Index: trunk/src/transform_field/ima_patch_detection.m
===================================================================
--- trunk/src/transform_field/ima_patch_detection.m	(revision 921)
+++ trunk/src/transform_field/ima_patch_detection.m	(revision 921)
@@ -0,0 +1,191 @@
+% 'ima_edge_detection': find edges 
+
+%------------------------------------------------------------------------
+%%%%  Use the general syntax for transform fields with a single input and parameters %%%%
+% OUTPUT: 
+% DataOut:   output field structure 
+%
+%INPUT:
+% DataIn:  input field structure
+% Param: matlab structure whose field Param.TransformInput contains the filter parameters
+%-----------------------------------
+
+%=======================================================================
+% Copyright 2008-2015, LEGI UMR 5519 / CNRS UJF G-INP, Grenoble, France
+%   http://www.legi.grenoble-inp.fr
+%   Joel.Sommeria - Joel.Sommeria (A) legi.cnrs.fr
+%
+%     This file is part of the toolbox UVMAT.
+%
+%     UVMAT is free software; you can redistribute it and/or modify
+%     it under the terms of the GNU General Public License as published
+%     by the Free Software Foundation; either version 2 of the license,
+%     or (at your option) any later version.
+%
+%     UVMAT is distributed in the hope that it will be useful,
+%     but WITHOUT ANY WARRANTY; without even the implied warranty of
+%     MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+%     GNU General Public License (see LICENSE.txt) for more details.
+%=======================================================================
+
+function DataOut=ima_patch_detection(DataIn,Param)
+
+%% request input parameters
+if isfield(DataIn,'Action') && isfield(DataIn.Action,'RUN') && isequal(DataIn.Action.RUN,0)
+    prompt = {'npx';'npy';'threshold'};
+    dlg_title = 'get the filter size in x and y';
+    num_lines= 3;
+    def     = { '50';'50';'0.3'};
+    if isfield(Param,'TransformInput')&&isfield(Param.TransformInput,'FilterBoxSize_x')&&...
+            isfield(Param.TransformInput,'FilterBoxSize_y')&&isfield(Param.TransformInput,'LumThreshold')
+        def={num2str(Param.TransformInput.FilterBoxSize_x);num2str(Param.TransformInput.FilterBoxSize_y);num2str(Param.TransformInput.LumThreshold)};
+    end
+    
+    
+    
+    %% create the GUI set_threshold
+    set(0,'Units','points')
+    ScreenSize=get(0,'ScreenSize');% get the size of the screen, to put the fig on the upper right
+    Width=350;% fig width in points (1/72 inch)
+    Height=min(0.8*ScreenSize(4),300);
+    Left=ScreenSize(3)- Width-40; %right edge close to the right, with margin=40
+    Bottom=ScreenSize(4)-Height-40; %put fig at top right
+    hfig=findobj(allchild(0),'Tag','set_threshold');
+    if isempty(hfig)
+        hfig=figure('name','set_threshold','tag','set_threshold','MenuBar','none','NumberTitle','off','Units',...
+            'pixels','Position',[Left,Bottom,Width,Height],'DeleteFcn',@closefcn)%);
+    else
+        figure(hfig)
+    end
+    BackgroundColor=get(hfig,'Color');
+    hh=0.14; % box height (relative)
+    ii=0.01; % gap between uicontrols
+    
+    ww=(1-5*ii)/4; % box width (relative)
+    % first raw of the GUI
+    %Amask=imread('/fsnet/project/coriolis/2015/15MINI_MEDDY/0_REF_FILES/mask_patch.png');
+    uicontrol('Style','text','Units','normalized', 'Position', [ii 0.95-2*ii-0.75*hh ww hh/2],'BackgroundColor',BackgroundColor,...
+        'String','Threshold','FontUnits','points','FontSize',12,'FontWeight','bold','ForegroundColor','blue','HorizontalAlignment','right');%title
+    % uicontrol('Style','edit','Units','normalized', 'Position', [2*ii+ww 0.95-2*ii-hh ww hh],'tag','num_Z_1','BackgroundColor',[1 1 1],...
+    %     'String',num2str(SliceCoord(1,3)),'FontUnits','points','FontSize',12,'FontWeight','bold','TooltipString','''num_Z_1'': z position of first slice');%edit box
+    hThreshold=uicontrol('Style','edit','Units','normalized', 'Position', [3*ii+2*ww 0.95-2*ii-hh ww hh],'tag','Threshold','BackgroundColor',[1 1 1],...
+        'FontUnits','points','FontSize',12,'FontWeight','bold');%edit box
+    uicontrol('Style','slider','Units','normalized', 'Position', [0.1 0.1 0.8 0.1],'tag','SetThreshold','BackgroundColor',[1 1 1],...
+        'FontUnits','points','FontSize',12,'FontWeight','bold','Callback',@(hObject,eventdata)SetThreshold_Callback(hObject,eventdata));%edit box
+  %  uiwait(hfig);
+    %
+    %
+    %     DataOut.TransformInput.FilterBoxSize_x=str2num(answer{1}); %size of the filtering window
+    %     DataOut.TransformInput.FilterBoxSize_y=str2num(answer{2}); %size of the filtering window
+    DataOut.TransformInput.LumThreshold=str2num(get(hThreshold,'String')) %size of the filtering window
+    
+ 
+    
+    return
+end
+
+DataOut=DataIn; %default
+%Amask=imread('/fsnet/project/coriolis/2015/15MINI_MEDDY/0_REF_FILES/mask_patch.png');
+plot_mask(DataIn.A,Param.TransformInput.LumThreshold)
+% Athreshold=Param.TransformInput.LumThreshold;
+% %
+% %     DataOut.A=zeros(size(DataIn.A,1),size(DataIn.A,2),3);
+% DataOut.A=(DataIn.A>Athreshold);%transform to the initial image format
+% %     DataOut.A(:,:,1)=DataIn.A;%transform to the initial image format, red
+% STATS = regionprops(DataOut.A, 'FilledArea','MinorAxisLength','MajorAxisLength','PixelIdxList');
+% Area=zeros(size(STATS));
+% for iobj=1:numel(STATS)
+%     Area(iobj)=STATS(iobj).FilledArea;
+% end
+% [Area, main_obj]=max(Area);
+% MajorAxisLength=STATS(main_obj).MajorAxisLength
+% MinorAxisLength=STATS(main_obj).MinorAxisLength
+% for iobj=1:numel(STATS)
+%     if iobj~=main_obj
+%         DataOut.A(STATS(iobj).PixelIdxList)=0;
+%     end
+% end
+% 
+% DataOut.A=Amax*DataOut.A;
+
+
+%------------------------------------------------------------------------
+% function called by selecting CheckRefraction in the GUI set_slices
+function SetThreshold_Callback(hObject,eventdata)
+%------------------------------------------------------------------------
+hfig=get(hObject,'parent');
+hThreshold=findobj(hfig,'Tag','Threshold');
+Threshold=get(hObject,'Value');
+
+huvmat=findobj(allchild(0),'Tag','uvmat');
+hhuvmat=guidata(huvmat);
+UvData=get(huvmat,'UserData');
+Amax=max(max(UvData.Field.A));
+Amin=min(min(UvData.Field.A));
+Threshold=Amin+(Amax-Amin)*Threshold;
+set(hThreshold,'String',num2str(Threshold))
+
+plot_mask(UvData.Field.A,Threshold)
+
+UvData.XmlData{1}.TransformInput.LumThreshold=Threshold;
+set(huvmat,'UserData',UvData)
+
+
+
+
+
+
+% h_refraction(1)=findobj(hset_slice,'String','surface');
+% h_refraction(2)=findobj(hset_slice,'Tag','num_H');
+% h_refraction(3)=findobj(hset_slice,'String','index');
+% h_refraction(4)=findobj(hset_slice,'Tag','num_RefractionIndex');
+% if isequal(get(hObject,'Value'),1)
+%     set(h_refraction,'Visible','on')
+% else
+%     set(h_refraction,'Visible','off')
+% end
+
+function plot_mask(A,Threshold)
+    
+A=(A>Threshold) ;%& Amask>100;%transform to binary image format
+try
+    STATS = regionprops(A, 'FilledArea','MinorAxisLength','MajorAxisLength','PixelIdxList');
+    Area=zeros(size(STATS));
+    for iobj=1:numel(STATS)
+        Area(iobj)=STATS(iobj).FilledArea;
+    end
+    [Area, main_obj]=max(Area);
+    MajorAxisLength=STATS(main_obj).MajorAxisLength;
+    MinorAxisLength=STATS(main_obj).MinorAxisLength;
+    for iobj=1:numel(STATS)
+        if iobj~=main_obj
+            A(STATS(iobj).PixelIdxList)=0;
+        end
+    end
+catch ME
+    disp('image toolbox not available, skipped')
+end
+[npy,npx]=size(A);
+A=cat(3,A,zeros(npy,npx,2));% make a color image
+
+huvmat=findobj(allchild(0),'Tag','uvmat');
+hhuvmat=guidata(huvmat);
+hmask=findobj(hhuvmat.PlotAxes,'Tag','MaskFig')
+if isempty(hmask)
+    axes(hhuvmat.PlotAxes)
+    hold on
+    imagesc([0.5 npx],[npy-0.5 0.5],A,'AlphaData',0.2,'Tag','MaskFig')
+else
+    set(hmask,'CData',A)
+    set(hmask,'AlphaData',0.2)
+end
+
+
+function closefcn(hObject,eventdata)
+
+huvmat=findobj(allchild(0),'Tag','uvmat');
+hhuvmat=guidata(huvmat);
+hmask=findobj(hhuvmat.PlotAxes,'Tag','MaskFig')
+if ~isempty(hmask)
+   delete(hmask)
+end