Rename config structs: *Params -> *Config

Breaking change: Renamed simulation config types for consistency:
- StaticSMLMParams -> StaticSMLMConfig
- DiffusionSMLMParams -> DiffusionSMLMConfig

Updated all source files, tests, and documentation.

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

Author: kalidke

CLAUDE.md

@@ -63,7 +63,7 @@ AbstractLabeling → FixedLabeling, PoissonLabeling, BinomialLabeling
 Molecule → GenericFluor
 
 # Simulation params
-SMLMSimParams → StaticSMLMParams, DiffusionSMLMParams
+SMLMSimParams → StaticSMLMConfig, DiffusionSMLMConfig
 ```
 
 ### Key Files by Function
@@ -81,8 +81,8 @@ SMLMSimParams → StaticSMLMParams, DiffusionSMLMParams
 ### Dispatch Pattern
 
 The `simulate()` function dispatches on parameter type:
-- `simulate(params::StaticSMLMParams; ...)` → static simulation (returns 3-tuple)
-- `simulate(params::DiffusionSMLMParams; ...)` → diffusion simulation (returns BasicSMLD)
+- `simulate(params::StaticSMLMConfig; ...)` → static simulation (returns 3-tuple)
+- `simulate(params::DiffusionSMLMConfig; ...)` → diffusion simulation (returns BasicSMLD)
 
 ## Code Style
 

README.md

@@ -35,7 +35,7 @@ using SMLMSim
 
 # Define a camera and simulation parameters
 camera = IdealCamera(128, 128, 0.1)  # 128×128 pixels, 100nm pixels
-params = StaticSMLMParams(density=1.0, σ_psf=0.13) # Density 1/μm², PSF 130nm
+params = StaticSMLMConfig(density=1.0, σ_psf=0.13) # Density 1/μm², PSF 130nm
 
 # Run simulation for an 8-molecule ring pattern
 smld_noisy, info = simulate(
@@ -58,7 +58,7 @@ Simulate molecules diffusing and interacting (e.g., dimerization).
 using SMLMSim
 
 # Set diffusion simulation parameters
-params = DiffusionSMLMParams(
+params = DiffusionSMLMConfig(
     density = 0.5,           # molecules per μm²
     box_size = 10.0,         # μm
     diff_monomer = 0.1,      # μm²/s
@@ -109,7 +109,7 @@ Create camera images from simulation results.
 using MicroscopePSFs # Needed for PSF types
 
 # Generate images from diffusion simulation output
-# Note: Frame timing is controlled by DiffusionSMLMParams (camera_framerate, camera_exposure)
+# Note: Frame timing is controlled by DiffusionSMLMConfig (camera_framerate, camera_exposure)
 # Multiple simulation timesteps are automatically integrated during simulate()
 psf = GaussianPSF(0.15) # 150nm PSF width
 images, img_info = gen_images(smld, psf;
@@ -132,7 +132,7 @@ using MicroscopePSFs
 camera_scmos = SCMOSCamera(128, 128, 0.1, 1.6)
 
 # Run static simulation with sCMOS camera
-params = StaticSMLMParams(density=1.0, σ_psf=0.13)
+params = StaticSMLMConfig(density=1.0, σ_psf=0.13)
 smld_noisy, info = simulate(
     params,
     pattern=Nmer2D(n=8, d=0.1),
@@ -145,7 +145,7 @@ psf = GaussianPSF(0.15)
 images_scmos, img_info = gen_images(smld_noisy, psf, bg=10.0, camera_noise=true)
 
 # For diffusion simulations
-diff_params = DiffusionSMLMParams(density=0.5, box_size=10.0)
+diff_params = DiffusionSMLMConfig(density=0.5, box_size=10.0)
 smld_diff, diff_info = simulate(diff_params; camera=camera_scmos, override_count=10)
 ```
 
@@ -165,7 +165,7 @@ using MicroscopePSFs
 
 # --- Simulation Setup ---
 camera = IdealCamera(128, 128, 0.1) # 128×128 pixels, 100nm pixels
-params = StaticSMLMParams(density=1.0, σ_psf=0.13)
+params = StaticSMLMConfig(density=1.0, σ_psf=0.13)
 smld_noisy, info = simulate(
     params,
     pattern=Nmer2D(n=6, d=0.2), # Hexamer
@@ -203,7 +203,7 @@ using Statistics
 camera_scmos = SCMOSCamera(64, 64, 0.1, 1.6)  # 64×64 pixels, 100nm/px, 1.6 e⁻ read noise
 
 # Run diffusion simulation
-params = DiffusionSMLMParams(
+params = DiffusionSMLMConfig(
     density = 1.0,           # 1 molecule/μm²
     box_size = 6.4,          # 6.4×6.4 μm field
     diff_monomer = 0.1,      # 0.1 μm²/s diffusion

api_overview.md

@@ -22,8 +22,8 @@ All simulations use consistent physical units:
 
 - `AbstractSim`: Base type for all simulation types
   - `SMLMSimParams`: Base type for simulation parameters
-    - `StaticSMLMParams`: Parameters for static SMLM simulation
-    - `DiffusionSMLMParams`: Parameters for diffusion simulation
+    - `StaticSMLMConfig`: Parameters for static SMLM simulation
+    - `DiffusionSMLMConfig`: Parameters for diffusion simulation
 
 - `SimInfo`: Metadata and intermediate results from simulation functions
 - `ImageInfo`: Metadata from image generation functions
@@ -50,12 +50,12 @@ All simulations use consistent physical units:
 
 ## Essential Types
 
-### StaticSMLMParams
+### StaticSMLMConfig
 
 Parameters for static SMLM simulation with fixed molecular patterns.
 
 ```julia
-Base.@kwdef mutable struct StaticSMLMParams <: SMLMSimParams
+Base.@kwdef mutable struct StaticSMLMConfig <: SMLMSimParams
     density::Float64 = 1.0          # density in particles per square micron
     σ_psf::Float64 = 0.13           # PSF width in microns
     minphotons::Int = 50            # minimum photons for detection
@@ -67,12 +67,12 @@ Base.@kwdef mutable struct StaticSMLMParams <: SMLMSimParams
 end
 ```
 
-### DiffusionSMLMParams
+### DiffusionSMLMConfig
 
 Parameters for diffusion-based SMLM simulation using Smoluchowski dynamics.
 
 ```julia
-Base.@kwdef mutable struct DiffusionSMLMParams <: SMLMSimParams
+Base.@kwdef mutable struct DiffusionSMLMConfig <: SMLMSimParams
     density::Float64 = 1.0          # number density (molecules/μm²)
     box_size::Float64 = 10.0        # simulation box size (μm)
     diff_monomer::Float64 = 0.1     # monomer diffusion coefficient (μm²/s)
@@ -222,21 +222,21 @@ end
 
 ```julia
 # Static SMLM with default parameters
-params_static = StaticSMLMParams()
+params_static = StaticSMLMConfig()
 
 # Custom parameters for static simulation
-params_static = StaticSMLMParams(
+params_static = StaticSMLMConfig(
     density = 2.0,        # 2 patterns per μm²
     σ_psf = 0.15,         # 150nm PSF width
     nframes = 2000,       # 2000 frames
     framerate = 20.0      # 20 fps
 )
 
 # Diffusion simulation with default parameters
-params_diff = DiffusionSMLMParams()
+params_diff = DiffusionSMLMConfig()
 
 # Custom parameters for diffusion simulation
-params_diff = DiffusionSMLMParams(
+params_diff = DiffusionSMLMConfig(
     density = 0.5,        # molecules per μm²
     box_size = 15.0,      # 15μm box size
     diff_monomer = 0.2,   # 0.2 μm²/s diffusion coefficient
@@ -338,7 +338,7 @@ All `simulate()` methods return a tuple: `(primary_output, info)`.
 ```julia
 # Static SMLM simulation
 # First create simulation parameters
-params = StaticSMLMParams()
+params = StaticSMLMConfig()
 
 # Then run simulation - returns (smld_noisy, SimInfo)
 smld_noisy, info = simulate(
@@ -363,7 +363,7 @@ smld_noisy, info = simulate(
 
 # Diffusion simulation
 # First create simulation parameters
-params_diff = DiffusionSMLMParams()
+params_diff = DiffusionSMLMConfig()
 
 # Then run simulation - returns (smld, SimInfo)
 smld, info = simulate(
@@ -498,7 +498,7 @@ single_frame, info = gen_image(
 # Example usage of diffusion analysis functions
 
 # First, run a diffusion simulation
-params = DiffusionSMLMParams()
+params = DiffusionSMLMConfig()
 smld, info = simulate(params)
 
 # Extract dimers from diffusion simulation
@@ -523,7 +523,7 @@ state_history = track_state_changes(smld)
 # Example usage of track utilities
 
 # First, run a simulation
-params = StaticSMLMParams()
+params = StaticSMLMConfig()
 smld_noisy, info = simulate(params)
 
 # Specify a track ID to extract
@@ -630,7 +630,7 @@ x, y, z, pattern_ids = uniform3D(density, pattern3d, field_x, field_y, zrange=[-
 
 ```julia
 # 1. Define parameters
-params = StaticSMLMParams(
+params = StaticSMLMConfig(
     density = 1.0,
     σ_psf = 0.13,
     nframes = 1000
@@ -674,7 +674,7 @@ images, img_info = gen_images(smld_model, psf;
 
 ```julia
 # 1. Define parameters
-params = DiffusionSMLMParams(
+params = DiffusionSMLMConfig(
     density = 0.5,        # molecules per μm²
     box_size = 10.0,      # μm
     diff_monomer = 0.1,   # μm²/s
@@ -714,7 +714,7 @@ using MicroscopePSFs
 
 # Define a camera and simulation parameters
 camera = IdealCamera(128, 128, 0.1)  # 128×128 pixels, 100nm pixels
-params = StaticSMLMParams(density=1.0, σ_psf=0.13, nframes=1000)
+params = StaticSMLMConfig(density=1.0, σ_psf=0.13, nframes=1000)
 
 # Run simulation for an 8-molecule ring pattern
 smld_noisy, info = simulate(
@@ -748,7 +748,7 @@ using SMLMSim
 using MicroscopePSFs
 
 # Set diffusion simulation parameters
-params = DiffusionSMLMParams(
+params = DiffusionSMLMConfig(
     density = 0.5,        # molecules per μm²
     box_size = 10.0,      # μm
     diff_monomer = 0.1,   # μm²/s
@@ -823,7 +823,7 @@ end
 
 # Create camera and parameters
 camera = IdealCamera(128, 128, 0.1)
-params = StaticSMLMParams(
+params = StaticSMLMConfig(
     density = 0.5,
     σ_psf = 0.13,
     nframes = 2000,

docs/src/core/noise.md

@@ -51,11 +51,11 @@ Note that the axial (z) uncertainty is typically 2-3× larger than the lateral (
 
 ## Uncertainty in Static Simulations
 
-The `StaticSMLMParams` includes a parameter `σ_psf` that controls the PSF width used for uncertainty calculations:
+The `StaticSMLMConfig` includes a parameter `σ_psf` that controls the PSF width used for uncertainty calculations:
 
 ```julia
 # Create simulation parameters with specific PSF width
-params = StaticSMLMParams(
+params = StaticSMLMConfig(
     σ_psf=0.15,  # 150nm PSF width
     ρ=1.0,       # 1 pattern per μm²
     nframes=1000

docs/src/diffusion/examples.md

@@ -26,7 +26,7 @@ using CairoMakie
 using MicroscopePSFs
 
 # Set up simulation parameters
-params = DiffusionSMLMParams(
+params = DiffusionSMLMConfig(
     density = 2.0,        # molecules per μm²
     box_size = 10.0,      # μm
     diff_monomer = 0.1,   # μm²/s
@@ -111,7 +111,7 @@ using MicroscopePSFs
 using CairoMakie
 
 # Set up diffusion parameters with high temporal resolution
-params = DiffusionSMLMParams(
+params = DiffusionSMLMConfig(
     density = 1.0,          # molecules per μm²
     box_size = 10.0,        # μm
     diff_monomer = 0.2,     # μm²/s (moderate diffusion)
@@ -176,15 +176,15 @@ using SMLMSim
 using CairoMakie
 
 # Set up simulations with different dissociation rates
-params_stable = DiffusionSMLMParams(
+params_stable = DiffusionSMLMConfig(
     density = 1.0,        # molecules per μm²
     diff_monomer = 0.1,   # μm²/s
     diff_dimer = 0.05,    # μm²/s
     k_off = 0.05,         # s⁻¹ (stable dimers)
     t_max = 20.0          # s
 )
 
-params_unstable = DiffusionSMLMParams(
+params_unstable = DiffusionSMLMConfig(
     density = 1.0,        # molecules per μm²
     diff_monomer = 0.1,   # μm²/s
     diff_dimer = 0.05,    # μm²/s
@@ -234,7 +234,7 @@ using CairoMakie
 using MicroscopePSFs
 
 # Set simulation parameters
-params = DiffusionSMLMParams(
+params = DiffusionSMLMConfig(
     density = 0.3,        # molecules per μm²
     box_size = 10.0,      # μm
     diff_monomer = 0.1,   # μm²/s
@@ -317,7 +317,7 @@ using SMLMSim
 using CairoMakie
 
 # Set up a minimal simulation with just two particles
-params = DiffusionSMLMParams(
+params = DiffusionSMLMConfig(
     box_size = 1.0,       # 1 μm box for close interactions
     diff_monomer = 0.1,   # μm²/s
     diff_dimer = 0.05,    # μm²/s

docs/src/diffusion/overview.md

@@ -43,13 +43,13 @@ All simulation parameters use consistent physical units:
 
 ### Running a Basic Simulation
 
-The main interface for running diffusion simulations is the `simulate` function with `DiffusionSMLMParams`:
+The main interface for running diffusion simulations is the `simulate` function with `DiffusionSMLMConfig`:
 
 ```julia
 using SMLMSim
 
 # Set simulation parameters
-params = DiffusionSMLMParams(
+params = DiffusionSMLMConfig(
     density = 0.5,        # molecules per μm²
     box_size = 10.0,      # μm
     diff_monomer = 0.1,   # μm²/s
@@ -69,11 +69,11 @@ The `smld` output is a `BasicSMLD` structure containing all emitters across all
 
 ## Simulation Parameters
 
-The `DiffusionSMLMParams` structure allows you to customize various aspects of the simulation:
+The `DiffusionSMLMConfig` structure allows you to customize various aspects of the simulation:
 
 ```julia
 # More complex simulation
-params = DiffusionSMLMParams(
+params = DiffusionSMLMConfig(
     density = 2.0,           # Higher density
     box_size = 20.0,         # Larger area
     diff_monomer = 0.2,      # Faster monomer diffusion

docs/src/images.md

@@ -32,7 +32,7 @@ using MicroscopePSFs
 
 # Create or load an SMLD object
 # (This could be from either static or diffusion simulation)
-params = StaticSMLMParams(density=1.0, σ_psf=0.13, nframes=1000)
+params = StaticSMLMConfig(density=1.0, σ_psf=0.13, nframes=1000)
 camera = IdealCamera(128, 128, 0.1)  # 128×128 pixels, 100nm pixels
 pattern = Nmer2D(n=6, d=0.2)  # Hexamer with 200nm diameter
 molecule = GenericFluor(1e4, [-50.0 50.0; 1e-2 -1e-2])  # Blinking model
@@ -132,7 +132,7 @@ using MicroscopePSFs
 camera_scmos = SCMOSCamera(128, 128, 0.1, 1.6)  # 1.6 e⁻ RMS read noise
 
 # Run simulation with sCMOS camera
-params = StaticSMLMParams(density=1.0, σ_psf=0.13)
+params = StaticSMLMConfig(density=1.0, σ_psf=0.13)
 smld_true, smld_model, smld_noisy = simulate(
     params,
     pattern=Nmer2D(n=8, d=0.1),

docs/src/index.md

@@ -72,7 +72,7 @@ smld_true, smld_model, smld_noisy = simulate(
 
 ```julia
 # Set diffusion simulation parameters
-params = DiffusionSMLMParams(
+params = DiffusionSMLMConfig(
     density = 0.5,        # molecules per μm²
     box_size = 10.0,      # μm
     diff_monomer = 0.1,   # μm²/s

docs/src/static/examples.md

@@ -18,7 +18,7 @@ using CairoMakie
 camera = IdealCamera(128, 64, 0.1)  # 128×64 pixels, 100nm pixels
 
 # Create simulation parameters
-params = StaticSMLMParams(
+params = StaticSMLMConfig(
     density = 1.0,        # patterns per μm²
     σ_psf = 0.13,         # PSF width in μm
 )
@@ -73,7 +73,7 @@ using CairoMakie
 camera = IdealCamera(128, 128, 0.1)  # 128×128 pixels, 100nm pixels
 
 # Create 3D simulation parameters
-params = StaticSMLMParams(
+params = StaticSMLMConfig(
     density = 0.5,        # emitters per μm²
     σ_psf = 0.13,         # PSF width in μm
     ndims = 3,            # 3D simulation
@@ -129,7 +129,7 @@ using CairoMakie
 camera = IdealCamera(128, 128, 0.1)  # 128×128 pixels, 100nm pixels
 
 # Create simulation parameters
-params = StaticSMLMParams(
+params = StaticSMLMConfig(
     density = 2.0,        # patterns per μm²
     σ_psf = 0.13,         # 130nm PSF width
     nframes = 100,        # 100 frames
@@ -247,7 +247,7 @@ camera = IdealCamera(64, 64, 0.1)
 grid = JitteredGrid2D()
 
 # Create simulation parameters
-params = StaticSMLMParams(
+params = StaticSMLMConfig(
     density = 0.2,        # Patterns per μm²
     nframes = 1000        # Number of frames
 )