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Update documentation for covariance fields
- Add σ_xy field to Emitter2DFit struct definitions - Add σ_xy, σ_xz, σ_yz fields to Emitter3DFit struct definitions - Update constructor examples to show covariance parameters Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
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api_overview.md

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@@ -87,6 +87,7 @@ mutable struct Emitter2DFit{T} <: AbstractEmitter
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bg::T # fitted background in photons/pixel
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σ_x::T # uncertainty in x position in microns
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σ_y::T # uncertainty in y position in microns
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σ_xy::T # covariance between x and y (microns², 0 = axis-aligned)
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σ_photons::T # uncertainty in photon count
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σ_bg::T # uncertainty in background level
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frame::Int # frame number in acquisition sequence
@@ -105,6 +106,9 @@ mutable struct Emitter3DFit{T} <: AbstractEmitter
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σ_x::T # uncertainty in x position in microns
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σ_y::T # uncertainty in y position in microns
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σ_z::T # uncertainty in z position in microns
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σ_xy::T # covariance between x and y (microns², 0 = uncorrelated)
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σ_xz::T # covariance between x and z (microns², 0 = uncorrelated)
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σ_yz::T # covariance between y and z (microns², 0 = uncorrelated)
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σ_photons::T # uncertainty in photon count
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σ_bg::T # uncertainty in background level
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frame::Int # frame number in acquisition sequence
@@ -138,6 +142,7 @@ emitter_2d_fit = Emitter2DFit{Float64}(
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1000.0, 10.0, # photons detected, background photons/pixel
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0.01, 0.01, # σ_x, σ_y: position uncertainties in microns
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50.0, 2.0; # σ_photons, σ_bg: photon count uncertainties
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σ_xy=0.005, # covariance (optional, default=0 for axis-aligned uncertainty)
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frame=5, # frame number in acquisition (1-based, default=1)
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dataset=1, # dataset identifier for multi-acquisition experiments
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track_id=2, # tracking ID for linked localizations (default=0 = unlinked)

docs/src/index.md

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@@ -71,6 +71,7 @@ mutable struct Emitter2DFit{T} <: AbstractEmitter
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bg::T # fitted background in photons/pixel
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σ_x::T # uncertainty in x position in microns
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σ_y::T # uncertainty in y position in microns
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σ_xy::T # covariance between x and y (microns², 0 = axis-aligned)
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σ_photons::T # uncertainty in photon count
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σ_bg::T # uncertainty in background level
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frame::Int # frame number in acquisition sequence
@@ -88,6 +89,9 @@ mutable struct Emitter3DFit{T} <: AbstractEmitter
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σ_x::T # uncertainty in x position in microns
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σ_y::T # uncertainty in y position in microns
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σ_z::T # uncertainty in z position in microns
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σ_xy::T # covariance between x and y (microns², 0 = uncorrelated)
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σ_xz::T # covariance between x and z (microns², 0 = uncorrelated)
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σ_yz::T # covariance between y and z (microns², 0 = uncorrelated)
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σ_photons::T # uncertainty in photon count
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σ_bg::T # uncertainty in background level
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frame::Int # frame number in acquisition sequence
@@ -118,6 +122,7 @@ emitter_2d_fit = Emitter2DFit{Float64}(
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1000.0, 10.0, # photons, background
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0.01, 0.01, # σ_x, σ_y (uncertainties in μm)
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50.0, 2.0; # σ_photons, σ_bg (uncertainties)
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σ_xy=0.005, # covariance (optional, 0 = axis-aligned)
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frame=5, # frame number
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dataset=1, # dataset identifier
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track_id=2, # tracking identifier (0 = unlinked)
@@ -130,6 +135,7 @@ emitter_3d_fit = Emitter3DFit{Float64}(
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1000.0, 10.0, # photons, background
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0.01, 0.01, 0.02, # σ_x, σ_y, σ_z (uncertainties in μm)
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50.0, 2.0; # σ_photons, σ_bg (uncertainties)
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σ_xy=0.005, σ_xz=0.002, σ_yz=0.003, # covariances (optional, 0 = uncorrelated)
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frame=5, # frame number
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dataset=1, # dataset identifier
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track_id=2, # tracking identifier (0 = unlinked)

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