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Author: amatov

changeImage.m

@@ -0,0 +1,118 @@
+function changeImage(key)
+
+% advances to the next image when a key is pressed
+%
+% SYNOPSIS changeImage(key)
+%
+% Alexandre Matov, 11-Mar-2004
+
+handles = guidata(findobj('Name','manTrack'));
+switch key
+    case 1
+        if handles.no>1 & handles.no<41
+            handles.no = handles.no - 1;
+            flag = -1;
+            if ishandle(handles.neighborPlot)
+                delete(handles.neighborPlot);
+            end
+            if ~isempty(handles.neighborPlot)
+                handles.neighborPlot = [];
+            end
+        else
+            msgbox('there are 40 images in the stack (min number 1 and max number 40)')
+            return
+        end
+    case 2
+        if handles.no>0 & handles.no<40
+            handles.no = handles.no + 1;
+            flag = 1;
+            if ishandle(handles.neighborPlot)
+                delete(handles.neighborPlot);
+            end
+            if ~isempty(handles.neighborPlot)
+                handles.neighborPlot = [];
+            end
+        else
+            msgbox('there are 40 images in the stack (min number 1 and max number 40)')
+            return
+        end
+end
+fh = findall(0, 'Name', 'Spindle'); 
+if handles.no>0 & handles.no<41
+    handles.image = Gauss2D(double(imread(char(handles.listImages(handles.no)))), 1);
+else
+    msgbox('there are 40 images in the stack')
+    return
+end
+figure(fh)
+set(handles.title,'String',['Frame ',num2str(handles.no)]);
+guidata(findobj('Name', 'manTrack'), handles);
+set(findobj('Type','image'),'CData', handles.image);
+refresh(fh);
+hold on
+delete(handles.currentSp);
+haSp=plot(handles.candsR.Lmax(2), handles.candsR.Lmax(1), 'r*');%initial speckle
+
+% Next, plot all the detected speckles. First, load in the cands structure
+if isunix == 1
+    temp_cands_fname = strcat('/unc/manTrackWT2s/speckles/cands0', num2str(handles.no+50), '.mat');
+else
+    temp_cands_fname = strcat('U:\manTrackWT2s\speckles\cands0', num2str(handles.no+50), '.mat');
+end
+load(temp_cands_fname); % Load in the new cand structure.
+cands=cands(find([cands.status]==1)); % do not consider the insignificant ones!!
+
+[temp0 length] = size(cands);
+% find the previous point that has already been recorded. 
+if ~isempty(handles.speckleCo)
+    list = sort([handles.speckleCo(:,1);handles.noInit]);
+    if handles.no > list(end)
+        indx = find(handles.speckleCo(:,1)==list(end));
+    elseif handles.no < list(1)
+        indx = find(handles.speckleCo(:,1)==list(1));
+    else
+        indx = find(handles.speckleCo(:,1)==(handles.no));
+        if isempty(indx)
+            indx = find(handles.speckleCo(:,1)==(handles.no-flag*1));
+            if isempty(indx)
+                indx = find(handles.speckleCo(:,1)==(handles.no-flag*2));
+            end
+        end
+    end
+    %     indx = find(handles.speckleCo(:, 1) == (handles.no - 1)); % Find saved coordinate ????flag*
+else
+    indx = []; % No previous saved coordinate. 
+end % indx can be improved - dont in one for loop!!
+RADIUS = 30;
+handles.neighbors.length = 0;
+if (handles.no == handles.noInit)
+    handles.currentSp = haSp;
+    guidata(findobj('Name','manTrack'),handles); 
+    return;
+end   
+if isempty(indx) % Previous point is the first speckle
+    previous_point = handles.candsR;
+    for i = 1 : length
+        temp0 = (cands(i).Lmax - previous_point.Lmax).^2;
+         if (temp0 < RADIUS^2)
+            handles.neighbors.length = handles.neighbors.length + 1;
+            handles.neighbors.points(handles.neighbors.length, 1:2) = cands(i).Lmax(1:2);
+                handles.neighborPlot(end + 1, 1) = plot(cands(i).Lmax(2), cands(i).Lmax(1), 'g.');
+                set(handles.neighborPlot(end, 1),'ButtonDownFcn','plotSpeckle');
+        end
+    end
+else
+    previous_point_coordinate = [handles.speckleCo(indx, 3) handles.speckleCo(indx, 2)];
+    for i = 1 : length
+        temp0 = (cands(i).Lmax - previous_point_coordinate).^2;
+        if (temp0 < RADIUS^2)
+           handles.neighbors.length = handles.neighbors.length + 1;
+           handles.neighbors.points(handles.neighbors.length, 1:2) = cands(i).Lmax(1:2);
+                handles.neighborPlot(end + 1, 1) = plot(cands(i).Lmax(2), cands(i).Lmax(1), 'g.');
+                set(handles.neighborPlot(end, 1),'ButtonDownFcn','plotSpeckle');
+        end
+    end
+end
+handles.tempCands = cands;
+handles.currentSp = haSp;
+guidata(findobj('Name','manTrack'),handles);

deleteSpeckle.m

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+function deleteSpeckle
+
+% allows to review a trajectory and delete a manually selected speckle
+% within it
+%
+% SYNOPSIS deleteSpeckle
+%
+% Alexandre Matov, 11-Mar-2004
+
+% delete the speckle (cands) index from the trajectory 
+delSpeck=questdlg('Would you like to delete this entry?','Delete entry','Yes','No','Yes');
+switch delSpeck
+    case 'Yes'
+        ha = gcbo;      
+        handles=guidata(findobj('Name','manTrack'));        
+        indxD = find(handles.hPlot == ha);
+        delete(handles.hPlot(indxD));
+        handles.hPlot(indxD) = [];
+        delete(handles.textB(indxD));
+        handles.textB(indxD) = [];
+        delete(handles.near(indxD));
+        handles.near(indxD)=[];
+        handles.speckleCo(indxD,:) = [];      
+        guidata(findobj('Name','manTrack'),handles);      
+    case 'No'
+        return;
+end % switch