From b4418bc3149fcfe553d692f32feeb22c1168864c Mon Sep 17 00:00:00 2001
From: Laurent Mercadier <laurent.mercadier@xfel.eu>
Date: Wed, 19 Mar 2025 07:59:37 +0100
Subject: [PATCH] Add mode for peak integration, return peak integration
attributes
---
src/toolbox_scs/detectors/digitizers.py | 36 ++++++++++++++++++++-----
1 file changed, 30 insertions(+), 6 deletions(-)
diff --git a/src/toolbox_scs/detectors/digitizers.py b/src/toolbox_scs/detectors/digitizers.py
index 506335d..e610171 100644
--- a/src/toolbox_scs/detectors/digitizers.py
+++ b/src/toolbox_scs/detectors/digitizers.py
@@ -32,7 +32,8 @@ log = logging.getLogger(__name__)
def peaks_from_raw_trace(traces, pulseStart, pulseStop, baseStart, baseStop,
- period=None, npulses=None, extra_dim=None):
+ period=None, npulses=None, extra_dim=None,
+ mode='trapz'):
"""
Computes peaks from raw digitizer traces by trapezoidal integration.
@@ -55,6 +56,9 @@ def peaks_from_raw_trace(traces, pulseStart, pulseStop, baseStart, baseStop,
number of pulses. Ignored if intstart is a 1D-array.
extra_dim: str
Name given to the dimension along the peaks. Defaults to 'pulseId'.
+ mode: str in ['trapz', 'sum', 'mean', 'ampl']
+ The operation performed over the integration region. `ampl` is the
+ amplitude between the baseline and the peak height.
Returns
-------
@@ -86,7 +90,15 @@ def peaks_from_raw_trace(traces, pulseStart, pulseStop, baseStart, baseStop,
results = xr.DataArray(np.empty((traces.shape[0], len(pulses))),
coords=coords,
dims=['trainId', extra_dim])
-
+ func = {'trapz': np.trapz, 'sum': np.sum,
+ 'mean': np.mean}.get(mode)
+ if mode == 'ampl':
+ def func(val, axis):
+ return np.max(val, axis=axis) - np.min(val, axis=axis)
+
+ if func is None:
+ raise ValueError('mode must be a string in ["trapz", "sum",'
+ '"mean", "ampl"]')
for i, p in enumerate(pulses):
a = pulseStart + p
b = pulseStop + p
@@ -96,7 +108,7 @@ def peaks_from_raw_trace(traces, pulseStart, pulseStop, baseStart, baseStop,
break
bg = np.outer(np.median(traces[:, bkga:bkgb], axis=1),
np.ones(b-a))
- results[:, i] = np.trapz(traces[:, a:b] - bg, axis=1)
+ results[:, i] = func(traces[:, a:b] - bg, axis=1)
return results
@@ -720,7 +732,7 @@ def digitizer_type(run, source):
def get_digitizer_peaks(proposal, runNB, mnemonic, merge_with=None,
- bunchPattern='sase3', integParams=None,
+ bunchPattern='sase3', integParams=None, mode='trapz',
save=False, subdir='usr/processed_runs'):
"""
Extract the peaks from digitizer raw traces. The result can be merged
@@ -753,6 +765,14 @@ def get_digitizer_peaks(proposal, runNB, mnemonic, merge_with=None,
{'pulseStart':100, 'pulsestop':200, 'baseStart':50,
'baseStop':99, 'period':24, 'npulses':500}.
If None, integration parameters are computed automatically.
+ mode: str in ['trapz', 'sum', 'mean', 'ampl']
+ The operation performed over the integration region. `ampl` is the
+ amplitude between the baseline and the peak height.
+ save: bool
+ If True, save the computed peaks and the average raw trace in a h5
+ file in the subdir + f'/r{runNB:04d}/ folder.
+ subdir: str
+ subdirectory to save the output in.
Returns
-------
@@ -793,7 +813,8 @@ def get_digitizer_peaks(proposal, runNB, mnemonic, merge_with=None,
run, mnemonic, trace, integParams, pattern)
# extract peaks
- peaks = peaks_from_raw_trace(traces, **params, extra_dim=extra_dim)
+ peaks = peaks_from_raw_trace(traces, **params,
+ extra_dim=extra_dim, mode=mode)
peaks = peaks.rename(mnemonic.replace('raw', 'peaks'))
# Align pulse id
@@ -812,13 +833,16 @@ def get_digitizer_peaks(proposal, runNB, mnemonic, merge_with=None,
if params[p] is None:
params[p] = 'None'
peaks.attrs[f'{peaks.name}_{p}'] = params[p]
+ peaks.attrs[f'{peaks.name}_mode'] = mode
+
# save peaks
if save:
save_peaks(proposal, runNB, peaks, trace, subdir)
# merge with existing dataset
- ds = mw_ds.merge(peaks, join='inner')
+ ds = mw_ds.merge(peaks.to_dataset(promote_attrs=True), join='inner',
+ combine_attrs='drop_conflicts')
return ds
--
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