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<?php |
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/** |
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Copyright (C) 2018-2020 KANOUN Salim |
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This program is free software; you can redistribute it and/or modify |
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it under the terms of the Affero GNU General Public v.3 License as published by |
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the Free Software Foundation; |
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This program is distributed in the hope that it will be useful, |
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but WITHOUT ANY WARRANTY; without even the implied warranty of |
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MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the |
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Affero GNU General Public Public for more details. |
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You should have received a copy of the Affero GNU General Public Public along |
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with this program; if not, write to the Free Software Foundation, Inc., |
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51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA |
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*/ |
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/** |
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* Fill Orthanc_Studies and Orthanc_Series table to link DICOM Orthanc storage with the web plateform |
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* Used in the validation process of the upload |
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*/ |
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class Fill_Orthanc_Table { |
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private $linkpdo; |
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private $username; |
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private $studyOrthancObject; |
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private $visitObject; |
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public function __construct($id_visit, String $username, PDO $linkpdo) { |
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$this->username=$username; |
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$this->linkpdo=$linkpdo; |
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$this->visitObject=new Visit($id_visit, $linkpdo); |
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} |
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/** |
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* return study details of a study stored in Orthanc |
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* @param String $studyID |
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* @return array |
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*/ |
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public function parseData(String $studyID) { |
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$studyData=new Orthanc_Study($studyID, null, null); |
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$studyData->retrieveStudyData(); |
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$this->studyOrthancObject=$studyData; |
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$studyDetails=get_object_vars($studyData); |
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return $studyDetails; |
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} |
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/** |
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* Fill data in the database, write data for study and for each series |
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* Once done trigger the change upload status of visit to update upload status and eventually skip |
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* local form and/or QC |
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*/ |
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public function fillDB($anonFromOrthancStudyId) { |
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//Check that original OrthancID is unknown for this study |
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if ($this->visitObject->getParentStudyObject()->isOriginalOrthancNeverKnown($anonFromOrthancStudyId)) { |
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try { |
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//Fill la database |
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$this->addToDbStudy($anonFromOrthancStudyId); |
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foreach ($this->studyOrthancObject->orthancSeries as $serie) { |
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//Fill series database |
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$this->addtoDbSerie($serie); |
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} |
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$this->visitObject->changeUploadStatus(Visit::DONE, $this->username); |
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} catch (Exception $e1) { |
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throw new Exception("Error during import ".$e1->getMessage()); |
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} |
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} else { |
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throw new Exception("Error during import Study Already Known"); |
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} |
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} |
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/** |
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* Private function to write into Orthanc_Studies DB |
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* @param string $anonFromOrthancStudyId |
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*/ |
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private function addToDbStudy(string $anonFromOrthancStudyId) { |
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$studyAcquisitionDate2=$this->parseDateTime($this->studyOrthancObject->studyDate, 1); |
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$studyAcquisitionTime2=$this->parseDateTime($this->studyOrthancObject->studyTime, 2); |
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if ($studyAcquisitionDate2 != null && $studyAcquisitionTime2 != null) { |
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$acquisitionDateTime=$studyAcquisitionDate2." ".$studyAcquisitionTime2; |
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} |
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$addBdd=$this->linkpdo->prepare('INSERT INTO orthanc_studies (id_visit, |
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uploader, |
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upload_date, |
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acquisition_date, |
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acquisition_time, |
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acquisition_datetime, |
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study_orthanc_id, |
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anon_from_orthanc_id, |
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study_uid, |
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study_description, |
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patient_orthanc_id, |
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patient_name, |
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patient_id, |
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number_of_series, |
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number_of_instances, |
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disk_size, |
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uncompressed_disk_size) |
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VALUES(:id_visit, |
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:uploader, |
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:upload_date, |
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:acquisition_date, |
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:acquisition_time, |
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:acquisition_datetime, |
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:study_orthanc_id, |
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:anon_from_orthanc_id, |
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:study_uid, |
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:study_description, |
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:patient_orthanc_id, |
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:patient_name, |
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:patient_id, |
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:number_of_series, |
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:number_of_instances, |
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:disk_size, |
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:uncompressed_disk_size) |
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ON DUPLICATE KEY UPDATE uploader=:uploader, |
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upload_date=:upload_date, |
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acquisition_date=:acquisition_date, |
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acquisition_time=:acquisition_time, |
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acquisition_datetime=:acquisition_datetime, |
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anon_from_orthanc_id=:anon_from_orthanc_id, |
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study_uid=:study_uid, |
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study_description=:study_description, |
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patient_orthanc_id=:patient_orthanc_id, |
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patient_name=:patient_name, |
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patient_id=:patient_id, |
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number_of_series=:number_of_series, |
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number_of_instances=:number_of_instances, |
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disk_size=:disk_size, |
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uncompressed_disk_size=:uncompressed_disk_size, |
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deleted=0 '); |
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$addBdd->execute(array( |
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'id_visit'=>$this->visitObject->id_visit, |
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'uploader'=>$this->username, |
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'upload_date'=>date("Y-m-d H:i:s"), |
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'acquisition_date'=>$this->studyOrthancObject->studyDate, |
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'acquisition_time'=>$this->studyOrthancObject->studyTime, |
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'acquisition_datetime'=> isset($acquisitionDateTime) ? $acquisitionDateTime : null, |
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'study_orthanc_id'=>$this->studyOrthancObject->studyOrthancID, |
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'anon_from_orthanc_id'=>$anonFromOrthancStudyId, |
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'study_uid'=>$this->studyOrthancObject->studyInstanceUID, |
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'study_description'=>$this->studyOrthancObject->studyDescription, |
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'patient_orthanc_id'=>$this->studyOrthancObject->parentPartientOrthancID, |
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'patient_name'=>$this->studyOrthancObject->parentPatientName, |
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'patient_id'=>$this->studyOrthancObject->parentPatientID, |
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'number_of_series'=>$this->studyOrthancObject->numberOfSeriesInStudy, |
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'number_of_instances'=>$this->studyOrthancObject->countInstances, |
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'disk_size'=>$this->studyOrthancObject->diskSizeMb, |
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'uncompressed_disk_size'=>$this->studyOrthancObject->uncompressedSizeMb |
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)); |
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} |
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/** |
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* Private function to write into the Orthanc_Series DB |
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* @param Orthanc_Serie $serie |
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*/ |
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private function addtoDbSerie(Orthanc_Serie $serie) { |
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$serieAcquisitionDate2=$this->parseDateTime($serie->seriesDate, 1); |
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$serieAcquisitionTime2=$this->parseDateTime($serie->seriesTime, 2); |
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if ($serieAcquisitionDate2 != null && $serieAcquisitionTime2 != null) { |
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$acquisitionDateTime=$serieAcquisitionDate2." ".$serieAcquisitionTime2; |
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} |
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$addBddSeries=$this->linkpdo->prepare('INSERT INTO orthanc_series ( |
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study_orthanc_id, |
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modality, |
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acquisition_date, |
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acquisition_time, |
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acquisition_datetime, |
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series_description, |
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injected_dose, |
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radiopharmaceutical, |
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half_life, |
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injected_time, |
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injected_activity, |
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series_orthanc_id, |
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number_of_instances, |
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serie_uid, |
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serie_number, |
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patient_weight, |
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serie_disk_size, |
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serie_uncompressed_disk_size, |
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manufacturer, |
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model_name, |
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injected_datetime) |
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VALUES( :Study_Orthanc_ID, |
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:Modality, |
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:Acquisition_Date, |
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:Acquisition_Time, |
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:Acquisition_DateTime, |
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:Series_Description, |
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:Injected_Dose, |
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:Radiopharmaceutical, |
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:HalfLife, |
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:Injected_Time, |
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:Injected_Activity, |
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:Series_Orthanc_ID, |
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:Number_Instances, |
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:Serie_UID, |
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:Serie_Number, |
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:Patient_Weight, |
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:Serie_Disk_Size, |
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:Serie_Uncompressed_Disk_Size, |
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:Manufacturer, |
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:Model_Name, :Injected_DateTime) |
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ON DUPLICATE KEY UPDATE study_orthanc_id=:Study_Orthanc_ID, modality=:Modality, acquisition_date=:Acquisition_Date, acquisition_time=:Acquisition_Time, acquisition_datetime=:Acquisition_DateTime, series_description=:Series_Description, injected_dose=:Injected_Dose, radiopharmaceutical=:Radiopharmaceutical, half_life=:HalfLife, injected_time=:Injected_Time, injected_activity=:Injected_Activity, number_of_instances=:Number_Instances, serie_number=:Serie_Number, patient_weight=:Patient_Weight, serie_disk_size=:Serie_Disk_Size, serie_uncompressed_disk_size=:Serie_Uncompressed_Disk_Size, manufacturer=:Manufacturer, model_name=:Model_Name, deleted=0, injected_datetime=:Injected_DateTime'); |
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$value=array( |
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'Study_Orthanc_ID'=>$this->studyOrthancObject->studyOrthancID, |
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'Modality'=>$serie->modality, |
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'Acquisition_Date'=>$serie->seriesDate, |
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'Acquisition_Time'=>$serie->seriesTime, |
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'Acquisition_DateTime'=> isset($acquisitionDateTime) ? $acquisitionDateTime : null, |
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'Series_Description'=> $serie->seriesDescription, |
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'Injected_Dose'=> is_numeric($serie->injectedDose) ? $serie->injectedDose : null, |
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'Radiopharmaceutical'=> $serie->radiopharmaceutical, |
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'HalfLife'=> is_numeric($serie->halfLife) ? $serie->halfLife : null, |
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'Injected_Time'=> $serie->injectedTime, |
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'Injected_DateTime'=> $this->parseDateTime($serie->injectedDateTime, 0), |
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'Injected_Activity'=> is_numeric($serie->injectedActivity) ? $serie->injectedActivity : null, |
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'Series_Orthanc_ID'=> $serie->serieOrthancID, |
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'Number_Instances'=> $serie->numberOfInstanceInOrthanc, |
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'Serie_UID'=> $serie->seriesInstanceUID, |
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'Serie_Number'=> $serie->seriesNumber, |
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'Patient_Weight'=>is_numeric($serie->patientWeight) ? $serie->patientWeight : null, |
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'Serie_Disk_Size'=> $serie->diskSizeMb, |
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'Serie_Uncompressed_Disk_Size' => $serie->uncompressedSizeMb, |
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'Manufacturer'=> $serie->seriesManufacturer, |
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'Model_Name'=>$serie->seriesModelName |
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); |
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$addBddSeries->execute($value); |
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} |
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/** |
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* Parse a DICOM date or Time string and return a string ready to send to database |
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* Return null if non parsable |
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* @param string $string |
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* @param type 0=dateTime, 1=Date, 2=Time |
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* return formated date for db saving, null if parse failed |
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*/ |
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private function parseDateTime($string, int $type) { |
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$parsedDateTime=null; |
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//If contain time split the ms (after.) which are not constant |
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if ($type == 0 || $type == 2) { |
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if (strpos($string, ".")) { |
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$timeWithoutms=explode(".", $string); |
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$string=$timeWithoutms[0]; |
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} |
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} |
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if ($type == 2) { |
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$dateObject=DateTime::createFromFormat('His', $string); |
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if ($dateObject !== false) { |
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$parsedDateTime=$dateObject->format('H:i:s'); |
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} |
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} else if ($type == 1) { |
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$dateObject=DateTime::createFromFormat('Ymd', $string); |
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if ($dateObject !== false) { |
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$parsedDateTime=$dateObject->format('Y-m-d'); |
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} |
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} else if ($type == 0) { |
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$dateObject=DateTime::createFromFormat('YmdHis', $string); |
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if ($dateObject !== false) { |
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$parsedDateTime=$dateObject->format('Y-m-d H:i:s'); |
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} |
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} |
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return $parsedDateTime; |
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} |
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} |
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