salimkanoun / GaelO

src/models/Orthanc.php

<?php 
/**
 Copyright (C) 2018-2020 KANOUN Salim
 This program is free software; you can redistribute it and/or modify
 it under the terms of the Affero GNU General Public v.3 License as published by
 the Free Software Foundation;
 This program is distributed in the hope that it will be useful,
 but WITHOUT ANY WARRANTY; without even the implied warranty of
 MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
 Affero GNU General Public Public for more details.
 You should have received a copy of the Affero GNU General Public Public along
 with this program; if not, write to the Free Software Foundation, Inc.,
 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
 */

use GuzzleHttp\Client;

The type GuzzleHttp\Client was not found. Maybe you did not declare it correctly or list all dependencies?

use Psr\Http\Message\StreamInterface;

The type Psr\Http\Message\StreamInterface was not found. Maybe you did not declare it correctly or list all dependencies?

/**
 * Main class for Orthanc communication, serve usefull APIs (get dicom tags, send to peer, download zip...)
 * 
 * If Orthanc is using HTTPS :
 * the php_openssl extension must exist and be enabled
 * In the php.ini file you should add this lines if not exists:
 * extension=php_openssl.dll
 * allow_url_fopen = On
*/

Class Orthanc {
	
	private $url;
	private $context;
	
	/**
	 * Build connexion string in Orthanc, boolean to connect with Orthanc Exposed or Orthanc PACS
	 * @param boolean $exposed
	 */
	public function __construct(bool $exposed=false) {
		//Set Time Limit at 3H as operation could be really long
		set_time_limit(10800);

		$this->client = new Client();

The property client does not exist. Although not strictly required by PHP, it is generally a best practice to declare properties explicitly.

		//Set address of Orthanc server
		if ($exposed) {
			$this->url=GAELO_ORTHANC_EXPOSED_INTERNAL_ADDRESS.':'.GAELO_ORTHANC_EXPOSED_INTERNAL_PORT;
			$this->login = GAELO_ORTHANC_EXPOSED_INTERNAL_LOGIN;

The property login does not exist. Although not strictly required by PHP, it is generally a best practice to declare properties explicitly.

			$this->password = GAELO_ORTHANC_EXPOSED_INTERNAL_PASSWORD;

The property password does not exist. Although not strictly required by PHP, it is generally a best practice to declare properties explicitly.

			$this->context=array(
				'http' => array(
					'header'  => "Authorization: Basic ".base64_encode(GAELO_ORTHANC_EXPOSED_INTERNAL_LOGIN.':'.GAELO_ORTHANC_EXPOSED_INTERNAL_PASSWORD)
	   			));
		}else {
			$this->url=GAELO_ORTHANC_PACS_ADDRESS.':'.GAELO_ORTHANC_PACS_PORT;
			$this->login = GAELO_ORTHANC_PACS_LOGIN;
			$this->password = GAELO_ORTHANC_PACS_PASSWORD;
			$this->context=array(
	   			'http' => array(
	   				'header'  => "Authorization: Basic ".base64_encode(GAELO_ORTHANC_PACS_LOGIN.':'.GAELO_ORTHANC_PACS_PASSWORD)
	   			) );
	   }

	}
	
	/**
	 * Return list of Peers declared in Orthanc
	 * @return mixed
	 */
	public function getPeers() {
		$context=stream_context_create($this->context);
		$json=file_get_contents($this->url.'/peers/', false, $context);
		$peers=json_decode($json, true);
		return $peers;
	}
	
	/**
	 * Search function in Orthanc, search the Patients/Studies/Series level in Orthanc and return the raw response in JSON
	 * @param string $level
	 * @param string $patientID
	 * @param string $patientName
	 * @param string $studyDate
	 * @param string $studyUID
	 * @param string $accessionNumber
	 * @param string $studyDescription
	 * @return string json
	 */
	public function searchInOrthanc(string $level, string $patientID, string $patientName, string $studyDate, string $studyUID, string $accessionNumber, string $studyDescription) {
		
		$queryDetails=array(
				'PatientID' => $patientID,
				'PatientName' => $patientName,
				'StudyDate' => $studyDate,
				'StudyInstanceUID' => $studyUID,
				'AccessionNumber'=> $accessionNumber,
				'StudyDescription'=> $studyDescription,
		);
		
		$query=array(
				'Level' => $level,
				'CaseSensitive' => false,
				'Expand' => false,
				'Query' => $queryDetails,
				
		);
		
		$opts=array('http' =>
				array(
						'method'  => 'POST',
						'content' => json_encode($query),
						'header'=>  ['Content-Type: application/json Accept: application/json ', $this->context['http']['header']]
				)
		);

		$context=stream_context_create($opts);
		$resultJson=file_get_contents($this->url.'/tools/find', false, $context);
		$result=json_decode($resultJson);
		
		return $result;
	}
	
	/**
	 * return the ZIP as temp file containing the Orthanc ID ressources dicoms
	 * @param array $uidList
	 * @return resource temporary file path
	 */
	public function getZipStream(array $uidList) : StreamInterface {
	   
		if (!is_array($uidList)) {

The condition is_array($uidList) is always true.

			$uidList=array($uidList);
		}

		$options = [
			'auth' => [$this->login, $this->password],
			'headers'  => ['content-type' => 'application/json', 'Accept' => 'application/zip'],
			'body' => json_encode(array('Transcode'=>'1.2.840.10008.1.2.1', 'Resources' => $uidList)),
			'stream' => true
		];

		$response = $this->client->request('POST', $this->url.'/tools/create-archive' , $options);

		$zipStream = $response->getBody();
		
		return $zipStream;

The expression return $zipStream returns the type Psr\Http\Message\StreamInterface which is incompatible with the documented return type resource.

	}
	
	
	/**
	 * Delete in Orthanc patients / study / series depending on Level and Orthanc ID
	 * @param  $level
	 * @param  $uidList
	 */
	public function deleteFromOrthanc(string $level, string $uid) {
	    
		$opts=array('http' =>
			array(
				'method'  => 'DELETE',
				'header'=>  ['Content-Type: application/json Accept: application/json', $this->context['http']['header']]
			)
		);
	    
		$context=stream_context_create($opts);
		file_get_contents($this->url.'/'.$level.'/'.$uid, false, $context);
	    
	}
	
	/**
	 * Add Peer declaration to Orthanc
	 * @param string $name name of the peer
	 * @param string $url URL with http / https and port
	 * @param string $username
	 * @param string $password
	 * @return mixed
	 */
	public function addPeer(string $name, string $url, string $username, string $password) {
	    
		$peerValues['Username']=$username;

$peerValues was never initialized. Although not strictly required by PHP, it is generally a good practice to add $peerValues = array(); before regardless.

		$peerValues['Password']=$password;
		$peerValues['Url']=$url;
		$opts=array('http' =>
			array(
				'method'  => 'PUT',
				'content' => json_encode($peerValues),
				'header'=>  ['Content-Type: application/json Accept: application/json ', $this->context['http']['header']]
			)
		);
	    
		$context=stream_context_create($opts);
		$resultJson=file_get_contents($this->url.'/peers/'.$name, false, $context);
	    
		$result=json_decode($resultJson);
		return $result;
	    
	}
	
	/**
	 * Remove Peer declaration from Orthanc
	 * @param string $name
	 */
	public function removePeer(string $name) {
	    
		$opts=array('http' =>
			array(
				'method'  => 'DELETE',
				'header'=>  ['Content-Type: application/json Accept: application/json ', $this->context['http']['header']]
			)
		);
	    
		$context=stream_context_create($opts);
		$resultJson=file_get_contents($this->url.'/peers/'.$name, false, $context);
	    
		$result=json_decode($resultJson);
	    
		return $result;
	}
	
	/**
	 * Remove all peers from orthanc
	 */
	public function removeAllPeers() {
	    
		$peers=$this->getPeers();
	    
		foreach ($peers as $peer) {
			$this->removePeer($peer);
		}
	    
	}
	
	/**
	 * Test if a peer has Orthanc Peer Accelerator
	 * @param string $peer
	 * @return boolean
	 */
	public function isPeerAccelerated(string $peer) {
		$context=stream_context_create($this->context);
		$json=file_get_contents($this->url.'/transfers/peers/', false, $context);
		$peersTest=json_decode($json, true);
	    
		if ($peersTest[$peer] == "installed") {
			return true;
		}
	    
		return false;
	}
	
	/**
	 * Send id list of DICOM to a peer
	 * @param string $peer
	 * @param array $ids
	 */
	public function sendToPeer(string $peer, array $ids) {
		
		$opts=array('http' =>
				array(
						'method'  => 'POST',
						"timeout" => 300, 
						'content' => json_encode($ids),
						'header'=>  ['Content-Type: application/json Accept: application/json', $this->context['http']['header']]
				)
		);
		
		$context=stream_context_create($opts);
		$result=file_get_contents($this->url.'/peers/'.$peer.'/store', false, $context);
		return $result;
	    
	}
	
	/**
	 * Send to Orthanc peer but asynchroneously
	 * @param string $peer
	 * @param array $ids
	 * @return string
	 */
	public function sendToPeerAsync(string $peer, array $ids) {
		$data['Synchronous']=false;

$data was never initialized. Although not strictly required by PHP, it is generally a good practice to add $data = array(); before regardless.

		$data['Resources']=$ids;
	    
		$opts=array('http' =>
			array(
				'method'  => 'POST',
				'content' => json_encode($data),
				'header'=>  ['Content-Type: application/json Accept: application/json', $this->context['http']['header']]
			)
		);
	    
		$context=stream_context_create($opts);
		$result=file_get_contents($this->url.'/peers/'.$peer.'/store', false, $context);
		return $result;
	}
	
	/**
	 * Send to peer with transfers accelerator plugin
	 * @param string $peer
	 * @param array $ids
	 * @param bool $gzip
	 * @return string
	 */
	public function sendToPeerAsyncWithAccelerator(string $peer, array $ids, bool $gzip) {
	    
		//If Peer dosen't have accelerated transfers fall back to regular orthanc peer transfers
		if (!$this->isPeerAccelerated($peer)) {
			$answer=$this->sendToPeerAsync($peer, $ids);
			return $answer;
		}
	    
		if (!$gzip) $data['Compression']="none"; else $data['Compression']="gzip";

$data was never initialized. Although not strictly required by PHP, it is generally a good practice to add $data = array(); before regardless.

	    
		$data['Peer']=$peer;
	    
	    
		foreach ($ids as $serieID) {
			$resourceSeries['Level']="Series";
			$resourceSeries['ID']=$serieID;
			$data['Resources'][]=$resourceSeries;

The variable $resourceSeries seems to be defined later in this foreach loop on line 311. Are you sure it is defined here?

		}
	    
		$opts=array('http' =>
			array(
				'method'  => 'POST',
				'content' => json_encode($data),
				'header'=>  ['Content-Type: application/json Accept: application/json', $this->context['http']['header']]
			)
		);
	    
		$context=stream_context_create($opts);
		$result=file_get_contents($this->url.'/transfers/send', false, $context);
	    
		return $result;
	    
	}
	
	/**
	 * Import a file in Orthanc using the POST API
	 * @param string $file (path)
	 * @return string
	 */
	public function importFile(string $file) {
	    
		try {
			$opts=array('http' =>
				array(
					'method'  => 'POST',
					'content' => file_get_contents($file),
					'header'=>  ['Content-Type: application/dicom Accept: application/json', "content-length: ".filesize($file), $this->context['http']['header']]
				)
			);
    	    
			$context=stream_context_create($opts);
			$result=file_get_contents($this->url.'/instances', false, $context);
    	    
		}catch (Exception $e1) {
			error_log("Error during import Dcm ".$e1->getMessage());
		}
		return $result;

	}

	/**
	 * This method has the advantage to stream the content and avoid running out memory
	 */
	public function importFileGuzzle(string $file){
		try{
			$body = fopen($file, 'r');

			$options = ['auth' => [$this->login, $this->password],
			'headers'  => ['content-type' => 'application/dicom', 'Accept' => 'application/json'],
			'body' => $body];

			$response = $this->client->request('POST', $this->url.'/instances' , $options);
			
			return (string) $response->getBody();
		} catch (Exception $e1) {
			error_log("Error during import Dcm ".$e1->getMessage());
		}
	}

	/**
	 * Anonymize a study ressources according to Anon Profile
	 * Return the Anonymized Orthanc ID
	 * @param string $studyID
	 * @param string $profile
	 * @param string $patientCode
	 * @param string $visitType
	 * @param string $studyName
	 * @return string
	 */
	public function Anonymize(string $studyID, string $profile, string $patientCode, string $visitType, string $studyName) {
	    
		$jsonAnonQuery=$this->buildAnonQuery($profile, $patientCode, $patientCode, $visitType, $studyName);
	    
		$opts=array('http' =>
			array(
				'method'  => 'POST',
				"timeout" => 300,
				'content' => json_encode($jsonAnonQuery),
				'header'=>  ['Content-Type: application/json Accept: application/json', $this->context['http']['header']]
			)
		);
	    
		$context=stream_context_create($opts);

		$result=file_get_contents($this->url."/studies/".$studyID."/anonymize", false, $context);
        
		//get the resulting Anonymized study Orthanc ID
		$anonAnswer=json_decode($result, true);
		$anonymizedID=$anonAnswer['ID'];
	    
		//Remove SC if any in the anonymized study
		$this->removeSC($anonymizedID);
	    
		return $anonymizedID;
	    
	}
	
	/**
	 * Build Anon Json post for Anon settings
	 * @param string $profile
	 * @param string $newPatientName
	 * @param string $newPatientID
	 * @param string $newStudyDescription
	 * @return string
	 */
	private function buildAnonQuery(string $profile, string $newPatientName, string $newPatientID, string $newStudyDescription, string $clinicalStudy) {
    	    
		$tagsObjects=[];
		if ($profile == "Default") {
			$date=TagAnon::KEEP;
			$body=TagAnon::KEEP;
            
			$tagsObjects[]=new TagAnon("0010,0030", TagAnon::REPLACE, "19000101"); // BirthDay
			$tagsObjects[]=new TagAnon("0008,1030", TagAnon::REPLACE, $newStudyDescription); //studyDescription
			$tagsObjects[]=new TagAnon("0008,103E", TagAnon::KEEP); //series Description
           
    
		}else if ($profile == "Full") {
			$date=TagAnon::CLEAR;
			$body=TagAnon::CLEAR;
            
			$tagsObjects[]=new TagAnon("0010,0030", TagAnon::REPLACE, "19000101"); // BirthDay
			$tagsObjects[]=new TagAnon("0008,1030", TagAnon::CLEAR); // studyDescription
			$tagsObjects[]=new TagAnon("0008,103E", TagAnon::CLEAR); //series Description
		}
        
		//List tags releted to Date
		$tagsObjects[]=new TagAnon("0008,0022", $date); // Acquisition Date

The variable $date does not seem to be defined for all execution paths leading up to this point.

		$tagsObjects[]=new TagAnon("0008,002A", $date); // Acquisition DateTime
		$tagsObjects[]=new TagAnon("0008,0032", $date); // Acquisition Time
		$tagsObjects[]=new TagAnon("0038,0020", $date); // Admitting Date
		$tagsObjects[]=new TagAnon("0038,0021", $date); // Admitting Time
		$tagsObjects[]=new TagAnon("0008,0035", $date); // Curve Time
		$tagsObjects[]=new TagAnon("0008,0025", $date); // Curve Date
		$tagsObjects[]=new TagAnon("0008,0023", $date); // Content Date
		$tagsObjects[]=new TagAnon("0008,0033", $date); // Content Time
		$tagsObjects[]=new TagAnon("0008,0024", $date); // Overlay Date
		$tagsObjects[]=new TagAnon("0008,0034", $date); // Overlay Time
		$tagsObjects[]=new TagAnon("0040,0244", $date); // ...Start Date
		$tagsObjects[]=new TagAnon("0040,0245", $date); // ...Start Time
		$tagsObjects[]=new TagAnon("0008,0021", $date); // Series Date
		$tagsObjects[]=new TagAnon("0008,0031", $date); // Series Time
		$tagsObjects[]=new TagAnon("0008,0020", $date); // Study Date
		$tagsObjects[]=new TagAnon("0008,0030", $date); // Study Time
		$tagsObjects[]=new TagAnon("0010,21D0", $date); // Last menstrual date
		$tagsObjects[]=new TagAnon("0008,0201", $date); // Timezone offset from UTC
		$tagsObjects[]=new TagAnon("0040,0002", $date); // Scheduled procedure step start date
		$tagsObjects[]=new TagAnon("0040,0003", $date); // Scheduled procedure step start time
		$tagsObjects[]=new TagAnon("0040,0004", $date); // Scheduled procedure step end date
		$tagsObjects[]=new TagAnon("0040,0005", $date); // Scheduled procedure step end time
    	
		// same for Body characteristics
		$tagsObjects[]=new TagAnon("0010,2160", $body); // Patient's ethnic group

The variable $body does not seem to be defined for all execution paths leading up to this point.

		$tagsObjects[]=new TagAnon("0010,21A0", $body); // Patient's smoking status
		$tagsObjects[]=new TagAnon("0010,0040", $body); // Patient's sex
		$tagsObjects[]=new TagAnon("0010,2203", $body); // Patient's sex neutered
		$tagsObjects[]=new TagAnon("0010,1010", $body); // Patient's age
		$tagsObjects[]=new TagAnon("0010,21C0", $body); // Patient's pregnancy status
		$tagsObjects[]=new TagAnon("0010,1020", $body); // Patient's size
		$tagsObjects[]=new TagAnon("0010,1030", $body); // Patient's weight
    
		//Others
		$tagsObjects[]=new TagAnon("0008,0050", TagAnon::REPLACE, $clinicalStudy); // Accession Number contains study name
		$tagsObjects[]=new TagAnon("0010,0020", TagAnon::REPLACE, $newPatientID); //new Patient Name
		$tagsObjects[]=new TagAnon("0010,0010", TagAnon::REPLACE, $newPatientName); //new Patient Name
    	
		// Keep some Private tags usefull for PET/CT or Scintigraphy
		$tagsObjects[]=new TagAnon("7053,1000", TagAnon::KEEP); //Phillips
		$tagsObjects[]=new TagAnon("7053,1009", TagAnon::KEEP); //Phillips
		$tagsObjects[]=new TagAnon("0009,103B", TagAnon::KEEP); //GE
		$tagsObjects[]=new TagAnon("0009,100D", TagAnon::KEEP); //GE
		$tagsObjects[]=new TagAnon("0011,1012", TagAnon::KEEP); //Other
    	
		$jsonArrayAnon=[];
		$jsonArrayAnon['KeepPrivateTags']=false;
		$jsonArrayAnon['Force']=true;
    	
		foreach ($tagsObjects as $tag) {
    	    
			if ($tag->choice == TagAnon::REPLACE) {
				$jsonArrayAnon['Replace'][$tag->tag]=$tag->newValue;
			}else if ($tag->choice == TagAnon::KEEP) {
				$jsonArrayAnon['Keep'][]=$tag->tag;
			}
            
		}
    	
		return $jsonArrayAnon;

The expression return $jsonArrayAnon returns the type array which is incompatible with the documented return type string.

    	
	}
    
	/**
	 * Remove secondary captures in the study
	 * @param string $orthancStudyID
	 */
	private function removeSC(string $orthancStudyID) {
    	
		$studyOrthanc=new Orthanc_Study($orthancStudyID, $this->url, $this->context);
		$studyOrthanc->retrieveStudyData();
		$seriesObjects=$studyOrthanc->orthancSeries;
		foreach ($seriesObjects as $serie) {
			if ($serie->isSecondaryCapture()) {
				$this->deleteFromOrthanc("series", $serie->serieOrthancID);
			}
		}
    	
	}
    
    
	/**
	 * Return JobId details (get request in Orthanc)
	 * @param String $jobId
	 * @return mixed
	 */
	public function getJobDetails(String $jobId) {
        
		$context=stream_context_create($this->context);
		$json=file_get_contents($this->url.'/jobs/'.$jobId, false, $context);
        
		return json_decode($json, true);
        
	}

}