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[NET-276] Allow txt and csv functional connectivity files #114

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Merged
pollaro merged 1 commit into from
May 13, 2025
Merged

[NET-276] Allow txt and csv functional connectivity files #114

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129 changes: 80 additions & 49 deletions +nla/+inputField/NetworkAtlasFuncConn.m
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Original file line number Diff line number Diff line change
Expand Up @@ -37,7 +37,9 @@
label_gap = LABEL_GAP;
h = LABEL_H * 2 + label_gap;

%% Create label
%% NETWORK ATLAS

% Create label
if ~isgraphics(obj.label)
obj.label = uilabel(parent);
end
Expand All @@ -46,14 +48,14 @@
obj.label.HorizontalAlignment = 'left';
obj.label.Position = [x, y - LABEL_H, label_w + label_gap, LABEL_H];

%% Create button
% Create button
if ~isgraphics(obj.button)
obj.button = uibutton(parent, 'push', 'ButtonPushedFcn', @(h,e)obj.buttonClickedCallback());
end
button_w = 100;
obj.button.Position = [x + label_w + label_gap, y - LABEL_H, button_w, LABEL_H];

%% Mesh inflation selector
% Mesh inflation selector
if ~isgraphics(obj.inflation_label)
obj.inflation_label = uilabel(parent);
obj.inflation_label.HorizontalAlignment = 'right';
Expand All @@ -70,15 +72,15 @@
end
obj.inflation_dropdown.Position = [0, y - LABEL_H, inflation_dropdown_w, LABEL_H];

%% 'View as surface parcel' checkbox
% 'View as surface parcel' checkbox
checkbox_surface_parcels_w = 108;
if ~isgraphics(obj.checkbox_surface_parcels)
obj.checkbox_surface_parcels = uicheckbox(parent);
obj.checkbox_surface_parcels.Text = ' Surface parcels';
end
obj.checkbox_surface_parcels.Position = [0, y - LABEL_H, checkbox_surface_parcels_w, LABEL_H];

%% Create view button
% Create view button
if ~isgraphics(obj.button_view_net_atlas)
obj.button_view_net_atlas = uibutton(parent, 'push', 'ButtonPushedFcn',...
@(h,e)obj.buttonViewNetAtlasClickedCallback());
Expand All @@ -88,8 +90,10 @@
obj.button_view_net_atlas.Position = [0, y - LABEL_H, button_view_net_atlas_w, LABEL_H];

w = label_w + label_gap + button_w + label_gap + checkbox_surface_parcels_w + label_gap + button_view_net_atlas_w;

%% Create label2
%%

%% FUNCTIONAL CONNECTIVITY
% Create label2
if ~isgraphics(obj.label2)
obj.label2 = uilabel(parent);
end
Expand All @@ -98,14 +102,14 @@
obj.label2.HorizontalAlignment = 'left';
obj.label2.Position = [x, y - h, label2_w + label_gap, LABEL_H];

%% Create button2
% Create button2
if ~isgraphics(obj.button2)
obj.button2 = uibutton(parent, 'push', 'ButtonPushedFcn', @(h,e)obj.button2ClickedCallback());
end
button2_w = 100;
obj.button2.Position = [x + label2_w + label_gap, y - h, button2_w, LABEL_H];

%% Create view button
% Create view button
if ~isgraphics(obj.button_view_fc_avg)
obj.button_view_fc_avg = uibutton(parent, 'push', 'ButtonPushedFcn', @(h,e)obj.buttonViewFCAvgClickedCallback());
end
Expand All @@ -116,6 +120,7 @@

w2 = label2_w + label_gap + button2_w + label_gap + button_view_fc_avg_w;
w = max(w, w2);
%%
end

function undraw(obj)
Expand Down Expand Up @@ -204,55 +209,81 @@ function buttonClickedCallback(obj, ~)
end

function button2ClickedCallback(obj, ~)
[file, path, idx] = uigetfile({'*.mat', 'Functional connectivity matrix (*.mat)'}, 'Select Functional Connectivity Matrix');
if idx == 1
prog = uiprogressdlg(obj.fig, 'Title', 'Loading functional connectivity data', 'Message',...
sprintf('Loading %s', file), 'Indeterminate', true);
drawnow;

[file, path, idx] = uigetfile(...
{'*.mat', 'MATLAB File (*.mat)'; '*.csv', 'Comma-separated Values (*.csv)'; '*.txt', 'Text file (*.txt)'},...
'Select Functional Connectivity Matrix', 'MultiSelect', 'on'...
);
text_file = file;
if iscell(file)
text_file = file{1};
end
prog = uiprogressdlg(obj.fig, 'Title', 'Loading functional connectivity data', 'Message',...
sprintf('Loading %s', text_file), 'Indeterminate', true);
drawnow;

fc_unordered = false;
if idx == 1
fc_data = load([path file]);
fc_unordered = false;
if isnumeric(fc_data)
fc_unordered = fc_data;
elseif isstruct(fc_data)
if isfield(fc_data, 'functional_connectivity')
fc_unordered = fc_data.functional_connectivity;
elseif isfield(fc_data, 'func_conn')
fc_unordered = fc_data.func_conn;
elseif isfield(fc_data, 'fc')
fc_unordered = fc_data.fc;
else
fn = fieldnames(fc_data);
if numel(fn) == 1
fname = fn{1};
if isnumeric(fc_data.(fname))
fc_unordered = fc_data.(fname);
end
else
if iscell(file)
fc_data = readmatrix([path file{1}]);
for current_file = 2:numel(file)
fc_data(:,:,current_file) = readmatrix([path file{current_file}]);
end
else
fc_data = readmatrix([path file]);
fc_data_size = size(fc_data);
if numel(fc_data_size) == 2 && fc_data_size(1) ~= fc_data_size(2)
greater_dimension = fc_data_size(2);
lesser_dimension = fc_data_size(1);
if fc_data_size(1) > fc_data_size(2)
greater_dimension = fc_data_size(1);
lesser_dimension = fc_data_size(2);
end
third_dimension = greater_dimension / lesser_dimension;
fc_data = reshape(fc_data, [lesser_dimension, lesser_dimension, third_dimension]);
end
end
end

% functional connectivity matrix (not ordered/trimmed according to network atlas yet)
if ~islogical(fc_unordered)
obj.func_conn_unordered = double(fc_unordered);

%% Transform R-values to Z-scores
% If this condition isn't true, it cannot be R values
% If it is true, it is almost certainly R values but might not be
if all(abs(obj.func_conn_unordered(:)) <= 1)
sel = uiconfirm(obj.fig, sprintf('Fisher Z transform functional connectivity data?\n(If you have provided R-values)'), 'Fisher Z transform?');
if strcmp(sel, 'Ok')
obj.func_conn_unordered = nla.fisherR2Z(obj.func_conn_unordered);
if isnumeric(fc_data)
fc_unordered = fc_data;
elseif isstruct(fc_data)
if isfield(fc_data, 'functional_connectivity')
fc_unordered = fc_data.functional_connectivity;
elseif isfield(fc_data, 'func_conn')
fc_unordered = fc_data.func_conn;
elseif isfield(fc_data, 'fc')
fc_unordered = fc_data.fc;
else
fn = fieldnames(fc_data);
if numel(fn) == 1
fname = fn{1};
if isnumeric(fc_data.(fname))
fc_unordered = fc_data.(fname);
end
end

obj.update();
close(prog);
else
close(prog);
uialert(obj.fig, sprintf('Could not load functional connectivity matrix from %s', file), 'Invalid functional connectivity file');
end
end

% functional connectivity matrix (not ordered/trimmed according to network atlas yet)
if ~islogical(fc_unordered)
obj.func_conn_unordered = double(fc_unordered);

%% Transform R-values to Z-scores
% If this condition isn't true, it cannot be R values
% If it is true, it is almost certainly R values but might not be
if all(abs(obj.func_conn_unordered(:)) <= 1)
sel = uiconfirm(obj.fig, sprintf('Fisher Z transform functional connectivity data?\n(If you have provided R-values)'), 'Fisher Z transform?');
if strcmp(sel, 'Ok')
obj.func_conn_unordered = nla.fisherR2Z(obj.func_conn_unordered);
end
end
obj.update();
else
uialert(obj.fig, sprintf('Could not load functional connectivity matrix from %s', file), 'Invalid functional connectivity file');
end
close(prog);
end

function buttonViewNetAtlasClickedCallback(obj)
Expand Down
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