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#!/usr/bin/env python
#/*##########################################################################
# Copyright (C) 2019-2021 European Synchrotron Radiation Facility
#
# This file is part of the PyMca X-ray Fluorescence Toolkit developed at
# the ESRF by the Software group.
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
# in the Software without restriction, including without limitation the rights
# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
# copies of the Software, and to permit persons to whom the Software is
# furnished to do so, subject to the following conditions:
#
# The above copyright notice and this permission notice shall be included in
# all copies or substantial portions of the Software.
#
# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
# THE SOFTWARE.
#
#############################################################################*/
__author__ = "V.A. Sole - ESRF Data Analysis"
__contact__ = "sole@esrf.fr"
__license__ = "MIT"
__copyright__ = "European Synchrotron Radiation Facility, Grenoble, France"
from collections import OrderedDict
import logging
_logger = logging.getLogger(__name__)
from bliss.config import get_sessions_list
from bliss.config.settings import scan as rdsscan
from bliss.data.node import get_node, get_nodes
_NODE_TYPES = [ "channel",
"lima",
"node_ref_channel",
"scan",
"scan_group"]
def get_node_list(node, node_type=None, name=None, db_name=None, dimension=None,
filter=None, unique=False, reverse=False, ignore_underscore=True):
"""
Return list of nodes matching the given filter
"""
if not hasattr(node, "name"):
input_node = get_node(node)
else:
input_node = node
if hasattr(input_node, "walk"):
if reverse:
iterator = input_node.walk_from_last
else:
iterator = input_node.walk
else:
if reverse:
iterator = input_node.iterator.walk_from_last
else:
iterator = input_node.iterator.walk
if node_type:
if hasattr(node_type, "lower"):
node_type = node_type.lower()
if node_type not in _NODE_TYPES:
_logger.warning("Node type %s ignored" % node_type)
node_type = None
output_list = []
# walk not waiting
if node_type or name or db_name or dimension:
for node in iterator(wait=False, include_filter=filter):
if ignore_underscore and hasattr(node.name, "startswith") and node.name.startswith("_"):
continue
if not _check_dimension(node, dimension):
continue
if node_type and (node.type == node_type):
output_list.append(node)
elif name and (node.name == name):
output_list.append(node)
elif db_name and node.db_name == db_name:
output_list.append(node)
else:
output_list.append(node)
if unique and len(output_list):
break
else:
for node in iterator(wait=False, include_filter=filter):
#print(node.name, node.db_name, node)
if ignore_underscore and hasattr(node.name, "startswith") and node.name.startswith("_"):
continue
output_list.append(node)
if unique:
break
return output_list
def _check_dimension(node, dimension=None):
if dimension is None:
return True
elif not hasattr(node, "shape"):
return False
elif len(node.shape) == dimension:
return True
else:
return False
def get_session_scan_list(session, filename=None):
"""
Returns a sorted list of actual scans. Last scan is last.
"""
nodes = list(_get_session_scans(session))
try:
nodes = sorted(nodes, key=lambda k: k.info["start_timestamp"])
except KeyError:
# slower but safe method
if _logger.getEffectiveLevel() == logging.DEBUG:
for node in nodes:
if "start_timestamp" not in node.info:
_logger.debug("start_timestamp missing in <%s>" % node.name)
break
nodes = [node for node in nodes if "start_timestamp" in node.info]
nodes = sorted(nodes, key=lambda k: k.info["start_timestamp"])
if filename:
nodes = [node for node in nodes
if scan_info(node)["filename"] == filename]
return nodes
def _get_session_scans(session):
if hasattr(session, "name"):
session_node = session
session_name = session.name
else:
session_node = get_node(session)
session_name = session
db_names = rdsscan( f"{session_name}:*_children_list",
count=1000000,
connection=session_node.db_connection,
)
# we are interested on actual scans, therefore we do not take scans
# whose name starts by underscore
return ( node
for node in get_nodes(
*(db_name.replace("_children_list", "") for db_name in db_names)
)
if node is not None and node.type == "scan" and \
hasattr(node.name, "startswith") and not node.name.startswith("_")
)
def get_session_last_scan(session):
return get_session_scan_list(session)[-1]
def get_session_filename(session):
"""
Return filename associated to last session scan or an empty string
"""
try:
info = get_session_last_scan(session).info.get_all()
except:
_logger.warning("Error reading info from last scan")
_logger.warning("attempting slower method")
info = {}
scan_list = get_session_scan_list(session)
scan_list.reverse()
for scan in scan_list:
try:
info = scan.info.get_all()
except:
info = {}
if "filename" in info:
break
return info.get("filename", "")
def get_scan_list(session_node):
return get_node_list(session_node, node_type="scan", filter="scan")
def get_data_channels(node, unique=False):
return get_node_list(node, node_type="channel", filter="channel", dimension=0, unique=unique)
def get_spectrum_nodes(node, dimension=1, unique=False):
return get_node_list(node, node_type="channel", filter="channel", dimension=1, unique=unique)
def get_spectra(node, unique=False):
spectra_nodes = get_spectrum_nodes(node, unique=unique)
if len(spectra_nodes):
return [spectra_node.get_as_array(0, -1) for spectra_node in spectra_nodes]
else:
return []
def get_filename(session_node):
scan_list = get_scan_list(session_node)
filename = ""
if len(scan_list):
info = scan_info(scan_list[-1])
if "filename" in info:
filename = info["filename"]
return filename
def get_filenames(node):
filenames = []
if node.type == "scan":
info = scan_info(node)
if "filename" in info:
filenames.append(info["filename"])
else:
scan_list = get_scan_list(node)
for scan in scan_list:
info = scan_info(scan)
if "filename" in info:
filename = info["filename"]
if filename not in filenames:
filenames.append(filename)
return filenames
def get_last_spectrum_instances(session_node, offset=None):
sc = get_scan_list(session_node)
sc.reverse()
spectra = OrderedDict()
if offset is None:
if len(sc) > 10:
start = 10
else:
start = 0
else:
start = offset
for scan in sc:
sp = get_spectra(scan)
names = [(x, x.name) for x in sp]
for obj, name in names:
if name not in spectra:
print("adding name ", obj.db_name, " scan = ", scan.name)
spectra[name] = (obj, scan)
return spectra
def shortnamemap(names, separator=":"):
"""
Map full Redis names to short (but still unique) names
:param list(str) names:
:param str separator:
:returns dict:
"""
if not names:
return {}
names = set(names)
parts = [name.split(separator) for name in names]
nparts = max(map(len, parts))
parts = [([""] * (nparts - len(lst))) + lst for lst in parts]
ret = {}
for i in reversed(range(-nparts, 0)):
joinednames = [separator.join(s for s in lst[i:] if s) for lst in parts]
newnames = joinednames + list(ret.values())
selection = [
(idx, (separator.join(s for s in lst if s), name))
for idx, (name, lst) in enumerate(zip(joinednames, parts))
if newnames.count(name) == 1
]
if selection:
idx, tuples = list(zip(*selection))
ret.update(tuples)
parts = [lst for j, lst in enumerate(parts) if j not in idx]
return ret
def get_scan_data(scan_node, unique=False, top_master=False):
data_channels = get_data_channels(scan_node, unique=unique)
if top_master:
try:
top_master, channels = \
next(iter(scan_node.info["acquisition_chain"].items()))
if "scalars" in channels:
_logger.info("Taking only scalar data from top master")
data_channels = [x for x in data_channels \
if x.name in channels["scalars"]]
except:
_logger.warning("Cannot perform top_master filtering")
names = shortnamemap(x.name for x in data_channels)
result = {}
i = 0
for channel in data_channels:
# names :mon and :det from ID10 are badly mapped
if channel.name not in names and channel.name.startswith(":"):
short_name = names[channel.name[1:]]
else:
short_name = names[channel.name]
result[short_name] = channel.get_as_array(0, -1)
i += 1
return result
def scan_info(scan_node):
"""
See https://gitlab.esrf.fr/bliss/bliss/-/blob/master/bliss/data/display.py
def collect_channels_info(self, scan_info):
#------------- scan_info example -------------------------------------------------------
# session_name = scan_info.get('session_name') # ex: 'test_session'
# user_name = scan_info.get('user_name') # ex: 'pguillou'
# filename = scan_info.get('filename') # ex: '/mnt/c/tmp/test_session/data.h5'
# node_name = scan_info.get('node_name') # ex: 'test_session:mnt:c:tmp:183_ascan'
# start_time = scan_info.get('start_time') # ex: datetime.datetime(2019, 3, 18, 15, 28, 17, 83204)
# start_time_str = scan_info.get('start_time_str') # ex: 'Mon Mar 18 15:28:17 2019'
# start_timestamp = scan_info.get('start_timestamp') # ex: 1552919297.0832036
# save = scan_info.get('save') # ex: True
# sleep_time = scan_info.get('sleep_time') # ex: None
# title = scan_info.get('title') # ex: 'ascan roby 0 10 10 0.01'
# scan_type = scan_info.get('type') # ex: ^
# start = scan_info.get('start') # ex: ^ = [0]
# stop = scan_info.get('stop') # ex: ^ = [10]
# npoints = scan_info.get('npoints') # ex: ^ = 10
# count_time = scan_info.get('count_time') # ex: ^ = 0.01
# total_acq_time = scan_info.get('total_acq_time') # ex: 0.1 ( = npoints * count_time )
# scan_nb = scan_info.get('scan_nb') # ex: 183
# positioners_dial = scan_info.get('positioners_dial') # ex: {'bad': 0.0, 'calc_mot1': 20.0, 'roby': 20.0, ... }
# positioners = scan_info.get('positioners') # ex: {'bad': 0.0, 'calc_mot1': 20.0, 'roby': 10.0, ...}
# acquisition_chain = scan_info.get('acquisition_chain')
# ex: {'axis':
# {
# 'master' : {'scalars': ['axis:roby'], 'spectra': [], 'images': [] },
# 'scalars': ['timer:elapsed_time', 'diode:diode'],
# 'spectra': [],
# 'images' : []
# }
# }
# master, channels = next(iter(scan_info["acquisition_chain"].items()))
# master = axis
# channels = {'master': {'scalars': ['axis:roby'],
# 'scalars_units': {'axis:roby': None},
# 'spectra': [],
# 'images': [],
# 'display_names': {'axis:roby': 'roby'}
# },
# 'scalars': ['timer:elapsed_time',
# 'timer:epoch',
# 'lima_simulator2:bpm:x',
# 'simulation_diode_sampling_controller:diode'],
#
# 'scalars_units': {'timer:elapsed_time': 's',
# 'timer:epoch': 's',
# 'lima_simulator2:bpm:x': 'px',
# 'simulation_diode_sampling_controller:diode': None},
# 'spectra': [],
# 'images': [],
# 'display_names': {'timer:elapsed_time': 'elapsed_time',
# 'timer:epoch': 'epoch',
# 'lima_simulator2:bpm:x': 'x',
# 'simulation_diode_sampling_controller:diode': 'diode'}}
# ONLY MANAGE THE FIRST ACQUISITION BRANCH (multi-top-masters scan are ignored)
top_master, channels = next(iter(scan_info["acquisition_chain"].items()))
"""
return scan_node.info.get_all()
if __name__ == "__main__":
import sys
# get the available sessions
scan_number = None
reference = None
_logger.setLevel(logging.DEBUG)
if len(sys.argv) > 1:
sessions = [sys.argv[1]]
if len(sys.argv) > 2:
scan_number = sys.argv[2]
else:
sessions = get_sessions_list()
for session_name in sessions:
print("SESSION <%s>" % session_name)
#connection = client.get_redis_connection(db=1)
#while not DataNode.exists(session_name, None, connection):
# gevent.sleep(1)
# get node
session_node = get_node(session_name)
if not session_node:
print("\tNot Available")
continue
scans = get_session_scan_list(session_node)
for scan in scans:
filenames = get_filenames(scan)
nFiles = len(filenames)
if not nFiles:
filename = "No FILE"
else:
if nFiles > 1:
print("WARNING, more than one file associated to scan")
filename = filenames[-1]
sInfo = scan_info(scan)
print(list(sInfo.keys()))
title = sInfo.get("title", "No COMMAND")
if scan_number:
if scan.name.startswith("161"):
reference = scan
else:
print("\t%s %s %s" % (scan.name, filename, title))
if len(sessions) == 1:
if reference:
scan = reference
else:
scan = scans[-1]
print("SCAN = %s" % scan)
print("NAME = %s" % scan.name)
print("TITLE = %s" % scan_info(scan).get("title", "No COMMAND"))
print("ACQUISITION_CHAIN = ", scan_info(scan).get("acquisition_chain", None))
#for master in scan_info(scan)["acquisition_chain"]:
# print(" master = ", master)
# print(" channels = ", list(scan_info(scan)[master].keys()))
top_master, channels = next(iter(scan.info["acquisition_chain"].items()))
print("N counters devices = ", len(channels["spectra"]))
print("N Mca devices = ", len(channels["spectra"]))
print(top_master)
print(channels)
sys.exit(0)
counters = get_data_channels(scan)
#for counter in counters:
# print(counter.name, counter.short_name, counter.dtype, counter.type, counter.info, counter.get_as_array(0, -1))
print(get_scan_data(scan))
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