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feat: use alternative ProgressBar function
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works both when parfor is run in parallel or in serial, without any further changes to the code
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@edkerk
edkerk committed Apr 11, 2024
1 parent f2b4a23 commit 8918962
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2 changes: 1 addition & 1 deletion core/parallelPoolRAVEN.m
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Original file line number Diff line number Diff line change
Expand Up @@ -46,7 +46,7 @@
else
pool = gcp('nocreate');
if isempty(pool)
parpool(IdleTimeout=120);
parpool('IdleTimeout',120)
end
end
end
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6 changes: 2 additions & 4 deletions core/runDynamicFBA.m
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Expand Up @@ -76,7 +76,7 @@
biomassVec = biomass;
timeVec(1) = 0;
[~,hsSol]=solveLP(model,1);
fprintf('Running dynamic FBA analysis... 0%% complete');
PB = ProgressBar2(nSteps,'Running dynamic FBA analysis','cli');
for stepNo = 1:nSteps
% Run FBA
[sol,hsSol] = solveLP(model,1,[],hsSol);
Expand Down Expand Up @@ -107,10 +107,8 @@
model.lb(excInd) = -uptakeBound;
timeVec(stepNo+1) = stepNo*timeStep;

progress=pad(num2str(floor(stepNo/nSteps*100)),3,'left');
fprintf('\b\b\b\b\b\b\b\b\b\b\b\b\b%s%% complete',progress);
count(PB);
end
fprintf('\b\b\b\b\b\b\b\b\b\b\b\b\bCOMPLETE\n');

selNonZero = any(concentrationMatrix>0,2);
concentrationMatrix = concentrationMatrix(selNonZero,:);
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5 changes: 2 additions & 3 deletions core/runPhenotypePhasePlane.m
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Expand Up @@ -49,10 +49,8 @@
shadowPrices2 = zeros(nPts);
[~,hsSol] = solveLP(model);
% Calulate points
fprintf('Running PhPP analysis... 0%% complete');
PB = ProgressBar2(nPts,'Running PhPP analysis','cli');
for i = 1:nPts %ind1
progress=pad(num2str(floor(i/nPts*100)),3,'left');
fprintf('\b\b\b\b\b\b\b\b\b\b\b\b\b%s%% complete',progress);
for j = 1:nPts %ind2
model1 = setParam(model,'eq',controlRxn1,-1*ind1(i));
model1 = setParam(model1,'eq',controlRxn2,-1*ind2(j));
Expand All @@ -63,6 +61,7 @@
shadowPrices2(j,i) = fbasol.sPrice(metID2);
end
end
count(PB);
end
fprintf('\b\b\b\b\b\b\b\b\b\b\b\b\bCOMPLETE\n');

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6 changes: 2 additions & 4 deletions core/runProductionEnvelope.m
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Expand Up @@ -33,12 +33,10 @@
targetUpperBound = nan(1,numel(biomassValues));
targetLowerBound = nan(1,numel(biomassValues));

fprintf('Creating production envelope... 0%% complete');
PB = ProgressBar2(length(biomassValues),'Creating production envelope','cli');
% Max/min for target production
model = setParam(model,'obj',targetRxn,1);
for i = 1:length(biomassValues)
progress=pad(num2str(floor(i/numel(biomassValues)*100)),3,'left');
fprintf('\b\b\b\b\b\b\b\b\b\b\b\b\b%s%% complete',progress);
model1 = setParam(model,'eq',biomassRxn,biomassValues(i));
sol = solveLP(model1,0,[],hsSol);
if (sol.stat > 0)
Expand All @@ -53,8 +51,8 @@
else
targetLowerBound(i) = NaN;
end
count(PB);
end
fprintf('\b\b\b\b\b\b\b\b\b\b\b\b\bCOMPLETE\n');

% Plot results
plot([biomassValues fliplr(biomassValues)],[targetUpperBound fliplr(targetLowerBound)],'blue','LineWidth',2);
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7 changes: 3 additions & 4 deletions core/runRobustnessAnalysis.m
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Expand Up @@ -50,16 +50,15 @@
redCost = zeros(nPoints,1);
controlFlux = linspace(solMin,solMax,nPoints)';

fprintf('Running robustness analysis... 0%% complete');

PB = ProgressBar2(length(controlFlux),'Running robustness analysis','cli');
for i=1:length(controlFlux)
progress=pad(num2str(floor(i/numel(controlFlux)*100)),3,'left');
fprintf('\b\b\b\b\b\b\b\b\b\b\b\b\b%s%% complete',progress);
modelControlled = setParam(baseModel,'eq',controlRxnIdx,controlFlux(i));
solControlled = solveLP(modelControlled);
objFlux(i) = solControlled.x(logical(modelControlled.c));
redCost(i) = solControlled.rCost(controlRxnIdx);
count(PB);
end
fprintf('\b\b\b\b\b\b\b\b\b\b\b\b\bCOMPLETE\n');

if plotRedCost
yyaxis right
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4 changes: 2 additions & 2 deletions doc/core/parallelPoolRAVEN.html
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Expand Up @@ -61,7 +61,7 @@ <h2><a name="_cross"></a>CROSS-REFERENCE INFORMATION <a href="#_top"><img alt="^
</ul>
This function is called by:
<ul style="list-style-image:url(../matlabicon.gif)">
<li><a href="findGeneDeletions.html" class="code" title="function [genes, fluxes, originalGenes, details, grRatioMuts]=findGeneDeletions(model,testType,analysisType,refModel,oeFactor)">findGeneDeletions</a> findGeneDeletions</li><li><a href="getAllowedBounds.html" class="code" title="function [minFluxes, maxFluxes, exitFlags]=getAllowedBounds(model,rxns,runParallel)">getAllowedBounds</a> getAllowedBounds</li><li><a href="randomSampling.html" class="code" title="function [solutions, goodRxns]=randomSampling(model,nSamples,replaceBoundsWithInf,supressErrors,runParallel,goodRxns,minFlux)">randomSampling</a> randomSampling</li></ul>
<li><a href="getAllowedBounds.html" class="code" title="function [minFluxes, maxFluxes, exitFlags]=getAllowedBounds(model,rxns,runParallel)">getAllowedBounds</a> getAllowedBounds</li><li><a href="randomSampling.html" class="code" title="function [solutions, goodRxns]=randomSampling(model,nSamples,replaceBoundsWithInf,supressErrors,runParallel,goodRxns,minFlux)">randomSampling</a> randomSampling</li></ul>
<!-- crossreference -->


Expand Down Expand Up @@ -115,7 +115,7 @@ <h2><a name="_source"></a>SOURCE CODE <a href="#_top"><img alt="^" border="0" sr
0046 <span class="keyword">else</span>
0047 pool = gcp(<span class="string">'nocreate'</span>);
0048 <span class="keyword">if</span> isempty(pool)
0049 parpool(IdleTimeout=120);
0049 parpool(<span class="string">'IdleTimeout'</span>,120)
0050 <span class="keyword">end</span>
0051 <span class="keyword">end</span>
0052 <span class="keyword">end</span>
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52 changes: 25 additions & 27 deletions doc/core/runDynamicFBA.html
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Expand Up @@ -158,7 +158,7 @@ <h2><a name="_source"></a>SOURCE CODE <a href="#_top"><img alt="^" border="0" sr
0076 biomassVec = biomass;
0077 timeVec(1) = 0;
0078 [~,hsSol]=solveLP(model,1);
0079 fprintf(<span class="string">'Running dynamic FBA analysis... 0%% complete'</span>);
0079 PB = ProgressBar2(nSteps,<span class="string">'Running dynamic FBA analysis'</span>,<span class="string">'cli'</span>);
0080 <span class="keyword">for</span> stepNo = 1:nSteps
0081 <span class="comment">% Run FBA</span>
0082 [sol,hsSol] = solveLP(model,1,[],hsSol);
Expand Down Expand Up @@ -189,32 +189,30 @@ <h2><a name="_source"></a>SOURCE CODE <a href="#_top"><img alt="^" border="0" sr
0107 model.lb(excInd) = -uptakeBound;
0108 timeVec(stepNo+1) = stepNo*timeStep;
0109
0110 progress=pad(num2str(floor(stepNo/nSteps*100)),3,<span class="string">'left'</span>);
0111 fprintf(<span class="string">'\b\b\b\b\b\b\b\b\b\b\b\b\b%s%% complete'</span>,progress);
0112 <span class="keyword">end</span>
0113 fprintf(<span class="string">'\b\b\b\b\b\b\b\b\b\b\b\b\bCOMPLETE\n'</span>);
0114
0115 selNonZero = any(concentrationMatrix&gt;0,2);
0116 concentrationMatrix = concentrationMatrix(selNonZero,:);
0117 excRxnNames = excRxnNames(selNonZero);
0118 selPlot = ismember(excRxnNames,plotRxns);
0119
0120 <span class="comment">% Plot concentrations as a function of time</span>
0121 clf
0122 subplot(1,2,1);
0123 plot(timeVec,biomassVec);
0124 axis tight
0125 title(<span class="string">'Biomass'</span>);
0126 xlabel(<span class="string">'Time (h)'</span>);
0127 ylabel(<span class="string">'Concentration (g/L)'</span>);
0128 subplot(1,2,2);
0129 plot(timeVec,concentrationMatrix(selPlot,:));
0130 axis tight
0131 title(<span class="string">'Substrates and/or products'</span>);
0132 xlabel(<span class="string">'Time (h)'</span>);
0133 ylabel(<span class="string">'Concentration (mmol/L)'</span>);
0134 legend(strrep(excRxnNames(selPlot),<span class="string">'EX_'</span>,<span class="string">''</span>));
0135 <span class="keyword">end</span></pre></div>
0110 count(PB);
0111 <span class="keyword">end</span>
0112
0113 selNonZero = any(concentrationMatrix&gt;0,2);
0114 concentrationMatrix = concentrationMatrix(selNonZero,:);
0115 excRxnNames = excRxnNames(selNonZero);
0116 selPlot = ismember(excRxnNames,plotRxns);
0117
0118 <span class="comment">% Plot concentrations as a function of time</span>
0119 clf
0120 subplot(1,2,1);
0121 plot(timeVec,biomassVec);
0122 axis tight
0123 title(<span class="string">'Biomass'</span>);
0124 xlabel(<span class="string">'Time (h)'</span>);
0125 ylabel(<span class="string">'Concentration (g/L)'</span>);
0126 subplot(1,2,2);
0127 plot(timeVec,concentrationMatrix(selPlot,:));
0128 axis tight
0129 title(<span class="string">'Substrates and/or products'</span>);
0130 xlabel(<span class="string">'Time (h)'</span>);
0131 ylabel(<span class="string">'Concentration (mmol/L)'</span>);
0132 legend(strrep(excRxnNames(selPlot),<span class="string">'EX_'</span>,<span class="string">''</span>));
0133 <span class="keyword">end</span></pre></div>
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75 changes: 37 additions & 38 deletions doc/core/runPhenotypePhasePlane.html
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Expand Up @@ -118,45 +118,44 @@ <h2><a name="_source"></a>SOURCE CODE <a href="#_top"><img alt="^" border="0" sr
0049 shadowPrices2 = zeros(nPts);
0050 [~,hsSol] = solveLP(model);
0051 <span class="comment">% Calulate points</span>
0052 fprintf(<span class="string">'Running PhPP analysis... 0%% complete'</span>);
0052 PB = ProgressBar2(nPts,<span class="string">'Running PhPP analysis'</span>,<span class="string">'cli'</span>);
0053 <span class="keyword">for</span> i = 1:nPts <span class="comment">%ind1</span>
0054 progress=pad(num2str(floor(i/nPts*100)),3,<span class="string">'left'</span>);
0055 fprintf(<span class="string">'\b\b\b\b\b\b\b\b\b\b\b\b\b%s%% complete'</span>,progress);
0056 <span class="keyword">for</span> j = 1:nPts <span class="comment">%ind2</span>
0057 model1 = <a href="setParam.html" class="code" title="function model=setParam(model, paramType, rxnList, params, var)">setParam</a>(model,<span class="string">'eq'</span>,controlRxn1,-1*ind1(i));
0058 model1 = <a href="setParam.html" class="code" title="function model=setParam(model, paramType, rxnList, params, var)">setParam</a>(model1,<span class="string">'eq'</span>,controlRxn2,-1*ind2(j));
0059 [fbasol,hsSol] = solveLP(model1,0,[],hsSol);
0060 <span class="keyword">try</span>
0061 growthRates(j,i) = fbasol.x(logical(model1.c));
0062 shadowPrices1(j,i) = fbasol.sPrice(metID1);
0063 shadowPrices2(j,i) = fbasol.sPrice(metID2);
0064 <span class="keyword">end</span>
0065 <span class="keyword">end</span>
0066 <span class="keyword">end</span>
0067 fprintf(<span class="string">'\b\b\b\b\b\b\b\b\b\b\b\b\bCOMPLETE\n'</span>);
0068
0069 <span class="comment">% Plot the points</span>
0070 figure(2);
0071 pcolor(ind1,ind2,shadowPrices1);
0072 xlabel(strrep(strcat(controlRxn1,<span class="string">' (mmol/g DW-hr)'</span>),<span class="string">'_'</span>,<span class="string">'\_'</span>)), ylabel(strrep(strcat(controlRxn2,<span class="string">' (mmol/g DW-hr)'</span>),<span class="string">'_'</span>,<span class="string">'\_'</span>)), zlabel(<span class="string">'growth rate (1/hr)'</span>);
0073 title([<span class="string">'Shadow price '</span> strrep(model.mets{metID1},<span class="string">'_'</span>,<span class="string">'-'</span>)]);
0074 colorbar();
0075 xticklabels(sprintfc(<span class="string">'%d'</span>, -xticks))
0076 yticklabels(sprintfc(<span class="string">'%d'</span>, -yticks))
0077 figure(3);
0078 pcolor(ind1,ind2,shadowPrices2);
0079 xlabel(strrep(strcat(controlRxn1,<span class="string">' (mmol/g DW-hr)'</span>),<span class="string">'_'</span>,<span class="string">'\_'</span>)), ylabel(strrep(strcat(controlRxn2,<span class="string">' (mmol/g DW-hr)'</span>),<span class="string">'_'</span>,<span class="string">'\_'</span>)), zlabel(<span class="string">'growth rate (1/hr)'</span>);
0080 title([<span class="string">'Shadow price '</span> strrep(model.mets{metID2},<span class="string">'_'</span>,<span class="string">'-'</span>)]);
0081 colorbar();
0082 xticklabels(sprintfc(<span class="string">'%d'</span>, -xticks))
0083 yticklabels(sprintfc(<span class="string">'%d'</span>, -yticks))
0084 figure(1);
0085 surfl(ind1,ind2,growthRates);
0086 xlabel(strrep(strcat(controlRxn1,<span class="string">' (mmol/g DW-hr)'</span>),<span class="string">'_'</span>,<span class="string">'\_'</span>)), ylabel(strrep(strcat(controlRxn2,<span class="string">' (mmol/g DW-hr)'</span>),<span class="string">'_'</span>,<span class="string">'\_'</span>)), zlabel(<span class="string">'growth rate (1/hr)'</span>);
0087 colormap(hsv(17));
0088 xticklabels(sprintfc(<span class="string">'%d'</span>, -xticks))
0089 yticklabels(sprintfc(<span class="string">'%d'</span>, -yticks))
0090 <span class="keyword">end</span></pre></div>
0054 <span class="keyword">for</span> j = 1:nPts <span class="comment">%ind2</span>
0055 model1 = <a href="setParam.html" class="code" title="function model=setParam(model, paramType, rxnList, params, var)">setParam</a>(model,<span class="string">'eq'</span>,controlRxn1,-1*ind1(i));
0056 model1 = <a href="setParam.html" class="code" title="function model=setParam(model, paramType, rxnList, params, var)">setParam</a>(model1,<span class="string">'eq'</span>,controlRxn2,-1*ind2(j));
0057 [fbasol,hsSol] = solveLP(model1,0,[],hsSol);
0058 <span class="keyword">try</span>
0059 growthRates(j,i) = fbasol.x(logical(model1.c));
0060 shadowPrices1(j,i) = fbasol.sPrice(metID1);
0061 shadowPrices2(j,i) = fbasol.sPrice(metID2);
0062 <span class="keyword">end</span>
0063 <span class="keyword">end</span>
0064 count(PB);
0065 <span class="keyword">end</span>
0066 fprintf(<span class="string">'\b\b\b\b\b\b\b\b\b\b\b\b\bCOMPLETE\n'</span>);
0067
0068 <span class="comment">% Plot the points</span>
0069 figure(2);
0070 pcolor(ind1,ind2,shadowPrices1);
0071 xlabel(strrep(strcat(controlRxn1,<span class="string">' (mmol/g DW-hr)'</span>),<span class="string">'_'</span>,<span class="string">'\_'</span>)), ylabel(strrep(strcat(controlRxn2,<span class="string">' (mmol/g DW-hr)'</span>),<span class="string">'_'</span>,<span class="string">'\_'</span>)), zlabel(<span class="string">'growth rate (1/hr)'</span>);
0072 title([<span class="string">'Shadow price '</span> strrep(model.mets{metID1},<span class="string">'_'</span>,<span class="string">'-'</span>)]);
0073 colorbar();
0074 xticklabels(sprintfc(<span class="string">'%d'</span>, -xticks))
0075 yticklabels(sprintfc(<span class="string">'%d'</span>, -yticks))
0076 figure(3);
0077 pcolor(ind1,ind2,shadowPrices2);
0078 xlabel(strrep(strcat(controlRxn1,<span class="string">' (mmol/g DW-hr)'</span>),<span class="string">'_'</span>,<span class="string">'\_'</span>)), ylabel(strrep(strcat(controlRxn2,<span class="string">' (mmol/g DW-hr)'</span>),<span class="string">'_'</span>,<span class="string">'\_'</span>)), zlabel(<span class="string">'growth rate (1/hr)'</span>);
0079 title([<span class="string">'Shadow price '</span> strrep(model.mets{metID2},<span class="string">'_'</span>,<span class="string">'-'</span>)]);
0080 colorbar();
0081 xticklabels(sprintfc(<span class="string">'%d'</span>, -xticks))
0082 yticklabels(sprintfc(<span class="string">'%d'</span>, -yticks))
0083 figure(1);
0084 surfl(ind1,ind2,growthRates);
0085 xlabel(strrep(strcat(controlRxn1,<span class="string">' (mmol/g DW-hr)'</span>),<span class="string">'_'</span>,<span class="string">'\_'</span>)), ylabel(strrep(strcat(controlRxn2,<span class="string">' (mmol/g DW-hr)'</span>),<span class="string">'_'</span>,<span class="string">'\_'</span>)), zlabel(<span class="string">'growth rate (1/hr)'</span>);
0086 colormap(hsv(17));
0087 xticklabels(sprintfc(<span class="string">'%d'</span>, -xticks))
0088 yticklabels(sprintfc(<span class="string">'%d'</span>, -yticks))
0089 <span class="keyword">end</span></pre></div>
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52 changes: 25 additions & 27 deletions doc/core/runProductionEnvelope.html
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Original file line number Diff line number Diff line change
Expand Up @@ -92,36 +92,34 @@ <h2><a name="_source"></a>SOURCE CODE <a href="#_top"><img alt="^" border="0" sr
0033 targetUpperBound = nan(1,numel(biomassValues));
0034 targetLowerBound = nan(1,numel(biomassValues));
0035
0036 fprintf(<span class="string">'Creating production envelope... 0%% complete'</span>);
0036 PB = ProgressBar2(length(biomassValues),<span class="string">'Creating production envelope'</span>,<span class="string">'cli'</span>);
0037 <span class="comment">% Max/min for target production</span>
0038 model = <a href="setParam.html" class="code" title="function model=setParam(model, paramType, rxnList, params, var)">setParam</a>(model,<span class="string">'obj'</span>,targetRxn,1);
0039 <span class="keyword">for</span> i = 1:length(biomassValues)
0040 progress=pad(num2str(floor(i/numel(biomassValues)*100)),3,<span class="string">'left'</span>);
0041 fprintf(<span class="string">'\b\b\b\b\b\b\b\b\b\b\b\b\b%s%% complete'</span>,progress);
0042 model1 = <a href="setParam.html" class="code" title="function model=setParam(model, paramType, rxnList, params, var)">setParam</a>(model,<span class="string">'eq'</span>,biomassRxn,biomassValues(i));
0043 sol = solveLP(model1,0,[],hsSol);
0044 <span class="keyword">if</span> (sol.stat &gt; 0)
0045 targetUpperBound(i) = sol.x(logical(model.c));
0046 <span class="keyword">else</span>
0047 targetUpperBound(i) = NaN;
0048 <span class="keyword">end</span>
0049 model1.c = -model1.c;
0050 sol = solveLP(model1,0,[],hsSol);
0051 <span class="keyword">if</span> (sol.stat &gt; 0)
0052 targetLowerBound(i) = sol.x(logical(model1.c));
0053 <span class="keyword">else</span>
0054 targetLowerBound(i) = NaN;
0055 <span class="keyword">end</span>
0056 <span class="keyword">end</span>
0057 fprintf(<span class="string">'\b\b\b\b\b\b\b\b\b\b\b\b\bCOMPLETE\n'</span>);
0058
0059 <span class="comment">% Plot results</span>
0060 plot([biomassValues fliplr(biomassValues)],[targetUpperBound fliplr(targetLowerBound)],<span class="string">'blue'</span>,<span class="string">'LineWidth'</span>,2);
0061 axis tight;
0062 ylabel([strrep(targetRxn,<span class="string">'_'</span>,<span class="string">'-'</span>) <span class="string">' (mmol/gDW h)'</span>]);
0063 xlabel(<span class="string">'Growth rate (1/h)'</span>);
0064 targetValues = [targetLowerBound; targetUpperBound];
0065 <span class="keyword">end</span></pre></div>
0040 model1 = <a href="setParam.html" class="code" title="function model=setParam(model, paramType, rxnList, params, var)">setParam</a>(model,<span class="string">'eq'</span>,biomassRxn,biomassValues(i));
0041 sol = solveLP(model1,0,[],hsSol);
0042 <span class="keyword">if</span> (sol.stat &gt; 0)
0043 targetUpperBound(i) = sol.x(logical(model.c));
0044 <span class="keyword">else</span>
0045 targetUpperBound(i) = NaN;
0046 <span class="keyword">end</span>
0047 model1.c = -model1.c;
0048 sol = solveLP(model1,0,[],hsSol);
0049 <span class="keyword">if</span> (sol.stat &gt; 0)
0050 targetLowerBound(i) = sol.x(logical(model1.c));
0051 <span class="keyword">else</span>
0052 targetLowerBound(i) = NaN;
0053 <span class="keyword">end</span>
0054 count(PB);
0055 <span class="keyword">end</span>
0056
0057 <span class="comment">% Plot results</span>
0058 plot([biomassValues fliplr(biomassValues)],[targetUpperBound fliplr(targetLowerBound)],<span class="string">'blue'</span>,<span class="string">'LineWidth'</span>,2);
0059 axis tight;
0060 ylabel([strrep(targetRxn,<span class="string">'_'</span>,<span class="string">'-'</span>) <span class="string">' (mmol/gDW h)'</span>]);
0061 xlabel(<span class="string">'Growth rate (1/h)'</span>);
0062 targetValues = [targetLowerBound; targetUpperBound];
0063 <span class="keyword">end</span></pre></div>
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