def analyse_n_cluster_per_event(scan_base,
include_no_cluster=False,
time_line_absolute=True,
combine_n_readouts=1000,
chunk_size=10000000,
plot_n_cluster_hists=False,
output_pdf=None,
output_file=None):
''' Determines the number of cluster per event as a function of time. Therefore the data of a fixed number of read outs are combined ('combine_n_readouts').
Parameters
----------
scan_base: list of str
scan base names (e.g.: ['//data//SCC_50_fei4_self_trigger_scan_390', ]
include_no_cluster: bool
Set to true to also consider all events without any hit.
combine_n_readouts: int
the number of read outs to combine (e.g. 1000)
max_chunk_size: int
the maximum chunk size used during read, if too big memory error occurs, if too small analysis takes longer
output_pdf: PdfPages
PdfPages file object, if none the plot is printed to screen
'''
time_stamp = []
n_cluster = []
start_time_set = False
for data_file in scan_base:
with tb.open_file(data_file + '_interpreted.h5',
mode="r+") as in_cluster_file_h5:
# get data and data pointer
meta_data_array = in_cluster_file_h5.root.meta_data[:]
cluster_table = in_cluster_file_h5.root.Cluster
# determine the event ranges to analyze (timestamp_start, start_event_number, stop_event_number)
parameter_ranges = np.column_stack(
(analysis_utils.get_ranges_from_array(
meta_data_array['timestamp_start'][::combine_n_readouts]),
analysis_utils.get_ranges_from_array(
meta_data_array['event_number'][::combine_n_readouts])))
# create a event_numer index (important for speed)
analysis_utils.index_event_number(cluster_table)
# initialize the analysis and set settings
analyze_data = AnalyzeRawData()
analyze_data.create_tot_hist = False
analyze_data.create_bcid_hist = False
# variables for read speed up
index = 0 # index where to start the read out, 0 at the beginning, increased during looping
best_chunk_size = chunk_size
total_cluster = cluster_table.shape[0]
progress_bar = progressbar.ProgressBar(widgets=[
'',
progressbar.Percentage(), ' ',
progressbar.Bar(marker='*', left='|', right='|'), ' ',
progressbar.AdaptiveETA()
],
maxval=total_cluster,
term_width=80)
progress_bar.start()
# loop over the selected events
for parameter_index, parameter_range in enumerate(
parameter_ranges):
logging.debug('Analyze time stamp ' + str(parameter_range[0]) +
' and data from events = [' +
str(parameter_range[2]) + ',' +
str(parameter_range[3]) + '[ ' + str(
int(
float(
float(parameter_index) /
float(len(parameter_ranges)) *
100.0))) + '%')
analyze_data.reset() # resets the data of the last analysis
# loop over the cluster in the actual selected events with optimizations: determine best chunk size, start word index given
readout_cluster_len = 0 # variable to calculate a optimal chunk size value from the number of hits for speed up
hist = None
for clusters, index in analysis_utils.data_aligned_at_events(
cluster_table,
start_event_number=parameter_range[2],
stop_event_number=parameter_range[3],
start_index=index,
chunk_size=best_chunk_size):
n_cluster_per_event = analysis_utils.get_n_cluster_in_events(
clusters['event_number']
)[:,
1] # array with the number of cluster per event, cluster per event are at least 1
if hist is None:
hist = np.histogram(n_cluster_per_event,
bins=10,
range=(0, 10))[0]
else:
hist = np.add(
hist,
np.histogram(n_cluster_per_event,
bins=10,
range=(0, 10))[0])
if include_no_cluster and parameter_range[
3] is not None: # happend for the last readout
hist[0] = (parameter_range[3] -
parameter_range[2]) - len(
n_cluster_per_event
) # add the events without any cluster
readout_cluster_len += clusters.shape[0]
total_cluster -= len(clusters)
progress_bar.update(index)
best_chunk_size = int(1.5 * readout_cluster_len) if int(
1.05 * readout_cluster_len
) < chunk_size else chunk_size # to increase the readout speed, estimated the number of hits for one read instruction
if plot_n_cluster_hists:
plotting.plot_1d_hist(
hist,
title='Number of cluster per event at ' +
str(parameter_range[0]),
x_axis_title='Number of cluster',
y_axis_title='#',
log_y=True,
filename=output_pdf)
hist = hist.astype('f4') / np.sum(
hist) # calculate fraction from total numbers
if time_line_absolute:
time_stamp.append(parameter_range[0])
else:
if not start_time_set:
start_time = parameter_ranges[0, 0]
start_time_set = True
time_stamp.append((parameter_range[0] - start_time) / 60.0)
n_cluster.append(hist)
progress_bar.finish()
if total_cluster != 0:
logging.warning(
'Not all clusters were selected during analysis. Analysis is therefore not exact'
)
if time_line_absolute:
plotting.plot_scatter_time(
time_stamp,
n_cluster,
title='Number of cluster per event as a function of time',
marker_style='o',
filename=output_pdf,
legend=('0 cluster', '1 cluster', '2 cluster',
'3 cluster') if include_no_cluster else
('0 cluster not plotted', '1 cluster', '2 cluster', '3 cluster'))
else:
plotting.plot_scatter(
time_stamp,
n_cluster,
title='Number of cluster per event as a function of time',
x_label='time [min.]',
marker_style='o',
filename=output_pdf,
legend=('0 cluster', '1 cluster', '2 cluster',
'3 cluster') if include_no_cluster else
('0 cluster not plotted', '1 cluster', '2 cluster', '3 cluster'))
if output_file:
with tb.open_file(output_file, mode="a") as out_file_h5:
cluster_array = np.array(n_cluster)
rec_array = np.array(zip(time_stamp, cluster_array[:, 0],
cluster_array[:, 1], cluster_array[:, 2],
cluster_array[:, 3], cluster_array[:, 4],
cluster_array[:, 5]),
dtype=[('time_stamp', float),
('cluster_0', float),
('cluster_1', float),
('cluster_2', float),
('cluster_3', float),
('cluster_4', float),
('cluster_5', float)
]).view(np.recarray)
try:
n_cluster_table = out_file_h5.create_table(
out_file_h5.root,
name='n_cluster',
description=rec_array,
title='Cluster per event',
filters=tb.Filters(complib='blosc',
complevel=5,
fletcher32=False))
n_cluster_table[:] = rec_array
except tb.exceptions.NodeError:
logging.warning(
output_file +
' has already a Beamspot note, do not overwrite existing.')
return time_stamp, n_cluster
def analyse_n_cluster_per_event(
scan_base,
include_no_cluster=False,
time_line_absolute=True,
combine_n_readouts=1000,
chunk_size=10000000,
plot_n_cluster_hists=False,
output_pdf=None,
output_file=None,
):
""" Determines the number of cluster per event as a function of time. Therefore the data of a fixed number of read outs are combined ('combine_n_readouts').
Parameters
----------
scan_base: list of str
scan base names (e.g.: ['//data//SCC_50_fei4_self_trigger_scan_390', ]
include_no_cluster: bool
Set to true to also consider all events without any hit.
combine_n_readouts: int
the number of read outs to combine (e.g. 1000)
max_chunk_size: int
the maximum chunk size used during read, if too big memory error occurs, if too small analysis takes longer
output_pdf: PdfPages
PdfPages file object, if none the plot is printed to screen
"""
time_stamp = []
n_cluster = []
start_time_set = False
for data_file in scan_base:
with tb.openFile(data_file + "_interpreted.h5", mode="r+") as in_cluster_file_h5:
# get data and data pointer
meta_data_array = in_cluster_file_h5.root.meta_data[:]
cluster_table = in_cluster_file_h5.root.Cluster
# determine the event ranges to analyze (timestamp_start, start_event_number, stop_event_number)
parameter_ranges = np.column_stack(
(
analysis_utils.get_ranges_from_array(meta_data_array["timestamp_start"][::combine_n_readouts]),
analysis_utils.get_ranges_from_array(meta_data_array["event_number"][::combine_n_readouts]),
)
)
# create a event_numer index (important for speed)
analysis_utils.index_event_number(cluster_table)
# initialize the analysis and set settings
analyze_data = AnalyzeRawData()
analyze_data.create_tot_hist = False
analyze_data.create_bcid_hist = False
# variables for read speed up
index = 0 # index where to start the read out, 0 at the beginning, increased during looping
best_chunk_size = chunk_size
total_cluster = cluster_table.shape[0]
progress_bar = progressbar.ProgressBar(
widgets=[
"",
progressbar.Percentage(),
" ",
progressbar.Bar(marker="*", left="|", right="|"),
" ",
analysis_utils.ETA(),
],
maxval=total_cluster,
term_width=80,
)
progress_bar.start()
# loop over the selected events
for parameter_index, parameter_range in enumerate(parameter_ranges):
logging.debug(
"Analyze time stamp "
+ str(parameter_range[0])
+ " and data from events = ["
+ str(parameter_range[2])
+ ","
+ str(parameter_range[3])
+ "[ "
+ str(int(float(float(parameter_index) / float(len(parameter_ranges)) * 100.0)))
+ "%"
)
analyze_data.reset() # resets the data of the last analysis
# loop over the cluster in the actual selected events with optimizations: determine best chunk size, start word index given
readout_cluster_len = (
0
) # variable to calculate a optimal chunk size value from the number of hits for speed up
hist = None
for clusters, index in analysis_utils.data_aligned_at_events(
cluster_table,
start_event_number=parameter_range[2],
stop_event_number=parameter_range[3],
start=index,
chunk_size=best_chunk_size,
):
n_cluster_per_event = analysis_utils.get_n_cluster_in_events(clusters["event_number"])[
:, 1
] # array with the number of cluster per event, cluster per event are at least 1
if hist is None:
hist = np.histogram(n_cluster_per_event, bins=10, range=(0, 10))[0]
else:
hist = np.add(hist, np.histogram(n_cluster_per_event, bins=10, range=(0, 10))[0])
if include_no_cluster and parameter_range[3] is not None: # happend for the last readout
hist[0] = (parameter_range[3] - parameter_range[2]) - len(
n_cluster_per_event
) # add the events without any cluster
readout_cluster_len += clusters.shape[0]
total_cluster -= len(clusters)
progress_bar.update(index)
best_chunk_size = (
int(1.5 * readout_cluster_len) if int(1.05 * readout_cluster_len) < chunk_size else chunk_size
) # to increase the readout speed, estimated the number of hits for one read instruction
if plot_n_cluster_hists:
plotting.plot_1d_hist(
hist,
title="Number of cluster per event at " + str(parameter_range[0]),
x_axis_title="Number of cluster",
y_axis_title="#",
log_y=True,
filename=output_pdf,
)
hist = hist.astype("f4") / np.sum(hist) # calculate fraction from total numbers
if time_line_absolute:
time_stamp.append(parameter_range[0])
else:
if not start_time_set:
start_time = parameter_ranges[0, 0]
start_time_set = True
time_stamp.append((parameter_range[0] - start_time) / 60.0)
n_cluster.append(hist)
progress_bar.finish()
if total_cluster != 0:
logging.warning("Not all clusters were selected during analysis. Analysis is therefore not exact")
if time_line_absolute:
plotting.plot_scatter_time(
time_stamp,
n_cluster,
title="Number of cluster per event as a function of time",
marker_style="o",
filename=output_pdf,
legend=("0 cluster", "1 cluster", "2 cluster", "3 cluster")
if include_no_cluster
else ("0 cluster not plotted", "1 cluster", "2 cluster", "3 cluster"),
)
else:
plotting.plot_scatter(
time_stamp,
n_cluster,
title="Number of cluster per event as a function of time",
x_label="time [min.]",
marker_style="o",
filename=output_pdf,
legend=("0 cluster", "1 cluster", "2 cluster", "3 cluster")
if include_no_cluster
else ("0 cluster not plotted", "1 cluster", "2 cluster", "3 cluster"),
)
if output_file:
with tb.openFile(output_file, mode="a") as out_file_h5:
cluster_array = np.array(n_cluster)
rec_array = np.array(
zip(
time_stamp,
cluster_array[:, 0],
cluster_array[:, 1],
cluster_array[:, 2],
cluster_array[:, 3],
cluster_array[:, 4],
cluster_array[:, 5],
),
dtype=[
("time_stamp", float),
("cluster_0", float),
("cluster_1", float),
("cluster_2", float),
("cluster_3", float),
("cluster_4", float),
("cluster_5", float),
],
).view(np.recarray)
try:
n_cluster_table = out_file_h5.createTable(
out_file_h5.root,
name="n_cluster",
description=rec_array,
title="Cluster per event",
filters=tb.Filters(complib="blosc", complevel=5, fletcher32=False),
)
n_cluster_table[:] = rec_array
except tb.exceptions.NodeError:
logging.warning(output_file + " has already a Beamspot note, do not overwrite existing.")
return time_stamp, n_cluster
def analyze_beam_spot(scan_base,
combine_n_readouts=1000,
chunk_size=10000000,
plot_occupancy_hists=False,
output_pdf=None,
output_file=None):
''' Determines the mean x and y beam spot position as a function of time. Therefore the data of a fixed number of read outs are combined ('combine_n_readouts'). The occupancy is determined
for the given combined events and stored into a pdf file. At the end the beam x and y is plotted into a scatter plot with absolute positions in um.
Parameters
----------
scan_base: list of str
scan base names (e.g.: ['//data//SCC_50_fei4_self_trigger_scan_390', ]
combine_n_readouts: int
the number of read outs to combine (e.g. 1000)
max_chunk_size: int
the maximum chunk size used during read, if too big memory error occurs, if too small analysis takes longer
output_pdf: PdfPages
PdfPages file object, if none the plot is printed to screen
'''
time_stamp = []
x = []
y = []
for data_file in scan_base:
with tb.open_file(data_file + '_interpreted.h5',
mode="r+") as in_hit_file_h5:
# get data and data pointer
meta_data_array = in_hit_file_h5.root.meta_data[:]
hit_table = in_hit_file_h5.root.Hits
# determine the event ranges to analyze (timestamp_start, start_event_number, stop_event_number)
parameter_ranges = np.column_stack(
(analysis_utils.get_ranges_from_array(
meta_data_array['timestamp_start'][::combine_n_readouts]),
analysis_utils.get_ranges_from_array(
meta_data_array['event_number'][::combine_n_readouts])))
# create a event_numer index (important)
analysis_utils.index_event_number(hit_table)
# initialize the analysis and set settings
analyze_data = AnalyzeRawData()
analyze_data.create_tot_hist = False
analyze_data.create_bcid_hist = False
analyze_data.histogram.set_no_scan_parameter()
# variables for read speed up
index = 0 # index where to start the read out, 0 at the beginning, increased during looping
best_chunk_size = chunk_size
progress_bar = progressbar.ProgressBar(widgets=[
'',
progressbar.Percentage(), ' ',
progressbar.Bar(marker='*', left='|', right='|'), ' ',
progressbar.AdaptiveETA()
],
maxval=hit_table.shape[0],
term_width=80)
progress_bar.start()
# loop over the selected events
for parameter_index, parameter_range in enumerate(
parameter_ranges):
logging.debug('Analyze time stamp ' + str(parameter_range[0]) +
' and data from events = [' +
str(parameter_range[2]) + ',' +
str(parameter_range[3]) + '[ ' + str(
int(
float(
float(parameter_index) /
float(len(parameter_ranges)) *
100.0))) + '%')
analyze_data.reset() # resets the data of the last analysis
# loop over the hits in the actual selected events with optimizations: determine best chunk size, start word index given
readout_hit_len = 0 # variable to calculate a optimal chunk size value from the number of hits for speed up
for hits, index in analysis_utils.data_aligned_at_events(
hit_table,
start_event_number=parameter_range[2],
stop_event_number=parameter_range[3],
start_index=index,
chunk_size=best_chunk_size):
analyze_data.analyze_hits(
hits) # analyze the selected hits in chunks
readout_hit_len += hits.shape[0]
progress_bar.update(index)
best_chunk_size = int(1.5 * readout_hit_len) if int(
1.05 * readout_hit_len
) < chunk_size else chunk_size # to increase the readout speed, estimated the number of hits for one read instruction
# get and store results
occupancy_array = analyze_data.histogram.get_occupancy()
projection_x = np.sum(occupancy_array, axis=0).ravel()
projection_y = np.sum(occupancy_array, axis=1).ravel()
x.append(
analysis_utils.get_mean_from_histogram(projection_x,
bin_positions=range(
0, 80)))
y.append(
analysis_utils.get_mean_from_histogram(projection_y,
bin_positions=range(
0, 336)))
time_stamp.append(parameter_range[0])
if plot_occupancy_hists:
plotting.plot_occupancy(
occupancy_array[:, :, 0],
title='Occupancy for events between ' + time.strftime(
'%H:%M:%S', time.localtime(parameter_range[0])) +
' and ' + time.strftime(
'%H:%M:%S', time.localtime(parameter_range[1])),
filename=output_pdf)
progress_bar.finish()
plotting.plot_scatter([i * 250 for i in x], [i * 50 for i in y],
title='Mean beam position',
x_label='x [um]',
y_label='y [um]',
marker_style='-o',
filename=output_pdf)
if output_file:
with tb.open_file(output_file, mode="a") as out_file_h5:
rec_array = np.array(zip(time_stamp, x, y),
dtype=[('time_stamp', float), ('x', float),
('y', float)])
try:
beam_spot_table = out_file_h5.create_table(
out_file_h5.root,
name='Beamspot',
description=rec_array,
title='Beam spot position',
filters=tb.Filters(complib='blosc',
complevel=5,
fletcher32=False))
beam_spot_table[:] = rec_array
except tb.exceptions.NodeError:
logging.warning(
output_file +
' has already a Beamspot note, do not overwrite existing.')
return time_stamp, x, y
def analyze_beam_spot(
scan_base,
combine_n_readouts=1000,
chunk_size=10000000,
plot_occupancy_hists=False,
output_pdf=None,
output_file=None,
):
""" Determines the mean x and y beam spot position as a function of time. Therefore the data of a fixed number of read outs are combined ('combine_n_readouts'). The occupancy is determined
for the given combined events and stored into a pdf file. At the end the beam x and y is plotted into a scatter plot with absolute positions in um.
Parameters
----------
scan_base: list of str
scan base names (e.g.: ['//data//SCC_50_fei4_self_trigger_scan_390', ]
combine_n_readouts: int
the number of read outs to combine (e.g. 1000)
max_chunk_size: int
the maximum chunk size used during read, if too big memory error occurs, if too small analysis takes longer
output_pdf: PdfPages
PdfPages file object, if none the plot is printed to screen
"""
time_stamp = []
x = []
y = []
for data_file in scan_base:
with tb.openFile(data_file + "_interpreted.h5", mode="r+") as in_hit_file_h5:
# get data and data pointer
meta_data_array = in_hit_file_h5.root.meta_data[:]
hit_table = in_hit_file_h5.root.Hits
# determine the event ranges to analyze (timestamp_start, start_event_number, stop_event_number)
parameter_ranges = np.column_stack(
(
analysis_utils.get_ranges_from_array(meta_data_array["timestamp_start"][::combine_n_readouts]),
analysis_utils.get_ranges_from_array(meta_data_array["event_number"][::combine_n_readouts]),
)
)
# create a event_numer index (important)
analysis_utils.index_event_number(hit_table)
# initialize the analysis and set settings
analyze_data = AnalyzeRawData()
analyze_data.create_tot_hist = False
analyze_data.create_bcid_hist = False
analyze_data.histograming.set_no_scan_parameter()
# variables for read speed up
index = 0 # index where to start the read out, 0 at the beginning, increased during looping
best_chunk_size = chunk_size
progress_bar = progressbar.ProgressBar(
widgets=[
"",
progressbar.Percentage(),
" ",
progressbar.Bar(marker="*", left="|", right="|"),
" ",
analysis_utils.ETA(),
],
maxval=hit_table.shape[0],
term_width=80,
)
progress_bar.start()
# loop over the selected events
for parameter_index, parameter_range in enumerate(parameter_ranges):
logging.debug(
"Analyze time stamp "
+ str(parameter_range[0])
+ " and data from events = ["
+ str(parameter_range[2])
+ ","
+ str(parameter_range[3])
+ "[ "
+ str(int(float(float(parameter_index) / float(len(parameter_ranges)) * 100.0)))
+ "%"
)
analyze_data.reset() # resets the data of the last analysis
# loop over the hits in the actual selected events with optimizations: determine best chunk size, start word index given
readout_hit_len = (
0
) # variable to calculate a optimal chunk size value from the number of hits for speed up
for hits, index in analysis_utils.data_aligned_at_events(
hit_table,
start_event_number=parameter_range[2],
stop_event_number=parameter_range[3],
start=index,
chunk_size=best_chunk_size,
):
analyze_data.analyze_hits(hits) # analyze the selected hits in chunks
readout_hit_len += hits.shape[0]
progress_bar.update(index)
best_chunk_size = (
int(1.5 * readout_hit_len) if int(1.05 * readout_hit_len) < chunk_size else chunk_size
) # to increase the readout speed, estimated the number of hits for one read instruction
# get and store results
occupancy_array = analyze_data.histograming.get_occupancy()
projection_x = np.sum(occupancy_array, axis=0).ravel()
projection_y = np.sum(occupancy_array, axis=1).ravel()
x.append(analysis_utils.get_mean_from_histogram(projection_x, bin_positions=range(0, 80)))
y.append(analysis_utils.get_mean_from_histogram(projection_y, bin_positions=range(0, 336)))
time_stamp.append(parameter_range[0])
if plot_occupancy_hists:
plotting.plot_occupancy(
occupancy_array[:, :, 0],
title="Occupancy for events between "
+ time.strftime("%H:%M:%S", time.localtime(parameter_range[0]))
+ " and "
+ time.strftime("%H:%M:%S", time.localtime(parameter_range[1])),
filename=output_pdf,
)
progress_bar.finish()
plotting.plot_scatter(
[i * 250 for i in x],
[i * 50 for i in y],
title="Mean beam position",
x_label="x [um]",
y_label="y [um]",
marker_style="-o",
filename=output_pdf,
)
if output_file:
with tb.openFile(output_file, mode="a") as out_file_h5:
rec_array = np.array(zip(time_stamp, x, y), dtype=[("time_stamp", float), ("x", float), ("y", float)])
try:
beam_spot_table = out_file_h5.createTable(
out_file_h5.root,
name="Beamspot",
description=rec_array,
title="Beam spot position",
filters=tb.Filters(complib="blosc", complevel=5, fletcher32=False),
)
beam_spot_table[:] = rec_array
except tb.exceptions.NodeError:
logging.warning(output_file + " has already a Beamspot note, do not overwrite existing.")
return time_stamp, x, y
