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R8218/CT/infoCT.m
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infoCT.m
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%% infoCT
% This script lists the technical and the personal informations linked to the dicoms for
% "Pathologic" and "Normal" patients and returns the excel file "InfoCT".
%
% Alex Terrier comment: This scipt only works with matlab R2015a from a Windows system. It is
% using a modified version of dicominfo.m (dicominfo2.m) and a modified
% private function directory. This script should be updated and abandoned.
% INPUT: 'normal' or 'pathologic'
% Author: RO-EPFL-LBO
% Date: 2016-09-05
%%
function infoCT
addpath(genpath('CT'));
addpath(genpath('XLS_MySQL_DB'));
addpath(genpath('muscles'));
addpath(genpath('anatomy'));
addpath(genpath('Generated_Amira_TCL_Scripts'));
XLSShoulderDatabaseLocation = '../../../data/Excel/'; % Location of the XLS ShoulderDatabase
list{1,1} = 'sCase.id';
list{1,2} = 'patient.IPP';
list{1,3} = 'patient.initials';
list{1,4} = 'patient.gender';
list{1,5} = 'patient.birth_date';
%list{1,6} = 'patient.age';
%list{1,7} = 'patient.ethnicity';
list{1,6} = 'patient.height';
list{1,7} = 'patient.weight';
%list{1,10} = 'patient.BMI';
list{1,8} = 'shoulder.side';
list{1,9} = 'CT.date';
list{1,10} = 'CT.kernel';
list{1,11} = 'CT.pixel_size';
list{1,12} = 'CT.slice_spacing';
list{1,13} = 'CT.slice_thickness';
list{1,14} = 'CT.tension';
list{1,15} = 'CT.current';
list{1,16} = 'CT.institution';
list{1,17} = 'CT.manufacturer';
list{1,18} = 'CT.model';
list{1,19} = 'CT.protocol';
directory = '../../../data';
%% Loop over all the normal and pathologic cases
location = 'N';
l=1;
rootDir = '../../../data/N';
for levelDir1 = 0:9
for levelDir2 = 0:9
curentDir = sprintf('%s/%d/%d/N*', rootDir, levelDir1, levelDir2);
folderInfo = dir(curentDir);
for i=1:1:numel(folderInfo)
name = folderInfo(i).name;
sCases_normal{l,1} = folderInfo(i).name;
sCases_normal{l,2} = levelDir1;
sCases_normal{l,3} = levelDir2;
sCases_normal{l,4} = 'N';
l=l+1;
end
end
end
location = 'P';
l=1;
rootDir = '../../../data/P';
for levelDir1 = 0:9
for levelDir2 = 0:9
curentDir = sprintf('%s/%d/%d/P*', rootDir, levelDir1, levelDir2);
folderInfo = dir(curentDir);
for i=1:1:numel(folderInfo)
name = folderInfo(i).name;
sCases_pathologic{l,1} = folderInfo(i).name;
sCases_pathologic{l,2} = levelDir1;
sCases_pathologic{l,3} = levelDir2;
sCases_pathologic{l,4} = 'P';
l=l+1;
end
end
end
sCases = [sCases_normal;sCases_pathologic];
%% Data exportation from dicom
for j=2:1:numel(sCases(:,1))+1
patient = char(sCases(j-1,1))
levelDir1 = cell2mat(sCases(j-1,2));
levelDir2 = cell2mat(sCases(j-1,3));
location = char(sCases(j-1,4));
finalDirectory = sprintf('%s/%s/%d/%d', directory, location, levelDir1, levelDir2);
if exist(sprintf('%s/%s/CT-%s-1/dicom', finalDirectory,patient,patient),'dir') == 7 %if a folder "dicom" exist, the patient name is added to the "measured" column
% directoryin=list(j,1);
% directoryin=char(directoryin);
ctdirectoryin = sprintf('%s/%s/CT-%s-1/dicom',finalDirectory, patient, patient);
images = dir(ctdirectoryin);
ct=images(10).name;
ct2=images(11).name;
inpath=[ctdirectoryin,'/',ct];
inpath2=[ctdirectoryin,'/',ct2];
info=dicominfo2(inpath);
info2=dicominfo2(inpath2);
%Patient#
list{j,1} = strtok(patient,'-');
%Weight
tf = isfield(info,'PatientWeight'); % Test si le champ "PatientWeight" existe
if tf==1
weight=info.PatientWeight;
else
weight=' ';
end
list{j,7} = weight;
%Height
tf = isfield(info,'PatientSize'); % Test si le champ "PatientSize" existe
if tf==1
Size=info.PatientSize;
Size=Size*100;
Size=round(Size,0);
else
Size=' ';
end
list{j,6} = Size;
%Gender
tf = isfield(info,'PatientSex'); % Test si le champ "PatientSex" existe
if tf==1
gender=info.PatientSex;
else
gender=' ';
end
list{j,4} = gender;
%Birth date
tf = isfield(info,'PatientBirthDate'); % Test si le champ "PatientBirthDate" existe
if tf==1
date=info.PatientBirthDate;
date=[date(1:4) '.' date(5:6) '.' date(7:8)];
else
date=' ';
end
list{j,5} = date;
%CT date
tf = isfield(info,'AcquisitionDate'); % Test si le champ "AcquisitionDate" existe
if tf==1
ctdate=info.AcquisitionDate;
ctdate=[ctdate(1:4) '.' ctdate(5:6) '.' ctdate(7:8)];
else
ctdate=' ';
end
list{j,9} = ctdate;
%IPP
tf = isfield(info,'PatientID'); % Test si le champ "PatientID" existe
if tf==1
id=info.PatientID;
else
id=' ';
end
list{j,2} = id;
%Kernel
tf = isfield(info,'ConvolutionKernel'); % Test si le champ "ConvolutionKernel" existe
if tf==1
kernel=info.ConvolutionKernel;
else
kernel=' ';
end
list{j,10} = kernel;
%Pixel Size
tf = isfield(info,'PixelSpacing'); % Test si le champ "PixelSpacing" existe
if tf==1
pixel1=info.PixelSpacing(1);
%pixel2=info.PixelSpacing(2);
pixel1=num2str(pixel1);
%pixel2=num2str(pixel2);
%pixel= ['[',pixel1,',',pixel2,']'];
pixel= [,pixel1,];
else
pixel=' ';
end
list{j,11} = pixel;
%Slice Thickness
tf = isfield(info,'SliceThickness'); % Test si le champ "SliceThickness" existe
if tf==1
thickness=info.SliceThickness;
else
thickness=' ';
end
list{j,13} = thickness;
%Tension
tf = isfield(info,'KVP'); % Test si le champ "KVP" existe
if tf==1
tension=info.KVP;
else
tension=' ';
end
list{j,14} = tension;
%Current
tf = isfield(info,'XrayTubeCurrent'); % Test si le champ "XrayTubeCurrent" existe
if tf==1
current=info.XrayTubeCurrent;
else
current=' ';
end
list{j,15} = current;
%Institution Name
tf = isfield(info,'InstitutionName'); % Test si le champ "InstitutionName" existe
if tf==1
instname=info.InstitutionName;
else
instname=' ';
end
list{j,16} = instname;
%Manufacturer
tf = isfield(info,'Manufacturer'); % Test si le champ "Manufacturer" existe
if tf==1
manufacturer=info.Manufacturer;
else
manufacturer=' ';
end
list{j,17} = manufacturer;
%Model Name
tf = isfield(info,'ManufacturerModelName'); % Test si le champ "ManufacturerModelName" existe
if tf==1
manufacturermn=info.ManufacturerModelName;
else
manufacturermn=' ';
end
list{j,18} = manufacturermn;
%Protocol Name
tf = isfield(info,'ProtocolName'); % Test si le champ "ProtocolName" existe
if tf==1
protocol=info.ProtocolName;
else
protocol=' ';
end
list{j,19} = protocol;
%Spacing Between Slices
tf = isfield(info,'ImagePositionPatient'); % Test si le champ "ImagePositionPatient" existe
if tf==1
pos1 = info.ImagePositionPatient(3);
pos2 = info2.ImagePositionPatient(3);
%pixel1=num2str(pixel1);
%pixel2=num2str(pixel2);
%pixel= ['[',pixel1,',',pixel2,']'];
space2= abs(pos1-pos2);
else
space2=' ';
end
list{j,12} = space2;
% %Patient Name
% tf = isfield(info,'PatientName'); % Test si le champ "PatientName" existe
%
% if tf==1
% name = info.PatientName.FamilyName;
%
% %pixel1=num2str(pixel1);
%
% else
% name=' ';
% end
% list{j,8} = name;
else
list{j,1} = strtok(patient,'-');
end
if strcmp(patient,'P410-95295')
end
end
delete([XLSShoulderDatabaseLocation 'xlsFromMatlab/CT.xls']);
xlswrite([XLSShoulderDatabaseLocation 'xlsFromMatlab/CT'], list)
addpath('XLS_MySQL_DB');
MainExcel2SQL;
end
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