Fix sCMOS scalar calibration and non-square image bug (Issue #37)

Allow sCMOS cameras to use scalar calibration values for modern uniform
sensors like Orca Fusion AND fix pre-existing bug with non-square sCMOS images.

Issue #37 - Scalar Calibration:
When CameraType='SCMOS' with scalar gain/offset/readnoise and empty
CalibrationFilePath, the code failed because sCMOS CUDA kernels expect
2D variance images to index into, not scalars.

Pre-existing Bug - Non-Square sCMOS Images:
The gauss_sCMOS() function had incorrect dimensions after permutation,
causing failures with ANY non-square sCMOS data (429×244, etc.), even
with proper 2D calibration arrays. This was hidden when using square
images (256×256) where transpose doesn't change dimensions.

Changes:
- FindROI.m constructor (lines 86-104): For sCMOS with scalar
  calibration, expand scalars to 2D variance image matching Data
  dimensions. THIS IS THE ONLY PLACE SCALARS NEED EXPANSION.

- FindROI.gauss_sCMOS (lines 366-368): Fix output array dimensions
  after permutation by allocating to match PermutedStack size, not
  original Stack size.

- SingleMoleculeFitting.m: Update documentation to clarify sCMOS
  supports both pixel-wise arrays and scalars (auto-expanded).

Why convertToPhotons doesn't need changes:
MATLAB handles scalar division correctly - the else branch at line 118
already works fine for scalars. Expansion is ONLY needed for sCMOS
variance image (Varim) used by CUDA kernels.

Testing:
- Non-square sCMOS with scalars: ✓ Works (429×244 verified)
- Non-square sCMOS with 2D arrays: ✓ Works (was broken, now fixed)
- Square sCMOS: ✓ Works (backward compatible)
- DataToPhotons unit tests: ✓ All pass (5/5)

Fixes #37 + non-square sCMOS bug

🤖 Generated with [Claude Code](https://claude.com/claude-code)

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

Author: kalidke

MATLAB/+smi_core/@FindROI/FindROI.m

@@ -83,11 +83,29 @@
                 switch SMF.Data.CameraType
                     case 'SCMOS'
                         obj.IsSCMOS = 1;
-                        obj.Varim = gpuArray(single(SMF.Data.CameraReadNoise./SMF.Data.CameraGain.^2)); 
+                        % For sCMOS with scalar calibration (modern uniform
+                        % sensors like Orca Fusion), expand to 2D variance image
+                        % matching data dimensions. This supports Issue #37 fix.
+                        CameraReadNoise = SMF.Data.CameraReadNoise;
+                        CameraGain = SMF.Data.CameraGain;
+                        if isscalar(CameraReadNoise) && isscalar(CameraGain)
+                            % Need 2D variance image for sCMOS CUDA kernels
+                            % Expand based on Data dimensions if available
+                            if nargin > 1 && ~isempty(Data)
+                                [NRows, NCols, ~] = size(Data);
+                                CameraReadNoise = CameraReadNoise * ones(NRows, NCols, 'single');
+                                CameraGain = CameraGain * ones(NRows, NCols, 'single');
+                            else
+                                % Data not yet available - will fail if used
+                                % This case shouldn't happen in normal workflow
+                                warning('FindROI: sCMOS with scalar calibration but no Data provided');
+                            end
+                        end
+                        obj.Varim = gpuArray(single(CameraReadNoise./CameraGain.^2));
                     otherwise
                         obj.IsSCMOS = 0;
                 end
-                
+
             end
 
             if nargin > 1
@@ -344,9 +362,11 @@ function showOverlay(obj)
         Out1 = feval(K_Gauss,gpuArray(Stack),Varim,Out1,size(Stack,1),Sigma);
 
         %Permuting and doing the other dimension
-        Out = gpuArray(zeros(size(Stack),'single'));
-        Out = feval(K_Gauss,permute(Out1,[2 1 3]),permute(Varim,[2 1]),Out,size(Stack,1),Sigma);
-        
+        % For non-square images, output dimensions must match permuted input
+        PermutedStack = permute(Out1,[2 1 3]);
+        Out = gpuArray(zeros(size(PermutedStack),'single'));
+        Out = feval(K_Gauss,PermutedStack,permute(Varim,[2 1]),Out,size(PermutedStack,1),Sigma);
+
         %Permute back
         Out = permute(Out,[2 1 3]);
 

MATLAB/+smi_core/@SingleMoleculeFitting/SingleMoleculeFitting.m

@@ -391,10 +391,11 @@
                 'precedence over the inclusion set']);
             obj.SMFFieldNotes.Data.CameraType.Tip = ...
                 sprintf(['Type of camera used to collect the raw data.\n', ...
-                'CameraGain, CameraOffset, CameraReadNoise) should be\n', ...
-                'scalars if the CameraType is EMCCD while if SCMOS,\n', ...
-                'square arrays taken from the file located at the ', ...
-                'CalibrationFilePath.']);
+                'CameraGain, CameraOffset, CameraReadNoise should be:\n', ...
+                '  EMCCD: scalars\n', ...
+                '  SCMOS: either square arrays from CalibrationFilePath\n', ...
+                '         OR scalars for uniform sensors (e.g., Orca Fusion).\n', ...
+                'Scalar values for SCMOS will be expanded automatically.']);
             obj.SMFFieldNotes.Data.CameraGain.Tip = ...
                 'Gain of the camera used to collect the raw data';
             obj.SMFFieldNotes.Data.CameraOffset.Tip = ...