def set_calibration_params(self, cmdline=None):
if not cmdline:
cmdline = []
try:
params, unk = calibration_parameters(cmdline,
self.input_file.origin)
except KeyError:
params = None
self.calib_params = params
def main():
script = os.path.splitext(os.path.basename(__file__))[0]
log.info("[SCRIPT] {}".format(script))
parser = argparse.ArgumentParser(
description='Display each event in the file')
parser.add_argument('-f',
'--file',
dest='input_path',
action='store',
default=get_path('gamma_test.simtel.gz'),
help='path to the input file. '
'Default = gamma_test.simtel.gz')
parser.add_argument('-O',
'--origin',
dest='origin',
action='store',
default='hessio',
help='origin of the file: {}. Default = hessio'.format(
InputFile.origin_list()))
parser.add_argument('-D',
dest='display',
action='store_true',
default=False,
help='display the camera events')
parser.add_argument('--pdf',
dest='output_path',
action='store',
default=None,
help='path to store a pdf output of the plots')
parser.add_argument('-t',
'--telescope',
dest='tel',
action='store',
type=int,
default=None,
help='telecope to view. '
'Default = All')
calibration_arguments(parser)
logger_detail = parser.add_mutually_exclusive_group()
logger_detail.add_argument('-q',
'--quiet',
dest='quiet',
action='store_true',
default=False,
help='Quiet mode')
logger_detail.add_argument('-v',
'--verbose',
dest='verbose',
action='store_true',
default=False,
help='Verbose mode')
logger_detail.add_argument('-d',
'--debug',
dest='debug',
action='store_true',
default=False,
help='Debug mode')
args = parser.parse_args()
print('DEBUG type(args) {}'.format(type(args)))
print('DEBUG args {}'.format(args))
params = calibration_parameters(args)
if args.quiet:
log.setLevel(40)
if args.verbose:
log.setLevel(20)
if args.debug:
log.setLevel(10)
log.debug("[file] Reading file")
input_file = InputFile(args.input_path, args.origin)
source = input_file.read()
# geom_dict is a dictionary of CameraGeometry, with keys of
# (num_pixels, focal_length), the parameters that are used to guess the
# geometry of the telescope. By using these keys, the geometry is
# calculated only once per telescope type as needed, reducing computation
# time.
# Creating a geom_dict at this point is optional, but is recommended, as
# the same geom_dict can then be shared between the calibration and
# CameraPlotter, again reducing computation time.
# The dictionary becomes filled as a result of a dictionary's mutable
# nature.
geom_dict = {}
# Calibrate events and fill geom_dict
calibrated_source = calibrate_source(source, params, geom_dict)
fig = plt.figure(figsize=(16, 7))
if args.display:
plt.show(block=False)
pp = PdfPages(args.output_path) if args.output_path is not None else None
for event in calibrated_source:
tels = list(event.dl0.tels_with_data)
if args.tel is None:
tel_loop = tels
else:
if args.tel not in tels:
continue
tel_loop = [args.tel]
log.debug(tels)
for tel_id in tel_loop:
display_telescope(event, tel_id, args.display, geom_dict, pp, fig)
if pp is not None:
pp.close()
log.info("[COMPLETE]")
def calculate_charge_resolutions(parser, chargeres_cmdlines):
run = 0
num_runs = len(chargeres_cmdlines)
chargeres_dict = {}
for name, cmdline in chargeres_cmdlines.items():
args, excess_args = parser.parse_known_args(cmdline)
run += 1
log.info("[run] Calculating charge resolution {}/{}"
.format(run, num_runs))
# Print event/args values
log.info("[files] {}".format(args.input_paths))
telescopes = "All" if args.tel is None else args.tel
log.info("[origin] {}".format(args.origin))
log.info("[telescopes] {}".format(telescopes))
# Obtain InputFiles (to check files exist)
input_file_list = []
for filepath in args.input_paths:
tilde_filepath = os.path.expanduser(filepath)
for globfile in glob.glob(tilde_filepath):
input_file_list.append(InputFile(globfile, args.origin))
# Find maxpe
maxpe = args.maxpe
if maxpe is None:
maxpe = 0
for input_file in input_file_list:
file_maxpe = input_file.find_max_true_npe(args.tel)
if file_maxpe > maxpe:
maxpe = file_maxpe
log.info("[maxpe] {}".format(maxpe))
params, unknown_args = calibration_parameters(excess_args,
args.origin,
args.calib_help)
chargeres = ChargeResolution(maxpe)
for input_file in input_file_list:
source = input_file.read()
calibrated_source = calibrate_source(source, params)
chargeres.add_source(calibrated_source, args.tel)
# Plot comparison graphs
if args.comparison is not None:
hist = chargeres.variation_hist
hist[hist == 0.0] = np.nan
xedges = chargeres.variation_xedges
yedges = chargeres.variation_yedges
fig = plt.figure(figsize=(10, 7))
ax = fig.add_subplot(111)
ax.set_title(name)
x, y = np.meshgrid(xedges, yedges)
x = np.power(10, x)
y = np.power(10, y)
hist_mask = np.ma.masked_where(np.isnan(hist), hist)
im = ax.pcolormesh(x, y, hist_mask, norm=LogNorm(),
cmap=plt.cm.viridis)
cb = plt.colorbar(im)
ax.set_aspect('equal')
ax.grid()
ax.set_xscale('log')
ax.set_yscale('log')
ax.set_xlabel(r'True Charge $Q_T$ (p.e.)')
ax.set_ylabel(r'Measured Charge $Q_M$ (p.e.)')
cb.ax.set_ylabel("Count")
line = np.linspace(*ax.get_xlim(), 100)
ax.plot(line, line, c='0.75', ls='--')
# Add minor ticks
lmin = floor(log10(hist_mask.min()))
lmax = ceil(log10(hist_mask.max()))
logticks = np.tile(np.arange(lmin, 10), lmax) * (
np.power(10, np.arange(lmax * 10) // 10))
logticks = im.norm(logticks[(logticks != 0) &
(logticks >= hist_mask.min()) &
(logticks <= hist_mask.max())])
cb.ax.yaxis.set_ticks(logticks, minor=True)
cb.ax.yaxis.set_tick_params(which='minor', length=5)
cb.ax.tick_params(length=10)
args.comparison = os.path.expanduser(args.comparison)
output_dir = dirname(args.comparison)
if not os.path.exists(output_dir):
log.info("[output] Creating directory: {}".format(output_dir))
os.makedirs(output_dir)
log.info("[output] {}".format(args.comparison))
warnings.filterwarnings("ignore", module="matplotlib")
with warnings.catch_warnings():
warnings.simplefilter("ignore")
fig.savefig(args.comparison, bbox_inches='tight')
chargeres_dict[name] = chargeres
log.info('[run] Charge resolution calculations finished')
return chargeres_dict
def argparsing():
parser = argparse.ArgumentParser(
formatter_class=argparse.ArgumentDefaultsHelpFormatter)
parser.add_argument('-f', '--file', dest='input_paths',
default=[get_path('gamma_test.simtel.gz')], nargs='*',
help='path to the input files to be combined for a '
'single charge resolution.')
parser.add_argument('-O', '--origin', dest='origin', action='store',
choices=InputFile.origin_list(),
default='hessio', help='origin of the file')
parser.add_argument('-t', '--telescope', dest='tel', action='store',
type=int, default=None, nargs='*',
help='list of telecopes to be included. '
'Default = All')
parser.add_argument('-o', '--output', dest='output_path', action='store',
default=None,
help='path to store a pdf output of the plots. '
'default = display on screen instead')
parser.add_argument('--comparison', dest='comparison', action='store',
default=None,
help='output path for a True Charge versus Measured'
'Charge graph. Default = do not plot graph')
parser.add_argument('-M', '--maxpe', dest='maxpe', action='store',
default=None, type=float,
help='maximum pe to calculate the charge resolution'
' up to. Default = maximum pe in file')
parser.add_argument('--maxpeplot', dest='maxpeplot', action='store',
default=None, type=float,
help='maximum pe to plot up to. Default = maxpe')
parser.add_argument('-B', '--binning', dest='binning', action='store',
default="log", choices=['none', 'normal', 'log'],
help='binning of the charge resoltion graph: '
'"none" = no binning, "normal" = bin, '
'"log" = bin in log space.')
parser.add_argument('--normalx', dest='normalx', action='store_true',
default=False,
help='Use a normal x axis instead of the defualt log'
'axis')
parser.add_argument('--normaly', dest='normaly', action='store_true',
default=False,
help='Use a normal y axis instead of the defualt log'
'axis')
parser.add_argument('-E', '--example', dest='example', action='store_true',
default=False,
help='print an example runcard')
parser.add_argument('-R', '--runcard', dest='runcard', action='store',
default=None,
help='path to a runcard text file with arguments that '
'override command line arguments. This run card '
'can allow complex combinations of files and '
'calibrations to compare the charge resolution '
'against each other.')
parser.add_argument('--chargeres-names', dest='chargeres_names',
default=['default'], nargs='*',
help='chargres calculation to include in plot. '
'Only used for runcards.')
parser.add_argument('--calib-help', dest='calib_help', action='store_true',
default=False,
help='display the arguments used for the camera '
'calibration')
logger_detail = parser.add_mutually_exclusive_group()
logger_detail.add_argument('-q', '--quiet', dest='quiet',
action='store_true', default=False,
help='Quiet mode')
logger_detail.add_argument('-v', '--verbose', dest='verbose',
action='store_true', default=False,
help='Verbose mode')
logger_detail.add_argument('-d', '--debug', dest='debug',
action='store_true', default=False,
help='Debug mode')
args, excess_args = parser.parse_known_args()
if args.quiet:
log.setLevel(40)
if args.verbose:
log.setLevel(20)
if args.debug:
log.setLevel(10)
if args.calib_help:
params, unknown_args = calibration_parameters(excess_args,
args.origin,
args.calib_help)
if args.example:
print("""
# Each charge resolution block starts with [chargeres] and the names for
# this charge resolution.
# The options in each block are equivalent to the scripts help message.
# Options that seem to apply to plotting will only have effect in a
# plotting block.
[chargeres] test_file_local
#-f gamma_test.simtel.gz
-f ~/Software/outputs/sim_telarray/simtel_run4_gcts_hnsb.gz
-O hessio
--integrator 4
--integration-window 7 3
--integration-sigamp 2 4
--integration-lwt 0
--integration-calib_scale 1.05
--comparison ~/Downloads/test_file_local.pdf
# A second charge resolution block to also calculate the resolution with
# a different integrator so the two resolutions can be plotted against
# each other.
[chargeres] test_file_nei
#-f gamma_test.simtel.gz
-f ~/Software/outputs/sim_telarray/simtel_run4_gcts_hnsb.gz
-O hessio
--integrator 5
--integration-window 7 3
--integration-sigamp 2 4
--integration-lwt 0
--integration-calib_scale 1.05
--comparison ~/Downloads/test_file_nei.pdf
# A plotting block configures an output plot
[plot] normal_plot
--chargeres-names test_file_local test_file_nei
-o ~/Downloads/normal_plot.pdf
--binning normal
--normalx
--normaly
[plot] log_plot
--chargeres-names test_file_local test_file_nei
-o ~/Downloads/log_plot.pdf""")
exit()
chargeres_cmdlines = {}
plot_cmdlines = {}
if args.runcard is None:
name = args.chargeres_names[0]
chargeres_cmdlines[name] = sys.argv[1:]
plot_cmdlines[name] = sys.argv[1:]
chargeres_args = {name: args}
plot_args = {name: args}
else:
chargeres_args = {}
plot_args = {}
current = None
runcard = open(args.runcard)
for line in runcard:
if line.strip() and not line.startswith('#'):
argument = line.split()[0]
if argument == '[chargeres]':
name = line.split()[1:][0]
chargeres_cmdlines[name] = []
current = chargeres_cmdlines[name]
continue
elif argument == '[plot]':
name = line.split()[1:][0]
plot_cmdlines[name] = []
current = plot_cmdlines[name]
continue
current.extend(line.split())
# Temp fill for checks
for name, cmdline in chargeres_cmdlines.items():
chargeres_args[name], unknown = parser.parse_known_args(cmdline)
for name, cmdline in plot_cmdlines.items():
plot_args[name], unknown = parser.parse_known_args(cmdline)
# Check all chargeres_names exist
for plot_name, args in plot_args.items():
for name in args.chargeres_names:
try:
if name not in chargeres_args:
raise IndexError
except IndexError:
log.exception("[chargeres_names] For plot: {}, no chargeres "
"has the name: {}".format(plot_name, name))
raise
return parser, chargeres_cmdlines, plot_cmdlines
def main():
script = os.path.splitext(os.path.basename(__file__))[0]
log.info("[SCRIPT] {}".format(script))
parser = argparse.ArgumentParser(
formatter_class=argparse.ArgumentDefaultsHelpFormatter)
parser.add_argument('-f',
'--file',
dest='input_path',
action='store',
default=get_path('gamma_test.simtel.gz'),
help='path to the input file')
parser.add_argument('-O',
'--origin',
dest='origin',
action='store',
choices=InputFile.origin_list(),
default='hessio',
help='origin of the file')
parser.add_argument('-o',
'--output',
dest='output_dir',
action='store',
default=None,
help='path of the output directory to store the '
'images (default = input file directory)')
parser.add_argument('-e',
'--event',
dest='event_req',
action='store',
default=0,
type=int,
help='event index to plot (not id!)')
parser.add_argument('--id',
dest='event_id_f',
action='store_true',
default=False,
help='-e will specify event_id instead '
'of index')
parser.add_argument('-t',
'--telescope',
dest='tel',
action='store',
type=int,
default=None,
help='telecope to view')
parser.add_argument('-c',
'--channel',
dest='chan',
action='store',
type=int,
default=0,
help='channel to view (default = 0 (HG))')
parser.add_argument('--calib-help',
dest='calib_help',
action='store_true',
default=False,
help='display the arguments used for the camera '
'calibration')
logger_detail = parser.add_mutually_exclusive_group()
logger_detail.add_argument('-q',
'--quiet',
dest='quiet',
action='store_true',
default=False,
help='Quiet mode')
logger_detail.add_argument('-v',
'--verbose',
dest='verbose',
action='store_true',
default=False,
help='Verbose mode')
logger_detail.add_argument('-d',
'--debug',
dest='debug',
action='store_true',
default=False,
help='Debug mode')
args, excess_args = parser.parse_known_args()
if args.quiet:
log.setLevel(40)
if args.verbose:
log.setLevel(20)
if args.debug:
log.setLevel(10)
telid = args.tel
chan = args.chan
log.debug("[file] Reading file")
input_file = InputFile(args.input_path, args.origin)
event = input_file.get_event(args.event_req, args.event_id_f)
# Print event/args values
log.info("[event_index] {}".format(event.count))
log.info("[event_id] {}".format(event.dl0.event_id))
log.info("[telescope] {}".format(telid))
log.info("[channel] {}".format(chan))
params, unknown_args = calibration_parameters(excess_args, args.origin,
args.calib_help)
if unknown_args:
parser.print_help()
calibration_parameters(unknown_args, args.origin, True)
msg = 'unrecognized arguments: %s'
parser.error(msg % ' '.join(unknown_args))
# Create a dictionary to store any geoms in
geom = CameraGeometry.guess(*event.meta.pixel_pos[telid],
event.meta.optical_foclen[telid])
geom_dict = {telid: geom}
calibrated_event = calibrate_event(event, params, geom_dict)
# Select telescope
tels = list(calibrated_event.dl0.tels_with_data)
if telid is None or telid not in tels:
log.error("[event] please specify one of the following telescopes "
"for this event: {}".format(tels))
exit()
# Extract required images
data_ped = calibrated_event.dl1.tel[telid].pedestal_subtracted_adc[chan]
true_pe = calibrated_event.mc.tel[telid].photo_electrons
measured_pe = calibrated_event.dl1.tel[telid].pe_charge
max_time = np.unravel_index(np.argmax(data_ped), data_ped.shape)[1]
max_charges = np.max(data_ped, axis=1)
max_pixel = int(np.argmax(max_charges))
min_pixel = int(np.argmin(max_charges))
# Get Neighbours
max_pixel_nei = geom.neighbors[max_pixel]
min_pixel_nei = geom.neighbors[min_pixel]
# Get Windows
windows = calibrated_event.dl1.tel[telid].integration_window[chan]
length = np.sum(windows, axis=1)
start = np.argmax(windows, axis=1)
end = start + length - 1
# Draw figures
ax_max_nei = {}
ax_min_nei = {}
fig_waveforms = plt.figure(figsize=(18, 9))
fig_waveforms.subplots_adjust(hspace=.5)
fig_camera = plt.figure(figsize=(15, 12))
ax_max_pix = fig_waveforms.add_subplot(4, 2, 1)
ax_min_pix = fig_waveforms.add_subplot(4, 2, 2)
ax_max_nei[0] = fig_waveforms.add_subplot(4, 2, 3)
ax_min_nei[0] = fig_waveforms.add_subplot(4, 2, 4)
ax_max_nei[1] = fig_waveforms.add_subplot(4, 2, 5)
ax_min_nei[1] = fig_waveforms.add_subplot(4, 2, 6)
ax_max_nei[2] = fig_waveforms.add_subplot(4, 2, 7)
ax_min_nei[2] = fig_waveforms.add_subplot(4, 2, 8)
ax_img_nei = fig_camera.add_subplot(2, 2, 1)
ax_img_max = fig_camera.add_subplot(2, 2, 2)
ax_img_true = fig_camera.add_subplot(2, 2, 3)
ax_img_cal = fig_camera.add_subplot(2, 2, 4)
plotter = CameraPlotter(event, geom_dict)
# Draw max pixel traces
plotter.draw_waveform(data_ped[max_pixel], ax_max_pix)
ax_max_pix.set_title("(Max) Pixel: {}, "
"True: {}, "
"Measured = {:.3f}".format(max_pixel,
true_pe[max_pixel],
measured_pe[max_pixel]))
ax_max_pix.set_ylabel("Amplitude-Ped (ADC)")
max_ylim = ax_max_pix.get_ylim()
plotter.draw_waveform_positionline(start[max_pixel], ax_max_pix)
plotter.draw_waveform_positionline(end[max_pixel], ax_max_pix)
for i, ax in ax_max_nei.items():
if len(max_pixel_nei) > i:
pix = max_pixel_nei[i]
plotter.draw_waveform(data_ped[pix], ax)
ax.set_title("(Max Nei) Pixel: {}, "
"True: {}, "
"Measured = {:.3f}".format(pix, true_pe[pix],
measured_pe[pix]))
ax.set_ylabel("Amplitude-Ped (ADC)")
ax.set_ylim(max_ylim)
plotter.draw_waveform_positionline(start[pix], ax)
plotter.draw_waveform_positionline(end[pix], ax)
# Draw min pixel traces
plotter.draw_waveform(data_ped[min_pixel], ax_min_pix)
ax_min_pix.set_title("(Min) Pixel: {}, "
"True: {}, "
"Measured = {:.3f}".format(min_pixel,
true_pe[min_pixel],
measured_pe[min_pixel]))
ax_min_pix.set_ylabel("Amplitude-Ped (ADC)")
ax_min_pix.set_ylim(max_ylim)
plotter.draw_waveform_positionline(start[min_pixel], ax_min_pix)
plotter.draw_waveform_positionline(end[min_pixel], ax_min_pix)
for i, ax in ax_min_nei.items():
if len(min_pixel_nei) > i:
pix = min_pixel_nei[i]
plotter.draw_waveform(data_ped[pix], ax)
ax.set_title("(Min Nei) Pixel: {}, "
"True: {}, "
"Measured = {:.3f}".format(pix, true_pe[pix],
measured_pe[pix]))
ax.set_ylabel("Amplitude-Ped (ADC)")
ax.set_ylim(max_ylim)
plotter.draw_waveform_positionline(start[pix], ax)
plotter.draw_waveform_positionline(end[pix], ax)
# Draw cameras
nei_camera = np.zeros_like(max_charges, dtype=np.int)
nei_camera[min_pixel_nei] = 2
nei_camera[min_pixel] = 1
nei_camera[max_pixel_nei] = 3
nei_camera[max_pixel] = 4
camera = plotter.draw_camera(telid, nei_camera, ax_img_nei)
camera.cmap = plt.cm.viridis
ax_img_nei.set_title("Neighbour Map")
plotter.draw_camera_pixel_annotation(telid, max_pixel, min_pixel,
ax_img_nei)
camera = plotter.draw_camera(telid, data_ped[:, max_time], ax_img_max)
camera.add_colorbar(ax=ax_img_max, label="Amplitude-Ped (ADC)")
ax_img_max.set_title("Max Timeslice (T = {})".format(max_time))
plotter.draw_camera_pixel_annotation(telid, max_pixel, min_pixel,
ax_img_max)
camera = plotter.draw_camera(telid, true_pe, ax_img_true)
camera.add_colorbar(ax=ax_img_true, label="True Charge (Photo-electrons)")
ax_img_true.set_title("True Charge")
plotter.draw_camera_pixel_annotation(telid, max_pixel, min_pixel,
ax_img_true)
int_dict, inverted = integrator_dict()
integrator_name = '' if 'integrator' not in params else \
params['integrator']
camera = plotter.draw_camera(telid, measured_pe, ax_img_cal)
camera.add_colorbar(ax=ax_img_cal, label="Calib Charge (Photo-electrons)")
ax_img_cal.set_title("Charge (integrator={})".format(integrator_name))
plotter.draw_camera_pixel_annotation(telid, max_pixel, min_pixel,
ax_img_cal)
fig_waveforms.suptitle("Integrator = {}".format(integrator_name))
fig_camera.suptitle("Camera = {}".format(geom.cam_id))
waveform_output_name = "{}_e{}_t{}_c{}_integrator{}_waveform.pdf"\
.format(input_file.filename, event.count, telid, chan,
inverted[params['integrator']])
camera_output_name = "{}_e{}_t{}_c{}_integrator{}_camera.pdf"\
.format(input_file.filename, event.count, telid, chan,
inverted[params['integrator']])
output_dir = args.output_dir if args.output_dir is not None else \
input_file.output_directory
output_dir = os.path.join(output_dir, script)
if not os.path.exists(output_dir):
log.info("[output] Creating directory: {}".format(output_dir))
os.makedirs(output_dir)
waveform_output_path = os.path.join(output_dir, waveform_output_name)
log.info("[output] {}".format(waveform_output_path))
fig_waveforms.savefig(waveform_output_path,
format='pdf',
bbox_inches='tight')
camera_output_path = os.path.join(output_dir, camera_output_name)
log.info("[output] {}".format(camera_output_path))
fig_camera.savefig(camera_output_path, format='pdf', bbox_inches='tight')
log.info("[COMPLETE]")
def main():
script = os.path.splitext(os.path.basename(__file__))[0]
log.info("[SCRIPT] {}".format(script))
parser = argparse.ArgumentParser(
description='Display each event in the file')
parser.add_argument('-f', '--file', dest='input_path', action='store',
default=get_path('gamma_test.simtel.gz'),
help='path to the input file. '
'Default = gamma_test.simtel.gz')
parser.add_argument('-O', '--origin', dest='origin', action='store',
default='hessio',
help='origin of the file: {}. Default = hessio'
.format(origin_list()))
parser.add_argument('-D', dest='display', action='store_true',
default=False, help='display the camera events')
parser.add_argument('--pdf', dest='output_path', action='store',
default=None,
help='path to store a pdf output of the plots')
parser.add_argument('-t', '--telescope', dest='tel', action='store',
type=int, default=None, help='telecope to view. '
'Default = All')
calibration_arguments(parser)
logger_detail = parser.add_mutually_exclusive_group()
logger_detail.add_argument('-q', '--quiet', dest='quiet',
action='store_true', default=False,
help='Quiet mode')
logger_detail.add_argument('-v', '--verbose', dest='verbose',
action='store_true', default=False,
help='Verbose mode')
logger_detail.add_argument('-d', '--debug', dest='debug',
action='store_true', default=False,
help='Debug mode')
args = parser.parse_args()
params = calibration_parameters(args)
if args.quiet:
log.setLevel(40)
if args.verbose:
log.setLevel(20)
if args.debug:
log.setLevel(10)
log.debug("[file] Reading file")
input_file = InputFile(args.input_path, args.origin)
source = input_file.read()
# geom_dict is a dictionary of CameraGeometry, with keys of
# (num_pixels, focal_length), the parameters that are used to guess the
# geometry of the telescope. By using these keys, the geometry is
# calculated only once per telescope type as needed, reducing computation
# time.
# Creating a geom_dict at this point is optional, but is recommended, as
# the same geom_dict can then be shared between the calibration and
# CameraPlotter, again reducing computation time.
# The dictionary becomes filled as a result of a dictionary's mutable
# nature.
geom_dict = {}
# Calibrate events and fill geom_dict
calibrated_source = calibrate_source(source, params, geom_dict)
fig = plt.figure(figsize=(16, 7))
if args.display:
plt.show(block=False)
pp = PdfPages(args.output_path) if args.output_path is not None else None
for event in calibrated_source:
tels = list(event.dl0.tels_with_data)
if args.tel is None:
tel_loop = tels
else:
if args.tel not in tels:
continue
tel_loop = [args.tel]
log.debug(tels)
for tel_id in tel_loop:
display_telescope(event, tel_id, args.display, geom_dict, pp, fig)
if pp is not None:
pp.close()
log.info("[COMPLETE]")
def calculate_charge_resolutions(parser, chargeres_cmdlines):
run = 0
num_runs = len(chargeres_cmdlines)
chargeres_dict = {}
for name, cmdline in chargeres_cmdlines.items():
args, excess_args = parser.parse_known_args(cmdline)
run += 1
log.info("[run] Calculating charge resolution {}/{}".format(
run, num_runs))
# Print event/args values
log.info("[files] {}".format(args.input_paths))
telescopes = "All" if args.tel is None else args.tel
log.info("[origin] {}".format(args.origin))
log.info("[telescopes] {}".format(telescopes))
# Obtain InputFiles (to check files exist)
input_file_list = []
for filepath in args.input_paths:
tilde_filepath = os.path.expanduser(filepath)
for globfile in glob.glob(tilde_filepath):
input_file_list.append(InputFile(globfile, args.origin))
# Find maxpe
maxpe = args.maxpe
if maxpe is None:
maxpe = 0
for input_file in input_file_list:
file_maxpe = input_file.find_max_true_npe(args.tel)
if file_maxpe > maxpe:
maxpe = file_maxpe
log.info("[maxpe] {}".format(maxpe))
params, unknown_args = calibration_parameters(excess_args, args.origin,
args.calib_help)
chargeres = ChargeResolution(maxpe)
for input_file in input_file_list:
source = input_file.read()
calibrated_source = calibrate_source(source, params)
chargeres.add_source(calibrated_source, args.tel)
# Plot comparison graphs
if args.comparison is not None:
hist = chargeres.variation_hist
hist[hist == 0.0] = np.nan
xedges = chargeres.variation_xedges
yedges = chargeres.variation_yedges
fig = plt.figure(figsize=(10, 7))
ax = fig.add_subplot(111)
ax.set_title(name)
x, y = np.meshgrid(xedges, yedges)
x = np.power(10, x)
y = np.power(10, y)
hist_mask = np.ma.masked_where(np.isnan(hist), hist)
im = ax.pcolormesh(x,
y,
hist_mask,
norm=LogNorm(),
cmap=plt.cm.viridis)
cb = plt.colorbar(im)
ax.set_aspect('equal')
ax.grid()
ax.set_xscale('log')
ax.set_yscale('log')
ax.set_xlabel(r'True Charge $Q_T$ (p.e.)')
ax.set_ylabel(r'Measured Charge $Q_M$ (p.e.)')
cb.ax.set_ylabel("Count")
line = np.linspace(*ax.get_xlim(), 100)
ax.plot(line, line, c='0.75', ls='--')
# Add minor ticks
lmin = floor(log10(hist_mask.min()))
lmax = ceil(log10(hist_mask.max()))
logticks = np.tile(np.arange(lmin, 10), lmax) * (np.power(
10,
np.arange(lmax * 10) // 10))
logticks = im.norm(
logticks[(logticks != 0) & (logticks >= hist_mask.min()) &
(logticks <= hist_mask.max())])
cb.ax.yaxis.set_ticks(logticks, minor=True)
cb.ax.yaxis.set_tick_params(which='minor', length=5)
cb.ax.tick_params(length=10)
args.comparison = os.path.expanduser(args.comparison)
output_dir = dirname(args.comparison)
if not os.path.exists(output_dir):
log.info("[output] Creating directory: {}".format(output_dir))
os.makedirs(output_dir)
log.info("[output] {}".format(args.comparison))
warnings.filterwarnings("ignore", module="matplotlib")
with warnings.catch_warnings():
warnings.simplefilter("ignore")
fig.savefig(args.comparison, bbox_inches='tight')
chargeres_dict[name] = chargeres
log.info('[run] Charge resolution calculations finished')
return chargeres_dict
def argparsing():
parser = argparse.ArgumentParser(
formatter_class=argparse.ArgumentDefaultsHelpFormatter)
parser.add_argument('-f',
'--file',
dest='input_paths',
default=[get_path('gamma_test.simtel.gz')],
nargs='*',
help='path to the input files to be combined for a '
'single charge resolution.')
parser.add_argument('-O',
'--origin',
dest='origin',
action='store',
choices=InputFile.origin_list(),
default='hessio',
help='origin of the file')
parser.add_argument('-t',
'--telescope',
dest='tel',
action='store',
type=int,
default=None,
nargs='*',
help='list of telecopes to be included. '
'Default = All')
parser.add_argument('-o',
'--output',
dest='output_path',
action='store',
default=None,
help='path to store a pdf output of the plots. '
'default = display on screen instead')
parser.add_argument('--comparison',
dest='comparison',
action='store',
default=None,
help='output path for a True Charge versus Measured'
'Charge graph. Default = do not plot graph')
parser.add_argument('-M',
'--maxpe',
dest='maxpe',
action='store',
default=None,
type=float,
help='maximum pe to calculate the charge resolution'
' up to. Default = maximum pe in file')
parser.add_argument('--maxpeplot',
dest='maxpeplot',
action='store',
default=None,
type=float,
help='maximum pe to plot up to. Default = maxpe')
parser.add_argument('-B',
'--binning',
dest='binning',
action='store',
default="log",
choices=['none', 'normal', 'log'],
help='binning of the charge resoltion graph: '
'"none" = no binning, "normal" = bin, '
'"log" = bin in log space.')
parser.add_argument('--normalx',
dest='normalx',
action='store_true',
default=False,
help='Use a normal x axis instead of the defualt log'
'axis')
parser.add_argument('--normaly',
dest='normaly',
action='store_true',
default=False,
help='Use a normal y axis instead of the defualt log'
'axis')
parser.add_argument('-E',
'--example',
dest='example',
action='store_true',
default=False,
help='print an example runcard')
parser.add_argument('-R',
'--runcard',
dest='runcard',
action='store',
default=None,
help='path to a runcard text file with arguments that '
'override command line arguments. This run card '
'can allow complex combinations of files and '
'calibrations to compare the charge resolution '
'against each other.')
parser.add_argument('--chargeres-names',
dest='chargeres_names',
default=['default'],
nargs='*',
help='chargres calculation to include in plot. '
'Only used for runcards.')
parser.add_argument('--calib-help',
dest='calib_help',
action='store_true',
default=False,
help='display the arguments used for the camera '
'calibration')
logger_detail = parser.add_mutually_exclusive_group()
logger_detail.add_argument('-q',
'--quiet',
dest='quiet',
action='store_true',
default=False,
help='Quiet mode')
logger_detail.add_argument('-v',
'--verbose',
dest='verbose',
action='store_true',
default=False,
help='Verbose mode')
logger_detail.add_argument('-d',
'--debug',
dest='debug',
action='store_true',
default=False,
help='Debug mode')
args, excess_args = parser.parse_known_args()
if args.quiet:
log.setLevel(40)
if args.verbose:
log.setLevel(20)
if args.debug:
log.setLevel(10)
if args.calib_help:
params, unknown_args = calibration_parameters(excess_args, args.origin,
args.calib_help)
if args.example:
print("""
# Each charge resolution block starts with [chargeres] and the names for
# this charge resolution.
# The options in each block are equivalent to the scripts help message.
# Options that seem to apply to plotting will only have effect in a
# plotting block.
[chargeres] test_file_local
#-f gamma_test.simtel.gz
-f ~/Software/outputs/sim_telarray/simtel_run4_gcts_hnsb.gz
-O hessio
--integrator 4
--integration-window 7 3
--integration-sigamp 2 4
--integration-lwt 0
--integration-calib_scale 1.05
--comparison ~/Downloads/test_file_local.pdf
# A second charge resolution block to also calculate the resolution with
# a different integrator so the two resolutions can be plotted against
# each other.
[chargeres] test_file_nei
#-f gamma_test.simtel.gz
-f ~/Software/outputs/sim_telarray/simtel_run4_gcts_hnsb.gz
-O hessio
--integrator 5
--integration-window 7 3
--integration-sigamp 2 4
--integration-lwt 0
--integration-calib_scale 1.05
--comparison ~/Downloads/test_file_nei.pdf
# A plotting block configures an output plot
[plot] normal_plot
--chargeres-names test_file_local test_file_nei
-o ~/Downloads/normal_plot.pdf
--binning normal
--normalx
--normaly
[plot] log_plot
--chargeres-names test_file_local test_file_nei
-o ~/Downloads/log_plot.pdf""")
exit()
chargeres_cmdlines = {}
plot_cmdlines = {}
if args.runcard is None:
name = args.chargeres_names[0]
chargeres_cmdlines[name] = sys.argv[1:]
plot_cmdlines[name] = sys.argv[1:]
chargeres_args = {name: args}
plot_args = {name: args}
else:
chargeres_args = {}
plot_args = {}
current = None
runcard = open(args.runcard)
for line in runcard:
if line.strip() and not line.startswith('#'):
argument = line.split()[0]
if argument == '[chargeres]':
name = line.split()[1:][0]
chargeres_cmdlines[name] = []
current = chargeres_cmdlines[name]
continue
elif argument == '[plot]':
name = line.split()[1:][0]
plot_cmdlines[name] = []
current = plot_cmdlines[name]
continue
current.extend(line.split())
# Temp fill for checks
for name, cmdline in chargeres_cmdlines.items():
chargeres_args[name], unknown = parser.parse_known_args(cmdline)
for name, cmdline in plot_cmdlines.items():
plot_args[name], unknown = parser.parse_known_args(cmdline)
# Check all chargeres_names exist
for plot_name, args in plot_args.items():
for name in args.chargeres_names:
try:
if name not in chargeres_args:
raise IndexError
except IndexError:
log.exception("[chargeres_names] For plot: {}, no chargeres "
"has the name: {}".format(plot_name, name))
raise
return parser, chargeres_cmdlines, plot_cmdlines
def main():
script = os.path.splitext(os.path.basename(__file__))[0]
log.info("[SCRIPT] {}".format(script))
parser = argparse.ArgumentParser(description='Create a gif of an event')
parser.add_argument('-f', '--file', dest='input_path', action='store',
required=True, help='path to the input file')
parser.add_argument('-O', '--origin', dest='origin', action='store',
required=True, help='origin of the file: {}'
.format(origin_list()))
parser.add_argument('-o', '--output', dest='output_dir', action='store',
default=None,
help='path of the output directory to store the '
'images (default = input file directory)')
parser.add_argument('-e', '--event', dest='event_req', action='store',
required=True, type=int,
help='event index to plot (not id!)')
parser.add_argument('--id', dest='event_id_f', action='store_true',
default=False, help='-e will specify event_id instead '
'of index')
parser.add_argument('-t', '--telescope', dest='tel', action='store',
type=int, default=None, help='telecope to view')
parser.add_argument('-c', '--channel', dest='chan', action='store',
type=int, default=0,
help='channel to view (default = 0 (HG))')
calibration_arguments(parser)
logger_detail = parser.add_mutually_exclusive_group()
logger_detail.add_argument('-q', '--quiet', dest='quiet',
action='store_true', default=False,
help='Quiet mode')
logger_detail.add_argument('-v', '--verbose', dest='verbose',
action='store_true', default=False,
help='Verbose mode')
logger_detail.add_argument('-d', '--debug', dest='debug',
action='store_true', default=False,
help='Debug mode')
args = parser.parse_args()
if args.quiet:
log.setLevel(40)
if args.verbose:
log.setLevel(20)
if args.debug:
log.setLevel(10)
telid = args.tel
chan = args.chan
log.debug("[file] Reading file")
input_file = InputFile(args.input_path, args.origin)
event = input_file.get_event(args.event_req, args.event_id_f)
# Print event/args values
log.info("[event_index] {}".format(event.count))
log.info("[event_id] {}".format(event.dl0.event_id))
log.info("[telescope] {}".format(telid))
log.info("[channel] {}".format(chan))
params = calibration_parameters(args)
# Create a dictionary to store any geoms in
geom = CameraGeometry.guess(*event.meta.pixel_pos[telid],
event.meta.optical_foclen[telid])
geom_dict = {telid: geom}
calibrated_event = calibrate_event(event, params, geom_dict)
# Select telescope
tels = list(calibrated_event.dl0.tels_with_data)
if telid is None or telid not in tels:
log.error("[event] please specify one of the following telescopes "
"for this event: {}".format(tels))
exit()
# Extract required images
data_ped = calibrated_event.dl1.tel[telid].pedestal_subtracted_adc[chan]
true_pe = calibrated_event.mc.tel[telid].photo_electrons
measured_pe = calibrated_event.dl1.tel[telid].pe_charge
max_time = np.unravel_index(np.argmax(data_ped), data_ped.shape)[1]
max_charges = np.max(data_ped, axis=1)
max_pixel = int(np.argmax(max_charges))
min_pixel = int(np.argmin(max_charges))
# Get Neighbours
max_pixel_nei = geom.neighbors[max_pixel]
min_pixel_nei = geom.neighbors[min_pixel]
# Get Windows
windows = calibrated_event.dl1.tel[telid].integration_window[chan]
length = np.sum(windows, axis=1)
start = np.argmax(windows, axis=1)
end = start + length - 1
# Draw figures
ax_max_nei = {}
ax_min_nei = {}
fig_waveforms = plt.figure(figsize=(24, 10))
fig_waveforms.subplots_adjust(hspace=.5)
fig_camera = plt.figure(figsize=(30, 24))
ax_max_pix = fig_waveforms.add_subplot(4, 2, 1)
ax_min_pix = fig_waveforms.add_subplot(4, 2, 2)
ax_max_nei[0] = fig_waveforms.add_subplot(4, 2, 3)
ax_min_nei[0] = fig_waveforms.add_subplot(4, 2, 4)
ax_max_nei[1] = fig_waveforms.add_subplot(4, 2, 5)
ax_min_nei[1] = fig_waveforms.add_subplot(4, 2, 6)
ax_max_nei[2] = fig_waveforms.add_subplot(4, 2, 7)
ax_min_nei[2] = fig_waveforms.add_subplot(4, 2, 8)
ax_img_nei = fig_camera.add_subplot(2, 2, 1)
ax_img_max = fig_camera.add_subplot(2, 2, 2)
ax_img_true = fig_camera.add_subplot(2, 2, 3)
ax_img_cal = fig_camera.add_subplot(2, 2, 4)
plotter = CameraPlotter(event, geom_dict)
# Draw max pixel traces
plotter.draw_waveform(data_ped[max_pixel], ax_max_pix)
ax_max_pix.set_title("(Max) Pixel: {}, "
"True: {}, "
"Measured = {}".format(max_pixel, true_pe[max_pixel],
measured_pe[max_pixel]))
ax_max_pix.set_ylabel("Amplitude-Ped (ADC)")
max_ylim = ax_max_pix.get_ylim()
plotter.draw_waveform_positionline(start[max_pixel], ax_max_pix)
plotter.draw_waveform_positionline(end[max_pixel], ax_max_pix)
for i, ax in ax_max_nei.items():
if len(max_pixel_nei) > i:
pix = max_pixel_nei[i]
plotter.draw_waveform(data_ped[pix], ax)
ax.set_title("(Max Nei) Pixel: {}, "
"True: {}, "
"Measured = {}".format(pix, true_pe[pix],
measured_pe[pix]))
ax.set_ylabel("Amplitude-Ped (ADC)")
ax.set_ylim(max_ylim)
plotter.draw_waveform_positionline(start[pix], ax)
plotter.draw_waveform_positionline(end[pix], ax)
# Draw min pixel traces
plotter.draw_waveform(data_ped[min_pixel], ax_min_pix)
ax_min_pix.set_title("(Min) Pixel: {}, "
"True: {}, "
"Measured = {}".format(min_pixel, true_pe[min_pixel],
measured_pe[min_pixel]))
ax_min_pix.set_ylabel("Amplitude-Ped (ADC)")
ax_min_pix.set_ylim(max_ylim)
plotter.draw_waveform_positionline(start[min_pixel], ax_min_pix)
plotter.draw_waveform_positionline(end[min_pixel], ax_min_pix)
for i, ax in ax_min_nei.items():
if len(min_pixel_nei) > i:
pix = min_pixel_nei[i]
plotter.draw_waveform(data_ped[pix], ax)
ax.set_title("(Min Nei) Pixel: {}, "
"True: {}, "
"Measured = {}".format(pix, true_pe[pix],
measured_pe[pix]))
ax.set_ylabel("Amplitude-Ped (ADC)")
ax.set_ylim(max_ylim)
plotter.draw_waveform_positionline(start[pix], ax)
plotter.draw_waveform_positionline(end[pix], ax)
# Draw cameras
nei_camera = np.zeros_like(max_charges, dtype=np.int)
nei_camera[min_pixel_nei] = 2
nei_camera[min_pixel] = 1
nei_camera[max_pixel_nei] = 3
nei_camera[max_pixel] = 4
camera = plotter.draw_camera(telid, nei_camera, ax_img_nei)
camera.cmap = plt.cm.viridis
ax_img_nei.set_title("Neighbour Map")
plotter.draw_camera_pixel_annotation(telid, max_pixel, min_pixel,
ax_img_nei)
camera = plotter.draw_camera(telid, data_ped[:, max_time], ax_img_max)
camera.add_colorbar(ax=ax_img_max, label="Amplitude-Ped (ADC)")
ax_img_max.set_title("Max Timeslice (T = {})".format(max_time))
plotter.draw_camera_pixel_annotation(telid, max_pixel, min_pixel,
ax_img_max)
camera = plotter.draw_camera(telid, true_pe, ax_img_true)
camera.add_colorbar(ax=ax_img_true, label="True Charge (Photo-electrons)")
ax_img_true.set_title("True Charge")
plotter.draw_camera_pixel_annotation(telid, max_pixel, min_pixel,
ax_img_true)
camera = plotter.draw_camera(telid, measured_pe, ax_img_cal)
camera.add_colorbar(ax=ax_img_cal, label="Calib Charge (Photo-electrons)")
ax_img_cal.set_title("Charge (integrator={})".format(params['integrator']))
plotter.draw_camera_pixel_annotation(telid, max_pixel, min_pixel,
ax_img_cal)
fig_waveforms.suptitle("Integrator = {}".format(params['integrator']))
fig_camera.suptitle("Camera = {}".format(geom.cam_id))
# TODO: another figure of all waveforms that have non-zero true charge
waveform_output_name = "{}_e{}_t{}_c{}_integrator{}_waveform.pdf"\
.format(input_file.filename, event.count, telid, chan, args.integrator)
camera_output_name = "{}_e{}_t{}_c{}_integrator{}_camera.pdf"\
.format(input_file.filename, event.count, telid, chan, args.integrator)
output_dir = args.output_dir if args.output_dir is not None else \
input_file.output_directory
output_dir = os.path.join(output_dir, script)
if not os.path.exists(output_dir):
log.info("[output] Creating directory: {}".format(output_dir))
os.makedirs(output_dir)
waveform_output_path = os.path.join(output_dir, waveform_output_name)
log.info("[output] {}".format(waveform_output_path))
fig_waveforms.savefig(waveform_output_path, format='pdf')
camera_output_path = os.path.join(output_dir, camera_output_name)
log.info("[output] {}".format(camera_output_path))
fig_camera.savefig(camera_output_path, format='pdf')
log.info("[COMPLETE]")
def initialize(self, argv=None):
self.log.info("Initializing the calibration pipeline...")
# Declare and parse command line option
parser = argparse.ArgumentParser(
description='Display each event in the file')
parser.add_argument('-f', '--file', dest='input_path',
action='store',
default=get_path('gamma_test.simtel.gz'),
help='path to the input file. '
' Default = gamma_test.simtel.gz')
parser.add_argument('-O', '--origin', dest='origin',
action='store',
default='hessio',
help='origin of the file: {}. '
'Default = hessio'
.format(origin_list()))
parser.add_argument('-D', dest='display', action='store_true',
default=False,
help='display the camera events')
parser.add_argument('--pdf', dest='output_path', action='store',
default=None,
help='path to store a pdf output of the plots')
parser.add_argument('-t', '--telescope', dest='tel',
action='store',
type=int, default=None,
help='telecope to view. Default = All')
calibration_arguments(parser)
logger_detail = parser.add_mutually_exclusive_group()
logger_detail.add_argument('-q', '--quiet', dest='quiet',
action='store_true', default=False,
help='Quiet mode')
logger_detail.add_argument('-v', '--verbose', dest='verbose',
action='store_true', default=False,
help='Verbose mode')
logger_detail.add_argument('-d', '--debug', dest='debug',
action='store_true', default=False,
help='Debug mode')
self.args = parser.parse_args()
self.params = calibration_parameters(self.args)
if self.args.quiet:
self.log.setLevel(40)
if self.args.verbose:
self.log.setLevel(20)
if self.args.debug:
self.log.setLevel(10)
self.log.debug("[file] Reading file")
input_file = InputFile(self.args.input_path, self.args.origin)
self.source = input_file.read()
# geom_dict is a dictionary of CameraGeometry, with keys of
# (num_pixels, focal_length), the parameters that are used to guess the
# geometry of the telescope. By using these keys, the geometry is
# calculated only once per telescope type as needed, reducing
# computation time.
# Creating a geom_dict at this point is optional, but is recommended,
# as the same geom_dict can then be shared between the calibration and
# CameraPlotter, again reducing computation time.
# The dictionary becomes filled as a result of a dictionary's mutable
# nature.def display_telescope(event, tel_id, display,
# geom_dict, pp, fig):
self.geom_dict = {}