Longitudinal

README.md

@@ -8,8 +8,9 @@ and for measuring field of view size using an EM grid.
 ## Main functions
 
 * `mpqc.record.PSF` to easily acquire PSF stacks with ScanImage.
-* `mpqc.record.lens_tissue` to acquire standardised data from lens tissue.
+* `mpqc.record.lens_paper` to acquire standardised data from lens tissue.
 * `mpqc.record.standard_light_source` to data from a standard light source
+* `mpqc.record.electrical_noise` to measure the electrical noise of the PMTs.
 * `measurePSF` to estimate PSF size. For a demo, run `measurePSF('demo')`. 
 * `Grid2MicsPerPixel`  measures the number of microns per pixel along x and y by analyzing an image of an EM grid. 
 * `mpqc.tools.meanFrame` plots the mean frame intensity as a function of time whilst you are scanning.

code/+mpqc/+longitudinal/long_electrical_noise.m

@@ -0,0 +1,151 @@
+function varargout = long_electrical_noise(data_dir,varargin)
+% Longitudinal electrical noise plots showing FWHM and max values over time
+%
+% mpqc.longitudinal.long_electrical_noise(maintenace_folder_path, varargin)
+% Optional inputs: Starting date- month-year
+%
+% Purpose
+% Plots of the maximum value and FWHM of electrical noise for each channel
+% with PMTs off. If there is significant change in electrical noise, the FWHM
+% distributions will likely increase in value.
+%
+%
+% Outputs
+% out (optional) - structure containing key information and data.
+%
+% Notes
+% Currently plots for 4 PMT channels regardless of actual number of
+% PMTs in system
+%
+%
+% Isabell Whiteley, SWC AMF 2025
+
+if nargin<1
+    data_dir = pwd;
+end
+
+
+debugPlots = true;
+
+maintenanceFiles = dir(fullfile(data_dir,'\**\*.tif')); 
+n=1;
+
+for ii=1:length(maintenanceFiles)
+    tmp = maintenanceFiles(ii);
+
+    if contains(tmp.name,'electrical_noise')
+        plotting_template(n) = generic_generator_template(tmp);
+        plotting_template(n).type = 'electrical_noise';
+        plotting_template(n).plotting_func = @mpqc.plot.electrical_noise;
+        plotting_template(n).date = string(datetime(regexp(tmp.name, '(\d{4}-\d{2}-\d{2})_(\d{2}-\d{2}-\d{2})','match'),'InputFormat','yyyy-MM-dd_HH-mm-ss'));
+        [pathstr,plotting_template(n).name,ext] = fileparts(tmp.name);
+        n=n+1;
+    end
+end
+if ~exist('plotting_template','var')
+    disp('No electrical noise files found')
+    varargout{1} = [];
+    return
+end
+
+% sort plotting_template data by the date/time
+date_list = [plotting_template.date];
+[~,order] = sort(datenum(date_list,'dd-mm-yyyy hh:MM:ss'),1,'ascend');
+plotting_template = plotting_template(order);
+
+if nargin > 1 % Optional variable for selecting starting date
+    startDate = datetime(varargin{1});
+    startIndex = 1;
+
+    while [plotting_template(startIndex).date] < startDate
+        startIndex = startIndex + 1;
+    end
+
+    plotting_template = plotting_template(startIndex:end);
+end
+
+for ii = 1:length(plotting_template)
+    if contains(plotting_template(ii).full_path_to_data, '.tif')
+        noiseData(:,:,:,ii) = mpqc.tools.scanImage_stackLoad(plotting_template(ii).full_path_to_data);
+    end
+end
+
+noiseData = single(noiseData);
+
+for q = 1:size(noiseData,4) % each date
+
+    if debugPlots
+        fig = mpqc.tools.returnFigureHandleForFile(sprintf('%s_%02d',mfilename,q));
+    end
+    for t = 1:size(noiseData,3) % each PMT
+
+        % Extract data
+        t_im = noiseData(:,:,t,q);
+        [n,x] = hist(t_im(:),100); % plots all data as histogram
+        m = smoothdata(n,'gaussian',5);
+        detail = interp1(x,m,[1:1000]);
+
+        maxVal(t,q) = max(detail(:));
+        halfMaxVal = maxVal(t,q)/2;
+        leftIndex = find(detail(:) >= halfMaxVal, 1, 'first');
+        rightIndex = find(detail(:) >= halfMaxVal, 1, 'last');
+        fwhm(t,q) = rightIndex -leftIndex;
+
+        % TODO Remove data where PMT does not exist
+
+        % Optionally plot
+        if debugPlots
+            subplot(2,2,t)
+            a=area(n);
+            a.EdgeColor=[0,0,0.75];
+            a.FaceColor=[0.5,0.5,1];
+            a.LineWidth=2;
+            hold on
+            b = plot(m);
+            b.LineWidth = 2;
+            sgtitle(plotting_template(q).date)
+            title(['PMT # ',num2str(t)])
+            hold off
+        end
+    end
+end
+
+for ii = 1:size(noiseData,3) % plotting FWHM and max value over time for each PMT
+    xlabels = {plotting_template.date};
+    fig = mpqc.tools.returnFigureHandleForFile(sprintf('%s_%02d',mfilename,ii));
+    subplot(2,1,1)
+    plot(maxVal(ii,:))
+    xticks(1:length(xlabels))
+    xticklabels(xlabels)
+    title('Max value')
+
+    subplot(2,1,2)
+    plot(fwhm(ii,:))
+    xticks(1:length(xlabels))
+    xticklabels(xlabels)
+    title('FWHM')
+    sgtitle(['PMT # ',num2str(ii)])
+end
+
+
+% Output of the main function
+if nargout>0
+    out.fileName = {plotting_template(:).name};
+    out.noiseData = noiseData;
+    out.fwhm = fwhm;
+    out.maxValues = maxVal;
+    out.date ={plotting_template(:).date};
+    varargout{1} = out;
+end
+
+end % close main funtion
+
+
+
+function out = generic_generator_template(t_dir)
+out.full_path_to_data = fullfile(t_dir.folder,t_dir.name);
+out.type = [];
+out.plotting_func = [];
+out.name = [];
+out.date = [];
+end

code/+mpqc/+longitudinal/long_power.m

@@ -0,0 +1,181 @@
+function varargout = long_power(data_dir,varargin)
+% Function to track the changes in laser power over time
+%
+% mpqc.longitudinal.long_power(maintenace_folder_path, varargin)
+%
+% Optional inputs: 
+% 'startDate', month-year
+% 'wavelength, value
+%
+% Purpose
+% Plots the power at the objective from 0-100% and compares maximum output
+% power over time. Used to monitor the health of a laser
+%
+%                
+% Outputs
+% out (optional) - structure containing key information and data.
+%
+%
+%
+% Isabell Whiteley, SWC AMF 2025
+
+if nargin<1
+    data_dir = pwd;
+end
+
+% For elseif statement of wavelength given in varargin
+ % % process inputs 
+ %    % addpath("+tools");
+ %    optInputs =  parseInputVariable(varargin{:});
+ % 
+ %    % Extract critical input variable
+ %    selectWavelength = optInputs.wavelength;
+ %   % TODO Add to parseInputVariable startDate
+
+debugPlots = true;
+
+maintenanceFiles = dir(fullfile(data_dir,'\**\*.mat')); 
+n=1;
+
+for ii=1:length(maintenanceFiles)
+    tmp = maintenanceFiles(ii);
+
+    if contains(tmp.name,'power')
+        plotting_template(n) = generic_generator_template(tmp);
+        plotting_template(n).type = 'power';
+        plotting_template(n).plotting_func = @mpqc.plot.power;
+        plotting_template(n).date = string(datetime(regexp(tmp.name, '(\d{4}-\d{2}-\d{2})_(\d{2}-\d{2}-\d{2})','match'),'InputFormat','yyyy-MM-dd_HH-mm-ss'));
+        plotting_template(n).wavelength = str2num(cell2mat(regexp(tmp.name,'\d*(?=nm)','match')));
+        [pathstr,plotting_template(n).name,ext] = fileparts(tmp.name);
+        n=n+1;
+    end
+end
+if ~exist('plotting_template','var')
+    disp('No power measurement files found')
+    varargout{1} = [];
+    return
+end
+
+% sort plotting_template data by the date/time
+date_list = [plotting_template.date];
+[~,order] = sort(datenum(date_list,'dd-mm-yyyy hh:MM:ss'),1,'ascend');
+plotting_template = plotting_template(order);
+
+if nargin > 1 % Optional variable for selecting starting date
+    startDate = datetime(varargin{1});
+    startIndex = 1;
+
+    while [plotting_template(startIndex).date] < startDate
+        startIndex = startIndex + 1;
+    end
+
+    plotting_template = plotting_template(startIndex:end);
+end
+
+if isequal(plotting_template(:).wavelength) % if wavelength is the same
+    for ii = 1:length(plotting_template)
+        if contains(plotting_template(ii).full_path_to_data, '.mat')
+            % If power data is found, load it and find max value
+            powerData(ii) = load(plotting_template(ii).full_path_to_data);
+            maxPower(ii) = powerData(ii).powerMeasurements.observedPower(end);
+
+            % Plot the power curves for each date
+            hold on
+            subplot(2,1,1)
+            plot([0:5:100],powerData(ii).powerMeasurements.observedPower,'.')
+            legend(plotting_template.date,'location', 'Northwest')
+            title(cell2mat(['Power at ', string(plotting_template(1).wavelength), 'nm']))
+            xlabel('Percent power')
+            ylabel('Power (mW)')
+            hold off
+        end
+    end
+    % Plot the maximum laser output over time
+    subplot(2,1,2)
+    plot(maxPower, '-*')
+    title('Maximum laser power')
+    xlabels = {plotting_template.date};
+    xticks(1:length(xlabels))
+    xticklabels(xlabels)
+    ylabel('Maximum power (mW)')
+
+% elseif isequal(plotting_template(:).wavelength,selectWavelength)
+% elseif ~isempty(selectWavelength)
+%     tempStruc = find(plotting_template(:).wavelength == selectWavelength);
+% % if wavelength given in varargin, plot only that wavelength and dates 
+
+else
+    % disp('Different wavelengths found')
+    % powerData = [];
+    % maxPower = [];
+    for i = 1:length(plotting_template)
+        allWave(i) = plotting_template(i).wavelength;
+    end
+    wavelengthVals = unique(allWave);
+    numWavelength = length(wavelengthVals);
+maxPower = cell(zeros(1:length(plotting_template)),zeros(1:length(wavelengthVals))); % Need to be cells because they will have empty values
+powerData = cell(zeros(1:length(plotting_template)),zeros(1:length(wavelengthVals)));
+ for jj = 1:length(numWavelength)
+     figure;
+     for ii = 1:length(plotting_template)
+
+        if contains(plotting_template(ii).full_path_to_data, '.mat') && isequal(plotting_template(ii).wavelength,wavelengthVals(jj))
+            % If power data is found, load it and find max value
+            powerData(ii,jj) = load(plotting_template(ii).full_path_to_data);
+            maxPower(ii,jj) = powerData(ii).powerMeasurements.observedPower(end);
+
+
+              hold on
+            subplot(2,1,1)
+            plot([0:5:100],powerData(ii,jj).powerMeasurements.observedPower,'.')
+            legend(plotting_template.date,'location', 'Northwest')
+            title(cell2mat(['Power at ', string(wavelengthVals(jj)), 'nm']))
+            xlabel('Percent power')
+            ylabel('Power (mW)')
+            hold off
+        end
+     end
+ end
+    % for ii = 1:length(numWavelength)       
+    % end
+    % separate plots for each wavelength
+    % tried groupcounts
+    % in R2025a numunique function may work
+
+    % plot wavelengths separately, but keep all dates - so assisgn NaN to
+    % unused dates. Make temporary structures so values are not permanently
+    %  replaced
+end
+
+
+
+% identify wavelength - done
+% plot curves on same plot - done
+% separate plots based on wavelength
+% max value to see decay of laser - done
+
+
+
+
+
+
+% Output of the main function
+if nargout>0
+    out.fileName = {plotting_template(:).name};
+    out.date ={plotting_template(:).date};
+    out.powerData = powerData;
+    out.maxPower = maxPower;
+    out.wavelength = {plotting_template(:).wavelength};
+    varargout{1} = out;
+end
+
+end
+
+function out = generic_generator_template(t_dir)
+out.full_path_to_data = fullfile(t_dir.folder,t_dir.name);
+out.type = [];
+out.plotting_func = [];
+out.name = [];
+out.date = [];
+out.wavelength = [];
+end

code/+mpqc/+longitudinal/long_standard_light_source.m

@@ -0,0 +1,38 @@
+function varargout = long_standard_light_source(data_dir,varargin)
+% Plots showing photon count of PMTs over time
+%
+%
+%
+%
+% Isabell Whiteley, SWC AMF 2025
+
+if nargin<1
+    data_dir = pwd;
+end
+
+
+debugPlots = true;
+
+maintenanceFiles = dir(fullfile(data_dir,'\**\*.tif')); 
+n=1;
+
+for ii=1:length(maintenanceFiles)
+    tmp = maintenanceFiles(ii);
+
+    if contains(tmp.name,'standard_light_source')
+        plotting_template(n) = generic_generator_template(tmp);
+        plotting_template(n).type = 'standard_light_source';
+        plotting_template(n).plotting_func = @mpqc.plot.electrical_noise;
+        plotting_template(n).date = string(datetime(regexp(tmp.name, '(\d{4}-\d{2}-\d{2})_(\d{2}-\d{2}-\d{2})','match'),'InputFormat','yyyy-MM-dd_HH-mm-ss'));
+        [pathstr,plotting_template(n).name,ext] = fileparts(tmp.name);
+        n=n+1;
+    end
+end
+if ~exist('plotting_template','var')
+    disp('No standard light source files found')
+    varargout{1} = [];
+    return
+end
+
+
+end

code/testscript.m

@@ -0,0 +1,2 @@
+a = 1
+[d,out] = mpqc.longitudinal.long_electrical_noise('C:\Users\Isabell\Desktop\2p-313_diagnostics\')