%
%
%  Track Plot Length Function for Imaris
%
%  Copyright Bitplane AG 2006
%
%
%  Installation:
%
%  - Copy this file into the XTensions folder in the Imaris installation directory.
%  - You will find this function in the Image Processing menu
%
%    <CustomTools>
%      <Menu>
%       <Submenu name="Tracks Functions">
%        <Item name="Plot Length of the Track" icon="Matlab" tooltip="Plot the length of the track steps.">
%          <Command>Matlab::BPTrackPlotLength(%i)</Command>
%        </Item>
%       </Submenu>
%      </Menu>
%      <SurpassTab>
%        <SurpassComponent name="bpTrack">
%          <Item name="Plot Length" icon="Matlab" tooltip="Plot the length of the track steps.">
%            <Command>Matlab::BPTrackPlotLength(%i)</Command>
%          </Item>
%        </SurpassComponent>
%      </SurpassTab>
%    </CustomTools>
% 
%
%  Description:
%   
%   Plot the length of the track steps. 
%   
%

function BPTrackPlotLength(aImarisApplicationID,aThreshold)

% connect to Imaris Com interface
if ~isa(aImarisApplicationID, 'COM.Imaris_Application')
  vImarisServer = actxserver('ImarisServer.Server');
  vImarisApplication = vImarisServer.GetObject(aImarisApplicationID);
else
  vImarisApplication = aImarisApplicationID;
end

% get the track
vTrack = vImarisApplication.mFactory.ToTrack(vImarisApplication.mSurpassSelection);

if ~vImarisApplication.mFactory.IsTrack(vTrack)  
    msgbox('Please select a Track!');
    return;
end


if nargin<2
    vAnswer = inputdlg(['Step length below the threshold is considered ', ...
        'as "pause" indicator. Please enter the threshold value:'],...
        'Plot track length',...
        1,{'0.4'});
    if isempty(vAnswer), return; end;
    vThreshold = sscanf(char(vAnswer),'%f');
else
    vThreshold = aThreshold;
end


% get the spots and edges
%vEdges = vTrack.GetEdges;
vSpots = vTrack.GetSpots;

[vSpotsXYZ,vSpotsTime,vSpotsRadius] = vSpots.Get;
vSpotsXYZ = vSpotsXYZ';

vNumberOfSpots = length(vSpotsRadius);

vTimeMin = min(vSpotsTime);
vTimeMax = max(vSpotsTime);

vSpotAtTime = zeros(1,vTimeMax-vTimeMin+1);
vSpotAtTime(vSpotsTime-vTimeMin+1) = 1:vNumberOfSpots;

vTime = sort(vSpotsTime);

vSpotsIndex = vSpotAtTime(vTime-vTimeMin+1);

vTimeLength = double(max(vTime(2:vNumberOfSpots)-vTime(1:vNumberOfSpots-1),1));
vStepLength = vSpotsXYZ(:,vSpotsIndex(2:vNumberOfSpots)) - ...
    vSpotsXYZ(:,vSpotsIndex(1:vNumberOfSpots-1));

vStepsSize = sqrt(sum( (vStepLength).^2 )) ./ vTimeLength;

vPause = length(find(vStepsSize<=vThreshold));

vTimes = vTime(1:vNumberOfSpots-1)-vTimeMin+1;

subplot(2,2,1)
plot(vTimes,vStepsSize,'b-')
hold on
plot(vTimes,zeros(1,vNumberOfSpots-1)+vThreshold,'r-')
hold off
title(sprintf('Steps size of %s (total length = %.2f)',vTrack.mName,sum(vStepsSize)));
xlabel(sprintf('Number of pause steps = %i (%.2f%%)',vPause,vPause/(vNumberOfSpots-1)*100));
ylabel('Step size [um]');

% finally plot the results
vStrings = {'X','Y','Z'};
for vPlot = 1:3
    subplot(2,2,vPlot+1)
    plot(vTimes,vStepLength(vPlot,:),'b-');
    title([vStrings{vPlot}, '-Step size of ', vTrack.mName]);
    xlabel('Time');
    ylabel('Step size [um]');
end