additional field untuk overlay MRI OHIF

src/dimse/parseMeta.ts

@@ -57,10 +57,44 @@ function parseFile(filename: string): Promise<ElementType> {
         const instanceNumber = dataset.string('x00200013');
         const sliceThickness = dataset.string('x00180050');
         const sliceLocation = dataset.string('x00201041');
-        const numberOfFrames = dataset.string('x00280008');
-        const recommendedDisplayFrameRate = dataset.string('x00082144');
-        const cineRate = dataset.string('x00180040');
-        const frameTime = dataset.string('x00181063');
+
+        // TODO: buat ini dynamic berdasarkan includefields atau modality
+        // TODO: hapus tambahan di bawah ini yang tidak diperlukan
+
+        // MR-specific tags for overlay
+        const spacingBetweenSlices = dataset.string('x00180088');
+        const percentPhaseFieldOfView = dataset.string('x00180094');
+        const fovDimensionElement = dataset.elements.x00181149;
+        const fovDimension = fovDimensionElement
+          ? [
+            dataset.uint16('x00181130', 0),
+            dataset.uint16('x00181130', 1),
+          ]
+          : null;
+        const acquisitionMatrixElement = dataset.elements.x00181310;
+        const acquisitionMatrix = acquisitionMatrixElement
+          ? [
+            dataset.uint16('x00181310', 0),
+            dataset.uint16('x00181310', 1),
+            dataset.uint16('x00181310', 2),
+            dataset.uint16('x00181310', 3),
+          ]
+          : null;
+        const scanningSequence = dataset.string('x00180020');
+        const repetitionTime = dataset.string('x00180080');
+        const echoTime = dataset.string('x00180081');
+        const inversionTime = dataset.string('x00180082');
+        const receiveCoilName = dataset.string('x00181250');
+        const mrAcquisitionType = dataset.string('x00180023');
+        const phaseEncodingDirection = dataset.string('x00181312');
+        const numOfAverages = dataset.string('x00180083');
+        const echoTrainLength = dataset.string('x00180091');
+        const flipAngle = dataset.string('x00181314');
+        const pixelBandwidth = dataset.string('x00180095');
+        const acquisitionTime = dataset.string('x00080032');
+        const acquistionDurationTotal = dataset.string('x00189073'); // in seconds
+        const acquistionDurationPerFrame = dataset.string('x00189220'); // in ms
+        const parallelAcquisitionTechnique = dataset.string('x00181316');
 
         // append to all results
         const result: ElementType = {
@@ -90,13 +124,29 @@ function parseFile(filename: string): Promise<ElementType> {
           ...(iop && { '00200037': { Value: iop, vr: 'DS' } }),
           ...(ipp && { '00200032': { Value: ipp, vr: 'DS' } }),
           '00200013': { Value: [instanceNumber], vr: 'IS' },
-          '00280008': { Value: [numberOfFrames], vr: 'IS' },
-          '00082144': { Value: [recommendedDisplayFrameRate], vr: 'IS' },
-          '00180040': { Value: [cineRate], vr: 'IS' },
-          '00181063': { Value: [frameTime], vr: 'DS' },
           '00180050': { Value: [sliceThickness], vr: 'DS' },
           '00201041': { Value: [sliceLocation], vr: 'DS' },
+          '00180088': { Value: [spacingBetweenSlices], vr: 'DS' },
+          '00180094': { Value: [percentPhaseFieldOfView], vr: 'DS' },
+          ...(fovDimension && { '00181149': { Value: fovDimension, vr: 'IS' } }),
+          ...(acquisitionMatrix && { '00181310': { Value: acquisitionMatrix, vr: 'US' } }),
+          '00180020': { Value: [scanningSequence], vr: 'CS' },
+          '00180080': { Value: [repetitionTime], vr: 'DS' },
+          '00180081': { Value: [echoTime], vr: 'DS' },
+          '00180082': { Value: [inversionTime], vr: 'DS' },
+          '00181250': { Value: [receiveCoilName], vr: 'SH' },
+          '00180023': { Value: [mrAcquisitionType], vr: 'CS' },
+          '00181312': { Value: [phaseEncodingDirection], vr: 'CS' },
+          '00180083': { Value: [numOfAverages], vr: 'DS' },
+          '00180091': { Value: [echoTrainLength], vr: 'IS' },
+          '00181314': { Value: [flipAngle], vr: 'DS' },
+          '00180095': { Value: [pixelBandwidth], vr: 'DS' },
+          '00080032': { Value: [acquisitionTime], vr: 'TM' },
+          '00189073': { Value: [acquistionDurationTotal], vr: 'DS' },
+          '00189220': { Value: [acquistionDurationPerFrame], vr: 'FD' },
+          '00181316': { Value: [parallelAcquisitionTechnique], vr: 'CS' },
         };
+
         resolve(result);
       });
     });
@@ -113,7 +163,7 @@ export function parseMeta(json: object, studyInstanceUID: string, seriesInstance
     const sopInstanceUid = json[key]['00080018'].Value[0];
     const pathname = path.join(storagePath, studyInstanceUID, sopInstanceUid);
     parsing.push(parseFile(pathname));
-    
+
   }
   return Promise.all(parsing);
 }

src/dimse/tags.ts

@@ -32,16 +32,7 @@ export const seriesLevelTags: Array<string> = [
   '00201209',
 ];
 
-export const imageLevelTags: Array<string> = [
-  '00080016', // SOPClassUID
-  '00080018', // SOPInstanceUID
-  '00200013', // InstanceNumber
-  '00280008', // NumberOfFrames
-  '00280010', // Rows
-  '00280011', // Columns
-  '00082144', // RecommendedDisplayFrameRate
-  '00180040', // CineRate
-];
+export const imageLevelTags: Array<string> = ['00080016', '00080018'];
 
 export function tagsForLevel(level: QUERY_LEVEL) {
   switch (level) {

src/dimse/wadoRs.ts

@@ -22,7 +22,7 @@ type WadoRsArgs = {
   seriesInstanceUid?: string;
   sopInstanceUid?: string;
   dataFormat?: DataFormat;
-  frame?: number;
+  frame?: number | number[];
 };
 type WadoRsResponse = {
   contentType: string;
@@ -91,10 +91,9 @@ interface AddFileToBuffer {
   filename: string,
   instanceInfo: InstanceInfo,
   dataFormat?: DataFormat,
-  frame?: number,
 }
 
-async function addFileToBuffer({ pathname, filename, dataFormat, instanceInfo, frame }: AddFileToBuffer): Promise<Buffer> {
+async function addFileToBuffer({ pathname, filename, dataFormat, instanceInfo }: AddFileToBuffer): Promise<Buffer> {
   const logger = LoggerSingleton.Instance;
   const filepath = path.join(pathname, filename);
   const buffArray: Buffer[] = [];
@@ -129,24 +128,8 @@ async function addFileToBuffer({ pathname, filename, dataFormat, instanceInfo, f
     // Get the pixeldata from the DICOM and add it to the buffer.
     const dataset = dicomParser.parseDicom(data);
     const pixeldataElement = dataset.elements.x7fe00010;
-    let dataOffset = pixeldataElement.dataOffset;
-    let dataLength = pixeldataElement.length;
-
-    // WADO-RS frame request: return only the requested frame's bytes.
-    // The file is recompressed to uncompressed (Implicit VR LE) above, so
-    // frames are contiguous and slicing by frame size is safe.
-    if (dataFormat === 'pixeldata' && typeof frame === 'number' && frame > 0) {
-      const rows = dataset.uint16('x00280010') ?? 0;
-      const cols = dataset.uint16('x00280011') ?? 0;
-      const samplesPerPixel = dataset.uint16('x00280002') ?? 1;
-      const bitsAllocated = dataset.uint16('x00280100') ?? 8;
-      const frameSize = rows * cols * samplesPerPixel * (bitsAllocated / 8);
-      dataOffset += (frame - 1) * frameSize;
-      dataLength = frameSize;
-    }
-
     buffArray.push(Buffer.from(`Content-Type:application/octet-stream;${term}`));
-    returnData = Buffer.from(dataset.byteArray.buffer, dataOffset, dataLength);
+    returnData = Buffer.from(dataset.byteArray.buffer, pixeldataElement.dataOffset, pixeldataElement.length);
     break;
   }
   case 'rendered': {
@@ -174,7 +157,7 @@ type InstanceInfo = {
   instance?: string
 }
 
-export async function doWadoRs({ studyInstanceUid, seriesInstanceUid, sopInstanceUid, dataFormat, frame }: WadoRsArgs): Promise<WadoRsResponse> {
+export async function doWadoRs({ studyInstanceUid, seriesInstanceUid, sopInstanceUid, dataFormat }: WadoRsArgs): Promise<WadoRsResponse> {
   const logger = LoggerSingleton.Instance;
   // Set up all the paths and query levels.
   const storagePath = config.get(ConfParams.STORAGE_PATH) as string;
@@ -254,14 +237,14 @@ export async function doWadoRs({ studyInstanceUid, seriesInstanceUid, sopInstanc
       buffers = await Promise.all(files.map(async (file) => {
         const instanceInfo = foundInstances.find((i) => i.instance === file)
         if (instanceInfo) {
-          return addFileToBuffer({ pathname, filename: file, dataFormat, instanceInfo, frame });
+          return addFileToBuffer({ pathname, filename: file, dataFormat, instanceInfo });
         }
       }))
     }
     else {
       // Attach the one file that we need to the return buffer
       const instanceInfo = { study: studyInstanceUid, series: seriesInstanceUid, instance: sopInstanceUid }
-      buffers = [await addFileToBuffer({ pathname: studyPath, filename, dataFormat, instanceInfo, frame })];
+      buffers = [await addFileToBuffer({ pathname: studyPath, filename, dataFormat, instanceInfo })];
     }
 
     // Set up the boundaries and join together all of the file buffers to form

src/routes/routes.ts

@@ -51,15 +51,16 @@ module.exports = function (server: FastifyInstance, opts: unknown, done: () => v
       const hasStudyDate = query.StudyDate !== undefined;
 
       if (!hasMedicalRecord && !hasAccessionNumber && !hasPatientName && !hasStudyInstanceUID && !hasStudyDate) {
+        // TODO: buat startDate tgl H-1 karena terkadang kena Bug beda timezone +-7 di file DICOM nya
         const startDate = moment().format('YYYYMMDD');
         const endDate = moment().format('YYYYMMDD');
         query.StudyDate = `${startDate}-${endDate}`;
-        
+
         // Add time range filter (entire day)
         const startTime = '000000';
         const endTime = '235959';
         query['00080030'] = `${startTime}-${endTime}`; // StudyTime (0008,0030)
-        
+
         logger.info(`Adding default date range filter: ${query.StudyDate}`);
         logger.info(`Adding default time range filter: ${query['00080030']}`);
       }
@@ -67,14 +68,14 @@ module.exports = function (server: FastifyInstance, opts: unknown, done: () => v
       logger.info(`Querying studies with filters: ${JSON.stringify(query)}`);
 
       const json = deepmerge.all(await doFind(QUERY_LEVEL.STUDY, query), options);
-      
+
       // Karena by default hasilnya urut StudyTime (ascending), 
       // Maka, jika butuh latest first (descending), maka dibalik urutannya
       if (Array.isArray(json) && json.length > 0) {
         logger.info(`Reversing order of ${json.length} studies to show latest first`);
         json.reverse();
       }
-      
+
       return reply.send(json);
     } catch (error) {
       logger.error(error);
@@ -360,12 +361,12 @@ module.exports = function (server: FastifyInstance, opts: unknown, done: () => v
   //------------------------------------------------------------------
 
   server.get<{
-    Params: IParamsImage & { frame: string };
+    Params: IParamsImage;
   }>('/rs/studies/:studyInstanceUid/series/:seriesInstanceUid/instances/:sopInstanceUid/frames/:frame', async (req, reply) => {
-    const { studyInstanceUid, seriesInstanceUid, sopInstanceUid, frame } = req.params;
+    const { studyInstanceUid, seriesInstanceUid, sopInstanceUid } = req.params;
 
     try {
-      const rsp = await doWadoRs({ studyInstanceUid, seriesInstanceUid, sopInstanceUid, dataFormat: 'pixeldata', frame: parseInt(frame, 10) });
+      const rsp = await doWadoRs({ studyInstanceUid, seriesInstanceUid, sopInstanceUid, dataFormat: 'pixeldata' });
       reply.header('Content-Type', rsp.contentType);
       return reply.send(rsp.buffer);
     } catch (error) {
@@ -410,6 +411,25 @@ module.exports = function (server: FastifyInstance, opts: unknown, done: () => v
     }
   });
 
+  server.get<{
+    Params: IParamsImage;
+    Querystring: QueryParams;
+  }>('/rs/studies/:studyInstanceUid/series/:seriesInstanceUid/instances/:sopInstanceUid/metadata', async (req, reply) => {
+    const { studyInstanceUid, seriesInstanceUid, sopInstanceUid } = req.params;
+    const { query } = req;
+    query.StudyInstanceUID = studyInstanceUid;
+    query.SeriesInstanceUID = seriesInstanceUid;
+    query.SOPInstanceUID = sopInstanceUid;
+
+    try {
+      const rsp = await fetchMeta(query, studyInstanceUid, seriesInstanceUid);
+      return reply.send(rsp);
+    } catch (error) {
+      logger.error(error);
+      return reply.send(500);
+    }
+  });
+
   done();
 };