function DisplayChart($data, $label, $height, $id) {
$colors = GenerateColorGradient();
?>
<table class="grayrounded" width="100%">
<tr>
<td class="title"><?php
echo $label;
?>
</td>
</tr>
<tr>
<td class="body">
<script>
$(function() {
var data = [
{
label: "<?php
echo $label;
?>
",
hoverable: true,
clickable: true,
data: [<?
foreach ($data as $date => $item) {
$value = $data[$date]['value'];
$date = $date*1000;
if (($date > 0) && ($value > 0)) {
$jsonstrings[] .= "['$date', $value]";
#$jsonstrings[] .= "['$date', " . number_format($value,1,'.','') . "]";
}
}
?><?php
echo implode2(',', $jsonstrings);
?>
]
}
];
var options = {
series: {
lines: { show: true, fill: false },
points: { show: true }
},
legend: { noColumns: 6 },
xaxis: { mode: "time", timeformat: "%Y-%m-%d" },
yaxis: { min: 0, tickDecimals: 1 },
selection: { mode: "x" },
};
var placeholder = $("#placeholder<?php
echo $id;
?>
");
var plot = $.plot(placeholder, data, options);
});
</script>
<div id="placeholder<?php
echo $id;
?>
" style="height:<?php
echo $height;
?>
px;" align="center"></div>
</td>
</tr>
<tr>
<td class="body">
<table class="tinytable">
<thead>
<th>Date</th>
<th>Subject</th>
<th>Study</th>
<th>Value</th>
</thead>
<tbody>
<?
// get min, max
$min = $data[0];
$max = $data[0];
foreach ($data as $date => $value) {
$value = $data[$date]['value'];
if ($value > $max) { $max = $value; }
if ($value < $min) { $min = $value; }
}
$range = $max - $min;
foreach ($data as $date => $value) {
$value = $data[$date]['value'];
$uid = $data[$date]['uid'];
$studynum = $data[$date]['studynum'];
$subjectid = $data[$date]['subjectid'];
$studyid = $data[$date]['studyid'];
if (($value > 0) && ($range > 0)) {
$cindex = round((($value - $min)/$range)*100);
if ($cindex > 100) { $cindex = 100; }
}
$date = $date;
$date = date("D, d M Y", $date);
?>
<tr>
<td><?php
echo $date;
?>
</td>
<td><a href="subjects.php?id=<?php
echo $subjectid;
?>
"><?php
echo $uid;
?>
</a></td>
<td><a href="subjects.php?id=<?php
echo $studyid;
?>
"><?php
echo $uid;
echo $studynum;
?>
</a></td>
<td align="right" bgcolor="<?php
echo $colors[$cindex];
?>
"><tt><?php
echo $value;
?>
<tt></td>
</tr>
<?
}
?>
</tbody>
</table>
</td>
</tr>
</table>
<?
}
function DisplayAnalysisList($id, $numperpage, $pagenum)
{
$sqlstring = "select pipeline_name, pipeline_level from pipelines where pipeline_id = {$id}";
$result = MySQLiQuery($sqlstring, __FILE__, __LINE__);
$row = mysqli_fetch_array($result, MYSQLI_ASSOC);
$pipeline_name = $row['pipeline_name'];
$pipeline_level = $row['pipeline_level'];
//$urllist['Analysis'] = "analysis.php";
$urllist['Pipelines'] = "pipelines.php";
$urllist["{$pipeline_name}"] = "pipelines.php?action=editpipeline&id={$id}";
$urllist["Analysis List"] = "pipelines.php?action=viewanalyses&id={$id}";
NavigationBar("Analysis", $urllist);
/* prep the pagination */
if ($numperpage == "") {
$numperpage = 500;
}
if ($pagenum == "" || $pagenum < 1) {
$pagenum = 1;
}
$limitstart = ($pagenum - 1) * $numperpage;
$limitcount = $numperpage;
/* create the color lookup table */
$colors = GenerateColorGradient();
//echo "<pre>";
//print_r($colors);
//echo "</pre>";
/* run the sql query here to get the row count */
$sqlstring = "select *, timediff(analysis_enddate, analysis_startdate) 'analysis_time', timediff(analysis_clusterenddate, analysis_clusterstartdate) 'cluster_time' from analysis a left join studies b on a.study_id = b.study_id left join enrollment c on b.enrollment_id = c.enrollment_id left join subjects d on c.subject_id = d.subject_id where a.pipeline_id = {$id} and analysis_status not in ('NoMatchingStudies','NoMatchingStudyDependency','IncompleteDependency','BadDependency')";
$result = MySQLiQuery($sqlstring, __FILE__, __LINE__);
$numrows = mysqli_num_rows($result);
$numpages = ceil($numrows / $numperpage);
if ($pagenum > $numpages) {
$pagenum = $numpages;
}
?>
<div id="dialogbox" title="Dialog Box" style="display:none;">Loading...</div>
<script type="text/javascript">
//$(document).ready(function() {
// $(".fancybox").fancybox();
//});
</script>
<script type="text/javascript">
//$(document).ready(function() {
$(function() {
$("#studiesall").click(function() {
var checked_status = this.checked;
$(".allstudies").find("input[type='checkbox']").each(function() {
this.checked = checked_status;
});
});
$("#analysesall").click(function() {
var checked_status = this.checked;
$(".allanalyses").find("input[type='checkbox']").each(function() {
this.checked = checked_status;
});
});
$("a.viewlog").click(function(e) {
var id = jQuery(this).attr("id");
e.preventDefault();
$("#dialogbox").load("viewanalysis.php?action=viewlogs&analysisid=" + id).dialog({height:800, width:1200});
});
$("a.viewfiles").click(function(e) {
var id = jQuery(this).attr("id");
e.preventDefault();
$("#dialogbox").load("viewanalysis.php?action=viewfiles&analysisid=" + id).dialog({height:800, width:1200});
});
$("a.viewresults").click(function(e) {
var id = jQuery(this).attr("id");
e.preventDefault();
$("#dialogbox").load("viewanalysis.php?action=viewresults&analysisid=" + id + "&studyid=<?php
echo $study_id;
?>
").dialog({height:800, width:1200});
});
});
</script>
<table width="100%" class="tablepage">
<form method="post" action="pipelines.php" id="numperpageform">
<input type="hidden" name="action" value="viewanalyses">
<input type="hidden" name="id" value="<?php
echo $id;
?>
">
<tr>
<td class="label"><?php
echo $numrows;
?>
analyses</td>
<td class="pagenum">
Page <?php
echo $pagenum;
?>
of <?php
echo $numpages;
?>
<span class="tiny">(<?php
echo $numperpage;
?>
/page)</span>
<select name="numperpage" title="Change number per page" onChange="numperpageform.submit()">
<option value="100" <?php
if ($numperpage == 100) {
echo "selected";
}
?>
>100
<option value="500" <?php
if ($numperpage == 500) {
echo "selected";
}
?>
>500
<option value="1000" <?php
if ($numperpage == 1000) {
echo "selected";
}
?>
>1,000
<option value="2000" <?php
if ($numperpage == 2000) {
echo "selected";
}
?>
>2,000
<option value="5000" <?php
if ($numperpage == 5000) {
echo "selected";
}
?>
>5,000
<option value="10000" <?php
if ($numperpage == 10000) {
echo "selected";
}
?>
>10,000
<option value="50000" <?php
if ($numperpage == 50000) {
echo "selected";
}
?>
>50,000
</select>
</td>
<td class="middle"> </td>
<td class="firstpage" title="First page"><a href="pipelines.php?action=viewanalyses&id=<?php
echo $id;
?>
&numperpage=<?php
echo $numperpage;
?>
&pagenum=1">«</a></td>
<td class="previouspage" title="Previous page"><a href="pipelines.php?action=viewanalyses&id=<?php
echo $id;
?>
&numperpage=<?php
echo $numperpage;
?>
&pagenum=<?php
echo $pagenum - 1;
?>
">‹</a></td>
<td title="Refresh page"><a href="" style="margin-left:20px; margin-right:20px; font-size:14pt">⟳</a></td>
<td class="nextpage" title="Next page"><a href="pipelines.php?action=viewanalyses&id=<?php
echo $id;
?>
&numperpage=<?php
echo $numperpage;
?>
&pagenum=<?php
echo $pagenum + 1;
?>
">›</a></td>
<td class="lastpage" title="Last page"><a href="pipelines.php?action=viewanalyses&id=<?php
echo $id;
?>
&numperpage=<?php
echo $numperpage;
?>
&pagenum=<?php
echo $numpages;
?>
">»</a></td>
</tr>
</form>
</table>
<form method="post" name="studieslist" action="pipelines.php">
<input type="hidden" name="action" value="deleteanalyses" id="studieslistaction">
<input type="hidden" name="destination" value="" id="studieslistdestination">
<input type="hidden" name="analysisnotes" value="">
<input type="hidden" name="analysisid" value="">
<input type="hidden" name="id" value="<?php
echo $id;
?>
">
<table id="analysistable" class="smallgraydisplaytable" width="100%">
<!--<table id="analysistable" class="tablesorter" width="100%">-->
<thead>
<tr>
<th><input type="checkbox" id="studiesall"> Study</th>
<th>Visit</th>
<th>Pipeline<br>version</th>
<?php
if ($pipeline_level == 1) {
?>
<th>Study date</th>
<th># series</th>
<?php
}
?>
<th>Status</th>
<th>Successful</th>
<th>Logs</th>
<th>Files</th>
<th>Results</th>
<th>Notes</th>
<th>Message</th>
<th>Size<br><span class="tiny">bytes</span></th>
<th>Hostname</th>
<th>Setup time<br><span class="tiny">completed date</span></th>
<th>Cluster time<br><span class="tiny">completed date</span></th>
<th>Operations<br><input type="checkbox" id="analysesall"></th>
</tr>
</thead>
<tbody>
<?php
$sqlstring = "select *, timediff(analysis_enddate, analysis_startdate) 'analysis_time', timediff(analysis_clusterenddate, analysis_clusterstartdate) 'cluster_time' from analysis a left join studies b on a.study_id = b.study_id left join enrollment c on b.enrollment_id = c.enrollment_id left join subjects d on c.subject_id = d.subject_id where a.pipeline_id = {$id} and a.analysis_status not in ('NoMatchingStudies','NoMatchingStudyDependency','IncompleteDependency','BadDependency') order by a.analysis_status desc, study_datetime desc limit {$limitstart}, {$limitcount}";
$result = MySQLiQuery($sqlstring, __FILE__, __LINE__);
while ($row = mysqli_fetch_array($result, MYSQLI_ASSOC)) {
$numcomplete += $row['analysis_iscomplete'];
$analysistimes[] = $row['analysis_time'];
$analysissizes[] = $row['analysis_disksize'];
$clustertimes[] = $row['cluster_time'];
}
$minsize = min($analysissizes);
$maxsize = max($analysissizes);
$minanalysistime = min($analysistimes);
$maxanalysistime = max($analysistimes);
$minclustertime = min($clustertimes);
$maxclustertime = max($clustertimes);
/* rewind the result */
mysqli_data_seek($result, 0);
while ($row = mysqli_fetch_array($result, MYSQLI_ASSOC)) {
$analysis_id = $row['analysis_id'];
$analysis_qsubid = $row['analysis_qsubid'];
$analysis_status = $row['analysis_status'];
$analysis_numseries = $row['analysis_numseries'];
$analysis_statusmessage = $row['analysis_statusmessage'];
$analysis_statusdatetime = $row['analysis_statusdatetime'];
$analysis_swversion = $row['analysis_swversion'];
$analysis_iscomplete = $row['analysis_iscomplete'];
$analysis_time = $row['analysis_time'];
$analysis_size = $row['analysis_disksize'];
$analysis_isbad = $row['analysis_isbad'];
$notes = $row['analysis_notes'];
$analysis_hostname = $row['analysis_hostname'];
$cluster_time = $row['cluster_time'];
$analysis_enddate = date('Y-m-d H:i', strtotime($row['analysis_enddate']));
if ($row['analysis_clusterenddate'] == "") {
$analysis_clusterenddate = "-";
} else {
$analysis_clusterenddate = date('Y-m-d H:i', strtotime($row['analysis_clusterenddate']));
}
$study_id = $row['study_id'];
$study_num = $row['study_num'];
$study_datetime = date('M j, Y H:i', strtotime($row['study_datetime']));
$uid = $row['uid'];
$visittype = $row['study_type'];
$pipeline_version = $row['pipeline_version'];
$pipeline_dependency = $row['pipeline_dependency'];
$sqlstringA = "select pipeline_submithost from pipelines where pipeline_id = {$id}";
//PrintSQL($sqlstringA);
$resultA = MySQLiQuery($sqlstringA, __FILE__, __LINE__);
$rowA = mysqli_fetch_array($resultA, MYSQLI_ASSOC);
$pipeline_submithost = $rowA['pipeline_submithost'];
if ($pipeline_submithost == "") {
$pipeline_submithost = $GLOBALS['cfg']['clustersubmithost'];
}
$sqlstringA = "select pipeline_name, pipeline_submithost from pipelines where pipeline_id = {$pipeline_dependency}";
$resultA = MySQLiQuery($sqlstringA, __FILE__, __LINE__);
$rowA = mysqli_fetch_array($resultA, MYSQLI_ASSOC);
$pipeline_dep_name = $rowA['pipeline_name'];
if ($notes == "") {
$notestitle = "Click to create notes";
$notescolor = "#DDD";
} else {
$notestitle = $notes;
$notescolor = "C00";
}
if ($analysis_isbad) {
$rowcolor = "#f2d7d7";
} else {
$rowcolor = "";
}
/* get color index for the size */
$sizeindex = 0;
if ($analysis_size > 0) {
$sizeindex = round($analysis_size / ($maxsize - $minsize) * 100.0);
if ($sizeindex > 100) {
$sizeindex = 100;
}
$sizecolor = $colors[$sizeindex];
} else {
$sizecolor = "#fff";
}
//echo "$analysis_size, $sizeindex, $sizecolor, $maxsize<br>";
?>
<script>
function GetAnalysisNotes<?php
echo $analysis_id;
?>
(){
var analysisnotes = prompt("Enter notes for this analysis","<?php
echo $notestitle;
?>
");
if (analysisnotes != null){
//$("#analysisnotes").attr("value", analysisnotes);
document.studieslist.analysisnotes.value = analysisnotes;
document.studieslist.action.value = 'setanalysisnotes';
document.studieslist.id.value = '<?php
echo $id;
?>
';
document.studieslist.analysisid.value = '<?php
echo $analysis_id;
?>
';
document.studieslist.submit();
}
}
</script>
<tr bgcolor="<?php
echo $rowcolor;
?>
">
<td class="allstudies" style="text-align:left"><input type="checkbox" name="studyid[]" value="<?php
echo $study_id;
?>
">
<a href="studies.php?id=<?php
echo $study_id;
?>
"><?php
echo $uid;
echo $study_num;
?>
</a></td>
<td><?php
echo $visittype;
?>
</td>
<td><?php
echo $pipeline_version;
?>
</td>
<?php
if ($pipeline_level == 1) {
?>
<td class="tiny"><?php
echo $study_datetime;
?>
</td>
<td><?php
echo $analysis_numseries;
?>
</td>
<?php
}
?>
<td>
<?php
if ($analysis_status == 'processing' && $analysis_qsubid != 0) {
//$systemstring = "SGE_ROOT=/sge/sge-root; export SGE_ROOT; SGE_CELL=nrccell; export SGE_CELL; cd /sge/sge-root/bin/lx24-amd64; ./qstat -j $analysis_qsubid";
$systemstring = "ssh {$pipeline_submithost} qstat -j {$analysis_qsubid}";
//echo "$systemstring";
//$out = shell_exec($systemstring);
if (trim($out) == "hi") {
?>
<img src="images/alert.png" title="Analysis is marked as running, but the cluster job is not.<br><br>This means the analysis is being setup and the data is being copied or the cluster job failed. Check log files for error"><?php
}
?>
<!--<a class="fancybox" title="SGE status" href="pipelines.php?action=viewjob&id=<?php
echo $analysis_qsubid;
?>
">processing</a>-->
<a href="<?php
echo $GLOBALS['cfg']['siteurl'];
?>
/pipelines.php?action=viewjob&id=<?php
echo $analysis_qsubid;
?>
">processing</a>
<?php
} else {
if ($analysis_qsubid == 0) {
echo "Preparing data";
} else {
echo $analysis_status;
}
}
?>
</td>
<td style="font-weight: bold; color: green"><?php
if ($analysis_iscomplete) {
echo "✓";
}
?>
</td>
<?php
if ($analysis_status != "") {
?>
<td><a href="#" class="viewlog" id="<?php
echo $analysis_id;
?>
"><img src="images/preview.gif"></a></td>
<td><a href="#" class="viewfiles" id="<?php
echo $analysis_id;
?>
"><img src="images/folder.gif"></a></td>
<td><a href="#" class="viewresults" id="<?php
echo $analysis_id;
?>
"><img src="images/chart-vertical.png"></a></td>
<?php
} else {
?>
<td></td>
<td></td>
<?php
}
?>
<td>
<span onClick="GetAnalysisNotes<?php
echo $analysis_id;
?>
();" style="cursor:hand; font-size:14pt; color: <?php
echo $notescolor;
?>
" title="<?php
echo $notestitle;
?>
">✎</span>
</td>
<td style="font-size:9pt; white-space:nowrap">
<?php
echo $analysis_statusmessage;
?>
<br>
<?php
if (strpos($analysis_statusmessage, "processing step") !== false) {
$parts = explode(" ", $analysis_statusmessage);
$stepnum = $parts[2];
$steptotal = $parts[4];
?>
<img src="horizontalchart.php?b=no&w=150&h=3&v=<?php
echo $stepnum;
?>
,<?php
echo $steptotal - $stepnum;
?>
&c=666666,DDDDDD" style="margin:2px"><br>
<?php
}
?>
<span class="tiny"><?php
echo $analysis_statusdatetime;
?>
</span>
</td>
<td align="right" style="font-size:8pt; border-bottom: 5px solid <?php
echo $sizecolor;
?>
; margin-bottom:0px; padding-bottom:0px" valign="bottom">
<?php
echo number_format($analysis_size, 0);
?>
<table cellspacing="0" cellpadding="0" border="0" width="100%" height="5px" style="margin-top:5px">
<tr>
<td width="100%" height="5px" style="background-color: <?php
echo $sizecolor;
?>
; height:5px; font-size: 1pt; border: 0px"> </td>
</tr>
</table>
</td>
<td><?php
echo $analysis_hostname;
?>
</td>
<td><?php
echo $analysis_time;
?>
<br><span class="tiny"><?php
echo $analysis_enddate;
?>
</span></td>
<td><?php
echo $cluster_time;
?>
<br><span class="tiny"><?php
echo $analysis_clusterenddate;
?>
</span></td>
<td class="allanalyses" ><input type="checkbox" name="analysisids[]" value="<?php
echo $analysis_id;
?>
"></td>
</tr>
<?php
}
?>
<script>
function GetDestination(){
var destination = prompt("Please enter a valid destination for the selected analyses","/home/<?php
echo $GLOBALS['username'];
?>
/onrc/data");
if (destination != null){
//document.studieslist.destination.value = desination;
document.studieslist.action='pipelines.php';
//document.studieslist.action.value='copyanalyses';
$("#studieslistaction").attr("value", "copyanalyses");
$("#studieslistdestination").attr("value", destination);
document.studieslist.submit();
}
}
function GetDestination2(){
var destination = prompt("Please enter a valid directory in which to create the 'data' directory and links","/home/<?php
echo $GLOBALS['username'];
?>
/onrc/data");
if (destination != null){
document.studieslist.action='pipelines.php';
$("#studieslistaction").attr("value", "createlinks");
$("#studieslistdestination").attr("value", destination);
document.studieslist.submit();
}
}
function MarkAnalysis(){
document.studieslist.action='pipelines.php';
document.studieslist.submit();
}
</script>
<tr style="color: #444; font-size:12pt; font-weight:bold">
<td colspan="8" valign="top" style="background-color: #fff">
<table>
<tr>
<td valign="top" style="color: #444; font-size:12pt; font-weight:bold; border-top:none">
Studies group
</td>
<td valign="top" style="border-top:none">
<select name="studygroupid" style="width:150px">
<?php
$sqlstring = "select * from groups where group_type = 'study'";
$result = MySQLiQuery($sqlstring, __FILE__, __LINE__);
while ($row = mysqli_fetch_array($result, MYSQLI_ASSOC)) {
$groupid = $row['group_id'];
$groupname = $row['group_name'];
?>
<option value="<?php
echo $groupid;
?>
"><?php
echo $groupname;
?>
<?php
}
?>
</select>
<input type="submit" name="addtogroup" value="Add" onclick="document.studieslist.action='groups.php';document.studieslist.action.value='addstudiestogroup'">
</td>
</tr>
</table>
</td>
<td colspan="8" align="right" style="background-color: #fff; font-size: 12pt">
With selected: <br><br>
<input type="submit" value="Delete" style="border: 1px solid red; background-color: pink; width:150px; margin:4px" onclick="document.studieslist.action.value='deleteanalyses';return confirm('Are you absolutely sure you want to DELETE the selected analyses?')" title="<b style='color:pink'>Pipeline will be disabled. Wait until the deletions are compelte before reenabling the pipeline</b><Br> This will delete the selected analyses, which will be regenerated using the latest pipeline version">
<br><br><br>
<input type="button" name="copyanalyses" value="Copy analyses to..." style="width: 150px; margin:4px" onclick="document.studieslist.action='pipelines.php';document.studieslist.action.value='copyanalyses';GetDestination()">
<br>
<input type="button" name="createlinks" value="Create links..." style="width: 150px; margin:4px" onclick="document.studieslist.action='pipelines.php';document.studieslist.action.value='createlinks';GetDestination2()" title="Creates a directory called 'data' which contains links to all of the selected studies">
<br>
<input type="button" name="rerunresults" value="Re-run results script" style="width: 150px; margin:4px" onclick="document.studieslist.action='pipelines.php';document.studieslist.action.value='rerunresults';document.studieslist.submit();" title="This will delete any existing results inserted into NiDB and re-run the results script">
<br>
<input type="button" name="runsupplement" value="Run supplement script" style="width: 150px; margin:4px" onclick="document.studieslist.action='pipelines.php';document.studieslist.action.value='runsupplement';document.studieslist.submit();" title="Run the script specified in the supplemental command script. This will not download new data or re-download existing data. It will only perform commands on the existing files in the analysis directory">
<br>
<input type="button" name="rechecksuccess" value="Re-check if successful" style="width: 150px; margin:4px" onclick="document.studieslist.action='pipelines.php';document.studieslist.action.value='rechecksuccess';document.studieslist.submit();" title="This option will check the selected analyses against the 'successfully completed files' field and mark them as successful if the file(s) exist">
<br><br>
<input type="button" name="markasbad" value="Mark as bad" style="width: 150px; margin:4px" onclick="document.studieslist.action='pipelines.php';document.studieslist.action.value='markbad'; MarkAnalysis()" title="Mark the analyses as bad so they will not be used in dependent pipelines">
<br>
<input type="button" name="markasgood" value="Mark as good" style="width: 150px; margin:4px" onclick="document.studieslist.action='pipelines.php';document.studieslist.action.value='markgood'; MarkAnalysis()" title="Unmark an analysis as bad">
</td>
</tr>
</tbody>
</table>
</form>
<?php
}
function DisplayMRSeries($id, $study_num, $uid, $audit, $fix) {
$colors = GenerateColorGradient();
/* get the subject information */
$sqlstring = "select * from subjects a left join enrollment b on a.subject_id = b.subject_id left join studies c on b.enrollment_id = c.enrollment_id where c.study_id = $id";
$result = MySQLQuery($sqlstring, __FILE__, __LINE__);
if (mysql_num_rows($result) > 0) {
$row = mysql_fetch_array($result, MYSQL_ASSOC);
$dbsubjectname = $row['name'];
$dbsubjectdob = $row['birthdate'];
$dbsubjectsex = $row['gender'];
$dbstudydatetime = $row['study_datetime'];
}
else {
echo "$sqlstring<br>";
}
/* get the movement & SNR stats by sequence name */
$sqlstring2 = "SELECT b.series_sequencename, max(a.move_maxx) 'maxx', min(a.move_minx) 'minx', max(a.move_maxy) 'maxy', min(a.move_miny) 'miny', max(a.move_maxz) 'maxz', min(a.move_minz) 'minz', avg(a.pv_snr) 'avgpvsnr', avg(a.io_snr) 'avgiosnr', std(a.pv_snr) 'stdpvsnr', std(a.io_snr) 'stdiosnr', min(a.pv_snr) 'minpvsnr', min(a.io_snr) 'miniosnr', max(a.pv_snr) 'maxpvsnr', max(a.io_snr) 'maxiosnr', min(a.motion_rsq) 'minmotion', max(a.motion_rsq) 'maxmotion', avg(a.motion_rsq) 'avgmotion', std(a.motion_rsq) 'stdmotion' FROM mr_qa a left join mr_series b on a.mrseries_id = b.mrseries_id where a.io_snr > 0 group by b.series_sequencename";
//echo "$sqlstring2<br>";
$result2 = MySQLQuery($sqlstring2, __FILE__, __LINE__);
while ($row2 = mysql_fetch_array($result2, MYSQL_ASSOC)) {
$sequence = $row2['series_sequencename'];
$pstats[$sequence]['rangex'] = abs($row2['minx']) + abs($row2['maxx']);
$pstats[$sequence]['rangey'] = abs($row2['miny']) + abs($row2['maxy']);
$pstats[$sequence]['rangez'] = abs($row2['minz']) + abs($row2['maxz']);
$pstats[$sequence]['avgpvsnr'] = $row2['avgpvsnr'];
$pstats[$sequence]['stdpvsnr'] = $row2['stdpvsnr'];
$pstats[$sequence]['minpvsnr'] = $row2['minpvsnr'];
$pstats[$sequence]['maxpvsnr'] = $row2['maxpvsnr'];
$pstats[$sequence]['avgiosnr'] = $row2['avgiosnr'];
$pstats[$sequence]['stdiosnr'] = $row2['stdiosnr'];
$pstats[$sequence]['miniosnr'] = $row2['miniosnr'];
$pstats[$sequence]['maxiosnr'] = $row2['maxiosnr'];
$pstats[$sequence]['avgmotion'] = $row2['avgmotion'];
$pstats[$sequence]['stdmotion'] = $row2['stdmotion'];
$pstats[$sequence]['minmotion'] = $row2['minmotion'];
$pstats[$sequence]['maxmotion'] = $row2['maxmotion'];
if ($row2['stdiosnr'] != 0) {
$pstats[$sequence]['maxstdiosnr'] = ($row2['avgiosnr'] - $row2['miniosnr'])/$row2['stdiosnr'];
} else { $pstats[$sequence]['maxstdiosnr'] = 0; }
if ($row2['stdpvsnr'] != 0) {
$pstats[$sequence]['maxstdpvsnr'] = ($row2['avgpvsnr'] - $row2['minpvsnr'])/$row2['stdpvsnr'];
} else { $pstats[$sequence]['maxstdpvsnr'] = 0; }
if ($row2['stdmotion'] != 0) {
$pstats[$sequence]['maxstdmotion'] = ($row2['avgmotion'] - $row2['minmotion'])/$row2['stdmotion'];
} else { $pstats[$sequence]['maxstdmotion'] = 0; }
}
//print_r($pstats);
?>
<script>
$(document).ready(function() {
$(".highlightblack").hide();
$(".highlightred").hide();
$(".highlightorange").hide();
$(".highlightyellow").hide();
$(".highlightgreen").hide();
$(".ratingdiv").hover( function() { $(this).children(".highlightblack").show(); }, function() { $(this).children(".highlightblack").hide(); } );
$(".ratingdiv").hover( function() { $(this).children(".highlightred").show(); }, function() { $(this).children(".highlightred").hide(); } );
$(".ratingdiv").hover( function() { $(this).children(".highlightorange").show(); }, function() { $(this).children(".highlightorange").hide(); } );
$(".ratingdiv").hover( function() { $(this).children(".highlightyellow").show(); }, function() { $(this).children(".highlightyellow").hide(); } );
$(".ratingdiv").hover( function() { $(this).children(".highlightgreen").show(); }, function() { $(this).children(".highlightgreen").hide(); } );
});
$(function() {
$( document ).tooltip({show:{effect:'appear'}, hide:{duration:0}});
});
</script>
<style type="text/css">
.edit_inline { background-color: lightyellow; padding-left: 2pt; padding-right: 2pt; }
.edit_textarea { background-color: lightyellow; }
textarea.inplace_field { background-color: white; font-family: courier new; font-size: 8pt; border: 1pt solid gray; width: 800px; }
input.inplace_field { background-color: white; font-size: 8pt; border: 1pt solid gray; width: 200px; }
</style>
<table class="smallgraydisplaytable" width="100%">
<thead>
<tr>
<th>Series</th>
<th>Upload Beh</th>
<th>Protocol</th>
<th title="Time of the start of the series acquisition">Time</th>
<th>Notes</th>
<th title="View movement graph and FFT">QA</th>
<th title="Analyst ratings and notes">Ratings</th>
<th title="Total displacement in X direction">X</th>
<th title="Total displacement in Y direction">Y</th>
<th title="Total displacement in Z direction">Z</th>
<th title="Per Voxel SNR (timeseries) - Calculated from the fslstats command">PV<br>SNR</th>
<th title="Inside-Outside SNR - This calculates the brain signal (center of brain-extracted volume) compared to the average of the volume corners">IO<br>SNR</th>
<th>Motion R<sup>2</sup></th>
<th>Sequence</th>
<th>Length<br><span class="tiny">approx.</span></th>
<th>TR<br><span class="tiny">ms</span></th>
<th>Spacing <br><span class="tiny">(x y z)</span></th>
<th>Image size <br><span class="tiny">(x y z)</span></th>
<th>BOLD reps</th>
<th># files</th>
<th>Size</th>
<th>Beh</th>
<? if ($GLOBALS['issiteadmin']) { ?>
<th>Hide</th>
<th>Reset QA</th>
<? } ?>
</tr>
</thead>
<tbody>
<?
/* just get a list of MR series ids */
$sqlstring = "select mrseries_id from mr_series where study_id = $id order by series_num";
$result = MySQLQuery($sqlstring, __FILE__, __LINE__);
while ($row = mysql_fetch_array($result, MYSQL_ASSOC)) {
$mrseriesids[] = $row['mrseries_id'];
}
/* get the rating information */
if (count($mrseriesids) < 1) {
?>
<tr>
<td colspan="22" align="center">No series found for this study</td>
</tr>
<?
}
else {
$sqlstring3 = "select * from ratings where rating_type = 'series' and data_modality = 'MR' and data_id in (" . implode(',',$mrseriesids) . ")";
$result3 = MySQLQuery($sqlstring3, __FILE__, __LINE__);
while ($row3 = mysql_fetch_array($result3, MYSQL_ASSOC)) {
$ratingseriesid = $row3['data_id'];
$ratings[$ratingseriesid][] = $row3['rating_value'];
}
//print_r($ratings);
/* get the actual MR series info */
mysql_data_seek($result,0);
$sqlstring = "select * from mr_series where study_id = $id order by series_num";
$result = MySQLQuery($sqlstring, __FILE__, __LINE__);
while ($row = mysql_fetch_array($result, MYSQL_ASSOC)) {
$mrseries_id = $row['mrseries_id'];
$series_datetime = date('g:ia',strtotime($row['series_datetime']));
$protocol = $row['series_protocol'];
$series_desc = $row['series_desc'];
$sequence = $row['series_sequencename'];
$series_num = $row['series_num'];
$series_tr = $row['series_tr'];
$series_te = $row['series_te'];
$series_flip = $row['series_flip'];
$phasedir = $row['phaseencodedir'];
$phaseangle = $row['phaseencodeangle'];
$series_spacingx = $row['series_spacingx'];
$series_spacingy = $row['series_spacingy'];
$series_spacingz = $row['series_spacingz'];
$series_fieldstrength = $row['series_fieldstrength'];
$img_rows = $row['img_rows'];
$img_cols = $row['img_cols'];
$img_slices = $row['img_slices'];
$bold_reps = $row['bold_reps'];
$numfiles = $row['numfiles'];
$series_size = $row['series_size'];
$series_status = $row['series_status'];
$series_notes = $row['series_notes'];
$beh_size = $row['beh_size'];
$numfiles_beh = $row['numfiles_beh'];
$data_type = $row['data_type'];
$lastupdate = $row['lastupdate'];
$image_type = $row['image_type'];
$image_comments = $row['image_comments'];
$ishidden = $row['ishidden'];
if (($numfiles_beh == '') || ($numfiles_beh == 0)) {
/* get the number and size of the beh files */
$behs = glob($GLOBALS['cfg']['archivedir'] . "/$uid/$study_num/$series_num/beh/*");
//print_r($behs);
$numfiles_beh = count($behs);
$totalsize = 0;
foreach ($behs as $behfile) {
$beh_size += filesize($behfile);
}
if ($numfiles_beh > 0) {
$sqlstring5 = "update mr_series set beh_size = '$beh_size', numfiles_beh = '$numfiles_beh' where mrseries_id = $mrseries_id";
$result5 = MySQLQuery($sqlstring5, __FILE__, __LINE__);
}
}
if ($phasedir == "COL") {
// A>>P or P>>A
if ($phaseangle == 0) {
$phase = "A >> P";
}
elseif ((abs($phaseangle) > 3.1) && (abs($phaseangle) < 3.2)) {
$phase = "P >> A";
}
else {
$phase = "COL";
}
}
else {
// R>>L or L>>R
if (($phaseangle > 1.5) && ($phaseangle < 1.6)) {
$phase = "R >> L";
}
elseif (($phaseangle < -1.5) && ($phaseangle > -1.6)) {
$phase = "L >> R";
}
else {
$phase = "ROW";
}
}
$behdir = "";
if (trim($protocol) == "") {
$protocol = "(blank)";
}
$scanlengthsec = ($series_tr * $numfiles)/1000.0;
//echo "[Secs: $scanlengthsecs]";
$scanlength = floor($scanlengthsec/60.0) . ":" . sprintf("%02d",round(fmod($scanlengthsec,60.0)));
if ( (preg_match("/epfid2d1/i",$sequence)) && ($numfiles_beh < 1)) { $behcolor = "red"; } else { $behcolor = ""; }
if ($numfiles_beh < 1) { $numfiles_beh = "-"; }
$thumbpath = $GLOBALS['cfg']['archivedir'] . "/$uid/$study_num/$series_num/thumb.png";
$gifthumbpath = $GLOBALS['cfg']['archivedir'] . "/$uid/$study_num/$series_num/thumb.gif";
$realignpath = $GLOBALS['cfg']['archivedir'] . "/$uid/$study_num/$series_num/MotionCorrection.txt";
$sqlstring2 = "select * from mr_qa where mrseries_id = $mrseries_id";
$result2 = MySQLQuery($sqlstring2, __FILE__, __LINE__);
$row2 = mysql_fetch_array($result2, MYSQL_ASSOC);
$iosnr = $row2['io_snr'];
$pvsnr = $row2['pv_snr'];
$move_minx = $row2['move_minx'];
$move_miny = $row2['move_miny'];
$move_minz = $row2['move_minz'];
$move_maxx = $row2['move_maxx'];
$move_maxy = $row2['move_maxy'];
$move_maxz = $row2['move_maxz'];
$acc_minx = $row2['acc_minx'];
$acc_miny = $row2['acc_miny'];
$acc_minz = $row2['acc_minz'];
$acc_maxx = $row2['acc_maxx'];
$acc_maxy = $row2['acc_maxy'];
$acc_maxz = $row2['acc_maxz'];
$motion_rsq = $row2['motion_rsq'];
$rangex = abs($move_minx) + abs($move_maxx);
$rangey = abs($move_miny) + abs($move_maxy);
$rangez = abs($move_minz) + abs($move_maxz);
$rangex2 = abs($acc_minx) + abs($acc_maxx);
$rangey2 = abs($acc_miny) + abs($acc_maxy);
$rangez2 = abs($acc_minz) + abs($acc_maxz);
$stdsmotion = 0;
/* calculate color based on voxel size... red (100) means more than 1 voxel displacement in that direction */
if ($series_spacingx > 0) {
$xindex = round(($rangex/$series_spacingx)*100); if ($xindex > 100) { $xindex = 100; }
$xindex2 = round(($rangex2/$series_spacingx)*100); if ($xindex2 > 100) { $xindex2 = 100; }
}
if ($series_spacingy > 0) {
$yindex = round(($rangey/$series_spacingy)*100); if ($yindex > 100) { $yindex = 100; }
$yindex2 = round(($rangey2/$series_spacingy)*100); if ($yindex2 > 100) { $yindex2 = 100; }
}
if ($series_spacingz > 0) {
$zindex = round(($rangez/$series_spacingz)*100); if ($zindex > 100) { $zindex = 100; }
$zindex2 = round(($rangez2/$series_spacingz)*100); if ($zindex2 > 100) { $zindex2 = 100; }
}
/* get standard deviations from the mean for SNR */
if ($pstats[$sequence]['stdiosnr'] != 0) {
if ($iosnr > $pstats[$sequence]['avgiosnr']) {
$stdsiosnr = 0;
}
else {
$stdsiosnr = (($iosnr - $pstats[$sequence]['avgiosnr'])/$pstats[$sequence]['stdiosnr']);
}
}
if ($pstats[$sequence]['stdpvsnr'] != 0) {
if ($pvsnr > $pstats[$sequence]['avgpvsnr']) {
$stdspvsnr = 0;
}
else {
$stdspvsnr = (($pvsnr - $pstats[$sequence]['avgpvsnr'])/$pstats[$sequence]['stdpvsnr']);
}
}
if ($pstats[$sequence]['stdmotion'] != 0) {
if ($motion_rsq > $pstats[$sequence]['avgmotion']) {
$stdmotion = 0;
}
else {
$stdmotion = (($motion_rsq - $pstats[$sequence]['avgmotion'])/$pstats[$sequence]['stdmotion']);
}
}
if ($pstats[$sequence]['maxstdpvsnr'] == 0) { $pvindex = 100; }
else { $pvindex = round(($stdspvsnr/$pstats[$sequence]['maxstdpvsnr'])*100); }
$pvindex = 100 + $pvindex;
if ($pvindex > 100) { $pvindex = 100; }
if ($pstats[$sequence]['maxstdiosnr'] == 0) { $ioindex = 100; }
else { $ioindex = round(($stdsiosnr/$pstats[$sequence]['maxstdiosnr'])*100); }
$ioindex = 100 + $ioindex;
if ($ioindex > 100) { $ioindex = 100; }
if ($ioindex < 0) { $ioindex = 0; }
if ($pstats[$sequence]['maxstdmotion'] == 0) { $motionindex = 100; }
else { $motionindex = round(($stdmotion/$pstats[$sequence]['maxstdmotion'])*100); }
$motionindex = 100 + $motionindex;
if ($motionindex > 100) { $motionindex = 100; }
if ($motionindex < 0) { $motionindex = 0; }
//echo "[ioindex: $ioindex]";
$maxpvsnrcolor = $colors[100-$pvindex];
$maxiosnrcolor = $colors[100-$ioindex];
$maxmotioncolor = $colors[100-$motionindex];
if ($pvsnr <= 0.0001) { $pvsnr = "-"; $maxpvsnrcolor = ""; }
else { $pvsnr = number_format($pvsnr,2); }
if ($iosnr <= 0.0001) { $iosnr = "-"; $maxiosnrcolor = ""; }
else { $iosnr = number_format($iosnr,2); }
//if ($motion_rsq <= 0.0001) { $motion_rsq = "-"; $maxmotioncolor = ""; }
//else { $motion_rsq = number_format($motion_rsq,2); }
/* setup movement colors */
$maxxcolor = $colors[$xindex];
$maxycolor = $colors[$yindex];
$maxzcolor = $colors[$zindex];
if ($rangex <= 0.0001) { $rangex = "-"; $maxxcolor = ""; }
else { $rangex = number_format($rangex,2); }
if ($rangey <= 0.0001) { $rangey = "-"; $maxycolor = ""; }
else { $rangey = number_format($rangey,2); }
if ($rangez <= 0.0001) { $rangez = "-"; $maxzcolor = ""; }
else { $rangez = number_format($rangez,2); }
/* setup acceleration colors */
$maxxcolor2 = $colors[$xindex2];
$maxycolor2 = $colors[$yindex2];
$maxzcolor2 = $colors[$zindex2];
if ($rangex2 <= 0.0001) { $rangex2 = "-"; $maxxcolor2 = ""; }
else { $rangex2 = number_format($rangex2,2); }
if ($rangey2 <= 0.0001) { $rangey2 = "-"; $maxycolor2 = ""; }
else { $rangey2 = number_format($rangey2,2); }
if ($rangez2 <= 0.0001) { $rangez2 = "-"; $maxzcolor2 = ""; }
else { $rangez2 = number_format($rangez2,2); }
/* format the motion r^2 value */
if ($motion_rsq == 0) {
$motion_rsq = '-';
$maxmotioncolor = "";
}
else {
$motion_rsq = number_format($motion_rsq,5);
}
/* get manually entered QA info */
$sqlstringC = "select avg(value) 'avgrating', count(value) 'count' from manual_qa where series_id = $mrseries_id and modality = 'MR'";
//PrintSQL($sqlstringC);
$resultC = MySQLQuery($sqlstringC, __FILE__, __LINE__);
$rowC = mysql_fetch_array($resultC, MYSQL_ASSOC);
$avgrating = $rowC['avgrating'];
$ratingcount = $rowC['count'];
if ($avgrating < 0.5) { $manualqacolor = "black"; }
if (($avgrating >= 0.5) && ($avgrating < 1.5)) { $manualqacolor = "#FF0000"; }
if (($avgrating >= 1.5) && ($avgrating <= 3.0)) { $manualqacolor = "#00FF00"; }
if ($ratingcount < 1) { $manualqacolor = "#EFEFEF"; }
/* check if this is real data, or unusable data based on the ratings, and get rating counts */
$isbadseries = false;
$istestseries = false;
$ratingcount2 = '';
$hasratings = false;
$rowcolor = '';
//print_r($ratings);
if (isset($ratings)) {
foreach ($ratings as $key => $ratingarray) {
if ($key == $mrseries_id) {
$hasratings = true;
if (in_array(5,$ratingarray)) {
$isbadseries = true;
}
if (in_array(6,$ratingarray)) {
$istestseries = true;
}
$ratingcount2 = count($ratingarray);
break;
}
}
}
if ($isbadseries) { $rowcolor = "red"; }
if ($istestseries) { $rowcolor = "#AAAAAA"; }
if ($ishidden) { $rowcolor = "AAA"; }
/* --- audit the dicom files --- */
$dupes = null;
$dcmcount = 0;
if ($audit) {
$dicoms = glob($GLOBALS['cfg']['archivedir'] . "/$uid/$study_num/$series_num/dicom/*.dcm");
//print_r($dicoms);
$dcmcount = count($dicoms);
if ($dcmcount > 0) {
//$filename = $dicoms[0];
$mergeddcms = null;
foreach ($dicoms as $dcmfile) {
$dicom = Nanodicom::factory($dcmfile, 'simple');
$dicom->parse(array(array(0x0010, 0x0010), array(0x0010, 0x0030), array(0x0010, 0x0040), array(0x0018, 0x1030), array(0x0008, 0x103E), array(0x0010, 0x0020), array(0x0020, 0x0012), array(0x0020, 0x0013), array(0x0008, 0x0020), array(0x0008, 0x0030), array(0x0008, 0x0032)));
$dicom->profiler_diff('parse');
$filesubjectname = trim($dicom->value(0x0010, 0x0010));
$filesubjectdob = trim($dicom->value(0x0010, 0x0030));
$filesubjectsex = trim($dicom->value(0x0010, 0x0040));
$fileprotocol = trim($dicom->value(0x0018, 0x1030));
$fileseriesdesc = trim($dicom->value(0x0008, 0x103E));
$fileseriesnum = trim($dicom->value(0x0020, 0x0011));
$filescanid = trim($dicom->value(0x0010, 0x0020));
$fileinstancenumber = trim($dicom->value(0x0020, 0x0013));
$fileslicenumber = trim($dicom->value(0x0020, 0x0012));
$fileacquisitiontime = trim($dicom->value(0x0008, 0x0032));
$filecontenttime = trim($dicom->value(0x0008, 0x0033));
$filestudydate = trim($dicom->value(0x0008, 0x0020));
$filestudytime = trim($dicom->value(0x0008, 0x0030));
unset($dicom);
//echo "<pre>$fileprotocol, $protocol -- $fileslicenumber, $fileinstancenumber - [$filestudydate $filestudytime] - [$dbstudydatetime]</pre><br>";
$filestudydatetime = $filestudydate . substr($filestudytime,0,6);
$dbstudydatetime = str_replace(array(":","-"," "),"",$dbstudydatetime);
$dbsubjectdob = str_replace(array(":","-"," "),"",$dbsubjectdob);
if (
($fileprotocol != $protocol) ||
($dbsubjectname != $filesubjectname) ||
($dbsubjectdob != $filesubjectdob) ||
($dbsubjectsex != $filesubjectsex) ||
($series_num != $fileseriesnum) ||
($filestudydatetime != $dbstudydatetime)
)
{
if ($fileprotocol != $protocol) {
//echo "Protocol does not match (File: $fileprotocol DB: $protocol)<br>";
//echo "files don't match DB<br>";
$errantdcms[]{'filename'} = $dcmfile;
$errantdcms[]{'error'} = "Protocol does not match (File: $fileprotocol DB: $protocol)";
}
if (strcasecmp($dbsubjectname,$filesubjectname) != 0) {
if (($dbsubjectname == "") && ($filesubjectname) != "") {
//echo "Patient name does not match (File: $filesubjectname DB: $dbsubjectname)<br>";
$errantdcms[]{'filename'} = $dcmfile;
$errantdcms[]{'error'} = "Patient name does not match (File: $filesubjectname DB: $dbsubjectname)";
}
elseif (($filesubjectname == "") && ($dbsubjectname) != "") {
//echo "Patient name does not match (File: $filesubjectname DB: $dbsubjectname)<br>";
$errantdcms[]{'filename'} = $dcmfile;
$errantdcms[]{'error'} = "Patient name does not match (File: $filesubjectname DB: $dbsubjectname)";
}
else {
if ((stristr($dbsubjectname, $filesubjectname) === false) && (stristr($filesubjectname, $dbsubjectname) === false)) {
//echo "Patient name does not match (File: $filesubjectname DB: $dbsubjectname)<br>";
$errantdcms[]{'filename'} = $dcmfile;
$errantdcms[]{'error'} = "Patient name does not match (File: $filesubjectname DB: $dbsubjectname)";
}
}
}
if ($dbsubjectdob != $filesubjectdob) {
//echo "Patient DOB does not match (File: $filesubjectdob DB: $dbsubjectdob)<br>";
$errantdcms[]{'filename'} = $dcmfile;
$errantdcms[]{'error'} = "Patient DOB does not match (File: $filesubjectdob DB: $dbsubjectdob)";
}
if ($dbsubjectsex != $filesubjectsex) {
//echo "Patient sex does not match (File: $filesubjectsex DB: $dbsubjectsex)<br>";
$errantdcms[]{'filename'} = $dcmfile;
$errantdcms[]{'error'} = "Patient sex does not match (File: $filesubjectsex DB: $dbsubjectsex)";
}
if ($series_num != $fileseriesnum) {
//echo "Series number does not match (File: $fileseriesnum DB: $series_num)<br>";
$errantdcms[]{'filename'} = $dcmfile;
$errantdcms[]{'error'} = "Series number does not match (File: $fileseriesnum DB: $series_num)";
}
if ($filestudydatetime != $dbstudydatetime) {
//echo "Study datetime does not match (File: $filestudydatetime DB: $dbstudydatetime)<br>";
$errantdcms[]{'filename'} = $dcmfile;
$errantdcms[]{'error'} = "Study datetime does not match (File: $filestudydatetime DB: $dbstudydatetime)";
}
}
$mergeddcms{$filesubjectname}{$filesubjectdob}{$filesubjectsex}{$filestudydate}{$filestudytime}{$fileseriesnum}{$fileslicenumber}{$fileinstancenumber}{$fileacquisitiontime}{$filecontenttime}[] = $dcmfile;
if (count($mergeddcms{$filesubjectname}{$filesubjectdob}{$filesubjectsex}{$filestudydate}{$filestudytime}{$fileseriesnum}{$fileslicenumber}{$fileinstancenumber}{$fileacquisitiontime}{$filecontenttime}) > 1) {
/* check the MD5 hash to see if the files really are the same */
//$hash1 = md5_file(
//echo "Series $fileseriesnum contains duplicate files<br>";
$dupes[$series_num] = 1;
if ($fix) {
/* move the duplicate file to the dicom/extra directory */
if (!file_exists($GLOBALS['cfg']['archivedir'] . "/$uid/$study_num/$series_num/dicom/duplicates")) {
mkdir($GLOBALS['cfg']['archivedir'] . "/$uid/$study_num/$series_num/dicom/duplicates");
}
echo "Moving [$dcmfile] -> [" . $GLOBALS['cfg']['archivedir'] . "/$uid/$study_num/$series_num/dicom/duplicates/" . GenerateRandomString(20) . ".dcm]<br>";
rename($dcmfile, $GLOBALS['cfg']['archivedir'] . "/$uid/$study_num/$series_num/dicom/duplicates/" . GenerateRandomString(20) . ".dcm");
}
}
}
}
/* move the errant files */
if ($fix) {
for($i=0;$i<count($errantdcms);$i++) {
echo "Moving [$errantdcms[$i]{'filename'}] -> [" . $GLOBALS['dicomincomingpath'] . "/" . GenerateRandomString(20) . ".dcm]<br>";
rename($errantdcms[$i]{'filename'},$GLOBALS['dicomincomingpath'] . "/" . GenerateRandomString(20) . ".dcm");
}
/* rename the files in the directory */
$dicoms = glob($GLOBALS['cfg']['archivedir'] . "/$uid/$study_num/$series_num/dicom/*.dcm");
//print_r($dicoms);
$dcmcount = count($dicoms);
if ($dcmcount > 0) {
$dcmsize = 0;
foreach ($dicoms as $dcmfile) {
$dicom = Nanodicom::factory($dcmfile, 'simple');
$dicom->parse(array(array(0x0010, 0x0010), array(0x0010, 0x0030), array(0x0010, 0x0040), array(0x0018, 0x1030), array(0x0008, 0x103E), array(0x0010, 0x0020), array(0x0020, 0x0012), array(0x0020, 0x0013), array(0x0008, 0x0020), array(0x0008, 0x0030), array(0x0008, 0x0032)));
$dicom->profiler_diff('parse');
$fileseriesnum = trim($dicom->value(0x0020, 0x0011));
$fileinstancenumber = trim($dicom->value(0x0020, 0x0013));
$fileslicenumber = trim($dicom->value(0x0020, 0x0012));
$fileacquisitiontime = trim($dicom->value(0x0008, 0x0032));
unset($dicom);
$dcmsize += filesize($dcmfile);
$newdcmfile = $GLOBALS['cfg']['archivedir'] . "/$uid/$study_num/$series_num/dicom/$uid" . "_$study_num" . "_$series_num" . "_" . sprintf("%05d",$fileslicenumber) . "_" . sprintf("%05d",$fileinstancenumber) . "_$fileacquisitiontime.dcm";
//if (file_exists($newdcmfile)) {
/* some DTI files are weird, so we'll append the aquisition time */
//}
echo "$dcmfile --> $newdcmfile<br>";
rename($dcmfile, $newdcmfile);
}
/* update the database with the new info */
$sqlstring5 = "update mr_series set series_size = $dcmsize, numfiles = $dcmcount where mrseries_id = $mrseries_id";
$result5 = MySQLQuery($sqlstring5, __FILE__, __LINE__);
}
}
}
?>
<script type="text/javascript">
$(document).ready(function(){
$(".edit_inline<? echo $mrseries_id; ?>").editInPlace({
url: "series_inlineupdate.php",
params: "action=editinplace&modality=MR&id=<? echo $mrseries_id; ?>",
default_text: "<i style='color:#AAAAAA'>Add notes...</i>",
bg_over: "white",
bg_out: "lightyellow",
});
});
</script>
<script type="text/javascript">
// Popup window code
function newPopup(url) {
popupWindow = window.open(
url,'popUpWindow','height=700,width=800,left=10,top=10,resizable=yes,scrollbars=yes,toolbar=yes,menubar=no,location=no,directories=no,status=yes')
}
</script>
<style>
.ui-tooltip {
padding: 7px 7px;
border-radius: 5px;
font-size: 10px;
border: 1px solid black;
}
</style>
<tr style="color: <?php
echo $rowcolor;
?>
">
<td><?php
echo $series_num;
?>
<?
if ($dupes[$series_num] == 1) {
?><span style="color: white; background-color: red; padding: 1px 5px; font-weight: bold; font-size: 8pt">Contains duplicates</span> <?
}
?>
</td>
<td><span id="uploader<?php
echo $mrseries_id;
?>
"></span></td>
<td title="<b>Series Description</b> <?php
echo $series_desc;
?>
<br><b>Protocol</b> <?php
echo $protocol;
?>
<br><b>Sequence Description</b> <?php
echo $sequence;
?>
<br><b>TE</b> <?php
echo $series_te;
?>
ms<br><b>Magnet</b> <?php
echo $series_fieldstrength;
?>
T<br><b>Flip angle</b> <?php
echo $series_flip;
?>
°<br><b>Image type</b> <?php
echo $image_type;
?>
<br><b>Image comment</b> <?php
echo $image_comments;
?>
<br><b>Phase encoding</b> <?php
echo $phase;
?>
">
<? if ($data_type == "dicom") {
$dicoms = glob($GLOBALS['cfg']['archivedir'] . "/$uid/$study_num/$series_num/dicom/*.dcm");
$dcmfile = $dicoms[0];
if (file_exists($dcmfile)) {
?><a href="series.php?action=scanparams&dcmfile=<?php
echo $dcmfile;
?>
"><?php
echo $series_desc;
?>
</a><?
}
else {
?><span style="color: red" title="Files missing from disk"><?php
echo $series_desc;
?>
</span><?
}
} else {
echo $series_desc;
}
?>
<br>
<? if (file_exists($thumbpath)) { ?>
<a href="preview.php?image=<?php
echo $thumbpath;
?>
" class="preview"><img src="images/preview.gif" border="0"></a>
<? } ?>
<? if (file_exists($gifthumbpath)) { ?>
<a href="preview.php?image=<?php
echo $gifthumbpath;
?>
" class="preview"><img src="images/movie.png" border="0"></a>
<? } ?>
<? if ($bold_reps < 2) { ?>
<a href="viewimage.php?modality=mr&type=dicom&seriesid=<?php
echo $mrseries_id;
?>
"><img src="images/colors.png" border="0"></a>
<? } ?>
</td>
<td style="font-size:8pt"><?php
echo $series_datetime;
?>
</td>
<td><span id="series_notes" class="edit_inline<? echo $mrseries_id; ?>" style="background-color: lightyellow; padding: 1px 3px; font-size: 8pt;"><? echo $series_notes; ?></span></td>
<td class="seriesrow" style="padding: 0px 5px;">
<a href="JavaScript:newPopup('mrseriesqa.php?id=<?php
echo $mrseries_id;
?>
');"><img src="images/chart.gif" border="0" title="View QA results, including movement correction"></a>
</td>
<td class="seriesrow" style="padding: 0px 5px;">
<span style="font-size:7pt"><?php
echo $ratingcount2;
?>
</span>
<div id="popup" style="display:none; min-width:800px; min-height:400px"></div>
<? if ($hasratings) { $image = "rating2.png"; } else { $image = "rating.png"; } ?>
<a href="JavaScript:newPopup('ratings.php?id=<?php
echo $mrseries_id;
?>
&type=series&modality=mr');"><img src="images/<?php
echo $image;
?>
" border="0" title="View ratings"></a>
</td>
<td class="seriesrow" align="right" style="padding:0px">
<table cellspacing="0" cellpadding="1" height="100%" width="100%" class="movementsubtable" style="border-radius:0px">
<tr><td title="Total X displacement" class="mainval" style="background-color: <?php
echo $maxxcolor;
?>
;"><?php
echo $rangex;
?>
</td></tr>
<tr><td title="Total X acceleration" class="subval" style="background-color: <?php
echo $maxxcolor2;
?>
;"><?php
echo $rangex2;
?>
</td></tr>
</table>
</td>
<td class="seriesrow" align="right" style="padding:0px;margin:0px;height:100%">
<table cellspacing="0" cellpadding="0" height="100%" width="100%" class="movementsubtable">
<tr><td title="Total Y displacement" class="mainval" style="background-color: <?php
echo $maxycolor;
?>
;height:100%"><?php
echo $rangey;
?>
</td></tr>
<tr><td title="Total Y acceleration" class="subval" style="background-color: <?php
echo $maxycolor2;
?>
;height:100%"><?php
echo $rangey2;
?>
</td></tr>
</table>
</td>
<td class="seriesrow" align="right" style="padding:0px">
<table cellspacing="0" cellpadding="1" height="100%" width="100%" class="movementsubtable">
<tr><td title="Total Z displacement" class="mainval" style="background-color: <?php
echo $maxzcolor;
?>
;"><?php
echo $rangez;
?>
</td></tr>
<tr><td title="Total Z acceleration" class="subval" style="background-color: <?php
echo $maxzcolor2;
?>
;"><?php
echo $rangez2;
?>
</td></tr>
</table>
</td>
<td class="seriesrow" align="right" style="background-color: <?php
echo $maxpvsnrcolor;
?>
; font-size:8pt">
<a href="stddevchart.php?h=40&w=450&min=<?php
echo $pstats[$sequence]['minpvsnr'];
?>
&max=<?php
echo $pstats[$sequence]['maxpvsnr'];
?>
&mean=<?php
echo $pstats[$sequence]['avgpvsnr'];
?>
&std=<?php
echo $pstats[$sequence]['stdpvsnr'];
?>
&i=<?php
echo $pvsnr;
?>
&b=yes" class="preview" style="color: black; text-decoration: none"><?php
echo $pvsnr;
?>
</a>
</td>
<td class="seriesrow" align="right" style="background-color: <?php
echo $maxiosnrcolor;
?>
; font-size:8pt">
<a href="stddevchart.php?h=40&w=450&min=<?php
echo $pstats[$sequence]['miniosnr'];
?>
&max=<?php
echo $pstats[$sequence]['maxiosnr'];
?>
&mean=<?php
echo $pstats[$sequence]['avgiosnr'];
?>
&std=<?php
echo $pstats[$sequence]['stdiosnr'];
?>
&i=<?php
echo $iosnr;
?>
&b=yes" class="preview" style="color: black; text-decoration: none"><?php
echo $iosnr;
?>
</a>
</td>
<td class="seriesrow" align="right" style="background-color: <?php
echo $maxmotioncolor;
?>
; font-size:8pt">
<a href="stddevchart.php?h=40&w=450&min=<?php
echo $pstats[$sequence]['minmotion'];
?>
&max=<?php
echo $pstats[$sequence]['maxmotion'];
?>
&mean=<?php
echo $pstats[$sequence]['avgmotion'];
?>
&std=<?php
echo $pstats[$sequence]['stdmotion'];
?>
&i=<?php
echo $motion_rsq;
?>
&b=yes" class="preview" style="color: black; text-decoration: none"><?php
echo $motion_rsq;
?>
</a>
</td>
<td><?php
echo $sequence;
?>
</td>
<td style="font-size:8pt"><?php
echo $scanlength;
?>
</td>
<td align="right" style="font-size:8pt"><?php
echo $series_tr;
?>
</td>
<td style="font-size:8pt"><?php
echo number_format($series_spacingx, 1);
?>
× <?php
echo number_format($series_spacingy, 1);
?>
× <?php
echo number_format($series_spacingz, 1);
?>
</td>
<td style="font-size:8pt"><?php
echo $img_cols;
?>
× <?php
echo $img_rows;
?>
× <?php
echo $img_slices;
?>
</td>
<td style="font-size:8pt"><?php
echo $bold_reps;
?>
</td>
<td style="font-size:8pt">
<?php
echo $numfiles;
?>
<? if (($dcmcount != $numfiles) && ($audit)) { ?><span style="color: white; background-color: red; padding: 1px 5px; font-weight: bold"><?php
echo $dcmcount;
?>
</span> <? } ?>
</td>
<td nowrap style="font-size:8pt">
<?php
echo HumanReadableFilesize($series_size);
?>
<a href="download.php?modality=mr&type=dicom&seriesid=<?php
echo $mrseries_id;
?>
" border="0"><img src="images/download16.png" title="Download <?php
echo $data_type;
?>
data"></a>
</td>
<td nowrap bgcolor="<?php
echo $behcolor;
?>
">
<? if ($numfiles_beh != "-") { ?>
<a href="managefiles.php?seriesid=<?php
echo $mrseries_id;
?>
&modality=mr&datatype=beh"><?php
echo $numfiles_beh;
?>
</a>
<? } else { ?>
<?php
echo $numfiles_beh;
?>
<? } ?>
<span class="tiny">
<?
if ($numfiles_beh > 0) {
echo "(" . HumanReadableFilesize($beh_size) . ")";
?>
<a href="download.php?modality=mr&type=beh&seriesid=<?php
echo $mrseries_id;
?>
" border="0"><img src="images/download16.png" title="Download behavioral data"></a>
<?
}
?>
</span>
</td>
<? if ($GLOBALS['issiteadmin']) {
if ($ishidden) { ?>
<td><a href="studies.php?action=unhidemrseries&id=<?php
echo $id;
?>
&seriesid=<?php
echo $mrseries_id;
?>
" title="Un-hide this series from search results.">Unhide</a></td>
<? } else { ?>
<td><a href="studies.php?action=hidemrseries&id=<?php
echo $id;
?>
&seriesid=<?php
echo $mrseries_id;
?>
" title="Hide this series from search results. It will be visible on this page, but nowhere else on NiDB">Hide</a></td>
<?
}
?>
<td><a href="studies.php?action=resetqa&seriesid=<?php
echo $mrseries_id;
?>
&id=<?php
echo $id;
?>
" color="red">X</a></td>
<?
}
?>
</tr>
<?
}
?>
<!-- uploader script for this series -->
<script>
function createUploaders(){
/* window.onload can only be called once, so make 1 function to create all uploaders */
<?
mysql_data_seek($result,0); /* reset the sql result, so we can loop through it again */
while ($row = mysql_fetch_array($result, MYSQL_ASSOC)) {
$mrseries_id = $row['mrseries_id'];
?>
var uploader<?php
echo $mrseries_id;
?>
= new qq.FileUploader({
element: document.getElementById('uploader<?php
echo $mrseries_id;
?>
'),
action: 'upload.php',
params: {modality: 'MRBEH', studyid: '<?php
echo $id;
?>
', seriesid: <?php
echo $mrseries_id;
?>
},
debug: true
});
<?
}
?>
}
// in your app create uploader as soon as the DOM is ready
// don't wait for the window to load
window.onload = createUploaders;
</script>
<?
}
?>
</tbody>
</table>
<?
}
function Search($s) {
//print_r($s);
/*
***************** steps to searching *****************
1) build the search string
2) run the query
3) depending on the query type, either...
a) display the query, then end
b) display the results
*/
/* --------- [1] get the SQL search string ---------- */
$sqlstring = BuildSQLString($s);
if ($sqlstring == "") { return; }
/* escape all the variables and put them back into meaningful variable names */
foreach ($s as $key => $value) {
if (is_scalar($value)) { $$key = mysql_real_escape_string($s[$key]); }
else { $$key = $s[$key]; }
}
/* make modality lower case to conform with table names... MySQL table names are case sensitive when using the 'show tables' command */
$s_studymodality = strtolower($s_studymodality);
/* ---------- [2] run the query ----------- */
$starttime = microtime(true);
$result = MySQLQuery($sqlstring, __FILE__, __LINE__);
$querytime = microtime(true) - $starttime;
if ($s_resultorder == "debug") {
?>
<span class="sublabel">Query returned <?php
echo mysql_num_rows($result);
?>
rows in <?php
echo number_format($querytime, 4);
?>
sec</span>
<div style="background-color: #EEEEEE"><?php
echo $sqlstring;
?>
</div><br>
<div style="background-color: #EEEEEE"><?php
echo getFormattedSQL($sqlstring);
?>
</div>
<br><br><br><br>
<?
return;
}
/* display the results */
if (mysql_num_rows($result) > 0) {
if ((mysql_num_rows($result) > 100000) && ($s_resultorder != "pipelinecsv")) {
?>
<div style="border: 2px solid darkred; background-color: #FFEEEE; text-align: left; padding:5px; border-radius: 5px">
<b>Your search returned <? echo number_format(mysql_num_rows($result),0); ?> results... which is a lot</b>
<br>
Try changing the search criteria to return fewer results or select a .csv format
</div>
<?
return;
}
/* generate a color gradient in an array (green to yellow to red) */
$colors = GenerateColorGradient();
$colors2 = GenerateColorGradient2();
/* display the number of rows and the search time */
?>
<span class="sublabel">Query returned <? echo number_format(mysql_num_rows($result),0); ?> rows in <?php
echo number_format($querytime, 4);
?>
sec</span>
<details>
<summary style="font-size:9pt">View SQL query:</summary>
<div style="background-color: #EEEEEE; font-family:courier new; font-size:10pt"><?php
echo getFormattedSQL($sqlstring);
?>
<br></div>
</details>
<style>
#preview {
position:absolute;
border:1px solid #ccc;
background:gray;
padding:0px;
display:none;
color:#fff;
}
</style>
<script type="text/javascript">
// Popup window code
function newPopup(url) {
popupWindow = window.open(
url,'popUpWindow','height=700,width=800,left=10,top=10,resizable=yes,scrollbars=yes,toolbar=no,menubar=no,location=no,directories=no,status=no')
}
</script>
<?
/* ---------- pipeline results ------------ */
if (($s_resultorder == "pipeline") || ($s_resultorder == "pipelinecsv")) {
if ($s_pipelineresulttype == "i") {
/* get the result names first (due to MySQL bug which prevents joining in this table in the main query) */
$sqlstringX = "select * from analysis_resultnames where result_name like '%$s_pipelineresultname%' ";
$resultX = MySQLQuery($sqlstringX,__FILE__,__LINE__);
while ($rowX = mysql_fetch_array($resultX, MYSQL_ASSOC)) {
$resultnames[$rowX['resultname_id']] = $rowX['result_name'];
}
/* and get the result unit (due to the same MySQL bug) */
$sqlstringX = "select * from analysis_resultunit where result_unit like '%$s_pipelineresultunit%' ";
$resultX = MySQLQuery($sqlstringX,__FILE__,__LINE__);
while ($rowX = mysql_fetch_array($resultX, MYSQL_ASSOC)) {
$resultunit[$rowX['resultunit_id']] = $rowX['result_unit'];
}
/* ---------------- pipeline results (images) --------------- */
while ($row = mysql_fetch_array($result, MYSQL_ASSOC)) {
//PrintVariable($row,'row');
$step = $row['analysis_step'];
$pipelinename = $row['pipeline_name'];
$uid = $row['uid'];
$subject_id = $row['subject_id'];
$gender = $row['gender'];
$study_id = $row['study_id'];
$study_num = $row['study_num'];
$type = $row['result_type'];
$size = $row['result_size'];
//$name = $row['result_name'];
$name = $resultnames[$row['result_nameid']];
$unit = $resultunit[$row['result_unitid']];
$filename = $row['result_filename'];
$swversion = $row['result_softwareversion'];
$important = $row['result_isimportant'];
$lastupdate = $row['result_lastupdate'];
switch($type) {
case "v": $thevalue = $value; break;
case "f": $thevalue = $filename; break;
case "t": $thevalue = $text; break;
case "h": $thevalue = $filename; break;
case "i": $thevalue = $filename; break;
}
$tables["$uid$study_num"][$name] = $thevalue;
$tables["$uid$study_num"]['subjectid'] = $subject_id;
$tables["$uid$study_num"]['studyid'] = $study_id;
$tables["$uid$study_num"]['studynum'] = $study_num;
$names[$name] = "blah";
}
//PrintVariable($tables,'Tables');
?>
<table cellspacing="0" class="multicoltable">
<thead>
<tr>
<th>UID</th>
<?
foreach ($names as $name => $blah) {
?>
<th align="center" style="font-size:9pt"><?php
echo $name;
?>
</th>
<?
}
?>
</tr>
</thead>
<?
$maximgwidth = 1200/count($names);
$maximgwidth -= ($maximgwidth*0.05); /* subtract 5% of image width to give a gap between them */
if ($maximgwidth < 100) { $maximgwidth = 100; }
foreach ($tables as $uid => $valuepair) {
?>
<tr style="font-weight: <?php
echo $bold;
?>
">
<td><a href="studies.php?id=<?php
echo $tables[$uid]['studyid'];
?>
"><b><?php
echo $uid;
?>
</b></a></td>
<?
foreach ($names as $name => $blah) {
if ($tables[$uid][$name] == "") { $dispval = "-"; }
else { $dispval = $tables[$uid][$name]; }
list($width, $height, $type, $attr) = getimagesize("/mount$filename");
$filesize = number_format(filesize("/mount$filename")/1000) . " kB";
?>
<td style="padding:2px"><a href="preview.php?image=/mount<?php
echo $dispval;
?>
" class="preview"><img src="preview.php?image=/mount<?php
echo $dispval;
?>
" style="max-width: <?php
echo $maximgwidth;
?>
px"></a></td>
<?
}
?>
</tr>
<?
}
?>
</table>
<br><br><br><br><br><br><br><br>
<?
}
else {
/* ---------------- pipeline results (values) --------------- */
/* get the result names first (due to MySQL bug which prevents joining in this table in the main query) */
$sqlstringX = "select * from analysis_resultnames where result_name like '%$s_pipelineresultname%' ";
$resultX = MySQLQuery($sqlstringX,__FILE__,__LINE__);
while ($rowX = mysql_fetch_array($resultX, MYSQL_ASSOC)) {
$resultnames[$rowX['resultname_id']] = $rowX['result_name'];
}
/* and get the result unit (due to the same MySQL bug) */
$sqlstringX = "select * from analysis_resultunit where result_unit like '%$s_pipelineresultunit%' ";
$resultX = MySQLQuery($sqlstringX,__FILE__,__LINE__);
while ($rowX = mysql_fetch_array($resultX, MYSQL_ASSOC)) {
$resultunit[$rowX['resultunit_id']] = $rowX['result_unit'];
}
/* load the data into a useful table */
while ($row = mysql_fetch_array($result, MYSQL_ASSOC)) {
$step = $row['analysis_step'];
$pipelinename = $row['pipeline_name'];
$uid = $row['uid'];
$subject_id = $row['subject_id'];
$study_id = $row['study_id'];
$study_num = $row['study_num'];
$birthdate = $row['birthdate'];
$gender = $row['gender'];
$study_datetime = $row['study_datetime'];
$type = $row['result_type'];
$size = $row['result_size'];
$name = $resultnames[$row['result_nameid']];
$name2 = $resultnames[$row['result_nameid']];
$unit = $resultunit[$row['result_unitid']];
$unit2 = $resultunit[$row['result_unitid']];
$text = $row['result_text'];
$value = $row['result_value'];
$filename = $row['result_filename'];
$swversion = $row['result_softwareversion'];
$important = $row['result_isimportant'];
$lastupdate = $row['result_lastupdate'];
/* calculate age at scan */
list($year, $month, $day) = explode("-", $birthdate);
$d1 = mktime(0,0,0,$month,$day,$year);
list($year, $month, $day, $extra) = explode("-", $study_datetime);
$d2 = mktime(0,0,0,$month,$day,$year);
$ageatscan = number_format((($d2-$d1)/31536000),1);
if (strpos($unit,'^') !== false) {
$unit = str_replace('^','<sup>',$unit);
$unit .= '</sup>';
}
switch($type) {
case "v": $thevalue = $value; break;
case "f": $thevalue = $filename; break;
case "t": $thevalue = $text; break;
case "h": $thevalue = $filename; break;
case "i":
?>
<a href="preview.php?image=/mount<?php
echo $filename;
?>
" class="preview"><img src="images/preview.gif" border="0"></a>
<?
break;
}
if (substr($name, -(strlen($unit))) != $unit) {
$name .= " <b>$unit</b>";
$name2 .= " " . $row['result_unit'];
}
$tables[$uid][$name] = $thevalue;
$tables[$uid][$name2] = $thevalue;
$tables[$uid]['age'] = $ageatscan;
$tables[$uid]['gender'] = $gender;
$tables[$uid]['subjectid'] = $subject_id;
$tables[$uid]['studyid'] = $study_id;
$tables[$uid]['studynum'] = $study_num;
//$names[$name] = "blah";
if (($thevalue > $names[$name]['max']) || ($names[$name]['max'] == "")) { $names[$name]['max'] = $thevalue; }
if (($thevalue < $names[$name]['min']) || ($names[$name]['min'] == "")) { $names[$name]['min'] = $thevalue; }
if (($thevalue > $names2[$name2]['max']) || ($names2[$name2]['max'] == "")) { $names2[$name2]['max'] = $thevalue; }
if (($thevalue < $names2[$name2]['min']) || ($names2[$name2]['min'] == "")) { $names2[$name2]['min'] = $thevalue; }
}
if ($s_resultorder == "pipelinecsv") {
$csv = "uid,studynum,sex,age";
foreach ($names2 as $name2 => $blah) {
$csv .= ",$name2";
}
$csv .= "\n";
foreach ($tables as $uid => $valuepair) {
$csv .= $uid . ',' . $tables[$uid]['studynum'] . ',' . $tables[$uid]['gender'] . ',' . $tables[$uid]['age'];
foreach ($names2 as $name2 => $blah) {
$csv .= ',' . $tables[$uid][$name2];
}
$csv .= "\n";
}
$filename = "query" . GenerateRandomString(10) . ".csv";
file_put_contents("/tmp/" . $filename, $csv);
?>
<br><br>
<div width="50%" align="center" style="background-color: #FAF8CC; padding: 5px;">
Download .csv file <a href="download.php?type=file&filename=<?php
echo "/tmp/{$filename}";
?>
"><img src="images/download16.png"></a>
</div>
<?
}
else {
?>
<br><br><br><br><br>
<br><br><br><br><br>
<br><br><br><br><br>
<style>
tr.rowhover:hover { background-color: ffff96; }
td.tdhover:hover { background-color: yellow; }
</style>
<table cellspacing="0">
<tr>
<td>UID</td>
<td>Sex</td>
<td>Age</td>
<?
$csv = "studyid,sex,age";
foreach ($names as $name => $blah) {
$csv .= ",$name";
?>
<td style="max-width:25px;"><span style="padding-left: 8px; font-size:10pt; white-space:nowrap; display: block; -webkit-transform: rotate(-70deg) translate3d(0,0,0); -moz-transform: rotate(-70deg);"><?php
echo $name;
?>
</span></td>
<?
}
$csv .= "\n";
?>
</tr>
<?
foreach ($tables as $uid => $valuepair) {
?>
<tr style="font-weight: <?php
echo $bold;
?>
" class="rowhover">
<td>
<a href="studies.php?id=<?php
echo $tables[$uid]['studyid'];
?>
"><b><?php
echo $uid;
?>
</b><?php
echo $tables[$uid]['studynum'];
?>
</a>
</td>
<td style="border-left: 1px solid #AAAAAA; border-top: 1px solid #AAAAAA; font-size:9pt; padding:2px;"><?php
echo $tables[$uid]['gender'];
?>
</td>
<td style="border-left: 1px solid #AAAAAA; border-top: 1px solid #AAAAAA; font-size:9pt; padding:2px;"><?php
echo $tables[$uid]['age'];
?>
</td>
<?
$stats[0][$tables[$uid]['gender']]++;
$stats[1][] = $tables[$uid]['age'];
$csv .= $tables[$uid]['studyid'] . ',' . $tables[$uid]['gender'] . ',' . $tables[$uid]['age'];
$i=2;
foreach ($names as $name => $blah) {
$val = $tables[$uid][$name];
$range = $names[$name]['max'] - $names[$name]['min'];
if (($val > 0) && ($range > 0)) {
$cindex = round((($val - $names[$name]['min'])/$range)*100);
//echo "[$val, $range, $cindex]<br>";
if ($cindex > 100) { $cindex = 100; }
}
if ($tables[$uid][$name] == "") {
$dispval = "-";
}
else {
$dispval = $tables[$uid][$name];
$stats[$i][] = $val;
//$stats[$i]['numintotal'] ++;
}
$csv .= ',' . $tables[$uid][$name];
if ($dispval != '-') {
if (($dispval + 0) > 10000) { $dispval = number_format($dispval,0); }
elseif (($dispval + 0) > 1000) { $dispval = number_format($dispval,2); }
else { $dispval = number_format($dispval,4); }
}
?>
<td class="tdhover" style="text-align: right; border-left: 1px solid #AAAAAA; border-top: 1px solid #AAAAAA; font-size:8pt; padding:2px; background-color: <? if ($s_pipelinecolorize) { if (trim($dispval) == '-') { echo "#EEE"; } else { echo $colors[$cindex]; } } ?>"><?php
echo $dispval;
?>
</td>
<?
$i++;
}
$csv .= "\n";
?>
</tr>
<?
}
if ($s_pipelineresultstats == 1) {
?>
<tr class="rowhover">
<td align="right"><b>N</b></td>
<td class="tdhover" style="text-align: right; border-left: 1px solid #AAAAAA; border-top: 1px solid #AAAAAA; font-size:8pt; padding:2px;">
<?
foreach ($stats[0] as $key => $value) { echo "$key -> $value<br>"; }
?>
</td>
<?
for($i=1;$i<count($stats);$i++) {
$count = count($stats[$i]);
?><td class="tdhover" style="text-align: right; border-left: 1px solid #AAAAAA; border-top: 1px solid #AAAAAA; font-size:8pt; padding:2px;"><?php
echo $count;
?>
</td><?
}
?>
</tr>
<tr class="rowhover">
<td align="right"><b>Min</b></td>
<td class="tdhover" style="text-align: right; border-left: 1px solid #AAAAAA; border-top: 1px solid #AAAAAA; font-size:8pt; padding:2px;"></td>
<?
for($i=1;$i<count($stats);$i++) {
$min = min($stats[$i]);
?><td class="tdhover" style="text-align: right; border-left: 1px solid #AAAAAA; border-top: 1px solid #AAAAAA; font-size:8pt; padding:2px;"><?php
echo $min;
?>
</td><?
}
?>
</tr>
<tr class="rowhover">
<td align="right"><b>Max</b></td>
<td class="tdhover" style="text-align: right; border-left: 1px solid #AAAAAA; border-top: 1px solid #AAAAAA; font-size:8pt; padding:2px;"></td>
<?
for($i=1;$i<count($stats);$i++) {
$max = max($stats[$i]);
?><td class="tdhover" style="text-align: right; border-left: 1px solid #AAAAAA; border-top: 1px solid #AAAAAA; font-size:8pt; padding:2px;"><?php
echo $max;
?>
</td><?
}
?>
</tr>
<tr class="rowhover">
<td align="right"><b>Mean</b></td>
<td class="tdhover" style="text-align: right; border-left: 1px solid #AAAAAA; border-top: 1px solid #AAAAAA; font-size:8pt; padding:2px;"></td>
<?
for($i=1;$i<count($stats);$i++) {
$avg = number_format(array_sum($stats[$i])/count($stats[$i]),2);
?><td class="tdhover" style="text-align: right; border-left: 1px solid #AAAAAA; border-top: 1px solid #AAAAAA; font-size:8pt; padding:2px;"><?php
echo $avg;
?>
</td><?
}
?>
</tr>
<tr class="rowhover">
<td align="right"><b>Median</b></td>
<td class="tdhover" style="text-align: right; border-left: 1px solid #AAAAAA; border-top: 1px solid #AAAAAA; font-size:8pt; padding:2px;"></td>
<?
for($i=1;$i<count($stats);$i++) {
$median = number_format(median($stats[$i]),2);
?><td class="tdhover" style="text-align: right; border-left: 1px solid #AAAAAA; border-top: 1px solid #AAAAAA; font-size:8pt; padding:2px;"><?php
echo $median;
?>
</td><?
}
?>
</tr>
<tr class="rowhover">
<td align="right"><b>Std Dev</b></td>
<td class="tdhover" style="text-align: right; border-left: 1px solid #AAAAAA; border-top: 1px solid #AAAAAA; font-size:8pt; padding:2px;"></td>
<?
for($i=1;$i<count($stats);$i++) {
$stdev = number_format(sd($stats[$i]),2);
?><td class="tdhover" style="text-align: right; border-left: 1px solid #AAAAAA; border-top: 1px solid #AAAAAA; font-size:8pt; padding:2px;"><?php
echo $stdev;
?>
</td><?
}
?>
</tr>
<?
}
?>
</table>
<? if ($s_pipelinecormatrix == 1) { ?>
<br><br><br><br>
<br><br><br><br>
<b>Correlation Matrix (r)</b><br>
<?
foreach ($names as $name => $blah) {
foreach ($tables as $uid => $valuepair) {
$lists['age'][] = $tables[$uid]['age'];
/* this loop gets the data into an array */
foreach ($names as $name => $blah) {
$lists[$name][] = $tables[$uid][$name];
}
}
}
?>
<table cellspacing="0">
<tr>
<td> </td>
<? foreach ($lists as $label => $vals1) { ?>
<td style="max-width:25px;"><span style="padding-left: 8px; font-size:10pt; white-space:nowrap; display: block; -webkit-transform: rotate(-70deg) translate3d(0,0,0); -moz-transform: rotate(-70deg);"><?php
echo $label;
?>
</span></td>
<? } ?>
</tr>
<?
$kashi = new Kashi();
foreach ($lists as $label => $vals1) {
for ($i=0;$i<count($vals1);$i++) {
if ($vals1[$i] == 0) { $vals1[$i] = 0.000001; }
}
?>
<tr class="rowhover">
<td align="right" style="font-size:10pt"><?php
echo $label;
?>
</td>
<?
foreach ($lists as $label => $vals2) {
$starttime1 = microtime(true);
/* compare vals1 to vals2 */
//$coeff = Correlation($vals1,$vals2);
for ($i=0;$i<count($vals2);$i++) {
if ($vals2[$i] == 0) { $vals2[$i] = 0.000001; }
}
$coeff = $kashi->cor($vals1,$vals2);
$coefftime = microtime(true) - $starttime1;
$cindex = round((($coeff - (-1))/2)*100);
//echo "[$val, $range, $cindex]<br>";
if ($cindex > 100) { $cindex = 100; }
/* display correlation coefficient */
?>
<td class="tdhover" style="text-align: right; border-left: 1px solid #AAAAAA; border-top: 1px solid #AAAAAA; font-size:8pt; padding:2px; background-color: <?php
echo $colors2[$cindex];
?>
"><?php
echo number_format($coeff, 3);
?>
</td>
<?
flush();
}
?>
</tr>
<?
}
?>
</table>
<?
}
}
}
}
elseif ($s_resultorder == 'subject') {
/* display only subject data */
SearchStudy($result);
}
elseif ($s_resultorder == 'uniquesubject') {
/* display only unique subject data */
SearchSubject($result);
}
elseif ($s_resultorder == 'long') {
/* display longitudinal data */
SearchLongitudinal($result);
}
else {
SearchDefault($result, $s, $colors, $colors2);
}
}
else {
?>
<span class="sublabel">Query returned <? echo number_format(mysql_num_rows($result),0); ?> rows in <?php
echo number_format($querytime, 4);
?>
sec</span>
<details>
<summary style="font-size:9pt">View SQL query:</summary>
<div style="background-color: #EEEEEE; font-family:courier new; font-size:10pt"><?php
echo getFormattedSQL($sqlstring);
?>
<br></div>
</details>
<br>
<?
}
}
function DisplayChart($data1, $data2, $data3, $title, $label1, $label2, $label3, $height, $id, $disptable)
{
$colors = GenerateColorGradient();
ksort($data1);
ksort($data2);
ksort($data3);
?>
<table class="smallgrayrounded" width="100%">
<tr>
<td class="title"><?php
echo $title;
?>
</td>
</tr>
<tr>
<td class="body">
<script>
$(function() {
var data1 = [<?php
foreach ($data1 as $date => $item) {
$value = $data1[$date]['value'];
$date = $date * 1000;
if ($date > 0 && $value > 0) {
$jsonstrings[] .= "['{$date}', {$value}]";
}
}
echo implode2(',', $jsonstrings);
?>
];
<?php
if ($label2 != "") {
?>
var data2 = [<?php
$jsonstrings = "";
foreach ($data2 as $date => $item) {
$value = $data2[$date]['value'];
$date = $date * 1000;
if ($date > 0 && $value > 0) {
$jsonstrings[] .= "['{$date}', {$value}]";
}
}
echo implode2(',', $jsonstrings);
?>
];
<?php
}
?>
<?php
if ($label3 != "") {
?>
var data3 = [<?php
$jsonstrings = "";
foreach ($data3 as $date => $item) {
$value = $data3[$date]['value'];
$date = $date * 1000;
if ($date > 0 && $value > 0) {
$jsonstrings[] .= "['{$date}', {$value}]";
}
}
echo implode2(',', $jsonstrings);
?>
];
<?php
}
?>
var options = {
series: {
lines: { show: true, fill: false },
points: { show: true }
},
grid: {
hoverable: true,
clickable: true
},
legend: { noColumns: 6 },
xaxis: { mode: "time", timeformat: "%Y-%m-%d" },
yaxis: { min: 0, tickDecimals: 1 },
selection: { mode: "x" },
};
var placeholder = $("#placeholder<?php
echo $id;
?>
");
var plot = $.plot(placeholder, [
{ label: "<?php
echo $label1;
?>
", color: '#F00', data: data1}<?php
if ($label2 != "") {
?>
, { label: "<?php
echo $label2;
?>
", color: '#4B4', data: data2} <?php
}
if ($label3 != "") {
?>
, { label: "<?php
echo $label3;
?>
", color: '#00F', data: data3} <?php
}
?>
],options);
});
</script>
<div id="placeholder<?php
echo $id;
?>
" style="height:<?php
echo $height;
?>
px;" align="center"></div>
</td>
</tr>
<?php
if ($disptable) {
?>
<tr>
<td class="body">
<table class="tinytable">
<thead>
<th>Date</th>
<th>Subject</th>
<th>Study</th>
<th>Value</th>
</thead>
<tbody>
<?php
// get min, max
$min = $data[0];
$max = $data[0];
foreach ($data as $date => $value) {
$value = $data[$date]['value'];
if ($value > $max) {
$max = $value;
}
if ($value < $min) {
$min = $value;
}
}
$range = $max - $min;
foreach ($data as $date => $value) {
$value = $data[$date]['value'];
$uid = $data[$date]['uid'];
$studynum = $data[$date]['studynum'];
$subjectid = $data[$date]['subjectid'];
$studyid = $data[$date]['studyid'];
if ($value > 0 && $range > 0) {
$cindex = round(($value - $min) / $range * 100);
if ($cindex > 100) {
$cindex = 100;
}
}
$date = $date;
$date = date("D, d M Y", $date);
?>
<tr>
<td><?php
echo $date;
?>
</td>
<td><a href="subjects.php?id=<?php
echo $subjectid;
?>
"><?php
echo $uid;
?>
</a></td>
<td><a href="subjects.php?id=<?php
echo $studyid;
?>
"><?php
echo $uid;
echo $studynum;
?>
</a></td>
<td align="right" bgcolor="<?php
echo $colors[$cindex];
?>
"><tt><?php
echo $value;
?>
<tt></td>
</tr>
<?php
}
?>
</tbody>
</table>
</td>
</tr>
<?php
}
?>
</table>
<?php
}
