tapas_physio_pca -> no voxel limitation

PhysIO/code/gui/tapas_physio_interactive_noiseROI_mask.m

@@ -0,0 +1,237 @@
+function tapas_physio_interactive_noiseROI_mask( mask_path )
+%TAPAS_PHYSIO_INTERACTIVE_NOISEROI_MASK function will help visualizing the
+%effect of 'threshold' and 'erosion' in tapas_physio_create_noise_rois_regressors()
+%
+% SYNTAX
+%   tapas_physio_interactive_noiseROI_mask() % a popup window will be used to select a mask
+%   tapas_physio_interactive_noiseROI_mask('path/to/my_mask.nii')
+%
+% NOTES
+%   The noiseROI will be created on the fly and kept in memory, it will not
+%   be written on disk.
+%   Selected values can be saved as global variables for latter usage.
+%
+
+default_threshold = 0.95; % from 0 to 1
+default_erosion   = 1;    % 0, 1, 2, ...
+
+
+%% Mask selection
+
+if nargin < 1
+    mask_path = spm_select(1,'image','Select a mask');
+    if isempty(mask_path)
+        return
+    end
+end
+
+
+%% Load mask & display it
+
+Vmask = spm_vol(mask_path);
+Ymask = spm_read_vols(Vmask);
+
+spm_check_registration(Vmask);
+spm_orthviews('context_menu','interpolation',3); % disable interpolation // 3->NN , 2->Trilin , 1->Sinc
+
+
+%% Vroi
+% the noiseROI will be computed and displayed on the fly without writting to the disk
+
+% copy header
+Vroi = Vmask;
+% change some settings so the volume remains "virtual"
+% thanks to @gllmflndn for helping on this part
+Vroi.dt = [spm_type('float64') 0];
+Vroi.pinfo = [1 ; 0 ; 0];
+
+[Yroi , descrip ] = threshold_erode_mask(Ymask, default_threshold, default_erosion);
+Vroi.fname = descrip; % only useful for the display in the menu
+
+Vroi.dat = Yroi; % this is not a file object, just a standard matrix
+print_stats( Yroi )
+
+
+%% UserData (useful for the GUI)
+
+UserData = struct;
+UserData.Vmask = Vmask;
+UserData.Ymask = Ymask;
+UserData.Vroi  = Vroi;
+
+
+%% GUI
+% add a panel so the user can enter the values in the SPM figure
+
+F = spm_figure('FindWin','Graphics');
+
+% this code might not work in old version of Matlab, since it use the "object" syntax
+% old versions might have to use get() & set() functions
+panel = uipanel(F,...
+    'Title','Threshold & Erosion',...
+    'Units', 'Normalized',...
+    'Position',[...
+    F.Children(2).Position(1)...
+    F.Children(4).Position(2)...
+    F.Children(2).Position(3)...
+    F.Children(4).Position(4)...
+    ],...
+    'UserData', UserData);
+
+% from botton to top, since matlab figure origin (0,0) is in the bottom left corner
+
+uicontrol(panel,...
+    'Tag', 'pushbutton_save',...
+    'Style','pushbutton',...
+    'Units','normalized',...
+    'Position',[0.1 0.1 0.8 0.2],...
+    'String', 'Save values & close',...
+    'Tooltip','Saved as global variables',...
+    'Callback',@save_values_Callback);
+
+uicontrol(panel,...
+    'Tag','text_erosion',...
+    'Style','Text',...
+    'Units', 'Normalized',...
+    'Position',[0.1 0.4 0.3 0.25],...
+    'String', '3D erosion');
+
+uicontrol(panel,...
+    'Tag','edit_erosion',...
+    'Style','Edit',...
+    'Units', 'Normalized',...
+    'Position',[0.4 0.4 0.4 0.25],...
+    'String', num2str(default_erosion),...
+    'Callback', @update_noiseROI_Callback,...
+    'Tooltip','integer values, like 0 1 2 3 ...');
+
+uicontrol(panel,...
+    'Tag','text_threshold',...
+    'Style','Text',...
+    'Units', 'Normalized',...
+    'Position',[0.1 0.7 0.3 0.25],...
+    'String', 'Threshold');
+
+uicontrol(panel,...
+    'Tag','edit_threshold',...
+    'Style','Edit',...
+    'Units', 'Normalized',...
+    'Position',[0.4 0.7 0.4 0.25],...
+    'String', num2str(default_threshold),...
+    'Callback', @update_noiseROI_Callback,...
+    'Tooltip', 'from 0 to 1');
+
+
+%% Add the overlay
+% code from spm_orthviews:add_c_image
+
+global st % global variable used by using spm_orthviews()
+
+r = 1;
+
+spm_orthviews('addcolouredimage',r,Vroi ,[1 0 0]);
+hlabel = sprintf('%s (%s)',Vroi.fname ,'Red');
+c_handle    = findobj(findobj(st.vols{r}.ax{1}.cm,'label','Overlay'),'Label','Remove coloured blobs');
+ch_c_handle = get(c_handle,'Children');
+set(c_handle,'Visible','on');
+uimenu(ch_c_handle(2),'Label',hlabel,'ForegroundColor',[1 0 0],...
+    'Callback','c = get(gcbo,''UserData'');spm_orthviews(''context_menu'',''remove_c_blobs'',2,c);',...
+    'Tag','noiseROI_menu');
+spm_orthviews('redraw')
+
+
+end % function
+
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+function [ Yroi , descrip ] = threshold_erode_mask(Ymask, threshold, erosion)
+
+Yroi = Ymask/max(abs(Ymask(:))); % normamalize input range to [0..1]
+Yroi(Yroi< threshold) = 0;
+Yroi(Yroi>=threshold) = 1;
+
+for i = 1 : erosion
+    Yroi = spm_erode(Yroi);
+end
+
+descrip = sprintf('threshold = %4.2f // erosion = %d', threshold, erosion);
+
+end % function
+
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+function print_stats( Yroi )
+
+fprintf('[%s]: n_Voxels_in_ROI = %6d \n', mfilename, sum(Yroi(:)));
+
+end % function
+
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+function update_noiseROI_Callback(hObject,~)
+
+global st % to overlay the final ROIs, using spm_orthviews
+
+% Retrieve UserData
+panel = get(hObject,'Parent');
+UserData = get(panel,'UserData');
+
+
+% Check values
+threshold = get( findobj('Tag', 'edit_threshold'), 'String');
+threshold = str2double(threshold);
+if threshold<0 || threshold>1 || isnan(threshold)
+    threshold = 0.95;
+    set( findobj('Tag', 'edit_threshold'), 'String', num2str(threshold));
+end
+
+erosion = get( findobj('Tag', 'edit_erosion'), 'String');
+erosion = str2double(erosion);
+erosion = round(erosion);
+if erosion<0 || erosion>999 || isnan(erosion)
+    erosion = 1;
+    set( findobj('Tag', 'edit_erosion'), 'String', num2str(erosion));
+end
+
+
+% Apply new values on mask
+[ Yroi , descrip ] = threshold_erode_mask(UserData.Ymask, threshold, erosion);
+UserData.Vroi.dat = Yroi;
+UserData.Vroi.name = descrip;
+print_stats( Yroi )
+
+
+% Redraw : update overlay
+st.vols{1}.blobs{1}.vol = UserData.Vroi;
+handles = findobj('Tag', 'noiseROI_menu');
+handles.Text = sprintf('%s (Red)', descrip);
+spm_orthviews('redraw')
+
+
+end % function
+
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+function save_values_Callback(~,~)
+
+F = spm_figure('FindWin','Graphics');
+
+threshold = get( findobj('Tag', 'edit_threshold'), 'String');
+threshold = str2double(threshold);
+
+erosion = get( findobj('Tag', 'edit_erosion'), 'String');
+erosion = str2double(erosion);
+erosion = round(erosion);
+
+global tapas_physio_interactive_noiseROI_mask_threshold tapas_physio_interactive_noiseROI_mask_erosion
+tapas_physio_interactive_noiseROI_mask_threshold = threshold;
+tapas_physio_interactive_noiseROI_mask_erosion   = erosion;
+
+fprintf('[%s]: Values saved in global variables : \n', mfilename);
+fprintf('tapas_physio_interactive_noiseROI_mask_threshold = %4.2f \n', threshold);
+fprintf('tapas_physio_interactive_noiseROI_mask_erosion   = %d \n', erosion);
+fprintf('Retrieve them using ''global tapas_physio_interactive_noiseROI_mask_threshold tapas_physio_interactive_noiseROI_mask_erosion'' \n')
+
+delete(F)
+
+end % function