Merge branch 'master' of https://github.com/isetbio/isetbio

external/psychtoolbox/+ptb/oiSetPtbOptics.m

@@ -94,10 +94,8 @@
 %% Get PTB optics as PSF
 switch (p.Results.opticsModel)
     case 'DeltaFunction'
-        theLsf = position1DMinutes*0;
-        centerPosition = round((numel(position1DMinutes)-1)/2);
-        theLsf(centerPosition+1) = 1;
-        thePsf = LsfToPsf(theLsf);
+        thePsf = zeros(size(xGridMinutes));
+        thePsf(centerPosition,centerPosition) = 1;
     case 'Geisler'
         theLsf = GeislerLSFMinutes(position1DMinutes);
         thePsf = LsfToPsf(theLsf);

isettools/eyemovement/fixationalEyeMovements/@fixationalEM/generateEMandMosaicComboVideo.m

@@ -88,7 +88,7 @@ function generateEMandMosaicComboVideo(fixEMobj, coneMosaic, varargin)
 for iTrial = 1:nTrials
     % Make figure
     hFig = figure();
-    clf
+
     set(hFig, 'Position', [10 10 figSize(1) figSize(2)], 'Color', [1 1 1]);
     % Make subplots axes
     if (showMovingMosaicOnSeparateSubFig)
@@ -113,11 +113,13 @@ function generateEMandMosaicComboVideo(fixEMobj, coneMosaic, varargin)
             plot(axMosaic, crossLengthMeters * [-1 1], [0 0], 'k-', ...
                 'LineWidth', 2.0);
         end
-
+        set(axMosaic, 'LineWidth', 1.0, 'FontSize', 20);
         hold(axMosaic, 'off');
         box(axMosaic, 'on');
     end
 
+
+
     % emPath for this trial
     theEMpathMeters = squeeze(fixEMobj.emPosMicrons(iTrial, :, :)) * 1e-6;
 
@@ -130,11 +132,25 @@ function generateEMandMosaicComboVideo(fixEMobj, coneMosaic, varargin)
             set(axMosaic, 'XLim', xo + visualizedSpaceMeters * ...
                 [-0.5 0.5] * 1.05, 'YLim', yo + visualizedSpaceMeters * ...
                 [-0.5 0.5] * 1.05, 'XTickLabel', {}, 'YTickLabel', {});
-            set(axMosaic, 'FontSize', 16, 'LineWidth', 1.0);
+            set(axMosaic, 'FontSize', 20, 'LineWidth', 1.0);
             title(axMosaic, ...
                 sprintf('%2.1f msec', 1000 * fixEMobj.timeAxis(timeBin)));
         end
 
+
+        % plot emPaths for previous trials
+        for k = 1: iTrial-1
+            theEMpathMetersOld = squeeze(fixEMobj.emPosMicrons(k, :, :)) * 1e-6;
+            plot(axEMpath, theEMpathMetersOld(:, 1), ...
+                theEMpathMetersOld(:, 2), 'k-',  ...
+                'LineWidth', 2.0);
+            if (k == 1)
+                hold(axEMpath, 'on');
+            end
+        end
+
+
+
         % Update the emPath
         plot(axEMpath, theEMpathMeters(1:timeBin, 1), ...
             theEMpathMeters(1:timeBin, 2), 'r-', 'Color', [1 0.5 0.5], ...
@@ -168,11 +184,15 @@ function generateEMandMosaicComboVideo(fixEMobj, coneMosaic, varargin)
         xlabel(axEMpath, 'space (degs)');
         grid(axEMpath, 'on');
         box(axEMpath, 'on');
-        set(axEMpath, 'LineWidth', 1.0);
+        set(axEMpath, 'LineWidth', 1.0, 'FontSize', 20);
 
         if (nTrials > 1)
-            title(axEMpath, sprintf('%2.1f msec (trial #%d)', ...
-                1000 * fixEMobj.timeAxis(timeBin), iTrial));
+            if (~showMovingMosaicOnSeparateSubFig)
+                title(axEMpath, sprintf('%2.1f msec (trial #%d)', ...
+                    1000 * fixEMobj.timeAxis(timeBin), iTrial));
+            else
+                title(axEMpath, sprintf('trial #%d', iTrial));
+            end
         else
             title(axEMpath, sprintf('%2.1f msec', ...
                 1000 * fixEMobj.timeAxis(timeBin)));

isettools/human/humanOTF.m

@@ -1,5 +1,5 @@
 function [OTF2D, fSupport, wave] = humanOTF(pRadius, D0, fSupport, wave)
-% Calculate the human OTF, including chromatic aberration
+% Calculate the Marimont-Wandell human OTF, including chromatic aberration
 %
 % Syntax:
 %   [OTF2D, fSupport, wave] = ...
@@ -44,6 +44,8 @@
 % History:
 %    xx/xx/03       Copyright ImagEval Consultants, LLC, 2003.
 %    06/25/18  jnm  Formatting, fix example to display both subplots
+%    08/20/18  dhb  Change fftshift -> ifftshift for storage of OTF.
+%                   See isetbio issue #373 on github.
 
 % Examples:
 %{
@@ -148,8 +150,9 @@
     % zero them out.
     tmp(l) = 0;
 
-    % This is the proper storage format for the OI-ShiftInvariant case.
-    OTF2D(:, :, ii) = fftshift(tmp);
+    % This is the proper storage format for the OI-ShiftInvariant case,
+    % where the DC component goes to the upper left corner.
+    OTF2D(:, :, ii) = ifftshift(tmp);
 end
 
 end

isettools/opticalimage/optics/opticsGet.m

@@ -188,8 +188,6 @@
 %      worth it.]
 %    * [Note - DHB: Not all options appear to be documented in the above
 %      header comments.]
-%    * [Note: JNM - Fixed issue with variable naming in diffraction limited
-%      psf data]
 %    * TODO: When 2015B phased out, replace strfind() with contains()
 %
 
@@ -198,6 +196,11 @@
 %    12/21/17  dhb  Use OtfToPsf to do the conversion, but with backwards
 %                   compatible control.
 %    03/14/18  jnm  Formatting
+%    08/30/18  dhb  Replace abs(fft2(OTF)) with OtfToPsf for M-W optics,
+%                   which was special cased for backward compatibility.
+%                   This is based on the view that what was being done was
+%                   not correct, and that we should bite the bullet and
+%                   change. See issue #373 on github.
 
 % Examples:
 %{
@@ -829,22 +832,12 @@
                     if nWave == 1
                         % Just do one specified wavelength
                         otf = opticsGet(optics,'otf data',thisWave);
-                        if strcmp(optics.name,'human-MW')
-                            val = fftshift(abs(fft2(otf)));
-                        else
-                            [~,~,val] = OtfToPsf([],[],fftshift(otf));
-                        end
+                        [~,~,val] = OtfToPsf([],[],fftshift(otf));
                     else
                         % Do all the wavelenghts
                         val = zeros(size(optics.OTF.OTF));
-                        if strcmp(optics.name,'human-MW')
-                            for ii=1:length(thisWave)
-                                val(:,:,ii) = fftshift(abs(fft2(optics.OTF.OTF(:,:,ii))));
-                            end
-                        else
-                            for ii=1:length(thisWave)
-                                [~,~,val(:,:,ii)] = OtfToPsf([],[],fftshift(optics.OTF.OTF(:,:,ii)));
-                            end
+                        for ii=1:length(thisWave)
+                            [~,~,val(:,:,ii)] = OtfToPsf([],[],fftshift(optics.OTF.OTF(:,:,ii)));
                         end
                     end