From 28f65b7567bab3ed004ed4120cee8d480a3e6a11 Mon Sep 17 00:00:00 2001
From: Laurent Mercadier <laurent.mercadier@xfel.eu>
Date: Tue, 13 Apr 2021 22:53:40 +0200
Subject: [PATCH] Added BAM detectors function, added is_pulse_at in
bunch_pattern_external
---
src/toolbox_scs/constants.py | 14 +--
src/toolbox_scs/detectors/__init__.py | 3 +
src/toolbox_scs/detectors/bam_detectors.py | 86 +++++++++++++++++++
src/toolbox_scs/detectors/digitizers.py | 18 +---
src/toolbox_scs/detectors/load_detectors.py | 11 ++-
src/toolbox_scs/misc/__init__.py | 2 +-
src/toolbox_scs/misc/bunch_pattern.py | 48 -----------
.../misc/bunch_pattern_external.py | 35 +++++++-
8 files changed, 142 insertions(+), 75 deletions(-)
create mode 100644 src/toolbox_scs/detectors/bam_detectors.py
diff --git a/src/toolbox_scs/constants.py b/src/toolbox_scs/constants.py
index 2b1789d..72eee76 100644
--- a/src/toolbox_scs/constants.py
+++ b/src/toolbox_scs/constants.py
@@ -30,15 +30,15 @@ mnemonics = {
'dim': ['pulse_slot']},
# Bunch Arrival Monitors
- "BAM5": {'source': 'SCS_ILH_LAS/DOOCS/BAM_414_B2:output',
- 'key': 'data.lowChargeArrivalTime',
- 'dim': ['BAMbunchId']},
- "BAM6": {'source': 'SCS_ILH_LAS/DOOCS/BAM_1932M_TL:output',
- 'key': 'data.lowChargeArrivalTime',
- 'dim': ['BAMbunchId']},
- "BAM7": {'source': 'SCS_ILH_LAS/DOOCS/BAM_1932S_TL:output',
+ "BAM414": {'source': 'SCS_ILH_LAS/DOOCS/BAM_414_B2:output',
'key': 'data.lowChargeArrivalTime',
'dim': ['BAMbunchId']},
+ "BAM1932M": {'source': 'SCS_ILH_LAS/DOOCS/BAM_1932M_TL:output',
+ 'key': 'data.lowChargeArrivalTime',
+ 'dim': ['BAMbunchId']},
+ "BAM1932S": {'source': 'SCS_ILH_LAS/DOOCS/BAM_1932S_TL:output',
+ 'key': 'data.lowChargeArrivalTime',
+ 'dim': ['BAMbunchId']},
# SA3
"nrj": {'source': 'SA3_XTD10_MONO/MDL/PHOTON_ENERGY',
diff --git a/src/toolbox_scs/detectors/__init__.py b/src/toolbox_scs/detectors/__init__.py
index c5a95de..716b46b 100644
--- a/src/toolbox_scs/detectors/__init__.py
+++ b/src/toolbox_scs/detectors/__init__.py
@@ -5,6 +5,7 @@ from .xgm import (
from .digitizers import (
get_peaks, get_tim_peaks, get_laser_peaks, get_digitizer_peaks,
check_peak_params)
+from .bam_detectors import get_bam
from .dssc_data import (
save_xarray, load_xarray, get_data_formatted, save_attributes_h5)
from .dssc_misc import (
@@ -27,6 +28,7 @@ __all__ = (
"get_laser_peaks",
"get_digitizer_peaks",
"check_peak_params",
+ "get_bam",
"save_xarray",
"load_xarray",
"get_data_formatted",
@@ -68,6 +70,7 @@ clean_ns = [
'xgm',
'digitizers',
'load_detectors'
+ 'bam_detectors'
]
diff --git a/src/toolbox_scs/detectors/bam_detectors.py b/src/toolbox_scs/detectors/bam_detectors.py
new file mode 100644
index 0000000..36fef4a
--- /dev/null
+++ b/src/toolbox_scs/detectors/bam_detectors.py
@@ -0,0 +1,86 @@
+""" Beam Arrival Monitor related sub-routines
+
+ Copyright (2021) SCS Team.
+
+ (contributions preferrably comply with pep8 code structure
+ guidelines.)
+"""
+
+import logging
+
+import numpy as np
+import xarray as xr
+import matplotlib.pyplot as plt
+from scipy.signal import find_peaks
+import re
+
+from ..constants import mnemonics as _mnemonics
+from ..misc.bunch_pattern_external import is_pulse_at
+from ..util.exceptions import ToolBoxValueError
+
+
+log = logging.getLogger(__name__)
+
+
+def get_bam(run, key=None, merge_with=None, bunchPattern='sase3'):
+ """
+ blablabla
+ """
+
+ # check if bunch pattern table exists
+ if bool(merge_with) and 'bunchPatternTable' in merge_with:
+ bpt = merge_with['bunchPatternTable']
+ log.debug('Using bpt from merge_with dataset.')
+ elif _mnemonics['bunchPatternTable']['source'] in run.all_sources:
+ bpt = run.get_array(*_mnemonics['bunchPatternTable'].values())
+ log.debug('Loaded bpt from extra_data run.')
+ else:
+ bpt = None
+ if key is None:
+ keys = ['BAM1932M'] if merge_with is None else []
+ else:
+ keys = key if isinstance(key, list) else [key]
+ if bool(merge_with):
+ bam_keys = [k for k in _mnemonics if 'BAM' in k]
+ mw_to_process = [k for k in merge_with if k in bam_keys and
+ len(merge_with[k].coords) == 1]
+ keys = [k for k in keys if k not in merge_with]
+ else:
+ mw_to_process = []
+
+ ds = xr.Dataset()
+ roi = np.s_[:5400:2]
+ if len(keys) > 0:
+ vals = []
+ for k in keys:
+ val = run.get_array(*_mnemonics[k].values(), roi=roi)
+ val[_mnemonics[k]['dim'][0]] = np.arange(2700)
+ vals.append(val)
+ aligned_vals = xr.align(*vals, join='inner')
+ ds = dict(zip(keys, aligned_vals))
+ ds = xr.Dataset(ds)
+ if len(mw_to_process) > 0:
+ vals = []
+ for k in mw_to_process:
+ val = merge_with[k].isel({_mnemonics[k]['dim'][0]: roi})
+ val[_mnemonics[k]['dim'][0]] = np.arange(2700)
+ vals.append(val)
+ aligned_vals = xr.align(*vals, join='inner')
+ ds_mw = dict(zip(mw_to_process, aligned_vals))
+ ds_mw = xr.Dataset(ds_mw)
+ ds = ds.merge(ds_mw)
+
+ if bpt is not None and len(ds.variables) > 0:
+ dim_names = {'sase3': 'sa3_pId', 'sase1': 'sa1_pId',
+ 'scs_ppl': 'ol_pId'}
+ mask = is_pulse_at(bpt, bunchPattern)
+ mask = mask.rename({'pulse_slot': dim_names[bunchPattern]})
+ ds = ds.rename({_mnemonics['BAM1932M']['dim'][0]: dim_names[bunchPattern]})
+ ds = ds.where(mask, drop=True)
+
+ if bool(merge_with):
+ result = merge_with.drop(mw_to_process)
+ result = result.merge(ds, join='inner')
+ return result
+
+ return ds
diff --git a/src/toolbox_scs/detectors/digitizers.py b/src/toolbox_scs/detectors/digitizers.py
index 642ace1..946f53d 100644
--- a/src/toolbox_scs/detectors/digitizers.py
+++ b/src/toolbox_scs/detectors/digitizers.py
@@ -15,7 +15,7 @@ from scipy.signal import find_peaks
import re
from ..constants import mnemonics as _mnemonics
-from ..misc.bunch_pattern_external import is_sase_1, is_sase_3, is_ppl
+from ..misc.bunch_pattern_external import is_pulse_at
from ..util.exceptions import ToolBoxValueError
@@ -127,12 +127,7 @@ def peaks_from_apd(array, params, digitizer, bpt, bunchPattern):
npulses_apd = params['npulses']
dim_names = {'sase3': 'sa3_pId', 'sase1': 'sa1_pId', 'scs_ppl': 'ol_pId'}
pulse_dim = dim_names[bunchPattern]
- if bunchPattern == 'sase3':
- mask = is_sase_3(bpt).rename({'pulse_slot': pulse_dim})
- if bunchPattern == 'sase1':
- mask = is_sase_1(bpt).rename({'pulse_slot': pulse_dim})
- if bunchPattern == 'scs_ppl':
- mask = is_ppl(bpt).rename({'pulse_slot': pulse_dim})
+ mask = is_pulse_at(bpt, bunchPattern).rename({'pulse_slot': pulse_dim})
mask = mask.sel(trainId=array.trainId)
mask = mask.assign_coords({pulse_dim: np.arange(2700)})
pid = np.sort(np.unique(np.where(mask)[1]))
@@ -299,12 +294,7 @@ def get_peaks(run,
dim_names = {'sase3': 'sa3_pId', 'sase1': 'sa1_pId', 'scs_ppl': 'ol_pId'}
extra_dim = dim_names[pattern]
valid_tid = np.intersect1d(arr.trainId, bpt.trainId, assume_unique=True)
- if pattern == 'sase3':
- mask = is_sase_3(bpt.sel(trainId=valid_tid))
- if pattern == 'sase1':
- mask = is_sase_1(bpt.sel(trainId=valid_tid))
- if pattern == 'scs_ppl':
- mask = is_ppl(bpt.sel(trainId=valid_tid))
+ mask = is_pulse_at(bpt.sel(trainId=valid_tid), pattern)
mask = mask.rename({'pulse_slot': extra_dim})
mask = mask.assign_coords({extra_dim: np.arange(2700)})
mask_on = mask.where(mask, drop=True).fillna(False).astype(bool)
@@ -648,7 +638,7 @@ def check_peak_params(run, key, raw_trace=None, ntrains=200, params=None,
sel = run.select_trains(np.s_[:ntrains])
bp_params = {}
bpt = sel.get_array(*_mnemonics['bunchPatternTable'].values())
- mask = is_sase_3(bpt) if bunchPattern == 'sase3' else is_ppl(bpt)
+ mask = is_pulse_at(bpt, bunchPattern)
pid = np.sort(np.unique(np.where(mask)[1]))
bp_params['npulses'] = len(pid)
if bp_params['npulses'] == 1:
diff --git a/src/toolbox_scs/detectors/load_detectors.py b/src/toolbox_scs/detectors/load_detectors.py
index 6da74b9..2ad3ed9 100644
--- a/src/toolbox_scs/detectors/load_detectors.py
+++ b/src/toolbox_scs/detectors/load_detectors.py
@@ -9,6 +9,7 @@
from ..constants import mnemonics as _mnemonics
from .digitizers import get_tim_peaks, get_laser_peaks
from .xgm import get_xgm
+from .bam_detectors import get_bam
def get_all_detectors(run, data, tim_bp='sase3', laser_bp='scs_ppl'):
@@ -32,10 +33,16 @@ def get_all_detectors(run, data, tim_bp='sase3', laser_bp='scs_ppl'):
adc peaks. See get_fast_adc_peaks for details.
"""
tim = [k for k in _mnemonics if 'MCP' in k and k in data]
+ ds = get_tim_peaks(run, key=tim, merge_with=data, bunchPattern=tim_bp)
+
laser = [k for k in _mnemonics if 'FastADC' in k and k in data]
+ ds = get_laser_peaks(run, key=laser, merge_with=ds, bunchPattern=laser_bp)
+
xgm = [k for k in _mnemonics if ('_SA3' in k or '_SA1' in k
or '_XGM' in k) and k in data]
- ds = get_tim_peaks(run, key=tim, merge_with=data, bunchPattern=tim_bp)
- ds = get_laser_peaks(run, key=laser, merge_with=ds, bunchPattern=laser_bp)
ds = get_xgm(run, key=xgm, merge_with=ds)
+
+ bam = [k for k in _mnemonics if 'BAM' in k and k in data]
+ ds = get_bam(run, key=bam, merge_with=ds)
+
return ds
diff --git a/src/toolbox_scs/misc/__init__.py b/src/toolbox_scs/misc/__init__.py
index 9afb2d9..5def83e 100644
--- a/src/toolbox_scs/misc/__init__.py
+++ b/src/toolbox_scs/misc/__init__.py
@@ -1,5 +1,5 @@
from .bunch_pattern import (extractBunchPattern, pulsePatternInfo,
- repRate, sortBAMdata,
+ repRate,
)
from .bunch_pattern_external import is_sase_3, is_sase_1, is_ppl
from .laser_utils import positionToDelay, degToRelPower
diff --git a/src/toolbox_scs/misc/bunch_pattern.py b/src/toolbox_scs/misc/bunch_pattern.py
index 2edf854..3f5939b 100644
--- a/src/toolbox_scs/misc/bunch_pattern.py
+++ b/src/toolbox_scs/misc/bunch_pattern.py
@@ -212,51 +212,3 @@ def repRate(data=None, runNB=None, proposalNB=None, key='sase3'):
return 0
f = 1/((a[0,1] - a[0,0])*12e-3/54.1666667)
return f
-
-def sortBAMdata(data, key='scs_ppl', sa3Offset=0):
- ''' Extracts beam arrival monitor data from the raw arrays 'BAM6', 'BAM7', etc...
- according to the bunchPatternTable. The BAM arrays contain 7220 values, which
- corresponds to FLASH busrt length of 800 us @ 9 MHz. The bunchPatternTable
- only has 2700 values, corresponding to XFEL 600 us burst length @ 4.5 MHz.
- Hence, the BAM arrays are truncated to 5400 with a stride of 2 and matched
- to the bunchPatternTable. If key is one of the sase, the given dimension name
- of the bam arrays is 'sa[sase number]_pId', to match other data (XGM, TIM...).
- If key is 'scs_ppl', the dimension is named 'ol_pId'
- Inputs:
- data: xarray Dataset containing BAM arrays
- key: str, ['sase1', 'sase2', 'sase3', 'scs_ppl']
- sa3Offset: int, used if key=='scs_ppl'. Offset in number of pulse_id
- between the first OL and FEL pulses. An offset of 40 means that
- the first laser pulse comes 40 pulse_id later than the FEL on a
- grid of 4.5 MHz. Negative values shift the laser pulse before
- the FEL one.
- Output:
- ndata: xarray Dataset with same keys as input data (but new bam arrays)
- '''
- a, b, mask = extractBunchPattern(key=key, runDir=data.attrs['run'])
- if key == 'scs_ppl':
- a3, b3, mask3 = extractBunchPattern(key='sase3', runDir=data.attrs['run'])
- firstSa3_pId = a3.where(b3>0, drop=True)[0,0].values.astype(int)
- mask = mask.roll(pulse_slot=firstSa3_pId+sa3Offset)
- mask = mask.rename({'pulse_slot':'BAMbunchId'})
- ndata = data
- dropList = []
- mergeList = []
- for k in data:
- if 'BAM' in k:
- dropList.append(k)
- bam = data[k].isel(BAMbunchId=slice(0,5400,2))
- bam = bam.where(mask, drop=True)
- if 'sase' in key:
- name = f'sa{key[4]}_pId'
- elif key=='scs_ppl':
- name = 'ol_pId'
- else:
- name = 'bam_pId'
- bam = bam.rename({'BAMbunchId':name})
- mergeList.append(bam)
- mergeList.append(data.drop(dropList))
- ndata = xr.merge(mergeList, join='inner')
- for k in data.attrs.keys():
- ndata.attrs[k] = data.attrs[k]
- return ndata
diff --git a/src/toolbox_scs/misc/bunch_pattern_external.py b/src/toolbox_scs/misc/bunch_pattern_external.py
index 0a5ca3b..993b584 100644
--- a/src/toolbox_scs/misc/bunch_pattern_external.py
+++ b/src/toolbox_scs/misc/bunch_pattern_external.py
@@ -19,7 +19,7 @@ def _convert_data(bpt_dec):
bpt_conv = bpt_dec
if type(bpt_dec).__module__ == 'xarray.core.dataarray':
- bpt_conv = bpt_dec.where(bpt_dec.values == True, other = 0)
+ bpt_conv = bpt_dec.where(bpt_dec.values == True, other=0)
elif type(bpt_dec).__module__ == 'numpy':
bpt_conv = bpt_dec.astype(int)
else:
@@ -30,13 +30,42 @@ def _convert_data(bpt_dec):
return bpt_conv
+def is_pulse_at(bpt, loc):
+ """
+ Check for prescence of a pulse at the location provided.
+
+ Parameters
+ ----------
+ bpt : numpy array, xarray DataArray
+ The bunch pattern data.
+ loc : str
+ The location where to check: {'sase1', 'sase3', 'scs_ppl'}
+
+ Returns
+ -------
+ boolean : numpy array, xarray DataArray
+ true if a pulse is present at *loc*.
+ """
+ if loc == 'sase3':
+ bpt_dec = ebp.is_sase(bpt, 3)
+ elif loc == 'sase1':
+ bpt_dec = ebp.is_sase(bpt, 1)
+ elif loc == 'scs_ppl':
+ bpt_dec = ebp.is_laser(bpt, laser=PPL_SCS)
+ else:
+ raise ValueError(f'loc argument is {loc}, expected "sase1", ' +
+ '"sase3" or "scs_ppl"')
+
+ return _convert_data(bpt_dec)
+
+
def is_sase_3(bpt):
"""
Check for prescence of a SASE3 pulse.
Parameters
----------
- data : numpy array, xarray DataArray
+ bpt : numpy array, xarray DataArray
The bunch pattern data.
Returns
@@ -54,7 +83,7 @@ def is_sase_1(bpt):
Parameters
----------
- data : numpy array, xarray DataArray
+ bpt : numpy array, xarray DataArray
The bunch pattern data.
Returns
--
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