experimental reference spec maker for ome-tiff

README.md

Create conda environment

$ conda create --name bioformats python=3.8
$ conda activate bioformats
$ conda install -c ome bioformats2raw raw2ometiff

Download source image and convert to ome-tiff

$ wget https://downloads.openmicroscopy.org/images/Vectra-QPTIFF/perkinelmer/PKI_scans/LuCa-7color_Scan1.qptiff
$ bioformats2raw LuCa-7color_Scan1.qptiff n5_tile_directory/
$ raw2ometiff n5_tile_directory/ LuCa-7color_Scan1.ome.tif --compression=zlib

Note the --compression=zlib flag is necessary because other TIFF codecs are not included in numcodecs

Create reference spec

$ python zarr_reference_utils.py LuCa-7color_Scan1.ome.tif LuCa-7color_Scan1.ome.tif_offsets.json

convert_zenodo_url.js

// convert zenodo deposit url to enable CORS
async function convertZenodoFileUrl(url) {
  const myRegexp = /https?:\/\/zenodo.org\/record\/([a-zA-Z0-9-]+)\/files\/(.*)/g;
  const match = myRegexp.exec(url);
  if (!match || match.length !== 3) {
    throw new Error("Invalid zenodo url");
  }
  const [fullUrl, depositId, fileName] = match;
  const blob = await fetch(
    `https://zenodo.org/api/records/${depositId}`
  ).then(r => r.blob());
  const data = JSON.parse(await new Response(blob).text());
  const fn = fileName.split("?")[0];
  const fileObj = data.files.filter(file => {
    return file.key === fn;
  })[0];
  return fileObj.links.self;
}

LuCa-7color_Scan1.ome.tif_offsets.json

{".zgroup": "{\n    \"zarr_format\": 2\n}", ".zattrs": "{\n    \"multiscales\": [\n        {\n            \"datasets\": [\n                {\n                    \"path\": \"0\"\n                },\n                {\n                    \"path\": \"1\"\n                },\n                {\n                    \"path\": \"2\"\n                },\n                {\n                    \"path\": \"3\"\n                },\n                {\n                    \"path\": \"4\"\n                },\n                {\n                    \"path\": \"5\"\n                },\n                {\n                    \"path\": \"6\"\n                },\n                {\n                    \"path\": \"7\"\n                },\n                {\n                    \"path\": \"8\"\n                }\n            ],\n            \"metadata\": {},\n            \"name\": \"resolution #1\",\n            \"version\": \"0.1\"\n        }\n    ]\n}", "0/.zarray": "{\n    \"chunks\": [\n        1,\n        1024,\n        1024\n    ],\n    \"compressor\": {\n        \"id\": \"zlib\",\n        \"level\": 8\n    },\n    \"dtype\": \"|u1\",\n    \"fill_value\": null,\n    \"filters\": null,\n    \"order\": \"C\",\n    \"shape\": [\n        5,\n        34560,\n        24960\n    ],\n    \"zarr_format\": 2\n}", "1/.zarray": "{\n    \"chunks\": [\n        1,\n        1024,\n        1024\n    ],\n    \"compressor\": {\n        \"id\": \"zlib\",\n        \"level\": 8\n    },\n    \"dtype\": \"|u1\",\n    \"fill_value\": null,\n    \"filters\": null,\n    \"order\": \"C\",\n    \"shape\": [\n        5,\n        17280,\n        12480\n    ],\n    \"zarr_format\": 2\n}", "2/.zarray": "{\n    \"chunks\": [\n        1,\n        1024,\n        1024\n    ],\n    \"compressor\": {\n        \"id\": \"zlib\",\n        \"level\": 8\n    },\n    \"dtype\": \"|u1\",\n    \"fill_value\": null,\n    \"filters\": null,\n    \"order\": \"C\",\n    \"shape\": [\n        5,\n        8640,\n        6240\n    ],\n    \"zarr_format\": 2\n}", "3/.zarray": "{\n    \"chunks\": [\n        1,\n        1024,\n        1024\n    ],\n    \"compressor\": {\n        \"id\": \"zlib\",\n        \"level\": 8\n    },\n    \"dtype\": \"|u1\",\n    \"fill_value\": null,\n    \"filters\": null,\n    \"order\": \"C\",\n    \"shape\": [\n        5,\n        4320,\n        3120\n    ],\n    \"zarr_format\": 2\n}", "4/.zarray": "{\n    \"chunks\": [\n        1,\n        1024,\n        1024\n    ],\n    \"compressor\": {\n        \"id\": \"zlib\",\n        \"level\": 8\n    },\n    \"dtype\": \"|u1\",\n    \"fill_value\": null,\n    \"filters\": null,\n    \"order\": \"C\",\n    \"shape\": [\n        5,\n        2160,\n        1560\n    ],\n    \"zarr_format\": 2\n}", "5/.zarray": "{\n    \"chunks\": [\n        1,\n        1024,\n        780\n    ],\n    \"compressor\": {\n        \"id\": \"zlib\",\n        \"level\": 8\n    },\n    \"dtype\": \"|u1\",\n    \"fill_value\": null,\n    \"filters\": null,\n    \"order\": \"C\",\n    \"shape\": [\n        5,\n        1080,\n        780\n    ],\n    \"zarr_format\": 2\n}", "6/.zarray": "{\n    \"chunks\": [\n        1,\n        540,\n        390\n    ],\n    \"compressor\": {\n        \"id\": \"zlib\",\n        \"level\": 8\n    },\n    \"dtype\": \"|u1\",\n    \"fill_value\": null,\n    \"filters\": null,\n    \"order\": \"C\",\n    \"shape\": [\n        5,\n        540,\n        390\n    ],\n    \"zarr_format\": 2\n}", "7/.zarray": "{\n    \"chunks\": [\n        1,\n        270,\n        195\n    ],\n    \"compressor\": {\n        \"id\": \"zlib\",\n        \"level\": 8\n    },\n    \"dtype\": \"|u1\",\n    \"fill_value\": null,\n    \"filters\": null,\n    \"order\": \"C\",\n    \"shape\": [\n        5,\n        270,\n        195\n    ],\n    \"zarr_format\": 2\n}", "8/.zarray": "{\n    \"chunks\": [\n        1,\n        135,\n        97\n    ],\n    \"compressor\": {\n        \"id\": \"zlib\",\n        \"level\": 8\n    },\n    \"dtype\": \"|u1\",\n    \"fill_value\": null,\n    \"filters\": null,\n    \"order\": \"C\",\n    \"shape\": [\n        5,\n        135,\n        97\n    ],\n    \"zarr_format\": 2\n}", "0/0.0.0": ["gc://viv-demo/LuCa-7color_Scan1.ome.tif", 1055, 1039], "0/0.0.1": ["gc://viv-demo/LuCa-7color_Scan1.ome.tif", 16, 1039], "0/0.0.2": ["gc://viv-demo/LuCa-7color_Scan1.ome.tif", 2094, 1039], "0/0.0.3": ["gc://viv-demo/LuCa-7color_Scan1.ome.tif", 3133, 80048], "0/0.0.4": ["gc://viv-demo/LuCa-7color_Scan1.ome.tif", 83181, 242570], "0/0.0.5": ["gc://viv-demo/LuCa-7color_Scan1.ome.tif", 325751, 270236], "0/0.0.6": ["gc://viv-demo/LuCa-7color_Scan1.ome.tif", 595987, 256366], "0/0.0.7": ["gc://viv-demo/LuCa-7color_Scan1.ome.tif", 1111311, 274383], "0/0.0.8": ["gc://viv-demo/LuCa-7color_Scan1.ome.tif", 852353, 257919], "0/0.0.9": ["gc://viv-demo/LuCa-7color_Scan1.ome.tif", 1434658, 278134], "0/0.0.10": ["gc://viv-demo/LuCa-7color_Scan1.ome.tif", 1720065, 261677], "0/0.0.11": 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["gc://viv-demo/LuCa-7color_Scan1.ome.tif", 1984516213, 601485], "4/3.0.1": ["gc://viv-demo/LuCa-7color_Scan1.ome.tif", 1982534396, 170942], "4/3.1.0": ["gc://viv-demo/LuCa-7color_Scan1.ome.tif", 1983989099, 527114], "4/3.1.1": ["gc://viv-demo/LuCa-7color_Scan1.ome.tif", 1982705338, 203251], "4/3.2.0": ["gc://viv-demo/LuCa-7color_Scan1.ome.tif", 1982519147, 13781], "4/3.2.1": ["gc://viv-demo/LuCa-7color_Scan1.ome.tif", 1982532928, 1468], "4/4.0.0": ["gc://viv-demo/LuCa-7color_Scan1.ome.tif", 1985328234, 581616], "4/4.0.1": ["gc://viv-demo/LuCa-7color_Scan1.ome.tif", 1983821914, 160856], "4/4.1.0": ["gc://viv-demo/LuCa-7color_Scan1.ome.tif", 1986011140, 514443], "4/4.1.1": ["gc://viv-demo/LuCa-7color_Scan1.ome.tif", 1985121538, 194793], "4/4.2.0": ["gc://viv-demo/LuCa-7color_Scan1.ome.tif", 1983809486, 12428], "4/4.2.1": ["gc://viv-demo/LuCa-7color_Scan1.ome.tif", 1983982770, 1438], "5/0.0.0": ["gc://viv-demo/LuCa-7color_Scan1.ome.tif", 1987160687, 391659], "5/0.1.0": ["gc://viv-demo/LuCa-7color_Scan1.ome.tif", 1983984208, 4891], "5/1.0.0": ["gc://viv-demo/LuCa-7color_Scan1.ome.tif", 1986798836, 361851], "5/1.1.0": ["gc://viv-demo/LuCa-7color_Scan1.ome.tif", 1985117698, 3840], "5/2.0.0": ["gc://viv-demo/LuCa-7color_Scan1.ome.tif", 1988185671, 310788], "5/2.1.0": ["gc://viv-demo/LuCa-7color_Scan1.ome.tif", 1985316331, 3639], "5/3.0.0": ["gc://viv-demo/LuCa-7color_Scan1.ome.tif", 1987801197, 384474], "5/3.1.0": ["gc://viv-demo/LuCa-7color_Scan1.ome.tif", 1985319970, 4314], "5/4.0.0": ["gc://viv-demo/LuCa-7color_Scan1.ome.tif", 1988496459, 371527], "5/4.1.0": ["gc://viv-demo/LuCa-7color_Scan1.ome.tif", 1985324284, 3950], "6/0.0.0": ["gc://viv-demo/LuCa-7color_Scan1.ome.tif", 1985909850, 101290], "6/1.0.0": ["gc://viv-demo/LuCa-7color_Scan1.ome.tif", 1986525583, 93460], "6/2.0.0": ["gc://viv-demo/LuCa-7color_Scan1.ome.tif", 1986619043, 80605], "6/3.0.0": ["gc://viv-demo/LuCa-7color_Scan1.ome.tif", 1986699648, 99188], "6/4.0.0": ["gc://viv-demo/LuCa-7color_Scan1.ome.tif", 1987609343, 95876], "7/0.0.0": ["gc://viv-demo/LuCa-7color_Scan1.ome.tif", 1987552346, 26107], "7/1.0.0": ["gc://viv-demo/LuCa-7color_Scan1.ome.tif", 1987578453, 24084], "7/2.0.0": ["gc://viv-demo/LuCa-7color_Scan1.ome.tif", 1987705219, 20942], "7/3.0.0": ["gc://viv-demo/LuCa-7color_Scan1.ome.tif", 1987775593, 25604], "7/4.0.0": ["gc://viv-demo/LuCa-7color_Scan1.ome.tif", 1987744511, 24686]}

VizarrReferenceStore.imjoy.html

<docs>
[TODO: write documentation for this plugin.]
</docs>

<config lang="json">
{
  "name": "VizarrReferenceStore",
  "type": "web-worker",
  "tags": [],
  "ui": "",
  "version": "0.1.0",
  "cover": "",
  "description": "Reading Vizarr using reference store",
  "icon": "extension",
  "inputs": null,
  "outputs": null,
  "api_version": "0.1.8",
  "env": "",
  "permissions": [],
  "requirements": ["https://unpkg.com/zarr@0.4.0/zarr.umd.js"],
  "dependencies": []
}
</config>

<script lang="javascript">

// Using the FileReferenceStore made by Trevor Manz
// https://observablehq.com/d/a417a770860fbb64
class FileReferenceStore {
  constructor(ref, target) {
    this.ref = ref;
    this.target = target;
  }

  _url(urlPath) {
    if(!urlPath){
      return this.target
    }
    const [protocol, path] = urlPath.split('://');
    if (protocol === 'https' || protocol === 'http') {
      return urlPath;
    }
    if (protocol === 'gc') {
      return 'https://storage.googleapis.com/' + path;
    }
    throw Error("Protocol not supported, got: " + JSON.stringify(protocol));
  }

  async getItem(key) {
    const res = this.ref[key];
    if (!res) {
      // Key not in store
      throw new zarr.KeyError(key);
    }
   
    if (res?.length !== 3) {
      // JSON data entry in reference 
      const meta = typeof res === 'string' ? res : JSON.stringify(res)
      const enc = new TextEncoder().encode(meta);
      return enc.buffer;
    }

    const [urlPath, offset, size] = res;
    const url = this._url(urlPath);
    const headers = {
      Range: `bytes=${offset}-${offset + size - 1}`
    };
    const value = await fetch(url, { headers }).then(res => res.arrayBuffer());
    return value;
  }

  containsItem(key) {
    return key in this.ref;
  }

  static async fromUrl(url, targetUrl) {
    const ref = await fetch(url).then(res => res.json());
    return new FileReferenceStore(ref, targetUrl);
  }
}

class ImJoyPlugin {
  async setup() {
    api.log('initialized')
  }

  async run(ctx) {
    const viewer = await api.createWindow({src: 'https://hms-dbmi.github.io/vizarr'})
    const refUrl = 'https://gist.githubusercontent.com/manzt/102eaa9652e181071d7e2c9fd0cc65d3/raw/5ae948a89c6bc78cbe57196ec8045cd1a988a0ff/LuCa-7color_Scan1.ome.tif_offsets.json'
    const targetUrl = 'gc://viv-demo/LuCa-7color_Scan1.ome.tif'
    const store = await FileReferenceStore.fromUrl(refUrl, targetUrl);
    const img = { "source": store, "name": "Demo Image", "contrast_limits": [0, 20]}
    viewer.add_image(img)
  }
}

api.export(new ImJoyPlugin())
</script>

zarr_reference_utils.py

"""Utilities for creating reference spec for zarr according to https://github.com/intake/fsspec-reference-maker
Made by Trevor Manz, see: https://gist.github.com/manzt/102eaa9652e181071d7e2c9fd0cc65d3
"""
import json
from typing import Dict, Tuple, Union

import zarr
from tifffile import TiffFile
from tifffile.tifffile import ZarrTiffStore
from zarr.indexing import BasicIndexer

ReferenceDict = Dict[str, Union[str, Tuple[str, int, int]]]


def get_zarr_meta(store: ZarrTiffStore, byteorder: str) -> Dict[str, str]:
    """Exports zarr metadata created by tifffile from the underlying store."""

    # Use first page to determine arr meta
    first_page = store._data[0][0]
    if first_page.compression.name != "ADOBE_DEFLATE":
        raise ValueError(
            f"Compression {first_page.compression.name} not supported by zarr."
        )

    # The ZarrTiffStore takes care of compression, so compressor is set to
    # null in array metadata. In order to read natively with Zarr, we need to
    # add the compression to the zarr metadata.
    #
    # This is fragile code. I'm sure there are other criteria that limit
    # whether a TIFF can be read directly as Zarr.
    compressor_config = {"id": "zlib", "level": first_page.compression.value}

    meta = dict()
    for key, value in store._store.items():
        if ".zarray" in key:
            # Override compression of None with config above
            value = json.loads(value)
            # We need to fix the byteorder
            # Because tifffile uses sys.byteorder
            # see here: https://github.com/cgohlke/tifffile/blob/d2fe871da182acc45f54b5a03bcf29a0b52a32ae/tifffile/tifffile.py#L8011
            value["dtype"] = byteorder + value["dtype"][1:]
            value["compressor"] = compressor_config
            value = ZarrTiffStore._json(value)

        meta[key] = value.decode("utf-8")
    return meta


def create_reference(store, byteorder, ref_url: str = None) -> ReferenceDict:

    if not isinstance(store, ZarrTiffStore):
        raise Exception("Must be ZarrTiffStore")

    if not store.is_multiscales:
        raise Exception("Not a multiscale zarr.")

    grp = zarr.open(store)
    datasets = grp.attrs["multiscales"][0]["datasets"]
    pyramid = [grp.get(d["path"]) for d in datasets]

    # Copy zarr metadata (.zattrs, .zarray, .zgroup) from the ZarrTiffStore
    ref = get_zarr_meta(store, byteorder)

    # Traverse all levels of pyramid and get the offset / bytecount for all chunks
    for level in pyramid:
        indexer = BasicIndexer(Ellipsis, level)
        for chunk_coord, *_ in indexer:
            ckey = level._chunk_key(chunk_coord)
            *_, offset, bytecount = level.store._parse_key(ckey)
            if offset == 0 or bytecount == 0:
                continue
            ref[ckey] = [ref_url, offset, bytecount]

    return ref


if __name__ == "__main__":
    import json
    import sys
    from pathlib import Path

    from tifffile import imread

    input_path, output_path = Path(sys.argv[1]), Path(sys.argv[2])
    print("Reading file from " + str(input_path))
    with TiffFile(input_path) as tif:
        byteorder = tif.byteorder
    store = imread(input_path, aszarr=True)
    print("Create reference file...")
    ref = create_reference(store, byteorder, None)

    print("Writing reference file...")
    with open(str(output_path), "w") as f:
        json.dump(ref, f)
    print("Reference file created: " + str(output_path))