From b5f4916bc9e4fb3e1b7d075ebb9b7719e79f67ce Mon Sep 17 00:00:00 2001
From: William Moore <w.moore@dundee.ac.uk>
Date: Wed, 29 Sep 2021 17:40:25 +0100
Subject: [PATCH 1/3] Display collection using Plate layout
---
src/io.ts | 6 ++--
src/ome.ts | 103 ++++++++++++++++++++++++++++++++++++++---------------
2 files changed, 78 insertions(+), 31 deletions(-)
diff --git a/src/io.ts b/src/io.ts
index 08458f3a..f201642b 100644
--- a/src/io.ts
+++ b/src/io.ts
@@ -1,7 +1,7 @@
import { DTYPE_VALUES, ImageLayer, MultiscaleImageLayer, ZarrPixelSource } from '@hms-dbmi/viv';
import { Group as ZarrGroup, openGroup, ZarrArray } from 'zarr';
import GridLayer from './gridLayer';
-import { loadOmeroMultiscales, loadPlate, loadWell } from './ome';
+import { loadCollection, loadOmeroMultiscales, loadWell } from './ome';
import type {
ImageLayerConfig,
LayerState,
@@ -111,8 +111,8 @@ export async function createSourceData(config: ImageLayerConfig): Promise<Source
if (node instanceof ZarrGroup) {
const attrs = (await node.attrs.asObject()) as Ome.Attrs;
- if ('plate' in attrs) {
- return loadPlate(config, node, attrs.plate);
+ if ('collection' in attrs || 'plate' in attrs) {
+ return loadCollection(config, node, attrs);
}
if ('well' in attrs) {
diff --git a/src/ome.ts b/src/ome.ts
index d9a4ea48..78cdd79e 100644
--- a/src/ome.ts
+++ b/src/ome.ts
@@ -107,25 +107,78 @@ export async function loadWell(config: ImageLayerConfig, grp: ZarrGroup, wellAtt
return sourceData;
}
-export async function loadPlate(config: ImageLayerConfig, grp: ZarrGroup, plateAttrs: Ome.Plate): Promise<SourceData> {
- if (!('columns' in plateAttrs) || !('rows' in plateAttrs)) {
- throw Error(`Plate .zattrs missing columns or rows`);
+async function getImagePaths(grp: ZarrGroup, omeAttrs: Ome.Attrs): Promise<string[]> {
+ if ('collection' in omeAttrs) {
+ return Object.keys(omeAttrs.collection.images);
+ } else if ('plate' in omeAttrs) {
+ // Load each Well to get a path/to/image/
+ const wellPaths = omeAttrs.plate.wells.map((well) => well.path);
+ async function getImgPath(wellPath: string) {
+ const wellAttrs = await getAttrsOnly<{ well: Ome.Well }>(grp, wellPath);
+ // Fields are by index and we assume at least 1 per Well
+ return join(wellPath, wellAttrs.well.images[0].path);
+ }
+ const imgPaths = await Promise.all(wellPaths.map(getImgPath));
+ return imgPaths;
+ } else {
+ return [];
}
+}
- const rows = plateAttrs.rows.map((row) => row.name);
- const columns = plateAttrs.columns.map((row) => row.name);
+export async function loadCollection(
+ config: ImageLayerConfig,
+ grp: ZarrGroup,
+ omeAttrs: Ome.Attrs
+): Promise<SourceData> {
+ const imagePaths = await getImagePaths(grp, omeAttrs);
+
+ let displayName = 'Collection';
+ let rows: string[];
+ let columns: string[];
+ let colCount: number;
+ let rowCount: number;
+ if ('plate' in omeAttrs) {
+ const plateAttrs = omeAttrs.plate;
+ if (!('columns' in plateAttrs) || !('rows' in plateAttrs)) {
+ throw Error(`Plate .zattrs missing columns or rows`);
+ }
+ rows = plateAttrs.rows.map((row) => row.name);
+ columns = plateAttrs.columns.map((row) => row.name);
+ displayName = plateAttrs.name || 'Collection';
+ colCount = columns.length;
+ rowCount = rows.length;
+ } else {
+ const imgCount = imagePaths.length;
+ colCount = Math.ceil(Math.sqrt(imgCount));
+ rowCount = Math.ceil(imgCount / colCount);
+ }
- // Fields are by index and we assume at least 1 per Well
- const wellPaths = plateAttrs.wells.map((well) => well.path);
+ function getImgSource(source: string, row: number, column: number) {
+ if (rows && columns) {
+ return join(source, rows[row], columns[column]);
+ } else {
+ return join(source, imagePaths[row * colCount + column]);
+ }
+ }
- // Use first image as proxy for others.
- const wellAttrs = await getAttrsOnly<{ well: Ome.Well }>(grp, wellPaths[0]);
- if (!('well' in wellAttrs)) {
- throw Error('Path for image is not valid, not a well.');
+ function getGridCoord(imgPath: string) {
+ let row, col, name;
+ if (rows && columns) {
+ const [rowName, colName] = imgPath.split('/');
+ row = rows.indexOf(rowName);
+ col = columns.indexOf(colName);
+ name = `${rowName}${colName}`;
+ } else {
+ const imgIndex = imagePaths?.indexOf(imgPath);
+ row = Math.floor(imgIndex / colCount);
+ col = imgIndex - row * colCount;
+ name = imgPath;
+ }
+ return { row, col, name };
}
- const imgPath = wellAttrs.well.images[0].path;
- const imgAttrs = (await grp.getItem(join(wellPaths[0], imgPath)).then((g) => g.attrs.asObject())) as Ome.Attrs;
+ const imgPath = imagePaths[0];
+ const imgAttrs = (await grp.getItem(imgPath).then((g) => g.attrs.asObject())) as Ome.Attrs;
if (!('omero' in imgAttrs)) {
throw Error('Path for image is not valid.');
}
@@ -133,16 +186,10 @@ export async function loadPlate(config: ImageLayerConfig, grp: ZarrGroup, plateA
const { datasets } = imgAttrs.multiscales[0];
const resolution = datasets[datasets.length - 1].path;
- async function getImgPath(wellPath: string) {
- const wellAttrs = await getAttrsOnly<{ well: Ome.Well }>(grp, wellPath);
- return join(wellPath, wellAttrs.well.images[0].path);
- }
- const wellImagePaths = await Promise.all(wellPaths.map(getImgPath));
-
// Create loader for every Well. Some loaders may be undefined if Wells are missing.
const mapper = ([key, path]: string[]) => grp.getItem(path).then((arr) => [key, arr]) as Promise<[string, ZarrArray]>;
const promises = await pMap(
- wellImagePaths.map((p) => [p, join(p, resolution)]),
+ imagePaths.map((p) => [p, join(p, resolution)]),
mapper,
{ concurrency: 10 }
);
@@ -151,11 +198,11 @@ export async function loadPlate(config: ImageLayerConfig, grp: ZarrGroup, plateA
const meta = parseOmeroMeta(imgAttrs.omero, axis_labels);
const tileSize = guessTileSize(data[0][1]);
const loaders = data.map((d) => {
- const [row, col] = d[0].split('/');
+ const coord = getGridCoord(d[0]);
return {
- name: `${row}${col}`,
- row: rows.indexOf(row),
- col: columns.indexOf(col),
+ name: coord.name,
+ row: coord.row,
+ col: coord.col,
loader: new ZarrPixelSource(d[1], axis_labels, tileSize),
};
});
@@ -172,9 +219,9 @@ export async function loadPlate(config: ImageLayerConfig, grp: ZarrGroup, plateA
colormap: config.colormap ?? '',
opacity: config.opacity ?? 1,
},
- name: plateAttrs.name || 'Plate',
- rows: rows.length,
- columns: columns.length,
+ name: displayName,
+ rows: rowCount,
+ columns: colCount,
};
// Us onClick from image config or Open Well in new window
sourceData.onClick = (info: any) => {
@@ -185,7 +232,7 @@ export async function loadPlate(config: ImageLayerConfig, grp: ZarrGroup, plateA
const { row, column } = gridCoord;
let imgSource = undefined;
if (typeof config.source === 'string' && grp.path && !isNaN(row) && !isNaN(column)) {
- imgSource = join(config.source, rows[row], columns[column]);
+ imgSource = getImgSource(config.source, row, column);
}
if (config.onClick) {
delete info.layer;
From 0a08418f6400f2012eef08e53eda485e00add735 Mon Sep 17 00:00:00 2001
From: William Moore <w.moore@dundee.ac.uk>
Date: Tue, 5 Oct 2021 09:56:23 +0100
Subject: [PATCH 2/3] Remove support for source=plate/acquisition/
This was only a TEMP format and never made it to the HCS spec. HCS images are now
/plate/A/1/0/ and the acquisition is not included in the URL
---
src/io.ts | 11 -----------
1 file changed, 11 deletions(-)
diff --git a/src/io.ts b/src/io.ts
index f201642b..e0cceeea 100644
--- a/src/io.ts
+++ b/src/io.ts
@@ -123,17 +123,6 @@ export async function createSourceData(config: ImageLayerConfig): Promise<Source
return loadOmeroMultiscales(config, node, attrs);
}
- if (Object.keys(attrs).length === 0 && node.path) {
- // No rootAttrs in this group.
- // if url is to a plate/acquisition/ check parent dir for 'plate' zattrs
- const parentPath = node.path.slice(0, node.path.lastIndexOf('/'));
- const parent = await openGroup(node.store, parentPath);
- const parentAttrs = (await parent.attrs.asObject()) as Ome.Attrs;
- if ('plate' in parentAttrs) {
- return loadPlate(config, parent, parentAttrs.plate);
- }
- }
-
if (!('multiscales' in attrs)) {
throw Error('Group is missing multiscales specification.');
}
From e307782ee35ac5a723d321bd9624300e8fd2ac88 Mon Sep 17 00:00:00 2001
From: William Moore <w.moore@dundee.ac.uk>
Date: Tue, 5 Oct 2021 10:05:37 +0100
Subject: [PATCH 3/3] Fix types
---
types/ome.ts | 5 +++++
1 file changed, 5 insertions(+)
diff --git a/types/ome.ts b/types/ome.ts
index c4c52ce3..ac3e5236 100644
--- a/types/ome.ts
+++ b/types/ome.ts
@@ -56,12 +56,17 @@ declare module Ome {
wells: { path: string }[];
}
+ interface Collection {
+ images: {};
+ }
+
interface Well {
images: { path: string; acquisition?: number }[];
version: Version;
}
type Attrs =
+ | { collection: Collection }
| { multiscales: Multiscale[] }
| { omero: Omero; multiscales: Multiscale[] }
| { plate: Plate }