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Fix/update brt ng metadata #339

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merged 2 commits into from
Oct 5, 2023
Merged

Fix/update brt ng metadata #339

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c934d56
convert output of visual_min_max to new callback format
philipmac Oct 4, 2023
5f3684c
use HedwigImages iface
philipmac Oct 4, 2023
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15 changes: 11 additions & 4 deletions em_workflows/brt/flow.py
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Original file line number Diff line number Diff line change
Expand Up @@ -38,6 +38,8 @@
from typing import Dict
import glob
import os

from pytools.HedwigZarrImages import HedwigZarrImages
from em_workflows.file_path import FilePath
import subprocess
import math
Expand All @@ -46,7 +48,6 @@
from prefect import task, Flow, Parameter, unmapped
from prefect.run_configs import LocalRun
from prefect.engine import signals
from pytools.workflow_functions import visual_min_max

from em_workflows.utils import utils
from em_workflows.utils import neuroglancer as ng
Expand Down Expand Up @@ -502,13 +503,19 @@ def gen_zarr(fp_in: FilePath):
def gen_ng_metadata(fp_in: FilePath) -> Dict:
file_path = fp_in
asset_fp = Path(f"{file_path.assets_dir}/{file_path.base}.zarr")

first_zarr_arr = Path(asset_fp.as_posix() + "/0/0")
zarr_fp = Path(f"{file_path.working_dir}/{file_path.base}.zarr")
hw_images = HedwigZarrImages(zarr_fp)
_, hw_image = next(hw_images.series())

ng_asset = file_path.gen_asset(
asset_type=AssetType.NEUROGLANCER_ZARR, asset_fp=asset_fp
)
ng_asset["metadata"] = visual_min_max(mad_scale=5, input_image=first_zarr_arr)
metadata = {
"shader": "Grayscale",
"dimensions": "XYZ",
"shaderParameters": hw_image.neuroglancer_shader_parameters(),
}
ng_asset["metadata"] = metadata
return ng_asset


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