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NORDIC.m
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NORDIC.m
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function NORDIC(file_filter,ARG)
%
% Processing of matlab files. Assume that the data is a 4D array, and
% that the 4th dimension has [vol_1 ... Vol_N noise_volume gfactor_map ]
% Variable should be stored in an array labelled KSP
% KSP should be in image-space and complex valued
% An auxilary variable called KSP_processed shoudl exist. It shoudl be
% all zeros, and have the length of the third dimension in KSP
% Copyright Board of Regents, University of Minnesota, 2022
NORDIC_threshold=1.0; % scaling the threshold relative to the largest singular value of the noise
ker=0; % if 0, the scaling is automatic to a 11:1 ratio
kernel_size=[ker ker ker]; % making a cubic patchsize
master_fast=1; % If 0, then indidvidual files will be saved. legacy option, not needed when patch_avg_sub<ker
soft_thrs=[]; % Parameter for switching between NORDIC and MPPCA (=10)
patch_avg_sub=2; % use for master_fast==1; Reduces the number of over lapping patches. Shift us 1/patch_avg_sub
patch_avg=0; % For subfunction use, of where patch averagign shoudl be performed.
file_idx=1;
DUAL=1; % Paramter to remove some final volumes from the end of [vol_1 ... Vol_N] leaving [ noise_volume gfactor_map ]
restart_list=0;
DIR=[pwd '/'];
NVR_LLR_3D_MP_2(DIR,file_filter,file_idx,NORDIC_threshold,DUAL,kernel_size,patch_avg,['kernel_' num2str(ker)],restart_list, master_fast,soft_thrs, patch_avg_sub);
return
function NVR_LLR_3D_MP_2(DIREC,file_filter,file_idx,NVR_threshold,DUAL,kernel_size,patch_average,APPEND_NAME, restart_list, master_fast,soft_thrs, patch_average_sub, NVR2, truncate_length)
% check if the NVR file exist, otherwise start the conversion
% there are three files, filename, filename_out filename_in
% check if the data is in the file; otherwise skip
% check if the file is being handled allready, otherwise only one slice can be processed
%
% start processing
% check if the output is saved in a file, otherwise start processing
% finish processing
% save the result to a file
% clear all temporary files
% if complete then load the file and do the normalization for averaging
% path('~moeller/matlab/Regularization',path)
%soft_thrs=10; disp('Using the MPPCA estimation method')
% soft_thrs=[]; disp('Using the NVR estimation method')
if ~exist('master_fast'); master_fast=0; end;
if ~exist('patch_average_sub'); ARG.patch_average_sub=1; else ; ARG.patch_average_sub=patch_average_sub; end
if ~exist('DUAL'); ARG.DUAL=1; else ; ARG.DUAL=DUAL; end
if ~exist('NVR_threshold'); ARG.NVR_threshold=1; else ; ARG.NVR_threshold=NVR_threshold; end
if ~exist('file_idx'); ARG.file_idx=1; else ; ARG.file_idx= file_idx; end
if ~exist('kernel_size'); ARG.kernel_size=[4 4 4];else ; ARG.kernel_size= kernel_size; end
if ~exist('patch_average'); ARG.patch_average=1; else ; ARG.patch_average=patch_average; end
if ~exist('APPEND_NAME'); ARG.APPEND_NAME=[];else ; ARG.APPEND_NAME=APPEND_NAME; end
if ~exist('NVR2'); ARG.NVR2=[]; else ; ARG.NVR2=NVR2; end
if ~exist('truncate_length'); ARG.truncate_length=[]; else ; ARG.truncate_length= truncate_length; end
if ~exist('restart_list'); ARG.restart_list=0;else ; ARG.restart_list= restart_list; end
if ~exist('soft_thrs'); ARG.soft_thrs=[] ;else ; ARG.soft_thrs= soft_thrs; end
if isempty(soft_thrs)
disp('Using the NVR estimation method')
elseif soft_thrs==10
disp('Using the MPPCA estimation method')
end
ARG.patch_scale=0;
PP=dir(file_filter) % PP=dir('M*SORT2*mat');
filename=PP(file_idx).name;%filename2%[1:2]+2+2+2%size(PP,1)/2:-1:1;%:-1:size(PP,1)/2
if sum(kernel_size)==0 % choose optimal kernel
tmp=matfile(filename);
matdim=size(tmp,'KSP');
ker=round((matdim(4)*11)^(1/3));
kernel_size=[ker ker ker], ARG.kernel_size=kernel_size;
APPEND_NAME=['kernel' num2str(ker)]; ARG.APPEND_NAME=APPEND_NAME;
end
ARG.filename=filename;
ARG.master_fast=master_fast;
filename_out=dir(['KSP_' filename(1:end-4) APPEND_NAME '.mat']); % FILE with the NVR reconstruction
filename_in=dir([filename(1:end-4) '_NVR.mat']); % file with the data that will be used in the NVR, IE phase normalized
if isempty(filename_out) |1 % process is not complete
if isempty(filename_in) | 1 % Initial file is missing, create
% STANDARD
disp('CHECK if the right input to NORDIC is used')
[KSP_phase_norm, meanphase, DD_phase] = sub_create_NVR_file(filename, ARG) ;
% [KSP_phase_norm, meanphase, DD_phase] = sub_create_NVR_file_HCP(filename, ARG) ;
% [KSP_phase_norm, meanphase, DD_phase] = sub_create_NVR_file_MPPCA(filename, ARG) ;
ARG.meanphase=meanphase;
ARG.DD_phase=DD_phase;
filename_in=dir([filename(1:end-4) '_NVR.mat']);
QQ=matfile(filename_in.name,'writable',true);
% return
for n1=1:1000; % update with the files that already exist
tmp=dir([ARG.filename 'slice' num2str(n1) '.mat']);
if ~isempty(tmp); QQ.KSP_processed(1,n1)=2; end
end
else
return; % Only the master gets to go. Usefull when the phase correction and saving is the slowest part
end
if ~isempty(filename_in) % check if it is being written to or if it is completed
filename_in_tmp=dir([filename(1:end-4) '_NVR.mat']);
if filename_in_tmp.bytes ~= filename_in.bytes | filename_in_tmp.bytes<1e3
disp('NVR file is being saved or processed. Stopping....')
% return
end
end
if restart_list~=2
filename_in=dir([filename(1:end-4) '_NVR.mat']);
QQ=matfile(filename_in.name,'writable',true);
if master_fast==1; QQ.writing_file=1; end
if QQ.writing_file==0
disp('I am a slave, just saving files')
end
end
if restart_list==3
%QQ.writing_file=1; % Make this the master
KSP_processed=QQ.KSP_processed;
if sum(KSP_processed)==2*size(KSP_processed,2) % all files are saved
QQ.writing_file=1;
else
KSP_processed(KSP_processed~=2)=0;
QQ.KSP_processed=KSP_processed;
% return
end
for n1=1:1000; % update with the files that already exist
tmp=dir([ARG.filename 'slice' num2str(n1) '.mat']);
if ~isempty(tmp); QQ.KSP_processed(1,n1)=2; end
end
end
if restart_list==2 % the _NVR file has been corrupted
% QQ.writing_file=0; % lock file for other to be maste
sub_create_NVR_file(filename, ARG)
filename_in=dir([filename(1:end-4) '_NVR.mat']);
QQ=matfile(filename_in.name,'writable',true);
for n1=1:1000; % update with the files that already exist
tmp=dir([ARG.filename 'slice' num2str(n1) '.mat']);
if ~isempty(tmp); QQ.KSP_processed(1,n1)=2; end
end
restart_list=1;
end
if restart_list==1
QQ.writing_file=1; % Make this the master
KSP_processed=QQ.KSP_processed;
KSP_processed(KSP_processed==1)=0;
KSP_processed(KSP_processed==3)=0;
QQ.KSP_processed=KSP_processed;
end
if QQ.writing_file==1
disp('I am master, I have control')
QQ.writing_file=0;
%KSP2=QQ.KSP2;
variableInfo=who('-file',filename_in.name);
if (ismember('KSP_recon',variableInfo) & restart_list==0)
KSP_recon=QQ.KSP_recon;
elseif ismember('size_KSP',variableInfo)
size_KSP=QQ.size_KSP;
KSP_recon=single(complex(zeros(size_KSP)));
KSP2=KSP_recon;
else
KSP_recon=single(complex(zeros(size(QQ,'KSP2'))));
KSP2=KSP_recon;
end
master=1;
else
% disp('I am slave')
KSP2=[];
KSP_recon=[];
master=0;
end
if restart_list==1;
%QQ.writing_file==1
if sum(QQ.KSP_processed)==size(QQ.KSP_processed,2)*3;
QQ.KSP_processed=QQ.KSP_processed*0+2; % set all files to be processed. If they are not they will be.
KSP_recon=single(complex(zeros(size(KSP2))));
end
for n1=1:1000; % update with the files that already exist
tmp=dir([ARG.filename 'slice' num2str(n1) '.mat']);
if ~isempty(tmp);
QQ.KSP_processed(1,n1)=2;
% else
% QQ.KSP_processed(1,n1)=0;
end
end
end
if ARG.patch_average==0
KSP_processed=QQ.KSP_processed*0;
for nw1=2:max(1,floor(ARG.kernel_size(1)/ARG.patch_average_sub));
KSP_processed(1,nw1 : max(1,floor(ARG.kernel_size(1)/ARG.patch_average_sub)):end)=2;
end
KSP_processed(end)=0; % disp
QQ.KSP_processed=KSP_processed;
end
if master_fast>0;
KSP2=KSP_phase_norm;
% KSP2=QQ.KSP2;
end
if master_fast==0
KSP_weight=KSP2(:,:,:,1)*0;
for n1=1:size(QQ,'KSP_processed',2)
fprintf( [num2str(n1) ' '])
[KSP_recon]=sub_NVR_for_one_slice(KSP_recon,KSP2,ARG,n1,QQ,master*0,[]) ; % save all files
fprintf( [num2str(n1) ' '])
if mod(n1,20)==0; disp(' ');end
end
elseif master_fast==1
KSP_weight=KSP2(:,:,:,1)*0;
NOISE=KSP_weight;
Component_threshold=KSP_weight;
energy_removed=KSP_weight;
for n1=1:size(QQ,'KSP_processed',2)
fprintf( [num2str(n1) ' '])
[KSP_recon,~,KSP_weight,NOISE,Component_threshold,energy_removed]=sub_NVR_for_one_slice(KSP_recon,KSP2,ARG,n1,QQ,master_fast,KSP_weight,NOISE,Component_threshold,energy_removed) ; % save all files
fprintf( [num2str(n1) ' '])
if mod(n1,20)==0; disp(' ');end
end
KSP_recon=KSP_recon./repmat((KSP_weight),[1 1 1 size(KSP2,4)]); % Assumes that the combination is with N instead of sqrt(N). Works for NVR not MPPCA
ARG.NOISE= NOISE./KSP_weight;
ARG.Component_threshold = Component_threshold./KSP_weight;
ARG.energy_removed = energy_removed./KSP_weight;
elseif master_fast==2
KSP_processed=QQ.KSP_processed;
KSP_weight=KSP2(:,:,:,1)*0;
KSP_recon2=KSP_recon;
for n1=1:size(QQ,'KSP_processed',2)
fprintf( [num2str(n1) ' '])
[KSP_recon2,~,KSP_weight]=sub_NVR_for_one_slice(KSP_recon2,abs(KSP2),ARG,n1,QQ,master_fast*0+1,KSP_weight) ; % save all files
fprintf( [num2str(n1) ' '])
if mod(n1,20)==0; disp(' ');end
end
KSP_recon2=KSP_recon2./repmat((KSP_weight),[1 1 1 size(KSP2,4)]); % Assumes that the combination is with N instead of sqrt(N). Works for NVR not MPPCA
QQ.KSP_processed=KSP_processed;
KSP_weight=KSP2(:,:,:,1)*0;
for n1=1:size(QQ,'KSP_processed',2)
fprintf( [num2str(n1) ' '])
[KSP_recon,~,KSP_weight]=sub_NVR_for_one_slice(KSP_recon,abs(KSP_recon2).*exp(1i*angle(KSP2)),ARG,n1,QQ,master_fast*0+1,KSP_weight) ; % save all files
fprintf( [num2str(n1) ' '])
if mod(n1,20)==0; disp(' ');end
end
KSP_recon=KSP_recon./repmat((KSP_weight),[1 1 1 size(KSP2,4)]); % Assumes that the combination is with N instead of sqrt(N). Works for NVR not MPPCA
elseif master_fast==3
KSP_weight=KSP2(:,:,:,1)*0;
for n1=1:size(QQ,'KSP_processed',2)
fprintf( [num2str(n1) ' '])
[KSP_recon,~,KSP_weight]=sub_NVR_for_one_slice(KSP_recon,abs(KSP2),ARG,n1,QQ,master_fast*0+1,KSP_weight) ; % save all files
fprintf( [num2str(n1) ' '])
if mod(n1,20)==0; disp(' ');end
end
KSP_recon=KSP_recon./repmat((KSP_weight),[1 1 1 size(KSP2,4)]); % Assumes that the combination is with N instead of sqrt(N). Works for NVR not MPPCA
end
if master_fast==0; % allready loaded
if master==1
KSP_processed=QQ.KSP_processed;
if sum(KSP_processed(KSP_processed<2))>0;pause(60*5);end % hopefully enough time for other processes to finish
for n1=1:size(QQ,'KSP_processed',2)
fprintf( [num2str(n1) ' '])
[KSP_recon]=sub_NVR_for_one_slice(KSP_recon,KSP2,ARG,n1,QQ,master) ; % have the master load the files in
fprintf( [num2str(n1) ' '])
if mod(n1,20)==0; disp(' ');end
end
end
end
% detrmine if this will be the master or slave process
% GOTTA SAVE THE RESULTS, and that goes into the *_NVR file
if restart_list==0
if master==1 & master_fast==0
QQ.KSP_recon=KSP_recon;
end
end
if master==1
if sum(QQ.KSP_processed,2)==3*size(QQ.KSP_processed,2) % all slices processed and included
disp('Complete process and save new file')
sub_complete_NVR(KSP_recon,QQ,ARG)
elseif master_fast>0
sub_complete_NVR(KSP_recon,QQ,ARG); % run in a single_file and DOES NOT average
else
disp('something went wrong for the master. Check ')
QQ.KSP_processed
sum(QQ.KSP_processed,2)
3*size(QQ.KSP_processed,2)
end
end
if master==1
% cleanup
filename_out=dir(['KSP_' filename(1:end-4) APPEND_NAME '.mat']); % FILE with the NVR reconstruction
if ~isempty(filename_out)
sub_remove_tmp_files(ARG)
end
end
end
function sub_remove_tmp_files(ARG)
filename_in=dir([ARG.filename(1:end-4) '_NVR.mat']); % file with the data that will be used in the NVR, IE phase normalized
eval(['!rm ' filename_in.name])
filename_in=dir([ARG.filename(1:end) 'slice*.mat']); % file with the data that will be used in the NVR, IE phase normalized
for n=1:size(filename_in,1)
eval(['!rm ' filename_in(n).name ]);
end
function sub_complete_NVR(KSP2a,QQ,ARG)
KSP2_weight_update=0*KSP2a(:,:,:,1);
filename=ARG.filename;
patch_average = ARG.patch_average;
APPEND_NAME = ARG.APPEND_NAME;
NVR_threshold = ARG.NVR_threshold;
w1=ARG.kernel_size(1);
w2=ARG.kernel_size(2);
w3=ARG.kernel_size(3);
% create KSP2_weight
if patch_average==1
if ~exist('patch_avg'); patch_avg=1;end
KSP2_weight=zeros((size(KSP2a(1:w1,:,:,1))));
for n2=1:size(KSP2a,2)-w2;
for n3=1:size(KSP2a,3)-w3;
if patch_avg==1
KSP2_weight(:,[1:w2]+(n2-1),[1:w3]+(n3-1),1) =...
KSP2_weight(:,[1:w2]+(n2-1),[1:w3]+(n3-1),1) +1;
else
KSP2_weight(:,round(w2/2)+(n2-1),round(w3/2)+(n3-1),1) =...
KSP2_weight(:,round(w2/2)+(n2-1),round(w3/2)+(n3-1),1) +1;
end
end
end
for n1= 1:size(KSP2a,1)-w1;
KSP2_weight_update([1:w1]+(n1-1),:,:,1)=KSP2_weight_update([1:w1]+(n1-1),:,:,1)+ KSP2_weight;
end
KSP_update=KSP2a./repmat(KSP2_weight_update,[1 1 1 size(KSP2a,4)]);
else
KSP_update=KSP2a;
end
if ARG.master_fast~=3
QQ1=matfile(ARG.filename);
g_factor_map=QQ1.KSP(:,:,:,size(QQ1,'KSP',4));
for niter=1:min(size(KSP_update,4),size(ARG.DD_phase,4) )
KSP_update(:,:,:,niter)= KSP_update(:,:,:,niter).*exp(1i*angle(ARG.meanphase )).*exp(1i*angle(ARG.DD_phase(:,:,:,niter) ));
end
for niter=1:size(KSP_update,4); KSP_update(:,:,:,niter)=KSP_update(:,:,:,niter).*(g_factor_map+eps); end
end
try
NOISE= ARG.NOISE; if ARG.soft_thrs~=10; NOISE=[]; end % empty it unless it is calculated
Component_threshold= ARG.Component_threshold;
energy_removed = ARG.energy_removed;
catch;end
KSP_update(isnan(KSP_update))=0;
KSP_update(isinf(KSP_update))=0;
% KSP_update=DATA_full;
% for niter=1:size(KSP_update,4); KSP_update(:,:,:,niter)=KSP_update(:,:,:,niter).*(g_factor_map+eps); end
try
if isempty(APPEND_NAME)
save(['KSP_' filename(1:end-4) '.mat'],'KSP_update','Component_threshold','energy_removed','NOISE','-v7.3')
else
save(['KSP_' filename(1:end-4) APPEND_NAME '.mat'],'KSP_update','Component_threshold','energy_removed','NOISE','-v7.3')
end
catch
if isempty(APPEND_NAME)
save(['KSP_' filename(1:end-4) '.mat'],'KSP_update','-v7.3')
else
save(['KSP_' filename(1:end-4) APPEND_NAME '.mat'],'KSP_update','-v7.3')
end
end
return
function [KSP_recon,KSP2,KSP2_weight,NOISE, Component_threshold,energy_removed]=sub_NVR_for_one_slice(KSP_recon,KSP2,ARG,n1,QQ,master,KSP2_weight,NOISE,Component_threshold,energy_removed)
if ~exist('NOISE'); NOISE=[]; end
if ~exist('Component_threshold');Component_threshold=[]; end
if ~exist('energy_removed'); energy_removed=[]; end
% QQ.KSP_processed 0 nothing done, 1 running, 2 saved 3 completed and averaged
if master==0 && ARG.patch_average==0
OPTION='NO_master_NO_PA';
elseif master==0 && ARG.patch_average==1
OPTION='NO_master_PA' ;
elseif master==1 && ARG.patch_average==0
OPTION='master_NO_PA' ;
elseif master==1 && ARG.patch_average==1
OPTION='master_PA' ;
end
switch OPTION
case 'NO_master_NO_PA'
case 'NO_master_PA'
case 'master_NO_PA'
case 'master_PA'
end
if QQ.KSP_processed(1,n1)~=1 && QQ.KSP_processed(1,n1)~=3 % not being processed also not completed yet
if QQ.KSP_processed(1,n1)==2 && master==1% processed but not added.
% loading instead of processing
% load file as soon as save, if more than 10 sec, just do the recon
% instead.
try % try to load otherwise go to next slice
load([ARG.filename 'slice' num2str(n1) '.mat'],'DATA_full2')
catch;
QQ.KSP_processed(1,n1)=0; % identified as bad file and being identified for reprocessing
return ;end
end
if QQ.KSP_processed(1,n1)~=2
QQ.KSP_processed(1,n1)=1; % block for other processes
if ~exist('DATA_full2')
ARG2=QQ.ARG;
if master==0
QQ.KSP_processed(1,n1)=1 ; % STARTING
KSP2a=QQ.KSP2([1:ARG.kernel_size(1)]+(n1-1),:,:,:); lambda=ARG2.LLR_scale*ARG.NVR_threshold;
else
QQ.KSP_processed(1,n1)=1 ; % STARTING
KSP2a=KSP2([1:ARG.kernel_size(1)]+(n1-1),:,:,:); lambda=ARG2.LLR_scale*ARG.NVR_threshold;
end
if ARG.patch_average==1
% [DATA_full2, ~,NOISE, Component_threshold] =subfunction_loop_for_NVR_avg(KSP2a,ARG.kernel_size(3),ARG.kernel_size(2),ARG.kernel_size(1),lambda,1,ARG.soft_thrs);
[DATA_full2, KSP2_weight] =subfunction_loop_for_NVR_avg(KSP2a,ARG.kernel_size(3),ARG.kernel_size(2),ARG.kernel_size(1),lambda,1,ARG.soft_thrs,KSP2_weight);
else
KSP2_weight_tmp =KSP2_weight([1:ARG.kernel_size(1)]+(n1-1),:,:,:);
NOISE_tmp =NOISE([1:ARG.kernel_size(1)]+(n1-1),:,:,:);
Component_threshold_tmp =Component_threshold([1:ARG.kernel_size(1)]+(n1-1),:,:,:);
energy_removed_tmp =energy_removed([1:ARG.kernel_size(1)]+(n1-1),:,:,:);
[DATA_full2,KSP2_weight_tmp,NOISE_tmp, Component_threshold_tmp,energy_removed_tmp] =...
subfunction_loop_for_NVR_avg_update(KSP2a,ARG.kernel_size(3),ARG.kernel_size(2),ARG.kernel_size(1),lambda,1,ARG.soft_thrs,KSP2_weight_tmp,ARG,NOISE_tmp,Component_threshold_tmp,energy_removed_tmp);
KSP2_weight([1:ARG.kernel_size(1)]+(n1-1),:,:,:)=KSP2_weight_tmp;
try; NOISE([1:ARG.kernel_size(1)]+(n1-1),:,:,:) =NOISE_tmp; catch;end
Component_threshold([1:ARG.kernel_size(1)]+(n1-1),:,:,:) = Component_threshold_tmp;
energy_removed([1:ARG.kernel_size(1)]+(n1-1),:,:,:) = energy_removed_tmp;
%DATA_full=subfunction_loop_for_NVR(KSP2a,ARG.kernel_size(3),ARG.kernel_size(2),ARG.kernel_size(1),lambda);
%DATA_full2(1, round(w2/2)+[1:size(DATA_full,1)],:,: )=DATA_full; % center plane only
end
end
end
if master==0
if QQ.KSP_processed(1,n1)~=2
save([ARG.filename 'slice' num2str(n1) '.mat'],'DATA_full2', '-v7.3' )
QQ.KSP_processed(1,n1)=2 ; % COMPLETED
end
else
if ARG.patch_average==1
tmp=KSP_recon([1:ARG.kernel_size(1)]+(n1-1),:,:,:) ;
KSP_recon([1:ARG.kernel_size(1)]+(n1-1),:,:,:)= tmp + DATA_full2;
else
KSP_recon([1:ARG.kernel_size(1)]+(n1-1) ,1:size(DATA_full2,2),:,:)= KSP_recon([1:ARG.kernel_size(1)]+(n1-1) ,1:size(DATA_full2,2),:,:) + DATA_full2;
end
QQ.KSP_processed(1,n1)=3 ;
end
end
return
function [KSP2, meanphase, DD_phase]=sub_create_NVR_file(filename,ARG)
tmp=1;
filename_in=([filename(1:end-4) '_NVR.mat']); % file with the data that will be used in the NVR, IE phase normalized
save(filename_in,'tmp'); % create nearly empty file
newname=load(filename,'KSP');
matdim=size(newname.KSP(:,:,:,1:end-(ARG.DUAL-1))); % just to indicate if the is noise + SB_refrence + gfactor or noise +gfactor added
% KSP=newname.KSP(:,:,:,1:end-(ARG.DUAL-1)); clear newname
KSP=newname.KSP;clear newname
for nsl=size(KSP,3):-1:1
% MASK(:,:,nsl)= bwmorph( abs(KSP(:,:,nsl,1))>0,'shrink',1);
end
if ARG.DUAL==3 | ARG.DUAL==1 | 1
g_factor_map=mean(KSP(:,:,:,end:end) ,4)*1;
else
g_factor_map=mean(KSP(:,:,:,end-(ARG.DUAL-1):end) ,4);
end
KSP=KSP(:,:,:,1:end-1-(ARG.DUAL-1)); % removes the gfactor and the SB reference if it is there.
for niter=1:size(KSP,4); KSP(:,:,:,niter)=KSP(:,:,:,niter)./(g_factor_map+eps); end
% D1=KSP(:,:,:,1); SNRMASK=abs(D1(:,:,:,end))<20;
% KSP_NOISE=D1.*SNRMASK.*MASK.*sqrt(size(D1,1))*pi/2;
% KSP_NOISE=D1.*SNRMASK.*MASK;%.*sqrt(size(D1,1))*pi/2;
KSP_NOISE = KSP(:,:,:,end);
% for niter=1:size(KSP,4); KSP(:,:,:,niter)=KSP(:,:,:,niter).*SNRMASK.*MASK;end
% clear MASK SNRMASK
meanphase=mean(KSP(:,:,:,[1:end-1]),4);
for slice=matdim(3):-1:1
for n=1:size(KSP,4)-1; % include the noise
KSP(:,:,slice,n)=KSP(:,:,slice,n).*exp(-i*angle(meanphase(:,:,slice)));
end
end
DD_phase=0*KSP;
for slice=matdim(3):-1:1
for n=1:size(KSP,4)-1;
tmp=KSP(:,:,slice,n);
for ndim=[1:2]; tmp=ifftshift(ifft(ifftshift( tmp ,ndim),[],ndim),ndim+0); end
[nx, ny, nc, nb] = size(tmp(:,:,:,:,1,1));
tmp = bsxfun(@times,tmp,reshape(tukeywin(ny,1).^10,[1 ny]));
tmp = bsxfun(@times,tmp,reshape(tukeywin(nx,1).^10,[nx 1]));
for ndim=[1:2]; tmp=fftshift(fft(fftshift( tmp ,ndim),[],ndim),ndim+0); end
DD_phase(:,:,slice,n)=tmp;
end
end
% DD_phase=0*KSP;
for slice=matdim(3):-1:1
for n=1:size(KSP,4);
KSP_update(:,:,slice,n)= KSP(:,:,slice,n).*exp(-i*angle( DD_phase(:,:,slice,n) ));
end
end
if 0 % 20200527
for slice=matdim(3):-1:1
DD=KSP(:,:,slice,:);
meanphase=mean(DD(:,:,1,[1:size(DD,4)-1]),4);
for n=1:size(DD,4); % include the noise
DD(:,:,1,n)=DD(:,:,1,n).*exp(-i*angle(meanphase));
end
% for n=1:size(DD,4);
% tmp=DD(:,:,1,n);
% for ndim=[1:2]; tmp=ifftshift(ifft(ifftshift( tmp ,ndim),[],ndim),ndim+0); end
% [nx, ny, nc, nb] = size(tmp(:,:,:,:,1,1));
% tmp = bsxfun(@times,tmp,reshape(tukeywin(ny,1).^10,[1 ny]));
% tmp = bsxfun(@times,tmp,reshape(tukeywin(nx,1).^10,[nx 1]));
% for ndim=[1:2]; tmp=fftshift(fft(fftshift( tmp ,ndim),[],ndim),ndim+0); end
% DD_phase(:,:,1,n)=tmp;
% end
% meanphase=mean(DD(:,:,1,[1:size(DD,4)-1]),4);
% for n=1:size(DD,4)-1; % not added to noise
% DD(:,:,1,n)=DD(:,:,1,n).*exp(-i*angle(meanphase));
% end
for n=1:size(DD,4);
tmp=DD(:,:,1,n);
for ndim=[1:2]; tmp=ifftshift(ifft(ifftshift( tmp ,ndim),[],ndim),ndim+0); end
[nx, ny, nc, nb] = size(tmp(:,:,:,:,1,1));
tmp = bsxfun(@times,tmp,reshape(tukeywin(ny,1).^10,[1 ny]));
tmp = bsxfun(@times,tmp,reshape(tukeywin(nx,1).^10,[nx 1]));
for ndim=[1:2]; tmp=fftshift(fft(fftshift( tmp ,ndim),[],ndim),ndim+0); end
DD_phase(:,:,1,n)=tmp;
end
for n=1:size(DD,4);
DD1(:,:,1,n)=DD(:,:,1,n).*exp(-i*angle( DD_phase(:,:,1,n) ));
end
KSP_update(:,:,slice,:)=DD1;
end
clear KSP DD1 DD DD_phase newname D1
end
KSP2=KSP_update(:,:,:,1:end-1);
KSP_NOISE_update = KSP_update(:,:,:,end);
clear KSP_update
if 0
% annoyinng noise_scale
Q=sq(abs(KSP2(end-3,3:end-3,:,end))); Q1=mean(Q(:)); % take image noise from the bottom of the volume, where the signal is lowest - JIC
Q=sq(abs(KSP2(end-3,3,:,:))); Q1=mean(Q(:)); % take image noise from the bottom of the volume, where the signal is lowest - JIC
Q=sq(abs(KSP_NOISE(:,:,:,end))); Q11=mean(Q(:));
KSP_NOISE=KSP_NOISE/Q11*Q1;
KSP_NOISE=KSP_NOISE(3:end-3,3:end-3,:);
% KSP_NOISE=KSP_NOISE/Q1;
end
if ARG.DUAL<3 % noise might not be acquired correctly
estimate_noise_from_data=0;
if estimate_noise_from_data==1
Q=sq((KSP2(end-3,2,:,:))); Q1a=mean(abs(Q(:))); % take image noise from the bottom of the volume, where the signal is lowest - JIC
Q=sq((KSP2(end-3,end-2,:,:))); Q1b=mean(abs(Q(:))); Q1=min(Q1a,Q1b);
Q=sq((KSP_NOISE(:,:,:,end))); Q11=mean(abs(Q(:)));
KSP_NOISE=KSP_NOISE/Q11*Q1;
else
KSP_NOISE= KSP_NOISE /1; %
disp('change the scaling to the recon program');
end
end
%w1=4; w2=4; w3=4;
%[w1 w2 w3]=kernel_size;
w1=ARG.kernel_size(1);
w2=ARG.kernel_size(2);
w3=ARG.kernel_size(3);
if ~isempty(ARG.truncate_length)
KSP2=KSP2(:,:,:,1:ARG.truncate_length);
end
if 0
[w4]=ceil([ (w1*w2*w3*size(KSP2,4))^(1/3)]);
stmp=size(KSP_NOISE);
tmp= KSP_NOISE(:); tmp=std(real(tmp));
tmp=complex(randn(w1*w2*w3*size(KSP2,4),1), randn(w1*w2*w3*size(KSP2,4),1))*tmp;
Noise=tmp(randperm(size(tmp,1),w1*w2*w3*size(KSP2,4)));
end
if 1
Noise=KSP_NOISE;
Noise=Noise(:);tmp=std(real(Noise));
Noise=complex(randn(w1*w2*w3*size(KSP2,4),1), randn(w1*w2*w3*size(KSP2,4),1))*tmp;
Noise=reshape(Noise(1:w1*w2*w3*size(KSP2,4)),[],size(KSP2,4));
TT=Noise;
[U,S,V]=svd(TT,'econ'); S=diag(S);
[S(1) S(2)]
else
TT=KSP2([5:end-5],3,:,:); %TT=KSP2([5:end-5],4,:,:);
TT=reshape(TT,[],size(KSP2,4));
[~,SS,~]=svd(TT(1:w1*w2*w3,:),'econ'); SS=diag(SS); [SS(1) SS(2) ]
end
ARG.LLR_scale=max(abs(S)) ;
for subrange=[10:5:size(TT,2)]
[U,S1,V]=svd(TT(:,[1:subrange]),'econ'); S1=diag(S1);
ARG.LLR_scale_subscale(subrange)=max(abs(S1)) ;
end
ARG.filename=filename;
KSP_processed=zeros(1,size(KSP2,1)-w1+1);
reading_file=1;
writing_file=1; % if I save it I am master, so don't let anyone else be master
% QQ.KSP2=KSP2;
%QQ.KSP_recon=complex(single(zeros(size(KSP2)))); SHOULD BE IN MEMEORY INSTEAD
% QQ.ARG=ARG;
if ARG.master_fast>0
size_KSP=size(KSP2);
save(filename_in,'size_KSP','ARG','writing_file','reading_file','KSP_processed','-v7.3'); % create nearly empty file
else
save(filename_in,'KSP2','ARG','writing_file','reading_file','KSP_processed','-v7.3'); % create nearly empty file
end
return
function [KSP2, meanphase, DD_phase]=sub_create_NVR_file_HCP(filename,ARG)
tmp=1;
filename_in=([filename(1:end-4) '_NVR.mat']); % file with the data that will be used in the NVR, IE phase normalized
save(filename_in,'tmp'); % create nearly empty file
newname=load(filename,'KSP');
matdim=size(newname.KSP(:,:,:,1:end-(ARG.DUAL-1))); % just to indicate if the is noise + SB_refrence + gfactor or noise +gfactor added
% KSP=newname.KSP(:,:,:,1:end-(ARG.DUAL-1)); clear newname
KSP=newname.KSP;clear newname
for nsl=size(KSP,3):-1:1
% MASK(:,:,nsl)= bwmorph( abs(KSP(:,:,nsl,1))>0,'shrink',1);
end
g_factor_map=mean(KSP(:,:,:,end) ,4);
KSP=KSP(:,:,:,1:end-1-(ARG.DUAL-1)); % removes the gfactor and the SB reference if it is there.
for niter=1:size(KSP,4); KSP(:,:,:,niter)=KSP(:,:,:,niter)./(g_factor_map+eps); end
KSP_NOISE = KSP(:,:,:,end);
meanphase=1+0*mean(KSP(:,:,:,[1:end-1]),4);
for slice=matdim(3):-1:1
for n=1:size(KSP,4)-1; % include the noise
KSP(:,:,slice,n)=KSP(:,:,slice,n).*exp(-i*angle(meanphase(:,:,slice)));
end
end
DD_phase=0*KSP;
for slice=matdim(3):-1:1
for n=1:size(KSP,4)-1;
tmp=KSP(:,:,slice,n);
for ndim=[1:2]; tmp=ifftshift(ifft(ifftshift( tmp ,ndim),[],ndim),ndim+0); end
[nx, ny, nc, nb] = size(tmp(:,:,:,:,1,1));
tmp = bsxfun(@times,tmp,reshape(tukeywin(ny,1).^10,[1 ny]));
tmp = bsxfun(@times,tmp,reshape(tukeywin(nx,1).^10,[nx 1]));
for ndim=[1:2]; tmp=fftshift(fft(fftshift( tmp ,ndim),[],ndim),ndim+0); end
DD_phase(:,:,slice,n)=tmp*0+1;
end
end
for slice=matdim(3):-1:1
for n=1:size(KSP,4);
KSP_update(:,:,slice,n)= KSP(:,:,slice,n).*exp(-i*angle( DD_phase(:,:,slice,n) ));
end
end
KSP2=KSP_update(:,:,:,1:end-1);
KSP_NOISE_update = KSP_update(:,:,:,end);
clear KSP_update
estimate_noise_from_data=1;
if estimate_noise_from_data==1
Q=sq((KSP2(end-3,2,:,:))); Q1a=mean(abs(Q(:))); % take image noise from the bottom of the volume, where the signal is lowest - JIC
Q=sq((KSP2(end-3,end-2,:,:))); Q1b=mean(abs(Q(:))); Q1=min(Q1a,Q1b);
Q=sq((KSP_NOISE(:,:,:,end))); Q11=mean(abs(Q(:)));
KSP_NOISE=KSP_NOISE/Q11*Q1;
else
KSP_NOISE= KSP_NOISE *pi; %
disp('change the scaling to the recon program');
end
%w1=4; w2=4; w3=4;
%[w1 w2 w3]=kernel_size;
w1=ARG.kernel_size(1);
w2=ARG.kernel_size(2);
w3=ARG.kernel_size(3);
if ~isempty(ARG.truncate_length)
KSP2=KSP2(:,:,:,1:ARG.truncate_length);
end
if 0
[w4]=ceil([ (w1*w2*w3*size(KSP2,4))^(1/3)]);
stmp=size(KSP_NOISE);
tmp= KSP_NOISE(:); tmp=std(real(tmp));
tmp=complex(randn(w1*w2*w3*size(KSP2,4),1), randn(w1*w2*w3*size(KSP2,4),1))*tmp;
Noise=tmp(randperm(size(tmp,1),w1*w2*w3*size(KSP2,4)));
end
if 1
Noise=KSP_NOISE;
Noise=Noise(:);tmp=std(real(Noise));
Noise=complex(randn(w1*w2*w3*size(KSP2,4),1), randn(w1*w2*w3*size(KSP2,4),1))*tmp;
Noise=reshape(Noise(1:w1*w2*w3*size(KSP2,4)),[],size(KSP2,4));
TT=Noise;
[U,S,V]=svd(TT,'econ'); S=diag(S);
[S(1) S(2)]
else
TT=KSP2([5:end-5],3,:,:); %TT=KSP2([5:end-5],4,:,:);
TT=reshape(TT,[],size(KSP2,4));
[~,SS,~]=svd(TT(1:w1*w2*w3,:),'econ'); SS=diag(SS); [SS(1) SS(2) ]
end
ARG.LLR_scale=max(abs(S)) ;
for subrange=[10:5:size(TT,2)]
[U,S1,V]=svd(TT(:,[1:subrange]),'econ'); S1=diag(S1);
ARG.LLR_scale_subscale(subrange)=max(abs(S1)) ;
end
ARG.filename=filename;
KSP_processed=zeros(1,size(KSP2,1)-w1+1);
reading_file=1;
writing_file=1; % if I save it I am master, so don't let anyone else be master
if ARG.master_fast>0
size_KSP=size(KSP2);
save(filename_in,'size_KSP','ARG','writing_file','reading_file','KSP_processed','-v7.3'); % create nearly empty file
else
save(filename_in,'KSP2','ARG','writing_file','reading_file','KSP_processed','-v7.3'); % create nearly empty file
end
return
function [KSP2, meanphase, DD_phase]=sub_create_NVR_file_MPPCA(filename,ARG)
tmp=1;
filename_in=([filename(1:end-4) '_NVR.mat']); % file with the data that will be used in the NVR, IE phase normalized
save(filename_in,'tmp'); % create nearly empty file
newname=load(filename,'KSP');
matdim=size(newname.KSP(:,:,:,1:end-(ARG.DUAL-1))); % just to indicate if the is noise + SB_refrence + gfactor or noise +gfactor added
% KSP=newname.KSP(:,:,:,1:end-(ARG.DUAL-1)); clear newname
KSP=abs(newname.KSP);clear newname % make it magnitude
for nsl=size(KSP,3):-1:1
% MASK(:,:,nsl)= bwmorph( abs(KSP(:,:,nsl,1))>0,'shrink',1);
end
g_factor_map=mean(KSP(:,:,:,end) ,4)*0+1; % no g-factor correction
KSP=KSP(:,:,:,1:end-1-(ARG.DUAL-1)); % removes the gfactor and the SB reference if it is there.
for niter=1:size(KSP,4); KSP(:,:,:,niter)=KSP(:,:,:,niter)./(g_factor_map+eps); end
KSP_NOISE = KSP(:,:,:,end);
meanphase=1+0*mean(KSP(:,:,:,[1:end-1]),4);
for slice=matdim(3):-1:1
for n=1:size(KSP,4)-1; % include the noise
KSP(:,:,slice,n)=KSP(:,:,slice,n).*exp(-i*angle(meanphase(:,:,slice)));
end
end
DD_phase=0*KSP;
for slice=matdim(3):-1:1
for n=1:size(KSP,4)-1;
tmp=KSP(:,:,slice,n);
for ndim=[1:2]; tmp=ifftshift(ifft(ifftshift( tmp ,ndim),[],ndim),ndim+0); end
[nx, ny, nc, nb] = size(tmp(:,:,:,:,1,1));
tmp = bsxfun(@times,tmp,reshape(tukeywin(ny,1).^10,[1 ny]));
tmp = bsxfun(@times,tmp,reshape(tukeywin(nx,1).^10,[nx 1]));
for ndim=[1:2]; tmp=fftshift(fft(fftshift( tmp ,ndim),[],ndim),ndim+0); end
DD_phase(:,:,slice,n)=tmp*0+1;
end
end
for slice=matdim(3):-1:1
for n=1:size(KSP,4);
KSP_update(:,:,slice,n)= KSP(:,:,slice,n).*exp(-i*angle( DD_phase(:,:,slice,n) ));
end
end
KSP2=KSP_update(:,:,:,1:end-1);
KSP_NOISE_update = KSP_update(:,:,:,end);
clear KSP_update
estimate_noise_from_data=1;
if estimate_noise_from_data==1
Q=sq((KSP2(end-3,2,:,:))); Q1a=mean(abs(Q(:))); % take image noise from the bottom of the volume, where the signal is lowest - JIC
Q=sq((KSP2(end-3,end-2,:,:))); Q1b=mean(abs(Q(:))); Q1=min(Q1a,Q1b);