Updates for Timepoint assocation (LT-60) and Conformance Checks (LT-92, LT-93, LT-94)

Packages/viewerbase/server/lib/namespace.js

@@ -1,3 +1,4 @@
 Services = {};
 Services.QIDO = {};
-Services.WADO = {};
+Services.WADO = {};
+Services.DIMSE = {};

Packages/viewerbase/server/methods/getStudyMetadata.js

@@ -3,13 +3,17 @@ Meteor.methods({
      * Retrieves Study metadata given a Study Instance UID
      * This Meteor method is available from both the client and the server
      */
-    'GetStudyMetadata' : function(studyInstanceUid) {
+    GetStudyMetadata: function(studyInstanceUid) {
         log.info('GetStudyMetadata(%s)', studyInstanceUid);
 
+        if (!Meteor.settings.dicomWeb) {
+            throw 'No properly configured server was available over DICOMWeb';
+        }
+
         // Get the server data. This is user-defined in the
         // config.json files used to run the Meteor server
         var server = Meteor.settings.dicomWeb.endpoints[0];
 
         return Services.WADO.RetrieveMetadata(server, studyInstanceUid);
     }
-});
+});

Packages/viewerbase/server/methods/worklistSearch.js

@@ -3,16 +3,17 @@ Meteor.methods({
      * Use the specified filter to conduct a search from the DICOM server
      * @param filter
      */
-    'WorklistSearch': function(filter) {
-        if (!Meteor.settings.dicomWeb) {
-            console.warn('No dicomWeb settings provided! Worklist search is not possible!')
-            return;
-        }
-        
-        // Get the server data. This is user-defined in the
-        // config.json files used to run the Meteor server
-        var server = Meteor.settings.dicomWeb.endpoints[0];
+    WorklistSearch: function(filter) {
+        if (Meteor.settings.dicomWeb && Meteor.settings.defaultServiceType === 'dicomWeb') {
+            // Get the server data. This is user-defined in the
+            // config.json files used to run the Meteor server
+            var server = Meteor.settings.dicomWeb.endpoints[0];
 
-        return Services.QIDO.Studies(server, filter);
+            return Services.QIDO.Studies(server, filter);
+        } else if (Meteor.settings.dimse && Meteor.settings.defaultServiceType === 'dimse') {
+            return Services.DIMSE.Studies(filter);
+        } else {
+            throw 'No properly configured server was available over DICOMWeb or DIMSE.';
+        }
     }
-});
+});

Packages/viewerbase/server/services/dimse/instances.js

@@ -0,0 +1,70 @@
+/**
+ * Parses data returned from a study search and transforms it into
+ * an array of series that are present in the study
+ *
+ * @param resultData
+ * @returns {Array} Series List
+ */
+function resultDataToStudyMetadata(resultData) {
+    var seriesMap = {};
+    var seriesList = [];
+
+    resultData.forEach(function(instanceRaw) {
+        var instance = instanceRaw.toObject();
+        // Use seriesMap to cache series data
+        // If the series instance UID has already been used to
+        // process series data, continue using that series
+        var seriesInstanceUid = instance[0x0020000E];
+        var series = seriesMap[seriesInstanceUid];
+
+        // If no series data exists in the seriesMap cache variable,
+        // process any available series data
+        if (!series) {
+            series = {
+                seriesInstanceUid: seriesInstanceUid,
+                seriesNumber: instance[0x00200011],
+                instances: []
+            };
+
+            // Save this data in the seriesMap cache variable
+            seriesMap[seriesInstanceUid] = series;
+            seriesList.push(series);
+        }
+
+        var host = Meteor.settings.dimse.host,
+            port = Meteor.settings.dimse.port;
+
+        var serverRoot = host + ':' + port;
+
+        log.info('INSTANCE');
+        log.info(instance);
+        var sopInstanceUid = instance[0x00080018];
+        var uri = serverRoot + '/studies/' + studyInstanceUid + '/series/' + seriesInstanceUid + '/instances/' + sopInstanceUid + '/frames/1';
+
+        // Add this instance to the current series
+        series.instances.push({
+            sopClassUid: instance[0x00080016],
+            sopInstanceUid: sopInstanceUid,
+            uri: uri,
+            instanceNumber: instance[0x00200013]
+        });
+    });
+    return seriesList;
+}
+
+/**
+ * Retrieve a set of instances using a DIMSE call
+ * @param studyInstanceUid
+ * @returns {{wadoUriRoot: String, studyInstanceUid: String, seriesList: Array}}
+ */
+Services.DIMSE.Instances = function(studyInstanceUid) {
+    //var url = buildUrl(server, studyInstanceUid);
+    var result = DIMSE.retrieveInstances(studyInstanceUid);
+
+    console.log("DIMSE Instance retrieval");
+    console.log(result);
+    return {
+        studyInstanceUid: studyInstanceUid,
+        seriesList: resultDataToStudyMetadata(result)
+    };
+};

Packages/viewerbase/server/services/dimse/retrieveMetadata.js

@@ -0,0 +1,162 @@
+/**
+ * Parses the SourceImageSequence, if it exists, in order
+ * to return a ReferenceSOPInstanceUID. The ReferenceSOPInstanceUID
+ * is used to refer to this image in any accompanying DICOM-SR documents.
+ *
+ * @param instance
+ * @returns {String} The ReferenceSOPInstanceUID
+ */
+function getSourceImageInstanceUid(instance) {
+    // TODO= Parse the whole Source Image Sequence
+    // This is a really poor workaround for now.
+    // Later we should probably parse the whole sequence.
+    var SourceImageSequence = instance[0x00082112];
+    log.info('SourceImageSequence ' + SourceImageSequence);
+    if (SourceImageSequence && SourceImageSequence.length) {
+        return SourceImageSequence[0][0x00081155];
+    }
+}
+
+/**
+ * Parses result data from a DIMSE search into Study MetaData
+ * Returns an object populated with study metadata, including the
+ * series list.
+ *
+ * @param resultData
+ * @returns {{seriesList: Array, patientName: *, patientId: *, accessionNumber: *, studyDate: *, modalities: *, studyDescription: *, imageCount: *, studyInstanceUid: *}}
+ */
+function resultDataToStudyMetadata(studyInstanceUid, resultData) {
+    var seriesMap = {};
+    var seriesList = [];
+
+    if (!resultData.length) {
+        return;
+    }
+
+    var anInstance = resultData[0].toObject();
+    if (!anInstance) {
+        return;
+    }
+
+    var studyData = {
+        seriesList: seriesList,
+        patientName: anInstance[0x00100010],
+        patientId: anInstance[0x00100020],
+        accessionNumber: anInstance[0x00080050],
+        studyDate: anInstance[0x00080020],
+        modalities: anInstance[0x00080061],
+        studyDescription: anInstance[0x00081030],
+        imageCount: anInstance[0x00201208],
+        studyInstanceUid: anInstance[0x0020000D]
+    };
+
+    resultData.forEach(function(instanceRaw) {
+        var instance = instanceRaw.toObject();
+        var seriesInstanceUid = instance[0x0020000E];
+        var series = seriesMap[seriesInstanceUid];
+        if (!series) {
+            series = {
+                seriesDescription: instance[0x0008103E],
+                modality: instance[0x00080060],
+                seriesInstanceUid: seriesInstanceUid,
+                seriesNumber: parseFloat(instance[0x00200011]),
+                instances: []
+            };
+            seriesMap[seriesInstanceUid] = series;
+            seriesList.push(series);
+        }
+
+        var sopInstanceUid = instance[0x00080018];
+
+        log.info('instance');
+        log.info(instance);
+        var instanceSummary = {
+            imageType: instance[0x00080008],
+            sopClassUid: instance[0x00080016],
+            sopInstanceUid: sopInstanceUid,
+            instanceNumber: parseFloat(instance[0x00200013]),
+            imagePositionPatient: instance[0x00200032],
+            imageOrientationPatient: instance[0x00200037],
+            frameOfReferenceUID: instance[0x00200052],
+            sliceLocation: parseFloat(instance[0x00201041]),
+            samplesPerPixel: parseFloat(instance[0x00280002]),
+            photometricInterpretation: instance[0x00280004],
+            rows: parseFloat(instance[0x00280010]),
+            columns: parseFloat(instance[0x00280011]),
+            pixelSpacing: instance[0x00280030],
+            bitsAllocated: parseFloat(instance[0x00280100]),
+            bitsStored: parseFloat(instance[0x00280101]),
+            highBit: parseFloat(instance[0x00280102]),
+            pixelRepresentation: parseFloat(instance[0x00280103]),
+            windowCenter: instance[0x00281050],
+            windowWidth: instance[0x00281051],
+            rescaleIntercept: parseFloat(instance[0x00281052]),
+            rescaleSlope: parseFloat(instance[0x00281053]),
+            sourceImageInstanceUid: getSourceImageInstanceUid(instance),
+            laterality: instance[0x00200062],
+            viewPosition: instance[0x00185101],
+            numFrames: parseFloat(instance[0x00280008]),
+            frameRate: parseFloat(instance[0x00181063])
+        };
+
+        var host = Meteor.settings.dimse.host,
+            port = Meteor.settings.dimse.port;
+
+        var serverRoot = host + ':' + port;
+
+        instanceSummary.wadorsuri = serverRoot + '/studies/' + studyInstanceUid + '/series/' + seriesInstanceUid + '/instances/' + sopInstanceUid + '/frames/1';
+
+        series.instances.push(instanceSummary);
+    });
+
+    return studyData;
+}
+
+/**
+ * Retrieved Study MetaData from a DICOM server using DIMSE
+ * @param studyInstanceUid
+ * @returns {{seriesList: Array, patientName: *, patientId: *, accessionNumber: *, studyDate: *, modalities: *, studyDescription: *, imageCount: *, studyInstanceUid: *}}
+ */
+Services.DIMSE.RetrieveMetadata = function(studyInstanceUid) {
+    console.log('DIMSE RetrieveMetadata');
+
+    var result = DIMSE.retrieveInstances(studyInstanceUid, null, {
+        0x00080050: '',
+        0x00080061: '',
+        0x00081030: '',
+        0x00201208: '',
+        0x00080060: '',
+        0x00080008: '',
+        0x00200032: '',
+        0x00200037: '',
+        0x00200052: '',
+        0x00201041: '',
+        0x00280002: '',
+        0x00280004: '',
+        0x00280030: '',
+        0x00280100: '',
+        0x00280101: '',
+        0x00280102: '',
+        0x00280103: '',
+        0x00281050: '',
+        0x00281051: '',
+        0x00281052: '',
+        0x00281053: '',
+        0x00200062: '',
+        0x00185101: '',
+        0x00280008: '',
+        0x00181063: '',
+        0x00082112: ''
+    });
+
+    var study = resultDataToStudyMetadata(studyInstanceUid, result);
+    if (!study) {
+        study = {};
+    }
+
+    study.studyInstanceUid = studyInstanceUid;
+
+    console.log(study);
+    console.log(study.seriesList[0].instances[0]);
+    return study;
+};

Packages/viewerbase/server/services/dimse/studies.js

@@ -0,0 +1,48 @@
+/**
+ * Parses resulting data from a QIDO call into a set of Study MetaData
+ *
+ * @param resultData
+ * @returns {Array} An array of Study MetaData objects
+ */
+function resultDataToStudies(resultData) {
+    var studies = [];
+
+    resultData.forEach(function(studyRaw) {
+        var study = studyRaw.toObject();
+        studies.push({
+            studyInstanceUid: study[0x0020000D],
+            // 00080005 = SpecificCharacterSet
+            studyDate: study[0x00080020],
+            studyTime: study[0x00080030],
+            accessionNumber: study[0x00080050],
+            referringPhysicianName: study[0x00080090],
+            // 00081190 = URL
+            patientName: study[0x00100010],
+            patientId: study[0x00100020],
+            patientBirthdate: study[0x00100030],
+            patientSex: study[0x00100040],
+            imageCount: study[0x00201208],
+            studyId: study[0x00200010],
+            studyDescription: study[0x00081030],
+            modalities: study[0x00080061]
+        });
+    });
+    return studies;
+}
+
+
+Services.DIMSE.Studies = function(filter) {
+    console.log('Services.DIMSE.Studies');
+    var parameters = {
+        0x00100010: filter.patientName,
+        0x00100020: filter.patientId,
+        0x00080050: filter.accessionNumber,
+        0x00081030: filter.studyDescription,
+        0x00100040: "",
+        0x00201208: "",
+        0x00080061: ""
+    };
+
+    var results = DIMSE.retrieveStudies(parameters);
+    return resultDataToStudies(results);
+};

Packages/viewerbase/server/services/qido/instances.js

@@ -30,10 +30,10 @@ function resultDataToStudyMetadata(server, studyInstanceUid, resultData) {
 
         // If no series data exists in the seriesMap cache variable,
         // process any available series data
-        if(!series) {
+        if (!series) {
             series = {
-                seriesInstanceUid : seriesInstanceUid,
-                seriesNumber : DICOMWeb.getString(instance['00200011']),
+                seriesInstanceUid: seriesInstanceUid,
+                seriesNumber: DICOMWeb.getString(instance['00200011']),
                 instances: []
             };
 
@@ -52,7 +52,7 @@ function resultDataToStudyMetadata(server, studyInstanceUid, resultData) {
         // manually create a WADO-URI from the UIDs
         // NOTE: Haven't been able to get Orthanc's WADO-URI to work yet - maybe its not configured?
         var sopInstanceUid = DICOMWeb.getString(instance['00080018']);
-        var uri = server.wadoUriRoot + '?requestType=WADO&studyUID=' + studyInstanceUid + '&seriesUID=' + seriesInstanceUid + '&objectUID=' + sopInstanceUid + "&contentType=application%2Fdicom";
+        var uri = server.wadoUriRoot + '?requestType=WADO&studyUID=' + studyInstanceUid + '&seriesUID=' + seriesInstanceUid + '&objectUID=' + sopInstanceUid + '&contentType=application%2Fdicom';
 
         // Add this instance to the current series
         series.instances.push({
@@ -61,8 +61,8 @@ function resultDataToStudyMetadata(server, studyInstanceUid, resultData) {
             uri: uri,
             instanceNumber: DICOMWeb.getString(instance['00200013'])
         });
-  });
-  return seriesList;
+    });
+    return seriesList;
 }
 
 /**
@@ -80,4 +80,4 @@ Services.QIDO.Instances = function(server, studyInstanceUid) {
         studyInstanceUid: studyInstanceUid,
         seriesList: resultDataToStudyMetadata(server, studyInstanceUid, result.data)
     };
-};
+};

Packages/viewerbase/server/services/qido/studies.js

@@ -16,6 +16,7 @@ function filterToQIDOURL(server, filter) {
         PatientName: filter.patientName,
         PatientID: filter.patientId,
         AccessionNumber: filter.accessionNumber,
+        StudyDescription: filter.studyDescription,
         limit: filter.limit || 20,
         includefield: server.qidoSupportsIncludeField ? 'all' : commaSeparatedFields
     };

Packages/viewerbase/server/services/wado/retrieveMetadata.js

@@ -105,7 +105,8 @@ function resultDataToStudyMetadata(server, studyInstanceUid, resultData) {
             laterality: DICOMWeb.getString(instance['00200062']),
             viewPosition: DICOMWeb.getString(instance['00185101']),
             numFrames: DICOMWeb.getNumber(instance['00280008']),
-            frameRate: DICOMWeb.getNumber(instance['00181063'])
+            frameRate: DICOMWeb.getNumber(instance['00181063']),
+            sliceThickness: DICOMWeb.getNumber(instance['00180050'])
         };
 
         if (server.imageRendering === 'wadouri') {