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Include physio processing #3

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9b538ee
added button for physio batch
Dec 13, 2019
56a102d
added vendor field, read in params
Dec 18, 2019
d0692df
only save, physio installation instruction
Dec 18, 2019
b94f10b
error message when physio not installed
Dec 18, 2019
ca0beae
changes with respect to first comments layout in UI changed
Jan 9, 2020
7091d6a
replaced spm select box
Jan 9, 2020
86215ba
settings tab, add figures to report
Jan 24, 2020
fc2cd7c
bugfix underscore missing
Feb 3, 2020
1ecdcab
export settings button
Feb 24, 2020
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221 changes: 215 additions & 6 deletions api-matlab/rtQC_display.m
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Original file line number Diff line number Diff line change
Expand Up @@ -59,6 +59,7 @@ function rtQC_display()

% Setup all UIcontrols and GUI components
rtQC_display_setup;

% Set callbacks
gui_data.tgroup.SelectionChangedFcn = @tabChangedCallback;
gui_data.pb_help.Callback = @linkToGithub;
Expand Down Expand Up @@ -91,6 +92,7 @@ function rtQC_display()
gui_data.pb_startRT.Callback = @startRT;
gui_data.pb_stopRT.Callback = @stopRT;
gui_data.popup_setDim.Callback = @setDim;
gui_data.popup_setVendor.Callback = @setVendor;
gui_data.sld_slice.Callback = @changeSlice;
gui_data.popup_setImg.Callback = @setImg;
gui_data.edit_structural_pre.Callback = @editStructural;
Expand All @@ -113,10 +115,39 @@ function rtQC_display()

gui_data.QCtgroup.SelectionChangedFcn = @QCtabChangedCallback;
gui_data.pb_open_qc_post.Callback = @generateReport;

gui_data.pb_get_physio_batch.Callback = @physioBatch;

% settings callback
gui_data.edit_physio_save_dir.Callback = @editphysio_save_dir ;
gui_data.edit_log_files_sampling_interval.Callback = @editlog_files_sampling_interval ;
gui_data.edit_log_files_relative_start_acquisition.Callback = @editlog_files_relative_start_acquisition ;
gui_data.edit_log_files_align_scan.Callback = @editlog_files_align_scan ;
gui_data.edit_sqpar_NslicesPerBeat.Callback = @editsqpar_NslicesPerBeat ;
gui_data.edit_sqpar_time_slice_to_slice.Callback = @editsqpar_time_slice_to_slice ;
gui_data.edit_sqpar_Nprep.Callback = @editsqpar_Nprep ;
gui_data.edit_sync_nominal.Callback = @editsync_nominal ;
gui_data.edit_auto_matched_min.Callback = @editauto_matched_min ;
gui_data.edit_auto_matched_file.Callback = @editauto_matched_file ;
gui_data.edit_posthoc_cpulse_select_off.Callback = @editposthoc_cpulse_select_off ;
gui_data.edit_model_output_multiple_regressors.Callback = @editmodel_output_multiple_regressors ;
gui_data.edit_model_output_physio.Callback = @editmodel_output_physio ;
gui_data.edit_model_orthogonalise.Callback = @editmodel_orthogonalise ;
gui_data.edit_model_censor_unreliable_recording_intervals.Callback = @editmodel_censor_unreliable_recording_intervals ;
gui_data.edit_order_c.Callback = @editorder_c;
gui_data.edit_order_r.Callback = @editorder_r ;
gui_data.edit_order_cr.Callback = @editorder_cr ;
gui_data.edit_rvt_no.Callback = @editrvt_no ;
gui_data.edit_hrv_no.Callback = @edithrv_no ;
gui_data.edit_noise_rois_no.Callback = @editnoise_rois_no ;
gui_data.edit_movement_no.Callback = @editmovement_no ;
gui_data.edit_other_no.Callback = @editother_no ;
gui_data.edit_verbose_level.Callback = @editverbose_level ;
gui_data.edit_verbose_fig_output_file.Callback = @editverbose_fig_output_file ;
gui_data.edit_verbose_use_tabs.Callback = @editverbose_use_tabs ;

gui_data.export_settings.Callback = @export_settings;

set(findall(fig, '-property', 'Interruptible'), 'Interruptible', 'on')

% Make figure visible after normalizing units
set(findall(fig, '-property', 'Units'), 'Units', 'Normalized')
fig.Visible = 'on';
Expand Down Expand Up @@ -205,6 +236,147 @@ function gotoTab2(hObject,eventdata)
guidata(fig,gui_data)
end

%%%% start settings tab functions

function export_settings(hObject,eventdata)
fig = ancestor(hObject,'figure');
gui_data = guidata(fig);
panels = {'general', 'physio', 'new'};
labels = {};
values = {};
counter = 1;
for i=1:length(panels)
children = eval(['gui_data.panel_set_' panels{i} '.Children']);
for j=1:length(children)
if strcmp(children(j).Style, 'text')
name = children(j).String;
name = strrep(name, '.', '_');
matching_edit = eval(['gui_data.edit_' name '.String']);
labels{counter} = [panels{i} '_' name];
values{counter} = matching_edit;
counter = counter+1;
end
end
end
% save to json file
enc = jsonencode(containers.Map(labels, values));
fid = fopen([gui_data.qc_out_dir filesep 'settings.json'], 'wt');
fprintf(fid, '%s', enc);
fclose(fid);
msgbox(['Saved settings in: ' gui_data.qc_out_dir], 'Success');
end

function editphysio_save_dir (hObject,eventdata)
fig = ancestor(hObject,'figure');
gui_data = guidata(fig);
end
function editlog_files_sampling_interval (hObject,eventdata)
fig = ancestor(hObject,'figure');
gui_data = guidata(fig);
end
function editlog_files_relative_start_acquisition (hObject,eventdata)
fig = ancestor(hObject,'figure');
gui_data = guidata(fig);
end
function editlog_files_align_scan (hObject,eventdata)
fig = ancestor(hObject,'figure');
gui_data = guidata(fig);
end
function editsqpar_NslicesPerBeat (hObject,eventdata)
fig = ancestor(hObject,'figure');
gui_data = guidata(fig);
end
function editsqpar_time_slice_to_slice (hObject,eventdata)
fig = ancestor(hObject,'figure');
gui_data = guidata(fig);
end
function editsqpar_Nprep (hObject,eventdata)
fig = ancestor(hObject,'figure');
gui_data = guidata(fig);
end
function editsync_nominal (hObject,eventdata)
fig = ancestor(hObject,'figure');
gui_data = guidata(fig);
end
function editauto_matched_min (hObject,eventdata)
fig = ancestor(hObject,'figure');
gui_data = guidata(fig);
end
function editauto_matched_file (hObject,eventdata)
fig = ancestor(hObject,'figure');
gui_data = guidata(fig);
end
function editposthoc_cpulse_select_off (hObject,eventdata)
fig = ancestor(hObject,'figure');
gui_data = guidata(fig);
end
function editmodel_output_multiple_regressors (hObject,eventdata)
fig = ancestor(hObject,'figure');
gui_data = guidata(fig);
end
function editmodel_output_physio (hObject,eventdata)
fig = ancestor(hObject,'figure');
gui_data = guidata(fig);
end
function editmodel_orthogonalise (hObject,eventdata)
fig = ancestor(hObject,'figure');
gui_data = guidata(fig);
end
function editmodel_censor_unreliable_recording_intervals (hObject,eventdata)
fig = ancestor(hObject,'figure');
gui_data = guidata(fig);
end
function editorder_c (hObject,eventdata)
fig = ancestor(hObject,'figure');
gui_data = guidata(fig);
end
function editorder_r (hObject,eventdata)
fig = ancestor(hObject,'figure');
gui_data = guidata(fig);
end
function editorder_cr (hObject,eventdata)
fig = ancestor(hObject,'figure');
gui_data = guidata(fig);
end
function editrvt_no (hObject,eventdata)
fig = ancestor(hObject,'figure');
gui_data = guidata(fig);
end
function edithrv_no (hObject,eventdata)
fig = ancestor(hObject,'figure');
gui_data = guidata(fig);
end
function editnoise_rois_no (hObject,eventdata)
fig = ancestor(hObject,'figure');
gui_data = guidata(fig);
end
function editmovement_no (hObject,eventdata)
fig = ancestor(hObject,'figure');
gui_data = guidata(fig);
end
function editother_no (hObject,eventdata)
fig = ancestor(hObject,'figure');
gui_data = guidata(fig);
end
function editverbose_level (hObject,eventdata)
fig = ancestor(hObject,'figure');
gui_data = guidata(fig);
end
function editverbose_fig_output_file(hObject,eventdata)
fig = ancestor(hObject,'figure');
gui_data = guidata(fig);
txt = get(hObject, 'String');
gui_data.editverbose_fig_output_file.String = txt;
% assignin('base', 'gui_data', gui_data)
guidata(fig,gui_data)
end
function editverbose_use_tabs (hObject,eventdata)
fig = ancestor(hObject,'figure');
gui_data = guidata(fig);
end

%%%%% end setting tab functions


function editFDthreshold(hObject,eventdata)
fig = ancestor(hObject,'figure');
Expand All @@ -226,7 +398,6 @@ function editFDthreshold(hObject,eventdata)
guidata(fig,gui_data)
end


function editSPMdir(hObject,eventdata)
fig = ancestor(hObject,'figure');
gui_data = guidata(fig);
Expand Down Expand Up @@ -457,6 +628,7 @@ function calcAndDispMI(hObject,eventdata)
return;
end


msgbox('Functionality to be added: plot 2D histogram and display mutual information measure');
% slice_nr = 20;
% im1 = spm_read_vols(spm_vol(gui_data.im1_dqchecks_fn));
Expand Down Expand Up @@ -492,6 +664,8 @@ function runPreProc(hObject,eventdata)
gui_data.functional0_fn = [gui_data.functional4D_fn ',1'];
% Preprocess structural and f0 images
[d, f, e] = fileparts(gui_data.structural_fn);
disp(d);
disp(f);
if exist([d filesep 'rc1' f e], 'file')
% 1) If preprocessing has already been done, assign variables
gui_data.preProc_status = 1;
Expand Down Expand Up @@ -1099,6 +1273,9 @@ function drawTHEPLOT(fig)
% guidata(fig, gui_data);
end

function setVendor(hObject,eventdata)

end

function setDim(hObject,eventdata)

Expand Down Expand Up @@ -1215,7 +1392,6 @@ function drawBrains(fig)
end



% Offline tab functions

function runOfflineQC(hObject,eventdata)
Expand Down Expand Up @@ -1424,7 +1600,7 @@ function generateReport(hObject,eventdata)
dt_str = [num2str(Y) num2str(MO) num2str(D) num2str(H) num2str(MI) num2str(round(S))];
t = datestr(dt);
log_name = [gui_data.subject_id '_' dt_str '.html'];
fid = fopen(log_name,'a');
fid = fopen([gui_data.qc_out_dir filesep log_name],'a');
fprintf(fid, '<H2>Log</H2>');
fprintf(fid, ['\n<BR>Subject: ' gui_data.subject_id]);
fprintf(fid, ['\n<BR>Date/time: ' t]);
Expand All @@ -1450,10 +1626,43 @@ function generateReport(hObject,eventdata)
fprintf(fid, '\n<TABLE><TR><TD><img src="tsnr_whole.png" alt="no picture" width=700 height=600></TD></TR></TABLE>' );
fprintf(fid, '\n<TABLE><TR><TD><img src="tsnr_brain.png" alt="no picture" width=700 height=600></TD></TR></TABLE>' );
fprintf(fid, '\n<TABLE><TR><TD><img src="mask_contour.png" alt="no picture" width=700 height=700></TD></TR></TABLE>' );
% add physio plots
phys_dir = gui_data.edit_physio_save_dir.String;
if exist([gui_data.qc_out_dir filesep phys_dir])
fprintf(fid, '<H2>Physio processing plots</H2>');
figure_file_gen = split(gui_data.edit_verbose_fig_output_file.String, '.');
figure_file = cell2mat(join([figure_file_gen(1) '_05.' figure_file_gen(2)], ''));
img_to_plot = [phys_dir '/' figure_file]; % possible option (this works if in settings tab just allow input of directory name
% add other figures
fprintf(fid, sprintf('\n<TABLE><TR><TD><img src="%s" alt="no picture" width=700 height=600></TD></TR></TABLE>', img_to_plot));
end
fclose(fid);
url = ['file:///' gui_data.qc_out_dir filesep log_name];
web(url, '-browser')
web(url, '-browser');

end

function physioBatch(hObject,eventdata)

% get guidata
fig = ancestor(hObject,'figure');
gui_data = guidata(fig);

vendor = gui_data.popup_setVendor.String(gui_data.popup_setVendor.Value);
if strcmp(vendor, 'select vendor...')
errordlg('First set vendor in drop down menu to the right of the button.');
end

%% read nr slices and nr scans from nifti header:
% hdr = spm_vol('C:\Users\nwiedemann\Downloads\rtQC_sample_data\rtQC_sample_data\sub-opennft\fanon-0007.nii')
% nr_scans = length(hdr)
% nr_slices = hdr(1).dim(3)
%%
% default path for cardiac and respiratory inputs:
default_path = gui_data.data_dir;
% default_path = 'C:\Users\nwiedemann\Downloads\tapas\tapas\misc\example\PhysIO';

wrapper_physiobatch(char(vendor), gui_data.qc_out_dir, default_path, gui_data);
end

function showFDoutliers(hObject,eventdata)
Expand Down
27 changes: 23 additions & 4 deletions api-matlab/rtQC_display_setup.m
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Original file line number Diff line number Diff line change
Expand Up @@ -34,6 +34,7 @@
gui_data.tab_pre = uitab('Parent', gui_data.tgroup, 'Title', 'Pre QC');
gui_data.tab_online = uitab('Parent', gui_data.tgroup, 'Title', 'Online QC');
gui_data.tab_post = uitab('Parent', gui_data.tgroup, 'Title', 'Post QC');
gui_data.tab_settings = uitab('Parent', gui_data.tgroup, 'Title', 'Settings');

% Set variable values
gui_data.current_dir = mfilename('fullpath');
Expand Down Expand Up @@ -964,26 +965,42 @@
'Style', 'push',...
'String', 'Show FD outliers', ...
'Units', 'Normalized',...
'Position', [0.8 0.7 0.18 0.3],...
'Position', [0.8 0.795 0.18 0.225],...
'CallBack', @showFDoutliers, ...
'UserData', 0,...
'fontsize', gui_data.button_font_size);
gui_data.pb_run_qc_post = uicontrol('Parent', gui_data.panel_rtsummary,...
'Style', 'push',...
'String', 'Run Offline QC', ...
'Units', 'Normalized',...
'Position', [0.8 0.38 0.18 0.3],...
'Position', [0.8 0.55 0.18 0.225],...
'CallBack', @runOfflineQC, ...
'UserData', 0,...
'fontsize', gui_data.button_font_size);
gui_data.pb_open_qc_post = uicontrol('Parent', gui_data.panel_rtsummary,...
'Style', 'push',...
'String', 'Generate report', ...
'Units', 'Normalized',...
'Position', [0.8 0.06 0.18 0.3],...
'Position', [0.8 0.06 0.18 0.225],...
'CallBack', @generateReport, ...
'UserData', 0,...
'fontsize', gui_data.button_font_size);
gui_data.pb_get_physio_batch = uicontrol('Parent', gui_data.panel_rtsummary,...

@jsheunis jsheunis Jan 7, 2020

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The positioning of the button and dropdown on the GUI is not great, when run on my Mac:
Screen Shot 2020-01-07 at 11 04 08

@NinaWie Does is render differently on your system?

Previously I haven't given much attention to cross-platform functionality, at least in the sense that the display of the GUI and buttons are fine. Maybe that needs some more attention.

For this specific case, maybe check if you can update the position of these UIcontrols, and perhaps others on the same tab and group, such that the layout is user friendly.

@NinaWie NinaWie Jan 9, 2020

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Yes, it renders perfectly fine on my system. But I now changed it such that "select vendor" is inside the drop down menu, which I like better than the label above the menu anyway. You can try again, the new commit should be part of the pull request already. Let me know if it's still ugly on the mac.

@jsheunis jsheunis Jan 16, 2020

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Perfect

'Style', 'push',...
'String', 'Get physio batch', ...
'Units', 'Normalized',...
'Position', [0.8 0.305 0.1 0.225],...
'CallBack', @physioBatch, ...
'UserData', 0,...
'fontsize', gui_data.button_font_size);
gui_data.popup_setVendor = uicontrol('Parent', gui_data.panel_rtsummary,...
'Style', 'popup',...
'String', {'select vendor...', 'BIDS','Philips','Biopac_Txt','GE','Siemens','Siemens_HCP','Siemens_Tics'},...
'Units', 'Normalized',...
'Position', [0.91 0.305 0.07 0.225],...
'Value', 1,...
'Callback', @setVendor,...
'fontsize', gui_data.button_font_size);


% Offline summary panel UIcontrols
Expand Down Expand Up @@ -1072,7 +1089,9 @@
% set(get(gui_data.panel_qcsummaryR,'Children'),'Enable','off')
% set(children(strcmpi ( get (children,'Type'),'UIControl')),'enable','off')


%% --------------- Create UIcontrols for PRE QC tab -------------------- %%
settings_tab;
%%

% Save GUI data
guidata(fig, gui_data)
Expand Down
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