locan.constants.PropertyKey#

class locan.constants.PropertyKey(value, names=None, *, module=None, qualname=None, type=None, start=1, boundary=None)[source]#

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()[source]#

Property keys for properties representing spatial coordinates

Return type:: list[str]

classmethod coordinate_properties()[source]#

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()[source]#

Property keys for properties representing photon intensities.

Return type:: list[str]

classmethod intensity_properties()[source]#

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()[source]#

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()[source]#

Property keys for properties representing spatial coordinate uncertainties.

Return type:: list[str]

classmethod uncertainty_properties()[source]#

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)')#