Merge pull request #23 from juancarlosfarah/22/addProcessAnatomicalIm…

…ageTest

feat: add test for processanatomicalimage

src/matlab/operations/ProcessAnatomicalImage.m

@@ -1,4 +1,4 @@
-function [status, result] = ProcessAnatomicalImage(pathToWorkspace, config)
+function [status, result, sentence] = ProcessAnatomicalImage(pathToWorkspace, config)
 %PROCESSANATOMICALIMAGE Processes an anatomical image using `fsl_anat`.
 %   Uses `fsl_anat` to process an anatomical image.
 %   

test/operations/ProcessAnatomicalImageTest.m

@@ -0,0 +1,99 @@
+%% main function to generate tests
+
+function tests = ProcessAnatomicalImageTest
+  tests = functiontests(localfunctions);
+end
+
+%% test functions
+
+function TestDefaultCommand(testCase)
+
+  % specify (arbitrary) input files 
+  pathToWorkspace = '.';
+  inputFile = 'sample.nii';
+  outputFolder = 'outputdir';
+
+  % these two steps allow us to pass a struct to the operation
+  config = struct('inputFile', inputFile, ...
+   'outputFolder', outputFolder, ...
+   'clobber', true, ...
+   'noReg', true, ...
+   'noNonLinReg', true, ...
+   'noSeg', true, ...
+   'weakBias', true, ...
+   'noReorient', true, ...
+   'noCrop', true, ...
+   'verbose', false);
+  configCell = namedargs2cell(config);
+
+  % run the operation to get the actual command
+  [~, ~, actualCommand] = ProcessAnatomicalImage(pathToWorkspace, configCell{:});
+
+  % this is the expected default command
+  inputfile = fullfile(pathToWorkspace, inputFile);
+  outputdirectory = fullfile(pathToWorkspace, outputFolder);
+  expectedCommand = ...
+   sprintf('fsl_anat --clobber --noreg --nononlinreg --noseg --weakbias --noreorient --nocrop -i %s -o %s', ...
+   inputfile, outputdirectory);
+
+  % verify equality
+  verifyEqual(testCase, actualCommand, expectedCommand);
+
+end
+
+function TestSpecifyingAllOptions(testCase)
+
+  % specify (arbitrary) input files 
+  pathToWorkspace = '.';
+  inputFile = 'sample.nii';
+  outputFolder = 'outputdir';
+
+  % these two steps allow us to pass a struct to the operation
+  config = struct('inputFile', inputFile, ...
+   'outputFolder', outputFolder, ...
+   'clobber', false, ...
+   'noReg', false, ...
+   'noNonLinReg', false, ...
+   'noSeg', false, ...
+   'weakBias', false, ...
+   'noReorient', false, ...
+   'noCrop', false, ...
+   'verbose', true);
+  configCell = namedargs2cell(config);
+
+  % run the operation to get the actual command
+  [~, ~, actualCommand] = ProcessAnatomicalImage(pathToWorkspace, configCell{:});
+
+  % this is the expected default command
+  inputfile = fullfile(pathToWorkspace, inputFile);
+  outputdirectory = fullfile(pathToWorkspace, outputFolder);
+  expectedCommand = sprintf('fsl_anat -i %s -o %s', inputfile, outputdirectory);
+
+  % verify equality
+  verifyEqual(testCase, actualCommand, expectedCommand);
+
+end
+
+%% optional file fixtures
+
+function setupOnce(testCase)
+ % do not change function name
+ % use to set a new path, for example
+end
+
+function teardownOnce(testCase)
+ % do not change function name
+ % use to change back to original path, for example
+end
+
+%% optional fresh fixtures
+
+function setup(testCase)
+ % do not change function name
+ % use to open a figure, for example
+end
+
+function teardown(testCase)
+ % do not change function name
+ % use to close a figure, for example
+end