-
Notifications
You must be signed in to change notification settings - Fork 0
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
- Loading branch information
Showing
12 changed files
with
238 additions
and
116 deletions.
There are no files selected for viewing
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file was deleted.
Oops, something went wrong.
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,25 @@ | ||
| function T=get_alignment_metrics(P) | ||
|
|
||
| T=table(); | ||
| Name={'Non-aligned','Translations','CaliAli','CaliAli+Neuron alignment'}; | ||
| for i=1:size(P,2) | ||
| Neuo=mat2gray(squeeze(P.(i)(1,:).(5){1,1}(:,:,1,:))); | ||
| T=[T;create_table(Neuo,Name{i},'Neurons')]; | ||
| end | ||
| % | ||
| % for i=1:size(P,2) | ||
| % BVo=mat2gray(P.(i)(1,:).BloodVessels{1,1}); | ||
| % T=[T;create_table(BVo,Name{i},'BV')]; | ||
| % end | ||
|
|
||
| end | ||
|
|
||
|
|
||
| function out=create_table(in,reference_projection,test_projection) | ||
| pr=get_matched_projection(in); | ||
| [c,~,s] = motion_metrics(in); | ||
| out=table(categorical(string(reference_projection)),categorical(string(test_projection)),{pr},{c},mean(c),s, ... | ||
| 'VariableNames',{'Transformation','Test. Projection','Aligned Projections','Correlation scores','Mean Corr. Score','Crispness'}); | ||
| end | ||
|
|
||
|
|
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,11 @@ | ||
| function out=get_matched_projection(in) | ||
| ref=in(:,:,round(size(in,3)/2)); | ||
|
|
||
| for i=1:size(in,3) | ||
| J = localHistMatch(mat2gray(ref), mat2gray(in(:,:,i)), [100,100], [50,50],0.001); | ||
| A=mat2gray(in(:,:,i)); | ||
| k=mat2gray(imgaussfilt(medfilt2(mat2gray(histeq(A.*J)).*mat2gray(ref),[4,4]))); | ||
| out(:,:,:,i)=cat(3,max(cat(3,A,k),[],3),max(cat(3,J,k),[],3),J*0); | ||
| end | ||
|
|
||
|
|
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,58 @@ | ||
| function opt=int_var(varargin) | ||
| %% INTIALIZE VARIABLES | ||
| inp = inputParser; | ||
| valid_v = @(x) isnumeric(x); | ||
| addParameter(inp,'gSig',2.5,valid_v) %Neuron Filter size. 2.5 default. | ||
| addParameter(inp,'sf',10,valid_v) %Frame rate. Defualt 10 fps | ||
| addParameter(inp,'n_enhanced',1) %MIN1PIE background substraciton. True is recommended. default True | ||
| addParameter(inp,'theFiles','pickup') %Cell array containing paths to the input video files, "pickup" let the user choose | ||
| addParameter(inp,'UseBV',1) %Use BVz for aligmen. Disable this i | ||
| addParameter(inp,'BVz',[]) %Size of blood vessels [min diameter max diameter] in pixels. | ||
| % defaults is in the range range [0.6*opt.gSig,0.9*opt.gSig]; | ||
| %Size of blood vessels [min diameter max diameter] in pixels. | ||
| addParameter(inp,'FinalAlignmentWithNeuronShapes',0) % Add an extra alignment iteration utilizing only neuron shapes after CaliAli | ||
| addParameter(inp,'FinalAlignmentWithNeuronShapes',0) % Add an extra alignment iteration utilizing only ne | ||
| %% | ||
| addParameter(inp,'dynamic_spatial',0) % not currently in use | ||
| addParameter(inp,'datename',0) % not currently in use | ||
| %% Internal variables | ||
| addParameter(inp,'Mask',[]) % Used internally | ||
| addParameter(inp,'T_Mask',[]) % Used internally | ||
| addParameter(inp,'NR_Mask',[]) % Used internally | ||
| addParameter(inp,'NR_Mask_n',[]) % Used internally | ||
| addParameter(inp,'F',[]) % Used internally | ||
| addParameter(inp,'T',[]) % Used internally | ||
| addParameter(inp,'shifts',[]) % Used internally | ||
| addParameter(inp,'shifts_n',[]) % Used internally | ||
| addParameter(inp,'BV_score',[]) % Used internally | ||
| addParameter(inp,'range',[]) % Used internally | ||
| addParameter(inp,'Cn_scale',[]) % Used internally | ||
| addParameter(inp,'date_v',[]) | ||
| varargin=varargin{1, :}; | ||
| if isstruct(varargin) | ||
| varargin = [fieldnames(varargin), struct2cell(varargin)]'; | ||
| end | ||
|
|
||
| inp.KeepUnmatched = true; | ||
| parse(inp,varargin{:}); | ||
| opt=inp.Results; | ||
|
|
||
| if isempty(opt.BVz) | ||
| opt.BVz=[0.6*opt.gSig,0.9*opt.gSig]; | ||
| end | ||
|
|
||
|
|
||
| if strcmpi(opt.theFiles,"pickup") | ||
| opt.theFiles = uipickfiles('FilterSpec','*mc.h5'); | ||
| end | ||
|
|
||
|
|
||
| if ~isempty(opt.theFiles) | ||
| [filepath,name]=fileparts(opt.theFiles{end}); | ||
| opt.out=strcat(filepath,filesep,name,'_aligned','.h5'); | ||
| opt.out_mat=strcat(filepath,filesep,name,'_aligned.mat'); | ||
| else | ||
| opt.out=[]; | ||
| opt.out_mat=[]; | ||
| end | ||
| end |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,106 @@ | ||
| function J = localHistMatch(Im, ref, win, patchOverlap, intensityThreshold) | ||
| % localHistMatch performs local histogram matching of an image with overlapping patches, | ||
| % ignoring regions below a certain intensity threshold. | ||
| % | ||
| % Inputs: | ||
| % Im - Input grayscale image (MxN matrix). | ||
| % ref - Reference grayscale image (MxN matrix). | ||
| % win - Window size [height, width] for local processing. | ||
| % patchOverlap - Overlap between patches [height, width]. | ||
| % intensityThreshold - Minimum intensity value to include in processing. | ||
| % | ||
| % Output: | ||
| % J - Image after local histogram matching. | ||
|
|
||
| % Validate inputs | ||
| if nargin ~= 5 | ||
| error('Five input arguments required: Im, ref, win, patchOverlap, and intensityThreshold.'); | ||
| end | ||
|
|
||
| if ~ismatrix(Im) || ~ismatrix(ref) | ||
| error('Input images must be grayscale (2D matrices).'); | ||
| end | ||
|
|
||
| if numel(win) ~= 2 || any(win <= 0) | ||
| error('Window size must be a vector with two positive integers.'); | ||
| end | ||
|
|
||
| if numel(patchOverlap) ~= 2 || any(patchOverlap < 0) | ||
| error('Patch overlap must be a vector with two non-negative integers.'); | ||
| end | ||
|
|
||
| if ~isscalar(intensityThreshold) || intensityThreshold < 0 | ||
| error('Intensity threshold must be a non-negative scalar.'); | ||
| end | ||
|
|
||
| % Convert images to grayscale if they are not already | ||
| if size(Im, 3) == 3 | ||
| Im = rgb2gray(Im); | ||
| end | ||
| if size(ref, 3) == 3 | ||
| ref = rgb2gray(ref); | ||
| end | ||
|
|
||
| % Ensure the reference image has the same size as the input image | ||
| [m, n] = size(Im); | ||
| [ref_m, ref_n] = size(ref); | ||
| if m ~= ref_m || n ~= ref_n | ||
| error('Input image and reference image must have the same dimensions.'); | ||
| end | ||
|
|
||
| % Create an empty image to store the result | ||
| J = zeros(size(Im), 'like', Im); | ||
|
|
||
| % Determine the window size and overlap | ||
| windowHeight = win(1); | ||
| windowWidth = win(2); | ||
| overlapHeight = patchOverlap(1); | ||
| overlapWidth = patchOverlap(2); | ||
|
|
||
| % Compute the step size based on window size and overlap | ||
| stepY = windowHeight - overlapHeight; | ||
| stepX = windowWidth - overlapWidth; | ||
|
|
||
| % Create a mask to keep track of valid pixels | ||
| mask = false(size(Im)); | ||
|
|
||
| % Process the image in overlapping local regions | ||
| for i = 1:stepY:m | ||
| for j = 1:stepX:n | ||
| % Define the window limits | ||
| rowRange = i:min(i+windowHeight-1, m); | ||
| colRange = j:min(j+windowWidth-1, n); | ||
|
|
||
| % Extract the local region from the input image | ||
| localRegion = Im(rowRange, colRange); | ||
| localMask = localRegion > intensityThreshold; | ||
|
|
||
| % Extract the local region from the reference image (same region) | ||
| refRegion = ref(rowRange, colRange); | ||
|
|
||
| % Apply mask to exclude low-intensity regions | ||
| if any(localMask(:)) | ||
| % Perform histogram matching | ||
| matchedRegion = imhistmatch(localRegion, refRegion); | ||
| if max(matchedRegion,[],"all")>1 | ||
| dummy=1; | ||
| end | ||
| % Apply the mask to the matched region | ||
| temp=Im(rowRange, colRange); | ||
|
|
||
| matchedRegion(~localMask) = temp(~localMask); | ||
|
|
||
| % Place the matched region back into the output image | ||
| J(rowRange, colRange) = matchedRegion; | ||
|
|
||
| % Update mask | ||
| mask(rowRange, colRange) = mask(rowRange, colRange) | localMask; | ||
| end | ||
| end | ||
| end | ||
|
|
||
| % Normalize the output image to account for overlapping regions | ||
| % J(mask) = J(mask) ./ (sum(mask(:)) / numel(J)); | ||
|
|
||
| % Ensure the output image is in the same format as the input | ||
| end |
Oops, something went wrong.