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Unify variable naming convention #182

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merged 13 commits into from
Dec 1, 2023
Merged

Unify variable naming convention #182

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1f5918f
Renames contrasts variables in target functions
DrPaulSharp Nov 30, 2023
43822ae
Renames fields in "problemDef" struct
DrPaulSharp Nov 30, 2023
670fc29
Replaces "nbair" with "bulkIn and "nbsub" with "bulkOut"
DrPaulSharp Nov 30, 2023
366f0f8
Renames variables in tests
DrPaulSharp Nov 30, 2023
064f372
Changes "sf" to "scalefactor" in target functions
DrPaulSharp Nov 30, 2023
cbc04c6
Changes "qshift" to "qzshift" in target functions
DrPaulSharp Nov 30, 2023
750616f
Tidies up "backSort.m" routine
DrPaulSharp Nov 30, 2023
c3abfb9
Renames "nba" and "nbs" to "bulkIn" and "bulkOut" respectively in tar…
DrPaulSharp Nov 30, 2023
bcfc20e
Restores use of "nba" and "nbs" as inputs in "processCustomFuncion.m"…
DrPaulSharp Nov 30, 2023
d68490e
Renames "nba" and "nbs" to "bulkIn" and "bulkOut" respectively in uti…
DrPaulSharp Nov 30, 2023
c63a777
Fixes typos
DrPaulSharp Nov 30, 2023
b2c34cb
Addresses review comments and fixes bugs
DrPaulSharp Dec 1, 2023
9d11d26
Tidies up code
DrPaulSharp Dec 1, 2023
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10 changes: 5 additions & 5 deletions 3rdParty/mcmcstat/%runDram.m
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Original file line number Diff line number Diff line change
Expand Up @@ -71,12 +71,12 @@

% Pre-processor directives for Matlab Coder.
coder.varsize('problem.ssubs',[Inf 1],[1 0]);
coder.varsize('problem.backgrounds',[Inf 1],[1 0]);
coder.varsize('problem.qshifts',[Inf 1],[1 0]);
coder.varsize('problem.backgroundParams',[Inf 1],[1 0]);
coder.varsize('problem.qzshifts',[Inf 1],[1 0]);
coder.varsize('problem.scalefactors',[Inf 1],[1 0]);
coder.varsize('problem.nbairs',[Inf 1],[1 0]);
coder.varsize('problem.nbsubs',[Inf 1],[1 0]);
coder.varsize('problem.resolutions',[Inf 1],[1 0]);
coder.varsize('problem.bulkIn',[Inf 1],[1 0]);
coder.varsize('problem.bulkOut',[Inf 1],[1 0]);
coder.varsize('problem.resolutionParams',[Inf 1],[1 0]);
coder.varsize('problem.ssubs',[Inf 1],[1 0]);
coder.varsize('problem.calculations.all_chis',[Inf 1],[1 0]);
coder.varsize('problem.calculations.sum_chi',[1 1],[0 0]);
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10 changes: 5 additions & 5 deletions API/RATMain.m
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Expand Up @@ -9,12 +9,12 @@
preAlloc = zeros(numberOfContrasts,1);

problem = struct('ssubs',preAlloc,...
'backgrounds',preAlloc,...
'qshifts',preAlloc,...
'backgroundParams',preAlloc,...
'qzshifts',preAlloc,...
'scalefactors',preAlloc,...
'nbairs',preAlloc,...
'nbsubs',preAlloc,...
'resolutions',preAlloc,...
'bulkIn',preAlloc,...
'bulkOut',preAlloc,...
'resolutionParams',preAlloc,...
'calculations',struct('all_chis',preAlloc,'sum_chi',0),...
'allSubRough',preAlloc,...
'resample',preAlloc);
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12 changes: 6 additions & 6 deletions API/parseClassToStructs.m
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Expand Up @@ -319,12 +319,12 @@
problemDef.contrastBulkIns = inputStruct.contrastBulkIns;
problemDef.contrastBulkOuts = inputStruct.contrastBulkOuts;
problemDef.contrastResolutions = contrastRes;
problemDef.backs = inputStruct.backgroundParamValues; %inputStruct.backgrounds; % **** note backPar workaround (todo) ****
problemDef.shifts = inputStruct.qzshiftValues;
problemDef.sf = inputStruct.scalefactorValues;
problemDef.nba = inputStruct.bulkInValues;
problemDef.nbs = inputStruct.bulkOutValues;
problemDef.res = inputStruct.resolutionParamValues; %inputStruct.resolutions; % **** note resolutionParam workaround (todo) ****
problemDef.backgroundParams = inputStruct.backgroundParamValues; %inputStruct.backgrounds; % **** note backPar workaround (todo) ****
problemDef.qzshifts = inputStruct.qzshiftValues;
problemDef.scalefactors = inputStruct.scalefactorValues;
problemDef.bulkIn = inputStruct.bulkInValues;
problemDef.bulkOut = inputStruct.bulkOutValues;
problemDef.resolutionParams = inputStruct.resolutionParamValues; %inputStruct.resolutions; % **** note resolutionParam workaround (todo) ****
problemDef.params = inputStruct.paramValues;
problemDef.numberOfLayers = inputStruct.numberOfLayers;
problemDef.modelType = inputStruct.modelType;
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51 changes: 26 additions & 25 deletions API/parseOutToProjectClass.m
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@@ -1,51 +1,52 @@
function outProblemDef = parseOutToProjectClass(problemDefInput,outProblemStruct)


%Reconstruct the problemDef class as an output
%Using the outputs from the calculation(s)
outProblemDef = problemDefInput;

%(1) Parameters
pars = outProblemStruct.params;
for i = 1:length(pars)
outProblemDef.setParameterValue(i,pars(i));
params = outProblemStruct.params;
for i = 1:length(params)
outProblemDef.setParameterValue(i,params(i));
end

%(2) Backgrounds
backs = outProblemStruct.backs;
for i = 1:length(backs)
outProblemDef.setBackgroundParamValue(i,backs(i));
backgroundParams = outProblemStruct.backgroundParams;
for i = 1:length(backgroundParams)
outProblemDef.setBackgroundParamValue(i,backgroundParams(i));
end

%(3) Scalefactors
scales = outProblemStruct.sf;
for i = 1:length(scales)
outProblemDef.setScalefactor(i,'value',scales(i));
scalefactors = outProblemStruct.scalefactors;
for i = 1:length(scalefactors)
outProblemDef.setScalefactor(i,'value',scalefactors(i));
end

%(4) Qzshifts
% shifts = outProblemStruct.shifts;
% outProblemDef.qzshifts = shifts;
qzshifts = outProblemStruct.qzshifts;
for i = 1:length(qzshifts)
outProblemDef.setQzshift(i,'value',qzshifts(i));
end

%(4) Nbairs
nbairs = outProblemStruct.nba;
for i = 1:length(nbairs)
outProblemDef.setBulkIn(i,'value',nbairs(i));
%(5) Bulk In
bulkIns = outProblemStruct.bulkIn;
for i = 1:length(bulkIns)
outProblemDef.setBulkIn(i,'value',bulkIns(i));
end

%(5) Nbsubs
nbsubs = outProblemStruct.nbs;
for i = 1:length(nbsubs)
outProblemDef.setBulkOut(i,'value',nbsubs(i));
%(6) Bulk Out
bulkOuts = outProblemStruct.bulkOut;
for i = 1:length(bulkOuts)
outProblemDef.setBulkOut(i,'value',bulkOuts(i));
end

%(5) Resolutions
resol = outProblemStruct.res;
for i = 1:length(resol)
outProblemDef.setResolutionParam(i,'value',resol(i));
%(7) Resolutions
resolutionParams = outProblemStruct.resolutionParams;
for i = 1:length(resolutionParams)
outProblemDef.setResolutionParam(i,'value',resolutionParams(i));
end

% (6) Domain ratio
% (8) Domain ratio
if strcmpi(outProblemStruct.TF,'domains')
domainRatios = outProblemStruct.domainRatio;
for i = 1:length(domainRatios)
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12 changes: 6 additions & 6 deletions compile/fullCompile/makeCompileArgsFull.m
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Expand Up @@ -23,12 +23,12 @@
ARGS_1_1.contrastBulkIns = coder.typeof(0,[1 maxArraySize],[0 1]);
ARGS_1_1.contrastBulkOuts = coder.typeof(0,[1 maxArraySize],[0 1]);
ARGS_1_1.contrastResolutions = coder.typeof(0,[1 maxArraySize],[0 1]);
ARGS_1_1.backs = coder.typeof(0,[1 maxArraySize],[0 1]);
ARGS_1_1.shifts = coder.typeof(0,[1 maxArraySize],[0 1]);
ARGS_1_1.sf = coder.typeof(0,[1 maxArraySize],[0 1]);
ARGS_1_1.nba = coder.typeof(0,[1 maxArraySize],[0 1]);
ARGS_1_1.nbs = coder.typeof(0,[1 maxArraySize],[0 1]);
ARGS_1_1.res = coder.typeof(0,[1 maxArraySize],[0 1]);
ARGS_1_1.backgroundParams = coder.typeof(0,[1 maxArraySize],[0 1]);
ARGS_1_1.qzshifts = coder.typeof(0,[1 maxArraySize],[0 1]);
ARGS_1_1.scalefactors = coder.typeof(0,[1 maxArraySize],[0 1]);
ARGS_1_1.bulkIn = coder.typeof(0,[1 maxArraySize],[0 1]);
ARGS_1_1.bulkOut = coder.typeof(0,[1 maxArraySize],[0 1]);
ARGS_1_1.resolutionParams = coder.typeof(0,[1 maxArraySize],[0 1]);
ARGS_1_1.params = coder.typeof(0,[1 maxArraySize],[0 1]);
ARGS_1_1.numberOfLayers = coder.typeof(0);
ARGS_1_1.modelType = coder.typeof('X',[1 maxArraySize],[0 1]);
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12 changes: 6 additions & 6 deletions compile/reflectivityCalculation/makeCompileArgs.m
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Expand Up @@ -23,12 +23,12 @@
ARGS_1_1.contrastBulkIns = coder.typeof(0,[1 maxArraySize],[0 1]);
ARGS_1_1.contrastBulkOuts = coder.typeof(0,[1 maxArraySize],[0 1]);
ARGS_1_1.contrastResolutions = coder.typeof(0,[1 maxArraySize],[0 1]);
ARGS_1_1.backs = coder.typeof(0,[1 maxArraySize],[0 1]);
ARGS_1_1.shifts = coder.typeof(0,[1 maxArraySize],[0 1]);
ARGS_1_1.sf = coder.typeof(0,[1 maxArraySize],[0 1]);
ARGS_1_1.nba = coder.typeof(0,[1 maxArraySize],[0 1]);
ARGS_1_1.nbs = coder.typeof(0,[1 maxArraySize],[0 1]);
ARGS_1_1.res = coder.typeof(0,[1 maxArraySize],[0 1]);
ARGS_1_1.backgroundParams = coder.typeof(0,[1 maxArraySize],[0 1]);
ARGS_1_1.qzshifts = coder.typeof(0,[1 maxArraySize],[0 1]);
ARGS_1_1.scalefactors = coder.typeof(0,[1 maxArraySize],[0 1]);
ARGS_1_1.bulkIn = coder.typeof(0,[1 maxArraySize],[0 1]);
ARGS_1_1.bulkOut = coder.typeof(0,[1 maxArraySize],[0 1]);
ARGS_1_1.resolutionParams = coder.typeof(0,[1 maxArraySize],[0 1]);
ARGS_1_1.params = coder.typeof(0,[1 maxArraySize],[0 1]);
ARGS_1_1.numberOfLayers = coder.typeof(0);
ARGS_1_1.modelType = coder.typeof('X',[1 maxArraySize],[0 1]);
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2 changes: 1 addition & 1 deletion minimisers/generalUtils/checkBounds.m
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Expand Up @@ -24,7 +24,7 @@

fitWhichNbas = problem.fitBulkIn;
fittingNbas = problem.nba(find(fitWhichNbas));
fittingNbaConstr = problem.nbairs_constr(find(fitWhichNbas),:);
fittingNbaConstr = problem.bulkIns_constr(find(fitWhichNbas),:);
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please remove the underscore

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I'll get on it, but we should be removing this file, as per #175.

fittingNbaNames = problem.nbaNames(find(fitWhichNbas));


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