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GrainMapping_fun.m
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GrainMapping_fun.m
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% GrainMapping for lab-base diffraction contrast tomography
% July 8, 2021
% Copyright by Haixing Fang, haixing.fang@grenoble-inp.fr; haixingfang868@gmail.com
% indexing grain orientations based on forward simulation
% shape reconstruction by growing neighboring voxels around indexed seeding voxels
% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% steps for grain mapping
% step 1: get geometry information using get_geometry.m and input those information to setup_exp.m
% step 2: get spots info, using get_spots.m; You may need to segment your images first
% step 3: get absorption tomo, run get_tomo_slices_create_h5.m
% step 4: check other parameters, e.g. RecBox, RecCenter, RecVoxelSize, S etc;
% note the coordinate differences betweeen DTU and Simap datasets
% step 5: run GrainMapping.m or GrainMapping_simap.m depending where the dataset is obtained
% step 5-1: input crytallographic parameters, experimental geometry, tomo h5 and spots info
% step 5-2: setup_hkl
% step 5-3: define reconstruction info: voxel size, volume, center and reconstruction parameters
% step 5-4: indexing and growing process (decoupled)
% step 5-5: merging process to define grains
% step 5-6: write out h5 ouput for DS
% step 5-7: fitting geometry for redoing the whole reconstruction
% step 5-8: end, when there is no need to redo the reconstruction given that good fitting parameters have been implemented
% version 2.0, Sep 24, 2021
% version 3.0, Dec 3, 2021
% version 4.0, Feb 10, 2022 (remove assigned spots from the spot list)
% version 5.0, April 8, 2022, compute by cpu, gpu_cuda_Gt, gpu_cuda_comp
function GrainMapping_fun(OutputFolder,fname_prefix,RecVolumePixel,SampleName,compute_opt)
%for testing
% SampleName='virtual_Fe_100um_6grains';
% RecVolumePixel=[1 60;
% 1 60;
% 1 80];
% OutputFolder='./virtual_Fe_100um_6grains_rec/fullvol_v4_simap_round_new_spots_gpu_Gt_test';
% fname_prefix='fullvol';
% SampleName='AlCu_8wt_580C_1h_nano_source';
% % RecVolumePixel=[1 338;
% % 1 305;
% % 1 425]; % full volume
% RecVolumePixel=[1 338;
% 1 305;
% 150 425]; % effective volume masked by tomo
% OutputFolder='./AlCu_8wt_580C_1h_nano_source_rec/fullvol_fitted_geo_gpu_test';
% fname_prefix='fullvol_v4';
% computation_options = [{'cpu'}, {'gpu_cuda_Gt'}, {'gpu_cuda_comp'}];
% compute_opt = computation_options{2};
fprintf('**********Computational choice: %s**********\n',compute_opt)
% set up all parameters: geometry, detector, sample, reconstruction, filefolders
% SampleName='AlCu8wt_middle_thinned_0930'; % 'simu_Fe'; 'AlCu8wt_middle_thinned_0930'
setup_para;
if ~exist('RotAxisOffset','var')
RotAxisOffset=0; % added on Aug 30, 2022
fprintf('RotAxisOffset set to 0 because it was not pre-set.\n')
end
fprintf('Tomo and spot files will be loaded from %s.\n',FileFolder)
fprintf('Output files will be written to %s.\n',OutputFolder)
% load tomographic volume data
fprintf('load tomo file: %s \n',fullfile(h5Folder_tomo,h5FileName_tomo))
tomo=get_tomo_fromh5(fullfile(h5Folder_tomo,h5FileName_tomo),1);
fprintf('tomo center = [%.4f %.4f %.4f] (mm).\n',tomo.Center)
if strcmp(SampleName,'AlCu_8wt_580C_1h_nanoS_CCD')
tomo.Center(3)=tomo.Center(3)-1/(Lsam2det/Lsam2sou+1);
end
fprintf('New tomo center = [%.4f %.4f %.4f] (mm). \n',tomo.Center)
% load DCT images for processing and spot segmentation, get binary images
fprintf('load spots file: %s \n',fullfile(FileFolder,SpotsFile))
load(fullfile(FileFolder,SpotsFile));
for i=1:length(proj_bin)
[proj_bin_bw(:,:,i),idx] = bwdist(double(proj_bin{i}));
end
rot_angles=rot_start:rot_step:rot_end;
% generate hkl for indexing
setup_hkl;
sprintf('Geometry: Lss = %.4f mm, Lsd = %.4f mm, dety00 = %.4f mm, detz00 = %.4f mm,\n tilt_xyz = [%.4f %.4f %.4f] degrees', ...
Lsam2sou, Lsam2det, dety00, detz00, tilt_x, tilt_y, tilt_z)
rng('shuffle');
%% Define the reconstruction volume
% figure;view0=orthosliceViewer(tomo.PhaseId,'Colormap',parula(256));
SampleVolumeDim=tomo.Dimension'.*tomo.VoxSize; % [mm]
% check orthoviewer to get the ROI
% note: in orthoview [x y] is reversed from conventionally defined system,
% should be switched
tomo_FOV_range=[1 tomo.Dimension(1);1 tomo.Dimension(2);1 tomo.Dimension(3)]; % [pixel]
VoxSize=tomo.VoxSize(1); % [x y z] [mm]
tomo_FOV_center=(tomo_FOV_range(:,2)-tomo_FOV_range(:,1))/2+tomo_FOV_range(:,1)-0.5; % [pixel]
RecVol_origin=(-tomo.Dimension'/2+tomo_FOV_center).*tomo.VoxSize; % [mm]
RecVol_origin(1:2)=-RecVol_origin(1:2); % add on Oct 7, 2021
RecVol_shift=RecVol_origin./VoxSize; % shift with respect to the tomo volume [pixel]
for i=1:3
RecVolume(i,1)=(RecVolumePixel(i,1)-1)*VoxSize-SampleVolumeDim(i)/2;
RecVolume(i,2)=RecVolumePixel(i,2)*VoxSize-SampleVolumeDim(i)/2;
RecBox(i)=-(RecVolume(i,1)-RecVol_origin(i))*2; % [mm]
end
for i=1:3
if RecVolumePixel(i,1)==0
RecVolumePixel(i,1)=1;
RecVolumePixel(i,2)=RecVolumePixel(i,2)+1;
end
end
dim=RecVolumePixel(:,2)-RecVolumePixel(:,1)+1;
dim=dim';
sprintf('The reconstructed volume has dimensions of %d*%d*%d pixel',dim)
if dim(1)>tomo.Dimension(1) || dim(2)>tomo.Dimension(2) || dim(3)>tomo.Dimension(3)
error('Error: reconstructed volume is larger than sample volume, please set a smaller volume for reconstruction.')
elseif dim(3)==1
error('Error: please set the volume_z >= 2 * VoxSize.')
end
% scale the tomo volume to have the same pixel size as RecVolume
tomo_scale=tomo;
if all(VoxSize~=tomo.VoxSize)
tomo_scale.PhaseId=imresize3(tomo.PhaseId,tomo.VoxSize(1)/VoxSize(1),'nearest');
tomo_scale.Mask=imresize3(tomo.Mask,tomo.VoxSize(1)/VoxSize(1),'nearest');
tomo_scale.Dimension=size(tomo_scale.Mask);
tomo_scale.VoxSize=[VoxSize VoxSize VoxSize];
end
% figure;view1=orthosliceViewer(tomo_scale.PhaseId,'Colormap',parula(256));
if RecVolumePixel(1,2)>tomo_scale.Dimension(1) || RecVolumePixel(2,2)>tomo_scale.Dimension(2) ...
|| RecVolumePixel(3,2)>tomo_scale.Dimension(3) || ~all(RecVolumePixel(:,1)>0)
error('Error: reconstructed volume is not properly set, please reset it.')
end
% initialize information for the reconstructed volume
DS.PhaseId=zeros(dim);
DS.Mask=zeros(dim);
DS.Completeness=zeros(dim);
DS.GrainId=zeros(dim);
DS.Rodrigues=zeros([3 dim]);
DS.EulerZXZ=zeros([3 dim]);
DS.IPF001=zeros([3 dim]);
DS.Dismedian=zeros(dim)+10; % median distance [mm]
DS.Ninter=zeros(dim); % number of intersected spots
DS.Icorr=zeros(dim); % intended for Icorr, but leave as no-use for the moment
DS.VisitFlag=zeros(dim)-1; % flag for visiting indexing, -1: non-visible; 0: not visited; 1: visited
clear allVoxel_indices;
[allVoxel_indices(:,1), allVoxel_indices(:,2), allVoxel_indices(:,3)]=ind2sub(dim, ...
find(tomo_scale.Mask(RecVolumePixel(1,1):RecVolumePixel(1,2),RecVolumePixel(2,1):RecVolumePixel(2,2), ...
RecVolumePixel(3,1):RecVolumePixel(3,2))==1));
for i=1:length(allVoxel_indices(:,1))
DS.Mask(allVoxel_indices(i,1),allVoxel_indices(i,2),allVoxel_indices(i,3))=1;
DS.PhaseId(allVoxel_indices(i,1),allVoxel_indices(i,2),allVoxel_indices(i,3))=1;
DS.VisitFlag(allVoxel_indices(i,1),allVoxel_indices(i,2),allVoxel_indices(i,3))=0;
DS.Dismedian(allVoxel_indices(i,1),allVoxel_indices(i,2),allVoxel_indices(i,3))=20;
end
allVoxel_indices=allVoxel_indices+RecVolumePixel(:,1)'-1;
if isempty(allVoxel_indices)
error('Error: please select a sample region containing grains to be reconstructed.');
end
allVoxel_indices=allVoxel_indices(randperm(length(allVoxel_indices(:,1))),:);
total_voxel=length(allVoxel_indices(:,1));
% generate seeding positions
pos_seed=generate_seeding_indexing_pos(1,allVoxel_indices,tomo_scale,VoxSize,simap_data_flag);
%% discretize orientation space
% nDiv=30;
% OR=ori_division(nDiv);
% OR=ori_division_mtex('cubic'); % using mtexfit_all_flag_track(i)
OR_folder='./ori_set_hyperspherical';
if strcmp(compute_opt, 'gpu_cuda_comp')
OR=get_ori_set(OR_folder,sgno,'1')
else
OR=get_ori_set(OR_folder,sgno)
end
vis_flag=0;
if vis_flag==1
cs = crystalSymmetry('cubic');
OR_ori=orientation(rotation(quaternion(OR.q(:,1),OR.q(:,2),OR.q(:,3),OR.q(:,4))),cs);
figure;
plot(OR_ori,'axisAngle','all');
end
%%%%%%%%%%%%%%%%%% grain mapping engine
SpotsForIndexing_select=0; % select spots which above certain size for indexing
if SpotsForIndexing_select==1
for i=1:length(Spots)
SpotsForIndex{i}=Spots{i}(Spots{i}(:,11)>20,:); % e.g. sizes should > 100 pixels
end
else
SpotsForIndex=Spots;
end
total_run_time=0; % total running time [s]
iter=0;
stop_grain_mapping=0;
indexed_voxel_fraction_min=0.999; % minimum allowed fraction of indexed voxels
% indexed_voxel_fraction_min=20000/total_voxel; % minimum allowed fraction of indexed voxels
FirstGrainID(1)=1;
indexing_final_all=[];
pos_seed_all=[];
Nr_indexed_voxel_all=[];
Nr_seed=50;
if strcmp(compute_opt,'gpu_cuda_comp')
Nr_seed=400;
end
% save parameters
save_para(Lsam2sou,Lsam2det,P0y,P0z,RotAxisOffset,dety00,detz00,tilt_x,tilt_y,tilt_z,RotDet, ...
pixelysize,pixelzsize,dety0,detz0,detysize,detzsize,BeamStopY,BeamStopZ, ...
drop_off,maxD,TrustComp,minComp,minEucDis,Ahkl,OR,VoxSize,RecVolumePixel, ...
FileFolder,OutputFolder,simap_data_flag,sample_no,fitted_geo_already,rot_angles, ...
tomo_scale,h5Folder_tomo,h5FileName_tomo,SpotsFile,maxDmedian);
save(fullfile(OutputFolder,'recon_init.mat'),'-v7.3');
if strcmp(compute_opt, 'cpu')
if isempty(gcp('nocreate'))
parpool('local',maxNumCompThreads);
end
elseif strcmp(compute_opt, 'gpu_cuda_Gt')
fprintf(['Note: you may need to modify the pre-assigned size for "float Gt_match" in "cuda_forward_Gt.cu".\n' ...
'It is recomended to set it as "float Gt_match[nr_spots*7]" where nr_spots = nr_projs*maximum spots per projection. \n']);
nr_spots = 0;
for i=1:length(Spots)
nr_spots = nr_spots + length(Spots{i}(:,1));
end
fprintf('There are in total %d spots.\n', nr_spots)
end
if ~exist('iter_end','var')
iter_end = 10; % define the gridding level
elseif iter_end > 10
iter_end=10;
end
check_fit_all=0;
if check_fit_all==1
sprintf("Grain mapping engine will check the need of fit_all mode for seeds.")
end
fprintf('*********** Start grain reconstruction engine **************\n')
while stop_grain_mapping~=1
iter=iter+1;
% generate seeding positions for indexing, April 14, 2022
% pos_seed = generate_uniform_seeding_pos(iter,RecVolumePixel,tomo_scale,VoxSize,simap_data_flag);
if iter>=10
Nr_seed=2500;
fprintf("Nr_seed switches its value to %d.\n", Nr_seed);
end
tStart=tic;
fprintf('Grain mapping engine starts with an iterative attempt of %d ...\n',iter)
fprintf('There are %d / %d unvisited voxels and %d / %d = %.3f voxels to be indexed ...\n', ...
length(find(DS.VisitFlag==0)),total_voxel,total_voxel-length(find(DS.GrainId>0)), ...
total_voxel,(total_voxel-length(find(DS.GrainId>0)))/total_voxel)
switch (compute_opt)
case 'cpu'
[indexing_final,pos_seed_new,DS_out,Nr_indexed_voxel]=GrainMapping_engine_cpu(pos_seed,OR,RotDet, ...
SpotsForIndex,proj_bin_bw,rot_angles,rot_start,rot_step,S,B,Ahkl,nrhkl,hklnumber,hkl_square, ...
hkl_family,hkl_family_square,d_possible,Glen_possible,thetamax,lambda_min,lambda_max, ...
Lsam2sou,Lsam2det,TrustComp,minComp,minEucDis,dety00,detz00,P0y,P0z,RotAxisOffset, ...
pixelysize,pixelzsize,dety0,detz0,detysize,detzsize,BeamStopY,BeamStopZ, ...
drop_off,maxD,DS,tomo_scale,VoxSize,RecVolumePixel,FirstGrainID(iter),simap_data_flag,maxDmedian,Nr_seed,OutputFolder,iter);
case 'gpu_cuda_Gt'
[indexing_final,pos_seed_new,DS_out,Nr_indexed_voxel]=GrainMapping_engine_gpu_Gt(pos_seed,OR,RotDet, ...
SpotsForIndex,proj_bin_bw,rot_angles,rot_start,rot_step,S,B,Ahkl,nrhkl,hklnumber,hkl_square, ...
hkl_family_square,d_possible,thetamax,lambda_min,lambda_max, ...
Lsam2sou,Lsam2det,TrustComp,minComp,minEucDis,dety00,detz00,P0y,P0z,RotAxisOffset, ...
pixelysize,pixelzsize,dety0,detz0,detysize,detzsize,BeamStopY,BeamStopZ, ...
drop_off,maxD,DS,tomo_scale,VoxSize,RecVolumePixel,FirstGrainID(iter),simap_data_flag, ...
maxDmedian,Nr_seed,OutputFolder,iter,check_fit_all);
case 'gpu_cuda_comp'
[indexing_final,pos_seed_new,DS_out,Nr_indexed_voxel]=GrainMapping_engine_gpu_comp(pos_seed,OR,RotDet, ...
SpotsForIndex,proj_bin_bw,rot_angles,S,B,Ahkl,nrhkl,thetamax,lambda_min,lambda_max, ...
Lsam2sou,Lsam2det,TrustComp,minComp,minEucDis,dety00,detz00,P0y,P0z,RotAxisOffset, ...
pixelysize,pixelzsize,dety0,detz0,detysize,detzsize,BeamStopY,BeamStopZ, ...
drop_off,maxD,DS,tomo_scale,VoxSize,RecVolumePixel,FirstGrainID(iter), ...
simap_data_flag,maxDmedian,Nr_seed,OutputFolder,iter,check_fit_all);
end
iter_time=toc(tStart);
sprintf('To complete iteration %d takes %.2f s and successful indexing rate = %.3f.',iter,iter_time, ...
length(find(indexing_final(:,7)>=minComp))/length(find(indexing_final(:,7)>0)))
save(fullfile(OutputFolder,[strcat('pos',num2str(iter)) '.mat']),'pos_seed','pos_seed_new');
%%%%%%%%%%%%%%%% store intermediate data
total_run_time=total_run_time+iter_time;
indexing_final_all=[indexing_final_all;indexing_final];
pos_seed_all=[pos_seed_all;pos_seed_new];
Nr_indexed_voxel_all=[Nr_indexed_voxel_all Nr_indexed_voxel];
% DS_record{iter}=DS_out;
indexed_voxel_fraction(iter)=length(find(DS_out.GrainId>0))/total_voxel;
if (length(find(indexing_final(:,7)>=minComp))/length(find(indexing_final(:,7)>0))<1/4 && Nr_seed<500) || iter>=iter_end
Nr_seed=500;
sprintf("Nr_seed switches its value to %d.", Nr_seed)
% not_remove_spot=1;
end
if iter>2 && indexed_voxel_fraction(iter)>0.95 && ...
abs(indexed_voxel_fraction(iter)-indexed_voxel_fraction(iter-1))<0.04
check_fit_all=1;
fprintf("OR fitting switches to fit_all mode.\n")
if Nr_seed<500
Nr_seed=500;
end
% if strcmp(compute_opt, 'gpu_cuda_comp')
% compute_opt = 'gpu_cuda_Gt';
% elseif strcmp(compute_opt, 'gpu_cuda_Gt')
% OR = get_ori_set(OR_folder,sgno,'1')
% end
end
if (iter>=2 && indexed_voxel_fraction(iter)>indexed_voxel_fraction_min && ...
abs(indexed_voxel_fraction(iter)-indexed_voxel_fraction(iter-1))*total_voxel<=2) || ...
(iter==1 && indexed_voxel_fraction(iter)>0.999) || (iter>=iter_end ...
&& (indexed_voxel_fraction(iter)>0.995 || (total_voxel-length(find(DS_out.GrainId>0)))<30000))
stop_grain_mapping=1;
sprintf('There are %d / %d voxels already indexed ...',length(find(DS_out.GrainId>0)),total_voxel)
else % continue to index unvisited voxel
FirstGrainID(iter+1)=FirstGrainID(iter)+length(pos_seed(:,1));
% clear un_visited_voxels;
% [un_visited_voxels(:,1), un_visited_voxels(:,2), un_visited_voxels(:,3)]=ind2sub(size(DS_out.VisitFlag), ...
% find(DS_out.VisitFlag>=0 & DS_out.VisitFlag<0.5));
% [un_visited_voxels(:,1), un_visited_voxels(:,2), un_visited_voxels(:,3)]=ind2sub(size(DS_out.VisitFlag), ...
% find(DS_out.VisitFlag==0));
% update on April 24, 2022
clear un_visited_voxels;
if indexed_voxel_fraction(iter)>0.99 || (total_voxel-length(find(DS_out.GrainId>0)))<30000
completeness_bin1=DS_out.Completeness>=TrustComp;
completeness_bin2=DS_out.VisitFlag==1;
completeness_bin=completeness_bin1+completeness_bin2>0;
completeness_bin_bw=bwdist(double(completeness_bin)); % the seeding candidates should far away from the indexed ones
[un_visited_voxels(:,1), un_visited_voxels(:,2), un_visited_voxels(:,3)]=ind2sub(size(DS_out.VisitFlag), ...
find(DS_out.VisitFlag>=0 & DS_out.VisitFlag<=0.5 & completeness_bin_bw>=3));
else
[un_visited_voxels(:,1), un_visited_voxels(:,2), un_visited_voxels(:,3)]=ind2sub(size(DS_out.VisitFlag), ...
find(DS_out.VisitFlag>=0 & DS_out.VisitFlag<0.5));
end
if (~isempty(un_visited_voxels) && length(un_visited_voxels(:,1))<total_voxel*0.05) || isempty(un_visited_voxels)
clear un_visited_voxels;
[un_visited_voxels(:,1), un_visited_voxels(:,2), un_visited_voxels(:,3)]=ind2sub(size(DS_out.VisitFlag), ...
find(DS_out.VisitFlag>=0 & DS_out.VisitFlag<0.5));
end
if ~isempty(un_visited_voxels)
un_visited_voxels=un_visited_voxels+RecVolumePixel(:,1)'-1;
pos_seed=generate_seeding_indexing_pos(iter+1,un_visited_voxels,tomo_scale,VoxSize,simap_data_flag);
else
stop_grain_mapping=1;
sprintf('There are %d / %d voxels already indexed ...',length(find(DS_out.GrainId>0)),total_voxel)
end
end
DS=DS_out;
save(fullfile(OutputFolder,strcat(num2str(iter), 'DS.mat')),'DS_out','-v7.3');
% % remove the assigned spots from the spot list
if strcmp(compute_opt,'gpu_cuda_Gt') && stop_grain_mapping~=1
for k=1:length(SpotsForIndex)
if isempty(SpotsForIndex)
not_remove_spot=1;
end
end
if iter>2 && not_remove_spot~=1
if (indexed_voxel_fraction(iter-1) == 0 && indexed_voxel_fraction(iter)>0.3 && iter>=9) ...
|| (indexed_voxel_fraction(iter-1)>0 && abs(indexed_voxel_fraction(iter)-indexed_voxel_fraction(iter-1))<0.1 && iter>=9)
[SpotsForIndex,~]=merge_regions_and_remove_spots(DS,proj_bin_bw,Spots,rot_start,rot_step,rot_angles,S,B,Ahkl,nrhkl,hklnumber, ...
hkl_square,RotDet,thetamax,lambda_min,lambda_max,Lsam2sou,Lsam2det,minEucDis,dety00,detz00,P0y,P0z,RotAxisOffset, ...
pixelysize,pixelzsize,dety0,detz0,detysize,detzsize,BeamStopY,BeamStopZ,tomo_scale,VoxSize,RecVolumePixel,simap_data_flag);
[proj,proj_bin,proj_bin_bw]=remove_spots_from_proj(proj,proj_bin,SpotsForIndex);
% GrainMapping_writer(DS_merge,tomo_scale.Center,[],[],atomparam.name, ...
% VoxSize,RecVolumePixel,tomo_scale.Dimension,OutputFolder,[SampleName '_temp'],[SampleName '_temp'],1);
end
end
end
end
% merge regions that have smaller misorientation than pre-defined threshold value
mtex_avail=0; % availability of mtex toolbox, 1: yes; 0: no (default).
if mtex_avail~=0
cs = crystalSymmetry('cubic'); % 'cubic', 'hexagonal', 'tetragonal', 'orthorhombic', 'monoclinic', 'trigonal'
else
cs = [];
end
min_misori = 0.5; % recommend to be 0.5 [deg]
[DS_merge,Ngrain,Nregion,Inherit_region_nr,CentroidComp]=merge_and_update_completeness(DS,mtex_avail, ...
cs,min_misori,proj_bin_bw,Spots,rot_start,rot_step,rot_angles,S,B,Ahkl,nrhkl,hklnumber,hkl_square, ...
RotDet,thetamax,lambda_min,lambda_max,Lsam2sou,Lsam2det,minEucDis,dety00,detz00,P0y,P0z,RotAxisOffset, ...
pixelysize,pixelzsize,dety0,detz0,detysize,detzsize,BeamStopY,BeamStopZ, ...
tomo_scale,VoxSize,RecVolumePixel,simap_data_flag);
iter_merge=1;
Ngrain_iter(iter_merge)=Ngrain;
iter_flag=1; % iterative merging
if iter_flag==1
stop_iter=0;
while stop_iter~=1
[DS_merge,Ngrain,Nregion,Inherit_region_nr,CentroidComp]=merge_and_update_completeness(DS_merge,mtex_avail, ...
cs,min_misori,proj_bin_bw,Spots,rot_start,rot_step,rot_angles,S,B,Ahkl,nrhkl,hklnumber,hkl_square, ...
RotDet,thetamax,lambda_min,lambda_max,Lsam2sou,Lsam2det,minEucDis,dety00,detz00,P0y,P0z,RotAxisOffset, ...
pixelysize,pixelzsize,dety0,detz0,detysize,detzsize,BeamStopY,BeamStopZ, ...
tomo_scale,VoxSize,RecVolumePixel,simap_data_flag);
iter_merge=iter_merge+1;
Ngrain_iter(iter_merge)=Ngrain;
if Ngrain_iter(iter_merge-1)-Ngrain_iter(iter_merge)<=0
stop_iter=1;
end
end
end
% revise indexing for the unindexed single voxel
[DS_merge]=revise_single_unindexed_voxel(DS_merge);
% write output as h5 file and generate dream3d and xdmf files for visualization
Center=tomo.Center; % [mm]
CenterShift=[];
PhaseNo=[];
PhaseName=atomparam.name;
ProjectName=fname_prefix;
regenerate_IPF=1;
[DS_new]=GrainMapping_writer(DS_merge,Center,CenterShift,PhaseNo,PhaseName, ...
VoxSize,RecVolumePixel,tomo_scale.Dimension,OutputFolder,fname_prefix,ProjectName,regenerate_IPF);
single_voxel_ID=find(DS_new.nVox==1);
if ~isempty(single_voxel_ID)
DS_merge=revise_single_voxel(DS_new,DS_merge);
[DS_new]=GrainMapping_writer(DS_merge,Center,CenterShift,PhaseNo,PhaseName, ...
VoxSize,RecVolumePixel,tomo_scale.Dimension,OutputFolder,fname_prefix,ProjectName,regenerate_IPF);
end
% basic grain information
grains=length(DS_new.SeedID); % number of grains
grainvolume=DS_new.nVox*DS_new.VoxSize(1)*DS_new.VoxSize(2)*DS_new.VoxSize(3)*1e9; % [um^3]
grainsize=2*(3*grainvolume/(4*pi)).^(1/3); % equivalent diameter of grain [um]
euler_grains=DS_new.EulerZXZ;% Euler angles [deg]: ([0 2*pi], [0 pi], [0 2*pi])
if false
figure;subplot(1,2,1);hist(grainsize);subplot(1,2,2);hist(DS_new.SeedComp);
end
GrainInfo=zeros(length(DS_new.SeedID),12);
for i=1:length(DS_new.SeedID)
if DS_new.nVox(i)>0
pos=((DS_new.Coord(i,:)+RecVolumePixel(:,1)'-1)-tomo_scale.Dimension/2).*VoxSize+tomo_scale.Center'; % [mm]
if simap_data_flag==1
pos(1:2)=-pos(1:2);
end
U=euler2u(DS_new.EulerZXZ(i,1)*pi/180,DS_new.EulerZXZ(i,2)*pi/180,DS_new.EulerZXZ(i,3)*pi/180);
% [Nr_simu,Nr_intersect,dis_median,SimuSpots,HittedSpots]=index_verify_v3(U,proj_bin_bw,Spots,pos,rot_angles,S,B,Ahkl,nrhkl,hklnumber,hkl_square, ...
% RotDet,thetamax,lambda_min,lambda_max,Lsam2sou,Lsam2det,minEucDis,dety00,detz00,P0y,P0z, ...
% pixelysize,pixelzsize,dety0,detz0,detysize,detzsize,BeamStopY,BeamStopZ);
[Nr_simu,Nr_intersect,dis_median]=forward_comp(U,proj_bin_bw,pos,rot_angles,S,B,Ahkl,nrhkl, ...
RotDet,thetamax,lambda_min,lambda_max,Lsam2sou,Lsam2det,minEucDis,dety00,detz00,P0y,P0z, ...
RotAxisOffset,pixelysize,pixelzsize,dety0,detz0,detysize,detzsize,BeamStopY,BeamStopZ);
GrainInfo(i,:)=[i pos DS_new.EulerZXZ(i,:) grainsize(i) Nr_intersect Nr_simu Nr_intersect/Nr_simu dis_median];
end
end
dlmwrite(fullfile(OutputFolder,'GrainInfo.txt'),GrainInfo,'delimiter',' ');
save(fullfile(OutputFolder,[fname_prefix '_recon.mat']),'-v7.3');
if false
%%%%%% fit geometry, select grains for fitting
fit_geometry=1; % whether to fit the geometry, 1: yes; 0: no
if fit_geometry==1
% select grains for fitting
comp_min=0.55;
grainsize_min=45; % [um]
hittedSpots_pair=[];
hittedSpots_pair_all=[];
select_ind=find(grainsize>grainsize_min & DS_new.SeedComp>=comp_min);
if isempty(select_ind)
[~,select_ind]=max(grainsize);
end
% select grains for fitting
DS_fit=DS_new;
eff_index=[];
for i=1:length(select_ind)
eff_index=[eff_index;find(DS_new.SeedID==select_ind(i))];
end
DS_fit.SeedID=DS_new.SeedID(eff_index);
DS_fit.SeedComp=DS_new.SeedComp(eff_index);
DS_fit.RodVec=DS_new.RodVec(eff_index,:);
DS_fit.nVox=DS_new.nVox(eff_index,:);
DS_fit.Coord=DS_new.Coord(eff_index,:);
DS_fit.EulerZXZ=DS_new.EulerZXZ(eff_index,:);
tic
Rsample=sqrt(SampleVolumeDim(1)^2+SampleVolumeDim(2)^2)/2; % [mm]
if length(DS_new.SeedID)>length(DS_fit.SeedID)
% for simulate spots for all grains, e.g. at -146 deg
[SpotNr_simu_all,SpotNr_obs_all,SpotsPair_all,GrainIndex_all,SubGrain_all,~,SmallGrID]=Forward_simu_spots_exp(DS_new, ...
Rsample,RecVolumePixel,tomo_scale,ExpTime,atomparam,proj,Spots,rot_start,rot_step, ...
S,B,Ahkl,nrhkl,hkl_square,Energy,lambda,V,K1,I0E,RotDet,thetamax,lambda_min,lambda_max,Lsam2sou,Lsam2det, ...
dety00,detz00,P0y,P0z,RotAxisOffset,pixelysize,pixelzsize,dety0,detz0,detysize,detzsize,BeamStopY,BeamStopZ, ...
simap_data_flag,strcat(OutputFolder,'./grains_all'),[rot_start:2*rot_step:rot_end-180]);
end
[SpotNr_simu,SpotNr_obs,SpotsPair,GrainIndex,SubGrain,rot_angles_calc,~]=Forward_simu_spots_exp(DS_fit, ...
Rsample,RecVolumePixel,tomo_scale,ExpTime,atomparam,proj,Spots,rot_start,rot_step, ...
S,B,Ahkl,nrhkl,hkl_square,Energy,lambda,V,K1,I0E,RotDet,thetamax,lambda_min,lambda_max,Lsam2sou,Lsam2det, ...
dety00,detz00,P0y,P0z,RotAxisOffset,pixelysize,pixelzsize,dety0,detz0,detysize,detzsize,BeamStopY,BeamStopZ, ...
simap_data_flag,strcat(OutputFolder,'./grains_forfit'),rot_angles);
if length(DS_new.SeedID)==length(DS_fit.SeedID)
SpotsPair_all=SpotsPair;
end
SpotsPair_all0=SpotsPair_all;
SpotsPair0=SpotsPair;
toc
% make spots pair unique and select the good ones for fitting
SpotsPair=make_unique_spot_pair(SpotsPair0);
SpotsPair_all=make_unique_spot_pair(SpotsPair_all0);
% SpotsPair=SpotsPair(SpotsPair(:,20)<25,:);
% col 13-14 forward simulated position; col 16-17 experimental position [pixel]
[ErrMean0,Err0,dis_y0,dis_z0]=dis_calc_spotspair([Lsam2sou Lsam2det dety00 detz00 tilt_x tilt_y tilt_z], ...
SpotsPair,S,B,P0y,P0z,RotAxisOffset,pixelysize,pixelzsize,dety0,detz0);
[ErrMean0_all,Err0_all,dis_y0_all,dis_z0_all]=dis_calc_spotspair([Lsam2sou Lsam2det dety00 detz00 tilt_x tilt_y tilt_z], ...
SpotsPair_all,S,B,P0y,P0z,RotAxisOffset,pixelysize,pixelzsize,dety0,detz0);
fprintf('%d spots are selected for fitting the geometry. \n',length(SpotsPair(:,1)));
fprintf('Average distance for selected grains is %.2f pixels. \n',ErrMean0);
fprintf('Average distance for all grains is %.2f pixels. \n',ErrMean0_all);
%%%% fitting options: 'FitWithouTilts'; 'FitAllOnce'; 'FitAll2Steps';
%%%% differences are small, by default use 'FitAll2Steps'
% [ParaFit,fval]=L_shift_tilt_fitting(SpotsPair,S,B,P0y,P0z,pixelysize,pixelzsize, ...
% dety0,detz0,Lsam2sou,Lsam2det,dety00,detz00,tilt_x,tilt_y,tilt_z,'FitWithouTilts');
% [ParaFit,fval]=L_shift_tilt_fitting(SpotsPair,S,B,P0y,P0z,pixelysize,pixelzsize, ...
% dety0,detz0,Lsam2sou,Lsam2det,dety00,detz00,tilt_x,tilt_y,tilt_z,'FitAllOnce');
% [ParaFit,fval]=L_shift_tilt_fitting(SpotsPair,S,B,P0y,P0z,pixelysize,pixelzsize, ...
% dety0,detz0,Lsam2sou,Lsam2det,dety00,detz00,tilt_x,tilt_y,tilt_z,'FitAll2Steps');
% P0y=ParaFit(3);P0z=ParaFit(4);
% ParaFit=ParaFit([1:2 5:end]);
% add on Nov 25, 2021, random testing on different initial values
iter_fit=100;
for j=1:iter_fit
if j==1
x0(j,:)=[Lsam2sou Lsam2det dety00 detz00 tilt_x tilt_y tilt_z];
else
x0(j,1)=Lsam2sou-1+rand(1)*2;
x0(j,2)=Lsam2det-1+rand(1)*2;
x0(j,3)=dety00-0.1+rand(1)*0.2;
x0(j,4)=detz00-0.2+rand(1)*0.2;
x0(j,5)=tilt_x-1+rand(1)*2;
x0(j,6)=tilt_y-1+rand(1)*2;
x0(j,7)=tilt_z-1+rand(1)*2;
end
[ParaFit(j,:),fval(j)]=L_shift_tilt_fitting(SpotsPair,S,B,P0y,P0z,RotAxisOffset,pixelysize,pixelzsize, ...
dety0,detz0,x0(j,1),x0(j,2),x0(j,3),x0(j,4),x0(j,5),x0(j,6),x0(j,7),'FitAllOnce');
j
end
[value,ind]=min(fval);
ParaFit=ParaFit(ind,:);
fval=fval(ind);
% col 13-14 forward simulated position; col 16-17 experimental position [pixel]
[ErrMean_fit,Err_fit,dis_y_fit,dis_z_fit]=dis_calc_spotspair(ParaFit,SpotsPair,S,B,P0y,P0z,RotAxisOffset, ...
pixelysize,pixelzsize,dety0,detz0);
[ErrMean_all_fit,Err_all_fit,dis_y_all_fit,dis_z_all_fit]=dis_calc_spotspair(ParaFit, ...
SpotsPair_all,S,B,P0y,P0z,RotAxisOffset,pixelysize,pixelzsize,dety0,detz0);
fprintf('Average distances for selected grains before and after fitting are %.2f and %.2f pixels,respectively. \n', ...
ErrMean0,ErrMean_fit);
fprintf('Average distances for all grains before and after fitting are %.2f and %.2f pixels,respectively. \n', ...
ErrMean0_all,ErrMean_all_fit);
Forward_simu_spots_exp_after_geo_fit(DS_fit,ParaFit, ...
Rsample,RecVolumePixel,tomo_scale,ExpTime,atomparam,proj,Spots,rot_start,rot_step, ...
S,B,Ahkl,nrhkl,hkl_square,Energy,lambda,V,K1,I0E,thetamax,lambda_min,lambda_max, ...
P0y,P0z,RotAxisOffset,pixelysize,pixelzsize,dety0,detz0,detysize,detzsize,BeamStopY,BeamStopZ, ...
simap_data_flag,OutputFolder,rot_angles);
end
if false
plot_dis;
slice0=slice_show(DS_new,round(DS_new.Dimension(3)/2),1,0,0)
end
save(fullfile(OutputFolder,[fname_prefix '_recon.mat']),'-v7.3');
end