Check and fix example codes from the README. They are in test_README.jl, which now works.

Author: kalidke

README.md

@@ -136,7 +136,7 @@ params = SmoluchowskiParams(
 systems = simulate(params)
 
 # Visualize the simulation
-visualize_sequence(systems, filename="diffusion.mp4", framerate=30)
+visualize_sequence(systems, filename="diffusion.mp4", framerate=round(Int64,1/params.dt))
 
 # Generate microscope images
 psf = Gaussian2D(0.15)  # 150nm PSF width
@@ -185,7 +185,8 @@ ax = Axis(fig[1, 1],
     title="Simulated SMLM Localizations",
     xlabel="x (μm)",
     ylabel="y (μm)",
-    aspect=DataAspect()
+    aspect=DataAspect(),
+    yreversed=true  # This makes (0,0) at top-left
 )
 
 # Scatter plot with photon counts as color
@@ -199,7 +200,7 @@ scatter!(ax, x_noisy, y_noisy,
 Colorbar(fig[1, 2], colormap=:viridis, label="Photons")
 
 # Show or save the figure
-# display(fig)
+display(fig)
 # save("smlm_simulation.png", fig)
 ```
 

dev/test_README.jl

@@ -1,10 +1,10 @@
 # using Pkg
 # Pkg.activate("dev")
 
-# using Revise
-using SMLMSim # must be 'dev'ed in the current environment
+using Revise
+using SMLMSim
 using CairoMakie
-
+using MicroscopePSFs
 #==========================================================================
 Basic Usage
 ==========================================================================#
@@ -25,7 +25,7 @@ smld_true, smld_model, smld_noisy = simulate(;
     framerate=50.0,       # frames per second
     pattern=Nmer2D(n=6, d=0.2),  # hexamer with 200nm diameter
     molecule=GenericFluor(; q=[0 50; 1e-2 0]),  # rates in 1/s
-    camera=IdealCamera(; ypixels=256, xpixels=128, pixelsize=0.1)  # pixelsize in μm
+    camera=IdealCamera(1:256, 1:128, 0.1)  # pixelsize in μm
 )
 
 #==========================================================================
@@ -77,7 +77,7 @@ params = SmoluchowskiParams(
 systems = simulate(params)
 
 # Visualize the simulation
-visualize_sequence(systems, filename="diffusion.mp4", framerate=30)
+visualize_sequence(systems, filename="diffusion.mp4", framerate=round(Int64,1/params.dt))
 
 # Generate microscope images
 psf = Gaussian2D(0.15)  # 150nm PSF width
@@ -121,7 +121,8 @@ ax = Axis(fig[1, 1],
     title="Simulated SMLM Localizations",
     xlabel="x (μm)",
     ylabel="y (μm)",
-    aspect=DataAspect()
+    aspect=DataAspect(),
+    yreversed=true  # This makes (0,0) at top-left
 )
 
 # Scatter plot with photon counts as color

src/SMLMSim.jl

@@ -4,6 +4,8 @@ using SMLMData
 using Distributions
 using LinearAlgebra
 
+# Re-export critical types from SMLMData to make them available to users
+export AbstractCamera, IdealCamera, AbstractEmitter, Emitter2D, Emitter3D, Emitter2DFit, Emitter3DFit, BasicSMLD
 
 include("molecules.jl")
 include("patterns.jl")
@@ -13,7 +15,14 @@ include("interface.jl")
 # Submodules
 include("diffusion/InteractionDiffusion.jl")
 
-using .InteractionDiffusion
+# Import specific functions from InteractionDiffusion
+using .InteractionDiffusion: DiffusingMolecule, DiffusingMoleculeSystem, 
+                            SmoluchowskiParams, get_dimers, 
+                            show_frame, visualize_sequence, visualize_simulation,
+                            gen_image, gen_image_sequence
+
+# Add this line to import the simulate method
+using .InteractionDiffusion: simulate
 
 # Export molecule types
 export
@@ -43,12 +52,13 @@ export
     SmoluchowskiParams,
 
     # Core simulation functions
-    simulate,
-    simulate_and_image,
-
+    simulate, # Will dispatch to appropriate method based on argument types
+    
     # Analysis functions
     get_dimers,
-    gen_dimer_images
+    gen_dimer_images,
+    gen_image,         # Add this
+    gen_image_sequence # Add this
 
 # Pattern simulation types and functions
 export
@@ -77,5 +87,4 @@ export
     visualize_sequence,
     visualize_simulation
 
-
 end

src/diffusion/InteractionDiffusion.jl

@@ -42,17 +42,20 @@ module InteractionDiffusion
 using SMLMData 
 using Distributions
 using MicroscopePSFs
-using SMLMSim
 
 using Printf
 using CairoMakie
 
+# Import the main simulate function to add our method
+import ..simulate
+
 include("types.jl")
 include("smoluchowski.jl")
 include("visualize.jl")
 include("microscope.jl")
 include("dimer.jl")
 
+
 # Core types and functions for diffusion simulation
 export
     # Core types
@@ -61,7 +64,7 @@ export
     SmoluchowskiParams,
 
     # Core simulation functions
-    simulate,
+    simulate,  # Export the function, but the implementation is a method
     simulate_and_image,
 
     # Analysis functions

src/diffusion/visualize.jl

@@ -164,9 +164,16 @@ function visualize_sequence(systems::Vector{<:DiffusingMoleculeSystem};
     xlims!(ax, (0, box_size))
     ylims!(ax, (box_size, 0))
 
-    # Add legend if showing dimers
+    # Store legend position for updates
+    legend_pos = (1, 2)
+    
+    # Create Observables for legend labels
     if show_dimers
-        leg = Legend(fig[1, 2], ["Monomers", "Dimers"], [:blue, :red])
+        legend_labels = Observable(["Monomers (0)", "Dimers (0)"])
+        leg = Legend(fig[legend_pos...],
+            [MarkerElement(color=:blue, marker=:circle),
+             MarkerElement(color=:red, marker=:circle)],
+            legend_labels[])
     end
 
     # Information display
@@ -185,10 +192,10 @@ function visualize_sequence(systems::Vector{<:DiffusingMoleculeSystem};
         if show_dimers
             sc.color = [mol.state == 2 ? :red : :blue for mol in systems[i].molecules]
 
-            # Update legend with counts
+            # Update legend labels
             n_monomers = count(mol -> mol.state == 1, systems[i].molecules)
             n_dimers = count(mol -> mol.state == 2, systems[i].molecules)
-            leg.labels = ["Monomers ($n_monomers)", "Dimers ($n_dimers)"]
+            legend_labels[] = ["Monomers ($n_monomers)", "Dimers ($n_dimers)"]
         end
 
         # Update info text