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Some fixes in file and error handling on Linux systems #1

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43 changes: 22 additions & 21 deletions Batch_Recon/Batch_Manager_KM.m
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Original file line number Diff line number Diff line change
Expand Up @@ -148,8 +148,8 @@ function Select_Batch(val)
try
script_batch_cDTI_KM(Batch_struct.struct_diff(cpt_diff),Batch_struct.UI);
Batch_struct.struct_diff(cpt_diff).hasError=false;
catch
disp(['Problem with ' Batch_struct.struct_diff(cpt_diff).Patient ' serie ' num2str(Batch_struct.struct_diff(cpt_diff).SerieNumber)]);
catch ME
disp(['Problem with ' Batch_struct.struct_diff(cpt_diff).Patient ' serie ' num2str(Batch_struct.struct_diff(cpt_diff).SerieNumber) ':' ME.message]);
Batch_struct.struct_diff(cpt_diff).hasError=true;
end

Expand Down Expand Up @@ -189,8 +189,8 @@ function Select_Batch(val)
try
script_batch_DICOM_KM(Batch_struct.struct_diff(cpt_diff));
Batch_struct.struct_diff(cpt_diff).hasDicomError=false;
catch
disp(['Problem with DICOM Recon ' Batch_struct.struct_diff(cpt_diff).Patient ' serie ' num2str(Batch_struct.struct_diff(cpt_diff).SerieNumber)]);
catch ME
disp(['Problem with DICOM Recon ' Batch_struct.struct_diff(cpt_diff).Patient ' serie ' num2str(Batch_struct.struct_diff(cpt_diff).SerieNumber) ':' ME.message]);
Batch_struct.struct_diff(cpt_diff).hasDicomError=true;
end
Update_Batch_Table();
Expand Down Expand Up @@ -226,7 +226,7 @@ function Select_Batch(val)


Batch_struct.UI=UIDiffRecon_KM(true);


listing=dir(fullfile(Batch_struct.dcm_dir, '**'));
listing=listing(~[listing.isdir]); % Remove folder
Expand All @@ -238,20 +238,19 @@ function Select_Batch(val)

listing_dcm=[];
for cpt_folder=1:length(listing_folder)

listing_dcm=[listing_dcm; dir(listing_folder(cpt_folder))];
%
contents = dir(strtrim(listing_folder(cpt_folder)));
listing_dcm=[listing_dcm; contents];
end

[struct_diff, struct_final, ListNames, ListSeries]=Analyze_Content_local(listing_dcm,[]); % Create a brand new list_update;

Batch_struct.struct_diff=struct_diff;
Batch_struct.struct_update=struct_final;
Batch_struct.DataUI = Struct2DataUI(struct_diff);

Batch_loaded=true;
end

function Load_Batch

[file path]=uigetfile('.mat');
Expand All @@ -274,12 +273,11 @@ function Select_Batch(val)
end
function Update_Batch_Table
if Batch_loaded

if UI_created % we update the batch from the UI only if the UI already exist
Batch_struct.struct_diff=DataUI2Struct(Batch_struct.struct_diff,uit.Data);
end

for cpt_diff=1:length(Batch_struct.struct_diff)

fullfile(string(Batch_struct.dcm_dir),'Batch_Recon','Maps_'+string(Batch_struct.struct_diff(cpt_diff).Patient)+'_'+Batch_struct.struct_diff(cpt_diff).SerieNumber+'_'+string(Batch_struct.name(1:end-4)));
Batch_struct.struct_diff(cpt_diff).ReconFolder=fullfile(string(Batch_struct.dcm_dir),'Batch_Recon','Maps_'+string(Batch_struct.struct_diff(cpt_diff).Patient)+'_'+Batch_struct.struct_diff(cpt_diff).SerieNumber+'_'+string(Batch_struct.name(1:end-4)));
Batch_struct.struct_diff(cpt_diff).ReconDcmFolder=fullfile(string(Batch_struct.dcm_dir),'Dicom_Recon','Maps_'+string(Batch_struct.struct_diff(cpt_diff).Patient)+'_'+Batch_struct.struct_diff(cpt_diff).SerieNumber+'_'+string(Batch_struct.name(1:end-4)));
Expand Down Expand Up @@ -323,13 +321,13 @@ function Select_Batch(val)
LL=Batch_struct.struct_update(cpt).Listing;
folderAlreadySorted=[folderAlreadySorted string(unique(string({LL(:).folder})))];
end
folderAlreadySorted=deblank(folderAlreadySorted);
folderAlreadySorted=strtrim(folderAlreadySorted);
% Idx=contains(folderAlreadySorted , 'Dicom_Recon' );
% folderAlreadySorted(Idx)=[];

for cpt_folder=1:length(listing_folder)
if( ~contains(deblank(listing_folder(cpt_folder)) , folderAlreadySorted))
listing_dcm=[listing_dcm; dir(listing_folder(cpt_folder))];
if( ~contains(strtrim(listing_folder(cpt_folder)) , folderAlreadySorted))
listing_dcm=[listing_dcm; dir(strtrim(listing_folder(cpt_folder)))];
end
%
end
Expand Down Expand Up @@ -397,7 +395,6 @@ function Select_Batch(val)
end
function struct_diff=DataUI2Struct(struct_diff,DataUI)


for cpt_diff=1:length(struct_diff)


Expand All @@ -424,13 +421,17 @@ function Select_Batch(val)
cpt_name=0;
k=1;
h = waitbar(0,'Analyzing the folders...');
for cpt=1:1:size(listing,1)
for cpt=1:1:size(listing,1)
if ~listing(cpt).isdir & isempty(strfind(listing(cpt).folder,'Batch_Recon'))

[FolderName, name, fExt] = fileparts(listing(cpt).name);
[FolderName, name, fExt] = fileparts(listing(cpt).name);

if (strcmp(fExt, '.dcm') | strcmp(fExt, '.IMA') | isempty(fExt)) & ~ strcmp('DICOMDIR',listing(cpt).name)
tmpInfo=dicominfo(fullfile(listing(cpt).folder , listing(cpt).name));
try
tmpInfo=dicominfo(fullfile(listing(cpt).folder , listing(cpt).name));
catch dicomerr
disp(['Failed to parse DICOM information from file ' string(listing(cpt).name)])
end
%tmpDcm=dicomread([listing(cpt).folder '\' listing(cpt).name]);
%Dcm(:,:,k)=double(dicomread(listing(cpt).name));
%Dcm(k)=tmpInfo.SeriesNumber;
Expand Down Expand Up @@ -480,7 +481,7 @@ function Select_Batch(val)
badc=~isempty(strfind(tmpImageType,'ADC'));
bfa=~isempty(strfind(tmpImageType,'FA'));
bten=~isempty(strfind(tmpImageType,'TENSOR'))&isempty(strfind(tmpImageType,'TENSOR_B0'));

if ~isfield (tmpInfo,'PatientID')
if isfield (tmpInfo,'OtherPatientID')
tmpInfo.PatientID=tmpInfo.OtherPatientID;
Expand Down
2 changes: 1 addition & 1 deletion Script_Recon/script_batch_DICOM_KM.m
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Original file line number Diff line number Diff line change
Expand Up @@ -29,7 +29,7 @@ function script_batch_DICOM_KM(struct_diff)
Recon_Local_Dicom_Maps(struct_diff,tmpMap.FA*1e3,tmpEnum,'FA',50000,[0 1e3]);
end

if isfile(fullfile(struct_diff.ReconFolder, 'HA.mat') && isfile(fullfile(struct_diff.ReconFolder, 'ROI.mat'))
if isfile(fullfile(struct_diff.ReconFolder, 'HA.mat')) && isfile(fullfile(struct_diff.ReconFolder, 'ROI.mat'))
tmpMap=load(fullfile(struct_diff.ReconFolder, 'HA.mat'));
tmpMap2=load(fullfile(struct_diff.ReconFolder, 'ROI.mat'));
Recon_Local_Dicom_Maps(struct_diff,(tmpMap.HA_filter2+90)*1e1.*tmpMap2.LV_Mask,tmpEnum,'HA',60000,[0 180*1e1]);
Expand Down