wip: safe pre_edge

58362d46 · Mauro Rovezzi · db20acaa · 58362d46 · 58362d46
Commit 58362d46 authored 4 months ago by Mauro Rovezzi
--- a/notebooks/devel_sandbox.ipynb
+++ b/notebooks/devel_sandbox.ipynb
@@ -57,7 +57,7 @@
    "# \"INFO\" -> useful messages\n",
    "# \"WARNING\" -> warnings only\n",
    "# \"ERROR\" -> only errors\n",
-    "_logger.setLevel(\"INFO\")\n",
+    "_logger.setLevel(\"DEBUG\")\n",
    "\n",
    "# show workflow version (and famewoks branch information)\n",
    "branch = os.popen(\"cd ~/devel/famewoks; git branch --show-current\").read()[:-1]\n",
@@ -153,11 +153,31 @@
    "    ynorm=\"area\",\n",
    "    show_slide=True,\n",
    "    show_i0=False,\n",
+    "    show_deriv=False,\n",
    "    show_e0=True,\n",
-    "    show_merge=\"rebin\",\n",
+    "    show_merge=True,\n",
    ")"
   ]
  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "fig.add_vline(x=dataset.fluo.e0)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "from famewoks.bliss2larch import safe_pre_edge\n",
+    "sg = safe_pre_edge(session, group=dataset.fluo)"
+   ]
+  },
  {
   "cell_type": "code",
   "execution_count": null,

 %% Cell type:markdown id: tags:

 # Development sandbox notebook

 This notebook is for development and testing of new features and bug fixes only.

 %% Cell type:code id: tags:

 ``` python
 %load_ext autoreload
 %autoreload 2

 # Uncomment the following two lines if the plots do not show in the notebook
 # import plotly.io as pio
 # pio.renderers.default = "iframe"

 import os
 from dataclasses import asdict
 from IPython.display import display
 from famewoks import __version__ as wkflver
 from famewoks.datamodel import (
    ExpSession,
    ExpCounters,
    CNTS_FLUO_XMAP,
    CNTS_FLUO,
    CNTS_CAS,
 )
 from famewoks.tests.datainfos import DATAINFOS, get_exp_session
 from famewoks.plots import plot_data, plot_eshift
 from famewoks.bliss2larch import (
    search_samples,
    show_samples_info,
    search_datasets,
    load_data,
    get_scans,
    get_group,
    set_enealign,
    apply_eshift,
    set_bad_fluo_channels,
    set_bad_scans,
    set_bad_samples,
    merge_data,
    save_data,
 )
 from famewoks.bliss2larch import _logger

 # adjust the logger level:
 # "DEBUG" -> show all messages
 # "INFO" -> useful messages
 # "WARNING" -> warnings only
 # "ERROR" -> only errors
-_logger.setLevel("INFO")
+_logger.setLevel("DEBUG")

 # show workflow version (and famewoks branch information)
 branch = os.popen("cd ~/devel/famewoks; git branch --show-current").read()[:-1]
 _logger.info(f"--> Using famewoks version: {wkflver} (branch: {branch})")

 # define the counters names or use those already defined for BM16: CNTS_FLUO_XMAP, CNTS_FLUO, CNTS_CAS
 CNTS_CAS_XPAD = ExpCounters(
    ene="energy_enc",
    ix=["p201_1_bkg_sub", "p201_3_bkg_sub", "p201_5_bkg_sub"],  #: I0, I1, I2
    fluo_roi=["xpad_roi1"],  # all detector names for ROI1
    fluo_corr=["xpad_roi1"],  # all detector names (DT corrected)
    fluo_time=["sec"],  # elapsed time, which is different for the spikes
    time="sec",  # "musst_timer"
 )
 # define the experimental session metadata manually
 session = ExpSession(
    flag=1,
    datadir="/data/visitor/a161838/bm16/20241113",
    proposal="a161838",
    session="20241113",
    proposer="Quantin",
    lc="AA, IK",
    elem="V",
    edge="K",
    comment="",
    counters=CNTS_CAS,  # *NOTE* give here the correct counters names!
    samples=[],
    bad_samples=[],
    bad_fluo_channels=None,
    enealign=None,
 )

 # (testing) otherwise it is possible to get the session from a collection of previous experiments
 # session = get_exp_session(DATAINFOS, proposer="Isaure",session="20241003")
 # session = get_exp_session(DATAINFOS, proposer="Rimondi",session="20241001")
 # session = get_exp_session(DATAINFOS, proposer="Biswas",session="20240924")
 # session = get_exp_session(DATAINFOS, proposer="Sanchez",session="20240716")
 # session = get_exp_session(DATAINFOS, proposer="Stellato",session="20240625")
 # session = get_exp_session(DATAINFOS, proposer="Bertrand",session="20240910")

 # display the session metadata
 #display(asdict(session))
 ```

 %% Cell type:code id: tags:

 ``` python
 samples = search_samples(session, ignore_names=["rack", "mount", "align", "bl_", "sample"])
 ```

 %% Cell type:code id: tags:

 ``` python
 sel_sample = 10
 datasets = search_datasets(session, sample=sel_sample)
 ```

 %% Cell type:code id: tags:

 ``` python
 sel_dataset = 0
 dataset = datasets[sel_dataset]
 load_data(
    session,
    dataset,
    use_fluo_corr=False,
    iskip=1, #: ignore the first point
    istrip=1, #: ignore the last point
    calc_eshift=True,
    merge=True,
    skip_scans=[],
 )
 ```

 %% Cell type:code id: tags:

 ``` python
 fig = plot_data(
    dataset,
    data="fluo",
    ynorm="area",
    show_slide=True,
    show_i0=False,
+    show_deriv=False,
    show_e0=True,
-    show_merge="rebin",
+    show_merge=True,
 )
 ```

 %% Cell type:code id: tags:

 ``` python
+fig.add_vline(x=dataset.fluo.e0)
+```
+
+%% Cell type:code id: tags:
+
+``` python
+from famewoks.bliss2larch import safe_pre_edge
+sg = safe_pre_edge(session, group=dataset.fluo)
+```
+
+%% Cell type:code id: tags:
+
+``` python
 ```

--- a/src/famewoks/bliss2larch.py
+++ b/src/famewoks/bliss2larch.py
@@ -32,6 +32,8 @@ from larch.io import AthenaProject
 from larch.xafs import pre_edge
 from larch.xafs.rebin_xafs import rebin_xafs

+from xraydb import xray_edge
+
 # from larch.xafs.pre_edge import energy_align
 from famewoks.energy import energy_align

@@ -45,6 +47,29 @@ _logger.setLevel("INFO")  # adjust logger level .DEBUG, .INFO, .WARNING, .ERROR
 _logger.debug(f"DataSourceSpecH5 version: {ds_version}")
 _logger.debug(f"workflow version: {wkfl_version}")

+def safe_pre_edge(session: ExpSession, group: Group, verbose: bool = True) -> Group:
+    """Apply `pre_edge` to a group, safely catching errors and checking for correct E0"""
+    infolab = group.filename
+    glabel = group.label if not None else ""
+    try:
+        e0ref = xray_edge(session.elem, session.edge).energy
+        _logger.debug(f"{infolab}_{glabel} -> safe_pre_ede() -> E0 for {session.elem} {session.edge} edge: {e0ref:.2f} eV")
+    except Exception as err:
+        _logger.error(f"{infolab}_{glabel} -> cannot get edge energy from session -> check element and edge")
+        _logger.debug(f"ERR---> {err}")
+        e0ref = 0
+    try:
+        pre_edge(group)
+    except Exception as err:
+        _logger.warning(f"{infolab}_{glabel} -> `pre_edge()` failed")
+        _logger.debug(f"ERR---> {err}")
+
+    e0thr = e0ref * 0.01
+    if abs(group.e0 - e0ref) > e0thr:
+        _logger.debug(f"{infolab}_{glabel} -> found E0 is out of 1% threshold from theory ({e0ref:.2f} eV) -> forced from {group.e0:.2f} to {e0ref:.2f} eV")
+        group.e0 = e0ref
+    return group
+

 def search_samples(
    session: ExpSession,