PixelDefectsEmulatorPostInclude Namespace Reference

Functions
def	emulateITkPixelDefects (flags, cfg, ModulePatterns=[[-2, 2, 0, 99,-99, 99,-99, 99, 0, 9999, 0, 1, 0]], DefectProbabilities=[[0., 1e-2, 1e-1, 0.]], NDefectFractionsPerPattern=[[1.,-1, 1.]], NoiseProbability=[], NoiseShape=[], CornerDefectParamsPerPattern=[], NCornerDefectFractionsPerPattern=[], RngPerDefectType=False, DefectsInputFiles=[], DefectsOutputFile=None, FillHistogramsPerPattern=False, FillEtaPhiHistogramsPerPattern=False, int MaxRandomPositionAttempts=10, str HistogramGroupName="ITkPixelDefects", str HistogramFileName="itk_pixel_defects_opt1.root", PropagateDefectsToStatus=True)
def	emulatePixelDefects (flags, cfg, ModulePatterns=None, DefectProbabilities=None, NDefectFractionsPerPattern=None, RngPerDefectType=False, DefectsInputFiles=[], DefectsOutputFile=None, FillHistogramsPerPattern=False, FillEtaPhiHistogramsPerPattern=False, str HistogramGroupName="PixelDefects", str HistogramFileName="pixel_defects.root")
def	poissonFractions (cc_defect_prob=1e-1, max_n=5)
def	quadProb (circuit_prob)
def	fractionsForExactlyNCoreColumnDefects (ExactlyNCoreColumnDefects=1)
def	makeITkDefectsParams (quad_cc_defect_prob, quad_fractions, circuit_cc_defect_prob, circuit_fractions, pixel_defect_prob=1e-2, module_defect_prob=0., cornerDefectProb=0., noiseProbability=None, noiseShape=[])
def	makeITkPixelNoise (noiseProb=0.)
def	emulateITkPixelDefectsOneCC (flags, cfg, FrontEndCCDefectProb=0.1, PixelDefectProb=1e-2, NumberOfCCDefects=1, ModuleDefectProb=0., CornerDefectProb=0., NoiseProb=0., RngPerDefectType=False, DefectsInputFiles=[], DefectsOutputFile=None, PropagateDefectsToStatus=True, HistogramFileName=None)
def	emulateITkPixelDefectsPoisson (flags, cfg, FrontEndCCDefectProb=0.1, PixelDefectProb=1e-2, ModuleDefectProb=0., CornerDefectProb=0., NoiseProb=0., RngPerDefectType=False, DefectsInputFiles=[], DefectsOutputFile=None, PropagateDefectsToStatus=True, HistogramFileName=None)
def	emulateITkPixelDefectsDefault (flags, cfg, FrontEndCCDefectProb=0.1, PixelDefectProb=1e-2, ModuleDefectProb=1e-2, CornerDefectProb=15e-2, NoiseProb=0., RngPerDefectType=False, DefectsInputFiles=[], DefectsOutputFile=None, PropagateDefectsToStatus=True, HistogramFileName=None)

Function Documentation

emulateITkPixelDefects()

def PixelDefectsEmulatorPostInclude.emulateITkPixelDefects	(		flags,
			cfg,
			ModulePatterns = [[-2,2,0,99,-99,99,-99,99,0,9999,0,1,0]],
			DefectProbabilities = [[0.,1e-2,1e-1,0.]],
			NDefectFractionsPerPattern = [[1.,-1, 1.]],
			NoiseProbability = [],
			NoiseShape = [],
			CornerDefectParamsPerPattern = [],
			NCornerDefectFractionsPerPattern = [],
			RngPerDefectType = False,
			DefectsInputFiles = [],
			DefectsOutputFile = None,
			FillHistogramsPerPattern = False,
			FillEtaPhiHistogramsPerPattern = False,
		int	MaxRandomPositionAttempts = 10,
		str	HistogramGroupName = "ITkPixelDefects",
		str	HistogramFileName = "itk_pixel_defects_opt1.root",
			PropagateDefectsToStatus = True
	)

Schedule conditions algorithm for emulated ITk pixel defects, and algorithms to drop RDOs overlapping with the emulated defects.
ModulePattern: criteria to match modules, which are lists of n-tuples where every two numbers of each n-tuple define a range
               to match parts of module identifiers (barrel/ec, layer/disk, eta., phi, columns, side) plus a flag (last
               element of each n-tuple), which is unused for pixel.
DefectProbabilities: list of n-tuples per criterion containing 4 probabilities: module, pixel to be defect, a module
                     to have at least one core column defect, circuit defect.
NDefectFractionsPerPattern: Fractions of exactly n-group defects (core-column, circuit) under condition that there is at least one
                            such group defect. There must be one n-tuple with fractions per criterion, and each fraction
                            n-tuple must contain for each group defect probability a non empty set of fractions of exactly 1, ... n defects.
                            Fractions for different group defects are separated by -1. There should be two sequences of
                            positive fractions separated by -1.
NoiseProbability: Empty or probabilities of a pixel to produce a spurious hit.
NoiseShape: binned PDF (i.e. list of fractions) to create tot values for spurious hits.
CornerDefectParamsPerPattern: parameters for corner defects per pattern can be created with e.g. makeCornerDefectParam
NCornerDefectFractionsPerPattern: fractions of 1,..4 corner defects
FillHistogramsPerPattern: if True histograms are filled per module pattern
FillEtaPhiHistogramsPerPattern: if True also fill xy, and rz histograms of defects per module.
HistogramGroupName: None (disables histogramming) or the histogram group name must be unique
HistogramFileName: None (disables histogramming) or a file name for writing the histograms.

Definition at line 38 of file PixelDefectsEmulatorPostInclude.py.

def emulateITkPixelDefects(flags,
                           cfg,
                           ModulePatterns=[[-2,2,0,99,-99,99,-99,99,0,9999,0,1,0]],
                           DefectProbabilities=[[0.,1e-2,1e-1,0.]],
                           NDefectFractionsPerPattern=[[1.,-1, 1.]],
                           NoiseProbability=[],
                           NoiseShape=[],
                           CornerDefectParamsPerPattern=[],
                           NCornerDefectFractionsPerPattern=[],
                           RngPerDefectType=False,
                           DefectsInputFiles=[],
                           DefectsOutputFile=None,
                           FillHistogramsPerPattern=False,
                           FillEtaPhiHistogramsPerPattern=False,
                           MaxRandomPositionAttempts: int=10,
                           HistogramGroupName: str="ITkPixelDefects",
                           HistogramFileName: str="itk_pixel_defects_opt1.root",
                           PropagateDefectsToStatus=True) :
    """
    Schedule conditions algorithm for emulated ITk pixel defects, and algorithms to drop RDOs overlapping with the emulated defects.
    ModulePattern: criteria to match modules, which are lists of n-tuples where every two numbers of each n-tuple define a range
                   to match parts of module identifiers (barrel/ec, layer/disk, eta., phi, columns, side) plus a flag (last
                   element of each n-tuple), which is unused for pixel.
    DefectProbabilities: list of n-tuples per criterion containing 4 probabilities: module, pixel to be defect, a module
                         to have at least one core column defect, circuit defect.
    NDefectFractionsPerPattern: Fractions of exactly n-group defects (core-column, circuit) under condition that there is at least one
                                such group defect. There must be one n-tuple with fractions per criterion, and each fraction
                                n-tuple must contain for each group defect probability a non empty set of fractions of exactly 1, ... n defects.
                                Fractions for different group defects are separated by -1. There should be two sequences of
                                positive fractions separated by -1.
    NoiseProbability: Empty or probabilities of a pixel to produce a spurious hit.
    NoiseShape: binned PDF (i.e. list of fractions) to create tot values for spurious hits.
    CornerDefectParamsPerPattern: parameters for corner defects per pattern can be created with e.g. makeCornerDefectParam
    NCornerDefectFractionsPerPattern: fractions of 1,..4 corner defects
    FillHistogramsPerPattern: if True histograms are filled per module pattern
    FillEtaPhiHistogramsPerPattern: if True also fill xy, and rz histograms of defects per module.
    HistogramGroupName: None (disables histogramming) or the histogram group name must be unique
    HistogramFileName: None (disables histogramming) or a file name for writing the histograms.
    """
 
    from InDetDefectsEmulation.PixelDefectsEmulatorConfig import (
        ITkPixelDefectsEmulatorCondAlgCfg,
        ITkPixelDefectsEmulatorAlgCfg,
        ITkPixelDefectsEmulatorToDetectorElementStatusCondAlgCfg,
        DefectsHistSvcCfg
    )
    from AthenaCommon.Constants import INFO
 
    if HistogramFileName is None or len(HistogramFileName) ==0 :
        HistogramGroupName = None
    if HistogramGroupName is not None :
        cfg.merge( DefectsHistSvcCfg(flags, HistogramGroup=HistogramGroupName, FileName=HistogramFileName))
 
    # schedule custom defects generating conditions alg
    cfg.merge( ITkPixelDefectsEmulatorCondAlgCfg(flags,
                                                 # to enable histogramming:
                                                 HistogramGroupName=f"/{HistogramGroupName}/EmulatedDefects/" if HistogramGroupName is not None else "",
                                                 ModulePatterns = ModulePatterns,
                                                 DefectProbabilities = DefectProbabilities,
                                                 NDefectFractionsPerPattern = NDefectFractionsPerPattern,
                                                 MaxRandomPositionAttempts=MaxRandomPositionAttempts,
                                                 CornerDefectParamsPerPattern=CornerDefectParamsPerPattern,
                                                 NCornerDefectFractionsPerPattern=NCornerDefectFractionsPerPattern,
                                                 RngPerDefectType=RngPerDefectType,
                                                 DefectsInputFiles=DefectsInputFiles,
                                                 DefectsOutputFile=DefectsOutputFile,
                                                 FillHistogramsPerPattern=FillHistogramsPerPattern,
                                                 FillEtaPhiHistogramsPerPattern=FillEtaPhiHistogramsPerPattern,
                                                 CheckerBoardDefects=False,
                                                 OddColToggle=False,
                                                 OddRowToggle=False,
                                                 WriteKey="ITkPixelEmulatedDefects", # the default should match the key below
                                                 ))
 
    # schedule the algorithm which drops elements from the ITk Pixel RDO collection
    cfg.merge( ITkPixelDefectsEmulatorAlgCfg(flags,
                                             # prevent default cond alg from being scheduled :
                                             EmulatedDefectsKey="ITkPixelEmulatedDefects",
                                             ModulePatterns = ModulePatterns,
                                             NoiseProbability = NoiseProbability,
                                             NoiseShape = NoiseShape,
                                             # to enable histogramming:
                                             HistogramGroupName=f"/{HistogramGroupName}/RejectedRDOs/" if HistogramGroupName is not None else "",
                                             OutputLevel=INFO))
 
    if PropagateDefectsToStatus :
        # propagate defects to detector element status
        cfg.merge(ITkPixelDefectsEmulatorToDetectorElementStatusCondAlgCfg(flags,
                                                                           name="ITkPixelDefectsEmulatorToDetectorElementStatusCondAlg",
                                                                           EmulatedDefectsKey="ITkPixelEmulatedDefects",
                                                                           WriteKey="ITkPixelDetectorElementStatusFromEmulatedDefects"))
        pixel_det_el_status_cond_alg=cfg.getCondAlgo("ITkPixelDetectorElementStatusCondAlgNoByteStreamErrors")
        pixel_det_el_status_cond_alg.ConditionsSummaryTool.PixelDetElStatusCondDataBaseKey="ITkPixelDetectorElementStatusFromEmulatedDefects"
 

emulateITkPixelDefectsDefault()

def PixelDefectsEmulatorPostInclude.emulateITkPixelDefectsDefault	(		flags,
			cfg,
			FrontEndCCDefectProb = 0.1,
			PixelDefectProb = 1e-2,
			ModuleDefectProb = 1e-2,
			CornerDefectProb = 15e-2,
			NoiseProb = 0.,
			RngPerDefectType = False,
			DefectsInputFiles = [],
			DefectsOutputFile = None,
			PropagateDefectsToStatus = True,
			HistogramFileName = None
	)

Enables all defects according to the current expectation.

Definition at line 424 of file PixelDefectsEmulatorPostInclude.py.

def emulateITkPixelDefectsDefault(flags,
                                  cfg,
                                  FrontEndCCDefectProb=0.1,
                                  PixelDefectProb=1e-2,
                                  ModuleDefectProb=1e-2,
                                  CornerDefectProb=15e-2,
                                  NoiseProb=0.,
                                  RngPerDefectType=False,
                                  DefectsInputFiles=[],
                                  DefectsOutputFile=None,
                                  PropagateDefectsToStatus=True,
                                  HistogramFileName=None) :
    """
    Enables all defects according to the current expectation.
    """
    emulateITkPixelDefectsPoisson(flags,cfg,
                                  FrontEndCCDefectProb,
                                  PixelDefectProb,
                                  ModuleDefectProb,
                                  CornerDefectProb,
                                  NoiseProb,
                                  RngPerDefectType=RngPerDefectType,
                                  DefectsInputFiles=DefectsInputFiles,
                                  DefectsOutputFile=DefectsOutputFile,
                                  PropagateDefectsToStatus=PropagateDefectsToStatus,
                                  HistogramFileName=HistogramFileName)

emulateITkPixelDefectsOneCC()

def PixelDefectsEmulatorPostInclude.emulateITkPixelDefectsOneCC	(		flags,
			cfg,
			FrontEndCCDefectProb = 0.1,
			PixelDefectProb = 1e-2,
			NumberOfCCDefects = 1,
			ModuleDefectProb = 0.,
			CornerDefectProb = 0.,
			NoiseProb = 0.,
			RngPerDefectType = False,
			DefectsInputFiles = [],
			DefectsOutputFile = None,
			PropagateDefectsToStatus = True,
			HistogramFileName = None
	)

Create exactly one core column defect per module where the probability is given
by module_prob, and create single pixel defects according to pixel_defect_prob

Definition at line 329 of file PixelDefectsEmulatorPostInclude.py.

def emulateITkPixelDefectsOneCC(flags,
                                cfg,
                                FrontEndCCDefectProb=0.1,
                                PixelDefectProb=1e-2,
                                NumberOfCCDefects=1,
                                ModuleDefectProb=0.,
                                CornerDefectProb=0.,
                                NoiseProb=0.,
                                RngPerDefectType=False,
                                DefectsInputFiles=[],
                                DefectsOutputFile=None,
                                PropagateDefectsToStatus=True,
                                HistogramFileName=None) :
    """
    Create exactly one core column defect per module where the probability is given
    by module_prob, and create single pixel defects according to pixel_defect_prob
    """
    noiseProbabilitySingle,noiseShapeSingle = makeITkPixelNoise(NoiseProb)
    fractions=fractionsForExactlyNCoreColumnDefects(NumberOfCCDefects)
    ModulePatterns, DefectProbabilities, NDefectFractionsPerPattern, NoiseProbability, NoiseShape,cornerDefectParam,cornerDefectFractions = makeITkDefectsParams(
        quad_cc_defect_prob=quadProb(FrontEndCCDefectProb),
        quad_fractions=fractions,    # same fractions for quads and other modules
        circuit_cc_defect_prob=FrontEndCCDefectProb,
        circuit_fractions=fractions,
        pixel_defect_prob=PixelDefectProb,
        module_defect_prob=ModuleDefectProb,
        cornerDefectProb=CornerDefectProb,
        noiseProbability=noiseProbabilitySingle,
        noiseShape=noiseShapeSingle)
 
    return emulateITkPixelDefects(flags,
                                  cfg,
                                  ModulePatterns=ModulePatterns,
                                  DefectProbabilities=DefectProbabilities,
                                  NDefectFractionsPerPattern=NDefectFractionsPerPattern,
                                  NoiseProbability=NoiseProbability,
                                  NoiseShape=NoiseShape,
                                  CornerDefectParamsPerPattern=cornerDefectParam,
                                  NCornerDefectFractionsPerPattern=cornerDefectFractions,
                                  RngPerDefectType=RngPerDefectType,
                                  DefectsInputFiles=DefectsInputFiles,
                                  DefectsOutputFile=DefectsOutputFile,
                                  FillHistogramsPerPattern=True,
                                  FillEtaPhiHistogramsPerPattern=True,
                                  PropagateDefectsToStatus=PropagateDefectsToStatus,
                                  HistogramFileName=HistogramFileName)
 
 

emulateITkPixelDefectsPoisson()

def PixelDefectsEmulatorPostInclude.emulateITkPixelDefectsPoisson	(		flags,
			cfg,
			FrontEndCCDefectProb = 0.1,
			PixelDefectProb = 1e-2,
			ModuleDefectProb = 0.,
			CornerDefectProb = 0.,
			NoiseProb = 0.,
			RngPerDefectType = False,
			DefectsInputFiles = [],
			DefectsOutputFile = None,
			PropagateDefectsToStatus = True,
			HistogramFileName = None
	)

Create Poisson distributed  core column defects per module where the probability for at least one
core column defect is given by front_end_cc_defect_prob for single chip modules and larger for
quads, respectively. Single pixel defects are controlled by pixel_defect_prob

Definition at line 377 of file PixelDefectsEmulatorPostInclude.py.

def emulateITkPixelDefectsPoisson(flags,
                                  cfg,
                                  FrontEndCCDefectProb=0.1,
                                  PixelDefectProb=1e-2,
                                  ModuleDefectProb=0.,
                                  CornerDefectProb=0.,
                                  NoiseProb=0.,
                                  RngPerDefectType=False,
                                  DefectsInputFiles=[],
                                  DefectsOutputFile=None,
                                  PropagateDefectsToStatus=True,
                                  HistogramFileName=None) :
    """
    Create Poisson distributed  core column defects per module where the probability for at least one
    core column defect is given by front_end_cc_defect_prob for single chip modules and larger for
    quads, respectively. Single pixel defects are controlled by pixel_defect_prob
    """
    noiseProbabilitySingle,noiseShapeSingle = makeITkPixelNoise(NoiseProb)
    quad_prob=quadProb(FrontEndCCDefectProb)
    ModulePatterns, DefectProbabilities, NDefectFractionsPerPattern, NoiseProbability, NoiseShape,cornerDefectParam,cornerDefectFractions = makeITkDefectsParams(
        quad_cc_defect_prob=quad_prob,
        quad_fractions=poissonFractions(quad_prob),
        circuit_cc_defect_prob=FrontEndCCDefectProb,
        circuit_fractions=poissonFractions(FrontEndCCDefectProb),
        pixel_defect_prob=PixelDefectProb,
        module_defect_prob=ModuleDefectProb,
        cornerDefectProb=CornerDefectProb,
        noiseProbability=noiseProbabilitySingle,
        noiseShape=noiseShapeSingle)
 
    return emulateITkPixelDefects(flags,
                                  cfg,
                                  ModulePatterns=ModulePatterns,
                                  DefectProbabilities=DefectProbabilities,
                                  NDefectFractionsPerPattern=NDefectFractionsPerPattern,
                                  NoiseProbability=NoiseProbability,
                                  NoiseShape=NoiseShape,
                                  CornerDefectParamsPerPattern=cornerDefectParam,
                                  NCornerDefectFractionsPerPattern=cornerDefectFractions,
                                  RngPerDefectType=RngPerDefectType,
                                  DefectsInputFiles=DefectsInputFiles,
                                  DefectsOutputFile=DefectsOutputFile,
                                  FillHistogramsPerPattern=True,
                                  FillEtaPhiHistogramsPerPattern=True,
                                  PropagateDefectsToStatus=PropagateDefectsToStatus,
                                  HistogramFileName=HistogramFileName)
 

emulatePixelDefects()

def PixelDefectsEmulatorPostInclude.emulatePixelDefects	(		flags,
			cfg,
			ModulePatterns = None,
			DefectProbabilities = None,
			NDefectFractionsPerPattern = None,
			RngPerDefectType = False,
			DefectsInputFiles = [],
			DefectsOutputFile = None,
			FillHistogramsPerPattern = False,
			FillEtaPhiHistogramsPerPattern = False,
		str	HistogramGroupName = "PixelDefects",
		str	HistogramFileName = "pixel_defects.root"
	)

Schedule algorithms to emulate run3 pixel defects, and algorithm to drop RDOs which overlap with these defects

Definition at line 132 of file PixelDefectsEmulatorPostInclude.py.

def emulatePixelDefects(flags,
                        cfg,
                        ModulePatterns=None,
                        DefectProbabilities=None,
                        NDefectFractionsPerPattern=None,
                        RngPerDefectType=False,
                        DefectsInputFiles=[],
                        DefectsOutputFile=None,
                        FillHistogramsPerPattern=False,
                        FillEtaPhiHistogramsPerPattern=False,
                        HistogramGroupName: str="PixelDefects",
                        HistogramFileName: str="pixel_defects.root") :
    """
    Schedule algorithms to emulate run3 pixel defects, and algorithm to drop RDOs which overlap with these defects
    """
    from InDetDefectsEmulation.PixelDefectsEmulatorConfig import (
        PixelDefectsEmulatorCondAlgCfg,
        PixelDefectsEmulatorAlgCfg,
        DefectsHistSvcCfg
    )
    from AthenaCommon.Constants import INFO
 
    if HistogramFileName is None or len(HistogramFileName) ==0 :
        HistogramGroupName = None
    if HistogramGroupName is not None :
        cfg.merge( DefectsHistSvcCfg(flags, HistogramGroup=HistogramGroupName, FileName=HistogramFileName))
 
    if ModulePatterns is None and DefectProbabilities is None and NDefectFractionsPerPattern is None:
        a_module_pattern_list, a_prob_list,fractions,ignore_NoiseProbability,ignore_NoiseShape, cornerDefectParam, cornerDefectFractions = combineModuleDefects([
                                         moduleDefect(bec=[-2,-2],layer=[0,99], phi_range=[-99,99],eta_range=[-99,99], # select all modules
                                                      columns_or_strips=[0,9999], # sensors with all kind of numbers of columns
                                                      side_range=[0,0],     # there is only a single side
                                                      all_rows=False,       # there is no connection between modules
                                                      probability=[1e-2,    # probability of a module to be defect
                                                                   1e-2,    # probability of a pixel to be defect
                                                                   0.,      # probability of a module to have at least one core-column defect
                                                                   0.       # probability of a module to have at least one defect circuit
                                                                   ])
                                                                   ])
        ModulePatterns =  a_module_pattern_list
        DefectProbabilities =  a_prob_list
        NDefectFractionsPerPattern = fractions
 
    # schedule custom defects generating conditions alg
    cfg.merge( PixelDefectsEmulatorCondAlgCfg(flags,
                                              ModulePatterns = ModulePatterns,
                                              DefectProbabilities = DefectProbabilities,
                                              NDefectFractionsPerPattern = NDefectFractionsPerPattern,
                                              CornerDefectParamsPerPattern=cornerDefectParam,
                                              NCornerDefectFractionsPerPattern=cornerDefectFractions,
                                              RngPerDefectType=RngPerDefectType,
                                              DefectsInputFiles=DefectsInputFiles,
                                              DefectsOutputFile=DefectsOutputFile,
                                              FillHistogramsPerPattern=FillHistogramsPerPattern,
                                              FillEtaPhiHistogramsPerPattern=FillEtaPhiHistogramsPerPattern,
                                              # to enable histogramming:
                                              HistogramGroupName=f"/{HistogramGroupName}/EmulatedDefects/" if HistogramGroupName is not None else "",
                                              WriteKey="PixelEmulatedDefects", # the default should match the key below
                                              ))
 
    # schedule the algorithm which drops elements from the ITk Pixel RDO collection
    cfg.merge( PixelDefectsEmulatorAlgCfg(flags,
                                             # prevent default cond alg from being scheduled :
                                             EmulatedDefectsKey="PixelEmulatedDefects",
                                             # to enable histogramming:
                                             HistogramGroupName=f"/{HistogramGroupName}/RejectedRDOs/" if HistogramGroupName is not None else "",
                                             # (prefix "/PixelDefects/" is assumed by THistSvc config)
                                             OutputLevel=INFO))
 
 

fractionsForExactlyNCoreColumnDefects()

def PixelDefectsEmulatorPostInclude.fractionsForExactlyNCoreColumnDefects

(

ExactlyNCoreColumnDefects = 1

)

Create fraction n-tuple, containing zero except for the element corresponding
to exactly n defects, which is set to 1.

Definition at line 227 of file PixelDefectsEmulatorPostInclude.py.

def fractionsForExactlyNCoreColumnDefects(ExactlyNCoreColumnDefects=1) :
    """
    Create fraction n-tuple, containing zero except for the element corresponding
    to exactly n defects, which is set to 1.
    """
    return [ 0. if idx != ExactlyNCoreColumnDefects else 1. for idx in range(1,ExactlyNCoreColumnDefects+1) ]
 

makeITkDefectsParams()

def PixelDefectsEmulatorPostInclude.makeITkDefectsParams	(		quad_cc_defect_prob,
			quad_fractions,
			circuit_cc_defect_prob,
			circuit_fractions,
			pixel_defect_prob = 1e-2,
			module_defect_prob = 0.,
			cornerDefectProb = 0.,
			noiseProbability = None,
			noiseShape = []
	)

Create different defects for quads and single chip modules, where the corresponding modules are selected by
the number of offline columns

Definition at line 234 of file PixelDefectsEmulatorPostInclude.py.

def makeITkDefectsParams( quad_cc_defect_prob,
                          quad_fractions,
                          circuit_cc_defect_prob,
                          circuit_fractions,
                          pixel_defect_prob=1e-2,
                          module_defect_prob=0.,
                          cornerDefectProb=0.,
                          noiseProbability=None,
                          noiseShape=[]) :
    """
    Create different defects for quads and single chip modules, where the corresponding modules are selected by
    the number of offline columns
    """
    # corner defects:
    # - 50% of ~30% of the 3D modules have disconnected corners area 2-4mm x 2-2.5mm,
    # - roughly circular shape with a sagitta (defined by circle crossing sensor edges) of ~0-2mm,
    # - impact on all 3D sensors which are all single chip modules i.e. modules with 384 or 400 columns
    corner_defects=makeCornerDefectParam(probability=cornerDefectProb,
                                         min_rx=2.,max_rx=8.4,
                                         min_ry=2.,max_ry=4.5,
                                         min_sagitta=0.,max_sagitta=2.2)
    # assume each corner has equal probability to suffer corner defects
    # Assume number of corners with defects Poisson distributed
    corner_defect_n_defect_corners=poissonFractions(cc_defect_prob=15e-2, max_n=4)
 
    return combineModuleDefects([
            moduleDefect(bec=[-2,2],layer=[0,99], phi_range=[-99,99],eta_range=[-99,99], # select all modules
                         columns_or_strips=[800,800], # but only quads
                         side_range=[0,0],     # there is only a single side
                         all_rows=False,       # there is no connection between modules
                         probability=[module_defect_prob,      # probability of a module to be defect
                                      pixel_defect_prob,    # probability of a pixel to be defect
                                      quad_cc_defect_prob, # probability of a module to have at least one core-column defect
                                      0.       # probability of a module to have at least one defect circuit
                                      ],
                         fractionsOfNDefects=[quad_fractions,[1.]], # dummy fractions for circuit defects
                         noiseProbability=noiseProbability,
                         noiseShape=noiseShape,
                         cornerDefectParam=[], # need empty lists here
                         cornerDefectNCornerFractions=[] # and here, otherwise resulting property will be non-conform,
                         ),
            moduleDefect(bec=[-2,2],layer=[0,1], phi_range=[-99,99],eta_range=[-99,99], # select all modules
                         columns_or_strips=[384,384], # but only ring triplet modules
                         side_range=[0,0],     # there is only a single side
                         all_rows=False,       # there is no connection between modules
                         probability=[module_defect_prob,      # probability of a module to be defect
                                      pixel_defect_prob,    # probability of a pixel to be defect
                                      circuit_cc_defect_prob,    # probability of a module to have at least one core-column defect
                                      0.       # probability of a module to have at least one defect circuit
                                      ],
                         fractionsOfNDefects=[circuit_fractions,[1.]], # dummy fractions for circuit defects
                         noiseProbability=noiseProbability,
                         noiseShape=noiseShape,
                         cornerDefectParam=corner_defects,
                         cornerDefectNCornerFractions=corner_defect_n_defect_corners,
                         ),
            moduleDefect(bec=[-2,2],layer=[0,1], phi_range=[-99,99],eta_range=[-99,99], # select all modules
                         columns_or_strips=[200,200], # but only barrel triplet modules
                         side_range=[0,0],     # there is only a single side
                         all_rows=False,       # there is no connection between modules
                         probability=[module_defect_prob,      # probability of a module to be defect
                                      pixel_defect_prob,    # probability of a pixel to be defect
                                      circuit_cc_defect_prob,    # probability of a module to have at least one core-column defect
                                      0.       # probability of a module to have at least one defect circuit
                                    ],
                         fractionsOfNDefects=[circuit_fractions,[1.]], # dummy fractions for circuit defects
                         noiseProbability=noiseProbability,
                         noiseShape=noiseShape,
                         cornerDefectParam=corner_defects,
                         cornerDefectNCornerFractions=corner_defect_n_defect_corners,
                         )
        ])
 

makeITkPixelNoise()

def PixelDefectsEmulatorPostInclude.makeITkPixelNoise

(

noiseProb = 0.

)

For NoiseProb>0. create phantasie noise tot shape, with mean at zero width of 0.7
truncated below a tot of 1.

Definition at line 307 of file PixelDefectsEmulatorPostInclude.py.

def makeITkPixelNoise(noiseProb=0.) :
    """
    For NoiseProb>0. create phantasie noise tot shape, with mean at zero width of 0.7
    truncated below a tot of 1.
    """
    if noiseProb > 0. :
        import math
        def norm(dist) :
            scale = sum(dist)
            return [elm/scale if scale > 0. else 0. for elm in dist]
        def gaussDist(mean, width, n) :
            scale = -1./(2*width)
            return norm([ math.exp( scale *math.pow(i - mean,2.) ) for i in range(0,n) ])
 
        # Guassian tot distribution with mean of 0 but tot >=1
        noiseShape=[ 0. ] + gaussDist(-1,0.7,4)
    else :
        noiseProb=None
        noiseShape=[]
    return noiseProb,noiseShape
 
 

poissonFractions()

def PixelDefectsEmulatorPostInclude.poissonFractions	(		cc_defect_prob = 1e-1,
			max_n = 5
	)

Create fractions for exactly 1..max_n defects, under the condition that
the probability for at least one such defects is cc_defect_prob, and
assuming that the fractions are Poisson distributed.

Definition at line 202 of file PixelDefectsEmulatorPostInclude.py.

def poissonFractions(cc_defect_prob=1e-1, max_n=5) :
    """
    Create fractions for exactly 1..max_n defects, under the condition that
    the probability for at least one such defects is cc_defect_prob, and
    assuming that the fractions are Poisson distributed.
    """
    if cc_defect_prob > 0. :
        def PoissonProb(expected, n) :
            return math.pow(expected,n)*math.exp(-expected)/math.gamma(n+1)
        def norm(fractions) :
            Norm = 1./sum (fractions)
            return [Norm*elm for elm in fractions ]
        expectation=-math.log(1-cc_defect_prob)
        return norm([ PoissonProb(expectation,i) for i in range(1,max_n+1) ])
    else :
        return [1.]
 

quadProb()

def PixelDefectsEmulatorPostInclude.quadProb

(

circuit_prob

)

Compute the defect probability for a quad module from the probabilities
of a single chip module, assuming that the defect is a "feature" of the
chip.

Definition at line 219 of file PixelDefectsEmulatorPostInclude.py.

def quadProb(circuit_prob) :
    """
    Compute the defect probability for a quad module from the probabilities
    of a single chip module, assuming that the defect is a "feature" of the
    chip.
    """
    return 1-math.pow(1-circuit_prob,4) # not (no defect core column on none of the sensors)