Merge branch 'dev'

data/sensor/colorfilters/auto/SONY/s_imx490QEdata.m

@@ -0,0 +1,41 @@
+%% Managing the IMX490 spectral QE
+%
+% Grabit on the scanned image in sonyIMX490.png produced the first
+% file.
+
+%%
+datadir = fullfile(isetRootPath,'data','sensor','colorfilters','auto','SONY');
+curdir = pwd;
+chdir(datadir);
+
+%% Data from grabit, via Zhenyi
+tmp = load('qe_imx490_scan.mat');
+
+% Scale to 0,1
+tmp.data = tmp.data/100;
+
+tmp.data(tmp.data<0) = 0;
+tmp.data(isnan(tmp.data)) = 0;
+
+ieNewGraphWin; plot(tmp.wavelength,tmp.data);
+xaxisLine;
+
+%% Write it out in the two formats.   Not sure why we have two.
+
+%% CF file
+tmp.filterNames = {'r','g','b'};
+tmp.comment = 'Cleaned up QE from grabit scan of LUCID curves.';
+
+cfFile = fullfile(datadir,'cf_imx490.mat');
+
+ieSaveColorFilter(tmp,cfFile);
+disp("Saved Sony imx490 spectral qe as a color filter.")
+disp('Read it using ieReadColorFilter')
+
+%% QE file
+qeFile = fullfile(datadir,'qe_imx490.mat');
+ieSaveSpectralFile(tmp.wavelength,tmp.data,tmp.comment,qeFile);
+disp("Saved Sony imx490 spectral qe as a color filter.")
+disp('Read it using ieReadSpectra.')
+
+%%

imgproc/demosaic/Demosaic.m

@@ -132,6 +132,8 @@
 switch lower(m)
     case {'iebilinear','bilinear'}
         method = 'ieBilinear';
+    case {'matlabbilinear'}
+        method = 'matlabbilinear';
     case {'multichannel'}
         method = 'multichannel';
     case {'adaptivelaplacian'}
@@ -174,7 +176,11 @@
             % Rarely go this computational path.  Mainly used for human retina.
             demosaicedImage = demosaicMultichannel(imgRGB,sensor,'interpolate');
         end
-
+    case {'matlabbilinear'}
+        % [1] Malvar, H.S., L. He, and R. Cutler, High quality linear
+        % interpolation for demosaicing of Bayer-patterned color
+        % images. ICASPP, Volume 34, Issue 11, pp. 2274-2282, May 2004.  
+        demosaicedImage = demosaic(imgRGB,sensorGet(sensor,'pattern'));
     case 'adaptivelaplacian'
         clipToRange = 0;
         if (strcmp(bPattern,'grbg') || ...

metrics/scielab/scPrepareFilters.m

@@ -33,18 +33,7 @@
 % The filters are a cell array.  The support defines the spatial support in
 % terms of degrees of visual angle.
 %
-% Example:
-%   params.deltaEversion = '2000';
-%   params.sampPerDeg    = 145;
-%   params.imageFormat   = 'LMS';
-%   params.filterSize    = 145;
-%   params.dimension     = 2;
-%   [filters,support]    = scPrepareFilters(params);
-%
-%   figure;   % Units are degrees of visual angle
-%   subplot(1,3,1), mesh(support,support,filters{1}); colormap(hsv(256));
-%   subplot(1,3,2), mesh(support,support,filters{2}); colormap(hsv(256));
-%   subplot(1,3,3), mesh(support,support,filters{3}); colormap(hsv(256));
+% The source code below contains a runnable example.
 %
 % In 1996, Xuemei Zhang used this routine
 %   [k1, k2, k3] = separableFilters(params.sampPerDeg,2);
@@ -59,6 +48,35 @@
 %
 % Copyright ImagEval Consultants, LLC, 2003.
 
+% Examples:
+%{
+  clear; close all; 
+  params.deltaEversion = '2000';
+  params.sampPerDeg    = 145;
+  params.imageFormat   = 'LMS';
+  params.filterSize    = 145;
+  params.dimension     = 2;
+  [filters,support]    = scPrepareFilters(params);
+  
+  % Units are degrees of visual angle
+  figure; clf;
+  subplot(1,3,1), mesh(support,support,filters{1}); colormap(hsv(256));
+  subplot(1,3,2), mesh(support,support,filters{2}); colormap(hsv(256));
+  subplot(1,3,3), mesh(support,support,filters{3}); colormap(hsv(256));
+    
+  % In 1996, Xuemei Zhang used this routine
+  [k1, k2, k3] = separableFilters(params.sampPerDeg,2);
+  figure; clf;
+  subplot(1,2,1); mesh(support,support,filters{3})
+  subplot(1,2,2); mesh(support,support,k1)
+   
+  % The values are the same aes shown by the zero difference
+  figure; clf;
+  subplot(1,3,1); mesh(support,support,k1-filters{1});
+  subplot(1,3,2); mesh(support,support,k2-filters{2});
+  subplot(1,3,3); mesh(support,support,k3-filters{3});
+%}
+
 % Check parameters
 if ieNotDefined('params'), error('Params required.'); end
 if ~checkfields(params,'sampPerDeg'), params.sampPerDeg = 224; end

opticalimage/oiCompute.m

@@ -18,7 +18,10 @@
 %
 %   crop - Crop the OI to the same size as the scene. (Logical)
 %          Default: false;
-%         (We could do a setprefs on these, but BW is resistant.)
+%
+%   pixel size - Spatial resolution of the oi image. A scalar in
+%                meters. Normally it is set to match the optics and
+%                scene properties.
 %
 % Return
 %   oi - The oi with computed photon irradiance
@@ -57,12 +60,12 @@
 % in opticsDLCompute. This blur and intensity in this computation depends
 % on the diffraction limited parameters (f/#) but little else.
 %
-% To create an image with no blur, set the f/# to a very small number.
-% This will provide an image that has the geometry and zero-blur as used in
-% computer graphics pinhole cameras.  The absolute light level, however,
-% will be higher than what would be seen through a small pinhole. You can
-% manage this by setting scaling the spectral irradiance
-% (oiAdjustIlluminance).
+% To create an image with no blur, set the f/# (focal length over the
+% aperture) to be a very small number. This image has the geometry and
+% zero-blur as used in computer graphics pinhole cameras.  The
+% absolute light level, however, will be higher than what would be
+% seen through a small pinhole. You can manage this by setting scaling
+% the spectral irradiance (oiAdjustIlluminance).
 %
 % * The second model is shift-invariant optics.  This depends on having a
 % wavelength-dependent OTF defined and included in the optics structure.
@@ -123,6 +126,13 @@
 oi = oiCompute(oi,scene,'pad value','border','crop',true);
 oiWindow(oi);
 %}
+%{
+% Almost right.  Off by 1 part in 100.  Need to fix. (BW).
+scene = sceneCreate;
+oi = oiCreate;
+oi = oiCompute(oi,scene,'pad value','border','crop',true,'pixel size',1e-6);
+oiWindow(oi);
+%}
 %% Parse
 varargin = ieParamFormat(varargin);
 p = inputParser;
@@ -135,28 +145,29 @@
 p.parse(oi,scene,varargin{:});
 
 % Ages ago, we some code flipped the order of scene and oi.  We think
-% we have caught all those cases, but we still test.  Maybe delete
-% this code by January 2024.
+% we have caught all those cases, but we still test, and are now forcing
+% the user to correct.
 if strcmp(oi.type,'scene') && (strcmp(scene.type,'opticalimage') ||...
         strcmp(scene.type,'wvf'))
-    warning('flipping oi and scene variables.')
-    tmp = scene; scene = oi; oi = tmp; clear tmp
+    error('You need to flip order oi and scene variables in the call to oiCompute')
+    % We used to help the user
+    % tmp = scene; scene = oi; oi = tmp; clear tmp
 end
-%% Adjust oi fov if user send in a pixel size
 
+%% Adjust oi fov if user sends in a pixel size
 if ~isempty(p.Results.pixelsize)
     pz = p.Results.pixelsize;
     sw = sceneGet(scene, 'cols');
     flengthM = oiGet(oi, 'focal length', 'm');
     wAngular = atand(pz*sw/2/flengthM)*2;
-    % oi use scene hFOV later.
+    % oi uses scene hFOV later.
     scene = sceneSet(scene, 'wAngular',wAngular);
 end
 
 %% Compute according to the selected model.
-
+%
 % Should we pad the scene before the call to these computes?
-
+%
 % We pass varargin because it may contain the key/val parameters
 % such as pad value and crop. But we only use pad value here.
 if strcmp(oi.type,'wvf')

opticalimage/oiCreate.m

@@ -10,6 +10,9 @@
 %
 % Inputs
 %   oiType -
+%     {'pinhole'}    - Turn off cos4th, infinite depth of field and
+%                      NaN focal length
+%
 %     {'diffraction limited'} -  Diffraction limited optics, no diffuser or
 %                         data (Default).  Equivalent to using the wvf or
 %                         shift-invariant with a zero wavefront
@@ -103,15 +106,6 @@
 %%
 scene = []; wvf = [];
 switch ieParamFormat(oiType)
-    case {'empty'}
-        % Just the basic shell of the oi struct
-        % Other terms will get added by the calling function
-        oi.type = 'opticalimage';
-        oi.name = vcNewObjectName('opticalimage');
-        oi.metadata = [];  % Store metadata typically for machine-learning apps
-        oi = oiSet(oi, 'diffuser method', 'skip');
-        oi = oiSet(oi,'wave',[]);
-
     case {'diffractionlimited','default'}
         % Diffraction limited is implemented using the dlMTF method.
         % This is like the wvf case, but the dl MTF is computed on the fly
@@ -136,6 +130,47 @@
             oi.optics.transmittance.scale = ones(length(370:730), 1);
         end
 
+    case {'pinhole'}
+        % Pinhole optics in an OI. 
+        % 
+        % We set the f/# (focal length over the aperture) to be a very
+        % small number. This image has zero-blur because the
+        % diffraction aperture is very large. That is the goal of the
+        % pinhole camera optics, but the way we achieve it is odd.
+        % 
+        % The absolute light level is high because a small fnumber
+        % means the focal length is very short compared to the
+        % aperture.
+        %
+        % With these default settings the focal length is 10 mm and the
+        % aperture diameter is 10 m.        
+        oi = oiCreate();
+        oi = oiSet(oi, 'name', 'pinhole');
+        oi = oiSet(oi, 'optics name','pinhole');
+
+        % This makes the computation a pinhole
+        oi = oiSet(oi,'optics model','skip');
+        oi = oiSet(oi, 'optics offaxis method', 'skip');
+        oi = oiSet(oi, 'diffuser method', 'skip');
+
+        % Not sure why we set these, but it is true that when we have
+        % a very small fnumber, we should have no blur - like a
+        % pinhole.
+        oi = oiSet(oi, 'optics fnumber',1e-3);
+        oi = oiSet(oi, 'optics focal length',1e-2);
+
+        % Pinhole do not have a focal length or fNumber.
+        wvf = [];
+
+    case {'empty'}
+        % Just the basic shell of the oi struct
+        % Other terms will get added by the calling function
+        oi.type = 'opticalimage';
+        oi.name = vcNewObjectName('opticalimage');
+        oi.metadata = [];  % Store metadata typically for machine-learning apps
+        oi = oiSet(oi, 'diffuser method', 'skip');
+        oi = oiSet(oi,'wave',[]);
+
     case {'shiftinvariant','wvf'}
         % We create via the wavefront method.  We create a wvf, convert it
         % to an oi using wvf2oi, which calls wvf2optics.  
@@ -277,21 +312,6 @@
         oi = oiSet(oi,'fov',100);        
         wvf = [];
 
-    case {'pinhole'}
-        % Pinhole camera version of OI
-        oi = oiCreate('shift invariant');
-        oi = oiSet(oi, 'optics model', 'skip');
-        oi = oiSet(oi, 'bit depth', 64);  % Forces double
-        oi = oiSet(oi, 'optics offaxis method', 'skip');
-        oi = oiSet(oi, 'diffuser method', 'skip');
-
-        % Pinhole do not have a focal length.  In this case, the focal
-        % length is used to say the image plane distance.
-        oi = oiSet(oi, 'optics focal length',NaN);
-        oi = oiSet(oi, 'optics name','pinhole');
-        oi = oiSet(oi, 'name', 'pinhole');
-        wvf = [];
-
     otherwise
         fprintf('\n--- Valid OI types: ---\n')
         for ii=1:length(validTypes)

opticalimage/oiGet.m

@@ -404,10 +404,12 @@
                 if ~isempty(varargin), val = val*ieUnitScaleFactor(varargin{1}); end
 
             case {'wangular','widthangular','hfov','horizontalfieldofview','fov'}
-                % oiCompute(oi,scene) assigns the angular field of view to the oi.
+                % oiCompute(oi,scene) assigns the angular field of
+                % view to the oi. 
+                %
                 % This horizontal FOV represents the size of the OI,
-                % usually after the computational padding.
-                % reflects the angle of the scene it represents.
+                % usually after the computational padding. Reflects
+                % the angle of the scene it represents.
                 if checkfields(oi,'wAngular')
                     val = oi.wAngular;
                 else
@@ -416,10 +418,12 @@
                     % 'focal plane distance'.
                     fprintf('*** The oi fov is not set yet.  ');
                     scene = vcGetObject('scene');
-                    if isempty(scene) % Default scene visual angle.
+                    if isempty(scene) 
+                        % Default scene visual angle.
                         fprintf('Using a default fov of 10.\n');
                         disp('oiGet:  No scene, arbitrary oi angle: 10 deg'), val = 10;
-                    else              % Use current scene angular width
+                    else              
+                        % Use current scene angular width
                         fprintf('Using the scene fov.\n');
                         val = sceneGet(scene,'wangular');
                     end