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Merged
AndyEck16 merged 2 commits into from
Mar 24, 2025
Merged

Net267 remove cohens d effect from user view #106

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a2b294b
[NET-267] Hide and disable cohens D, make cohens D calculations zero.…
Mar 24, 2025
00ab959
Exported mlapp files
actions-user Mar 24, 2025
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8 changes: 4 additions & 4 deletions +nla/+gfx/+plots/MatrixPlot.m
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Original file line number Diff line number Diff line change
Expand Up @@ -21,7 +21,7 @@
figure_size % Size to display. Either nla.gfx.FigSize.SMALL or nla.gfx.FigSize.LARGE
draw_legend % Legend on/off
draw_colorbar % Colorbar on/off
color_map % Colormap to use (enter 'turbo(256)' for default)
color_map % Colormap to use (enter 'jet(1000)' for default)
marked_networks % networks to mark with a symbol
discrete_colorbar % colorbar as discrete. TRUE == discrete, FALSE == continuous
network_clicked_callback % Button function to add to each network. Used for clickable networks
Expand Down Expand Up @@ -55,7 +55,7 @@
end

properties (Constant)
colormap_choices = {"Parula", "Turbo", "HSV", "Hot", "Cool", "Spring", "Summer", "Autumn", "Winter", "Gray",...
colormap_choices = {"Jet", "Parula", "Turbo", "HSV", "Hot", "Cool", "Spring", "Summer", "Autumn", "Winter", "Gray",...
"Bone", "Copper", "Pink"}; % Colorbar choices
end

Expand All @@ -82,7 +82,7 @@
% figure_margins = nla.gfx.FigMargins.WHITESPACE
% draw_legend = true
% draw_colorbar = true
% color_map = turbo(256)
% color_map = jet(1000)
% lower_limit = -0.3
% upper_limit = 0.3
% x_position = 0
Expand All @@ -104,7 +104,7 @@
addParameter(matrix_input_parser, 'figure_margins', nla.gfx.FigMargins.WHITESPACE, @isenum);
addParameter(matrix_input_parser, 'draw_legend', true, @islogical);
addParameter(matrix_input_parser, 'draw_colorbar', true, @islogical);
addParameter(matrix_input_parser, 'color_map', turbo(256));
addParameter(matrix_input_parser, 'color_map', jet(1000)); %reverted to jet(1000) by request
addParameter(matrix_input_parser, 'lower_limit', -0.3, validNumberInput);
addParameter(matrix_input_parser, 'upper_limit', 0.3, validNumberInput);
addParameter(matrix_input_parser, 'x_position', 0, validNumberInput);
Expand Down
Binary file modified +nla/+net/+result/+plot/NetworkTestPlotApp.mlapp
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52 changes: 34 additions & 18 deletions +nla/+net/+result/+plot/NetworkTestPlotApp_exported.m
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Expand Up @@ -175,28 +175,41 @@ function getPlotTitle(app)
methods (Access = private)

function cohens_d_filter = createSignificanceFilter(app)
cohens_d_filter = nla.TriMatrix(app.edge_test_options.net_atlas.numNets, "logical", nla.TriMatrixDiag.KEEP_DIAGONAL);
if isequal(app.CohensDThresholdCheckBox.Enable, true) && isequal(app.CohensDThresholdCheckBox.Value, true)
if isequal(app.test_method, "no_permutations") && ~isequal(app.network_test_result.no_permutations, false)

end
if isequal(app.test_method, "full_connectome") && ~isequal(app.network_test_result.full_connectome, false)
cohens_d_filter.v = (app.network_test_result.full_connectome.d.v >= app.network_test_options.d_max);
end
if ~isequal(app.network_test_result.within_network_pair, false) && isfield(app.network_test_result.within_network_pair, "d")...
&& ~isequal(app.test_method, "full_connectome")
cohens_d_filter.v = (app.network_test_result.within_network_pair.d.v >= app.network_test_options.d_max);
end
else
cohens_d_filter.v = true(numel(cohens_d_filter.v), 1);
end
%REMOVE COHENS D FILTERING UNTIL WE DETERMINE CORRECT CALCULATION FOR IT - ADE 2025MAR24
num_nets = app.edge_test_options.net_atlas.numNets;
cohens_d_filter = nla.TriMatrix(num_nets, "logical", nla.TriMatrixDiag.KEEP_DIAGONAL);
cohens_d_filter.v = true(numel(cohens_d_filter.v), 1);
return;

% cohens_d_filter = nla.TriMatrix(app.edge_test_options.net_atlas.numNets, "logical", nla.TriMatrixDiag.KEEP_DIAGONAL);
% if isequal(app.CohensDThresholdCheckBox.Enable, true) && isequal(app.CohensDThresholdCheckBox.Value, true)
% if isequal(app.test_method, "no_permutations") && ~isequal(app.network_test_result.no_permutations, false)
%
% end
% if isequal(app.test_method, "full_connectome") && ~isequal(app.network_test_result.full_connectome, false)
% cohens_d_filter.v = (app.network_test_result.full_connectome.d.v >= app.network_test_options.d_max);
% end
% if ~isequal(app.network_test_result.within_network_pair, false) && isfield(app.network_test_result.within_network_pair, "d")...
% && ~isequal(app.test_method, "full_connectome")
% cohens_d_filter.v = (app.network_test_result.within_network_pair.d.v >= app.network_test_options.d_max);
% end
% else
% cohens_d_filter.v = true(numel(cohens_d_filter.v), 1);
% end
end

function applyScaleChange(app)
progress_bar = uiprogressdlg(app.UIFigure, "Title", "Please Wait", "Message", "Applying Changes...", "Indeterminate", true);
progress_bar.Message = "Chaning scale of existing TriMatrix...";
app.matrix_plot.applyScale(false, false, app.UpperLimitEditField.Value, app.LowerLimitEditField.Value, app.PlotScaleDropDown.Value, app.ColormapDropDown.Value)
end

function hideCohensDControls(app)
app.CohensDThresholdEditField.Visible = false;
app.CohensDThresholdCheckBox.Visible = false;
app.CohensDThresholdEditFieldLabel.Visible = false;

end
end


Expand All @@ -213,6 +226,8 @@ function startupFcn(app, network_test_result, edge_test_result, flags, edge_test
test_method = "within_network_pair";
end

app.hideCohensDControls(); %keep cohens d controls in code, but hide from user until we get right calcluations - ADE2025MAR24

app.network_test_result = network_test_result;
app.edge_test_result = edge_test_result;
app.test_method = test_method;
Expand All @@ -232,7 +247,7 @@ function startupFcn(app, network_test_result, edge_test_result, flags, edge_test
app.ColormapDropDown.Items = app.colormap_choices;
app.ColormapDropDown.Value = app.colormap_choices{1};

app.drawTriMatrixPlot()
app.drawTriMatrixPlot();
end

% Callback function
Expand Down Expand Up @@ -451,13 +466,14 @@ function createComponents(app)
% Create CohensDThresholdEditFieldLabel
app.CohensDThresholdEditFieldLabel = uilabel(app.Panel);
app.CohensDThresholdEditFieldLabel.HorizontalAlignment = 'right';
app.CohensDThresholdEditFieldLabel.Enable = 'off';
app.CohensDThresholdEditFieldLabel.Position = [195 237 118 22];
app.CohensDThresholdEditFieldLabel.Text = 'Cohen''s D Threshold';

% Create CohensDThresholdEditField
app.CohensDThresholdEditField = uieditfield(app.Panel, 'numeric');
app.CohensDThresholdEditField.Enable = 'off';
app.CohensDThresholdEditField.Position = [339 237 52 22];
app.CohensDThresholdEditField.Value = 0.5;

% Create ColormapDropDownLabel
app.ColormapDropDownLabel = uilabel(app.Panel);
Expand Down Expand Up @@ -501,9 +517,9 @@ function createComponents(app)

% Create CohensDThresholdCheckBox
app.CohensDThresholdCheckBox = uicheckbox(app.Panel);
app.CohensDThresholdCheckBox.Enable = 'off';
app.CohensDThresholdCheckBox.Text = 'Cohen''s D Threshold';
app.CohensDThresholdCheckBox.Position = [257 207 134 22];
app.CohensDThresholdCheckBox.Value = true;

% Create ROIcentroidsonbrainplotsCheckBox
app.ROIcentroidsonbrainplotsCheckBox = uicheckbox(app.Panel);
Expand Down
59 changes: 34 additions & 25 deletions +nla/+net/CohenDTest.m
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Expand Up @@ -15,31 +15,40 @@
end

function result_object = run(obj, edge_test_results, network_atlas, result_object)
import nla.TriMatrix nla.TriMatrixDiag

number_of_networks = network_atlas.numNets();

for row = 1:number_of_networks
for column = 1:row

network_rho = edge_test_results.coeff.get(network_atlas.nets(row).indexes,...
network_atlas.nets(column).indexes);

single_sample_d = abs(mean(network_rho)) / std(network_rho);
d = abs((mean(network_rho) - mean(edge_test_results.coeff.v)) / sqrt(((std(network_rho).^2)) +...
(std(edge_test_results.coeff.v).^2)));

if isprop(result_object, "no_permutations") && ~isequal(result_object.no_permutations, false)
result_object.no_permutations.d.set(row, column, single_sample_d);
end
if isprop(result_object, "full_connectome") && ~isequal(result_object.full_connectome, false)
result_object.full_connectome.d.set(row, column, d);
end
if isprop(result_object, "within_network_pair") && ~isequal(result_object.within_network_pair, false)
result_object.within_network_pair.d.set(row, column, single_sample_d);
end
end
end


%DETERMINED THAT CURRENT COHEN'S D CALC IS INVALID
%RETURN WITHOUT MODIFYING EXISTING D PLACEHOLDER VALUE FROM 0
%RECOMMEND THAT, WHEN REENABLED, THIS FN BE CHANGED TO ACCEPT
%VECTOR OF INPUT AND RETURN VECTOR OF OUTPUT RATHER THAN
%RESULTS CLASS
%ADE 2025MAR24
return;




%LEAVING COMMENTED CODE BELOW THAT WOULD MODIFY FIELDS AS DONE
%PREVIOUSLY FOR REFERENCE.
% number_of_networks = network_atlas.numNets();
%
% for row = 1:number_of_networks
% for column = 1:row
%
% if isprop(result_object, "no_permutations") && ~isequal(result_object.no_permutations, false)
% %this_netpair_nonperm_d = COMPUTE NONPERMUTED D HERE;
% result_object.no_permutations.d.set(row, column, this_netpair_nonperm_d);
% end
% if isprop(result_object, "full_connectome") && ~isequal(result_object.full_connectome, false)
% %this_netpair_fullconn_d = COMPUTE FULLCONN D HERE;
% result_object.full_connectome.d.set(row, column, this_netpair_fullconn_d);
% end
% if isprop(result_object, "within_network_pair") && ~isequal(result_object.within_network_pair, false)
% %this_netpair_withinNP_d = COMPUTE WITHIN NET PAIR D HERE
% result_object.within_network_pair.d.set(row, column, this_netpair_withinNP_d);
% end
% end
% end
end
end
end
20 changes: 12 additions & 8 deletions +nla/TestPool.m
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Expand Up @@ -64,8 +64,7 @@
function ranked_results = collateNetworkPermutationResults(obj, nonpermuted_edge_test_results, network_atlas, nonpermuted_network_test_results,...
permuted_network_test_results, network_test_options)

% Run Cohen's D
cohen_d_test = nla.net.CohenDTest();


% Warning: Hacky code. Because of the way non-permuted network tests and permuted are called from the front, they are stored
% in different objects. (Notice the input argument for non-permuted network results). Eventually, it should probably be done
Expand All @@ -78,10 +77,15 @@
end
end
end
for test_index = 1:numNetTests(obj)
permuted_network_test_results{test_index} = cohen_d_test.run(nonpermuted_edge_test_results, network_atlas,...
permuted_network_test_results{test_index});
end

% REMOVE CALL TO COHENS D UNTIL WE DETERMINE CORRECT CALC FOR IT ADE 2025MAR24
% Run Cohen's D
% cohen_d_test = nla.net.CohenDTest();
% for test_index = 1:numNetTests(obj)
%
% permuted_network_test_results{test_index} = cohen_d_test.run(nonpermuted_edge_test_results, network_atlas,...
% permuted_network_test_results{test_index});
% end

ranked_results = obj.rankResults(network_test_options, permuted_network_test_results, network_atlas.numNetPairs());
end
Expand Down Expand Up @@ -274,11 +278,11 @@
end

function ranked_results = rankResults(obj, input_options, permuted_network_results, number_of_network_pairs)
import nla.net.ResultRank


ranked_results = permuted_network_results;
for test = 1:numNetTests(obj)
ranker = ResultRank(permuted_network_results{test}, number_of_network_pairs);
ranker = nla.net.ResultRank(permuted_network_results{test}, number_of_network_pairs);
ranked_results_object = ranker.rank();
ranked_results{test} = ranked_results_object;
if any(strcmp(ranked_results{test}.test_name, obj.correlation_input_tests))
Expand Down
Binary file modified NLAResult.mlapp
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5 changes: 1 addition & 4 deletions NLAResult_exported.m
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Expand Up @@ -293,9 +293,7 @@ function initFromResult(app, result, file_name, ~, old_data)
app.results = false;
end

if ~islogical(result.network_test_results)
app.genadjustableNetParams();
end

end

function enableNetButtons(app, val)
Expand Down Expand Up @@ -416,7 +414,6 @@ function RunButtonPushed(app, event)
drawnow();

app.setNesting();
app.genadjustableNetParams();

close(prog);
end
Expand Down
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