feat(b-values): implement parsing for multiple b-value formats and update default setting
This commit is contained in:
Ross
@@ -123,6 +123,64 @@
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"wadouri:https://www.penracourses.org.uk/media/atlas/dicom/IMG_596_stFfHXn.dcm",
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],
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},
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{
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i: [
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"wadouri:https://www.penracourses.org.uk/media/atlas/dicom/IMG_792_og2P5S6.dcm",
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"wadouri:https://www.penracourses.org.uk/media/atlas/dicom/IMG_793_3tKkg87.dcm",
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"wadouri:https://www.penracourses.org.uk/media/atlas/dicom/IMG_794_s8FB3dq.dcm",
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"wadouri:https://www.penracourses.org.uk/media/atlas/dicom/IMG_795_8HeRpXV.dcm",
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"wadouri:https://www.penracourses.org.uk/media/atlas/dicom/IMG_796_tllvzjH.dcm",
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"wadouri:https://www.penracourses.org.uk/media/atlas/dicom/IMG_797_AXieNgu.dcm",
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"wadouri:https://www.penracourses.org.uk/media/atlas/dicom/IMG_798_L8YapjK.dcm",
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"wadouri:https://www.penracourses.org.uk/media/atlas/dicom/IMG_799_kvuLUsW.dcm",
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"wadouri:https://www.penracourses.org.uk/media/atlas/dicom/IMG_800_i2eSNzF.dcm",
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"wadouri:https://www.penracourses.org.uk/media/atlas/dicom/IMG_801_dR3KPL5.dcm",
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"wadouri:https://www.penracourses.org.uk/media/atlas/dicom/IMG_802_cDgm138.dcm",
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"wadouri:https://www.penracourses.org.uk/media/atlas/dicom/IMG_803_Bj3PZyX.dcm",
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"wadouri:https://www.penracourses.org.uk/media/atlas/dicom/IMG_804_CEqcWo2.dcm",
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"wadouri:https://www.penracourses.org.uk/media/atlas/dicom/IMG_805_5R2LmiA.dcm",
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"wadouri:https://www.penracourses.org.uk/media/atlas/dicom/IMG_806_RgmKU6b.dcm",
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"wadouri:https://www.penracourses.org.uk/media/atlas/dicom/IMG_807_BKTkmJv.dcm",
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"wadouri:https://www.penracourses.org.uk/media/atlas/dicom/IMG_808_OQOf2MC.dcm",
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"wadouri:https://www.penracourses.org.uk/media/atlas/dicom/IMG_809_lxnU3mr.dcm",
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"wadouri:https://www.penracourses.org.uk/media/atlas/dicom/IMG_810_8vG5Ett.dcm",
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"wadouri:https://www.penracourses.org.uk/media/atlas/dicom/IMG_811_poX6D2s.dcm",
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"wadouri:https://www.penracourses.org.uk/media/atlas/dicom/IMG_812_k46Ws88.dcm",
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"wadouri:https://www.penracourses.org.uk/media/atlas/dicom/IMG_813_7Ft4JOE.dcm",
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"wadouri:https://www.penracourses.org.uk/media/atlas/dicom/IMG_814_V5lJKxR.dcm",
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"wadouri:https://www.penracourses.org.uk/media/atlas/dicom/IMG_815_1hFehRl.dcm",
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"wadouri:https://www.penracourses.org.uk/media/atlas/dicom/IMG_816_34UqY7Z.dcm",
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"wadouri:https://www.penracourses.org.uk/media/atlas/dicom/IMG_817_YG28gpL.dcm",
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"wadouri:https://www.penracourses.org.uk/media/atlas/dicom/IMG_818_wonhIz5.dcm",
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"wadouri:https://www.penracourses.org.uk/media/atlas/dicom/IMG_819_bv3zaOx.dcm",
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"wadouri:https://www.penracourses.org.uk/media/atlas/dicom/IMG_820_xEjnfcI.dcm",
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"wadouri:https://www.penracourses.org.uk/media/atlas/dicom/IMG_821_cH9fPxl.dcm",
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"wadouri:https://www.penracourses.org.uk/media/atlas/dicom/IMG_822_lWmBHxs.dcm",
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"wadouri:https://www.penracourses.org.uk/media/atlas/dicom/IMG_823_ybix6Gz.dcm",
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"wadouri:https://www.penracourses.org.uk/media/atlas/dicom/IMG_824_q430lCK.dcm",
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"wadouri:https://www.penracourses.org.uk/media/atlas/dicom/IMG_825_28trFVc.dcm",
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"wadouri:https://www.penracourses.org.uk/media/atlas/dicom/IMG_826_7BF6HBF.dcm",
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"wadouri:https://www.penracourses.org.uk/media/atlas/dicom/IMG_827_ipmO3HH.dcm",
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"wadouri:https://www.penracourses.org.uk/media/atlas/dicom/IMG_828_Zuppb9h.dcm",
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"wadouri:https://www.penracourses.org.uk/media/atlas/dicom/IMG_829_TMuror5.dcm",
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"wadouri:https://www.penracourses.org.uk/media/atlas/dicom/IMG_830_Mnaj7oR.dcm",
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"wadouri:https://www.penracourses.org.uk/media/atlas/dicom/IMG_831_2U6zI7M.dcm",
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"wadouri:https://www.penracourses.org.uk/media/atlas/dicom/IMG_832_V9fvVdM.dcm",
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"wadouri:https://www.penracourses.org.uk/media/atlas/dicom/IMG_833_AAFaoOW.dcm",
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"wadouri:https://www.penracourses.org.uk/media/atlas/dicom/IMG_834_vxBJLIn.dcm",
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"wadouri:https://www.penracourses.org.uk/media/atlas/dicom/IMG_835_ZppFa6u.dcm",
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"wadouri:https://www.penracourses.org.uk/media/atlas/dicom/IMG_836_adRHoD3.dcm",
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"wadouri:https://www.penracourses.org.uk/media/atlas/dicom/IMG_837_jjfHCn3.dcm",
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"wadouri:https://www.penracourses.org.uk/media/atlas/dicom/IMG_838_N21h3ne.dcm",
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"wadouri:https://www.penracourses.org.uk/media/atlas/dicom/IMG_839_n6FWmeX.dcm",
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"wadouri:https://www.penracourses.org.uk/media/atlas/dicom/IMG_840_dErur0M.dcm",
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"wadouri:https://www.penracourses.org.uk/media/atlas/dicom/IMG_841_PcoTakk.dcm",
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"wadouri:https://www.penracourses.org.uk/media/atlas/dicom/IMG_842_UmTu7Fg.dcm",
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"wadouri:https://www.penracourses.org.uk/media/atlas/dicom/IMG_843_USByQXH.dcm",
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],
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}
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],
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stackIdx: [0, 2, 1],
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stackPos: [0, 0, 2],
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+104
-21
@@ -232,7 +232,7 @@ const GROUPING_RULE_DEFINITIONS: GroupingRuleDefinition[] = [
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id: "contentTime",
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label: "Content/Acquisition time",
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description: "Content Time (0008,0033) / Acquisition Time (0008,0032)",
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defaultEnabled: true,
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defaultEnabled: false,
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},
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{
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id: "echoTime",
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@@ -296,6 +296,66 @@ function parseNumericValueList(raw?: string | null): number[] {
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.filter((value) => Number.isFinite(value));
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}
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/**
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* Extract b-value(s) from a dicomParser DataSet. Handles multiple VR encodings:
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* - (0018,9087) DiffusionBValue — VR FD (double) in Enhanced MR, DS (string) in some classic MR
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* - (0019,100C) GE private — VR DS
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* - (0043,1039) GE legacy — VR IS/DS
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* - (2001,1003) Philips private — VR FL (32-bit float)
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*/
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function parseBValuesFromDataSet(dataSet: any): number[] {
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if (!dataSet || typeof dataSet !== "object") return [];
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const tryNumeric = (tagId: string): number | null => {
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// DS/IS string form
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if (typeof dataSet.string === "function") {
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const raw = dataSet.string(tagId);
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if (raw != null && raw !== "") {
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const vals = parseNumericValueList(raw);
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if (vals.length > 0 && Number.isFinite(vals[0]) && vals[0] >= 0) return vals[0];
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}
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}
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// FD — 64-bit double (standard DiffusionBValue in Enhanced MR)
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if (typeof dataSet.double === "function") {
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try {
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const v = dataSet.double(tagId);
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if (Number.isFinite(v) && v >= 0) return v;
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} catch (_) {}
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}
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// FL — 32-bit float (Philips private (2001,1003))
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if (typeof dataSet.float === "function") {
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try {
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const v = dataSet.float(tagId);
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if (Number.isFinite(v) && v >= 0) return v;
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} catch (_) {}
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}
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return null;
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};
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// Standard (0018,9087) DiffusionBValue
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const v1 = tryNumeric("x00189087");
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if (v1 !== null) return [v1];
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// GE private (0019,100C)
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const v2 = tryNumeric("x0019100c");
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if (v2 !== null) return [v2];
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// GE legacy (0043,1039) — IS format, first value is b-value
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if (typeof dataSet.string === "function") {
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const raw = dataSet.string("x00431039");
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if (raw) {
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const parts = parseNumericValueList(raw);
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if (parts.length > 0 && Number.isFinite(parts[0]) && parts[0] >= 0) return [parts[0]];
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}
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}
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// Philips private (2001,1003) — VR FL
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const v3 = tryNumeric("x20011003");
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if (v3 !== null) return [v3];
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return [];
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}
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function normalizeToWadouriOrExternal(imageId: string): string {
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if (imageId.startsWith("wadouri:") || imageId.startsWith("external:")) {
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return imageId;
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@@ -1439,19 +1499,6 @@ export default function App({ container_id, imageStacks, autoCacheStack, annotat
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const cached = bValuesByBaseImageRef.current[baseUrl];
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if (cached) return cached;
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const parseBValuesFromDataSet = (dataSet: any): number[] => {
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if (!dataSet || typeof dataSet.string !== "function") return [];
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const standard = parseNumericValueList(dataSet.string("x00189087")); // DiffusionBValue
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if (standard.length > 0) return standard;
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const gePrivate = parseNumericValueList(dataSet.string("x0019100c"));
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if (gePrivate.length > 0) return gePrivate;
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const geLegacyPrivate = parseNumericValueList(dataSet.string("x00431039"));
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if (geLegacyPrivate.length > 0) return geLegacyPrivate;
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const privatePhilips = parseNumericValueList(dataSet.string("x20011003"));
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if (privatePhilips.length > 0) return privatePhilips;
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return [];
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};
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try {
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const cacheManager = cornerstoneDICOMImageLoader?.wadouri?.dataSetCacheManager;
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if (cacheManager?.get) {
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@@ -1466,13 +1513,42 @@ export default function App({ container_id, imageStacks, autoCacheStack, annotat
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// Continue with fetch fallback.
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}
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// Helper: parse bytes tolerating truncation (header-only range requests)
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const tryParseBytes = (bytes: Uint8Array): number[] => {
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try {
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return parseBValuesFromDataSet(dicomParser.parseDicom(bytes));
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} catch (e: any) {
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// dicomParser throws on truncation but attaches partial dataSet
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if (e?.dataSet) {
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const partial = parseBValuesFromDataSet(e.dataSet);
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if (partial.length > 0) return partial;
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}
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return [];
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}
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};
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// Range request — first 64 KB is enough to find b-value tags in the header
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try {
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const rangeResponse = await fetch(baseUrl, { headers: { Range: "bytes=0-65535" } });
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if (rangeResponse.ok || rangeResponse.status === 206) {
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const buf = await rangeResponse.arrayBuffer();
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const result = tryParseBytes(new Uint8Array(buf));
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if (result.length > 0 || rangeResponse.status === 200) {
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bValuesByBaseImageRef.current[baseUrl] = result;
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return result;
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}
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}
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} catch (e) {
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// Fall through to full fetch.
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}
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// Full fetch fallback (only if range request failed or server doesn't support Range)
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try {
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const response = await fetch(baseUrl);
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const arrayBuffer = await response.arrayBuffer();
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const dataSet = dicomParser.parseDicom(new Uint8Array(arrayBuffer));
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const fromFetch = parseBValuesFromDataSet(dataSet);
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bValuesByBaseImageRef.current[baseUrl] = fromFetch;
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return fromFetch;
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const buf = await response.arrayBuffer();
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const result = tryParseBytes(new Uint8Array(buf));
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bValuesByBaseImageRef.current[baseUrl] = result;
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return result;
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} catch (e) {
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bValuesByBaseImageRef.current[baseUrl] = [];
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return [];
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@@ -1656,8 +1732,15 @@ export default function App({ container_id, imageStacks, autoCacheStack, annotat
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.map((candidate) => candidate.ruleValues[ruleId])
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.filter((value): value is string => !!value);
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const distinct = new Set(values);
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// Ignore rules that are constant (or effectively unique per image) to avoid over-fragmentation.
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return distinct.size > 1 && distinct.size < Math.max(2, candidates.length);
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// Only activate when:
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// 1. Multiple distinct values (not constant across the series)
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// 2. Not effectively unique per-image (would produce a group of 1 per image)
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// 3. At least 70% of images have a value for this rule — avoids fragmenting when
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// only a handful of images returned metadata (e.g., b-value fetch failed for most)
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const coverage = values.length / candidates.length;
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return distinct.size > 1
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&& distinct.size < Math.max(2, candidates.length)
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&& coverage >= 0.7;
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})
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: [];
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