def test_efficiency_calculation(self):
efficiencies = result_analysis.calculate_efficiency(
input_tracks_file=analysis_utils.get_data(
'fixtures/result_analysis/Tracks_result.h5'),
input_alignment_file=analysis_utils.get_data(
'fixtures/result_analysis/Alignment_result.h5'),
output_efficiency_file=os.path.join(self.output_folder,
'Efficiency.h5'),
bin_size=[(250, 50)] * 4,
sensor_size=[(250 * 80., 336 * 50.)] * 4,
pixel_size=[(250, 50)] * 4,
n_pixels=[(80, 336)] * 4,
minimum_track_density=2,
use_duts=None,
cut_distance=500,
max_distance=500,
#col_range=[(1250, 17500)]*4,
#row_range=[(1000, 16000)]*4,
force_prealignment=True)
self.assertAlmostEqual(efficiencies[0],
100.000,
msg='DUT 0 efficiencies do not match',
places=3)
self.assertAlmostEqual(efficiencies[1],
98.7013,
msg='DUT 1 efficiencies do not match',
places=3)
self.assertAlmostEqual(efficiencies[2],
97.4684,
msg='DUT 2 efficiencies do not match',
places=3)
self.assertAlmostEqual(efficiencies[3],
100.000,
msg='DUT 3 efficiencies do not match',
places=3)
def run_analysis():
# The location of the example data files, one file per DUT
data_files = [
r'H:\Testbeam_05052016_LFCMOS\Telescope_data\kartel-converted-synchronized_plane0.h5',
r'H:\Testbeam_05052016_LFCMOS\Telescope_data\kartel-converted-synchronized_plane1.h5',
r'H:\Testbeam_05052016_LFCMOS\Telescope_data\kartel-converted-synchronized_plane2.h5',
r'H:\Testbeam_05052016_LFCMOS\Telescope_data\fe_dut-converted-synchronized_plane0.h5',
r'H:\Testbeam_05052016_LFCMOS\Telescope_data\fe_dut-converted-synchronized_plane1.h5',
r'H:\Testbeam_05052016_LFCMOS\Telescope_data\kartel-converted-synchronized_plane3.h5',
r'H:\Testbeam_05052016_LFCMOS\Telescope_data\kartel-converted-synchronized_plane4.h5',
r'H:\Testbeam_05052016_LFCMOS\Telescope_data\kartel-converted-synchronized_plane5.h5'
] # The first device is the reference for the coordinate system
# Pixel dimesions and matrix size of the DUTs
pixel_size = [(18.4, 18.4), (18.4, 18.4), (18.4, 18.4), (250, 50),
(250, 50), (18.4, 18.4), (18.4, 18.4),
(18.4, 18.4)] # (Column, row) pixel pitch in um
n_pixels = [(1152, 576), (1152, 576), (1152, 576), (80, 336), (80, 336),
(1152, 576), (1152, 576),
(1152, 576)] # (Column, row) dimensions of the pixel matrix
z_positions = [
0., 20000, 40000, 40000 + 101000, 40000 + 101000 + 23000, 247000,
267000, 287000
] # in um
dut_names = ("Tel 0", "Tel 1", "Tel 2", "LFCMOS3", "FEI4 Reference",
"Tel 3", "Tel 4", "Tel 5") # Friendly names for plotting
# Folder where all output data and plots are stored
output_folder = r'H:\Testbeam_05052016_LFCMOS\output'
# The following shows a complete test beam analysis by calling the seperate function in correct order
# Generate noisy pixel mask for all DUTs
threshold = [2, 2, 2, 10, 10, 2, 2, 2]
for i, data_file in enumerate(data_files):
hit_analysis.generate_pixel_mask(input_hits_file=data_file,
n_pixel=n_pixels[i],
pixel_mask_name='NoisyPixelMask',
pixel_size=pixel_size[i],
threshold=threshold[i],
dut_name=dut_names[i])
# Cluster hits from all DUTs
column_cluster_distance = [3, 3, 3, 2, 2, 3, 3, 3]
row_cluster_distance = [3, 3, 3, 3, 3, 3, 3, 3]
frame_cluster_distance = [0, 0, 0, 0, 0, 0, 0, 0]
for i, data_file in enumerate(data_files):
hit_analysis.cluster_hits(
input_hits_file=data_file,
input_noisy_pixel_mask_file=os.path.splitext(data_files[i])[0] +
'_noisy_pixel_mask.h5',
min_hit_charge=0,
max_hit_charge=13,
column_cluster_distance=column_cluster_distance[i],
row_cluster_distance=row_cluster_distance[i],
frame_cluster_distance=frame_cluster_distance[i],
dut_name=dut_names[i])
# Generate filenames for cluster data
input_cluster_files = [
os.path.splitext(data_file)[0] + '_clustered.h5'
for data_file in data_files
]
# Correlate the row / column of each DUT
dut_alignment.correlate_cluster(input_cluster_files=input_cluster_files,
output_correlation_file=os.path.join(
output_folder, 'Correlation.h5'),
n_pixels=n_pixels,
pixel_size=pixel_size,
dut_names=dut_names)
# Create prealignment relative to the first DUT from the correlation data
dut_alignment.prealignment(
input_correlation_file=os.path.join(output_folder, 'Correlation.h5'),
output_alignment_file=os.path.join(output_folder, 'Alignment.h5'),
z_positions=z_positions,
pixel_size=pixel_size,
dut_names=dut_names,
fit_background=True,
non_interactive=False
) # Tries to find cuts automatically; deactivate to do this manualy
# Merge the cluster tables to one merged table aligned at the event number
dut_alignment.merge_cluster_data(input_cluster_files=input_cluster_files,
output_merged_file=os.path.join(
output_folder, 'Merged.h5'),
n_pixels=n_pixels,
pixel_size=pixel_size)
# Apply the prealignment to the merged cluster table to create tracklets
dut_alignment.apply_alignment(
input_hit_file=os.path.join(output_folder, 'Merged.h5'),
input_alignment_file=os.path.join(output_folder, 'Alignment.h5'),
output_hit_file=os.path.join(output_folder, 'Tracklets_prealigned.h5'),
force_prealignment=True)
# Find tracks from the prealigned tracklets and stores the with quality indicator into track candidates table
track_analysis.find_tracks(
input_tracklets_file=os.path.join(output_folder,
'Tracklets_prealigned.h5'),
input_alignment_file=os.path.join(output_folder, 'Alignment.h5'),
output_track_candidates_file=os.path.join(
output_folder, 'TrackCandidates_prealignment.h5'))
# Select tracks with a hit in the time reference (DUT 4) and all position devices to increase analysis speed due to data reduction
data_selection.select_hits(hit_file=os.path.join(
output_folder, 'TrackCandidates_prealignment.h5'),
track_quality=0b11110111,
track_quality_mask=0b11110111)
# Do an alignment step with the track candidates, corrects rotations and is therefore much more precise than simple prealignment
dut_alignment.alignment(
input_track_candidates_file=os.path.join(
output_folder, 'TrackCandidates_prealignment_reduced.h5'),
input_alignment_file=os.path.join(output_folder, 'Alignment.h5'),
# Order of combinaions of planes to align, one should start with high resoultion planes (here: telescope planes)
align_duts=[
[0, 1, 2, 5, 6, 7], # align the telescope planes first
[4], # align the time reference after the telescope alignment
[3]
], # align the DUT last and not with the reference since it is rather small and would make the time reference alinmnt worse
# The DUTs to be used in the fit, always just the high resolution Mimosa26 planes used
select_fit_duts=[0, 1, 2, 5, 6, 7],
# The DUTs to be required to have a hit for the alignment
select_hit_duts=[
[0, 1, 2, 4, 5, 6, 7], # Take tracks with time reference hit
[0, 1, 2, 4, 5, 6, 7], # Take tracks with time reference hit
[0, 1, 2, 3, 4, 5, 6, 7]
], # Also require hit in the small DUT
# The required track quality per alignment step and DUT
selection_track_quality=[
[1, 1, 1, 0, 1, 1,
1], # Do not require a good hit in the time refernce
[1, 1, 1, 1, 1, 1, 1],
[1, 1, 1, 1, 0, 1, 1, 1]
], # Do not require a good hit in the small DUT
initial_rotation=[
[0., 0., 0.],
[0., 0., 0.],
[0., 0., 0.],
# Devices 3, 4 are heavily rotated (inverted), this is not implemented now
# Thus one has to set the correct rotation angles here manually
[np.pi - 0.05, -0.05, -0.005],
[np.pi - 0.01, -0.02, -0.0005],
[0., 0, 0.],
[0., 0, 0.],
[0., 0, 0.]
],
initial_translation=[
[0., 0, 0.],
[0., 0, 0.],
[0., 0, 0.],
# Devices 3, 4 are heavily rotated (inverted), this is not implemented now
# Thus one has to set the correct positions here manually
[11540, 18791, 0.],
[710., 9851., 0.],
[0., 0, 0.],
[0., 0, 0.],
[0., 0, 0.]
],
n_pixels=n_pixels,
use_n_tracks=
200000, # Do the alignment only on a subset of data, needed for reasonable run time
pixel_size=pixel_size)
# Apply new alignment to data
# Revert alignment from track candidates. Usually one would just apply the alignment to the merged data.
# Due to the large beam angle track finding fails on aligned data. Thus rely on the found tracks from prealignment.
dut_alignment.apply_alignment(
input_hit_file=os.path.join(output_folder,
'TrackCandidates_prealignment_reduced.h5'),
input_alignment_file=os.path.join(output_folder, 'Alignment.h5'),
output_hit_file=os.path.join(
output_folder, 'Merged_small.h5'
), # This is the new not aligned but preselected merged data file to apply (pre-) alignment on
inverse=True,
force_prealignment=True)
# Apply the alignment to the merged cluster table to create tracklets
dut_alignment.apply_alignment(
input_hit_file=os.path.join(output_folder, 'Merged_small.h5'),
input_alignment_file=os.path.join(output_folder, 'Alignment.h5'),
output_hit_file=os.path.join(output_folder, 'TrackCandidates.h5'))
# Fit track using alignment
track_analysis.fit_tracks(
input_track_candidates_file=os.path.join(output_folder,
'TrackCandidates.h5'),
input_alignment_file=os.path.join(output_folder, 'Alignment.h5'),
output_tracks_file=os.path.join(output_folder, 'Tracks.h5'),
select_hit_duts=[0, 1, 2, 4, 5, 6, 7],
select_fit_duts=[0, 1, 2, 5, 6, 7],
selection_track_quality=1
) # Take all tracks with good hits, do not care about time reference hit quality
# Create unconstrained residuals with aligned data
result_analysis.calculate_residuals(
input_tracks_file=os.path.join(output_folder, 'Tracks.h5'),
input_alignment_file=os.path.join(output_folder, 'Alignment.h5'),
output_residuals_file=os.path.join(output_folder, 'Residuals.h5'),
n_pixels=n_pixels,
pixel_size=pixel_size)
# Calculate efficiency with aligned data
result_analysis.calculate_efficiency(
input_tracks_file=os.path.join(output_folder, 'Tracks.h5'),
input_alignment_file=os.path.join(output_folder, 'Alignment.h5'),
output_efficiency_file=os.path.join(output_folder, 'Efficiency.h5'),
bin_size=(10, 10),
use_duts=[3],
sensor_size=[(20000, 10000), (20000, 10000), (20000, 10000),
(20000, 20000), (20000, 10000), (20000, 10000),
(20000, 10000)])
# Fit tracks using prealignmend
track_analysis.fit_tracks(
input_track_candidates_file=os.path.join(
output_folder, 'TrackCandidates_prealignment_reduced.h5'),
input_alignment_file=os.path.join(output_folder, 'Alignment.h5'),
output_tracks_file=os.path.join(output_folder,
'Tracks_prealignment.h5'),
force_prealignment=True,
select_hit_duts=[0, 1, 2, 4, 5, 6, 7],
select_fit_duts=[0, 1, 2, 5, 6, 7],
selection_track_quality=1
) # Take all tracks with good hits, do not care about time reference hit quality
# Create unconstrained residuals with prealigned data
result_analysis.calculate_residuals(
input_tracks_file=os.path.join(output_folder,
'Tracks_prealignment.h5'),
input_alignment_file=os.path.join(output_folder, 'Alignment.h5'),
output_residuals_file=os.path.join(output_folder,
'Residuals_prealignment.h5'),
force_prealignment=True,
n_pixels=n_pixels,
pixel_size=pixel_size)
# Create efficiency plot with prealigned data
result_analysis.calculate_efficiency(
input_tracks_file=os.path.join(output_folder,
'Tracks_prealignment.h5'),
input_alignment_file=os.path.join(output_folder, 'Alignment.h5'),
output_efficiency_file=os.path.join(output_folder,
'Efficiency_prealignment.h5'),
force_prealignment=True,
bin_size=(10, 10),
use_duts=[3],
sensor_size=[(20000, 10000), (20000, 10000), (20000, 10000),
(20000, 20000), (20000, 10000), (20000, 10000),
(20000, 10000)])
def run_analysis(hit_files):
# Create output subfolder where all output data and plots are stored
output_folder = os.path.join(
os.path.split(hit_files[0])[0], 'output_fei4_telescope')
if not os.path.exists(output_folder):
os.makedirs(output_folder)
mask_files = [(os.path.splitext(hit_file)[0] + '_mask.h5')
for hit_file in hit_files]
cluster_files = [(os.path.splitext(hit_file)[0] + '_clustered.h5')
for hit_file in hit_files]
z_positions = [0.0, 19500.0, 108800.0, 128300.0] # in um
initial_configuration = os.path.join(output_folder, 'telescope.yaml')
telescope = Telescope()
telescope.add_dut(dut_type="FEI4",
dut_id=0,
translation_x=0,
translation_y=0,
translation_z=z_positions[0],
rotation_alpha=0,
rotation_beta=0,
rotation_gamma=0,
name="Telescope 1")
telescope.add_dut(dut_type="FEI4",
dut_id=1,
translation_x=0,
translation_y=0,
translation_z=z_positions[1],
rotation_alpha=0,
rotation_beta=0,
rotation_gamma=0,
name="Telescope 2")
telescope.add_dut(dut_type="FEI4",
dut_id=2,
translation_x=0,
translation_y=0,
translation_z=z_positions[2],
rotation_alpha=0,
rotation_beta=0,
rotation_gamma=0,
name="Telescope 3")
telescope.add_dut(dut_type="FEI4",
dut_id=3,
translation_x=0,
translation_y=0,
translation_z=z_positions[3],
rotation_alpha=0,
rotation_beta=0,
rotation_gamma=0,
name="Telescope 4")
telescope.save_configuration(initial_configuration)
prealigned_configuration = os.path.join(output_folder,
'telescope_prealigned.yaml')
aligned_configuration = os.path.join(output_folder,
'telescope_aligned.yaml')
check_files = hit_analysis.check(
telescope_configuration=initial_configuration,
input_hit_files=hit_files)
# Generate noisy pixel mask for all DUTs
thresholds = [100, 100, 100, 100]
pixel_mask_names = ["NoisyPixelMask"] * len(thresholds)
mask_files = hit_analysis.mask(
telescope_configuration=initial_configuration,
input_hit_files=hit_files,
pixel_mask_names=pixel_mask_names,
thresholds=thresholds)
# Cluster hits from all DUTs
use_positions = [False, False, False, False]
min_hit_charges = [0, 0, 0, 0]
max_hit_charges = [13, 13, 13, 13]
column_cluster_distances = [1, 1, 1, 1]
row_cluster_distances = [3, 3, 3, 3]
frame_cluster_distances = [4, 4, 4, 4]
cluster_files = hit_analysis.cluster(
telescope_configuration=initial_configuration,
select_duts=None,
input_hit_files=hit_files,
input_mask_files=[
None if val else mask_files[i]
for i, val in enumerate(use_positions)
],
use_positions=use_positions,
min_hit_charges=min_hit_charges,
max_hit_charges=max_hit_charges,
column_cluster_distances=column_cluster_distances,
row_cluster_distances=row_cluster_distances,
frame_cluster_distances=frame_cluster_distances)
# Correlate each DUT with the first DUT
hit_analysis.correlate(telescope_configuration=initial_configuration,
input_files=cluster_files,
output_correlation_file=os.path.join(
output_folder, 'Correlation.h5'),
resolution=(250.0, 50.0),
select_reference_duts=0)
# Create pre-alignment, take first DUT as reference
prealigned_configuration = dut_alignment.prealign(
telescope_configuration=initial_configuration,
input_correlation_file=os.path.join(output_folder, 'Correlation.h5'),
reduce_background=True,
select_reference_dut=0)
# Merge all cluster tables into a single table
hit_analysis.merge_cluster_data(
telescope_configuration=initial_configuration,
input_cluster_files=cluster_files,
output_merged_file=os.path.join(output_folder, 'Merged.h5'))
# Create alignment, take first and last DUT as reference (telescope DUTs)
aligned_configuration = dut_alignment.align(
telescope_configuration=prealigned_configuration,
input_merged_file=os.path.join(output_folder, 'Merged.h5'),
select_duts=[[0, 1, 2, 3]], # align all planes at once
select_telescope_duts=[
0, 3
], # add outermost planes, z-axis positions are fixed for telescope DUTs, if not stated otherwise (see select_alignment_parameters)
select_fit_duts=[0, 1, 2, 3], # use all DUTs for track fit
select_hit_duts=[[0, 1, 2, 3]], # require hits in all DUTs
max_iterations=[
7
], # number of alignment iterations, the higher the number the more precise
max_events=(100000), # limit number of events to speed up alignment
quality_distances=[(250.0, 50.0), (250.0, 50.0), (250.0, 50.0),
(250.0, 50.0)],
isolation_distances=(1000.0, 1000.0),
use_limits=True,
plot=True)
# Find tracks from the tracklets and create a track candidates table
track_analysis.find_tracks(telescope_configuration=aligned_configuration,
input_merged_file=os.path.join(
output_folder, 'Merged.h5'),
output_track_candidates_file=os.path.join(
output_folder,
'TrackCandidates_aligned.h5'),
align_to_beam=True)
# Fit the track candidates, assign quality flags, and create a track table
track_analysis.fit_tracks(
telescope_configuration=aligned_configuration,
input_track_candidates_file=os.path.join(output_folder,
'TrackCandidates_aligned.h5'),
output_tracks_file=os.path.join(output_folder, 'Tracks_aligned.h5'),
select_duts=[0, 1, 2, 3],
select_fit_duts=(0, 1, 2, 3),
select_hit_duts=(0, 1, 2, 3),
exclude_dut_hit=True,
quality_distances=[(250.0, 50.0), (250.0, 50.0), (250.0, 50.0),
(250.0, 50.0)],
isolation_distances=(1000.0, 1000.0),
use_limits=False,
plot=True)
# Do additional track selection cuts on the tracks table
data_selection.select_tracks(
telescope_configuration=aligned_configuration,
input_tracks_file=os.path.join(output_folder, 'Tracks_aligned.h5'),
output_tracks_file=os.path.join(output_folder,
'Tracks_aligned_selected.h5'),
select_duts=[0, 1, 2, 3],
select_hit_duts=[[1, 2, 3], [0, 2, 3], [0, 1, 3], [0, 1, 2]],
select_no_hit_duts=None,
select_quality_duts=[[1, 2, 3], [0, 2, 3], [0, 1, 3], [0, 1, 2]],
query='(track_chi2 < 10)')
# Calculate the unconstrained residuals from final tracks to check the alignment
result_analysis.calculate_residuals(
telescope_configuration=aligned_configuration,
input_tracks_file=os.path.join(output_folder,
'Tracks_aligned_selected.h5'),
output_residuals_file=os.path.join(output_folder,
'Residuals_aligned.h5'),
select_duts=[0, 1, 2, 3],
nbins_per_pixel=20,
use_limits=True)
# Plotting of the tracks angles of the final tracks
result_analysis.histogram_track_angle(
telescope_configuration=aligned_configuration,
input_tracks_file=os.path.join(output_folder,
'Tracks_aligned_selected.h5'),
output_track_angle_file=None,
n_bins=200,
select_duts=[0, 1, 2, 3],
plot=True)
# Plotting of the 2D tracks density of the final tracks
plot_utils.plot_track_density(
telescope_configuration=aligned_configuration,
input_tracks_file=os.path.join(output_folder,
'Tracks_aligned_selected.h5'),
select_duts=[0, 1, 2, 3])
# Plotting of the 2D charge distribution of the final tracks
plot_utils.plot_charge_distribution(
telescope_configuration=aligned_configuration,
input_tracks_file=os.path.join(output_folder,
'Tracks_aligned_selected.h5'),
select_duts=[0, 1, 2, 3])
# Plotting of some final tracks (or track candidates) from selected event range
plot_utils.plot_events(
telescope_configuration=aligned_configuration,
input_tracks_file=os.path.join(output_folder,
'Tracks_aligned_selected.h5'),
output_pdf_file=os.path.join(output_folder, 'Events.pdf'),
select_duts=[1],
event_range=(0, 40))
# Create final efficiency plots from final tracks
result_analysis.calculate_efficiency(
telescope_configuration=aligned_configuration,
input_tracks_file=os.path.join(output_folder,
'Tracks_aligned_selected.h5'),
output_efficiency_file=os.path.join(output_folder, 'Efficiency.h5'),
select_duts=[0, 1, 2, 3],
resolutions=(250, 50),
extend_areas=(2000, 2000),
plot_ranges=None,
efficiency_regions=None,
minimum_track_density=1,
cut_distances=(1000.0, 1000.0))
def run_analysis(n_events):
# Start simulator with random seed 0
sim = SimulateData(random_seed=0)
# All simulator std. settings are listed here and can be changed
# Dimensions are in um, angles in mRad, temperatures in Kelvin
# voltages in Volt
# General setup
sim.n_duts = 6 # Number of DUTs in the simulation
sim.z_positions = [i * 10000 for i in range(sim.n_duts)]
sim.offsets = [(-10000 + 111 * 0., -10000 + 111 * 0.)
for i in range(sim.n_duts)]
sim.rotations = [(0, 0, 0)] * sim.n_duts # in rotation around x, y, z axis
sim.temperature = 300 # needed for charge sharing calculation
# Beam related settings
sim.beam_position = (0, 0) # Average beam position in x, y at z = 0
sim.beam_position_sigma = (2000, 2000) # in x, y at z = 0
sim.beam_momentum = 3200 # MeV
sim.beam_angle = 0 # Average beam angle in theta at z = 0
sim.beam_angle_sigma = 2 # Deviation of average beam angle in theta
sim.tracks_per_event = 3 # Average number of tracks per event
# Deviation from the average number of tracks
# Allows for no track per event possible!
sim.tracks_per_event_sigma = 1
# Device specific settings
sim.dut_bias = [50] * sim.n_duts # Sensor bias voltage
sim.dut_thickness = [200] * sim.n_duts # Sensor thickness
# Detection threshold for each device in electrons, influences efficiency!
sim.dut_threshold = [0.] * sim.n_duts
sim.dut_noise = [0.] * sim.n_duts # Noise for each device in electrons
sim.dut_pixel_size = [(50, 18.4)] * sim.n_duts # Pixel size in x / y
sim.dut_n_pixel = [(400, 1100)] * sim.n_duts # Number of pixel in x / y
# Efficiency for each device from 0. to 1. for hits above threshold
sim.dut_efficiencies = [1.] * sim.n_duts
# The effective material budget (sensor + passive compoonents) given in
# total material distance / total radiation length
# (https://cdsweb.cern.ch/record/1279627/files/PH-EP-Tech-Note-2010-013.pdf)
# 0 means no multiple scattering; std. setting is the sensor thickness made
# of silicon as material budget
sim.dut_material_budget = [
sim.dut_thickness[i] * 1e-4 / 9.370 for i in range(sim.n_duts)
]
# Digitization settings
sim.digitization_charge_sharing = True
# Shuffle hits per event to challenge track finding
sim.digitization_shuffle_hits = True
# Translate hit position on DUT plane to channel indices (column / row)
sim.digitization_pixel_discretization = True
# Create the data
output_folder = 'simulation' # Define a folder for output data
if not os.path.exists(output_folder):
os.makedirs(output_folder)
sim.create_data_and_store(os.path.join(output_folder, 'simulated_data'),
n_events=n_events)
# The simulated data files, one file per DUT
data_files = [
os.path.join(output_folder, r'simulated_data_DUT%d.h5' % i)
for i in range(sim.n_duts)
]
# The following shows a complete test beam analysis by calling the separate
# function in correct order
# Cluster hits from all DUTs
for i, data_file in enumerate(data_files):
hit_analysis.cluster_hits(input_hits_file=data_file,
min_hit_charge=1,
max_hit_charge=2**16,
column_cluster_distance=1,
row_cluster_distance=1,
frame_cluster_distance=2,
dut_name=data_files[i])
# Generate filenames for cluster data
input_cluster_files = [
os.path.splitext(data_file)[0] + '_clustered.h5'
for data_file in data_files
]
# Correlate the row / column of each DUT
dut_alignment.correlate_cluster(input_cluster_files=input_cluster_files,
output_correlation_file=os.path.join(
output_folder, 'Correlation.h5'),
n_pixels=sim.dut_n_pixel,
pixel_size=sim.dut_pixel_size)
# Create alignment data for the DUT positions to the first DUT from the
# correlation data. When needed, set offset and error cut for each DUT
# as list of tuples
dut_alignment.prealignment(
input_correlation_file=os.path.join(output_folder, 'Correlation.h5'),
output_alignment_file=os.path.join(output_folder, 'Alignment.h5'),
z_positions=sim.z_positions,
pixel_size=sim.dut_pixel_size,
# Deactivate if you have a large dataset, enhances alignment slightly
no_fit=True,
fit_background=False
if not (sim.tracks_per_event or sim.tracks_per_event_sigma) else True,
# Tries to find cuts automatically; deactivate to do this manualy
non_interactive=True)
# Correct all DUT hits via alignment information and merge the cluster
# tables to one tracklets table aligned at the event number
dut_alignment.merge_cluster_data(input_cluster_files=input_cluster_files,
output_merged_file=os.path.join(
output_folder, 'Merged.h5'),
n_pixels=sim.dut_n_pixel,
pixel_size=sim.dut_pixel_size)
dut_alignment.apply_alignment(
input_hit_file=os.path.join(output_folder, 'Merged.h5'),
input_alignment_file=os.path.join(output_folder, 'Alignment.h5'),
output_hit_file=os.path.join(output_folder, 'Tracklets_prealigned.h5'),
# If there is already an alignment info in the alignment file this has
# to be set
force_prealignment=True)
# Find tracks from the tracklets and stores the with quality indicator
# into track candidates table
track_analysis.find_tracks(
input_tracklets_file=os.path.join(output_folder,
'Tracklets_prealigned.h5'),
input_alignment_file=os.path.join(output_folder, 'Alignment.h5'),
output_track_candidates_file=os.path.join(
output_folder, 'TrackCandidates_prealigned.h5'))
# Fit the track candidates and create new track table
track_analysis.fit_tracks(
input_track_candidates_file=os.path.join(
output_folder, 'TrackCandidates_prealigned.h5'),
input_alignment_file=os.path.join(output_folder, 'Alignment.h5'),
output_tracks_file=os.path.join(output_folder, 'Tracks_prealigned.h5'),
# To get unconstrained residuals do not use DUT hit for track fit
exclude_dut_hit=True,
selection_track_quality=0,
# To get close to excact efficiency heavily avoid merged tracks
min_track_distance=1000,
force_prealignment=True)
result_analysis.calculate_efficiency(
input_tracks_file=os.path.join(output_folder, 'Tracks_prealigned.h5'),
input_alignment_file=os.path.join(output_folder, 'Alignment.h5'),
output_efficiency_file=os.path.join(output_folder, 'Efficiency.h5'),
bin_size=[(250, 50)],
sensor_size=[(250. * 80, 50. * 336)],
minimum_track_density=2,
use_duts=None,
cut_distance=500,
max_distance=500,
col_range=None,
row_range=None,
pixel_size=sim.dut_pixel_size,
n_pixels=sim.dut_n_pixel,
force_prealignment=True,
show_inefficient_events=True)