From 87cfeec60937da6d083981e210173c29471634fe Mon Sep 17 00:00:00 2001
From: mercadil <laurent.mercadier@xfel.eu>
Date: Sun, 24 Mar 2019 04:43:40 +0100
Subject: [PATCH] Fixed TIM functions: using bunchpattern and apd parameters to
extract correct pulses with getTIMapd() and mcpPeaks()
---
xgm.py | 51 +++++++++++++++++++++++++++++++++++----------------
1 file changed, 35 insertions(+), 16 deletions(-)
diff --git a/xgm.py b/xgm.py
index 4cd3a38..73eb3d5 100644
--- a/xgm.py
+++ b/xgm.py
@@ -361,13 +361,17 @@ def mcpPeaks(data, intstart, intstop, bkgstart, bkgstop, mcp=1, t_offset=None, n
keyraw = 'MCP{}raw'.format(mcp)
if keyraw not in data:
raise ValueError("Source not found: {}!".format(keyraw))
- sa3 = data['sase3'].where(data['sase3']>1)
- step = sa3.where(data['npulses_sase3']>0, drop=True)[0,:2].values
- step = int(step[1] - step[0])
- if t_offset is None:
- t_offset = 440 * step
if npulses is None:
- npulses = int((sa3.max().values - sa3.min().values + step)/step)
+ npulses = int(data['npulses_sase3'].max().values)
+ sa3 = data['sase3'].where(data['sase3']>1)
+ if npulses > 1:
+ step = sa3.where(data['npulses_sase3']>1, drop=True)[0,:2].values
+ step = int(step[1] - step[0])
+ if t_offset is None:
+ t_offset = 440 * step
+ else:
+ if t_offset is None:
+ t_offset = 1
results = xr.DataArray(np.empty((sa3.shape[0], npulses)), coords=sa3.coords,
dims=['trainId', 'MCP{}fromRaw'.format(mcp)])
for i in range(npulses):
@@ -381,7 +385,7 @@ def mcpPeaks(data, intstart, intstop, bkgstart, bkgstop, mcp=1, t_offset=None, n
def getTIMapd(data, mcp=1, use_apd=True, intstart=None, intstop=None,
- bkgstart=None, bkgstop=None, t_offset=1760, npulses=None):
+ bkgstart=None, bkgstop=None, t_offset=None, npulses=None):
''' Extract peak-integrated data from TIM where pulses are from SASE3 only.
If use_apd is False it calculates integration from raw traces.
The missing values, in case of change of number of pulses, are filled
@@ -400,19 +404,34 @@ def getTIMapd(data, mcp=1, use_apd=True, intstart=None, intstop=None,
tim: DataArray of shape trainId only for SASE3 pulses x N
with N=max(number of pulses per train)
'''
- key = 'MCP{}apd'.format(mcp)
+ sa3 = data['sase3'].where(data['sase3']>1, drop=True)
+ npulses_sa3 = data['npulses_sase3']
+ maxpulses = int(npulses_sa3.max().values)
+ step = 1
+ if maxpulses > 1:
+ step = sa3.where(data['npulses_sase3']>1, drop=True)[0,:2].values
+ step = int(step[1] - step[0])
if use_apd:
- apd = data[key]
+ apd = data['MCP{}apd'.format(mcp)]
+ initialDelay = data.attrs['run'].get_array(
+ 'SCS_UTC1_ADQ/ADC/1', 'board1.apd.channel_0.initialDelay.value')[0].values
+ upperLimit = data.attrs['run'].get_array(
+ 'SCS_UTC1_ADQ/ADC/1', 'board1.apd.channel_0.upperLimit.value')[0].values
+ nsamples = upperLimit - initialDelay
+ npulses_per_apd = int(nsamples/440)
+ sa3 /= npulses_per_apd
else:
- apd = mcpPeaks(data, intstart, intstop, bkgstart, bkgstop, t_offset, mcp, npulses)
- npulses_sa3 = data['npulses_sase3']
- sa3 = data['sase3'].where(data['sase3']>1, drop=True)/4
+ apd = mcpPeaks(data, intstart, intstop, bkgstart, bkgstop, mcp=mcp,
+ t_offset=t_offset, npulses=npulses)
+ sa3 /= step
sa3 -= sa3[:,0]
sa3 = sa3.astype(int)
if np.all(npulses_sa3 == npulses_sa3[0]):
tim = apd[:, sa3[0].values]
return tim
- maxpulses = int(npulses_sa3.max().values)
+ stride = 1
+ if use_apd:
+ stride = np.max([stride,int(step/npulses_per_apd)])
diff = npulses_sa3.diff(dim='trainId')
#only keep trainIds where a change occured:
diff = diff.where(diff != 0, drop=True)
@@ -430,7 +449,7 @@ def getTIMapd(data, mcp=1, use_apd=True, intstart=None, intstop=None,
else:
l = idx_change[i+1]
b = npulses_sa3[idx].values
- temp = apd[idx:l,:maxpulses].copy()
+ temp = apd[idx:l,:maxpulses*stride:stride].copy()
temp[:,b:] = np.NaN
if tim is None:
tim = temp
@@ -440,7 +459,7 @@ def getTIMapd(data, mcp=1, use_apd=True, intstart=None, intstop=None,
def calibrateTIM(data, rollingWindow=200, mcp=1, plot=False, use_apd=True, intstart=None,
- intstop=None, bkgstart=None, bkgstop=None, t_offset=1760, npulses_apd=None):
+ intstop=None, bkgstart=None, bkgstop=None, t_offset=None, npulses_apd=None):
''' Calibrate TIM signal (Peak-integrated signal) to the slow ion signal of SCS_XGM
(photocurrent read by Keithley, channel 'pulseEnergy.photonFlux.value').
The aim is to find F so that E_tim_peak[uJ] = F x TIM_peak. For this, we want to
@@ -469,7 +488,6 @@ def calibrateTIM(data, rollingWindow=200, mcp=1, plot=False, use_apd=True, intst
bkgstart: trace index of background start
bkgstop: trace index of background stop
t_offset: index separation between two pulses
- mcp: MCP channel number
npulses_apd: number of pulses
Output:
@@ -560,6 +578,7 @@ def calibrateTIM(data, rollingWindow=200, mcp=1, plot=False, use_apd=True, intst
return F
+
''' TIM calibration table
Dict with key= photon energy and value= array of polynomial coefficients for each MCP (1,2,3).
The polynomials correspond to a fit of the logarithm of the calibration factor as a function
--
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