[API] Added features for dicoms : PatientName and images: isPhantom (a…

…ces#6899) Patientname is added to dicoms endpoint view and IsPhantom is added to images endpoint view.
AlexandraLivadas · Jun 29, 2021 · b34fdef · b34fdef
1 parent 9ec7bed
commit b34fdef
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Showing 11 changed files with 239 additions and 13 deletions.
diff --git a/modules/api/docs/LorisRESTAPI_v0.0.4-dev.md b/modules/api/docs/LorisRESTAPI_v0.0.4-dev.md
@@ -553,6 +553,7 @@ the form:
         "OutputType" : "native",
         "Filename" : "abc.mnc",
         "AcquisitionType" : "t1w/t2w/etc",
+        "IsPhantom" : "true|false",
     }, /* More files */]
 }
 ```
@@ -810,6 +811,7 @@ object of the form:
     [
         {
             "Tarname" : "DCM_yyyy-mm-dd_ImagingUpload-hh-mm-abc123.tar",
+            "Patientname" : "DCM123_123456_V1",
             "SeriesInfo" :
                 [{
                     "SeriesDescription" : "MPRAGE_ipat2",
@@ -834,6 +836,7 @@ object of the form:
         },
         {
             "Tarname" : "DCM_yyyy-mm-dd_ImagingUpload-hh-mm-def456.tar",
+            "Patientname" : "DCM456_654321_V1",
             "SeriesInfo" :
                 [{
                 "SeriesDescription" : "MPRAGE_ipat2",

diff --git a/modules/api/php/endpoints/candidate/visit/dicoms.class.inc b/modules/api/php/endpoints/candidate/visit/dicoms.class.inc
@@ -133,11 +133,19 @@ class Dicoms extends Endpoint implements \LORIS\Middleware\ETagCalculator
             $request->getAttribute('user')
         );
 
-        $view = (new \LORIS\api\Views\Visit\Dicoms(
-            $this->_visit,
-            ...$dicomtars
-        ))->toArray();
-
+        $version = $request->getAttribute('LORIS-API-Version');
+        switch($version) {
+        case "v0.0.3":
+            $view = (new \LORIS\api\Views\Visit\Dicoms(
+                $this->_visit,
+                ...$dicomtars
+            ))->toArray();
+        default:
+            $view = (new \LORIS\api\Views\Visit\Dicoms_0_0_4_Dev(
+                $this->_visit,
+                ...$dicomtars
+            ))->toArray();
+        }
         $this->_cache = new \LORIS\Http\Response\JsonResponse($view);
 
         return $this->_cache;

diff --git a/modules/api/php/endpoints/candidate/visit/electrophysiology/channels.class.inc b/modules/api/php/endpoints/candidate/visit/electrophysiology/channels.class.inc
@@ -143,4 +143,4 @@ class Channels extends Endpoint implements \LORIS\Middleware\ETagCalculator
     {
         return md5(json_encode($this->_handleGET($request)->getBody()));
     }
-}
+}
diff --git a/modules/api/php/endpoints/candidate/visit/electrophysiology/metadata.class.inc b/modules/api/php/endpoints/candidate/visit/electrophysiology/metadata.class.inc
@@ -156,4 +156,4 @@ class Metadata extends Endpoint implements \LORIS\Middleware\ETagCalculator
     {
         return md5(json_encode($this->_handleGET($request)->getBody()));
     }
-}
+}
diff --git a/modules/api/php/endpoints/candidate/visit/electrophysiology/recording.class.inc b/modules/api/php/endpoints/candidate/visit/electrophysiology/recording.class.inc
@@ -218,4 +218,4 @@ class Recording extends Endpoint implements \LORIS\Middleware\ETagCalculator
 
         return md5(json_encode($signature));
     }
-}
+}
diff --git a/modules/api/php/endpoints/candidate/visit/images.class.inc b/modules/api/php/endpoints/candidate/visit/images.class.inc
@@ -133,10 +133,20 @@ class Images extends Endpoint implements \LORIS\Middleware\ETagCalculator
             $request->getAttribute('user')
         );
 
-        $view = (new \LORIS\api\Views\Visit\Images(
-            $this->_visit,
-            ...$images
-        ))->toArray();
+        $version = $request->getAttribute('LORIS-API-Version');
+        switch($version) {
+        case 'v0.0.3':
+            $view = (new \LORIS\api\Views\Visit\Images(
+                $this->_visit,
+                ...$images
+            ))->toArray();
+
+        default:
+            $view = (new \LORIS\api\Views\Visit\Images_0_0_4_Dev(
+                $this->_visit,
+                ...$images
+            ))->toArray();
+        }
 
         $this->_cache = new \LORIS\Http\Response\JsonResponse($view);
 

diff --git a/modules/api/php/endpoints/project/recordings.class.inc b/modules/api/php/endpoints/project/recordings.class.inc
@@ -181,4 +181,4 @@ class Recordings extends Endpoint implements \LORIS\Middleware\ETagCalculator
     {
         return md5(json_encode($this->_handleGET($request)->getBody()));
     }
-}
+}
diff --git a/modules/api/php/views/visit/dicoms_0_0_4_dev.class.inc b/modules/api/php/views/visit/dicoms_0_0_4_dev.class.inc
@@ -0,0 +1,112 @@
+<?php declare(strict_types=1);
+/**
+ * PHP Version 7
+ *
+ * @category ApiViews
+ * @package  Loris
+ * @author   Xavier Lecours Boucher <[email protected]>
+ * @license  http://www.gnu.org/licenses/gpl-3.0.txt GPLv3
+ * @link     https://www.github.com/aces/Loris/
+ */
+
+namespace LORIS\api\Views\Visit;
+
+use \LORIS\Data\Models\DicomTarDTO;
+use \LORIS\Data\Models\DicomSeriesDTO;
+/**
+ * Creates a representation of a visit dicoms following the api response
+ * specifications.
+ *
+ * @category ApiViews
+ * @package  Loris
+ * @author   Xavier Lecours Boucher <[email protected]>
+ * @license  http://www.gnu.org/licenses/gpl-3.0.txt GPLv3
+ * @link     https://www.github.com/aces/Loris/
+ */
+
+class Dicoms_0_0_4_Dev
+{
+    private $_timepoint;
+    private $_dicoms;
+
+    /**
+     * Constructor which sets the instance variables based on the provided timepoint
+     *
+     * @param \Timepoint  $timepoint The timepoint to represent
+     * @param DicomTarDTO ...$dicoms An array of dicomtars
+     */
+    public function __construct(\Timepoint $timepoint, DicomTarDTO ...$dicoms)
+    {
+        $this->_timepoint = $timepoint;
+        $this->_dicoms    = $dicoms;
+    }
+
+    /**
+     * This is a mapper function that formats a dicomtar following the
+     * API specifications.
+     *
+     * @param DicomTarDTO $dicom The dicomtar to format.
+     *
+     * @return array
+     */
+    private static function _formatDicomTars(DicomTarDTO $dicom): array
+    {
+        return [
+            'Tarname'     => $dicom->getTarname(),
+            'Patientname' => $dicom->getPatientname(),
+            'SeriesInfo'  => array_map(
+                [
+                    'self',
+                    '_formatSeries'
+                ],
+                $dicom->getSeries()
+            ),
+        ];
+    }
+
+    /**
+     * This is a mapper function that formats a dicom series following the
+     * API specifications.
+     *
+     * @param DicomSeriesDTO $series The series to format.
+     *
+     * @return array
+     */
+    private static function _formatSeries(DicomSeriesDTO $series): array
+    {
+        return [
+            'SeriesDescription' => $series->getSeriesDescription(),
+            'SeriesNumber'      => $series->getSeriesNumber(),
+            'EchoTime'          => $series->getEchotime(),
+            'RepetitionTime'    => $series->getRepetitiontime(),
+            'InversionTime'     => $series->getInversiontime(),
+            'SliceThickness'    => $series->getSlicethickness(),
+            'Modality'          => $series->getModality(),
+            'SeriesUID'         => $series->getSeriesuid(),
+        ];
+    }
+
+    /**
+     * Creates an serializable array of this object's data
+     *
+     * @return array
+     */
+    public function toArray(): array
+    {
+        $meta = [
+            'CandID' => $this->_timepoint->getCandID(),
+            'Visit'  => $this->_timepoint->getVisitLabel(),
+        ];
+
+        $dicomtars = array_map(
+            'self::_formatDicomTars',
+            $this->_dicoms
+        );
+
+        return [
+            'Meta'      => $meta,
+            'DicomTars' => $dicomtars,
+        ];
+    }
+}
+
diff --git a/modules/api/php/views/visit/images_0_0_4_dev.class.inc b/modules/api/php/views/visit/images_0_0_4_dev.class.inc
@@ -0,0 +1,72 @@
+<?php declare(strict_types=1);
+/**
+ * PHP Version 7
+ *
+ * @category ApiViews
+ * @package  Loris
+ * @author   Xavier Lecours Boucher <[email protected]>
+ * @license  http://www.gnu.org/licenses/gpl-3.0.txt GPLv3
+ * @link     https://www.github.com/aces/Loris/
+ */
+
+namespace LORIS\api\Views\Visit;
+
+use \LORIS\Data\Models\ImageDTO;
+/**
+ * Creates a representation of a visit images following the api response
+ * specifications.
+ *
+ * @category ApiViews
+ * @package  Loris
+ * @author   Xavier Lecours Boucher <[email protected]>
+ * @license  http://www.gnu.org/licenses/gpl-3.0.txt GPLv3
+ * @link     https://www.github.com/aces/Loris/
+ */
+
+class Images_0_0_4_Dev
+{
+    private $_timepoint;
+    private $_images;
+
+    /**
+     * Constructor which sets the instance variables based on the provided timepoint
+     *
+     * @param \Timepoint $timepoint The timepoint to represent
+     * @param ImageDTO   ...$images An array of images
+     */
+    public function __construct(\Timepoint $timepoint, ImageDTO ...$images)
+    {
+        $this->_timepoint = $timepoint;
+        $this->_images    = $images;
+    }
+
+    /**
+     * Creates an serializable array of this object's data
+     *
+     * @return array
+     */
+    public function toArray(): array
+    {
+        $meta = [
+            'CandID' => $this->_timepoint->getCandID(),
+            'Visit'  => $this->_timepoint->getVisitLabel(),
+        ];
+
+        $imagesdata = array_map(
+            function ($image) {
+                return [
+                    'OutputType'      => $image->getOutputType(),
+                    'Filename'        => $image->getFilename(),
+                    'AcquisitionType' => $image->getAcquisitionprotocol(),
+                    'IsPhantom'       => $image->isPhantom(),
+                ];
+            },
+            $this->_images
+        );
+
+        return [
+            'Meta'  => $meta,
+            'Files' => $imagesdata,
+        ];
+    }
+}
diff --git a/raisinbread/test/api/LorisApiDicomsTest.php b/raisinbread/test/api/LorisApiDicomsTest.php
@@ -73,6 +73,18 @@ public function testGetCandidatesCandidVisitDicoms(): void
             ),
             'array'
         );
+        $this->assertSame(
+            gettype(
+                $dicomArray['DicomTars']['0']['Tarname']
+            ),
+            'string'
+        );
+        $this->assertSame(
+            gettype(
+                $dicomArray['DicomTars']['0']['Patientname']
+            ),
+            'string'
+        );
         $this->assertSame(
             gettype(
                 $dicomArray['DicomTars']['0']['SeriesInfo']['0']
@@ -150,6 +162,10 @@ public function testGetCandidatesCandidVisitDicoms(): void
             'Tarname',
             $dicomArray['DicomTars']['0']
         );
+        $this->assertArrayHasKey(
+            'Patientname',
+            $dicomArray['DicomTars']['0']
+        );
 
         $this->assertArrayHasKey(
             'SeriesInfo',

diff --git a/raisinbread/test/api/LorisApiImagesTest.php b/raisinbread/test/api/LorisApiImagesTest.php
@@ -67,6 +67,10 @@ public function testGetCandidatesCandidVisitImages(): void
             gettype($imagesArray['Files']['0']['AcquisitionType']),
             'string'
         );
+        $this->assertSame(
+            gettype($imagesArray['Files']['0']['IsPhantom']),
+            'boolean'
+        );
 
         $this->assertArrayHasKey('Meta', $imagesArray);
         $this->assertArrayHasKey('CandID', $imagesArray['Meta']);
@@ -75,6 +79,7 @@ public function testGetCandidatesCandidVisitImages(): void
         $this->assertArrayHasKey('OutputType', $imagesArray['Files']['0']);
         $this->assertArrayHasKey('Filename', $imagesArray['Files']['0']);
         $this->assertArrayHasKey('AcquisitionType', $imagesArray['Files']['0']);
+        $this->assertArrayHasKey('IsPhantom', $imagesArray['Files']['0']);
     }
 
     /**