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ea_checkinstall.m
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function [success, commands] = ea_checkinstall(cmd,checkonly,robot,prefs)
success=1;
if ~exist('checkonly','var')
checkonly=0;
end
if ~exist('robot','var')
robot=0;
end
if ~exist('prefs','var')
prefs = [];
end
python_envs = dir(fullfile(ea_getearoot, 'classes', 'conda_utils', 'environments', '*.yml'));
python_envs = cellfun(@(x) x(1:end-4), {python_envs.name}', 'UniformOutput', false);
menuItems = {'Redownload data files'
'Install development version of LeadDBS'
'Python Environment (beta)'
python_envs
'MNI152NLin2009bAsym Nonlinear Flip Transform'
'7T Cardiac Gated FLASH MRI (Backdrop visualization)'
'7T Ex Vivo 100um Brain Atlas (Backdrop visualization)'
'Macroscale Human Connectome Atlas (Yeh 2018)'
'Structural Group Connectome 19 subjects Gibbs-tracker (Horn 2013)'
'Structural Group Connectome 169 NKI-RS subjects Gibbs-tracker (Horn 2016)'
'Structural Group Connectome 32 MGH-USC HCP subjects GQI (Horn 2017)'
'Structural Group Connectome 85 PPMI PD-patients GQI (Ewert 2017)'
'Functional Group Connectome 74 PPMI PD-patients 15 controls (Horn 2017)'
'Functional Group Connectome 75 Toronto PD-patients (Loh & Boutet 2020)'
'Allan Institute Genetics Database'};
downloadIDs = {'leaddata'
'hotfix'
'pyenv'
python_envs
'fliplr'
'7tcgflash'
'7tev100um'
'macroscalehc'
'group2013'
'group2016'
'group2017'
'group2017_ppmi'
'fgroup2017_ppmi'
'TorPD'
'allengenetics'};
assetNames = menuItems(5:end);
assetsIDs = downloadIDs(5:end);
if ismember(cmd, assetsIDs)
assetName = assetNames{ismember(assetsIDs, cmd)};
end
switch cmd
case 'list' % simply return list of installable datasets
success = menuItems;
commands = downloadIDs;
case 'leaddata'
checkf=[ea_space,'bb.nii'];
force=ea_alreadyinstalled(checkf,checkonly,robot);
if checkonly
success=~force;
return;
end
if force==-1
success=-1;
return;
end
if ~exist(checkf,'file') || force
success=ea_downloadasset('LeadDBS Data Files',...
[],...
'');
else
disp('LeadDBS data files is installed.')
end
case 'hotfix'
if ~checkonly
success=ea_hotfix;
end
case 'fliplr'
checkf=[ea_space, 'fliplr', filesep, 'normmethod.json'];
force=ea_alreadyinstalled(checkf,checkonly,robot);
if checkonly
success=~force;
return;
end
if force==-1
success=-1;
return;
end
if ~exist(checkf,'file') || force
success=ea_downloadasset(assetName,...
[ea_space,'fliplr.zip'],...
cmd);
else
disp([assetName, ' is installed.'])
end
case '7tcgflash'
space = ea_space;
if exist([space,'backdrops',filesep,'7T_Flash_Horn_2018.mat'], 'file')
movefile([space,'backdrops',filesep,'7T_Flash_Horn_2018.mat'], ...
[space,'backdrops',filesep,'7T_Flash_Horn_2019.mat']);
fid = fopen([space,'backdrops',filesep,'backdrops.txt'], 'r');
text = fread(fid, inf, '*char')';
fclose(fid);
text = strrep(text, '7T_Flash_Horn_2018.mat', '7T_Flash_Horn_2019.mat');
fid = fopen([space,'backdrops',filesep,'backdrops.txt'], 'w');
fwrite(fid, text);
fclose(fid);
end
checkf=[space,'backdrops',filesep,'7T_Flash_Horn_2019.mat'];
force=ea_alreadyinstalled(checkf,checkonly,robot);
if checkonly
success=~force;
return;
end
if force==-1
success=-1;
return;
end
if ~exist(checkf,'file') || force
ea_mkdir([space,'backdrops']);
success=ea_downloadasset(assetName,...
[ea_space,'backdrops',filesep,'7T_Flash_Horn_2019.mat'],...
cmd);
m = matfile([space,'backdrops',filesep,'7T_Flash_Horn_2019.mat'],'Writable',true);
m.fname = [space,'backdrops',filesep,'7T_Flash_Horn_2019.nii'];
fid=fopen([space,'backdrops',filesep,'backdrops.txt'],'a');
fprintf(fid,'%s %s\n','7T_Flash_Horn_2019.mat','7T_Cardiac_Gated_Flash_MRI_(Horn_2019)');
fclose(fid);
else
disp([assetName, ' is installed.'])
end
case '7tev100um'
space = ea_space;
checkf=[space,'backdrops',filesep,'7T_100um_Edlow_2019.mat'];
force=ea_alreadyinstalled(checkf,checkonly,robot);
if checkonly
success=~force;
return;
end
if force==-1
success=-1;
return;
end
if ~exist(checkf,'file') || force
ea_mkdir([space,'backdrops']);
success=ea_downloadasset(assetName,...
[ea_space,'backdrops',filesep,'7T_100um_Edlow_2019.mat'],...
cmd);
m = matfile([space,'backdrops',filesep,'7T_100um_Edlow_2019.mat'],'Writable',true);
m.fname = [space,'backdrops',filesep,'7T_100um_Edlow_2019.nii'];
fid=fopen([space,'backdrops',filesep,'backdrops.txt'],'a');
fprintf(fid,'%s %s\n','7T_100um_Edlow_2019.mat','7T_Ex_Vivo_100um_Brain_Atlas_(Edlow_2019)');
fclose(fid);
else
disp([assetName, ' is installed.'])
end
case 'macroscalehc'
space=ea_space;
checkf=[space,'atlases',filesep,'Macroscale Human Connectome Atlas (Yeh 2018)',filesep,'atlas_index.mat'];
force=ea_alreadyinstalled(checkf,checkonly,robot);
if checkonly
success=~force;
return;
end
if force==-1
success=-1;
return;
end
if ~exist(checkf,'file') || force
success=ea_downloadasset(assetName,...
[space,'atlases',filesep,'Macroscale_Human_Connectome_Atlas_Yeh_2018.zip'],...
cmd);
else
disp([assetName, ' is installed.'])
end
case 'group2013'
checkf=[ea_getconnectomebase('dmri',prefs),'Global Tracking 19 (Horn 2013) Full',filesep,'data.mat'];
force=ea_alreadyinstalled(checkf,checkonly,robot);
if checkonly
success=~force;
return;
end
if force==-1
success=-1;
return;
end
if ~exist(checkf,'file') || force
success=ea_downloadasset(assetName,...
[ea_getconnectomebase('dmri',prefs),'groupconnectome2013.zip'],...
cmd);
else
disp([assetName, ' is installed.'])
end
case 'group2016'
checkf=[ea_getconnectomebase('dmri',prefs),'NKI-RS 169 (Horn 2016)',filesep,'data.mat'];
force=ea_alreadyinstalled(checkf,checkonly,robot);
if checkonly
success=~force;
return;
end
if force==-1
success=-1;
return;
end
if ~exist(checkf,'file') || force
success=ea_downloadasset(assetName,...
[ea_getconnectomebase('dmri',prefs),'groupconnectome2016.zip'],...
cmd);
else
disp([assetName, ' is installed.'])
end
case 'group2017'
checkf=[ea_getconnectomebase('dmri',prefs),'MGH-USC HCP 32 (Horn 2017)',filesep,'data.mat'];
force=ea_alreadyinstalled(checkf,checkonly,robot);
if checkonly
success=~force;
return;
end
if force==-1
success=-1;
return;
end
if ~exist(checkf,'file') || force
success=ea_downloadasset(assetName,...
[ea_getconnectomebase('dmri',prefs),'groupconnectome2017.zip'],...
cmd);
else
disp([assetName, ' is installed.'])
end
case 'group2017_ppmi'
checkf=[ea_getconnectomebase('dmri',prefs),'PPMI 85 (Ewert 2017)',filesep,'data.mat'];
force=ea_alreadyinstalled(checkf,checkonly,robot);
if checkonly
success=~force;
return;
end
if force==-1
success=-1;
return;
end
if ~exist(checkf,'file') || force
success=ea_downloadasset(assetName,...
[ea_getconnectomebase('dmri',prefs),'groupconnectome_ppmi2017.zip'],...
cmd);
else
disp([assetName, ' is installed.'])
end
case 'fgroup2017_ppmi'
checkf=[ea_getconnectomebase('fmri',prefs),'PPMI 74 Patients 15 Controls (Horn 2017)',filesep,'dataset_info.json'];
force=ea_alreadyinstalled(checkf,checkonly,robot);
if checkonly
success=~force;
return;
end
if force==-1
success=-1;
return;
end
if ~exist(checkf,'file') || force
success=ea_downloadasset(assetName,...
[ea_getconnectomebase('fmri',prefs),'fgroupconnectome_ppmi2017.zip'],...
cmd);
else
disp([assetName, ' is installed.'])
end
case 'TorPD'
checkf=[ea_getconnectomebase('fmri',prefs),'Tor PD (Loh & Boutet 2020)',filesep,'dataset_info.json'];
force=ea_alreadyinstalled(checkf,checkonly,robot);
if checkonly
success=~force;
return;
end
if force==-1
success=-1;
return;
end
if ~exist(checkf,'file') || force
success=ea_downloadasset(assetName,...
[ea_getconnectomebase('fmri',prefs),'TorPD_Loh_Boutet_2020.zip'],...
cmd);
else
disp([assetName, ' is installed.'])
end
case 'allengenetics'
checkf = [ea_space, 'genetics', filesep, 'geneinfo.mat'];
force=ea_alreadyinstalled(checkf,checkonly,robot);
if checkonly
success=~force;
return;
end
if force==-1
success=-1;
return;
end
if ~exist(checkf,'file') || force
success=ea_downloadasset(assetName,...
[ea_space,'genetics.zip'],...
cmd);
else
disp([assetName, ' is installed.'])
end
case python_envs
py_env = ea_conda_env(cmd);
if ~checkonly
if ~ea_conda.is_installed
ea_conda.install;
end
py_env.force_create;
end
success = py_env.is_created;
end
function success=ea_downloadasset(assetname,destination,id)
if strcmp(assetname,'LeadDBS Data Files')
ea_update_data('full');
success=1;
else
downloadurl = 'https://www.lead-dbs.org/release/download.php';
success=1;
if ~exist(fileparts(destination), 'dir')
mkdir(fileparts(destination));
end
% get the file size and display it to inform user of size
try
fsize = ea_getassetfilesize(id); % get the filesize in bytes from the server
catch
fsize = 0;
end
if fsize ~= 0
fprintf('Downloading %s with a size of %.2f GB\nFilename: %s\n', assetname, fsize*1e-9, destination);
else
fprintf('Downloading %s\nFilename: %s\n', ea_getspace, destination);
disp('This could take a while...');
end
% first see if parallel toolbox is installed and can be utilized to
% download in the backgroung
if license('test', 'Distrib_Computing_Toolbox') % check if parallel toolbox is installed
disp('Parallel toolbox detected, downloading via background worker')
try
ea_downloadasset_parallel(downloadurl, assetname, destination, id, fsize);
catch
try
delete(findall(0,'type','figure','tag','TMWWaitbar')); % delete waitbar if error occured
disp('Download using parallel toolbox failed, trying websave...')
webopts=weboptions('Timeout',Inf);
websave(destination,downloadurl,'id',id,webopts);
catch
disp('Parallel toolbox not detected, downloading via websave...')
try
disp('''websave'' failed, trying ''urlwrite''.');
urlwrite([downloadurl,'?id=',id],destination,'Timeout',Inf);
catch
disp('''urlwrite'' failed.');
success=0;
end
end
end
else
try
disp('Trying ''websave''.');
webopts=weboptions('Timeout',Inf);
% uncomment this if you encounter problems with certificate validation
% (see https://www.mathworks.com/matlabcentral/answers/400086-how-to-read-data-form-website-url)
%webopts.CertificateFilename=('');
websave(destination,downloadurl,'id',id,webopts);
catch
try
disp('''websave'' failed, trying ''urlwrite''.');
urlwrite([downloadurl,'?id=',id],destination,'Timeout',Inf);
catch
disp('''urlwrite'' failed.');
success=0;
end
end
end
[loc,~,ext] = fileparts(destination);
if success
disp(['Installing ',assetname,'...'])
try
if strcmp(ext,'.gz')
gunzip(destination, loc);
ea_delete(destination);
elseif strcmp(ext,'.zip')
unzip(destination, loc);
ea_delete(destination);
end
catch
disp('Installation failed.');
success=0;
end
end
if ~success
fprintf(['\nDownload / install error! You may try to download the file manually from:\n',...
'%s\nand then extract it into %s.\n\n'], [downloadurl,'?id=',id], loc);
msgbox('Please check the command window for more information.','Download error!','Error')
return
end
end
function force=ea_alreadyinstalled(checkf,checkonly,robot)
if ~isfile(checkf) % then file not there, should install anyways.
force=1;
return
end
if checkonly % return here.
force=0;
return
end
if ~robot
choice = questdlg('This dataset seems already to be installed. Do you wish to re-download it?', ...
'Redownload Dataset?', ...
'Yes','No','No');
if strcmp(choice,'Yes')
force=1;
else
force=-1;
end
else
force=0;
end