@fnndsc/salsa 3.15.0 → 3.17.0

package/dist/dicom/dictionary.d.ts

@@ -0,0 +1,42 @@
+/**
+ * @file The static knowledge a tag listing needs beyond the DICOM dictionary:
+ * which module a tag belongs to, which tags carry identifying information,
+ * and how a handful of coded values read in words.
+ *
+ * All three are surfaces' concerns as much as the kernel's, so they live
+ * once, here, and every surface renders from the same answer: grouping
+ * decides where a row sits, the PHI flag decides whether it is shown or
+ * redacted, decoding gives a human the meaning of `MR` or `HFS`. The kernel
+ * flags and decodes; it never strips.
+ *
+ * @module
+ */
+/** Where a tag sits in a grouped listing. */
+export type DicomTagGroup = 'meta' | 'patient' | 'study' | 'series' | 'image' | 'equipment' | 'private' | 'other';
+/** The groups in the order a listing shows them. */
+export declare const DICOM_TAG_GROUPS: readonly DicomTagGroup[];
+/**
+ * Places a tag in its listing group.
+ *
+ * @param groupNumber - The tag's group number (the `gggg` of `(gggg,eeee)`).
+ * @param name - The dictionary name, when the tag has one.
+ * @returns The listing group.
+ */
+export declare function tagGroup_of(groupNumber: number, name: string | undefined): DicomTagGroup;
+/**
+ * Tags that identify a person or an institution. Flagged on the model so a
+ * surface can redact; never stripped by the kernel.
+ */
+export declare const DICOM_PHI_TAGS: ReadonlySet<string>;
+/** Transfer syntaxes by UID. A renderer's decoder support is judged against these. */
+export declare const TRANSFER_SYNTAX_NAMES: Readonly<Record<string, string>>;
+/**
+ * Reads a coded value in words, for the short list of tags a reader meets
+ * first. SOP class UIDs are named by the caller through the dictionary.
+ *
+ * @param name - The tag's dictionary name.
+ * @param value - The tag's formatted value.
+ * @returns The decoded words, or undefined when the tag is not coded or the
+ *   code is unknown.
+ */
+export declare function tagValue_decode(name: string, value: string): string | undefined;

package/dist/dicom/dictionary.js

@@ -0,0 +1,221 @@
+"use strict";
+/**
+ * @file The static knowledge a tag listing needs beyond the DICOM dictionary:
+ * which module a tag belongs to, which tags carry identifying information,
+ * and how a handful of coded values read in words.
+ *
+ * All three are surfaces' concerns as much as the kernel's, so they live
+ * once, here, and every surface renders from the same answer: grouping
+ * decides where a row sits, the PHI flag decides whether it is shown or
+ * redacted, decoding gives a human the meaning of `MR` or `HFS`. The kernel
+ * flags and decodes; it never strips.
+ *
+ * @module
+ */
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.TRANSFER_SYNTAX_NAMES = exports.DICOM_PHI_TAGS = exports.DICOM_TAG_GROUPS = void 0;
+exports.tagGroup_of = tagGroup_of;
+exports.tagValue_decode = tagValue_decode;
+/** The groups in the order a listing shows them. */
+exports.DICOM_TAG_GROUPS = [
+    'patient',
+    'study',
+    'series',
+    'image',
+    'equipment',
+    'meta',
+    'private',
+    'other',
+];
+/**
+ * Named tags whose module the group number alone gets wrong. Group 0008 mixes
+ * study, series and image identity; 0018 mixes acquisition and equipment;
+ * 0020 mixes study, series and image position.
+ */
+const GROUP_BY_NAME = {
+    // 0008: series identity and content
+    Modality: 'series',
+    SeriesDate: 'series',
+    SeriesTime: 'series',
+    SeriesDescription: 'series',
+    BodyPartExamined: 'series',
+    ProtocolName: 'series',
+    // 0008: image identity
+    SOPClassUID: 'image',
+    SOPInstanceUID: 'image',
+    ImageType: 'image',
+    ContentDate: 'image',
+    ContentTime: 'image',
+    AcquisitionDate: 'image',
+    AcquisitionTime: 'image',
+    AcquisitionNumber: 'image',
+    // 0008: equipment
+    Manufacturer: 'equipment',
+    ManufacturerModelName: 'equipment',
+    StationName: 'equipment',
+    InstitutionName: 'equipment',
+    InstitutionAddress: 'equipment',
+    InstitutionalDepartmentName: 'equipment',
+    // 0018: equipment
+    DeviceSerialNumber: 'equipment',
+    SoftwareVersions: 'equipment',
+    MagneticFieldStrength: 'equipment',
+    // 0020: study
+    StudyInstanceUID: 'study',
+    StudyID: 'study',
+    // 0020: series
+    SeriesInstanceUID: 'series',
+    SeriesNumber: 'series',
+    FrameOfReferenceUID: 'series',
+    PositionReferenceIndicator: 'series',
+    PatientPosition: 'series',
+    // 0020: image
+    InstanceNumber: 'image',
+    ImagePositionPatient: 'image',
+    ImageOrientationPatient: 'image',
+    SliceLocation: 'image',
+    ImageComments: 'image',
+    NumberOfFrames: 'image',
+};
+/** Module by tag group number, for tags the name table does not place. */
+const GROUP_BY_NUMBER = {
+    0x0002: 'meta',
+    0x0008: 'study',
+    0x0010: 'patient',
+    0x0018: 'series',
+    0x0020: 'image',
+    0x0028: 'image',
+    0x0032: 'study',
+    0x0038: 'patient',
+    0x0040: 'study',
+    0x0054: 'series',
+    0x0070: 'image',
+    0x0088: 'series',
+    0x3006: 'image',
+    0x7fe0: 'image',
+};
+/**
+ * Places a tag in its listing group.
+ *
+ * @param groupNumber - The tag's group number (the `gggg` of `(gggg,eeee)`).
+ * @param name - The dictionary name, when the tag has one.
+ * @returns The listing group.
+ */
+function tagGroup_of(groupNumber, name) {
+    if (groupNumber % 2 === 1)
+        return 'private';
+    if (name !== undefined && GROUP_BY_NAME[name] !== undefined)
+        return GROUP_BY_NAME[name];
+    return GROUP_BY_NUMBER[groupNumber] ?? 'other';
+}
+/**
+ * Tags that identify a person or an institution. Flagged on the model so a
+ * surface can redact; never stripped by the kernel.
+ */
+exports.DICOM_PHI_TAGS = new Set([
+    'PatientName',
+    'PatientID',
+    'PatientBirthDate',
+    'PatientBirthTime',
+    'PatientAddress',
+    'PatientTelephoneNumbers',
+    'OtherPatientIDs',
+    'OtherPatientNames',
+    'PatientMotherBirthName',
+    'InstitutionName',
+    'InstitutionAddress',
+    'ReferringPhysicianName',
+    'PerformingPhysicianName',
+    'OperatorsName',
+    'PhysiciansOfRecord',
+    'NameOfPhysiciansReadingStudy',
+    'AccessionNumber',
+]);
+/** Words for the coded values a reader meets first. */
+const MODALITY_NAMES = {
+    MR: 'Magnetic Resonance',
+    CT: 'Computed Tomography',
+    PT: 'Positron Emission Tomography',
+    NM: 'Nuclear Medicine',
+    US: 'Ultrasound',
+    CR: 'Computed Radiography',
+    DX: 'Digital Radiography',
+    MG: 'Mammography',
+    RF: 'Radio Fluoroscopy',
+    XA: 'X-Ray Angiography',
+    OT: 'Other',
+    SR: 'Structured Report',
+    SEG: 'Segmentation',
+    RTSTRUCT: 'RT Structure Set',
+    RTDOSE: 'RT Dose',
+    RTPLAN: 'RT Plan',
+    PR: 'Presentation State',
+    KO: 'Key Object Selection',
+    DOC: 'Document',
+};
+const PATIENT_SEX_NAMES = {
+    M: 'Male',
+    F: 'Female',
+    O: 'Other',
+};
+const PATIENT_POSITION_NAMES = {
+    HFS: 'Head First Supine',
+    HFP: 'Head First Prone',
+    HFDR: 'Head First Decubitus Right',
+    HFDL: 'Head First Decubitus Left',
+    FFS: 'Feet First Supine',
+    FFP: 'Feet First Prone',
+    FFDR: 'Feet First Decubitus Right',
+    FFDL: 'Feet First Decubitus Left',
+};
+const PHOTOMETRIC_NAMES = {
+    MONOCHROME1: 'Greyscale, minimum is white',
+    MONOCHROME2: 'Greyscale, minimum is black',
+    RGB: 'Colour, RGB',
+    'PALETTE COLOR': 'Colour, palette',
+    YBR_FULL: 'Colour, YBR full',
+    YBR_FULL_422: 'Colour, YBR 4:2:2',
+    YBR_RCT: 'Colour, YBR reversible',
+    YBR_ICT: 'Colour, YBR irreversible',
+};
+/** Transfer syntaxes by UID. A renderer's decoder support is judged against these. */
+exports.TRANSFER_SYNTAX_NAMES = {
+    '1.2.840.10008.1.2': 'Implicit VR Little Endian',
+    '1.2.840.10008.1.2.1': 'Explicit VR Little Endian',
+    '1.2.840.10008.1.2.1.99': 'Deflated Explicit VR Little Endian',
+    '1.2.840.10008.1.2.2': 'Explicit VR Big Endian',
+    '1.2.840.10008.1.2.4.50': 'JPEG Baseline (8-bit)',
+    '1.2.840.10008.1.2.4.51': 'JPEG Extended (12-bit)',
+    '1.2.840.10008.1.2.4.57': 'JPEG Lossless',
+    '1.2.840.10008.1.2.4.70': 'JPEG Lossless SV1',
+    '1.2.840.10008.1.2.4.80': 'JPEG-LS Lossless',
+    '1.2.840.10008.1.2.4.81': 'JPEG-LS Near-Lossless',
+    '1.2.840.10008.1.2.4.90': 'JPEG 2000 Lossless',
+    '1.2.840.10008.1.2.4.91': 'JPEG 2000',
+    '1.2.840.10008.1.2.4.201': 'High-Throughput JPEG 2000 Lossless',
+    '1.2.840.10008.1.2.4.202': 'High-Throughput JPEG 2000 Lossless RPCL',
+    '1.2.840.10008.1.2.4.203': 'High-Throughput JPEG 2000',
+    '1.2.840.10008.1.2.5': 'RLE Lossless',
+};
+/** Decoders by tag name; each answers with words or nothing. */
+const DECODERS = {
+    Modality: (value) => MODALITY_NAMES[value],
+    PatientSex: (value) => PATIENT_SEX_NAMES[value],
+    PatientPosition: (value) => PATIENT_POSITION_NAMES[value],
+    PhotometricInterpretation: (value) => PHOTOMETRIC_NAMES[value],
+    TransferSyntaxUID: (value) => exports.TRANSFER_SYNTAX_NAMES[value],
+};
+/**
+ * Reads a coded value in words, for the short list of tags a reader meets
+ * first. SOP class UIDs are named by the caller through the dictionary.
+ *
+ * @param name - The tag's dictionary name.
+ * @param value - The tag's formatted value.
+ * @returns The decoded words, or undefined when the tag is not coded or the
+ *   code is unknown.
+ */
+function tagValue_decode(name, value) {
+    const decoder = DECODERS[name];
+    return decoder === undefined ? undefined : decoder(value);
+}
+//# sourceMappingURL=dictionary.js.map

package/dist/dicom/dictionary.js.map

@@ -0,0 +1 @@
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package/dist/dicom/index.d.ts

@@ -0,0 +1,7 @@
+/**
+ * @file DICOM in the kernel: tag reading and the series as a folder.
+ * @module
+ */
+export * from './dictionary.js';
+export * from './tags.js';
+export * from './series.js';

package/dist/dicom/index.js

@@ -0,0 +1,24 @@
+"use strict";
+var __createBinding = (this && this.__createBinding) || (Object.create ? (function(o, m, k, k2) {
+    if (k2 === undefined) k2 = k;
+    var desc = Object.getOwnPropertyDescriptor(m, k);
+    if (!desc || ("get" in desc ? !m.__esModule : desc.writable || desc.configurable)) {
+      desc = { enumerable: true, get: function() { return m[k]; } };
+    }
+    Object.defineProperty(o, k2, desc);
+}) : (function(o, m, k, k2) {
+    if (k2 === undefined) k2 = k;
+    o[k2] = m[k];
+}));
+var __exportStar = (this && this.__exportStar) || function(m, exports) {
+    for (var p in m) if (p !== "default" && !Object.prototype.hasOwnProperty.call(exports, p)) __createBinding(exports, m, p);
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+/**
+ * @file DICOM in the kernel: tag reading and the series as a folder.
+ * @module
+ */
+__exportStar(require("./dictionary.js"), exports);
+__exportStar(require("./tags.js"), exports);
+__exportStar(require("./series.js"), exports);
+//# sourceMappingURL=index.js.map

package/dist/dicom/index.js.map

@@ -0,0 +1 @@
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package/dist/dicom/series.d.ts

@@ -0,0 +1,120 @@
+/**
+ * @file The series as the kernel knows it.
+ *
+ * A DICOM series in ChRIS is a folder of files. Files are the truth; a
+ * viewer hides them. This module answers "what is this folder as a series"
+ * without walking every file: the listing gives the count, the bytes and
+ * the order (oxidicom names each file by its InstanceNumber, so the name
+ * sorts the stack), and one header read gives identity, modality and
+ * geometry. A full positional sort is a volume renderer's business and is
+ * deferred to it.
+ *
+ * Headers read once are kept, keyed by path, so a tag listing that follows
+ * a scroll costs nothing on the second visit.
+ *
+ * @module
+ */
+import { type Result } from '@fnndsc/cumin';
+import type { VFSItem } from '../vfs/provider.js';
+import { type DicomTagSet } from './tags.js';
+/** How a folder is read; injected so the summary is testable without a daemon. */
+export interface DicomFolderIO {
+    list(path: string): Promise<Result<VFSItem[]>>;
+    readBinary(path: string): Promise<Result<Buffer>>;
+}
+/** The real folder reader: the VFS for listings, CFS for bytes. */
+export declare const dicomFolderIO_default: DicomFolderIO;
+/** How a folder's files are ordered into a stack. */
+export type DicomSeriesOrder = 'filename' | 'unknown';
+/** The voxel grid, from one header. */
+export interface DicomGeometry {
+    rows: number;
+    columns: number;
+    /** Row and column spacing in mm. */
+    pixelSpacing?: [number, number];
+    sliceThickness?: number;
+    spacingBetweenSlices?: number;
+}
+/** What one folder is as a series. */
+export interface DicomSeriesSummary {
+    path: string;
+    seriesInstanceUID?: string;
+    studyInstanceUID?: string;
+    modality: string;
+    seriesDescription: string;
+    seriesNumber?: number;
+    /** DICOM files in the folder. */
+    instances: number;
+    /** Frames in the header read; one for a classic single-frame file. */
+    frames: number;
+    order: DicomSeriesOrder;
+    geometry?: DicomGeometry;
+    transferSyntax?: {
+        uid: string;
+        name?: string;
+    };
+    /** Sum of the folder's DICOM file sizes. */
+    bytes: number;
+    /** The file whose header answered, first in stack order. */
+    header: string;
+    /** Files ordered for a stack, first to last. */
+    files: string[];
+    /** Annotation files found for the series' UID. */
+    annotations: string[];
+}
+/** Options for a series summary. */
+export interface DicomSeriesOptions {
+    /** Where annotation folders live; `<root>/<SeriesInstanceUID>` is listed when given. */
+    annotationRoot?: string;
+}
+/** A folder's DICOM files, ordered. */
+export interface DicomFolderListing {
+    files: Array<{
+        path: string;
+        size: number;
+    }>;
+    order: DicomSeriesOrder;
+}
+/**
+ * Reads one file's header through the cache.
+ *
+ * @param path - The file's VFS path.
+ * @param io - The folder reader.
+ * @returns The tag set, or an error when the file could not be read or parsed.
+ */
+export declare function dicomHeader_get(path: string, io?: DicomFolderIO): Promise<Result<DicomTagSet>>;
+/**
+ * Forgets every cached header.
+ */
+export declare function dicomHeaderCache_clear(): void;
+/**
+ * Lists a folder's DICOM files in stack order.
+ *
+ * Order is `filename` when every file starts with a number and a dash
+ * (oxidicom's `<InstanceNumber>-<SOPInstanceUID>.dcm`), sorted by that number;
+ * otherwise `unknown`, sorted by name.
+ *
+ * @param folder - The folder's VFS path.
+ * @param io - The folder reader.
+ * @returns The ordered files with sizes, or an error when the folder cannot be listed.
+ */
+export declare function dicomFolder_list(folder: string, io?: DicomFolderIO): Promise<Result<DicomFolderListing>>;
+/**
+ * Picks at most `cap` files spread evenly across the stack, always keeping
+ * the first and the last.
+ *
+ * @param files - The ordered files.
+ * @param cap - The most to keep.
+ * @returns The chosen files, in order.
+ */
+export declare function dicomFiles_sample<T>(files: T[], cap: number): T[];
+/**
+ * Summarizes a folder as a series from its listing and one header.
+ *
+ * @param folder - The folder's VFS path.
+ * @param options - Where to look for annotations.
+ * @param io - The folder reader.
+ * @returns The summary; an error when the folder cannot be listed, holds no
+ *   DICOM files, or its first file cannot be read.
+ */
+export declare function dicomSeries_summarize(folder: string, options?: DicomSeriesOptions, io?: DicomFolderIO): Promise<Result<DicomSeriesSummary>>;

package/dist/dicom/series.js

@@ -0,0 +1,209 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.dicomFolderIO_default = void 0;
+exports.dicomHeader_get = dicomHeader_get;
+exports.dicomHeaderCache_clear = dicomHeaderCache_clear;
+exports.dicomFolder_list = dicomFolder_list;
+exports.dicomFiles_sample = dicomFiles_sample;
+exports.dicomSeries_summarize = dicomSeries_summarize;
+/**
+ * @file The series as the kernel knows it.
+ *
+ * A DICOM series in ChRIS is a folder of files. Files are the truth; a
+ * viewer hides them. This module answers "what is this folder as a series"
+ * without walking every file: the listing gives the count, the bytes and
+ * the order (oxidicom names each file by its InstanceNumber, so the name
+ * sorts the stack), and one header read gives identity, modality and
+ * geometry. A full positional sort is a volume renderer's business and is
+ * deferred to it.
+ *
+ * Headers read once are kept, keyed by path, so a tag listing that follows
+ * a scroll costs nothing on the second visit.
+ *
+ * @module
+ */
+const cumin_1 = require("@fnndsc/cumin");
+const dispatcher_js_1 = require("../vfs/dispatcher.js");
+const index_js_1 = require("../files/index.js");
+const dictionary_js_1 = require("./dictionary.js");
+const tags_js_1 = require("./tags.js");
+/** The real folder reader: the VFS for listings, CFS for bytes. */
+exports.dicomFolderIO_default = {
+    list: (path) => dispatcher_js_1.vfsDispatcher.list(path),
+    readBinary: (path) => (0, index_js_1.fileContent_getBinary)(path),
+};
+/** Headers kept by path. Bounded; the oldest entry leaves first. */
+const HEADER_CACHE_LIMIT = 4096;
+const headerCache = new Map();
+/**
+ * Reads one file's header through the cache.
+ *
+ * @param path - The file's VFS path.
+ * @param io - The folder reader.
+ * @returns The tag set, or an error when the file could not be read or parsed.
+ */
+async function dicomHeader_get(path, io = exports.dicomFolderIO_default) {
+    const cached = headerCache.get(path);
+    if (cached !== undefined)
+        return (0, cumin_1.Ok)(cached);
+    const bytes = await io.readBinary(path);
+    if (!bytes.ok)
+        return (0, cumin_1.Err)();
+    const parsed = (0, tags_js_1.dicomTags_read)(bytes.value);
+    if (!parsed.ok)
+        return (0, cumin_1.Err)();
+    if (headerCache.size >= HEADER_CACHE_LIMIT) {
+        const oldest = headerCache.keys().next().value;
+        if (oldest !== undefined)
+            headerCache.delete(oldest);
+    }
+    headerCache.set(path, parsed.value);
+    return parsed;
+}
+/**
+ * Forgets every cached header.
+ */
+function dicomHeaderCache_clear() {
+    headerCache.clear();
+}
+/**
+ * Lists a folder's DICOM files in stack order.
+ *
+ * Order is `filename` when every file starts with a number and a dash
+ * (oxidicom's `<InstanceNumber>-<SOPInstanceUID>.dcm`), sorted by that number;
+ * otherwise `unknown`, sorted by name.
+ *
+ * @param folder - The folder's VFS path.
+ * @param io - The folder reader.
+ * @returns The ordered files with sizes, or an error when the folder cannot be listed.
+ */
+async function dicomFolder_list(folder, io = exports.dicomFolderIO_default) {
+    const listing = await io.list(folder);
+    if (!listing.ok)
+        return (0, cumin_1.Err)();
+    const base = folder.endsWith('/') ? folder.slice(0, -1) : folder;
+    const entries = listing.value.filter((item) => item.type === 'file' && /\.dcm$/i.test(item.name));
+    const numbered = entries.length > 0 && entries.every((item) => /^\d+-/.test(item.name));
+    const sorted = [...entries].sort((a, b) => numbered ? parseInt(a.name, 10) - parseInt(b.name, 10) || a.name.localeCompare(b.name) : a.name.localeCompare(b.name));
+    return (0, cumin_1.Ok)({
+        files: sorted.map((item) => ({ path: `${base}/${item.name}`, size: item.size })),
+        order: numbered ? 'filename' : 'unknown',
+    });
+}
+/**
+ * Picks at most `cap` files spread evenly across the stack, always keeping
+ * the first and the last.
+ *
+ * @param files - The ordered files.
+ * @param cap - The most to keep.
+ * @returns The chosen files, in order.
+ */
+function dicomFiles_sample(files, cap) {
+    if (cap <= 0)
+        return [];
+    if (files.length <= cap)
+        return files;
+    if (cap === 1)
+        return [files[0]];
+    const chosen = [];
+    const step = (files.length - 1) / (cap - 1);
+    for (let i = 0; i < cap; i++)
+        chosen.push(files[Math.round(i * step)]);
+    return chosen;
+}
+/**
+ * Summarizes a folder as a series from its listing and one header.
+ *
+ * @param folder - The folder's VFS path.
+ * @param options - Where to look for annotations.
+ * @param io - The folder reader.
+ * @returns The summary; an error when the folder cannot be listed, holds no
+ *   DICOM files, or its first file cannot be read.
+ */
+async function dicomSeries_summarize(folder, options = {}, io = exports.dicomFolderIO_default) {
+    const listed = await dicomFolder_list(folder, io);
+    if (!listed.ok || listed.value.files.length === 0)
+        return (0, cumin_1.Err)();
+    const files = listed.value.files;
+    const header = await dicomHeader_get(files[0].path, io);
+    if (!header.ok)
+        return (0, cumin_1.Err)();
+    const tags = header.value.tags;
+    const seriesInstanceUID = tagText_of(tags, 'SeriesInstanceUID');
+    const summary = {
+        path: folder,
+        ...(seriesInstanceUID !== undefined ? { seriesInstanceUID } : {}),
+        ...(tagText_of(tags, 'StudyInstanceUID') !== undefined ? { studyInstanceUID: tagText_of(tags, 'StudyInstanceUID') } : {}),
+        modality: tagText_of(tags, 'Modality') ?? 'OT',
+        seriesDescription: tagText_of(tags, 'SeriesDescription') ?? '',
+        ...(tagNumber_of(tags, 'SeriesNumber') !== undefined ? { seriesNumber: tagNumber_of(tags, 'SeriesNumber') } : {}),
+        instances: files.length,
+        frames: tagNumber_of(tags, 'NumberOfFrames') ?? 1,
+        order: listed.value.order,
+        ...(geometry_of(tags) !== undefined ? { geometry: geometry_of(tags) } : {}),
+        ...(header.value.transferSyntaxUID !== undefined
+            ? {
+                transferSyntax: {
+                    uid: header.value.transferSyntaxUID,
+                    ...(dictionary_js_1.TRANSFER_SYNTAX_NAMES[header.value.transferSyntaxUID] !== undefined ? { name: dictionary_js_1.TRANSFER_SYNTAX_NAMES[header.value.transferSyntaxUID] } : {}),
+                },
+            }
+            : {}),
+        bytes: files.reduce((total, file) => total + file.size, 0),
+        header: files[0].path,
+        files: files.map((file) => file.path),
+        annotations: [],
+    };
+    if (options.annotationRoot !== undefined && seriesInstanceUID !== undefined) {
+        const root = options.annotationRoot.endsWith('/') ? options.annotationRoot.slice(0, -1) : options.annotationRoot;
+        const found = await io.list(`${root}/${seriesInstanceUID}`);
+        if (found.ok) {
+            summary.annotations = found.value
+                .filter((item) => item.type === 'file')
+                .map((item) => `${root}/${seriesInstanceUID}/${item.name}`)
+                .sort();
+        }
+    }
+    return (0, cumin_1.Ok)(summary);
+}
+/**
+ * A tag's text, or nothing when absent or empty.
+ */
+function tagText_of(tags, name) {
+    const tag = (0, tags_js_1.dicomTag_find)(tags, name);
+    return tag === undefined || tag.value === '' ? undefined : tag.value;
+}
+/**
+ * A tag's first value as a number, or nothing when absent or not numeric.
+ */
+function tagNumber_of(tags, name) {
+    const text = tagText_of(tags, name);
+    if (text === undefined)
+        return undefined;
+    const parsed = Number(text.split('\\')[0]);
+    return Number.isFinite(parsed) ? parsed : undefined;
+}
+/**
+ * The voxel grid from a header, when it has one.
+ */
+function geometry_of(tags) {
+    const rows = tagNumber_of(tags, 'Rows');
+    const columns = tagNumber_of(tags, 'Columns');
+    if (rows === undefined || columns === undefined)
+        return undefined;
+    const geometry = { rows, columns };
+    const spacing = tagText_of(tags, 'PixelSpacing');
+    if (spacing !== undefined) {
+        const parts = spacing.split('\\').map(Number);
+        if (parts.length === 2 && parts.every(Number.isFinite))
+            geometry.pixelSpacing = [parts[0], parts[1]];
+    }
+    const thickness = tagNumber_of(tags, 'SliceThickness');
+    if (thickness !== undefined)
+        geometry.sliceThickness = thickness;
+    const between = tagNumber_of(tags, 'SpacingBetweenSlices');
+    if (between !== undefined)
+        geometry.spacingBetweenSlices = between;
+    return geometry;
+}
+//# sourceMappingURL=series.js.map

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