Fix SCMOSCamera matrix convention to match Julia standard (#34)

* Fix SCMOSCamera matrix convention to match Julia standard

The validation check for calibration matrices (readnoise, gain, offset, qe)
was expecting size (nx, ny) but Julia arrays use [row, col] indexing, so
matrices should be (ny, nx) where ny=rows and nx=cols.

This bug was masked by square camera tests but would cause:
- BoundsError for rectangular cameras when downstream code accesses map[y, x]
- Semantic errors for square cameras (data transposed)

Changes:
- Fix _validate_camera_param to expect (ny, nx) instead of (nx, ny)
- Update docstrings to clarify the convention
- Fix existing rectangular test that used wrong convention
- Add explicit test verifying semantic access pattern

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

* Bump version to 0.5.1

---------

Co-authored-by: Claude Opus 4.5 <noreply@anthropic.com>

Author: kalidke

Project.toml

@@ -1,7 +1,7 @@
 name = "SMLMData"
 uuid = "5488f106-40b8-4660-84c5-84a168990d1b"
 authors = ["klidke@unm.edu"]
-version = "0.5.0"
+version = "0.5.1"
 
 [deps]
 Adapt = "79e6a3ab-5dfb-504d-930d-738a2a938a0e"

src/types/cameras.jl

@@ -422,7 +422,7 @@ Construct sCMOS camera from pixel dimensions and calibration parameters.
 - `gain::Union{T, Matrix{T}} = 1`: Conversion gain in e⁻/ADU
 - `qe::Union{T, Matrix{T}} = 1`: Quantum efficiency (0-1)
 
-Each parameter can be scalar (uniform) or Matrix{T} with size (nx, ny).
+Each parameter can be scalar (uniform) or Matrix{T} with size (ny, nx) following Julia's [row, col] convention.
 
 # Examples
 ```julia
@@ -483,7 +483,7 @@ Construct sCMOS camera with custom pixel edge positions.
 - `gain::Union{T, Matrix{T}} = 1`: Conversion gain in e⁻/ADU
 - `qe::Union{T, Matrix{T}} = 1`: Quantum efficiency (0-1)
 
-Matrix parameters must have size (nx, ny) where nx = length(pixel_edges_x) - 1.
+Matrix parameters must have size (ny, nx) following Julia's [row, col] convention, where nx = length(pixel_edges_x) - 1 and ny = length(pixel_edges_y) - 1.
 
 # Example
 ```julia
@@ -515,9 +515,11 @@ function SCMOSCamera(
 end
 
 # Validation helper
+# Matrix parameters use Julia standard (row, col) = (y, x) convention
+# So for a camera with nx columns and ny rows, matrices should be (ny, nx)
 function _validate_camera_param(param::AbstractMatrix, nx, ny, name)
-    size(param) == (nx, ny) ||
-        throw(DimensionMismatch("$name size $(size(param)) must match ($nx, $ny)"))
+    size(param) == (ny, nx) ||
+        throw(DimensionMismatch("$name size $(size(param)) must match ($ny, $nx) [rows, cols]"))
 end
 _validate_camera_param(param::Real, nx, ny, name) = nothing
 

test/test_cameras.jl

@@ -252,10 +252,12 @@ end
         @test cam.readnoise === 1.5
         @test cam.gain === 0.5
 
-        # Matrix parameters
-        noise_map = ones(Float64, 10, 5) .* 1.2
+        # Matrix parameters - size must be (ny, nx) = (rows, cols) following Julia convention
+        # edges_x has 11 elements → nx = 10 columns
+        # edges_y has 6 elements → ny = 5 rows
+        noise_map = ones(Float64, 5, 10) .* 1.2  # (ny, nx) = (5, 10)
         cam2 = SCMOSCamera(edges_x, edges_y, readnoise=noise_map)
-        @test size(cam2.readnoise) == (10, 5)
+        @test size(cam2.readnoise) == (5, 10)
     end
 
     @testset "Type stability" begin
@@ -286,6 +288,27 @@ end
         @test_throws DimensionMismatch SCMOSCamera(10, 10, 0.1, 1.5, qe=wrong_size_map)
     end
 
+    @testset "Matrix convention (ny, nx) for rectangular cameras" begin
+        # Rectangular camera: 512 columns (x), 256 rows (y)
+        # Matrix must be (ny, nx) = (256, 512) following Julia [row, col] convention
+        nx, ny = 512, 256
+
+        # Create noise map with a marker at known position
+        noise_map = ones(Float64, ny, nx)  # (256, 512) = (rows, cols)
+        noise_map[100, 300] = 5.0  # row 100, col 300 → pixel (x=300, y=100)
+
+        cam = SCMOSCamera(nx, ny, 0.1, noise_map)
+        @test size(cam.readnoise) == (ny, nx)
+        @test size(cam.readnoise) == (256, 512)
+
+        # Verify semantic access: map[y, x] gives value for pixel at (x, y)
+        @test cam.readnoise[100, 300] == 5.0
+
+        # Transposed matrix should fail
+        wrong_map = ones(Float64, nx, ny)  # (512, 256) - WRONG
+        @test_throws DimensionMismatch SCMOSCamera(nx, ny, 0.1, wrong_map)
+    end
+
     @testset "Realistic use cases" begin
         # ORCA-Flash4.0 V3
         cam_flash = SCMOSCamera(