Collection thumbs

[will-moore]

This is not even a draft PR, but just me learning and exploring options for viewing a collection. (See #123 and #124).
Very rough - barely working at this stage; just pushing as part of the discussion...

But locally I managed to view this collection https://minio-dev.openmicroscopy.org/idr/v0.3/datasets/idr0062/8dc4707/7754.zarr
which has only 11 images but they are different sizes and can't be viewed by #124
(From Dataset at http://idr.openmicroscopy.org/webclient/?show=dataset-7754)

[will-moore]

Re-opening this PR with a view to updating it to support "bioformats2raw.layout": 3 collections of images as described at ome/ngff#112.

[will-moore]

Something has probably changed since I had this running previously, but now I can't get Thumbnails to render

And also hit a blocker trying to fix TypeScript

$ npm run check

> @hms-dbmi/[email protected] check
> tsc

src/components/NgffCollection/ImageThumbnail.tsx:103:7 - error TS2345: Argument of type '{ loader: ZarrPixelSource<string[]>; loaderSelection: (number | undefined)[][]; colorValues: number[][]; sliderValues: number[][]; channelIsOn: boolean[]; }' is not assignable to parameter of type 'Viv<LayerProps, string[]>'.
  Object literal may only specify known properties, and 'loaderSelection' does not exist in type 'Viv<LayerProps, string[]>'.

103       loaderSelection: chunks,
          ~~~~~~~~~~~~~~~~~~~~~~~

src/vizarr.tsx:29:19 - error TS2345: Argument of type '(prevSourceInfo: WithId<SourceData>[]) => (WithId<SourceData> | { name?: string | undefined; images: any[]; id: string; })[]' is not assignable to parameter of type 'SetStateAction<WithId<SourceData>[]>'.
  Type '(prevSourceInfo: WithId<SourceData>[]) => (WithId<SourceData> | { name?: string | undefined; images: any[]; id: string; })[]' is not assignable to type '(prev: WithId<SourceData>[]) => WithId<SourceData>[]'.
    Type '(WithId<SourceData> | { name?: string | undefined; images: any[]; id: string; })[]' is not assignable to type 'WithId<SourceData>[]'.
      Type 'WithId<SourceData> | { name?: string | undefined; images: any[]; id: string; }' is not assignable to type 'WithId<SourceData>'.
        Type '{ name?: string | undefined; images: any[]; id: string; }' is not assignable to type 'WithId<SourceData>'.
          Type '{ name?: string | undefined; images: any[]; id: string; }' is missing the following properties from type 'SourceData': loader, channel_axis, colors, names, and 5 more.

29     setSourceInfo((prevSourceInfo) => {
                     ~~~~~~~~~~~~~~~~~~~~~

[manzt]

Should be able to have a look in the next day or so. My guess is that there are some changes to state organization that merging might have messed with.

[manzt]

Hi will, as for the second type error:

setSourceInfo((prevSourceInfo) => {

The issue is that the type gaurd:

   if ('images' in sourceData && sourceData["images"].length > 0) {
      // This is a Collection

Doesn't sufficiently narrow the type. There is a case where sourceData is CollectionData but the length of the images is 0, so when setSourceInfo is called the type of sourceData: SourceData | CollectionData. If were just,

   if ('images' in sourceData) {
      // This is a Collection

Typescript could appropriately narrow correctly infer sourceData: SourceData

[manzt]

@will-moore, The ImageLayer from Viv has an updated API since they last time you worked on this (which was upgrade in #126). I fixed (from what I can tell) the rendering, and you will just need to figure out how to resolve the one type error from above.

[manzt]

[will-moore]

Thanks @manzt - I'm away for rest of this week but will take a look ASAP...

[will-moore]

Hi @manzt - Unfortunately I have no clue how to fix:

src/vizarr.tsx:29:19 - error TS2345: Argument of type '(prevSourceInfo: WithId<SourceData>[]) => (WithId<SourceData> | { name?: string | undefined; images: any[]; id: string; })[]' is not assignable to parameter of type 'SetStateAction<WithId<SourceData>[]>'.
  Type '(prevSourceInfo: WithId<SourceData>[]) => (WithId<SourceData> | { name?: string | undefined; images: any[]; id: string; })[]' is not assignable to type '(prev: WithId<SourceData>[]) => WithId<SourceData>[]'.
    Type '(WithId<SourceData> | { name?: string | undefined; images: any[]; id: string; })[]' is not assignable to type 'WithId<SourceData>[]'.
      Type 'WithId<SourceData> | { name?: string | undefined; images: any[]; id: string; }' is not assignable to type 'WithId<SourceData>'.
        Type '{ name?: string | undefined; images: any[]; id: string; }' is not assignable to type 'WithId<SourceData>'.
          Type '{ name?: string | undefined; images: any[]; id: string; }' is missing the following properties from type 'SourceData': loader, channel_axis, colors, names, and 5 more.

29     setSourceInfo((prevSourceInfo) => {

That line didn't change in this PR, so I'm not sure where to start...?

[manzt]

That line didn't change in this PR, so I'm not sure where to start...?

Hi will, the issue is that this PR widens the return type of createSourceData:

// previously SourceData, now SourceData | CollectionData
const sourceData = await createSourceData(config);

TypeScript is forcing you to handle each case (SourceData and CollectionData) in the rest of the function body, and the compiler error is saying the current code does not sufficiently handle the types as you intended and there is a bug. To demonstrate,

const sourceData: SourceData | CollectionData = { images: [], /* ... */ }; // we know this is a collection, but TS does not yet
if ('images' in sourceData && images.length > 0) {
  sourceData // CollectionData, we know this can only be CollectionData
  setCollectionState(sourceData);
  return;
};
sourceData // SourceData | CollectionData! source data _or_ collection with empty image list

The issue is that the guard 'images' in sourceData && images.length > 0 doesn't capture all instances of CollectionData since the expression isn't always true for CollectionData (e.g., a collection with images.length === 0), so the type is not sufficiently narrowed to just SourceData after the if block with early return.

setSourceInfo can only handle SourceData in the return so TS is letting you know there is a case where CollectionData can reach this bit of code and that is invalid. You can easily remove errors but forcing this condition to be more strict:

const sourceData: SourceData | CollectionData = { images: [], /* ... */ }
if ('images' in sourceData) {
  sourceData // CollectionData
  setCollectionState(sourceData);
  return;
};
sourceData // SourceData since the above captures _all_ instances of CollectionData

[will-moore]

Got it! Thanks for the explanation @manzt

[will-moore]

See #149 (comment)