@fnndsc/brasa 0.22.0 → 0.23.1

package/dist/builtins/res/image.js

@@ -0,0 +1,96 @@
+/**
+ * @file `image` — show a DICOM series or a volume, as the kernel sees it.
+ *
+ * `image <path>` is a KERNEL command, not a surface verb: it resolves what
+ * the path is and emits an `image.view` intent for whatever surface is
+ * listening. A graphical surface (ARGUS) opens a rendered pane from the
+ * intent; a text surface (chell on a TTY) prints the reflection this command
+ * renders. So `image ~/uploads/sag-anon` works the same from a browser and
+ * from a terminal sharing one CALYPSO session.
+ *
+ * Usage:
+ *   image [--force] <path>   a series folder, a .dcm, or a NIfTI/MGZ volume
+ *
+ * The path resolves to a series (via the same reader `dcm series` uses) or a
+ * volume file; anything else is refused by name. `--force` rides through the
+ * volume-size guard a graphical surface would otherwise hold at.
+ *
+ * @module
+ */
+import { envelope_ok, envelope_error } from '@fnndsc/cumin';
+import { context_getSingle, dicomSeries_summarize, dicomSlice_gray } from '@fnndsc/salsa';
+import { IMAGE_MODEL_KINDS } from '@fnndsc/menu';
+import chalk from 'chalk';
+import { commandArgs_process, path_resolve } from '../utils.js';
+import { args_checkHasHelpFlag, help_render } from '../help.js';
+import { surface_get } from '../../core/surface.js';
+import { series_render } from './dicom.js';
+import { thumbnail_render } from './thumbnail.js';
+/** Path endings a volume renderer answers to. */
+const VOLUME_PATTERN = /\.(nii|nii\.gz|mgz|mgh)$/i;
+/** One DICOM file; its folder is the series. */
+const DICOM_FILE_PATTERN = /\.dcm$/i;
+/**
+ * Handles `image [--force] <path>`.
+ *
+ * @param args - The command arguments.
+ * @returns An envelope carrying the reflection text and the `image.view` intent.
+ */
+export async function builtin_image(args) {
+    if (args_checkHasHelpFlag(args, 'image'))
+        return envelope_ok(help_render('image'));
+    const parsed = commandArgs_process(args, { booleanLongOptions: ['force'] });
+    const target = parsed._[0];
+    if (target === undefined)
+        return envelope_ok(help_render('image'));
+    const force = parsed.force === true;
+    const resolved = await path_resolve(target);
+    // A volume file: the intent names it; a text surface has no volume to draw.
+    if (VOLUME_PATTERN.test(resolved)) {
+        const name = resolved.split('/').pop() ?? resolved;
+        const model = { path: resolved, target: 'volume', ...(force ? { force } : {}) };
+        return envelope_ok(`${chalk.cyan('image')} ${name}\n${chalk.gray('  a volume; a graphical surface renders it, a terminal shows this line.')}\n`, { kind: IMAGE_MODEL_KINDS.view, data: model });
+    }
+    // A series: the folder the path names, or the folder a .dcm sits in.
+    const folder = DICOM_FILE_PATTERN.test(resolved) ? resolved.slice(0, resolved.lastIndexOf('/')) : resolved;
+    const annotationRoot = await annotationRoot_get();
+    const summary = await dicomSeries_summarize(folder, annotationRoot !== undefined ? { annotationRoot } : {});
+    if (!summary.ok) {
+        process.exitCode = 1;
+        return envelope_error('', undefined, `${chalk.red(`image: ${target}: not a readable DICOM series, study, or volume`)}\n`);
+    }
+    const series = summary.value;
+    const model = { path: resolved, target: 'series', ...(force ? { force } : {}) };
+    // The reflection: the same facts `dcm series` shows, under an `image` line,
+    // and a thumbnail of the middle slice so a text surface shows the image too.
+    const thumbnail = await sliceThumbnail_render(series);
+    const reflection = `${chalk.cyan('image')} ${series.seriesDescription || folder}\n${series_render(series)}${thumbnail}`;
+    return envelope_ok(reflection, { kind: IMAGE_MODEL_KINDS.view, data: model });
+}
+/**
+ * Renders the middle slice of a series as a terminal thumbnail: an ASCII ramp,
+ * or ANSI half-blocks when the surface renders colour. A slice this build
+ * cannot decode (compressed pixels) says so in one line; anything else that
+ * cannot be read leaves the reflection with its facts and no picture.
+ *
+ * @param series - The resolved series.
+ * @returns The thumbnail block (leading newline), a one-line note, or empty.
+ */
+async function sliceThumbnail_render(series) {
+    const slice = series.files[Math.floor(series.files.length / 2)] ?? series.header;
+    if (slice === undefined)
+        return '';
+    const gray = await dicomSlice_gray(slice);
+    if (!gray.ok)
+        return '';
+    if (gray.value.kind === 'compressed') {
+        return `\n${chalk.gray(`  (${gray.value.transferSyntax} — compressed pixels; no text preview in this build)`)}\n`;
+    }
+    return `\n${thumbnail_render(gray.value, surface_get().capabilities.color)}`;
+}
+/** Where the session's annotations live: `/home/<user>/annotations`. */
+async function annotationRoot_get() {
+    const user = (await context_getSingle()).user;
+    return user === null ? undefined : `/home/${user}/annotations`;
+}
+//# sourceMappingURL=image.js.map

package/dist/builtins/res/image.js.map

@@ -0,0 +1 @@
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package/dist/builtins/res/pipeline.js

@@ -201,7 +201,15 @@ async function pipelineRun_handle(args) {
     }
     sink_dataLine(chalk.green(`✓ Workflow ${workflowId} created — ${pluginInstanceIds.length} node(s) queued`));
     sink_dataLine(chalk.gray(`  Instance IDs: ${pluginInstanceIds.join(', ')}`));
-    return envelope_ok('');
+    // A scheduled run is a model, as a plugin's is: a surface lights the feed
+    // it landed in rather than reading the id out of the text.
+    const firstInstance = pluginInstanceIds[0];
+    if (feedID === undefined || firstInstance === undefined)
+        return envelope_ok('');
+    return envelope_ok('', {
+        kind: 'run.scheduled',
+        data: { pluginName: pipelineResult.value.name, instanceId: firstInstance, feedId: feedID, newFeed: false, outputPath: '' },
+    });
 }
 /**
  * Handles `pipeline source <name|id>`.

package/dist/builtins/res/pipeline.js.map

@@ -1 +1 @@
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package/dist/builtins/res/plugininstance.js

@@ -10,6 +10,38 @@ import { commandArgs_process, cliOptions_from } from '../utils.js';
 import { pluginInstances_fetchList } from '@fnndsc/chili/commands/plugininstances/list.js';
 import { pluginInstanceFields_fetch } from '@fnndsc/chili/commands/plugininstances/fields.js';
 import { table_render } from '@fnndsc/chili/screen/screen.js';
+/**
+ * Projects a listed row onto the wire's instance model: the fields the
+ * listing selected, typed; a field the listing did not select is absent.
+ *
+ * @param row - One table row as chili fetched it.
+ * @returns The typed row.
+ */
+function instanceRow_project(row) {
+    const text = (key) => (typeof row[key] === 'string' && row[key] !== '' ? String(row[key]) : undefined);
+    const numeric = (key) => {
+        const value = row[key];
+        if (value === undefined || value === null || value === '')
+            return undefined;
+        const parsed = typeof value === 'number' ? value : Number(value);
+        return Number.isFinite(parsed) ? parsed : undefined;
+    };
+    const pluginName = text('plugin_name');
+    const pluginVersion = text('plugin_version');
+    const feedId = numeric('feed_id');
+    const owner = text('owner_username');
+    const status = text('status');
+    const startedAt = text('start_date');
+    return {
+        id: numeric('id') ?? 0,
+        ...(pluginName !== undefined ? { pluginName } : {}),
+        ...(pluginVersion !== undefined ? { pluginVersion } : {}),
+        ...(feedId !== undefined ? { feedId } : {}),
+        ...(owner !== undefined ? { owner } : {}),
+        ...(status !== undefined ? { status } : {}),
+        ...(startedAt !== undefined ? { startedAt } : {}),
+    };
+}
 /**
  * Builtin handler for the `plugininstance` command.
  *
@@ -21,10 +53,13 @@ export async function builtin_plugininstance(args) {
     if (!subcommand || subcommand === 'list') {
         try {
             const { pluginInstances, selectedFields, totalCount } = await pluginInstances_fetchList(cliOptions_from(parsed));
+            // The listing is a model as well as a table: the run history a surface
+            // reads (a catalogue's RECENT block) rather than scrapes.
+            const model = { kind: 'plugininstance.list', data: pluginInstances.map(instanceRow_project) };
             if (pluginInstances.length === 0) {
-                return envelope_ok(`${chalk.gray('No plugin instances found.')}\n`);
+                return envelope_ok(`${chalk.gray('No plugin instances found.')}\n`, model);
             }
-            return envelope_ok(table_render(pluginInstances, selectedFields, { title: { title: 'Plugin Instances', justification: 'center' }, pagination: totalCount !== undefined ? { shown: pluginInstances.length, total: totalCount } : undefined }));
+            return envelope_ok(table_render(pluginInstances, selectedFields, { title: { title: 'Plugin Instances', justification: 'center' }, pagination: totalCount !== undefined ? { shown: pluginInstances.length, total: totalCount } : undefined }), model);
         }
         catch (e) {
             process.exitCode = 1;

package/dist/builtins/res/plugininstance.js.map

@@ -1 +1 @@
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package/dist/builtins/res/thumbnail.d.ts

@@ -0,0 +1,12 @@
+import type { DicomGray } from '@fnndsc/salsa';
+/** How wide a thumbnail is, in character cells. */
+export declare const THUMBNAIL_COLS: number;
+/**
+ * Renders a grayscale grid as an indented terminal thumbnail.
+ *
+ * @param grid - The slice luminance.
+ * @param color - Whether the surface renders ANSI colour.
+ * @param cols - Thumbnail width in cells; defaults to {@link THUMBNAIL_COLS}.
+ * @returns The thumbnail, lines indented by two spaces, trailing newline.
+ */
+export declare function thumbnail_render(grid: DicomGray, color: boolean, cols?: number): string;

package/dist/builtins/res/thumbnail.js

@@ -0,0 +1,83 @@
+/**
+ * @file A grayscale grid as a terminal thumbnail.
+ *
+ * One pipeline, two renderings chosen by the surface: an ASCII ramp that any
+ * pipe can print, and ANSI truecolour half-blocks (`▀`, two pixel rows per
+ * character cell) for a colour terminal. The grid is box-downsampled to the
+ * cell width, correcting for the ~2:1 aspect of a character cell so the image
+ * is not stretched. The plain ramp is always the floor; colour is an upgrade,
+ * never a requirement.
+ *
+ * @module
+ */
+import chalk from 'chalk';
+/** Luminance ramp, darkest to brightest; ten steps read well at thumbnail size. */
+const RAMP = ' .:-=+*#%@';
+/** How wide a thumbnail is, in character cells. */
+export const THUMBNAIL_COLS = 44;
+/**
+ * Box-averages a grid into `cols`×`rows` cells of 0..255.
+ *
+ * @param grid - The source luminance.
+ * @param cols - Target columns.
+ * @param rows - Target rows.
+ * @returns The downsampled cells, `out[y * cols + x]`.
+ */
+function downsample(grid, cols, rows) {
+    const { width: w, height: h, gray } = grid;
+    const out = new Float32Array(cols * rows);
+    for (let cy = 0; cy < rows; cy++) {
+        const y0 = Math.floor((cy * h) / rows);
+        const y1 = Math.max(y0 + 1, Math.floor(((cy + 1) * h) / rows));
+        for (let cx = 0; cx < cols; cx++) {
+            const x0 = Math.floor((cx * w) / cols);
+            const x1 = Math.max(x0 + 1, Math.floor(((cx + 1) * w) / cols));
+            let sum = 0;
+            let n = 0;
+            for (let y = y0; y < y1; y++)
+                for (let x = x0; x < x1; x++) {
+                    sum += gray[y * w + x];
+                    n++;
+                }
+            out[cy * cols + cx] = n === 0 ? 0 : sum / n;
+        }
+    }
+    return out;
+}
+/**
+ * Renders a grayscale grid as an indented terminal thumbnail.
+ *
+ * @param grid - The slice luminance.
+ * @param color - Whether the surface renders ANSI colour.
+ * @param cols - Thumbnail width in cells; defaults to {@link THUMBNAIL_COLS}.
+ * @returns The thumbnail, lines indented by two spaces, trailing newline.
+ */
+export function thumbnail_render(grid, color, cols = THUMBNAIL_COLS) {
+    // A character cell is about twice as tall as wide; halve the row count so a
+    // square image stays square. Half-blocks pack two pixel rows per cell.
+    const charRows = Math.max(1, Math.round(cols * (grid.height / grid.width) * 0.5));
+    if (!color) {
+        const cells = downsample(grid, cols, charRows);
+        let out = '';
+        for (let y = 0; y < charRows; y++) {
+            let line = '';
+            for (let x = 0; x < cols; x++)
+                line += RAMP[Math.round((cells[y * cols + x] / 255) * (RAMP.length - 1))];
+            out += `  ${line}\n`;
+        }
+        return out;
+    }
+    const cells = downsample(grid, cols, charRows * 2);
+    let out = '';
+    for (let y = 0; y < charRows; y++) {
+        let line = '';
+        for (let x = 0; x < cols; x++) {
+            const top = Math.round(cells[(2 * y) * cols + x]);
+            const bottom = Math.round(cells[(2 * y + 1) * cols + x]);
+            line += chalk.bgRgb(bottom, bottom, bottom).rgb(top, top, top)('▀');
+        }
+        out += `  ${line}\n`;
+    }
+    return out;
+}
+//# sourceMappingURL=thumbnail.js.map

package/dist/builtins/res/thumbnail.js.map

@@ -0,0 +1 @@
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package/dist/builtins/utils.d.ts

@@ -49,6 +49,16 @@ export interface PathContext {
  * @param context - User and CWD context.
  * @returns The absolute path.
  */
+/**
+ * The identity's home directory in the CUBE filesystem.
+ *
+ * CUBE roots every user at `/home/<username>`; with no identity there is no
+ * home, and the root stands in.
+ *
+ * @param user - The identity's username, or null when there is none.
+ * @returns The home path.
+ */
+export declare function homePath_of(user: string | null | undefined): string;
 export declare function path_resolvePure(inputPath: string, context: PathContext): string;
 /**
  * Resolves a path argument, handling `~` expansion and relative paths.

package/dist/builtins/utils.js

@@ -79,11 +79,23 @@ export function commandArgs_process(args, options = {}) {
  * @param context - User and CWD context.
  * @returns The absolute path.
  */
+/**
+ * The identity's home directory in the CUBE filesystem.
+ *
+ * CUBE roots every user at `/home/<username>`; with no identity there is no
+ * home, and the root stands in.
+ *
+ * @param user - The identity's username, or null when there is none.
+ * @returns The home path.
+ */
+export function homePath_of(user) {
+    return user ? `/home/${user}` : '/';
+}
 export function path_resolvePure(inputPath, context) {
     let resolved = inputPath;
     const { user, cwd } = context;
     if (inputPath.startsWith('~')) {
-        const home = user ? `/home/${user}` : '/';
+        const home = homePath_of(user);
         if (inputPath === '~' || inputPath === '~/') {
             resolved = home;
         }

package/dist/builtins/utils.js.map

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package/dist/core/dispatch.js

@@ -14,7 +14,7 @@
  */
 import { writeFileSync, appendFileSync } from 'fs';
 import chalk from 'chalk';
-import { builtin_cd, builtin_ls, builtin_pwd, builtin_connect, builtin_logout, builtin_cat, builtin_cp, builtin_mv, builtin_upload, builtin_pacs, builtin_pipeline, builtin_pull, builtin_query, builtin_cubepath, builtin_dcm, builtin_rm, builtin_setfacl, builtin_getfacl, builtin_touch, builtin_mkdir, builtin_plugin, builtin_feed, builtin_compute, builtin_tag, builtin_group, builtin_user, builtin_pluginmeta, builtin_plugininstance, builtin_workflow, builtin_download, builtin_edit, builtin_config, builtin_files, builtin_links, builtin_dirs, builtin_context, builtin_parametersofplugin, builtin_physicalmode, builtin_timing, builtin_id, builtin_whoami, builtin_whereami, builtin_version, builtin_fortune, builtin_date, builtin_cal, builtin_debug, builtin_help, builtin_tree, builtin_du, builtin_store, error_stripDebugPrefix } from '../builtins/index.js';
+import { builtin_cd, builtin_ls, builtin_pwd, builtin_connect, builtin_logout, builtin_cat, builtin_cp, builtin_mv, builtin_upload, builtin_pacs, builtin_pipeline, builtin_pull, builtin_query, builtin_cubepath, builtin_dcm, builtin_image, builtin_rm, builtin_setfacl, builtin_getfacl, builtin_touch, builtin_mkdir, builtin_plugin, builtin_feed, builtin_compute, builtin_tag, builtin_group, builtin_user, builtin_pluginmeta, builtin_plugininstance, builtin_workflow, builtin_download, builtin_edit, builtin_config, builtin_files, builtin_links, builtin_dirs, builtin_context, builtin_parametersofplugin, builtin_physicalmode, builtin_timing, builtin_id, builtin_whoami, builtin_whereami, builtin_version, builtin_fortune, builtin_date, builtin_cal, builtin_debug, builtin_help, builtin_tree, builtin_du, builtin_store, error_stripDebugPrefix } from '../builtins/index.js';
 import { builtin_executePlugin } from '../builtins/pluginExecute.js';
 import { builtin_proc } from '../builtins/proc.js';
 import { shellWords_expand } from '../builtins/wildcard.js';
@@ -86,6 +86,7 @@ export const ENVELOPE_HANDLERS = {
     logout: builtin_logout,
     cubepath: builtin_cubepath,
     dcm: builtin_dcm,
+    image: builtin_image,
     query: builtin_query,
     feed: builtin_feed,
     feeds: builtin_feed,
@@ -152,6 +153,7 @@ export const COMMAND_HANDLERS = {
     query: envelopeHandler_wrap(builtin_query),
     cubepath: envelopeHandler_wrap(builtin_cubepath),
     dcm: envelopeHandler_wrap(builtin_dcm),
+    image: envelopeHandler_wrap(builtin_image),
     download: envelopeHandler_wrap(builtin_download),
     edit: envelopeHandler_wrap(builtin_edit),
     config: envelopeHandler_wrap(builtin_config),

package/dist/core/dispatch.js.map

@@ -1 +1 @@
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package/dist/core/engine.d.ts

@@ -180,7 +180,14 @@ export declare function file_write(filePath: string, bytes: Buffer): Promise<voi
  * Reads one ChRIS file's raw bytes through ChILI, resolved against the
  * session's working directory.
  *
- * @param filePath - The file's path (absolute or cwd-relative).
+ * Resolved, as its twin {@link file_write} is: a surface addresses a file
+ * the way the session does, and the session's paths include the relative
+ * ones and the `/proc` projections. Handing the raw path to ChILI meant a
+ * volume produced by a run could not be read at the address the graph
+ * itself gives for it — the node's own `data` — while the same bytes read
+ * fine under `/home`. One file, two names, one of them refused.
+ *
+ * @param filePath - The file's path (absolute, cwd-relative, or projected).
  * @returns The file's bytes.
  * @throws {Error} When the path does not resolve to a readable file.
  */

package/dist/core/engine.js

@@ -299,13 +299,35 @@ export async function file_write(filePath, bytes) {
  * Reads one ChRIS file's raw bytes through ChILI, resolved against the
  * session's working directory.
  *
- * @param filePath - The file's path (absolute or cwd-relative).
+ * Resolved, as its twin {@link file_write} is: a surface addresses a file
+ * the way the session does, and the session's paths include the relative
+ * ones and the `/proc` projections. Handing the raw path to ChILI meant a
+ * volume produced by a run could not be read at the address the graph
+ * itself gives for it — the node's own `data` — while the same bytes read
+ * fine under `/home`. One file, two names, one of them refused.
+ *
+ * @param filePath - The file's path (absolute, cwd-relative, or projected).
  * @returns The file's bytes.
  * @throws {Error} When the path does not resolve to a readable file.
  */
 export async function file_read(filePath) {
+    const { path_resolve } = await import('../builtins/utils.js');
+    const resolved = await path_resolve(filePath);
+    const { vfsDispatcher } = await import('@fnndsc/salsa');
+    // A projection is read by the provider that owns it — `/proc/jobs/…/data`
+    // follows the node's own data link and delegates to the file behind it.
+    // ChILI's cat knows only CFS, so a path under a projection reached this
+    // route and 404'd: the volume a run had just produced could not be read
+    // at the address its own graph gives for it.
+    if (vfsDispatcher.path_isVirtual(resolved)) {
+        const projected = await vfsDispatcher.readBinary(resolved);
+        if (!projected.ok) {
+            throw new Error(`cannot read ${filePath}`);
+        }
+        return projected.value;
+    }
     const { files_catBinary } = await import('@fnndsc/chili/commands/fs/cat.js');
-    const result = await files_catBinary(filePath);
+    const result = await files_catBinary(resolved);
     if (!result.ok) {
         throw new Error(`cannot read ${filePath}`);
     }