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<?php
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/**
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* The Leginon software is Copyright 2003
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* The Scripps Research Institute, La Jolla, CA
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* For terms of the license agreement
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* see http://ami.scripps.edu/software/leginon-license
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*/
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// if the config file is not exist, redirect to setup wizard.
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if( !file_exists(dirname(__FILE__).'/../../config.php') ){
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$location = 'location:'.substr($_SERVER['REQUEST_URI'], 0, -11).'setup/index.php';
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header($location);
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exit();
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}
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require_once dirname(__FILE__).'/../../config.php';
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require_once "inc/mysql.inc";
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require_once "inc/path.inc";
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class particledata {
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var $crlf="\n";
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var $baseurl=PROCESSING_BASE_URL;
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function particledata () {
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$this->mysql = new mysql(
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DB_HOST,
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DB_USER,
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DB_PASS,
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PARTICLE_DB);
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}
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function getPathFromId ($pathId) {
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$q = "SELECT "
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."p.path AS path "
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."FROM ApPathData as p "
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."WHERE "
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." p.`DEF_id` = '$pathId' "
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."LIMIT 1 ";
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//echo $q."<br/><br/>\n";
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$r = $this->mysql->getSQLResult($q);
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//echo print_r($r)."<br/><br/>\n";
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$path = $r[0]['path'];
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//echo "$path<br/><br/>\n";
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return $path;
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}
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function getImageNameFromId ($imageId) {
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$q = "SELECT "
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."img.filename "
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."FROM ".DB_LEGINON.".AcquisitionImageData as img "
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."WHERE "
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." img.`DEF_id` = '$imageId' "
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."LIMIT 1 ";
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//echo $q."<br/><br/>\n";
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$r = $this->mysql->getSQLResult($q);
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//echo print_r($r)."<br/><br/>\n";
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$filename = $r[0]['filename'];
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//echo "$filename<br/><br/>\n";
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return $filename;
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}
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function getSessionData ($sessionId) {
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$q = "SELECT "
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."s.* "
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."FROM ".DB_LEGINON.".SessionData as s "
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."WHERE "
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." s.`DEF_id` = ".$sessionId." ";
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//echo $q."<br/><br/>\n";
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$r = $this->mysql->getSQLResult($q);
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//echo print_r($r)."<br/><br/>\n";
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return $r[0];
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}
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function getFilenamesFromLabel($runId, $label) {
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$q = "select "
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."distinct p.`REF|leginondata|AcquisitionImageData|image` as `id`, i.`MRC|Image` as `name` "
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."from ApParticleData p "
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."left join ".DB_LEGINON.".AcquisitionImageData i "
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."on (i.DEF_id = p.`REF|leginondata|AcquisitionImageData|image`) "
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."where "
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."p.`REF|ApSelectionRunData|selectionrun`=".$runId." and "
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."p.label='".$label."'";
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$r = $this->mysql->getSQLResult($q);
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return $r;
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}
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//------ -------------------- ---------//
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//------ General DB summary functions ---------//
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//------ -------------------- ---------//
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function getTotalAceStats(){
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$q = "SELECT count(DISTINCT `REF|ApAceRunData|acerun`) AS runs, "
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."COUNT(DISTINCT `REF|leginondata|AcquisitionImageData|image`) AS img "
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."FROM `ApCtfData` ";
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$r = $this->mysql->getSQLResult($q);
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$results = $r[0];
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$q = "SELECT COUNT(DISTINCT `REF|leginondata|AcquisitionImageData|image`) as i "
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."FROM `ApCtfData` "
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."WHERE (`confidence`>=0.8 OR `confidence_d`>=0.8)";
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$r = $this->mysql->getSQLResult($q);
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$results['conf']=$r[0]['i'];
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$q = "SELECT COUNT(DISTINCT `REF|leginondata|SessionData|session`) as i "
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."FROM `ApAceRunData` ";
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$r = $this->mysql->getSQLResult($q);
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$results['sessions']=$r[0]['i'];
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return $results;
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}
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function getTotalParticleStats(){
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$q = "SELECT count(*) AS particles, "
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."COUNT(DISTINCT p.`REF|ApSelectionRunData|selectionrun`) AS runs "
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."FROM `ApSelectionRunData` AS s "
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."LEFT JOIN `ApParticleData` AS p "
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."ON s.`DEF_id` = p.`REF|ApSelectionRunData|selectionrun` ";
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$r = $this->mysql->getSQLResult($q);
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return $r[0];
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}
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function getSloppyTotalParticleStats(){
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$q = "SELECT count(*) AS runs, "
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."COUNT(DISTINCT `REF|ApDogParamsData|dogparams`) AS dog, "
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."COUNT(DISTINCT `REF|ApManualParamsData|manparams`) AS manual, "
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."COUNT(DISTINCT `REF|ApTiltAlignParamsData|tiltparams`) AS tilt, "
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."COUNT(DISTINCT `REF|leginondata|SessionData|session`) AS sessions "
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."FROM `ApSelectionRunData`";
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$r = $this->mysql->getSQLResult($q);
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$results = $r[0];
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$q = "SELECT count(`DEF_id`) AS p, "
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."COUNT(DISTINCT `REF|leginondata|AcquisitionImageData|image`) AS i "
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."FROM `ApParticleData`";
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$r = $this->mysql->getSQLResult($q);
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$results['particles']=$r[0]['p'];
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$results['imgs']=$r[0]['i'];
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return $results;
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}
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function getTotalStackStats(){
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$q = "SELECT count(*) AS particles, "
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."COUNT(DISTINCT p.`REF|ApStackData|stack`) AS stacks "
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."FROM `ApStackData` AS s "
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."LEFT JOIN `ApStackParticleData` AS p "
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."ON s.`DEF_id` = p.`REF|ApStackData|stack` ";
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$r = $this->mysql->getSQLResult($q);
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return $r[0];
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}
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function getSloppyTotalStackStats(){
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$q = "SELECT count(*) AS s "
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."FROM `ApStackData`";
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$r = $this->mysql->getSQLResult($q);
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$results=array();
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$results['stacks']=$r[0]['s'];
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$q = "SELECT count(*) AS p "
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."FROM `ApStackParticleData`";
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$r = $this->mysql->getSQLResult($q);
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$results['particles']=$r[0]['p'];
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return $results;
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}
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function getTotalReconStats(){
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$q = "SELECT count(*) AS particles, "
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."COUNT(DISTINCT p.`REF|ApRefineIterData|refineIter`) AS iter, "
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."COUNT(DISTINCT i.`REF|ApRefineRunData|refineRun`) AS runs "
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."FROM `ApRefineIterData` AS i "
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."LEFT JOIN `ApRefineParticleData` AS p "
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."ON i.`DEF_id` = p.`REF|ApRefineIterData|refineIter` ";
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$r = $this->mysql->getSQLResult($q);
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return $r[0];
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}
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function getSloppyTotalReconStats(){
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$q = "SELECT count(*) AS i "
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."FROM `ApRefineIterData`";
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$r = $this->mysql->getSQLResult($q);
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$results=array();
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$results['iter']=$r[0]['i'];
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$q = "SELECT count(*) AS p "
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."FROM `ApRefineParticleData`";
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$r = $this->mysql->getSQLResult($q);
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$results['particles']=$r[0]['p'];
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$q = "SELECT count(*) AS r "
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."FROM `ApRefineRunData`";
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$r = $this->mysql->getSQLResult($q);
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$results['runs']=$r[0]['r'];
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return $results;
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}
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function getTotalTemplates(){
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$q = "SELECT count(*) AS templates "
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."FROM ApTemplateImageData";
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$r = $this->mysql->getSQLResult($q);
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return $r[0];
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}
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function getTotalModels(){
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$q = "SELECT count(*) AS models "
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."FROM ApInitialModelData";
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$r = $this->mysql->getSQLResult($q);
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return $r[0];
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}
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//------ -------------------- ---------//
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//------ Tomo functions ---------//
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//------ -------------------- ---------//
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function getTomoAlignmentRunsFromSession($sessionId,$showHidden=False){
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if (!$this->mysql->SQLTableExists("ApTomoAlignmentRunData")) return;
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$q = "SELECT a.`DEF_id` as `alignrunid`, "
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."t.`REF|leginondata|TiltSeriesData|tiltseries` as tiltseries "
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."FROM `ApTomoAlignmentRunData` a "
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."LEFT JOIN `ApTiltsInAlignRunData` t "
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."ON t.`REF|ApTomoAlignmentRunData|alignrun` = a.`DEF_id` "
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."WHERE a.`REF|leginondata|SessionData|session` = " .$sessionId." ";
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$fields = $this->mysql->getFields('ApTomoAlignmentRunData');
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if (!$showHidden && in_array('hidden',$fields))
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$q .= " AND ( a.`hidden` = 0 OR a.`hidden` IS NULL ) ";
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$q .= "ORDER BY `tiltseries` ASC ";
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$results = $this->mysql->getSQLResult($q);
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if (count(array($results))) {
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$finalresults = array();
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if ($results) {
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foreach ($results as $result) {
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$info = $this->getTomoAlignmentInfo($result['alignrunid']);
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$result = array_merge($result,$info);
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if ($result['protomoid']) {
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$result['method'] = 'protomo';
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} else {
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if ($result['imodid']) {
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$result['method'] = 'imod';
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} elseif ($result['xleginonid']) {
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$result['method'] = 'leginon';
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} else {
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$result['method'] = 'unknown';
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}
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}
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$finalresults[] = $result;
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}
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}
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} else {
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$finalresults = $results;
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}
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return $finalresults;
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}
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function getTomoAlignmentInfo($alignrunId){
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// This gives the method and parameter-of-the-method id of an alignment run
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$q = "SELECT a.`DEF_id` as `alignrun id`, "
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."a.name as `alignrun name`, "
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."a.bin as bin, "
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."a.badAlign as badAlign, "
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."path.`path`, "
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."tilt.`number` as `tilt number`, "
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."tia.`REF|leginondata|TiltSeriesData|tiltseries` as tiltseries, ";
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if ($this->mysql->SQLTableExists('ApImodXcorrParamsData')) {
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$q .= "a.`REF|ApImodXcorrParamsData|coarseImodParams` as imodid, "
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."imod.`FilterSigma1` as sigma1, "
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."imod.`FilterSigma2` as sigma2, "
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."imod.`FilterRadius2` as radius2, ";
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}
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if ($this->mysql->SQLTableExists('ApRaptorParamsData')) {
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$q .= "a.`REF|ApRaptorParamsData|raptorParams` as raptorid, "
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."";
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}
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if ($this->mysql->SQLTableExists('ApProtomoParamsData')) {
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$q .= "a.`REF|ApProtomoParamsData|fineProtomoParams` as protomoid, "
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."";
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}
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$q .= ""
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."a.`REF|leginondata|TomographySettingsData|coarseLeginonParams` as xleginonid, "
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."a.`description`, "
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."a.`hidden` "
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."FROM `ApTomoAlignmentRunData` a "
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."LEFT JOIN `ApPathData` path "
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."ON a.`REF|ApPathData|path` = path.`DEF_id` ";
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if ($this->mysql->SQLTableExists('ApImodXcorrParamsData')) {
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$q .= ""
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."LEFT JOIN `ApImodXcorrParamsData` imod "
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."ON a.`REF|ApImodXcorrParamsData|coarseImodParams` = imod.`DEF_id` ";
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}
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if ($this->mysql->SQLTableExists('ApRaptorParamsData')) {
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$q .= ""
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."LEFT JOIN `ApRaptorParamsData` raptor "
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."ON a.`REF|ApRaptorParamsData|raptorParams` = raptor.`DEF_id` ";
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}
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$q .= ""
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."LEFT JOIN `ApTiltsInAlignRunData` tia "
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."ON tia.`REF|ApTomoAlignmentRunData|alignrun` = a.`DEF_id` "
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."LEFT JOIN ".DB_LEGINON.".`TiltSeriesData` tilt ON tia.`REF|leginonData|TiltSeriesData|tiltseries` = tilt.`DEF_id` "
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."WHERE a.`DEF_id` = " .$alignrunId;
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list($r) = $this->mysql->getSQLResult($q);
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if ($r['protomoid']) {
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$r['method'] = 'protomo';
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} elseif ($r['raptorid']) {
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$r['method'] = 'raptor';
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} else {
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if ($r['imodid']) {
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$r['method'] = 'imod';
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$r['filter sigmas'] = '('.$r['sigma1'].','.$r['sigma2'].')';
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$r['filter radius2'] = $r['radius2'];
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unset($r['sigma1']);
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unset($r['sigma2']);
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unset($r['radius2']);
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} elseif ($r['xleginonid']) {
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$r['method'] = 'leginon';
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} else {
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$r['method'] = 'unknown';
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}
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}
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return $r;
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}
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function getTomoAlignerInfoFromAlignmentRun($alignid,$showiHidden=false) {
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// Workaround the possibility of missing these fields in appion_extra.xml
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// refs #1223
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$refinefields = $this->mysql->getFields('ApProtomoRefinementParamsData');
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$fselect = (in_array('SUBD|alibox|x',$refinefields)) ?
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" f.`SUBD|alibox|x` as `align box x`, "
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." f.`SUBD|alibox|y` as `align box y`, "
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:'';
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// Protomo has more than one iteration(cycle)
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$q = " SELECT a.`DEF_id` as alignerid, "
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." a.`REF|ApTomoAlignmentRunData|alignrun` as `alignrunid`, "
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." a.`REF|ApProtomoRefinementParamsData|refine_cycle` as `cycleid`, "
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." a.`REF|ApProtomoRefinementParamsData|good_cycle` as `goodid`, "
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." p.`series_name`, "
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." f.`cycle` as `refine cycle`, "
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." g.`cycle` as `good cycle`, "
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." f.`alismp` as `align sampling`, "
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.$fselect
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." f.`cormod`, "
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." f.`imgref`as `refnum`, "
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." f.`REF|leginondata|AcquisitionImageData|reference` as `refimg`, "
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#." f.`imgref` as `imgref number`, "
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." a.* "
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."FROM `ApTomoAlignerParamsData` a "
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."LEFT JOIN `ApProtomoRefinementParamsData` f "
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."ON a.`REF|ApProtomoRefinementParamsData|refine_cycle` = f.`DEF_id` "
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."LEFT JOIN `ApProtomoRefinementParamsData` g "
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."ON a.`REF|ApProtomoRefinementParamsData|good_cycle` = g.`DEF_id` "
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."LEFT JOIN `ApProtomoParamsData` p "
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."ON a.`REF|ApProtomoParamsData|protomo` = p.`DEF_id` "
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."LEFT JOIN `ApTomoAlignmentRunData` r "
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."ON a.`REF|ApTomoAlignmentRunData|alignrun` = r.`DEF_id` "
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."WHERE r.`DEF_id`=".$alignid." ";
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if (!$showHidden) {
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$q .= " AND ( a.`hidden` = 0 OR a.`hidden` IS NULL ) ";
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}
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$q .= "ORDER BY f.`cycle` ";
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$r = $this->mysql->getSQLResult($q);
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return $r;
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}
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function getTomoAlignersFromAlignmentRun($alignid,$showiHidden=false) {
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$q = " SELECT a.`DEF_id` as alignerid "
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."FROM `ApTomoAlignerParamsData` a "
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."LEFT JOIN `ApTomoAlignmentRunData` r "
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."ON a.`REF|ApTomoAlignmentRunData|alignrun` = r.`DEF_id` "
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."WHERE r.`DEF_id`=".$alignid." ";
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if (!$showHidden) {
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$q .= " AND ( a.`hidden` = 0 OR a.`hidden` IS NULL ) ";
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}
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$r = $this->mysql->getSQLResult($q);
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return $r;
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}
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function getAlignerInfo($alignerid) {
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$q = " SELECT ar.`DEF_id` as alignerid, "
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." FROM `ApTomoAlignerParamsData` ar "
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."WHERE ar.`DEF_id`=".$alignerid." ";
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$r = $this->mysql->getSQLResult($q);
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if (!$r[0]['REF|ApProtomoParamsData|protomo']) {
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$q = " SELECT ar.`DEF_id` as alignerid, "
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." arun.`DEF_id` as alignrunid, "
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." arun.`name` as runname, "
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." arun.`bin` as bin, "
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." path.`path`, "
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." tilts.`REF|leginondata|TiltSeriesData|tiltseries` as `tiltseries` "
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." FROM `ApTomoAlignerParamsData` ar "
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."LEFT JOIN `ApTomoAlignmentRunData` arun "
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."ON ar.`REF|ApTomoAlignmentRunData|alignrun` = arun.`DEF_id` "
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."LEFT JOIN `ApTiltsInAlignRunData` tilts "
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."ON tilts.`REF|ApTomoAlignmentRunData|alignrun` = arun.`DEF_id` "
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."LEFT JOIN `ApPathData` path "
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."ON arun.`REF|ApPathData|path` = path.`DEF_id` "
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."WHERE ar.`DEF_id`=".$alignerid." "
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."AND tilts.`primary_tiltseries` = 1 ";
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$r = $this->mysql->getSQLResult($q);
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return $r;
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} else {
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return $this->getProtomoAlignmentInfo($alignerid);
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}
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}
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function getProtomoAlignmentInfo($alignerid) {
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$q = " SELECT m.`DEF_id` as modelid, "
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." a.`REF|ApTomoAlignerParamsData|aligner` as `alignerid`, "
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." a.`REF|leginondata|AcquisitionImageData|image` as `image`, "
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." a.`number`, "
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." a.`rotation`, "
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." a.`SUBD|shift|x` as `shift x`, "
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." a.`SUBD|shift|y` as `shift y`, "
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." m.`psi`, "
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." m.`theta`, "
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." m.`phi`, "
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." m.`azimuth`, "
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." arun.`DEF_id` as alignrunid, "
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." arun.`name` as runname, "
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." arun.`bin` as bin, "
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." path.`path`, "
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." tilts.`REF|leginondata|TiltSeriesData|tiltseries` as `tiltseries`, "
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." r.* "
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."FROM `ApProtomoAlignmentData` a "
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."LEFT JOIN `ApProtomoModelData` m "
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."ON a.`REF|ApTomoAlignerParamsData|aligner` = m.`REF|ApTomoAlignerParamsData|aligner` "
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."LEFT JOIN `ApTomoAlignerParamsData` ar "
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."ON a.`REF|ApTomoAlignerParamsData|aligner` = ar.`DEF_id` "
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."LEFT JOIN `ApProtomoRefinementParamsData` r "
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."ON ar.`REF|ApProtomoRefinementParamsData|refine_cycle` = r.`DEF_id` "
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."LEFT JOIN `ApTomoAlignmentRunData` arun "
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."ON ar.`REF|ApTomoAlignmentRunData|alignrun` = arun.`DEF_id` "
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."LEFT JOIN `ApTiltsInAlignRunData` tilts "
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."ON tilts.`REF|ApTomoAlignmentRunData|alignrun` = arun.`DEF_id` "
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."LEFT JOIN `ApPathData` path "
|
|
."ON arun.`REF|ApPathData|path` = path.`DEF_id` "
|
|
."WHERE ar.`DEF_id`=".$alignerid." "
|
|
."AND tilts.`primary_tiltseries` = 1 ";
|
|
$r = $this->mysql->getSQLResult($q);
|
|
return $r;
|
|
}
|
|
function getFullTomogramInfo($tomogramId){
|
|
# check to see if ApFullTomogramRunData is linked. Old data does not have it.
|
|
$q = "SELECT t.* "
|
|
."FROM `ApFullTomogramData` t "
|
|
."WHERE t.`DEF_id` = " .$tomogramId;
|
|
list($r) = $this->mysql->getSQLResult($q);
|
|
if ($r['REF|ApFullTomogramRunData|reconrun']) $has_run=True;
|
|
if ($r['REF|ApTomoReconParamsData|reconparam']) $has_param=True;
|
|
|
|
$q = "SELECT t.`DEF_id` as DEF_id, ";
|
|
if ($has_run) {
|
|
$q .= "r.`runname` as runname, "
|
|
."r.`method` as `recon method`, ";
|
|
}
|
|
if ($has_param) {
|
|
$q .= "pa.`tilt_angle_offset`, "
|
|
."pa.`z_shift`, "
|
|
."pa.`tilt_axis_tilt_out_xyplane`, "
|
|
."pa.`tilt_axis_rotation_in_xyplane`, ";
|
|
}
|
|
$q .= "t.name as tomofilename, "
|
|
."t.description as description, "
|
|
."t.`REF|leginondata|TiltSeriesData|tiltseries` as tiltseries, "
|
|
."tilt.number as 'tiltseries number', "
|
|
." p.`path` as path, "
|
|
."t.`REF|ApTomoAlignerParamsData|aligner` as aligner, "
|
|
."t.`REF|leginondata|AcquisitionImageData|zprojection` as zproj_id, "
|
|
." t.`hidden` ";
|
|
if ($has_run)
|
|
$q .= ", r.`SEQ|excluded` as 'excluded imageIds' ";
|
|
$q .= "FROM `ApFullTomogramData` t ";
|
|
if ($has_run) {
|
|
$q .= "LEFT JOIN `ApFullTomogramRunData` r ON t.`REF|ApFullTomogramRunData|reconrun` = r.`DEF_id` "
|
|
."LEFT JOIN `ApPathData` p ON r.`REF|ApPathData|path` = p.`DEF_id` ";
|
|
} else {
|
|
$q .= "LEFT JOIN `ApPathData` p ON t.`REF|ApPathData|path` = p.`DEF_id` ";
|
|
}
|
|
if ($has_param) {
|
|
$q .= "LEFT JOIN `ApTomoReconParamsData` pa ON t.`REF|ApTomoReconParamsData|reconparam` = pa.`DEF_id` ";
|
|
}
|
|
$q .= "LEFT JOIN ".DB_LEGINON.".`TiltSeriesData` tilt ON t.`REF|leginonData|TiltSeriesData|tiltseries` = tilt.`DEF_id` "
|
|
."WHERE t.`DEF_id` = " .$tomogramId;
|
|
|
|
list($r) = $this->mysql->getSQLResult($q);
|
|
if (!$r['runname']) {
|
|
$r['runname'] = array_pop(explode('/',$r['path']));
|
|
}
|
|
return $r;
|
|
}
|
|
|
|
function getTomogramInfo($tomogramId){
|
|
$q = "SELECT t.`DEF_id` as DEF_id, "
|
|
."t.`REF|ApFullTomogramData|fulltomogram` as full, "
|
|
."t.name as name, "
|
|
."t.number as number, "
|
|
."t.pixelsize, "
|
|
."t.description as description, "
|
|
."t.`REF|leginondata|TiltSeriesData|tiltseries` as tiltseries, "
|
|
."t.offsetz as offsetz, "
|
|
."t.`SUBD|dimension|x` as dx, "
|
|
."t.`SUBD|dimension|y` as dy, "
|
|
."t.`SUBD|dimension|z` as dz, "
|
|
."tilt.`number` as tiltnumber, "
|
|
."prtl.xcoord as centerx, "
|
|
."prtl.ycoord as centery, "
|
|
."prtl.`REF|leginondata|AcquisitionImageData|image` as prtlimage, "
|
|
." p.`path` "
|
|
."FROM `ApTomogramData` t "
|
|
."LEFT JOIN `ApPathData` p ON t.`REF|ApPathData|path` = p.`DEF_id` "
|
|
."LEFT JOIN ".DB_LEGINON.".`TiltSeriesData` tilt ON t.`REF|leginonData|TiltSeriesData|tiltseries` = tilt.`DEF_id` "
|
|
."LEFT JOIN `ApParticleData` prtl ON t.`REF|ApParticleData|center` = prtl.`DEF_id` "
|
|
."WHERE t.`DEF_id` = " .$tomogramId;
|
|
list($r) = $this->mysql->getSQLResult($q);
|
|
return $r;
|
|
}
|
|
|
|
function getTomoCenter($centerx,$centery,$image1id,$tiltseriesid){
|
|
$q = "SELECT "
|
|
.$centerx." + p1.`SUBD|predicted shift|x` - p0.`SUBD|predicted shift|x` as x, "
|
|
.$centery." + p1.`SUBD|predicted shift|y` - p0.`SUBD|predicted shift|y` as y "
|
|
."FROM ".DB_LEGINON.".`TomographyPredictionData` p0 "
|
|
."LEFT JOIN "
|
|
. "(SELECT * "
|
|
."FROM ".DB_LEGINON.".`AcquisitionImageData` image0 "
|
|
."WHERE image0.`REF|TiltSeriesData|tilt series` = ".$tiltseriesid." "
|
|
."ORDER BY image0.`DEF_timestamp` ASC limit 1 ) image0 "
|
|
."ON p0.`REF|AcquisitionImageData|image` = image0.`DEF_id` "
|
|
.", ".DB_LEGINON.".`TomographyPredictionData` p1 "
|
|
."WHERE p1.`REF|AcquisitionImageData|image`=$image1id "
|
|
."";
|
|
list($r) = $this->mysql->getSQLResult($q);
|
|
if (count($r) == 0)
|
|
$r = array(x=>$centerx,y=>$centery);
|
|
return $r;
|
|
}
|
|
|
|
function getFullTomogramsFromSession($sessionId,$showHidden=False,$showDummy=False){
|
|
$q = "SELECT t.`DEF_id` as DEF_id "
|
|
."FROM `ApFullTomogramData` t "
|
|
."WHERE t.`REF|leginondata|SessionData|session` = " .$sessionId." ";
|
|
if (!$showDummy)
|
|
$q .= "AND t.name NOT LIKE 'dummy'";
|
|
$fields = $this->mysql->getFields('ApFullTomogramData');
|
|
if (!$showHidden && in_array('hidden',$fields))
|
|
$q .= " AND ( t.`hidden` = 0 OR t.`hidden` IS NULL ) ";
|
|
return $this->mysql->getSQLResult($q);
|
|
}
|
|
|
|
function getUnfinishedETomoRunsFromSession($sessionId) {
|
|
$q = "SELECT t.* "
|
|
.", p.path as rundir "
|
|
."FROM `ApFullTomogramRunData` t "
|
|
."LEFT JOIN `ApPathData` p "
|
|
."ON p.`DEF_id` = t.`REF|ApPathData|path` "
|
|
."WHERE t.`REF|leginondata|SessionData|session` = " .$sessionId." "
|
|
."AND t.`method` LIKE 'etomo' ";
|
|
$runs = $this->mysql->getSQLResult($q);
|
|
if (!is_array($runs) || count($runs)==0) return array();
|
|
|
|
$ready_for_etomo = array();
|
|
// only include ones with no full tomogram record in the database
|
|
foreach ($runs as $r) {
|
|
$q = "SELECT `DEF_id` "
|
|
."FROM `ApFullTomogramData` "
|
|
."WHERE `REF|ApFullTomogramRunData|reconrun`=".$r['DEF_id'];
|
|
$tomos = $this->mysql->getSQLResult($q);
|
|
if ( !is_array($tomos) || count($tomos) == 0)
|
|
$ready_for_etomo[]= $r;
|
|
}
|
|
return $ready_for_etomo;
|
|
}
|
|
|
|
function getTomogramsFromSession($sessionId){
|
|
$q = "SELECT t.`DEF_id` as DEF_id "
|
|
."FROM `ApTomogramData` t "
|
|
."WHERE t.`REF|leginondata|SessionData|session` = " .$sessionId;
|
|
return $this->mysql->getSQLResult($q);
|
|
}
|
|
function getSubTomoRunFromStack($stackId){
|
|
$currentstackId = $stackId;
|
|
while (!$r['subtomorunid'] && $currentstackId) {
|
|
$q = "SELECT `DEF_id` as subtomorunid "
|
|
."FROM `ApSubTomogramRunData` "
|
|
."WHERE `REF|ApStackdata|stack` = " .$currentstackId." "
|
|
."LIMIT 1";
|
|
list($r) = $this->mysql->getSQLResult($q);
|
|
if (!$r['subtomorunid']) {
|
|
$selectionruns = $this->getParticleRunsFromStack($currentstackId);
|
|
if (count($selectionruns) > 1) return;
|
|
$selectionrunid = $selectionruns[0][0]['DEF_id'];
|
|
$q = "SELECT `DEF_id` as subtomorunid "
|
|
."FROM `ApSubTomogramRunData` "
|
|
."WHERE `REF|ApSelectionRundata|pick` = " .$selectionrunid." "
|
|
."LIMIT 1";
|
|
list($r) = $this->mysql->getSQLResult($q);
|
|
}
|
|
if (!$r['subtomorunid']) {
|
|
$parentstack = $this->getParentStackId($currentstackId);
|
|
$currentstackId = $parentstack['parentid'];
|
|
}
|
|
}
|
|
return $r['subtomorunid'];
|
|
}
|
|
|
|
function getOrphanSubTomogramsFromSession($sessionId){
|
|
$q = "SELECT t.`DEF_id` as DEF_id "
|
|
."FROM `ApTomogramData` t "
|
|
."WHERE t.`REF|leginondata|SessionData|session` = " .$sessionId. " "
|
|
."AND t.`REF|ApFullTomogramData|fulltomogram` IS NULL";
|
|
return $this->mysql->getSQLResult($q);
|
|
}
|
|
|
|
function getSubTomogramStackIds($sessionId){
|
|
// subtomograms picked by stack
|
|
$q = "SELECT s.`DEF_id` as stackid, "
|
|
."t.`DEF_id` as subtomorunid, "
|
|
."s.* "
|
|
."FROM `ApSubTomogramRunData` t "
|
|
."LEFT JOIN `ApStackData` s "
|
|
."ON t.`REF|ApStackData|stack` = s.`DEF_id` "
|
|
."WHERE t.`REF|leginondata|SessionData|session` = " .$sessionId. " "
|
|
."AND s.`DEF_id` IS NOT NULL "
|
|
." ";
|
|
$r = $this->mysql->getSQLResult($q);
|
|
// subtomograms picked by particle selection (pick)
|
|
$q = "SELECT s.`DEF_id` as stackid, "
|
|
."sp1.`REF|ApStackData|stack` as oldstackid, "
|
|
."sp1.`REF|ApStackRunData|stackRun` as stackrunid, "
|
|
."pr . `DEF_id` as selectionid, "
|
|
."t. `DEF_id` as subtomorunid, "
|
|
."s.* "
|
|
."FROM ( "
|
|
."SELECT st.*, stpm.`DEF_id` as stackparamsid "
|
|
."FROM `ApStackParticleData` as st "
|
|
."LEFT JOIN `ApStackRunData` as str "
|
|
."ON st.`REF|ApStackRunData|stackRun` = str.`DEF_id` "
|
|
."LEFT JOIN `ApStackParamsData` as stpm "
|
|
."ON str.`REF|ApStackParamsData|stackParams` = stpm.`DEF_id` "
|
|
."group by "
|
|
."st.`REF|ApStackRunData|stackRun` "
|
|
.") sp1 "
|
|
."LEFT JOIN `ApParticleData` p "
|
|
."ON p .`DEF_id` = sp1 . `REF|ApParticleData|particle` "
|
|
."LEFT JOIN `ApSelectionRunData` pr ON "
|
|
."pr . `DEF_id` = p . `REF|ApSelectionRunData|selectionrun` "
|
|
."LEFT JOIN `ApStackData` s "
|
|
."ON s.`REF|ApStackData|oldstack` = sp1.`REF|ApStackData|stack` "
|
|
."LEFT JOIN `ApSubTomogramRunData` t "
|
|
."ON t.`REF|ApSelectionRunData|pick` = pr.`DEF_id` "
|
|
."WHERE t.`REF|leginondata|SessionData|session` = " .$sessionId. " "
|
|
."AND s.`DEF_id` IS NOT NULL "
|
|
." ";
|
|
$r1 = $this->mysql->getSQLResult($q);
|
|
$r = array_merge($r,$r1);
|
|
return $r;
|
|
}
|
|
|
|
function getAveragedTomogramsFromSession($sessionId,$showHidden=False){
|
|
$q = "SELECT t.`DEF_id` as `avgid`, "
|
|
."t.`description`, "
|
|
."t.`runname`, "
|
|
."t.`REF|ApStackData|stack` as stackid, "
|
|
."t.`hidden` as hidden, "
|
|
."stack.`substackname` as substackname "
|
|
."FROM `ApTomoAverageRunData` t "
|
|
."LEFT JOIN `ApSubTomogramRunData` sub "
|
|
."ON t.`REF|ApSubTomogramRunData|subtomorun` = sub.DEF_id "
|
|
."LEFT JOIN `ApStackData` stack "
|
|
."ON t.`REF|ApStackData|stack` = stack.DEF_id "
|
|
."WHERE sub.`REF|leginondata|SessionData|session` = " .$sessionId." ";
|
|
$fields = $this->mysql->getFields('ApTomoAverageRunData');
|
|
if (!$showHidden && in_array('hidden',$fields))
|
|
$q .= " AND ( t.`hidden` = 0 OR t.`hidden` IS NULL ) ";
|
|
$q .= "ORDER BY `avgid` ASC ";
|
|
return $this->mysql->getSQLResult($q);
|
|
}
|
|
|
|
function getAveragedTomogramInfo($avgId){
|
|
$q = "SELECT avgt.`DEF_id` as `avgid`, "
|
|
."avgt.`description`, "
|
|
."avgt.`runname`, "
|
|
."avgt.`REF|ApStackData|stack` as stackid, "
|
|
."subt.`DEF_id` as `subtomoid`, "
|
|
."sub.`DEF_id` as `subtomorunid`, "
|
|
."path.`path` "
|
|
."FROM `ApTomoAverageRunData` avgt "
|
|
."LEFT JOIN `ApPathData` path "
|
|
."ON avgt.`REF|ApPathData|path` = path.`DEF_id` "
|
|
."LEFT JOIN `ApSubTomogramRunData` sub "
|
|
."ON avgt.`REF|ApSubTomogramRunData|subtomorun` = sub.DEF_id "
|
|
."LEFT JOIN `ApStackData` stack "
|
|
."ON avgt.`REF|ApStackData|stack` = stack.DEF_id "
|
|
."LEFT JOIN `ApStackParticleData` stackp "
|
|
."ON stackp.`REF|ApStackData|stack` = stack.DEF_id "
|
|
."LEFT JOIN `ApParticleData` p "
|
|
."ON stackp.`REF|ApParticleData|particle` = p.DEF_id "
|
|
."LEFT JOIN `ApTomogramData` subt "
|
|
."ON subt.`REF|ApParticleData|center` = p.DEF_id "
|
|
."LEFT JOIN `ApTomoAvgParticleData` tap "
|
|
."ON tap.`REF|ApTomoAverageRunData|avgrun` = avgt.DEF_id "
|
|
."WHERE avgt.`DEF_id` = " .$avgId." "
|
|
."AND tap.`REF|ApTomogramData|subtomo` = subt.DEF_id "
|
|
." ";
|
|
return $this->mysql->getSQLResult($q);
|
|
}
|
|
|
|
function getTomoAlignedParticleInfo($avgid,$subtomoid){
|
|
$q = "SELECT p.`DEF_id` as `alignpid`, "
|
|
."p.`xshift`, "
|
|
."p.`yshift`, "
|
|
."p.`rotation`, "
|
|
."p.`mirror`, "
|
|
."avgtp.`z_shift` as zshift, "
|
|
."p.`REF|ApAlignStackData|alignstack` as `alignstack` "
|
|
."FROM `ApTomoAvgParticleData` avgtp "
|
|
."LEFT JOIN `ApTomogramData` sub "
|
|
."ON avgtp.`REF|ApTomogramData|subtomo` = sub.DEF_id "
|
|
."LEFT JOIN `ApAlignParticleData` p "
|
|
."ON avgtp.`REF|ApAlignParticleData|aligned_particle` = p.DEF_id "
|
|
."WHERE avgtp.`REF|ApTomoAverageRunData|avgrun` = " .$avgid." "
|
|
."AND avgtp.`REF|ApTomogramData|subtomo` = ".$subtomoid." ";
|
|
$r = $this->mysql->getSQLResult($q);
|
|
return $r[0];
|
|
}
|
|
|
|
function getsubTomogramsFromFullTomogram($fullId){
|
|
$q = "SELECT t.`DEF_id` as DEF_id "
|
|
."FROM `ApTomogramData` t "
|
|
."WHERE t.`REF|ApFullTomogramData|fulltomogram` = " .$fullId;
|
|
return $this->mysql->getSQLResult($q);
|
|
}
|
|
|
|
function getTiltSeries($sessionId) {
|
|
if($sessionId == NULL)
|
|
return array();
|
|
$query = "SELECT `DEF_id` as id, "
|
|
."UNIX_TIMESTAMP(DEF_timestamp) as timestamp, "
|
|
."`number` "
|
|
."FROM ".DB_LEGINON.".`TiltSeriesData` "
|
|
."WHERE `REF|SessionData|session`=".$sessionId." "
|
|
."ORDER BY DEF_timestamp "
|
|
." ";
|
|
return $this->mysql->getSQLResult($query);
|
|
}
|
|
|
|
function getTiltSeriesSelector($tiltSeries, $tiltSeriesId=NULL,$selectname='tiltseriesId') {
|
|
$selector = '<select name="'.$selectname.'" '
|
|
.'size=5 '
|
|
.'onchange=submit()>';
|
|
$length = strlen(count($tiltSeries));
|
|
for ($i = 0; $i < count($tiltSeries); $i++) {
|
|
$series = $tiltSeries[$i];
|
|
# use real series number if exist
|
|
if (!is_null($series['number'])) {
|
|
$number = $series['number'];
|
|
} else {
|
|
$number = $i + 1;
|
|
}
|
|
$selector .= '<option class="fixed" value='.$series['id'];
|
|
if ($series['id'] == $tiltSeriesId) {
|
|
$selector .= ' selected ';
|
|
$selected_number = $number;
|
|
}
|
|
$shownumber = str_pad($number, $length, ' ', STR_PAD_LEFT).'. ';
|
|
$shownumber = str_replace(" ", " ", $shownumber);
|
|
$timestamp = date('m/d/y H:i:s', $series['timestamp']);
|
|
$selector .= '>'.$shownumber.$timestamp.'</option>';
|
|
}
|
|
$selector .= '</select>';
|
|
return array($selector,$selected_number);
|
|
}
|
|
|
|
function getTomoAlignerSelector($aligners, $alignerId=NULL,$selectname='goodalignerId') {
|
|
$selector = '<select name="'.$selectname.'" '
|
|
.'size=1 '
|
|
.'onchange=submit()>';
|
|
$length = strlen(count($aligners));
|
|
for ($i = 0; $i < count($aligners); $i++) {
|
|
$data = $aligners[$i];
|
|
$aligner = $data['alignerid'];
|
|
$selector .= '<option class="fixed" value='.$i;
|
|
if ($i == $alignerId) {
|
|
$selector .= ' selected ';
|
|
$selected_number = $aligner;
|
|
}
|
|
$shownumber = str_pad($data['refine cycle'], $length, ' ', STR_PAD_LEFT).'. ';
|
|
$shownumber = str_replace(" ", " ", $shownumber);
|
|
$selector .= '>'.$shownumber.'sampling@'.$data['align sampling'].'</option>';
|
|
}
|
|
$selector .= '</select>';
|
|
return array($selector,$selected_number);
|
|
}
|
|
|
|
function getTomoAlignRunAlignerSelector($aligners, $selectedId=NULL,$selectname='goodalignerId') {
|
|
$selector = '<select name="'.$selectname.'" '
|
|
.'size=1 '
|
|
.'onchange=submit()>';
|
|
$length = strlen(count($aligners));
|
|
for ($i = 0; $i < count($aligners); $i++) {
|
|
$data = $aligners[$i];
|
|
$runinfo = $this -> getTomoAlignmentInfo($data['alignrunid']);
|
|
$alignerid = $data['alignerid'];
|
|
$selector .= '<option class="fixed" value='.$alignerid;
|
|
if ($alignerid == $selectedId) {
|
|
$selector .= ' selected ';
|
|
$selected_aligner = $alignerid;
|
|
}
|
|
if ($runinfo['method'] == 'protomo') {
|
|
if ($data['refine_cycle'] != 0) {
|
|
$showmethod = $runinfo['method'];
|
|
$showstr = str_pad(': itr '.$data['refine_cycle'], $length, ' ', STR_PAD_LEFT).'. ';
|
|
$showstr = str_replace(" ", " ", $showstr);
|
|
$showstr .= ' sampling@'.$data['align sampling'];
|
|
} else {
|
|
$showmethod = 'leginon';
|
|
$showstr = '';
|
|
}
|
|
} else {
|
|
$showmethod = $runinfo['method'];
|
|
$showstr = '';
|
|
}
|
|
$selector .= '>'.$runinfo['alignrun name'].'-'.$showmethod.$showstr.'</option>';
|
|
}
|
|
$selector .= '</select>';
|
|
return array($selector,$selected_aligner);
|
|
}
|
|
|
|
function checkforTomogram($tiltseriesId){
|
|
$q = "SELECT t.name , p.`path` "
|
|
."FROM `ApTomogramData` t "
|
|
."LEFT JOIN `ApPathData` p ON t.`REF|ApPathData|path` = p.`DEF_id` "
|
|
."WHERE t.`REF|leginondata|TiltSeriesData|tiltseries` = " .$tiltseriesId;
|
|
return $this->mysql->getSQLResult($q);
|
|
}
|
|
|
|
function checkforFullTomogram($tiltseriesId,$showHidden=False){
|
|
$q = "SELECT t.`DEF_id`, t.name as `tomofilename` "
|
|
."FROM `ApFullTomogramData` t "
|
|
."WHERE t.`REF|leginondata|TiltSeriesData|tiltseries` = " .$tiltseriesId;
|
|
$r = $this->mysql->getSQLResult($q);
|
|
$result = array();
|
|
if ($r && count($r)) {
|
|
foreach ($r as $full) {
|
|
$fullinfo = $this->getFullTomogramInfo($full['DEF_id']);
|
|
$fullinfo['subtomo'] = $this->countSubTomograms($full['DEF_id']);
|
|
if ($showHidden || !$fullinfo['hidden']) $result[] = $fullinfo;
|
|
}
|
|
}
|
|
return $result;
|
|
}
|
|
|
|
function getTiltSeriesInfo($tiltseriesId){
|
|
// get image bin and the most recent pixel calibration
|
|
$q="SELECT pd.`SUBD|binning|x` as imgbin, "
|
|
."pc.`pixelsize` as ccdpixelsize, "
|
|
."a.`REF|SessionData|session` as session, "
|
|
."a.`filename` as filename, "
|
|
."a.`DEF_id` as imageid, "
|
|
."t.`number` as number "
|
|
."FROM ".DB_LEGINON.".`AcquisitionImageData` a "
|
|
."left join ".DB_LEGINON.".`TiltSeriesData` t "
|
|
."on (a.`REF|TiltSeriesData|tilt series`= t.`DEF_id`) "
|
|
."left join ".DB_LEGINON.".`PresetData` pd "
|
|
."on (a.`REF|PresetData|preset`=pd.`DEF_id`) "
|
|
.", ".DB_LEGINON.".`PixelSizeCalibrationData` pc "
|
|
."WHERE a.`REF|TiltSeriesData|tilt series`='$tiltseriesId' "
|
|
."AND pc.`REF|InstrumentData|tem`= pd.`REF|InstrumentData|tem` "
|
|
."AND pc.`magnification`= pd.`magnification` "
|
|
."AND pd.`name` NOT LIKE 'Zproj' "
|
|
."AND "
|
|
."pc.`REF|InstrumentData|ccdcamera`= pd.`REF|InstrumentData|ccdcamera` "
|
|
."AND "
|
|
."pc.`DEF_timestamp`< a.`DEF_timestamp` "
|
|
."ORDER BY pc.`DEF_timestamp` DESC ";
|
|
$r = $this->mysql->getSQLResult($q);
|
|
return $r;
|
|
|
|
}
|
|
|
|
function countSubTomograms($fulltomogramId){
|
|
if (!$this->mysql->SQLTableExists("ApTomogramData")) return 0;
|
|
$q="SELECT * "
|
|
."FROM ApTomogramData "
|
|
."WHERE `REF|ApFullTomogramData|fulltomogram`=".$fulltomogramId;
|
|
$r = $this->mysql->getSQLResult($q);
|
|
return count($r);
|
|
}
|
|
|
|
function getTomoAlignmentRuns($tiltseriesId){
|
|
$q="SELECT *, "
|
|
."`REF|ApTomoAlignmentRunData|alignrun` as alignrunId "
|
|
."FROM ApTiltsInAlignRunData "
|
|
."WHERE `REF|leginondata|TiltSeriesData|tiltseries`=".$tiltseriesId;
|
|
$r = $this->mysql->getSQLResult($q);
|
|
return $r;
|
|
}
|
|
function countTomoAlignmentRuns($tiltseriesId){
|
|
$r = $this->getTomoAlignmentRuns($tiltseriesId);
|
|
return ($r)? count($r) : 0;
|
|
}
|
|
|
|
function countFullTomograms($tiltseriesId){
|
|
$r = $this->checkforFullTomogram($tiltseriesId,True);
|
|
return ($r)? count($r) : 0;
|
|
}
|
|
|
|
function countTomogramsByAlignment($tiltseriesId,$alignrunname){
|
|
$q="SELECT t.* "
|
|
."FROM ApTomoAlignmentRunData a "
|
|
."LEFT JOIN ApFullTomogramData f "
|
|
."on f.`REF|ApTomoAlignmentRunData|alignrun` = a.`DEF_id` "
|
|
."LEFT JOIN ApTomogramData t "
|
|
."on t.`REF|ApFullTomogramData|fulltomogram` = f.`DEF_id` "
|
|
."WHERE a.`REF|leginondata|TiltSeriesData|tiltseries`=".$tiltseriesId." "
|
|
."AND a.name LIKE '".$alignrunname."' ";
|
|
$r = $this->mysql->getSQLResult($q);
|
|
return ($r)? count($r) : 0;
|
|
}
|
|
|
|
// --- loads tomo z profile --- //
|
|
function loadTomoZProfile($filename) {
|
|
$data = array();
|
|
if (file_exists($filename)) {
|
|
$lines = file ($filename);
|
|
foreach ($lines as $line) {
|
|
list($k, $v) = explode(' ', $line);
|
|
$data[]=trim($v);
|
|
}
|
|
}
|
|
$r = array();
|
|
foreach(array_keys($data) as $i) $r[] = array('z'=>$i,'profile'=>$data[$i]);
|
|
return array($r);
|
|
}
|
|
|
|
// ------CTF data functions -------//
|
|
function hasCtfData($sessionId) {
|
|
$d = ($this->getLastCtfRun($sessionId)) ? true : false;
|
|
return $d;
|
|
}
|
|
|
|
function hasCtfTiltData($sessionId) {
|
|
$d = ($this->getLastCtfTiltRun($sessionId)) ? true : false;
|
|
return $d;
|
|
}
|
|
|
|
function getLastCtfRun($sessionId) {
|
|
$q = "select max(DEF_id) as runId "
|
|
."from `ApAceRunData` where `REF|leginondata|SessionData|session`='$sessionId'";
|
|
list($r) = $this->mysql->getSQLResult($q);
|
|
return $r['runId'];
|
|
}
|
|
|
|
function getLastCtfTiltRun($sessionId) {
|
|
$q = "select max(DEF_id) as runId "
|
|
."from `ApCtfTiltRunData` where `REF|leginondata|SessionData|session`='$sessionId'";
|
|
list($r) = $this->mysql->getSQLResult($q);
|
|
return $r['runId'];
|
|
}
|
|
|
|
function getCtfRunIds($sessionId, $showHidden=False, $ctffind=False) {
|
|
$q = "SELECT * "
|
|
."FROM `ApAceRunData` AS a "
|
|
."WHERE "
|
|
." `REF|leginondata|SessionData|session` = '$sessionId' ";
|
|
if (!$showHidden )
|
|
$q .= " AND ( a.`hidden` = 0 OR a.`hidden` IS NULL ) ";
|
|
if ($ctffind)
|
|
$q .= " AND `REF|ApCtfTiltParamsData|ctftilt_params` IS NOT NULL ";
|
|
$q .= "ORDER BY a.`DEF_id` DESC ";
|
|
$r = $this->mysql->getSQLResult($q);
|
|
return $r;
|
|
}
|
|
|
|
function getAceParams($acerunId) {
|
|
$q = "SELECT *, path.`path` as path, acerun.`DEF_id` as acerun "
|
|
."FROM ApAceRunData AS acerun "
|
|
."LEFT JOIN ApAceParamsData AS aceparams "
|
|
." ON (aceparams.`DEF_id` = acerun.`REF|ApAceParamsData|aceparams`) "
|
|
."LEFT JOIN ApCtfTiltParamsData AS ctftilt "
|
|
." ON (ctftilt.`DEF_id` = acerun.`REF|ApCtfTiltParamsData|ctftilt_params`) "
|
|
."LEFT JOIN ApAce2ParamsData AS ace2params "
|
|
." ON (ace2params.`DEF_id` = acerun.`REF|ApAce2ParamsData|ace2_params`) "
|
|
."LEFT JOIN ApPathData AS path "
|
|
." ON (path.`DEF_id` = acerun.`REF|ApPathData|path`) "
|
|
."where acerun.`DEF_id` = '$acerunId'";
|
|
//echo $q."<br/><br/>\n";
|
|
$r = $this->mysql->getSQLResult($q);
|
|
//echo print_r($r)."<br/><br/>\n";
|
|
if ($r) return end($r);
|
|
}
|
|
|
|
function getCtfInfoWithNominal($sessionId, $runId=false) {
|
|
$q = "select "
|
|
."c.`REF|leginondata|AcquisitionImageData|image`, "
|
|
."s.`defocus`, "
|
|
."c.`defocus1`, "
|
|
."c.`defocus2`, "
|
|
."c.`defocusinit`, "
|
|
."c.`amplitude_contrast`, "
|
|
."c.`angle_astigmatism`, "
|
|
."c.`noise1`, "
|
|
."c.`noise2`, "
|
|
."c.`noise3`, "
|
|
."c.`noise4`, "
|
|
."c.`envelope1`, "
|
|
."c.`envelope2`, "
|
|
."c.`envelope3`, "
|
|
."c.`envelope4`, "
|
|
."c.`lowercutoff`, "
|
|
."c.`uppercutoff`, "
|
|
."c.`confidence` , "
|
|
."c.`confidence_d` , "
|
|
."c.`snr` , "
|
|
."c.`graph1` , "
|
|
."c.`graph2` , "
|
|
."(c.`defocus1`+c.`defocus2`)/2+s.`defocus` as difference "
|
|
."from ApCtfData c left join ApAceRunData r on (c.`REF|ApAceRunData|acerun` = r.`DEF_id`) "
|
|
."left join ".DB_LEGINON.".AcquisitionImageData i on (c.`REF|leginondata|AcquisitionImageData|image` = i.`DEF_id`) "
|
|
."left join ".DB_LEGINON.".ScopeEMData s on (i.`REF|ScopeEMData|scope` = s.`DEF_id`) "
|
|
."where i.`REF|SessionData|session`='$sessionId' ";
|
|
if ($runId)
|
|
$q .= "and r.`DEF_id`='$runId' ";
|
|
else
|
|
$q .= "and c.`DEF_id`=(select max(c2.`DEF_id`) from ApCtfData c2 where c2.`REF|leginondata|AcquisitionImageData|image` = c.`REF|leginondata|AcquisitionImageData|image`)";
|
|
echo $q."<br/><br/>\n";
|
|
return $this->mysql->getSQLResult($q);
|
|
}
|
|
|
|
function getCtfInfo($runId) {
|
|
$q = "select "
|
|
."c.`REF|leginondata|AcquisitionImageData|image`, "
|
|
."s.`defocus`, "
|
|
."c.`defocus1`, "
|
|
."c.`defocus2`, "
|
|
."c.`defocusinit`, "
|
|
."c.`amplitude_contrast`, "
|
|
."c.`angle_astigmatism`, "
|
|
."c.`noise1`, "
|
|
."c.`noise2`, "
|
|
."c.`noise3`, "
|
|
."c.`noise4`, "
|
|
."c.`envelope1`, "
|
|
."c.`envelope2`, "
|
|
."c.`envelope3`, "
|
|
."c.`envelope4`, "
|
|
."c.`lowercutoff`, "
|
|
."c.`uppercutoff`, "
|
|
."c.`confidence` , "
|
|
."c.`confidence_d` , "
|
|
."c.`snr` , "
|
|
."c.`graph1` , "
|
|
."c.`graph2` "
|
|
."from ApCtfData c left join ApAceRunData r on (c. `REF|ApAceRunData|acerun` = r.`DEF_id`) "
|
|
."left join ".DB_LEGINON.".AcquisitionImageData i on (c.`REF|leginondata|AcquisitionImageData|image` = i.`DEF_id`) "
|
|
."left join ".DB_LEGINON.".ScopeEMData s on (i.`REF|ScopeEMData|scope` = s.`DEF_id`) "
|
|
."where c.`REF|ApAceRunData|acerun`='$runId'";
|
|
|
|
return $this->mysql->getSQLResult($q);
|
|
|
|
}
|
|
|
|
function getCtfInfoFromImageId($imageId, $order=false, $method='') {
|
|
$q = "select "
|
|
."c.`DEF_id`, "
|
|
."c.`REF|leginondata|AcquisitionImageData|image`, "
|
|
."s.`defocus`, "
|
|
."c.`defocus1`, "
|
|
."c.`defocus2`, "
|
|
."c.`defocusinit`, "
|
|
."c.`amplitude_contrast`, "
|
|
."c.`angle_astigmatism`, "
|
|
."c.`confidence` , "
|
|
."c.`confidence_d` , "
|
|
."c.`cross_correlation` , "
|
|
."c.`snr` , "
|
|
."r.`DEF_id` as acerunId , "
|
|
."r.`name` as runname , "
|
|
."p.`path`, "
|
|
."c.`graph1` , "
|
|
."c.`graph2` , "
|
|
."(c.`defocus1`+c.`defocus2`)/2+s.`defocus` as difference "
|
|
."from ApCtfData c "
|
|
."left join(ApAceRunData r, ApPathData p) "
|
|
."on ( r.DEF_id=c.`REF|ApAceRunData|acerun` and p.DEF_id=r.`REF|ApPathData|path`) "
|
|
."left join ".DB_LEGINON.".AcquisitionImageData i "
|
|
."on (c.`REF|leginondata|AcquisitionImageData|image` = i.`DEF_id`) "
|
|
."left join ".DB_LEGINON.".ScopeEMData s on (i.`REF|ScopeEMData|scope` = s.`DEF_id`) "
|
|
."where c.`REF|leginondata|AcquisitionImageData|image`='$imageId' ";
|
|
$q .= " AND c.`graph1` IS NOT NULL ";
|
|
|
|
if ($method === 'ace1') $q .= "AND r.`REF|ApAceParamsData|aceparams` IS NOT NULL ";
|
|
elseif ($method === 'ace2') $q .= "AND r.`REF|ApAce2ParamsData|ace2_params` IS NOT NULL ";
|
|
elseif ($method === 'ctffind') $q .= "AND r.`REF|ApCtfTiltParamsData|ctftilt_params` IS NOT NULL ";
|
|
|
|
if ($method === 'ctffind') $q .="ORDER BY (c.`cross_correlation`) DESC";
|
|
else $q .= "ORDER BY (c.`confidence`*c.`confidence_d`) DESC";
|
|
if ($order) {
|
|
$fields = $order['fields'];
|
|
$q .= " order by ".join(", ",$fields);
|
|
}
|
|
return $this->mysql->getSQLResult($q);
|
|
}
|
|
|
|
function getBestCtfInfoForSessionId($sessionId, $limit=false) {
|
|
$q = "select ctfdata.* "
|
|
."from "
|
|
." ( "
|
|
." select "
|
|
." i.`filename`, "
|
|
." c.`REF|leginondata|AcquisitionImageData|image`, "
|
|
." i.`DEF_id`, "
|
|
." p.`name`, "
|
|
." s.`defocus`, "
|
|
." c.`defocus1`, c.`defocus2`, c.`defocusinit`, c.`angle_astigmatism`, c.`amplitude_contrast`, "
|
|
." c.`noise1`, c.`noise2`, c.`noise3`, c.`noise4`, "
|
|
." c.`envelope1`, c.`envelope2`, c.`envelope3`, c.`envelope4`, c.`lowercutoff`, c.`uppercutoff`, c.`snr`, "
|
|
." c.`confidence`,c.`confidence_d` , c.`cross_correlation`, "
|
|
." abs(c.`defocus1`+c.`defocus2`)/2-abs(s.`defocus`) as difference "
|
|
." from `ApCtfData` c "
|
|
." left join ".DB_LEGINON.".`AcquisitionImageData` i on (i.`DEF_id` = c.`REF|leginondata|AcquisitionImageData|image`) "
|
|
." left join ".DB_LEGINON.".`PresetData` p on (p.DEF_id = i.`REF|PresetData|preset`) "
|
|
." left join ".DB_LEGINON.".`ScopeEMData` s on (i.`REF|ScopeEMData|scope` = s.`DEF_id`) "
|
|
." where "
|
|
." c.`REF|leginondata|AcquisitionImageData|image` in "
|
|
." ( "
|
|
." select a.`DEF_id` from ".DB_LEGINON.".`AcquisitionImageData` a "
|
|
." where a.`REF|SessionData|session`='$sessionId' "
|
|
." AND "
|
|
." ABS(s.`SUBD|stage position|a`) < 0.9 "
|
|
." ) "
|
|
." order by (greatest(COALESCE(confidence,0),COALESCE(confidence_d,0),COALESCE(cross_correlation,0))) desc "
|
|
." ) ctfdata ";
|
|
// if $limit is specified, report only values with confidences > $limit
|
|
if ($limit) {
|
|
$q .= " where ctfdata.confidence > $limit || ctfdata.confidence_d > $limit ";
|
|
}
|
|
$q .= " group by ctfdata.DEF_id ";
|
|
//echo $q."<br/><br/>\n";
|
|
return $this->mysql->getSQLResult($q);
|
|
}
|
|
|
|
function getCTFParameterFields() {
|
|
$q = "SELECT *, path.`path` as path, acerun.`DEF_id` as acerun "
|
|
."FROM ApAceRunData AS acerun ";
|
|
if ($this->mysql->SQLTableExists("ApAceParamsData")) {
|
|
$q .= "LEFT JOIN ApAceParamsData AS aceparams "
|
|
." ON (aceparams.`DEF_id` = acerun.`REF|ApAceParamsData|aceparams`) ";
|
|
}
|
|
if ($this->mysql->SQLTableExists("ApCtfTiltParamsData")) {
|
|
$q .= "LEFT JOIN ApCtfTiltParamsData AS ctftilt "
|
|
." ON (ctftilt.`DEF_id` = acerun.`REF|ApCtfTiltParamsData|ctftilt_params`) ";
|
|
}
|
|
if ($this->mysql->SQLTableExists("ApAce2ParamsData")) {
|
|
$q .= "LEFT JOIN ApAce2ParamsData AS ace2params "
|
|
." ON (ace2params.`DEF_id` = acerun.`REF|ApAce2ParamsData|ace2_params`) ";
|
|
}
|
|
$q .= "LEFT JOIN ApPathData AS path "
|
|
." ON (path.`DEF_id` = acerun.`REF|ApPathData|path`) "
|
|
." LIMIT 1; ";
|
|
//echo $q."<br/><br/>\n";
|
|
$r = $this->mysql->getSQLResult($q);
|
|
//echo print_r($r)."<br/><br/>\n";
|
|
return $r[0];
|
|
}
|
|
|
|
function getCTFStats($fields, $sessionId, $runId=false) {
|
|
if (!is_array($fields))
|
|
return False;
|
|
foreach ($fields as $field) {
|
|
$selects[$field] = "c.`REF|leginondata|AcquisitionImageData|image` as id, s.defocus, "
|
|
. "count(c.DEF_id) as `nb`, "
|
|
. "min(c.`$field`) as `min`, "
|
|
. "max(c.`$field`) as `max`, "
|
|
. "avg(c.`$field`) as `avg`, "
|
|
. "stddev(c.`$field`) as `stddev`";
|
|
}
|
|
if (!is_array($selects))
|
|
return False;
|
|
$stats = array();
|
|
foreach ($selects as $k=>$select) {
|
|
$q = "select ".$select." "
|
|
."from ApCtfData c left join ".DB_LEGINON.".AcquisitionImageData i "
|
|
."on (c.`REF|leginondata|AcquisitionImageData|image`=i.`DEF_id`) "
|
|
."left join ".DB_LEGINON.".`ScopeEMData` s "
|
|
."on (i.`REF|ScopeEMData|scope` = s.`DEF_id`) "
|
|
."left join ".DB_LEGINON.".`PresetData` p "
|
|
."on (`p`.`DEF_id`=`i`.`REF|PresetData|preset`) "
|
|
."where i.`REF|SessionData|session`='$sessionId' ";
|
|
if ($runId)
|
|
$q .= "and c.`REF|ApAceRunData|acerun`='$runId' ";
|
|
else
|
|
$q .= "and c.`DEF_id`=(select max(c2.`DEF_id`) from ApCtfData c2 where c2.`REF|leginondata|AcquisitionImageData|image` = c.`REF|leginondata|AcquisitionImageData|image`)";
|
|
$q .= "group by p.`name`";
|
|
//echo $q."<br/><br/>\n";
|
|
$r = $this->mysql->getSQLResult($q);
|
|
$stats[$k] = $r;
|
|
//echo print_r($r)."<br/><br/>\n";
|
|
}
|
|
return $stats;
|
|
}
|
|
|
|
function getAceRunIdFromPath($path){
|
|
$q= "SELECT r.* "
|
|
. "FROM `ApAceRunData` AS r "
|
|
. "LEFT JOIN ApPathData AS p "
|
|
. "ON (r.`REF|ApPathData|path` = p.`DEF_id`) "
|
|
. "WHERE p.`path` LIKE '$path%'";
|
|
$r = $this->mysql->getSQLResult($q);
|
|
return $r;
|
|
}
|
|
|
|
function getBestStats($fields, $sessionId, $limit=false) {
|
|
if (!is_array($fields))
|
|
return False;
|
|
foreach ($fields as $field) {
|
|
$selects[$field] = " ctfdata.name , "
|
|
. "count(ctfdata.`$field`) as `nb`, "
|
|
. "min(abs(ctfdata.`$field`)) as `min`, "
|
|
. "max(abs(ctfdata.`$field`)) as `max`, "
|
|
. "avg(ctfdata.`$field`) as `avg`, "
|
|
. "stddev(ctfdata.`$field`) as `stddev` ";
|
|
}
|
|
|
|
if (!is_array($selects))
|
|
return False;
|
|
$stats = array();
|
|
foreach ($selects as $k=>$select) {
|
|
$q = "select $select "
|
|
."from "
|
|
." ( "
|
|
." select allctfdata.* "
|
|
." from "
|
|
." ( "
|
|
." select "
|
|
." c.`REF|leginondata|AcquisitionImageData|image`, "
|
|
." c.`DEF_id`, "
|
|
." p.`name`, "
|
|
." s.`defocus`, "
|
|
." c.`defocus1`, c.`defocus2`, c.`defocusinit`, c.`angle_astigmatism`, "
|
|
." c.`confidence`,c.`confidence_d` , c.`cross_correlation` , "
|
|
." (c.`defocus1`+c.`defocus2`)/2+s.`defocus` as difference "
|
|
." from `ApCtfData` c "
|
|
." left join ".DB_LEGINON.".`AcquisitionImageData` i on (i.DEF_id=c.`REF|leginondata|AcquisitionImageData|image`) "
|
|
." left join ".DB_LEGINON.".`PresetData` p on (p.DEF_id=i.`REF|PresetData|preset`) "
|
|
." left join ".DB_LEGINON.".`ScopeEMData` s on (i.`REF|ScopeEMData|scope` = s.`DEF_id`) "
|
|
." where "
|
|
." c.`REF|leginondata|AcquisitionImageData|image` in "
|
|
." ( "
|
|
." select a.`DEF_id` from ".DB_LEGINON.".`AcquisitionImageData` a "
|
|
." where a.`REF|SessionData|session`='$sessionId' "
|
|
." ) "
|
|
." order by (if(confidence_d>confidence, confidence_d, confidence)) desc "
|
|
." ) allctfdata "
|
|
." group by allctfdata.`REF|leginondata|AcquisitionImageData|image` "
|
|
." ) ctfdata ";
|
|
// if $limit is specified, report only values with confidences > $limit
|
|
if ($limit){
|
|
$q .= " where sqrt(ctfdata.confidence * ctfdata.confidence_d) > $limit ";
|
|
}
|
|
$q .= " group by ctfdata.name; ";
|
|
//echo $q;
|
|
$r = $this->mysql->getSQLResult($q);
|
|
$stats[$k] = $r;
|
|
}
|
|
return $stats;
|
|
}
|
|
|
|
function getData($fields, $sessionId, $runId=false) {
|
|
if (!is_array($fields))
|
|
return False;
|
|
foreach ($fields as $field) {
|
|
$selects[$field] = "c.`REF|leginondata|AcquisitionImageData|image` as id, s.`defocus`, "
|
|
. "`$field`";
|
|
}
|
|
if (!is_array($selects))
|
|
return False;
|
|
$stats = array();
|
|
foreach ($selects as $k=>$select) {
|
|
$q = "select ".$select." "
|
|
."from ctf c left join ".DB_LEGINON.".AcquisitionImageData i"
|
|
."on (c.`REF|leginondata|AcquisitionImageData|image`=i.`DEF_id`) "
|
|
."left join ".DB_LEGINON.".ScopeEMData s on (s.`DEF_id` = i.`REF|ScopeEMData|scope`) "
|
|
."where i.`REF|SessionData|session`='$sessionId' ";
|
|
if ($runId)
|
|
$q .= "and c.`REF|ApAceRunData|acerun`='$runId' ";
|
|
else
|
|
$q .= "and c.`DEF_id`=(select max(c2.`DEF_id`) from ApCtfData c2 where c2.`REF|leginondata|AcquisitionImageData|image` = c.`REF|leginondata|AcquisitionImageData|image`)";
|
|
$r = $this->mysql->getSQLResult($q);
|
|
$stats[$k] = $r;
|
|
}
|
|
return $stats;
|
|
}
|
|
|
|
//------ -------------------- ---------//
|
|
//-------particle functions --------//
|
|
//------ -------------------- ---------//
|
|
//TODO: the next 2 display functions do not belong in this file!!!
|
|
function displayParameters ($title,$params,$exclude_fields,$expId,$hide_button_field='',$inform=false) {
|
|
//standard parameter table display
|
|
|
|
//Array of $params keys that are shown as a link to another report
|
|
$links=array(
|
|
'stackId'=>"stackreport.php?expId=$expId&sId="
|
|
,'particleSelection'=>"particlerunreport.php?expId=$expId&rId="
|
|
,'objectTracing'=>"particlerunreport.php?expId=$expId&rId="
|
|
,'aligner'=>"tomoalignercyclereport.php?expId=$expId&aId="
|
|
,'sizingreport'=>"sizingreport.php?expId=$expId&sizingId="
|
|
);
|
|
if (count($params) ==0) return;
|
|
echo "<h4>".$title."</h4>";
|
|
echo "<table class='tableborder' border='1' cellspacing='1' cellpadding='2'>\n";
|
|
$selection_fields = array_keys($params);
|
|
foreach($selection_fields as $key) {
|
|
$exclude = false;
|
|
foreach($exclude_fields as $bad) {
|
|
if ($key == $bad) {
|
|
$exclude = true;
|
|
break;
|
|
}
|
|
}
|
|
//Display only non-excluded fields
|
|
if (!$exclude) {
|
|
// Clean up referenced key for display
|
|
$displaykeyarray = explode('Data|',$key);
|
|
if (count($displaykeyarray)>1) {
|
|
$displaykey = array_pop($displaykeyarray);
|
|
$refkey = array_pop($displaykeyarray);
|
|
} else {
|
|
$displaykeyarray = explode('DEF_',$key);
|
|
$displaykey = array_pop($displaykeyarray);
|
|
$refkey = $displaykey;
|
|
}
|
|
// Display only non-null params
|
|
if (gettype($params[$key])!='NULL') {
|
|
if (!$hide_button_field) $hide_button_field = $key;
|
|
echo "<tr>\n";
|
|
echo "</td>";
|
|
echo "<td><span class='datafield0'>$displaykey</span></td>";
|
|
echo "<td>";
|
|
$type='text';
|
|
foreach(array_keys($links) as $linkkey) {
|
|
if ($linkkey ==$refkey) {
|
|
$type='link';
|
|
$link = $links[$linkkey];
|
|
}
|
|
}
|
|
if ($type!='link') {
|
|
if (!is_array($params[$key])) {
|
|
//plain display
|
|
echo $params[$key];
|
|
} else {
|
|
//array item display
|
|
$text = '';
|
|
foreach (array_keys($params[$key]) as $akey)
|
|
$text .= ($params[$key][$akey]).',';
|
|
echo trim($text,',');
|
|
}
|
|
} else {
|
|
//Specify different values for the displayed data and link if available
|
|
if (!is_array($params[$key])) {
|
|
$datadisplay = $params[$key];
|
|
$datalink = $datadisplay;
|
|
} else {
|
|
$datadisplay = $params[$key]['display'];
|
|
$datalink = $params[$key]['link'];
|
|
}
|
|
$link = $link.$datalink;
|
|
echo "<a href='".$link."'>".$datadisplay."</a>";
|
|
}
|
|
if ($hide_button_field == $key) {
|
|
$hideid = $params[$hide_button_field];
|
|
if ($params['hidden'] == 1) {
|
|
echo "<font color='#cc0000'>HIDDEN</font>\n";
|
|
if ($inform)
|
|
echo " <input class='edit' type='submit' name='unhideItem".$hideid."' value='unhide'>\n";
|
|
} else {
|
|
if ($inform)
|
|
echo "<input class='edit' type='submit' name='hideItem".$hideid."' value='hide'>\n";
|
|
}
|
|
}
|
|
echo "</td></tr>\n";
|
|
}
|
|
}
|
|
}
|
|
echo "</table>\n";
|
|
}
|
|
|
|
function displayParametersInSummary ($params,$display_fields,$expId,$primary_field='DEF_id') {
|
|
//standard parameter row display
|
|
/* Use $params[key] =
|
|
array('link'=>linkid,'display'=>display_string) to create
|
|
a link of a key in $params found in the array $links
|
|
set $primary_field='' to avoid editing/hiding buttons
|
|
*/
|
|
//Array of $params keys that are shown as a link to another report
|
|
$links=array(
|
|
'stackId'=>"stackreport.php?expId=$expId&sId="
|
|
,'stack'=>"stackreport.php?expId=$expId&sId="
|
|
,'particleSelection'=>"particlerunreport.php?expId=$expId&rId="
|
|
,'fulltomoid'=>"fulltomoreport.php?expId=$expId&tomoId="
|
|
,'avgid'=>"tomoavgreport.php?expId=$expId&avgId="
|
|
,'subtomo'=>"subtomosummary.php?expId=$expId&fullId="
|
|
,'alignrun id'=>"tomoalignercyclesummary.php?expId=$expId&alignId="
|
|
,'alignerid'=>"tomoalignercyclereport.php?expId=$expId&aId="
|
|
,'refine cycle'=>"tomoalignercyclereport.php?expId=$expId&aId="
|
|
);
|
|
$html = '<tr>';
|
|
foreach($display_fields as $key) {
|
|
// Clean up referenced key for display
|
|
$displaykeyarray = explode('Data|',$key);
|
|
if (count($displaykeyarray)>1) {
|
|
$displaykey = array_pop($displaykeyarray);
|
|
$refkey = array_pop($displaykeyarray);
|
|
} else {
|
|
$displaykeyarray = explode('DEF_',$key);
|
|
$displaykey = array_pop($displaykeyarray);
|
|
$refkey = $displaykey;
|
|
}
|
|
if (!$hide_button_field) $hide_button_field = $key;
|
|
$html .= "<td>\n";
|
|
$type='text';
|
|
foreach(array_keys($links) as $linkkey) {
|
|
if ($linkkey ==$refkey && $params[$key]) {
|
|
$type='link';
|
|
$link = $links[$linkkey];
|
|
}
|
|
}
|
|
if ($type!='link') {
|
|
if (!is_array($params[$key])) {
|
|
//plain display
|
|
$html .= $params[$key];
|
|
} else {
|
|
//array item display
|
|
$text = '';
|
|
foreach (array_keys($params[$key]) as $akey)
|
|
$text .= ($params[$key][$akey]).',';
|
|
$html .= trim($text,',');
|
|
}
|
|
} else {
|
|
//Specify different values for the displayed data and link if available
|
|
if (!is_array($params[$key])) {
|
|
$datadisplay = $params[$key];
|
|
$datalink = $datadisplay;
|
|
} else {
|
|
$datadisplay = $params[$key]['display'];
|
|
$datalink = $params[$key]['link'];
|
|
}
|
|
$link = $link.$datalink;
|
|
$html .= "<a href='".$link."'>".$datadisplay."</a>";
|
|
}
|
|
if ($primary_field == $key && $_SESSION['username']) {
|
|
$primary_id = $params[$key];
|
|
if ($params['hidden'] == 1) {
|
|
$html .= "<font color='#cc0000'>HIDDEN</font>\n";
|
|
$html .= " <input class='edit' type='submit' name='unhideItem".$primary_id."' value='unhide'>\n";
|
|
} else $html .= " <input class='edit' type='submit' name='hideItem".$primary_id."' value='hide'>\n";
|
|
}
|
|
if ('description' == $key && $primary_field) {
|
|
$descDiv = ($_SESSION['username']) ? editButton($primary_id,$t['description']) : $t['description'];
|
|
$html .= "$descDiv\n";
|
|
}
|
|
$html .= "</td>\n";
|
|
}
|
|
$html .= "</tr>";
|
|
return $html;
|
|
}
|
|
|
|
function getTemplatesFromProject ($projectId, $getHidden=False) {
|
|
$q="SELECT temp.*, path.path "
|
|
."FROM `ApTemplateImageData` AS temp "
|
|
."LEFT JOIN ApPathData AS path ON "
|
|
."(temp.`REF|ApPathData|path`=path.`DEF_id`) "
|
|
."WHERE `REF|projectdata|projects|project`='$projectId' ";
|
|
if (!$getHidden) $q.= "AND (temp.`hidden` IS NULL OR temp.`hidden` = 0) ";
|
|
$q.= "ORDER BY temp.`DEF_id` DESC";
|
|
$r = $this->mysql->getSQLResult($q);
|
|
return $r;
|
|
}
|
|
|
|
function getTemplatesFromId ($templateId) {
|
|
$q = "SELECT t.*, p.path "
|
|
."FROM `ApTemplateImageData` AS t "
|
|
."LEFT JOIN ApPathData AS p ON "
|
|
."(t.`REF|ApPathData|path`=p.`DEF_id`) "
|
|
."WHERE t.`DEF_id` = '$templateId' ";
|
|
$r = $this->mysql->getSQLResult($q);
|
|
return $r[0];
|
|
}
|
|
|
|
function getRecentTemplateRunFromId ($templateId) {
|
|
$q = "SELECT trun.* "
|
|
."FROM `ApTemplateRunData` AS trun "
|
|
."LEFT JOIN ApTemplateImageData AS timg ON "
|
|
."(trun.`REF|ApTemplateImageData|template` = timg.`DEF_id`) "
|
|
."WHERE timg.`DEF_id` = '$templateId' "
|
|
."ORDER BY trun.`DEF_id` DESC "
|
|
."LIMIT 1 ";
|
|
$r = $this->mysql->getSQLResult($q);
|
|
return $r[0];
|
|
}
|
|
|
|
function getTemplateStacksFromProject ($projectId, $getHidden=False, $type=False) {
|
|
$q = "SELECT stack.*, path.path "
|
|
."FROM ApTemplateStackData as stack "
|
|
."LEFT JOIN ApPathData AS path ON "
|
|
."(stack.`REF|ApPathData|path`=path.`DEF_id`) "
|
|
."WHERE `REF|projectdata|projects|project`='$projectId' ";
|
|
if (!$getHidden) $q.= "AND (stack.`hidden` IS NULL OR stack.`hidden` = 0) ";
|
|
if ($type == "clsavg") $q.= "AND (stack.`cls_avgs` = 1) ";
|
|
if ($type == "forward") $q.= "AND (stack.`forward_proj` = 1) ";
|
|
$q .= "ORDER BY stack.`DEF_id` DESC";
|
|
$r = $this->mysql->getSQLResult($q);
|
|
return $r;
|
|
}
|
|
|
|
function getTemplateStacksFromSession ($expId, $getHidden=False, $type=False) {
|
|
$q = "SELECT stack.*, path.path "
|
|
."FROM ApTemplateStackData as stack "
|
|
."LEFT JOIN ApPathData AS path ON "
|
|
."(stack.`REF|ApPathData|path`=path.`DEF_id`) "
|
|
."WHERE stack.`REF|leginondata|SessionData|session`='$expId' ";
|
|
if (!$getHidden) $q.= "AND (stack.`hidden` IS NULL OR stack.`hidden` = 0) ";
|
|
if ($type == "clsavg") $q.= "AND (stack.`cls_avgs` = 1) ";
|
|
if ($type == "forward") $q.= "AND (stack.`forward_proj` = 1) ";
|
|
$q .= "ORDER BY stack.`DEF_id` DESC";
|
|
$r = $this->mysql->getSQLResult($q);
|
|
return $r;
|
|
}
|
|
|
|
function getTemplateStackParams ($templateStackId, $getHidden=False, $type=False) {
|
|
$q = "SELECT ts.*, path.path "
|
|
."FROM ApTemplateStackData as ts "
|
|
." LEFT JOIN ApPathData as path ON "
|
|
."(ts.`REF|ApPathData|path`=path.`DEF_id`) "
|
|
." WHERE ts.`DEF_id`='$templateStackId' ";
|
|
$r = $this->mysql->getSQLResult($q);
|
|
return $r[0];
|
|
}
|
|
|
|
function getStackSelector($stackIds,$stackidval,$onchange) {
|
|
/* THIS FUNCTION SHOULD BE MOVED TO summarytables.inc */
|
|
# $stackinfo[0] = stackid
|
|
# $stackinfo[1] = pixel size in angstrums / pixels
|
|
# $stackinfo[2] = stack boxsize (length in either direction) in pixels
|
|
# $stackinfo[3] = number of particles in the stack
|
|
# $stackinfo[4] = appion stackfile path
|
|
# $stackinfo[5] = Imagic stack header file name, including extension but not path
|
|
# $stackinfo[6] = Imagic stack data file name, including extension but not path
|
|
# examples:
|
|
# $stackinfo[4] = '/your_disk/appion/09aug267/stacks/stack1'
|
|
# $stackinfo[5] = 'start.hed'
|
|
# $stackinfo[6] = 'start.img'
|
|
echo "<SELECT NAME='stackval'";
|
|
if ($onchange) echo "onchange='".$onchange."'";
|
|
echo ">\n";
|
|
foreach ($stackIds as $stackid){
|
|
// get stack parameters from database
|
|
$s=$this->getStackParams($stackid['stackid']);
|
|
// get number of particles in each stack
|
|
$totalp=$this->getNumStackParticles($stackid['stackid']);
|
|
$nump=commafy($totalp);
|
|
// get pixel size of stack
|
|
$apix=($this->getStackPixelSizeFromStackId($stackid['stackid']))*1e10;
|
|
// truncated pixel size
|
|
$showapix=sprintf("%.2f",$apix);
|
|
// get box size
|
|
$box = $s['boxsize'];
|
|
// get stack path with name
|
|
$opvals = "$stackid[stackid]|--|$apix|--|$box|--|$totalp|--|$s[path]|--|$s[name]";
|
|
// if imagic stack, send both hed & img files for dmf
|
|
if (ereg('\.hed', $s['name'])) $opvals.='|--|'.ereg_replace('hed','img',$s['name']);
|
|
if (ereg('\.img', $s['name'])) $opvals.='|--|'.ereg_replace('img','hed',$s['name']);
|
|
|
|
echo "<OPTION VALUE='$opvals'";
|
|
// select previously set stack on resubmita
|
|
if ($stackid['stackid']==$stackidval) echo " SELECTED";
|
|
echo">$s[shownstackname] ID: $stackid[stackid] ($nump particles, $showapix Å/pix, ".$box."x".$box.")</OPTION>\n";
|
|
}
|
|
echo "</SELECT>\n";
|
|
return $apix;
|
|
/* THIS FUNCTION SHOULD BE MOVED TO summarytables.inc */
|
|
}
|
|
|
|
function getParticlesFromImageId ($runId, $imageId){
|
|
$fields = $this->mysql->getFields('ApParticleData');
|
|
$labelselect = (in_array('label',$fields)) ? "p.label, ":" ";
|
|
$q = "select p.DEF_id as id, "
|
|
.$labelselect
|
|
."p.xcoord, p.ycoord, p.correlation, "
|
|
."p.`REF|ApTemplateImageData|template` as templateId, "
|
|
."p.diameter "
|
|
."from ApParticleData p "
|
|
."where p.`REF|ApSelectionRunData|selectionrun` = '$runId' "
|
|
."and p.`REF|leginondata|AcquisitionImageData|image` = '$imageId' ";
|
|
$r=$this->mysql->getSQLResult($q);
|
|
return $r;
|
|
}
|
|
|
|
function getTracesFromImageId ($runId, $imageId){
|
|
$q = "select p.DEF_id as id, "
|
|
."p.name "
|
|
."from ApContourData p "
|
|
."where p.`REF|ApSelectionRunData|selectionrun` = '$runId' "
|
|
."and p.`REF|leginondata|AcquisitionImageData|image` = '$imageId' ";
|
|
$r=$this->mysql->getSQLResult($q);
|
|
|
|
$allpoints = array();
|
|
if (!empty($r)) {
|
|
foreach ($r as $contour) {
|
|
$q = "select p.x,p.y "
|
|
."from ApContourPointData p "
|
|
."where p.`REF|ApContourData|contour` = ".$contour['id']." ";
|
|
$r=$this->mysql->getSQLResult($q);
|
|
$allpoints[$contour['id']] = $r;
|
|
}
|
|
}
|
|
return $allpoints;
|
|
}
|
|
|
|
function getLastAssessmentRun ($sessionId){
|
|
$q = "select max(DEF_id) as runId "
|
|
." from ApAssessmentRunData where `REF|leginondata|SessionData|session` = '$sessionId'";
|
|
list($r) = $this->mysql->getSQLResult($q);
|
|
return $r[runId];
|
|
}
|
|
|
|
function getAssessmentRunIds ($sessionId) {
|
|
$q = "select * "
|
|
."from ApAssessmentRun where `REF|leginondata|SessionData|session` = '$sessionId'";
|
|
list($r) = $this->mysql->getSQLResult($q);
|
|
return $r;
|
|
}
|
|
|
|
function getKeepStatus ($imageId,$runId){
|
|
// returns a boolean value, 0 if rejected, 1 if keeping,
|
|
// null if no status in database
|
|
$q = "select * "
|
|
."from ApAssessmentData "
|
|
."where `REF|leginondata|AcquisitionImageData|image` = '$imageId' "
|
|
."and `REF|ApAssessmentRunData|assessmentrun` = '$runId' ";
|
|
list($r)=$this->mysql->getSQLResult($q);
|
|
if ($r) {
|
|
if ($r['selectionkeep']==0) $keep='no';
|
|
elseif ($r['selectionkeep']==1) $keep='yes';
|
|
}
|
|
return $keep;
|
|
// return $r['selectionkeep'];
|
|
}
|
|
|
|
function updateKeepStatus ($imageId,$runId,$value){
|
|
// update image status : 0 if rejected, 1 if keeping,
|
|
|
|
$exists=($this->getKeepStatus($imageId,$runId)) ? true : false;
|
|
if ($exists) {
|
|
$data = array('selectionkeep'=>$value);
|
|
$where = array('REF|leginondata|AcquisitionImageData|image'=>$imageId);
|
|
$where['REF|ApAssessmentRunData|assessmentrun']=$runId;
|
|
$this->mysql->SQLUpdate('ApAssessmentData',$data,$where);
|
|
}
|
|
else {
|
|
$data['selectionkeep']=$value;
|
|
$data['REF|leginondata|AcquisitionImageData|image']=$imageId;
|
|
$data['REF|ApAssessmentRunData|assessmentrun']=$runId;
|
|
$this->mysql->SQLInsert('ApAssessmentData',$data);
|
|
}
|
|
}
|
|
|
|
function getAssessmentDataForRun ($runId){
|
|
$q = "select i.filename, a.selectionkeep as keep "
|
|
."from ApAssessmentData a "
|
|
."left join ".DB_LEGINON.".AcquisitionImageData i "
|
|
."on (a.`REF|leginondata|AcquisitionImageData|image` = i.`DEF_id`) "
|
|
."where a.`REF|ApAssessmentRunData|assessmentrun` = '$runId' ";
|
|
//echo "$q";
|
|
$r=$this->mysql->getSQLResult($q);
|
|
return $r;
|
|
}
|
|
|
|
function getSelectionRunData($runId) {
|
|
$q = "select * from ApSelectionRunData "
|
|
." where `DEF_id` = '$runId' ";
|
|
list($r) = $this->mysql->getSQLResult($q);
|
|
|
|
return $r;
|
|
}
|
|
|
|
|
|
function getSelectionParams ($runId, $returntype=False) {
|
|
$r = $this->getSelectionRunData($runId);
|
|
|
|
//print_r ($r);
|
|
//echo $r['REF|ApSelectionParamsData|params'];
|
|
$q = "select s.*, r.name, path.path AS path, r.`REF|leginondata|SessionData|session` ";
|
|
|
|
if ($r['REF|ApSelectionParamsData|params']) {
|
|
$selectionparamid=$r['REF|ApSelectionParamsData|params'];
|
|
$q .= "from ApSelectionParamsData s "
|
|
."left join ApSelectionRunData r on (s.`DEF_id` = r.`REF|ApSelectionParamsData|params`) ";
|
|
$type = "Template Correlator";
|
|
}
|
|
elseif ($r['REF|ApDogParamsData|dogparams']) {
|
|
$dogparamid=$r['REF|ApDogParamsData|dogparams'];
|
|
$q .= "from ApDogParamsData s "
|
|
."left join ApSelectionRunData r on (s.`DEF_id` = r.`REF|ApDogParamsData|dogparams`) ";
|
|
$type = "DOG Picker";
|
|
}
|
|
elseif ($r['REF|ApManualParamsData|manparams']) {
|
|
$manparamid=$r['REF|ApManualParamsData|manparams'];
|
|
$q .= "from ApManualParamsData s "
|
|
."left join ApSelectionRunData r on (s.`DEF_id` = r.`REF|ApManualParamsData|manparams`) ";
|
|
$type = "Manual Picker";
|
|
}
|
|
elseif ($r['REF|ApTiltAlignParamsData|tiltparams']) {
|
|
$manparamid=$r['REF|ApTiltAlignParamsData|tiltparams'];
|
|
$q .= "from ApTiltAlignParamsData s "
|
|
."left join ApSelectionRunData r on (s.`DEF_id` = r.`REF|ApTiltAlignParamsData|tiltparams`) ";
|
|
$type = "Tilt Picker";
|
|
}
|
|
$q .= "LEFT JOIN ApPathData AS path "
|
|
." ON (path.`DEF_id` = r.`REF|ApPathData|path`) ";
|
|
|
|
if ($returntype) return $type;
|
|
|
|
$q .= "where r.`DEF_id` = '$runId' ";
|
|
$r=$this->mysql->getSQLResult($q);
|
|
return $r;
|
|
}
|
|
|
|
function getObjectTracingRuns($sessionId) {
|
|
if ($this->mysql->SQLTableExists("ApContourData")) {
|
|
$q = "SELECT sr.*, count(*) as total_object_traced "
|
|
." FROM ApSelectionRunData AS sr "
|
|
." LEFT JOIN ApManualParamsData as p "
|
|
." ON sr.`REF|ApManualParamsData|manparams` = p.`DEF_id` "
|
|
." LEFT JOIN ApContourData as c "
|
|
." ON c.`REF|ApSelectionRunData|selectionrun` = sr.`DEF_id` "
|
|
." WHERE sr.`REF|leginondata|SessionData|session` = $sessionId "
|
|
." AND "
|
|
." p.`trace` = 1 "
|
|
." GROUP BY sr.`DEF_id` "
|
|
." ";
|
|
$r=$this->mysql->getSQLResult($q);
|
|
return $r;
|
|
} else {
|
|
return array();
|
|
}
|
|
}
|
|
|
|
function getParticleLabels($runId) {
|
|
$q = "select label, count(DEF_id) as `number particle` from ApParticleData where `REF|ApSelectionRunData|selectionrun`=".$runId." and label is not NULL group by `label`";
|
|
$r=$this->mysql->getSQLResult($q);
|
|
return $r;
|
|
}
|
|
|
|
function getMaxTiltAngle ($sessionId) {
|
|
$q = "SELECT MAX(ABS(s.`SUBD|stage position|a`))*180.0/PI() AS angle "
|
|
."FROM ".DB_LEGINON.".`AcquisitionImageData` AS im "
|
|
."LEFT JOIN ".DB_LEGINON.".`ScopeEMData` AS s "
|
|
."ON s.`DEF_id` = im.`REF|ScopeEMData|scope` "
|
|
."WHERE im.`REF|SessionData|session` = '$sessionId' ";
|
|
$r = $this->mysql->getSQLResult($q);
|
|
return $r[0]['angle'];
|
|
}
|
|
|
|
function getTemplateRunParams ($runId) {
|
|
$q="SELECT i.DEF_id as id, p.path, i.templatename as tname, i.apix, i.description, "
|
|
."t.range_start, t.range_end, t.range_incr, "
|
|
."r.name "
|
|
."from ApTemplateRunData AS t "
|
|
."left join ApTemplateImageData i on (t.`REF|ApTemplateImageData|template`=i.`DEF_id`) "
|
|
."LEFT JOIN ApPathData AS p ON (i.`REF|ApPathData|path`=p.`DEF_id`) "
|
|
."left join ApSelectionRunData r on (t.`REF|ApSelectionRunData|selectionrun` = r.`DEF_id`) "
|
|
."where t.`REF|ApSelectionRunData|selectionrun` = '$runId' ";
|
|
$r=$this->mysql->getSQLResult($q);
|
|
return $r;
|
|
}
|
|
|
|
function getParticles ($runId) {
|
|
$q="select p.DEF_id, p.xcoord, p.ycoord, p.correlation, p.`REF|leginondata|AcquisitionImageData|image`, a.`filename` "
|
|
."from ApParticleData p "
|
|
."left join ".DB_LEGINON.".`AcquisitionImageData` a "
|
|
."on p.`REF|leginondata|AcquisitionImageData|image` = a.`DEF_id` "
|
|
."where p.`REF|ApSelectionRunData|selectionrun` = '$runId' ";
|
|
$r=$this->mysql->getSQLResult($q);
|
|
return $r;
|
|
}
|
|
|
|
function getParticlesDataWithDeforcusPair($runId){
|
|
|
|
$q="SELECT p.`DEF_id`,p.xcoord, p.ycoord, p.`REF|leginondata|acquisitionImageData|image` as imageNum, "
|
|
."a.`filename`, "
|
|
."t.`REF|leginondata|AcquisitionImageData|image2` as pImage, t.shiftx, t.shifty "
|
|
."FROM ApParticleData as p "
|
|
."LEFT JOIN ApImageTransformationData t "
|
|
."ON (p.`REF|leginondata|acquisitionImageData|image` = t.`REF|leginondata|AcquisitionImageData|image1`) "
|
|
."left join ".DB_LEGINON.".`AcquisitionImageData` a "
|
|
."on p.`REF|leginondata|AcquisitionImageData|image` = a.`DEF_id` "
|
|
."WHERE p.`REF|ApSelectionRunData|selectionrun` = '$runId' ";
|
|
$r=$this->mysql->getSQLResult($q);
|
|
return $r;
|
|
|
|
}
|
|
|
|
function getImgIdFromSelectionRun ($runId) {
|
|
$q="SELECT "
|
|
." p.`REF|leginondata|AcquisitionImageData|image` AS imgid "
|
|
."FROM ApParticleData AS p "
|
|
."WHERE "
|
|
." p.`REF|ApSelectionRunData|selectionrun` = '$runId' "
|
|
."ORDER BY p.`REF|leginondata|AcquisitionImageData|image` DESC "
|
|
."LIMIT 1 ";
|
|
$r=$this->mysql->getSQLResult($q);
|
|
return $r[0]['imgid'];
|
|
}
|
|
|
|
function getParticleCorrelationStats($runId) {
|
|
}
|
|
|
|
function hasParticleData ($sessionId) {
|
|
$r= ($this->getLastParticleRun($sessionId)) ? true : false;
|
|
return $r;
|
|
}
|
|
|
|
function getStats ($runId, $inspect=false, $selexval=false) {
|
|
$q="select count(p.`DEF_id`) as `totparticles`, "
|
|
."count(distinct p.`REF|leginondata|AcquisitionImageData|image`) as num, "
|
|
."max(p.`REF|leginondata|AcquisitionImageData|image`) as lastimage, "
|
|
."min(p.correlation) as `min`, "
|
|
."max(p.correlation) as `max`, "
|
|
."avg(p.correlation) as `avg`, "
|
|
."stddev(p.correlation) as `stddev` "
|
|
."from ApParticleData p ";
|
|
// use the latest inspection value. This should be changed later
|
|
if ($inspect) {
|
|
$q.= "left join ApAssessmentData ad "
|
|
."on (ad.`REF|leginondata|AcquisitionImageData|image` = p.`REF|leginondata|AcquisitionImageData|image`) ";
|
|
}
|
|
$q.="WHERE ";
|
|
if ($inspect) {
|
|
$q.= "ad.`DEF_id`=(select max(ad2.`DEF_id`) from ApAssessmentData ad2 "
|
|
."where ad2.`REF|leginondata|AcquisitionImageData|image` = ad.`REF|leginondata|AcquisitionImageData|image`) "
|
|
."and ad.selectionkeep=1 AND ";
|
|
}
|
|
if ($selexval)
|
|
$q.="p.`correlation`>='$selexval' AND ";
|
|
$q.="p.`REF|ApSelectionRunData|selectionrun` = '$runId' ";
|
|
list($r) = $this->mysql->getSQLResult($q);
|
|
$tracestats = $this->getTraceStats($runId);
|
|
# not to replace $r['lastimage'] if no real trace stats
|
|
if (!$tracestats['lastimage']) $tracestats['lastimge'] = $r['lastimage'];
|
|
$r = array_merge($r,$tracestats);
|
|
$q = "select p.`name` "
|
|
." from ".DB_LEGINON.".AcquisitionImageData a"
|
|
." , ".DB_LEGINON.".PresetData p"
|
|
." where a.`REF|PresetData|preset` = p.`DEF_id`"
|
|
." and a.`DEF_id` = ".$r['lastimage'];
|
|
list($r1) = $this->mysql->getSQLResult($q);
|
|
if ($r1) {
|
|
$r['preset'] = $r1['name'];
|
|
} else {
|
|
$r['preset'] = 'n/a';
|
|
}
|
|
return $r;
|
|
|
|
}
|
|
|
|
function getTraceStats ($runId) {
|
|
if (!$this->mysql->SQLTableExists("ApContourData"))
|
|
return array();
|
|
$q = "SELECT count(*) as total_object_traced, "
|
|
."c.`REF|leginondata|AcquisitionImageData|image` as lastimage "
|
|
." FROM ApSelectionRunData AS sr "
|
|
." LEFT JOIN ApManualParamsData as p "
|
|
." ON sr.`REF|ApManualParamsData|manparams` = p.`DEF_id` "
|
|
." LEFT JOIN ApContourData as c "
|
|
." ON c.`REF|ApSelectionRunData|selectionrun` = sr.`DEF_id` "
|
|
." WHERE sr.`DEF_id` = $runId "
|
|
." AND "
|
|
." p.`trace` = 1 "
|
|
." AND "
|
|
." c.`DEF_id` is not null "
|
|
." GROUP BY sr.`DEF_id` ";
|
|
list($r)=$this->mysql->getSQLResult($q);
|
|
if (!$r) $r=array('total_object_traced'=>0);
|
|
return $r;
|
|
}
|
|
|
|
function getNumImgs ($runId){
|
|
$q="SELECT count(distinct `REF|leginondata|AcquisitionImageData|image`) as num "
|
|
. "FROM `ApParticleData` "
|
|
. "WHERE `REF|ApSelectionRunData|selectionrun`='$runId' ";
|
|
$r = $this->mysql->getSQLResult($q);
|
|
return $r[0]['num'];
|
|
}
|
|
|
|
function getNumImgsFromSessionId ($sessionId){
|
|
$q= "SELECT "
|
|
. " COUNT(DISTINCT p.`REF|leginondata|AcquisitionImageData|image`) AS num "
|
|
. "FROM `ApParticleData` AS p "
|
|
. "LEFT JOIN `ApSelectionRunData` AS r "
|
|
. " ON (p.`REF|ApSelectionRunData|selectionrun` = r.`DEF_id`) "
|
|
. "WHERE r.`REF|leginondata|SessionData|session`='$sessionId' ";
|
|
#. " ORDER BY num LIMIT 10";
|
|
#echo $q;
|
|
$r = $this->mysql->getSQLResult($q);
|
|
return $r[0]['num'];
|
|
}
|
|
|
|
function getSelectionRunIdFromPath($path){
|
|
$q= "SELECT r.* "
|
|
. "FROM `ApSelectionRunData` AS r "
|
|
. "LEFT JOIN ApPathData AS p "
|
|
. "ON (r.`REF|ApPathData|path` = p.`DEF_id`) "
|
|
. "WHERE p.`path` LIKE '$path%'";
|
|
$r = $this->mysql->getSQLResult($q);
|
|
return $r;
|
|
}
|
|
#--------- IMAGE ASSESSMENT FUNCTIONS ---------------#
|
|
|
|
function getNumAssessedImages ($sessionId) {
|
|
$rid = $this->getLastAssessmentRun($sessionId);
|
|
$q = "SELECT COUNT(assess.`DEF_id`) as num "
|
|
."FROM `ApAssessmentData` AS assess "
|
|
."LEFT JOIN ".DB_LEGINON.".`ViewerImageStatus` AS viewer"
|
|
." ON viewer.`REF|AcquisitionImageData|image` = assess.`REF|leginondata|AcquisitionImageData|image` "
|
|
."WHERE "
|
|
." ( assess.`selectionkeep` IS NOT NULL "
|
|
."OR "
|
|
." viewer.`status` IS NOT NULL ) "
|
|
."AND `REF|ApAssessmentRunData|assessmentrun` = '$rid'";
|
|
list($r) = $this->mysql->getSQLResult($q);
|
|
return $r['num'];
|
|
}
|
|
|
|
function getNumViewerPrefImages ($sessionId) {
|
|
$q = "SELECT "
|
|
. " COUNT(DISTINCT p.`REF|leginondata|AcquisitionImageData|image`) as num "
|
|
. "FROM `ApParticleData` AS p "
|
|
. "LEFT JOIN `ApSelectionRunData` AS r "
|
|
. " ON (p.`REF|ApSelectionRunData|selectionrun` = r.`DEF_id`) "
|
|
. "LEFT JOIN ".DB_LEGINON.".`ViewerImageStatus` AS viewer"
|
|
. " ON viewer.`REF|AcquisitionImageData|image` = p.`REF|leginondata|AcquisitionImageData|image` "
|
|
. "WHERE "
|
|
. " viewer.`status` IS NOT NULL "
|
|
. " AND "
|
|
. " r.`REF|leginondata|SessionData|session`='$sessionId' ";
|
|
#echo $q.";<br/><br/>\n";
|
|
list($r) = $this->mysql->getSQLResult($q);
|
|
return $r['num'];
|
|
}
|
|
|
|
function getNumTotalAssessImages ($sessionId) {
|
|
$rid = $this->getLastAssessmentRun($sessionId);
|
|
$q = "SELECT "
|
|
. " COUNT(DISTINCT part.`REF|leginondata|AcquisitionImageData|image`) as num "
|
|
. "FROM `ApParticleData` AS part "
|
|
. "LEFT JOIN `ApSelectionRunData` AS partrun "
|
|
. " ON (part.`REF|ApSelectionRunData|selectionrun` = partrun.`DEF_id`) "
|
|
. "LEFT JOIN ".DB_LEGINON.".`ViewerImageStatus` AS viewer"
|
|
. " ON viewer.`REF|AcquisitionImageData|image` = part.`REF|leginondata|AcquisitionImageData|image` "
|
|
. "LEFT JOIN `ApAssessmentData` AS assess "
|
|
. " ON assess.`REF|leginondata|AcquisitionImageData|image` = part.`REF|leginondata|AcquisitionImageData|image` "
|
|
. "WHERE ("
|
|
. " ( assess.`selectionkeep` IS NOT NULL AND `REF|ApAssessmentRunData|assessmentrun` = '$rid' )"
|
|
. "OR "
|
|
. " viewer.`status` IS NOT NULL "
|
|
. ") AND "
|
|
. " partrun.`REF|leginondata|SessionData|session` = '$sessionId' ";
|
|
#echo $q.";<br/><br/>\n";
|
|
list($r) = $this->mysql->getSQLResult($q);
|
|
return $r['num'];
|
|
}
|
|
|
|
function getNumRejectAssessedImages ($sessionId) {
|
|
$rid = $this->getLastAssessmentRun($sessionId);
|
|
$q = "SELECT COUNT(assess.`DEF_id`) as num "
|
|
."FROM `ApAssessmentData` AS assess "
|
|
."WHERE "
|
|
." assess.`selectionkeep` = 0 "
|
|
."AND `REF|ApAssessmentRunData|assessmentrun` = '$rid'";
|
|
list($r) = $this->mysql->getSQLResult($q);
|
|
return $r['num'];
|
|
}
|
|
|
|
function getNumHiddenImages ($sessionId) {
|
|
$q = "SELECT "
|
|
. " COUNT(DISTINCT p.`REF|leginondata|AcquisitionImageData|image`) as num "
|
|
. "FROM `ApParticleData` AS p "
|
|
. "LEFT JOIN `ApSelectionRunData` AS r "
|
|
. " ON (p.`REF|ApSelectionRunData|selectionrun` = r.`DEF_id`) "
|
|
. "LEFT JOIN ".DB_LEGINON.".`ViewerImageStatus` AS viewer"
|
|
. " ON viewer.`REF|AcquisitionImageData|image` = p.`REF|leginondata|AcquisitionImageData|image` "
|
|
. "WHERE "
|
|
. " viewer.`status` = 'hidden' "
|
|
. "AND "
|
|
. " r.`REF|leginondata|SessionData|session`='$sessionId' ";
|
|
list($r) = $this->mysql->getSQLResult($q);
|
|
return $r['num'];
|
|
}
|
|
|
|
function getNumTotalRejectImages ($sessionId) {
|
|
$rid = $this->getLastAssessmentRun($sessionId);
|
|
$q = "SELECT "
|
|
. " COUNT(DISTINCT part.`REF|leginondata|AcquisitionImageData|image`) as num "
|
|
. "FROM `ApParticleData` AS part "
|
|
. "LEFT JOIN `ApSelectionRunData` AS partrun "
|
|
. " ON (part.`REF|ApSelectionRunData|selectionrun` = partrun.`DEF_id`) "
|
|
. "LEFT JOIN ".DB_LEGINON.".`ViewerImageStatus` AS viewer"
|
|
. " ON viewer.`REF|AcquisitionImageData|image` = part.`REF|leginondata|AcquisitionImageData|image` "
|
|
. "LEFT JOIN `ApAssessmentData` AS assess "
|
|
. " ON assess.`REF|leginondata|AcquisitionImageData|image` = part.`REF|leginondata|AcquisitionImageData|image` "
|
|
. "WHERE ("
|
|
. " ( assess.`selectionkeep` = 0 AND `REF|ApAssessmentRunData|assessmentrun` = '$rid' )"
|
|
. "OR "
|
|
. " viewer.`status` = 'hidden' "
|
|
. ") AND "
|
|
. " partrun.`REF|leginondata|SessionData|session` = '$sessionId' ";
|
|
#echo $q.";<br/><br/>\n";
|
|
list($r) = $this->mysql->getSQLResult($q);
|
|
return $r['num'];
|
|
}
|
|
|
|
function getNumKeepAssessedImages ($sessionId) {
|
|
$rid = $this->getLastAssessmentRun($sessionId);
|
|
$q = "SELECT COUNT(assess.`DEF_id`) as num "
|
|
."FROM `ApAssessmentData` AS assess "
|
|
."LEFT JOIN ".DB_LEGINON.".`ViewerImageStatus` AS viewer"
|
|
." ON viewer.`REF|AcquisitionImageData|image` = assess.`REF|leginondata|AcquisitionImageData|image` "
|
|
."WHERE "
|
|
." assess.`selectionkeep` = 1 "
|
|
."AND `REF|ApAssessmentRunData|assessmentrun` = '$rid'";
|
|
list($r) = $this->mysql->getSQLResult($q);
|
|
return $r['num'];
|
|
}
|
|
|
|
function getNumExemplarImages ($sessionId) {
|
|
$q = "SELECT "
|
|
. " COUNT(DISTINCT p.`REF|leginondata|AcquisitionImageData|image`) as num "
|
|
. "FROM `ApParticleData` AS p "
|
|
. "LEFT JOIN `ApSelectionRunData` AS r "
|
|
. " ON (p.`REF|ApSelectionRunData|selectionrun` = r.`DEF_id`) "
|
|
. "LEFT JOIN ".DB_LEGINON.".`ViewerImageStatus` AS viewer"
|
|
. " ON viewer.`REF|AcquisitionImageData|image` = p.`REF|leginondata|AcquisitionImageData|image` "
|
|
. "WHERE "
|
|
. " viewer.`status` = 'exemplar' "
|
|
. "AND "
|
|
. " r.`REF|leginondata|SessionData|session`='$sessionId' ";
|
|
#echo $q.";<br/><br/>\n";
|
|
list($r) = $this->mysql->getSQLResult($q);
|
|
return $r['num'];
|
|
}
|
|
|
|
function getNumTotalKeepImages ($sessionId) {
|
|
$rid = $this->getLastAssessmentRun($sessionId);
|
|
$q = "SELECT "
|
|
. " COUNT(DISTINCT part.`REF|leginondata|AcquisitionImageData|image`) as num "
|
|
. "FROM `ApParticleData` AS part "
|
|
. "LEFT JOIN `ApSelectionRunData` AS partrun "
|
|
. " ON (part.`REF|ApSelectionRunData|selectionrun` = partrun.`DEF_id`) "
|
|
. "LEFT JOIN ".DB_LEGINON.".`ViewerImageStatus` AS viewer"
|
|
. " ON viewer.`REF|AcquisitionImageData|image` = part.`REF|leginondata|AcquisitionImageData|image` "
|
|
. "LEFT JOIN `ApAssessmentData` AS assess "
|
|
. " ON assess.`REF|leginondata|AcquisitionImageData|image` = part.`REF|leginondata|AcquisitionImageData|image` "
|
|
. "WHERE ( "
|
|
. " ( assess.`selectionkeep` = 1 AND `REF|ApAssessmentRunData|assessmentrun` = '$rid' )"
|
|
. "OR "
|
|
. " viewer.`status` = 'exemplar' "
|
|
. ") AND "
|
|
. " partrun.`REF|leginondata|SessionData|session` = '$sessionId' ";
|
|
#echo $q.";<br/><br/>\n";
|
|
list($r) = $this->mysql->getSQLResult($q);
|
|
return $r['num'];
|
|
}
|
|
|
|
// return the last Def_id value in the provided table
|
|
function getLastDefId($sessionId, $table)
|
|
{
|
|
$q = "select DEF_id as runId "
|
|
."from `".$table."` "
|
|
."where `REF|leginondata|SessionData|session` = '$sessionId' "
|
|
."order by DEF_id desc limit 1";
|
|
list($r) = $this->mysql->getSQLResult($q);
|
|
return $r['runId'];
|
|
}
|
|
|
|
function getLastParticleRun($sessionId)
|
|
{
|
|
return $this->getLastDefId($sessionId, "ApSelectionRunData");
|
|
}
|
|
|
|
function getLastDDStackRun($sessionId)
|
|
{
|
|
return $this->getLastDefId($sessionId, "ApDDStackRunData");
|
|
}
|
|
|
|
function hasDDstackData($sessionId)
|
|
{
|
|
$r= ($this->getLastDDStackRun($sessionId)) ? true : false;
|
|
return $r;
|
|
}
|
|
|
|
function getParticleRunData($partRunId)
|
|
{
|
|
return getRunData($partRunId, "ApSelectionRunData" );
|
|
}
|
|
|
|
function getDDStackRunData($partRunId)
|
|
{
|
|
return getRunData($partRunId, "ApSelectionRunData" );
|
|
}
|
|
|
|
function getRunData($runId, $table)
|
|
{
|
|
$q = "SELECT r.*, p.path "
|
|
."FROM `".$table."` AS r "
|
|
."LEFT JOIN ApPathData AS p ON (r.`REF|ApPathData|path` = p.`DEF_id`) "
|
|
."WHERE r.`DEF_id` = '$runId'";
|
|
list($r) = $this->mysql->getSQLResult($q);
|
|
return $r;
|
|
}
|
|
|
|
// Warning: this counts the number of runs, it does not return the
|
|
// last run id number used. Since a user can modify the runname,
|
|
// this is not a safe number to use for a defualt run name. Try
|
|
// getMaxRunNumber() instead.
|
|
function getLastRunNumberForType ($sessionId, $table, $field='name') {
|
|
$q = "SELECT r.`".$field."` "
|
|
."FROM `".$table."` AS r "
|
|
."WHERE r.`REF|leginondata|SessionData|session` = '$sessionId' "
|
|
."ORDER BY r.`".$field."` DESC "
|
|
." ";
|
|
$r = $this->mysql->getSQLResult($q);
|
|
if ($r && count($r) > 0) {
|
|
return count($r);
|
|
}
|
|
return 0;
|
|
}
|
|
|
|
function getRunIds($sessionId, $table, $showHidden=False)
|
|
{
|
|
$q = "SELECT r.*, p.path "
|
|
."FROM `".$table."` AS r "
|
|
."LEFT JOIN ApPathData AS p "
|
|
."ON (r.`REF|ApPathData|path` = p.`DEF_id`) "
|
|
."WHERE r.`REF|leginondata|SessionData|session` = '$sessionId' ";
|
|
if (!$showHidden) $q.= " AND (r.`hidden` IS NULL OR r.`hidden` = 0) ";
|
|
$q.= "ORDER BY r.`DEF_id` DESC ";
|
|
//echo $q."<br/>\n";
|
|
$r = $this->mysql->getSQLResult($q);
|
|
//echo print_r($r)."<br/>\n";
|
|
return $r;
|
|
}
|
|
|
|
function getParticleRunIds($sessionId,$showHidden=False)
|
|
{
|
|
return $this->getRunIds($sessionId, "ApSelectionRunData", $showHidden);
|
|
}
|
|
|
|
function getDDStackRunIds($sessionId,$showHidden=False)
|
|
{
|
|
return $this->getRunIds($sessionId, "ApDDStackRunData", $showHidden);
|
|
}
|
|
|
|
#--------- MAKE STACK FUNCTIONS---------------#
|
|
|
|
function getParticleRunsFromStack($stackid) {
|
|
// return all the particle runs contributing to a stack,
|
|
// accounting for multiple runs in 1 stack (combinestack)
|
|
$q = "SELECT `REF|ApStackRunData|stackRun` as stackrun "
|
|
. "FROM `ApRunsInStackData` as rs "
|
|
. "WHERE `REF|ApStackData|stack` = $stackid ";
|
|
$r = $this->mysql->getSQLResult($q);
|
|
$pruns = array();
|
|
foreach ($r as $srun) {
|
|
// get particle run from the first stack particle of
|
|
// each run
|
|
$q = "SELECT `REF|ApSelectionRunData|selectionrun` as DEF_id "
|
|
. "FROM `ApParticleData` as p "
|
|
. "LEFT JOIN `ApStackParticleData` AS sp "
|
|
. "ON sp.`REF|ApParticleData|particle` = p.`DEF_id` "
|
|
. "WHERE sp.`REF|ApStackRunData|stackRun`=".$srun['stackrun']." "
|
|
. "LIMIT 1 ";
|
|
$pruns[] = $this->mysql->getSQLResult($q);
|
|
}
|
|
return $pruns;
|
|
}
|
|
|
|
function getStackRunIdFromPath($path){
|
|
$q= "SELECT sd.* "
|
|
. "FROM `ApStackData` AS sd "
|
|
. "LEFT JOIN ApPathData AS p "
|
|
. "ON (sd.`REF|ApPathData|path` = p.`DEF_id`) "
|
|
. "WHERE p.`path` LIKE '$path%'";
|
|
$r = $this->mysql->getSQLResult($q);
|
|
return $r;
|
|
}
|
|
|
|
function getStackIds ($sessionId, $showHidden=False, $syntheticOnly=False, $noctf=False) {
|
|
$q = "SELECT "
|
|
." DISTINCT(r.`REF|ApStackData|stack`) as stackid , "
|
|
." st.*, "
|
|
." s.`REF|leginondata|SessionData|session` AS sessionid "
|
|
."FROM ApRunsInStackData as r "
|
|
."LEFT JOIN ApStackRunData as s ON "
|
|
." (r.`REF|ApStackRunData|stackRun`=s.`DEF_id`) "
|
|
."LEFT JOIN ApStackData as st ON "
|
|
." (r.`REF|ApStackData|stack` = st.`DEF_id`) ";
|
|
if ($noctf) {
|
|
$q.= "LEFT JOIN ApStackParamsData as param ON "
|
|
." (s.`REF|ApStackParamsData|stackParams` = param.`DEF_id`) ";
|
|
}
|
|
$q.="WHERE "
|
|
." s.`REF|leginondata|SessionData|session` = '$sessionId' ";
|
|
if (!$showHidden)
|
|
$q.= " AND st.`hidden` != 1 ";
|
|
if ($syntheticOnly)
|
|
$q.= " AND s.`REF|ApSyntheticStackParamsData|syntheticStackParams` is NOT NULL ";
|
|
if ($noctf)
|
|
$q.= " AND param.`fliptype` IS NULL ";
|
|
$q.= "ORDER BY stackid DESC";
|
|
//echo $q."<br/>\n";
|
|
$r = $this->mysql->getSQLResult($q);
|
|
//echo print_r($r)."<br/>\n";
|
|
return $r;
|
|
}
|
|
|
|
function getPrimaryStackIds ($sessionId) {
|
|
$q = "SELECT "
|
|
." DISTINCT(r.`REF|ApStackData|stack`) as stackid , "
|
|
." st.*, "
|
|
." s.`REF|leginondata|SessionData|session` AS sessionid "
|
|
."FROM ApRunsInStackData as r "
|
|
."LEFT JOIN ApStackRunData as s ON "
|
|
." (r.`REF|ApStackRunData|stackRun`=s.`DEF_id`) "
|
|
."LEFT JOIN ApStackData as st ON "
|
|
." (r.`REF|ApStackData|stack` = st.`DEF_id`) "
|
|
."WHERE "
|
|
." s.`REF|leginondata|SessionData|session` = '$sessionId' "
|
|
." AND st.`REF|ApStackData|oldstack` IS NULL "
|
|
."ORDER BY stackid DESC ";
|
|
//echo $q."<br/><br/>\n";
|
|
$r = $this->mysql->getSQLResult($q);
|
|
//echo print_r($r)."<br/><br/>\n";
|
|
return $r;
|
|
}
|
|
|
|
function getParentStackId ($substackId) {
|
|
$q = "SELECT "
|
|
." `REF|ApStackData|oldstack` as parentid "
|
|
." FROM ApStackData "
|
|
." WHERE `DEF_id` = ".$substackId." ";
|
|
$r = $this->mysql->getSQLResult($q);
|
|
return $r[0];
|
|
}
|
|
|
|
function getSubStackIds ($sessionId, $primarystackid, $showHidden=False) {
|
|
$q = "SELECT "
|
|
." DISTINCT(r.`REF|ApStackData|stack`) as stackid , "
|
|
." st.*, "
|
|
." s.`REF|leginondata|SessionData|session` AS sessionid "
|
|
."FROM ApRunsInStackData as r "
|
|
."LEFT JOIN ApStackRunData as s ON "
|
|
." (r.`REF|ApStackRunData|stackRun`=s.`DEF_id`) "
|
|
."LEFT JOIN ApStackData as st ON "
|
|
." (r.`REF|ApStackData|stack` = st.`DEF_id`) "
|
|
."WHERE "
|
|
." s.`REF|leginondata|SessionData|session` = '$sessionId' "
|
|
." AND st.`REF|ApStackData|oldstack` = '$primarystackid' ";
|
|
if (!$showHidden)
|
|
$q.= " AND st.`hidden` != 1 ";
|
|
$q.= "ORDER BY stackid DESC";
|
|
//echo $q."<br/><br/>\n";
|
|
$r = $this->mysql->getSQLResult($q);
|
|
//echo print_r($r)."<br/><br/>\n";
|
|
return $r;
|
|
}
|
|
|
|
function getClusterRefNumsFromSubStack ($substackid,$clusterstackid) {
|
|
$q = "SELECT "
|
|
."cp.`refnum` as classnum "
|
|
."FROM `ApClusteringParticleData` as cp "
|
|
."LEFT JOIN `ApAlignParticleData` as ap "
|
|
."ON cp.`REF|ApAlignParticleData|alignparticle` = ap.`DEF_id` "
|
|
."LEFT JOIN `ApStackParticleData` as pst "
|
|
."ON ap.`REF|ApStackParticleData|stackpart` = pst.`DEF_id` "
|
|
."LEFT JOIN `ApParticleData` as pp "
|
|
."ON pst.`REF|ApParticleData|particle` = pp.`DEF_id` "
|
|
."LEFT JOIN `ApStackParticleData` as sst "
|
|
."ON sst.`REF|ApParticleData|particle` = pp.`DEF_id` "
|
|
."WHERE "
|
|
."sst.`REF|ApStackData|stack` = ".$substackid." "
|
|
."AND cp.`REF|ApClusteringStackData|clusterstack` = ".$clusterstackid." "
|
|
."GROUP BY cp.`refnum` "
|
|
." ";
|
|
return $this->mysql->getSQLResult($q);
|
|
}
|
|
|
|
function getSubStackAlignCluster($substackinfo) {
|
|
$conditions = array(
|
|
'alignsub'=>array('alias'=>'ast','data'=>'ApAlignStackData'),
|
|
'clustersub'=>array('alias'=>'cst','data'=>'ApClausteringStackData')
|
|
);
|
|
$substackname = $substackinfo['substackname'];
|
|
foreach (array_keys($conditions) as $key) {
|
|
if (ereg($key,$substackname)) {
|
|
$conditionid = str_replace($key, '', $substackname);
|
|
$condition = $key;
|
|
} else {
|
|
echo ereg($key,$substackname);
|
|
}
|
|
}
|
|
if ($condition) {
|
|
$q = "SELECT ";
|
|
if ('clustersub' == $condition) {
|
|
$q.= "cst.`DEF_id` as clusterstackid, ";
|
|
$q.= "cr.`DEF_id` as clusterrunid, ";
|
|
}
|
|
$q.= " ast.`REF|ApStackData|stack` as primarystackid , "
|
|
." ast.`DEF_id` as alignstackid, "
|
|
." ar.`DEF_id` as alignrunid "
|
|
."FROM ApAlignStackData as ast "
|
|
."LEFT JOIN ApAlignRunData as ar ON "
|
|
." (ast.`REF|ApAlignRunData|alignRun`=ar.`DEF_id`) ";
|
|
if ('clustersub' == $condition) {
|
|
$q.= "LEFT JOIN ApClusteringRunData as cr ON "
|
|
."(cr.`REF|ApAlignStackData|alignstack` = ast.`DEF_id`) "
|
|
."LEFT JOIN ApClusteringStackData as cst ON "
|
|
."(cst.`REF|ApClusteringRunData|clusterrun` = cr.`DEF_id`) "
|
|
."WHERE "
|
|
." cst.`DEF_id` = '$conditionid' ";
|
|
} else {
|
|
$q.="WHERE "
|
|
." ast.`DEF_id` = '$conditionid' ";
|
|
}
|
|
$r = $this->mysql->getSQLResult($q);
|
|
if (count($r)) return $r[0];
|
|
}
|
|
return array();
|
|
}
|
|
|
|
function getTiltedStackIds ($sessionId, $showHidden=False) {
|
|
$q = "SELECT "
|
|
." DISTINCT(stack.`DEF_id`) as stackid "
|
|
."FROM ApRunsInStackData as runs "
|
|
."LEFT JOIN ApStackRunData as stackrun ON "
|
|
." (runs.`REF|ApStackRunData|stackRun` = stackrun.`DEF_id`) "
|
|
."LEFT JOIN ApStackData as stack ON "
|
|
." (runs.`REF|ApStackData|stack` = stack.`DEF_id`) "
|
|
."WHERE "
|
|
." stack.`REF|leginondata|SessionData|session` = '$sessionId' "
|
|
."AND "
|
|
." ( stackrun.`tiltangle` != 'notilt' AND stackrun.`tiltangle` != 'all' )";
|
|
if (!$showHidden)
|
|
$q.= " AND st.`hidden` != 1 ";
|
|
$q.= "ORDER BY stackid DESC";
|
|
$r = $this->mysql->getSQLResult($q);
|
|
return $r;
|
|
}
|
|
|
|
function getNamedSubStackIds ($sessionId, $primarystackid, $name, $showHidden=False) {
|
|
$q = "SELECT "
|
|
." DISTINCT(s.`DEF_id`) as stackid, "
|
|
." s.* "
|
|
."FROM ApStackData as s "
|
|
."WHERE "
|
|
." s.`REF|ApStackData|oldstack` = '$primarystackid' ";
|
|
if ($name)
|
|
$q.= "AND s.`substackname` REGEXP '".$name."' ";
|
|
if (!$showHidden)
|
|
$q.= " AND s.`hidden` != 1 ";
|
|
$q.= "ORDER BY stackid DESC";
|
|
$r = $this->mysql->getSQLResult($q);
|
|
return $r;
|
|
}
|
|
|
|
function getStackIdsForProject ($projectId, $showHidden=False) {
|
|
$q = "SELECT "
|
|
." DISTINCT(st.`DEF_id`) as stackid "
|
|
."FROM ApStackData as st ";
|
|
if (!$showHidden)
|
|
$q.= " WHERE st.`hidden` != 1 ";
|
|
$q.= "ORDER BY stackid DESC";
|
|
//echo $q."<br/>\n";
|
|
$r = $this->mysql->getSQLResult($q);
|
|
//echo print_r($r)."<br/>\n";
|
|
return $r;
|
|
}
|
|
|
|
function getStackIdsOld ($sessionId) {
|
|
$q = "select spar.stackid "
|
|
."from ("
|
|
."select `REF|ApParticleData|particle` as pid, `REF|ApStackRunData|stackRun` as stackid "
|
|
."from ApStackParticleData group by `REF|ApStackRunData|stackRun`) spar "
|
|
."left join ApParticleData p on (p.`DEF_id` = spar.pid) "
|
|
."left join ApSelectionRunData r on (p.`REF|ApSelectionRunData|selectionrun` = r.`DEF_id` ) "
|
|
."where r.`REF|leginondata|SessionData|session` = '$sessionId'";
|
|
$r = $this->mysql->getSQLResult($q);
|
|
return $r;
|
|
}
|
|
|
|
function getStackParams ($stackId) {
|
|
$q = "SELECT DISTINCT(sd.`DEF_id`) as `stackId`, sd.*, pd.`path`"
|
|
."FROM ApStackData as sd "
|
|
."LEFT JOIN ApPathData AS pd ON "
|
|
."(sd.`REF|ApPathData|path` = pd.`DEF_id`) "
|
|
."WHERE sd.`DEF_id` = '$stackId'";
|
|
//echo $q."<br/>\n";
|
|
list($stack_primary_array) = $this->mysql->getSQLResult($q);
|
|
if (!$stack_primary_array) return;
|
|
// Get runs in stack
|
|
$q = "SELECT r.`REF|ApStackRunData|stackRun` as runid "
|
|
."FROM ApRunsInStackData as r "
|
|
."WHERE r.`REF|ApStackData|stack` = '$stackId'";
|
|
//echo $q."<br/>\n";
|
|
$stackrunIds = $this->mysql->getSQLResult($q);
|
|
// Parameters of original stack of the runs in stack
|
|
$selectionstacks = array();
|
|
foreach ($stackrunIds as $runid) {
|
|
$stackrunId = $runid[runid];
|
|
$rstack = $this->getOriginalStackFromStackRun($stackrunId);
|
|
$childstackId = $rstack['stackId'];
|
|
//Get Parameters
|
|
$q = "SELECT DISTINCT(sd.`DEF_id`) as `stackId`, s.`DEF_id` as runid, s.*, p.*,sd.*,"
|
|
."s.`REF|leginondata|SessionData|session` AS sessionid "
|
|
."FROM ApRunsInStackData as r "
|
|
."LEFT JOIN ApStackRunData as s "
|
|
."ON (r.`REF|ApStackRunData|stackRun`=s.`DEF_id`) "
|
|
."LEFT JOIN ApStackData as sd "
|
|
."ON (r.`REF|ApStackData|stack`=sd.`DEF_id`) "
|
|
."LEFT JOIN ApPathData AS pd ON "
|
|
."(sd.`REF|ApPathData|path` = pd.`DEF_id`) "
|
|
."LEFT JOIN `ApStackParamsData` p "
|
|
."ON (p.`DEF_id` = s.`REF|ApStackParamsData|stackParams`) "
|
|
."WHERE r.`REF|ApStackData|stack` = '$childstackId'";
|
|
list($r) = $this->mysql->getSQLResult($q);
|
|
//echo $q."<br/>\n";
|
|
$params[]=$r;
|
|
$selectionstacks[] = $childstackId;
|
|
}
|
|
//handle multiple runs in stack
|
|
if (count($stackrunIds) > 1) {
|
|
$patharray = explode('/',$stack_primary_array[path]);
|
|
$runname = $patharray[count($patharray)-1];
|
|
$extra=0;
|
|
} else {
|
|
$extra=1;
|
|
$runname=$params[0]['stackRunName'];
|
|
}
|
|
//substack has no other parameter but oldstack reference
|
|
if ($stack_primary_array['REF|ApStackData|oldstack']) {
|
|
$r = array();
|
|
$r = array_merge($r, $stack_primary_array);
|
|
$r = array_merge($r,$this->getSubStackAlignCluster($stack_primary_array));
|
|
$r['shownstackname'] = $runname.'-'.$stack_primary_array['substackname'];
|
|
$r['REF|ApStackData|oldstack'] = $stack_primary_array['REF|ApStackData|oldstack'];
|
|
//add needed parent stackrun parameters, but not all since they overwrites the primary values
|
|
$r['tiltangle'] = $params[0]['tiltangle'];
|
|
$r['phaseFlipped'] = $params[0]['phaseFlipped'];
|
|
$r['fliptype'] = $params[0]['fliptype'];
|
|
$r['inverted'] = $params[0]['inverted'];
|
|
return $r;
|
|
}
|
|
$runarray = array();
|
|
$runarray['shownstackname'] = $runname;
|
|
$runarray['count'] = count($stackrunIds);
|
|
$runarray = array_merge($runarray,$stack_primary_array);
|
|
//use first run parameters for basic stack info
|
|
if ($extra) {
|
|
//use first run parameters for extra info
|
|
$r = array_merge($params[0],$runarray);
|
|
} else {
|
|
$r = $runarray;
|
|
$r['tiltangle'] = $params[0]['tiltangle'];
|
|
$r['phaseFlipped'] = $params[0]['phaseFlipped'];
|
|
$r['fliptype'] = $params[0]['fliptype'];
|
|
$r['inverted'] = $params[0]['inverted'];
|
|
$r['pixelsize'] = $params[0]['pixelsize'];
|
|
$r['boxsize'] = $params[0]['boxsize'];
|
|
}
|
|
$r['selectionstacks'] = $selectionstacks;
|
|
return $r;
|
|
}
|
|
|
|
function getOriginalStackFromStackRun($stackrunId) {
|
|
//get the original stack when a stackrun is also used in combined stacks
|
|
$q = "SELECT DISTINCT(rs.`REF|ApStackData|stack`) as stackId from `ApRunsInStackData` rs"
|
|
. " WHERE"
|
|
. " rs.`REF|ApStackRunData|stackRun`=".$stackrunId." "
|
|
. " AND"
|
|
. " rs.`REF|ApStackData|stack` NOT IN"
|
|
. " (SELECT `REF|ApStackData|stack` as stack FROM "
|
|
. " (SELECT count(*) as count ,`REF|ApStackData|stack`"
|
|
. " FROM `ApRunsInStackData`"
|
|
. " WHERE 1"
|
|
. " GROUP BY `REF|ApStackData|stack`) runs"
|
|
. " where runs.`count` > 1)";
|
|
list($rstack) = $this->mysql->getSQLResult($q);
|
|
return $rstack;
|
|
}
|
|
|
|
function getStackSelectionRun ($stackId) {
|
|
$q = "SELECT pr . `DEF_id` selectionid , "
|
|
." pr . `name`, "
|
|
." pr . `REF|leginondata|SessionData|session` as sessionId "
|
|
." FROM ( SELECT * FROM `ApStackParticleData` "
|
|
." WHERE `REF|ApStackData|stack` = ".$stackId." "
|
|
." group by `REF|ApStackRunData|stackRun` ) sp1 "
|
|
." LEFT JOIN `ApParticleData` p "
|
|
." ON p . `DEF_id` = sp1 . `REF|ApParticleData|particle` "
|
|
." LEFT JOIN `ApSelectionRunData` pr "
|
|
." ON pr . `DEF_id` = p . `REF|ApSelectionRunData|selectionrun` "
|
|
." ";
|
|
$r = $this->mysql->getSQLResult($q);
|
|
return $r;
|
|
}
|
|
|
|
function getStacksFromSelectionRun ($pickrunid) {
|
|
$q = "SELECT DISTINCT(sp1.`REF|ApStackData|stack`) as stackid, "
|
|
."sp1.`REF|ApStackRunData|stackRun` as stackrunid, "
|
|
."pr . `DEF_id` as selectionid "
|
|
."FROM ( "
|
|
."SELECT st.*, stpm.`DEF_id` as stackparamsid "
|
|
."FROM `ApStackParticleData` as st "
|
|
."LEFT JOIN `ApStackRunData` as str "
|
|
."ON st.`REF|ApStackRunData|stackRun` = str.`DEF_id` "
|
|
."LEFT JOIN `ApStackParamsData` as stpm "
|
|
."ON str.`REF|ApStackParamsData|stackParams` = stpm.`DEF_id` "
|
|
."group by "
|
|
."st.`REF|ApStackRunData|stackRun` "
|
|
.") sp1 "
|
|
."LEFT JOIN `ApParticleData` p "
|
|
."ON p .`DEF_id` = sp1 . `REF|ApParticleData|particle` "
|
|
."LEFT JOIN `ApSelectionRunData` pr ON "
|
|
."pr . `DEF_id` = p . `REF|ApSelectionRunData|selectionrun` "
|
|
."WHERE pr.`DEF_id` =".$pickrunid." "
|
|
." ";
|
|
$r = $this->mysql->getSQLResult($q);
|
|
return $r;
|
|
}
|
|
|
|
function getStackMeanAndStdev ($stackId) {
|
|
$q= "SELECT stackpart.mean AS mean, stackpart.stdev AS stdev "
|
|
."FROM `ApStackParticleData` AS stackpart "
|
|
."WHERE `REF|ApStackData|stack` = '$stackId'";
|
|
//echo $q."<br/><br/>\n";
|
|
$r = $this->mysql->getSQLResult($q);
|
|
//echo print_r($r[0])."<br/><br/>\n";
|
|
return $r;
|
|
}
|
|
|
|
function getParticlesFromStack($stackId){
|
|
$q= "SELECT `REF|ApParticleData|particle` AS particleId, mean, stdev, skew, "
|
|
."kurtosis, edgemean, edgestdev, centermean, centerstdev, min, max "
|
|
."FROM `ApStackParticleData` "
|
|
."WHERE `REF|ApStackData|stack` = '$stackId'";
|
|
|
|
$r = $this->mysql->getSQLResult($q);
|
|
return $r;
|
|
}
|
|
|
|
function getParticlePicksFromStack($stackId) {
|
|
$q="SELECT s.particleNumber as particle, "
|
|
."p.`REF|leginondata|AcquisitionImageData|image` as imgid, "
|
|
."p.xcoord, p.ycoord, p.helixnum, p.angle "
|
|
."FROM `ApStackParticleData` AS s "
|
|
."LEFT JOIN `ApParticleData` AS p "
|
|
."ON s.`REF|ApParticleData|particle` = p.`DEF_id` "
|
|
."WHERE s.`REF|ApStackData|stack` = '$stackId' "
|
|
."ORDER BY s.particleNumber";
|
|
$r = $this->mysql->getSQLResult($q);
|
|
return $r;
|
|
}
|
|
|
|
function getNumStackParticles ($stackId) {
|
|
$q= "SELECT count(DEF_id) as num "
|
|
."FROM `ApStackParticleData` "
|
|
."WHERE `REF|ApStackData|stack` = '$stackId'";
|
|
list($r) = $this->mysql->getSQLResult($q);
|
|
return $r['num'];
|
|
}
|
|
|
|
function getNumStackImages ($stackId) {
|
|
$q= "SELECT DISTINCT im.`DEF_id` AS imgid "
|
|
."FROM ApStackParticleData AS stpart "
|
|
."LEFT JOIN ApParticleData AS part "
|
|
."ON stpart.`REF|ApParticleData|particle` = part.`DEF_id` "
|
|
."LEFT JOIN ".DB_LEGINON.".`AcquisitionImageData` AS im "
|
|
."ON part.`REF|leginondata|AcquisitionImageData|image` = im.`DEF_id` "
|
|
."WHERE `REF|ApStackData|stack` = '$stackId'";
|
|
$r = $this->mysql->getSQLResult($q);
|
|
return count($r);
|
|
}
|
|
|
|
function getParticleMovieRunFromId($movierunid) {
|
|
$q = "SELECT pr . `DEF_id` as runid , "
|
|
." pr . `movieRunName`, "
|
|
." path . `path`, "
|
|
." pr . `REF|leginondata|SessionData|session` as sessionId, "
|
|
." pr . `REF|ApSelectionRunData|selectionrun` as selectionId "
|
|
." FROM `ApParticleMovieRunData` pr "
|
|
." LEFT JOIN `ApPathData` path "
|
|
." ON pr.`REF|ApPathData|path` = path.`DEF_id` "
|
|
." WHERE pr.`DEF_id` = ".$movierunid." "
|
|
." ";
|
|
list($r) = $this->mysql->getSQLResult($q);
|
|
return $r;
|
|
}
|
|
|
|
function getNumRefImages ($alignrun) {
|
|
$q = "SELECT count(DEF_id) as num "
|
|
."FROM `ApAlignReferenceData` "
|
|
."WHERE `REF|ApAlignRunData|alignrun` = '$alignrun'";
|
|
list($r) = $this->mysql->getSQLResult($q);
|
|
return $r['num'];
|
|
}
|
|
|
|
function removeAlignStackById($alignStackId) {
|
|
// Get alignment run for this stack
|
|
$q = "SELECT `REF|ApAlignRunData|alignrun` as alignrun "
|
|
. "FROM `ApAlignStackData` "
|
|
. "WHERE `DEF_id`=$alignStackId ";
|
|
$r = $this->mysql->getSQLResult($q);
|
|
$alignrun = $r[0]['alignrun'];
|
|
|
|
// delete entry in ApAlignRunData
|
|
$q = "DELETE from `ApAlignRunData` "
|
|
. "WHERE `DEF_id`=$alignrun ";
|
|
$r = $this->mysql->getSQLResult($q);
|
|
$status = "Removed Alignment ID $alignrun from ApAlignRunData table<br>\n";
|
|
|
|
// delete entry in ApAlignReferenceData
|
|
$q = "DELETE from `ApAlignReferenceData` "
|
|
. "WHERE `REF|ApAlignRunData|alignrun`=$alignrun ";
|
|
$r = $this->mysql->getSQLResult($q);
|
|
$status.= "Removed Aligned References from ApAlignReferenceData table<br>\n";
|
|
|
|
// get path the Stack entry in ApStackData
|
|
$q = "SELECT `REF|ApPathData|path` as path from ApAlignStackData "
|
|
."WHERE DEF_id=$alignStackId";
|
|
$r = $this->mysql->getSQLResult($q);
|
|
$pathid = $r[0]['path'];
|
|
// this path is used to remove the corresponding
|
|
// entry from ApAppionJobData
|
|
$q = "DELETE from ApAppionJobData "
|
|
."WHERE `REF|ApPathData|path`=$pathid ";
|
|
$this->mysql->getSQLResult($q);
|
|
$status.= "Removed associated job from ApAppionJobData<br/>\n";
|
|
|
|
// remove stack from ApStackData
|
|
$q = "DELETE from `ApAlignStackData` "
|
|
. "WHERE `DEF_id`=$alignStackId ";
|
|
$r = $this->mysql->getSQLResult($q);
|
|
$status.= "Removed Aligned Stack ID $alignStackId from ApAlignStackData table<br>\n";
|
|
// count the number of particles in ApStackParticleData
|
|
$q = "SELECT count(DEF_id) as num "
|
|
."FROM `ApAlignParticleData` "
|
|
."WHERE `REF|ApAlignStackData|alignstack`=$alignStackId ";
|
|
list($r) = $this->mysql->getSQLResult($q);
|
|
$q = "DELETE FROM `ApAlignParticleData` "
|
|
."WHERE `REF|ApAlignStackData|alignstack`=$alignStackId ";
|
|
$this->mysql->getSQLResult($q);
|
|
$status.= "Removed ".$r['num']." particles from ApAlignParticleData<br/>\n";
|
|
|
|
return $status;
|
|
}
|
|
|
|
function removeStackById($stackId) {
|
|
// Now get the stack run(s) used for this stack
|
|
$q = "SELECT `REF|ApStackRunData|stackRun` as stackrun "
|
|
. "FROM `ApRunsInStackData` as rs "
|
|
. "WHERE `REF|ApStackData|stack` = $stackId ";
|
|
$r = $this->mysql->getSQLResult($q);
|
|
|
|
// delete entry in ApRunsInStackData
|
|
$q = "delete from `ApRunsInStackData` "
|
|
. "WHERE `REF|ApStackData|stack` = $stackId";
|
|
$this->mysql->getSQLResult($q);
|
|
$status = "Removed Stack ID $stackId from ApRunsInStackData table<br>\n";
|
|
// check if there are still runs for each stack run:
|
|
foreach ($r as $srun) {
|
|
$srunid=$srun['stackrun'];
|
|
$q = "SELECT count(*) as num from `ApRunsInStackData` "
|
|
. "WHERE `REF|ApStackRunData|stackRun` = $srunid";
|
|
$r = $this->mysql->getSQLResult($q);
|
|
// if no entries left, remove entry in ApStackRunData
|
|
if ($r[0]['num']==0 ) {
|
|
$q = "DELETE from `ApStackRunData` "
|
|
. "WHERE `DEF_id` = $srunid";
|
|
$this->mysql->getSQLResult($q);
|
|
$status.= "Removed Stack Run ID $srunid from ApStackRunData table<br/>\n";
|
|
}
|
|
else $status.= "Stack Run ID $srunid is used in other stacks, not removing it from the ApStackRunData table<br/>\n";
|
|
}
|
|
// get path the Stack entry in ApStackData
|
|
$q = "SELECT `REF|ApPathData|path` as path from ApStackData "
|
|
."WHERE DEF_id=$stackId";
|
|
$r = $this->mysql->getSQLResult($q);
|
|
$pathid = $r[0]['path'];
|
|
// this path is used to remove the corresponding
|
|
// entry from ApAppionJobData
|
|
$q = "DELETE from ApAppionJobData "
|
|
."WHERE `REF|ApPathData|path`=$pathid ";
|
|
$this->mysql->getSQLResult($q);
|
|
$status.= "Removed associated job from ApAppionJobData<br/>\n";
|
|
// remove stack from ApStackData
|
|
$q = "DELETE from ApStackData "
|
|
." WHERE DEF_id=$stackId ";
|
|
$this->mysql->getSQLResult($q);
|
|
$status.= "Removed Stack ID $stackId from ApStackData<br/>\n";
|
|
// count the number of particles in ApStackParticleData
|
|
$q = "SELECT count(DEF_id) as num "
|
|
."FROM `ApStackParticleData` "
|
|
."WHERE `REF|ApStackData|stack` = '$stackId'";
|
|
list($r) = $this->mysql->getSQLResult($q);
|
|
$q = "DELETE from `ApStackParticleData` "
|
|
. "WHERE `REF|ApStackData|stack` = '$stackId'";
|
|
$this->mysql->getSQLResult($q);
|
|
$status.= "Removed ".$r['num']." particles from ApStackParticleData<br/>\n";
|
|
return $status;
|
|
}
|
|
|
|
//////// fix me ////////
|
|
function getStackIdFromReconId ($reconId) {
|
|
$q= "SELECT * "
|
|
."FROM `ApRefineRunData` "
|
|
."WHERE `DEF_id` = '$reconId'";
|
|
list($r) = $this->mysql->getSQLResult($q);
|
|
return $r['REF|ApStackData|stack'];
|
|
}
|
|
|
|
function getStackPixelSizeFromStackId ($stackId) {
|
|
// first see if it's stored in the ApStackData Table (easiest)
|
|
$q="SELECT pixelsize FROM ApStackData WHERE DEF_id=$stackId";
|
|
$r = $this->mysql->getSQLResult($q);
|
|
$apix = $r[0]['pixelsize'];
|
|
if ($apix && $apix != 0) return $apix;
|
|
$preset = $this->getPresetFromStackId($stackId);
|
|
return $preset['stackpixelsize'];
|
|
}
|
|
|
|
function getPresetFromStackId ($stackId) {
|
|
//get the first image of the stack assume using defocpair if not specified
|
|
$q="SELECT "
|
|
." IF( ( pimage . `defocpair` IS NULL OR pimage . `defocpair` = 1 ) , "
|
|
." sbimage . image , pimage . image ) as image , "
|
|
." pimage.image as pimage, "
|
|
." pimage.`stackbin` "
|
|
." FROM "
|
|
." ( SELECT "
|
|
." p . `REF|leginondata|AcquisitionImageData|image` as image , pa . `defocpair` ,"
|
|
." pa.`bin` as stackbin "
|
|
." FROM `ApStackParticleData` sp "
|
|
." LEFT JOIN `ApStackRunData` r ON "
|
|
." ( sp . `REF|ApStackRunData|stackRun` = r . `DEF_id` ) "
|
|
." LEFT JOIN `ApStackParamsData` pa ON "
|
|
." ( pa . `DEF_id` = r . `REF|ApStackParamsData|stackParams` ) "
|
|
." LEFT JOIN `ApParticleData` p ON "
|
|
." sp . `REF|ApParticleData|particle` = p . `DEF_id` "
|
|
." WHERE sp . `REF|ApStackData|stack` = ".$stackId." "
|
|
." limit 1 ) pimage , "
|
|
." ( SELECT "
|
|
." sb . `REF|leginondata|AcquisitionImageData|image2` as image "
|
|
." FROM `ApStackParticleData` sp "
|
|
." LEFT JOIN `ApStackRunData` r ON "
|
|
." ( sp . `REF|ApStackRunData|stackRun` = r . `DEF_id` ) "
|
|
." LEFT JOIN `ApStackParamsData` pa ON "
|
|
." ( pa . `DEF_id` = r . `REF|ApStackParamsData|stackParams` ) "
|
|
." LEFT JOIN `ApParticleData` p ON "
|
|
." sp . `REF|ApParticleData|particle` = p . `DEF_id` "
|
|
." LEFT JOIN `ApImageTransformationData` sb ON "
|
|
." (sb . `REF|leginondata|AcquisitionImageData|image1` "
|
|
." = p . `REF|leginondata|AcquisitionImageData|image`) "
|
|
." WHERE sp . `REF|ApStackData|stack`= ".$stackId." "
|
|
." limit 1 ) sbimage ";
|
|
list($r1)= $this->mysql->getSQLResult($q);
|
|
//if no sibling image when defocpair param is not specified, use the original image
|
|
$imgId = ($r1['image']) ? $r1['image'] : $r1['pimage'];
|
|
// get image bin and the most recent pixel calibration
|
|
$q="SELECT pd.`SUBD|binning|x` as imgbin, "
|
|
." pc.`pixelsize` as ccdpixelsize, pd.*, "
|
|
." pscope.`high tension` as hightension "
|
|
."FROM ".DB_LEGINON.".`AcquisitionImageData` a "
|
|
."left join ".DB_LEGINON.".`PresetData` pd "
|
|
." on (a.`REF|PresetData|preset`=pd.`DEF_id`) "
|
|
."LEFT JOIN ".DB_LEGINON.".`ScopeEMData` pscope "
|
|
." ON (pscope.`DEF_id` = a.`REF|ScopeEMData|scope`) "
|
|
.", ".DB_LEGINON.".PixelSizeCalibrationData pc "
|
|
."WHERE a.`DEF_id`='$imgId' "
|
|
."AND pc.`REF|InstrumentData|tem`= pd.`REF|InstrumentData|tem` "
|
|
."AND pc.`magnification`= pd.`magnification` "
|
|
."AND "
|
|
."pc.`REF|InstrumentData|ccdcamera`= pd.`REF|InstrumentData|ccdcamera` "
|
|
."AND "
|
|
."pc.`DEF_timestamp`< a.`DEF_timestamp` "
|
|
."ORDER BY pc.`DEF_timestamp` DESC ";
|
|
list($r2)=$this->mysql->getSQLResult($q);
|
|
if (!is_null($r1['stackbin']) ) {
|
|
settype($r1['stackbin'],"integer");
|
|
$stackbin = $r1['stackbin'];
|
|
} else {
|
|
$stackbin = 1;
|
|
}
|
|
$r2['stackpixelsize'] = $r2['ccdpixelsize']*$r2['imgbin']*$stackbin;
|
|
return $r2;
|
|
}
|
|
|
|
function getPixelSizeFromImgIdPresetQuery($imgid) {
|
|
$q="SELECT pd.`SUBD|binning|x` as imgbin, "
|
|
." pc.`pixelsize` as ccdpixelsize "
|
|
."FROM ".DB_LEGINON.".`AcquisitionImageData` AS a "
|
|
."LEFT JOIN ".DB_LEGINON.".`PresetData` AS pd "
|
|
." ON (a.`REF|PresetData|preset` = pd.`DEF_id`) "
|
|
.", ".DB_LEGINON.".PixelSizeCalibrationData pc "
|
|
."WHERE "
|
|
." a.`DEF_id`='$imgid' "
|
|
."AND "
|
|
." pc.`REF|InstrumentData|tem` = pd.`REF|InstrumentData|tem` "
|
|
."AND "
|
|
." pc.`magnification` = pd.`magnification` "
|
|
."AND "
|
|
." pc.`REF|InstrumentData|ccdcamera` = pd.`REF|InstrumentData|ccdcamera` "
|
|
."AND "
|
|
." pc.`DEF_timestamp` <= a.`DEF_timestamp` "
|
|
."ORDER BY pc.`DEF_timestamp` DESC ";
|
|
return $q;
|
|
}
|
|
|
|
function getPixelSizeFromImgIdEMQuery($imgid) {
|
|
// This is the more reliable query for pixel size but may take longer?
|
|
$q="SELECT ce.`SUBD|binning|x` as imgbin, "
|
|
." pc.`pixelsize` as ccdpixelsize "
|
|
."FROM ".DB_LEGINON.".`AcquisitionImageData` AS a "
|
|
."LEFT JOIN ".DB_LEGINON.".`CameraEMData` AS ce "
|
|
." ON (a.`REF|CameraEMData|camera` = ce.`DEF_id`) "
|
|
."LEFT JOIN ".DB_LEGINON.".`ScopeEMData` AS se "
|
|
." ON (a.`REF|ScopeEMData|scope` = se.`DEF_id`) "
|
|
.", ".DB_LEGINON.".PixelSizeCalibrationData pc "
|
|
."WHERE "
|
|
." a.`DEF_id`='$imgid' "
|
|
."AND "
|
|
." pc.`REF|InstrumentData|tem` = se.`REF|InstrumentData|tem` "
|
|
."AND "
|
|
." pc.`magnification` = se.`magnification` "
|
|
."AND "
|
|
." pc.`REF|InstrumentData|ccdcamera` = ce.`REF|InstrumentData|ccdcamera` "
|
|
."AND "
|
|
." pc.`DEF_timestamp` <= a.`DEF_timestamp` "
|
|
."ORDER BY pc.`DEF_timestamp` DESC ";
|
|
return $q;
|
|
}
|
|
|
|
function getPixelSizeFromImgId ($imgid) {
|
|
$q = $this->getPixelSizeFromImgIdPresetQuery($imgid);
|
|
//echo $q."<br/>\n";
|
|
list($r2)=$this->mysql->getSQLResult($q);
|
|
//echo print_r($r2)."<br/>\n";
|
|
if ($r2 === null) {
|
|
// If the session has only manual images, there is no preset.
|
|
$q = $this->getPixelSizeFromImgIdEMQuery($imgid);
|
|
list($r2)=$this->mysql->getSQLResult($q);
|
|
}
|
|
if ($r2['imgbin']) {
|
|
$pixelsize = $r2['ccdpixelsize']*$r2['imgbin'];
|
|
} else {
|
|
$pixelsize = $r2['ccdpixelsize'];
|
|
}
|
|
return $pixelsize;
|
|
}
|
|
|
|
function displayParticleStats ($particleruns, $display_keys, $inspect=False, $selexval=False, $dispImg=True) {
|
|
$expId=$_GET['expId'];
|
|
if (!is_array($particleruns))
|
|
return ;
|
|
$html = "\n<table class='tableborder' border='1' cellspacing='1' cellpadding='5'>\n";
|
|
$html .= "<tr> <td><span class='datafield0'>name</span></td>";
|
|
$html .= "<td><span class='datafield0'>dbid</span></td>";
|
|
foreach($display_keys as $key) {
|
|
$html .= "<td> <span class='datafield0'>".$key."</span> </td> ";
|
|
}
|
|
$html .= "</tr>";
|
|
foreach ($particleruns as $particle) {
|
|
$runId=$particle['DEF_id'];
|
|
if ($particle['hidden']) continue;
|
|
$particlestats = $this->getStats($runId, $inspect, $selexval);
|
|
$html .= "<tr>";
|
|
$numptl=$particlestats['totparticles'];
|
|
$numimg=$particlestats['num'];
|
|
$ppimg = ($numimg > 0) ? (sprintf("%.1f", $numptl/$numimg)) : 0;
|
|
$particlestats['numimgs']=$numimg.'<br />('.$ppimg.' prtl/img)';
|
|
if ($dispImg = True)
|
|
$particlestats['img'] = '<a href="'.$this->baseurl.'particlegraph.php?hg=1&run='.$runId.'">'
|
|
.'<img border="0" '
|
|
.'src="'.$this->baseurl.'particlegraph.php?w=150&hg=1&run='
|
|
.$runId.'"></a>';
|
|
$q = "select name from `ApSelectionRunData` where `DEF_id` = $runId";
|
|
list($r0) = $this->mysql->getSQLResult($q);
|
|
$html .= '<td><a href="'.$this->baseurl.'particlerunreport.php?expId='.$expId.'&rId='.$runId.'">'.$r0['name'].'</a></td>';
|
|
$html .= '<td>'.$runId.'</td>';
|
|
foreach($display_keys as $field) {
|
|
$data=$particlestats[$field];
|
|
if (eregi('^min|^max|^avg|^stddev', $field)) $data=format_sci_number($data,4);
|
|
$html .= "<td> $data </td> \n";
|
|
}
|
|
$html .= "</tr>\n";
|
|
}
|
|
$html .= "</table>\n";
|
|
return $html;
|
|
}
|
|
|
|
#--------- ALIGN STACK FUNCTIONS ---------------#
|
|
|
|
function getAlignStackIds ($sessionId, $showHidden=False) {
|
|
//$projectId = (int) getProjectFromExpId($expId);
|
|
// get session name, since original stack may be deleted
|
|
$q = "SELECT name from ".DB_LEGINON.".SessionData "
|
|
."WHERE DEF_id=$sessionId";
|
|
$r = $this->mysql->getSQLResult($q);
|
|
$sname = $r[0]['name'];
|
|
$q = "SELECT ast.`DEF_id` AS alignstackid "
|
|
."FROM ApAlignStackData AS ast "
|
|
."LEFT JOIN ApStackData AS st ON "
|
|
." (ast.`REF|ApStackData|stack` = st.`DEF_id`) "
|
|
."LEFT JOIN ApRunsInStackData as runsin ON "
|
|
." (runsin.`REF|ApStackData|stack` = st.`DEF_id`) "
|
|
."LEFT JOIN ApStackRunData as strun ON "
|
|
." (runsin.`REF|ApStackRunData|stackRun`=strun.`DEF_id`) "
|
|
."LEFT JOIN ApPathData ON "
|
|
." (ast.`REF|ApPathData|path`=ApPathData.`DEF_id`) "
|
|
."WHERE "
|
|
." (strun.`REF|leginondata|SessionData|session` = '$sessionId' "
|
|
."OR "
|
|
." ApPathData.`path` LIKE \"%$sname%\") ";
|
|
if (!$showHidden)
|
|
$q.= " AND ast.`hidden` != 1 ";
|
|
$q.= "ORDER BY alignstackid DESC";
|
|
//echo $q."<br/>\n";
|
|
$r = $this->mysql->getSQLResult($q);
|
|
//echo $r."<br/>\n";
|
|
return $r;
|
|
}
|
|
|
|
function getAlignStackIdsWithAnalysis ($sessionId, $projectId) {
|
|
//$projectId = (int) getProjectFromExpId($expId);
|
|
// get session name, since original stack may be deleted
|
|
$q = "SELECT name from ".DB_LEGINON.".SessionData "
|
|
."WHERE DEF_id=$sessionId";
|
|
$r = $this->mysql->getSQLResult($q);
|
|
$sname = $r[0]['name'];
|
|
$q = "SELECT DISTINCT ast.`DEF_id` AS alignstackid "
|
|
."FROM ApAlignStackData AS ast "
|
|
."LEFT JOIN ApAlignAnalysisRunData AS analysis ON "
|
|
." (analysis.`REF|ApAlignStackData|alignstack` = ast.`DEF_id`) "
|
|
."LEFT JOIN ApStackData AS st ON "
|
|
." (ast.`REF|ApStackData|stack` = st.`DEF_id`) "
|
|
."LEFT JOIN ApRunsInStackData as runsin ON "
|
|
." (runsin.`REF|ApStackData|stack` = st.`DEF_id`) "
|
|
."LEFT JOIN ApStackRunData as strun ON "
|
|
." (runsin.`REF|ApStackRunData|stackRun`=strun.`DEF_id`) "
|
|
."LEFT JOIN ApPathData ON "
|
|
." (ast.`REF|ApPathData|path`=ApPathData.`DEF_id`) "
|
|
."WHERE "
|
|
." (strun.`REF|leginondata|SessionData|session` = '$sessionId' "
|
|
."OR "
|
|
." ApPathData.`path` LIKE \"%$sname%\") "
|
|
."AND "
|
|
." ast.`hidden` != 1 "
|
|
."AND "
|
|
." analysis.`hidden` != 1 "
|
|
."AND "
|
|
." analysis.`DEF_id` IS NOT NULL "
|
|
."ORDER BY alignstackid DESC";
|
|
//echo $q."<br/><br/>\n";
|
|
$r = $this->mysql->getSQLResult($q);
|
|
//echo print_r($r)."<br/><br/>\n";
|
|
return $r;
|
|
}
|
|
|
|
function getAlignStackIdsWithClusterRun ($sessionId, $projectId) {
|
|
$q = "SELECT name from ".DB_LEGINON.".SessionData "
|
|
."WHERE DEF_id=$sessionId";
|
|
$r = $this->mysql->getSQLResult($q);
|
|
$sname = $r[0]['name'];
|
|
$q = "SELECT DISTINCT ast.`DEF_id` AS alignstackid "
|
|
."FROM ApAlignStackData AS ast "
|
|
."LEFT JOIN ApClusteringRunData AS cluster ON "
|
|
." (cluster.`REF|ApAlignStackData|alignstack` = ast.`DEF_id`)"
|
|
."LEFT JOIN ApStackData AS st ON "
|
|
." (ast.`REF|ApStackData|stack` = st.`DEF_id`) "
|
|
."LEFT JOIN ApRunsInStackData as runsin ON "
|
|
." (runsin.`REF|ApStackData|stack` = st.`DEF_id`) "
|
|
."LEFT JOIN ApStackRunData as strun ON "
|
|
." (runsin.`REF|ApStackRunData|stackRun`=strun.`DEF_id`) "
|
|
."LEFT JOIN ApPathData ON "
|
|
." (ast.`REF|ApPathData|path`=ApPathData.`DEF_id`) "
|
|
."WHERE "
|
|
." (strun.`REF|leginondata|SessionData|session` = '$sessionId' "
|
|
."OR "
|
|
." ApPathData.`path` LIKE \"%$sname%\") "
|
|
."AND "
|
|
." ast.`hidden` != 1 "
|
|
."AND "
|
|
." cluster.`DEF_id` IS NOT NULL "
|
|
."ORDER BY alignstackid DESC";
|
|
//echo $q."<br/><br/>\n";
|
|
$r = $this->mysql->getSQLResult($q);
|
|
//echo print_r($r)."<br/><br/>\n";
|
|
return $r;
|
|
}
|
|
|
|
function getAlignStackParams ($alignstackid) {
|
|
$q = "SELECT ar.*, ast.*, "
|
|
."ar.runname AS runname, "
|
|
."pd.`path` AS path "
|
|
."FROM ApAlignStackData as ast "
|
|
."LEFT JOIN ApPathData AS pd ON "
|
|
."(ast.`REF|ApPathData|path` = pd.`DEF_id`) "
|
|
."LEFT JOIN ApAlignRunData AS ar ON "
|
|
."(ast.`REF|ApAlignRunData|alignrun` = ar.`DEF_id`) "
|
|
."WHERE ast.`DEF_id` = '$alignstackid'";
|
|
$r = $this->mysql->getSQLResult($q);
|
|
$packagerefs = array(
|
|
'spidernoref'=>'REF|ApSpiderNoRefRunData|norefrun',
|
|
'spiderefbased'=>'REF|ApRefBasedRunData|refbasedrun',
|
|
'maxlike'=>'REF|ApMaxLikeRunData|maxlikerun',
|
|
'imagicMRA'=>'REF|ApMultiRefAlignRunData|imagicMRA',
|
|
'editerrun'=>'REF|ApEdIterRunData|editerrun',
|
|
);
|
|
foreach (array_keys($packagerefs) as $package) {
|
|
if ($r[0][$packagerefs[$package]]) $r[0]['package'] = $package;
|
|
}
|
|
return $r[0];
|
|
}
|
|
|
|
function getNumAlignStackParticles ($alignstackid) {
|
|
$q= "SELECT count(DEF_id) as num "
|
|
."FROM `ApAlignParticleData` "
|
|
."WHERE `REF|ApAlignStackData|alignstack` = '$alignstackid'";
|
|
|
|
//echo $q."<br/>\n";
|
|
list($r) = $this->mysql->getSQLResult($q);
|
|
return $r['num'];
|
|
}
|
|
|
|
function getNumAlignStackReferences ($alignstackid) {
|
|
$q= "SELECT count(aref.`DEF_id`) as num "
|
|
."FROM `ApAlignReferenceData` AS aref "
|
|
."LEFT JOIN ApAlignStackData AS astack ON "
|
|
." (astack.`REF|ApAlignRunData|alignrun` = aref.`REF|ApAlignRunData|alignrun`) "
|
|
."WHERE astack.`DEF_id` = '$alignstackid'"
|
|
." AND "
|
|
." astack.`iteration` = aref.`iteration` ";
|
|
//echo $q."<br/>\n";
|
|
list($r) = $this->mysql->getSQLResult($q);
|
|
//echo print_r($r)."<br/><br/>\n";
|
|
return $r['num'];
|
|
}
|
|
|
|
function getAnalysisRuns ($sessionId, $projectId, $showHidden=False) {
|
|
// This query left join ApCoranRun probably for historical reason
|
|
// get session name, since original stack may be deleted
|
|
$q = "SELECT name from ".DB_LEGINON.".SessionData "
|
|
."WHERE DEF_id=$sessionId";
|
|
$r = $this->mysql->getSQLResult($q);
|
|
$sname = $r[0]['name'];
|
|
|
|
$q = "SELECT analysis.`DEF_id` AS analysisid, analysis.* ";
|
|
if ($this->mysql->SQLTableExists("ApCoranRunData")) {
|
|
$q .= ", coran.* ";
|
|
}
|
|
$q .= "FROM ApAlignAnalysisRunData AS analysis "
|
|
."LEFT JOIN ApAlignStackData AS ast ON "
|
|
." (analysis.`REF|ApAlignStackData|alignstack` = ast.`DEF_id`) "
|
|
."LEFT JOIN ApStackData AS st ON "
|
|
." (ast.`REF|ApStackData|stack` = st.`DEF_id`) "
|
|
."LEFT JOIN ApRunsInStackData as runsin ON "
|
|
." (runsin.`REF|ApStackData|stack` = st.`DEF_id`) "
|
|
."LEFT JOIN ApStackRunData as strun ON "
|
|
." (runsin.`REF|ApStackRunData|stackRun`=strun.`DEF_id`) ";
|
|
if ($this->mysql->SQLTableExists("ApCoranRunData")) {
|
|
$q .= "LEFT JOIN ApCoranRunData as coran ON "
|
|
." (analysis.`REF|ApCoranRunData|coranrun` = coran.`DEF_id`) ";
|
|
}
|
|
$q .= "LEFT JOIN ApPathData ON "
|
|
." (ast.`REF|ApPathData|path`=ApPathData.`DEF_id`) "
|
|
."WHERE "
|
|
." (strun.`REF|leginondata|SessionData|session` = '$sessionId' "
|
|
."OR "
|
|
." ApPathData.`path` LIKE \"%$sname%\") ";
|
|
if (!$showHidden)
|
|
$q.= " AND analysis.`hidden` != 1 AND ast.`hidden` != 1 ";
|
|
$q .= "ORDER BY analysisid DESC ";
|
|
//echo $q."<br/><br/>\n";
|
|
$r = $this->mysql->getSQLResult($q);
|
|
//echo print_r($r)."<br/><br/>\n";
|
|
return $r;
|
|
}
|
|
|
|
function getAnalysisRunForAlignStack ($alignstackId, $projectId, $showHidden=False) {
|
|
$q = "SELECT analysis.`DEF_id` AS analysisid, analysis.* ";
|
|
if ($this->mysql->SQLTableExists("ApCoranRunData")) {
|
|
$q .= ", coran.* ";
|
|
}
|
|
$q .= "FROM ApAlignAnalysisRunData AS analysis ";
|
|
if ($this->mysql->SQLTableExists("ApCoranRunData")) {
|
|
$q .= "LEFT JOIN ApCoranRunData as coran ON "
|
|
." (analysis.`REF|ApCoranRunData|coranrun`=coran.`DEF_id`) ";
|
|
}
|
|
$q .= "WHERE "
|
|
." analysis.`REF|ApAlignStackData|alignstack` = $alignstackId ";
|
|
if (!$showHidden)
|
|
$q.= " AND analysis.`hidden` != 1 ";
|
|
$q .= "ORDER BY analysisid DESC ";
|
|
//echo $q."<br/>\n";
|
|
$r = $this->mysql->getSQLResult($q);
|
|
//echo print_r($r)."<br/>\n";
|
|
return $r;
|
|
}
|
|
|
|
function getAnalysisParams ($analysisid) {
|
|
$q = "SELECT analysis.`DEF_id` AS analysisid, analysis.*, path.path AS path ";
|
|
if ($this->mysql->SQLTableExists("ApCoranRunData")) {
|
|
$q .= ", coran.* ";
|
|
}
|
|
$q .= "FROM ApAlignAnalysisRunData AS analysis "
|
|
."LEFT JOIN ApAlignStackData AS ast ON "
|
|
." (analysis.`REF|ApAlignStackData|alignstack` = ast.`DEF_id`) "
|
|
."LEFT JOIN ApPathData AS path ON "
|
|
." (analysis.`REF|ApPathData|path` = path.`DEF_id`) ";
|
|
if ($this->mysql->SQLTableExists("ApCoranRunData")) {
|
|
$q .= "LEFT JOIN ApCoranRunData as coran ON "
|
|
." (analysis.`REF|ApCoranRunData|coranrun`=coran.`DEF_id`) ";
|
|
}
|
|
$q .= "WHERE "
|
|
." analysis.`DEF_id` = $analysisid "
|
|
."LIMIT 1 ";
|
|
//echo $q."<br/>\n";
|
|
$r = $this->mysql->getSQLResult($q);
|
|
//echo print_r($r)."<br/>\n";
|
|
return $r[0];
|
|
}
|
|
function getImagicAnalysisParams ($analysisid) {
|
|
$q = "SELECT analysis.`DEF_id` AS analysisid, analysis.*, data.*, path.path AS path "
|
|
."FROM ApAlignAnalysisRunData AS analysis "
|
|
."LEFT JOIN ApImagicAlignAnalysisData as data ON "
|
|
." (analysis.`REF|ApImagicAlignAnalysisData|imagicMSArun`=data.`DEF_id`) "
|
|
."LEFT JOIN ApPathData AS path ON "
|
|
." (analysis.`REF|ApPathData|path` = path.`DEF_id`) "
|
|
."WHERE "
|
|
." analysis.`DEF_id` = $analysisid "
|
|
."LIMIT 1 ";
|
|
$r = $this->mysql->getSQLResult($q);
|
|
return $r[0];
|
|
}
|
|
|
|
function getCoranEigenDataFromAnalysis ($analysisid) {
|
|
$q = "SELECT "
|
|
."ce.factor_num AS num, "
|
|
."ce.image_name AS name, "
|
|
."ce.percent_contrib AS contrib, "
|
|
."p.path AS path "
|
|
."FROM ApCoranEigenImageData AS ce "
|
|
."LEFT JOIN ApPathData AS p "
|
|
." ON (ce.`REF|ApPathData|path` = p.`DEF_id`) "
|
|
."LEFT JOIN ApCoranRunData AS cr "
|
|
." ON (ce.`REF|ApCoranRunData|coranRun` = cr.`DEF_id`) "
|
|
."LEFT JOIN ApAlignAnalysisRunData AS a "
|
|
." ON (a.`REF|ApCoranRunData|coranRun` = cr.`DEF_id`) "
|
|
."WHERE "
|
|
." a.`DEF_id` = '$analysisid' "
|
|
."ORDER BY ce.`factor_num` ASC";
|
|
//echo $q."<br/><br/>\n";
|
|
$r = $this->mysql->getSQLResult($q);
|
|
//echo print_r($r)."<br/><br/>\n";
|
|
return $r;
|
|
}
|
|
|
|
function getFinishedMaxLikeJobs ($projectId) {
|
|
$q = "SELECT maxjob.*, path.path "
|
|
."FROM ApMaxLikeJobData AS maxjob "
|
|
."LEFT JOIN ApPathData as path ON "
|
|
." maxjob.`REF|ApPathData|path` = path.`DEF_id` ";
|
|
if ($this->mysql->SQLTableExists("ApMaxLikeRunData")) {
|
|
$q .= "LEFT JOIN ApMaxLikeRunData as maxrun ON "
|
|
." maxrun.`REF|ApMaxLikeJobData|job` = maxjob.`DEF_id` ";
|
|
}
|
|
$q .= "WHERE "
|
|
." maxjob.`REF|projectdata|projects|project` = '$projectId' "
|
|
." AND "
|
|
." maxjob.`finished` = '1' "
|
|
." AND "
|
|
." maxjob.`hidden` != '1' ";
|
|
if ($this->mysql->SQLTableExists("ApMaxLikeRunData")) {
|
|
$q .= " AND "
|
|
." maxrun.`REF|ApMaxLikeJobData|job` IS NULL ";
|
|
}
|
|
$q .= " ORDER BY maxjob.`DEF_id` DESC ";
|
|
//echo $q."<br/><br/>\n";
|
|
$r = $this->mysql->getSQLResult($q);
|
|
//echo print_r($r)."<br/><br/>\n";
|
|
return $r;
|
|
}
|
|
|
|
function getFinishedCL2DJobs ($projectId) {
|
|
$q = "SELECT cl2djob.*, path.path "
|
|
."FROM ApCL2DRunData AS cl2djob "
|
|
."LEFT JOIN ApPathData as path ON "
|
|
." cl2djob.`REF|ApPathData|path` = path.`DEF_id` ";
|
|
$q .= "WHERE "
|
|
." cl2djob.`REF|projectdata|projects|project` = '$projectId' "
|
|
." AND "
|
|
." cl2djob.`finished` = '1' ";
|
|
$q .= " ORDER BY cl2djob.`DEF_id` DESC ";
|
|
//echo $q."<br/><br/>\n";
|
|
$r = $this->mysql->getSQLResult($q);
|
|
//echo print_r($r)."<br/><br/>\n";
|
|
return $r;
|
|
}
|
|
|
|
function getClusteringStacks ($sessionId, $projectId, $showHidden=False) {
|
|
// get session name, since original stack may be deleted
|
|
$q = "SELECT name from ".DB_LEGINON.".SessionData "
|
|
."WHERE DEF_id=$sessionId";
|
|
$r = $this->mysql->getSQLResult($q);
|
|
$sname = $r[0]['name'];
|
|
|
|
$q = "SELECT cluster.`DEF_id` AS clusterid, clusterrun.*, cluster.*, pd.`path` "
|
|
."FROM ApClusteringStackData AS cluster "
|
|
."LEFT JOIN ApClusteringRunData AS clusterrun ON "
|
|
." (cluster.`REF|ApClusteringRunData|clusterrun` = clusterrun.`DEF_id`) "
|
|
."LEFT JOIN ApAlignStackData AS ast ON "
|
|
." (clusterrun.`REF|ApAlignStackData|alignstack` = ast.`DEF_id`) "
|
|
."LEFT JOIN ApStackData AS st ON "
|
|
." (ast.`REF|ApStackData|stack` = st.`DEF_id`) "
|
|
."LEFT JOIN ApRunsInStackData as runsin ON "
|
|
." (runsin.`REF|ApStackData|stack` = st.`DEF_id`) "
|
|
."LEFT JOIN ApStackRunData as strun ON "
|
|
." (runsin.`REF|ApStackRunData|stackRun`=strun.`DEF_id`) "
|
|
."LEFT JOIN ApPathData AS pd ON "
|
|
." (cluster.`REF|ApPathData|path` = pd.`DEF_id`) "
|
|
."LEFT JOIN ApPathData ON "
|
|
." (ast.`REF|ApPathData|path`=ApPathData.`DEF_id`) "
|
|
."WHERE "
|
|
." (strun.`REF|leginondata|SessionData|session` = '$sessionId' "
|
|
."OR "
|
|
." ApPathData.`path` LIKE \"%$sname%\") ";
|
|
if (!$showHidden)
|
|
$q.= " AND cluster.`hidden` != 1 AND ast.`hidden` != 1 ";
|
|
$q .= "ORDER BY clusterid DESC ";
|
|
//echo $q."<br/><br/>\n";
|
|
$r = $this->mysql->getSQLResult($q);
|
|
//echo print_r($r)."<br/><br/>\n";
|
|
return $r;
|
|
}
|
|
|
|
function getAlignStackIdsWithCluster ($sessionId, $projectId) {
|
|
$q = "SELECT DISTINCT ast.`DEF_id` AS alignstackid "
|
|
."FROM ApAlignStackData AS ast "
|
|
."LEFT JOIN ApClusteringRunData AS clusterrun ON "
|
|
." (clusterrun.`REF|ApAlignStackData|alignstack` = ast.`DEF_id`) "
|
|
."LEFT JOIN ApClusteringStackData AS cluster ON "
|
|
." (cluster.`REF|ApClusteringRunData|clusterrun` = clusterrun.`DEF_id`) "
|
|
."LEFT JOIN ApStackData AS st ON "
|
|
." (ast.`REF|ApStackData|stack` = st.`DEF_id`) "
|
|
."LEFT JOIN ApRunsInStackData as runsin ON "
|
|
." (runsin.`REF|ApStackData|stack` = st.`DEF_id`) "
|
|
."LEFT JOIN ApStackRunData as strun ON "
|
|
." (runsin.`REF|ApStackRunData|stackRun`=strun.`DEF_id`) "
|
|
."LEFT JOIN ApAlignAnalysisRunData AS analysis ON "
|
|
." (analysis.`REF|ApAlignStackData|alignstack` = ast.`DEF_id`) "
|
|
."WHERE "
|
|
." strun.`REF|leginondata|SessionData|session` = '$sessionId' "
|
|
."AND "
|
|
." ast.`hidden` != 1 "
|
|
."AND "
|
|
." analysis.`hidden` != 1 "
|
|
."AND "
|
|
." cluster.`hidden` != 1 "
|
|
."AND "
|
|
." clusterrun.`DEF_id` IS NOT NULL "
|
|
."ORDER BY alignstackid DESC";
|
|
//echo $q."<br/><br/>\n";
|
|
$r = $this->mysql->getSQLResult($q);
|
|
//echo print_r($r)."<br/><br/>\n";
|
|
return $r;
|
|
}
|
|
|
|
function getAlignStackIdFromClusterId ($clusterId) {
|
|
$q = "SELECT DISTINCT ast.`DEF_id` AS alignstackid "
|
|
."FROM ApAlignStackData AS ast "
|
|
."LEFT JOIN ApClusteringRunData AS clusterrun ON "
|
|
." (clusterrun.`REF|ApAlignStackData|alignstack` = ast.`DEF_id`) "
|
|
."LEFT JOIN ApClusteringStackData AS cluster ON "
|
|
." (cluster.`REF|ApClusteringRunData|clusterrun` = clusterrun.`DEF_id`) "
|
|
."WHERE "
|
|
." cluster.`DEF_id` = '$clusterId' "
|
|
."ORDER BY alignstackid DESC";
|
|
//echo $q."<br/><br/>\n";
|
|
$r = $this->mysql->getSQLResult($q);
|
|
//echo print_r($r)."<br/><br/>\n";
|
|
return $r[0]['alignstackid'];
|
|
}
|
|
|
|
function getClusteringStacksForAlignStack ($alignstackId, $showHidden=false) {
|
|
$q = "SELECT cluster.`DEF_id` AS clusterid, path.path AS path, clusterrun.*, cluster.* ";
|
|
if ($this->mysql->SQLTableExists("ApSpiderClusteringParamsData")) {
|
|
$q .= ", spider.* ";
|
|
}
|
|
$q .= "FROM ApClusteringStackData AS cluster "
|
|
."LEFT JOIN ApClusteringRunData as clusterrun ON "
|
|
." (cluster.`REF|ApClusteringRunData|clusterrun`=clusterrun.`DEF_id`) "
|
|
."LEFT JOIN ApPathData as path ON "
|
|
." (cluster.`REF|ApPathData|path`=path.`DEF_id`) ";
|
|
if ($this->mysql->SQLTableExists("ApSpiderClusteringParamsData")) {
|
|
$q .= "LEFT JOIN ApSpiderClusteringParamsData as spider ON "
|
|
." (clusterrun.`REF|ApSpiderClusteringParamsData|spiderparams`=spider.`DEF_id`) ";
|
|
}
|
|
$q .= "WHERE "
|
|
." clusterrun.`REF|ApAlignStackData|alignstack` = $alignstackId ";
|
|
if (!$showHidden)
|
|
$q.= " AND cluster.`hidden` != 1 ";
|
|
$q .= "ORDER BY clusterid DESC ";
|
|
//echo $q."<br/>\n";
|
|
$r = $this->mysql->getSQLResult($q);
|
|
//echo print_r($r)."<br/>\n";
|
|
return $r;
|
|
}
|
|
|
|
function getClusteringRunParams ($clusterrunid) {
|
|
$q = "SELECT clustrun.* "
|
|
."FROM ApClusteringRunData AS clustrun "
|
|
."WHERE clustrun.`DEF_id` = '$clusterrunid'";
|
|
//echo $q."<br/>\n";
|
|
$r = $this->mysql->getSQLResult($q);
|
|
//echo print_r($r)."<br/>\n";
|
|
return $r[0];
|
|
}
|
|
|
|
function getClusteringStackParams ($clusterstackid) {
|
|
$q = "SELECT clustrun.*, cluststack.*, path.`path` AS path "
|
|
."FROM ApClusteringStackData AS cluststack "
|
|
."LEFT JOIN ApPathData AS path ON "
|
|
." (cluststack.`REF|ApPathData|path` = path.`DEF_id`) "
|
|
."LEFT JOIN ApClusteringRunData AS clustrun ON "
|
|
." (cluststack.`REF|ApClusteringRunData|clusterrun` = clustrun.`DEF_id`) "
|
|
."WHERE cluststack.`DEF_id` = '$clusterstackid'";
|
|
//echo $q."<br/>\n";
|
|
$r = $this->mysql->getSQLResult($q);
|
|
//echo print_r($r)."<br/>\n";
|
|
return $r[0];
|
|
}
|
|
|
|
function getClusteringRunsForAlignStack ($alignstackId, $showHidden=false) {
|
|
$q = "SELECT clusterrun.`DEF_id` AS clusterrunid, "
|
|
." clusterrun.*, analysis.`REF|ApImagicAlignAnalysisData|imagicMSArun` ";
|
|
if ($this->mysql->SQLTableExists("ApSpiderClusteringParamsData")) {
|
|
$q .= ", spider.* ";
|
|
}
|
|
$q .= "FROM ApClusteringRunData AS clusterrun ";
|
|
if ($this->mysql->SQLTableExists("ApSpiderClusteringParamsData")) {
|
|
$q .= "LEFT JOIN ApSpiderClusteringParamsData as spider ON "
|
|
." (clusterrun.`REF|ApSpiderClusteringParamsData|spiderparams`=spider.`DEF_id`) ";
|
|
}
|
|
$q .= "LEFT JOIN ApAlignAnalysisRunData as analysis ON "
|
|
." (clusterrun.`REF|ApAlignAnalysisRunData|analysisrun`=analysis.`DEF_id`) "
|
|
."WHERE "
|
|
." clusterrun.`REF|ApAlignStackData|alignstack` = $alignstackId "
|
|
."ORDER BY clusterrunid DESC ";
|
|
//echo $q."<br/>\n";
|
|
$r = $this->mysql->getSQLResult($q);
|
|
//echo print_r($r)."<br/>\n";
|
|
return $r;
|
|
}
|
|
|
|
function getClusteringStacksForClusteringRun ($clusterrunId, $showHidden=false) {
|
|
$q = "SELECT cluster.`DEF_id` AS clusterid, path.path AS path, "
|
|
." clusterrun.*, cluster.*, analysis.`REF|ApImagicAlignAnalysisData|imagicMSArun` ";
|
|
if ($this->mysql->SQLTableExists("ApSpiderClusteringParamsData")) {
|
|
$q .= ", spider.* ";
|
|
}
|
|
$q .= "FROM ApClusteringStackData AS cluster "
|
|
."LEFT JOIN ApClusteringRunData as clusterrun ON "
|
|
." (cluster.`REF|ApClusteringRunData|clusterrun`=clusterrun.`DEF_id`) "
|
|
."LEFT JOIN ApAlignAnalysisRunData as analysis ON "
|
|
." (clusterrun.`REF|ApAlignAnalysisRunData|analysisrun`=analysis.`DEF_id`) "
|
|
."LEFT JOIN ApPathData as path ON "
|
|
." (cluster.`REF|ApPathData|path`=path.`DEF_id`) ";
|
|
if ($this->mysql->SQLTableExists("ApSpiderClusteringParamsData")) {
|
|
$q .= "LEFT JOIN ApSpiderClusteringParamsData as spider ON "
|
|
." (clusterrun.`REF|ApSpiderClusteringParamsData|spiderparams`=spider.`DEF_id`) ";
|
|
}
|
|
$q .= "WHERE "
|
|
." clusterrun.`DEF_id` = $clusterrunId ";
|
|
if (!$showHidden)
|
|
$q.= " AND cluster.`hidden` != 1 ";
|
|
$q .= "ORDER BY clusterid DESC ";
|
|
//echo $q."<br/>\n";
|
|
$r = $this->mysql->getSQLResult($q);
|
|
//echo print_r($r)."<br/>\n";
|
|
return $r;
|
|
}
|
|
|
|
#--------- MAKE MASK FUNCTIONS---------------#
|
|
|
|
function getMaskMakerRunIds ($sessionId) {
|
|
$q = "select * "
|
|
."from `ApMaskMakerRunData` where `REF|leginondata|SessionData|session` = '$sessionId'";
|
|
$r = $this->mysql->getSQLResult($q);
|
|
return $r;
|
|
}
|
|
|
|
function getMaskAssessRunIds ($sessionId) {
|
|
$q = "select * "
|
|
."from `ApMaskAssessmentRunData` where `REF|leginondata|SessionData|session` = '$sessionId'";
|
|
$r = $this->mysql->getSQLResult($q);
|
|
return $r;
|
|
}
|
|
|
|
function hasMaskMakerData ($sessionId) {
|
|
$r= ($this->getLastMaskMakerRun($sessionId)) ? true : false;
|
|
return $r;
|
|
}
|
|
|
|
function getLastMaskMakerRun ($sessionId) {
|
|
$q = "select max(DEF_id) as runId "
|
|
."from `ApMaskMakerRunData` where `REF|leginondata|SessionData|session` = '$sessionId'";
|
|
list($r) = $this->mysql->getSQLResult($q);
|
|
return $r[runId];
|
|
}
|
|
|
|
function getMaskMakerParams ($runId) {
|
|
$q = "select * from ApMaskMakerRunData "
|
|
." where `DEF_id` = '$runId' ";
|
|
list($r)=$this->mysql->getSQLResult($q);
|
|
|
|
//print_r ($r);
|
|
//echo $r['REF|ApMaskMakerParamsData|params'];
|
|
$q = "select s.*, r.name, r.`REF|leginondata|SessionData|session` ";
|
|
|
|
if ($r['REF|ApMaskMakerParamsData|params']) {
|
|
$maskparamid=$r['REF|ApSelectionParamsData|params'];
|
|
$q .= "from ApMaskMakerParamsData s "
|
|
."left join ApMaskMakerRunData r on (s.`DEF_id` = r.`REF|ApMaskMakerParamsData|params`) "
|
|
."LEFT JOIN ApPathData AS p ON "
|
|
."(r.`REF|ApPathData|path`= p.`DEF_id`) ";
|
|
}
|
|
|
|
$q .= "where r.`DEF_id` = '$runId' ";
|
|
//echo $q;
|
|
$r=$this->mysql->getSQLResult($q);
|
|
//print_r ($r);
|
|
return $r;
|
|
}
|
|
|
|
function getMaskRegions ($runId) {
|
|
$q="select r.DEF_id, r.x, r.y, r.area, r.mean, r.stdev "
|
|
."from ApMaskRegionData r "
|
|
."where r.`REF|ApMaskMakerRunData|maskrun` = ".$runId." ";
|
|
$r=$this->mysql->getSQLResult($q);
|
|
return $r;
|
|
}
|
|
|
|
function getMaskRegionStats ($runId, $inspect=False){
|
|
$q="select count(r.`DEF_id`) as `totregions`, "
|
|
."count(distinct r.`REF|leginondata|AcquisitionImageData|image`) as num, "
|
|
."avg(r.area) as `areamean`, "
|
|
."avg(r.mean) as `Imean`, "
|
|
."avg(r.stdev) as `Istddev` "
|
|
."from ApMaskRegionData r ";
|
|
// use the latest inspection value. This should be changed later
|
|
if ($inspect) {
|
|
$q.= "left join ApAssessmentData ad "
|
|
."on (ad.`REF|leginondata|AcquisitionImageData|image` = r.`REF|leginondata|AcquisitionImageData|image`) ";
|
|
}
|
|
$q.="WHERE ";
|
|
if ($inspect) {
|
|
$q.= "ad.`DEF_id`=(select max(ad2.`DEF_id`) from ApAssessmentData ad2 where ad2.`REF|leginondata|AcquisitionImageData|image` = ad.`REF|leginondata|AcquisitionImageData|image`) "
|
|
."and ad.selectionkeep=1 AND ";
|
|
}
|
|
$q.="r.`REF|ApMaskMakerRunData|maskrun` = '$runId' ";
|
|
$r = $this->mysql->getSQLResult($q);
|
|
return $r[0];
|
|
|
|
}
|
|
|
|
function displayMaskRegionStats ($expId,$particleruns, $display_keys, $inspect=False, $selexval=False) {
|
|
if (!is_array($particleruns))
|
|
return ;
|
|
$html = "<BR>\n<table class='tableborder' border='1' cellspacing='1' cellpadding='5'>\n";
|
|
$html .= "<tr> <td> </td>";
|
|
foreach($display_keys as $key) {
|
|
$html .= "<td> <span class='datafield0'>".$key."</span> </td> ";
|
|
}
|
|
$html .= "</tr>";
|
|
|
|
foreach ($particleruns as $particle) {
|
|
$runId=$particle['DEF_id'];
|
|
$regionstats = $this->getMaskRegionStats($runId, $inspect);
|
|
$html .= "<tr>";
|
|
$numregn=$regionstats['totregions'];
|
|
$numimg=$regionstats['num'];
|
|
$rpimg = ($numimg > 0) ? (sprintf("%.1f", $numregn/$numimg)) : 0;
|
|
$regionstats['numimgs']=$numimg.'<BR>('.$rpimg.' regions/img)';
|
|
$regionstats['img'] = '<a href="maskregiongraph.php?hg=1&run='.$runId.'">'
|
|
.'<img border="0" '
|
|
.'src="maskregiongraph.php?w=150&hg=1&run='
|
|
.$runId.'"></a>';
|
|
$q = "select name from `ApMaskMakerRunData` where `DEF_id` = $runId";
|
|
$r = $this->mysql->getSQLResult($q);
|
|
$r0 = $r[0];
|
|
$html .= "<td><a target='params' href='maskrunreport.php?expId=$expId&rId=$runId'>".$r0['name']."</a></td>";
|
|
foreach($display_keys as $field) {
|
|
$data=$regionstats[$field];
|
|
if (eregi('^areamean|^Imean|^Istddev', $field)) $data=format_sci_number($data,4);
|
|
$html .= "<td> $data </td> \n";
|
|
}
|
|
$html .= "</tr>\n";
|
|
}
|
|
$html .= "</table>\n";
|
|
return $html;
|
|
}
|
|
|
|
function getMaskAssessRunByName ($sessionId,$name){
|
|
$q = "select * "
|
|
."from `ApMaskAssessmentRunData` "
|
|
."where "
|
|
."`REF|leginondata|SessionData|session` = '$sessionId' AND "
|
|
." `name` = '$name' ";
|
|
$r = $this->mysql->getSQLResult($q);
|
|
return $r;
|
|
}
|
|
|
|
function getMaskAssessNames ($sessionId){
|
|
$q = "select `name` "
|
|
."from `ApMaskAssessmentRunData` "
|
|
."where `REF|leginondata|SessionData|session` = '$sessionId' "
|
|
." group by `name` ";
|
|
$r = $this->mysql->getSQLResult($q);
|
|
if ($r) {
|
|
$names=array();
|
|
foreach ($r as $ra) $names[]=$ra[name];
|
|
}
|
|
return $names;
|
|
}
|
|
|
|
function getMaskAssessStats ($runId, $inspect=False){
|
|
$q="select count(m.`keep`) as `totkeeps`, "
|
|
."count(distinct r.`REF|leginondata|AcquisitionImageData|image`) as num "
|
|
."from ApMaskAssessmentData m "
|
|
."left join ApMaskRegionData r "
|
|
." on m.`REF|ApMaskRegionData|region` = r.`DEF_id` ";
|
|
// use the latest inspection value. This should be changed later
|
|
if ($inspect) {
|
|
$q.= "left join ApAssessmentData ad "
|
|
."on (ad.`REF|leginondata|AcquisitionImageData|image` = r.`REF|leginondata|AcquisitionImageData|image`) ";
|
|
}
|
|
$q.="WHERE ";
|
|
if ($inspect) {
|
|
$q.= "ad.`DEF_id`=(select max(ad2.`DEF_id`) from ApAssessmentData ad2 where ad2.`REF|leginondata|AcquisitionImageData|image` = ad.`REF|leginondata|AcquisitionImageData|image`) "
|
|
."and ad.selectionkeep=1 AND ";
|
|
}
|
|
$q.="m.`REF|ApMaskAssessmentRunData|run` = '$runId' AND "
|
|
."m.`keep` = 1 ";
|
|
$r = $this->mysql->getSQLResult($q);
|
|
return $r[0];
|
|
|
|
}
|
|
|
|
#---------RECONSTRUCTION FUNCTIONS---------------#
|
|
|
|
function getSymmetries($order=true) {
|
|
$q="SELECT * "
|
|
."FROM `ApSymmetryData`";
|
|
if ($order)
|
|
$q.=" order by symmetry ";
|
|
$r=$this->mysql->getSQLResult($q);
|
|
if (!$r) {
|
|
echo "<font size='+2' color='#cc3333'> Major Error: no symmetry info found in database</font>\n";
|
|
exit;
|
|
}
|
|
return $r;
|
|
}
|
|
|
|
function getSymInfo ($symId){
|
|
return $this->getSymmetryInfo($symId);
|
|
}
|
|
|
|
function getSymmetryInfo($id) {
|
|
$q="SELECT * "
|
|
."FROM `ApSymmetryData` WHERE DEF_id = $id";
|
|
list($r)=$this->mysql->getSQLResult($q);
|
|
return $r;
|
|
}
|
|
|
|
function getSymmetryDataFromEmanName($emansym) {
|
|
$q="SELECT * "
|
|
."FROM `ApSymmetryData` "
|
|
."WHERE eman_name = '$emansym' "
|
|
."LIMIT 1 ";
|
|
#echo $q."<br/>";
|
|
$r = $this->mysql->getSQLResult($q);
|
|
#echo print_r($r[0])."<br/>";
|
|
return $r[0];
|
|
}
|
|
|
|
function getModelsFromProject ($projectId, $getHidden=False) {
|
|
$q="SELECT i.*, p.path "
|
|
."FROM `ApInitialModelData` i "
|
|
."LEFT JOIN `ApPathData` p "
|
|
." ON (p.`DEF_id` = i.`REF|ApPathData|path`) "
|
|
."WHERE i.`REF|projectdata|projects|project`='$projectId' ";
|
|
if (!$getHidden) $q.= "AND (i.`hidden` IS NULL OR i.`hidden` = 0) ";
|
|
$q.= "ORDER BY i.`DEF_id` DESC";
|
|
//echo $q."\n<BR/>\n";
|
|
$r = $this->mysql->getSQLResult($q);
|
|
return $r;
|
|
}
|
|
|
|
function getModelsFromRefineID( $refineID )
|
|
{
|
|
$q = "SELECT model.*, refmodel.filename "
|
|
. " FROM `ApRefineInitModelData` AS refmodel, ApInitialModelData AS model "
|
|
. " WHERE refmodel.`REF|ApPrepRefineData|preprefine` = $refineID "
|
|
. " AND refmodel.`REF|ApInitialModelData|refmodel` = model.`DEF_id` ";
|
|
|
|
//echo $q."<br/><br/>\n";
|
|
$r = $this->mysql->getSQLResult($q);
|
|
//echo print_r($r)."<br/><br/>\n";
|
|
return $r;
|
|
}
|
|
|
|
|
|
function updateExemplar($table, $id, $value) {
|
|
$q = "SELECT exemplar "
|
|
."FROM `".$table."` "
|
|
."WHERE `DEF_id`=".$id." ";
|
|
$olddata = $this->mysql->getSQLResult($q);
|
|
if (array_key_exists('exemplar',$olddata[0])) {
|
|
$data = array();
|
|
$data['exemplar']=$value;
|
|
$where = array('DEF_id'=>$id);
|
|
$this->mysql->SQLUpdate($table,$data,$where);
|
|
}
|
|
}
|
|
|
|
function getMiscInfoFromProject ($projectId) {
|
|
$q="SELECT i.*, p.path "
|
|
."FROM `ApMiscData` i "
|
|
."LEFT JOIN `ApPathData` p "
|
|
." ON (p.`DEF_id` = i.`REF|ApPathData|path`) "
|
|
."WHERE i.`REF|projectdata|projects|project`='$projectId' "
|
|
."ORDER BY i.`DEF_id` DESC";
|
|
$r = $this->mysql->getSQLResult($q);
|
|
return $r;
|
|
}
|
|
|
|
function getJobTypesLike( $expId, $pattern )
|
|
{
|
|
$q="SELECT DISTINCT(j.`jobtype`) "
|
|
."FROM `ApAppionJobData` AS j "
|
|
."WHERE j.`REF|leginondata|SessionData|session` = $expId "
|
|
."AND j.`jobtype` LIKE '$pattern' ";
|
|
|
|
$r = $this->mysql->getSQLResult($q);
|
|
|
|
return $r;
|
|
}
|
|
|
|
function getJobIdsFromSession($expId, $jobtype=False, $status=False, $ignore=True) {
|
|
$q="SELECT j.*, "
|
|
."p.path as appath "
|
|
."FROM `ApAppionJobData` AS j "
|
|
."LEFT JOIN `ApPathData` AS p ON "
|
|
."(j.`REF|ApPathData|path` = p.`DEF_id`) "
|
|
."WHERE j.`REF|leginondata|SessionData|session` = $expId";
|
|
if ($jobtype) $q.=" AND j.`jobtype` = '$jobtype'";
|
|
if ($status) $q.=" AND j.`status` = '$status'";
|
|
if ($ignore) $q.=" AND j.`status` != 'I'";
|
|
$q.=" ORDER BY j.`DEF_id` DESC ";
|
|
$r = $this->mysql->getSQLResult($q);
|
|
return $r;
|
|
}
|
|
|
|
function getFscFromRefinementDataId ($id) {
|
|
$q = "SELECT * "
|
|
."FROM ApFSCData "
|
|
."WHERE `REF|ApRefineIterData|refineIter` = $id "
|
|
."ORDER BY pix";
|
|
//echo $q."<br/><br/>\n";
|
|
$r = $this->mysql->getSQLResult($q);
|
|
//echo print_r($r)."<br/><br/>\n";
|
|
return $r;
|
|
}
|
|
|
|
function getJobInfoFromId($jobid) {
|
|
$q="SELECT j.*, "
|
|
."p.path as appath, "
|
|
."d.path as dmfpath, "
|
|
."c.path as clusterpath "
|
|
."FROM `ApAppionJobData` AS j "
|
|
."LEFT JOIN ApPathData AS p ON "
|
|
."(j.`REF|ApPathData|path` = p.`DEF_id`) "
|
|
."LEFT JOIN ApPathData AS d ON "
|
|
."(j.`REF|ApPathData|dmfpath` = d.`DEF_id`) "
|
|
."LEFT JOIN ApPathData AS c ON "
|
|
."(j.`REF|ApPathData|clusterpath` = c.`DEF_id`) "
|
|
."WHERE j.`DEF_id` = $jobid";
|
|
$r = $this->mysql->getSQLResult($q);
|
|
return $r[0];
|
|
}
|
|
|
|
function getJobFileFromPath($path,$name) {
|
|
$q="SELECT j.*, p.path "
|
|
."FROM `ApAppionJobData` AS j "
|
|
."LEFT JOIN ApPathData AS p ON "
|
|
."(j.`REF|ApPathData|path` = p.`DEF_id`) "
|
|
."WHERE p.`path` = '$path' AND j.`name` = '$name'";
|
|
$r = $this->mysql->getSQLResult($q);
|
|
return $r;
|
|
}
|
|
|
|
function insertClusterJobData($host,$pathdir,$dmfpathdir,$clusterdir,$name,$expId,$jobtype,$user=NULL) {
|
|
// put appion path in db
|
|
$q = "SELECT DEF_id "
|
|
."FROM `ApPathData` "
|
|
."WHERE `path`='$pathdir'";
|
|
$r = $this->mysql->getSQLResult($q);
|
|
$pathid=$r[0]['DEF_id'];
|
|
if (!$pathid) {
|
|
$pdata['path']=$pathdir;
|
|
$pathid=$this->mysql->SQLInsert('ApPathData',$pdata);
|
|
}
|
|
// put dmf path in db
|
|
$q = "SELECT DEF_id "
|
|
."FROM `ApPathData` "
|
|
."WHERE `path`='$dmfpathdir'";
|
|
$r = $this->mysql->getSQLResult($q);
|
|
$dmfpathid=$r[0]['DEF_id'];
|
|
if (!$dmfpathid) {
|
|
$pdata['path']=$dmfpathdir;
|
|
$dmfpathid=$this->mysql->SQLInsert('ApPathData',$pdata);
|
|
}
|
|
// put cluster path in db
|
|
$q = "SELECT DEF_id "
|
|
."FROM `ApPathData` "
|
|
."WHERE `path`='$clusterdir'";
|
|
$r = $this->mysql->getSQLResult($q);
|
|
$clusterpathid=$r[0]['DEF_id'];
|
|
if (!$clusterpathid) {
|
|
$pdata['path']=$clusterdir;
|
|
$clusterpathid=$this->mysql->SQLInsert('ApPathData',$pdata);
|
|
}
|
|
// find if job is in database
|
|
$q = "SELECT DEF_id "
|
|
."FROM `ApAppionJobData` "
|
|
."WHERE `REF|ApPathData|path` = $pathid AND "
|
|
."`name` = '$name' AND "
|
|
."`REF|leginondata|SessionData|session` = $expId "
|
|
." AND `jobtype` = $jobtype ";
|
|
$r = $this->mysql->getSQLResult($q);
|
|
$jid=$r[0]['DEF_id'];
|
|
// if not in database, insert
|
|
if (!$jid) {
|
|
$jdata['REF|ApPathData|path'] = $pathid;
|
|
$jdata['name'] = $name;
|
|
$jdata['jobtype'] = $jobtype;
|
|
$jdata['REF|leginondata|SessionData|session'] = $expId;
|
|
$jdata['REF|ApPathData|dmfpath'] = $dmfpathid;
|
|
$jdata['REF|ApPathData|clusterpath'] = $clusterpathid;
|
|
$jdata['cluster'] = $host;
|
|
$jdata['user'] = $user;
|
|
$jid=$this->mysql->SQLInsert('ApAppionJobData',$jdata);
|
|
}
|
|
return $jid;
|
|
}
|
|
|
|
function displayHidingOption($expId,$allruns,$shownruns,$show = False) {
|
|
if (!$_GET['showHidden'] && count($allruns) != count($shownruns)) {
|
|
$numhidden = count($allruns) - count($shownruns);
|
|
$html = "<a href='".$_SERVER['PHP_SELF']."?expId=$expId&showHidden=1'>[Show ".$numhidden." hidden runs]</a><br/><br/>\n";
|
|
} elseif ($_GET['showHidden']) {
|
|
$html .= "<a href='".$_SERVER['PHP_SELF']."?expId=$expId&showHidden=0'>[Hide hidden runs]</a><br/><br/>\n";
|
|
}
|
|
return $html;
|
|
}
|
|
|
|
function updateDescription($table, $id, $newtext) {
|
|
$q = "SELECT description "
|
|
."FROM `".$table."` "
|
|
."WHERE `DEF_id`=".$id." ";
|
|
$olddata = $this->mysql->getSQLResult($q);
|
|
if (array_key_exists('description',$olddata[0])) {
|
|
$data = array();
|
|
$data['description']=$newtext;
|
|
$where = array('DEF_id'=>$id);
|
|
$this->mysql->SQLUpdate($table,$data,$where);
|
|
}
|
|
}
|
|
|
|
function updateHide($table, $id, $value) {
|
|
$q = "SELECT hidden "
|
|
."FROM `".$table."` "
|
|
."WHERE `DEF_id`=".$id." ";
|
|
$olddata = $this->mysql->getSQLResult($q);
|
|
if (array_key_exists('hidden',$olddata[0])) {
|
|
$data = array();
|
|
$data['hidden']=$value;
|
|
$where = array('DEF_id'=>$id);
|
|
$this->mysql->SQLUpdate($table,$data,$where);
|
|
}
|
|
}
|
|
|
|
function updateTableDescriptionAndHiding($post,$updatetable,$updateid) {
|
|
//update description if posted
|
|
if ($post['updateDesc'.$updateid]) {
|
|
$this->updateDescription($updatetable, $updateid, $post['newdescription'.$updateid]);
|
|
}
|
|
//update hidden if posted
|
|
if ($post['hideItem'.$updateid] == 'hide') {
|
|
$this->updateHide($updatetable, $updateid, '1');
|
|
} elseif ($_POST['unhideItem'.$updateid] == 'unhide') {
|
|
$this->updateHide($updatetable, $updateid, '0');
|
|
}
|
|
}
|
|
|
|
function updateClusterQueue($jobid,$queueid,$status) {
|
|
$data = array('clusterjobid'=>$queueid);
|
|
$data['status']=$status;
|
|
$where = array('DEF_id'=>$jobid);
|
|
$this->mysql->SQLUpdate('ApAppionJobData',$data,$where);
|
|
}
|
|
|
|
function updateClusterJobStatus($jobid, $status) {
|
|
$data = array('status'=>$status);
|
|
$where = array('DEF_id'=>$jobid);
|
|
$this->mysql->SQLUpdate('ApAppionJobData',$data, $where);
|
|
}
|
|
|
|
function abortClusterJob($jobid, $user=false) {
|
|
$data = array('status'=>'A');
|
|
$where = array('DEF_id'=>$jobid);
|
|
if ($user)
|
|
$where['user'] = $user;
|
|
$this->mysql->SQLUpdate('ApAppionJobData', $data, $where);
|
|
}
|
|
|
|
function getSubmittedJobs($expId) {
|
|
$q="SELECT * "
|
|
."FROM `ApAppionJobData` "
|
|
."WHERE `REF|leginondata|SessionData|session`=$expId";
|
|
$r = $this->mysql->getSQLResult($q);
|
|
return $r;
|
|
}
|
|
|
|
function getReconIdFromAppionJobId($jobid) {
|
|
$q="SELECT * "
|
|
."FROM `ApRefineRunData` "
|
|
."WHERE `REF|ApAppionJobData|job` = $jobid";
|
|
$r = $this->mysql->getSQLResult($q);
|
|
return $r[0];
|
|
}
|
|
|
|
function getJobNamesFromJobType( $jobtype, $sessionId )
|
|
{
|
|
$q = "select name from `ApAppionJobData` "
|
|
."where `REF|leginondata|SessionData|session` = $sessionId "
|
|
."and jobtype = '$jobtype'";
|
|
$r = $this->mysql->getSQLResult($q);
|
|
|
|
if ( $r === False ) {
|
|
$dberror = $this->mysql->getError();
|
|
error_log("Error: database error in particledata.inc, getDefaultJobName(): $dberror /n");
|
|
}
|
|
return $r;
|
|
}
|
|
|
|
// parse the runname into its components
|
|
static function getJobRunIdFromRunname( $runname )
|
|
{
|
|
// step 1: strip the jobtype and id from the runname
|
|
|
|
// check if the runname has a timestamp appended seperated by '-'
|
|
// explode returns an empty array if the delimiter is not found and the limit is negative
|
|
list($baseRunName, $extension) = explode( "-", $runname, -1 );
|
|
|
|
// check if the jobtype and id are followed by a '.' with other stuff
|
|
if ( !$baseRunName ) {
|
|
list($baseRunName, $extension) = explode( ".", $runname, -1 );
|
|
}
|
|
if ( !$baseRunName ) {
|
|
error_log("Error: unable to parse the 'runname' in particledata.inc, getJobRunIdFromRunname./n");
|
|
}
|
|
|
|
// step 2: match the $baseRunName with letters in the front and id with numbers at the end of the string
|
|
preg_match('/(\D+)(\d+)$/', $baseRunName, $matches);
|
|
$program = $matches[1];
|
|
$runId = $matches[2];
|
|
return $runId;
|
|
}
|
|
|
|
function getMaxRunNumber( $jobtype, $sessionId )
|
|
{
|
|
// get job names corresponding to the desired type for this session
|
|
$names = $this->getJobNamesFromJobType( $jobtype, $sessionId );
|
|
|
|
// find the name with the greatest incremental id ex. recon4 is greater than recon3
|
|
$maxRunNumber = 0;
|
|
foreach ( $names as $name ) {
|
|
$runNumber = $this->getJobRunIdFromRunname( $name['name'] );
|
|
$maxRunNumber = ( $runNumber > $maxRunNumber ) ? $runNumber : $maxRunNumber;
|
|
}
|
|
|
|
return $maxRunNumber;
|
|
}
|
|
|
|
function getDefaultJobName( $jobtype, $sessionId )
|
|
{
|
|
// check input values
|
|
if ( !$jobtype ) {
|
|
error_log("Error: 'jobtype' Parameter in particledata.inc, getDefaultJobName() is not set./n");
|
|
return False;
|
|
}
|
|
|
|
if ( !$sessionId ) {
|
|
error_log("Error: 'sessionId' Parameter in particledata.inc, getDefaultJobName() is not set./n");
|
|
return False;
|
|
}
|
|
|
|
$lastRunNumber = $this->getMaxRunNumber( $jobtype, $sessionId );
|
|
|
|
// increment the current run number and append it to the jobtype to create new jobname
|
|
$lastRunNumber++;
|
|
$jobName = $jobtype . $lastRunNumber;
|
|
|
|
return $jobName;
|
|
}
|
|
|
|
// Warning: do not use this function for counting the number of runs to create a new runname.
|
|
// try getMaxRunNumber instead.
|
|
function getReconIdsFromSession($sessionId, $showHidden=false, $package=false) {
|
|
$q = "SELECT DISTINCT(refrun.`DEF_id`) AS refid, refrun.*, path.path AS path "
|
|
." FROM `ApRefineRunData` AS refrun "
|
|
."LEFT JOIN ApRunsInStackData AS runs "
|
|
." ON refrun.`REF|ApStackData|stack` = runs.`REF|ApStackData|stack` "
|
|
."LEFT JOIN ApStackRunData AS stackrun "
|
|
." ON runs.`REF|ApStackRunData|stackRun` = stackrun.`DEF_id` "
|
|
."LEFT JOIN ApPathData AS path "
|
|
." ON refrun.`REF|ApPathData|path` = path.`DEF_id` "
|
|
."WHERE stackrun.`REF|leginondata|SessionData|session` = '$sessionId' ";
|
|
if (!$showHidden) $q.= " AND (refrun.`hidden` IS NULL OR refrun.`hidden` = 0) ";
|
|
if ($package) $q.= " AND (refrun.`package` = '$package') ";
|
|
$q.= " ORDER BY refrun.`DEF_id` DESC";
|
|
//echo $q."<br/><br/>\n";
|
|
$r = $this->mysql->getSQLResult($q);
|
|
//echo print_r($r)."<br/>\n";
|
|
return $r;
|
|
}
|
|
|
|
// Warning: do not use this function for counting the number of runs to create a new runname.
|
|
// try getMaxRunNumber instead.
|
|
function getMultiModelReconIdsFromSession($sessionId, $showHidden=false, $package=false) {
|
|
$q = "SELECT DISTINCT(refrun.`DEF_id`) AS refid, refrun.*, path.path AS path "
|
|
." FROM `ApRefineRunData` AS refrun "
|
|
."LEFT JOIN ApRunsInStackData AS runs "
|
|
." ON refrun.`REF|ApStackData|stack` = runs.`REF|ApStackData|stack` "
|
|
."LEFT JOIN ApStackRunData AS stackrun "
|
|
." ON runs.`REF|ApStackRunData|stackRun` = stackrun.`DEF_id` "
|
|
."LEFT JOIN ApPathData AS path "
|
|
." ON refrun.`REF|ApPathData|path` = path.`DEF_id` "
|
|
."WHERE stackrun.`REF|leginondata|SessionData|session` = '$sessionId' "
|
|
." AND refrun.`REF|ApMultiModelRefineRunData|multiModelRefineRun` IS NOT NULL ";
|
|
if (!$showHidden) $q.= " AND (refrun.`hidden` IS NULL OR refrun.`hidden` = 0) ";
|
|
if ($package) $q.= " AND (refrun.`package` = '$package') ";
|
|
$q.= " ORDER BY refrun.`DEF_id` DESC";
|
|
//echo $q."<br/><br/>\n";
|
|
$r = $this->mysql->getSQLResult($q);
|
|
//echo print_r($r)."<br/>\n";
|
|
return $r;
|
|
}
|
|
|
|
// Warning: do not use this function for counting the number of runs to create a new runname.
|
|
// try getMaxRunNumber instead.
|
|
function getSingleModelReconIdsFromSession($sessionId, $showHidden=false, $package=false) {
|
|
$q = "SELECT DISTINCT(refrun.`DEF_id`) AS refid, refrun.*, path.path AS path "
|
|
." FROM `ApRefineRunData` AS refrun "
|
|
."LEFT JOIN ApRunsInStackData AS runs "
|
|
." ON refrun.`REF|ApStackData|stack` = runs.`REF|ApStackData|stack` "
|
|
."LEFT JOIN ApStackRunData AS stackrun "
|
|
." ON runs.`REF|ApStackRunData|stackRun` = stackrun.`DEF_id` "
|
|
."LEFT JOIN ApPathData AS path "
|
|
." ON refrun.`REF|ApPathData|path` = path.`DEF_id` "
|
|
."WHERE stackrun.`REF|leginondata|SessionData|session` = '$sessionId' "
|
|
." AND refrun.`REF|ApMultiModelRefineRunData|multiModelRefineRun` IS NULL ";
|
|
if (!$showHidden) $q.= " AND (refrun.`hidden` IS NULL OR refrun.`hidden` = 0) ";
|
|
if ($package) $q.= " AND (refrun.`package` = '$package') ";
|
|
$q.= " ORDER BY refrun.`DEF_id` DESC";
|
|
//echo $q."<br/><br/>\n";
|
|
$r = $this->mysql->getSQLResult($q);
|
|
//if ($e=$this->mysql->getError()) {
|
|
//echo "error -> $e \n";
|
|
//}
|
|
//echo print_r($r)."<br/>\n";
|
|
return $r;
|
|
}
|
|
|
|
function getReconIterIdRelatedToStackid($stackId, $showHidden=False) {
|
|
// First get a three random particle ids from the stack id
|
|
$q = "SELECT `REF|ApParticleData|particle` AS partid "
|
|
." FROM ApStackParticleData AS stpart "
|
|
."WHERE `REF|ApStackData|stack` = '$stackId' "
|
|
." ORDER BY RAND() LIMIT 3 ";
|
|
//echo $q."<br/><br/>\n";
|
|
$r1 = $this->mysql->getSQLResult($q);
|
|
//echo print_r($r1)."<br/><br/>\n";
|
|
$partId1 = $r1[0]['partid'];
|
|
$partId2 = $r1[1]['partid'];
|
|
$partId3 = $r1[2]['partid'];
|
|
|
|
// Second get all recons using those particles
|
|
$q = "SELECT refrun.* "
|
|
." FROM ApRefineParticleData AS refpart "
|
|
."LEFT JOIN ApStackParticleData AS stpart "
|
|
." ON refpart.`REF|ApStackParticleData|particle` = stpart.`DEF_id` "
|
|
."LEFT JOIN ApRefineIterData AS refiter "
|
|
." ON refpart.`REF|ApRefineIterData|refineIter` = refiter.`DEF_id` "
|
|
."LEFT JOIN ApRefineRunData AS refrun "
|
|
." ON refiter.`REF|ApRefineRunData|refineRun` = refrun.`DEF_id` "
|
|
."WHERE "
|
|
." stpart.`REF|ApParticleData|particle` = '$partId1' "
|
|
."OR "
|
|
." stpart.`REF|ApParticleData|particle` = '$partId2' "
|
|
."OR "
|
|
." stpart.`REF|ApParticleData|particle` = '$partId3' "
|
|
." GROUP BY refrun.`DEF_id` "
|
|
." ORDER BY refrun.`DEF_id` DESC ";
|
|
//echo $q."<br/><br/>\n";
|
|
$r2 = $this->mysql->getSQLResult($q);
|
|
//echo print_r($r2)."<br/><br/>\n";
|
|
return $r2;
|
|
}
|
|
|
|
function getExemplarReconsFromSession($sessionId, $showHidden=False) {
|
|
$q = "SELECT refdata.`DEF_id` as refdataid, "
|
|
."refrun.`DEF_id` as refrunid, "
|
|
."refdata.*, refrun.*, stackrun.*, runs.*, p.*, params.* "
|
|
." FROM `ApRefineIterData` AS refdata "
|
|
."LEFT JOIN `ApRefineRunData` AS refrun "
|
|
. "ON refdata.`REF|ApRefineRunData|refineRun` = refrun.`DEF_id` "
|
|
."LEFT JOIN `ApEmanRefineIterData` AS params "
|
|
." ON (refdata.`REF|ApEmanRefineIterData|emanParams` = params.`DEF_id`) "
|
|
."LEFT JOIN ApRunsInStackData AS runs "
|
|
." ON refrun.`REF|ApStackData|stack` = runs.`REF|ApStackData|stack` "
|
|
."LEFT JOIN ApStackRunData AS stackrun "
|
|
." ON runs.`REF|ApStackRunData|stackRun` = stackrun.`DEF_id` "
|
|
."LEFT JOIN ApPathData as p "
|
|
." ON refrun.`REF|ApPathData|path` = p.`DEF_id` "
|
|
."WHERE refdata.exemplar = 1 "
|
|
."AND stackrun.`REF|leginondata|SessionData|session` = '$sessionId' ";
|
|
if (!$showHidden) $q.= " AND (refrun.`hidden` IS NULL OR refrun.`hidden` = 0) ";
|
|
$q.= " ORDER BY refrun.`DEF_id` DESC";
|
|
//echo $q."<br/><br/>\n";
|
|
$r = $this->mysql->getSQLResult($q);
|
|
//echo print_r($r)."<br/>\n";
|
|
return $r;
|
|
}
|
|
|
|
function getReconIds($stackId, $showHidden=False) {
|
|
$q = "SELECT * "
|
|
."FROM `ApRefineRunData` AS r ";
|
|
if (!$showHidden)
|
|
$q.= "LEFT JOIN ApStackData AS s "
|
|
." ON r.`REF|ApStackData|stack` = s.`DEF_id` ";
|
|
$q.= "WHERE r.`REF|ApStackData|stack` = '$stackId'";
|
|
if (!$showHidden)
|
|
$q.= " AND (s.`hidden` IS NULL OR s.`hidden` = 0) "
|
|
." AND (r.`hidden` IS NULL OR r.`hidden` = 0) ";
|
|
$q.= "ORDER BY r.`DEF_id` DESC";
|
|
$r = $this->mysql->getSQLResult($q);
|
|
return $r;
|
|
}
|
|
|
|
function getRefinementRunInfo($refineRunId) {
|
|
$q="select r.*, p.path "
|
|
."FROM `ApRefineRunData` AS r "
|
|
."LEFT JOIN ApPathData AS p ON "
|
|
."(r.`REF|ApPathData|path` = p.`DEF_id`) "
|
|
."WHERE r.`DEF_id` = '$refineRunId' ";
|
|
//echo $q."<br/><br/>\n";
|
|
list($r) = $this->mysql->getSQLResult($q);
|
|
//echo print_r($r)."<br/>\n";
|
|
return $r;
|
|
}
|
|
|
|
function getPostProcsFromRefId($refid, $getHidden=False) {
|
|
$q = "SELECT d.*, "
|
|
."p.path as path , a.path as amppath "
|
|
."FROM `Ap3dDensityData` AS d "
|
|
."LEFT JOIN `ApPathData` AS p ON "
|
|
."(d.`REF|ApPathData|path` = p.`DEF_id`) "
|
|
."LEFT JOIN `ApPathData` AS a ON "
|
|
."(d.`REF|ApPathData|ampPath` = a.`DEF_id`) "
|
|
."WHERE d.`REF|ApRefineIterData|refineIter` = $refid ";
|
|
if (!$getHidden) $q.= "AND (d.`hidden` IS NULL OR d.`hidden` = 0) ";
|
|
$r = $this->mysql->getSQLResult($q);
|
|
return $r;
|
|
}
|
|
|
|
function getDensityIdFromFile($rundir,$filename) {
|
|
$q = "SELECT d.`DEF_id` "
|
|
."FROM `Ap3dDensityData` AS d "
|
|
."LEFT JOIN ApPathData AS p ON "
|
|
."(d.`REF|ApPathData|path` = p.`DEF_id`) "
|
|
."WHERE d.`name` LIKE '$filename' "
|
|
."AND p.`path` LIKE '$rundir' ";
|
|
list($r) = $this->mysql->getSQLResult($q);
|
|
return $r['DEF_id'];
|
|
}
|
|
|
|
function get3dDensityInfo ($densityId) {
|
|
$q = "SELECT d.*,p.path "
|
|
."FROM `Ap3dDensityData` AS d "
|
|
."LEFT JOIN ApPathData AS p ON "
|
|
."(d.`REF|ApPathData|path` = p.`DEF_id`) "
|
|
."WHERE d.`DEF_id` = '$densityId' ";
|
|
list($r) = $this->mysql->getSQLResult($q);
|
|
return $r;
|
|
}
|
|
|
|
function getInitModelInfo ($modelId) {
|
|
$q = "SELECT d.*,p.path "
|
|
."FROM `ApInitialModelData` AS d "
|
|
."LEFT JOIN ApPathData AS p ON "
|
|
."(d.`REF|ApPathData|path` = p.`DEF_id`) "
|
|
."WHERE d.`DEF_id` = '$modelId' ";
|
|
list($r) = $this->mysql->getSQLResult($q);
|
|
return $r;
|
|
}
|
|
|
|
function getResolutionInfo ($resId) {
|
|
$q = "SELECT * "
|
|
."FROM `ApResolutionData` WHERE `DEF_id` = '$resId'";
|
|
list($r) = $this->mysql->getSQLResult($q);
|
|
return $r;
|
|
}
|
|
|
|
function getRMeasureInfo ($resId) {
|
|
$q = "SELECT * "
|
|
."FROM `ApRMeasureData` WHERE `DEF_id` = '$resId'";
|
|
list($r) = $this->mysql->getSQLResult($q);
|
|
return $r;
|
|
}
|
|
|
|
function getHighestResForRecon ($reconid) {
|
|
$q = "SELECT ref.iteration AS iter, res.half AS half, rmeas.rMeasure AS rmeas "
|
|
."FROM `ApRefineIterData` AS ref "
|
|
."LEFT JOIN `ApResolutionData` AS res "
|
|
." ON (ref.`REF|ApResolutionData|resolution` = res.`DEF_id`) "
|
|
."LEFT JOIN `ApRMeasureData` AS rmeas "
|
|
." ON (ref.`REF|ApRMeasureData|rMeasure` = rmeas.`DEF_id`) "
|
|
."WHERE ref.`REF|ApRefineRunData|refineRun` = '$reconid' "
|
|
//."ORDER by rmeas.rMeasure ";
|
|
."ORDER by res.half ";
|
|
$r = $this->mysql->getSQLResult($q);
|
|
return $r[0];
|
|
}
|
|
|
|
function getHighestRMeasureForRecon ($reconid) {
|
|
$q = "SELECT ref.iteration AS iter, res.half AS half, rmeas.rMeasure AS rmeas "
|
|
."FROM `ApRefineIterData` AS ref "
|
|
."LEFT JOIN `ApResolutionData` AS res "
|
|
." ON (ref.`REF|ApResolutionData|resolution` = res.`DEF_id`) "
|
|
."LEFT JOIN `ApRMeasureData` AS rmeas "
|
|
." ON (ref.`REF|ApRMeasureData|rMeasure` = rmeas.`DEF_id`) "
|
|
."WHERE ref.`REF|ApRefineRunData|refineRun` = '$reconid' "
|
|
."ORDER by rmeas.rMeasure ";
|
|
//."ORDER by res.half ";
|
|
$r = $this->mysql->getSQLResult($q);
|
|
return $r[0];
|
|
}
|
|
|
|
function getIterationInfo ($reconId,$iteration=0) {
|
|
$q = "SELECT * "
|
|
."FROM `ApRefineIterData` r "
|
|
."WHERE r.`REF|ApRefineRunData|refineRun` = '$reconId' "
|
|
."ORDER BY r.`iteration` ASC ";
|
|
$r = $this->mysql->getSQLResult($q);
|
|
if ($r[0]['REF|ApEmanRefineIterData|emanParams']) {
|
|
$q = "SELECT * "
|
|
."FROM `ApRefineIterData` r "
|
|
."LEFT JOIN `ApEmanRefineIterData` p "
|
|
."ON (r.`REF|ApEmanRefineIterData|emanParams` = p.`DEF_id`) "
|
|
."WHERE r.`REF|ApRefineRunData|refineRun` = '$reconId' "
|
|
."ORDER BY r.`iteration` ASC ";
|
|
} elseif ($r[0]['REF|ApXmippRefineIterData|xmippParams']) {
|
|
$q = "SELECT * "
|
|
."FROM `ApRefineIterData` r "
|
|
."LEFT JOIN `ApXmippRefineIterData` p "
|
|
."ON (r.`REF|ApXmippRefineIterData|xmippParams` = p.`DEF_id`) "
|
|
."WHERE r.`REF|ApRefineRunData|refineRun` = '$reconId' "
|
|
."ORDER BY r.`iteration` ASC ";
|
|
} elseif ($r[0]['REF|ApFrealignIterData|frealignParams']) {
|
|
$q = "SELECT * "
|
|
."FROM `ApRefineIterData` r "
|
|
."LEFT JOIN `ApFrealignIterData` p "
|
|
."ON (r.`REF|ApFrealignIterData|frealignParams` = p.`DEF_id`) "
|
|
."WHERE r.`REF|ApRefineRunData|refineRun` = '$reconId' "
|
|
."ORDER BY r.`iteration` ASC ";
|
|
}
|
|
//echo $q."<br/><br/>\n";
|
|
$r = $this->mysql->getSQLResult($q);
|
|
//echo print_r($r)."<br/><br/>\n";
|
|
if ($iteration >0) {
|
|
return $r[$iteration-1];
|
|
}
|
|
return $r;
|
|
}
|
|
|
|
function getRefinementData ($refineRunId, $iteration=False) {
|
|
$q = "SELECT * "
|
|
."FROM `ApRefineIterData` "
|
|
."WHERE `REF|ApRefineRunData|refineRun` = $refineRunId ";
|
|
if ($iteration) $q.="AND `iteration` = $iteration";
|
|
$r = $this->mysql->getSQLResult($q);
|
|
return $r;
|
|
}
|
|
|
|
function getParamsFromRefinementDataId ($refineIterId) {
|
|
$q = "SELECT * "
|
|
."FROM `ApRefineIterData` AS refineIter "
|
|
."LEFT JOIN `ApEmanRefineIterData` emanparams "
|
|
." ON (refineIter.`REF|ApEmanRefineIterData|emanParams` = emanparams.`DEF_id`) "
|
|
."WHERE refineIter.`DEF_id` = $refineIterId";
|
|
//echo $q."<br/><br/>\n";
|
|
$r = $this->mysql->getSQLResult($q);
|
|
//echo print_r($r)."<br/><br/>\n";
|
|
return $r[0];
|
|
}
|
|
|
|
function getStackFromRefineIter ($refineIterId) {
|
|
$q = "SELECT r.*, rr.*, s.*, path.path "
|
|
."FROM `ApRefineIterData` r "
|
|
."LEFT JOIN `ApRefineRunData` rr "
|
|
."ON (r.`REF|ApRefineRunData|refineRun` = rr.`DEF_id`) "
|
|
."LEFT JOIN `ApStackData` s "
|
|
."ON (rr.`REF|ApStackData|stack` = s.`DEF_id`) "
|
|
."LEFT JOIN `ApPathData` path "
|
|
."ON (s.`REF|ApPathData|path` = path.`DEF_id`) "
|
|
."WHERE r.`DEF_id` = $refineIterId";
|
|
$r = $this->mysql->getSQLResult($q);
|
|
return $r[0];
|
|
}
|
|
|
|
function getRefineParticleCounts($refineIterId) {
|
|
//check for cached values
|
|
$q = "SELECT * "
|
|
."FROM `ApRefineGoodBadParticleData` gb "
|
|
."WHERE gb.`REF|ApRefineIterData|refine` = '$refineIterId' ";
|
|
//echo $q."<br/><br/>\n";
|
|
$r = $this->mysql->getSQLResult($q);
|
|
//echo print_r($r)."<br/><br/>\n";
|
|
if (!$r)
|
|
return;
|
|
return $r[0];
|
|
}
|
|
|
|
function getSubsetParticlesInStack ($refineIterId, $subset, $refinetype='refine') {
|
|
$q = "SELECT particleNumber as p ";
|
|
$q .= "FROM `ApRefineParticleData` AS refinepart "
|
|
."LEFT JOIN `ApStackParticleData` AS stackpart "
|
|
." ON (refinepart.`REF|ApStackParticleData|particle` = stackpart.`DEF_id`) "
|
|
."WHERE refinepart.`REF|ApRefineIterData|refineIter` = '$refineIterId' ";
|
|
if ($refinetype == 'postRefine') {
|
|
if ($subset=='bad')
|
|
$q.="AND (refinepart.`postRefine_keep` = 0 OR refinepart.`postRefine_keep` IS NULL) ";
|
|
else
|
|
$q.="AND refinepart.`postRefine_keep` = 1 ";
|
|
} else {
|
|
if ($subset=='bad')
|
|
$q.="AND (refinepart.`refine_keep` = 0 OR refinepart.`refine_keep` IS NULL) ";
|
|
elseif (stripos($subset,';')!==false) {
|
|
$bits = explode(';',$subset);
|
|
$threeDref_num = $bits[0];
|
|
$twoDclass_num = $bits[1];
|
|
if (is_numeric($threeDref_num) && is_numeric($twoDclass_num) && $threeDref_num > 0 && $twoDclass_num >= 0)
|
|
$q.="AND (refinepart.`3Dref_num` = $threeDref_num AND refinepart.`2Dclass_num` = $twoDclass_num) ";
|
|
} else
|
|
$q.="AND refinepart.`refine_keep` = 1 ";
|
|
}
|
|
$q.= "ORDER BY stackpart.`particleNumber` ASC ";
|
|
//echo $q."<br/><br/>\n";
|
|
$r = $this->mysql->getSQLResult($q);
|
|
//echo print_r($r)."<br/><br/>\n";
|
|
return $r;
|
|
}
|
|
|
|
function getNumParticlesFromRefineIter($refineIterId)
|
|
{
|
|
$q = "SELECT COUNT(*) as num_parts ";
|
|
$q .= "FROM `ApRefineParticleData` AS refinepart "
|
|
."WHERE refinepart.`REF|ApRefineIterData|refineIter` = '$refineIterId' ";
|
|
//echo $q."<br/><br/>\n";
|
|
$r = $this->mysql->getSQLResult($q);
|
|
//echo print_r($r)."<br/><br/>\n";
|
|
return $r;
|
|
}
|
|
|
|
function getPreparedFrealignJobs ($jobid=False, $path=False, $showHidden=true) {
|
|
$q = "SELECT fre.*, path.path, job.`DEF_id` AS jobid "
|
|
. " FROM `ApFrealignPrepareData` AS fre "
|
|
. " LEFT JOIN ApPathData AS path ON ( fre.`REF|ApPathData|path` = path.`DEF_id` ) "
|
|
. " LEFT JOIN ApAppionJobData AS job ON ( fre.`REF|ApAppionJobData|job` = job.`DEF_id` ) ";
|
|
if ($jobid) {
|
|
$q .= " WHERE fre.`DEF_id` = '$jobid' ";
|
|
} elseif ($path) {
|
|
$q .= " WHERE path.`path` = '$path' ";
|
|
} elseif (!$showHidden) {
|
|
$q .= " WHERE fre.`hidden` != '1' AND job.`status` = 'D' ";
|
|
}
|
|
$q .= " ORDER BY fre.`DEF_id` DESC ";
|
|
//echo $q."<br/><br/>\n";
|
|
$r = $this->mysql->getSQLResult($q);
|
|
//echo print_r($r)."<br/><br/>\n";
|
|
return $r;
|
|
}
|
|
|
|
function getPreparedRefineJobs ($jobid=False, $path=False, $showHidden=true, $name=False) {
|
|
$q = "SELECT ref.*, path.path, job.`DEF_id` AS jobid "
|
|
. " FROM `ApPrepRefineData` AS ref "
|
|
. " LEFT JOIN ApPathData AS path ON ( ref.`REF|ApPathData|path` = path.`DEF_id` ) "
|
|
. " LEFT JOIN ApAppionJobData AS job ON ( ref.`REF|ApAppionJobData|job` = job.`DEF_id` ) ";
|
|
if ($jobid) {
|
|
$q .= " WHERE job.`DEF_id` = '$jobid' ";
|
|
} elseif ($path) {
|
|
$q .= " WHERE ref.`REF|ApPathData|path` = '$path' ";
|
|
} elseif ($name) {
|
|
$q .= " WHERE ref.`name` = '$name' ";
|
|
} elseif (!$showHidden) {
|
|
$q .= " WHERE ref.`hidden` != '1' AND job.`status` = 'D' ";
|
|
}
|
|
$q .= " ORDER BY ref.`DEF_id` DESC ";
|
|
//echo $q."<br/><br/>\n";
|
|
$r = $this->mysql->getSQLResult($q);
|
|
//echo print_r($r)."<br/><br/>\n";
|
|
return $r;
|
|
}
|
|
|
|
function getPreparedRefineStackData ( $refineid ) {
|
|
$q = "SELECT stack.* "
|
|
. " FROM ApRefineStackData AS stack "
|
|
. " WHERE stack.`REF|ApPrepRefineData|preprefine` = $refineid ";
|
|
//echo $q."<br/><br/>\n";
|
|
$r = $this->mysql->getSQLResult($q);
|
|
//echo print_r($r)."<br/><br/>\n";
|
|
return $r;
|
|
}
|
|
|
|
function getUploadFrealignJobs ($jobid=False, $path=False, $showHidden=true) {
|
|
$q = "SELECT fre.*, path.path "
|
|
. " FROM `ApFrealignPrepareData` AS fre "
|
|
. " LEFT JOIN ApPathData AS path ON ( fre.`REF|ApPathData|path` = path.`DEF_id` ) "
|
|
. " LEFT JOIN ApAppionJobData AS job ON ( fre.`REF|ApAppionJobData|job` = job.`DEF_id` ) ";
|
|
if ($jobid) {
|
|
$q .= " WHERE fre.`DEF_id` = '$jobid' ";
|
|
} elseif ($path) {
|
|
$q .= " WHERE path.`path` = '$path' ";
|
|
} elseif (!$showHidden) {
|
|
$q .= " WHERE fre.`hidden` != '1' ";
|
|
}
|
|
$q .= " ORDER BY fre.`DEF_id` DESC ";
|
|
//echo $q."<br/><br/>\n";
|
|
$r = $this->mysql->getSQLResult($q);
|
|
//echo print_r($r)."<br/><br/>\n";
|
|
return $r;
|
|
}
|
|
|
|
function getClusterJobByTypeAndPath ($type, $path) {
|
|
$q = "SELECT job.* "
|
|
. " FROM `ApAppionJobData` AS job "
|
|
. " LEFT JOIN ApPathData AS path "
|
|
. " ON ( job.`REF|ApPathData|path` = path.`DEF_id` ) "
|
|
. " WHERE "
|
|
. " path.`path` = '$path' "
|
|
. " AND "
|
|
. " job.`jobtype` = '$type' "
|
|
. " ORDER BY job.`DEF_id` DESC ";
|
|
//echo $q."<br/><br/>\n";
|
|
$r = $this->mysql->getSQLResult($q);
|
|
//echo print_r($r)."<br/><br/>\n";
|
|
return $r;
|
|
}
|
|
|
|
function getRawStackFromCluster ($clusterStackId) {
|
|
$q = "SELECT asd.*, path.path "
|
|
. " FROM `ApClusteringParticleData` acpd "
|
|
. " LEFT JOIN ApAlignParticleData aapd ON ( acpd.`REF|ApAlignParticleData|alignparticle` = aapd.`DEF_id` ) "
|
|
. " LEFT JOIN ApStackParticleData aspd ON ( aapd.`REF|ApStackParticleData|stackpart` = aspd.`DEF_id`) "
|
|
. " LEFT JOIN ApStackData asd ON ( aspd.`REF|ApStackData|stack` = asd.`DEF_id`) "
|
|
. " LEFT JOIN `ApPathData` path ON ( asd.`REF|ApPathData|path` = path.`DEF_id`) "
|
|
. " WHERE acpd.`REF|ApClusteringStackData|clusterstack` = '$clusterStackId' ";
|
|
$r = $this->mysql->getSQLResult($q);
|
|
return $r[0];
|
|
}
|
|
|
|
function getRawStackFromAlign ($alignStackId) {
|
|
$q = "SELECT asd.*, path.path "
|
|
. " FROM ApAlignParticleData aapd "
|
|
. " LEFT JOIN ApStackParticleData aspd ON ( aapd.`REF|ApStackParticleData|stackpart` = aspd.`DEF_id`) "
|
|
. " LEFT JOIN ApStackData asd ON ( aspd.`REF|ApStackData|stack` = asd.`DEF_id`) "
|
|
. " LEFT JOIN `ApPathData` path ON ( asd.`REF|ApPathData|path` = path.`DEF_id`) "
|
|
. " WHERE aapd.`REF|ApAlignStackData|alignstack` = '$alignStackId' ";
|
|
$r = $this->mysql->getSQLResult($q);
|
|
return $r[0];
|
|
}
|
|
|
|
function getAlignedStackFromCluster ($clusterStackId) {
|
|
$q = "SELECT aasd.*, path.path "
|
|
. " FROM `ApClusteringParticleData` acpd "
|
|
. " LEFT JOIN ApAlignParticleData aapd ON ( acpd.`REF|ApAlignParticleData|alignparticle` = aapd.`DEF_id` ) "
|
|
. " LEFT JOIN ApAlignStackData aasd ON ( aapd.`REF|ApAlignStackData|alignstack` = aasd.`DEF_id`) "
|
|
. " LEFT JOIN `ApPathData` path ON ( aasd.`REF|ApPathData|path` = path.`DEF_id`) "
|
|
. " WHERE acpd.`REF|ApClusteringStackData|clusterstack` = '$clusterStackId' ";
|
|
$r = $this->mysql->getSQLResult($q);
|
|
return $r[0];
|
|
}
|
|
|
|
function getAlignedStackFromAlign ($alignStackId) {
|
|
$q = "SELECT aasd.*, path.path "
|
|
. " FROM ApAlignParticleData aapd "
|
|
. " LEFT JOIN ApAlignStackData aasd ON ( aapd.`REF|ApAlignStackData|alignstack` = aasd.`DEF_id`) "
|
|
. " LEFT JOIN `ApPathData` path ON ( aasd.`REF|ApPathData|path` = path.`DEF_id`) "
|
|
. " WHERE aapd.`REF|ApAlignStackData|alignstack` = '$alignStackId' ";
|
|
$r = $this->mysql->getSQLResult($q);
|
|
return $r[0];
|
|
}
|
|
|
|
function getSubsetParticlesFromCluster ($clusterStackId, $refnums, $count=False) {
|
|
$q = "SELECT particleNumber as p ";
|
|
if ($count) $q = "SELECT count(particleNumber) as p ";
|
|
$q .= "FROM `ApClusteringParticleData` acpd "
|
|
."LEFT JOIN ApAlignParticleData aapd ON ( acpd.`REF|ApAlignParticleData|alignparticle` = aapd.`DEF_id` )"
|
|
."LEFT JOIN ApStackParticleData aspd ON ( aapd.`REF|ApStackParticleData|stackpart` = aspd.`DEF_id`)"
|
|
."LEFT JOIN ApStackData asd ON ( aspd.`REF|ApStackData|stack` = asd.`DEF_id`)"
|
|
."WHERE acpd.`REF|ApClusteringStackData|clusterstack` = '$clusterStackId' AND (";
|
|
|
|
foreach ($refnums as $refnum) {
|
|
$refnum = strval(intval($refnum)+1);
|
|
$q .= " acpd.`refnum` = '$refnum' OR ";
|
|
}
|
|
|
|
$q = substr($q, 0, -3);
|
|
$q .= ")";
|
|
|
|
//if (!$count) $q.= "ORDER BY aspd.`DEF_id` ASC ";
|
|
$r = $this->mysql->getSQLResult($q);
|
|
if ($count) return $r[0]['p'];
|
|
return $r;
|
|
}
|
|
|
|
function getSubsetParticlesFromAlign ($alignStackId, $refnums, $count=False) {
|
|
$q = "SELECT particleNumber as p ";
|
|
if ($count) $q = "SELECT count(particleNumber) as p ";
|
|
$q .= "FROM `ApAlignParticleData` aapd "
|
|
."LEFT JOIN ApAlignReferenceData aard ON ( aapd.`REF|ApAlignReferenceData|ref` = aard.`DEF_id`)"
|
|
."LEFT JOIN ApStackParticleData aspd ON ( aapd.`REF|ApStackParticleData|stackpart` = aspd.`DEF_id`)"
|
|
."LEFT JOIN ApStackData asd ON ( aspd.`REF|ApStackData|stack` = asd.`DEF_id`)"
|
|
."WHERE aapd.`REF|ApAlignStackData|alignstack` = '$alignStackId' AND (";
|
|
|
|
foreach ($refnums as $refnum) {
|
|
$refnum = strval(intval($refnum)+1);
|
|
$q .= " aard.`refnum` = '$refnum' OR ";
|
|
}
|
|
|
|
$q = substr($q, 0, -3);
|
|
$q .= ")";
|
|
|
|
//if (!$count) $q.= "ORDER BY aspd.`DEF_id` ASC ";
|
|
$r = $this->mysql->getSQLResult($q);
|
|
if ($count) return $r[0]['p'];
|
|
return $r;
|
|
}
|
|
|
|
function listAllStackParticles ($stackId) {
|
|
$q="SELECT sp.`particleNumber`, db.`MRC|image`, "
|
|
."p.`xcoord` , p.`ycoord` "
|
|
."FROM `ApStackParticleData` sp "
|
|
."LEFT JOIN ApParticleData p ON "
|
|
."( sp.`REF|ApParticleData|particle` = p.`DEF_id` ) "
|
|
."LEFT JOIN ".DB_LEGINON.".AcquisitionImageData db ON "
|
|
."( p.`REF|leginondata|AcquisitionImageData|image` = db.`DEF_id` ) "
|
|
."WHERE sp.`REF|ApStackData|stack`=$stackId";
|
|
$r = $this->mysql->getSQLResult($q);
|
|
return $r;
|
|
}
|
|
|
|
function getAverageMedianJump ($refineRunId) {
|
|
$q = "SELECT "
|
|
."COUNT(e.`median`) AS count, "
|
|
."AVG(e.`median`) AS average, "
|
|
."STDDEV(e.`median`) AS stdev "
|
|
."FROM ApEulerJumpData AS e "
|
|
."WHERE "
|
|
." e.`REF|ApRefineRunData|refineRun` = '$refineRunId' "
|
|
."GROUP BY e.`REF|ApRefineRunData|refineRun` ";
|
|
//echo $q."<br/><br/>\n";
|
|
$r = $this->mysql->getSQLResult($q);
|
|
//echo print_r($r)."<br/><br/>\n";
|
|
return $r[0];
|
|
}
|
|
|
|
function getEulerJumpsMM ($multiModelRefineRunId) {
|
|
$q="SELECT "
|
|
." e.`DEF_id`, "
|
|
." e.`median` "
|
|
."FROM ApEulerJumpData AS e "
|
|
."WHERE "
|
|
." e.`REF|ApMultiModelRefineRunData|multiModelRefineRun` = '$multiModelRefineRunId' ";
|
|
//."ORDER BY e.`median` ASC "
|
|
//."LIMIT 20 ";
|
|
$r=$this->mysql->getSQLResult($q);
|
|
return $r;
|
|
}
|
|
|
|
function getAverageMedianJumpMM ($multiModelRefineRunId) {
|
|
$q = "SELECT "
|
|
."COUNT(e.`median`) AS count, "
|
|
."AVG(e.`median`) AS average, "
|
|
."STDDEV(e.`median`) AS stdev "
|
|
."FROM ApEulerJumpData AS e "
|
|
."WHERE "
|
|
." e.`REF|ApMultiModelRefineRunData|multiModelRefineRun` = '$multiModelRefineRunId' "
|
|
."GROUP BY e.`REF|ApMultiModelRefineRunData|multiModelRefineRun` ";
|
|
//echo $q."<br/><br/>\n";
|
|
$r = $this->mysql->getSQLResult($q);
|
|
//echo print_r($r)."<br/><br/>\n";
|
|
return $r[0];
|
|
}
|
|
|
|
function getEulerJumps ($refineRunId) {
|
|
$q="SELECT "
|
|
." e.`DEF_id`, "
|
|
." e.`median` "
|
|
."FROM ApEulerJumpData AS e "
|
|
."WHERE "
|
|
." e.`REF|ApRefineRunData|refineRun` = '$refineRunId' ";
|
|
//."ORDER BY e.`median` ASC "
|
|
//."LIMIT 20 ";
|
|
$r=$this->mysql->getSQLResult($q);
|
|
return $r;
|
|
}
|
|
|
|
// no more ApEulerData tables
|
|
//function getParticleEuler ($refinementDataId) {
|
|
// $q = "SELECT distinct(`REF|ApEulerData|eulers`) as eulers "
|
|
// ."FROM `ApRefineParticleData` "
|
|
// ."WHERE `REF|ApRefineIterData|refineIter` = '$refinementDataId' ";
|
|
// $r = $this->mysql->getSQLResult($q);
|
|
// return $r;
|
|
//}
|
|
|
|
//function getNumInClass ($refinementDataId,$eulerId) {
|
|
// $q = "SELECT count(DEF_id) as num "
|
|
// ."FROM `ApRefineParticleData` "
|
|
// ."WHERE `REF|ApRefineIterData|refineIter` = '$refinementDataId' "
|
|
// ."AND `REF|ApEulerData|eulers` = $eulerId";
|
|
// list($r) = $this->mysql->getSQLResult($q);
|
|
// return $r['num'];
|
|
//}
|
|
|
|
function getEulerAngles ($eulerId) {
|
|
$q = "SELECT * "
|
|
."FROM `ApEulerData` "
|
|
."WHERE `DEF_id` = $eulerId";
|
|
$r = $this->mysql->getSQLResult($q);
|
|
return $r[0];
|
|
}
|
|
|
|
function getCommonParticles ($refine1, $refine2) {
|
|
# compare 2 iterations, get all the particles that were used in both
|
|
# reconstructions (ignore those that were thrown out) and return the eulers"
|
|
$q = "SELECT cls1.`REF|ApStackParticleData|particle` as prtl, "
|
|
."spd.particleNumber, "
|
|
."cls1.euler1 as euler1_1, "
|
|
."cls1.euler2 as euler1_2, "
|
|
."cls1.euler3 as euler1_3, "
|
|
."cls2.euler1 as euler2_1, "
|
|
."cls2.euler2 as euler2_2, "
|
|
."cls2.euler3 as euler2_3, "
|
|
."cls1.`shiftx` as shiftx1, "
|
|
."cls2.`shiftx` as shiftx2, "
|
|
."cls1.`shifty` as shifty1, "
|
|
."cls2.`shifty` as shifty2, "
|
|
."cls1.`euler3` as rot1, "
|
|
."cls2.`euler3` as rot2, "
|
|
."cls1.`quality_factor` as qf1, "
|
|
."cls2.`quality_factor` as qf2 "
|
|
."FROM (`ApRefineParticleData` as cls1) "
|
|
."LEFT JOIN ( "
|
|
." `ApRefineParticleData` as cls2, "
|
|
." `ApStackParticleData` as spd) "
|
|
//." `ApEulerData` euler1, `ApEulerData` euler2) "
|
|
."ON ( "
|
|
."cls1.`REF|ApStackParticleData|particle`=cls2.`REF|ApStackParticleData|particle` "
|
|
."AND spd.DEF_id=cls1.`REF|ApStackParticleData|particle` "
|
|
."AND cls1.`refine_keep`=1 AND cls2.`refine_keep`=1 "
|
|
//."AND euler1.DEF_id=cls1.`REF|ApEulerData|eulers` "
|
|
//."AND euler2.DEF_id=cls2.`REF|ApEulerData|eulers` "
|
|
.") "
|
|
."WHERE (cls1.`REF|ApRefineIterData|refineIter`=$refine1 "
|
|
."AND cls2.`REF|ApRefineIterData|refineIter`=$refine2 "
|
|
.") "
|
|
."ORDER by prtl";
|
|
$r = $this->mysql->getSQLResult($q);
|
|
return $r;
|
|
}
|
|
|
|
function getParticlesFromRefinementId($refine1) {
|
|
# compare 2 iterations, get all the particles that were used in both
|
|
# reconstructions (ignore those that were thrown out) and return the eulers"
|
|
$q = "SELECT cls1.`REF|ApStackParticleData|particle` as prtl, "
|
|
."spd.particleNumber, "
|
|
."cls1.euler1 as euler1_1, "
|
|
."cls1.euler2 as euler1_2, "
|
|
."cls1.euler3 as euler1_3, "
|
|
."cls1.`shiftx` as shiftx1, "
|
|
."cls1.`shifty` as shifty1, "
|
|
."cls1.`inplane_rotation` as rot1, "
|
|
."cls1.`quality_factor` as qf1 "
|
|
."FROM (`ApRefineParticleData` as cls1) "
|
|
."LEFT JOIN ( "
|
|
." `ApStackParticleData` as spd) "
|
|
//." `ApEulerData` euler1) "
|
|
."ON ( "
|
|
."spd.DEF_id=cls1.`REF|ApStackParticleData|particle` "
|
|
."AND cls1.`refine_keep`=1 "
|
|
//."AND euler1.DEF_id=cls1.`REF|ApEulerData|eulers` "
|
|
.") "
|
|
."WHERE ( "
|
|
." cls1.`REF|ApRefineIterData|refineIter`=$refine1 "
|
|
.") "
|
|
."ORDER by prtl";
|
|
$r = $this->mysql->getSQLResult($q);
|
|
return $r;
|
|
}
|
|
|
|
function getStackParticleNum ($particleId) {
|
|
$q = "SELECT particleNumber "
|
|
."FROM `ApStackParticleData` "
|
|
."WHERE `DEF_id` = $particleId";
|
|
list($r) = $this->mysql->getSQLResult($q);
|
|
return $r['particleNumber'];
|
|
}
|
|
|
|
function getMiscInfoFromReconId ($reconid) {
|
|
$q = "SELECT m.*, p.path "
|
|
."FROM `ApMiscData` AS m "
|
|
."LEFT JOIN ApPathData AS p ON "
|
|
."(m.`REF|ApPathData|path` = p.`DEF_id`) "
|
|
."WHERE m.`REF|ApRefineRunData|refineRun` = $reconid";
|
|
$r = $this->mysql->getSQLResult($q);
|
|
return $r;
|
|
}
|
|
|
|
function getEulerStats($reconId, $iterId1, $iterId2) {
|
|
$q = "SELECT difference, eulers, mean from `ApProcEulerData` "
|
|
." WHERE `reconId`=$reconId AND `iter1`=$iterId1 AND `iter2`=$iterId2";
|
|
$r=$this->mysql->getSQLResult($q);
|
|
|
|
return $r;
|
|
}
|
|
|
|
function getReconInfoFromRefinementId($refineid) {
|
|
$q="SELECT *"
|
|
."FROM "
|
|
."`ApRefineIterData` AS `ApRefineIterData` "
|
|
."LEFT JOIN `ApRefineRunData` AS `ApRefineRunData` "
|
|
."ON (`ApRefineRunData`.`DEF_id`=`ApRefineIterData`.`REF|ApRefineRunData|refineRun`) "
|
|
."LEFT JOIN `ApPathData` AS `ApPathData` "
|
|
."ON (`ApPathData`.`DEF_id`=`ApRefineRunData`.`REF|ApPathData|path`) "
|
|
."WHERE `ApRefineIterData`.`DEF_id`=$refineid ";
|
|
$r=$this->mysql->getSQLResult($q);
|
|
return $r[0];
|
|
}
|
|
|
|
function insertEulerStats($stats) {
|
|
$mean = $stats->myMean;
|
|
$errors = $stats->myData;
|
|
$reconId=$stats->myReconId;
|
|
$iterId1=$stats->myIterId1;
|
|
$iterId2=$stats->myIterId2;
|
|
$eulers=$stats->eulers1;
|
|
$min = $stats->myMin;
|
|
$max = $stats->myMax;
|
|
$stdev = $stats->myStandardDeviation;
|
|
|
|
$euler = array_map('simplify',$eulers);
|
|
|
|
$table="ApProcEulerData";
|
|
# $this->mysql->SQLInsert($table, $data);
|
|
$q = "SELECT DEF_id from `ApProcEulerData` "
|
|
." WHERE `reconId`=$reconId AND `iter1`=$iterId1 AND `iter2`=$iterId2";
|
|
//--- print_r($r=$this->mysql->SQLQuery($q));
|
|
//--- if (!$r=$this->mysql->getSQLResult($q)) {
|
|
$q = "INSERT INTO `ApProcEulerData` "
|
|
."(`reconId`, `iter1`, `iter2`, `difference`, `eulers`, `mean`, `min`, `max`, `stdev`) "
|
|
." VALUES "
|
|
."($reconId, $iterId1, $iterId2, "
|
|
."'".implode(",",$errors)."',"
|
|
."'".implode(",",$euler)."',"
|
|
."$mean, $min, $max, $stdev)";
|
|
$r=$this->mysql->SQLQuery($q);
|
|
if ($e=$this->mysql->getError()) {
|
|
echo "error -> $e \n";
|
|
exit;
|
|
}
|
|
//--- }
|
|
return $r;
|
|
|
|
}
|
|
|
|
function getAlignParticleNumber($alignId) {
|
|
$q="SELECT "
|
|
." ref.`refnum` AS classNumber, "
|
|
." count(part.`DEF_id`) as number, "
|
|
." ROUND(ref.`ssnr_resolution`,3) AS resolution "
|
|
."FROM ApAlignParticleData AS part "
|
|
."LEFT JOIN ApAlignReferenceData AS ref "
|
|
." ON (part.`REF|ApAlignReferenceData|ref` = ref.`DEF_id`) "
|
|
."WHERE part.`REF|ApAlignStackData|alignstack` = '$alignId' "
|
|
."GROUP BY ref.`refnum` "
|
|
."ORDER BY ref.`refnum` ";
|
|
//echo $q."<br/><br/>\n";
|
|
$r=$this->mysql->getSQLResult($q);
|
|
//echo print_r($r)."<br/><br/>\n";
|
|
return $r;
|
|
}
|
|
|
|
function getAlignParticleData ($alignid) {
|
|
$q="SELECT "
|
|
." a.`partnum`, "
|
|
." a.`spread`, "
|
|
." a.`correlation`, "
|
|
." a.`score` "
|
|
."FROM ApAlignParticleData AS a "
|
|
."WHERE "
|
|
." a.`REF|ApAlignStackData|alignstack` = '$alignid' ";
|
|
//."ORDER BY e.`median` "
|
|
//."LIMIT 100 ";
|
|
//echo $q."<br/><br/>\n";
|
|
$r=$this->mysql->getSQLResult($q);
|
|
//echo print_r($r)."<br/><br/>\n";
|
|
return $r;
|
|
}
|
|
|
|
function getClusteringParticleNumber($clusterId) {
|
|
$q="SELECT part.`refnum` AS classNumber, "
|
|
." COUNT(part.`DEF_id`) AS number, "
|
|
." ROUND(ref.`ssnr_resolution`,3) AS resolution "
|
|
."FROM ApClusteringParticleData AS part "
|
|
."LEFT JOIN ApClusteringReferenceData AS ref "
|
|
." ON (part.`REF|ApClusteringReferenceData|clusterreference` = ref.`DEF_id`) "
|
|
."WHERE part.`REF|ApClusteringStackData|clusterstack` = '$clusterId' "
|
|
."GROUP BY part.`refnum` "
|
|
."ORDER BY part.`refnum` ";
|
|
//echo $q."<br/><br/>\n";
|
|
$r=$this->mysql->getSQLResult($q);
|
|
//echo print_r($r)."<br/><br/>\n";
|
|
return $r;
|
|
}
|
|
|
|
function getNumberOfRctRuns($sessionId, $showHidden=False) {
|
|
$q="SELECT count(rctrun.`DEF_id`) AS number "
|
|
."FROM ApRunsInStackData as runsin "
|
|
."LEFT JOIN ApStackRunData AS strun "
|
|
." ON (runsin.`REF|ApStackRunData|stackRun` = strun.`DEF_id`) "
|
|
."LEFT JOIN ApRctRunData AS rctrun "
|
|
." ON rctrun.`REF|ApStackData|tiltstack` = runsin.`REF|ApStackData|stack` "
|
|
."WHERE strun.`REF|leginondata|SessionData|session` = '$sessionId' ";
|
|
if (!$showHidden )
|
|
$q .= " AND ( rctrun.`hidden` = 0 OR rctrun.`hidden` IS NULL ) ";
|
|
//echo $q."<br/><br/>\n";
|
|
$r=$this->mysql->getSQLResult($q);
|
|
//echo $r[0]['number']."<br/><br/>\n";
|
|
return $r[0]['number'];
|
|
}
|
|
|
|
function getNumberOfOtrRuns($sessionId, $showHidden=False) {
|
|
$q="SELECT count(otrrun.`DEF_id`) AS number "
|
|
."FROM ApRunsInStackData as runsin "
|
|
."LEFT JOIN ApStackRunData AS strun "
|
|
." ON (runsin.`REF|ApStackRunData|stackRun` = strun.`DEF_id`) "
|
|
."LEFT JOIN ApOtrRunData AS otrrun "
|
|
." ON otrrun.`REF|ApStackData|tiltstack` = runsin.`REF|ApStackData|stack` "
|
|
."WHERE strun.`REF|leginondata|SessionData|session` = '$sessionId' ";
|
|
if (!$showHidden )
|
|
$q .= " AND ( otrrun.`hidden` = 0 OR otrrun.`hidden` IS NULL ) ";
|
|
//echo $q."<br/><br/>\n";
|
|
$r=$this->mysql->getSQLResult($q);
|
|
//echo $r[0]['number']."<br/><br/>\n";
|
|
return $r[0]['number'];
|
|
}
|
|
|
|
function getRctRunsFromSession($sessionId, $showHidden=False) {
|
|
$q="SELECT rctrun.*, "
|
|
." path.`path` AS path, "
|
|
." rmeas.`half` AS rmeas, "
|
|
." fsc.`half` AS fsc, "
|
|
." fsc.`fscfile` AS fscfile, "
|
|
." stparam.`boxSize` AS boxsize "
|
|
."FROM ApRunsInStackData as runsin "
|
|
."LEFT JOIN ApStackRunData AS strun "
|
|
." ON (runsin.`REF|ApStackRunData|stackRun` = strun.`DEF_id`) "
|
|
."LEFT JOIN ApRctRunData AS rctrun "
|
|
." ON rctrun.`REF|ApStackData|tiltstack` = runsin.`REF|ApStackData|stack` "
|
|
."LEFT JOIN ApStackParamsData AS stparam "
|
|
." ON strun.`REF|ApStackParamsData|stackParams` = stparam.`DEF_id` "
|
|
."LEFT JOIN ApPathData AS path "
|
|
." ON rctrun.`REF|ApPathData|path` = path.`DEF_id` "
|
|
."LEFT JOIN ApResolutionData AS rmeas "
|
|
." ON rctrun.`REF|ApResolutionData|rmeasure_resolution` = rmeas.`DEF_id` "
|
|
."LEFT JOIN ApResolutionData AS fsc "
|
|
." ON rctrun.`REF|ApResolutionData|fsc_resolution` = fsc.`DEF_id` "
|
|
."WHERE "
|
|
." rctrun.`DEF_id` IS NOT NULL "
|
|
."AND "
|
|
." strun.`REF|leginondata|SessionData|session` = '$sessionId' ";
|
|
if (!$showHidden )
|
|
$q .= " AND ( rctrun.`hidden` = 0 OR rctrun.`hidden` IS NULL ) ";
|
|
$q .= "ORDER BY rctrun.`DEF_id` DESC ";
|
|
$r=$this->mysql->getSQLResult($q);
|
|
return $r;
|
|
}
|
|
|
|
function getRctRunDataFromId($rctId) {
|
|
$q="SELECT rctrun.*, "
|
|
." path.`path` AS path, "
|
|
." rmeas.`half` AS rmeas, "
|
|
." fsc.`half` AS fsc, "
|
|
." fsc.`fscfile` AS fscfile, "
|
|
." stparam.`boxSize` AS boxsize "
|
|
."FROM ApRctRunData as rctrun "
|
|
."LEFT JOIN ApRunsInStackData AS runsin "
|
|
." ON rctrun.`REF|ApStackData|tiltstack` = runsin.`REF|ApStackData|stack` "
|
|
."LEFT JOIN ApStackRunData AS strun "
|
|
." ON (runsin.`REF|ApStackRunData|stackRun` = strun.`DEF_id`) "
|
|
."LEFT JOIN ApStackParamsData AS stparam "
|
|
." ON strun.`REF|ApStackParamsData|stackParams` = stparam.`DEF_id` "
|
|
."LEFT JOIN ApPathData AS path "
|
|
." ON rctrun.`REF|ApPathData|path` = path.`DEF_id` "
|
|
."LEFT JOIN ApResolutionData AS rmeas "
|
|
." ON rctrun.`REF|ApResolutionData|rmeasure_resolution` = rmeas.`DEF_id` "
|
|
."LEFT JOIN ApResolutionData AS fsc "
|
|
." ON rctrun.`REF|ApResolutionData|fsc_resolution` = fsc.`DEF_id` "
|
|
."WHERE "
|
|
." rctrun.`DEF_id` = '$rctId' ";
|
|
$r=$this->mysql->getSQLResult($q);
|
|
return $r[0];
|
|
}
|
|
|
|
function getOtrRunsFromSession($sessionId, $showHidden=False) {
|
|
$q="SELECT otrrun.*, "
|
|
." path.`path` AS path, "
|
|
." rmeas.`half` AS rmeas, "
|
|
." fsc.`half` AS fsc, "
|
|
." fsc.`fscfile` AS fscfile, "
|
|
." stparam.`boxSize` AS boxsize "
|
|
."FROM ApRunsInStackData as runsin "
|
|
."LEFT JOIN ApStackRunData AS strun "
|
|
." ON (runsin.`REF|ApStackRunData|stackRun` = strun.`DEF_id`) "
|
|
."LEFT JOIN ApOtrRunData AS otrrun "
|
|
." ON otrrun.`REF|ApStackData|tiltstack` = runsin.`REF|ApStackData|stack` "
|
|
."LEFT JOIN ApStackParamsData AS stparam "
|
|
." ON strun.`REF|ApStackParamsData|stackParams` = stparam.`DEF_id` "
|
|
."LEFT JOIN ApPathData AS path "
|
|
." ON otrrun.`REF|ApPathData|path` = path.`DEF_id` "
|
|
."LEFT JOIN ApResolutionData AS rmeas "
|
|
." ON otrrun.`REF|ApResolutionData|rmeasure_resolution` = rmeas.`DEF_id` "
|
|
."LEFT JOIN ApResolutionData AS fsc "
|
|
." ON otrrun.`REF|ApResolutionData|fsc_resolution` = fsc.`DEF_id` "
|
|
."WHERE "
|
|
." otrrun.`DEF_id` IS NOT NULL "
|
|
."AND "
|
|
." strun.`REF|leginondata|SessionData|session` = '$sessionId' ";
|
|
if (!$showHidden )
|
|
$q .= " AND ( otrrun.`hidden` = 0 OR otrrun.`hidden` IS NULL ) ";
|
|
$q .= "ORDER BY otrrun.`DEF_id` DESC ";
|
|
$r=$this->mysql->getSQLResult($q);
|
|
return $r;
|
|
}
|
|
|
|
function getOtrRunDataFromId($otrId) {
|
|
$q="SELECT otrrun.*, "
|
|
." path.`path` AS path, "
|
|
." rmeas.`half` AS rmeas, "
|
|
." fsc.`half` AS fsc, "
|
|
." fsc.`fscfile` AS fscfile, "
|
|
." stparam.`boxSize` AS boxsize "
|
|
."FROM ApOtrRunData as otrrun "
|
|
."LEFT JOIN ApRunsInStackData AS runsin "
|
|
." ON otrrun.`REF|ApStackData|tiltstack` = runsin.`REF|ApStackData|stack` "
|
|
."LEFT JOIN ApStackRunData AS strun "
|
|
." ON (runsin.`REF|ApStackRunData|stackRun` = strun.`DEF_id`) "
|
|
."LEFT JOIN ApStackParamsData AS stparam "
|
|
." ON strun.`REF|ApStackParamsData|stackParams` = stparam.`DEF_id` "
|
|
."LEFT JOIN ApPathData AS path "
|
|
." ON otrrun.`REF|ApPathData|path` = path.`DEF_id` "
|
|
."LEFT JOIN ApResolutionData AS rmeas "
|
|
." ON otrrun.`REF|ApResolutionData|rmeasure_resolution` = rmeas.`DEF_id` "
|
|
."LEFT JOIN ApResolutionData AS fsc "
|
|
." ON otrrun.`REF|ApResolutionData|fsc_resolution` = fsc.`DEF_id` "
|
|
."WHERE "
|
|
." otrrun.`DEF_id` = '$otrId' ";
|
|
$r=$this->mysql->getSQLResult($q);
|
|
return $r[0];
|
|
}
|
|
|
|
function get3dDensitysFromSession($sessionId, $showHidden=False) {
|
|
$q="SELECT "
|
|
." dens.*, "
|
|
." path.`path` AS path ";
|
|
if ($this->mysql->SQLTableExists('ApRefineIterData')) {
|
|
$q .= ", refineiter.`REF|ApRefineRunData|refineRun` AS refrun ";
|
|
}
|
|
$q .= "FROM Ap3dDensityData as dens "
|
|
."LEFT JOIN ApPathData AS path "
|
|
." ON dens.`REF|ApPathData|path` = path.`DEF_id` ";
|
|
if ($this->mysql->SQLTableExists('ApRefineIterData')) {
|
|
$q .= "LEFT JOIN ApRefineIterData AS refineiter "
|
|
." ON dens.`REF|ApRefineIterData|refineIter` = refineiter.`DEF_id` ";
|
|
}
|
|
$q .= "WHERE "
|
|
." dens.`REF|leginondata|SessionData|session` = '$sessionId' ";
|
|
if (!$showHidden )
|
|
$q .= " AND ( dens.`hidden` = 0 OR dens.`hidden` IS NULL ) ";
|
|
$q .= "ORDER BY dens.`DEF_id` DESC ";
|
|
//echo $q."<br/><br/>\n";
|
|
$r=$this->mysql->getSQLResult($q);
|
|
//echo print_r($r[0])."<br/><br/>\n";
|
|
return $r;
|
|
}
|
|
|
|
function get3dDensityFromId($densityId) {
|
|
$q="SELECT "
|
|
." dens.*, "
|
|
." path.`path` AS path ";
|
|
if ($this->mysql->SQLTableExists('ApRefineIterData')) {
|
|
$q .= ", refineIter.`REF|ApRefineRunData|refineRun` AS refrun ";
|
|
}
|
|
$q .= "FROM Ap3dDensityData as dens "
|
|
."LEFT JOIN ApPathData AS path "
|
|
." ON dens.`REF|ApPathData|path` = path.`DEF_id` ";
|
|
if ($this->mysql->SQLTableExists('ApRefineIterData')) {
|
|
$q .= "LEFT JOIN ApRefineIterData AS refineIter "
|
|
." ON dens.`REF|ApRefineIterData|refineIter` = refineIter.`DEF_id` ";
|
|
}
|
|
$q .= "WHERE "
|
|
." dens.`DEF_id` = '$densityId' ";
|
|
$r=$this->mysql->getSQLResult($q);
|
|
return $r[0];
|
|
}
|
|
|
|
function getAngularReconstitutionRuns($sessionId) {
|
|
$q="SELECT "
|
|
." ar.*, "
|
|
." path.`path` AS path "
|
|
."FROM ApBootstrappedAngularReconstitutionRunData as ar "
|
|
."LEFT JOIN ApPathData AS path "
|
|
." ON ar.`REF|ApPathData|path` = path.`DEF_id` "
|
|
### add a session entry to table
|
|
."LEFT JOIN ApTemplateStackData AS ts "
|
|
." ON ar.`REF|ApTemplateStackData|templatestackid` = ts.`DEF_id` "
|
|
."LEFT JOIN SessionData AS sd "
|
|
." ON ts.`REF|leginondata|SessionData|session` = sd.`DEF_id` "
|
|
|
|
."LEFT JOIN ApClusteringStackData AS clusterstack "
|
|
." ON ar.`REF|ApClusteringStackData|clusterid` = clusterstack.`DEF_id` "
|
|
."LEFT JOIN ApClusteringRunData AS clusterrun ON "
|
|
." (clusterstack.`REF|ApClusteringRunData|clusterrun` = clusterrun.`DEF_id`) "
|
|
."LEFT JOIN ApAlignStackData AS ast ON "
|
|
." (clusterrun.`REF|ApAlignStackData|alignstack` = ast.`DEF_id`) "
|
|
."LEFT JOIN ApStackData AS stack "
|
|
." ON ast.`REF|ApStackData|stack` = stack.`DEF_id` "
|
|
."LEFT JOIN ApRunsInStackData AS runsinstack "
|
|
." ON stack.`DEF_id` = runsinstack.`REF|ApStackData|stack` "
|
|
."LEFT JOIN ApStackRunData AS stackrun "
|
|
." ON stackrun.`DEF_id` = runsinstack.`REF|ApStackRunData|stackRun` "
|
|
."WHERE "
|
|
." stackrun.`REF|leginondata|SessionData|session` = '$sessionId'";
|
|
$r=$this->mysql->getSQLResult($q);
|
|
return $r;
|
|
}
|
|
|
|
function getImagic3dRefinementRunsFromSessionId($sessionId) {
|
|
$q="SELECT "
|
|
." refinement.*, "
|
|
." path.`path` AS path "
|
|
."FROM ApImagic3dRefineRunData as refinement "
|
|
."LEFT JOIN ApPathData AS path "
|
|
." ON refinement.`REF|ApPathData|path` = path.`DEF_id` "
|
|
."LEFT JOIN ApStackData AS stack "
|
|
." ON refinement.`REF|ApStackData|stackrun` = stack.`DEF_id` "
|
|
."LEFT JOIN ApRunsInStackData AS runsinstack "
|
|
." ON stack.`DEF_id` = runsinstack.`REF|ApStackData|stack` "
|
|
."LEFT JOIN ApStackRunData AS stackrun "
|
|
." ON stackrun.`DEF_id` = runsinstack.`REF|ApStackRunData|stackRun` "
|
|
."WHERE "
|
|
." stackrun.`REF|leginondata|SessionData|session` = '$sessionId'";
|
|
$r=$this->mysql->getSQLResult($q);
|
|
return $r;
|
|
}
|
|
|
|
function getImagic3dRefinementParamsFromRefineId ($refineId) {
|
|
$q = "SELECT param.*, run.*, pd.path, symmetry.symmetry "
|
|
."FROM ApImagic3dRefineRunData as run "
|
|
."LEFT JOIN ApImagic3dRefineIterationData as param "
|
|
." ON (param.`REF|ApImagic3dRefineRunData|refinement_run`=run.`DEF_id`) "
|
|
."LEFT JOIN ApPathData AS pd ON "
|
|
." (run.`REF|ApPathData|path` = pd.`DEF_id`) "
|
|
."LEFT JOIN ApSymmetryData as symmetry "
|
|
." ON param.`REF|ApSymmetryData|symmetry`=symmetry.`DEF_id` "
|
|
."WHERE run.`DEF_id` = '$refineId'";
|
|
$r = $this->mysql->getSQLResult($q);
|
|
|
|
return $r;
|
|
}
|
|
|
|
#------------HELICAL FUNCTIONS---------------#
|
|
|
|
function getHIPIdsFromSession ($sessionId, $showHidden=false, $package=false) {
|
|
$q = "SELECT DISTINCT (ApHipRunData.`DEF_id`) AS refid, ApHipRunData.*, path.path AS path "
|
|
." FROM `ApHipRunData` "
|
|
."LEFT JOIN ApRunsInStackData AS runs "
|
|
." ON ApHipRunData.`REF|ApStackData|stack` = runs.`REF|ApStackData|stack` "
|
|
."LEFT JOIN ApStackRunData AS stackrun "
|
|
." ON runs.`REF|ApStackRunData|stackRun` = stackrun.`DEF_id` "
|
|
."LEFT JOIN ApPathData AS path "
|
|
." ON ApHipRunData.`REF|ApPathData|path` = path.`DEF_id` "
|
|
."WHERE stackrun.`REF|leginondata|SessionData|session` = '$sessionId' ";
|
|
if (!$showHidden) $q.= " AND (ApHipRunData.`hidden` IS NULL OR ApHipRunData.`hidden` = 0) ";
|
|
$q.= " ORDER BY ApHipRunData.`DEF_id` DESC";
|
|
$r = $this->mysql->getSQLResult($q);
|
|
return $r;
|
|
}
|
|
|
|
function getHipRunIds ($sessionId) {
|
|
$q = "SELECT r.*, p.path "
|
|
."FROM `ApHipRunData` AS r "
|
|
."LEFT JOIN ApPathData AS p "
|
|
."ON (r.`REF|ApPathData|path` = p.`DEF_id`) "
|
|
."WHERE r.`REF|leginondata|SessionData|session` = '$sessionId' ";
|
|
//if (!$showHidden) $q.= " AND (r.`hidden` IS NULL OR r.`hidden` = 0) ";
|
|
$q.= "ORDER BY r.`DEF_id` DESC ";
|
|
$r = $this->mysql->getSQLResult($q);
|
|
return $r;
|
|
}
|
|
|
|
function getHipRunInfo($hipId) {
|
|
$q="select r.*, p.path "
|
|
."FROM `ApHipRunData` AS r "
|
|
."LEFT JOIN ApPathData AS p ON "
|
|
."(r.`REF|ApPathData|path` = p.`DEF_id`) "
|
|
."WHERE r.`DEF_id` = '$hipId' ";
|
|
list($r) = $this->mysql->getSQLResult($q);
|
|
return $r;
|
|
}
|
|
|
|
function getHipParamsInfo($hipId) {
|
|
$q = "SELECT * "
|
|
."FROM `ApHipParamsData` r "
|
|
."WHERE r.`REF|ApHipRunData|hipRun` = '$hipId' ";
|
|
list($r) = $this->mysql->getSQLResult($q);
|
|
return $r;
|
|
}
|
|
|
|
function getStackIdFromHipId ($hipId) {
|
|
$q= "SELECT * "
|
|
."FROM `ApHipRunData` "
|
|
."WHERE `DEF_id` = '$hipId'";
|
|
list($r) = $this->mysql->getSQLResult($q);
|
|
return $r['REF|ApStackData|stack'];
|
|
}
|
|
|
|
function getHipInfoFromRefinementId($refineid) {
|
|
$q="SELECT *"
|
|
."FROM "
|
|
."`ApHipIterData` AS `ApHipIterData` "
|
|
."LEFT JOIN `ApHipRunData` AS `ApHipRunData` "
|
|
."ON (`ApHipRunData`.`DEF_id`=`ApHipIterData`.`REF|ApHipRunData|hipRun`) "
|
|
."LEFT JOIN `ApPathData` AS `ApPathData` "
|
|
."ON (`ApPathData`.`DEF_id`=`ApHipRunData`.`REF|ApPathData|path`) "
|
|
."WHERE `ApHipIterData`.`DEF_id`=$refineid ";
|
|
$r=$this->mysql->getSQLResult($q);
|
|
return $r[0];
|
|
}
|
|
|
|
function getHipRefinementData ($hipRunId, $iteration=False) {
|
|
$q = "SELECT * "
|
|
."FROM `ApHipIterData` "
|
|
."WHERE `REF|ApHipRunData|hipRun` = $hipRunId ";
|
|
if ($iteration) $q.="AND `iteration` = $iteration";
|
|
$r = $this->mysql->getSQLResult($q);
|
|
return $r;
|
|
}
|
|
|
|
function getHipIterInfo ($hipId,$iteration=0) {
|
|
$q = "SELECT * "
|
|
."FROM `ApHipIterData` r "
|
|
."WHERE r.`REF|ApHipRunData|hipRun` = '$hipId' "
|
|
."ORDER BY r.`iteration` ASC ";
|
|
$r = $this->mysql->getSQLResult($q);
|
|
if ($iteration >0) {
|
|
return $r[$iteration-1];
|
|
}
|
|
return $r;
|
|
}
|
|
|
|
function getHighestResForHip ($hipid) {
|
|
$q = "SELECT ref.iteration AS iter, res.half AS half, rmeas.rMeasure AS rmeas "
|
|
."FROM `ApHipIterData` AS ref "
|
|
."LEFT JOIN `ApResolutionData` AS res "
|
|
." ON (ref.`REF|ApResolutionData|resolution` = res.`DEF_id`) "
|
|
."LEFT JOIN `ApRMeasureData` AS rmeas "
|
|
." ON (ref.`REF|ApRMeasureData|rMeasure` = rmeas.`DEF_id`) "
|
|
."WHERE ref.`REF|ApHipRunData|hipRun` = '$hipid' "
|
|
//."ORDER by rmeas.rMeasure ";
|
|
."ORDER by res.half ";
|
|
$r = $this->mysql->getSQLResult($q);
|
|
return $r[0];
|
|
}
|
|
|
|
function getPostProcsFromHipRefId($refid, $getHidden=False) {
|
|
$q = "SELECT d.*, "
|
|
."p.path as path , a.path as amppath "
|
|
."FROM `Ap3dDensityData` AS d "
|
|
."LEFT JOIN `ApPathData` AS p ON "
|
|
."(d.`REF|ApPathData|path` = p.`DEF_id`) "
|
|
."LEFT JOIN `ApPathData` AS a ON "
|
|
."(d.`REF|ApPathData|ampPath` = a.`DEF_id`) "
|
|
."WHERE d.`REF|ApHipIterData|hipIter` = $refid ";
|
|
if (!$getHidden) $q.= "AND (d.`hidden` IS NULL OR d.`hidden` = 0) ";
|
|
$r = $this->mysql->getSQLResult($q);
|
|
return $r;
|
|
}
|
|
|
|
//------ -------------------- ---------//
|
|
//------ Loop again functions ---------//
|
|
//------ -------------------- ---------//
|
|
|
|
function getJobProgramRunsInSession ($sessionid,$jobtype) {
|
|
$q = "SELECT DISTINCT "
|
|
." progrun.`DEF_id` "
|
|
.", progrun.`runname` "
|
|
.", runpath.`path` AS rundir "
|
|
."FROM ApAppionJobData job "
|
|
."LEFT JOIN ScriptProgramRun as progrun "
|
|
." ON job.`DEF_id` = progrun.`REF|ApAppionJobData|job` "
|
|
."LEFT JOIN ApPathData as runpath "
|
|
." ON runpath.`DEF_id` = progrun.`REF|ApPathData|rundir` "
|
|
."WHERE "
|
|
." job.`REF|leginondata|SessionData|session` = $sessionid "
|
|
."AND "
|
|
." job.`jobtype` = '".$jobtype."' "
|
|
."; ";
|
|
//echo $q."<br/><br/>\n";
|
|
$r = $this->mysql->getSQLResult($q);
|
|
//echo print_r($r)."<br/><br/>\n";
|
|
return $r;
|
|
}
|
|
|
|
function getLoopProgramRuns () {
|
|
$q = "SELECT DISTINCT "
|
|
." progrun.`DEF_id` AS id "
|
|
."FROM ScriptProgramRun as progrun "
|
|
."LEFT JOIN ScriptParamValue AS paramvalue "
|
|
." ON paramvalue.`REF|ScriptProgramRun|progrun` = progrun.`DEF_id` "
|
|
."LEFT JOIN ScriptParamName AS paramname "
|
|
." ON paramvalue.`REF|ScriptParamName|paramname` = paramname.`DEF_id` "
|
|
."WHERE "
|
|
." progrun.`REF|ApAppionJobData|job` IS NOT NULL "
|
|
."AND "
|
|
." paramname.`name` = 'preset' "
|
|
."; ";
|
|
//echo $q."<br/><br/>\n";
|
|
$r = $this->mysql->getSQLResult($q);
|
|
//echo print_r($r)."<br/><br/>\n";
|
|
return $r;
|
|
}
|
|
|
|
function getProgramRunFromJob ($jobid) {
|
|
$q = "SELECT "
|
|
." progrun.`DEF_id` AS id "
|
|
."FROM ScriptProgramRun as progrun "
|
|
."WHERE `REF|ApAppionJobData|job` = ".$jobid." "
|
|
."ORDER BY progrun.`DEF_timestamp` DESC "
|
|
."LIMIT 1 ";
|
|
list($r) = $this->mysql->getSQLResult($q);
|
|
return $r;
|
|
}
|
|
function getProgramRunParams ($progrunid) {
|
|
$q = "SELECT "
|
|
." progrun.`DEF_id` AS id, "
|
|
." progname.`name` AS progname, "
|
|
." progrun.`runname` AS runname, "
|
|
." session.`name` AS sessionname, "
|
|
." username.`name` AS username "
|
|
."FROM ScriptProgramRun as progrun "
|
|
."LEFT JOIN ScriptProgramName AS progname "
|
|
." ON progrun.`REF|ScriptProgramName|progname` = progname.`DEF_id` "
|
|
."LEFT JOIN ScriptUserName AS username "
|
|
." ON progrun.`REF|ScriptUserName|username` = username.`DEF_id` "
|
|
."LEFT JOIN ApAppionJobData AS job "
|
|
." ON progrun.`REF|ApAppionJobData|job` = job.`DEF_id` "
|
|
."LEFT JOIN ".DB_LEGINON.".SessionData AS session "
|
|
." ON job.`REF|leginondata|SessionData|session` = session.`DEF_id` "
|
|
."WHERE "
|
|
." progrun.`DEF_id` = $progrunid "
|
|
."; ";
|
|
//echo $q."<br/><br/>\n";
|
|
$r = $this->mysql->getSQLResult($q);
|
|
//echo print_r($r[0])."<br/><br/>\n";
|
|
return $r[0];
|
|
}
|
|
|
|
function getProgramCommands ($progrunid) {
|
|
$q = "SELECT "
|
|
." paramvalue.*, paramname.*, "
|
|
." session.`name` AS sessionname "
|
|
."FROM ScriptParamValue as paramvalue "
|
|
."LEFT JOIN ScriptParamName AS paramname "
|
|
." ON paramvalue.`REF|ScriptParamName|paramname` = paramname.`DEF_id` "
|
|
|
|
."LEFT JOIN ScriptProgramRun AS progrun "
|
|
." ON paramvalue.`REF|ScriptProgramRun|progrun` = progrun.`DEF_id` "
|
|
."LEFT JOIN ApAppionJobData AS job "
|
|
." ON progrun.`REF|ApAppionJobData|job` = job.`DEF_id` "
|
|
."LEFT JOIN ".DB_LEGINON.".SessionData AS session "
|
|
." ON job.`REF|leginondata|SessionData|session` = session.`DEF_id` "
|
|
|
|
."WHERE "
|
|
." paramvalue.`REF|ScriptProgramRun|progrun` = $progrunid "
|
|
."ORDER BY LENGTH(paramvalue.`value`) "
|
|
."; ";
|
|
//echo $q."<br/><br/>\n";
|
|
$r = $this->mysql->getSQLResult($q);
|
|
//echo print_r($r)."<br/><br/>\n";
|
|
return $r;
|
|
}
|
|
|
|
function getJobCommandParams($jobid) {
|
|
$progrun = $this-> getProgramRunFromJob ($jobid);
|
|
$samplecommand = $this->getProgramCommands ($progrun['id']);
|
|
$s = array();
|
|
if (is_array($samplecommand) && count($samplecommand) > 0)
|
|
foreach ($samplecommand as $c) $s[$c['name']] = $c['value'];
|
|
return $s;
|
|
}
|
|
}
|
|
|
|
// For euler angles, takes alpha beta gamma and returns a,b,c, maybe?
|
|
function simplify($e) {
|
|
return $e['a'].','.$e['b'].','.$e['c'];
|
|
}
|
|
|
|
//TODO: the following functions should not be in this file!
|
|
function displayCTFstats($stats, $display_keys) {
|
|
if (!is_array($stats) || !is_array($display_keys))
|
|
return ;
|
|
$html = "<table class='tableborder' border='1' cellspacing='1' cellpadding='5'>";
|
|
foreach($stats as $field=>$data) {
|
|
if (!$head) {
|
|
$head = true;
|
|
$html .= "<th>\n";
|
|
foreach($display_keys as $kh) {
|
|
$html .= "<td><span class='datafield0'>".$kh."</span></td>";
|
|
}
|
|
$html .= "</th>\n";
|
|
}
|
|
$html .= "<tr>\n";
|
|
$html .= "<td rowspan='".(count($data)+1)."'><span class='datafield0'>".$field."</span></td>\n";
|
|
foreach($data as $row) {
|
|
$html .= "<tr>\n";
|
|
foreach($display_keys as $key) {
|
|
if (!is_array($row))
|
|
continue;
|
|
if (array_key_exists($key, $row))
|
|
$val = $row[$key];
|
|
else
|
|
continue;
|
|
if (eregi('defocus', $key))
|
|
$val = format_micro_number($val);
|
|
if (eregi('^min|^max|^avg|^stddev', $key))
|
|
if (eregi('defocus', $field) || eregi('nominal', $field)) {
|
|
$val = format_micro_number($val);
|
|
} else {
|
|
$val = format_sci_number($val, 3);
|
|
}
|
|
$html .= "<td>";
|
|
$html .= " ".$val."<br>\n";
|
|
$html .= "</td>";
|
|
}
|
|
$html .= "</tr>\n";
|
|
}
|
|
$html .= "</tr>\n";
|
|
}
|
|
$html .= "</table>";
|
|
return $html;
|
|
}
|
|
|
|
function displayCTFdata($data, $display_keys) {
|
|
$html = "<table class='tableborder' border='1' cellspacing='1' cellpadding='5'>";
|
|
$html .= "<tr>\n";
|
|
foreach($display_keys as $key) {
|
|
$html .= "<th>";
|
|
$html .= " ".$key."<br>\n";
|
|
$html .= "</th>";
|
|
}
|
|
$html .= "</tr>\n";
|
|
$html .= "<tr>\n";
|
|
foreach($data as $row) {
|
|
foreach($display_keys as $key) {
|
|
$val = $row[$key];
|
|
if (eregi('defocus', $key)) {
|
|
$val = format_micro_number($val);
|
|
}
|
|
$html .= "<td>";
|
|
$html .= " ".$val."<br>\n";
|
|
$html .= "</td>";
|
|
}
|
|
$html .= "</tr>\n";
|
|
}
|
|
$html .= "</table>";
|
|
return $html;
|
|
}
|
|
|
|
function getBaseAppionPath($sessioninfo,$new_base='appion') {
|
|
if (!is_array($sessioninfo)) {
|
|
if (!is_string($sessioninfo) && !empty($sessioninfo)) {
|
|
echo "ERROR: NO session information";
|
|
} else {
|
|
echo "ERROR: string input option not yet implemented";
|
|
}
|
|
}
|
|
|
|
if (defined('DEFAULT_APPION_PATH') && DEFAULT_APPION_PATH !='') {
|
|
return Path::formatEndPath(DEFAULT_APPION_PATH).$sessioninfo['Name'];
|
|
} else {
|
|
// get from leginon session image path
|
|
$leginon_imagepath = $sessioninfo['Image path'];
|
|
// use this in case that the word leginon is used in two parts of the path
|
|
ereg("(.*)leginon(.*)rawdata", $leginon_imagepath, $reg_match);
|
|
if (!is_null($reg_match)) {
|
|
$path_pieces = explode('leginon',$leginon_imagepath);
|
|
$pieces_count = count($path_pieces);
|
|
$appion_basepath = implode('leginon',array_slice($path_pieces,0,$pieces_count-1)).$new_base.$path_pieces[$pieces_count-1];
|
|
$appion_basepath=ereg_replace("/rawdata","",$appion_basepath);
|
|
$appion_basepath=ereg_replace("/appion2/","/appion/",$appion_basepath);
|
|
} else {
|
|
$extra="ERROR: could not determine Appion Path directory automatically. Please enter manually";
|
|
echo $extra;
|
|
}
|
|
}
|
|
return $appion_basepath;
|
|
}
|
|
|
|
?>
|