Merge pull request #707 from Pixilib/GaelO2-dev

Add Azure storage, TmtvProcessing Service, improved coverage calculation

.github/workflows/php-stan.yml

@@ -19,7 +19,7 @@ jobs:
  - name: 'Setup PHP'
  uses: shivammathur/setup-php@v2
  with:
- php-version: '8.1'
+ php-version: '8.2'
 
  - name: 'Copy .env'
  working-directory: ./GaelO2

.github/workflows/publish.yml

@@ -5,7 +5,6 @@ on:
  branches:
  - GaelO2
  - GaelO2-dev
- - tmtv-inference
  tags:
  - '*'
 

.github/workflows/tests.yml

@@ -20,7 +20,7 @@ jobs:
  - name: 'Setup PHP'
  uses: shivammathur/setup-php@v2
  with:
- php-version: '8.1'
+ php-version: '8.2'
 
  - name: 'Copy .env'
  working-directory: ./GaelO2

.gitignore

@@ -3,3 +3,4 @@ composer.phar
 .VSCodeCounter/*
 
 src/*
+GaelO2/app/Console/Commands/RealysaTmtvInference.php

Dockerfile

@@ -1,6 +1,7 @@
-FROM php:8.1.3-apache-bullseye
+FROM php:8.2.13-apache-bullseye
 
 ENV PHP_OPCACHE_VALIDATE_TIMESTAMPS="0"
+ENV TZ="UTC"
 
 RUN apt-get update -qy && \
  apt-get install -y --no-install-recommends apt-utils\
@@ -25,7 +26,7 @@ RUN apt-get update -qy && \
  postgresql-client-13 && \
  apt-get clean && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
 
-RUN pecl install pcov redis memcached-3.1.5
+RUN pecl install pcov redis memcached
 RUN docker-php-ext-install gd zip pdo pdo_mysql pdo_pgsql mbstring bcmath ctype fileinfo xml bz2 pcntl
 RUN docker-php-ext-configure opcache --enable-opcache \
  && docker-php-ext-install opcache

GaelO2/.env.example

@@ -36,6 +36,11 @@ AZURE_SUBSCRIPTION_ID=''
 AZURE_CONTAINER_GROUP=''
 AZURE_RESOURCE_GROUP=''
 
+FILESYSTEM_DISK='local'
+AZURE_BLOB_DSN=''
+AZURE_CONTAINER_NAME=''
+AZURE_BLOB_PREFIX=''
+
 BROADCAST_DRIVER=log
 CACHE_DRIVER=file
 QUEUE_CONNECTION=database

GaelO2/app/Console/Kernel.php

@@ -6,6 +6,7 @@
 use Illuminate\Console\Scheduling\Schedule;
 use Illuminate\Foundation\Console\Kernel as ConsoleKernel;
 use Illuminate\Support\Facades\Log;
+use DateTimeZone;
 
 class Kernel extends ConsoleKernel
 {
@@ -34,8 +35,8 @@ protected function schedule(Schedule $schedule)
  $schedule->call(function () {
  Log::info("Scheduler Probe");
  })
- ->hourly()
- ->sentryMonitor('gaelo-scheduler'); 
+  ->hourly()
+  ->sentryMonitor('gaelo-scheduler');
  }
 
  /**
@@ -45,8 +46,13 @@ protected function schedule(Schedule $schedule)
  */
  protected function commands()
  {
- $this->load(__DIR__.'/Commands');
+ $this->load(__DIR__ . '/Commands');
 
  require base_path('routes/console.php');
  }
+
+ protected function scheduleTimezone(): DateTimeZone|string|null
+ {
+ return 'UTC';
+ }
 }

GaelO2/app/GaelO/Adapters/JobAdapter.php

@@ -4,7 +4,6 @@
 
 use App\GaelO\Interfaces\Adapters\JobInterface;
 use App\Jobs\JobQcReport;
-use App\Jobs\JobRadiomicsReport;
 
 class JobAdapter implements JobInterface
 {
@@ -13,8 +12,4 @@ public function sendQcReportJob(int $visitId): void
  JobQcReport::dispatch($visitId);
  }
 
- public function sendRadiomicsReport(int $visitId, ?int $behalfUserId, ?array $destinatorEmails): void
- {
- JobRadiomicsReport::dispatch($visitId, $behalfUserId, $destinatorEmails);
- }
 }

GaelO2/app/GaelO/Adapters/MimeAdapter.php

@@ -3,7 +3,6 @@
 namespace App\GaelO\Adapters;
 
 use App\GaelO\Interfaces\Adapters\MimeInterface;
-use Illuminate\Support\Facades\Log;
 use League\MimeTypeDetection\ExtensionMimeTypeDetector;
 use League\MimeTypeDetection\GeneratedExtensionToMimeTypeMap;
 
@@ -12,12 +11,14 @@ class MimeAdapter implements MimeInterface
 
  public static function getExtensionsFromMime(string $mime): array
  {
+ if ($mime === 'application/dicom') return ['dcm'];
  $mimes = new ExtensionMimeTypeDetector();
  return $mimes->lookupAllExtensions($mime);
  }
 
  public static function getMimeFromExtension(string $extension): string
  {
+ if ($extension === 'dcm') return 'application/dicom';
  $mimes = new GeneratedExtensionToMimeTypeMap();
  return $mimes->lookupMimeType($extension);
  }

GaelO2/app/GaelO/Constants/Enums/ProcessingMaskEnum.php

@@ -0,0 +1,10 @@
+<?php
+
+namespace App\GaelO\Constants\Enums;
+
+enum ProcessingMaskEnum: string
+{
+ case RTSS = 'rtss';
+ case SEG = 'seg';
+ case NIFTI = 'nifti';
+}

GaelO2/app/GaelO/Interfaces/Adapters/JobInterface.php

@@ -5,5 +5,4 @@
 interface JobInterface
 {
  public function sendQcReportJob(int $visitId) : void;
- public function sendRadiomicsReport(int $visitId, ?int $behalfUserId, ?array $destinatorEmails) :void;
 }

GaelO2/app/GaelO/Interfaces/Repositories/DicomSeriesRepositoryInterface.php

@@ -20,7 +20,7 @@ public function getSeries(string $seriesInstanceUID, bool $withTrashed) : array
 
  public function getRelatedVisitIdFromSeriesInstanceUID(array $seriesInstanceUID, bool $withTrashed) : array ;
 
- public function getSeriesOrthancIDOfSeriesInstanceUID(array $seriesInstanceUID, bool $withTrashed) : array ;
+ public function getSeriesOrthancIDsOfSeriesInstanceUIDs(array $seriesInstanceUID, bool $withTrashed) : array ;
 
  public function getDicomSeriesOfStudyInstanceUIDArray(array $studyInstanceUID, bool $withTrashed) : array ;
 

GaelO2/app/GaelO/Interfaces/Repositories/VisitGroupRepositoryInterface.php

@@ -9,7 +9,7 @@ public function find($id) ;
 
  public function delete($id) : void ;
 
- public function createVisitGroup(String $studyName, String $name, String $modality) : void ;
+ public function createVisitGroup(String $studyName, String $name, String $modality) : array ;
 
  public function hasVisitTypes(int $visitGroupId) : bool ;
 

GaelO2/app/GaelO/Repositories/DicomSeriesRepository.php

@@ -90,7 +90,7 @@ public function getRelatedVisitIdFromSeriesInstanceUID(array $seriesInstanceUID,
  return $query->get()->pluck('dicomStudy.visit_id')->unique()->toArray();
  }
 
- public function getSeriesOrthancIDOfSeriesInstanceUID(array $seriesInstanceUID, bool $withTrashed): array
+ public function getSeriesOrthancIDsOfSeriesInstanceUIDs(array $seriesInstanceUID, bool $withTrashed): array
  {
  $query = $this->dicomSeriesModel
  ->whereIn('series_uid', $seriesInstanceUID)

GaelO2/app/GaelO/Repositories/VisitGroupRepository.php

@@ -26,14 +26,15 @@ public function delete($id): void
  $this->visitGroupModel->findOrFail($id)->delete();
  }
 
- public function createVisitGroup(String $studyName, String $name, String $modality): void
+ public function createVisitGroup(String $studyName, String $name, String $modality): array
  {
 
  $visitGroup = new VisitGroup();
  $visitGroup->name = $name;
  $visitGroup->study_name = $studyName;
  $visitGroup->modality = $modality;
  $visitGroup->save();
+ return $visitGroup->toArray();
  }
 
  public function hasVisitTypes(int $visitGroupId): bool

GaelO2/app/GaelO/Services/FormService/FormService.php

@@ -125,7 +125,7 @@ public function attachFile(array $reviewEntity, string $key, string $mimeType, s
  return $filename;
  }
 
- public function removeFile(array $reviewEntity, string $key): void
+ public function deleteFile(array $reviewEntity, string $key): void
  {
  if (empty($reviewEntity['sent_files'][$key])) {
  throw new GaelOBadRequestException('Non exisiting key file in review');

GaelO2/app/GaelO/Services/GaelOProcessingService/GaelOProcessingService.php

@@ -5,7 +5,6 @@
 use App\GaelO\Constants\SettingsConstants;
 use App\GaelO\Interfaces\Adapters\FrameworkInterface;
 use App\GaelO\Interfaces\Adapters\HttpClientInterface;
-use Illuminate\Support\Facades\Log;
 
 class GaelOProcessingService
 {

GaelO2/app/GaelO/Services/GaelOProcessingService/MaskProcessingService.php

@@ -0,0 +1,91 @@
+<?php
+
+namespace App\GaelO\Services\GaelOProcessingService;
+
+use App\GaelO\Constants\Enums\ProcessingMaskEnum;
+use App\GaelO\Services\GaelOProcessingService\GaelOProcessingService;
+use App\GaelO\Services\OrthancService;
+
+class MaskProcessingService
+{
+
+ private string $maskId;
+ private string $petId;
+ private string $petSeriesOrthancId;
+ private GaelOProcessingService $gaelOProcessingService;
+ private OrthancService $orthancService;
+
+ public function __construct(
+ OrthancService $orthancService,
+ GaelOProcessingService $gaelOProcessingService,
+ ) {
+ $this->gaelOProcessingService = $gaelOProcessingService;
+ $this->orthancService = $orthancService;
+ $this->orthancService->setOrthancServer(true);
+ }
+
+ public function setMaskId(string $maskId)
+ {
+ $this->maskId = $maskId;
+ }
+
+ public function getMaskId(): string
+ {
+ return $this->maskId;
+ }
+
+ public function setPetId(string $petId, string $petSeriesOrthancId)
+ {
+ $this->petId = $petId;
+ $this->petSeriesOrthancId = $petSeriesOrthancId;
+ }
+
+ public function getMaskAs(ProcessingMaskEnum $type, ?string $orientation = null) : string
+ {
+ if ($type === ProcessingMaskEnum::NIFTI) {
+ $exportFile = $this->gaelOProcessingService->getMaskDicomOrientation($this->maskId, $orientation, true);
+ } else if ($type === ProcessingMaskEnum::RTSS) {
+ $rtssId = $this->gaelOProcessingService->createRtssFromMask($this->petSeriesOrthancId, $this->maskId);
+ $exportFile = $this->gaelOProcessingService->getRtss($rtssId);
+ //remove downloaded data from processing
+ $this->gaelOProcessingService->deleteRessource("rtss", $rtssId);
+ } else if ($type === ProcessingMaskEnum::SEG) {
+ $segId = $this->gaelOProcessingService->createSegFromMask($this->petSeriesOrthancId, $this->maskId);
+ $exportFile = $this->gaelOProcessingService->getSeg($segId);
+ //remove downloaded data from processing
+ $this->gaelOProcessingService->deleteRessource("seg", $segId);
+ }
+
+ return $exportFile;
+ }
+
+ public function getStatsOfMask(): array
+ {
+ return $this->gaelOProcessingService->getStatsMaskSeries($this->maskId, $this->petId);
+ }
+
+ public function fragmentMask(): MaskProcessingService
+ {
+ $fragmentedMaskId = $this->gaelOProcessingService->fragmentMask($this->petId, $this->maskId, true);
+ $maskProcessingService = new MaskProcessingService($this->orthancService, $this->gaelOProcessingService);
+ $maskProcessingService->setMaskId($fragmentedMaskId);
+ $maskProcessingService->setPetId($this->petId, $this->petSeriesOrthancId);
+ return $maskProcessingService;
+ }
+
+ public function thresholdMaskTo41(): MaskProcessingService
+ {
+ $threshold41MaskId = $this->gaelOProcessingService->thresholdMask($this->maskId, $this->petId, "41%");
+ $maskProcessingService = new MaskProcessingService($this->orthancService, $this->gaelOProcessingService);
+ $maskProcessingService->setMaskId($threshold41MaskId);
+ $maskProcessingService->setPetId($this->petId, $this->petSeriesOrthancId);
+ return $maskProcessingService;
+ }
+
+ public function createTepMaskMip(): string
+ {
+ $mipFragmentedPayload = ['maskId' => $this->maskId, 'delay' => 0.3, 'min' => 0, 'max' => 5, 'inverted' => true, 'orientation' => 'LPI'];
+ $mipMask = $this->gaelOProcessingService->createMIPForSeries($this->petId, $mipFragmentedPayload);
+ return $mipMask;
+ }
+}