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AndyEck16 merged 3 commits into from
Mar 3, 2026
Merged

Smaller main screen #139

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fd88daa
Smaller Main GUI Screen
Mar 3, 2026
32e3eab
Exported mlapp files
actions-user Mar 3, 2026
17c6595
Update GUI reshape branch with master changes (#138)
AndyEck16 Mar 3, 2026
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68 changes: 0 additions & 68 deletions +nla/+net/+test/KolmogorovSmirnovTest.m
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64 changes: 64 additions & 0 deletions +nla/+qualityControl/checkNormalityWithKS.m
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Original file line number Diff line number Diff line change
@@ -0,0 +1,64 @@
function checkNormalityWithKS(fig, input_struct, test_pool)

prog = uiprogressdlg(...
fig, 'Title', 'Checking Normaility', 'Message', 'Running Kolmogorov-Smirnov Test'...
);
prog.Value = 0.02;

prog.Value = 0.25;
edge_test_result = test_pool.runEdgeTest(input_struct);

prog.Value = 0.5;
ks_result = runKolmogorovSmirnovTest(input_struct, edge_test_result);

prog.Value = 0.75;
qcKSOutput(ks_result.p, input_struct)

end

function ks_result = runKolmogorovSmirnovTest(input_struct, edge_result)
import nla.TriMatrix nla.TriMatrixDiag

ks_result = struct();
number_of_networks = input_struct.net_atlas.numNets();
ks_result.p = TriMatrix(number_of_networks, TriMatrixDiag.KEEP_DIAGONAL);
ks_result.ks = TriMatrix(number_of_networks, TriMatrixDiag.KEEP_DIAGONAL);

for network1 = 1:number_of_networks
for network2 = 1:network1
network_rho = edge_result.coeff.get(input_struct.net_atlas.nets(network1).indexes,...
input_struct.net_atlas.nets(network2).indexes);
[~, p, ks] = kstest(network_rho);
ks_result.p.set(network1, network2, p);
ks_result.ks.set(network1, network2, ks);
end
end
end

function qcKSOutput(ks_result_p_value, edge_test_options)
% This will open the qc figure for the KS test

network_test_options = nla.net.genBaseInputs();
network_test_options.full_connectome = false;
network_test_options.within_network_pair = false;
network_test_options.fdr_correction = nla.net.mcc.None();
edge_test_options.prob_max = 0.05;
default_discrete_colors = 1000;

p_value_max = network_test_options.fdr_correction.correct(edge_test_options.net_atlas,...
edge_test_options, '');

color_map = nla.net.result.NetworkResultPlotParameter.getColormap(default_discrete_colors,...
p_value_max);

fig = nla.gfx.createFigure();
% Also remember to move this in read the docs
matrix_plot = nla.gfx.plots.MatrixPlot(fig, sprintf("Non-permuted Kolmogorov-Smirnov Test p-value\nSmaller values are less normal"), ks_result_p_value, edge_test_options.net_atlas.nets, nla.gfx.FigSize.LARGE,...
'lower_limit', 0.00, 'upper_limit', p_value_max, 'color_map', color_map);
matrix_plot.displayImage();
width = matrix_plot.image_dimensions('image_width');
height = matrix_plot.image_dimensions('image_height');

fig.Position(3) = width;
fig.Position(4) = height;
end
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167 changes: 86 additions & 81 deletions NLA_GUI_exported.m
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Original file line number Diff line number Diff line change
Expand Up @@ -6,24 +6,25 @@
FileMenu matlab.ui.container.Menu
OpenpreviousresultMenu matlab.ui.container.Menu
GridLayout matlab.ui.container.GridLayout
Panel_7 matlab.ui.container.Panel
RunQualityControlButton matlab.ui.control.Button
MethodsPanel matlab.ui.container.Panel
NonPermutedCheckBox matlab.ui.control.CheckBox
FullConnCheckBox matlab.ui.control.CheckBox
WithinNetPairCheckBox matlab.ui.control.CheckBox
NetInputsPanel matlab.ui.container.Panel
Panel_3 matlab.ui.container.Panel
NoneButton matlab.ui.control.Button
NetTestSelector matlab.ui.control.ListBox
NetworkleveltestsCtrlclickformultipleLabel matlab.ui.control.Label
BranchLabel matlab.ui.control.Label
EdgeInputsPanel matlab.ui.container.Panel
NetInputsPanel matlab.ui.container.Panel
Panel matlab.ui.container.Panel
EdgeTestSelector matlab.ui.control.DropDown
EdgeleveltestDropDownLabel matlab.ui.control.Label
Panel_2 matlab.ui.container.Panel
BranchLabel matlab.ui.control.Label
Panel_5 matlab.ui.container.Panel
RunButton matlab.ui.control.Button
MethodsPanel matlab.ui.container.Panel
NonPermutedCheckBox matlab.ui.control.CheckBox
FullConnCheckBox matlab.ui.control.CheckBox
WithinNetPairCheckBox matlab.ui.control.CheckBox
RunQualityControlButton matlab.ui.control.Button
PermutationcountLabel matlab.ui.control.Label
PermutationcountEditField_2Label matlab.ui.control.Label
PermutationcountEditField matlab.ui.control.NumericEditField
end

Expand Down Expand Up @@ -304,7 +305,7 @@ function createComponents(app)

% Create NetworkLevelAnalysisUIFigure and hide until all components are created
app.NetworkLevelAnalysisUIFigure = uifigure('Visible', 'off');
app.NetworkLevelAnalysisUIFigure.Position = [100 100 1151 718];
app.NetworkLevelAnalysisUIFigure.Position = [100 100 786 620];
app.NetworkLevelAnalysisUIFigure.Name = 'NetworkLevelAnalysis';

% Create FileMenu
Expand All @@ -319,12 +320,59 @@ function createComponents(app)

% Create GridLayout
app.GridLayout = uigridlayout(app.NetworkLevelAnalysisUIFigure);
app.GridLayout.ColumnWidth = {'1x', 598};
app.GridLayout.RowHeight = {38, 100, '1x', 53, 1};
app.GridLayout.ColumnWidth = {'4x', '2x'};
app.GridLayout.RowHeight = {38, 200, '1x', 40};
app.GridLayout.ColumnSpacing = 8.66666666666667;
app.GridLayout.RowSpacing = 3.4;
app.GridLayout.Padding = [8.66666666666667 3.4 8.66666666666667 3.4];

% Create Panel_7
app.Panel_7 = uipanel(app.GridLayout);
app.Panel_7.BorderType = 'none';
app.Panel_7.Layout.Row = 3;
app.Panel_7.Layout.Column = 2;

% Create RunQualityControlButton
app.RunQualityControlButton = uibutton(app.Panel_7, 'push');
app.RunQualityControlButton.ButtonPushedFcn = createCallbackFcn(app, @RunQualityControlButtonPushed, true);
app.RunQualityControlButton.Position = [107 8 138 24];
app.RunQualityControlButton.Text = 'Run Quality Control';

% Create MethodsPanel
app.MethodsPanel = uipanel(app.Panel_7);
app.MethodsPanel.Title = 'MethodsPanel';
app.MethodsPanel.Position = [1 39 253 112];

% Create NonPermutedCheckBox
app.NonPermutedCheckBox = uicheckbox(app.MethodsPanel);
app.NonPermutedCheckBox.ValueChangedFcn = createCallbackFcn(app, @MethodButtonGroupSelectionChanged, true);
app.NonPermutedCheckBox.Tag = 'nonpermuted';
app.NonPermutedCheckBox.Enable = 'off';
app.NonPermutedCheckBox.Text = 'Non-permuted';
app.NonPermutedCheckBox.Position = [9 65 99 22];
app.NonPermutedCheckBox.Value = true;

% Create FullConnCheckBox
app.FullConnCheckBox = uicheckbox(app.MethodsPanel);
app.FullConnCheckBox.ValueChangedFcn = createCallbackFcn(app, @MethodButtonGroupSelectionChanged, true);
app.FullConnCheckBox.Tag = 'full_con';
app.FullConnCheckBox.Text = 'Full connectome';
app.FullConnCheckBox.Position = [9 35 110 22];
app.FullConnCheckBox.Value = true;

% Create WithinNetPairCheckBox
app.WithinNetPairCheckBox = uicheckbox(app.MethodsPanel);
app.WithinNetPairCheckBox.ValueChangedFcn = createCallbackFcn(app, @MethodButtonGroupSelectionChanged, true);
app.WithinNetPairCheckBox.Tag = 'within_net_pair';
app.WithinNetPairCheckBox.Text = 'Within Net-pair';
app.WithinNetPairCheckBox.Position = [9 5 101 22];
app.WithinNetPairCheckBox.Value = true;

% Create NetInputsPanel
app.NetInputsPanel = uipanel(app.Panel_7);
app.NetInputsPanel.Title = 'NetInputsPanel';
app.NetInputsPanel.Position = [1 164 253 162];

% Create Panel_3
app.Panel_3 = uipanel(app.GridLayout);
app.Panel_3.BorderType = 'none';
Expand All @@ -334,42 +382,29 @@ function createComponents(app)
% Create NoneButton
app.NoneButton = uibutton(app.Panel_3, 'push');
app.NoneButton.ButtonPushedFcn = createCallbackFcn(app, @NoneButtonPushed, true);
app.NoneButton.Position = [85 80 48 21];
app.NoneButton.Position = [145 206 48 21];
app.NoneButton.Text = 'None';

% Create NetTestSelector
app.NetTestSelector = uilistbox(app.Panel_3);
app.NetTestSelector.Items = {};
app.NetTestSelector.Multiselect = 'on';
app.NetTestSelector.ValueChangedFcn = createCallbackFcn(app, @NetTestSelectorValueChanged, true);
app.NetTestSelector.Position = [146 2 182 138];
app.NetTestSelector.Position = [1 8 193 192];
app.NetTestSelector.Value = {};

% Create NetworkleveltestsCtrlclickformultipleLabel
app.NetworkleveltestsCtrlclickformultipleLabel = uilabel(app.Panel_3);
app.NetworkleveltestsCtrlclickformultipleLabel.HorizontalAlignment = 'right';
app.NetworkleveltestsCtrlclickformultipleLabel.Position = [6 110 125 28];
app.NetworkleveltestsCtrlclickformultipleLabel.Position = [1 205 125 28];
app.NetworkleveltestsCtrlclickformultipleLabel.Text = {'Network-level tests'; '(Ctrl+click for multiple)'};

% Create BranchLabel
app.BranchLabel = uilabel(app.Panel_3);
app.BranchLabel.HorizontalAlignment = 'right';
app.BranchLabel.FontColor = [0.8 0.8 0.8];
app.BranchLabel.Position = [336 123 263 22];
app.BranchLabel.Text = 'gui | unknown_branch:0000000';

% Create EdgeInputsPanel
app.EdgeInputsPanel = uipanel(app.GridLayout);
app.EdgeInputsPanel.Title = 'Edge-level inputs';
app.EdgeInputsPanel.Layout.Row = [2 4];
app.EdgeInputsPanel.Layout.Row = [2 3];
app.EdgeInputsPanel.Layout.Column = 1;

% Create NetInputsPanel
app.NetInputsPanel = uipanel(app.GridLayout);
app.NetInputsPanel.Title = 'Network-level inputs';
app.NetInputsPanel.Layout.Row = 3;
app.NetInputsPanel.Layout.Column = 2;

% Create Panel
app.Panel = uipanel(app.GridLayout);
app.Panel.AutoResizeChildren = 'off';
Expand All @@ -390,69 +425,39 @@ function createComponents(app)
app.EdgeleveltestDropDownLabel.Position = [1 8 85 22];
app.EdgeleveltestDropDownLabel.Text = 'Edge-level test';

% Create Panel_2
app.Panel_2 = uipanel(app.GridLayout);
app.Panel_2.AutoResizeChildren = 'off';
app.Panel_2.BorderType = 'none';
app.Panel_2.Layout.Row = 4;
app.Panel_2.Layout.Column = 2;
% Create BranchLabel
app.BranchLabel = uilabel(app.GridLayout);
app.BranchLabel.FontColor = [0.8 0.8 0.8];
app.BranchLabel.Layout.Row = 4;
app.BranchLabel.Layout.Column = 1;
app.BranchLabel.Text = 'gui | unknown_branch:0000000';

% Create Panel_5
app.Panel_5 = uipanel(app.GridLayout);
app.Panel_5.BorderType = 'none';
app.Panel_5.Layout.Row = 4;
app.Panel_5.Layout.Column = 2;

% Create RunButton
app.RunButton = uibutton(app.Panel_2, 'push');
app.RunButton = uibutton(app.Panel_5, 'push');
app.RunButton.ButtonPushedFcn = createCallbackFcn(app, @RunButtonPushed, true);
app.RunButton.Position = [544 3 53 20];
app.RunButton.BackgroundColor = [0.8902 0.9882 0.851];
app.RunButton.Position = [191 6 53 30];
app.RunButton.Text = 'Run';

% Create MethodsPanel
app.MethodsPanel = uipanel(app.Panel_2);
app.MethodsPanel.AutoResizeChildren = 'off';
app.MethodsPanel.Title = 'Methods';
app.MethodsPanel.Position = [1 2 345 48];

% Create NonPermutedCheckBox
app.NonPermutedCheckBox = uicheckbox(app.MethodsPanel);
app.NonPermutedCheckBox.ValueChangedFcn = createCallbackFcn(app, @MethodButtonGroupSelectionChanged, true);
app.NonPermutedCheckBox.Tag = 'nonpermuted';
app.NonPermutedCheckBox.Enable = 'off';
app.NonPermutedCheckBox.Text = 'Non-permuted';
app.NonPermutedCheckBox.Position = [10 3 99 22];
app.NonPermutedCheckBox.Value = true;

% Create FullConnCheckBox
app.FullConnCheckBox = uicheckbox(app.MethodsPanel);
app.FullConnCheckBox.ValueChangedFcn = createCallbackFcn(app, @MethodButtonGroupSelectionChanged, true);
app.FullConnCheckBox.Tag = 'full_con';
app.FullConnCheckBox.Text = 'Full connectome';
app.FullConnCheckBox.Position = [118 3 110 22];
app.FullConnCheckBox.Value = true;

% Create WithinNetPairCheckBox
app.WithinNetPairCheckBox = uicheckbox(app.MethodsPanel);
app.WithinNetPairCheckBox.ValueChangedFcn = createCallbackFcn(app, @MethodButtonGroupSelectionChanged, true);
app.WithinNetPairCheckBox.Tag = 'within_net_pair';
app.WithinNetPairCheckBox.Text = 'Within Net-pair';
app.WithinNetPairCheckBox.Position = [236 3 101 22];
app.WithinNetPairCheckBox.Value = true;

% Create RunQualityControlButton
app.RunQualityControlButton = uibutton(app.Panel_2, 'push');
app.RunQualityControlButton.ButtonPushedFcn = createCallbackFcn(app, @RunQualityControlButtonPushed, true);
app.RunQualityControlButton.Position = [472 29 125 21];
app.RunQualityControlButton.Text = 'Run Quality Control';

% Create PermutationcountLabel
app.PermutationcountLabel = uilabel(app.Panel_2);
app.PermutationcountLabel.HorizontalAlignment = 'right';
app.PermutationcountLabel.Position = [359 2 106 22];
app.PermutationcountLabel.Text = 'Permutation count:';
% Create PermutationcountEditField_2Label
app.PermutationcountEditField_2Label = uilabel(app.Panel_5);
app.PermutationcountEditField_2Label.HorizontalAlignment = 'right';
app.PermutationcountEditField_2Label.Position = [6 8 106 26];
app.PermutationcountEditField_2Label.Text = 'Permutation count:';

% Create PermutationcountEditField
app.PermutationcountEditField = uieditfield(app.Panel_2, 'numeric');
app.PermutationcountEditField = uieditfield(app.Panel_5, 'numeric');
app.PermutationcountEditField.Limits = [0 Inf];
app.PermutationcountEditField.RoundFractionalValues = 'on';
app.PermutationcountEditField.ValueDisplayFormat = '%11d';
app.PermutationcountEditField.ValueChangedFcn = createCallbackFcn(app, @PermutationcountEditFieldValueChanged, true);
app.PermutationcountEditField.Position = [480 2 53 22];
app.PermutationcountEditField.Position = [127 7 53 27];
app.PermutationcountEditField.Value = 10000;

% Show the figure after all components are created
Expand Down
10 changes: 0 additions & 10 deletions docs/source/network_level_tests.rst
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Expand Up @@ -53,16 +53,6 @@ Provided Tests
* :math:`\textstyle E_i = \sum_{}\frac{\text{thresholded & binarized ROIs}}{\text{number of ROIs}} \scriptstyle * (\text{number of ROIs in the network-pair of interest})`
* :math:`O_i`: non-permuted, nominally thresholded, and binarized edge-level *p*-values for the network-pair of interest

* **Kolmogorov-Smirnov**

* MATLAB `kstest2 <https://www.mathworks.com/help/stats/kstest2.html>`_ function.

*Inputs:*
* Edge-level correlation coefficients for the network-pair of interest
* Edge-level correlation coefficients across the full connectome

* **Note**: This input is not used for single-sample tests

* **Wilcoxon rank-sum test**

* MATLAB `ranksum <https://www.mathworks.com/help/stats/ranksum.html>`_ function.
Expand Down
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