first commit

.gitattributes

@@ -0,0 +1,2 @@
+# Auto detect text files and perform LF normalization
+* text=auto

.gitignore

@@ -0,0 +1 @@
+*.asv

App/MIRO_app.prj

@@ -0,0 +1,141 @@
+<deployment-project plugin="plugin.apptool" plugin-version="1.0">
+  <configuration build-checksum="3022029705" file="C:\Users\biagi\Documents\MATLAB\MIRO-master\App\MIRO_app.prj" location="C:\Users\biagi\Documents\MATLAB\MIRO-master\App" name="MIRO_app" target="target.mlapps" target-name="Package App">
+    <param.appname>MIRO_app</param.appname>
+    <param.authnamewatermark>B. Mandracchia</param.authnamewatermark>
+    <param.email />
+    <param.company />
+    <param.icon>${PROJECT_ROOT}\MIRO_app_resources\icon_24.png</param.icon>
+    <param.icons>
+      <file>${PROJECT_ROOT}\MIRO_app_resources\icon_48.png</file>
+      <file>${PROJECT_ROOT}\MIRO_app_resources\icon_24.png</file>
+      <file>${PROJECT_ROOT}\MIRO_app_resources\icon_16.png</file>
+    </param.icons>
+    <param.summary>MATLAB Graphical User Interface for MIRO noise correction</param.summary>
+    <param.description />
+    <param.screenshot>C:\Users\biagi\AppData\Local\Temp\tp6677b93d_7e8b_4eca_83c9_d5ecd91e1423.png</param.screenshot>
+    <param.version>1.0</param.version>
+    <param.products.name />
+    <param.products.id />
+    <param.products.version />
+    <param.platforms>
+      <item>win64</item>
+    </param.platforms>
+    <param.output>${PROJECT_ROOT}</param.output>
+    <param.guid>fd3d6f83-e7c4-44f7-b209-b7753781f6e8</param.guid>
+    <unset>
+      <param.email />
+      <param.company />
+      <param.description />
+      <param.version />
+      <param.products.name />
+      <param.products.id />
+      <param.products.version />
+      <param.output />
+    </unset>
+    <fileset.main>
+      <file>${PROJECT_ROOT}\MIRO_app.mlapp</file>
+    </fileset.main>
+    <fileset.depfun>
+      <file>C:\Users\biagi\Documents\MATLAB\MIRO-master\Imdecorr\apodImRect.m</file>
+      <file>C:\Users\biagi\Documents\MATLAB\MIRO-master\Imdecorr\getCorrcoef.m</file>
+      <file>C:\Users\biagi\Documents\MATLAB\MIRO-master\Imdecorr\getDcorr.m</file>
+      <file>C:\Users\biagi\Documents\MATLAB\MIRO-master\Imdecorr\getDcorrMax.m</file>
+      <file>C:\Users\biagi\Documents\MATLAB\MIRO-master\Imdecorr\getRadAvg.m</file>
+      <file>C:\Users\biagi\Documents\MATLAB\MIRO-master\Imdecorr\im2pol.m</file>
+      <file>C:\Users\biagi\Documents\MATLAB\MIRO-master\Imdecorr\linmap.m</file>
+      <file>C:\Users\biagi\Documents\MATLAB\MIRO-master\Imdecorr\ResolutionFinder.m</file>
+      <file>C:\Users\biagi\Documents\MATLAB\MIRO-master\MIRO.m</file>
+      <file>C:\Users\biagi\Documents\MATLAB\MIRO-master\MIRO_functions\Fast Wiener\fast_wiener.mexw64</file>
+      <file>C:\Users\biagi\Documents\MATLAB\MIRO-master\MIRO_functions\Fast Wiener\fast_wiener_video.mexw64</file>
+      <file>C:\Users\biagi\Documents\MATLAB\MIRO-master\MIRO_functions\Fast Wiener\MIRO_Fast_Wiener.m</file>
+      <file>C:\Users\biagi\Documents\MATLAB\MIRO-master\MIRO_functions\Fast Wiener\MIRO_Fast_Wiener_Video.m</file>
+      <file>C:\Users\biagi\Documents\MATLAB\MIRO-master\MIRO_functions\FPN Correction\MIRO_FPN_correction.m</file>
+      <file>C:\Users\biagi\Documents\MATLAB\MIRO-master\MIRO_functions\FPN Correction\MIRO_Hotspot.m</file>
+      <file>C:\Users\biagi\Documents\MATLAB\MIRO-master\MIRO_functions\MIRO_Default_Parameters.m</file>
+      <file>C:\Users\biagi\Documents\MATLAB\MIRO-master\MIRO_functions\MIRO_main.m</file>
+      <file>C:\Users\biagi\Documents\MATLAB\MIRO-master\MIRO_functions\MIRO_parse_inputs.m</file>
+      <file>C:\Users\biagi\Documents\MATLAB\MIRO-master\MIRO_functions\Multiscale Wiener\MIRO_Aggregation.m</file>
+      <file>C:\Users\biagi\Documents\MATLAB\MIRO-master\MIRO_functions\Multiscale Wiener\MIRO_Collaborative_Wiener_dct.m</file>
+      <file>C:\Users\biagi\Documents\MATLAB\MIRO-master\MIRO_functions\Multiscale Wiener\MIRO_Collaborative_Wiener_Initialization.m</file>
+      <file>C:\Users\biagi\Documents\MATLAB\MIRO-master\MIRO_functions\Multiscale Wiener\MIRO_Needle_match.m</file>
+      <file>C:\Users\biagi\Documents\MATLAB\MIRO-master\MIRO_functions\Multiscale Wiener\MIRO_patch_3DFiltering.m</file>
+      <file>C:\Users\biagi\Documents\MATLAB\MIRO-master\MIRO_functions\Multiscale Wiener\MIRO_patch_matching_and_processing.m</file>
+      <file>C:\Users\biagi\Documents\MATLAB\MIRO-master\MIRO_functions\NLM\MIRO_image2vectors_double.mexw64</file>
+      <file>C:\Users\biagi\Documents\MATLAB\MIRO-master\MIRO_functions\NLM\MIRO_nlm.m</file>
+      <file>C:\Users\biagi\Documents\MATLAB\MIRO-master\MIRO_functions\NLM\MIRO_vectors_nlmeans_double.mexw64</file>
+      <file>C:\Users\biagi\Documents\MATLAB\MIRO-master\MIRO_functions\Shearlet Shrinkage\MIRO_Hotspot2.m</file>
+      <file>C:\Users\biagi\Documents\MATLAB\MIRO-master\MIRO_functions\Shearlet Shrinkage\MIRO_Shearlet_thresholding.m</file>
+      <file>C:\Users\biagi\Documents\MATLAB\MIRO-master\MIRO_functions\Shearlet Shrinkage\MIRO_SLcheckFilterSizes.m</file>
+      <file>C:\Users\biagi\Documents\MATLAB\MIRO-master\MIRO_functions\Shearlet Shrinkage\MIRO_SLgetShearletSystem2D.m</file>
+      <file>C:\Users\biagi\Documents\MATLAB\MIRO-master\MIRO_functions\Shearlet Shrinkage\MIRO_SLprepareFilters2D.m</file>
+      <file>C:\Users\biagi\Documents\MATLAB\MIRO-master\MIRO_functions\Shearlet Shrinkage\MIRO_Spectral_weighting.m</file>
+      <file>C:\Users\biagi\Documents\MATLAB\MIRO-master\MIRO_functions\Shearlet Shrinkage\MIRO_tophat.m</file>
+      <file>C:\Users\biagi\Documents\MATLAB\MIRO-master\MIRO_utils\animated_comparison.m</file>
+      <file>C:\Users\biagi\Documents\MATLAB\MIRO-master\MIRO_utils\Block_distance.m</file>
+      <file>C:\Users\biagi\Documents\MATLAB\MIRO-master\MIRO_utils\cprintf.m</file>
+      <file>C:\Users\biagi\Documents\MATLAB\MIRO-master\MIRO_utils\Define_SearchWindow.m</file>
+      <file>C:\Users\biagi\Documents\MATLAB\MIRO-master\MIRO_utils\Display_results_percentage.m</file>
+      <file>C:\Users\biagi\Documents\MATLAB\MIRO-master\MIRO_utils\Locate_blk.m</file>
+      <file>C:\Users\biagi\Documents\MATLAB\MIRO-master\MIRO_utils\nrm.m</file>
+      <file>C:\Users\biagi\Documents\MATLAB\MIRO-master\MIRO_utils\Pyramid.m</file>
+      <file>C:\Users\biagi\Documents\MATLAB\MIRO-master\MIRO_utils\ReadTiff.m</file>
+      <file>C:\Users\biagi\Documents\MATLAB\MIRO-master\MIRO_utils\removePad.m</file>
+      <file>C:\Users\biagi\Documents\MATLAB\MIRO-master\MIRO_utils\Sigma_estimation.m</file>
+      <file>C:\Users\biagi\Documents\MATLAB\MIRO-master\MIRO_utils\Spectral_filter.m</file>
+      <file>C:\Users\biagi\Documents\MATLAB\MIRO-master\MIRO_utils\textprogressbar.m</file>
+      <file>C:\Users\biagi\Documents\MATLAB\MIRO-master\ShearLab\dfilters.m</file>
+      <file>C:\Users\biagi\Documents\MATLAB\MIRO-master\ShearLab\dmaxflat.m</file>
+      <file>C:\Users\biagi\Documents\MATLAB\MIRO-master\ShearLab\MakeONFilter.m</file>
+      <file>C:\Users\biagi\Documents\MATLAB\MIRO-master\ShearLab\mctrans.m</file>
+      <file>C:\Users\biagi\Documents\MATLAB\MIRO-master\ShearLab\MirrorFilt.m</file>
+      <file>C:\Users\biagi\Documents\MATLAB\MIRO-master\ShearLab\modulate2.m</file>
+      <file>C:\Users\biagi\Documents\MATLAB\MIRO-master\ShearLab\SLdshear.m</file>
+      <file>C:\Users\biagi\Documents\MATLAB\MIRO-master\ShearLab\SLfiltersToGPU2D.m</file>
+      <file>C:\Users\biagi\Documents\MATLAB\MIRO-master\ShearLab\SLgetShearletIdxs2D.m</file>
+      <file>C:\Users\biagi\Documents\MATLAB\MIRO-master\ShearLab\SLgetShearlets2D.m</file>
+      <file>C:\Users\biagi\Documents\MATLAB\MIRO-master\ShearLab\SLgetWedgeBandpassAndLowpassFilters2D.m</file>
+      <file>C:\Users\biagi\Documents\MATLAB\MIRO-master\ShearLab\SLpadArray.m</file>
+      <file>C:\Users\biagi\Documents\MATLAB\MIRO-master\ShearLab\SLsheardec2D.m</file>
+      <file>C:\Users\biagi\Documents\MATLAB\MIRO-master\ShearLab\SLshearrec2D.m</file>
+      <file>C:\Users\biagi\Documents\MATLAB\MIRO-master\ShearLab\SLupsample.m</file>
+    </fileset.depfun>
+    <fileset.resources />
+    <fileset.package />
+    <build-deliverables>
+      <file location="C:\Users\biagi\Documents\MATLAB\MIRO-master" name="App" optional="false">C:\Users\biagi\Documents\MATLAB\MIRO-master\App</file>
+    </build-deliverables>
+    <workflow />
+    <matlab>
+      <root>C:\Program Files\MATLAB\R2021b</root>
+      <toolboxes>
+        <toolbox name="matlabcoder" />
+        <toolbox name="neuralnetwork" />
+      </toolboxes>
+      <toolbox>
+        <matlabcoder>
+          <enabled>true</enabled>
+        </matlabcoder>
+      </toolbox>
+      <toolbox>
+        <neuralnetwork>
+          <enabled>true</enabled>
+        </neuralnetwork>
+      </toolbox>
+    </matlab>
+    <platform>
+      <unix>false</unix>
+      <mac>false</mac>
+      <windows>true</windows>
+      <win2k>false</win2k>
+      <winxp>false</winxp>
+      <vista>false</vista>
+      <linux>false</linux>
+      <solaris>false</solaris>
+      <osver>10.0</osver>
+      <os32>false</os32>
+      <os64>true</os64>
+      <arch>win64</arch>
+      <matlab>true</matlab>
+    </platform>
+  </configuration>
+</deployment-project>

Demo/MIRO_Demo.m

@@ -0,0 +1,147 @@
+%% MIRO Demo
+% Demo file to demonstrate MIRO processing workflow. You can modify this 
+% code and use with your own data.
+
+%% Load Data
+
+% Paths
+FilePath_calibration = '.\Calibration_files\';
+FilePath_data = '.\Raw_data\';
+SavePath = '.\Results\';
+
+% Load calibration data
+load([FilePath_calibration, 'sCMOS_calibration.mat'],'Offset','Var','Gain');
+Var = Var./(Gain^2);
+
+% Load shearlet system
+% This is not necessary but it can speed up processing if MIRO is called
+% more than once. If you don't want to use it, just put shearletSystem = []
+% or remove the corresponding line in the MIRO options
+shearletSystem = getSLsys(Offset, 6);
+
+% load colormap
+load([FilePath_calibration, 'cmap.mat'],'glow');
+
+% load images
+D = dir([FilePath_data  '\*.mat']);
+
+% experimental parameters
+expT = [10 20 50 100];
+lambda_ch1 = .461;
+lambda_ch2 = .512;
+lambda_ch3 = .599;
+
+% load reference image
+load('.\GT\GT');
+
+S = zeros(length(expT),2,3);
+P = zeros(length(expT),2,3);
+
+for i = 1:length(D)
+
+    disp(i)
+    load([D(i).folder '\' D(i).name]);
+
+    %% MIRO
+
+    [miro1, Parameters] = MIRO(im1, ...
+        'Offset',Offset,...
+        'Gain',Gain,...
+        'Var',Var,...
+        'Lambda',lambda_ch1,...
+        'DisplayImages',1, ...
+        'Mode','s',...
+        'h',6,...
+        'Exp_time',expT(i)/1e3,...
+        'shearletSystem',shearletSystem);
+    colormap(glow)
+    title(['Channel 1, T = ' num2str(expT(i)) ' ms'])
+    pause(.01)
+
+    miro2 = MIRO(im2,...
+        'Offset',Offset,...
+        'Gain',Gain,...
+        'Var',Var,...
+        'Lambda',lambda_ch2,...
+        'DisplayImages',1,...
+        'Mode','s',...
+        'h',4,...
+        'Exp_time',expT(i)/1e3,...
+        'shearletSystem',shearletSystem);
+    colormap(glow)
+    title(['Channel 2, T = ' num2str(expT(i)) ' ms'])
+    pause(.01)
+
+    miro3 = MIRO(im3,...
+        'Offset',Offset,...
+        'Gain',Gain,...
+        'Var',Var,...
+        'Lambda',lambda_ch3,...
+        'DisplayImages',1,...
+        'Mode','s',...
+        'h',4,...
+        'Exp_time',expT(i)/1e3,...
+        'k',0,...
+        'shearletSystem',shearletSystem);
+    colormap(glow)
+    title(['Channel 3, T = ' num2str(expT(i)) ' ms'])
+    pause(.01)
+
+    %% Calculate SSIM & PSNR
+
+    S_mean_ch1(1) = calculate_SSIM(gt1,im1);
+    S_mean_ch1(2) = calculate_SSIM(gt1,miro1);
+
+    S_mean_ch2(1) = calculate_SSIM(gt2,im2);
+    S_mean_ch2(2) = calculate_SSIM(gt2,miro2);
+
+    S_mean_ch3(1) = calculate_SSIM(gt3,im3);
+    S_mean_ch3(2) = calculate_SSIM(gt3,miro3);
+
+
+    P_mean_ch1(1) = calculate_PSNR(gt1,im1);
+    P_mean_ch1(2) = calculate_PSNR(gt1,miro1);
+
+    P_mean_ch2(1) = calculate_PSNR(gt2,im2);
+    P_mean_ch2(2) = calculate_PSNR(gt2,miro2);
+
+    P_mean_ch3(1) = calculate_PSNR(gt3,im3);
+    P_mean_ch3(2) = calculate_PSNR(gt3,miro3);
+
+    S(i,:,1) = S_mean_ch1;
+    P(i,:,1) = P_mean_ch1;
+    S(i,:,2) = S_mean_ch2;
+    P(i,:,2) = P_mean_ch2;
+    S(i,:,3) = S_mean_ch3;
+    P(i,:,3) = P_mean_ch3;
+
+    %% Save
+    save(fullfile(SavePath,['MIRO_' num2str(expT(i),'%1.4u')]), 'miro1','miro2','miro3','Parameters',...
+        'P_mean_ch1','P_mean_ch2','P_mean_ch3','S_mean_ch1','S_mean_ch2','S_mean_ch3');
+
+    options.overwrite = true;
+    saveastiff(uint16(miro1),fullfile(SavePath,['MIRO_' num2str(expT(i),'%1.4u') '_ch1.tif']),options);
+    saveastiff(uint16(miro2),fullfile(SavePath,['MIRO_' num2str(expT(i),'%1.4u') '_ch2.tif']),options);
+    saveastiff(uint16(miro3),fullfile(SavePath,['MIRO_' num2str(expT(i),'%1.4u') '_ch3.tif']),options);
+
+end
+
+%% Display results
+f = figure('Name','Measured SSIM & PSNR','NumberTitle','off');
+f.Position(3:4) = [700 420]; f.Color = [1 1 1];
+tiledlayout(2,3);
+for i = 1:3
+nexttile
+plot(expT,S(:,:,i),'o','MarkerFaceColor','auto','LineWidth',2)
+title(['Channel ' num2str(i)])
+ylabel SSIM
+xlabel 'Exp. Time (ms)'
+set(gca,'TickDir','out','FontSize',10,'Box','off')
+end
+for i = 1:3
+nexttile
+plot(expT,P(:,:,i),'o','MarkerFaceColor','auto','LineWidth',2)
+ylabel PSNR
+xlabel 'Exp. Time (ms)'
+set(gca,'TickDir','out','FontSize',10,'Box','off')
+end

Demo/calculate_PSNR.m

@@ -0,0 +1,16 @@
+function [S_mean, S_std, S] = calculate_PSNR(ref,im)
+
+
+ref = nrm(ref);
+im = nrm(im);
+
+
+for idx = 1:size(im,3)
+    S(idx) = psnr(ref,im(:,:,idx));
+end
+
+S_mean = mean(S);
+S_std = std(S);
+
+
+end

Demo/calculate_SSIM.m

@@ -0,0 +1,16 @@
+function [S_mean, S_std, S] = calculate_SSIM(ref,im)
+
+
+ref = nrm(ref);
+im = nrm(im);
+
+
+for idx = 1:size(im,3)
+    S(idx) = ssim(ref,im(:,:,idx));
+end
+
+S_mean = mean(S);
+S_std = std(S);
+
+
+end