added HDF5Helper

aod/AodHRVolumeReader.m

@@ -0,0 +1,114 @@
+
+classdef AodHRVolumeReader < HDF5Helper
+    properties
+        x = [];
+        y = [];
+        z = [];
+        reps = [];
+        version = [];
+        vfilename = [];
+    end
+
+    methods
+        function self = AodHRVolumeReader(filename,vfilename)
+
+            self = self@HDF5Helper(filename, 'ImData');
+
+            isHRV = (H5Tools.existAttribute(self.fp,'CellFocussedVolume') && ...
+                H5Tools.readAttribute(self.fp, 'CellFocussedVolume') == 1);
+            self.version = H5Tools.readAttribute(self.fp, 'Version');
+            assert((H5Tools.existAttribute(self.fp,'ScanType') && ...
+                strncmp(H5Tools.readAttribute(self.fp, 'ScanType')', 'Volume', 6) == 1) ...
+                || isHRV , ...
+                'Not a volume scan file');
+
+
+            coord = AodCoordinatesReader(self.filename,self.version);
+            coords =  coord(:);
+            numPoints = size(coords,1);
+            self.reps = floor(self.sz(1) / numPoints);
+
+            ar = aodReader(vfilename,'Volume');
+
+            self.x = ar.x;
+            self.y = ar.y;
+            self.z = ar.z;
+            self.vfilename = vfilename;
+
+        end
+
+        function volume = subsref(self, s)
+
+            ar = aodReader(self.filename,'Functional');
+            data = ar(:,:,:);
+            coord = AodCoordinatesReader(self.filename,self.version);
+            coords =  coord(:);
+            volume = nan(length(self.x),length(self.y),length(self.z),size(data,1),size(data,3));
+
+            for i = 1:size(coords,1)
+                xind = find(single(coords(i,1))==single(self.x));
+                yind = find(single(coords(i,2))==single(self.y));
+                zind = find(single(coords(i,3))==single(self.z));
+                volume(xind,yind,zind,:,:) = squeeze(data(:,i,:));
+            end
+
+            if(strcmp(s(1).type,'()') == 0)
+                if 0 && ismember(s.subs,properties(self))
+                    volume = self.(s.subs);
+                    return;
+                end
+                volume = subsref@HDF5Helper(self,s);
+                return
+            end
+
+            % make sure subscripting has the right form
+            assert(numel(s) == 1 && strcmp(s.type, '()') && numel(s.subs) == 5 || ...
+                numel(s) == 1 && strcmp(s.type, '()') && numel(s.subs) == 4 || ...
+                numel(s) == 1 && strcmp(s.type, '()') && numel(s.subs) == 3, ...
+                'MATLAB:badsubscript', 'Only subscripting of the form (samples, channels) is allowed!')
+
+            % samples and channels
+            x = s(1).subs{1};
+            y = s(1).subs{2};
+            z = s(1).subs{3};
+
+            if numel(s(1).subs)<5
+                chan = 1;
+            else
+                chan = s(1).subs{5};
+            end
+
+            if numel(s(1).subs) < 4
+                reps = 1:self.reps;
+            else
+                reps = s(1).subs{4};
+            end
+
+            % all samples requested?
+            if ~HDF5Helper.iscolon(x)
+                volume = volume(x,:,:,:,:);
+            end
+
+            % all samples requested?
+            if ~HDF5Helper.iscolon(y)
+                volume = volume(:,y,:,:,:);
+            end
+
+            % all samples requested?
+            if ~HDF5Helper.iscolon(z)
+                volume = volume(:,:,z,:,:);
+            end
+
+            % all samples requested?
+            if ~HDF5Helper.iscolon(reps)
+                volume = volume(:,:,:,reps,:);
+            end
+
+            % all channels requested?
+            if ~HDF5Helper.iscolon(chan)
+                volume = volume(:,:,:,:,chan);
+            end
+
+        end
+    end
+end

aod/aodReader.m

@@ -45,6 +45,8 @@
     br = AodMotionReader(fileName);
 elseif strcmp(dataset, 'Volume') == 1
     br = AodVolumeReader(fileName);
+elseif strcmp(dataset, 'HRVolume') ==1
+    br = AodHRVolumeReader(fileName,varargin{1});
 else
     error('Unknown dataset.  Options are Temporal, Functional,Volume and Motion.');
 end