analysis¶

analysis.beamline¶

analysis.beamline.averagePhotonEnergy(evt, records, outkey='averagePhotonEnergy')[source]¶

Averages across given photon energies and adds it to evt[“analysis”][outkey].

Args:

evt:	The event variable
records:	A dictionary of photon energy `Records`

Kwargs:

outkey(str):	Data key of resulting `Record`, default is ‘averagePhotonEnergy’

Authors:	Benedikt J. Daurer

analysis.beamline.averagePulseEnergy(evt, records, outkey='averagePulseEnergy')[source]¶

Averages across given pulse energies and adds it to evt[“analysis”][outkey].

Args:

evt:	The event variable
records:	A dictionary of pulse energy `Records`

Kwargs:

outkey(str):	Data key of resulting `Record`, default is ‘averagePulseEnergy’

Authors:	Filipe Maia Benedikt J. Daurer

analysis.beamline.printPhotonEnergy(photonEnergies)[source]¶: Expects a dictionary of photon energy Records and prints photon energies to screen.

analysis.beamline.printPulseEnergy(pulseEnergies)[source]¶: Expects a dictionary of pulse energy Records and prints pulse energies to screen.

analysis.event¶

analysis.event.printKeys(evt, group=None)[source]¶: prints available keys of Hummingbird events

analysis.event.printNativeKeys(evt)[source]¶: prints available keys of Native event

analysis.event.printProcessingRate()[source]¶: Prints processing rate to screen

analysis.hitfinding¶

analysis.hitfinding.baglivo_score(evt, poisson_mask, outkey='')[source]¶

analysis.hitfinding.countHits(evt, hit, outkey='nrHits')[source]¶

Counts hits and adds the total nr. of hits to evt["analysis"][outkey].

Args:

evt:	The event variable
hit:	A boolean (True for hit, False for miss)

Kwargs:

outkey(str):	Data key of resulting `Record`, default is “nrHits”

Authors:	Benedikt J. Daurer (benedikt@xray.bmc.uu.se) Jonas Sellberg Tomas Ekeberg

analysis.hitfinding.countHitscore(evt, hitscore, hitscoreThreshold=200, outkey='')[source]¶

A simple hitfinder that performs a limit test against an already defined hitscore and adds the result to evt["analysis"][outkey + "isHit"], and the hitscore to evt["analysis"][outkey + "hitscore"].

Args:

evt:	The event variable
hitscore:	A pre-defined hitscore

Kwargs:

hitscoreThreshold(int):
	Events with hitscore above this threshold are hits, default=200

Authors:	Carl Nettelblad (carl.nettelblad@it.uu.se) Benedikt J. Daurer

analysis.hitfinding.countLitPixels(evt, record, aduThreshold=20, hitscoreThreshold=200, hitscoreDark=0, hitscoreMax=None, mask=None, outkey='litpixel: ')[source]¶

A simple hitfinder that counts the number of lit pixels and adds the result to evt["analysis"][outkey + "isHit"], evt["analysis"][outkey + "isMiss"], and the hitscore to evt["analysis"][outkey + "hitscore"].

Args:

evt:	The event variable
record:	A pixel detector `Record`

Kwargs:

aduThreshold(int):
	only pixels above this threshold (in ADUs) are valid, default=20
hitscoreThreshold(int):
	events with hitscore (Nr. of lit pixels) above this threshold are hits, default=200
mask(int, bool):
	only use masked pixel (mask == True or 1) for countin
outkey(str):	Prefix of data key of resulting `Record`, default is “litpixel: “

Authors:	Benedikt J. Daurer (benedikt@xray.bmc.uu.se)

analysis.hitfinding.countPhotonsAgainstEnergyFunction(evt, photonscore_record, energy_record, energyFunction=<function <lambda>>, outkey='photons: ')[source]¶

A hitfinder that tests given photon score (e.g. photon count) against a predicted photon threshold that is dependent on some given energy and adds a boolean to evt["analysis"][outkey + "isHit"], the hitscore to evt["analysis"][outkey + "hitscore"] and the limit to ``evt[“analysis”][outkey + “photonLimit”]

Args:

photonscore_record:
evt:	The event variable
	A `Record` containting a photon score, e.g. total photon count

:energy_record:” A Record containting an energy value, e.g. from gas monitor detector

Kwargs:

energyFunction(function with double argument):
	function that computes the photon threshold, given the energy
outkey(str):	Prefix of data key of resulting `Record`, default is “photons: “

Authors:	Carl Nettelblad (carl.nettelblad@it.uu.se)

analysis.hitfinding.countPhotonsAgainstEnergyPolynomial(evt, photonscore_record, energy_record, energyPolynomial=[200], outkey='photons: ')[source]¶

A hitfinder that tests photon score (e.g. photon count) against a predicted photon threshold that is dependent on some given energy and adds a boolean to evt["analysis"][outkey + "isHit"], the hitscore to evt["analysis"][outkey + "hitscore"] and the limit to ``evt[“analysis”][outkey + “photonLimit”]

Args:

photonscore_record:
evt:	The event variable
	A `Record` containting a photon score, e.g. total photon count

:energy_record:” A Record containting an energy value, e.g. from gas monitor detector

Kwargs:

energyPolynomial:
	array_like with polynomial coefficients fed to polyval (polynomial order one less than list length)
outkey(str):	Prefix of data key of resulting `Record`, default is “photons: “

Authors:	Carl Nettelblad (carl.nettelblad@it.uu.se)

analysis.hitfinding.countTof(evt, record, signalThreshold=1, minWindow=0, maxWindow=-1, hitscoreThreshold=2, outkey='tof: ')[source]¶

A simple hitfinder that performs a peak counting test on a time-of-flight detector signal, in a specific subwindow and adds the result to evt["analysis"][outkey + "isHit"], and the hitscore to evt["analysis"][outkey + "hitscore"].

Args:

evt:	The event variable
record:	A ToF detector record

Kwargs:

signalThreshold(str):
	The threshold of the signal, anything above this contributes to the score, default=1
minWindow(int):	Lower limit of window, default=0
maxWindow(int):	Upper limit of window, default=1
hitscoreThreshold(int):
	events with hitscore (Nr. of photons) above this threshold are hits, default=2
outkey(str):	Prefix of data key of resulting `Record`, default is “tof: “

Authors:	Carl Nettelblad (carl.nettelblad@it.uu.se)

analysis.hitfinding.generate_radial_mask(mask, cx, cy, radius)[source]¶

analysis.hitfinding.hitrate(evt, hit, history=100, unit='percent', outkey='hitrate')[source]¶

Counts hits and adds current hit rate to evt["analysis"][outkey].

Args:

evt:	The event variable
hit:	A boolean (True for hit, False for miss)

Kwargs:

history(int):	Buffer length, default = 100
outkey(str):	Data key of resulting `Record`, default is “hitrate”
unit(str):	Unit of hitrate, ‘fraction’ or ‘percent’, default is ‘fraction’

Authors:	Benedikt J. Daurer (benedikt@xray.bmc.uu.se) Tomas Ekeberg

analysis.hitfinding.lambda_values(evt, pulse_energy, sum_over_bkg_frames, fit_bkg, sample_params, outkey='')[source]¶

analysis.hitfinding.photon_count_frame(evt, front_type_s, front_key_s, aduThreshold, outkey='')[source]¶

analysis.hitfinding.stat_hitfinder(evt, pulse_energy, thr_params, bag_bkg, outkey='bagscore: ')[source]¶

analysis.sizing¶

analysis.sizing.absolute_error(evt, type_a, key_a, type_b, key_b, out_key=None)[source]¶: Returning the absolute error between two records as a new record.

analysis.sizing.findCenter(evt, type, key, mask=None, x0=0, y0=0, maxshift=10, threshold=0.5, blur=4)[source]¶

Estimating the center of diffraction based on pair-wise correlation enforcing friedel-symmetry and adding the estimated off center shifts cx and cy to evt['analysis']['offCenterX'] and evt['analysis']['offCenterX'].

Note

For this function, libspimage needs to be installed.

Args:

evt:	The event variable
type(str):	The event type of detectors, e.g. photonPixelDetectors
key(str):	The event key of a detector, e.g. CCD

Kwargs:

mask(bool or int):
	Only valid pixels (mask == True or 1) are used (default: all pixels are valid)
x0(int):	Initial guess for off center shift in x given in pixels (default = 0)
y0(int):	Initial guess for off center shift in y given in pixels (default = 0)
maxshift(int):	Maximum shift (in both directions) in pixels that is used for searching optimum (default = 10)
threshold(float):
	Intensities below this threshold are set to zero (default = 0.5)
blur(int):	Radius of the blurring kernel used to find the solution quickly (default = 4)

Authors:	Benedikt J. Daurer (benedikt@xray.bmc.uu.se), Filipe Maia, Tomas Ekeberg

analysis.sizing.fitSphere(evt, type, key, mask=None, x0=0, y0=0, d0=100, i0=1.0, wavelength=1.0, pixelsize=110, distance=1000, adu_per_photon=1, quantum_efficiency=1, material='virus', mask_radius=100, downsampling=1, brute_evals=10, photon_counting=True)[source]¶

Estimating the size of particles based on diffraction data using sphere model fitting. Adds results to evt['analysis'][RESULT] where RESULT is ‘size’, ‘intensity’, ‘centerx’, ‘centery’, ‘goodness’.

Note

For this function, libspimage needs to be installed.

Args:

evt:	The event variable
type(str):	The event type of detectors, e.g. photonPixelDetectors
key(str):	The event key of a detector, e.g. CCD

Kwargs:

wavelength(float):
x0(int):	Initial guess for off center shift in x (default = 0)
y0(int):	Initial guess for off center shift in y (default = 0)
d0(int):	Initial guess for diameter [nm] (default = 100)
i0(int):	Initial guess for intensity [mJ/um2] (default = 1)
	Photon wavelength [nm] (default = 1)
pixelsize(int):	Side length of a pixel [um] (default=110)
distance(int):	Distance from interaction to detector [mm] (default = 1000)
adu_per_photon(int):
	ADUs per photon (default = 1)
quantum_efficiency(float):
	Quantum efficiency of the detector (default = 1)
material(str):	Material of particle, e.g. virus, protein, water, ... (default = virus)
mask_radius(int):
	Radius in pixels used for circular mask defining valid pixels for fitting (default=100)
downsampling(int):
	Factor of downsampling, 1 means no downsampling (default = 1)
brute_evals(int):
	Nr. of brute force evaluations for estimating the size (default = 10)
photon_counting(bool):
	If True, Do photon conversion (discretization) before fitting (default = True)

Authors:	Benedikt J. Daurer (benedikt@xray.bmc.uu.se), Max Hantke, Filipe Maia

analysis.sizing.fitSphereRadial(evt, type, radial_distance_key, radial_average_key, mask_r=None, d0=100, i0=1.0, wavelength=1.0, pixelsize=110, distance=1000, adu_per_photon=1, quantum_efficiency=1, material='virus', mask_radius=100, brute_evals=10, photon_counting=True)[source]¶

Estimating the size of particles based on diffraction data using radial sphere model fitting. Adds results to evt['analysis'][RESULT] where RESULT is ‘diameter’, ‘intensity’, ‘error’.

Note

For this function, libspimage needs to be installed.

Args:

evt:	The event variable
type(str):	The event type of detectors, e.g. photonPixelDetectors
key(str):	The event key of a detector radial average, e.g. radial average - CCD

Kwargs:

wavelength(float):
d0(int):	Initial guess for diameter [nm] (default = 100)
i0(int):	Initial guess for intensity [mJ/um2] (default = 1)
	Photon wavelength [nm] (default = 1)
pixelsize(int):	Side length of a pixel [um] (default=110)
distance(int):	Distance from interaction to detector [mm] (default = 1000)
adu_per_photon(int):
	ADUs per photon (default = 1)
quantum_efficiency(float):
	Quantum efficiency of the detector (default = 1)
material(str):	Material of particle, e.g. virus, protein, water, ... (default = virus)
mask_radius(int):
	Radius in pixels used for circular mask defining valid pixels for fitting (default=100)
brute_evals(int):
	Nr. of brute force evaluations for estimating the size (default = 10)
photon_counting(bool):
	If True, Do photon conversion (discretization) before fitting (default = True)

Authors:	Max Hantke (hantke@xray.bmc.uu.se), Benedikt J. Daurer (benedikt@xray.bmc.uu.se), Filipe Maia

analysis.sizing.photon_error(evt, type_data, key_data, type_fit, key_fit, adu_per_photon)[source]¶

analysis.sizing.sphereModel(evt, type, key_centerx, key_centery, key_diameter, key_intensity, shape, wavelength=1.0, pixelsize=110, distance=1000, adu_per_photon=1, quantum_efficiency=1, material='virus', poisson=False)[source]¶

Return sphere model.

Note

For this function, libspimage needs to be installed.

Args:

key_centerx(str):
evt:	The event variable
type(str):	The event type, e.g. analysis
	The event key of the estimated off center shift in x
key_centery(str):
	The event key of the estimated off center shift in y
key_diameter(str):
	The event key of the estimated diameter
key_intensity(str):
	The event key of the estimated intensity
shape(tuple):	The shape of the fit

Kwargs:

wavelength(float):
	Photon wavelength [nm] (default = 1)
pixelsize(int):	Side length of a pixel [um] (default=110)
distance(int):	Distance from interaction to detector [mm] (default = 1000)
adu_per_photon(int):
	ADUs per photon (default = 1)
quantum_efficiency(float):
	Quantum efficiency of the detector (default = 1)
material(str):	Material of particle, e.g. virus, protein, water, ... (default = virus)
poisson(bool):	If True, apply poisson sampling (default = False)

Authors:	Benedikt J. Daurer (benedikt@xray.bmc.uu.se), Max Hantke, Filipe Maia

analysis.pixel_detector¶

analysis.pixel_detector.assemble(evt, type, key, x, y, nx=None, ny=None, subset=None, outkey=None, initkey=None)[source]¶

Asesembles a detector image given some geometry and adds assembled image to evt["analysis"]["assembled - " + key].

Args:

evt:	The event variable
type(str):	The event type (e.g. photonPixelDetectors)
key(str):	The event key (e.g. CCD)
x(int ndarray):	X coordinates
y(int ndarray):	Y coordinates

Kwargs:

nx(int):	Total width of assembled image (zero padding)
ny(int):	Total height of assembled image (zero padding)

Authors:	Benedikt J. Daurer (benedikt@xray.bmc.uu.se)

analysis.pixel_detector.bin(evt, type, key, binning, mask=None)[source]¶

Bin a detector image given a binning factor (and mask). Adds the records evt["analysis"]["binned image - " + key] and evt["analysis"]["binned mask - " + key].

Note

This feature depends on the python package libspimage.

Args:

evt:	The event variable
type(str):	The event type (e.g. photonPixelDetectors)
key(str):	The event key (e.g. CCD)
binning(int):	The linear binning factor

Kwargs:

mask:	Binary mask, pixels that are masked out are not counted into the binned value.

Authors:	Max F. Hantke (hantke@xray.bmc.uu.se)

analysis.pixel_detector.commonModeCSPAD2x2(evt, type, key, mask=None)[source]¶

Subtraction of common mode using median value of masked pixels (left and right half of detector are treated separately). Adds a record evt["analysis"]["cm_corrected - " + key].

Args:

evt:	The event variable
type(str):	The event type (e.g. photonPixelDetectors)
key(str):	The event key (e.g. CCD)

Kwargs:

mask:	Binary mask

Authors:	Max F. Hantke (hantke@xray.bmc.uu.se) Benedikt J. Daurer (benedikt@xray.bmc.uu.se)

analysis.pixel_detector.commonModeLines(evt, record, outkey=None, direction='vertical')[source]¶

Common mode correction subtracting the median along lines.

Args:

evt:	The event variable
record:	A pixel detector Record`

Kwargs:

outkey:	The event key for the corrected detecor image, default is “corrected”
direction:	The direction of the lines across which median is taken, default is vertical

analysis.pixel_detector.commonModePNCCD(evt, type, key, outkey=None, transpose=False, signal_threshold=None)[source]¶

Common mode correction for PNCCDs.

For each row its median value is subtracted (left and right half of detector are treated separately). Adds a record evt["analysis"][outkey].

Args:

evt:	The event variable
type(str):	The event type (e.g. photonPixelDetectors)
key(str):	The event key (e.g. CCD)

Kwargs:

transpose(bool):
outkey(str):	The event key for the corrected image, default is “corrected - ” + key
	Apply procedure on transposed image
signal_threshold(float):
	Apply procedure by using only pixels below given value

Authors:	Max F. Hantke (hantke@xray.bmc.uu.se) Benedikt J. Daurer (benedikt@xray.bmc.uu.se)

analysis.pixel_detector.cropAndCenter(evt, data_rec, cx=None, cy=None, w=None, h=None, outkey='cropped')[source]¶

analysis.pixel_detector.getCentral4Asics(evt, type, key)[source]¶

Adds a one-dimensional stack of its 4 centermost asics to evt["analysis"]["central4Asics"].

Args:

evt:	The event variable
type(str):	The event type (e.g. photonPixelDetectors)
key(str):	The event key (e.g. CCD)

Authors:	Carl Nettelblad (carl.nettelblad@it.uu.se) Benedikt J. Daurer (benedikt@xray.bmc.uu.se)

analysis.pixel_detector.getSubsetAsics(evt, type, key, subset, output)[source]¶

Adds a one-dimensional stack of an arbitrary subset of asics to evt["analysis"][output].

Args:

evt:	The event variable
type(str):	The event type (e.g. photonPixelDetectors)
key(str):	The event key (e.g. CCD)
subset(list):	Asic indices
output:	The output key in analysis

Authors:	Carl Nettelblad (carl.nettelblad@it.uu.se) Benedikt J. Daurer (benedikt@xray.bmc.uu.se)

analysis.pixel_detector.maxPhotonValue(evt, record, aduPhoton=1, outkey=None)[source]¶

Estimates the maximum number of photons on one pixel on the detector and adds it to evt["analysis"][outkey].

Args:

evt:	The event variable
record:	The data record (e.g. evt[‘photonPixelDetectors’][‘CCD’])

Kwargs:

aduPhoton(int):	ADU count per photon, default = 1
outkey(str):	Data key of resulting data record, default is ‘maxPhotons’

Authors:	Tomas Ekeberg (ekeberg@xray.bmc.uu.se) Benedikt J. Daurer (benedikt@xray.bmc.uu.se)

analysis.pixel_detector.moveHalf(evt, record, vertical=0, horizontal=0, outkey='half-moved')[source]¶

analysis.pixel_detector.pnccdGain(evt, record, gainmode)[source]¶

Returns gain (Number of ADUs per photon) based on photon energy record and gain mode.

Args:

evt:	The event variable
record:	A photon energy `Record` given in eV
gainmode:	The gain mode of PNCCD (3,4,5,6) or 0 for no gain

analysis.pixel_detector.printStatistics(detectors)[source]¶

analysis.pixel_detector.radial(evt, type, key, mask=None, cx=None, cy=None)[source]¶

Compute the radial average of a detector image given the center position (and a mask). Adds the records evt["analysis"]["radial average - " + key] and evt["analysis"]["radial distance - " + key].

Note

This feature depends on the python package libspimage.

Args:

evt:	The event variable
type(str):	The event type (e.g. photonPixelDetectors)
key(str):	The event key (e.g. CCD)

Kwargs:

mask:	Binary mask, pixels that are masked out are not counted into the radial average.
cx(float):	X-coordinate of the center position. If None the center will be in the middle.
cy(float):	Y-coordinate of the center position. If None the center will be in the middle.

Authors:	Max F. Hantke (hantke@xray.bmc.uu.se)

analysis.pixel_detector.rotate90(evt, data_rec, k=1, outkey='rotated')[source]¶

analysis.pixel_detector.subtractImage(evt, type, key, image, outkey=None)[source]¶

Subtract an image.

Adds a record evt["analysis"][outkey].

Args:

evt: The event variable

type(str): The event type (e.g. photonPixelDetectors)

key(str): The event key (e.g. CCD)

Kwargs:

outkey(str):	The event key for the subtracted image, default is “subtraced - ” + key

Authors:	Max F. Hantke (hantke@xray.bmc.uu.se) Benedikt J. Daurer (benedikt@xray.bmc.uu.se)

analysis.pixel_detector.threshold(evt, record, threshold, outkey=None)[source]¶

Set all values in an array that are lower than the threshold to zero.

Args:

evt:	The event variable
record:	The data record
threshold:	Set everything lower than this number to zero

Kwargs:

aduPhoton(int):	ADU count per photon, default = 1
outkey(str):	Data key of resulting data record, default is ‘maxPhotons’

Authors:	Tomas Ekeberg (ekeberg@xray.bmc.uu.se)

analysis.pixel_detector.totalNrPhotons(evt, record, aduPhoton=1, aduThreshold=0.5, outkey=None)[source]¶

Estimates the total nr. of photons on the detector and adds it to evt["analysis"][outkey].

Args:

evt:	The event variable
record:	The data record (e.g. evt[‘photonPixelDetectors’][‘CCD’])

Kwargs:

aduThreshold(int):
aduPhoton(int):	ADU count per photon, default = 1
	only pixels above this threshold given in units of ADUs are valid, default = 0.5
outkey(str):	Data key of resulting data record, default is ‘nrPhotons’

Authors:	Benedikt J. Daurer (benedikt@xray.bmc.uu.se)

analysis.template¶

analysis.template.someAnalysis(evt, type, key, keyword=None)[source]¶

An example for an analysis module. Please document here in the docstring:

what the module is doing
what arguments need to be passed
what the module returns (adds to the event variable)
who the authors are

Args:

evt:	The event variable
type(str):	The event type
key(str):	The event key

Kwargs:

keyword(type):	Kewyword description (default = None)

Authors:	Name (email), Name (email)