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common/.MATLABDriveTag

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+9e035526-0524-4e7b-9704-746305f4da3c

common/Bin_Signal.m

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+function binned = Bin_Signal(signal,step,type)
+% Bin the signal given a given step and type from a logical signal. Each
+% rise time will be taken to start the bin.
+%
+%       binned = Bin_Signal(signal,step,type)
+%
+% Perez-Ortega Jesus - May 2019
+
+signal = double(signal);
+switch type
+    case 'single'
+        if step == 0
+            binned = (Find_Peaks_Or_Valleys(signal,0.5,true,true,0,1,true)>0)';
+        elseif step<0
+            binned = Find_Peaks_Or_Valleys(signal,0.5,true,true,0,step,true)>0;
+            binned = (Find_Peaks_Or_Valleys(double(binned),0.5,true,true,0,1,true)>0)';
+        else
+            binned = Find_Peaks_Or_Valleys(signal,0.5,true,true,0,step,true)>0;
+            binned = (Find_Peaks_Or_Valleys(double(binned),0.5,true,false,0,-1,true)>0)';
+        end
+    case 'after_onset'
+        binned = (Find_Peaks_Or_Valleys(signal,0.5,true,true,0,step,true)>0)';
+    case 'after'
+        binned = (Find_Peaks_Or_Valleys(signal,0.5,true,false,0,step,true)>0)';
+    case 'before'
+        binned = (Find_Peaks_Or_Valleys(signal,0.5,true,true,0,-step,true)>0)';
+end

common/Circle_Mask.m

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+function mask = Circle_Mask(image_size,xy_center,radius)
+% Create a circle mask
+%
+% Jesus Perez-Ortega, [email protected]
+% March, 2019
+
+% Get size of image
+h = image_size(1);
+w = image_size(2);
+[x,y] = meshgrid(1:w,1:h);
+
+% Get mask
+mask = sqrt((x-xy_center(1)).^2 + (y-xy_center(2)).^2) < radius;

common/Downsample_And_Crop_Stim.m

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+function stim = Downsample_And_Crop_Stim(stimuli,period_ms,samples)
+% Get the visual stimulus of the same length of the imaging
+% 
+% The signal should be recorded in ms, and period should be a integer
+% number of ms.
+%
+%       stim = Downsample_And_Crop_Stim(stimuli,period_ms,samples)
+%
+% By Jesus Perez-Ortega, July 2019
+
+stim = downsample(round(stimuli*2),period_ms);
+stim = stim(1:samples);

common/Find_Peaks_Or_Valleys.m

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+function [indices,widths,amplitudes,ini_fin] = Find_Peaks_Or_Valleys(data,threshold,join,...
+detect_peaks,minimum_width,fixed_width,ignore_ini_fin)
+% Find peaks from signal by a given threshold.
+%
+%   [indices,widths,amplitudes,ini_fin] = Find_Peaks_Or_Valleys(data,threshold,join,...
+%    detect_peaks,minimum_width,fixed_width,ignore_ini_fin)
+%
+%           default: threshold = 0; join = true; detect_peaks = true;
+%                    minimum_width = 0; fixed_width = 0; ignore_ini_fin = false;
+%
+% Inputs
+% data = data as vector Fx1 (F = #frames)
+% threshold = threshold
+% join = set mode to get peaks (0 = each vector above threshold is a peak;
+%        1 = joining of adjacent vectors above the threshold is a peak)
+%
+% Outputs
+% indices = Fx1 vector containing the peak indices
+%
+% 1. Get indices above threshold
+% 2. Ignore initial and final peaks (or valleys)    - Optional
+% 3. Restriction to minimum width                   - Optional
+% 4. Set a fixed width                              - Optional
+% 5. Set the number at each peak (or valley)
+% 6. Join peaks or valleys                          - Optional
+%
+% by Jesus E. Perez-Ortega, Feb-2012
+% last modification July-2019
+
+switch nargin
+    case 6
+        ignore_ini_fin = false;
+    case 5      
+        ignore_ini_fin = false;
+        fixed_width = 0;
+    case 4
+        ignore_ini_fin = false;
+        fixed_width = 0;
+        minimum_width = 0;
+    case 3
+        ignore_ini_fin = false;
+        fixed_width = 0;
+        minimum_width = 0;
+        detect_peaks = true;
+    case 2
+        ignore_ini_fin = false;
+        fixed_width = 0;
+        minimum_width = 0;
+        detect_peaks = true;
+        join = true;
+    case 1
+        ignore_ini_fin = false;
+        fixed_width = 0;
+        minimum_width = 0;
+        detect_peaks = true;
+        join = true;
+        threshold = 0;
+end
+
+% 0. Correct signal data
+if(size(data,1)==1)
+    data = data';
+end
+original_data = data;
+
+% 1. Get peak or valley indices 
+[idx,count] = Get_Peak_Or_Valley_Indices(data,threshold,detect_peaks);
+% Size of data
+F = numel(data);
+indices=zeros(F,1);
+if ~count
+    if(detect_peaks)
+        disp('No peaks found!')
+        widths = [];
+        amplitudes = [];
+        ini_fin = [];
+    else
+        disp('No valleys found!')
+        widths = [];
+        amplitudes = [];
+        ini_fin = [];
+    end
+    return
+end
+
+% 2. Ignore initial and final peak
+if ignore_ini_fin
+
+    % Delete if start above threshold
+    last=1;
+    idx=idx';
+    for i=idx
+        if(last==i)
+            if detect_peaks
+                data(i)=threshold-1;
+            else
+                data(i)=threshold+1;
+            end
+            last=last+1;
+        else
+            break;
+        end
+    end
+
+    % Delete if ends above threshold
+    last = F;
+    idx = fliplr(idx);
+    for i = idx
+        if last==i
+            if detect_peaks
+                data(i)=threshold-1;
+            else
+                data(i)=threshold+1;
+            end
+            last=last-1;
+        else
+            break;
+        end
+    end
+
+    % Get peak or valley indices 
+    [idx,count] = Get_Peak_Or_Valley_Indices(data,threshold,detect_peaks);
+    if ~count
+        if detect_peaks
+            disp('No peaks found!')
+        else
+            disp('No valleys found!')
+        end
+        return
+    end
+end
+
+% 3. Minimum width (after join peaks or valleys)
+if minimum_width
+
+    % Join peaks or valleys
+    is = find(idx~=[0; idx(1:numel(idx)-1)+1]);    % index of same peak
+    % number of total peaks or valleys
+    count = numel(is);                                       
+    if count
+        for j = 1:count-1
+            indices(idx(is(j)):idx(is(j+1)-1),1)=j;    % set #peak
+        end
+        indices(idx(is(count)):max(idx),1)=count;
+    end
+
+    % Get peaks or valleys width
+    widths=[];
+    for i=1:count
+        widths(i)=length(find(indices==i));
+    end
+
+    % Evaluate peaks less than or equal to minimum width
+    idx_eval=find(widths<=minimum_width);
+    widths=widths(idx_eval);
+
+    % number of peaks to eliminate
+    count_less=length(widths);
+
+    % Detect initial and final times
+    if count_less>0
+        for i=1:count_less
+            peak=find(indices==idx_eval(i));
+            ini_peak=peak(1);
+            end_peak=peak(end);
+            if(detect_peaks)
+                data(ini_peak:end_peak)=threshold-1;
+            else
+                data(ini_peak:end_peak)=threshold+1;
+            end
+        end
+    end
+
+    % Get peak or valley indices 
+    [idx,count] = Get_Peak_Or_Valley_Indices(data,threshold,detect_peaks);
+    if ~count
+        if(detect_peaks)
+            disp('No peaks found!')
+        else
+            disp('No valleys found!')
+        end
+        return
+    end
+end
+
+% 4. Set fixed width 
+if fixed_width
+    last_end = -1;
+    end_before = false;
+    for i = idx'
+        if i==last_end+1
+            if detect_peaks
+                data(i) = threshold-1;
+            else
+                data(i) = threshold+1;
+            end
+            if end_before
+                end_before = false;
+            else
+                last_end = i;
+            end
+        else
+            if i>last_end
+                if fixed_width<0
+                    ini = i+fixed_width;
+                    fin = i-1;
+                    if ini<1
+                        ini = 1;
+                    end    
+                    fixed_width_peak = ini:fin;
+                    last_end = fin+1;
+                else
+                    fin = i+fixed_width-1;
+                    if(fin>F)
+                        fin = F;
+                    end    
+                    fixed_width_peak = i:fin;
+                    last_end = fin;
+                end
+
+                if detect_peaks
+                    data(fixed_width_peak) = threshold+1;
+                    if fixed_width<0
+                        fixed_width_peak = fixed_width_peak+length(fixed_width_peak);
+                        data(fixed_width_peak) = threshold-1;
+                    elseif sum(data(fixed_width_peak)<threshold)
+                        end_before = true;
+                    end
+                else
+                    data(fixed_width_peak) = threshold-1;
+                    if fixed_width<0
+                        data(fixed_width_peak-fixed_width) = threshold+1;
+                    elseif sum(data(fixed_width_peak)>threshold)
+                        end_before = true;
+                    end
+                end
+            end
+        end
+    end
+
+    % Get peak or valley indices 
+    [idx,count] = Get_Peak_Or_Valley_Indices(data,threshold,detect_peaks);
+end
+
+% 5. Put numbers to peaks
+indices=zeros(F,1);
+for i=1:count
+    indices(idx(i))=i;
+end
+
+% 6. Join peaks or valleys
+if join
+    is = find(idx~=[0; idx(1:numel(idx)-1)+1]);    % index of same peak
+
+    % number of total peaks
+    count = numel(is);                                       
+    if count
+        for j = 1:count-1
+            indices(idx(is(j)):idx(is(j+1)-1),1)=j;    % set #peak
+        end
+        indices(idx(is(count)):max(idx),1)=count;
+    end
+end
+
+% Get peaks or valleys width
+widths = zeros(count,1);
+ini_fin = zeros(count,2);
+for i = 1:count
+    id = find(indices==i);
+    ini_fin(i,1) = id(1);
+    ini_fin(i,2) = id(end);
+    widths(i) = length(id);
+end
+
+% Get peaks or valleys amplitud
+amplitudes = zeros(count,1);
+for i = 1:count
+    if detect_peaks
+        value = max(original_data(indices==i));
+    else
+        value = min(original_data(indices==i));
+    end
+    amplitudes(i) = value;
+end

common/Find_Threshold_In_Cumulative_Distribution.m

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+% Find the threshold upper a given alpha
+%
+% Jesús Pérez-Ortega nov 2018
+
+function th = Find_Threshold_In_Cumulative_Distribution(data,alpha)
+
+    if(min(data)==max(data))
+       th = max(data)+1; 
+    else
+        if(max(data)<=1)
+            x = 0:0.001:1;
+        elseif(max(data)<=10)
+            x = 0:0.01:10;
+        else
+            x = 0:max(data);
+        end
+        y = hist(data,x);
+        cdy = cumsum(y);
+        cdy = cdy/max(cdy);
+        id = find(cdy>(1-alpha),1,'first');
+        th = x(id);
+    end
+end

common/Get_Indices_Before_And_After_Stimulus.m

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+function indices = Get_Indices_Before_And_After_Stimulus(stimulus,before_samples,after_samples)
+% Get the indices befor and after and stimulus 
+%
+%       indices = Get_Indices_Before_And_After_Stimulus(stimulus,before_samples,after_samples)
+%
+% Jesus Perez-Ortega May 2019
+
+during = stimulus>0; 
+before = Bin_Signal(during,before_samples,'before');
+after = Bin_Signal(during,after_samples,'after');
+indices = find(before | during' | after);
+