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clean release
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@dmitrishastin
dmitrishastin committed Jul 29, 2022
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306 changes: 306 additions & 0 deletions Class_files/init_class.m
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classdef init_class

properties % Pipeline settings with default values

% Initiation:

fod
fs_dir
work_dir
logt % hidden flag

% Freesurfer related:

slab = 'cortex';

% Tractography related:

surfseed = true;
tckgen = '';
noseed = '';
sl_weights = '';
maxlen = 90;
final_init % hidden flag

% Pipeline options:

remesh_seeds = false;
registration = 'SAF_registration_default';
noregister = false;
notrunc = false;
fa = '';
wrks = '';
optmodules = '';
scalar2surf = '';

% Filter settings:

fastx = true;
pialfilter = false;
gwg_hard = false;
gg_margin = 0;

% General:

mrtrix_prefix = '';
outf = -1;
force = false;
dgn = false;
quiet = false;
version = '1.0.0';

end

methods

%% parse custom parameters
function this = init_class(parsed_input)

% values not required (set to true if not provided)
arguments_bool = {'dgn', 'notrunc', 'noregister', 'force', 'quiet', ...
'pialfilter', 'remesh_seeds', 'gwg_hard', 'surfseed', 'fastx'};

% can take multiple arguments
arguments_multi = {'optmodules','scalar2surf'};

% arguments pointing to a file
arguments_path = {'fod', 'fa', 'noseed', 'sl_weights'};

while ~isempty(parsed_input)

% if PS from a previous run is passed, accept its values and move on
old_PS = cellfun(@(x) isa(x, 'init_class'), parsed_input);
if any(old_PS)
this = parsed_input{old_PS};
this.logt = '';
this.final_init = '';
this.force = true;
parsed_input(old_PS) = [];
continue
end

% get the name-value combinations
iname = parsed_input{1}; parsed_input(1) = [];
assert(any(strcmp(iname, fieldnames(this))), 'wrong input provided');
ival = {};
while ~isempty(parsed_input) && (~ischar(parsed_input{1}) || ~any(strcmp(parsed_input{1}, fieldnames(this))))
if iscell(parsed_input{1})
ival(end + 1: end + numel(parsed_input(1))) = parsed_input(1);
else
ival(end + 1) = parsed_input(1);
end
parsed_input(1) = [];
end

% for input providing external files - make sure path not relative
if any(strcmp(iname, arguments_path))
ival = make_full_path(ival);
end

switch numel(ival)
case 0
assert(any(strcmp(arguments_bool, iname)), [iname ' requires values to proceed'])
this.(iname) = true;
case 1
if any(strcmp(arguments_bool, iname))
switch ival{1}
case {'on' 1}
ival{1} = true;
case {'off' 0}
ival{1} = false;
end
end
if any(strcmp(arguments_multi, iname))
this.(iname) = [this.(iname) ival{1}];
else
this.(iname) = ival{1};
end
otherwise
assert(any(strcmp(arguments_multi, iname)), [iname ' does not take multiple values'])
this.(iname) = [this.(iname) ival];
end
end

% if {''} is passed to multivalue inputs, the whole lot is purged
for mvi = arguments_multi
if iscell(this.(mvi{1})) && any(cellfun(@isempty, this.(mvi{1})))
this.(mvi{1}) = {};
end
end

this = workdir(this);
this = sortFS(this);
this = n_wrks(this);
this = start_log(this);

% checks
assert(~isempty(this.fod) && ~isempty(this.fs_dir), 'FOD file and FreeSurfer dir must be provided');
assert(~isempty(this.fa) || this.noregister, 'Provide FA for registration or ensure "noregister" flag is on');
assert(isempty(this.tckgen) || isempty(this.noseed), 'Either "tckgen" or "noseed" must be empty');

if this.dgn
this.quiet = false;
end

% switches off maxlen if streamlines already shorter via tckgen
if ~isempty(this.maxlen) && ~isempty(this.tckgen)
[~, tckgen_maxlen] = regexp(this.tckgen, '-maxlength ', 'once');
if ~isempty(tckgen_maxlen)
tckgen_maxlen = sscanf(this.tckgen(tckgen_maxlen + 1:end), '%d{1}');
if tckgen_maxlen < this.maxlen
this.maxlen = [];
end
end
end
end

%% sort out parallel workers
function this = n_wrks(this)

if isempty(this.wrks)

this.wrks = parcluster(parallel.defaultClusterProfile);
this.wrks = this.wrks.NumWorkers;

elseif ischar(this.wrks)

this.wrks = str2double(this.wrks);

end
end

%% create work folder if needed
function this = workdir(this)

if this.outf == -1 % set default unless specified otherwise
this.work_dir = [Supp_gz_fileparts(this.fod) filesep 'SAF_output'];
else % ensure full path
if strcmp(Supp_gz_fileparts(this.outf), '')
this.work_dir = [Supp_gz_fileparts(this.fod) filesep this.outf];
else
this.work_dir = this.outf;
end
end

if ~exist(this.work_dir, 'dir') % create the folder if it doesn't exist
mkdir(this.work_dir);
end

cd(this.work_dir); % open the folder

end

%% initiate log

function this = start_log(this)

if isempty(this.fa)
fa = 'not provided';
else
fa = this.fa;
end

this.logt = { ...
'Log for SAF_pipeline.m run on:' datestr(datetime('now')); ...
'Version:' this.version; ...
'' ''; ...
'FreeSurfer directory:' this.fs_dir; ...
'FOD file:' this.fod; ...
'FA file:' fa; ...
'Output directory:' this.work_dir; ...
'' ''};

if this.noregister
this.logt(end+1,:) = {'Registration:' 'already co-aligned'};
else
this.logt(end+1,:) = {'Registration:' this.registration};
end

if isempty(this.noseed)
this.logt(end+1:end+3,:) = { ...
'Seed from surface mesh vertices for tractography:' this.surfseed; ...
'Surface label for seeding:' this.slab; ...
'Additional tckgen options:' this.tckgen};
else
this.logt(end+1,:) = {'Tractography file:' this.noseed};
end

if isempty(this.sl_weights)
this.logt(end+1,:) = {'Streamline weights:' 'not provided'};
else
this.logt(end+1,:) = {'Streamline weights:' this.sl_weights};
end

this.logt(end+1:end+10,:) = { ...
'MRtrix command prefix: ' this.mrtrix_prefix; ...
'Fast mesh-streamline intersection detection: ' this.fastx; ...
'Extra margin during GG: ' this.gg_margin; ...
'Hard 2-point intersection during GWG:' this.gwg_hard; ...
'Do not truncate streamline at the WSM:' this.notrunc; ...
'Apply pial filtering:' this.pialfilter; ...
'Diagnostics:' this.dgn; ...
'Force overwrite:' this.force; ...
'Quiet:' this.quiet; ...
'' ''};

if isempty(this.scalar2surf)
this.logt(end+1,:) = {'Scalars provided for projection on the surface:' 'none'};
else
this.logt(end+1,:) = {'Scalars provided for projection on the surface:' strjoin(this.scalar2surf, ', ')};
end

if isempty(this.optmodules)
this.logt(end+1,:) = {'Optional modules:' 'none'};
else
this.logt(end+1,:) = {'Optional modules:' strjoin(this.optmodules, ', ')};
end

this.logt(end+1, :) = {'' ''};

end

%% ensure fs_dir is not in fact a file (in which case run recon-all)
function this = sortFS(this)

def_dir = [Supp_gz_fileparts(this.fod) filesep 'FS_reconall'];

if ~exist(this.fs_dir) && ~exist(def_dir, 'dir')

error('fs_dir not provided correctly')

elseif ~exist(this.fs_dir)

warning(['fs_dir not provided correctly but a default freesurfer directory found. Use the default directory? ' def_dir])
if strcmp(input('y/n? ', 's'), 'y')
this.fs_dir = def_dir;
else
error('fs_dir not provided correctly')
end

elseif ~isdir(this.fs_dir) && exist(def_dir, 'dir')

warning('fs_dir points to a file but a default freesurfer directory found. Use the default directory instead of re-running recon-all? ')
if strcmp(input('y/n? ', 's'), 'y')
this.fs_dir = def_dir;
else
verb_msg(['Running Freesurfer recon-all on ' this.fs_dir '... will take a while ;)'], this)
sys_exec(['recon-all -subject FS_reconall -sd ' Supp_gz_fileparts(this.fod) filesep ' -i ' this.fs_dir ' -all'], this);
this.fs_dir = def_dir;
end

elseif isdir(this.fs_dir) && exist(def_dir, 'dir')

warning('A default freesurfer directory was found but fs_dir points to a different directory. Using the provided directory')
this.fs_dir = make_full_path(this.fs_dir);

elseif ~isdir(this.fs_dir) && ~exist(def_dir, 'dir')

verb_msg(['Running Freesurfer recon-all on ' this.fs_dir '... will take a while ;)'], this)
sys_exec(['recon-all -subject FS_reconall -sd ' Supp_gz_fileparts(this.fod) filesep ' -i ' this.fs_dir ' -all'], this);
this.fs_dir = def_dir;

end
end
end
end

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