From 34145d7a49e00fea68ca094633ebbdf9a2b4e828 Mon Sep 17 00:00:00 2001
From: Laurent Mercadier <laurent.mercadier@xfel.eu>
Date: Thu, 27 Oct 2022 10:53:50 +0200
Subject: [PATCH] Add conversion to delay, improve plotting
---
src/toolbox_scs/routines/Reflectivity.py | 66 ++++++++++++++----------
1 file changed, 38 insertions(+), 28 deletions(-)
diff --git a/src/toolbox_scs/routines/Reflectivity.py b/src/toolbox_scs/routines/Reflectivity.py
index 6813233..c6bba0e 100644
--- a/src/toolbox_scs/routines/Reflectivity.py
+++ b/src/toolbox_scs/routines/Reflectivity.py
@@ -9,11 +9,7 @@ import matplotlib.pyplot as plt
import numpy as np
import xarray as xr
import re
-from functools import partial
from toolbox_scs.misc.laser_utils import positionToDelay as pTd
-from toolbox_scs.misc.laser_utils import delayToPosition as dTp
-from toolbox_scs.base.knife_edge import (prepare_arrays,
- function_fit)
from toolbox_scs.routines.XAS import xas
__all__ = [
@@ -59,9 +55,10 @@ def prepare_reflectivity_ds(ds, Iokey, Irkey, alternateTrains,
def reflectivity(data, Iokey='FastADC5peaks', Irkey='FastADC3peaks',
- delaykey='PP800_DelayLine', binWidth=0.05,
+ delaykey='PP800_DelayLine', binWidth=0.05,
+ positionToDelay=True, origin=None, invert=False,
pumpedOnly=False, alternateTrains=False, pumpOnEven=True,
- Ioweights=False, plot=True, plotErrors=True, origin=None,
+ Ioweights=False, plot=True, plotErrors=True, units='mm'
):
"""
Computes the reflectivity R = 100*(Ir/Io[pumped] / Ir/Io[unpumped] - 1)
@@ -85,6 +82,9 @@ def reflectivity(data, Iokey='FastADC5peaks', Irkey='FastADC3peaks',
optical delay in ps)
binWidth: float
width of bin in units of delay variable
+ positionToDelay: bool
+ origin: float
+ invert: bool
pumpedOnly: bool
Assumes that all trains and pulses are pumped. In this case,
Delta R is defined as Ir/Io.
@@ -102,8 +102,6 @@ def reflectivity(data, Iokey='FastADC5peaks', Irkey='FastADC3peaks',
If True, plots the results.
plotErrors: bool
If True, plots the 95% confidence interval.
- origin: float
- Used for plotting a vertical line at the position.
Output
------
@@ -114,18 +112,18 @@ def reflectivity(data, Iokey='FastADC5peaks', Irkey='FastADC3peaks',
# select relevant variables from dataset
variables = [Iokey, Irkey, delaykey]
ds = data[variables]
-
# prepare dataset according to pulse pattern
ds = prepare_reflectivity_ds(ds, Iokey, Irkey, alternateTrains,
pumpOnEven, pumpedOnly)
-
+
if (len(ds[delaykey].dims) > 1) and (ds[delaykey].dims !=
ds[Iokey].dims):
raise ValueError("Dimensions mismatch: delay variable has dims "
f"{ds[delaykey].dims} but (It, Io) variables have "
- f"dims {ds['deltaR'].dims}.")
+ f"dims {ds[Iokey].dims}.")
bin_delays = binWidth * np.round(ds[delaykey] / binWidth)
+ ds[delaykey+'_binned'] = bin_delays
counts = xr.ones_like(ds[Iokey]).groupby(bin_delays).sum(...)
if Ioweights is False:
ds['deltaR'] = ds[Irkey]/ds[Iokey]
@@ -164,42 +162,54 @@ def reflectivity(data, Iokey='FastADC5peaks', Irkey='FastADC3peaks',
name='counts',
coords={delaykey: xas_pumped['nrj']})
binned = xr.merge([deltaR, stddev, stderr, counts])
-
+
# copy attributes
for key, val in data.attrs.items():
binned.attrs[key] = val
+ binned = binned.rename({delaykey: 'delay'})
+
if plot:
- plot_reflectivity(binned, delaykey, origin, plotErrors)
+ plot_reflectivity(binned, delaykey, positionToDelay,
+ origin, invert, plotErrors, units)
return binned
-def plot_reflectivity(data, delaykey, origin, plotErrors):
- fig, ax = plt.subplots(figsize=(6,3.5), constrained_layout=True)
- ax.plot(data[delaykey], data['deltaR'], 'o-', color='C0')
- ax.set_xlabel(delaykey)
- ax.set_ylabel(r'$\Delta R$ [%]', color='C0')
- ax.grid()
+def plot_reflectivity(data, delaykey, positionToDelay, origin,
+ invert, plotErrors, units):
+ fig, ax = plt.subplots(figsize=(6, 4), constrained_layout=True)
+ ax.plot(data['delay'], data['deltaR'], 'o-', color='C0')
+ xlabel = delaykey + f' [{units}]'
if plotErrors:
- ax.fill_between(data[delaykey],
+ ax.fill_between(data['delay'],
data['deltaR'] - 1.96*data['deltaR_stderr'],
data['deltaR'] + 1.96*data['deltaR_stderr'],
color='C0', alpha=0.2)
ax2 = ax.twinx()
- ax2.bar(data[delaykey], data['counts'],
- width=0.80*(data[delaykey][1]-data[delaykey][0]),
- color='C1', alpha=0.2)
- ax2.set_ylabel('counts', color='C1')
+ ax2.bar(data['delay'], data['counts'],
+ width=0.80*(data['delay'][1]-data['delay'][0]),
+ color='C1', alpha=0.2)
+ ax2.set_ylabel('counts', color='C1', fontsize=13)
ax2.set_ylim(0, data['counts'].max()*3)
if origin is not None:
ax.axvline(origin, color='grey', ls='--')
+ if positionToDelay:
+ ax3 = ax.twiny()
+ xmin, xmax = ax.get_xlim()
+ ax3.set_xlim(pTd(xmin, origin, invert),
+ pTd(xmax, origin, invert),)
+ ax3.set_xlabel('delay [ps]', fontsize=13)
try:
proposalNB = int(re.findall(r'p(\d{6})',
data.attrs['runFolder'])[0])
runNB = int(re.findall(r'r(\d{4})', data.attrs['runFolder'])[0])
- ax.set_title(f'run {runNB} p{proposalNB}')
- except Exception as err:
+ ax.set_title(f'run {runNB} p{proposalNB}', fontsize=14)
+ except Exception:
if 'plot_title' in data.attrs:
- fig.suptitle(data.attrs['plot_title'])
- print('error', err)
+ ax.set_title(data.attrs['plot_title'])
+ ax.set_xlabel(xlabel, fontsize=13)
+ ax.set_ylabel(r'$\Delta R$ [%]', color='C0', fontsize=13)
+ ax.grid()
+
+ return fig, ax
--
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