update to BLISS/HDF5 files

larch/io/rixs_esrf_fame.py

@@ -10,16 +10,159 @@
 .. note: BM16 is FAME-UHD, French CRG beamline
 
 """
+
 import os
 import time
 import numpy as np
-from larch.io.specfile_reader import DataSourceSpecH5, _mot2array
+from larch.io.specfile_reader import DataSourceSpecH5, _mot2array, _str2rng
 from silx.io.dictdump import dicttoh5
 from larch.utils.logging import getLogger
 
 _logger = getLogger("io_rixs_bm16")
 
 
+def get_rixs_bm16(
+    fname,
+    scans=None,
+    sample_name=None,
+    mode="rixs",
+    mot_axis2="emi",
+    counter_signal="xpad_roi1",
+    counter_mon="p201_1_bkg_sub",
+    out_dir=None,
+    save_rixs=False,
+):
+    """Build RIXS map as X,Y,Z 1D arrays
+
+    Parameters
+    ----------
+    fname : str
+        path string to the BLISS/HDF5 file
+    scans : str or list of strings or list of ints, optional [None -> all scans in the file]
+        list of scans to load (the string is parsed by larch.io.specfile_reader._str2rng)
+    sample_name : str, optional ['UNKNOWN_SAMPLE']
+        name of the sample measured
+    mode : str, optional ['rixs']
+        RIXS acqusition mode (affects 'mot_axis2')
+            - 'rixs' -> incoming energy scans
+            - 'rixs_et' -> emitted energy scans
+    mot_axis2 : str ['emi']
+        name of the counter to use as second axis
+    counter_signal : str ['xpad_roi1']
+        name of the counter to use as signal
+    counter_mon : str ['p201_1_bkg_sub']
+        name of the counter to use as incoming beam monitor
+    out_dir : str, optional
+        path to save the data [None -> data_dir]
+    save_rixs : bool
+        if True -> save outdict to disk (in 'out_dir')
+
+    Returns
+    -------
+    outdict : dict
+        {
+        '_x': array, energy in
+        '_y': array, energy out
+        '_z': array, signal
+        'mode': str
+        'scans': list, scans
+        'writer_name': str,
+        'writer_version': str,
+        'writer_timestamp': str,
+        'counter_signal': str, counter_signal,
+        'counter_mon': str, counter_mon,
+        'mon_axis2': str, mot_axis2,
+        'sample_name': str, sample_name,
+        'ene_unit': "eV",
+        'rixs_header': None,
+        'data_dir': str, data_dir,
+        'out_dir': str, out_dir,
+        'fname_ine': str, full path raw data
+        'fname_out': str, full path
+        }
+    """
+    _writer = "get_rixs_bm16"
+    _writer_version = "1.5.1"  #: used for reading back in RixsData.load_from_h5()
+    _writer_timestamp = "{0:04d}-{1:02d}-{2:02d}_{3:02d}{4:02d}".format(
+        *time.localtime()
+    )
+    if sample_name is None:
+        sample_name = "SAMPLE_UNKNOWN"
+
+    data_dir = os.path.join(os.sep, *fname.split(os.sep)[1:-1])
+    _logger.debug(f"data_dir: {data_dir}")
+    if out_dir is None:
+        out_dir = data_dir
+    ds = DataSourceSpecH5(fname)
+
+    if isinstance(scans, str):
+        scans = _str2rng(scans)
+    if scans is None:
+        scans = [scn[0] for scn in ds.get_scans()]
+    assert isinstance(scans, list), "scans should be a list"
+
+    mode = mode.lower()
+    assert mode in ("rixs", "rixs_et"), "RIXS mode not valid"
+
+    _counter = 0
+    for scan in scans:
+        try:
+            ds.set_scan(scan)
+            xscan, sig, lab, attrs = ds.get_curve(counter_signal, mon=counter_mon)
+        except Exception:
+            _logger.error(f"cannot load scan {scan}!")
+            continue
+        # keV -> eV
+        escan = xscan * 1000
+        estep = ds.get_motor_position(mot_axis2) * 1000
+        if mode == "rixs":
+            x = escan
+            y = _mot2array(estep, escan)
+        if mode == "rixs_et":
+            x = _mot2array(estep, escan)
+            y = escan
+        if _counter == 0:
+            xcol = x
+            ycol = y
+            zcol = sig
+        else:
+            xcol = np.append(xcol, x)
+            ycol = np.append(ycol, y)
+            zcol = np.append(zcol, sig)
+        _counter += 1
+        _logger.info(f"Loaded scan {scan}: {estep:.1f} eV")
+
+    outdict = {
+        "_x": xcol,
+        "_y": ycol,
+        "_z": zcol,
+        "mode": mode,
+        "scans": scans,
+        "writer_name": _writer,
+        "writer_version": _writer_version,
+        "writer_timestamp": _writer_timestamp,
+        "counter_signal": counter_signal,
+        "counter_mon": counter_mon,
+        "mon_axis2": mot_axis2,
+        "sample_name": sample_name,
+        "ene_unit": "eV",
+        "rixs_header": None,
+        "data_dir": data_dir,
+        "out_dir": out_dir,
+    }
+
+    if save_rixs:
+        fnstr = fname.split("/")[-1].split(".")[0]
+        fnout = "{0}_rixs.h5".format(fnstr)
+        fname_out = os.path.join(out_dir, fnout)
+        dicttoh5(outdict, fname_out)
+        outdict["fname_in"] = fname
+        outdict["fname_out"] = fname_out
+        _logger.info("RIXS saved to {0}".format(fnout))
+
+    return outdict
+
+
 def _parse_header(fname):
     """Get parsed header for the RIXS_###.log file
     Return
@@ -43,7 +186,7 @@ def _parse_header(fname):
     return header
 
 
-def get_rixs_bm16(
+def get_rixs_bm16_spec(
     rixs_logfn,
     sample_name=None,
     out_dir=None,
@@ -52,7 +195,8 @@ def get_rixs_bm16(
     interp_ene_in=True,
     save_rixs=False,
 ):
-    """Build RIXS map as X,Y,Z 1D arrays
+    """Build RIXS map as X,Y,Z 1D arrays (version for Spec files - *DEPRECATED*)
+
     Parameters
     ----------
     rixs_logfn : str
@@ -138,8 +282,8 @@ def get_rixs_bm16(
         _logger.info(f"Loaded scan {scan}: {estep} eV")
 
     outdict = {
-        "_x": xcol * 1000, #to eV
-        "_y": ycol * 1000, #to eV
+        "_x": xcol * 1000,  # to eV
+        "_y": ycol * 1000,  # to eV
         "_z": zcol,
         "writer_name": _writer,
         "writer_version": _writer_version,