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DrPaulSharpDrPaulSharp
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Refactors contrasts class and struct (#179)
* Renames field of "priors" struct * Renames "nba" and "nbs" to "bulkIn" and "bulkOut" respectively in "contrastsClass.m" * Refactors "getNames" routines * Renames fields in contrasts struct * Renames contrasts fields in "parseClassToStructs" * Renames "packpriors.m" and "unpackpriors.m" to camel case * Fixes priors bug
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‎3rdParty/mcmcstat/%runDram.m

Lines changed: 3 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -2,14 +2,14 @@
22
debug = 0;
33

44
checks = controls.checks;
5-
[problemDef,fitNames] = packparams(problemDef,problemDefCells,problemDefLimits,checks);
5+
[problemDef,fitNames] = packParams(problemDef,problemDefCells,problemDefLimits,checks);
66
%fitPriors = packPriors(priors,checks);
77

88
% Seed the Random Number Generator
99
rng(0);
1010

1111

12-
%fitPriors = packpriors(priors,checks);
12+
%fitPriors = packPriors(priors,checks);
1313

1414
%First deal with priors.
1515
%Make uniform priors from the
@@ -66,7 +66,7 @@
6666
bayesResults.predlims = output.predlims;
6767

6868
problemDef.fitpars = output.bestPars;
69-
problemDef = unpackparams(problemDef,controls);
69+
problemDef = unpackParams(problemDef,controls);
7070
[problem,result] = reflectivityCalculation(problemDef,problemDefCells,controls);
7171

7272
% Pre-processor directives for Matlab Coder.

‎3rdParty/mcmcstat/refModel.m

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -36,7 +36,7 @@
3636
problemDefCells = problem{4};
3737

3838
problemDef.fitpars = pars;
39-
problemDef = unpackparams(problemDef,controls);
39+
problemDef = unpackParams(problemDef,controls);
4040
[problem,result] = reflectivityCalculation(problemDef,problemDefCells,controls);
4141

4242
ySim = result{1}{contrast};

‎3rdParty/mcmcstat/refModel_scaled.m

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -43,7 +43,7 @@
4343
pars = unscalePars(pars,constr);
4444

4545
problemDef.fitpars = pars;
46-
problemDef = unpackparams(problemDef,controls);
46+
problemDef = unpackParams(problemDef,controls);
4747
[problem,result] = reflectivityCalculation(problemDef,problemDefCells,controls);
4848

4949
ySim = result{1}{contrast};

‎3rdParty/mcmcstat/reflectivity_fitModel.m

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -13,7 +13,7 @@
1313

1414

1515
problemDef.fitpars = pars;
16-
problemDef = unpackparams(problemDef,controls);
16+
problemDef = unpackParams(problemDef,controls);
1717
%setappdata(0,'problem',problem);
1818
%problem = reflectivityCalculation(problem);
1919
[problemDef,result] = reflectivityCalculation(problemDef,problemDefCells,controls);

‎3rdParty/mcmcstat/reflectivity_fitModel_scaled.m

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -14,7 +14,7 @@
1414
pars = unscalePars(pars,constr);
1515

1616
problemDef.fitpars = pars;
17-
problemDef = unpackparams(problemDef,controls);
17+
problemDef = unpackParams(problemDef,controls);
1818
%setappdata(0,'problem',problem);
1919
%problem = reflectivityCalculation(problem);
2020
[problemDef,result] = reflectivityCalculation(problemDef,problemDefCells,controls);

‎3rdParty/mcmcstat/runBayes.m

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -90,7 +90,7 @@
9090
% outSld = mcmcpred_compile_sld(results,chain,[],data,problem,500);
9191
%
9292
% problemDef.fitpars = output.bestPars;
93-
% problemDef = unpackparams(problemDef,controls);
93+
% problemDef = unpackParams(problemDef,controls);
9494
% [problem,result] = reflectivityCalculation(problemDef,problemDefCells,controls);
9595
%
9696
% output.bestFits = result{1};

‎3rdParty/mcmcstat/runDram.m

Lines changed: 52 additions & 52 deletions
Original file line numberDiff line numberDiff line change
@@ -5,13 +5,13 @@
55
%coder.varsize('problemDef.contrastBacks',[1 Inf],[0 1]);
66

77
checks = controls.checks;
8-
[problemDef,fitNames] = packparams(problemDef,problemDefCells,problemDefLimits,checks);
8+
[problemDef,fitNames] = packParams(problemDef,problemDefCells,problemDefLimits,checks);
99
%fitPriors = packPriors(priors,checks);
1010

1111
% Seed the Random Number Generator
1212
rng(0);
1313

14-
%fitPriors = packpriors(priors,checks);
14+
%fitPriors = packPriors(priors,checks);
1515

1616
%First deal with priors.
1717
prior = {};
@@ -23,83 +23,83 @@
2323
params{i} = cell(1,6);
2424
end
2525

26-
% We have a list of 'fitPars' which is created by packparams.m
27-
% packparams doesn't do the same for our priors however. So we need
26+
% We have a list of 'fitPars' which is created by packParams.m
27+
% packParams doesn't do the same for our priors however. So we need
2828
% to make an array of the priors for the fitted parameters
2929
% so that we can then build the params array for the algorithm
3030

3131
% Put all the priors into one array
3232
% ** This won't work for code generation **
33-
% priorsGroup = [priors.paramPriors ; ...
34-
% priors.backgroundParamPriors ; ...
35-
% priors.resolutionParamPriors ; ...
36-
% priors.bulkInPriors ; ...
37-
% priors.bulkOutPriors ; ...
38-
% priors.qzshiftPriors ;
39-
% priors.scalefactorPriors];
40-
41-
% totalNumber = size(priors.paramPriors,1) + size(priors.backgroundParamPriors,1) + ...
42-
% size(priors.resolutionParamPriors,1) + size(priors.bulkInPriors,1) + size(priors.bulkOutPriors,1) + ...
43-
% size(priors.qzshiftPriors,1) + size(priors.scalefactorPriors,1);
33+
% priorsGroup = [priors.param ; ...
34+
% priors.backgroundParam ; ...
35+
% priors.resolutionParam ; ...
36+
% priors.bulkIn ; ...
37+
% priors.bulkOut ; ...
38+
% priors.qzshift ;
39+
% priors.scalefactor];
40+
41+
% totalNumber = size(priors.param,1) + size(priors.backgroundParam,1) + ...
42+
% size(priors.resolutionParam,1) + size(priors.bulkIn,1) + size(priors.bulkOut,1) + ...
43+
% size(priors.qzshift,1) + size(priors.scalefactor,1);
4444

4545
% Expand the individual cells..
4646
%allPriors = cell(totalNumber,2); %Will be a char type....
4747
% allPriors = strings(totalNumber,2);
4848
% allPriorVals = cell(totalNumber,2);
4949
% cellCount = 1;
50-
% for i = 1:size(priors.paramPriors,1)
51-
% allPriors(cellCount,1) = string(priors.paramPriors{i}{1});
52-
% allPriors(cellCount,2) = string(priors.paramPriors{i}{2});
53-
% allPriorVals{cellCount,1} = priors.paramPriors{i}{3};
54-
% allPriorVals{cellCount,2} = priors.paramPriors{i}{4};
50+
% for i = 1:size(priors.param,1)
51+
% allPriors(cellCount,1) = string(priors.param{i}{1});
52+
% allPriors(cellCount,2) = string(priors.param{i}{2});
53+
% allPriorVals{cellCount,1} = priors.param{i}{3};
54+
% allPriorVals{cellCount,2} = priors.param{i}{4};
5555
% cellCount = cellCount + 1;
5656
% end
5757
%
58-
% for i = 1:size(priors.backgroundParamPriors,1)
59-
% allPriors(cellCount,1) = priors.backgroundParamPriors{i}{1};
60-
% allPriors(cellCount,2) = priors.backgroundParamPriors{i}{2};
61-
% allPriorVals{cellCount,1} = priors.backgroundParamPriors{i}{3};
62-
% allPriorVals{cellCount,2} = priors.backgroundParamPriors{i}{4};
58+
% for i = 1:size(priors.backgroundParam,1)
59+
% allPriors(cellCount,1) = priors.backgroundParam{i}{1};
60+
% allPriors(cellCount,2) = priors.backgroundParam{i}{2};
61+
% allPriorVals{cellCount,1} = priors.backgroundParam{i}{3};
62+
% allPriorVals{cellCount,2} = priors.backgroundParam{i}{4};
6363
% cellCount = cellCount + 1;
6464
% end
6565
%
66-
% for i = 1:size(priors.resolutionParamPriors,1)
67-
% allPriors(cellCount,1) = priors.resolutionParamPriors{i}{1};
68-
% allPriors(cellCount,2) = priors.resolutionParamPriors{i}{2};
69-
% allPriorVals{cellCount,1} = priors.resolutionParamPriors{i}{3};
70-
% allPriorVals{cellCount,2} = priors.resolutionParamPriors{i}{4};
66+
% for i = 1:size(priors.resolutionParam,1)
67+
% allPriors(cellCount,1) = priors.resolutionParam{i}{1};
68+
% allPriors(cellCount,2) = priors.resolutionParam{i}{2};
69+
% allPriorVals{cellCount,1} = priors.resolutionParam{i}{3};
70+
% allPriorVals{cellCount,2} = priors.resolutionParam{i}{4};
7171
% cellCount = cellCount + 1;
7272
% end
7373
%
74-
% for i = 1:size(priors.bulkInPriors,1)
75-
% allPriors(cellCount,1) = priors.bulkInPriors{i}{1};
76-
% allPriors(cellCount,2) = priors.bulkInPriors{i}{2};
77-
% allPriorVals{cellCount,1} = priors.bulkInPriors{i}{3};
78-
% allPriorVals{cellCount,2} = priors.bulkInPriors{i}{4};
74+
% for i = 1:size(priors.bulkIn,1)
75+
% allPriors(cellCount,1) = priors.bulkIn{i}{1};
76+
% allPriors(cellCount,2) = priors.bulkIn{i}{2};
77+
% allPriorVals{cellCount,1} = priors.bulkIn{i}{3};
78+
% allPriorVals{cellCount,2} = priors.bulkIn{i}{4};
7979
% cellCount = cellCount + 1;
8080
% end
8181
%
82-
% for i = 1:size(priors.bulkOutPriors,1)
83-
% allPriors(cellCount,1) = priors.bulkOutPriors{i}{1};
84-
% allPriors(cellCount,2) = priors.bulkOutPriors{i}{2};
85-
% allPriorVals{cellCount,1} = priors.bulkOutPriors{i}{3};
86-
% allPriorVals{cellCount,2} = priors.bulkOutPriors{i}{4};
82+
% for i = 1:size(priors.bulkOut,1)
83+
% allPriors(cellCount,1) = priors.bulkOut{i}{1};
84+
% allPriors(cellCount,2) = priors.bulkOut{i}{2};
85+
% allPriorVals{cellCount,1} = priors.bulkOut{i}{3};
86+
% allPriorVals{cellCount,2} = priors.bulkOut{i}{4};
8787
% cellCount = cellCount + 1;
8888
% end
8989
%
90-
% for i = 1:size(priors.qzshiftPriors,1)
91-
% allPriors(cellCount,1) = priors.qzshiftPriors{i}{1};
92-
% allPriors(cellCount,2) = priors.qzshiftPriors{i}{2};
93-
% allPriorVals{cellCount,1} = priors.qzshiftPriors{i}{3};
94-
% allPriorVals{cellCount,2} = priors.qzshiftPriors{i}{4};
90+
% for i = 1:size(priors.qzshift,1)
91+
% allPriors(cellCount,1) = priors.qzshift{i}{1};
92+
% allPriors(cellCount,2) = priors.qzshift{i}{2};
93+
% allPriorVals{cellCount,1} = priors.qzshift{i}{3};
94+
% allPriorVals{cellCount,2} = priors.qzshift{i}{4};
9595
% cellCount = cellCount + 1;
9696
% end
9797
%
98-
% for i = 1:size(priors.scalefactorPriors,1)
99-
% allPriors(cellCount,1) = priors.scalefactorPriors{i}{1};
100-
% allPriors(cellCount,2) = priors.scalefactorPriors{i}{2};
101-
% allPriorVals{cellCount,1} = priors.scalefactorPriors{i}{3};
102-
% allPriorVals{cellCount,2} = priors.scalefactorPriors{i}{4};
98+
% for i = 1:size(priors.scalefactor,1)
99+
% allPriors(cellCount,1) = priors.scalefactor{i}{1};
100+
% allPriors(cellCount,2) = priors.scalefactor{i}{2};
101+
% allPriorVals{cellCount,1} = priors.scalefactor{i}{3};
102+
% allPriorVals{cellCount,2} = priors.scalefactor{i}{4};
103103
% cellCount = cellCount + 1;
104104
% end
105105

@@ -171,15 +171,15 @@
171171
%
172172
% % Calulate Max best fit curves
173173
% problemDef.fitpars = bestPars_max;
174-
% problemDef = unpackparams(problemDef,controls);
174+
% problemDef = unpackParams(problemDef,controls);
175175
% [outProblem,result] = reflectivityCalculation(problemDef,problemDefCells,controls);
176176
% bestFitMax_Ref = result(1);
177177
% bestFitMax_Sld = result(5);
178178
% bestFitMax_chi = outProblem.calculations.sum_chi;
179179
%
180180
% % Calculate 'mean' best fit curves
181181
% problemDef.fitpars = bestPars_mean;
182-
% problemDef = unpackparams(problemDef,controls);
182+
% problemDef = unpackParams(problemDef,controls);
183183
% [outProblem,result] = reflectivityCalculation(problemDef,problemDefCells,controls);
184184
% bestFitMean_Ref = result(1);
185185
% bestFitMean_Sld = result(5);

‎3rdParty/mcmcstat/sldModel.m

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -31,7 +31,7 @@
3131
controls.calcSldDuringFit = true;
3232

3333
problemDef.fitpars = pars;
34-
problemDef = unpackparams(problemDef,controls);
34+
problemDef = unpackParams(problemDef,controls);
3535
[~,result] = reflectivityCalculation(problemDef,problemDefCells,controls);
3636

3737
sld = result{5}{contrast};

‎3rdParty/paramonte/pmLogFunction.m

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -23,7 +23,7 @@
2323
problem = unscalePars(problem);
2424
end
2525

26-
problem = unpackparams(problem,obj.controls);
26+
problem = unpackParams(problem,obj.controls);
2727

2828
[outProblem,~] = reflectivityCalculation_mex(problem,obj.problemDefCells,obj.controls);
2929
chi = outProblem.calculations.sum_chi;

‎3rdParty/paramonte/processParamonteRuns.m

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -7,7 +7,7 @@
77

88
[problemDef,problemDefCells,problemDefLimits,~,controls] = parseClassToStructs(problem,controls);
99

10-
[problemDef,fitNames] = packparams(problemDef,problemDefCells,problemDefLimits,controls.checks);
10+
[problemDef,fitNames] = packParams(problemDef,problemDefCells,problemDefLimits,controls.checks);
1111

1212
pm = paramonte();
1313
pmpd = pm.ParaDRAM();
@@ -55,7 +55,7 @@
5555

5656
result = mergeStructs(result,bayesResults);
5757

58-
[~,fitNames] = packparams(problemDef,problemDefCells,problemDefLimits,controls.checks);
58+
[~,fitNames] = packParams(problemDef,problemDefCells,problemDefLimits,controls.checks);
5959
result.fitNames = fitNames;
6060

6161
outProblemDef = parseOutToProjectClass(problem,problemDef);

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