V16

ConditionAnalysis/GetDataName.m

@@ -0,0 +1,6 @@
+function name = GetDataName(SourceDir)
+    [~,dir,~]=fileparts(SourceDir);
+    name=[dir '_data.mat'];
+    name=fullfile(SourceDir,name);
+end
+

ConditionAnalysis/GetDefaultDataName.m

@@ -0,0 +1,4 @@
+function fileName = GetDefaultDataName
+    fileName='data.mat';
+end
+

ConditionAnalysis/getAppearanceGrowth.m

@@ -0,0 +1,107 @@
+function [AppearanceGrowth,NotBigEnough,Merged] = getAppearanceGrowth(SourceDirs, lb, ub,BeginTimes)
+% [ColoniesGrowth, ColoniesAppearance,ColoniesIndices,AreaGap,...
+%                              NotBigEnough,MergedBeforUpper]
+%% [ColoniesGrowth, ColoniesAppearance] = getAppearanceGrowth(
+%                                                          FileDir, lb, ub)
+% -------------------------------------------------------------------------
+% Purpose: This function calculates the growth rate and appearance time for
+%   each relevant colony.
+% 
+% Description: This function calculates the growth rate and appearance time for
+%   each relevant colony. Relevant colonies are the colonies that are not
+%   excluded and far enough from the border. For colonies that that became
+%   one we take data only till the first merging time.
+% 
+% Arguments: FileDir - The directory of the data
+%       lb - lower bound size in pixels
+%       ub - upper bound size in pixels
+%
+% Returns: ColoniesIndices - The indices of colonies that entered to
+%                            statistics.
+%          AreaGap - The diffrence between the first area that exceeded lb
+%          and the first area that exceeded ub for each colony that entered
+%          to statistics.
+%
+%          ColoniesGrowth - vector of the times it take for each colony to
+%                               reach from lb size to ub size.
+%          ColoniesAppearance - Colony's first appearance
+%
+%          NotBigEnough - colonies with last area < ub (not in statistics)
+%
+%          MergedBeforUpper - colonies that merged before exceeding the ub
+%                             (not in statistics)
+% -------------------------------------------------------------------------
+% Nir Dick. 9.2013
+    dataFlag=0;
+    if nargin<4
+        dataFlag=1;
+        BeginTimes=zeros(size(SourceDirs));
+    end
+
+    if(~iscell(SourceDirs))
+        SourceDirs = {SourceDirs};
+    end
+
+    numOfSources=length(SourceDirs);
+
+    % AppearanceGrowth init
+    AppearanceGrowth.plate=[];
+    AppearanceGrowth.id=[];
+    AppearanceGrowth.growth=[]; 
+    AppearanceGrowth.appearance=[];
+    AppearanceGrowth.areaGap=[];
+
+    % NotBigEnough init
+    NotBigEnough.plate=[];
+    NotBigEnough.id=[];
+
+    % Merged init
+    Merged.plate=[];
+    Merged.id=[];
+
+    for i=1:numOfSources
+        currAppearance=[];
+        if (lb>ub)
+            disp 'Invalid arguments lb > up';
+        else
+            % Load data file
+            FileDir=SourceDirs{i};
+            data=load(GetDataName(FileDir));
+
+            [currIndices,currGrowth,currGap,currNotBigEnough,currMerged]=...
+                                    getColoniesGrowthRate(FileDir, lb, ub);
+            coloniesNum=size(currIndices,1);
+            for k=1:coloniesNum
+                AppearenceIndex = find(data.Area(:,currIndices(k)),1,'first');
+                currAppearance=[currAppearance;data.FilesDateTime(AppearenceIndex)];
+            end 
+        end
+
+        if dataFlag&&isfield(data,'StartingTime')
+            currStarting=data.StartingTime;
+        else
+            currStarting=BeginTimes(i);
+        end
+
+        currAppearance=currAppearance-currStarting;
+
+        if currStarting
+            currAppearance=round(currAppearance*24*60);
+        end
+
+        % AppearanceGrowth building
+        AppearanceGrowth.plate=[AppearanceGrowth.plate; i*ones(size(currIndices))];
+        AppearanceGrowth.id=[AppearanceGrowth.id; currIndices];
+        AppearanceGrowth.growth=[AppearanceGrowth.growth;currGrowth];
+        AppearanceGrowth.appearance=[AppearanceGrowth.appearance;currAppearance];
+        AppearanceGrowth.areaGap=[AppearanceGrowth.areaGap;currGap];
+
+        % NotBigEnough building
+        NotBigEnough.plate=[NotBigEnough.plate;i*ones(size(currNotBigEnough))];
+        NotBigEnough.id=[NotBigEnough.id;currNotBigEnough];
+
+        % Merged building
+        Merged.plate=[Merged.plate;i*ones(size(currMerged))];
+        Merged.id=[Merged.id;currMerged];
+    end
+end

ConditionAnalysis/getAppearanceTime.m

@@ -0,0 +1,44 @@
+function [ApperanceTime] = getAppearanceTime(SourceDirs,BeginTimes)
+    dataFlag=0;
+    if nargin<2
+        dataFlag=1;
+        BeginTimes=zeros(size(SourceDirs));
+    end
+
+    if(~iscell(SourceDirs))
+        SourceDirs = {SourceDirs};
+    end
+
+    numOfSources=length(SourceDirs);
+
+    ApperanceTime.plate=[];
+    ApperanceTime.id=[];
+    ApperanceTime.time=[];
+
+    for i=1:numOfSources
+        % Load data file
+        data=load(GetDataName(SourceDirs{i}));
+
+        if dataFlag&&isfield(data,'StartingTime')
+            currBeginTime=data.StartingTime;
+        else
+            currBeginTime=BeginTimes(i);
+        end
+
+        indexes = 1:length(data.IgnoredColonies);
+        indexes = indexes(~data.IgnoredColonies);
+
+        [~,I]=max(data.Area(:,indexes)>0,[],1);
+        PlateAppearanceTime = data.FilesDateTime(I);
+
+        PlateAppearanceTime=PlateAppearanceTime-currBeginTime;
+
+        if currBeginTime
+            PlateAppearanceTime=round(PlateAppearanceTime*24*60);
+        end
+
+        ApperanceTime.plate=[ApperanceTime.plate,i*ones(size(indexes))];
+        ApperanceTime.id=[ApperanceTime.id,indexes];
+        ApperanceTime.time=[ApperanceTime.time,PlateAppearanceTime];
+    end
+end

ScannerTimeLapse/V15/getColoniesGrowthRate.m → ConditionAnalysis/getColoniesGrowthRate.m

@@ -1,6 +1,5 @@
-function [ColoniesIndices,ColoniesGrowth,AreaGap,...
-                              NotBigEnough,RemovedMerged]=...
-                                    getColoniesGrowthRate(FileDir, lb, ub)
+function [ColoniesIndices,ColoniesGrowth,AreaGap,NotBigEnough,RemovedMerged]=...
+                                                getColoniesGrowthRate(dataInfo, lb, ub)
 %% ColonisGrowth = getColoniesGrowthRate(FileDir)
 % -------------------------------------------------------------------------
 % Purpose: This function calculates the growth rate of each colony
@@ -17,30 +16,28 @@
 %       indicesBeforeMerged - Colony's index respectivly
 % -------------------------------------------------------------------------
 % Nir Dick. 9.2013
-
     %% Loading data and initializations
-    DirName = fullfile(FileDir, 'Results');
-    load(fullfile(DirName,'VecArea'));
-    load(fullfile(DirName,'ExcludedBacteria.txt'));
-    load(fullfile(DirName,'TimeAxis'));
-
-    allColonies = FindColoniesInWorkingArea(FileDir);
+    if isstruct(dataInfo)
+        data=dataInfo;
+    % Data info is the location of the file
+    else
+        data=load(GetDataName(dataInfo));
+    end
+
+    allColonies = find(data.IgnoredColonies==0);
 
     % Return an array of not big enough colonies
-    NotBigEnough=find(VecArea(:,end)<ub);
+    NotBigEnough=find(data.Area(end,:)<ub);
     NotBigEnough=intersect(NotBigEnough,allColonies);
-
-    % Remove excluded and not big enough
-    indicesBeforeMerged=setdiff(allColonies,ExcludedBacteria);
-    indicesBeforeMerged=setdiff(indicesBeforeMerged,NotBigEnough);
+    indicesBeforeMerged=setdiff(allColonies,NotBigEnough);
 
     %% Remove colonies that merged between lb to ub and for the rest 
     % calculate rate
     RemovedMerged=[];
     ColoniesGrowth=[];
     ColoniesIndices=[];
     AreaGap=[];
-    allMerged=getMergedColonies(DirName);
+    allMerged=getMergedColonies(data.Centroid);
     CINum=length(indicesBeforeMerged);
     for j=1:CINum
         currCol=indicesBeforeMerged(j);
@@ -50,31 +47,31 @@
 
         % Check if current colony merged while growing from lb to ub
         if mergeTimeIdx>0  
-            % Doesn't make sense, but stil....
+            % Doesn't make sense, but stil we cant calcullate prev
+            % index in this case
             if (mergeTimeIdx==1)
                 removeMerged=1;
             else
                 % Get area of current colony before merging time
-                currArea=VecArea(currCol,mergeTimeIdx-1);
+                currArea=data.Area(mergeTimeIdx-1,currCol);
                 if currArea<ub
                     removeMerged=1;
                 end
             end
-
         end
 
         % Add current colony to the removed colonies for merging reasons
         if (removeMerged)
             RemovedMerged=[RemovedMerged;currCol];
         % Add current colony to the result arrays
         else
-            lbIndex = find(VecArea(currCol,:)>=lb,1,'first');
-            ubIndex = find(VecArea(currCol,:)>=ub,1,'first');
+            lbIndex = find(data.Area(:,currCol)>=lb,1,'first');
+            ubIndex = find(data.Area(:,currCol)>=ub,1,'first');
             ColoniesIndices=[ColoniesIndices;currCol];
             ColoniesGrowth=...
-                [ColoniesGrowth;TimeAxis(ubIndex)-TimeAxis(lbIndex)];
+                [ColoniesGrowth;data.FilesDateTime(ubIndex)-data.FilesDateTime(lbIndex)];
             AreaGap=...
-               [AreaGap;VecArea(currCol,ubIndex)-VecArea(currCol,lbIndex)];
+               [AreaGap;data.Area(ubIndex,currCol)-data.Area(lbIndex,currCol)];
         end
     end
 

ConditionAnalysis/getDistrStatistics.m

@@ -0,0 +1,26 @@
+function [Stat] = getDistrStatistics(Distr)
+% Stat = ExperimentStatistics(Distr)
+% -------------------------------------------------------------------------
+% Purpose: checking statistical parmeters for a histogram
+% Arguments: TimeAxis - Time
+%       Distr - appearance time for each bacteria (not a histogram)
+% Returns: Stat.total
+%              .Avg
+%              .std
+%              .skw
+%              .mode
+%              .median
+%              .stdMed
+% -------------------------------------------------------------------------
+% Irit Levin Reisman. 2015
+    Stat.total = length(Distr);
+    Stat.Avg   = mean(Distr);
+    Stat.std   = std(Distr);
+    Stat.skw   = skewness(Distr);
+%     h          = hist(Distr, TimeAxis);
+%     [val, Ind] = max(h);
+%   Stat.max   = TimeAxis(Ind);
+    Stat.mode  = mode(Distr);
+    Stat.median= median(Distr);
+    Stat.stdMed= sqrt(sum((Distr - Stat.median).^2)/Stat.total);
+end

ScannerTimeLapse/V15/getMergedColonies.m → ConditionAnalysis/getMergedColonies.m

@@ -1,4 +1,4 @@
-function [result] = getMergedColonies(DirName)
+function [result] = getMergedColonies(VecCen)
 %% [result] = getMergedColonies()
 % -------------------------------------------------------------------------
 % Purpose: This function return for each colony the first time it merged.
@@ -12,11 +12,9 @@
 % relevant index or 0 if colony didn't merge.
 % -------------------------------------------------------------------------
 % Nir Dick. 9.2013
-
-    load(fullfile(DirName,'VecCen'));
 
-    coloniesNum=size(VecCen,1);
-    timesNum=size(VecCen,3);
+    coloniesNum=size(VecCen,2);
+    timesNum=size(VecCen,1);
 
     result=zeros(coloniesNum,1);
 
@@ -26,10 +24,10 @@
     for j=1:coloniesNum
         for k=1:timesNum
             % Get colony center
-            cen=VecCen(j,:,k);
-            if (cen ~= [0 0])
+            cen=[VecCen(k,j,1) VecCen(k,j,2)];
+            if ((cen(1) ~= 0) || (cen(2) ~= 0))
                 cenColoniesNum=...
-                      sum(VecCen(:,1,k)==cen(1,1)&VecCen(:,2,k)==cen(1,2));
+                      sum(VecCen(k,:,1)==cen(1,1)&VecCen(k,:,2)==cen(1,2));
 
                 if (cenColoniesNum>1)
                     result(j,1)=k;

ConditionAnalysis/getPropInTime.m

@@ -0,0 +1,28 @@
+function [id,Time,Area,Centroid] = getPropInTime(SourceDirs)
+    if(~iscell(SourceDirs))
+        SourceDirs = {SourceDirs};
+    end
+
+    numOfDirs=length(SourceDirs);
+
+    id = cell(1,numOfDirs);
+    Time=cell(1,numOfDirs);
+    Area=cell(1,numOfDirs);
+    Centroid=cell(1,numOfDirs);
+
+   for i=1:numOfDirs
+        % Load data file
+        data=load(GetDataName(SourceDirs{i}));
+
+        % Build the id vecs - colonie's id and source dir
+        indexes = 1:length(data.IgnoredColonies);
+        indexes = indexes(~data.IgnoredColonies);
+        id{i}=indexes;
+
+        % Load add the times arrea
+        Time{i}=data.FilesDateTime;
+        Area{i}=data.Area(:,indexes);
+        Centroid{i}=data.Centroid(:,indexes,:);
+   end
+end
+

ConditionAnalysis/getSurvivalCurve.m

@@ -0,0 +1,23 @@
+function [SurvivalCurveX, SurvivalCurveY] = getSurvivalCurve(SourceDirs,BeginTimes)
+%%[Time, DC] = plotDeathCurve(DirVec)
+% -------------------------------------------------------------------------
+% Purpose: creating a death curve
+% Arguments: DirVec - a cell array of the dir names
+%       ShowPlot - (1) plot the results. (0) no plot [default]
+% Returns: Time - Time axis till TimeLimit
+%       DC - Death Curve
+% -------------------------------------------------------------------------
+% Irit Levin Reisman. 2015
+    sentBegin=false;
+    if nargin>1
+        sentBegin=true;
+    end
+
+    if sentBegin
+        totalAppearenceTime=getAppearanceTime(SourceDirs,BeginTimes);
+    else
+        totalAppearenceTime=getAppearanceTime(SourceDirs);
+    end 
+    SurvivalCurveX = sort(totalAppearenceTime.time);
+    SurvivalCurveY  = length(totalAppearenceTime.time):-1:1;
+end