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50 lines
1.4 KiB
Python
Executable File
50 lines
1.4 KiB
Python
Executable File
import argparse
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import json
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from pathlib import Path
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import numpy as np
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from sfdata import SFDataFile, SFProcFile
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from utils.helpers import get_acq_from_pth
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parser = argparse.ArgumentParser()
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parser.add_argument("--input", "-f", required=True)
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parser.add_argument("--background", "-b", required=True)
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args = parser.parse_args()
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filename = Path(args.input)
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out_pth = Path(
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str(filename).replace("/raw/", "/res/processed/").replace(".CAMERAS.h5", ".PROCESSED.h5")
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)
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out_pth.parent.mkdir(parents=True, exist_ok=True)
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bgs = {}
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with SFDataFile(args.background) as fdata:
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for name, chan in fdata.items():
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if chan.ndim > 1:
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bgs[name] = np.mean(chan.data, axis=0)
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sums = {}
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with SFDataFile(args.input) as fdata, SFProcFile(out_pth) as fproc:
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for name, chan in fdata.items():
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if chan.ndim > 1:
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proj = np.sum(chan.data - bgs[name], axis=1)
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fproc[f"{name}.projection"] = (chan.pids, proj)
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sums[name] = np.sum(chan.data - bgs[name])
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meta_pth = Path(str(filename).replace("/raw/", "/res/processed/").replace("/data/ac", "/meta/ac"))
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acq = get_acq_from_pth(str(filename))
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meta_pth = meta_pth.with_name(f"apo_acq{acq}.json")
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meta_pth.parent.mkdir(parents=True, exist_ok=True)
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meta_data = {
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"some key": "some value"
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}
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meta_data.update(sums)
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with open(meta_pth, "w") as f:
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json.dump(meta_data, f)
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