Adds wrapper for python and dylib custom function (#157)

* Adds wrapper for python and dylib custom function

* Adds unit tests and modifies customFileClass to use wrapper instead

* Addresses review comments

API/parseClassToStructs.m

@@ -92,7 +92,6 @@
 %% Start by removing the cell arrays
 contrastLayers = inputStruct.contrastLayers;
 layersDetails = inputStruct.layersDetails;
-customFiles = inputStruct.files;
 
 % If any of the contrastLayers are empty, replace the empty cells by zero
 % thickness layers
@@ -108,15 +107,6 @@
     layersDetails = {0};
 end
 
-% When there are custom files, we need to strip the file extension
-% from the filename if it's present
-for i = 1:length(customFiles)
-    thisCustomFileCell = customFiles{i};
-    [~,name,~] = fileparts(thisCustomFileCell{1});
-    thisCustomFileCell{1} = name;
-    customFiles{i} = thisCustomFileCell;
-end
-
 % Pull out all the cell arrays (except priors) into one array
 problemDefCells{1} = inputStruct.contrastRepeatSLDs;
 problemDefCells{2} = inputStruct.allData;
@@ -131,7 +121,7 @@
 problemDefCells{11} = inputStruct.nbairNames;
 problemDefCells{12} = inputStruct.nbsubNames;
 problemDefCells{13} = inputStruct.resolParNames;
-problemDefCells{14} = customFiles';
+problemDefCells{14} = inputStruct.files;
 problemDefCells{15} = cellstr(inputStruct.backgroundTypes');
 problemDefCells{16} = cellstr(inputStruct.resolutionTypes');
 problemDefCells{17} = inputStruct.allOilChiData;
@@ -181,7 +171,7 @@
 
 % Also the custom files array..
 if isempty(problemDefCells{14})
-    problemDefCells{14} = {{'','',''}};
+    problemDefCells{14} = {''};
 end
 
 

API/projectClass/customFileClass.m

@@ -2,10 +2,13 @@
 
     % A container class for holding custom files for either
     % models, backgrounds or resolutions.
+   properties (SetAccess = private, Hidden = true)
+        wrappers = {}
+   end
 
     properties(Access = private, Constant, Hidden)
         invalidLanguageMessage = sprintf('Language must be a supportedLanguages enum or one of the following strings (%s)', ...
-                                         strjoin(supportedLanguages.values(), ', '))
+                                         strjoin(supportedLanguages.values(), ', '))    
     end
 
     methods
@@ -27,25 +30,34 @@
             end          
         end
 
+        function delete(obj)
+            % Destroys the wrappers
+            for i=1:length(obj.wrappers) 
+                delete(obj.wrappers{i});
+            end
+            obj.wrappers = {};
+        end
+
         function obj = addCustomFile(obj, varargin)
             % Add an entry to the file table.
             % A custom file entry can be added with no parameters, just the
             % name of the custom file entry, the name of the entry
             % alongside a filename, or can be fully defined by specifying
             % the name of the custom file entry, filename, language, and
-            % file path
+            % file path. For MATLAB, the provided path must be in the
+            % matlab path
             %
             % customFiles.addCustomFile()
             % customFiles.addCustomFile('New Row')
             % customFiles.addCustomFile('New Row', 'file.m')
-            % customFiles.addCustomFile('New Row', 'file.m', 'matlab', 'pwd')
+            % customFiles.addCustomFile('New Row', 'file.py', 'python', 'C:/stuff')
             if isempty(varargin)
 
                 % Nothing supplied - add empty data row
                 nameVal = obj.autoNameCounter();
                 newName = sprintf('New custom file %d', nameVal);
 
-                newRow = {newName, '', supportedLanguages.Matlab.value, 'pwd'};
+                newRow = {newName, '', supportedLanguages.Matlab.value, ''};
 
             else
 
@@ -62,7 +74,7 @@
                             throw(invalidType('Single input is expected to be a custom object name'));
                         end
 
-                        newRow = {newName, '', supportedLanguages.Matlab.value, 'pwd'};
+                        newRow = {newName, '', supportedLanguages.Matlab.value, ''};
 
                     case 2
 
@@ -71,7 +83,7 @@
                         newName = char(inputs{1});
                         newFile = char(inputs{2});
 
-                        newRow = {newName, newFile, supportedLanguages.Matlab.value, 'pwd'};
+                        newRow = {newName, newFile, supportedLanguages.Matlab.value, ''};
 
                     case 4
 
@@ -93,8 +105,7 @@
 
             % Check language is valid, then add the new entry
             newRow{3} = validateOption(newRow{3}, 'supportedLanguages', obj.invalidLanguageMessage).value;
-            obj.addRow(newRow{:});
-
+            obj.addRow(newRow{:});            
         end
 
         function obj = setCustomFile(obj, row, varargin)
@@ -218,31 +229,43 @@ function displayTable(obj)
             % Convert the custom files class to a struct
             %
             % customFiles.toStruct()
-            numberOfFiles = obj.rowCount;
-
+            fileStruct.files = {};
+            numberOfFiles = obj.rowCount;      
             if numberOfFiles > 0
                 filesList = cell(numberOfFiles, 1);
                 for i = 1:numberOfFiles
                     thisRow = obj.varTable{i,:};
                     thisFile = thisRow{2};
                     thisType = thisRow{3};
-                    thisPath = thisRow{4};
-
-                    if strcmpi(thisPath,'pwd')
-                        thisPath = pwd;
+                    thisPath = thisRow{4};                    
+                    [~, functionName, ~] = fileparts(thisFile);
+                    libpath = fullfile(thisPath, thisFile);
+                    wrapper = [];
+                    if i <= length(obj.wrappers)
+                        wrapper = obj.wrappers{i};                        
                     end
-                    filesList{i} = {thisFile, thisType, thisPath};
+                    if isempty(wrapper) || ~strcmp(wrapper.libPath, libpath) || ~strcmp(wrapper.functionName, functionName)
+                        if strcmpi(thisType, supportedLanguages.Python.value)
+                            wrapper = pythonWrapper(libpath, functionName);
+                            thisFile = wrapper.getHandle();
+                        elseif strcmpi(thisType, supportedLanguages.Cpp.value)
+                            wrapper = dyLibWrapper(libpath, functionName);
+                            thisFile = wrapper.getHandle();
+                        end
+                        obj.wrappers{i} = wrapper;
+                    else
+                        thisFile = wrapper.getHandle();
+                    end
+                    [~, handle, ~] = fileparts(thisFile);
+                    filesList{i} = handle;
                 end
                 fileStruct.files = filesList;
-            else
-                fileStruct.files = {};
             end
         end
 
     end
 
     methods(Access = protected)
-
         function obj = setCustomLanguage(obj, row, language)
            % Check whether a specified language is supported, and set the
            % file entry if so.

API/projectClass/dyLibWrapper.m

@@ -0,0 +1,46 @@
+classdef dyLibWrapper < handle
+    % A custom function wrapper for c++ dynamic library. The library should be a .dll
+    % (Windows), .so (Linux), or .dylib (MacOS).
+    properties (SetAccess = private)
+        functionName
+        libPath
+    end
+
+    properties (Access = private, Hidden = true)
+        objectHandle % Handle to the underlying C++ class instance
+        mexHandle % Handle to the mex function
+    end
+
+    methods
+        function obj = dyLibWrapper(libPath, functionName)
+            % Creates a dyLibWrapper object. It creates a callback interface for the 
+            % library via wrapperMex.The arguments should be full or relative path of 
+            % the library with extension and the name of the function to call in the dynamic library
+            %
+            % wrapper = dyLibWrapper('customBilayer.so', 'customBilayer');
+            % wrapper = dyLibWrapper('D:/MATLAB/customBilayer.dll', 'customDomains');
+            obj.mexHandle = @wrapperMex;
+            obj.objectHandle = obj.mexHandle('new', libPath, functionName);
+            obj.libPath = libPath;
+            obj.functionName = functionName;
+        end
+
+        function delete(obj)
+            % Destroys the callback class instance in wrapperMex
+            if ~isempty(obj.objectHandle)
+                obj.mexHandle('delete', obj.objectHandle);
+            end
+            obj.objectHandle = [];
+        end
+
+        function handle = getHandle(obj)
+            % Gets the wrapper object handle
+            handle = obj.objectHandle;
+        end      
+
+        function disp(obj)
+            % Displays libarary path and function name
+            fprintf('Dynamic library wrapper for %s function in %s\n', obj.functionName, obj.libPath);
+        end
+    end
+end

API/projectClass/projectClass.m

@@ -136,6 +136,11 @@
             obj.contrasts = contrastsClass();               
         end
 
+        function delete(obj)
+            % Destroys the wrappers
+            delete(obj.customFile);
+        end
+
         function domainsObj = toDomainsClass(obj)
             % Alias of the converter routine from projectClass to
             % domainsClass.

API/projectClass/pythonWrapper.m

@@ -0,0 +1,59 @@
+classdef pythonWrapper < handle
+    % A custom function wrapper for a python file. 
+
+    properties (SetAccess = private)
+        functionName
+        libPath
+    end
+
+    properties (SetAccess = private, Hidden = true)
+        tempFolder
+        tempName
+        filename
+    end
+
+    methods
+        function obj = pythonWrapper(libPath, functionName)
+            % Creates a pythonWrapper object. It creates a temporary function which runs 
+            % the python code using the python executable connected to MATLAB pyenv. The 
+            % arguments should be full or relative path of the python file with extension and 
+            % the name of the function to call in the python file
+            %
+            % wrapper = pythonWrapper('customBilayer.py', 'customBilayer');
+            % wrapper = pythonWrapper('D:/MATLAB/customBilayer.py', 'customDomains');
+            obj.tempFolder = tempname();
+            obj.libPath = libPath;
+            obj.functionName = functionName;
+
+            fnstr = ['function [output,sub_rough] = %s(varargin)\n' ...
+                     '  [output, sub_rough] = pyRunner("%s", "%s", varargin);\n' ...
+                     'end\n'];
+
+            mkdir(obj.tempFolder);
+            filename = sprintf('%s.m', tempname(obj.tempFolder));
+            fid = fopen(filename, 'w+');
+            [~, obj.tempName, ~] = fileparts(filename);
+            fprintf(fid, fnstr, obj.tempName, obj.libPath, obj.functionName);
+            fclose(fid);
+            addpath(obj.tempFolder);
+        end
+
+        function delete(obj)
+            % Removes the temporary runner file
+            rmpath(obj.tempFolder);
+            if exist(obj.tempFolder, 'dir')
+                rmdir(obj.tempFolder, 's');
+            end
+        end
+
+        function handle = getHandle(obj)
+            % Gets the name of the temporary runner file
+            handle = obj.tempName;
+        end      
+
+        function disp(obj)
+            % Displays library path and function name
+            fprintf('Python wrapper for %s function in %s\n', obj.functionName, obj.libPath);
+        end
+    end
+end

addPaths.m

@@ -25,6 +25,7 @@
 
     fullfile(root,'compile','DE');
     eventCompilePath;
+    fullfile(root,'compile','customWrapper');
     fullfile(root,'compile','reflectivityCalculation');
     fullfile(root,'compile','simplex');
     fullfile(root,'compile');
@@ -46,7 +47,6 @@
     fullfile(root,'targetFunctions','common','callCustomFunction');
     fullfile(root,'targetFunctions','common','callCustomFunction','callMatlabFunction');
     fullfile(root,'targetFunctions','common','callCustomFunction','callCppFunction');
-    fullfile(root,'targetFunctions','common','callCustomFunction','callPythonFunction');
 
     fullfile(root,'targetFunctions','common','callReflectivity');
     fullfile(root,'targetFunctions','common','costFunctions','chiSquared');
@@ -88,8 +88,7 @@
 
 addpath(root);
 setappdata(0, 'root', root);
-includedir = {fullfile(root, 'targetFunctions', 'common', 'customModelsIncludes'),...
-              fullfile(root, 'compile', 'events')};
+includedir = {fullfile(root, 'compile', 'customWrapper'), eventCompilePath};
 setappdata(0, 'includeDirs', includedir);
 
 % Add the folder with the eventManager dynamic library to the system path so 

buildScript.m

@@ -18,16 +18,18 @@
 % need to change RAT paths to exclude these files from the source generation
 % setCompilePaths('lib');
 % 
-% % Now generate the source....
-% reflectivityCalculationCodeOnlyScript;
+% Now generate the source....
+reflectivityCalculationCodeOnlyScript;
 
 % Finally, change the paths back or the tests might fail...
 % setCompilePaths('mex');
-
 compilePath = fullfile(thisPath, 'compile', 'events');
 cd(compilePath);
-
 eventCompileScript;
 
+compilePath = fullfile(thisPath, 'compile', 'customWrapper');
+cd(compilePath);
+wrapperCompileScript;
+
 % Return to RAT root directory
 cd(thisPath);

compile/Dram_compile/makeCompileArgs.m

@@ -68,8 +68,7 @@
 ARG = coder.typeof('X',[1 maxArraySize],[0 1]);
 ARGS_1_2{13} = coder.typeof({ARG}, [1 maxArraySize],[0 1]);
 ARG = coder.typeof('X',[1 maxArraySize],[0 1]);
-ARG = coder.typeof({ARG}, [1 3]);
-ARGS_1_2{14} = coder.typeof({ARG}, [1 maxArraySize],[0 1]);
+ARGS_1_2{14} = coder.typeof({ARG}, [1 maxArraySize], [0 1]);
 ARG = coder.typeof('X',[1 maxArraySize],[1 1]);
 ARGS_1_2{15} = coder.typeof({ARG}, [1 maxArraySize],[0 1]);
 ARG = coder.typeof('X',[1 maxArraySize],[1 1]);

compile/RAT_main_compile/makeCompileArgs.m

@@ -68,8 +68,7 @@
 ARG = coder.typeof('X',[1 maxArraySize],[0 1]);
 ARGS_1_2{13} = coder.typeof({ARG}, [1 maxArraySize],[0 1]);
 ARG = coder.typeof('X',[1 maxArraySize],[0 1]);
-ARG = coder.typeof({ARG}, [1 3]);
-ARGS_1_2{14} = coder.typeof({ARG}, [1 maxArraySize],[0 1]);
+ARGS_1_2{14} = coder.typeof({ARG}, [1 maxArraySize], [0 1]);
 ARG = coder.typeof('X',[1 maxArraySize],[1 1]);
 ARGS_1_2{15} = coder.typeof({ARG}, [1 maxArraySize],[0 1]);
 ARG = coder.typeof('X',[1 maxArraySize],[1 1]);