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Diffusion Imaris Cell Densities - Julie Meystre (master) Browse

xt-cell-densities/functions/getAllData.m
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getAllData.m
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function [allIds allSubId allClus allPos allInt allRadii allnSpots] = getAllData()
% for the current folder that is selected
% Go through the clusters
% Get the cluster number
% Get the subcluster number
% Get the positions
% Get the intensities for the needed channels
global X;
% All data is to be appended
% Which channels for the intensity
% get from the User Interface the list of channels of interest
channelsList = getChannelIndexes();
%Get the statistic on which to base clustering
chosenStat = 'Intensity Mean';
% Z compensation
zComp = getFromTag('txt_z_compensation_factor', 'Number');
% Which object to Read the data from?
nFolders = X.GetNumberOf('Group');
if (nFolders > 1)
sel = X.SelectDialog('Group');
else
folder = X.GetObject('Type','Group', 'Number', 1);
sel = folder.GetName;
end
mainFolder = X.GetObject('Type','Group', 'Name', sel);
% Iterate through the clusters
nClusters = X.GetNumberOf('Group', 'Parent', mainFolder);
allPos = [];
allIds = [];
allInt = [];
allSub = [];
allClus = [];
allnSpots = [];
allRadii = [];
for i=1:nClusters
currCluster = X.GetObject('Type', 'Group', 'Number', i, 'Parent', mainFolder);
disp(['Currently Processing Cluster ' num2str(i)]);
% Get number of subclusters
nSubClus = X.GetNumberOf('Spots', 'Parent', currCluster);
clusName = X.GetName(currCluster);
clusNum = str2num(clusName(8:end));
%Iterate through each subcluster
for subClus = 1:nSubClus
%Infer the number of the subcluster, which will give us the subID
spot = X.GetObject('Type', 'Spots', 'Number', subClus, 'Parent', currCluster);
name = X.GetName(spot);
subClusNum = str2num(name(11:end));
% Get the spots positions
posXYZ = spot.GetPositionsXYZ();
nSpots = size(posXYZ,1);
allPos = [allPos ; posXYZ];
% Ids from the spots, simple enough?
allIds = [allIds 1:nSpots];
% SubIDs
allSub = [allSub; repmat(subClusNum, nSpots,1)];
% Cluster ID
allClus= [allClus; repmat(clusNum, nSpots,1)];
%Number of spots per subcluster
allnSpots = [ allnSpots nSpots ];
% Now the intensities
allInt = [allInt; getStatsOnSelectedChannels(spot, chosenStat, channelsList)];
allRadii = [allRadii; spot.GetRadii()];
end
end
allSubId = 100000*allClus + allSub;
end
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