@fnndsc/salsa 3.17.0 → 3.18.0

package/dist/dicom/index.d.ts

@@ -5,3 +5,4 @@
 export * from './dictionary.js';
 export * from './tags.js';
 export * from './series.js';
+export * from './pixels.js';

package/dist/dicom/index.js

@@ -21,4 +21,5 @@ Object.defineProperty(exports, "__esModule", { value: true });
 __exportStar(require("./dictionary.js"), exports);
 __exportStar(require("./tags.js"), exports);
 __exportStar(require("./series.js"), exports);
+__exportStar(require("./pixels.js"), exports);
 //# sourceMappingURL=index.js.map

package/dist/dicom/index.js.map

@@ -1 +1 @@
-{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/dicom/index.ts"],"names":[],"mappings":";;;;;;;;;;;;;;;;AAAA;;;GAGG;AACH,kDAAgC;AAChC,4CAA0B;AAC1B,8CAA4B"}
+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/dicom/index.ts"],"names":[],"mappings":";;;;;;;;;;;;;;;;AAAA;;;GAGG;AACH,kDAAgC;AAChC,4CAA0B;AAC1B,8CAA4B;AAC5B,8CAA4B"}

package/dist/dicom/pixels.d.ts

@@ -0,0 +1,28 @@
+import { type Result } from '@fnndsc/cumin';
+import { type DicomFolderIO } from './series.js';
+/** A slice's luminance: `gray[y * width + x]`, 0 (black) to 255 (white). */
+export interface DicomGray {
+    width: number;
+    height: number;
+    gray: Uint8Array;
+}
+/**
+ * The outcome of reading a slice for a thumbnail: the grid, or the news that
+ * the pixels are compressed and this build cannot decode them. An unreadable
+ * or non-DICOM file is an error, not an outcome.
+ */
+export type DicomGrayOutcome = ({
+    kind: 'gray';
+} & DicomGray) | {
+    kind: 'compressed';
+    transferSyntax: string;
+};
+/**
+ * Reads one DICOM slice as an 8-bit grayscale grid.
+ *
+ * @param path - The slice file's VFS path.
+ * @param io - The reader, injected for tests.
+ * @returns The grid, the compressed verdict, or an error when the bytes are
+ *   not a readable DICOM file.
+ */
+export declare function dicomSlice_gray(path: string, io?: DicomFolderIO): Promise<Result<DicomGrayOutcome>>;

package/dist/dicom/pixels.js

@@ -0,0 +1,129 @@
+"use strict";
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.dicomSlice_gray = dicomSlice_gray;
+/**
+ * @file One DICOM slice as an 8-bit grayscale grid, for a text thumbnail.
+ *
+ * The kernel reads a slice's pixels, applies the modality rescale and a
+ * window/level (the file's own, or an auto range when it declares none), and
+ * normalises to 0..255 with MONOCHROME1 inverted so bright always reads high.
+ * A surface then renders that grid — an ASCII ramp on any pipe, ANSI
+ * half-blocks on a colour terminal — without knowing anything about DICOM.
+ *
+ * Only uncompressed transfer syntaxes are read here; a compressed one (the
+ * JPEG family, RLE) needs a codec the kernel does not carry, and says so
+ * rather than pretending. dcmjs decodes the endianness of the uncompressed
+ * ones, so the pixels arrive native-endian in the naturalised dataset.
+ *
+ * @module
+ */
+const dcmjs_1 = __importDefault(require("dcmjs"));
+const cumin_1 = require("@fnndsc/cumin");
+const series_js_1 = require("./series.js");
+/** Transfer syntaxes the kernel cannot decode without a codec: JPEG* and RLE. */
+const COMPRESSED_SYNTAX = /^1\.2\.840\.10008\.1\.2\.[45]/;
+/**
+ * Reads one DICOM slice as an 8-bit grayscale grid.
+ *
+ * @param path - The slice file's VFS path.
+ * @param io - The reader, injected for tests.
+ * @returns The grid, the compressed verdict, or an error when the bytes are
+ *   not a readable DICOM file.
+ */
+async function dicomSlice_gray(path, io = series_js_1.dicomFolderIO_default) {
+    const bytes = await io.readBinary(path);
+    if (!bytes.ok)
+        return (0, cumin_1.Err)();
+    try {
+        const buffer = new Uint8Array(bytes.value).slice().buffer;
+        const message = dcmjs_1.default.data.DicomMessage.readFile(buffer, { ignoreErrors: true });
+        const meta = dcmjs_1.default.data.DicomMetaDictionary.naturalizeDataset(message.meta);
+        const ds = dcmjs_1.default.data.DicomMetaDictionary.naturalizeDataset(message.dict);
+        const transferSyntax = typeof meta.TransferSyntaxUID === 'string' ? meta.TransferSyntaxUID : '';
+        if (COMPRESSED_SYNTAX.test(transferSyntax))
+            return (0, cumin_1.Ok)({ kind: 'compressed', transferSyntax });
+        const height = numberOf(ds.Rows) ?? 0;
+        const width = numberOf(ds.Columns) ?? 0;
+        if (height === 0 || width === 0)
+            return (0, cumin_1.Err)();
+        const count = width * height;
+        const pixelData = Array.isArray(ds.PixelData) ? ds.PixelData[0] : ds.PixelData;
+        if (!(pixelData instanceof ArrayBuffer))
+            return (0, cumin_1.Err)();
+        const bits = numberOf(ds.BitsAllocated) ?? 16;
+        const signed = numberOf(ds.PixelRepresentation) === 1;
+        const src = new Float64Array(count);
+        if (bits === 16) {
+            const view = signed ? new Int16Array(pixelData, 0, count) : new Uint16Array(pixelData, 0, count);
+            for (let i = 0; i < count; i++)
+                src[i] = view[i];
+        }
+        else if (bits === 8) {
+            const view = new Uint8Array(pixelData, 0, count);
+            for (let i = 0; i < count; i++)
+                src[i] = view[i];
+        }
+        else {
+            return (0, cumin_1.Err)();
+        }
+        // Modality rescale: stored value to a physical unit (HU for CT, etc.).
+        const slope = numberOf(ds.RescaleSlope) ?? 1;
+        const intercept = numberOf(ds.RescaleIntercept) ?? 0;
+        if (slope !== 1 || intercept !== 0)
+            for (let i = 0; i < count; i++)
+                src[i] = src[i] * slope + intercept;
+        // The file's own window/level, or an auto range when it declares none.
+        let center = firstNumber(ds.WindowCenter);
+        let width_wl = firstNumber(ds.WindowWidth);
+        if (center === undefined || width_wl === undefined || width_wl <= 0) {
+            const auto = autoWindow(src);
+            center = auto.center;
+            width_wl = auto.width;
+        }
+        const low = center - width_wl / 2;
+        const invert = ds.PhotometricInterpretation === 'MONOCHROME1';
+        const gray = new Uint8Array(count);
+        for (let i = 0; i < count; i++) {
+            let t = ((src[i] - low) / width_wl) * 255;
+            t = t < 0 ? 0 : t > 255 ? 255 : t;
+            gray[i] = invert ? 255 - t : t;
+        }
+        return (0, cumin_1.Ok)({ kind: 'gray', width, height, gray });
+    }
+    catch {
+        return (0, cumin_1.Err)();
+    }
+}
+/** The first number of a DICOM value that may be a number, an array, or a DS string. */
+function firstNumber(value) {
+    const one = Array.isArray(value) ? value[0] : value;
+    if (typeof one === 'number')
+        return Number.isFinite(one) ? one : undefined;
+    if (typeof one === 'string') {
+        const parsed = Number.parseFloat(one);
+        return Number.isFinite(parsed) ? parsed : undefined;
+    }
+    return undefined;
+}
+/** A whole number from a DICOM value that may arrive as a number or a string. */
+function numberOf(value) {
+    if (typeof value === 'number')
+        return value;
+    if (typeof value === 'string') {
+        const parsed = Number.parseInt(value, 10);
+        return Number.isFinite(parsed) ? parsed : undefined;
+    }
+    return undefined;
+}
+/** A window from the robust range of the data: its 2nd to 98th percentile. */
+function autoWindow(src) {
+    const sorted = src.slice().sort();
+    const low = sorted[Math.floor(sorted.length * 0.02)] ?? 0;
+    const high = sorted[Math.floor(sorted.length * 0.98)] ?? low + 1;
+    const width = Math.max(1, high - low);
+    return { center: low + width / 2, width };
+}
+//# sourceMappingURL=pixels.js.map

package/dist/dicom/pixels.js.map

@@ -0,0 +1 @@
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package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@fnndsc/salsa",
-  "version": "3.17.0",
+  "version": "3.18.0",
   "description": "Shared Application Logic and Service Assets for ChRIS",
   "repository": {
     "type": "git",
@@ -60,7 +60,7 @@
     "adm-zip": "npm:empty-npm-package@1.0.0"
   },
   "dependencies": {
-    "@fnndsc/cumin": "^3.22.0",
+    "@fnndsc/cumin": "^3.22.1",
     "axios": "^1.6.8",
     "dcmjs": "^0.52.0",
     "ws": "^8.21.0"