write($fname);
$zip->addFile($fname);
}
$zip->writeToFileNamed($tempfilename.'.zip');
$self->render(data=>cellfinder_image::readFile($tempfilename.'.zip'), format=>'zip');
system('rm '.$tempfilename.'*');
} elsif($spc eq 'mp4')
{ my $f= cellfinder_image::readImageFunctionForIDAndWidth($self->db, 0, undef, undef, undef, undef, $idstack, $idcomposition, $self->param('composite'));
my $p = $f->(0);
my $i=1;
my $tempfilename=cellfinder_image::tempFileName('/tmp/cellf');
for(@$p)
{ my $fname=$tempfilename.sprintf('%04d', $i++).'.jpg';
$_->Write($fname);
}
system('/usr/local/bin/ffmpeg -i '.$tempfilename.'%04d.jpg -pix_fmt yuv420p '.$tempfilename.'.mp4');
$self->render(data=>cellfinder_image::readFile($tempfilename.'.mp4'), format=>'mp4');
system('rm '.$tempfilename.'*');
}
};
get '/IMG/STACK/DELALL/:idtrial'=> [idtrial =>qr/\d+/] => sub
{ my $self=shift;
my $idtrial= $self->param("idtrial");
my $sql=qq{delete from montages where idtrial=?};
my $sth = $self->db->prepare( $sql );
$sth->execute(($idtrial));
$self->render(data=>'OK', format =>'txt' );
};
get '/IMG/import/:idtrial/:name/:uri'=> [name=>qr/.+/, uri=>qr/.+/] => sub
{ my $self=shift;
my $idtrial= $self->param("idtrial");
my $name= $self->param("name");
my $uri= $self->param("uri");
my $ua = Mojo::UserAgent->new;
my $data= $ua->get($uri)->res->body;
my $suffix='.jpg'; # sensible default
$suffix=$1 if $uri =~/^.+\.(.+)$/o;
my $idimage= cellfinder_image::uploadImageFromData($self->db, $idtrial, $name, $suffix, $data);
$self->render(text=>$idimage);
};
post '/IMG/import_stack/:idtrial/:name'=> [name=>qr/.+/] => sub
{ use TempFileNames;
my $self=shift;
my $name= $self->param("name");
my $idtrial= $self->param("idtrial");
my $jsonR = decode_json( $self->req->body );
my $suffix='.jpg'; # sensible default
my @image_ids;
my $i=0;
foreach my $dc_name (@$jsonR) # import every image
{ my $ua = Mojo::UserAgent->new;
my $data=$ua->get('http://augimageserver'.$dc_name)->res->body;
$suffix=$1 if $dc_name =~/^.+\.(.+)$/o;
my $idimage= cellfinder_image::uploadImageFromData($self->db, $idtrial, $name. ($i? "_$i":''), $suffix, $data);
push @image_ids, $idimage;
$i++;
}
my $idmontage=cellfinder_image::insertObjectIntoTable($self->db, 'montages', 'id', {idtrial=> $idtrial, name=> $name} );
my $idref;
foreach my $id (@image_ids)
{ my $idanalysis=cellfinder_image::insertObjectIntoTable($self->db, 'analyses', 'id', { idimage=> $id } );
$idref=$idanalysis unless $idref;
cellfinder_image::insertObjectIntoTable($self->db, 'montage_images', 'id', {idimage=> $id, idanalysis=> $idanalysis, idanalysis_reference=>$idref, idmontage=> $idmontage} );
}
$self->render(data=>'OK', format =>'txt' );
};
helper getLastAnaOfImageID => sub { my ($self, $idimage)=@_;
my $query=qq/select max(id) from analyses where idimage=?/;
my $sth = $self->db->prepare($query);
$sth->execute(($idimage));
my $a=$sth->fetchall_arrayref();
return $a->[0]->[0] if $a;
return undef;
};
post '/IMG/makestack/:idtrial/:name'=> [name=>qr/.+/] => sub
{ my $self=shift;
my $name= $self->param("name");
my $idtrial= $self->param("idtrial");
# warn $self->req->body;
my $jsonR = decode_json( $self->req->body );
my @image_ids=@$jsonR;
my $idmontage=cellfinder_image::insertObjectIntoTable($self->db, 'montages', 'id', {idtrial=> $idtrial, name=> $name} );
my $idref;
my $trial = cellfinder_image::getObjectFromDBHandID($self->db, 'trials', $idtrial);
$self->db->{AutoCommit}=0;
foreach my $id (@image_ids)
{ my $idanalysis=$self->getLastAnaOfImageID( $id );
cellfinder_image::insertObjectIntoTable($self->db, 'montage_images', 'id', {idcomposition_for_editing => $trial->{composition_for_editing}, idimage=> $id, idanalysis=> $idanalysis, idanalysis_reference=>$idref, idmontage=> $idmontage} );
$idref=$idanalysis unless $idref;
}
$self->db->{AutoCommit}=1;
$self->render(data=>$idmontage, format =>'txt' );
};
helper makeidentiystackFolder => sub { my ($self, $dbh, $idtrial, $folder_name)=@_;
my $sql=qq{select folder_content.idimage, min(analyses.id) as idanalysis from folder_content join analyses on analyses.idimage = folder_content.idimage where linkname = ? group by folder_content.idimage, name order by name};
my $sth = $dbh->prepare( $sql );
my $linkname= $idtrial.$folder_name;
$sth->execute(($linkname));
my $first = $sth->fetchrow_arrayref();
my $trial = cellfinder_image::getObjectFromDBHandID($dbh, 'trials', $idtrial);
my $idmontage=cellfinder_image::insertObjectIntoTable($dbh, 'montages', 'id', {idtrial=> $idtrial, name=> $folder_name} );
my $idreference=$first->[1];
cellfinder_image::insertObjectIntoTable($dbh, 'montage_images', 'id', {idcomposition_for_editing => $trial->{composition_for_editing}, idimage=> $first->[0], idanalysis=> $idreference, idmontage=> $idmontage} );
$dbh->{AutoCommit}=0;
while(my $curr=$sth->fetchrow_arrayref())
{
cellfinder_image::insertObjectIntoTable($dbh, 'montage_images', 'id', {idcomposition_for_editing => $trial->{composition_for_editing}, idimage=> $curr->[0], idanalysis=> $curr->[1], idanalysis_reference=>$idreference, idmontage=> $idmontage, parameter=> '1,0,0,1,0,0'} );
}
$dbh->{AutoCommit}=1;
return $idmontage;
};
post '/IMG/makeidentiystack_folder/:idtrial/:folder_name'=> [idtrial=>qr/[0-9]+/, folder_name =>qr/.+/] => sub
{ my $self=shift;
my $idtrial= $self->param("idtrial");
my $folder_name = $self->param("folder_name");
my $dbh=$self->db;
my $idmontage=$self->makeidentiystackFolder($dbh, $idtrial, $folder_name);
$self->render(data=>$idmontage, format =>'txt' );
};
post '/IMG/analyze/:idtrial/:name'=> [idtrial=>qr/[0-9]+/, name=>qr/.+/] => sub
{ my $self= shift;
my $idtrial= $self->param("idtrial");
my $name= $self->param("name");
my $uri= $self->req->body;
my $ua = Mojo::UserAgent->new;
my $data= $ua->get($uri)->res->body;
my $suffix='.jpg'; # sensible default
$suffix=$1 if $uri =~/^.+\.(.+)$/o;
my $trial = cellfinder_image::getObjectFromDBHandID($self->db, 'trials', $idtrial);
my $idimage = cellfinder_image::uploadImageFromData($self->db, $idtrial, $name, $suffix, $data);
my $d = { idimage=>$idimage, idcomposition_for_editing => $trial->{composition_for_editing}, idcomposition_for_analysis=> $trial->{composition_for_celldetection} };
my $idanalysis=cellfinder_image::insertObjectIntoTable($self->db, 'analyses', 'id', $d );
my $f= cellfinder_image::readImageFunctionForIDAndWidth($self->db, $idimage);
cellfinder_image::imageForComposition($self->db, $d->{idcomposition_for_analysis}, $f, $f->(0), 0, $idanalysis);
my $sql='INSERT INTO tags (idimage, idtag) (select ? as idimage, tag_repository.id as idtag from tag_repository where tag_repository.idtrial=?)';
my $sth = $self->db->prepare($sql);
$sth->execute(($idimage, $idtrial));
$self->render(data=>'OK', format =>'txt' );
};
get '/IMG/analyze_folder/:idtrial/:folder_name'=> [idtrial=>qr/[0-9]+/, folder_name =>qr/.+/] => sub
{ my $self=shift;
my $idtrial= $self->param("idtrial");
my $folder_name = $self->param("folder_name");
my $linkname= $idtrial.$folder_name;
my $dbh=$self->db;
my $trial = cellfinder_image::getObjectFromDBHandID($dbh, 'trials', $idtrial);
my $sql=qq{select idimage, name from folder_content where linkname=? order by 2};
my $sth = $dbh->prepare( $sql );
$sth->execute(($linkname));
warn $linkname;
my $sqldel = SQL::Abstract->new;
while(my $curr=$sth->fetchrow_arrayref())
{ my $idimage=$curr->[0];
warn Dumper $curr;
my $d={idimage=>$idimage, idcomposition_for_editing => $trial->{composition_for_editing}, idcomposition_for_analysis=> $trial->{composition_for_celldetection} };
my($stmt, @bind) = $sqldel->delete('analyses', {idimage=>$idimage} );
my $sthdel = $dbh->prepare($stmt);
$sthdel->execute(@bind);
my $idanalysis=cellfinder_image::insertObjectIntoTable($dbh, 'analyses', 'id', $d );
my $f= cellfinder_image::readImageFunctionForIDAndWidth($dbh, $idimage);
cellfinder_image::imageForComposition($dbh, $d->{idcomposition_for_analysis}, $f, $f->(0), 0, $idanalysis);
}
$self->render(data=>'OK', format =>'txt' );
};
get '/IMG/automatch_folder/:idtrial/:idransac/:folder_name'=> [idtrial=>qr/[0-9]+/, idransac=>qr/[0-9]+/, folder_name =>qr/.+/] => sub
{ my $self=shift;
my $idtrial= $self->param("idtrial");
my $idransac= $self->param("idransac");
my $folder_name = $self->param("folder_name");
my $params=$self-> getRANSACParams($idransac);
my $linkname= $idtrial.$folder_name;
my $dbh=$self->db;
my $sql=qq{select idimage, name from folder_content where linkname=? order by 2};
my $sth = $dbh->prepare( $sql );
$sth->execute(($linkname));
my ($idimage1, $idimage2, $next_idimage);
while( my $curr=$sth->fetchrow_arrayref() )
{ $next_idimage=$curr->[0];
$idimage1=$next_idimage unless $idimage1;
my ($idana1, $idana2)=($self->getLastAnaOfImageID($idimage1), $self->getLastAnaOfImageID($next_idimage));
if(!$idana1)
{ $idimage1=undef;
next;
}
next unless $idana2;
$idimage2=$next_idimage;
if($idana1 && $idana2 && $idana1 != $idana2)
{ my $par= cellfinder_image::runRANSACRegistrationRCode($idana1, $idana2,$params->{thresh}, $params->{identityradius}, $params->{iterations}, $params->{aiterations}, $params->{cfunc});
eval{
$par= cellfinder_image::reverseAffineMatrix(cellfinder_image::runRANSACRegistrationRCode($idana2, $idana1,$params->{thresh}, $params->{identityradius}, $params->{iterations}, $params->{aiterations}, $params->{cfunc})) unless $par; # try reversed RANSAC
};
my $name=$par? "$idana1 $idana2":"X$idana1 $idana2";
my $idmontage=cellfinder_image::insertObjectIntoTable($self->db, 'montages', 'id', {idtrial=> $idtrial, name=>$name} );
cellfinder_image::insertObjectIntoTable($dbh, 'montage_images', 'id', {idimage=> $idimage1, idanalysis=> $idana1, idanalysis_reference=>undef, idmontage=> $idmontage} );
cellfinder_image::insertObjectIntoTable($dbh, 'montage_images', 'id', {idimage=> $idimage2, idanalysis=> $idana2, idanalysis_reference=>$idana1, idmontage=> $idmontage, parameter=> $par} );
}
($idimage1, $idimage2)=($idimage2, $next_idimage);
}
$self->render(data=>'OK', format =>'txt' );
};
helper deleteOrphanedMIsInTrial => sub { my ($self, $idtrial)=@_;
my $sql=qq{delete from montages where id in ( select id from (select montages.id, coalesce(count,0) as count from montages left join (select count(*), idmontage from montage_images group by idmontage) a on a.idmontage=montages.id where idtrial=?) a where count<2)};
my $sth = $self->db->prepare( $sql );
$sth->execute(($idtrial));
};
get '/IMG/collect/:samebase/:idmontage'=> [samebase => qr/[0-9]+/, idmontage => qr/[0-9]+/] => sub
{ my $self=shift;
my $idbase = $self->param('samebase');
my $idmontage = $self->param('idmontage');
my $sql=qq{update montage_images set idmontage = ? where idanalysis_reference = ?};
my $sth = $self->db->prepare( $sql );
$sth->execute( ($idmontage, $idbase) );
$self->render(data=>'0', format =>'txt' );
};
get '/IMG/autostitch/:idmontage'=> [idmontage =>qr/[0-9]+/] => sub
{ my $self=shift;
my $idmontage= $self->param('idmontage');
my $move=1;
sub iterateAnalysesOfMontageIDAndMatrix { my ($dbh, $move, $idmontage_orig, $current_matrix, $idanalysis_ref, $idanalysis, $idmontage, $idimage, $seenR)=@_;
$seenR=[] unless $seenR;
return if $idmontage ~~ @$seenR;
push @$seenR, $idmontage;
my $query= qq/select idanalysis, idanalysis_reference, parameter, idmontage, idimage, id from montage_images where (idanalysis_reference=?) and idmontage not in (?,?)/;
my $sth = $dbh->prepare($query);
$idmontage = $idmontage_orig unless $idmontage;
$sth->execute(($idanalysis, $idmontage, $idmontage_orig));
my $anchors= $sth->fetchall_arrayref();
foreach my $curr_anchor (@$anchors)
{ if( $curr_anchor->[2] )
{ if ($current_matrix) {
$current_matrix = cellfinder_image::multiplyAffineMatrixes($current_matrix, $curr_anchor->[2]);
} else {
$current_matrix = $curr_anchor->[2];
}
cellfinder_image::uniquelyInsertObjectIntoTable($dbh, 'montage_images', 'id', {idimage=> $curr_anchor->[4], idanalysis=> $curr_anchor->[0], idanalysis_reference => $idanalysis_ref, idmontage=> $idmontage_orig, parameter=> $current_matrix} );
cellfinder_image::deleteObjectFromTable($dbh, 'montage_images', {id=> $curr_anchor->[5]}) if($move);
iterateAnalysesOfMontageIDAndMatrix($dbh, $move, $idmontage_orig, $current_matrix, $idanalysis_ref, $curr_anchor->[0], $curr_anchor->[3], $curr_anchor->[4], $seenR );
}
}
}
my $query=qq/select idanalysis, idanalysis_reference, parameter, idmontage, idimage, idtrial from montage_images join montages on idmontage=montages.id where idmontage = ? and idanalysis_reference is not null/;
my $sth = $self->db->prepare($query);
$sth->execute(($idmontage));
my $anchor= $sth->fetchrow_hashref();
iterateAnalysesOfMontageIDAndMatrix($self->db, $move, $idmontage, $anchor->{parameter}, $anchor->{idanalysis_reference}, $anchor->{idanalysis} );
if($move)
{
$self-> deleteOrphanedMIsInTrial($anchor->{idtrial});
$self->render(data=>'0', format =>'txt' );
} else
{ $self->render(data=>$idmontage, format =>'txt' );
}
};
helper getRANSACParams => sub { my ($self, $idransac)=@_;
my $compo=cellfinder_image::getObjectFromDBHandID($self->db, 'patch_compositions', $idransac);
my $paramstr = '{'.cellfinder_image::getObjectFromDBHandID($self->db, 'patch_chains_with_parameters', $compo->{primary_chain})->{params}.'}';
warn "$idransac : $paramstr";
return eval($paramstr); #<!> fixme: use real parser
};
get '/IMG/bridgestitch/:idtrial/:idransac/:idmontage1/:idmontage2'=> [idtrial => qr/[0-9]+/, idransac => qr/[0-9]+/, idmontage1 => qr/[0-9]+/, idmontage2 => qr/[0-9]+/] => sub
{ my $self=shift;
my $idtrial= $self->param("idtrial");
my $idransac= $self->param("idransac");
my $idmontage1= $self->param('idmontage1');
my $idmontage2= $self->param('idmontage2');
my $all= $self->param('all');
my $params=$self->getRANSACParams($idransac);
my $query=qq/select a.idanalysis as ida_a, b.idanalysis as ida_b, a.idimage as idm_a, b.idimage as idm_b from montage_images a, montage_images b where a.idmontage=? and b.idmontage=?/;
my $sth = $self->db->prepare($query);
$sth->execute(($idmontage1, $idmontage2));
while( my $curr=$sth->fetchrow_arrayref() )
{ my($idana1, $idana2, $idimage1, $idimage2)=($curr->[0], $curr->[1], $curr->[2], $curr->[3]);
my $par= cellfinder_image::runRANSACRegistrationRCode($idana2, $idana1,$params->{thresh}, $params->{identityradius}, $params->{iterations}, $params->{aiterations}, $params->{cfunc});
if($par)
{ my $name="B$idana1 $idana2";
my $idmontage=cellfinder_image::insertObjectIntoTable($self->db, 'montages', 'id', {idtrial=> $idtrial, name=> $name} );
cellfinder_image::insertObjectIntoTable($self->db, 'montage_images', 'id', {idimage=> $idimage1, idanalysis=> $idana1, idanalysis_reference=>$idana2, idmontage=> $idmontage, parameter=> $par} );
last unless $all;
}
}
$self->render(data=>'0', format =>'txt' );
};
helper rebaseMontageID => sub { my ($self, $idmontageimage)=@_;
my $montage_image=cellfinder_image::getObjectFromDBHandID($self->db, 'montage_images', $idmontageimage);
my ($oldbase, $newbase, $orig_matrix, $idstack)=( $montage_image->{idanalysis_reference}, $montage_image->{idanalysis},
$montage_image->{parameter}, $montage_image->{idmontage} );
my $inverted_matrix= $orig_matrix? cellfinder_image::reverseAffineMatrix($orig_matrix):'1,0,0,1,0,0';
my $sql=SQL::Abstract->new();
my($stmt, @bind) = $sql->select('montage_images',undef, {idmontage => $idstack} );
my $sth = $self->db->prepare($stmt);
$sth->execute(@bind);
while( my $curr_line = $sth->fetchrow_hashref() )
{ my $matrix= $curr_line->{parameter};
if($curr_line->{idanalysis} == $newbase)
{ $matrix=undef;
} elsif($curr_line->{idanalysis} == $oldbase)
{ $matrix=$inverted_matrix;
} else
{ $matrix = cellfinder_image::multiplyAffineMatrixes($matrix, $inverted_matrix);
}
my($stmt, @bind) = $sql->update('montage_images', {parameter=> $matrix, idanalysis_reference=> $newbase}, {id=>$curr_line->{id} } );
my $sth = $self->db->prepare($stmt);
$sth->execute(@bind);
}
return $idstack;
};
#<!>fixme
get '/IMG/setup_cam/:source'=> [source =>qr/[0-9a-z]+/i] =>sub
{ my $self=shift;
my $source = $self->param('source');
if($source =~ /hhb/i)
{ Mojo::UserAgent->new->get('http://10.210.21.44/SetChannel.cgi?Channel=3')->res->body;
sleep(1);
Mojo::UserAgent->new->get('http://10.210.21.44/ChangeResolution.cgi?ResType=3')->res->body;
}
$self->render(data=>'OK', format =>'txt' );
};
get '/IMG/trigger/:loc/:piz'=> [loc =>qr/[0-9a-z]+/i, piz=>qr/[0-9a]{8,9}/i] => sub
{ my $self=shift;
my $piz = $self->param('piz');
my $loc = $self->param('loc');
my $ua = Mojo::UserAgent->new;
my $data= $ua->get("http://auginfo/scanuploaddocscal/$loc/$piz")->res->body;
$self->render(data=>'OK', format =>'txt' );
};
get '/IMG/rebase/:idmontageimage'=> [idmontageimage => qr/[0-9]+/] => sub
{ my $self=shift;
my $idmontageimage = $self->param('idmontageimage');
my $idstack=$self->rebaseMontageID($idmontageimage);
$self->render(data=> $idstack, format =>'txt' );
};
helper getFirstObjectInTableForDict => sub { my ($self, $table, $dict)=@_;
my $sql=SQL::Abstract->new();
my($stmt, @bind) = $sql->select($table, undef, $dict );
my $sth = $self->db->prepare($stmt);
$sth->execute(@bind);
return $sth->fetchrow_hashref();
};
get '/IMG/rebase_merge/:idmontage'=> [idmontage => qr/[0-9]+/] => sub
{ my $self=shift;
my $idmontage = $self->param('idmontage');
my $query=qq/select * from (select a.idmontage as a, b.idmontage as b, c.idmontage as c, a.idanalysis as aa, a.idanalysis_reference as ab, a.parameter from montage_images a join montage_images b on a.idanalysis=b.idanalysis join montage_images c on a.idanalysis_reference=c.idanalysis where a.idmontage=?) a where a!=b and a!=c/;
my $sth = $self->db->prepare($query);
$sth->execute(($idmontage));
my $a= $sth->fetchall_arrayref()->[0];
my ($idmontage_a, $idmontage_b, $idanalysis_a, $idanalysis_b, $parameter)=($a->[1], $a->[2], $a->[3], $a->[4], $a->[5]);
my $montagea= $self->getFirstObjectInTableForDict('montage_images', {idmontage => $idmontage_a, idanalysis => $idanalysis_a});
my $montageb= $self->getFirstObjectInTableForDict('montage_images', {idmontage => $idmontage_b, idanalysis => $idanalysis_b});
if($montageb && $montagea)
{ my ($idmontageimagea , $idmontageimageb)=($montagea->{id}, $montageb->{id});