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experimental reference spec maker for ome-tiff

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 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;
}
{".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], 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["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]}
<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>
"""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))
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