/
restructure_pin_record.m
178 lines (163 loc) · 6.28 KB
/
restructure_pin_record.m
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function Results = restructure_pin_record(Results)
%% Restructure raw record of pin releases from stochastic simulations
%
% Syntax: Results = restructure_pin_record(Results)
%
% Inputs:
% Results::struct Raw results of stochastic simulations
%
% Outputs:
% Results::struct Simulation results with restructured pin record
%
% m-file Requirements:
% -none-
%
% Author: Chris Norman, University of Warwick
% Source: https://github.com/ChrisAlexNorman/SytSim
%------------- BEGIN CODE --------------
fprintf('\nRestructuring record of SNAREpin releases:\n')
if ~isfield(Results,'PinRec')
fprintf('!!! Pin data not recorded !!!\n')
else
PinV = Results.PinRec;
Results = rmfield(Results,'PinRec');
nSNAREs = Results.metaData.nSNAREs;
nVesicleSites = Results.metaData.nVesicleSites;
% Initialise event times
num_event_times = 0;
for v = 1:length(PinV)
num_event_times = num_event_times + size(PinV{v},1) - 1;
end
event_times = zeros(1,num_event_times);
% Estimate variable sizes from event times
freePins = zeros(nSNAREs+2,ceil(length(event_times)/3)+1);
priPins = zeros(nSNAREs+2,ceil(length(event_times)/3)+1);
triPins = zeros(nSNAREs+2,ceil(length(event_times)/3)+1);
clear('event_times')
Pins_on_release = zeros(2,length(Results.releaseTimes));
freePins(2,1) = nVesicleSites; priPins(2,1) = nVesicleSites; triPins(2,1) = nVesicleSites;
fpn = 2; ppn = 2; tpn = 2; rpn = 1;
fprintf('Unpacking PinRec data... \nOf %d : ',length(PinV))
for v = 1:length(PinV)
% Display progress
if ~mod(v,10000) || v == length(PinV)
if v > 10000
for j=1:length(num2str(v-1))
fprintf('\b'); % delete previous counter display
end
end
fprintf('%d',v)
end
if ~(size(PinV{v},1) == 1)
for ti = 2:size(PinV{v},1)
if PinV{v}(ti,4) == nSNAREs+1
% Vesicle released
Pins_on_release(1,rpn) = PinV{v}(ti,1);
Pins_on_release(2,rpn) = PinV{v}(ti-1,4);
freePins(1,fpn) = PinV{v}(ti,1);
freePins(PinV{v}(ti-1,4)+2,fpn) = -1;
priPins(1,ppn) = PinV{v}(ti,1);
priPins(PinV{v}(ti-1,2)+2,ppn) = -1;
triPins(1,tpn) = PinV{v}(ti,1);
triPins(PinV{v}(ti-1,3)+2,tpn) = -1;
rpn=rpn+1; fpn=fpn+1; ppn=ppn+1; tpn=tpn+1;
else
if PinV{v}(ti,2) ~= PinV{v}(ti-1,2)
% primary Pin released
priPins(1,ppn) = PinV{v}(ti,1);
priPins(PinV{v}(ti,2)+2,ppn) = 1;
if PinV{v}(ti-1,4) <= nSNAREs
priPins(PinV{v}(ti-1,2)+2,ppn) = -1;
end
ppn = ppn + 1;
end
if PinV{v}(ti,3) ~= PinV{v}(ti-1,3)
% tripartite Pin released
triPins(1,tpn) = PinV{v}(ti,1);
triPins(PinV{v}(ti,3)+2,tpn) = 1;
if PinV{v}(ti-1,4) <= nSNAREs
triPins(PinV{v}(ti-1,3)+2,tpn) = -1;
end
tpn = tpn + 1;
end
if PinV{v}(ti,4) ~= PinV{v}(ti-1,4)
% check if both Pins released
freePins(1,fpn) = PinV{v}(ti,1);
freePins(PinV{v}(ti,4)+2,fpn) = 1;
if PinV{v}(ti-1,4) <= nSNAREs
freePins(PinV{v}(ti-1,4)+2,fpn) = -1;
end
fpn = fpn+1;
end
end
end
end
end
clear('PinV')
fprintf(' Done.\nRe-structuring freePins... ')
freePins(:,fpn:end)=[];
try
freePins = sortrows(freePins',1)';
catch
fprintf('\nRan out of memory. Trying slower method... ')
[freePins(1,:),sortfpn] = sort(freePins(1,:));
for n = 1:nSNAREs
freePins(n+1,:) = freePins(n+1,sortfpn);
end
clear('sortfpn');
end
fprintf(' Done.\nRe-structuring priPins... ')
priPins(:,ppn:end) = [];
try
priPins = sortrows(priPins',1)';
catch
fprintf('\nRan out of memory. Trying slower method... ')
[priPins(1,:),sortppn] = sort(priPins(1,:));
for n = 1:nSNAREs
priPins(n+1,:) = priPins(n+1,sortppn);
end
clear('sortppn');
end
fprintf(' Done.\nRe-structuring triPins... ')
triPins(:,tpn:end) = [];
try
triPins = sortrows(triPins',1)';
catch
fprintf('\nRan out of memory. Trying slower method... ')
[triPins(1,:),sorttpn] = sort(triPins(1,:));
for n = 1:nSNAREs
triPins(n+1,:) = triPins(n+1,sorttpn);
end
clear('sorttpn');
end
fprintf(' Done.\nRe-structuring Pins_on_release... ')
try
Pins_on_release = sortrows(Pins_on_release',1)';
catch
fprintf('\nRan out of memory. Trying slower method... ')
[Pins_on_release(1,:),sortrpn] = sort(Pins_on_release(1,:));
Pins_on_release(2,:) = Pins_on_release(2,sortrpn);
clear('sortrpn');
end
Pins_on_release = Pins_on_release(2,:);
fprintf(' Done.\nSumming rows... ')
for n = 1:nSNAREs+1
freePins(n+1,:) = cumsum(freePins(n+1,:));
priPins(n+1,:) = cumsum(priPins(n+1,:));
triPins(n+1,:) = cumsum(triPins(n+1,:));
end
fprintf(' Done.\nThinning...')
freePins = freePins(:,floor(linspace(1,size(freePins,2),min(size(freePins,2),1e6))));
priPins = priPins(:,floor(linspace(1,size(priPins,2),min(size(priPins,2),1e6))));
triPins = triPins(:,floor(linspace(1,size(triPins,2),min(size(triPins,2),1e6))));
Results.priPins = priPins;
Results.triPins = triPins;
Results.freePins = freePins;
Results.Pins_on_release = Pins_on_release;
fprintf(' Done.\n')
end
metaData = Results.metaData;
Results = rmfield(Results,'metaData');
Results.metaData = metaData;
fprintf('All done!\n')
%------------- END OF CODE --------------