The alpha version. The first working version.

GIFT_Clean/GiftIcaReport.m

@@ -5,17 +5,45 @@ classdef GiftIcaReport<handle
     % some guidlines can be found below!
     % https://doi.org/10.1016/j.neuroimage.2016.12.036
     
+    % to do: auto scale images
+    % to do: check slices to be plotted actually exist!!
+    % to do: create the output
     properties
-        ICAfile     = {};   % .nii file containing the ICA images
+        ICAfile     = {};       % .nii file containing the ICA images
-        TCfile      = {};   % .nii file containing the TimeCourse data
+        TCfile      = {};       % .nii file containing the TimeCourse data
-        Orientation = 'sag';% orientation of images to create
+        Orientation = 'sag';    % orientation of images to create
-        SliceNumbers = [];   % slice numbers to plot
+        DirOut          = '.'   %default uses the current directory
+        FileOut         = 'Report.png'; %default report name
+        Layout          = 'north';     %define the location of the TC plot
+        Colormap=gray;          % colormap for images
         
     end
+    properties (Dependent=true)
+        PlotSliceNumbers       % slice numbers to plot
+        NPlots            % number of slices to plot
+        ImageLimits       %defines the minium and max value for colorbar
+    end
     
     properties (Access=private)
-        OrientationOptions={'tra','sag','cor','all'};
         SPMPath
+        FigureObject
+        ImageData
+        TimeCourseData
+        VData
+        VTimeCourse
+        PData
+        PTimeCourse
+        SliceNumbersInternal
+        NSlicesInternal = 10;
+        TCPlot  %subplot containing the time course
+        SLPlot  %subplot containing the 
+        CLim = [0,1]; %limits for plotting
+        %% the matlab reporting gives an licence error.
+        % ReportObj               % the place holder for the Report object
+        
+    end
+    properties (Constant,Access=private)
+        OrientationOptions={'tra','sag','cor','all'}; %option all still needs to be implemented
     end
     
     methods %constructor, set and get functions
@@ -23,6 +51,18 @@ classdef GiftIcaReport<handle
             %GIFTICAREPORT Construct an instance of this class
             %   Detailed explanation goes here
             obj.SPMPath=[]; %check if SPM is in the path
+            obj.FigureObject=figure; %create a figure
+            %% the matlab reporting gives an licence error at the CNC
+            %import mlreportgen.report.*
+            %obj.ReportObj = Report(fullfile(obj.DirOut,obj.FileOut));
+        end
+        
+        function delete(obj)
+            if ~isempty(obj.FigureObject)
+                if isa(obj.FigureObject,'matlab.ui.Figure')
+                    close(obj.FigureObject);
+                end
+            end
         end
         
         function set.SPMPath(obj,~)
@@ -37,41 +77,287 @@ classdef GiftIcaReport<handle
         end
         
         function set.TCfile(obj,val)
-           obj.TCfile=obj.setfile(val);
+            obj.TCfile=obj.setfile(val);
         end
         
         function set.ICAfile(obj,val)
-           obj.ICAfile=obj.setfile(val);
+            obj.ICAfile=obj.setfile(val);
         end
         
         function set.Orientation(obj,val)
             switch lower(val)
-                case obj.OrientationOptions %#ok<MCSUP>
+                case obj.OrientationOptions 
                     obj.Orientation=val;
                 otherwise
                     id = 'GiftIcaReport:set_orientation:invalid_orientation';
                     msg = sprintf('%s\n%s\n%s\t%s\t%s\n',...
                         'invalid option for orientation',...
                         'pick one of the following options',...
-                        obj.OrientationOptions{:}); %#ok<MCSUP>
+                        obj.OrientationOptions{:}); 
                     throw(MException(id,msg));
             end
         end
         
-        function set.SliceNumbers(obj,val)
+        function set.PlotSliceNumbers(obj,val)
-            if isnumeric(val) && ~any(val<1)
+            if isempty(val)
-                   obj.SliceNumbers=val;
+                if ~isempty(obj.ImageData) && ~isempty(obj.NPlots)
+                    %autofill the plotslicenumbers
+                    switch lower(obj.Orientation)
+                        case 'tra'
+                            nmax=size(obj.ImageData,3)
+                        case 'cor'
+                            nmax=size(obj.ImageData,2)
+                        case 'sag'
+                            nmax=size(obj.ImageData,1);
+                        otherwise
+                            return;
+                    end
+                    obj.SliceNumbersInternal=round(linspace(1,nmax,obj.NPlots));
+                end
             else
-                id = 'GiftIcaReport:set_slicenumbers:invalid_input';
+                if isnumeric(val) && ~any(val<1)
+                    obj.SliceNumbersInternal=val;
+                    obj.NSlicesInternal=numel(val);
+                else
+                    id = 'GiftIcaReport:set_slicenumbers:invalid_input';
+                    msg = sprintf('invalid input for slicenumbers');
+                    throw(MException(id,msg));
+                end
+            end
+        end
+        
+        function val=get.PlotSliceNumbers(obj)
+            val=obj.SliceNumbersInternal;
+        end
+        
+        function set.NPlots(obj,val)
+            if isnumeric(val) && numel(val)==1 && val>0
+                tmp=obj.SliceNumbersInternal;
+                if ~isempty(tmp) && val<=numel(tmp)
+                    obj.PlotSliceNumbers=tmp(1:val);
+                else
+                    obj.NSlicesInternal=val;
+                    obj.PlotSliceNumbers=[];
+                end
+            else
+                id = 'GiftIcaReport:set_NSlices:invalid_input';
                 msg = sprintf('invalid input for slicenumbers');
                 throw(MException(id,msg));
             end
+        end
     
+        function val=get.NPlots(obj)
+            val=obj.NSlicesInternal;
+        end
+        
+        function set.ImageLimits(obj,val)
+            if isnumeric(val) && numel(val)==2
+                obj.CLim=transpose(sort(val(:))); %guarante it is a row vector
+            else
+                id = 'GiftIcaReport:setImageLimits:invalid_input';
+                msg = sprintf('Invalid input, set limits to [min max]');
+                throw(MException(id,msg));
+            end
+        end
+        
+        function val=get.ImageLimits(obj)
+            val=obj.CLim;
+        end
+        
+        function set.Layout(obj,val)
+            switch lower(val)
+                case {'north','south','east','west',''}
+                    obj.Layout=val;
+                otherwise
+                    id = 'GiftIcaReport:setLayout:invalid_input';
+                    msg = sprintf('Invalid input for Layout.\n Use north east south, west or empty value');
+                    throw(MException(id,msg));
+            end
+        end
+    end
+    methods %user callable functions
+        function LoadData(obj)
+            % read ICA file
+            [d,f,~]=fileparts(obj.ICAfile{1});
+            obj.PData=spm_select('ExtFPList',d,f,1:10000);
+            obj.VData=spm_vol(obj.PData);
+            obj.ImageData=spm_read_vols(obj.VData);
+            % read TimeCourse file
+            [d,f,~]=fileparts(obj.TCfile{1});
+            obj.PTimeCourse=spm_select('ExtFPList',d,f,1:10000);
+            obj.VTimeCourse=spm_vol(obj.PTimeCourse);
+            obj.TimeCourseData=spm_read_vols(obj.VTimeCourse);
+            if isempty(obj.PlotSliceNumbers) %auto set the slice numbers
+                obj.PlotSliceNumbers([]);
+            end
+        end
+        
+        function BuildFigure(obj)
+            if isempty(obj.FigureObject)
+                obj.FigureObject=figure;
+            end
+            figure(obj.FigureObject);
+            clf;
+            [nrow,ncol] = obj.getrowcol;
+            obj.TCPlot={};
+            obj.SLPlot=cell(nrow,ncol);
+            switch lower(obj.Layout)
+                case {'north','n'}
+                    r=nrow+1;
+                    c=ncol;
+                    PlRow=setdiff(1:r,1);
+                    PlCol=1:c;
+                    obj.TCPlot={subplot(r,1,1)};
+                case {'east','e'}
+                    r=nrow;
+                    c=ncol+1;
+                    PlRow=1:r;
+                    PlCol=setdiff(1:c,1);
+                    obj.TCPlot={subplot(1,c,c)};
+                case {'south','s'}
+                    r=nrow+1;
+                    c=ncol;
+                    PlRow=setdiff(1:r,r);
+                    PlCol=1:c;
+                    obj.TCPlot={subplot(r,1,r)};
+                case {'west','w'}
+                    r=nrow;
+                    c=ncol+1;
+                    PlRow=1:r;
+                    PlCol=setdiff(1:c,1);
+                    obj.TCPlot={subplot(1,c,1)};
+                otherwise %center option
+                    r=nrow+1;
+                    c=ncol;
+                    PlRow=setdiff(1:r,floor(r/2));
+                    PlCol=1:c;
+                    obj.TCPlot={subplot(r,1,floor(r/2))};
+            end
+            [x,y]=ndgrid(PlRow,PlCol);
+            x=transpose(x);
+            y=transpose(y);
+            for k=1:obj.NPlots
+                p=(x(k)-1)*c+y(k);
+                obj.SLPlot{k}=subplot(r,c,p);
+            end        
+        end
+        
+        function PlotTimeCourse(obj,IC)
+            if isempty(obj.TimeCourseData)
+                id = 'GiftIcaReport:PlotTC:NoDataToPlot';
+                msg = 'No time data to plot';
+                throw(MException(id,msg));
+            end
+            if IC>size(obj.TimeCourseData,2)
+                id = 'GiftIcaReport:PlotTC:InvalidComponent';
+                msg = 'invalid component';
+                throw(MException(id,msg));
+            end
+            axes(obj.TCPlot{1});
+            plot(obj.TimeCourseData(:,IC));
+        end
+        
+        function PlotSlices(obj,IC)
+            if isempty(obj.ImageData)
+                id = 'GiftIcaReport:PlotTC:NoDataToPlot';
+                msg = 'No time data to plot';
+                throw(MException(id,msg));
+            end
+            if IC>size(obj.ImageData,4)
+                id = 'GiftIcaReport:PlotTC:InvalidComponent';
+                msg = 'invalid component';
+                throw(MException(id,msg));
+            end
+            for k=1:obj.NPlots
+                axes(obj.SLPlot{k}); %#ok<LAXES>
+                switch lower(obj.Orientation)
+                    case 'cor'
+                        if obj.PlotSliceNumbers(k)>size(obj.ImageData,2);continue;end
+                        im=squeeze(obj.ImageData(:,obj.PlotSliceNumbers(k),:,IC));
+                    case 'tra'
+                        if obj.PlotSliceNumbers(k)>size(obj.ImageData,3);continue;end
+                        im=squeeze(obj.ImageData(:,:,obj.PlotSliceNumbers(k),IC));
+                    case 'sag'
+                        if obj.PlotSliceNumbers(k)>size(obj.ImageData,1);continue;end
+                        im=squeeze(obj.ImageData(obj.PlotSliceNumbers(k),:,:,IC));
+                    case 'all'
+                end
+                imagesc(im,obj.CLim);
+                camroll(90)
+                colormap(obj.Colormap);
+                axis image
+                axis off
+            end
+        end
+        
+        function GenReport(obj)
+            % load all info if not already present
+            if isempty(obj.ImageData)||isempty(obj.TimeCourseData)
+                obj.LoadData;
+            end
+            obj.BuildFigure;
+            % loop over IC
+            for IC=1:size(obj.TimeCourseData,2)
+                obj.PlotTimeCourse(IC);
+                obj.PlotSlices(IC);
+                
+                obj.TCPlot{1}.Title.String= sprintf('IC:%.4d',IC);
+                [~,f,e]=fileparts(obj.FileOut);
+                switch lower(e)
+                    case '.png'
+                        fout=fullfile(obj.DirOut,sprintf('%s_%.4d.png',f,IC));
+                        type=-'png';
+                    otherwise
+                       id = 'GiftIcaReport:GenReport:invalidFileType';
+                       msg = sprintf('Filetype not implemented');
+                       throw(MException(id,msg));
+                end
+                saveas(gcf,fout,type);
+            end
+            %% this block of code gives a licence error. weird as I could create the object ?
+            %             if isempty(obj.ReportObj)
+            %                 id  = 'GiftIcaReport:GenReport:EmptyReportObject';
+            %                 msg = 'No report object set in constructor of this object';
+            %                 throw(MException(id,msg));
+            %             end
+            %             if ~isa(obj.ReportObj,'mlreportgen.report.Report')
+            %                 id  = 'GiftIcaReport:GenReport:WrongClassReportObject';
+            %                 msg = 'No report object set in constructor of this object';
+            %                 throw(MException(id,msg));
+            %             end
+            %             import mlreportgen.report.*
+            %             %open(obj.ReportObj)
+            %             % generate the figure
+            %             surf(peaks) %just for testing
+            %             add(obj.ReportObj,Figure)
+            %             %close(obj.ReportObj)
+            %             disp(obj.ReportObj)
+            %%
         end
     end
     methods %private methods
-       function out = setfile(~,val)
+        function [nrow,ncol]=getrowcol(obj)
-             if isempty(val)
+            p=factor(obj.NPlots);
+            while numel(p)>2
+                p(1)=p(1)*p(end);
+                p(end)=[];
+                p=sort(p);
+            end
+            if numel(p)==1 % catch primes
+                p(2)=1;
+                p=sort(p);
+            end
+            if 9*p(2)>16*p(1) %very elongated plot
+                ncol=ceil(sqrt(obj.NPlots));
+                nrow=ceil(obj.NPlots/ncol);
+            else
+                nrow=p(1);
+                ncol=p(2);
+            end
+        end
+        
+        function out = setfile(~,val)
+            if isempty(val)
                 out={};
                 return
             end
@@ -98,7 +384,7 @@ classdef GiftIcaReport<handle
                     return
                 end
             end
-       end
+        end
     end
 end
 

GIFT_Clean/UnityTestGiftIcaReport.m

@@ -8,8 +8,9 @@ P={'X:\My Documents\MATLAB\Projects\fMRI_script\GIFT_Clean\TestData\g_sub01_comp
 if not(exist(P{1},'file'));error('Test file not found,unity test not performed');end
 P2={'X:\My Documents\MATLAB\Projects\fMRI_script\GIFT_Clean\TestData\g_sub01_timecourses_ica_s1_.nii'};
 if not(exist(P2{1},'file'));error('Test file not found,unity test not performed');end
-%% basic call 
+%% basic call and close 
 Q = GiftIcaReport;
+clear('Q')
 %% basic call with no SPM error
 try 
     tmp=fileparts(which('spm'));
@@ -25,6 +26,7 @@ catch ME
     end
 end
 %% test set ICAfile
+Q = GiftIcaReport;
 Q.ICAfile=[]; %set to empty
 try
     Q.ICAfile = 'junk';
@@ -41,7 +43,7 @@ Q.ICAfile=P{1};
 %Q.ICAfile='ui'; % request a user interface
 %% test set TC file
 %Q.TCfile='ui';
-Q.ICAfile=P2;
+Q.TCfile=P2;
 %% test set orientation
 try
     Q.Orientation='junk';
@@ -53,13 +55,14 @@ catch ME
         disp(ME)
     end
 end
+Q.Orientation='all';
 Q.Orientation='tra';
 Q.Orientation='cor';
 Q.Orientation='sag';
 
 %% test setting slice numbers I
 try 
-    Q.SliceNumbers=0:5;
+    Q.PlotSliceNumbers=0:5;
 catch ME
     if ~strcmpi(ME.identifier,'GiftIcaReport:set_slicenumbers:invalid_input')
         rethrow(ME);
@@ -70,7 +73,7 @@ catch ME
 end
 %% test setting slice numbers II
 try 
-    Q.SliceNumbers='junk';
+    Q.PlotSliceNumbers='junk';
 catch ME
     if ~strcmpi(ME.identifier,'GiftIcaReport:set_slicenumbers:invalid_input')
         rethrow(ME);
@@ -79,4 +82,17 @@ catch ME
         disp(ME);
     end
 end
-Q.SliceNumbers=1:2:100;
+%% test ImageLimits
+Q.ImageLimits = [0 1]; %to do check on properly working error
+%% test NPlots set
+Q.NPlots=25;
+disp(Q.PlotSliceNumbers);
+%
+%Q.PlotSliceNumbers=1:2:100;
+Q.Layout='north'; % to do build error handling check
+Q.LoadData;
+Q.NPlots=9; %if PlotSliceNumbers is empty, auto set the slices to plot
+Q.PlotSliceNumbers=[]; %auto set the slices to plot
+Q.BuildFigure;
+Q.GenReport;
+