locan.constants.PropertyKey

class locan.constants.PropertyKey(value)

Bases: Enum

Property descriptions for standard properties used in locan.LocData and throughout locan.

Methods

coordinate_properties()	Property descriptions for properties representing spatial coordinates
coordinate_keys()	Property keys for properties representing spatial coordinates
uncertainty_properties()	Property descriptions for properties representing spatial coordinate uncertainties
uncertainty_keys()	Property keys for properties representing spatial coordinate uncertainties.
intensity_properties()	Property descriptions for properties representing photon intensities.
intensity_keys()	Property keys for properties representing photon intensities.
summary()	A formatted string representation of PropertyKey showing all elements with attributes.

Attributes

index
original_index
position_x
position_y
position_z
frame
frames_number
frames_missing
time
intensity
local_background
local_background_sigma
signal_noise_ratio
signal_background_ratio
chi_square
two_kernel_improvement
psf_amplitude
psf_width
psf_width_x
psf_width_y
psf_width_z
psf_half_width
psf_half_width_x
psf_half_width_y
psf_half_width_z
psf_sigma
psf_sigma_x
psf_sigma_y
psf_sigma_z
uncertainty
uncertainty_x
uncertainty_y
uncertainty_z
channel
slice_z
plane
cluster_label

channel = PropertyDescription(name='channel', type='integer', unit_SI=None, unit=None, description='identifier for an imaging channel')

chi_square = PropertyDescription(name='chi_square', type='float', unit_SI=None, unit=None, description='chi-square value of the fitting procedure as estimated by the fitter')

cluster_label = PropertyDescription(name='cluster_label', type='integer', unit_SI=None, unit=None, description='identifier for a localization cluster')

classmethod coordinate_keys()

Property keys for properties representing spatial coordinates

Return type:

list[str]

classmethod coordinate_properties()

Property descriptions for properties representing spatial coordinates

Return type:

list[PropertyKey]

frame = PropertyDescription(name='frame', type='integer', unit_SI=None, unit=None, description='frame  number in which the localization occurs')

frames_missing = PropertyDescription(name='frames_missing', type='integer', unit_SI=None, unit=None, description='number of frames that occurred between two successive localizations')

frames_number = PropertyDescription(name='frames_number', type='integer', unit_SI=None, unit=None, description='number of frames that contribute to a merged localization')

index = PropertyDescription(name='index', type='integer', unit_SI=None, unit=None, description='a positive integer identifying the localization')

intensity = PropertyDescription(name='intensity', type='float', unit_SI=None, unit=None, description='intensity or emission strength as estimated by the fitter')

classmethod intensity_keys()

Property keys for properties representing photon intensities.

Return type:

list[str]

classmethod intensity_properties()

Property descriptions for properties representing photon intensities.

Return type:

list[PropertyKey]

local_background = PropertyDescription(name='local_background', type='float', unit_SI=None, unit=None, description='background in the neighborhood of localization as estimated by the fitter')

local_background_sigma = PropertyDescription(name='local_background_sigma', type='float', unit_SI=None, unit=None, description='variation of local background in terms of standard deviation')

original_index = PropertyDescription(name='original_index', type='integer', unit_SI=None, unit=None, description='')

plane = PropertyDescription(name='plane', type='integer', unit_SI=None, unit=None, description='identifier for an imaging plane')

position_x = PropertyDescription(name='position_x', type='float', unit_SI='m', unit=None, description='spatial coordinate.')

position_y = PropertyDescription(name='position_y', type='float', unit_SI='m', unit=None, description='spatial coordinate.')

position_z = PropertyDescription(name='position_z', type='float', unit_SI='m', unit=None, description='spatial coordinate.')

psf_amplitude = PropertyDescription(name='psf_amplitude', type='float', unit_SI=None, unit=None, description='')

psf_half_width = PropertyDescription(name='psf_half_width', type='float', unit_SI=None, unit=None, description='')

psf_half_width_x = PropertyDescription(name='psf_half_width_x', type='float', unit_SI=None, unit=None, description='')

psf_half_width_y = PropertyDescription(name='psf_half_width_y', type='float', unit_SI=None, unit=None, description='')

psf_half_width_z = PropertyDescription(name='psf_half_width_z', type='float', unit_SI=None, unit=None, description='')

psf_sigma = PropertyDescription(name='psf_sigma', type='float', unit_SI=None, unit=None, description='sigma of the fitted Gauss-function - being isotropic or representing the root-mean-square of psf_sigma_c for all dimensions')

psf_sigma_x = PropertyDescription(name='psf_sigma_x', type='float', unit_SI=None, unit=None, description='sigma of the fitted Gauss-function in x-dimension as estimated by the fitter')

psf_sigma_y = PropertyDescription(name='psf_sigma_y', type='float', unit_SI=None, unit=None, description='sigma of the fitted Gauss-function in y-dimension as estimated by the fitter')

psf_sigma_z = PropertyDescription(name='psf_sigma_z', type='float', unit_SI=None, unit=None, description='sigma of the fitted Gauss-function in z-dimension as estimated by the fitter')

psf_width = PropertyDescription(name='psf_width', type='float', unit_SI=None, unit=None, description='full-width-half-max of the fitted Gauss-function - being isotropic or representing the root-mean-square of psf_width_c for all dimensions')

psf_width_x = PropertyDescription(name='psf_width_x', type='float', unit_SI=None, unit=None, description='full-width-half-max of the fitted Gauss-function in x-dimension as estimated by the fitter')

psf_width_y = PropertyDescription(name='psf_width_y', type='float', unit_SI=None, unit=None, description='full-width-half-max of the fitted Gauss-function in y-dimension as estimated by the fitter')

psf_width_z = PropertyDescription(name='psf_width_z', type='float', unit_SI=None, unit=None, description='full-width-half-max of the fitted Gauss-function in z-dimension as estimated by the fitter')

signal_background_ratio = PropertyDescription(name='signal_background_ratio', type='float', unit_SI=None, unit=None, description='ratio between mean intensity (i.e. intensity for a single localization) and the local_background')

signal_noise_ratio = PropertyDescription(name='signal_noise_ratio', type='float', unit_SI=None, unit=None, description='ratio between mean intensity (i.e. intensity for a single localization) and the standard deviation of local_background (i.e. local_background_sigma for a single localization)')

slice_z = PropertyDescription(name='slice_z', type='float', unit_SI=None, unit=None, description='identifier for an imaging slice')

classmethod summary()

A formatted string representation of PropertyKey showing all elements with attributes.

Return type:

str

time = PropertyDescription(name='time', type='float', unit_SI='s', unit=None, description='')

two_kernel_improvement = PropertyDescription(name='two_kernel_improvement', type='float', unit_SI=None, unit=None, description='a rapidSTORM parameter describing the improvement from two kernel fitting')

uncertainty = PropertyDescription(name='uncertainty', type='float', unit_SI=None, unit=None, description='localization error for all dimensions or representing a value proportional to psf_sigma / sqrt(intensity) or representing the root-mean-square of uncertainty_c for all dimensions.')

classmethod uncertainty_keys()

Property keys for properties representing spatial coordinate uncertainties.

Return type:

list[str]

classmethod uncertainty_properties()

Property descriptions for properties representing spatial coordinate uncertainties

Return type:

list[PropertyKey]

uncertainty_x = PropertyDescription(name='uncertainty_x', type='float', unit_SI=None, unit=None, description='localization error in x-dimension estimated by a fitter or representing a value proportional to psf_sigma_x / sqrt(intensity)')

uncertainty_y = PropertyDescription(name='uncertainty_y', type='float', unit_SI=None, unit=None, description='localization error in y-dimension estimated by a fitter or representing a value proportional to psf_sigma_y / sqrt(intensity)')

uncertainty_z = PropertyDescription(name='uncertainty_z', type='float', unit_SI=None, unit=None, description='localization error in z-dimension estimated by a fitter or representing a value proportional to psf_sigma_z / sqrt(intensity)')