bg fix

.gitmodules

@@ -0,0 +1,3 @@
+[submodule "stackin"]
+	path = stackin
+	url = https://github.com/RJ3/stackin.git

LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2019 Damon McCullough
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

README.md

@@ -8,11 +8,16 @@ Rhythm is a MATLAB-based graphical user interface to display, condition, and ana
 * Ability to create movies and export individual signals
 
 # Requirements
-We recommend the latest release of 64-bit MATLAB on a 64-bit machine. We have tested this package on both windows and mac platforms. This code was originally created for a mac. While functionality is unchanged on windows machines, GUI display may be a bit irregular on MATLAB for windows.
+We recommend the latest release of 64-bit MATLAB on a 64-bit machine. We have tested this package on both windows and mac platforms. This code was originally created for a mac. While functionality is unchanged on windows machines, GUI display may be a bit irregular on MATLAB for windows.  
+
+*MATLAB 9.5  
+*Signal Processing Toolbox 8.1  
+*Image Processing Toolbox 10.3  
+*Statistics and Machine Learning Toolbox 11.4  
 
 # Contributions
 If you would like to contribute to this project, please contact Dr. Igor Efimov at igor@wustl.edu. If you find this code helpful, please reference our review paper describing proper analysis of optical mapping data found at http://www.ncbi.nlm.nih.gov/pubmed/22821993
 
-# Nottice!!!
+# Notice!!!
 Until we can fully perfect the use of Github distribution, we recommend the URL (Google Drive) below for the most up-to-date release of Rhythm
 https://drive.google.com/folderview?id=0BxA1B_i6ZEvlflptaFlBUlJVNTUtTVUyQzJldnNGc3hneldhVHhVNmhhTjV2M3VmNHY5TlE&usp=sharing

aMap.m

@@ -1,4 +1,4 @@
-function [actMap1] = aMap(data,stat,endp,Fs,bg,cmap,filename)
+function [actMap1] = aMap(data,startt,endt,Fs,bg,cmap,filename,dir)
 %% aMap is the central function for creating conduction velocity maps
 % [actMap1] = aMap(data,stat,endp,Fs,bg) calculates the activation map
 % for a single action potential upstroke.
@@ -19,6 +19,8 @@
 % cmap = a colormap input that facilites the potential inversion of the
 % colormap. cmap is stored in the handles structure as handles.cmap.
 %
+% dir = directory to output csv to
+%
 %
 % OUTPUT
 % actMap1 = activation map
@@ -48,8 +50,8 @@
 
 %% Code
 % Create initial variables
-stat=round(stat*Fs);
-endp=round(endp*Fs);
+stat=round(startt*Fs);
+endp=round(endt*Fs);
 actMap = zeros(size(data,1),size(data,2));
 mask2 = zeros(size(data,1),size(data,2));
 temp = data(:,:,stat:endp); % windowed signal
@@ -79,9 +81,10 @@
 actMap1 = actMap1/Fs*1000; %% time in ms
 
 % Plot Map
-zz = figure('Name','Activation Map');
+actMapPeriod = " " + num2str(round(startt, 3)) + " - " + num2str(round(endt, 3));
+zz = figure('Name',strcat('Activation Map: ',actMapPeriod));
 contourf(flipud(actMap1),endp-stat,'LineColor','none')
-title('Activation Map')
+title(strcat('Activation Map: ',actMapPeriod))
 axis image
 axis off
 colormap(cmap);
@@ -90,15 +93,22 @@
 % User prompt for input to create csv
 prompt1 = {'Save activation map for CV analysis?'};
 dlg_title1 = 'Save activation map';
-num_lines1 = 1;
-direc='/home/lab/Documents/Langendorff-MEHP/ActMaps/';
-def1 = {strcat(direc,'ActMap-',filename,'.csv')};
+num_lines1 = [1 60];
+direc=dir;
+file = strtok(filename,'.');    % Get filename without extension 
+def1 = {strcat(direc,'/ActMaps/ActMap-',file,'.csv')};
 answer = inputdlg(prompt1,dlg_title1,num_lines1,def1);
 % process user inputs
 if isempty(answer)      % cancel save if user clicks "cancel"
     return
 end
 filename = answer{1};
+
+% create the ActMaps folder if it doesn't exist already.
+newSubFolder = strcat(direc,'/ActMaps/');
+if ~exist(newSubFolder, 'dir')
+  mkdir(newSubFolder);
+end
 csvwrite(filename,actMap1);
 
 

apdMap.m

@@ -1,4 +1,4 @@
-function [apdMap] = apdMap(data,start,endp,Fs,percent,cmap)
+function [apdMap] = apdMap(data,start,endp,Fs,percent,cmap,filename,dir)
 %% the function apdMap creates a visual representation of the action potential duration 
 %
 % INPUTS
@@ -100,4 +100,27 @@
 figure('Name','Histogram of APD')
 hist(reshape(apdMap,[],1),floor(APD_max-APD_min))
 %xlim([APD_min APD_max])
+
+
+
+% User prompt for input to create csv
+prompt1 = {'Save APD map?'};
+dlg_title1 = 'Save APD map';
+num_lines1 = [1 60];
+file = strtok(filename,'.');    % Get filename without extension 
+def1 = {strcat(dir,'/APDMaps/APD-',file,'.csv')};
+answer = inputdlg(prompt1,dlg_title1,num_lines1,def1);
+% process user inputs
+if isempty(answer)      % cancel save if user clicks "cancel"
+    return
+end
+filename = answer{1};
+
+% create the APDMaps folder if it doesn't exist already.
+newSubFolder = strcat(dir,'/APDMaps/');
+if ~exist(newSubFolder, 'dir')
+  mkdir(newSubFolder);
+end
+csvwrite(filename,apdMap);
+
 end

binning.m

@@ -19,8 +19,10 @@
 data(data==0) = NaN;
 
 avePattern = ones(N,N);
-for i = 1:size(data,3)
+parfor i = 1:size(data,3)  % for each frame of the data
+    % get the N*N cmos data for the frame
     temp = data(:,:,i);
+    % replace temp with 
     temp = 1/N/N*conv2(temp,avePattern,'same');
     data(:,:,i) = temp;
 end

filter_data.m

@@ -32,7 +32,7 @@
     %% Apply Filter
     temp = reshape(data,[],size(data,3));
     filt_temp = zeros(size(temp));
-    for i = 1:size(temp,1)
+    parfor i = 1:size(temp,1)
         if sum(temp(i,:)) ~= 0
         filt_temp(i,:) = filtfilt(b,a,temp(i,:)); % needed to create 0 phase offset
         end

normalize_data.m

@@ -14,9 +14,28 @@
 % divides by the difference between the min and max. 
 
 %% Code
-min_data = repmat(min(data,[],3),[1 1 size(data,3)]);
-diff_data = repmat(max(data,[],3)-min(data,[],3),[1 1 size(data,3)]);
-normData = (data-min_data)./(diff_data);
+disp('(normalize_data.m) Starting ')
+
+disp('(normalize_data.m) Calculation min_data... ')
+min_data = repmat(min(data,[],3), [1 1 size(data,3)]);
+
+disp('(normalize_data.m) Calculation diff_data... ')
+diff_data = repmat(max(data,[],3) - min(data,[],3), [1 1 size(data,3)]);
+% normData = (data-min_data)./(diff_data);
+% data_temp = data - min_data;
+
+% Subtraction
+disp('(normalize_data.m) Subtraction... ')
+% data_temp = bsxfun(@minus, data, min_data);
+data = bsxfun(@minus, data, min_data);
+clear min_data
+
+% Division
+disp('(normalize_data.m) Division... ')
+normData = rdivide(data, diff_data);
+clear diff_data
+
+disp('(normalize_data.m) Done ')
 % % %% NON RECTANGULAR POLYGON MOD
 % % min_data = repmat(min(data,[],2),[1 size(data,2)]);
 % % diff_data = repmat(max(data,[],2),[1 size(data,2)])-min_data;

remove_BKGRD.m

@@ -99,7 +99,7 @@
 BG = mat2gray(bg);
 level = graythresh(BG);
 BW = im2bw(BG,level*thresh);
-BW2 = bwareaopen(BW, perc_ex*size(BG,1)*size(BG,2));
+BW2 = bwareaopen(BW, floor(perc_ex*size(BG,1)*size(BG,2)));
 BW3 = imfill(BW2,'holes');
 mask = repmat(BW3,[1 1 size(data,3)]);
 new_data = data.*mask;

remove_Drift.m

@@ -34,7 +34,7 @@
 tempy = reshape(data,size(data,1)*size(data,2),[]);
 temp_ord = ord_str{1};
 ord = str2num(temp_ord(1));
-for i = 1:size(data,1)*size(data,2)
+parfor i = 1:size(data,1)*size(data,2)
     if sum(tempy(i,:)) ~= 0
     [p,s,mu] = polyfit(tempx,tempy(i,:),ord);
     y_poly = polyval(p,tempx,s,mu);