Motivation: Currently we initialize each <code class="notranslate"

[feature] Reuse zarr metadata from one image for others in plate about vizarr HOT 3 OPEN

hms-dbmi commented on June 13, 2024

[feature] Reuse zarr metadata from one image for others in plate

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Comments (3)

will-moore commented on June 13, 2024

I like the idea. Makes sense and certainly most of the plates I've seen do have identical sized images in every Well.
But it's probably too restrictive to say that ALL Plates must have all Images the same size. So we could maybe 'consolidate' that info into a parameter like "all_images_same_size" in the plate metadata?
Maybe open an issue at https://github.com/ome/ngff ?

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manzt commented on June 13, 2024

Sure, I'll look into opening an issue. It's worth noting that in order to render to the grid currently (for plate or well), we require identically sized images:

vizarr/src/gridLayer.ts

Lines 44 to 55 in 1ef2163

 function validateWidthHeight(d: { data: { width: number; height: number } }[]) { 

 const [first] = d; 

 // Return early if no grid data. Maybe throw an error? 

 const { width, height } = first.data; 

 // Verify that all grid data is same shape (ignoring undefined) 

 d.forEach(({ data }) => { 

 if (data?.width !== width || data?.height !== height) { 

 throw new Error('Grid data is not same shape.'); 

 } 

 }); 

 return { width, height }; 

 }

And vizarr will throw an error otherwise. So this issue is suggesting that we make that assumption initially as well, when initializing arrays.

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joshmoore commented on June 13, 2024

Maybe open an issue at https://github.com/ome/ngff ?

Agreed. I think we have something along the lines of "all dtypes for the multiresolutions will be of the same type" and we might could generalize that for "all items in a certain type of collection".

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[feature] Reuse zarr metadata from one image for others in plate about vizarr HOT 3 OPEN

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	function validateWidthHeight(d: { data: { width: number; height: number } }[]) {
	const [first] = d;
	// Return early if no grid data. Maybe throw an error?
	const { width, height } = first.data;
	// Verify that all grid data is same shape (ignoring undefined)
	d.forEach(({ data }) => {
	if (data?.width !== width \|\| data?.height !== height) {
	throw new Error('Grid data is not same shape.');
	}
	});
	return { width, height };
	}