Merge pull request #1 from haoershi/main

update unit tests

.github/workflows/matlab.yml

@@ -2,10 +2,13 @@ name: MATLAB Unit Tests
 
 on:
   push:
-    branches:
-      - main
+    branches: [ "main" ]
     paths:
-      - './matlab/**' 
+      - 'matlab/**' 
+  pull_request:
+    branches: [ "main" ]
+    paths:
+      - 'matlab/**' 
   workflow_dispatch: 
 
 jobs:
@@ -20,10 +23,23 @@ jobs:
         uses: matlab-actions/setup-matlab@v1
         with:
           matlab-version: R2021b  # Adjust to your MATLAB version
-          license-server: your-license-server-address  # Optional if using a network license
 
       - name: Run MATLAB Unit Tests
+        env:
+          IEEG_USERNAME: ${{ secrets.IEEG_USERNAME }}
+          IEEG_PASSWORD: ${{ secrets.IEEG_PASSWORD }}
         run: |
-          matlab -batch "runtests('test','IncludeSubfolders',true)"
-        working-directory: ./matlab
+          matlab -batch "import matlab.unittest.TestRunner; import matlab.unittest.TestSuite; import matlab.unittest.plugins.XMLPlugin; suite = testsuite('matlab/test','IncludeSubfolders',true); runner = TestRunner.withNoPlugins; xmlFile = 'matlab/test-results.xml'; p = XMLPlugin.producingJUnitFormat(xmlFile); runner.addPlugin(p); result = runner.run(suite); if any([result.Failed]) exit(1); end"
+      
+      - name: Upload Test Results
+        uses: actions/upload-artifact@v2
+        with:
+          name: test-results
+          path: matlab/test-results.xml
+
+      - name: Display Test Results
+        uses: mikepenz/action-junit-report@v4
+        if: success() || failure() # always run even if the previous step fails
+        with:
+          report_paths: 'matlab/test-results.xml'
 

.github/workflows/python.yml

@@ -7,12 +7,12 @@ on:
   push:
     branches: [ "main" ]
     paths:
-      - './python/**' 
+      - 'python/**' 
   pull_request:
     branches: [ "main" ]
     paths:
-      - './python/**' 
-  # workflow_dispatch: 
+      - 'python/**' 
+  workflow_dispatch: 
 
 jobs:
   build:
@@ -34,8 +34,11 @@ jobs:
         python -m pip install --upgrade pip
         python -m pip install flake8 pytest
         if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
-      working-directory: ./python
+      working-directory: python
     - name: Test with pytest
+      env:
+        IEEG_USERNAME: ${{ secrets.IEEG_USERNAME }}
+        IEEG_PASSWORD: ${{ secrets.IEEG_PASSWORD }}
       run: |
         pytest
-      working-directory: ./python
+      working-directory: python

matlab/iEEGData.m

@@ -47,6 +47,7 @@ The ending time (in seconds) of the data clip.
         dura
         data
         fs
+        nchs
         ch_names
         ref_chnames
         raw
@@ -94,6 +95,8 @@ The ending time (in seconds) of the data clip.
             obj.data = p.Results.data;
             obj.fs = p.Results.fs;
             obj.ch_names = p.Results.ch_names;
+            assert(size(obj.data,2)==length(obj.ch_names));
+            obj.nchs = length(obj.ch_names);
             obj.ref_chnames = {};
             obj.index = [];
             obj.power = struct();
@@ -108,6 +111,7 @@ function download(obj, user)
             obj.data = output.values;
             obj.fs = output.fs;
             obj.ch_names = output.chLabels;
+            obj.nchs = length(obj.ch_names);
             obj.raw = obj.data;
             obj.raw_chs = obj.ch_names;
             obj.username = user.usr;
@@ -142,6 +146,7 @@ function reject_nonieeg(obj)
             obj.nonieeg = find_non_ieeg(obj.ch_names);
             obj.data = obj.data(:, ~obj.nonieeg);
             obj.ch_names = obj.ch_names(~obj.nonieeg);
+            obj.nchs = length(obj.ch_names);
             obj.history{end + 1} = 'reject_nonieeg';
         end
 
@@ -151,6 +156,7 @@ function reject_artifact(obj)
             [obj.bad, obj.reject_details] = identify_bad_chs(obj.data, obj.fs);
             obj.data = obj.data(:, ~obj.bad);
             obj.ch_names = obj.ch_names(~obj.bad);
+            obj.nchs = length(obj.ch_names);
             obj.history{end + 1} = 'reject_artifact';
         end
 
@@ -196,9 +202,9 @@ function filter(obj, varargin)
                 end
             end
             p = inputParser;
-            addOptional(p, 'low_freq', 1, @isnumeric);
-            addOptional(p, 'high_freq', 120, @isnumeric);
-            addOptional(p, 'notch_freq', 60, @isnumeric);
+            addOptional(p, 'low_freq', defaults{1}, @isnumeric);
+            addOptional(p, 'high_freq', defaults{2}, @isnumeric);
+            addOptional(p, 'notch_freq', defaults{3}, @isnumeric);
             parse(p, varargin{:});
             low_freq = p.Results.low_freq;
             high_freq = p.Results.high_freq;
@@ -224,6 +230,7 @@ function bipolar(obj)
             obj.data(:, inds) = [];
             obj.ch_names(inds) = [];
             obj.ref_chnames(inds) = [];
+            obj.nchs = length(obj.ch_names);
             obj.history{end + 1} = 'bipolar';
         end
 
@@ -271,6 +278,7 @@ function laplacian(obj, varargin)
             obj.data(:, inds) = [];
             obj.ch_names(inds) = [];
             obj.ref_chnames(inds) = [];
+            obj.nchs = length(obj.ch_names);
             obj.history{end + 1} = 'laplacian';
         end
 
@@ -328,6 +336,7 @@ function reref(obj, ref, varargin)
                     obj.ch_names(inds) = [];
                     obj.ref_chnames(inds) = [];
             end
+            obj.nchs = length(obj.ch_names);
             obj.history{end + 1} = ['reref-', ref];
         end
 
@@ -356,7 +365,7 @@ If False (default), return the absolute power.
             %}
             freqs = default_freqs;
             p = inputParser;
-            defaults = {freqs,nan,false};
+            defaults = {freqs,[],false};
             for i = 1:length(varargin)
                 if isempty(varargin{i})
                     varargin{i} = defaults{i};
@@ -373,7 +382,7 @@ If False (default), return the absolute power.
             nbands = size(band,1);
             for i = 1:nbands
                 obj.power(i).freq = band(i,:);
-                obj.power(i).power = bandpower(obj.data, obj.fs, obj.power(i).freq, window, relative);
+                obj.power(i).power = band_power(obj.data, obj.fs, obj.power(i).freq, window, relative);
             end
             obj.history{end + 1} = 'bandpower';
         end
@@ -634,7 +643,6 @@ function heatmap_settings(obj,varargin)
             % or apply customized settings
             % customized color could be 1:colormap of size nX3, 
             % 2:cell/string array of color hex codes
-            nchs = size(obj.data,2); % add formula here
 
             % default colors
             blue = hex2rgb('#3c5488');red = hex2rgb('#a5474e'); white = [1,1,1]; 
@@ -653,7 +661,7 @@ function heatmap_settings(obj,varargin)
             h.CellLabelColor = 'none';
             % fix figure size
             % Calculate approximate figure size
-            figureHeight = nchs * (h.FontSize) / 0.8;
+            figureHeight = obj.nchs * (h.FontSize) / 0.8;
             figureWidth = figureHeight + 50;
             h.Position = [100, 100, figureWidth, figureHeight];
             % fix colormap
@@ -714,6 +722,7 @@ function reverse(obj)
             % Reverse by one processing step.
             obj.data = obj.rev_data;
             obj.ch_names = obj.rev_chs;
+            obj.nchs = length(obj.ch_names);
             obj.ref_chnames = obj.rev_refchs;
             obj.history{end + 1} = 'reverse';
         end

matlab/iEEGPreprocess.m

@@ -112,9 +112,15 @@ function load_data(obj, path, varargin)
         >>> session.load_data("/path/to/saved_data.mat", replace = True)
         %}
             p = inputParser;
+            defaults = {false,true};
+            for i = 1:length(varargin)
+                if isempty(varargin{i})
+                    varargin{i} = defaults{i};
+                end
+            end
             addRequired(p, 'path', @(x) isstring(x) || ischar(x));
-            addOptional(p, 'replace',false, @(x) ismember(x,[0,1]));
-            addOptional(p, 'default_folder',true, @(x) ismember(x,[0,1]));
+            addOptional(p, 'replace',defaults{1}, @(x) ismember(x,[0,1]));
+            addOptional(p, 'default_folder',defaults{2}, @(x) ismember(x,[0,1]));
             parse(p, path, varargin{:});
             path = p.Results.path;
             replace = p.Results.replace;
@@ -205,7 +211,11 @@ The stop time (in seconds) of the data segment to download.
             username = p.Results.username;
 
             if isempty(obj.user)
-                obj.login('username', username);
+                if ~isempty(username)
+                    obj.login(username);
+                else
+                    obj.login()
+                end
             end
             data = iEEGData(filename, start, stop, select_elecs, ignore_elecs);
             data.download(obj.user); 
@@ -224,6 +234,7 @@ function remove_data(obj, dataIndex)
             % Remove data instance from current session.
             obj.meta(dataIndex, :) = [];
             obj.datasets(dataIndex) = [];
+            obj.num_data = size(obj.meta, 1);
         end
 
         function save(obj, filename, varargin) 

matlab/test/authTest.m

@@ -0,0 +1,39 @@
+%% Test Class Definition
+classdef authTest < matlab.unittest.TestCase
+    %% Test Method Block
+    methods (Test)
+        % includes unit test functions
+        function testAuth(testCase)   
+            % see https://www.mathworks.com/help/matlab/matlab_prog/types-of-qualifications.html
+            % for qualification method
+            % addpath(genpath('./../..')); % always add to ensure loading of other files/func
+            paths;
+            assert(exist(USER_DIR,'dir') == 7);
+            if ~isempty(getenv('GITHUB_ACTIONS'))
+                % Use GitHub secrets to retrieve credentials
+                config.usr = getenv('IEEG_USERNAME');
+                config.pwd = getenv('IEEG_PASSWORD');
+                pwd_path = fullfile(USER_DIR, strcat(config.usr(1:3), '_ieeglogin.bin'));
+                PATH = IEEGSession.createPwdFile(config.usr, config.pwd, pwd_path);
+                config.pwd = strcat(config.usr(1:3), '_ieeglogin.bin');
+                file_name = fullfile(USER_DIR, strcat(config.usr(1:3), '_config.json'));
+                jsonStr = jsonencode(config);
+                fid = fopen(file_name, 'w');
+                fprintf(fid, '%s', jsonStr);
+                fclose(fid);
+                fprintf('-- -- IEEG user config file saved -- --\n');
+                user_data_dir = fullfile(DATA_DIR, config.usr(1:3));
+            end
+            files = dir(fullfile(USER_DIR,'*.json'));
+            if isempty(files)
+                error('Login info unavailable.')
+            else
+                for i = 1:length(files)
+                    f = fullfile(files(i).folder, files(i).name);
+                    login = jsondecode(fileread(f));
+                    assert(exist(fullfile(USER_DIR,login.pwd)))
+                end
+            end
+        end
+    end
+end

matlab/test/bandPowerTest.m

@@ -0,0 +1,74 @@
+classdef bandPowerTest < matlab.unittest.TestCase
+
+    methods (Test)
+        function testBandPowerAbsolute(tc)
+            addpath(genpath('./..')); 
+            % Generate example data with known band power in the alpha range
+            fs = 250;
+            duration = 10; % seconds
+            time = [0:1/fs:duration-1/fs]';
+            alpha_band = [8, 12];
+            alpha_power = 0.5; % Known alpha band power
+
+            data = zeros(length(time), 1);
+            data = data + sin(2*pi*10*time) + 0.1 * randn(size(time)); % Alpha band (10 Hz)
+
+            % Call the function under test
+            bp = band_power(data, fs, alpha_band);
+
+            % Assertions
+            tc.verifyEqual(bp, alpha_power, 'Alpha band power mismatch', 'AbsTol', 0.1); % Allow some tolerance
+
+            % Generate example data
+            data = randn(100, 5);
+            fs = 250;
+            band = [1, 30];
+
+            % Call the function under test
+            bp = band_power(data, fs, band);
+
+            % Assertions
+            tc.verifyEqual(size(bp), [1, size(data, 2)], 'Band power size mismatch');
+            tc.verifyGreaterThan(bp, 0, 'Band power should be greater than zero');
+        end
+
+        function testBandPowerRelative(tc)
+            addpath(genpath('./..')); 
+            % Generate example data with known band power in the alpha range
+            fs = 250;
+            duration = 10; % seconds
+            time = [0:1/fs:duration-1/fs]';
+
+            % Simulate data with power in two frequency bands
+            alpha_band = [8, 12];
+            beta_band = [15, 30];
+            alpha_power = 0.6; % Known power ratio
+            beta_power = 0.4;  % Known power ratio
+
+            data_alpha = sin(2*pi*10*time); % Alpha band (10 Hz)
+            data_beta = sin(2*pi*20*time);  % Beta band (20 Hz)
+
+            data = alpha_power * data_alpha + beta_power * data_beta + 0.1 *randn(size(time));
+            % Call the function under test with relative power
+            bp = band_power(data, fs, alpha_band, [], true);
+
+            % Assertions
+            tc.verifyEqual(bp, alpha_power, 'Relative alpha band power mismatch', 'AbsTol', 0.1); % Allow some tolerance
+
+
+            % Generate example data
+            data = randn(100, 5);
+            fs = 250;
+            band = [1, 30];
+
+            % Call the function under test with relative power
+            bp = band_power(data, fs, band, [], true);
+
+            % Assertions
+            tc.verifyEqual(size(bp), [1, size(data, 2)], 'Relative band power size mismatch');
+            tc.verifyGreaterThanOrEqual(bp, 0, 'Relative band power should be greater than or equal to zero');
+            tc.verifyLessThanOrEqual(bp, 1, 'Relative band power should be less than or equal to one');
+        end
+    end
+
+end

matlab/test/bandpassFilterTest.m

@@ -0,0 +1,17 @@
+classdef bandpassFilterTest < matlab.unittest.TestCase
+
+    methods (Test)
+        function test_BandpassFilter(tc)
+            % Test with default parameters
+
+            addpath(genpath('./..')); % always add to ensure loading of other files/func
+            paths;
+            load(fullfile(TESTDATA_DIR,'sampleData.mat'));
+            values = bandpass_filter(old_values, fs);
+            tc.verifyEqual(size(values), size(old_values), 'Output size mismatch');
+            values = bandpass_filter(old_values, fs, 5, 50, 6);
+            tc.verifyEqual(size(values), size(old_values), 'Output size mismatch');
+        end
+    end
+
+end

matlab/test/refBipolarTest/refBipolarTest.m → matlab/test/bipolarTest.m

@@ -1,5 +1,5 @@
 %% Test Class Definition
-classdef refBipolarTest < matlab.unittest.TestCase
+classdef bipolarTest < matlab.unittest.TestCase
     % This is a test class defined for the decompose_labels function
     % Import test cases from decompLabel_testInput.csv file, which include 
     % input, expected output, and notes describes the test scenairo of the
@@ -9,14 +9,19 @@
     %% Test Method Block
     methods (Test)
         % includes unit test functions
-        function testrefBipolar(testCase)   
+        function testBipolar(testCase)   
             % This part test for wrong input types
             % see https://www.mathworks.com/help/matlab/matlab_prog/types-of-qualifications.html
             % for qualification method
-            addpath(genpath('./../..')); % always add to ensure loading of other files/func
-            load refBipolar_testInput.mat;
+            addpath(genpath('./..')); % always add to ensure loading of other files/func
+            paths;
+            load(fullfile(TESTDATA_DIR,'reref_testInput.mat'));
             f = @() bipolar(old_values,labels);
             testCase.verifyWarningFree(f)
+            [out_values,out_labels] = bipolar(old_values,labels);
+            n = length(find(strcmp('-',out_labels)));
+            testCase.verifyEqual(n,15);
+
         end
     end
 end