function getZoomData($uisubject, $SubjectKey, $StudyEventOID, $StudyEventRepeatKey)
{
require dirname(__FILE__) . "/../../../lib/nanodicom/nanodicom.php";
$importPathAnon = $uisubject->m_tblConfig["IMPORT_BASE_PATH"] . "dicom/anonymizedDICOM/";
$imageDir = $uisubject->m_tblConfig["PATH_TO_AJAXZOOM_PICT"];
$files = array();
//Populate $files array
if ($handle = opendir($imageDir)) {
while ($file = readdir($handle)) {
if ($file != "." && $file != "..") {
$fileinfo = explode("_", $file);
$file_SubjectKey = $fileinfo[0];
$file_StudyEventOID = $fileinfo[1];
$file_StudyEventRepeatKey = $fileinfo[2];
if ($file_SubjectKey == $SubjectKey && $file_StudyEventOID == $StudyEventOID && $file_StudyEventRepeatKey == $StudyEventRepeatKey) {
$files[$file] = $file;
}
}
}
closedir($handle);
}
ksort($files);
$zoomData = array();
$i = 1;
foreach ($files as $file) {
$zoomData[$i]['f'] = $file;
// File
$zoomData[$i]['p'] = "/pic/zoom/dicom/";
// Path
$i++;
}
$dicomFilename = $importPathAnon . substr($zoomData[1]['f'], 0, strpos($zoomData[1]['f'], "."));
$dicom = Nanodicom::factory($dicomFilename, 'simple');
$dicom->parse(array('PixelSpacing'));
$pixArr = explode("\\", $dicom->PixelSpacing);
$pixelSpacingH = $pixArr[0];
$pixelSpacingV = $pixArr[1];
//Turn the array $zoomData into a string that can be passed over query string in one variable
$zoomData = strtr(base64_encode(addslashes(gzcompress(serialize($zoomData), 9))), '+/=', '-_,');
$zoomDatas = array($zoomData, $i - 1, $pixelSpacingH, $pixelSpacingV);
return $zoomDatas;
}
/**
*/
public function provider()
{
$samples_dir = realpath(dirname(__FILE__)) . DIRECTORY_SEPARATOR . 'samples' . DIRECTORY_SEPARATOR;
$output_dir = realpath(dirname(__FILE__)) . DIRECTORY_SEPARATOR . 'tests' . DIRECTORY_SEPARATOR;
$files = array();
if ($handle = opendir($samples_dir)) {
while (false !== ($file = readdir($handle))) {
if ($file != "." && $file != ".." && is_file($samples_dir . $file)) {
$files[] = $file;
}
}
closedir($handle);
}
$data = array();
foreach ($files as $file) {
$filename = $samples_dir . $file;
$dicom = Nanodicom::factory($filename);
$data[] = array($dicom->summary(), file_get_contents($output_dir . $file . '.summary.txt'));
unset($dicom);
}
return $data;
}
/**
* Parses the object.
*
* If the list of elements has a tag name, dictionaries will be loaded. For performance
* is better to pass only arrays of the form:
* array(group, element) where group and element are numbers (hex or decimal equivalents or any other base).
* @param mixed array for a list of elements tags to read. parsing stops when all found. Or TRUE to force
* load dictionaries when parsing. This tool force the reading of dictionaries
* @param boolean a flag to test if dicom file has DCM header only.
* @return this
*/
public function parse($vr_reading_list = TRUE, $check_dicom_preamble = FALSE)
{
return parent::parse($vr_reading_list, $check_dicom_preamble);
}
function DisplayCTSeries($id, $study_num, $uid, $audit, $fix) {
/* 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>";
}
?>
<!--<a href="studies.php?id=<?$id?>&action=addseries&modality=CT">Add Series</a>-->
<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>
<span class="smallnote"><b>Upload file(s) by clicking the button or drag-and-drop (Firefox and Chrome only)</b><br>
DICOM files will only be associated with the study under which they were originally run... If you upload files from a different study, they won't show up here.</span>
<br><br>
<div id="file-uploader-demo1">
<noscript>
<p>Please enable JavaScript to use file uploader.</p>
<!-- or put a simple form for upload here -->
</noscript>
</div>
<br>
<table class="smalldisplaytable" width="100%">
<thead>
<tr>
<th>Series</th>
<th>Desc</th>
<th>Protocol</th>
<th>Time</th>
<th>Notes</th>
<th>Contrast</th>
<th>Body part</th>
<th>Options</th>
<th>KVP</th>
<th>Collection Dia</th>
<th>Contrast Route</th>
<th>Rotation Dir</th>
<th>Exposure</th>
<th>Tube current</th>
<th>Filter type</th>
<th>Power</th>
<th>Kernel</th>
<th>Spacing</th>
<th>Image size</th>
<th># files</th>
<th>Size</th>
</tr>
</thead>
<tbody>
<?
$sqlstring = "select * from ct_series where study_id = $id order by series_num";
$result = MySQLQuery($sqlstring, __FILE__, __LINE__);
while ($row = mysql_fetch_array($result, MYSQL_ASSOC)) {
$ctseries_id = $row['ctseries_id'];
$series_datetime = date('g:ia',strtotime($row['series_datetime']));
$series_desc = $row['series_desc'];
$protocol = $row['series_protocol'];
$sequence = $row['series_sequencename'];
$series_num = $row['series_num'];
$series_contrastbolusagent = $row['series_contrastbolusagent'];
$series_bodypartexamined = $row['series_bodypartexamined'];
$series_scanoptions = $row['series_scanoptions'];
$series_kvp = $row['series_kvp'];
$series_datacollectiondiameter = $row['series_datacollectiondiameter'];
$series_contrastbolusroute = $row['series_contrastbolusroute'];
$series_rotationdirection = $row['series_rotationdirection'];
$series_exposuretime = $row['series_exposuretime'];
$series_xraytubecurrent = $row['series_xraytubecurrent'];
$series_filtertype = $row['series_filtertype'];
$series_generatorpower = $row['series_generatorpower'];
$series_convolutionkernel = $row['series_convolutionkernel'];
$series_spacingx = $row['series_spacingx'];
$series_spacingy = $row['series_spacingy'];
$series_spacingz = $row['series_spacingz'];
$img_rows = $row['series_imgrows'];
$img_cols = $row['series_imgcols'];
$img_slices = $row['series_imgslices'];
$numfiles = $row['numfiles'];
$series_size = $row['series_size'];
$series_status = $row['series_status'];
$series_notes = $row['series_notes'];
$data_type = $row['data_type'];
$lastupdate = $row['lastupdate'];
if ( (preg_match("/epfid2d1/i",$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";
$realignpath = $GLOBALS['cfg']['archivedir'] . "/$uid/$study_num/$series_num/MotionCorrection.txt";
/* --- audit the dicom files --- */
if ($audit) {
$dicoms = glob($GLOBALS['cfg']['archivedir'] . "/$uid/$study_num/$series_num/dicom/*.dcm");
//print_r($dicoms);
$dcmcount = count($dicoms);
$dupes = null;
if ($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));
$filestudydate = trim($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} = $dcmfile;
$mergeddcms{$filesubjectname}{$filesubjectdob}{$filesubjectsex}{$filestudydate}{$filestudytime}{$fileseriesnum}{$fileslicenumber}{$fileinstancenumber}{$fileacquisitiontime}++;
if ($mergeddcms{$filesubjectname}{$filesubjectdob}{$filesubjectsex}{$filestudydate}{$filestudytime}{$fileseriesnum}{$fileslicenumber}{$fileinstancenumber}{$fileacquisitiontime} > 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");
}
}
}
}
echo "<pre>";
//print_r($mergeddcms);
print_r($errantdcms);
echo "</pre>";
/* 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 ct_series set series_size = $dcmsize, numfiles = $dcmcount where ctseries_id = $ctseries_id";
$result5 = MySQLQuery($sqlstring5, __FILE__, __LINE__);
}
}
}
?>
<script type="text/javascript">
$(document).ready(function(){
$(".edit_inline<? echo $ctseries_id; ?>").editInPlace({
url: "series_inlineupdate.php",
params: "action=editinplace&modality=CT&id=<? echo $ctseries_id; ?>",
default_text: "<i style='color:#AAAAAA'>Add notes...</i>",
bg_over: "white",
bg_out: "lightyellow",
});
});
</script>
<tr>
<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><?php
echo $series_desc;
?>
</td>
<td><?php
echo $protocol;
?>
<a href="preview.php?image=<?php
echo $thumbpath;
?>
" class="preview"><img src="images/preview.gif" border="0"></a></td>
<td><?php
echo $series_datetime;
?>
</td>
<td><span id="series_notes" class="edit_inline<? echo $ctseries_id; ?>" style="background-color: lightyellow; padding: 1px 3px; font-size: 8pt;"><? echo $series_notes; ?></span></td>
<td><?php
echo $series_contrastbolusagent;
?>
</td>
<td><?php
echo $series_bodypartexamined;
?>
</td>
<td><?php
echo $series_scanoptions;
?>
</td>
<td><?php
echo $series_kvp;
?>
<span class="tiny">V</span></td>
<td><?php
echo $series_datacollectiondiameter;
?>
<span class="tiny">mm</span></td>
<td><?php
echo $series_contrastbolusroute;
?>
</td>
<td><?php
echo $series_rotationdirection;
?>
</td>
<td><?php
echo $series_exposuretime;
?>
<span class="tiny">ms</span></td>
<td><?php
echo $series_xraytubecurrent;
?>
<span class="tiny">mA</span></td>
<td><?php
echo $series_filtertype;
?>
</td>
<td><?php
echo $series_generatorpower;
?>
<span class="tiny">V</span></td>
<td><?php
echo $series_convolutionkernel;
?>
</td>
<td><?php
echo number_format($series_spacingx, 1);
?>
× <?php
echo number_format($series_spacingy, 1);
?>
× <?php
echo number_format($series_spacingz, 1);
?>
</td>
<td><?php
echo $img_cols;
?>
× <?php
echo $img_rows;
?>
× <?php
echo $img_slices;
?>
</td>
<td>
<?php
echo $numfiles;
?>
<? if (($dcmcount != $numfiles) && ($audit)) { ?><span style="color: white; background-color: red; padding: 1px 5px; font-weight: bold"><?php
echo $dcmcount;
?>
</span> <? } ?>
</td>
<td nowrap><?php
echo HumanReadableFilesize($series_size);
?>
<a href="download.php?modality=ct&type=dicom&seriesid=<?php
echo $ctseries_id;
?>
" border="0"><img src="images/download16.png" title="Download <?php
echo $data_type;
?>
data"></a></td>
</tr>
<?
}
?>
</tbody>
</table>
<?
}
/**
* Public method to get the summary of the given file.
*
* @param string how the output is returned. Either as string (ready to be echoed) or array
* @return mixed|false Either a string, array or FALSE (when file is not DICOM)
*/
public function summary($output = 'string')
{
// Parse the file
$this->parse();
$transfer_syntax = trim($this->get(0x2, 0x10, 'UN'));
$transfer_syntax .= ($transfer_syntax == 'UN' or !array_key_exists($transfer_syntax, Nanodicom_Dictionary::$transfer_syntaxes)) ? ' - Unknow' : ' - Parsed using: ' . Nanodicom_Dictionary::$transfer_syntaxes[$transfer_syntax][0];
//.'. Parsed using: '.Nanodicom_Dictionary::$transfer_syntaxes[$this->_transfer_syntax][0];
if ($transfer_syntax == 'UN - Unknow') {
$transfer_syntax .= ' [Parsed Using: ' . $this->_transfer_syntax . ' - ' . Nanodicom_Dictionary::$transfer_syntaxes[$this->_transfer_syntax][0] . ']';
}
// Checking for "rows" since that value should be set for images.
$has_images = $this->get(0x28, 0x10, 'N/A') != 'N/A' ? 'YES' : 'NO';
$statuses = array('Not parsed yet', 'Partially parsed. Some tags were found', 'Successfully parsed!', 'Failed');
$values = array('Filename: ' => basename($this->_location), 'Transfer Syntax: ' => $transfer_syntax, 'DICOM file? ' => $statuses[$this->status], 'Has DCM preamble? ' => $this->has_dicom_preamble === TRUE ? 'YES' : 'NO', 'Has Metadata? ' => $this->get(0x2, 0x0, FALSE) ? 'YES' : 'NO', 'Modality: ' => $this->get(0x8, 0x60, 'UN'), 'Patient Name: ' => $this->get(0x10, 0x10, 'N/A'), 'Images? ' => $has_images);
$pixel_representation = array('0' => 'Unsigned Integer. Only positive values allowed.', '1' => '2\'s complement. Negative and positive allowed.', 'N/A' => 'Not available');
$planar_configuration = array('0' => 'Color-by-pixel: RGB, RGB, RGB..', '1' => 'Color-by-plane: RRR..., GGG..., BBB...', 'N/A' => 'Not available');
if ($has_images == 'YES') {
$values = $values + array('Rows: ' => $this->get(0x28, 0x10, 'N/A'), 'Cols: ' => $this->get(0x28, 0x11, 'N/A'), 'Samples per pixel: ' => $this->get(0x28, 0x2, 'N/A'), 'Bits Allocated: ' => $this->get(0x28, 0x100, 'N/A'), 'Bits Stored: ' => $this->get(0x28, 0x101, 'N/A'), 'High bit: ' => $this->get(0x28, 0x102, 'N/A'), 'Dose scaling: ' => $this->get(0x3004, 0xe, 'N/A'), 'Window Width: ' => $this->get(0x28, 0x1051, 'N/A'), 'Window Center: ' => $this->get(0x28, 0x1050, 'N/A'), 'Rescale intercept: ' => $this->get(0x28, 0x1052, 'N/A'), 'Rescale slope: ' => $this->get(0x28, 0x1053, 'N/A'), 'Number of Frames: ' => $this->get(0x28, 0x8, 'N/A'), 'Photometric Inter: ' => $this->get(0x28, 0x4, 'N/A'), 'Px Representation: ' => $this->get(0x28, 0x103, 'N/A') . ' - ' . Nanodicom::array_get($pixel_representation, $this->get(0x28, 0x103, 'N/A'), 'Wrong'), 'Planar Config: ' => $this->get(0x28, 0x6, 'N/A') . ' - ' . Nanodicom::array_get($planar_configuration, $this->get(0x28, 0x6, 'N/A'), 'Wrong'));
}
if ($output == 'string') {
$output = '';
foreach ($values as $index => $value) {
$output .= $index . "\t" . $value . "\n";
}
// Set the output back to values
$values = $output;
}
return $values;
}
$result = mysql_query($sqlstring) or die("Query failed: " . mysql_error() . "<br><i>{$sqlstring}</i><br>");
$row = mysql_fetch_array($result, MYSQL_ASSOC);
if (mysql_num_rows($result) > 0) {
$found = 1;
$seriesid = $row['ppiseries_id'];
}
if ($found) {
/* check the dicom files */
$dicoms = glob("{$archivedir}/{$subject}/{$study}/{$series}/dicom/*.dcm");
//print_r($dicoms);
$dcmcount = count($dicoms);
if ($dcmcount > 0) {
$filename = $dicoms[0];
//echo "$filename\n";
/* open the dicom file, check the 3 important tags */
$dicom = Nanodicom::factory($filename, 'simple');
$dicom->parse(array(array(0x10, 0x10), array(0x10, 0x30), array(0x10, 0x40)));
/* patient name,dob,sex */
// Only a small subset of the dictionary entries were loaded
$dicom->profiler_diff('parse');
//echo 'Patient name if exists: '.$dicom->value(0x0010, 0x0010)."\n"; // Patient Name if exists
// This will return nothing because dictionaries were not loaded
//echo 'Patient name should be empty here: '.$dicom->PatientName."\n";
$filesubjectname = trim($dicom->value(0x10, 0x10));
$filesubjectdob = trim($dicom->value(0x10, 0x30));
$filesubjectsex = trim($dicom->value(0x10, 0x40));
$fileprotocol = trim($dicom->value(0x18, 0x1030));
$fileseriesdesc = trim($dicom->value(0x8, 0x103e));
$filescanid = trim($dicom->value(0x10, 0x20));
//print_r($dicom);
if (strcasecmp($subjectname, $filesubjectname) != 0) {
/**
* Public method to get the images from the dicom object
*
* @param integer a default window width
* @param integer a default window center
* @return mixed false if something is missing or not image data found, otherwise an
* array of GD objects
*/
public function get_images($width = NULL, $center = NULL)
{
// Parse the object if not parsed yet
$this->parse();
// Set the profiler
$this->profiler['pixel']['start'] = microtime(TRUE);
$return = $this->_check_driver();
// If FALSE, driver not found
if (!$return) {
return FALSE;
}
// Supported transfer syntaxes
if (!array_key_exists(trim($this->_transfer_syntax), self::$reading_image_transfer_syntaxes)) {
// Not supported transfer syntax found
throw new Nanodicom_Exception('Transfer syntax ":syntax" not supported', array(':syntax' => $this->_transfer_syntax), 300);
}
// Let's read some values from DICOM file
$rows = $this->get(0x28, 0x10);
$cols = $this->get(0x28, 0x11);
if ($rows == NULL or $cols === NULL) {
// There is no rows, no samples per pixel, no pixel data or malformed dicom file
throw new Nanodicom_Exception('There is no rows, no samples per pixel, no pixel data or malformed dicom file', NULL, 301);
}
$samples_per_pixel = $this->get(0x28, 0x2, 1);
$bits_allocated = $this->get(0x28, 0x100);
$bits_stored = $this->get(0x28, 0x101);
$high_bit = $this->get(0x28, 0x102);
$dose_scaling = $this->get(0x3004, 0xe, 1);
$window_width = $width == NULL ? $this->get(0x28, 0x1051, 0) : $width;
$window_center = $center == NULL ? $this->get(0x28, 0x1050, 0) : $center;
$rescale_intercept = $this->get(0x28, 0x1052, 0);
$rescale_slope = $this->get(0x28, 0x1053, 1);
$number_of_frames = (int) $this->get(0x28, 0x8, 1);
$pixel_representation = $this->get(0x28, 0x103);
$photometric_interpretation = trim($this->get(0x28, 0x4, 'NONE'));
$planar_configuration = $this->get(0x28, 0x6, 0);
$transfer_syntax_uid = trim($this->get(0x2, 0x10));
$blob = $this->get(0x7fe0, 0x10);
// Save some values for internal use
// TODO: improve this, probably using $this->pixeler[]?
$this->_rows = $rows;
$this->_cols = $cols;
$this->_dose_scaling = $dose_scaling;
$this->_rescale_slope = $rescale_slope;
$this->_rescale_intercept = $rescale_intercept;
$this->_samples_per_pixel = $samples_per_pixel;
$this->_pixel_representation = $pixel_representation;
// Window Center and Width can have multiple values. By now, just reading the first one.
// It assumes the delimiter is the "\"
if (!(strpos($window_center, "\\") === FALSE)) {
$temp = explode("\\", $window_center);
$window_center = (int) $temp[0];
}
if (!(strpos($window_width, "\\") === FALSE)) {
$temp = explode("\\", $window_width);
$window_width = (int) $temp[0];
}
// Setting some values
$images = array();
$max = array();
$min = array();
$current_position = $starting_position = 0;
$current_image = 0;
$bytes_to_read = (int) $bits_allocated / 8;
$image_size = $cols * $rows * $samples_per_pixel * $bytes_to_read;
list($vr_mode, $endian) = Nanodicom::decode_transfer_syntax($transfer_syntax_uid);
$this->_vr_mode = $vr_mode;
$this->_endian = $endian;
if ($transfer_syntax_uid == '1.2.840.10008.1.2.4.50') {
// This is jpeg lossy 8-bits. Just get the data.
$images = array();
$counter = 0;
foreach ($blob as $group => $elements) {
foreach ($elements as $element => $indexes) {
if ($element == Nanodicom::SEQUENCE_DELIMITER) {
continue;
}
foreach ($indexes as $values) {
$data = $values;
if ($counter == 0) {
// Read Basic Offset Table
} else {
// It is a real Item
if (!isset($data['done'])) {
// Read value if not read yet
$this->_read_value_from_blob($data, $group, $element);
}
$images[] = $this->_read_image_blob($data['val']);
}
$counter++;
}
}
}
return $images;
}
if ($transfer_syntax_uid == '1.2.840.10008.1.2.5') {
// It is "RLE - Run Length Encoding, Lossless"
$counter = 0;
$temp = array();
foreach ($blob as $group => $elements) {
foreach ($elements as $element => $indexes) {
if ($element == Nanodicom::SEQUENCE_DELIMITER) {
continue;
}
foreach ($indexes as $values) {
$data = $values;
$data['g'] = $group;
$data['e'] = $element;
if ($counter == 0) {
// Read Basic Offset Table
} else {
// It is a real Item
$dir = realpath(dirname($this->_location)) . DIRECTORY_SEPARATOR;
$file = basename($this->_location);
if (!isset($data['done'])) {
// Read value if not read yet
$this->_read_value_from_blob($data, $group, $element);
}
// This is the item data
$item = $data['val'];
// Save the header
$header = array();
// 16 Unsigned Long values
for ($i = 0; $i <= 16; $i++) {
$chunk = substr($item, 4 * $i, 4);
$header[] = $this->{Nanodicom::$_read_int}(4, Nanodicom::LITTLE_ENDIAN, 4, Nanodicom::UNSIGNED, $chunk);
}
$total_segments = array_shift($header);
$segment_index = 0;
foreach ($header as $starting_byte_of_segment) {
// This is a segment, do the uncompression
if ($starting_byte_of_segment == 0) {
// Only process if the segment has a positive starting value
break;
}
$size_of_segment = $header[$segment_index + 1] == 0 ? strlen($item) - $starting_byte_of_segment : $header[$segment_index + 1] - $starting_byte_of_segment;
$temp[$counter - 1][$segment_index] = '';
$expected_segment_size = $cols * $rows * $bytes_to_read / $total_segments;
$bytes_count = $current_segment_size = 0;
while ($bytes_count < $size_of_segment) {
$tmp = $starting_byte_of_segment + $bytes_count;
// Read "n"
$n = substr($item, $starting_byte_of_segment + $bytes_count, 1);
$n = $this->{Nanodicom::$_read_int}(1, Nanodicom::LITTLE_ENDIAN, 1, Nanodicom::SIGNED, $n);
// Add 1
$bytes_count++;
if ($n >= 0 and $n <= 127) {
$temp[$counter - 1][$segment_index] .= substr($item, $starting_byte_of_segment + $bytes_count, $n + 1);
$bytes_count = $bytes_count + $n + 1;
$current_segment_size = $current_segment_size + $n + 1;
} elseif ($n <= -1 and $n >= -127) {
$byte = substr($item, $starting_byte_of_segment + $bytes_count, 1);
$temp[$counter - 1][$segment_index] .= str_repeat($byte, -$n + 1);
$bytes_count++;
$current_segment_size = $current_segment_size - $n + 1;
} else {
// Do nothing
}
}
$segment_index++;
}
}
// Increment counter
$counter++;
}
}
}
$counter--;
$blob = '';
for ($count = 0; $count < $counter; $count++) {
if ($photometric_interpretation == 'RGB') {
if ($planar_configuration == 1) {
// Color-by-plane: RRR..., GGG..., BBB...
$blob .= implode('', $temp[$count]);
} else {
// Color-by-pixel: RGB, RGB, RGB..
}
} else {
$dimension = $cols * $rows;
for ($i = 0; $i < $dimension; $i++) {
$part = '';
foreach ($temp[$count] as $segment) {
$part = substr($segment, $i, 1) . $part;
}
$blob .= $part;
}
}
}
}
// Blob here has "uncompressed" data (from raw or RLE)
if ($photometric_interpretation == 'PALETTE COLOR') {
$this->_samples_per_pixel = 3;
$palettes = array();
$palettes['R'] = array($this->get(0x28, 0x1101), $this->get(0x28, 0x1201));
$palettes['G'] = array($this->get(0x28, 0x1102), $this->get(0x28, 0x1202));
$palettes['B'] = array($this->get(0x28, 0x1103), $this->get(0x28, 0x1203));
$palettes['A'] = array($this->get(0x28, 0x1104), $this->get(0x28, 0x1204));
$entries = (int) $palettes['R'][0]['val1'];
$entries = $entries == 0 ? pow(2, 16) : $entries;
$first = $palettes['R'][0]['val2'];
$size = $palettes['R'][0]['val3'];
$palette_byte_size = (int) $size / 8;
$offset = 8;
$current_position = 0;
$colors = array('R', 'G', 'B');
// Now let's create the right values for the images
for ($index = 0; $index < $number_of_frames; $index++) {
// Create the image object
$image = self::create_image($cols, $rows);
for ($y = 0; $y < $rows; $y++) {
for ($x = 0; $x < $cols; $x++) {
$rgb = array();
$value = $this->_read_gray($blob, $current_position, $bytes_to_read);
$palette_index = $value <= $first ? $first : ($value > $first + $entries ? $first + $entries - 1 : $value);
$current_position += $bytes_to_read;
for ($sample = 0; $sample < 3; $sample++) {
$tmp = $this->_read_gray($palettes[$colors[$sample]][1], $palette_byte_size * $palette_index, $palette_byte_size);
$rgb[$sample] = $tmp >> 8;
}
// Set the color
$color = $this->_allocate_color_rgb($image, $rgb);
$rgb = NULL;
// Set the pixel value
$this->_set_pixel($image, $x, $y, $color);
$color = NULL;
}
}
// Append the current image
$images[] = $image;
$image = NULL;
}
return $images;
} else {
// Do this if no window center and window width are set and when samples per pixel is 1 (gray images).
if (($window_center == 0 or $window_width == 0) and $samples_per_pixel == 1) {
$length = strlen($blob);
// This is costly performance wise! :(
while ($current_position < $starting_position + $length) {
if ($current_position == $starting_position + $current_image * $image_size) {
// A new image has been found
$x = 0;
$y = 0;
$max[$current_image] = -200000;
// Small enough so it will be properly calculated
$min[$current_image] = 200000;
// Large enough so it wil be properly calculated
$current_image++;
}
$gray = $this->_read_gray($blob, $current_position, $bytes_to_read);
$current_position += $bytes_to_read;
// Getting the max
if ($gray > $max[$current_image - 1]) {
// max
$max[$current_image - 1] = $gray;
}
// Getting the min
if ($gray < $min[$current_image - 1]) {
// min
$min[$current_image - 1] = $gray;
}
$y++;
if ($y == $cols) {
// Next row
$x++;
$y = 0;
}
}
}
}
$current_position = $starting_position = 0;
// Now let's create the right values for the images
for ($index = 0; $index < $number_of_frames; $index++) {
if ($samples_per_pixel == 1) {
// Real max and min according to window center & width (if set)
$maximum = ($window_center != 0 and $window_width != 0) ? round($window_center + $window_width / 2) : $max[$index];
$minimum = ($window_center != 0 and $window_width != 0) ? round($window_center - $window_width / 2) : $min[$index];
// Check if window and level are sent
$maximum = (!empty($window) and !empty($level)) ? round($level + $window / 2) : $maximum;
$minimum = (!empty($window) and !empty($level)) ? round($level - $window / 2) : $minimum;
if ($maximum == $minimum) {
// Something wrong. Avoid having a zero division
throw new Nanodicom_Exception('Division by zero', NULL, 302);
}
}
// Create the image object
$image = self::create_image($cols, $rows);
$pixels = array();
for ($y = 0; $y < $rows; $y++) {
for ($x = 0; $x < $cols; $x++) {
switch ($samples_per_pixel) {
case 1:
$gray = $this->_read_gray($blob, $current_position, $bytes_to_read);
$current_position += $bytes_to_read;
// truncating pixel values over max and below min
$gray = $gray > $maximum ? $maximum : $gray;
$gray = $gray < $minimum ? $minimum : $gray;
// Converting to gray value
$gray = ($gray - $minimum) / ($maximum - $minimum) * 255;
// For MONOCHROME1 we have to invert the pixel values.
if ($photometric_interpretation == 'MONOCHROME1') {
$gray = 255 - $gray;
}
// Set the (gray) color
$color = $this->_allocate_color_gray($image, $gray);
$gray = NULL;
break;
case 3:
// It has 3 colors
$rgb = array();
for ($sample = 0; $sample < $samples_per_pixel; $sample++) {
$current_position = $planar_configuration == 0 ? $current_position : $sample * ($rows * $cols) + ($y * $cols + $x);
$rgb[$sample] = $this->_read_gray($blob, $current_position, $bytes_to_read);
$current_position += $bytes_to_read;
}
// Set the color
$color = $this->_allocate_color_rgb($image, $rgb);
$rgb = NULL;
break;
default:
break;
}
// Set the pixel value
$this->_set_pixel($image, $x, $y, $color);
$color = NULL;
}
}
// Append the current image
$images[] = $image;
$image = NULL;
}
// Collect the ending time for the profiler
$this->profiler['pixel']['end'] = microtime(TRUE);
return $images;
}
function DisplayAllScanParamaters($filename)
{
$urllist['Home'] = "index.php";
$urllist['Scan Params'] = "series.php";
NavigationBar("MR Scan Parameters", $urllist);
$dicom = Nanodicom::factory($filename, 'dumper');
$tags = $dicom->dump();
//print_r($tags);
$lines = explode("\n", $tags);
?>
<div align="center">
<table style="font-size: 10pt; border: 1px solid #DDDDDD" cellspacing="0" cellpadding="2">
<tr>
<td colspan="3" style="font-weight: bold; font-size: 14pt; text-align: center; padding:10px; border-bottom: 2px solid #666666">MR Sequence Parameters <span style="color:darkred">(CONTAINS PHI - DO NOT SHARE)</span></td>
</tr>
<?php
$lasttag1 = '';
foreach ($lines as $line) {
preg_match('/.*(\\w{4}):(\\w{4})\\s+(\\w+)\\s+([A-Z]{2})\\s+(\\d+)\\s+\\[(.*)\\].*/', $line, $matches);
//print_r($matches);
$tag1 = $matches[1];
$tag2 = $matches[2];
$name = $matches[3];
$value = $matches[6];
if (trim($tag1) == "") {
continue;
}
preg_match_all('/((?:^|[A-Z])[a-z]+)/', $name, $matches2);
$pieces = $matches2[0];
$name = implode(' ', $pieces);
if ($tag1 == "0018") {
switch ($tag2) {
case '0050':
$units = 'mm';
break;
case '0080':
$units = 'ms';
break;
case '0081':
$units = 'ms';
break;
case '0082':
$units = 'ms';
break;
case '0084':
$units = 'Hz';
break;
case '0087':
$units = 'T';
break;
case '0093':
$units = '%';
break;
case '0094':
$units = '%';
break;
case '1314':
$units = '°';
break;
default:
$units = '';
}
}
if ($lasttag1 != $tag1) {
$style = "border-top: solid 2px #666666";
} else {
$style = "border-top: solid 1px #CCCCCC";
}
?>
<tr>
<td style="color:darkblue; <?php
echo $style;
?>
"><?php
echo $tag1;
?>
:<?php
echo $tag2;
?>
</td>
<td style="<?php
echo $style;
?>
"><?php
echo $name;
?>
</td>
<td style="<?php
echo $style;
?>
"><?php
echo $value;
?>
<span class="tiny"><?php
echo $units;
?>
</span></td>
</tr>
<?php
$lasttag1 = $tag1;
}
?>
<tr>
<td colspan="3" style="font-size:8pt; border-top: solid 2px #666666; padding:8px">Generated by NiDB <?php
echo date("D M j, Y g:i a T");
?>
. Tags extracted using <a href="http://www.nanodicom.org">Nanodicom</a>
<br>Based on DICOM file [<?php
echo $filename;
?>
]</td>
</tr>
</table>
</div>
<?php
unset($dicom);
}
/**
*Extract image from DICOM file and save it as PNG
*Saved image are stored in the data directory, dicom_images folder
*Naming convention $SubjectKey_$StudyEventOID_$StudyEventRepeatKey_$FormOID_$FormRepeatKey_$imageSuffix_UID.png
* allow the identification of the image
*@author wlt
**/
public function saveImage($file, $SubjectKey, $StudyEventOID, $StudyEventRepeatKey, $FormOID = "", $FormRepeatKey = "", $imageSuffix = "")
{
$this->addLog(__METHOD__ . "({$file},{$SubjectKey},{$StudyEventOID},{$StudyEventRepeatKey},{$FormOID},{$FormRepeatKey},{$imageSuffix})", TRACE);
$importPath = $this->m_tblConfig["IMPORT_BASE_PATH"] . "dicom";
$exportPath = $this->m_tblConfig["PATH_TO_AJAXZOOM_PICT"];
$filename = $importPath . "/" . $file;
//Checking filename parameter
if (!file_exists($filename)) {
$this->addLog(__METHOD__ . " File {$filename} does not exists", FATAL);
}
//We need at least a StudyEventOID and a StudyEventRepeatKey
if ($StudyEventOID == "" || $StudyEventRepeatKey == "") {
$this->addLog(__METHOD__ . " StudyEventOID and StudyEventRepeatKey must be set", FATAL);
}
//Handle of Exception must be done at the upper level, to be added to the import report
$dicom = Nanodicom::factory($filename, 'pixeler');
$imageFilename = $SubjectKey . "_" . $StudyEventOID . "_" . $StudyEventRepeatKey . "_" . $FormOID . "_" . $FormRepeatKey . "_" . $imageSuffix . "_" . $file;
if (!file_exists($imageFilename . '.0.jpg')) {
$images = $dicom->get_images();
if ($images !== FALSE) {
foreach ($images as $index => $image) {
$dicom->write_image($image, $exportPath . "/" . $imageFilename . '.' . $index);
}
} else {
throw new Exception("For file {$filename} there are no DICOM images or transfer syntax not supported yet");
}
$images = NULL;
$dicom = Nanodicom::factory($filename, 'anonymizer');
file_put_contents(dirname($filename) . "/anonymizedDICOM/{$imageFilename}", $dicom->anonymize());
unset($dicom);
} else {
throw new Exception("File {$imageFilename}.0.jpg is already here");
}
unset($dicom);
}
// If using another library, for example, imagemagick, the following should be done:
// $images = $dicom->set_driver('imagick')->get_images();
if ($images !== FALSE) {
foreach ($images as $index => $image) {
// Defaults to jpg
$dicom->write_image($image, $dir . $file . '.' . $index);
// To write another format, pass the format in second parameter.
// This will write a png image instead
// $dicom->write_image($image, $dir.$file.'.'.$index, 'png');
}
} else {
echo "There are no DICOM images or transfer syntax not supported yet.\n";
}
$images = NULL;
} else {
echo "Image already exists\n";
}
unset($dicom);
} catch (Nanodicom_Exception $e) {
echo 'File failed. ' . $e->getMessage() . "\n";
}
// 21) Prints summary report
try {
echo "21) Prints summary report\n";
$dicom = Nanodicom::factory($filename);
echo $dicom->summary();
unset($dicom);
} catch (Nanodicom_Exception $e) {
echo 'File failed. ' . $e->getMessage() . "\n";
}
}
