Diffusion ShoulderDB_ImportSegmentMeasureAnalyze (Bashardoust_SystCoord) Browse

R8218/dicominfoSCase.m
54ddcc3bd331Bashardoust_SystCoord

dicominfoSCase.m
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			function outputArg = dicominfoSCase(varargin)
			%DICOMINFOSCASE Get info from dicom fields and save in csv, xls, mat, and SQL
			% This function should be started from /shoulder/methods/matlab/database
			% A logfile is written during execution in
			% /shoulder/methods/matlab/database/log/dicominfoSCase.log
			%
			% The fonction can be run from server with
			% matlab -nojvm -nodisplay -nosplash -r "dicominfoSCase;quit" &
			% For 700 cases, it takes ~25 seconds from server
			%
			% This funtion replaces
			% /home/shoulder/methods/matlab/database/CTinfoCT.m
			% which only works matlab R2015a on a Windows system

			% Syntax: outputArg = dicominfoSCase(varargin)
			%
			% Input:
			% varargin: can be nothing (all cases), 'N', 'P', or a sCaseId
			%
			% Output:
			% outputArg: 1 if ok and 0 otherwise
			%
			% Example: CTdicomInfo('P315')
			% Other M-files required:
			% Subfunctions: listSCase
			% See also: measureSCase
			%
			% Author: Alexandre Terrier
			% EPFL-LBO
			% Creation date: 2018-07-01
			% Revision date: 2018-08-13
			%
			% TO DO:
			% Re-check for double slash in paths
			% We should implement the ShoulderCase class
			% We should save data in sCase/matlab directory
			% We might family name, given name (to check anonimity)
			% We should first read csv and then update
			% We should update MySQL
			% Check 'Index exceeds matrix dimensions' when 'using dicomdisp'
			% Remove xls before writing csv


			%% Initialization
			% This should be in a function call
			dataDir = '../../../data/'; % location of data
			xlsDataDir = strcat(dataDir, 'Excel/xlsFromMatlab/'); % Location of the XLS ShoulderDatabase
			logDir = 'log'; % log file in current directory

			%% Open log file
			filename = 'dicominfoSCase.log';
			filename = [logDir '/' filename];
			logFileId = fopen(filename, 'w');

			fprintf(logFileId, 'dicominfoSCase log file\n');
			fprintf(logFileId, '\nDate: ');
			fprintf(logFileId, datestr(datetime));
			fprintf(logFileId, '\n');
			fprintf(logFileId, '\nGet dicom info of sCases');
			fprintf(logFileId, '\n');

			%% Get list of sCases
			sCaseList = listSCase(varargin);

			%% Read dicom info

			tic; % Start stopwatch timer
			fprintf(logFileId, '\n\nRead dicom meta data\n'); % log file message

			% Struct below correponds to regular dicom field names, except sCase_id
			sCaseDicom = struct(...
			'sCase_id' ,[],...
			'PatientID' ,[],...
			'PatientSex' ,[],...
			'PatientAge' ,[],...
			'PatientBirthDate' ,[],...
			'PatientSize' ,[],...
			'PatientWeight' ,[],...
			'PatientFamilyName' ,[],...
			'PatientGivenName' ,[],...
			'AcquisitionDate' ,[],...
			'ConvolutionKernel' ,[],...
			'PixelSpacing' ,[],...
			'SpacingBetweenSlices' ,[],...
			'SliceThickness' ,[],...
			'KVP' ,[],...
			'XrayTubeCurrent' ,[],...
			'InstitutionName' ,[],...
			'StudyDescription' ,[],...
			'SeriesDescription' ,[],... % Might describe shoulder side
			'Manufacturer' ,[],...
			'ManufacturerModelName' ,[],...
			'ProtocolName' ,[]...
			);

			% Loop over all sCases collected above
			for sCase_idx=1:1:numel(sCaseList)
			sCase_id = sCaseList(sCase_idx).id;
			dicomDir = [sCaseList(sCase_idx).dir '/dicom'];
			dicomFiles = dir([dicomDir, '/*.dcm']);
			dicomFile1 = [dicomDir, '/', dicomFiles(10).name]; % seems better to check 10th than 1st !
			dicomInfoError = false;
			fprintf(logFileId, '\n');
			fprintf(logFileId, sCaseList(sCase_idx).id);
			fprintf(logFileId, ': ');
			% Try first with matlab function dicominfo
			try
			dicomInfo1 = dicominfo(dicomFile1, 'UseVRHeuristic', true);
			fprintf(logFileId, 'dicominfo ok');
			% If dicominfo didn't worked, try with matlab function dicomdisp
			catch ME
			dicomInfoError = true;
			fprintf(logFileId, '\n');
			fprintf(logFileId, 'dicominfo error --> using dicomdisp');
			fprintf(logFileId, ['\n' ME.message]);
			dicomdispStr = evalc('dicomdisp(dicomFile1)');
			end

			% If dicominfo didn't worked, continue with output of dicomdisp
			if dicomInfoError % get dicom info from dicomdisp()
			PatientID = extractAfter(dicomdispStr,'PatientID');
			PatientID = extractAfter(PatientID,'[');
			PatientID = extractBefore(PatientID,']');

			PatientSex = extractAfter(dicomdispStr,'PatientSex');
			PatientSex = extractAfter(PatientSex,'[');
			PatientSex = extractBefore(PatientSex,']');

			PatientAge = extractAfter(dicomdispStr,'PatientAge');
			PatientAge = extractAfter(PatientAge,'[');
			PatientAge = extractBefore(PatientAge,']');

			PatientBirthDate = extractAfter(dicomdispStr,'PatientBirthDate');
			PatientBirthDate = extractAfter(PatientBirthDate,'[');
			PatientBirthDate = extractBefore(PatientBirthDate,']');

			PatientSize = extractAfter(dicomdispStr,'PatientSize');
			PatientSize = extractAfter(PatientSize,'[');
			PatientSize = extractBefore(PatientSize,']');
			PatientSize = str2double(PatientSize);

			PatientWeight = extractAfter(dicomdispStr,'PatientWeight');
			PatientWeight = extractAfter(PatientWeight,'[');
			PatientWeight = extractBefore(PatientWeight,']');
			PatientWeight = str2double(PatientWeight);

			AcquisitionDate = extractAfter(dicomdispStr,'AcquisitionDate');
			AcquisitionDate = extractAfter(AcquisitionDate,'[');
			AcquisitionDate = extractBefore(AcquisitionDate,']');

			ConvolutionKernel = extractAfter(dicomdispStr,'ConvolutionKernel');
			ConvolutionKernel = extractAfter(ConvolutionKernel,'[');
			ConvolutionKernel = extractBefore(ConvolutionKernel,']');

			PixelSpacing = extractAfter(dicomdispStr,'PixelSpacing');
			PixelSpacing = extractAfter(PixelSpacing,'[');
			PixelSpacing = extractBefore(PixelSpacing,'\');

			SpacingBetweenSlices = extractAfter(dicomdispStr,'SpacingBetweenSlices');
			SpacingBetweenSlices = extractAfter(SpacingBetweenSlices,'[');
			SpacingBetweenSlices = extractBefore(SpacingBetweenSlices,']');
			SpacingBetweenSlices = str2double(SpacingBetweenSlices);

			SliceThickness = extractAfter(dicomdispStr,'SliceThickness');
			SliceThickness = extractAfter(SliceThickness,'[');
			SliceThickness = extractBefore(SliceThickness,']');
			SliceThickness = str2double(SliceThickness);

			KVP = extractAfter(dicomdispStr,'KVP');
			KVP = extractAfter(KVP,'[');
			KVP = extractBefore(KVP,']');
			KVP = str2double(KVP);

			XrayTubeCurrent = extractAfter(dicomdispStr,'XrayTubeCurrent');
			XrayTubeCurrent = extractAfter(XrayTubeCurrent,'[');
			XrayTubeCurrent = extractBefore(XrayTubeCurrent,']');
			XrayTubeCurrent = str2double(XrayTubeCurrent);

			InstitutionName = extractAfter(dicomdispStr,'InstitutionName');
			InstitutionName = extractAfter(InstitutionName,'[');
			InstitutionName = extractBefore(InstitutionName,']');

			Manufacturer = extractAfter(dicomdispStr,'Manufacturer');
			Manufacturer = extractAfter(Manufacturer,'[');
			Manufacturer = extractBefore(Manufacturer,']');

			ManufacturerModelName = extractAfter(dicomdispStr,'ManufacturerModelName');
			ManufacturerModelName = extractAfter(ManufacturerModelName,'[');
			ManufacturerModelName = extractBefore(ManufacturerModelName,']');

			ProtocolName = extractAfter(dicomdispStr,'ProtocolName');
			ProtocolName = extractAfter(ProtocolName,'[');
			ProtocolName = extractBefore(ProtocolName,']');

			SeriesDescription = extractAfter(dicomdispStr,'SeriesDescription');
			SeriesDescription = extractAfter(SeriesDescription,'[');
			SeriesDescription = extractBefore(SeriesDescription,']');

			else % dicomInfo exists
			if isfield(dicomInfo1,'PatientID')
			PatientID = dicomInfo1.PatientID;
			else
			PatientID = '';
			end
			if isfield(dicomInfo1,'PatientSex')
			PatientSex = dicomInfo1.PatientSex;
			else
			PatientSex = '';
			end
			if isfield(dicomInfo1,'PatientBirthDate')
			PatientBirthDate = dicomInfo1.PatientBirthDate;
			else
			PatientBirthDate = '';
			end
			if isfield(dicomInfo1,'PatientAge')
			PatientAge = dicomInfo1.PatientAge;
			else
			PatientAge = '';
			end
			if isfield(dicomInfo1,'PatientSize')
			PatientSize = dicomInfo1.PatientSize;
			else
			PatientSize = '';
			end
			if isfield(dicomInfo1,'PatientWeight')
			PatientWeight = dicomInfo1.PatientWeight;
			else
			PatientWeight='';
			end
			if isfield(dicomInfo1,'AcquisitionDate')
			AcquisitionDate = dicomInfo1.AcquisitionDate;
			else
			AcquisitionDate = '';
			end
			if isfield(dicomInfo1,'ConvolutionKernel')
			ConvolutionKernel = dicomInfo1.ConvolutionKernel;
			else
			ConvolutionKernel = '';
			end
			if isfield(dicomInfo1,'PixelSpacing')
			PixelSpacing = dicomInfo1.PixelSpacing(1);
			PixelSpacing = num2str(PixelSpacing);
			% PixelSpacing = [,PixelSpacing,]; % Commented because I (AT) don't
			% understand the effect
			else
			PixelSpacing='';
			end
			if isfield(dicomInfo1,'SpacingBetweenSlices')
			SpacingBetweenSlices = dicomInfo1.SpacingBetweenSlices;
			else % SpacingBetweenSlices estimated from 2 slices
			% fprintf(logFileID, '\n');
			fprintf(logFileId, ', SpacingBetweenSlices estimated from 2 slices');
			dicomFile2 = [dicomDir, '/', dicomFiles(11).name];
			dicomInfo2 = dicominfo(dicomFile2, 'UseVRHeuristic', true);
			ImagePositionPatient1 = dicomInfo1.ImagePositionPatient(3);
			ImagePositionPatient2 = dicomInfo2.ImagePositionPatient(3);
			posdDiff = abs(ImagePositionPatient2 - ImagePositionPatient1);
			InstanceNumber1 = dicomInfo1.InstanceNumber;
			InstanceNumber2 = dicomInfo2.InstanceNumber;
			InstanceNumberDiff = abs(InstanceNumber2 - InstanceNumber1);
			if InstanceNumberDiff == 0
			InstanceNumberDiff=1;
			end
			SpacingBetweenSlices = posdDiff/InstanceNumberDiff;
			end
			if isfield(dicomInfo1,'SliceThickness')
			SliceThickness = dicomInfo1.SliceThickness;
			else
			SliceThickness='';
			end
			if isfield(dicomInfo1,'KVP')
			KVP = dicomInfo1.KVP;
			else
			KVP= '';
			end
			if isfield(dicomInfo1,'XrayTubeCurrent')
			XrayTubeCurrent = dicomInfo1.XrayTubeCurrent;
			else
			XrayTubeCurrent = '';
			end
			if isfield(dicomInfo1,'InstitutionName')
			InstitutionName = dicomInfo1.InstitutionName;
			else
			InstitutionName = '';
			end
			if isfield(dicomInfo1,'Manufacturer')
			Manufacturer = dicomInfo1.Manufacturer;
			else
			Manufacturer ='';
			end
			if isfield(dicomInfo1,'ManufacturerModelName')
			ManufacturerModelName = dicomInfo1.ManufacturerModelName;
			else
			ManufacturerModelName = '';
			end
			if isfield(dicomInfo1,'ProtocolName')
			ProtocolName = dicomInfo1.ProtocolName;
			else
			ProtocolName = '';
			end
			if isfield(dicomInfo1,'SeriesDescription')
			SeriesDescription = dicomInfo1.SeriesDescription;
			else
			SeriesDescription = '';
			end
			% End of reading dimcom info
			end

			%% Format data
			PatientBirthDate = datetime(PatientBirthDate,'InputFormat','yyyyMMdd');
			PatientBirthDate = datestr(PatientBirthDate, 'yyyy-mm-dd');
			PatientAge = str2double(strtok(PatientAge,'Y'));
			PatientSize = round(100 * PatientSize);
			if PatientSize == 0
			PatientSize = '';
			end
			PatientWeight = round(PatientWeight);
			if PatientWeight == 0
			PatientWeight = '';
			end
			AcquisitionDate = datetime(AcquisitionDate,'InputFormat','yyyyMMdd');
			AcquisitionDate = datestr(AcquisitionDate, 'yyyy-mm-dd');

			PixelSpacing = str2double(PixelSpacing);
			PixelSpacing = round(PixelSpacing, 3);
			SpacingBetweenSlices = round(SpacingBetweenSlices, 3);
			SliceThickness = round(SliceThickness, 3);
			KVP = round(KVP);
			XrayTubeCurrent = round(XrayTubeCurrent);
			% Replace any ',' by ' ' to avoid problem in csv
			InstitutionName = strrep(InstitutionName,',',' ');
			Manufacturer = strrep(Manufacturer,',',' ');
			ManufacturerModelName = strrep(ManufacturerModelName,',',' ');
			ProtocolName = strrep(ProtocolName,',',' ');
			SeriesDescription = strrep(SeriesDescription,',',' ');

			%% Add data in sCaseDicom structure
			% This could be directly in sCase.CT object
			sCaseDicom(sCase_idx).id = sCase_id;
			sCaseDicom(sCase_idx).PatientID = PatientID;
			sCaseDicom(sCase_idx).PatientSex = PatientSex;
			sCaseDicom(sCase_idx).PatientBirthDate = PatientBirthDate;
			sCaseDicom(sCase_idx).PatientAge = PatientAge;
			sCaseDicom(sCase_idx).PatientSize = PatientSize;
			sCaseDicom(sCase_idx).PatientWeight = PatientWeight;
			sCaseDicom(sCase_idx).AcquisitionDate = AcquisitionDate;
			sCaseDicom(sCase_idx).ConvolutionKernel = ConvolutionKernel;
			sCaseDicom(sCase_idx).PixelSpacing = PixelSpacing;
			sCaseDicom(sCase_idx).SpacingBetweenSlices = SpacingBetweenSlices;
			sCaseDicom(sCase_idx).SliceThickness = SliceThickness;
			sCaseDicom(sCase_idx).KVP = KVP;
			sCaseDicom(sCase_idx).XrayTubeCurrent = XrayTubeCurrent;
			sCaseDicom(sCase_idx).InstitutionName = InstitutionName;
			sCaseDicom(sCase_idx).Manufacturer = Manufacturer;
			sCaseDicom(sCase_idx).ManufacturerModelName = ManufacturerModelName;
			sCaseDicom(sCase_idx).ProtocolName = ProtocolName;
			sCaseDicom(sCase_idx).SeriesDescription = SeriesDescription;
			end
			fprintf(logFileId, '\n\nElapsed time (s): %s', num2str(toc)); % stopwatch timer

			%% Write csv file
			% This might be a function. The input would be a filename and a structure
			% data

			dataHeader = [...
			'sCase_id,' ...
			'patient_IPP,' ...
			'patient_gender,' ...
			'patient_birthDate,' ...
			'patient_age,' ...
			'patient_height,' ...
			'patient_weight,' ...
			'CT_date,' ...
			'CT_kernel,' ...
			'CT_pixelSize,' ...
			'CT_sliceSpacing,' ...
			'CT_sliceThickness,' ...
			'CT_tension,' ...
			'CT_current,' ...
			'CT_institution,' ...
			'CT_manufacturer,' ...
			'CT_model,' ...
			'CT_protocol,' ...
			'CT_SeriesDescription' ...
			];

			csvFilename = strcat(xlsDataDir, 'CTdicomInfo.csv');
			csvFileId = fopen(csvFilename, 'w');
			fprintf(csvFileId,dataHeader);
			for sCase_idx=1:1:numel(sCaseDicom) % Loop on all sCase provided by listsCase()
			fprintf(csvFileId,'\n%s,%s,%s,%s,%f,%f,%f,%s,%s,%f,%f,%f,%f,%f,%s,%s,%s,%s,%s',...
			sCaseDicom(sCase_idx).id,...
			sCaseDicom(sCase_idx).PatientID,...
			sCaseDicom(sCase_idx).PatientSex,...
			sCaseDicom(sCase_idx).PatientBirthDate,...
			sCaseDicom(sCase_idx).PatientAge,...
			sCaseDicom(sCase_idx).PatientSize,...
			sCaseDicom(sCase_idx).PatientWeight,...
			sCaseDicom(sCase_idx).AcquisitionDate,...
			sCaseDicom(sCase_idx).ConvolutionKernel,...
			sCaseDicom(sCase_idx).PixelSpacing,...
			sCaseDicom(sCase_idx).SpacingBetweenSlices,...
			sCaseDicom(sCase_idx).SliceThickness,...
			sCaseDicom(sCase_idx).KVP,...
			sCaseDicom(sCase_idx).XrayTubeCurrent,...
			sCaseDicom(sCase_idx).InstitutionName,...
			sCaseDicom(sCase_idx).Manufacturer,...
			sCaseDicom(sCase_idx).ManufacturerModelName,...
			sCaseDicom(sCase_idx).ProtocolName,...
			sCaseDicom(sCase_idx).SeriesDescription...
			);
			end
			fclose(csvFileId);

			fprintf(logFileId, ['\n\nSaved csv file: ' csvFilename]);

			%% Write xls file (Windows only)
			[~,message] = csv2xlsSCase(csvFilename);
			fprintf(logFileId, message);

			%% Update MySQL
			% To be done
			%{
			addpath('XLS_MySQL_DB');
			MainExcel2SQL;
			%}

			%% Final log
			fprintf(logFileId, '\n\nsCases treated: %s', num2str(numel(sCaseDicom))); % Number of sCases treated
			fprintf(logFileId, '\nElapsed time (s): %s', num2str(toc)); % stopwatch timer
			fclose(logFileId); % Close log file

			outputArg = 1; % Might be extended
			end

R8218/dicominfoSCase.m54ddcc3bd331Bashardoust_SystCoord

dicominfoSCase.mView Options

R8218/dicominfoSCase.m
54ddcc3bd331Bashardoust_SystCoord

dicominfoSCase.m
View Options