First scripts

reduce.py

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+import numpy as np
+import json, os, glob, yaml
+import argparse, pickle, h5py
+from pathlib import Path
+from sfdata import SFDataFile, SFDataFiles
+
+from alvra_tools.load_data import load_data_compact_pump_probe
+#from alvra_tools.channels import *
+#from alvra_tools.utils import *
+#from alvra_tools.XAS_functions import *
+#from alvra_tools.XAS_utils import *
+
+def get_acq_from_pth(path):
+    import re
+    return re.search(r"acq(\d+)", path).group(1).zfill(4)
+
+parser = argparse.ArgumentParser()
+parser.add_argument("--input", "-i", required=True)
+parser.add_argument("channels_file")
+args = parser.parse_args()
+
+filename = Path(args.input)
+output_file = Path(str(filename).replace("/raw/", "/res/processed/").replace(".h5",".PROCESSED.h5") )
+output_file.parent.mkdir(parents=True, exist_ok=True, mode=0o775)
+
+acq = get_acq_from_pth(args.input)
+acq_meta_pth = Path(str(filename).replace("/data/ac", "/meta/ac")).parent
+acq_info_pth = acq_meta_pth.joinpath(f"acq{acq}.json")
+
+#if not acq_info_pth.exists():
+#    write_apo_meta(apo_meta_pth, apo_meta_dic)
+#    msg = f"Acq info(.json)  file does not exist: {acq_info_pth}"
+#    raise IOError(msg)
+
+with open(acq_info_pth, "r") as f:
+    acq_parameters = json.load(f)
+    rbk_value = acq_parameters.get("scan_info", {}).get("scan_readbacks", 0)
+    scan_value = acq_parameters.get("scan_info", {}).get("scan_values", 0)
+    xlabel = acq_parameters.get("scan_info", {}).get("name", 'None')
+    units = acq_parameters.get("scan_info", {}).get("units", 'None')
+
+with open(args.channels_file, "r") as f:
+    channels_aliases = yaml.safe_load(f)
+
+channels_mapping = channels_aliases["channels"]
+channels_pp = list(channels_mapping[ch] for ch in channels_aliases["channels_pump"])
+channels_all = channels_pp
+
+with SFDataFile(args.input) as step:
+    resultsPP, results, _, _ = load_data_compact_pump_probe(channels_pp, channels_all, step)
+
+res = {}
+for name, chan in channels_mapping.items():
+    ch = resultsPP[chan]
+    if name in channels_aliases["channels_pump"]:
+        res[name + "_pump"] = ch.pump
+    if name in channels_aliases["channels_unpump"]:
+        res[name + "_unpump"] = ch.unpump
+
+with h5py.File(output_file, 'w') as f:
+    gr1 = f.create_group("allShots")
+    for key, value in results.items():
+        gr1[key] = value
+    gr2 = f.create_group("OnOff")
+    for key, value in res.items():
+        gr2[key] = value
+    gr3 = f.create_group("meta")
+    gr3["readback_value"] = np.atleast_1d(rbk_value)
+    gr3["scan_value"] = np.atleast_1d(scan_value)
+    gr3["xlabel"] = xlabel
+    gr3["units"]  = units
+