Fixes memory bugs and removes unused code and routines (#264)

* Fixes bug and removes unused routines * Resolves seg faults and removes unnecessary code * Adds test for running RAT without any layers * Adjusts build
RascalSoftware · Sep 11, 2024 · 253fde5 · 253fde5
1 parent b3cf660
commit 253fde5
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Showing 32 changed files with 29 additions and 475 deletions.
diff --git a/API/parseClassToStructs.m b/API/parseClassToStructs.m
@@ -90,34 +90,16 @@
 %        Each cell is {1 x Inf char}
 
 
-% First parse the class to a structure variable.
+%% First parse the class to a structure variable.
 inputStruct = project.toStruct();
 
-%% Start by removing the cell arrays
-contrastLayers = inputStruct.contrastLayers;
-layerDetails = inputStruct.layerDetails;
-
-% If any of the contrastLayers are empty, replace the empty cells by zero
-% thickness layers
-for i = 1:length(contrastLayers)
-    thisLayer = contrastLayers{i};
-    if isempty(thisLayer)
-        contrastLayers{i} = 0;
-    end
-end
-
-% Do the same for layerDetails
-if isempty(layerDetails)
-    layerDetails = {0};
-end
-
-% Pull out all the cell arrays (except priors) into one array
+%% Pull out all the cell arrays (except priors) into one array
 problemCells{1} = inputStruct.contrastRepeatSLDs;
 problemCells{2} = inputStruct.data;
 problemCells{3} = inputStruct.dataLimits;
 problemCells{4} = inputStruct.simLimits;
-problemCells{5} = contrastLayers;
-problemCells{6} = layerDetails;
+problemCells{5} = inputStruct.contrastLayers;
+problemCells{6} = inputStruct.layerDetails;
 problemCells{7} = inputStruct.paramNames;
 problemCells{8} = inputStruct.backgroundParamNames;
 problemCells{9} = inputStruct.scalefactorNames;
@@ -137,39 +119,15 @@
 
 % Now deal with domains cell arrays
 if isa(project, 'domainsClass') && isa(project.domainContrasts, 'domainContrastsClass')
-
-    domainContrastLayers = inputStruct.domainContrastLayers;
-
-    % If any of the domainContrastLayers are empty, replace the empty
-    % cells by zero thickness layers
-    for i = 1:length(domainContrastLayers)
-        thisLayer = domainContrastLayers{i};
-        if isempty(thisLayer)
-            domainContrastLayers{i} = 0;
-        end
-    end
 
     problemCells{18} = inputStruct.domainContrastRepeatSLDs;
-    problemCells{19} = domainContrastLayers;
+    problemCells{19} = inputStruct.domainContrastLayers;
 end
 
 if isa(project, 'domainsClass')
     problemCells{20} = inputStruct.domainRatioNames;
 end
 
-% Fix for cell array bug with custom layers - is this needed still??
-if strcmpi(inputStruct.modelType,'custom layers') || strcmpi(inputStruct.modelType,'custom xy')
-    for i = 1:length(problemCells{5})
-        problemCells{5}{i} = 0;
-    end
-    for i = 1:length(problemCells{19})
-        problemCells{19}{i} = 0;
-    end
-
-    problemCells{6} = {0};
-
-end
-
 % Also the custom files array..
 if isempty(problemCells{14})
     problemCells{14} = {''};

diff --git a/API/projectClass/contrastsClass.m b/API/projectClass/contrastsClass.m
@@ -108,7 +108,7 @@
                         contrastLayers{i} = thisArray;
                         contrastCustomFile(i) = NaN;
                     otherwise
-                        contrastLayers{i} = {};
+                        contrastLayers{i} = [];
                         whichFile = thisContrast.model;
                         thisContrastFileNum = find(strcmpi(whichFile, allowedNames.customFileNames));
                         contrastCustomFile(i) = thisContrastFileNum;

diff --git a/compile/fullCompile/makeCompileArgsFull.m b/compile/fullCompile/makeCompileArgsFull.m
@@ -54,7 +54,7 @@
 ARG = coder.typeof(0,[1 maxArraySize],[1 1]);
 ARGS_1_2{5} = coder.typeof({ARG}, [1 maxArraySize],[0 1]);
 ARG = coder.typeof(0,[1 10],[1 1]);
-ARGS_1_2{6} = coder.typeof({ARG}, [maxArraySize 1],[1 0]);
+ARGS_1_2{6} = coder.typeof({ARG}, [maxArraySize 1],[1 1]);
 ARG = coder.typeof('X',[1 maxArraySize],[0 1]);
 ARGS_1_2{7} = coder.typeof({ARG}, [1 maxArraySize],[0 1]);
 ARG = coder.typeof('X',[1 maxArraySize],[0 1]);

diff --git a/compile/reflectivityCalculation/makeCompileArgs.m b/compile/reflectivityCalculation/makeCompileArgs.m
@@ -54,7 +54,7 @@
 ARG = coder.typeof(0,[1 maxArraySize],[1 1]);
 ARGS_1_2{5} = coder.typeof({ARG}, [1 maxArraySize],[0 1]);
 ARG = coder.typeof(0,[1 10],[1 1]);
-ARGS_1_2{6} = coder.typeof({ARG}, [maxArraySize 1],[1 0]);
+ARGS_1_2{6} = coder.typeof({ARG}, [maxArraySize 1],[1 1]);
 ARG = coder.typeof('X',[1 maxArraySize],[0 1]);
 ARGS_1_2{7} = coder.typeof({ARG}, [1 maxArraySize],[0 1]);
 ARG = coder.typeof('X',[1 maxArraySize],[0 1]);

diff --git a/minimisers/NS/plotLivePointsWithEllipses.m b/minimisers/NS/plotLivePointsWithEllipses.m
diff --git a/targetFunctions/common/groupLayers/allocateLayersForContrast.m b/targetFunctions/common/groupLayers/allocateLayersForContrast.m
@@ -1,4 +1,4 @@
-function     thisContrastLayers = allocateLayersForContrast(contrastLayers,outParameterisedLayers,useImaginary)
+function thisContrastLayers = allocateLayersForContrast(contrastLayers,outParameterisedLayers,useImaginary)
 % Decide which layers are needed for a particular contrast.
 % This function takes the master array of all layers
 % and extracts which parameters are required for 
@@ -8,30 +8,14 @@
 %     outParameterisedLayers - List of all the available layers
 %     thisContrastLayers     - Array detailing which layers are required for this contrast
 
-coder.varsize('thisContrastLayers',[1000 6],[1 1]);
-
 if useImaginary
     thisContrastLayers = zeros(length(contrastLayers),6);
 else
     thisContrastLayers = zeros(length(contrastLayers),5);
 end
 
- for i = 1:length(contrastLayers)
-    if (contrastLayers(i) ~= 0)
-        thisLayer = outParameterisedLayers{contrastLayers(i)};
-
-%         % Check the length of thisLayer. If it's 6, then we have an
-%         % imaginary SLD defined. Combile them into one complex number at
-%         % this point.
-%         if length(thisLayer) == 6
-%             compSLD = complex(thisLayer(2),thisLayer(3));
-%             thisLayer = [thisLayer(1) compSLD thisLayer(4:end)];
-%         end
-
-        thisContrastLayers(i,:) = thisLayer;
-    else
-        thisContrastLayers(1,:) = [];
-    end
+for i = 1:length(contrastLayers)
+    thisContrastLayers(i,:) = outParameterisedLayers{contrastLayers(i)};
 end
 
-end
+end
diff --git a/targetFunctions/common/groupLayers/allocateLayersForDomainsContrast.m b/targetFunctions/common/groupLayers/allocateLayersForDomainsContrast.m
diff --git a/targetFunctions/common/resampleLayers/SLDFunction.m b/targetFunctions/common/resampleLayers/SLDFunction.m
@@ -26,11 +26,9 @@
 if ~isempty(where)
     sldVal = rho(where);
 else
-    belowVals = find(x > z);
-    aboveVals = find(x < z);
-    below = belowVals(end);
-    above = aboveVals(1);
-
+    below = find(x > z, 1, 'last');
+    above = find(x < z, 1);
+
     belowY = rho(below);
     aboveY = rho(above);
 

diff --git a/tests/domainsTFReflectivityCalculation/domainsCustomLayersInputs.mat b/tests/domainsTFReflectivityCalculation/domainsCustomLayersInputs.mat
diff --git a/tests/domainsTFReflectivityCalculation/domainsCustomLayersOutputs.mat b/tests/domainsTFReflectivityCalculation/domainsCustomLayersOutputs.mat
diff --git a/tests/domainsTFReflectivityCalculation/domainsCustomLayersTFParams.mat b/tests/domainsTFReflectivityCalculation/domainsCustomLayersTFParams.mat
diff --git a/tests/domainsTFReflectivityCalculation/domainsCustomXYInputs.mat b/tests/domainsTFReflectivityCalculation/domainsCustomXYInputs.mat
diff --git a/tests/domainsTFReflectivityCalculation/domainsCustomXYOutputs.mat b/tests/domainsTFReflectivityCalculation/domainsCustomXYOutputs.mat
diff --git a/tests/domainsTFReflectivityCalculation/domainsCustomXYTFParams.mat b/tests/domainsTFReflectivityCalculation/domainsCustomXYTFParams.mat
diff --git a/tests/domainsTFReflectivityCalculation/domainsStandardLayersInputs.mat b/tests/domainsTFReflectivityCalculation/domainsStandardLayersInputs.mat
diff --git a/tests/domainsTFReflectivityCalculation/domainsStandardLayersOutputs.mat b/tests/domainsTFReflectivityCalculation/domainsStandardLayersOutputs.mat
diff --git a/tests/domainsTFReflectivityCalculation/domainsStandardLayersTFParams.mat b/tests/domainsTFReflectivityCalculation/domainsStandardLayersTFParams.mat
diff --git a/tests/nonPolarisedTFReflectivityCalculation/customLayersInputs.mat b/tests/nonPolarisedTFReflectivityCalculation/customLayersInputs.mat
diff --git a/tests/nonPolarisedTFReflectivityCalculation/customLayersOutputs.mat b/tests/nonPolarisedTFReflectivityCalculation/customLayersOutputs.mat
diff --git a/tests/nonPolarisedTFReflectivityCalculation/customLayersTFParams.mat b/tests/nonPolarisedTFReflectivityCalculation/customLayersTFParams.mat
diff --git a/tests/nonPolarisedTFReflectivityCalculation/customXYInputs.mat b/tests/nonPolarisedTFReflectivityCalculation/customXYInputs.mat
diff --git a/tests/nonPolarisedTFReflectivityCalculation/customXYOutputs.mat b/tests/nonPolarisedTFReflectivityCalculation/customXYOutputs.mat
diff --git a/tests/nonPolarisedTFReflectivityCalculation/customXYTFParams.mat b/tests/nonPolarisedTFReflectivityCalculation/customXYTFParams.mat
diff --git a/tests/nonPolarisedTFReflectivityCalculation/standardLayersInputs.mat b/tests/nonPolarisedTFReflectivityCalculation/standardLayersInputs.mat
diff --git a/tests/nonPolarisedTFReflectivityCalculation/standardLayersOutputs.mat b/tests/nonPolarisedTFReflectivityCalculation/standardLayersOutputs.mat
diff --git a/tests/nonPolarisedTFReflectivityCalculation/standardLayersTFParams.mat b/tests/nonPolarisedTFReflectivityCalculation/standardLayersTFParams.mat
diff --git a/tests/nonPolarisedTFReflectivityCalculation/testReflectivityCalculations.m b/tests/nonPolarisedTFReflectivityCalculation/testReflectivityCalculations.m
@@ -119,6 +119,19 @@ function loadTFParams(testCase, TFFile)
     methods (Test, ParameterCombination='exhaustive')
 %% Test High Level RAT Routines
 
+        function testRATEmpty(testCase)
+            % Test that RAT runs for a project without any layers.
+            emptyProject = projectClass();
+            emptyProject.addContrast('data', 'Simulation',...
+                                     'background', 'Background 1',...
+                                     'bulkIn', 'SLD Air',...
+                                     'bulkOut', 'SLD D2O',...
+                                     'scalefactor', 'Scalefactor 1',...
+                                     'resolution', 'Resolution 1');
+
+            [~, ~] = RAT(emptyProject,testCase.controlsInput);
+        end
+
         function testRAT(testCase)
             [projectOutput, result] = RAT(testCase.project,testCase.controlsInput);
 

diff --git a/tests/testContrastsClass.m b/tests/testContrastsClass.m
@@ -499,7 +499,7 @@ function testToStructCustomLayers(testCase)
             for i=1:testCase.numContrasts
                 testCase.exampleClass.contrasts{i}.model = {'DSPC Model'};
             end
-            testCase.exampleStruct.contrastLayers = {{} {} {}};
+            testCase.exampleStruct.contrastLayers = {[] [] []};
             testCase.exampleStruct.contrastCustomFile = [1 1 1];
 
             testCase.verifyEqual(testCase.exampleClass.toStruct(testCase.allowedNames, 'custom layers', testCase.varTable), testCase.exampleStruct);

diff --git a/tests/testProjectConversion/DSPCBilayerProjectClass.mat b/tests/testProjectConversion/DSPCBilayerProjectClass.mat
diff --git a/tests/testProjectConversion/monolayerVolumeModelProjectClass.mat b/tests/testProjectConversion/monolayerVolumeModelProjectClass.mat
diff --git a/utilities/misc/hdrload.m b/utilities/misc/hdrload.m