First commit

.dropbox

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+{"ns": 677615433, "tag": "shared"}

.gitignore

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+Data
+Icon
+.DS_Store
+*.sublime-project
+*.sublime-workspace

.ipynb_checkpoints/pytrack_test-checkpoint.ipynb

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+{
+ "metadata": {
+  "name": "",
+  "signature": "sha256:5eea78c4a82cf7843b080601e5d46c05d35982c43bb39098da90a82d13f5bd49"
+ },
+ "nbformat": 3,
+ "nbformat_minor": 0,
+ "worksheets": []
+}

LICENSE.md

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+The MIT License (MIT)
+
+Copyright (c) 2015 John Lian
+
+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

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+# MATLAB Particle Tracker
+This is an application that can be used to track particles with a series of images. It uses algorithms adopted from the [The Matlab Particle Tracking Code Repository](http://site.physics.georgetown.edu/matlab/).
+
+Detailed manual coming soon!

default_config.m

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+% parameter structure for particle tracking
+% 	color = imread(fullfile(img.path, img.name));
+% 	a = rgb2gray(color);
+% 	b = bpass(a, param.ln, param.d);
+% 	pk = pkfnd(b, param.th, param.sz);  
+% 	cnt = cntrd(b, pk, param.szz);
+
+% param = struct;
+
+param.fps = 600; % frames per second with which the footage was captured
+
+% image analysis parameters
+param.ln = 1;	% characteristic lengthscale of noise in pixels.
+param.d = 10;   % diameter of blobs 
+param.th = 40;  % threshhold
+param.sz = 11;  % set to be slighly larger than diameter of particle
+param.szz = param.sz + 2; % for cnt
+
+% particle tracking parameters
+param.mem = 10;    % number of times steps that a particle can be lost for
+param.dim = 2;     % default is 2
+param.good = 10;   % eliminates trajectories with less than this many positions
+param.quiet = 1;   % default is 1
+param.maxdisp = 20;     % max number of pixels a particle would move in one time interval
+
+param.pxperm = 0.8636/432;

lib/analyseImgs.m

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+function [ positionList ] = analyseImgs( imgs, param )
+% analyse the input image and outputs the positions of the centroids
+% of each particle in the image
+%   input:	imgs - full file path + file name of the image
+% 			param: the parameters needed i.e. sz, d, etc.
+%   output: an array listing the scrambled coordinates and data 
+%			of the different particles at different times, such that:
+%			positionlist(0:d-1,*): contains the d coordinates and
+%			data for all the particles, at the different times. must be positve
+%			positionlist(d,*): contains the time t that the position 
+%			was determined, must be integers (e.g. frame number.  These values must 
+%           be monotonically increasing and uniformly gridded in time.
+
+i = 1;
+positionList = [];
+
+for img = imgs'
+
+	color = imread(fullfile(img.path, img.name));
+
+	% make sure the code can handle already gray images
+	[~, ~, numberOfColorChannels] = size(color);
+	if numberOfColorChannels > 1
+	  a = rgb2gray(color);
+	else
+	  a = color; % It's already gray.
+	end
+
+% 	% for some reason matlab cannot read images properly!!!!
+% 	a = 255-a;
+
+	b = bpass(a, param.ln, param.d);
+	pk = pkfnd(b, param.th, param.sz);  
+	cnt = cntrd(b, pk, param.szz);
+	positionList = [positionList; create_positionList(cnt,i)];
+	i = i + 1;
+
+end
+
+return;
+
+end
+

lib/animate.m

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+function animate(y, T, param)
+%% math
+% makes animation of all the particles
+L = 0.8636;
+
+%% graphics
+
+% set up first frame
+figure('Color', 'white');
+set(gcf,'Position',[100 678 640 360]);
+
+%% animation sub plot
+subplot(1,5,1);
+
+% vertical line
+plot([0;0],[0 L],'k'); 
+
+hold on
+par = plot(0,y(1,:),'sr','MarkerSize',3,'MarkerFaceColor','r');
+hold off
+
+ht = title(sprintf('Time: %0.2f sec', T(1)));
+ylim([0 L]); axis 'auto x'; ylabel('Position (m)');
+
+%% the position  sub plot 
+subplot(1,5,[2 3 4 5]);
+
+% plot only the displacements i.e. odd columns
+pFig = plot(T, y, 'LineWidth', 1);
+
+
+% n moving markers
+mar = line(T(1), y(1,:), 'Marker', '.', 'MarkerSize', 10);
+axis([0 T(length(T)) 0 L]);
+xlabel('Time (s)'); 
+ah = gca;
+
+% get figure size
+ahh = gcf;
+pos = get(gcf, 'Position');
+width = pos(3); height = pos(4);
+
+% preallocate data (for storing frame data)
+mov = zeros(height, width, 1, length(T), 'uint8');
+
+%% animation loop
+
+display('Animating...');
+
+% loop through by changing XData and YData
+for id = 1:length(T)
+    % update graphics data. This is more efficient than recreating plots.
+    % convert to cell otherwise the vector-set function doesn't work    
+    set(mar, 'XData', T(id), {'YData'}, num2cell(y(id, :))');
+    set(par,{'YData'}, num2cell(y(id, :))');
+
+    set(ht, 'String', sprintf('%0.2f s, frame(%d)', T(id),id));
+
+    % get frame as an image
+    f = getframe(ahh);
+
+    % create a colormap for the first frame. For the rest of the frames,
+    % use the same colormap
+    if id == 1
+        [mov(:,:,1,id), map] = rgb2ind(f.cdata, 256, 'nodither');
+    else
+        mov(:,:,1,id) = rgb2ind(f.cdata, map, 'nodither');
+    end
+end
+
+%% gif
+
+gif_button = uicontrol('Style', 'pushbutton', 'String', 'GIF',...
+        'Position', [20 20 50 20],...
+        'Callback', {@GIF,param,mov, map});        
+% the pushbutton string callback
+% calls the gif function to make gif
+
+%% export 
+
+export_button = uicontrol('Style', 'pushbutton', 'String', 'Save',...
+        'Position', [20 50 50 20],...
+        'Callback', {@newPlot,param,ah});        
+% the pushbutton string callback
+% calls the ploter and export
+
+if ~exist(fullfile(param.path, 'Analysis'), 'dir')
+	mkdir(param.path, 'Analysis')
+end
+
+
+end
+
+function GIF(~,~,param, mov, map) 
+
+gif_fps = param.fps/10; 
+
+outGIF = fullfile(param.path, 'Analysis','Animation.gif');
+
+display('Saving as GIF...');
+
+imwrite(mov, map, outGIF, 'LoopCount', inf, 'DelayTime', 1/gif_fps);
+
+fprintf('GIF saved as:\n "%s"\n', outGIF);
+
+end
+
+function newPlot(~,~,param, gca)
+
+display('Saving...');
+
+outPlot = fullfile(param.path, 'Analysis','TrajectoriesPlot');
+set(get(gca,'YLabel'),'String','Position (m)')
+set(get(gca,'XLabel'),'String','Time (s)')
+
+export_fig(gca, outPlot, '-pdf','-png','-m2');
+
+fprintf('Plot saved as:\n "%s"\n', outPlot);
+
+
+end
+

lib/chooseDiag.m

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+function reply = chooseDiag( prompt )
+% Construct a questdlg with two options
+choice = questdlg( prompt, ...
+	'Choices', ...
+	'Yes','No','Yes');
+% Handle response
+switch choice
+    case 'Yes'
+        reply = 1;
+    case 'No'
+        reply = 2;
+end
+
+end
+

lib/convert.m

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+classdef convert
+
+    properties (Constant)
+        % 1 pixel = 0.0001461870504 meters
+        a = 0.8636/923;
+
+        % 1 frame = 1/600 seconds
+        b = 1/600;
+
+        % set the equillibrium position in meters
+        eq = 0;
+
+        % set mass of one magnet in kg
+        m = 0.009601;
+
+        % set the offset of the bottom fixed magent in number of pixels
+        o = 20.5;
+
+        % set the pull force in lbs
+        pf = 11.33;
+    end
+
+    methods (Static)
+
+        function output = pixelsToMeters(X, pxperm)
+            for i=1:size(X,2)
+                for j = 1:size(X,1)
+                output(j,i) = X(j,i)*pxperm; 
+                end
+            end 
+        end
+
+        function output = framesToSeconds(Y)
+            for i=1:size(Y,2)
+                output(i) = Y(i)*convert.b; 
+            end 
+        end
+
+        function output = velToMetric(vel)
+            for i=1:size(vel,2)
+                output(i) = vel(i)*convert.a/convert.b;
+            end
+        end
+
+        function output = accToMetric(acc)
+            for i=1:size(acc,2)
+                output(i) = acc(i)*convert.a/convert.b/convert.b;
+            end 
+        end
+
+        function output = NTolb(force) 
+            for i=1:size(force,2) 
+                output(i) = force(i)*0.22481;
+            end
+        end
+
+        function output = metersToInches(disp)
+            for i=1:size(disp, 2) 
+                output(i) = disp(i)*39.3701; 
+            end
+        end
+
+    end
+
+end
+

lib/create_positionList.m

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+function [ positionList ] = create_positionList( cnt, index )
+% create positionlist vector by appending data to the end
+% for track.m
+
+positionList(:,1) = cnt(:,2);     % x-coordinate
+positionList(:,2) = cnt(:,1);     % y-coordinate
+positionList(1:size(cnt,1),3) = index;      % frame number
+
+return;
+
+end
+

lib/export_fig/.gitignore

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+/.ignore
+*.txt
+*.asv
+*~
+*.mex*

lib/export_fig/LICENSE

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+Copyright (c) 2014, Oliver J. Woodford
+All rights reserved.
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+
+* Redistributions of source code must retain the above copyright notice, this
+  list of conditions and the following disclaimer.
+
+* Redistributions in binary form must reproduce the above copyright notice,
+  this list of conditions and the following disclaimer in the documentation
+  and/or other materials provided with the distribution.
+
+* Neither the name of the {organization} nor the names of its
+  contributors may be used to endorse or promote products derived from
+  this software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
+FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.