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makeimage_poly_3Dmesh_v3_SingleGrain.m
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makeimage_poly_3Dmesh_v3_SingleGrain.m
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% makeimage script produces tiff diffraction images using the reflection information in A
% Haixing Fang March 2019
% used for produces tiff diffraction images for polychromatic X-ray diffraction
% modified on Sep 25, 2019: use the searching method to find unique
% reflections to avoid connecting issues caused by using 'measure'
% employ Gaussian point spread
% To create images for a single grain
% last updated on March 30, 2020
if peakshape==1
peakfwhm=2;
end
no=0;
totalrefl=0;
label_unique_flag=1;
if peakshape == 0
peakwsig = 0;
pixellimit = 0;
elseif peakshape == 1
pixellimit = ceil(peakfwhm);
end
nr = size(A_gr,1);
nrefl=0;
frame = zeros(detzsize,detysize);
no = no+1;
for jj=1:nr
int=A_gr(jj,21);
% Changed such that dety,detz has 0,0 in the center of the
% lower right corner instead of 0,0 at the border.
dety=round(A_gr(jj,17))+1;
detz=round(A_gr(jj,18))+1;
% Do not consider reflections with A_gr CMS further away from the
% detector than 5*fwhm of the spot
if (-5*pixellimit >= dety) || (dety >= detysize+5*pixellimit) || (-5*pixellimit >= detz) || (detz >= detzsize+5*pixellimit)
%disp(['reflection outside detector; y,z: ',num2str(dety),', ',num2str(detz)])
else
nrefl=nrefl+1;
Arefl(nrefl,:) = A_gr(jj,:);
totalrefl=totalrefl+1;
NOMAT(totalrefl)=jj;
if peakshape == 0 % spike peak
pixelnr_fit(1)=0.0943; % 14-14, calibrated
pixelnr_fit(2)=1.1679; % 14-14
if SubGrain{A_gr(jj,2)}(A_gr(jj,23),6)>1 && SubGrain{A_gr(jj,2)}(A_gr(jj,23),6)<100 % use um
% pixelnr=fix(SubGrain{A_gr(jj,2)}(A_gr(jj,23),6)./(2*1000*mean([pixelysize pixelzsize]))); % [2 1.75 1.5 1.25]
pixelnr=SubGrain{A_gr(jj,2)}(A_gr(jj,23),6)*pixelnr_fit(1)+pixelnr_fit(2); % 14-14
elseif SubGrain{A_gr(jj,2)}(A_gr(jj,23),6)==Inf
pixelnr=5;
else
% pixelnr=fix(SubGrain{A_gr(jj,2)}(A_gr(jj,23),6)./(2*mean([pixelysize pixelzsize]))); % use mm
pixelnr=SubGrain{A_gr(jj,2)}(A_gr(jj,23),6)*1000*pixelnr_fit(1)+pixelnr_fit(2); % 14-14
end
pixelnr=pixelnr*(Lsam2det/Lsam2sou);
% pixelnr=5;
% % randomize the position to avoid 'jaggie' artifacts
% dety = randi([dety-round(pixelnr/2),dety+round(pixelnr/2)],1,1);
% detz = randi([detz-round(pixelnr/2),detz+round(pixelnr/2)],1,1);
dety_delta=randi([dety-round(pixelnr/2),dety+round(pixelnr/2)],1,1)-dety;
dety = dety+dety_delta;
rand_direction=rand(1);
if rand_direction>0.5
detz = detz+dety_delta*tand(26.6); % rotated grid method
else
detz = detz-dety_delta*tand(26.6); % rotated grid method
end
for k1=round(dety-pixelnr):round(dety+pixelnr)
for k2=round(detz-pixelnr):round(detz+pixelnr)
if (0 < k1) && (k1 <= detysize) && (0 < k2) && (k2 <= detzsize)
frame(k2,k1)=frame(k2,k1)+int;
end
end
end
elseif peakshape == 1 % Anisotropic Gaussian type peak
% find factor of peak on this frame
factor=1/(1/(2*pi*4*4)*exp(-1))*0.8;
if SubGrain{A_gr(jj,2)}(A_gr(jj,23),6)>1 && SubGrain{A_gr(jj,2)}(A_gr(jj,23),6)<100 % use um
pixelnr=(SubGrain{A_gr(jj,2)}(A_gr(jj,23),6)./(2*1000*mean([pixelysize pixelzsize]))); % [2 1.75 1.5 1.25]
elseif SubGrain{A_gr(jj,2)}(A_gr(jj,23),6)==Inf
pixelnr=5;
else
pixelnr=(SubGrain{A_gr(jj,2)}(A_gr(jj,23),6)./(2*mean([pixelysize pixelzsize]))); % use mm
end
pixelnr=pixelnr*(Lsam2det/Lsam2sou);
if pixelnr<=0
pixelnr=1;
end
peakfwhm=sqrt(2)*pixelnr;
pixelnr=9/20*2.355*peakfwhm;% FWHM/FWTM = 5/9
gaussian1=fspecial('Gaussian',round(2*pixelnr)+1,peakfwhm);
PSF2=fspecial('motion',pixelnr*2,90-abs(A_gr(jj,16)-90)); % anisotropic filter
PSF2=conv2(PSF2,gaussian1);
for k1=1:size(PSF2,2)
for k2=1:size(PSF2,1)
if (0 < round(k1+dety-size(PSF2,2)/2)) && (round(k1+dety-size(PSF2,2)/2) <= detysize) ...
&& (0 < round(k2+detz-size(PSF2,1)/2)) && (round(k2+detz-size(PSF2,1)/2) <= detzsize)
frame(round(k2+detz-size(PSF2,1)/2),round(k1+dety-size(PSF2,2)/2))= ...
frame(round(k2+detz-size(PSF2,1)/2),round(k1+dety-size(PSF2,2)/2))+int*factor*PSF2(k2,k1);
end
end
end
end
end
end
% frame = frame./(sum(I0E)*ExpTime*(pixelysize*pixelzsize)).*(2^16-1); % normalized by empty sample beam
% frame=frame./max(max(frame)).*(2^16-1); % normalized by the strongest signal
% bgint_gen; % generate background noise
frame = frame + bgint*ones(detzsize,detysize); % Add background counts
% bgint_gen_v2; % generate background noise
% frame = frame + bgint*ones(detzsize,detysize); % Add constant background counts
% frame = frame + Ibg; % Add background counts
frame_image=uint16(frame);
% thres1=fix(bgint)+1;
% thres1=bgint+sqrt(bgint);
% thres1=2*bgint;
% thres1=7*bgint;
frame_bin = frame_image>thres1;
if thres1~=(bgint+sqrt(bgint))
frame_image=double(frame_image).*double(frame_bin)+thres1.*double(~frame_bin);
frame_image=uint16(frame_image);
end
% add beam stop
if ~isempty(BeamStopY) && ~isempty(BeamStopZ)
frame_image_BeamStop=frame_image;
frame_image_BeamStop(BeamStopZ(1):BeamStopZ(2),BeamStopY(1):BeamStopY(2))=0;
frame_bin_BeamStop=frame_bin;
frame_bin_BeamStop(BeamStopZ(1):BeamStopZ(2),BeamStopY(1):BeamStopY(2))=0;
end
label_BeamStop=1;
if label_BeamStop~=1
frame_label = label(frame_bin,1,0,detzsize*detysize);
frame_label_im=uint16(frame_label);
frame_measure = measure(frame_label,frame_image,{'dimension','DimensionsCube','gravity','size','feret'});
else
frame_label = label(frame_bin_BeamStop,1,0,detzsize*detysize);
frame_label_im=uint16(frame_label);
frame_measure = measure(frame_label,frame_image,{'dimension','DimensionsCube','gravity','size','feret'});
end
clear GrainIndex;
clear label_str;
label_pos=[];
Gr_unique=unique(A_gr(:,2),'rows');
n=0; % spot number
n_pos=0; % number for label string
for m=1:length(Gr_unique)
hklIndex=A_gr(find(A_gr(:,2)==Gr_unique(m)),4:6);
[hklIndex,ia,ic] = unique(hklIndex,'rows');
hklIndex_unique=[];
for n1=1:length(hklIndex(:,1))
hkl_rest=setdiff(hklIndex,hklIndex(n1,:),'rows');
if ~ismember(hklIndex(n1,:)/2,hkl_rest,'rows') && ~ismember(hklIndex(n1,:)/3,hkl_rest,'rows') ...
&& ~ismember(hklIndex(n1,:)/4,hkl_rest,'rows') && ~ismember(hklIndex(n1,:)/5,hkl_rest,'rows')
hklIndex_unique=[hklIndex_unique;hklIndex(n1,:)]; % get rid of multiple reflections such as 111 222
end
end
hklIndex_unique(:,4)=hklIndex_unique(:,1).^2+hklIndex_unique(:,2).^2+hklIndex_unique(:,3).^2;
hklIndex_unique = sortrows(hklIndex_unique,4);
hklIndex_unique=hklIndex_unique(:,1:3);
% m
% length(hklIndex_unique(:,1))
for nn=1:length(hklIndex_unique(:,1))
clear A_filted;
A_filted=A_gr(find(A_gr(:,2)==Gr_unique(m) & ((A_gr(:,4)==hklIndex_unique(nn,1) & ...
A_gr(:,5)==hklIndex_unique(nn,2) & A_gr(:,6)==hklIndex_unique(nn,3)) | ...
(A_gr(:,4)==hklIndex_unique(nn,1)*2 & ...
A_gr(:,5)==hklIndex_unique(nn,2)*2 & A_gr(:,6)==hklIndex_unique(nn,3)*2) | ...
(A_gr(:,4)==hklIndex_unique(nn,1)*3 & ...
A_gr(:,5)==hklIndex_unique(nn,2)*3 & A_gr(:,6)==hklIndex_unique(nn,3)*3))),:);
if ~isempty(A_filted)
if label_BeamStop==1 && ~(round(min(A_filted(:,18)))>=BeamStopZ(1) && round(max(A_filted(:,18)))<=BeamStopZ(2) ...
&& round(min(A_filted(:,17)))>=BeamStopY(1) && round(max(A_filted(:,17)))<=BeamStopY(2))
n=n+1;
A_rest=setdiff(A_gr,A_filted,'rows');
if exist('ismembertol','builtin')==0
LIA=ismember(A_filted(:,17:18),A_rest(:,17:18),'Rows');
else
LIA=ismembertol(A_filted(:,17:18),A_rest(:,17:18),2,'DataScale',1,'ByRows',true); % tolerance is 2 pixels
end
CropROI(1)=round(min(A_filted(:,17)))-20;
CropROI(2)=round(min(A_filted(:,18)))-20;
CropROI(3)=round(max(A_filted(:,17))-min(A_filted(:,17)))+40;
CropROI(4)=round(max(A_filted(:,18))-min(A_filted(:,18)))+40;
if CropROI(1)<1
CropROI(1)=1;
end
if CropROI(2)<1
CropROI(2)=1;
end
% [xmin ymin width height]
if CropROI(1)+CropROI(3)>=detysize
CropROI(3)=detysize-CropROI(1);
end
if CropROI(2)+CropROI(4)>=detzsize
CropROI(4)=detzsize-CropROI(2);
end
frame_select=imcrop(frame_image_BeamStop,[CropROI(1) CropROI(2) CropROI(3)-1 CropROI(4)-1]); % [xmin ymin width height]
if sum(sum(frame_select==0))>0 || sum(sum(frame_select==mean(mean(frame_select))))/numel(frame_select)
frame_select_bg=1.1*thres1;
frame_select_bin = frame_select>frame_select_bg; % in touch with the beam stop
else
% [frame_select_bin,frame_select_bg] = threshold(frame_select,'otsu',Inf);
% [frame_select_bin,frame_select_bg] = threshold(frame_select,'background',Inf);
% if size(frame_select,1)/size(frame_select,2)>=10 || size(frame_select,1)/size(frame_select,2)<=0.1
% if max(max(frame_select))<=thres1*1.5
[frame_select_bin,frame_select_bg1] = threshold(frame_select,'otsu',Inf);
% else
[frame_select_bin,frame_select_bg2] = threshold(frame_select,'background',Inf);
% end
frame_select_bg=1/2*frame_select_bg1+1/2*frame_select_bg2;
frame_select_bin=frame_select>frame_select_bg;
if frame_select_bg<thres1
frame_select_bin=frame_select>thres1;
end
frame_select_bin=double(frame_select_bin);
end
frame_select_bin=frame_select_bin>0;
if sum(LIA)==0 % no overlap with other spots
GrainIndex(n,1)=n; % ID of diffraction spot
% GrainIndex(n,2)=sum(frame_select_measure.Size); % size of the diffraction spot [pixel*pixel]
GrainIndex(n,2)=sum(sum(frame_select_bin));
GrainIndex(n,3)=A_filted(1,2); % ID of grain
GrainIndex(n,4:6)=hklIndex_unique(nn,:); % (h k l)
GrainIndex(n,7)=sum(sum(double(frame_select_bin).*double(frame_select)))/GrainIndex(n,2);% average intensity of the diffraction spot
GrainIndex(n,8)=A_filted(1,1); % ID of Reflection number
GrainIndex(n,9)=0; % overlapped area fraction, flag 0-no, 1-yes
GrainIndex(n,10)=sum(sum(double(frame_select_bin).*double(frame_select)))- ...
sum(sum(double(frame_select_bin).*max([thres1 frame_select_bg]))); % IntInt, modified on March 28, 2020
% AllSpotsNr(rot_number)=AllSpotsNr(rot_number)+1;
else % overlap with other spots
% frame_select=imcrop(frame_image,[round(min(A_filted(:,17))) round(min(A_filted(:,18))) ...
% round(max(A_filted(:,17))-min(A_filted(:,17))) ...
% round(max(A_filted(:,18))-min(A_filted(:,18)))]); % [xmin ymin width height]
% frame_select_bin = frame_select>thres1;
% % frame_select_label = label(frame_select_bin,1,0,size(frame_select,1)*size(frame_select,2));
% % frame_select_measure = measure(frame_select_label,frame_select,{'gravity','size'});
GrainIndex(n,1)=n; % ID of diffraction spot
% GrainIndex(n,2)=sum(frame_select_measure.Size); % size of the diffraction spot [pixel*pixel]
GrainIndex(n,2)=sum(sum(frame_select_bin));
GrainIndex(n,3)=A_filted(1,2); % ID of grain
GrainIndex(n,4:6)=hklIndex_unique(nn,:); % (h k l)
GrainIndex(n,7)=sum(sum(double(frame_select_bin).*double(frame_select)))/GrainIndex(n,2);% average intensity of the diffraction spot
GrainIndex(n,8)=A_filted(1,1); % ID of Reflection number
GrainIndex(n,9)=length(find(LIA==1))/length(LIA); % overlapped area fraction, flag 0-no, 1-yes
GrainIndex(n,10)=sum(sum(double(frame_select_bin).*double(frame_select)))- ...
sum(sum(double(frame_select_bin).*max([thres1 frame_select_bg]))); % IntInt, modified on March 28, 2020
% AllSpotsNr(rot_number)=AllSpotsNr(rot_number)+1;
% SpotOverlapNr(rot_number)=SpotOverlapNr(rot_number)+1;
end
if GrainIndex(n,2)>0
n_pos=n_pos+1;
label_str{n_pos} = strcat([num2str(GrainIndex(n,4)) num2str(GrainIndex(n,5)) ...
num2str(GrainIndex(n,6))],strcat(', No.',num2str(GrainIndex(n,3))));
% if rot>=0
% label_pos = [label_pos;frame_measure(n).Gravity(1) frame_measure(n).Gravity(2)];
% else
% label_pos = [label_pos;detysize-frame_measure(n).Gravity(1) frame_measure(n).Gravity(2)];
% end
label_pos = [label_pos;detysize-mean(A_filted(:,17)) detzsize-mean(A_filted(:,18))];
end
end
end
end
end
% unique label annotations
if exist('label_str','var')
if label_unique_flag==1
[label_str_unique,idx,idc]=unique(label_str);
label_pos_unique=label_pos(idx,:);
else
label_str_unique=label_str;
label_pos_unique=label_pos;
end
end
% flipud(fliplr) is to rotate the image by 180 degrees in clockwise direction
%Write out tiff file for grey value image
filename = sprintf('%s/%s%0.4d_grey.tif',direc,prefix,rot_number-1); % Generate FILENAME of frame
frame_image = flipud(fliplr(frame_image)); %flip frame to output images in correct direction
% if rot<0
% frame_image = fliplr(frame_image);
% end
% imwrite(frame_image,filename,'tif'); % Write out tiff file
%Write out tiff file for binary image
filename = sprintf('%s/%s%0.4d_binary.tif',direc,prefix,rot_number-1); % Generate FILENAME of frame
frame_bin = flipud(fliplr(frame_bin)); %flip frame to output images in correct direction
% if rot<0
% frame_bin = fliplr(frame_bin);
% end
% imwrite(frame_bin,filename,'tif'); % Write out tiff file
%Write out tiff file for label image
filename = sprintf('%s/%s%0.4d_label.tif',direc,prefix,rot_number-1); % Generate FILENAME of frame
frame_label_im = flipud(fliplr(frame_label_im)); %flip frame to output images in correct direction
% if rot<0
% frame_label_im = fliplr(frame_label_im);
% end
% imwrite(frame_label_im,filename,'tif'); % Write out tiff file
%Write out tiff file for label image
if exist('label_pos_unique','var') && exist('insertText.m','file')~=0
if ~isempty(label_pos_unique)
filename = sprintf('%s/%s%0.4d_label_annot.tif',direc,prefix,rot_number-1); % Generate FILENAME of frame
% frame_label_im = flipud(fliplr(image_label_annot)); %flip frame to output images in correct direction
frame_label_annot = insertText(frame_label_im, label_pos_unique, label_str_unique, 'FontSize', 30,'BoxOpacity', 0.4);
% imwrite(frame_label_annot,filename,'tif'); % Write out tiff file
end
end
%Write out tiff file for grey value image with beam stop
filename = sprintf('%s/%s%0.4d_beamstop.tif',direc,prefix,rot_number-1); % Generate FILENAME of frame
frame_image_BeamStop = flipud(fliplr(frame_image_BeamStop));
% imwrite(frame_image_BeamStop,filename,'tif'); % Write out tiff file
%Write out tiff file for grey value image with beam stop
filename = sprintf('%s/%s%0.4d_beamstop_bin.tif',direc,prefix,rot_number-1); % Generate FILENAME of frame
frame_bin_BeamStop = flipud(fliplr(frame_bin_BeamStop));
% imwrite(frame_bin_BeamStop,filename,'tif'); % Write out tiff file
% record the effective index of diffraction spots
if exist('GrainIndex','var')
hklIndex=GrainIndex(:,3:6);
[hklIndex_unique,ia,ic] = unique(hklIndex,'rows');
% GrainIndex_unique=GrainIndex(ia,:); % size of diffraction spot may not be true
% GrainIndex_unique=sortrows(GrainIndex_unique);
GrainIndex_unique=GrainIndex(find(GrainIndex(:,2)>0),:);
end