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Create recon metadata JSON artifact #182

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Merged
yousefmoazzam merged 1 commit into from
Apr 29, 2026
Merged

Create recon metadata JSON artifact #182

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31 changes: 23 additions & 8 deletions httomo/templates/visr-tomo-recon.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -134,22 +134,33 @@ spec:
- name: recon-dir-path
- name: tmpdir-path
value: /tmp
- name: output-filename
- name: raw-recon-filename
value: recon.raw
- name: metadata-filename
value: metadata.json
script:
image: ghcr.io/diamondlightsource/httomo:latest
command: [/opt/conda/bin/python]
source: |
from pathlib import Path
import h5py
import json

OUT_PATH = "{{`{{ inputs.parameters.tmpdir-path }}`}}/{{`{{ inputs.parameters.output-filename }}`}}"
RECON_DIR = Path("{{`{{ inputs.parameters.recon-dir-path }}`}}")
RECON_FILENAME_PATTERN = "*-httomolib-rescale_to_int.h5"
recon_data_path = list(RECON_DIR.glob(RECON_FILENAME_PATTERN))[0]
RAW_RECON_PATH = "{{`{{ inputs.parameters.tmpdir-path }}`}}/{{`{{ inputs.parameters.raw-recon-filename }}`}}"
HDF5_RECON_DIR = Path("{{`{{ inputs.parameters.recon-dir-path }}`}}")
HDF5_RECON_FILENAME_PATTERN = "*-httomolib-rescale_to_int.h5"
hdf5_recon_data_path = list(HDF5_RECON_DIR.glob(HDF5_RECON_FILENAME_PATTERN))[0]

with h5py.File(recon_data_path, "r") as f:
f["/data"][:].tofile(OUT_PATH)
with h5py.File(hdf5_recon_data_path, "r") as f:
data = f["/data"][:]
data.tofile(RAW_RECON_PATH)

METADATA_PATH = "{{`{{ inputs.parameters.tmpdir-path }}`}}/{{`{{ inputs.parameters.metadata-filename }}`}}"

order = "C" if data.flags.c_contiguous else "F"
metadata = {"shape": list(data.shape), "dtype": str(data.dtype), "order": order}
with open(METADATA_PATH, "w") as f:
f.write(json.dumps(metadata, indent=2))
volumeMounts:
- name: session
mountPath: "{{`{{ workflow.parameters.visitdir }}`}}"
Expand All @@ -163,6 +174,10 @@ spec:
outputs:
artifacts:
- name: recon
path: "{{`{{ inputs.parameters.tmpdir-path }}`}}/{{`{{ inputs.parameters.output-filename }}`}}"
path: "{{`{{ inputs.parameters.tmpdir-path }}`}}/{{`{{ inputs.parameters.raw-recon-filename }}`}}"
archive:
none: { }
- name: metadata
path: "{{`{{ inputs.parameters.tmpdir-path }}`}}/{{`{{ inputs.parameters.metadata-filename }}`}}"
archive:
none: { }