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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 create.py LuCa-7color_Scan1.ome.tif gc://viv-demo/LuCa-7color_Scan1.ome.tif
import zarr
from zarr.indexing import BasicIndexer
from tifffile import imread
from tifffile.tifffile import ZarrTiffStore
from pathlib import Path
import sys
import json
from typing import Dict, Union, Tuple
ReferenceDict = Dict[str, Union[str, Tuple[str, int, int]]]
def get_zarr_meta(store: ZarrTiffStore) -> 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)
value["compressor"] = compressor_config
value = ZarrTiffStore._json(value)
meta[key] = value.decode("utf-8")
return meta
def create_reference(store: ZarrTiffStore, 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)
# 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__":
fp, ref_url = Path(sys.argv[1]), sys.argv[2]
store = imread(fp, aszarr=True)
ref = create_reference(store, ref_url)
with open(str(fp) + "_offsets.json", "w") as f:
json.dump(ref, f)
{".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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