def analyze(self):
with AnalyzeRawData(raw_data_file=self.output_filename,
create_pdf=True) as analyze_raw_data:
analyze_raw_data.interpreter.set_warning_output(False)
analyze_raw_data.create_source_scan_hist = True
analyze_raw_data.create_hit_table = False
analyze_raw_data.interpret_word_table()
analyze_raw_data.plot_histograms()
analyze_raw_data.interpreter.print_summary()
with tb.open_file(analyze_raw_data._analyzed_data_file,
'r') as out_file_h5:
occ_hist = out_file_h5.root.HistOcc[:, :, 0].T
self.occ_mask = np.zeros(shape=occ_hist.shape,
dtype=np.dtype('>u1'))
# noisy pixels are set to 1
self.occ_mask[occ_hist > self.abs_occ_limit] = 1
# make inverse
self.inv_occ_mask = invert_pixel_mask(self.occ_mask)
if self.overwrite_mask:
for mask in self.disable_for_mask:
self.register.set_pixel_register_value(
mask, self.inv_occ_mask)
else:
for mask in self.disable_for_mask:
enable_mask = np.logical_and(
self.inv_occ_mask,
self.register.get_pixel_register_value(mask))
self.register.set_pixel_register_value(mask, enable_mask)
if self.overwrite_mask:
for mask in self.enable_for_mask:
self.register.set_pixel_register_value(mask, self.occ_mask)
else:
for mask in self.enable_for_mask:
disable_mask = np.logical_or(
self.occ_mask,
self.register.get_pixel_register_value(mask))
self.register.set_pixel_register_value(mask, disable_mask)
plot_occupancy(self.occ_mask.T,
title='Noisy Pixels',
z_max=1,
filename=analyze_raw_data.output_pdf)
plot_fancy_occupancy(self.occ_mask.T,
z_max=1,
filename=analyze_raw_data.output_pdf)
for mask in self.disable_for_mask:
mask_name = self.register.pixel_registers[mask]['name']
plot_occupancy(self.register.get_pixel_register_value(mask).T,
title='%s Mask' % mask_name,
z_max=1,
filename=analyze_raw_data.output_pdf)
for mask in self.enable_for_mask:
mask_name = self.register.pixel_registers[mask]['name']
plot_occupancy(self.register.get_pixel_register_value(mask).T,
title='%s Mask' % mask_name,
z_max=1,
filename=analyze_raw_data.output_pdf)
def analyze(self):
with AnalyzeRawData(raw_data_file=self.output_filename,
create_pdf=True) as analyze_raw_data:
analyze_raw_data.create_tot_hist = True
if self.enable_tdc:
analyze_raw_data.create_tdc_counter_hist = True # histogram all TDC words
analyze_raw_data.create_tdc_hist = True # histogram the hit TDC information
analyze_raw_data.interpret_word_table()
analyze_raw_data.plot_histograms()
analyze_raw_data.interpreter.print_summary()
occ_hist = analyze_raw_data.out_file_h5.root.HistOcc[:, :, 0].T
occ_mask = np.zeros(shape=occ_hist.shape, dtype=np.dtype('>u1'))
occ_mask[occ_hist > 1] = 1
inv_occ_mask = invert_pixel_mask(occ_mask)
if self.overwrite_mask:
for mask in self.disable_for_mask:
self.register.set_pixel_register_value(mask, inv_occ_mask)
else:
for mask in self.disable_for_mask:
enable_mask = np.logical_and(
inv_occ_mask,
self.register.get_pixel_register_value(mask))
self.register.set_pixel_register_value(mask, enable_mask)
if self.overwrite_mask:
for mask in self.enable_for_mask:
self.register.set_pixel_register_value(mask, occ_mask)
else:
for mask in self.enable_for_mask:
disable_mask = np.logical_or(
occ_mask, self.register.get_pixel_register_value(mask))
self.register.set_pixel_register_value(mask, disable_mask)
plot_occupancy(occ_mask.T,
title='Merged Pixels',
z_max=1,
filename=analyze_raw_data.output_pdf)
plot_fancy_occupancy(occ_mask.T,
z_max=1,
filename=analyze_raw_data.output_pdf)
for mask in self.disable_for_mask:
mask_name = self.register.pixel_registers[mask]['name']
plot_occupancy(self.register.get_pixel_register_value(mask).T,
title='%s Mask' % mask_name,
z_max=1,
filename=analyze_raw_data.output_pdf)
for mask in self.enable_for_mask:
mask_name = self.register.pixel_registers[mask]['name']
plot_occupancy(self.register.get_pixel_register_value(mask).T,
title='%s Mask' % mask_name,
z_max=1,
filename=analyze_raw_data.output_pdf)
def analyze(self):
self.register.set_global_register_value("Vthin_AltFine", self.threshold[0])
self.register.set_pixel_register_value('TDAC', self.new_tdac[0])
self.register.set_pixel_register_value('Enable', self.new_enable_mask[0]) # use enable mask from the lowest point to mask bad pixels
# write configuration to avaoid high current states
commands = []
commands.extend(self.register.get_commands("ConfMode"))
commands.extend(self.register.get_commands("WrRegister", name=["Vthin_AltFine"]))
commands.extend(self.register.get_commands("WrFrontEnd", same_mask_for_all_dc=False, name="TDAC"))
commands.extend(self.register.get_commands("WrFrontEnd", same_mask_for_all_dc=False, name="Enable"))
self.register_utils.send_commands(commands)
with AnalyzeRawData(raw_data_file=self.output_filename, create_pdf=True) as analyze_raw_data:
analyze_raw_data.create_source_scan_hist = True
analyze_raw_data.interpreter.set_warning_output(False)
analyze_raw_data.interpret_word_table()
analyze_raw_data.interpreter.print_summary()
analyze_raw_data.plot_histograms()
last_step = None
for step in range(self.plot_n_steps, -1, -1):
if self.threshold[step] is not None:
plot_occupancy(self.occupancy_hist[step].T, title='Occupancy at Vthin_AltFine %d Step %d' % (self.threshold[step], self.tdac_step[step]), filename=analyze_raw_data.output_pdf)
plot_fancy_occupancy(self.occupancy_hist[step].T, filename=analyze_raw_data.output_pdf)
plot_occupancy(self.occupancy_mask[step].T, title='Noisy pixels at Vthin_AltFine %d Step %d' % (self.threshold[step], self.tdac_step[step]), z_max=1, filename=analyze_raw_data.output_pdf)
plot_fancy_occupancy(self.occupancy_mask[step].T, filename=analyze_raw_data.output_pdf)
plot_three_way(self.tdac[step].T, title='TDAC at Vthin_AltFine %d Step %d' % (self.threshold[step], self.tdac_step[step]), x_axis_title="TDAC", filename=analyze_raw_data.output_pdf, maximum=31, bins=32)
plot_occupancy(self.tdac[step].T, title='TDAC at Vthin_AltFine %d Step %d' % (self.threshold[step], self.tdac_step[step]), z_max=31, filename=analyze_raw_data.output_pdf)
plot_occupancy(self.enable_mask[step].T, title='Enable mask at Vthin_AltFine %d Step %d' % (self.threshold[step], self.tdac_step[step]), z_max=1, filename=analyze_raw_data.output_pdf)
# adding Poisson statistics plots
fig = Figure()
FigureCanvas(fig)
ax = fig.add_subplot(111)
ax.set_title("Hit statistics")
hist, bin_edges = np.histogram(self.occupancy_hist[step], bins=np.arange(0.0, np.max(self.occupancy_hist[step]) + 2, 1.0))
try:
_, idx = hist_quantiles(hist, [0.0, 0.9], return_indices=True)
except IndexError:
idx = [0, 1]
bins = np.arange(0, np.maximum(bin_edges[idx[1]], stats.poisson.ppf(0.9999, mu=self.occupancy_limit * self.n_triggers * self.consecutive_lvl1)) + 2, 1)
ax.hist(self.occupancy_hist[step].flatten(), bins=bins, align='left', alpha=0.5, label="Measured occupancy")
ax.bar(x=bins[:-1], height=stats.poisson.pmf(k=bins[:-1], mu=self.occupancy_limit * self.n_triggers * self.consecutive_lvl1) * self.enable_mask[step].sum(), alpha=0.5, width=1.0, color="r", label="Expected occupancy (Poisson statistics)")
# ax.hist(stats.poisson.rvs(mu=self.occupancy_limit * self.n_triggers * self.consecutive_lvl1, size=self.enable_mask[step].sum()), bins=bins, align='left', alpha=0.5, label="Expected occupancy (Poisson statistics)")
ax.set_xlabel('#Hits')
ax.set_ylabel('#Pixels')
ax.legend()
analyze_raw_data.output_pdf.savefig(fig)
last_step = step
if last_step is not None:
plot_three_way(self.new_tdac[last_step].T, title='Final TDAC after Vthin_AltFine %d Step %d' % (self.threshold[last_step], self.tdac_step[last_step]), x_axis_title="TDAC", filename=analyze_raw_data.output_pdf, maximum=31, bins=32)
plot_occupancy(self.new_tdac[last_step].T, title='Final TDAC after Vthin_AltFine %d Step %d' % (self.threshold[last_step], self.tdac_step[last_step]), z_max=31, filename=analyze_raw_data.output_pdf)
plot_occupancy(self.new_enable_mask[last_step].T, title='Final Enable mask after Vthin_AltFine %d Step %d' % (self.threshold[last_step], self.tdac_step[last_step]), z_max=1, filename=analyze_raw_data.output_pdf)
def analyze(self):
self.register.set_global_register_value("Vthin_AltFine", self.last_good_threshold[self.increase_threshold])
self.register.set_pixel_register_value('TDAC', self.last_good_tdac[self.increase_threshold])
self.register.set_pixel_register_value('Enable', self.last_good_enable_mask[0]) # use enable mask from the lowest point to mask bad pixels
# write configuration to avaoid high current states
commands = []
commands.extend(self.register.get_commands("ConfMode"))
commands.extend(self.register.get_commands("WrRegister", name=["Vthin_AltFine"]))
commands.extend(self.register.get_commands("WrFrontEnd", same_mask_for_all_dc=False, name="TDAC"))
commands.extend(self.register.get_commands("WrFrontEnd", same_mask_for_all_dc=False, name="Enable"))
self.register_utils.send_commands(commands)
with AnalyzeRawData(raw_data_file=self.output_filename, create_pdf=True) as analyze_raw_data:
analyze_raw_data.create_source_scan_hist = True
analyze_raw_data.interpreter.set_warning_output(False)
analyze_raw_data.interpret_word_table()
analyze_raw_data.interpreter.print_summary()
analyze_raw_data.plot_histograms()
plot_occupancy(self.last_occupancy_hist[self.increase_threshold].T, title='Noisy Pixels at Vthin_AltFine %d Step %d' % (self.last_reg_val[self.increase_threshold], self.last_step[self.increase_threshold]), filename=analyze_raw_data.output_pdf)
plot_fancy_occupancy(self.last_occupancy_hist[self.increase_threshold].T, filename=analyze_raw_data.output_pdf)
plot_occupancy(self.last_occupancy_mask[self.increase_threshold].T, title='Occupancy Mask at Vthin_AltFine %d Step %d' % (self.last_reg_val[self.increase_threshold], self.last_step[self.increase_threshold]), z_max=1, filename=analyze_raw_data.output_pdf)
plot_fancy_occupancy(self.last_occupancy_mask[self.increase_threshold].T, filename=analyze_raw_data.output_pdf)
plot_three_way(self.last_good_tdac[self.increase_threshold].T, title='TDAC at Vthin_AltFine %d Step %d' % (self.last_reg_val[self.increase_threshold], self.last_step[self.increase_threshold]), x_axis_title="TDAC", filename=analyze_raw_data.output_pdf, maximum=31, bins=32)
plot_occupancy(self.last_good_tdac[self.increase_threshold].T, title='TDAC at Vthin_AltFine %d Step %d' % (self.last_reg_val[self.increase_threshold], self.last_step[self.increase_threshold]), z_max=31, filename=analyze_raw_data.output_pdf)
plot_occupancy(self.last_good_enable_mask[self.increase_threshold].T, title='Intermediate Enable Mask at Vthin_AltFine %d Step %d' % (self.last_reg_val[self.increase_threshold], self.last_step[self.increase_threshold]), z_max=1, filename=analyze_raw_data.output_pdf)
plot_fancy_occupancy(self.last_good_enable_mask[self.increase_threshold].T, filename=analyze_raw_data.output_pdf)
plot_occupancy(self.last_good_enable_mask[0].T, title='Final Enable Mask at Vthin_AltFine %d Step %d' % (self.last_reg_val[0], self.last_step[0]), z_max=1, filename=analyze_raw_data.output_pdf)
plot_fancy_occupancy(self.last_good_enable_mask[0].T, filename=analyze_raw_data.output_pdf)
def analyze(self):
with AnalyzeRawData(raw_data_file=self.output_filename, create_pdf=True) as analyze_raw_data:
analyze_raw_data.create_cluster_size_hist = False
analyze_raw_data.create_source_scan_hist = True
analyze_raw_data.create_cluster_tot_hist = False
analyze_raw_data.interpreter.set_warning_output(False)
analyze_raw_data.clusterizer.set_warning_output(False)
analyze_raw_data.interpret_word_table()
analyze_raw_data.interpreter.print_summary()
analyze_raw_data.plot_histograms()
with tb.open_file(analyze_raw_data._analyzed_data_file, 'r') as out_file_h5:
occ_hist = out_file_h5.root.HistOcc[:, :, 0].T
self.occ_mask = np.zeros(shape=occ_hist.shape, dtype=np.dtype('>u1'))
# n largest elements
n_largest_elements = np.sort(occ_hist[occ_hist > self.low_value])[-self.mask_high_count:]
# noisy pixels are set to 1
if n_largest_elements.shape[0] > 0:
self.occ_mask[occ_hist >= n_largest_elements[0]] = 1
# make inverse
self.inv_occ_mask = invert_pixel_mask(self.occ_mask)
if self.overwrite_mask:
for mask in self.disable_for_mask:
self.register.set_pixel_register_value(mask, self.inv_occ_mask)
else:
for mask in self.disable_for_mask:
enable_mask = np.logical_and(self.inv_occ_mask, self.register.get_pixel_register_value(mask))
self.register.set_pixel_register_value(mask, enable_mask)
if self.overwrite_mask:
for mask in self.enable_for_mask:
self.register.set_pixel_register_value(mask, self.occ_mask)
else:
for mask in self.enable_for_mask:
disable_mask = np.logical_or(self.occ_mask, self.register.get_pixel_register_value(mask))
self.register.set_pixel_register_value(mask, disable_mask)
plot_occupancy(self.occ_mask.T, title='Noisy Pixels', z_max=1, filename=analyze_raw_data.output_pdf)
plot_fancy_occupancy(self.occ_mask.T, z_max=1, filename=analyze_raw_data.output_pdf)
for mask in self.disable_for_mask:
mask_name = self.register.pixel_registers[mask]['name']
plot_occupancy(self.register.get_pixel_register_value(mask).T, title='%s Mask' % mask_name, z_max=1, filename=analyze_raw_data.output_pdf)
for mask in self.enable_for_mask:
mask_name = self.register.pixel_registers[mask]['name']
plot_occupancy(self.register.get_pixel_register_value(mask).T, title='%s Mask' % mask_name, z_max=1, filename=analyze_raw_data.output_pdf)
def analyze(self):
with AnalyzeRawData(raw_data_file=self.output_filename, create_pdf=True) as analyze_raw_data:
analyze_raw_data.interpreter.set_warning_output(False)
analyze_raw_data.create_source_scan_hist = True
analyze_raw_data.create_hit_table = False
analyze_raw_data.interpret_word_table()
analyze_raw_data.plot_histograms()
analyze_raw_data.interpreter.print_summary()
with tb.open_file(analyze_raw_data._analyzed_data_file, 'r') as out_file_h5:
occ_hist = out_file_h5.root.HistOcc[:, :, 0].T
self.occ_mask = np.zeros(shape=occ_hist.shape, dtype=np.dtype('>u1'))
# noisy pixels are set to 1
if self.trig_count == 0:
consecutive_lvl1 = (2 ** self.register.global_registers['Trig_Count']['bitlength'])
else:
consecutive_lvl1 = self.trig_count
self.occ_mask[occ_hist > self.occupancy_limit * self.n_triggers * consecutive_lvl1] = 1
# make inverse
self.inv_occ_mask = invert_pixel_mask(self.occ_mask)
if self.overwrite_mask:
for mask in self.disable_for_mask:
self.register.set_pixel_register_value(mask, self.inv_occ_mask)
else:
for mask in self.disable_for_mask:
enable_mask = np.logical_and(self.inv_occ_mask, self.register.get_pixel_register_value(mask))
self.register.set_pixel_register_value(mask, enable_mask)
if self.overwrite_mask:
for mask in self.enable_for_mask:
self.register.set_pixel_register_value(mask, self.occ_mask)
else:
for mask in self.enable_for_mask:
disable_mask = np.logical_or(self.occ_mask, self.register.get_pixel_register_value(mask))
self.register.set_pixel_register_value(mask, disable_mask)
plot_occupancy(self.occ_mask.T, title='Noisy Pixels', z_max=1, filename=analyze_raw_data.output_pdf)
plot_fancy_occupancy(self.occ_mask.T, z_max=1, filename=analyze_raw_data.output_pdf)
for mask in self.disable_for_mask:
mask_name = self.register.pixel_registers[mask]['name']
plot_occupancy(self.register.get_pixel_register_value(mask).T, title='%s Mask' % mask_name, z_max=1, filename=analyze_raw_data.output_pdf)
for mask in self.enable_for_mask:
mask_name = self.register.pixel_registers[mask]['name']
plot_occupancy(self.register.get_pixel_register_value(mask).T, title='%s Mask' % mask_name, z_max=1, filename=analyze_raw_data.output_pdf)
def analyze(self):
self.register.set_global_register_value("Vthin_AltFine", self.last_good_threshold + self.increase_threshold)
self.register.set_pixel_register_value('TDAC', self.last_good_tdac)
self.register.set_pixel_register_value('Enable', self.last_good_enable_mask)
# write configuration to avaoid high current states
commands = []
commands.extend(self.register.get_commands("ConfMode"))
commands.extend(self.register.get_commands("WrRegister", name=["Vthin_AltFine"]))
commands.extend(self.register.get_commands("WrFrontEnd", same_mask_for_all_dc=False, name="TDAC"))
commands.extend(self.register.get_commands("WrFrontEnd", same_mask_for_all_dc=False, name="Enable"))
self.register_utils.send_commands(commands)
with AnalyzeRawData(raw_data_file=self.output_filename, create_pdf=True) as analyze_raw_data:
analyze_raw_data.create_source_scan_hist = True
analyze_raw_data.interpreter.set_warning_output(False)
analyze_raw_data.interpret_word_table()
analyze_raw_data.interpreter.print_summary()
analyze_raw_data.plot_histograms()
plot_occupancy(self.last_occupancy_hist.T, title='Noisy Pixels at Vthin_AltFine %d Step %d' % (self.last_reg_val, self.last_step), filename=analyze_raw_data.output_pdf)
plot_fancy_occupancy(self.last_occupancy_hist.T, filename=analyze_raw_data.output_pdf)
plot_occupancy(self.last_occupancy_mask.T, title='Occupancy Mask at Vthin_AltFine %d Step %d' % (self.last_reg_val, self.last_step), z_max=1, filename=analyze_raw_data.output_pdf)
plot_fancy_occupancy(self.last_occupancy_mask.T, filename=analyze_raw_data.output_pdf)
plot_three_way(self.last_tdac_distribution.T, title='TDAC at Vthin_AltFine %d Step %d' % (self.last_reg_val, self.last_step), x_axis_title="TDAC", filename=analyze_raw_data.output_pdf, maximum=31, bins=32)
plot_occupancy(self.last_tdac_distribution.T, title='TDAC at Vthin_AltFine %d Step %d' % (self.last_reg_val, self.last_step), z_max=31, filename=analyze_raw_data.output_pdf)
plot_occupancy(self.register.get_pixel_register_value('Enable').T, title='Enable Mask', z_max=1, filename=analyze_raw_data.output_pdf)
plot_fancy_occupancy(self.register.get_pixel_register_value('Enable').T, filename=analyze_raw_data.output_pdf)
def analyze(self):
with AnalyzeRawData(raw_data_file=self.output_filename, create_pdf=True) as analyze_raw_data:
analyze_raw_data.create_tot_hist = True
if self.enable_tdc:
analyze_raw_data.create_tdc_counter_hist = True # histogram all TDC words
analyze_raw_data.create_tdc_hist = True # histogram the hit TDC information
analyze_raw_data.interpreter.use_tdc_word(True) # align events at the TDC word
analyze_raw_data.interpret_word_table()
analyze_raw_data.plot_histograms()
analyze_raw_data.interpreter.print_summary()
with tb.open_file(analyze_raw_data._analyzed_data_file, 'r') as out_file_h5:
occ_hist = out_file_h5.root.HistOcc[:, :, 0].T
occ_mask = np.zeros(shape=occ_hist.shape, dtype=np.dtype('>u1'))
occ_mask[occ_hist > 1] = 1
inv_occ_mask = invert_pixel_mask(occ_mask)
if self.overwrite_mask:
for mask in self.disable_for_mask:
self.register.set_pixel_register_value(mask, inv_occ_mask)
else:
for mask in self.disable_for_mask:
enable_mask = np.logical_and(inv_occ_mask, self.register.get_pixel_register_value(mask))
self.register.set_pixel_register_value(mask, enable_mask)
if self.overwrite_mask:
for mask in self.enable_for_mask:
self.register.set_pixel_register_value(mask, occ_mask)
else:
for mask in self.enable_for_mask:
disable_mask = np.logical_or(occ_mask, self.register.get_pixel_register_value(mask))
self.register.set_pixel_register_value(mask, disable_mask)
plot_occupancy(occ_mask.T, title='Merged Pixels', z_max=1, filename=analyze_raw_data.output_pdf)
plot_fancy_occupancy(occ_mask.T, z_max=1, filename=analyze_raw_data.output_pdf)
for mask in self.disable_for_mask:
mask_name = self.register.pixel_registers[mask]['name']
plot_occupancy(self.register.get_pixel_register_value(mask).T, title='%s Mask' % mask_name, z_max=1, filename=analyze_raw_data.output_pdf)
for mask in self.enable_for_mask:
mask_name = self.register.pixel_registers[mask]['name']
plot_occupancy(self.register.get_pixel_register_value(mask).T, title='%s Mask' % mask_name, z_max=1, filename=analyze_raw_data.output_pdf)
def analyze(self):
self.register.set_global_register_value("Vthin_AltFine",
self.last_good_threshold)
self.register.set_pixel_register_value('TDAC', self.last_good_tdac)
self.register.set_pixel_register_value('Enable',
self.last_good_enable_mask)
with AnalyzeRawData(raw_data_file=self.output_filename,
create_pdf=True) as analyze_raw_data:
analyze_raw_data.create_source_scan_hist = True
analyze_raw_data.interpreter.set_warning_output(False)
analyze_raw_data.interpret_word_table()
analyze_raw_data.interpreter.print_summary()
analyze_raw_data.plot_histograms()
plot_occupancy(self.last_occupancy_hist.T,
title='Noisy Pixels at Vthin_AltFine %d Step %d' %
(self.last_reg_val, self.last_step),
filename=analyze_raw_data.output_pdf)
plot_fancy_occupancy(self.last_occupancy_hist.T,
filename=analyze_raw_data.output_pdf)
plot_occupancy(self.last_occupancy_mask.T,
title='Occupancy Mask at Vthin_AltFine %d Step %d' %
(self.last_reg_val, self.last_step),
z_max=1,
filename=analyze_raw_data.output_pdf)
plot_fancy_occupancy(self.last_occupancy_mask.T,
filename=analyze_raw_data.output_pdf)
plotThreeWay(self.last_tdac_distribution.T,
title='TDAC at Vthin_AltFine %d Step %d' %
(self.last_reg_val, self.last_step),
x_axis_title="TDAC",
filename=analyze_raw_data.output_pdf,
maximum=31,
bins=32)
plot_occupancy(self.last_tdac_distribution.T,
title='TDAC at Vthin_AltFine %d Step %d' %
(self.last_reg_val, self.last_step),
z_max=31,
filename=analyze_raw_data.output_pdf)
plot_occupancy(self.register.get_pixel_register_value('Enable').T,
title='Enable Mask',
z_max=1,
filename=analyze_raw_data.output_pdf)
plot_fancy_occupancy(
self.register.get_pixel_register_value('Enable').T,
filename=analyze_raw_data.output_pdf)
def analyze(self):
self.register.set_global_register_value("Vthin_AltFine", self.last_good_threshold + self.increase_threshold)
self.register.set_pixel_register_value('TDAC', self.last_good_tdac)
self.register.set_pixel_register_value('Enable', self.last_good_enable_mask)
with AnalyzeRawData(raw_data_file=self.output_filename, create_pdf=True) as analyze_raw_data:
analyze_raw_data.create_source_scan_hist = True
analyze_raw_data.interpreter.set_warning_output(False)
analyze_raw_data.interpret_word_table()
analyze_raw_data.interpreter.print_summary()
analyze_raw_data.plot_histograms()
plot_occupancy(self.last_occupancy_hist.T, title='Noisy Pixels at Vthin_AltFine %d Step %d' % (self.last_reg_val, self.last_step), filename=analyze_raw_data.output_pdf)
plot_fancy_occupancy(self.last_occupancy_hist.T, filename=analyze_raw_data.output_pdf)
plot_occupancy(self.last_occupancy_mask.T, title='Occupancy Mask at Vthin_AltFine %d Step %d' % (self.last_reg_val, self.last_step), z_max=1, filename=analyze_raw_data.output_pdf)
plot_fancy_occupancy(self.last_occupancy_mask.T, filename=analyze_raw_data.output_pdf)
plot_three_way(self.last_tdac_distribution.T, title='TDAC at Vthin_AltFine %d Step %d' % (self.last_reg_val, self.last_step), x_axis_title="TDAC", filename=analyze_raw_data.output_pdf, maximum=31, bins=32)
plot_occupancy(self.last_tdac_distribution.T, title='TDAC at Vthin_AltFine %d Step %d' % (self.last_reg_val, self.last_step), z_max=31, filename=analyze_raw_data.output_pdf)
plot_occupancy(self.register.get_pixel_register_value('Enable').T, title='Enable Mask', z_max=1, filename=analyze_raw_data.output_pdf)
plot_fancy_occupancy(self.register.get_pixel_register_value('Enable').T, filename=analyze_raw_data.output_pdf)
def analyze(self):
with AnalyzeRawData(raw_data_file=self.output_filename, create_pdf=True) as analyze_raw_data:
analyze_raw_data.interpreter.set_warning_output(False)
analyze_raw_data.create_source_scan_hist = True
analyze_raw_data.create_hit_table = False
analyze_raw_data.interpret_word_table()
analyze_raw_data.plot_histograms()
analyze_raw_data.interpreter.print_summary()
# get occupancy hist
occ_hist = analyze_raw_data.out_file_h5.root.HistOcc[:, :, 0].T
self.occ_mask = np.zeros(shape=occ_hist.shape, dtype=np.dtype('>u1'))
# noisy pixels are set to 1
self.occ_mask[occ_hist > self.abs_occ_limit] = 1
# make inverse
self.inv_occ_mask = invert_pixel_mask(self.occ_mask)
# generate masked occupancy hist
masked_occ_hist = occ_hist.copy()
masked_occ_hist[self.occ_mask == 1] = 0
if self.overwrite_mask:
for mask in self.disable_for_mask:
self.register.set_pixel_register_value(mask, self.inv_occ_mask)
else:
for mask in self.disable_for_mask:
enable_mask = self.register.get_pixel_register_value(mask)
new_enable_mask = np.logical_and(self.inv_occ_mask, enable_mask)
self.register.set_pixel_register_value(mask, new_enable_mask)
if self.overwrite_mask:
for mask in self.enable_for_mask:
self.register.set_pixel_register_value(mask, self.occ_mask)
else:
for mask in self.enable_for_mask:
disable_mask = self.register.get_pixel_register_value(mask)
new_disable_mask = np.logical_or(self.occ_mask, disable_mask)
self.register.set_pixel_register_value(mask, new_disable_mask)
plot_occupancy(self.occ_mask.T, title='Noisy Pixels', z_max=1, filename=analyze_raw_data.output_pdf)
plot_fancy_occupancy(self.occ_mask.T, z_max=1, filename=analyze_raw_data.output_pdf)
for mask in self.disable_for_mask:
mask_name = self.register.pixel_registers[mask]['name']
plot_occupancy(self.register.get_pixel_register_value(mask).T, title='%s Mask' % mask_name, z_max=1, filename=analyze_raw_data.output_pdf)
for mask in self.enable_for_mask:
mask_name = self.register.pixel_registers[mask]['name']
plot_occupancy(self.register.get_pixel_register_value(mask).T, title='%s Mask' % mask_name, z_max=1, filename=analyze_raw_data.output_pdf)
# adding Poisson statistics plots
fig = Figure()
FigureCanvas(fig)
ax = fig.add_subplot(111)
ax.set_title("Hit statistics")
hist, bin_edges = np.histogram(occ_hist, bins=np.arange(0, np.max(occ_hist) + 2, 1))
try:
_, idx = hist_quantiles(hist, [0.0, 0.9], return_indices=True)
except IndexError:
idx = [0, 1]
bins = np.arange(0, np.maximum(bin_edges[idx[1]], stats.poisson.ppf(0.9999, mu=self.occupancy_limit * self.n_triggers * self.consecutive_lvl1)) + 2, 1)
ax.hist(occ_hist.flatten(), bins=bins, align='left', alpha=0.5, label="Measured occupancy before masking noisy pixels")
ax.hist(masked_occ_hist.flatten(), bins=bins, align='left', alpha=0.5, label="Measured occupancy after masking noisy pixels")
ax.bar(x=bins[:-1], height=stats.poisson.pmf(k=bins[:-1], mu=self.occupancy_limit * self.n_triggers * self.consecutive_lvl1) * self.register.get_pixel_register_value("Enable").sum(), alpha=0.5, width=1.0, color="r", label="Expected occupancy (Poisson statistics)")
# ax.hist(stats.poisson.rvs(mu=self.occupancy_limit * self.n_triggers * self.consecutive_lvl1, size=self.register.get_pixel_register_value("Enable").sum()), bins=bins, align='left', alpha=0.5, label="Expected occupancy (Poisson statistics)")
ax.set_xlabel('#Hits')
ax.set_ylabel('#Pixels')
ax.legend()
analyze_raw_data.output_pdf.savefig(fig)
def analyze(self):
with AnalyzeRawData(raw_data_file=self.output_filename,
create_pdf=True) as analyze_raw_data:
analyze_raw_data.create_cluster_size_hist = False
analyze_raw_data.create_source_scan_hist = True
analyze_raw_data.create_cluster_tot_hist = False
analyze_raw_data.interpreter.set_warning_output(False)
analyze_raw_data.interpret_word_table()
analyze_raw_data.interpreter.print_summary()
analyze_raw_data.plot_histograms()
occ_hist = analyze_raw_data.out_file_h5.root.HistOcc[:, :, 0].T
self.occ_mask = np.zeros(shape=occ_hist.shape,
dtype=np.dtype('>u1'))
# n largest elements
n_largest_elements = np.sort(
occ_hist[occ_hist > self.low_value])[-self.mask_high_count:]
# noisy pixels are set to 1
if n_largest_elements.shape[0] > 0:
self.occ_mask[occ_hist >= n_largest_elements[0]] = 1
# make inverse
self.inv_occ_mask = invert_pixel_mask(self.occ_mask)
if self.overwrite_mask:
for mask in self.disable_for_mask:
self.register.set_pixel_register_value(
mask, self.inv_occ_mask)
else:
for mask in self.disable_for_mask:
enable_mask = np.logical_and(
self.inv_occ_mask,
self.register.get_pixel_register_value(mask))
self.register.set_pixel_register_value(mask, enable_mask)
if self.overwrite_mask:
for mask in self.enable_for_mask:
self.register.set_pixel_register_value(mask, self.occ_mask)
else:
for mask in self.enable_for_mask:
disable_mask = np.logical_or(
self.occ_mask,
self.register.get_pixel_register_value(mask))
self.register.set_pixel_register_value(mask, disable_mask)
plot_occupancy(self.occ_mask.T,
title='Noisy Pixels',
z_max=1,
filename=analyze_raw_data.output_pdf)
plot_fancy_occupancy(self.occ_mask.T,
z_max=1,
filename=analyze_raw_data.output_pdf)
for mask in self.disable_for_mask:
mask_name = self.register.pixel_registers[mask]['name']
plot_occupancy(self.register.get_pixel_register_value(mask).T,
title='%s Mask' % mask_name,
z_max=1,
filename=analyze_raw_data.output_pdf)
for mask in self.enable_for_mask:
mask_name = self.register.pixel_registers[mask]['name']
plot_occupancy(self.register.get_pixel_register_value(mask).T,
title='%s Mask' % mask_name,
z_max=1,
filename=analyze_raw_data.output_pdf)
