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Cowenupdates #1

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0e74639
minor changes. initialized a variable and defined some values before …
cowenowner Nov 9, 2020
eed1755
Update .gitignore
cowenowner Nov 9, 2020
6d446a4
Update Main_assemblies_detection.m
cowenowner Nov 9, 2020
30cf39e
mods to allow custom binning
cowenowner Nov 17, 2020
7771c91
updates
cowenowner Nov 19, 2020
0b007dd
Update FindAssemblies_recursive.m
cowenowner Nov 29, 2020
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2 changes: 2 additions & 0 deletions .gitignore
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Original file line number Diff line number Diff line change
@@ -0,0 +1,2 @@
*.asv

189 changes: 103 additions & 86 deletions Programs_and_data/Assembly_activity_function.m
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Expand Up @@ -4,14 +4,14 @@
% ARGUMENTS:
% As_across_bins := structure containing assembly information output of ASSEMBLIES_ACROSS_BINS;
% assembly := structure containing assembly information output of Main_assemblies_detection.m
% spM := matrix with population spike trains; each row is the spike train (time stamps, not binned) relative to a unit.
% spM := matrix with population spike trains; each row is the spike train (time stamps, not binned) relative to a unit.
% BinSizes := vector of bin sizes to be tested;
%
% (optional) lagChoice - The user can chose if to consider only the assembly activation (marked at
% the occurrence of the first assembly unit spike) or the activity of the whole
%
% (optional) lagChoice - The user can chose if to consider only the assembly activation (marked at
% the occurrence of the first assembly unit spike) or the activity of the whole
% assembly (from the spike of the first assembly unit to the spike of the last assembly unit)
% lagChoice='beginning' ---> only assembly activation
% lagChoice='duration' ---> activity stays up during the whole assembly duration
% lagChoice='beginning' ---> only assembly activation
% lagChoice='duration' ---> activity stays up during the whole assembly duration


% (optional) act_count - options on how to count activity
Expand All @@ -25,8 +25,8 @@


% RETURNS:
% assembly_activity - assembly activation profile across recording time
% according to different possible definitions.
% assembly_activity - assembly activation profile across recording time
% according to different possible definitions.
%
%
%
Expand All @@ -35,98 +35,123 @@
%
% last update 11/01/2016
%
% Cowen: more work to do here to get this to work with custion binnned
% spike time matrices.


if nargin<5 || isempty(lagChoice), lagChoice='duration'; end;
if nargin<6 || isempty(act_count), act_count='full'; end;
if nargin<5 || isempty(lagChoice), lagChoice='duration'; end
if nargin<6 || isempty(act_count), act_count='full'; end


as=As_across_bins;
assembly_activity=cell(length(as),1);

for n=1:length(as)

tb=assembly.bin{find(BinSizes==as{n}.bin)}.bin_edges;

switch act_count
case 'full'
[activity]=DetectAssembly(spM ,as{n},tb); % only full assembly occurrences are considered
case 'partial'
[activity]=DetectAssembly_additive(spM ,as{n},tb); % partial activations are also took into account
case 'combined'
[activity]=DetectAssembly_additive_weighted(spM ,as{n},tb); % partial activations are also took into account but weighting differently full assembly contributions from partial assembly contributions.
end
ta=tb(1:end-1)+as{n}.bin/2; %tb are the binning edges, I want the center
WOO=[ta',activity'];



switch lagChoice
case 'beginning'
assembly_activity{n}=WOO;
case 'duration'

alag=As_across_bins{n}.lag(end);
activity_lag=activity;
for j=1:alag
ix = find(BinSizes==as{n}.bin);
tb=assembly.bin{ix}.bin_edges;

switch act_count
case 'full'
if iscell(spM)
[activity]=DetectAssembly(spM{ix} ,as{n}); % only full assembly occurrences are considered
else
[activity]=DetectAssembly(spM ,as{n},tb); % only full assembly occurrences are considered
end
case 'partial'
if iscell(spM)
[activity]=DetectAssembly_additive(spM{ix} ,as{n}); % only full assembly occurrences are considered
else
[activity]=DetectAssembly_additive(spM ,as{n},tb); % partial activations are also took into account
end
case 'combined'
if iscell(spM)
[activity]=DetectAssembly_additive_weighted(spM{ix} ,as{n}); % only full assembly occurrences are considered
else
[activity]=DetectAssembly_additive_weighted(spM ,as{n},tb); % partial activations are also took into account but weighting differently full assembly contributions from partial assembly contributions.
end
end
ta=tb(1:end-1)+as{n}.bin/2; %tb are the binning edges, I want the center
WOO=[ta',activity'];



switch lagChoice
case 'beginning'
assembly_activity{n}=WOO;
case 'duration'

alag=As_across_bins{n}.lag(end);
activity_lag=activity;
for j=1:alag
activity_lag=[activity_lag; [zeros(1,j), activity(1:end-j)]];
end
VOO=[ta',sum(activity_lag,1)'];

assembly_activity{n}=VOO;
end

end
VOO=[ta',sum(activity_lag,1)'];
assembly_activity{n}=VOO;
end
end

end






function [activity]=DetectAssembly(spM, Assembly, tb)
% only occurrences of full assemblies are considered. The 'activity' vector
% returns the number of times the complete set of assembly units is firing
% in a bin.
% in a bin.

eelements=Assembly.elements;
alag=Assembly.lag;
Sbin_assembly=zeros(length(eelements),length(tb)-1);
for i=1:length(eelements)
[Sbin_assembly(i,:),~] = histcounts(spM(eelements(i),:),tb);
if nargin < 3
Sbin_assembly=zeros(length(eelements),size(spM,2));
for i=1:length(eelements)
Sbin_assembly(i,:) = spM(eelements(i),:);
end
else
Sbin_assembly=zeros(length(eelements),length(tb)-1);
for i=1:length(eelements)
[Sbin_assembly(i,:),~] = histcounts(spM(eelements(i),:),tb);
end
end

Sbin_shifted=nan(size(Sbin_assembly));
for e1=1:length(Assembly.elements)
if alag(e1)==0
Sbin_shifted(e1,:)=Sbin_assembly(e1,:);
elseif alag(e1)>0
Sbin_shifted(e1,1:end-alag(e1))=Sbin_assembly(e1,1+alag(e1):end);
Sbin_shifted(e1,1:end-alag(e1))=Sbin_assembly(e1,1+alag(e1):end);
else
Sbin_shifted(e1,1-alag(e1):end)=Sbin_assembly(e1,1:end+alag(e1));
end
end
aus=sum(Sbin_shifted,1);
Sbin_shifted(:,isnan(aus))=0; % cut at the borders
activity=min(Sbin_shifted,[],1);
activity=min(Sbin_shifted,[],1);
end


function [activationtot]=DetectAssembly_additive(spM, Assembly, tb)

eelements=Assembly.elements;
alag=Assembly.lag;
Sbin_assembly=zeros(length(eelements),length(tb)-1);
for i=1:length(eelements)
[Sbin_assembly(i,:),~] = histcounts(spM(eelements(i),:),tb);

if nargin < 3
Sbin_assembly=zeros(length(eelements),size(spM,2));
for i=1:length(eelements)
Sbin_assembly(i,:) = spM(eelements(i),:);
end
else
Sbin_assembly=zeros(length(eelements),length(tb)-1);
for i=1:length(eelements)
[Sbin_assembly(i,:),~] = histcounts(spM(eelements(i),:),tb);
end
end

maxrate=max(Sbin_assembly(:));
maxrate=max(Sbin_assembly(:));
Sbin_p=cell(1,maxrate);
for i=1:maxrate
Sbin_p{i}=zeros(size(Sbin_assembly));
Sbin_p{i}(find(Sbin_assembly>=i))=1;
Sbin_p{i}(Sbin_assembly>=i)=1;
end

activity=zeros(maxrate,size(Sbin_assembly,2));
Expand All @@ -136,16 +161,16 @@
if alag(e1)==0
Sbin_shifted(e1,:)=Sbin_p{i}(e1,:);
elseif alag(e1)>0
Sbin_shifted(e1,1:end-alag(e1))=Sbin_p{i}(e1,1+alag(e1):end);
Sbin_shifted(e1,1:end-alag(e1))=Sbin_p{i}(e1,1+alag(e1):end);
else
Sbin_shifted(e1,1-alag(e1):end)=Sbin_p{i}(e1,1:end+alag(e1));
end
end
activity(i,:)=sum(Sbin_shifted,1);
activity(i,find(activity(i,:)==1))=0;
activity(i,:)=sum(Sbin_shifted,1);
activity(i,activity(i,:)==1)=0;
end
activationtot=sum(activity,1);

activationtot=sum(activity,1);
activationtot(isnan(activationtot))=0;
activationtot=activationtot/length(eelements);
end
Expand All @@ -156,16 +181,23 @@

eelements=Assembly.elements;
alag=Assembly.lag;
Sbin_assembly=zeros(length(eelements),length(tb)-1);
for i=1:length(eelements)
[Sbin_assembly(i,:),~] = histcounts(spM(eelements(i),:),tb);
if nargin < 3
Sbin_assembly=zeros(length(eelements),size(spM,2));
for i=1:length(eelements)
Sbin_assembly(i,:) = spM(eelements(i),:);
end
else
Sbin_assembly=zeros(length(eelements),length(tb)-1);
for i=1:length(eelements)
[Sbin_assembly(i,:),~] = histcounts(spM(eelements(i),:),tb);
end
end

maxrate=max(Sbin_assembly(:));
maxrate=max(Sbin_assembly(:));
Sbin_p=cell(1,maxrate);
for i=1:maxrate
Sbin_p{i}=zeros(size(Sbin_assembly));
Sbin_p{i}(find(Sbin_assembly>=i))=1;
Sbin_p{i}(Sbin_assembly>=i)=1;
end


Expand All @@ -176,35 +208,20 @@
if alag(e1)==0
Sbin_shifted(e1,:)=Sbin_p{i}(e1,:);
elseif alag(e1)>0
Sbin_shifted(e1,1:end-alag(e1))=Sbin_p{i}(e1,1+alag(e1):end);
Sbin_shifted(e1,1:end-alag(e1))=Sbin_p{i}(e1,1+alag(e1):end);
else
Sbin_shifted(e1,1-alag(e1):end)=Sbin_p{i}(e1,1:end+alag(e1));
end
end
activity(i,:)=sum(Sbin_shifted,1);
activity(i,:)=sum(Sbin_shifted,1);
activity(i,:)= activity(i,:).^5;
activity(i,find(activity(i,:)==1))=0;
activity(i,activity(i,:)==1)=0;
end
activationtot=sum(activity,1);

activationtot=sum(activity,1);
activationtot(isnan(activationtot))=0;
activationtot=activationtot/length(eelements)^5;
end


















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