fix: #6

# Problems - When I retrieve DICOM instances that contain ANN (label), I got the error because ANN did not have pixel - Furthermore, thumbnail have same issues too (may get no pixel instance in median) # Solutions - Exclude sop class UID that do not contain pixel in query
Chinlinlee · May 12, 2023 · 9f1948a · 9f1948a
1 parent dd407c9
commit 9f1948a
Show file tree

Hide file tree

Showing 10 changed files with 162 additions and 80 deletions.
diff --git a/api/controller.class.js b/api/controller.class.js
@@ -53,6 +53,19 @@ class Controller {
 
         this.postProcess();
     }
+
+    /**
+     * @return {string}
+     */
+    paramsToString() {
+        let strArr = [];
+        let keys = Object.keys(this.request.params);
+        for(let i = 0 ; i < keys.length; i++) {
+            let key = keys[i];
+            strArr.push(`${key}: ${this.request.params[key]}`);
+        }
+        return strArr.join(" ");
+    }
 }
 
 module.exports.Controller = Controller;
diff --git a/api/dicom-web/controller/STOW-RS/service/dicom-jpeg-generator.js b/api/dicom-web/controller/STOW-RS/service/dicom-jpeg-generator.js
@@ -1,6 +1,7 @@
 const fs = require("fs");
 const { Dcm2JpgExecutor } = require("../../../../../models/DICOM/dcm4che/wrapper/org/github/chinlinlee/dcm2jpg/Dcm2JpgExecutor");
 const { Dcm2JpgExecutor$Dcm2JpgOptions } = require("../../../../../models/DICOM/dcm4che/wrapper/org/github/chinlinlee/dcm2jpg/Dcm2JpgExecutor$Dcm2JpgOptions");
+const notImageSOPClass = require("../../../../../models/DICOM/dicomWEB/notImageSOPClass");
 const { logger } = require("../../../../../utils/logs/log");
 const dicomToJpegTask = require("../../../../../models/mongodb/models/dicomToJpegTask");
 const colorette = require("colorette");
@@ -28,6 +29,10 @@ class DicomJpegGenerator {
 
     async generateAllFrames() {
         try {
+
+            if (notImageSOPClass.includes(this.dicomJsonModel.getSopClassUid())) {
+                return;
+            }
 
             await this.insertStartTask_();
 

diff --git a/api/dicom-web/controller/WADO-RS/rendered/instanceFrames.js b/api/dicom-web/controller/WADO-RS/rendered/instanceFrames.js
@@ -1,5 +1,6 @@
 const _ = require("lodash");
 const renderedService = require("../service/rendered.service");
+const dicomModel = require("../../../../../models/mongodb/models/dicom");
 const { MultipartWriter } = require("../../../../../utils/multipartWriter");
 const errorResponse = require("../../../../../utils/errorResponse/errorResponseMessage");
 const { ApiLogger } = require("../../../../../utils/logs/api-logger");
@@ -11,8 +12,8 @@ class RetrieveRenderedInstanceFramesController extends Controller {
     }
 
     async mainProcess() {
-        let apiLogger = new ApiLogger(this.request, "WADO-RS");
-        apiLogger.addTokenValue();
+        this.apiLogger = new ApiLogger(this.request, "WADO-RS");
+        this.apiLogger.addTokenValue();
 
         let {
             studyUID,
@@ -21,7 +22,7 @@ class RetrieveRenderedInstanceFramesController extends Controller {
             frameNumber
         } = this.request.params;
 
-        apiLogger.logger.info(`Get study's series' rendered instances' frames, study UID: ${studyUID}, series UID: ${seriesUID}, instance UID: ${instanceUID}, frame: ${frameNumber}`);
+        this.apiLogger.logger.info(`Get study's series' rendered instances' frames, study UID: ${studyUID}, series UID: ${seriesUID}, instance UID: ${instanceUID}, frame: ${frameNumber}`);
 
         let headerAccept = _.get(this.request.headers, "accept", "");
         if (!headerAccept.includes("*/*") && !headerAccept.includes("image/jpeg")) {
@@ -33,25 +34,19 @@ class RetrieveRenderedInstanceFramesController extends Controller {
         }
 
         try {
+            let imagePathObj = await dicomModel.getPathOfInstance(this.request.params);
+
+            if(!imagePathObj) {
+                return this.responseNotFound();
+            }
+
             let instanceFramesObj = await renderedService.getInstanceFrameObj(this.request.params);
-            if (!instanceFramesObj) {
-                this.response.writeHead(404, {
-                    "Content-Type": "application/dicom+json"
-                });
-                let notFoundMessage = errorResponse.getNotFoundErrorMessage(`Not Found Instance, Instance UID: ${
-                    instanceUID
-                }, Series UID: ${
-                    seriesUID
-                }, Study UID: ${
-                    studyUID
-                }`);
-
-                let notFoundMessageStr = JSON.stringify(notFoundMessage);
-
-                apiLogger.logger.warn(`[${notFoundMessageStr}]`);
-
-                return this.response.end(notFoundMessageStr);
+            if (_.isUndefined(instanceFramesObj)) {
+                return this.response.status(400).json(
+                    errorResponse.getBadRequestErrorMessage(`instance: ${this.request.params.instanceUID} doesn't have pixel data`)
+                );
             }
+
             let dicomNumberOfFrames = _.get(instanceFramesObj, "00280008.Value.0", 1);
             dicomNumberOfFrames = parseInt(dicomNumberOfFrames);
 
@@ -65,7 +60,7 @@ class RetrieveRenderedInstanceFramesController extends Controller {
 
                     let badRequestMessageStr = JSON.stringify(badRequestMessage);
 
-                    apiLogger.logger.warn(badRequestMessageStr);
+                    this.apiLogger.logger.warn(badRequestMessageStr);
 
                     return this.response.end(JSON.stringify(badRequestMessageStr));
                 }
@@ -78,7 +73,7 @@ class RetrieveRenderedInstanceFramesController extends Controller {
                     this.response.writeHead(200, {
                         "Content-Type": "image/jpeg"
                     });
-                    apiLogger.logger.info(`Get instance's frame successfully, instance UID: ${instanceUID}, frame number: ${frameNumber[0]}`);
+                    this.apiLogger.logger.info(`Get instance's frame successfully, instance UID: ${instanceUID}, frame number: ${frameNumber[0]}`);
                     return this.response.end(postProcessResult.magick.toBuffer(), "binary");
                 }
                 throw new Error(`Can not process this image, instanceUID: ${instanceFramesObj.instanceUID}, frameNumber: ${this.request.frameNumber[0]}`);
@@ -87,7 +82,7 @@ class RetrieveRenderedInstanceFramesController extends Controller {
                 await renderedService.writeSpecificFramesRenderedImages(this.request, frameNumber, instanceFramesObj, multipartWriter);
                 multipartWriter.writeFinalBoundary();
 
-                apiLogger.logger.info(`Get instance's frame successfully, instance UID: ${instanceUID}, frame numbers: ${frameNumber}`);
+                this.apiLogger.logger.info(`Get instance's frame successfully, instance UID: ${instanceUID}, frame numbers: ${frameNumber}`);
 
                 return this.response.end();
             }
@@ -99,6 +94,18 @@ class RetrieveRenderedInstanceFramesController extends Controller {
             this.response.end(JSON.stringify(e, Object.getOwnPropertyNames(e), 4), "utf8");
         }
     }
+
+    responseNotFound() {
+        let notFoundStr = `Not Found Instance, ${this.paramsToString()}`;
+
+        this.apiLogger.logger.warn(notFoundStr);
+
+        let notFoundMessage = errorResponse.getNotFoundErrorMessage(
+            notFoundStr
+        );
+
+        return this.response.status(404).json(notFoundMessage);
+    }
 }
 /**
  * 

diff --git a/api/dicom-web/controller/WADO-RS/rendered/instances.js b/api/dicom-web/controller/WADO-RS/rendered/instances.js
@@ -34,6 +34,11 @@ class RetrieveRenderedInstancesController extends Controller {
             if (imagePathObj) {
                 let multipartWriter = new MultipartWriter([], this.request, this.response);
                 let instanceFramesObj = await renderedService.getInstanceFrameObj(imagePathObj);
+                if (_.isUndefined(instanceFramesObj)) {
+                    return this.response.status(400).json(
+                        errorResponse.getBadRequestErrorMessage(`instance: ${this.request.params.instanceUID} doesn't have pixel data`)
+                    );
+                }
                 let dicomNumberOfFrames = _.get(instanceFramesObj, "00280008.Value.0", 1);
                 dicomNumberOfFrames = parseInt(dicomNumberOfFrames);
                 await renderedService.writeRenderedImages(this.request, dicomNumberOfFrames, instanceFramesObj, multipartWriter);

diff --git a/api/dicom-web/controller/WADO-RS/rendered/series.js b/api/dicom-web/controller/WADO-RS/rendered/series.js
@@ -30,6 +30,7 @@ class RetrieveRenderedSeriesController extends Controller {
 
                 for(let imagePathObj of instancesInSeries) {
                     let instanceFramesObj = await renderedService.getInstanceFrameObj(imagePathObj);
+                    if (_.isUndefined(instanceFramesObj)) continue;
                     let dicomNumberOfFrames = _.get(instanceFramesObj, "00280008.Value.0", 1);
                     dicomNumberOfFrames = parseInt(dicomNumberOfFrames);
                     await renderedService.writeRenderedImages(this.request, dicomNumberOfFrames, instanceFramesObj, multipartWriter);

diff --git a/api/dicom-web/controller/WADO-RS/rendered/study.js b/api/dicom-web/controller/WADO-RS/rendered/study.js
@@ -34,6 +34,7 @@ class RetrieveRenderedStudyController extends Controller {
 
                 for(let imagePathObj of pathGroupOfInstancesInStudy) {
                     let instanceFramesObj = await renderedService.getInstanceFrameObj(imagePathObj);
+                    if(_.isUndefined(instanceFramesObj)) continue;
                     let dicomNumberOfFrames = _.get(instanceFramesObj, "00280008.Value.0", 1);
                     dicomNumberOfFrames = parseInt(dicomNumberOfFrames);
                     await renderedService.writeRenderedImages(this.request, dicomNumberOfFrames, instanceFramesObj, multipartWriter);

diff --git a/api/dicom-web/controller/WADO-RS/service/WADO-RS.service.js b/api/dicom-web/controller/WADO-RS/service/WADO-RS.service.js
@@ -168,7 +168,11 @@ class InstanceImagePathFactory extends ImagePathFactory {
 
     async getImagePaths() {
         let imagePath = await dicomModel.getPathOfInstance(this.uids);
-        this.imagePaths = [imagePath];
+
+        if(imagePath)
+            this.imagePaths = [imagePath];
+        else
+            this.imagePaths = [];
     }
 }
 

diff --git a/api/dicom-web/controller/WADO-RS/service/rendered.service.js b/api/dicom-web/controller/WADO-RS/service/rendered.service.js
@@ -4,6 +4,7 @@ const fs = require("fs");
 const sharp = require("sharp");
 const { Dcm2JpgExecutor } = require("../../../../../models/DICOM/dcm4che/wrapper/org/github/chinlinlee/dcm2jpg/Dcm2JpgExecutor");
 const { Dcm2JpgExecutor$Dcm2JpgOptions } = require("../../../../../models/DICOM/dcm4che/wrapper/org/github/chinlinlee/dcm2jpg/Dcm2JpgExecutor$Dcm2JpgOptions");
+const notImageSOPClass = require("../../../../../models/DICOM/dicomWEB/notImageSOPClass");
 const Magick = require("../../../../../models/magick");
 const _ = require("lodash");
 
@@ -105,6 +106,7 @@ const { raccoonConfig } = require("../../../../../config-class");
 async function getInstanceFrameObj(iParam, otherFields={}) {
     let { studyUID, seriesUID, instanceUID } = iParam;
     try {
+        /** @type { import("mongoose").FilterQuery<any> } */
         let query = {
             $and: [
                 {
@@ -115,6 +117,11 @@ async function getInstanceFrameObj(iParam, otherFields={}) {
                 },
                 {
                     instanceUID: instanceUID
+                },
+                {
+                    "00080016.Value": {
+                        $nin: notImageSOPClass
+                    }
                 }
             ]
         };

diff --git a/models/DICOM/dicom-json-model.js b/models/DICOM/dicom-json-model.js
@@ -238,6 +238,10 @@ class DicomJsonModel {
         return _.get(this.dicomJson, "00020010.Value.0");
     }
 
+    getSopClassUid() {
+        return _.get(this.dicomJson, "00080016.Value.0");
+    }
+
     getStudyDate() {
         return _.get(this.dicomJson, "00080020.Value.0");
     }

diff --git a/models/DICOM/dicomWEB/notImageSOPClass.js b/models/DICOM/dicomWEB/notImageSOPClass.js
@@ -1,77 +1,112 @@
 /**
- * ### 非影像類SOP Class
-
-1.2.840.10008.5.1.4.1.1.104.1 Encapsulated PDF Storage
-1.2.840.10008.5.1.4.1.1.11.1 Grayscale Softcopy Presentation State Storage SOP Class
-1.2.840.10008.5.1.4.1.1.11.2 Color Softcopy Presentation State Storage SOP Class
-1.2.840.10008.5.1.4.1.1.11.3 Pseudocolor Softcopy Presentation Stage Storage SOP Class
-1.2.840.10008.5.1.4.1.1.11.4 Blending Softcopy Presentation State Storage SOP Class
-
-1.2.840.10008.5.1.4.1.1.481.2 Radiation Therapy Dose Storage
-1.2.840.10008.5.1.4.1.1.481.3 Radiation Therapy Structure Set Storage
-1.2.840.10008.5.1.4.1.1.481.4 Radiation Therapy Beams Treatment Record Storage
-1.2.840.10008.5.1.4.1.1.481.5 Radiation Therapy Plan Storage
-1.2.840.10008.5.1.4.1.1.481.6 Radiation Therapy Brachy Treatment Record Storage
-1.2.840.10008.5.1.4.1.1.481.7 Radiation Therapy Treatment Summary Record Storage
-1.2.840.10008.5.1.4.1.1.481.8 Radiation Therapy Ion Plan Storage
-1.2.840.10008.5.1.4.1.1.481.9 Radiation Therapy Ion Beams Treatment Record Storage
-
-1.2.840.10008.5.1.4.1.1.66 Raw Data Storage
-1.2.840.10008.5.1.4.1.1.66.1 Spatial Registration Storage
-1.2.840.10008.5.1.4.1.1.66.2 Spatial Fiducials Storage
-1.2.840.10008.5.1.4.1.1.66.3 Deformable Spatial Registration Storage
-1.2.840.10008.5.1.4.1.1.66.4 Segmentation Storage
-1.2.840.10008.5.1.4.1.1.67 Real World Value Mapping Storage
-
-1.2.840.10008.5.1.4.1.1.88.11 Basic Text SR
-1.2.840.10008.5.1.4.1.1.88.22 Enhanced SR
-1.2.840.10008.5.1.4.1.1.88.33 Comprehensive SR
-1.2.840.10008.5.1.4.1.1.88.40 Procedure Log Storage
-1.2.840.10008.5.1.4.1.1.88.50 Mammography CAD SR
-1.2.840.10008.5.1.4.1.1.88.59 Key Object Selection Document
-1.2.840.10008.5.1.4.1.1.88.65 Chest CAD SR
-1.2.840.10008.5.1.4.1.1.88.67 X-Ray Radiation Dose SR
-
-1.2.840.10008.5.1.4.1.1.9.1.1 12-lead ECG Waveform Storage
-1.2.840.10008.5.1.4.1.1.9.1.2 General ECG Waveform Storage
-1.2.840.10008.5.1.4.1.1.9.1.3 Ambulatory ECG Waveform Storage
-1.2.840.10008.5.1.4.1.1.9.2.1 Hemodynamic Waveform Storage
-1.2.840.10008.5.1.4.1.1.9.3.1 Cardiac Electrophysiology Waveform Storage
-1.2.840.10008.5.1.4.1.1.9.4.1 Basic Voice Audio Waveform Storage
+ * The list of sop class name that one's name not contains "image storage"
  */
-module.exports = [
-    "1.2.840.10008.5.1.4.1.1.104.1",
+module.exports=[
+    "1.2.840.10008.5.1.4.1.1.4.2",
+    "1.2.840.10008.5.1.4.1.1.6.2",
+    "1.2.840.10008.5.1.4.1.1.9.1.1",
+    "1.2.840.10008.5.1.4.1.1.9.1.2",
+    "1.2.840.10008.5.1.4.1.1.9.1.3",
+    "1.2.840.10008.5.1.4.1.1.9.2.1",
+    "1.2.840.10008.5.1.4.1.1.9.3.1",
+    "1.2.840.10008.5.1.4.1.1.9.4.1",
+    "1.2.840.10008.5.1.4.1.1.9.4.2",
+    "1.2.840.10008.5.1.4.1.1.9.5.1",
+    "1.2.840.10008.5.1.4.1.1.9.6.1",
+    "1.2.840.10008.5.1.4.1.1.9.6.2",
+    "1.2.840.10008.5.1.4.1.1.9.7.1",
+    "1.2.840.10008.5.1.4.1.1.9.7.2",
+    "1.2.840.10008.5.1.4.1.1.9.7.3",
+    "1.2.840.10008.5.1.4.1.1.9.7.4",
+    "1.2.840.10008.5.1.4.1.1.9.8.1",
     "1.2.840.10008.5.1.4.1.1.11.1",
     "1.2.840.10008.5.1.4.1.1.11.2",
     "1.2.840.10008.5.1.4.1.1.11.3",
     "1.2.840.10008.5.1.4.1.1.11.4",
-    "1.2.840.10008.5.1.4.1.1.481.2",
-    "1.2.840.10008.5.1.4.1.1.481.3",
-    "1.2.840.10008.5.1.4.1.1.481.4",
-    "1.2.840.10008.5.1.4.1.1.481.5",
-    "1.2.840.10008.5.1.4.1.1.481.6",
-    "1.2.840.10008.5.1.4.1.1.481.7",
-    "1.2.840.10008.5.1.4.1.1.481.8",
-    "1.2.840.10008.5.1.4.1.1.481.9",
+    "1.2.840.10008.5.1.4.1.1.11.5",
+    "1.2.840.10008.5.1.4.1.1.11.6",
+    "1.2.840.10008.5.1.4.1.1.11.7",
+    "1.2.840.10008.5.1.4.1.1.11.8",
+    "1.2.840.10008.5.1.4.1.1.11.9",
+    "1.2.840.10008.5.1.4.1.1.11.10",
+    "1.2.840.10008.5.1.4.1.1.11.11",
+    "1.2.840.10008.5.1.4.1.1.11.12",
+    "1.2.840.10008.5.1.4.1.1.30",
     "1.2.840.10008.5.1.4.1.1.66",
     "1.2.840.10008.5.1.4.1.1.66.1",
     "1.2.840.10008.5.1.4.1.1.66.2",
     "1.2.840.10008.5.1.4.1.1.66.3",
     "1.2.840.10008.5.1.4.1.1.66.4",
+    "1.2.840.10008.5.1.4.1.1.66.5",
+    "1.2.840.10008.5.1.4.1.1.66.6",
     "1.2.840.10008.5.1.4.1.1.67",
+    "1.2.840.10008.5.1.4.1.1.68.1",
+    "1.2.840.10008.5.1.4.1.1.68.2",
+    "1.2.840.10008.5.1.4.1.1.77.1.5.3",
+    "1.2.840.10008.5.1.4.1.1.77.1.5.8",
+    "1.2.840.10008.5.1.4.1.1.78.1",
+    "1.2.840.10008.5.1.4.1.1.78.2",
+    "1.2.840.10008.5.1.4.1.1.78.3",
+    "1.2.840.10008.5.1.4.1.1.78.4",
+    "1.2.840.10008.5.1.4.1.1.78.5",
+    "1.2.840.10008.5.1.4.1.1.78.6",
+    "1.2.840.10008.5.1.4.1.1.78.7",
+    "1.2.840.10008.5.1.4.1.1.78.8",
+    "1.2.840.10008.5.1.4.1.1.79.1",
+    "1.2.840.10008.5.1.4.1.1.80.1",
+    "1.2.840.10008.5.1.4.1.1.81.1",
+    "1.2.840.10008.5.1.4.1.1.82.1",
     "1.2.840.10008.5.1.4.1.1.88.11",
     "1.2.840.10008.5.1.4.1.1.88.22",
     "1.2.840.10008.5.1.4.1.1.88.33",
+    "1.2.840.10008.5.1.4.1.1.88.34",
+    "1.2.840.10008.5.1.4.1.1.88.35",
     "1.2.840.10008.5.1.4.1.1.88.40",
     "1.2.840.10008.5.1.4.1.1.88.50",
     "1.2.840.10008.5.1.4.1.1.88.59",
     "1.2.840.10008.5.1.4.1.1.88.65",
     "1.2.840.10008.5.1.4.1.1.88.67",
-    "1.2.840.10008.5.1.4.1.1.9.1.1",
-    "1.2.840.10008.5.1.4.1.1.9.1.2",
-    "1.2.840.10008.5.1.4.1.1.9.1.3",
-    "1.2.840.10008.5.1.4.1.1.9.2.1",
-    "1.2.840.10008.5.1.4.1.1.9.3.1",
-    "1.2.840.10008.5.1.4.1.1.9.4.1",
-    "1.2.840.10008.5.1.4.1.1.91.1"
+    "1.2.840.10008.5.1.4.1.1.88.68",
+    "1.2.840.10008.5.1.4.1.1.88.69",
+    "1.2.840.10008.5.1.4.1.1.88.70",
+    "1.2.840.10008.5.1.4.1.1.88.71",
+    "1.2.840.10008.5.1.4.1.1.88.72",
+    "1.2.840.10008.5.1.4.1.1.88.73",
+    "1.2.840.10008.5.1.4.1.1.88.74",
+    "1.2.840.10008.5.1.4.1.1.88.75",
+    "1.2.840.10008.5.1.4.1.1.88.76",
+    "1.2.840.10008.5.1.4.1.1.90.1",
+    "1.2.840.10008.5.1.4.1.1.91.1",
+    "1.2.840.10008.5.1.4.1.1.104.1",
+    "1.2.840.10008.5.1.4.1.1.104.2",
+    "1.2.840.10008.5.1.4.1.1.104.3",
+    "1.2.840.10008.5.1.4.1.1.104.4",
+    "1.2.840.10008.5.1.4.1.1.104.5",
+    "1.2.840.10008.5.1.4.1.1.131",
+    "1.2.840.10008.5.1.4.1.1.200.2",
+    "1.2.840.10008.5.1.4.1.1.200.8",
+    "1.2.840.10008.5.1.4.1.1.481.2",
+    "1.2.840.10008.5.1.4.1.1.481.3",
+    "1.2.840.10008.5.1.4.1.1.481.4",
+    "1.2.840.10008.5.1.4.1.1.481.5",
+    "1.2.840.10008.5.1.4.1.1.481.6",
+    "1.2.840.10008.5.1.4.1.1.481.7",
+    "1.2.840.10008.5.1.4.1.1.481.8",
+    "1.2.840.10008.5.1.4.1.1.481.9",
+    "1.2.840.10008.5.1.4.1.1.481.10",
+    "1.2.840.10008.5.1.4.1.1.481.11",
+    "1.2.840.10008.5.1.4.1.1.481.12",
+    "1.2.840.10008.5.1.4.1.1.481.13",
+    "1.2.840.10008.5.1.4.1.1.481.14",
+    "1.2.840.10008.5.1.4.1.1.481.15",
+    "1.2.840.10008.5.1.4.1.1.481.16",
+    "1.2.840.10008.5.1.4.1.1.481.17",
+    "1.2.840.10008.5.1.4.1.1.481.18",
+    "1.2.840.10008.5.1.4.1.1.481.19",
+    "1.2.840.10008.5.1.4.1.1.481.20",
+    "1.2.840.10008.5.1.4.1.1.481.21",
+    "1.2.840.10008.5.1.4.1.1.481.22",
+    "1.2.840.10008.5.1.4.1.1.481.25",
+    "1.2.840.10008.5.1.4.34.7",
+    "1.2.840.10008.5.1.4.34.10"
 ];