/normxcorr/trunk

% written by Chris

function [rasterx, rastery, validx,validy,x,y]=ppselection_func(validx,validy,x,y);

% Code to analyze the displacement data (contained by validx and validy)

% Programmed by Chris

% Last revision: 8/24/06

% Prompt user for displacement data

if exist('validx')==0

    [validx,Pathvalidx] = uigetfile('*.mat','Open validx.mat');

    if validx==0

        return;

    end

    cd(Pathvalidx);

    validx=importdata(validx,'\t');

end

if exist('validy')==0

    [validy,Pathvalidy] = uigetfile('*.mat','Open validy.mat');

    if validy==0

        return;

    end

    cd(Pathvalidy);

    validy=importdata(validy,'\t');

end

% Checking for plot orientation and give standard orientations

if exist('x')==0

    x=1;

    y=2;

end

if x~1|2|3

    x=1;

    y=2;

end

validxbackup=validx;

validybackup=validy;

% Choose an image

[looppoints loopimages]=size(validx);

selectedimage=0;

prompt = {'From which image do you want to select the view?'};

dlg_title = 'Marker selection';

num_lines= 1;

if selectedimage==0

    defaultimage=loopimages;

end

if selectedimage~0

    defaultimage=selectedimage;

end

def     = {num2str(defaultimage)};

answer = inputdlg(prompt,dlg_title,num_lines,def);

selectedimage = str2num(cell2mat(answer(1,1)));

if selectedimage>loopimages

    selectedimage=loopimages;

end

if selectedimage<1

    selectedimage=1;

end

rasterx=0;

rastery=0;

% Call the selection tool

[rasterx, rastery, validx,validy,x,y]=gridtypeselection(validx,validy,x,y,selectedimage,rasterx,rastery);

return

%-------------------------------

%

% Decide which type of raster you want to analyze

function [rasterx, rastery, validx,validy,x,y] = gridtypeselection(validx,validy,x,y,selectedimage,rasterx,rastery);

gridselection = menu(sprintf('Which type of grid do you want to use'),...

    'Two Markers','Rectangular','Two Rectangles of Markers','Circular','Line','Change view','Cancel');

if gridselection==1

    [validx,validy,rasterx, rastery,selectedimage,x,y]=twop_grid_displ(validx,validy,x,y,selectedimage,rasterx,rastery);

    exist('validx');

    exist('validy');

    exist('rasterx');

    exist('rastery');

    exist('x');

    exist('y');

    return

end

if gridselection==2

    [validx,validy,rasterx, rastery,selectedimage,x,y]=rect_grid_displ(validx,validy,x,y,selectedimage,rasterx,rastery);

    exist('validx');

    exist('validy');

    exist('rasterx');

    exist('rastery');

    exist('x');

    exist('y');

    return

end

if gridselection==5

    [validx,validy,rasterx, rastery,selectedimage,x,y]=line_grid_displ(validx,validy,x,y,selectedimage,rasterx,rastery);

    exist('validx');

    exist('validy');

    exist('rasterx');

    exist('rastery');

    exist('x');

    exist('y');

    return

end

if gridselection==3

    [validx,validy,rasterx, rastery,selectedimage,x,y]=tworect_grid_displ(validx,validy,x,y,selectedimage,rasterx,rastery);

    exist('validx');

    exist('validy');

    exist('rasterx');

    exist('rastery');

    exist('x');

    exist('y');

    return

end

if gridselection==4

    [validx,validy,rasterx, rastery,selectedimage,x,y]=circ_grid_displ(validx,validy,x,y,selectedimage,rasterx,rastery);

    exist('validx');

    exist('validy');

    exist('rasterx');

    exist('rastery');

    exist('x');

    exist('y');

    return

end

if gridselection==6

    [validx,validy,x,y,selectedimage,rasterx,rastery] = change_view_displ(validx,validy,x,y,selectedimage,rasterx,rastery);

    exist('validx');

    exist('validy');

    exist('rasterx');

    exist('rastery');

    exist('x');

    exist('y');

end

if gridselection==7

    close all

    exist('validx');

    exist('validy');

    exist('rasterx');

    exist('rastery');

    exist('x');

    exist('y');

    if exist('validx')==0

        validx=0;

        validy=0;

    end

    if exist('rasterx')==0

        rasterx=0;

        rastery=0;

    end

    if exist('x')==0

        x=0;

        y=0;

    end

end

if exist('validx')==0

    validx=0

    validy=0

end

if exist('rasterx')==0

    rasterx=0

    rastery=0

end

if exist('x')==0

    x=0

    y=0

end

return

%-------------------------------

%

% Change the view

function [validx,validy,x,y,selectedimage,rasterx,rastery] = change_view_displ(validx,validy,x,y,selectedimage,rasterx,rastery);

[looppoints loopimages]=size(validx);

if x==1

    pos=validx;

end

if x==2

    pos=validy;

end

if x==3

    validxfirst=zeros(size(validx));

    validxfirst=validx(:,1)*ones(1,loopimages);

    pos=validx-validxfirst;

end

if x==4

    validyfirst=zeros(size(validy));

    validyfirst=validy(:,1)*ones(1,loopimages);

    pos=validy-validyfirst;

end

if y==1

    displ=validx;

end

if y==2

    displ=validy;

end

if y==3

    validxfirst=zeros(size(validx));

    validxfirst=validx(:,1)*ones(1,loopimages);

    displ=validx-validxfirst;

end

if y==4

    validyfirst=zeros(size(validy));

    validyfirst=validy(:,1)*ones(1,loopimages);

    displ=validy-validyfirst;

end

h=figure;

plot(pos(:,selectedimage),displ(:,selectedimage),'o','MarkerEdgeColor','k','MarkerFaceColor','g')

title(sprintf('View.') )

changeviewselection = menu(sprintf('Do you want to change the coordinate system to select markers?'),...

    'x-position vs. y-position','x-position vs. x-displacement','y-position vs. x-displacement',...

    'x-position vs. y-displacement','y-position vs. y-displacement','Change image #','Go back to grid-type selection');

if changeviewselection==1

    close all

    x=1;

    y=2;

    [validx,validy,x,y,selectedimage,rasterx,rastery] = change_view_displ(validx,validy,x,y,selectedimage,rasterx,rastery);

end

if changeviewselection==2

    close all

    x=1;

    y=3;

    [validx,validy,x,y,selectedimage,rasterx,rastery] = change_view_displ(validx,validy,x,y,selectedimage,rasterx,rastery);

end

if changeviewselection==3

    close all

    x=2;

    y=3;

    [validx,validy,x,y,selectedimage,rasterx,rastery] = change_view_displ(validx,validy,x,y,selectedimage,rasterx,rastery);

end

if changeviewselection==4

    close all

    x=1;

    y=4;

    [validx,validy,x,y,selectedimage,rasterx,rastery] = change_view_displ(validx,validy,x,y,selectedimage,rasterx,rastery);

end

if changeviewselection==5

    close all

    x=2;

    y=4;

    [validx,validy,x,y,selectedimage,rasterx,rastery] = change_view_displ(validx,validy,x,y,selectedimage,rasterx,rastery);

end

if changeviewselection==6

    prompt = {'From which image do you want to select the view?'};

    dlg_title = 'Marker selection';

    num_lines= 1;

    if selectedimage==0

        defaultimage=loopimages;

    end

    if selectedimage~0

        defaultimage=selectedimage;

    end

    def     = {num2str(defaultimage)};

    answer = inputdlg(prompt,dlg_title,num_lines,def);

    selectedimage = str2num(cell2mat(answer(1,1)));

    if selectedimage>loopimages

        selectedimage=loopimages;

    end

    if selectedimage<1

        selectedimage=1;

    end

    [validx,validy,x,y,selectedimage,rasterx,rastery] = change_view_displ(validx,validy,x,y,selectedimage,rasterx,rastery);

end

if changeviewselection==7

    close all

    [rasterx, rastery, validx,validy,x,y]=gridtypeselection(validx,validy,x,y,selectedimage,rasterx,rastery);

end

%-------------------------------

%

% Define two rectangles and add them to one marker array

function [validx,validy,rasterx,rastery,selectedimage,x,y] = tworect_grid_displ(validx,validy,x,y,selectedimage,rasterx,rastery);

[validx,validy,rasterx1, rastery1,selectedimage]=rect_grid_displ(validx,validy,x,y,selectedimage,rasterx,rastery);

[validx,validy,rasterx2, rastery2,selectedimage]=rect_grid_displ(validx,validy,x,y,selectedimage,rasterx,rastery);

% if size(rasterx1)~size(rasterx2)

%     close all

%     rasterx=0;rastery=0;

%     return

% end

rasterx=[rasterx1; rasterx2];

rastery=[rastery1; rastery2];

if x==1

    pos1=validx;pos2=rasterx;

end

if x==2

    pos1=validy;pos2=rasterx;

end

if x==3

    validxfirst=zeros(size(validx));rasterxfirst=zeros(size(rasterx));

    validxfirst=validx(:,1)*ones(1,loopimages);rasterxfirst=rasterx(:,1)*ones(1,loopimages);

    pos1=validx-validxfirst;pos2=rasterx-rasterxfirst;

end

if x==4

    validyfirst=zeros(size(validy));rasteryfirst=zeros(size(rastery));

    validyfirst=validy(:,1)*ones(1,loopimages);rasteryfirst=rastery(:,1)*ones(1,loopimages);

    pos1=validy-validyfirst;pos2=rastery-rasteryfirst;

end

if y==1

    displ1=validx;displ2=rasterx;

end

if y==2

    displ1=validy;displ2=rastery;

end

if y==3

    validyfirst=zeros(size(validy));rasteryfirst=zeros(size(rastery));

    validyfirst=validy(:,1)*ones(1,loopimages);rasteryfirst=rastery(:,1)*ones(1,loopimages);

    displ1=validy-validyfirst;displ2=rastery-rasteryfirst;

end

[looppoints loopimages]=size(validx);

defaultimage=loopimages;

prompt = {'From which image do you want to select the rectangles?'};

dlg_title = 'Marker selection';

num_lines= 1;

if selectedimage==0

    defaultimage=loopimages;

end

if selectedimage~0

    defaultimage=selectedimage;

end

def     = {num2str(defaultimage)};

answer = inputdlg(prompt,dlg_title,num_lines,def);

selectedimage = str2num(cell2mat(answer(1,1)));

if selectedimage>loopimages

    selectedimage=loopimages;

end

if selectedimage<1

    selectedimage=1;

end

h=figure;

plot(pos1(:,selectedimage),displ1(:,selectedimage),'o','MarkerEdgeColor','k','MarkerFaceColor','g')

hold on

plot(pos2(:,selectedimage),displ2(:,selectedimage),'o','MarkerEdgeColor','k','MarkerFaceColor','r')

% Accept the chosen markers, try again or give up 

confirmcircselection = menu(sprintf('Do you want to use these markers?'),...

    'Yes','No, try again','Go back to grid-type selection');

if confirmcircselection==2

    close all

    [validx,validy,rasterx,rastery,selectedimage,x,y] = tworect_grid_displ(validx,validy,x,y,selectedimage,rasterx,rastery);

end

if confirmcircselection==3

    close all

    [rasterx, rastery,validx,validy, x,y] = gridtypeselection(validx,validy,x,y,selectedimage,rasterx,rastery);

end

if confirmcircselection==1

    close all

end

%-------------------------------

%

% Define line and find markers

function [validx,validy,rasterx,rastery,selectedimage,x,y]=line_grid_displ(validx,validy,x,y,selectedimage,rasterx,rastery);

[looppoints loopimages]=size(validx);

defaultimage=loopimages;

if x==1

    pos=validx;

end

if x==2

    pos=validy;

end

if x==3

    validxfirst=zeros(size(validx));

    validxfirst=validx(:,1)*ones(1,loopimages);

    pos=validx-validxfirst;

end

if x==4

    validyfirst=zeros(size(validy));

    validyfirst=validy(:,1)*ones(1,loopimages);

    pos=validy-validyfirst;

end

if y==1

    displ=validx;

end

if y==2

    displ=validy;

end

if y==3

    validxfirst=zeros(size(validx));

    validxfirst=validx(:,1)*ones(1,loopimages);

    displ=validx-validxfirst;

end

if y==4

    validyfirst=zeros(size(validy));

    validyfirst=validy(:,1)*ones(1,loopimages);

    displ=validy-validyfirst;

end

prompt = {'From which image do you want to select markers?'};

dlg_title = 'Marker selection';

num_lines= 1;

if selectedimage==0

    defaultimage=loopimages;

end

if selectedimage~0

    defaultimage=selectedimage;

end

def     = {num2str(defaultimage)};

answer = inputdlg(prompt,dlg_title,num_lines,def);

selectedimage = str2num(cell2mat(answer(1,1)));

if selectedimage>loopimages

    selectedimage=loopimages;

end

if selectedimage<1

    selectedimage=1;

end

h=figure;

plot(pos(:,selectedimage),displ(:,selectedimage),'o','MarkerEdgeColor','k','MarkerFaceColor','g')

title(sprintf('Pick two points on the sample.') )

[xpos(1,1),ypos(1,1)]=ginput(1);

hold on

plot(xpos(1,1),ypos(1,1),'+g')

[xpos(2,1),ypos(2,1)]=ginput(1);

plot(xpos(2,1),ypos(2,1),'+g')

centerpoint=[xpos(1,1)+(xpos(2,1)-xpos(1,1))/2; ypos(1,1)+(ypos(2,1)-ypos(1,1))/2];

plot(centerpoint(1,1),centerpoint(2,1),'+b')

linelength=sqrt((xpos(2,1)-xpos(1,1))*(xpos(2,1)-xpos(1,1))+(ypos(2,1)-ypos(1,1))*(ypos(2,1)-ypos(1,1)));

lineslope=(ypos(2,1)-ypos(1,1))/(xpos(2,1)-xpos(1,1));

intersecty=ypos(1,1)-lineslope*xpos(1,1);

ycalc=zeros(2,1);

ycalc=lineslope*xpos+intersecty;

plot(xpos(:,1),ycalc(:,1),'-b')

intercept=[0; centerpoint(2,1)-centerpoint(1,1)*(-1/lineslope)];

distancefromline=(abs((xpos(2,1)-xpos(1,1))*(ypos(1,1)-displ(:,selectedimage))-(xpos(1,1)-pos(:,selectedimage))*(ypos(2,1)-ypos(1,1))))/sqrt((xpos(2,1)-xpos(1,1))*(xpos(2,1)-xpos(1,1))+(ypos(2,1)-ypos(1,1))*(ypos(2,1)-ypos(1,1)));

distancefromcenterpoint=(abs((intercept(1,1)-centerpoint(1,1))*(centerpoint(2,1)-displ(:,selectedimage))-(centerpoint(1,1)-pos(:,selectedimage))*(intercept(2,1)-centerpoint(2,1))))/sqrt((intercept(1,1)-centerpoint(1,1))*(intercept(1,1)-centerpoint(1,1))+(intercept(2,1)-centerpoint(2,1))*(intercept(2,1)-centerpoint(2,1)));

linewidthquestion=0;

linewidth=20;

while linewidthquestion==0

    prompt = {'Enter the width of the line in [pixel]:'};

    dlg_title = 'Input for grid creation';

    num_lines= 1;

    def     = {num2str(linewidth)};

    answer = inputdlg(prompt,dlg_title,num_lines,def);

    linewidth = str2num(cell2mat(answer(1,1)))

    selectpoints=find(distancefromline<linewidth & distancefromcenterpoint<linelength/2);

    plot(pos(selectpoints,selectedimage),displ(selectpoints,selectedimage),'.r')

    drawnow

    confirmlineselection = menu(sprintf('Do you want to use these markers?'),...

        'Yes','No, try different linewidth','No, different line','Go back to grid-type selection');

    if confirmlineselection==1

        close all

        linewidthquestion=1;

        rasterx=[validx(selectpoints,:);validx(selectpoints,:)];

        rastery=[validy(selectpoints,:);validy(selectpoints,:)];

        close all

    end

    if confirmlineselection==2

        hold off

        plot(pos(:,selectedimage),displ(:,selectedimage),'o','MarkerEdgeColor','k','MarkerFaceColor','g')

        hold on

        plot(xpos(:,1),ycalc(:,1),'-b')

        plot(xpos(1,1),ypos(1,1),'+g')

        plot(xpos(2,1),ypos(2,1),'+g')

    end

    if confirmlineselection==3

        close all

        linewidthquestion=1;

        [validx,validy,rasterx, rastery,selectedimage,x,y]=line_grid_displ(validx,validy,x,y,selectedimage,rasterx,rastery);

    end

    if confirmlineselection==4

        close all

        linewidthquestion=1;

        [rasterx, rastery,validx,validy, x,y] = gridtypeselection(validx,validy,x,y,selectedimage,rasterx,rastery);

    end

end

%-------------------------------

%

% Choose two markers

function [validx,validy,rasterx, rastery,selectedimage,x,y]=twop_grid_displ(validx,validy,x,y,selectedimage,rasterx,rastery);

[looppoints loopimages]=size(validx);

defaultimage=loopimages;

if x==1

    pos=validx;

end

if x==2

    pos=validy;

end

if x==3

    validxfirst=zeros(size(validx));

    validxfirst=validx(:,1)*ones(1,loopimages);

    pos=validx-validxfirst;

end

if x==4

    validyfirst=zeros(size(validy));

    validyfirst=validy(:,1)*ones(1,loopimages);

    pos=validy-validyfirst;

end

if y==1

    displ=validx;

end

if y==2

    displ=validy;

end

if y==3

    validxfirst=zeros(size(validx));

    validxfirst=validx(:,1)*ones(1,loopimages);

    displ=validx-validxfirst;

end

if y==4

    validyfirst=zeros(size(validy));

    validyfirst=validy(:,1)*ones(1,loopimages);

    displ=validy-validyfirst;

end

prompt = {'From which image do you want to select markers?'};

dlg_title = 'Marker selection';

num_lines= 1;

if selectedimage==0

    defaultimage=loopimages;

end

if selectedimage~0

    defaultimage=selectedimage;

end

def     = {num2str(defaultimage)};

answer = inputdlg(prompt,dlg_title,num_lines,def);

selectedimage = str2num(cell2mat(answer(1,1)));

if selectedimage>loopimages

    selectedimage=loopimages;

end

if selectedimage<1

    selectedimage=1;

end

h=figure;

plot(pos(:,selectedimage),displ(:,selectedimage),'o','MarkerEdgeColor','k','MarkerFaceColor','g')

title(sprintf('Pick two markers.') )

[xpos(1,1),ypos(1,1)]=ginput(1);

whereisthispoint=abs(pos(:,selectedimage)-xpos(1,1))+abs(displ(:,selectedimage)-ypos(1,1));

selectedpoint1=find(whereisthispoint==min(whereisthispoint));

hold on

plot(pos(selectedpoint1,selectedimage),displ(selectedpoint1,selectedimage),'+r')

[xpos(2,1),ypos(2,1)]=ginput(1);

whereisthispoint=abs(pos(:,selectedimage)-xpos(2,1))+abs(displ(:,selectedimage)-ypos(2,1));

selectedpoint2=find(whereisthispoint==min(whereisthispoint));

plot(pos(selectedpoint2,selectedimage),displ(selectedpoint2,selectedimage),'+r')

% Accept the chosen markers, try again or give up 

confirmcircselection = menu(sprintf('Do you want to use these two markers?'),...

    'Yes','No, try again','Go back to grid-type selection');

if confirmcircselection==2

    close all

    hold off

    [validx,validy,rasterx,rastery,selectedimage,x,y]=twop_grid_displ(validx,validy,x,y,selectedimage,rasterx,rastery);

end

if confirmcircselection==3

    close all

    [rasterx,rastery,validx,validy,x,y]=gridtypeselection(validx,validy,x,y,selectedimage,rasterx,rastery);