function dicom = spm_cfg_dicom
% SPM Configuration file for DICOM Import
%__________________________________________________________________________
% Copyright (C) 2005-2017 Wellcome Trust Centre for Neuroimaging

% $Id: spm_cfg_dicom.m 7201 2017-11-08 11:13:25Z guillaume $

%-------------------------------------------------------------------------
% data DICOM files
%--------------------------------------------------------------------------
data         = cfg_files;
data.tag     = 'data';
data.name    = 'DICOM files';
data.help    = {'Select the DICOM files to convert.'};
data.filter  = 'any';
data.ufilter = '.*';
data.num     = [1 Inf];

%--------------------------------------------------------------------------
% outdir Output directory
%--------------------------------------------------------------------------
outdir         = cfg_files;
outdir.tag     = 'outdir';
outdir.name    = 'Output directory';
outdir.val{1}  = {''};
outdir.help    = {'Files produced by this function will be written into this output directory. If no directory is given, images will be written to current working directory.'};
outdir.filter  = 'dir';
outdir.ufilter = '.*';
outdir.num     = [0 1];

%--------------------------------------------------------------------------
% root Directory structure
%--------------------------------------------------------------------------
root         = cfg_menu;
root.tag     = 'root';
root.name    = 'Directory structure';
root.help    = {'Choose root directory of converted file tree. The options are:'
                ''
                '* Output directory: ./<StudyDate-StudyTime>: Automatically determine the project name and try to convert into the output directory, starting with a StudyDate-StudyTime subdirectory. This option is useful if automatic project recognition fails and one wants to convert data into a project directory.'
                ''
                '* Output directory: ./<PatientID>: Convert into the output directory, starting with a PatientID subdirectory.'
                ''
                '* Output directory: ./<ProtocolName>: Convert into the output directory, starting with a ProtocolName subdirectory.'
                ''
                '* No directory hierarchy: Convert all files into the output directory, without sequence/series subdirectories'}';
root.labels  = {'Output directory: ./<StudyDate-StudyTime>/<ProtocolName>'
                'Output directory: ./<PatientID>/<ProtocolName>'
                'Output directory: ./<PatientID>/<StudyDate-StudyTime>/<ProtocolName>'
                'Output directory: ./<ProtocolName>'
                'No directory hierarchy'}';
% removed 'Output directory: ./<PatientName>/<ProtocolName>' for anonymity purposes
root.values  = {'date_time'
                'patid'
                'patid_date'
                'series'
                'flat'}';
root.def     = @(val)spm_get_defaults('dicom.root', val{:});

%--------------------------------------------------------------------------
% protfilter Protocol name filter
%--------------------------------------------------------------------------
protfilter         = cfg_entry;
protfilter.tag     = 'protfilter';
protfilter.name    = 'Protocol name filter';
protfilter.help    = {'A regular expression to filter protocol names. DICOM images whose protocol names do not match this filter will not be converted.'};
protfilter.strtype = 's';
protfilter.num     = [0 Inf];
protfilter.val     = {'.*'};

%--------------------------------------------------------------------------
% format Output image format
%--------------------------------------------------------------------------
format         = cfg_menu;
format.tag     = 'format';
format.name    = 'Output image format';
format.help    = {'Output files can be written as .img + .hdr, or the two can be combined into a single .nii file.'
                  'In any case, only 3D image files will be produced.'}';
format.labels  = {'Two file (img+hdr) NIfTI'
                  'Single file (nii) NIfTI'}';
format.values  = {'img' 'nii'};
format.def     = @(val)spm_get_defaults('images.format', val{:});

%--------------------------------------------------------------------------
% meta Export metadata
%--------------------------------------------------------------------------
meta        = cfg_menu;
meta.tag    = 'meta';
meta.name   = 'Export metadata';
meta.help   = {'Save DICOM fields in a sidecar JSON file.'};
meta.labels = {'No', 'Yes'};
meta.values = {0 1};
meta.val    = {0};

%--------------------------------------------------------------------------
% icedims Use ICEDims in filename
%--------------------------------------------------------------------------
icedims        = cfg_menu;
icedims.tag    = 'icedims';
icedims.name   = 'Use ICEDims in filename';
icedims.help   = {'If image sorting fails, one can try using the additional SIEMENS ICEDims information to create unique filenames. Use this only if there would be multiple volumes with exactly the same file names.'};
icedims.labels = {'No' 'Yes'};
icedims.values = {0 1};
icedims.val    = {0};

%--------------------------------------------------------------------------
% convopts Conversion options
%--------------------------------------------------------------------------
convopts       = cfg_branch;
convopts.tag   = 'convopts';
convopts.name  = 'Conversion options';
convopts.val   = {format meta icedims};
convopts.help  = {''};

%--------------------------------------------------------------------------
% dicom DICOM Import
%--------------------------------------------------------------------------
dicom          = cfg_exbranch;
dicom.tag      = 'dicom';
dicom.name     = 'DICOM Import';
dicom.val      = {data root outdir protfilter convopts};
dicom.help     = {
    'DICOM Conversion.'
    'Most scanners produce data in DICOM format. This routine attempts to convert DICOM files into SPM compatible image volumes, which are written into the current directory by default. Note that not all flavours of DICOM can be handled, as DICOM is a very complicated format, and some scanner manufacturers use their own fields, which are not in the official documentation at http://medical.nema.org/'
    }';
dicom.prog     = @spm_run_dicom;
dicom.vout     = @vout;


%==========================================================================
function dep = vout(job)
dep            = cfg_dep;
dep.sname      = 'Converted Images';
dep.src_output = substruct('.','files');
dep.tgt_spec   = cfg_findspec({{'filter','image','strtype','e'}});