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francesco changes in cross_correlation_rect #19

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francescotoselli Mar 1, 2016
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francescotoselli Mar 1, 2016
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francescotoselli Mar 2, 2016
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7 changes: 5 additions & 2 deletions cross_correlate_rect.m
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Original file line number Diff line number Diff line change
@@ -1,4 +1,4 @@
function [c] = cross_correlate_rect(a2,b2,NfftHeight,NfftWidth)
function [c,c2] = cross_correlate_rect(a2,b2,NfftHeight,NfftWidth)

% temprorary solution
a2 = a2 - mean2(a2);
Expand All @@ -13,8 +13,11 @@

% another option not implemented yet, but b2 shall be larger than a2
% see >> help normxcorr2
a3=a2(2:end-1,2:end-1); %taglio bordi di a2
b2 = b2(end:-1:1,end:-1:1); %raddrizzo l'immagine
c2 = normxcorr2(a3,b2); %calcolo correlazione normalizzata
% c = normxcorr2(b2,a2);

c(c<0) = 0;

c2(c2<0) = 0;
return
4 changes: 3 additions & 1 deletion fill_holes.m
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Expand Up @@ -7,7 +7,9 @@
%

vector(abs(vector)==0) = NaN;
vector = inpaint_nans(real(vector)) + i*inpaint_nans(imag(vector));
%vector = inpaint_nans(real(vector)) + i*inpaint_nans(imag(vector));
%%SOSTITUZIONE MIA
vector = inpaint_nans(vector,3);

% [indx,indy] = find(~abs(vector));
%
Expand Down
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48 changes: 30 additions & 18 deletions openpivgui.m
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Expand Up @@ -472,7 +472,6 @@ function pushbutton_start_Callback(hObject, eventdata, handles)

switch handles.filesType
case{'sequence'}

for fileind = 1:handles.amount-jump % main loop, for whole file list
% while (get(handles.pushbutton_start,'UserData') ==1)

Expand All @@ -493,9 +492,9 @@ function pushbutton_start_Callback(hObject, eventdata, handles)
% Prepare the results storage;
numcols = floor((horSize-ittWidth)/ovlapHor+1);
numrows = floor((verSize-ittHeight)/ovlapVer+1);
res = zeros(numcols*numrows,5);
res = zeros(numcols*numrows,6);
resind = 0;

%%%%
a2 = zeros(ittHeight,ittWidth);
b2 = zeros(ittHeight,ittWidth);
NfftWidth = 2*ittWidth;
Expand All @@ -516,7 +515,9 @@ function pushbutton_start_Callback(hObject, eventdata, handles)
% a2 = prepfun(a2);
% b2 = prepfun(b2);

c = cross_correlate_rect(a2,b2,NfftHeight,NfftWidth);
[c,c2] = cross_correlate_rect(a2,b2,NfftHeight,NfftWidth);

corr=max(max(c2));
% c = cross_correlate_rect(a2,b2,Nfftx,Nffty);
if ~any(c(:)), % completely "black"
u = 0;
Expand All @@ -525,7 +526,7 @@ function pushbutton_start_Callback(hObject, eventdata, handles)
x = origin(1) + k + ittWidth/2 - 1;
resind = resind + 1;
s2n = 0;
res(resind,:) = [x y u v s2n];
res(resind,:) = [x y u v corr s2n];
continue
end

Expand All @@ -540,7 +541,7 @@ function pushbutton_start_Callback(hObject, eventdata, handles)
x = origin(1) + k + ittWidth/2-1;

resind = resind + 1;
res(resind,:) = [x y u v s2n];
res(resind,:) = [x y u v corr s2n];
% quiver(x+cropvec(1),y+cropvec(2),u,v,'y');
if u ~= 0 || v ~= 0
% quiver(x,y,u,v,5,'y','Linewidth',1);
Expand All @@ -562,17 +563,22 @@ function pushbutton_start_Callback(hObject, eventdata, handles)
% Reshape U and V matrices in two-dimensional grid and produce
% velocity vector in U + i*V form (real and imaginary parts):

u = reshape(res(:,3), numrows,numcols);
v = reshape(res(:,4), numrows,numcols);
vector = u + sqrt(-1)*v;
u = reshape(res(:,3), numcols,numrows); %addition
v = reshape(res(:,4), numcols,numrows); %addition
u=u'; %addition
v=v'; %addition
vector=u + sqrt(-1)*v; %addition
% u = reshape(res(:,3), numrows,numcols);
% v = reshape(res(:,4), numrows,numcols);
% vector = u + sqrt(-1)*v;

% Remove outlayers - GLOBAL FILTERING
vector(abs(vector)>mean(abs(vector(vector~=0)))*outl) = 0;
u = real(vector);
v = imag(vector);

% Adaptive Local Median filtering

%kernel = [-1 -1 -1 -1 -1; -1 2 2 2 -1; -1 2 8 2 -1; -1 2 2 2 -1; -1 -1 -1 -1 -1];
kernel = [-1 -1 -1; -1 8 -1; -1 -1 -1];
tmpv = abs(conv2(v,kernel,'same'));
tmpu = abs(conv2(u,kernel,'same'));
Expand All @@ -591,17 +597,20 @@ function pushbutton_start_Callback(hObject, eventdata, handles)
% Let's throw the outlayers out:
u(u_out) = 0; u(v_out) = 0;
v(v_out) = 0; v(u_out) = 0;
vector = u + sqrt(-1)*v;

vector = u + sqrt(-1)*v;
vector=vector'; %addition
res(:,3) = reshape(real(vector),numrows*numcols,1);
res(:,4) = reshape(imag(vector),numrows*numcols,1);
res(:,4) = reshape(-imag(vector),numrows*numcols,1);%modified

% Filtered results will be stored in '.._flt.txt' file
filt_res = res;


vector=vector'; %addition
vector = fill_holes(vector,numrows,numcols);
vector=vector'; %addition
res(:,3) = reshape(real(vector),numrows*numcols,1);
res(:,4) = reshape(imag(vector),numrows*numcols,1);
res(:,4) = reshape(-imag(vector),numrows*numcols,1);%modified


% scale the pixels and apply the dt
Expand All @@ -627,21 +636,24 @@ function pushbutton_start_Callback(hObject, eventdata, handles)
% Save results as ASCII (text) files:
% Final (filtered, interpolated) results
% fid = fopen([dirname,filesep,filenames(fileind,1:end-4),baseext],'w');

basename = handles.files{fileind}(1:end-4);
baseext = '.vec';

final = fullfile(handles.path,[basename,baseext]);
finaltxt = fullfile(handles.path,[basename,'_final.txt']);
write_openpiv_vec(final,res,xUnits,tUnits,numrows,numcols);
write_openpiv_txt(finaltxt,res,xUnits,tUnits,numrows,numcols);

% Unfiltered, uninterpolated: (comment with % sign if you don't need it)
nofilt = fullfile(handles.path,[basename,'_noflt.txt']);
write_openpiv_vec(nofilt,no_filt_res,xUnits,tUnits,numrows,numcols);
write_openpiv_txt(nofilt,no_filt_res,xUnits,tUnits,numrows,numcols);


% Filtered, but not interpolated:
filtered = fullfile(handles.path,[basename,'_flt.txt']);
write_openpiv_vec(filtered,filt_res,xUnits,tUnits,numrows,numcols);
%filtered2 = fullfile(handles.path,[basename,'_flt2.txt']);
write_openpiv_txt(filtered,filt_res,xUnits,tUnits,numrows,numcols);
%write_openpiv_txt(filtered2,filt_res2,xUnits,tUnits,numrows,numcols);


% Results visualization
Expand Down Expand Up @@ -1207,7 +1219,7 @@ function next_image_Callback(hObject, eventdata, handles)


% --------------------------------------------------------------------
function exit_Callback(hObject, eventdata, handles)
function exit_Callback(~, ~, handles)
% hObject handle to exit (see GCBO)
% eventdata reserved - to be defined in a future version of MATLAB
% handles structure with handles and user data (see GUIDATA)
Expand Down
46 changes: 46 additions & 0 deletions write_openpiv_txt.m
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Original file line number Diff line number Diff line change
@@ -0,0 +1,46 @@
function success = write_openpiv_txt(filename,data,xUnits,tUnits,numrows,numcols)
% success = write_openpiv_txt(filename,data,,xUnits,uUnits)
% originally it was just
% fid = fopen(fullfile(handles.path,[handles.files{fileind}(1:end-4),'.txt']),'w');
% fprintf(fid,'%3d %3d %7.4f %7.4f %7.4f\n',res');
% fclose(fid);

% minimal implementation
% filename is a full path
% fullfile(handles.path,[handles.files{fileind}(1:end-4),'.txt'])
fid = fopen(filename,'w');

% data is called res in OpenPIV and it shall be N rows x 5 cols
% in print, it's rotated to 5 rows x N cols
if size(data,2) == 6
data = data';
elseif size(data,1) ~= 6
error('Wrong number of columns');
end

% print the header
% example of the VEC header
% TITLE="E:\2CM_FP500_5%G_68K\C001H001S0015CC\Soapfilmone\Analysis\Run00000
% 1.T000.D000.P000.H001.L.vec" VARIABLES="X mm", "Y mm", "U m/s", "V m/s",
% "CHC", DATASETAUXDATA Application="PIV" DATASETAUXDATA
% SourceImageWidth="1024" DATASETAUXDATA SourceImageHeight="1024"
% DATASETAUXDATA MicrometersPerPixelX="19.530001" DATASETAUXDATA
% MicrometersPerPixelY="19.530001" DATASETAUXDATA LengthUnit="mm"
% DATASETAUXDATA OriginInImageX="0.000000" DATASETAUXDATA
% OriginInImageY="0.000000" DATASETAUXDATA
% MicrosecondsPerDeltaT="2000.000000" DATASETAUXDATA TimeUnit="ms"
% DATASETAUXDATA SecondaryPeakNumber="0" DATASETAUXDATA
% DewarpedImageSource="0" ZONE I=63, J=63, F=POINT

zone = sprintf('ZONE I=%d, J=%d',numrows,numcols);
header = sprintf('VARIABLES= "X %s", "Y %s", "U %s/%s", "V %s/%s", "corr", "CHC", %s\n',...
xUnits,xUnits,xUnits,tUnits,xUnits,tUnits,zone);

% "CHC"

%fprintf(fid,'%s',header);
% print the data
fprintf(fid,'%3d %3d %7.4f %7.4f %7.4f %7.4f\n',data);
fclose(fid);

if fid ~= -1, success = true; else success = false; end
8 changes: 4 additions & 4 deletions write_openpiv_vec.m
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Original file line number Diff line number Diff line change
Expand Up @@ -12,9 +12,9 @@

% data is called res in OpenPIV and it shall be N rows x 5 cols
% in print, it's rotated to 5 rows x N cols
if size(data,2) == 5
if size(data,2) == 6
data = data';
elseif size(data,1) ~= 5
elseif size(data,1) ~= 6
error('Wrong number of columns');
end

Expand All @@ -33,14 +33,14 @@
% DewarpedImageSource="0" ZONE I=63, J=63, F=POINT

zone = sprintf('ZONE I=%d, J=%d',numrows,numcols);
header = sprintf('VARIABLES= "X %s", "Y %s", "U %s/%s", "V %s/%s", "CHC", %s\n',...
header = sprintf('VARIABLES= "X %s", "Y %s", "U %s/%s", "V %s/%s", "corr", "CHC", %s\n',...
xUnits,xUnits,xUnits,tUnits,xUnits,tUnits,zone);

% "CHC"

fprintf(fid,'%s',header);
% print the data
fprintf(fid,'%3d %3d %7.4f %7.4f %7.4f\n',data);
fprintf(fid,'%3d %3d %7.4f %7.4f %7.4f %7.4f\n',data);
fclose(fid);

if fid ~= -1, success = true; else success = false; end