added development version of addROIgrow.m which correctly loops throu…

…gh slices in order to grow 3D ROIs in the Volume

mrvista_development/addROIgrow.m

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+function vw = addROIgrow(vw,sgn,fillholes)
+% vw = addROIgrow(vw,[sgn],[filholes]);
+%
+% Grows a ROI region in 3D (ie not just in current slice) using a
+% three-dimensional six-connected neighborhood.
+%
+% If sgn~=0, adds user-specified rectangle to selected ROI in
+% current slice. If sgn==0, removes the rectangle from the ROI.
+%
+% If fillholes~=0, [default = 0] then fill holes in ROI 
+% (regardless of their value).
+%
+% 27/06/2005 SOD
+% 2013 March 31 RD, fixed looping through slices
+
+if notDefined('sgn'), sgn = 1; end
+if notDefined('fillholes'), fillholes = 0; end;
+
+% error if no current ROI
+if vw.selectedROI==0, myErrorDlg('No current ROI'); return; end
+
+% Get current ROI coords
+curCoords = getCurROIcoords(vw);
+
+% Save prevSelpts for undo
+vw.prevCoords = curCoords;
+
+% Get curSlice
+curSlice = viewGet(vw, 'Current Slice');
+
+% Get starting point from user.
+% (rgn is short for region)
+rgn = round(ginput(1));
+
+% Note: ginput hands them back in x, y order (1st col is x and
+% 2nd col is y).  But we use them in the opposite order (y then
+% x), so flip 'em.
+rgn = fliplr(rgn);
+
+% ras 01/06: allow clicking on an axis to auto-update the orientation,
+% without needing to click the orientation buttons
+if checkfields(vw, 'ui', 'axiAxesHandle')
+    h=[vw.ui.axiAxesHandle vw.ui.corAxesHandle vw.ui.sagAxesHandle];
+    ori = find(h==gca);
+    setCurSliceOri(vw, ori);
+    curSlice = vw.loc(ori);  % take different current slice
+end
+
+
+% % Check if outside image
+% dims = size(get(findobj('Parent', gca, 'Type', 'Image'), 'CData'));
+% if (min(rgn(:,1))< 1 | max(rgn(:,1))>dims(1)),
+%     myWarnDlg('Must choose starting point within image boundaries');
+%     return;
+% end;
+
+% Compute new coordinates
+newCoords = zeros(3,1);
+newCoords(1,:) = rgn(1,1);
+newCoords(2,:) = rgn(1,2);
+newCoords(3,:) = curSlice;
+
+% for montage views, convert from montage coords to vw coords
+if checkfields(vw, 'ui', 'montageSize')
+    newCoords = montage2Coords(vw,newCoords);
+end
+
+% Convert coords to canonical frame of reference
+newCoords = curOri2CanOri(vw,newCoords);
+
+% get thesholds
+cothresh =  getCothresh(vw);
+phWindow =  getPhWindow(vw);
+mapWindow = getMapWindow(vw);
+curScan =   getCurScan(vw);
+
+% get data, above cothresh, between phthresh and mapthresh
+% coherence
+data = [];
+if ~isempty(vw.co) & cothresh~=0,
+    tmp  = getCurData(vw,'co',curScan);
+    data = tmp>cothresh;
+end;
+
+% phase
+if ~isempty(vw.ph),
+    tmp = getCurData(vw,'ph',curScan);
+
+    % we need to check whether there is a phase wrap
+    if phWindow(2) > phWindow(1),
+        tmp = tmp>=phWindow(1) & tmp<=phWindow(2);
+    else
+        tmp = tmp>=phWindow(1) | tmp<=phWindow(2);
+    end
+
+    if isempty(data),
+        data = tmp;
+    else,
+        data = tmp.*data;
+    end;
+end;
+
+% map
+if ~isempty(vw.map),
+    tmp = getCurData(vw,'map',curScan);
+    tmp = tmp>=mapWindow(1) & tmp<=mapWindow(2);
+    if isempty(data),
+        data = tmp;
+    else,
+        data = tmp.*data;
+    end;
+end;
+
+if isempty(data),
+    data = viewGet(vw,'anatomy');
+end;
+
+% find clusters
+[imgLabel] = bwlabeln(data, 6);
+
+% correct for upsample factor of ui
+uiScale = upSampleFactor(vw,curScan);
+newCoords(1:2,:) = round(newCoords(1:2,:)./uiScale(1:2)');
+
+% find our cluster
+Label = imgLabel(newCoords(1),newCoords(2),newCoords(3));
+if Label==0, % no data so quit
+    return;
+end;
+
+% data with only our cluster
+data = imgLabel==Label;
+
+if fillholes~=0,
+  % find clusters again, flipped to we get background only
+  imgLabel2 = bwlabeln(data*-1+1,6);
+  % loop over clusters and make the ones that are larger than the ROI
+  % background - assume smaller clusters are holes
+  roisize = sum(data(:));
+  % another loop... sigh
+  labels = unique(imgLabel2)';
+  labels = labels(find(labels>0));
+  for n=labels,
+    label = find(imgLabel2==n);
+    if length(label) >= roisize,
+      data(label) = 0;
+    else,
+      data(label) = 1;
+    end;
+  end;
+end;
+
+% apply upsample factor again for each slice
+dims = viewSize(vw);
+sliceWithData = find(squeeze(max(max(data))));
+datanew = zeros(dims);
+% for slice = sliceWithData, % loops...
+%     datanew(:,:,slice)=imresize(data(:,:,slice),dims(1:2),'nearest',0);
+% end;
+for iSlice = 1:numel(sliceWithData), % loops... % edited by RD
+    slice = sliceWithData(iSlice);
+    datanew(:,:,slice)=imresize(data(:,:,slice),dims(1:2),'nearest',0);
+end;
+data = datanew;
+
+% convert matrix to coords
+[i1, i2, i3] = ind2sub(size(data),find(data>.5));
+newCoords = [i1 i2 i3]';
+
+% Merge/remove coordinates
+if sgn
+    coords = mergeCoords(curCoords,newCoords);
+else
+    coords = removeCoords(newCoords,curCoords);
+end
+vw.ROIs(vw.selectedROI).coords = coords;
+
+vw.ROIs(vw.selectedROI).modified = datestr(now);
+
+return;