void MainWindow::documentOpen(void)
{
PluginFileIOFactory *fileIOFactory = sharedPluginFileIOFactory();
QString filter = tr("Dunnart diagrams (") +
fileIOFactory->openableFileTypesString() + ")";
// Determine the working directory.
QSettings settings;
QString workingDir(QDir::homePath());
QVariant workingDirSetting =
settings.value("workingDirectory");
if (workingDirSetting.isValid())
{
workingDir = workingDirSetting.toString();
}
QString fileNameString = QFileDialog::getOpenFileName(this,
tr("Open Diagram"), workingDir, filter);
if (!fileNameString.isEmpty())
{
QSettings settings;
settings.setValue("workingDirectory", QFileInfo(fileNameString).absolutePath());
settings.sync();
loadDiagram(fileNameString);
}
}
void
RunPotentialParamsQueue::updateTable(const utility::DataTable::Key & key,
const StructureDataType * const structureData)
{
utility::insertStructureInfoAndPotentialParams(key, *structureData,
workingDir(), myTableSupport.getTable());
}
bool validate(const FilePath& userHomePath,
bool projectSharingEnabled) const
{
// ensure the scratch path and properties paths exist
if (!scratchPath_.exists() || !propertiesPath_.exists())
return false;
// ensure the properties are there
if (project().empty() || workingDir().empty() || (lastUsed() == 0))
return false;
// for projects validate that the base directory still exists
std::string theProject = project();
if (theProject != kProjectNone)
{
FilePath projectDir = FilePath::resolveAliasedPath(theProject,
userHomePath);
if (!projectDir.exists())
return false;
// check for project file
FilePath projectPath = r_util::projectFromDirectory(projectDir);
if (!projectPath.exists())
return false;
// if we got this far the scope is valid, do one final check for
// trying to open a shared project if sharing is disabled
if (!projectSharingEnabled &&
r_util::isSharedPath(projectPath.absolutePath(), userHomePath))
return false;
}
// validated!
return true;
}
iCelHNavStruct* celHNavStructBuilder::LoadHNavStruct (iVFS* vfs, const char* directory)
{
csRef<iDocumentSystem> docsys = csLoadPluginCheck<iDocumentSystem>(objectRegistry, "crystalspace.documentsystem.tinyxml");
if (!docsys)
{
return 0;
}
// Mount file
csString workingDir(vfs->GetCwd());
vfs->ChDir(directory);
// Read XML file
csRef<iDocument> doc = docsys->CreateDocument();
csRef<iFile> xmlFile = vfs->Open("navstruct.xml", VFS_FILE_READ);
if(!xmlFile.IsValid())
{
return 0;
}
const char* log = doc->Parse(xmlFile);
if (log)
{
return 0;
}
csRef<iDocumentNode> root = doc->GetRoot();
csRef<iDocumentNode> mainNode = root->GetNode("iCelHNavStruct");
// Read parameters
csRef<iDocumentNode> paramsNode = mainNode->GetNode("parameters");
csRef<iCelNavMeshParams> params;
params.AttachNew(new celNavMeshParams());
ParseParameters(paramsNode, params);
// Create navigation structure
csRef<celHNavStruct> navStruct;
navStruct.AttachNew(new celHNavStruct(params, objectRegistry));
// Read navigation meshes
csRef<iDocumentNode> meshesNode = mainNode->GetNode("navmeshes");
csHash<csRef<iSector>, const char*> sectors;
if(!ParseMeshes(meshesNode, sectors, navStruct, vfs, params))
{
return 0;
}
// Read high level graph
csRef<iDocumentNode> graphNode = mainNode->GetNode("highlevelgraph");
csRef<iCelGraph> graph = scfCreateInstance<iCelGraph>("cel.celgraph");
if(!ParseGraph(graphNode, graph, sectors))
{
return 0;
}
navStruct->SetHighLevelGraph(graph);
this->navStruct = navStruct;
vfs->ChDir(workingDir.GetDataSafe());
return navStruct;
}
int dir(vector<string>argVector)
{
//Execute dir command
char workingDir_Cstr[FILENAME_MAX];
vector<string> dirContents;
GetWorkingDir(workingDir_Cstr, sizeof(workingDir_Cstr));
string workingDir(workingDir_Cstr);
cout << workingDir << '\n';
#ifdef WINDOWS
workingDir = workingDir + "\\*";
WIN32_FIND_DATA fileData;
HANDLE hFind;
hFind = FindFirstFile(workingDir.c_str(), &fileData);
if (hFind == INVALID_HANDLE_VALUE)
{
cout << "\n Failure accessing directory\n";
return 0;
}
while (FindNextFile(hFind, &fileData))
{
if (fileData.dwFileAttributes & FILE_ATTRIBUTE_DIRECTORY)
{
cout << "\t <DIR> " << fileData.cFileName << '\n';
}
else
{
cout << "\t" << fileData.cFileName << '\n';
}
}
#else
DIR *dp;
struct dirent *dirp;
string DIRstr;
if ((dp = opendir(workingDir.c_str())) == NULL)
{
cout << "\n Failure accessing directory\n";
return 0;
}
while ((dirp = readdir(dp)) != NULL)
{
if (dirp->d_type == DT_DIR)
{
DIRstr = dirp->d_name;
if ((DIRstr != ".") && (DIRstr != "..")) cout << "\t <DIR> " << dirp->d_name << '\n';
}
else
{
cout << "\t" << dirp->d_name << '\n';
}
}
closedir(dp);
#endif
return 0;
}
wxString MemCheckPlugin::PrepareCommand(const wxString& projectName, wxString& wd)
{
wd.clear();
if(!clCxxWorkspaceST::Get()->IsOpen()) { return ""; }
ProjectPtr proj = clCxxWorkspaceST::Get()->GetProject(projectName);
if(!proj) {
clWARNING() << "MemCheckPlugin::PrepareCommand(): could not find project:" << projectName;
return wxEmptyString;
}
BuildConfigPtr bldConf = clCxxWorkspaceST::Get()->GetProjBuildConf(projectName, wxEmptyString);
if(!bldConf) {
clWARNING() << "MemCheckPlugin::PrepareCommand(): failed to find project configuration for project:"
<< projectName;
return wxEmptyString;
}
wxString projectPath = proj->GetFileName().GetPath();
// expand variables
wxString cmd = bldConf->GetCommand();
cmd = MacroManager::Instance()->Expand(cmd, NULL, projectName);
wxString cmdArgs = bldConf->GetCommandArguments();
cmdArgs = MacroManager::Instance()->Expand(cmdArgs, NULL, projectName);
// Execute command & cmdArgs
wd = bldConf->GetWorkingDirectory();
wd = MacroManager::Instance()->Expand(wd, NULL, projectName);
wxFileName workingDir(wd, "");
if(workingDir.IsRelative()) { workingDir.MakeAbsolute(projectPath); }
wxFileName fileExe(cmd);
if(fileExe.IsRelative()) { fileExe.MakeAbsolute(workingDir.GetPath()); }
fileExe.Normalize();
#ifdef __WXMSW__
if(!fileExe.Exists() && fileExe.GetExt().IsEmpty()) {
// Try with .exe
wxFileName withExe(fileExe);
withExe.SetExt("exe");
if(withExe.Exists()) { fileExe = withExe; }
}
#endif
wd = workingDir.GetPath();
cmd = fileExe.GetFullPath();
cmd = ::WrapWithQuotes(cmd);
cmd << " " << cmdArgs;
clDEBUG() << "Command to execute:" << cmd;
clDEBUG() << "Working directory:" << wd;
return cmd;
}
void CefIPCPipeClient::startService()
{
#ifdef DEBUG
const char* exeName = "desura_browserhost-d.exe";
#else
const char* exeName = "desura_browserhost.exe";
#endif
UserAgentFN userAgent = (UserAgentFN)WebCore::FactoryBuilder(WEBCORE_USERAGENT);
gcString ua = userAgent();
gcString exe(exeName);
gcString params("{3} {0} {1} {2}", m_szPipeId, m_szHostName, UTIL::STRING::base64_encode(ua.c_str(), ua.size()), exeName);
DWORD dwExitCode = 0;
STARTUPINFOA siStartupInfo;
PROCESS_INFORMATION piProcessInfo;
memset(&siStartupInfo, 0, sizeof(siStartupInfo));
memset(&piProcessInfo, 0, sizeof(piProcessInfo));
siStartupInfo.cb = sizeof(siStartupInfo);
gcString workingDir(UTIL::OS::getCurrentDir());
UINT oldErrMode = SetErrorMode(0);
BOOL res = CreateProcessA(const_cast<char*>(exe.c_str()), const_cast<char*>(params.c_str()), 0, 0, false, CREATE_DEFAULT_ERROR_MODE, 0, workingDir.c_str(), &siStartupInfo, &piProcessInfo);
DWORD lastError = GetLastError();
SetErrorMode(oldErrMode);
CloseHandle( piProcessInfo.hThread );
if (res == false)
{
CloseHandle( piProcessInfo.hProcess );
throw gcException(ERR_LAUNCH, lastError, "Failed to start render helper");
}
else
{
#ifdef DEBUG
WaitForInputIdle(piProcessInfo.hProcess, INFINITE);
#else
WaitForInputIdle(piProcessInfo.hProcess, 5000);
#endif
CloseHandle( piProcessInfo.hProcess );
}
}
bool celHNavStruct::SaveToFile (iVFS* vfs, const char* directory)
{
csRef<iDocumentSystem> docsys = csLoadPluginCheck<iDocumentSystem>(objectRegistry, "crystalspace.documentsystem.tinyxml");
if (!docsys)
{
return false;
}
csString workingDir(vfs->GetCwd());
vfs->ChDir(directory);
// Create XML file
csRef<iDocument> doc = docsys->CreateDocument();
csRef<iDocumentNode> root = doc->CreateRoot();
csRef<iDocumentNode> mainNode = root->CreateNodeBefore(CS_NODE_ELEMENT);
mainNode->SetValue("iCelHNavStruct");
// Create parameters subtree
csRef<iDocumentNode> params = mainNode->CreateNodeBefore(CS_NODE_ELEMENT);
params->SetValue("parameters");
SaveParameters(params);
// Create navmeshes subtree
csRef<iDocumentNode> navmeshes = mainNode->CreateNodeBefore(CS_NODE_ELEMENT);
navmeshes->SetValue("navmeshes");
SaveNavMeshes(navmeshes, vfs);
// Create highlevelgraph subtree
csRef<iDocumentNode> hlgraph = mainNode->CreateNodeBefore(CS_NODE_ELEMENT);
hlgraph->SetValue("highlevelgraph");
csRef<iDocumentNode> nodes = hlgraph->CreateNodeBefore(CS_NODE_ELEMENT);
nodes->SetValue("nodes");
csRef<iDocumentNode> edges = hlgraph->CreateNodeBefore(CS_NODE_ELEMENT);
edges->SetValue("edges");
SaveHighLevelGraph(nodes, edges);
// Write xml file
const char* log = doc->Write(vfs, "navstruct.xml");
vfs->ChDir(workingDir.GetDataSafe());
vfs->Sync();
if (log)
{
return false;
}
return true;
}
status_t
SVNSourceControl::DeleteRepository(const char *path)
{
if (!path || strlen(path) < 1)
return B_ERROR;
DPath workingDir(path);
DPath repoPath(sRepoPath);
repoPath << workingDir.GetFileName();
BString command("rm -r ");
command << "'" << repoPath.GetFullPath() << "'";
BString out;
RunCommand(command, out);
return B_OK;
}
status_t
SVNSourceControl::CreateRepository(const char *path)
{
// The SourceControl class runs under the DSCM idea of the local directory
// being a repository. Seeing how SVN doesn't allow for this, we create a
// repository elsewhere on the hard drive, check it out to the path we were
// given, and add the files to the repository. Checking in is not part of
// this call, however.
DPath workingDir(path);
DPath repoPath(sRepoPath);
repoPath << workingDir.GetFileName();
BDirectory dir(sRepoPath.String());
if (dir.InitCheck() != B_OK)
create_directory(sRepoPath.String(), 0777);
BString command("svnadmin create ");
command << "'" << repoPath.GetFullPath() << "'";
BString out;
RunCommand(command, out);
BString repoURL = "file://";
repoURL << repoPath.GetFullPath();
SetURL(repoURL.String());
SetWorkingDirectory(path);
CloneRepository(repoURL.String(), path);
BPath svnpath(path);
svnpath.Append(".svn");
if (!BEntry(svnpath.Path()).Exists())
return B_ERROR;
command = "";
command << "cd '" << path << "'; "
<< "svn add --non-interactive *";
RunCommand(command, out);
return B_OK;
}
void FileTestContext::inputFile(const char* filename)
{
UtlString inputPath;
inputFilePath(filename, inputPath);
UtlString workingPath;
workingFilePath(filename, workingPath);
OsPath input(inputPath);
OsPath working(workingPath);
OsPath workingDirPath(working.getDirName());
workingDirPath.strip(UtlString::trailing, OsPath::separator(0));
OsDir workingDir(workingDirPath);
if (!workingDir.exists())
{
UtlString msg;
msg.append("FileTestContext::inputFile failed to create working directory '");
msg.append(working.getDirName().data());
msg.append("'");
CPPUNIT_ASSERT_EQUAL_MESSAGE(msg.data(),
OS_SUCCESS,OsFileSystem::createDir(workingDirPath,TRUE));
}
UtlString msg;
msg.append("FileTestContext::inputFile copy failed from '");
msg.append(inputPath);
msg.append("' -> '");
msg.append(workingPath);
msg.append("'");
CPPUNIT_ASSERT_EQUAL_MESSAGE(msg.data(),
OS_SUCCESS,
OsFileSystem::copy(input, working)
);
Os::Logger::instance().log(FAC_UNIT_TEST, PRI_NOTICE, "FileTestContext::inputFile '%s' -> '%s'",
inputPath.data(), workingPath.data());
}
void
SearchStoichiometries::releaseBufferedStructures(
const utility::DataTable::Key & tableKey)
{
// Send any finished structure data down my pipe
utility::DataTable & table = myTableSupport.getTable();
ssio::ResourceLocator lastSavedRelative;
BOOST_FOREACH(StructureDataType * const structure, myBuffer)
{
lastSavedRelative = common::getRelativeSavePath(*structure, workingDir());
if(!lastSavedRelative.empty())
{
// Insert the relative path to the last place this structre was saved
table.insert(tableKey, "lowest", lastSavedRelative.string());
}
if(const unsigned int * const spacegroup = structure->properties().find(
structure_properties::general::SPACEGROUP_NUMBER))
{
table.insert(tableKey, "sg",
boost::lexical_cast< std::string>(*spacegroup));
}
// Try to calculate the energy/atom
if(const double * const internalEnergy = structure->properties().find(
structure_properties::general::ENERGY_INTERNAL))
{
const size_t numAtoms = structure->getNumAtoms();
if(numAtoms != 0)
table.insert(tableKey, "energy/atom",
common::toString(*internalEnergy / numAtoms));
}
// Pass the structure on
out(structure);
}
bool QGenieExport2DiskFileThread::copyFile(const QString &filePath,const QString &destDir)
{
qDebug () << "Copyt " << filePath << "to " << destDir;
QString path2MK = filePath.mid(2,filePath.lastIndexOf("/") - 2);
QDir workingDir(destDir);
if(!workingDir.mkpath(path2MK))
{
return false;
}
QDir destDir_(destDir);
QString fileName = destDir_.absolutePath() + QDir::separator() + filePath.mid(2);
if(QFile::exists(fileName))
{
QFile::setPermissions(fileName,QFile::WriteOther);
QFile::remove(fileName);
}
return QFile::copy(filePath,fileName);
}
// Inject webinos.js
// The file is loaded from the webinos\test\client folder if possible.
// If this fails, the current folder is used.
void ClientApp::InjectWebinos(CefRefPtr<CefFrame> frame)
{
CefRefPtr<CefCommandLine> commandLine = AppGetCommandLine();
// First try and load the platform-supplied webinos.js
#if defined(OS_WIN)
FilePath workingDir(commandLine->GetProgram().ToWString().c_str());
FilePath webinosJSPath = workingDir.DirName().Append(L"..\\..\\webinos\\web_root\\webinos.js");
#else
FilePath workingDir(commandLine->GetProgram());
FilePath webinosJSPath = workingDir.DirName().Append("..\\..\\webinos\\web_root\\webinos.js");
#endif
int64 webinosJSCodeSize;
bool gotJSFile = file_util::GetFileSize(webinosJSPath, &webinosJSCodeSize);
if (!gotJSFile)
{
// Unable to load the platform-supplied webinos.js, use the installed version.
#if defined(OS_WIN)
workingDir = FilePath(commandLine->GetProgram().ToWString().c_str());
webinosJSPath = workingDir.DirName().Append(L"webinos.js");
#else
workingDir = FilePath(commandLine->GetProgram());
webinosJSPath = workingDir.DirName().Append("webinos.js");
#endif
gotJSFile = file_util::GetFileSize(webinosJSPath, &webinosJSCodeSize);
}
if (gotJSFile)
{
char* webinosJSCode = new char[webinosJSCodeSize+1];
file_util::ReadFile(webinosJSPath, webinosJSCode, webinosJSCodeSize);
webinosJSCode[webinosJSCodeSize] = 0;
if (frame == NULL)
{
// Register as a Cef extension.
CefRegisterExtension("webinos", webinosJSCode, NULL);
}
else
{
// Run the code in the frame javascript context right now,
// but only if the URL refers to the widget server.
int widgetServerPort;
AppGetWebinosWRTConfig(NULL,&widgetServerPort);
char injectionCandidate[MAX_URL_LENGTH];
sprintf(injectionCandidate,"http://localhost:%d",widgetServerPort);
std::string url = frame->GetURL();
if (url.substr(0,strlen(injectionCandidate)) == injectionCandidate)
frame->ExecuteJavaScript(webinosJSCode, url, 0);
}
delete[] webinosJSCode;
}
else
{
LOG(ERROR) << "Can't find webinos.js";
}
}
int main( int argc, char *argv[] )
{
// try {
time_t programStartTime(time(NULL) );
boost::filesystem::path workingDir( boost::filesystem::current_path() );
// ========== PROGRAM PARAMETERS ==========
std::string progName( "buildrandctree" );
std::string configFilename( "/home/raid2/moreno/Code/hClustering/config/"+progName+".cfg" );
// program parameters
std::string roiFilename, inputFolder, outputFolder;
float memory( 0.5 ), maxNbDist( 1 );
unsigned int nbLevel( 26 ), threads( 0 );
bool keepDiscarded( false ), niftiMode( true ), debug( false );
TC_GROWTYPE growType( TC_GROWOFF );
size_t baseSize( 0 );
// Declare a group of options that will be allowed only on command line
boost::program_options::options_description genericOptions( "Generic options" );
genericOptions.add_options()
( "version", "Program version" )
( "help,h", "Produce extended program help message" )
( "roi,r", boost::program_options::value< std::string >(&roiFilename), "file with the seed voxels coordinates." )
( "inputf,I", boost::program_options::value< std::string >(&inputFolder), "input data folder (seed tractograms)." )
( "outputf,O", boost::program_options::value< std::string >(&outputFolder), "output folder" )
( "maxnbdist,d", boost::program_options::value< float >(&maxNbDist)->implicit_value(1), "[opt] maximum dissimilarity a seed voxel tract must have to its most similar neighbor not be discarded. (0,1]." )
( "cnbhood,c", boost::program_options::value< unsigned int >(&nbLevel)->implicit_value(26), "[opt] centroid method neighborhood level. Valid values: 6, 18, 26(default), 32, 96, 124." )
( "basesize,S", boost::program_options::value< size_t >(&baseSize), "[opt] grow homogeneous base nodes (meta-leaves) of size S. (>=2)." )
( "basenum,N", boost::program_options::value< size_t >(&baseSize), "[opt] grow N homogeneous base nodes (meta-leaves). (>=10)." )
;
// Declare a group of options that will be allowed both on command line and in config file
boost::program_options::options_description configOptions( "Configuration" );
configOptions.add_options()
( "verbose,v", "[opt] verbose output." )
( "vista", "[opt] use vista file format (default is nifti)." )
( "cache-mem,m", boost::program_options::value< float >(&memory)->implicit_value(0.5), "[opt] maximum of memory (in GBytes) to use for tractogram cache memory. Default: 0.5." )
( "keep-disc,k", "[opt] keep discarded voxels data in a section of the tree file." )
( "debugout", "[opt] write additional detailed outputs meant for debug." )
( "pthreads,p", boost::program_options::value< unsigned int >(&threads), "[opt] number of processing cores to run the program in. Default: all available." )
;
// Hidden options, will be allowed both on command line and in config file, but will not be shown to the user.
boost::program_options::options_description hiddenOptions( "Hidden options" );
//hiddenOptions.add_options() ;
boost::program_options::options_description cmdlineOptions;
cmdlineOptions.add(genericOptions).add(configOptions).add(hiddenOptions);
boost::program_options::options_description configFileOptions;
configFileOptions.add(configOptions).add(hiddenOptions);
boost::program_options::options_description visibleOptions( "Allowed options" );
visibleOptions.add(genericOptions).add(configOptions);
boost::program_options::positional_options_description posOpt; //this arguments do not need to specify the option descriptor when typed in
//posOpt.add( "roi", -1);
boost::program_options::variables_map variableMap;
store(boost::program_options::command_line_parser(argc, argv).options(cmdlineOptions).positional(posOpt).run(), variableMap);
std::ifstream ifs(configFilename.c_str() );
store(parse_config_file(ifs, configFileOptions), variableMap);
notify( variableMap);
if ( variableMap.count( "help" ) )
{
std::cout << "---------------------------------------------------------------------------" << std::endl;
std::cout << std::endl;
std::cout << " Project: hClustering" << std::endl;
std::cout << std::endl;
std::cout << " Whole-Brain Connectivity-Based Hierarchical Parcellation Project" << std::endl;
std::cout << " David Moreno-Dominguez" << std::endl;
std::cout << " [email protected]" << std::endl;
std::cout << " [email protected]" << std::endl;
std::cout << " www.cbs.mpg.de/~moreno" << std::endl;
std::cout << std::endl;
std::cout << " For more reference on the underlying algorithm and research they have been used for refer to:" << std::endl;
std::cout << " - Moreno-Dominguez, D., Anwander, A., & Knösche, T. R. (2014)." << std::endl;
std::cout << " A hierarchical method for whole-brain connectivity-based parcellation." << std::endl;
std::cout << " Human Brain Mapping, 35(10), 5000-5025. doi: http://dx.doi.org/10.1002/hbm.22528" << std::endl;
std::cout << " - Moreno-Dominguez, D. (2014)." << std::endl;
std::cout << " Whole-brain cortical parcellation: A hierarchical method based on dMRI tractography." << std::endl;
std::cout << " PhD Thesis, Max Planck Institute for Human Cognitive and Brain Sciences, Leipzig." << std::endl;
std::cout << " ISBN 978-3-941504-45-5" << std::endl;
std::cout << std::endl;
std::cout << " hClustering is free software: you can redistribute it and/or modify" << std::endl;
std::cout << " it under the terms of the GNU Lesser General Public License as published by" << std::endl;
std::cout << " the Free Software Foundation, either version 3 of the License, or" << std::endl;
std::cout << " (at your option) any later version." << std::endl;
std::cout << " http://creativecommons.org/licenses/by-nc/3.0" << std::endl;
std::cout << std::endl;
std::cout << " hClustering is distributed in the hope that it will be useful," << std::endl;
std::cout << " but WITHOUT ANY WARRANTY; without even the implied warranty of" << std::endl;
std::cout << " MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the" << std::endl;
std::cout << " GNU Lesser General Public License for more details." << std::endl;
std::cout << std::endl;
std::cout << "---------------------------------------------------------------------------" << std::endl << std::endl;
std::cout << "buildrandctree" << std::endl << std::endl;
std::cout << "Build a centroid hierarchical tree from a set of artificially pre-generated set of tractograms yoielding a uniformly random similarity matrix and a seed neighborhood information voxel list." << std::endl << std::endl;
std::cout << "* Arguments:" << std::endl << std::endl;
std::cout << " --version: Program version." << std::endl << std::endl;
std::cout << " -h --help: Produce extended program help message." << std::endl << std::endl;
std::cout << " -r --roi: A text file with the seed voxel coordinates and the corresponding tractogram index (if tractogram naming is based on index rather than coordinates)." << std::endl << std::endl;
std::cout << " -I --inputf: input data folder (containing the compact tractograms)." << std::endl << std::endl;
std::cout << " -O --outputf: Output folder where tree files will be written." << std::endl << std::endl;
std::cout << "[-d --maxnbdist]: Maximum dissimilarity a seed voxel tract must have to its most similar neighbor not be discarded." << std::endl;
std::cout << " Valid values: (0,1] Use a value of 1 (default) if no discarding is desired." << std::endl << std::endl;
std::cout << "[-c --cnbhood]: Use centroid method with C neighborhood level. Valid values: 6, 18, 24(default), 32, 96, 124." << std::endl << std::endl;
std::cout << "[-S --basesize]: Merge homogeneous base nodes of size S. (mutually exclusive with -N option). Default: 0 (no homogeneous merging)." << std::endl << std::endl;
std::cout << "[-N --basenum]: Grow N homogeneous base nodes. (mutually exclusive with -S option). Default: 0 (no homogeneous merging)." << std::endl << std::endl;
std::cout << "[-v --verbose]: Verbose output (recommended)." << std::endl << std::endl;
std::cout << "[--vista]: Read/write vista (.v) files [default is nifti (.nii) and compact (.cmpct) files]." << std::endl << std::endl;
std::cout << "[-m --cache-mem]: Maximum amount of RAM memory (in GBytes) to use for temporal tractogram cache storing. Valid values [0.1,50]. Default: 0.5." << std::endl << std::endl;
std::cout << "[-k --keep-disc]: Keep discarded voxel information in a specialiced section of the tree." << std::endl << std::endl;
std::cout << "[--debugout]: Write additional detailed outputs meant to be used for debugging." << std::endl << std::endl;
std::cout << "[-p --pthreads]: Number of processing threads to run the program in parallel. Default: use all available processors." << std::endl << std::endl;
std::cout << std::endl;
std::cout << "* Usage example:" << std::endl << std::endl;
std::cout << " buildrandctree -r roi_lh.txt -I tractograms/ -O results/ -c 26 -N 1000 -k -m 2 -v " << std::endl << std::endl;
std::cout << std::endl;
std::cout << "* Outputs (in output folder defined at option -O):" << std::endl << std::endl;
std::cout << " - 'cX_bin_nmt.txt' - (where X is the neighborhood level defined at option -c) non-monotonic binary-branching hierarchical tree without tree processing (if desired use processtree command)." << std::endl;
std::cout << " - 'baselist_nmt.txt' - meta-leaves (base nodes defined by the us of option -N or -S) list with IDs corresponding to the non-monotonic tree file." << std::endl;
std::cout << " - 'success.txt' - An empty file created when the program has sucessfully exited after completion (to help for automatic re-running scripting after failure)." << std::endl;
std::cout << " - 'buildrandtree_log.txt' - A text log file containing the parameter details and in-run and completion information of the program." << std::endl;
std::cout << std::endl;
std::cout << " [extra outputs when using --debugout option)" << std::endl << std::endl;
std::cout << " - 'cX_bin_nmt_debug.txt' - version of the counterpart file without '_debug' suffix with redundant information for debugging purposes." << std::endl;
std::cout << std::endl;
exit(0);
}
if ( variableMap.count( "verbose" ) ) {
std::cout << "verbose output" << std::endl;
verbose=true;
}
if ( variableMap.count( "pthreads" ) )
{
if ( threads == 1 )
{
std::cout << "Using a single processor" << std::endl;
}
else if( threads == 0 || threads >= omp_get_num_procs() )
{
threads = omp_get_num_procs();
std::cout << "Using all available processors ( " << threads << " )." << std::endl;
}
else
{
std::cout << "Using a maximum of " << threads << " processors " << std::endl;
}
omp_set_num_threads( threads );
}
else
{
threads = omp_get_num_procs();
omp_set_num_threads( threads );
std::cout << "Using all available processors ( " << threads << " )." << std::endl;
}
if ( variableMap.count( "vista" ) )
{
if( verbose )
{
std::cout << "Using vista format" << std::endl;
}
fileManagerFactory fmf;
fmf.setVista();
niftiMode = false;
}
else
{
if( verbose )
{
std::cout << "Using nifti format" << std::endl;
}
fileManagerFactory fmf;
fmf.setNifti();
niftiMode = true;
}
if ( variableMap.count( "debugout" ) )
{
if( verbose )
{
std::cout << "Debug output files activated" << std::endl;
}
debug = true;
}
if ( variableMap.count( "version" ) )
{
std::cout << progName << ", version 2.0" << std::endl;
exit(0);
}
if ( variableMap.count( "roi" ) )
{
if( !boost::filesystem::is_regular_file( boost::filesystem::path( roiFilename ) ) )
{
std::cerr << "ERROR: roi file \"" <<roiFilename<< "\" is not a regular file" << std::endl;
std::cerr << visibleOptions << std::endl;
exit(-1);
}
else if( verbose )
{
std::cout << "Seed voxels roi file: " << roiFilename << std::endl;
}
}
else
{
std::cerr << "ERROR: no seed voxels roi file stated" << std::endl;
std::cerr << visibleOptions << std::endl;
exit(-1);
}
if( verbose )
{
std::cout << "Maximum distance to most similar neighbor: " << maxNbDist << std::endl;
}
if ( maxNbDist <= 0 || maxNbDist > 1 )
{
std::cerr << "ERROR: distance value used is out of bounds please use a value within (0,1]" << std::endl;
std::cerr << visibleOptions << std::endl;
exit(-1);
}
else if ( maxNbDist == 1 && verbose )
{
std::cout << "No neighbor distance restrictions will be applied" << std::endl;
}
else if( verbose )
{
std::cout << "Seed voxels with no neighbors with tract dissimilarity lower than " << maxNbDist << " will be discarded as outliers" << std::endl;
}
if( verbose )
{
std::cout << "Centroid neighborhood level: " << nbLevel << std::endl;
}
if ( ( nbLevel != 6 ) && ( nbLevel != 18 ) && ( nbLevel != 26 ) && ( nbLevel != 32 ) && ( nbLevel != 92 ) && ( nbLevel != 124 ) )
{
std::cerr << "ERROR: invalid nbhood level, only (6,18,26,32,92,124) are accepted" << std::endl;
std::cerr << visibleOptions << std::endl;
exit(-1);
}
if ( ( variableMap.count( "basesize" ) && variableMap.count( "basenum" ) ) )
{
std::cerr << "ERROR: options --basesize (-S) and --basenum (-N) are mutually exclusive" << std::endl;
std::cerr << visibleOptions << std::endl;
exit(-1);
}
if ( variableMap.count( "basesize" ) )
{
if( baseSize <= 1 )
{
std::cerr << "ERROR: base node (meta-leaf) size must be greater than 1" << std::endl;
std::cerr << visibleOptions << std::endl;
exit(-1);
}
else
{
if( verbose )
{
std::cout << "Initial merging stage up to homogeneous base nodes of size: " << baseSize << std::endl;
}
growType = TC_GROWSIZE;
}
}
if ( variableMap.count( "basenum" ) )
{
if( baseSize < 10 )
{
std::cerr << "ERROR: base node (meta-leaf) number must be equal or greater than 10" << std::endl;
std::cerr << visibleOptions << std::endl;
exit(-1);
}
else
{
if( verbose )
{
std::cout << "Initial merging stage up to " << baseSize << " homogeneous base nodes (meta-leaves)" << std::endl;
}
growType = TC_GROWNUM;
}
}
if( growType == TC_GROWOFF && verbose )
{
std::cout << "No homogeneous merging stage" << std::endl;
}
if ( variableMap.count( "keep-disc" ) )
{
if( verbose )
{
std::cout << "Discarded voxel coordinates will be saved in an special section fo the tree file" << std::endl;
}
keepDiscarded = true;
}
else
{
if( verbose )
{
std::cout << "Discarded voxel coordinates will not be saved" << std::endl;
}
keepDiscarded = false;
}
if ( variableMap.count( "inputf" ) )
{
if( !boost::filesystem::is_directory( boost::filesystem::path( inputFolder ) ) )
{
std::cerr << "ERROR: input seed tractogram folder \"" <<inputFolder<< "\" is not a directory" << std::endl;
std::cerr << visibleOptions << std::endl;
exit(-1);
}
else if( verbose )
{
std::cout << "Input seed tractogram folder: " << inputFolder << std::endl;
}
}
else
{
std::cerr << "ERROR: no input seed tractogram stated" << std::endl;
std::cerr << visibleOptions << std::endl;
exit(-1);
}
if ( variableMap.count( "outputf" ) )
{
if( !boost::filesystem::is_directory( boost::filesystem::path( outputFolder ) ) )
{
std::cerr << "ERROR: output folder \"" <<outputFolder<< "\" is not a directory" << std::endl;
std::cerr << visibleOptions << std::endl;
exit(-1);
}
else if( verbose )
{
std::cout << "Output folder: " << outputFolder << std::endl;
}
}
else
{
std::cerr << "ERROR: no output folder stated" << std::endl;
std::cerr << visibleOptions << std::endl;
exit(-1);
}
if ( memory < 0.1 || memory > 50)
{
std::cerr << "ERROR: cache size must be a positive float between 0.1 and 50 (GB)" << std::endl;
std::cerr << visibleOptions << std::endl;
exit(-1);
}
else if( verbose )
{
std::cout << "Tractogram cache memory: " << memory << " GBytes" << std::endl;
}
std::string logFilename(outputFolder+"/"+progName+"_log.txt" );
std::ofstream logFile(logFilename.c_str() );
if(!logFile)
{
std::cerr << "ERROR: unable to open log file: \"" <<logFilename<< "\"" << std::endl;
exit(-1);
}
logFile << "Start Time:\t" << ctime(&programStartTime) << std::endl;
logFile << "Working directory:\t" << workingDir.string() << std::endl;
logFile << "Verbose:\t" << verbose << std::endl;
logFile << "Processors used:\t" << threads << std::endl;
if( niftiMode )
{
logFile << "Using nifti file format" << std::endl;
}
else
{
logFile << "Using vista file format" << std::endl;
}
logFile << "Vista mode flag:\t" << verbose << std::endl;
logFile << "Roi file:\t" << roiFilename << std::endl;
logFile << "Max nb distance:\t" << maxNbDist << std::endl;
logFile << "Nbhood restriction level:\t" <<nbLevel<< std::endl;
switch(growType)
{
case TC_GROWOFF:
logFile << "Region growing: None" << std::endl;
break;
case TC_GROWSIZE:
logFile << "Region growing: Size: " << baseSize << std::endl;
break;
case TC_GROWNUM:
logFile << "Region growing: Number: " << baseSize << std::endl;
break;
}
logFile << "Input seed tract folder:\t" << inputFolder << std::endl;
logFile << "Output folder:\t" << outputFolder << std::endl;
logFile << "Memory cache size:\t" << memory << " GB" << std::endl;
logFile << "Debug outputr:\t" << debug << std::endl;
logFile << "-------------" << std::endl;
/////////////////////////////////////////////////////////////////
randCnbTreeBuilder builder( roiFilename, verbose );
logFile << "Roi size:\t" << builder.roiSize() << std::endl;
builder.log( &logFile );
builder.setInputFolder( inputFolder );
builder.setOutputFolder( outputFolder );
builder.setDebugOutput( debug );
builder.buildRandCentroid( nbLevel, memory, growType, baseSize, keepDiscarded );
/////////////////////////////////////////////////////////////////
// save and print total time
time_t programEndTime(time(NULL) );
int totalTime( difftime(programEndTime,programStartTime) );
std::cout << "Program Finished, total time: " << totalTime/3600 << "h " << (totalTime%3600)/60 << "' " << ((totalTime%3600)%60) << "\" " << std::endl;
logFile << "-------------" << std::endl;
logFile << "Finish Time:\t" << ctime(&programEndTime) << std::endl;
logFile << "Elapsed time : " << totalTime/3600 << "h " << (totalTime%3600)/60 << "' " << ((totalTime%3600)%60) << "\"" << std::endl;
// create file that indicates process was finished successfully
std::string successFilename(outputFolder+"/success.txt" );
std::ofstream successFile(successFilename.c_str() );
if(!successFile)
{
std::cerr << "ERROR: unable to create success file: \"" <<successFile<< "\"" << std::endl;
exit(-1);
}
successFile << "success";
// }
// catch(std::exception& e)
// {
// std::cout << e.what() << std::endl;
// return 1;
// }
return 0;
}
int main( int argc, char *argv[] )
{
// try {
time_t programStartTime(time(NULL));
boost::filesystem::path workingDir( boost::filesystem::current_path());
// ========== PROGRAM PARAMETERS ==========
std::string progName("partitiontree");
std::string configFilename("../../config/"+progName+".cfg");
unsigned int threads(0), levelDepth(3), filterRadius(0);
bool verbose(false), niftiMode( true );
// program parameters
std::string treeFilename, outputFolder;
// Declare a group of options that will be allowed only on command line
boost::program_options::options_description genericOptions("Generic options");
genericOptions.add_options()
( "version", "Program version" )
( "help,h", "Produce extended program help message" )
( "tree,t", boost::program_options::value< std::string >(&treeFilename), "file with the tree to compute partitions from")
( "outputf,O", boost::program_options::value< std::string >(&outputFolder), "output folder where partition files will be written")
( "search-depth,d", boost::program_options::value< unsigned int >(&levelDepth)->implicit_value(3), "[opt] optimal partition search depth (default = 3)")
( "filter-radius,r", boost::program_options::value< unsigned int >(&filterRadius)->implicit_value(0), "[opt] output partition filter kernel radius (default = 0 | no filtering)")
( "hoz", "[opt] obtain horizontal cut partitions (instead of Spread-Separation ones)")
( "maxgran,m", "[opt] obtain only the maximum granularity partition")
;
// Declare a group of options that will be allowed both on command line and in config file
boost::program_options::options_description configOptions("Configuration");
configOptions.add_options()
( "verbose,v", "[opt] verbose output." )
( "vista", "[opt] use vista file format (default is nifti)." )
( "pthreads,p", boost::program_options::value< unsigned int >(&threads), "[opt] number of processing threads to run the program in parallel, default: all available")
;
// Hidden options, will be allowed both on command line and in config file, but will not be shown to the user.
boost::program_options::options_description hiddenOptions("Hidden options");
//hiddenOptions.add_options() ;
boost::program_options::options_description cmdlineOptions;
cmdlineOptions.add(genericOptions).add(configOptions).add(hiddenOptions);
boost::program_options::options_description configFileOptions;
configFileOptions.add(configOptions).add(hiddenOptions);
boost::program_options::options_description visibleOptions("Allowed options");
visibleOptions.add(genericOptions).add(configOptions);
boost::program_options::positional_options_description posOpt; //this arguments do not need to specify the option descriptor when typed in
//posOpt.add("roi-file", -1);
boost::program_options::variables_map variableMap;
store(boost::program_options::command_line_parser(argc, argv).options(cmdlineOptions).positional(posOpt).run(), variableMap);
std::ifstream ifs(configFilename.c_str());
store(parse_config_file(ifs, configFileOptions), variableMap);
notify(variableMap);
if (variableMap.count("help"))
{
std::cout << "---------------------------------------------------------------------------" << std::endl;
std::cout << std::endl;
std::cout << " Project: hClustering" << std::endl;
std::cout << std::endl;
std::cout << " Whole-Brain Connectivity-Based Hierarchical Parcellation Project" << std::endl;
std::cout << " David Moreno-Dominguez" << std::endl;
std::cout << " [email protected]" << std::endl;
std::cout << " [email protected]" << std::endl;
std::cout << " www.cbs.mpg.de/~moreno" << std::endl;
std::cout << std::endl;
std::cout << " For more reference on the underlying algorithm and research they have been used for refer to:" << std::endl;
std::cout << " - Moreno-Dominguez, D., Anwander, A., & Knösche, T. R. (2014)." << std::endl;
std::cout << " A hierarchical method for whole-brain connectivity-based parcellation." << std::endl;
std::cout << " Human Brain Mapping, 35(10), 5000-5025. doi: http://dx.doi.org/10.1002/hbm.22528" << std::endl;
std::cout << " - Moreno-Dominguez, D. (2014)." << std::endl;
std::cout << " Whole-brain cortical parcellation: A hierarchical method based on dMRI tractography." << std::endl;
std::cout << " PhD Thesis, Max Planck Institute for Human Cognitive and Brain Sciences, Leipzig." << std::endl;
std::cout << " ISBN 978-3-941504-45-5" << std::endl;
std::cout << std::endl;
std::cout << " hClustering is free software: you can redistribute it and/or modify" << std::endl;
std::cout << " it under the terms of the GNU Lesser General Public License as published by" << std::endl;
std::cout << " the Free Software Foundation, either version 3 of the License, or" << std::endl;
std::cout << " (at your option) any later version." << std::endl;
std::cout << " http://creativecommons.org/licenses/by-nc/3.0" << std::endl;
std::cout << std::endl;
std::cout << " hClustering is distributed in the hope that it will be useful," << std::endl;
std::cout << " but WITHOUT ANY WARRANTY; without even the implied warranty of" << std::endl;
std::cout << " MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the" << std::endl;
std::cout << " GNU Lesser General Public License for more details." << std::endl;
std::cout << std::endl;
std::cout << "---------------------------------------------------------------------------" << std::endl << std::endl;
std::cout << "partitiontree" << std::endl << std::endl;
std::cout << "Obtain tree partitions at all granularity levels using the Spread-Separation method (finding the the partition with highest SS index at each granularity)." << std::endl;
std::cout << " Optimal SS value for each partition is searched within a defined search-depth hierarchical levels. Final partitions can be filtered with a defined kernel size." << std::endl;
std::cout << " to keep local SS maxima within that kernel. For SS index refer to (Moreno-Dominguez, 2014)" << std::endl;
std::cout << " For an interactive 3D partition management with more options please use the Hierarchcial Clustering module developed in OpenWalnut (www.openwalnut.org)." << std::endl << std::endl;
std::cout << "* Arguments:" << std::endl << std::endl;
std::cout << " --version: Program version." << std::endl << std::endl;
std::cout << " -h --help: produce extended program help message." << std::endl << std::endl;
std::cout << " -t --tree: File with the hierarchical tree to extract partitions from." << std::endl << std::endl;
std::cout << " -O --outputf: Output folder where partition files will be written." << std::endl << std::endl;
std::cout << "[-d --search-depth]: Search optimal partition for each granularity within d hierarchical levels." << std::endl;
std::cout << " A higher value will produce more optimized partition but will increase computing time." << std::endl;
std::cout << " Default: 3. Recommendened values: 3 for good quality and fast computation, 4 for enhanced quality." << std::endl << std::endl;
std::cout << "[-r --filter-radius]: Filter output partitions to keep only local SS (partition quality) maxima" << std::endl;
std::cout << " within a r-sized kernel across the granularity dimension." << std::endl << std::endl;
std::cout << "[-h --hoz]: Write horizontal cut partitions instead of SS ones (optimal partition search is still based on SS index)." << std::endl << std::endl;
std::cout << "[-m --maxgran]: Compute and write only the maximum granularity (meta-leaves) partition." << std::endl << std::endl;
std::cout << "[-v --verbose]: verbose output (recommended)." << std::endl << std::endl;
std::cout << "[--vista]: write output tree in vista coordinates (default is nifti)." << std::endl << std::endl;
std::cout << "[-p --pthreads]: number of processing threads to run the program in parallel. Default: use all available processors." << std::endl << std::endl;
std::cout << std::endl;
std::cout << "* Usage example:" << std::endl << std::endl;
std::cout << " partitiontree -t tree_lh.txt -O results/ -d 3 -r 50 -v" << std::endl << std::endl;
std::cout << std::endl;
std::cout << "* Outputs (in output folder defined at option -O):" << std::endl << std::endl;
std::cout << " (default outputs)" << std::endl;
std::cout << " - 'allSSparts_dX.txt' - (where X is the search depth level defined at parameter -d) Contains a summary of the partition information (cut value and size) for all granularities." << std::endl;
std::cout << " - 'TREE_SSparts_dX.txt' - (where TREE is the filename of the input tree defined at parameter -t) contains a copy of the original tree file with the partitions at all granularities included in the relevant fields." << std::endl;
std::cout << " - 'partitiontree_log.txt' - A text log file containing the parameter details and in-run and completion information of the program." << std::endl;
std::cout << std::endl;
std::cout << " (additional if using option -r)" << std::endl;
std::cout << " - 'filtSSparts_dX_rY.txt' - (where Y is the filter radius defined at parameter -r) Contains a summary of the resulting filtered partitions." << std::endl;
std::cout << " - 'TREE_SSparts_dX_rY.txt' - contains a copy of the original tree file with the resulting filtered partitions included in the relevant fields." << std::endl;
std::cout << std::endl;
std::cout << " (when using --hoz option, the prefix 'SS' will be replaced by 'Hoz'')" << std::endl;
std::cout << std::endl;
std::cout << " (alternative outputs when using option --maxgran)" << std::endl;
std::cout << " - 'fmaxgranPart.txt' - Contains the size information of the resulting maximal granularity partition for that tree." << std::endl;
std::cout << " - 'TREE_maxgranPart.txt' - contains a copy of the original tree file with the resulting max granularity partition included in the relevant fields." << std::endl;
std::cout << std::endl;
exit(0);
}
if (variableMap.count("version"))
{
std::cout << progName <<", version 2.0"<<std::endl;
exit(0);
}
if (variableMap.count("verbose"))
{
std::cout << "verbose output"<<std::endl;
verbose=true;
}
if (variableMap.count("pthreads"))
{
if (threads==1)
{
std::cout <<"Using a single processor"<< std::endl;
}
else if(threads==0 || threads>=omp_get_num_procs())
{
threads = omp_get_num_procs();
std::cout <<"Using all available processors ("<< threads <<")." << std::endl;
}
else
{
std::cout <<"Using a maximum of "<< threads <<" processors "<< std::endl;
}
omp_set_num_threads( threads );
}
else
{
threads = omp_get_num_procs();
omp_set_num_threads( threads );
std::cout <<"Using all available processors ("<< threads <<")." << std::endl;
}
if ( variableMap.count( "vista" ) )
{
if( verbose )
{
std::cout << "Using vista format" << std::endl;
}
fileManagerFactory fmf;
fmf.setVista();
niftiMode = false;
}
else
{
if( verbose )
{
std::cout << "Using nifti format" << std::endl;
}
fileManagerFactory fmf;
fmf.setNifti();
niftiMode = true;
}
if (variableMap.count("tree"))
{
if(!boost::filesystem::is_regular_file(boost::filesystem::path(treeFilename)))
{
std::cerr << "ERROR: tree file \""<<treeFilename<<"\" is not a regular file"<<std::endl;
std::cerr << visibleOptions << std::endl;
exit(-1);
}
std::cout << "Roi voxels file: "<< treeFilename << std::endl;
}
else
{
std::cerr << "ERROR: no tree file stated"<<std::endl;
std::cerr << visibleOptions << std::endl;
exit(-1);
}
if (variableMap.count("outputf"))
{
if(!boost::filesystem::is_directory(boost::filesystem::path(outputFolder)))
{
std::cerr << "ERROR: output folder \""<<outputFolder<<"\" is not a directory"<<std::endl;
std::cerr << visibleOptions << std::endl;
exit(-1);
}
std::cout << "Output folder: "<< outputFolder << std::endl;
}
else
{
std::cerr << "ERROR: no output folder stated"<<std::endl;
std::cerr << visibleOptions << std::endl;
exit(-1);
}
if (variableMap.count("maxgran"))
{
std::cout<<"Obtaining only max. granularity partition..."<<std::endl;
WHtree tree(treeFilename);
std::cout<<tree.getReport( false )<<std::endl;
if( tree.testRootBaseNodes() )
{
std::vector<size_t > maxpart( tree.getRootBaseNodes() );
std::vector<std::vector<size_t > > partitionVector( 1, maxpart);
std::vector<float > partitionValues(1,0);
std::cout<<"maxgranpart size: "<<std::endl<<maxpart.size()<<std::endl;
WHtreePartition partitioner(&tree);
std::string outPartFilename( outputFolder + "/maxgranPart.txt" );
partitioner.writePartitionSet( outPartFilename, partitionValues,partitionVector);
tree.insertPartitions( partitionVector, partitionValues );
std::string outTreeFilename( outputFolder + "/" + tree.getName() + "_maxgranPart" );
outTreeFilename += ( ".txt" );
tree.writeTree( outTreeFilename, niftiMode );
return 0;
}
else
{
std::cout<<"ERROR: tree does not have a maximum granularity meta-leaf partition"<<std::endl;
return(-1);
}
}
if( levelDepth > 5 )
{
std::cout << "Level depth indicated: " << levelDepth << " is too high, setting to a maximum of 5" << std::endl;
levelDepth = 5;
}
std::cout << "Using a search depth of: " << levelDepth << std::endl;
if( filterRadius > 1000 )
{
std::cout << "filter radius indicated: " << filterRadius << " is too high (max is 1000), setting to 100" << std::endl;
filterRadius = 10;
}
if( filterRadius == 0 )
{
std::cout << "using no filtering (radius 0)" << std::endl;
}
else if( filterRadius < 0 )
{
std::cout << "filter radius indicated: " << filterRadius << " must be positive. using no filtering (radius 0)" << std::endl;
filterRadius = 0;
}
else
{
std::cout << "Using a filter radius of: " << filterRadius << std::endl;
}
/////////////////////////////////////////////////////////////////
std::string logFilename(outputFolder+"/"+progName+"_log.txt");
std::ofstream logFile(logFilename.c_str());
if(!logFile) {
std::cerr << "ERROR: unable to open log file: \""<<logFilename<<"\""<<std::endl;
exit(-1);
}
logFile <<"Start Time:\t"<< ctime(&programStartTime) <<std::endl;
logFile <<"Working directory:\t"<< workingDir.string() <<std::endl;
logFile <<"Verbose:\t"<< verbose <<std::endl;
logFile <<"Tree file:\t"<< treeFilename <<std::endl;
logFile <<"Output folder:\t"<< outputFolder <<std::endl;
logFile <<"Verbose:\t"<< verbose <<std::endl;
if( niftiMode )
{
logFile << "Using nifti file format" << std::endl;
}
else
{
logFile << "Using vista file format" << std::endl;
}
WHtree tree(treeFilename);
logFile << tree.getReport( false ) <<std::endl;
std::cout<<tree.getReport( false )<<std::endl;
std::vector< float > partitionValues;
std::vector< std::vector< size_t> > partitionVector;
WHtreePartition treePartition(&tree);
std::string prefix;
if (variableMap.count("hoz"))
{
prefix = "Hoz";
std::cout <<"getting hoz partitions at all levels..." <<std::endl;
treePartition.scanHozPartitions( &partitionValues, &partitionVector );
std::cout << partitionValues.size() << " Partitions obtained, writing to file..." <<std::endl;
logFile <<"Initial partitions:\t"<< partitionValues.size() <<std::endl;
std::string outPartFilename( outputFolder + "/all" + prefix + "parts.txt" );
treePartition.writePartitionSet( outPartFilename, partitionValues, partitionVector);
tree.insertPartitions( partitionVector, partitionValues );
std::string outTreeFilename( outputFolder + "/" + tree.getName() + "_" + prefix + "parts_d" + boost::lexical_cast<std::string>(levelDepth) );
outTreeFilename += ( ".txt" );
tree.writeTree( outTreeFilename, niftiMode );
}
else
{
prefix = "SS";
std::cout <<"getting SS partitions at all levels..." <<std::endl;
treePartition.scanOptimalPartitions( levelDepth, &partitionValues, &partitionVector );
std::cout << partitionValues.size() << " Partitions obtained, writing to file..." <<std::endl;
logFile <<"Initial partitions:\t"<< partitionValues.size() <<std::endl;
std::string outPartFilename( outputFolder + "/all" + prefix + "parts_d" + boost::lexical_cast<std::string>(levelDepth) + ".txt" );
treePartition.writePartitionSet( outPartFilename, partitionValues, partitionVector);
tree.insertPartitions( partitionVector, partitionValues );
std::string outTreeFilename( outputFolder + "/" + tree.getName() + "_" + prefix + "parts_d" + boost::lexical_cast<std::string>(levelDepth) );
outTreeFilename += ( ".txt" );
tree.writeTree( outTreeFilename, niftiMode );
}
std::vector < unsigned int > filterRadii;
//filterRadii.reserve( 6 );
// filterRadii.push_back( 1 );
// filterRadii.push_back( 2 );
// filterRadii.push_back( 5 );
// filterRadii.push_back( 10 );
// filterRadii.push_back( 15 );
// filterRadii.push_back( 20 );
filterRadii.push_back( filterRadius );
for(size_t i=0; i< filterRadii.size(); ++i)
{
if( filterRadii[i] <= 0 )
{
continue;
}
std::vector< float > filtPartValues( partitionValues );
std::vector< std::vector< size_t> > filtPartVector( partitionVector );
std::cout << "Filtering with a radius of "<< filterRadii[i] << "..." <<std::endl;
treePartition.filterMaxPartitions( filterRadii[i], &filtPartValues, &filtPartVector );
std::cout << filtPartValues.size() << " Filtered partitions obtained, writing to file..." <<std::endl;
logFile <<"Filtered partitions:\t"<< filtPartValues.size() <<std::endl;
std::string outPartFilename( outputFolder + "/filt" + prefix + "parts_d" + boost::lexical_cast<std::string>(levelDepth) );
outPartFilename += ( "_r" + boost::lexical_cast<std::string>(filterRadii[i]) + ".txt" );
treePartition.writePartitionSet(outPartFilename, filtPartValues, filtPartVector);
std::cout << "Adding filtered partitions to tree and writing..." <<std::endl;
std::string outTreeFilename( outputFolder + "/" + tree.getName() + "_" + prefix + "parts_d" + boost::lexical_cast<std::string>(levelDepth) );
outTreeFilename += ( "_r" + boost::lexical_cast<std::string>(filterRadii[i]) + ".txt" );
tree.insertPartitions( filtPartVector, filtPartValues );
tree.writeTree( outTreeFilename, niftiMode );
}
/////////////////////////////////////////////////////////////////
// save and print total time
time_t programEndTime(time(NULL));
int totalTime( difftime(programEndTime,programStartTime) );
std::cout <<"Program Finished, total time: "<< totalTime/3600 <<"h "<< (totalTime%3600)/60 <<"' "<< ((totalTime%3600)%60) <<"\" "<< std::endl;
logFile <<"-------------"<<std::endl;
logFile <<"Finish Time:\t"<< ctime(&programEndTime) <<std::endl;
logFile <<"Elapsed time : "<< totalTime/3600 <<"h "<< (totalTime%3600)/60 <<"' "<< ((totalTime%3600)%60) <<"\""<< std::endl;
// }
// catch(std::exception& e)
// {
// std::cout << e.what() << std::endl;
// return 1;
// }
return 0;
}
void MainWindow::documentExport(void)
{
Canvas *currCanvas = canvas();
QString currFilename = currCanvas->filename();
currFilename.chop(4);
if (currFilename.isEmpty())
{
// Determine the working directory.
QSettings settings;
QString workingDir(QDir::homePath());
QVariant workingDirSetting =
settings.value("workingDirectory");
if (workingDirSetting.isValid())
{
workingDir = workingDirSetting.toString();
}
currFilename = workingDir + "/untitled";
}
QString filename = QFileDialog::getSaveFileName(this, tr("Export Diagram"),
currFilename, tr("SVG (*.svg);;PDF (*.pdf);;Postscript (*.ps)"));
if (filename.isEmpty())
{
return;
}
QRectF pageRect = currCanvas->pageRect();
if (pageRect.size().isEmpty())
{
// There is no page set, so use a page equal to diagram bounds
double padding = 10;
pageRect = expandRect(diagramBoundingRect(currCanvas->items()), padding);
}
QFileInfo file(filename);
if (file.suffix() == "svg")
{
QSvgGenerator generator;
generator.setFileName(filename);
QRectF targetRect(QPointF(0, 0), currCanvas->sceneRect().size());
QPointF topLeft = pageRect.topLeft() -
currCanvas->sceneRect().topLeft();
QRectF viewbox(topLeft, pageRect.size());
generator.setSize(viewbox.size().toSize());
generator.setViewBox(viewbox);
generator.setTitle(QFileInfo(filename).fileName());
generator.setDescription(tr("This file was exported from Dunnart. "
"http://www.dunnart.org/"));
QPainter painter;
if (painter.begin(&generator))
{
painter.setRenderHint(QPainter::Antialiasing);
currCanvas->setRenderingForPrinting(true);
currCanvas->render(&painter, targetRect,
currCanvas->sceneRect(),
Qt::IgnoreAspectRatio);
currCanvas->setRenderingForPrinting(false);
painter.end();
}
else
{
qDebug("Export SVG painter failed to begin.");
}
}
else
{
// Use QPrinter for PDF and PS.
QPrinter printer;
printer.setOutputFileName(filename);
printer.setPaperSize(pageRect.size(),
QPrinter::Millimeter);
QPainter painter;
if (painter.begin(&printer))
{
painter.setRenderHint(QPainter::Antialiasing);
currCanvas->setRenderingForPrinting(true);
currCanvas->render(&painter, QRectF(),
expandRect(pageRect, -3),
Qt::IgnoreAspectRatio);
currCanvas->setRenderingForPrinting(false);
}
else
{
qDebug("Export PDF/PS painter failed to begin.");
}
}
}
int main( int argc, char *argv[] )
{
// try {
time_t programStartTime(time(NULL));
boost::filesystem::path workingDir( boost::filesystem::current_path());
// ========== PROGRAM PARAMETERS ==========
std::string progName("matchpartition");
std::string configFilename("../../config/"+progName+".cfg");
// program parameters
std::string refTreeFilename, targetTreeFilename, matchTableFilename, outputFolder;
unsigned int searchDepth(1);
float lambda(0);
bool signaturePart(false), colorMatching(false), overlapPart(false), exclusive(false);
bool verbose(false), niftiMode( true );
// Declare a group of options that will be allowed only on command line
boost::program_options::options_description genericOptions("Generic options");
genericOptions.add_options()
( "version", "Program version" )
( "help,h", "Produce extended program help message" )
( "reference,r", boost::program_options::value< std::string >(&refTreeFilename), "file with reference partitioned tree" )
( "target,t", boost::program_options::value< std::string >(&targetTreeFilename), "file with target tree to be partitioned-matched" )
( "leafmatch,m", boost::program_options::value< std::string >(&matchTableFilename), "file with meta-leaves (base-nodes) matching table" )
( "outputf,O", boost::program_options::value< std::string >(&outputFolder), "output folder where partition-matched trees will be written" )
( "signature,s", boost::program_options::value< float >(&lambda), "[xor with -o and -c] Signature-based partition matching, inster lambda coefficient value" )
( "overlap,o", "[xor with -s and -c] Meta-leaf overlap-based partition matching")
( "depth,d", boost::program_options::value< unsigned int >(&searchDepth)->implicit_value(0), "[opt] partition search depth. Default: 0 (automatic partition-size based adaptive depth, recommended)")
( "justcolor,c", "[xor with -s and -o] Perform only olor matching (requires pre-computed partitions in both trees)")
( "excl,x", "[opt] color exclusively clusters that have a match, clusters without match will be white")
;
// Declare a group of options that will be allowed both on command line and in config file
boost::program_options::options_description configOptions("Configuration");
configOptions.add_options()
( "verbose,v", "[opt] verbose output." )
( "vista", "[opt] Write output tree in vista coordinates (default is nifti)." )
;
// Hidden options, will be allowed both on command line and in config file, but will not be shown to the user.
boost::program_options::options_description hiddenOptions("Hidden options");
//hiddenOptions.add_options() ;
boost::program_options::options_description cmdlineOptions;
cmdlineOptions.add(genericOptions).add(configOptions).add(hiddenOptions);
boost::program_options::options_description configFileOptions;
configFileOptions.add(configOptions).add(hiddenOptions);
boost::program_options::options_description visibleOptions("Allowed options");
visibleOptions.add(genericOptions).add(configOptions);
boost::program_options::positional_options_description posOpt; //this arguments do not need to specify the option descriptor when typed in
//posOpt.add("roi-file", -1);
boost::program_options::variables_map variableMap;
store(boost::program_options::command_line_parser(argc, argv).options(cmdlineOptions).positional(posOpt).run(), variableMap);
std::ifstream ifs(configFilename.c_str());
store(parse_config_file(ifs, configFileOptions), variableMap);
notify(variableMap);
if (variableMap.count( "help" ) )
{
std::cout << "---------------------------------------------------------------------------" << std::endl;
std::cout << std::endl;
std::cout << " Project: hClustering" << std::endl;
std::cout << std::endl;
std::cout << " Whole-Brain Connectivity-Based Hierarchical Parcellation Project" << std::endl;
std::cout << " David Moreno-Dominguez" << std::endl;
std::cout << " [email protected]" << std::endl;
std::cout << " [email protected]" << std::endl;
std::cout << " www.cbs.mpg.de/~moreno" << std::endl;
std::cout << std::endl;
std::cout << " For more reference on the underlying algorithm and research they have been used for refer to:" << std::endl;
std::cout << " - Moreno-Dominguez, D., Anwander, A., & Knösche, T. R. (2014)." << std::endl;
std::cout << " A hierarchical method for whole-brain connectivity-based parcellation." << std::endl;
std::cout << " Human Brain Mapping, 35(10), 5000-5025. doi: http://dx.doi.org/10.1002/hbm.22528" << std::endl;
std::cout << " - Moreno-Dominguez, D. (2014)." << std::endl;
std::cout << " Whole-brain cortical parcellation: A hierarchical method based on dMRI tractography." << std::endl;
std::cout << " PhD Thesis, Max Planck Institute for Human Cognitive and Brain Sciences, Leipzig." << std::endl;
std::cout << " ISBN 978-3-941504-45-5" << std::endl;
std::cout << std::endl;
std::cout << " hClustering is free software: you can redistribute it and/or modify" << std::endl;
std::cout << " it under the terms of the GNU Lesser General Public License as published by" << std::endl;
std::cout << " the Free Software Foundation, either version 3 of the License, or" << std::endl;
std::cout << " (at your option) any later version." << std::endl;
std::cout << " http://creativecommons.org/licenses/by-nc/3.0" << std::endl;
std::cout << std::endl;
std::cout << " hClustering is distributed in the hope that it will be useful," << std::endl;
std::cout << " but WITHOUT ANY WARRANTY; without even the implied warranty of" << std::endl;
std::cout << " MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the" << std::endl;
std::cout << " GNU Lesser General Public License for more details." << std::endl;
std::cout << std::endl;
std::cout << "---------------------------------------------------------------------------" << std::endl << std::endl;
std::cout << "matchpartition" << std::endl << std::endl;
std::cout << "Finds the best matching corresponding partitions in a target tree to those present in an unrelated reference tree (meta-leaf matching across these two trees must have been precomputed using comparetrees)." << std::endl;
std::cout << " Two partition matching algorithms are available: signature matching and overlap matching. Found target partitions will be color-matched as best as possible." << std::endl;
std::cout << " There is also the possibility of only color-matching predefined partitions of the target tree to predefined partitions of the reference tree." << std::endl << std::endl;
std::cout << "* Arguments:" << std::endl << std::endl;
std::cout << " --version: Program version." << std::endl << std::endl;
std::cout << " -h --help: produce extended program help message." << std::endl << std::endl;
std::cout << " -r --reference: The tree file with the reference partitioned tree." << std::endl << std::endl;
std::cout << " -t --target: The tree file with the target tree to find matching partitions in (or with partitions to be color-matched)." << std::endl << std::endl;
std::cout << " -m --leafmatch File with the meta-leaf matching information across both trees (output of comparetrees command)." << std::endl << std::endl;
std::cout << " -O --outputf: Output folder where partitioned/color matched tree files will be written." << std::endl << std::endl;
std::cout << "[-s --signature]: Signature-based partition matching, instert lambda coefficient value. [xor with -o and -c]." << std::endl;
std::cout << " In this method a pair signature matrices are computed for each reference-target partitions to find the quality of the match." << std::endl;
std::cout << " Each signature matrix defines a value for each pair of base-nodes of the tree it belongs to: 1 the base nodes are found in the same cluster, 0 if otherwise." << std::endl;
std::cout << " The higher the correlation between the reference and target-derived matrices, the best match is the target tree partition to the reference tree one." << std::endl;
std::cout << " A smart hierarchical search through possible partritions is conducted to find the one with best signature matching." << std::endl;
std::cout << " The lambda coefficient determines if and how a similar number of clusters in both partitions affects the matching quality value," << std::endl;
std::cout << " Lambda=0 -> cluster number does not affect the quality value. Lambda=1 -> cluster value similarity has as much weight as singature correlation." << std::endl << std::endl;
std::cout << "[-o --overlap]: Overlap-based partition matching. [xor with -o and -c]." << std::endl;
std::cout << " A match between two partititionsis found by iteratively matching clusters with higher base-node overlap and resolving possible ambiguities." << std::endl;
std::cout << " The matching quality between partitions is defined as the number of base-nodes pairs that are classified in the same way in both partitions" << std::endl;
std::cout << " (both in the smae cluster r both in different clusters) against the total number of pair combinations." << std::endl;
std::cout << " A smart hierarchical search through possible partritions is conducted to find the one with best signature matching." << std::endl << std::endl;
std::cout << "[-d --depth]: Partition search depth (for signature and overlap matching. A higher value will mean a more exhaustive search of the possible partitions," << std::endl;
std::cout << " but also a higher computation time, specially if the partition to be matched has a high number of clusters (>100)." << std::endl;
std::cout << " The default value (0, recommended) will adaptively give high search depth to low-cluster partitions and lower search depth to high-cluster partittions." << std::endl << std::endl;
std::cout << "[-c --justcolor]: Perform only color matching across reference and target tree parttitions (both trees need to have the same number of precompouted partitions)." << std::endl;
std::cout << " In multiple-to-one matching cases clusters from the reference tree might also be recolored to better identify matching relationships across partitions." << std::endl << std::endl;
std::cout << "[-x --excl]: Color exclusively clusters that have a match, clusters without match will be recolored white (on both reference and target trees)" << std::endl << std::endl;
std::cout << "[-v --verbose]: Verbose output (recommended)." << std::endl << std::endl;
std::cout << "[--vista]: Write output tree files in vista coordinates (default is nifti)." << std::endl << std::endl;
std::cout << std::endl;
std::cout << "* Usage example:" << std::endl << std::endl;
std::cout << " matchpartition -r refTree.txt -t targetTree.txt -m matching.txt -O results/ -s 0.5 -v" << std::endl << std::endl;
exit(0);
}
if (variableMap.count( "version" ) )
{
std::cout << progName <<", version 2.0"<<std::endl;
exit(0);
}
if ( variableMap.count( "verbose" ) )
{
std::cout << "verbose output" << std::endl;
verbose=true;
}
if ( variableMap.count( "vista" ) )
{
if( verbose )
{
std::cout << "Using vista coordinates" << std::endl;
}
fileManagerFactory fmf;
fmf.setVista();
niftiMode = false;
}
else
{
if( verbose )
{
std::cout << "Using nifti coordinates" << std::endl;
}
fileManagerFactory fmf;
fmf.setNifti();
niftiMode = true;
}
if (variableMap.count("reference"))
{
if(!boost::filesystem::is_regular_file( boost::filesystem::path( refTreeFilename ) ) )
{
std::cerr << "ERROR: reference tree file \""<<refTreeFilename<<"\" is not a regular file"<<std::endl;
std::cerr << visibleOptions << std::endl;
exit(-1);
}
std::cout << "Reference tree file: "<< refTreeFilename << std::endl;
}
else
{
std::cerr << "ERROR: no reference tree file stated"<<std::endl;
std::cerr << visibleOptions << std::endl;
exit(-1);
}
if (variableMap.count( "target" ) )
{
if(!boost::filesystem::is_regular_file(boost::filesystem::path( targetTreeFilename ) ) )
{
std::cerr << "ERROR: target tree file \""<<targetTreeFilename<<"\" is not a regular file"<<std::endl;
std::cerr << visibleOptions << std::endl;
exit(-1);
}
std::cout << "Target tree file: "<< targetTreeFilename << std::endl;
} else {
std::cerr << "ERROR: no target tree file stated"<<std::endl;
std::cerr << visibleOptions << std::endl;
exit(-1);
}
if (variableMap.count( "leafmatch" ) )
{
if(!boost::filesystem::is_regular_file(boost::filesystem::path( matchTableFilename ) ) )
{
std::cerr << "ERROR: match table file \""<<matchTableFilename<<"\" is not a regular file"<<std::endl;
std::cerr << visibleOptions << std::endl;
exit(-1);
}
std::cout << "Match table file: "<< matchTableFilename << std::endl;
}
else
{
std::cerr << "ERROR: no match Table file stated"<<std::endl;
std::cerr << visibleOptions << std::endl;
exit(-1);
}
if( variableMap.count( "signature" ) + variableMap.count( "overlap" ) + variableMap.count( "justcolor" ) > 1 )
{
std::cerr << "ERROR: multiple matching types selected, please use only one from -s, -o, -c."<<std::endl;
std::cerr << visibleOptions << std::endl;
exit(-1);
}
if (variableMap.count( "signature" ) )
{
std::cout << "Performing Signature partition matching (and color matching)" << std::endl;
std::cout <<" Using a lambda factor of "<< lambda << std::endl;
signaturePart = true;
colorMatching = true;
}
else if (variableMap.count( "overlap" ) )
{
std::cout << "Performing Overlap partition matching (and color matching): " << std::endl;
overlapPart = true;
colorMatching = true;
}
else if (variableMap.count( "justcolor" ) )
{
std::cout << "Performing only color matching: " << std::endl;
colorMatching = true;
}
else
{
std::cerr << "ERROR: no matching type selected, select signature, overlap or color matching"<<std::endl;
std::cerr << visibleOptions << std::endl;
exit(-1);
}
if (variableMap.count( "excl" ) )
{
std::cout << "Color exclusively matched clusters (unmatched clusters will be white) " << std::endl;
exclusive = true;
}
if( signaturePart || overlapPart )
{
if( searchDepth > 5 )
{
std::cout << "Level depth indicated: " << searchDepth << " is too high, setting to a maximum of 5" << std::endl;
searchDepth = 5;
}
else if ( searchDepth = 0 )
{
std::cout << "Using automatic parttion-size based adaptive search depth " << std::endl;
}
else
{
std::cout << "Using a search depth of: " << searchDepth << std::endl;
}
}
if (variableMap.count( "outputf" ) )
{
if(!boost::filesystem::is_directory(boost::filesystem::path( outputFolder ) ) )
{
std::cerr << "ERROR: output folder \""<<outputFolder<<"\" is not a directory"<<std::endl;
std::cerr << visibleOptions << std::endl;
exit(-1);
}
std::cout << "Output folder: "<< outputFolder << std::endl;
}
else
{
std::cerr << "ERROR: no output folder stated"<<std::endl;
std::cerr << visibleOptions << std::endl;
exit(-1);
}
std::string logFilename(outputFolder+"/"+progName+"_log.txt");
std::ofstream logFile(logFilename.c_str());
if(!logFile) {
std::cerr << "ERROR: unable to open log file: \""<<logFilename<<"\""<<std::endl;
exit(-1);
}
logFile <<"Start Time:\t"<< ctime(&programStartTime) <<std::endl;
logFile <<"Working directory:\t"<< workingDir.string() <<std::endl;
logFile <<"Verbose:\t"<< verbose <<std::endl;
logFile <<"Reference tree:\t"<< refTreeFilename <<std::endl;
logFile <<"Target tree:\t"<< targetTreeFilename <<std::endl;
logFile <<"Matching table:\t"<< matchTableFilename <<std::endl;
logFile <<"Output folder:\t"<< outputFolder <<std::endl;
if( niftiMode )
{
logFile << "Using nifti coordinates" << std::endl;
}
else
{
logFile << "Using vista coordinates" << std::endl;
}
logFile <<"-------------"<<std::endl;
/////////////////////////////////////////////////////////////////
WHtree refTree( refTreeFilename );
WHtree targetTree( targetTreeFilename );
if (!refTree.isLoaded() || !targetTree.isLoaded() )
{
throw std::runtime_error ("ERROR @ compareTrees(): trees are not loaded");
}
logFile <<"Reference Tree: "<< refTree.getReport(false) <<std::endl;
logFile <<"Target Tree: "<< targetTree.getReport(false) <<std::endl;
if (refTree.getDataSize() != targetTree.getDataSize() )
{
std::cerr <<"Reference Tree: "<< refTree.getReport() <<std::endl;
std::cerr <<"Target Tree: "<< targetTree.getReport() <<std::endl;
throw std::runtime_error ("ERROR @ compareTrees() datasets have different dimensions");
}
if (verbose) {
std::cout <<"Reference Tree: "<< refTree.getReport(false) <<std::endl;
std::cout <<"Target Tree: "<< targetTree.getReport(false) <<std::endl;
}
partitionMatcher matcher(&refTree,&targetTree,matchTableFilename, verbose);
std::string depthString;
if( searchDepth > 0 )
{
depthString = "_d"+string_utils::toString< unsigned int >( searchDepth ) ;
}
std::cout <<matcher.reportBaseNodes()<<std::endl;
std::string suffixPart("_pm_Signature_l" + string_utils::toString< float >( lambda ) + depthString + ".txt");
std::string suffixNew("_pm_Overlap" + depthString + ".txt");
std::string suffixColor("_colorMatch.txt");
bool refTreeColorsChanged( false );
if( signaturePart )
{
logFile << "Signature Matching" << std::endl;
logFile << "Lambda:\t" << lambda <<std::endl;
logFile << "Search depth:\t" << searchDepth <<std::endl;
matcher.findMatchingPartitions( lambda );
}
else if ( overlapPart )
{
logFile << "Overlap Matching" <<std::endl;
logFile << "Search depth:\t" << searchDepth <<std::endl;
matcher.findMatchingPartitions( -1 );
}
if( colorMatching )
{
logFile << "Color Matching" <<std::endl;
refTreeColorsChanged = matcher.matchColors( exclusive );
}
std::string refOutput;
std::string targetOutput;
if ( signaturePart )
{
targetOutput = outputFolder + "/" + targetTree.getName() + suffixPart;
}
else if ( overlapPart )
{
targetOutput = outputFolder + "/" + targetTree.getName() + suffixNew ;
}
else
{
targetOutput = outputFolder + "/" + targetTree.getName() + suffixColor;
}
if( refTreeColorsChanged )
{
refOutput = outputFolder + "/" + refTree.getName() + suffixColor;
}
else
{
refOutput = outputFolder + "/" + refTree.getName() + ".txt";
}
if( verbose )
{
std::cout << "Writing output target tree file to " << targetOutput << std::endl;
std::cout << "Writing output reference tree file to " << refOutput << std::endl;
}
targetTree.writeTree( targetOutput, niftiMode );
refTree.writeTree( refOutput, niftiMode );
logFile << "Written output target tree file to " << targetOutput << std::endl;
logFile << "Written output reference tree file to " << refOutput << std::endl;
/////////////////////////////////////////////////////////////////
// save and print total time
time_t programEndTime( time( NULL ) );
int totalTime( difftime( programEndTime, programStartTime ) );
std::cout <<"Program Finished, total time: "<< totalTime/3600 <<"h "<< (totalTime%3600)/60 <<"' "<< ((totalTime%3600)%60) <<"\" "<< std::endl;
logFile <<"-------------"<<std::endl;
logFile <<"Finish Time:\t"<< ctime(&programEndTime) <<std::endl;
logFile <<"Elapsed time : "<< totalTime/3600 <<"h "<< (totalTime%3600)/60 <<"' "<< ((totalTime%3600)%60) <<"\""<< std::endl;
// }
// catch(std::exception& e)
// {
// std::cout << e.what() << std::endl;
// return 1;
// }
return 0;
}
int main( int argc, char *argv[] )
{
// try {
time_t programStartTime(time(NULL));
boost::filesystem::path workingDir( boost::filesystem::current_path());
// ========== PROGRAM PARAMETERS ==========
std::string progName("cpcc");
std::string configFilename("../../config/"+progName+".cfg");
// program parameters
std::string treeFilename;
std::string distMatrixFolder;
unsigned int threads(0);
bool niftiMode( true );
bool verbose(false);
// Declare a group of options that will be allowed only on command line
boost::program_options::options_description genericOptions("Generic options");
genericOptions.add_options()
( "version", "Program version" )
( "help,h", "Produce extended program help message" )
( "tree,t", boost::program_options::value< std::string >(&treeFilename), "file with the hierarchical tree to compute the cpcc value from")
( "inputf,I", boost::program_options::value< std::string >(&distMatrixFolder), "Input data folder with the distance matrix files.")
;
// Declare a group of options that will be allowed both on command line and in config file
boost::program_options::options_description configOptions("Configuration");
configOptions.add_options()
( "verbose,v", "[opt] verbose output." )
( "vista", "[opt] use vista file format (default is nifti)." )
( "pthreads,p", boost::program_options::value< unsigned int >(&threads), "[opt] number of processing cores to run the program in. Default: all available." )
;
// Hidden options, will be allowed both on command line and in config file, but will not be shown to the user.
boost::program_options::options_description hiddenOptions("Hidden options");
//hiddenOptions.add_options() ;
boost::program_options::options_description cmdlineOptions;
cmdlineOptions.add(genericOptions).add(configOptions).add(hiddenOptions);
boost::program_options::options_description configFileOptions;
configFileOptions.add(configOptions).add(hiddenOptions);
boost::program_options::options_description visibleOptions("Allowed options");
visibleOptions.add(genericOptions).add(configOptions);
boost::program_options::positional_options_description posOpt; //this arguments do not need to specify the option descriptor when typed in
posOpt.add("tree", -1);
boost::program_options::variables_map variableMap;
store(boost::program_options::command_line_parser(argc, argv).options(cmdlineOptions).positional(posOpt).run(), variableMap);
std::ifstream ifs(configFilename.c_str());
store(parse_config_file(ifs, configFileOptions), variableMap);
notify(variableMap);
if (variableMap.count("help"))
{
std::cout << "---------------------------------------------------------------------------" << std::endl;
std::cout << std::endl;
std::cout << " Project: hClustering" << std::endl;
std::cout << std::endl;
std::cout << " Whole-Brain Connectivity-Based Hierarchical Parcellation Project" << std::endl;
std::cout << " David Moreno-Dominguez" << std::endl;
std::cout << " [email protected]" << std::endl;
std::cout << " [email protected]" << std::endl;
std::cout << " www.cbs.mpg.de/~moreno" << std::endl;
std::cout << std::endl;
std::cout << " For more reference on the underlying algorithm and research they have been used for refer to:" << std::endl;
std::cout << " - Moreno-Dominguez, D., Anwander, A., & Knösche, T. R. (2014)." << std::endl;
std::cout << " A hierarchical method for whole-brain connectivity-based parcellation." << std::endl;
std::cout << " Human Brain Mapping, 35(10), 5000-5025. doi: http://dx.doi.org/10.1002/hbm.22528" << std::endl;
std::cout << " - Moreno-Dominguez, D. (2014)." << std::endl;
std::cout << " Whole-brain cortical parcellation: A hierarchical method based on dMRI tractography." << std::endl;
std::cout << " PhD Thesis, Max Planck Institute for Human Cognitive and Brain Sciences, Leipzig." << std::endl;
std::cout << " ISBN 978-3-941504-45-5" << std::endl;
std::cout << std::endl;
std::cout << " hClustering is free software: you can redistribute it and/or modify" << std::endl;
std::cout << " it under the terms of the GNU Lesser General Public License as published by" << std::endl;
std::cout << " the Free Software Foundation, either version 3 of the License, or" << std::endl;
std::cout << " (at your option) any later version." << std::endl;
std::cout << " http://creativecommons.org/licenses/by-nc/3.0" << std::endl;
std::cout << std::endl;
std::cout << " hClustering is distributed in the hope that it will be useful," << std::endl;
std::cout << " but WITHOUT ANY WARRANTY; without even the implied warranty of" << std::endl;
std::cout << " MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the" << std::endl;
std::cout << " GNU Lesser General Public License for more details." << std::endl;
std::cout << std::endl;
std::cout << "---------------------------------------------------------------------------" << std::endl << std::endl;
std::cout << "cpcc" << std::endl << std::endl;
std::cout << "Compute the cophenetic correlation coefficient (Farris, 1969) of a hierarchical tree." << std::endl << std::endl;
std::cout << "* Arguments:" << std::endl << std::endl;
std::cout << " --version: Program version." << std::endl << std::endl;
std::cout << " -h --help: produce extended program help message." << std::endl << std::endl;
std::cout << " -t --tree: File with the hierarchical tree to compute cpcc from." << std::endl << std::endl;
std::cout << " -I --inputf: Input data folder containing the blocks of the precomputed tract pairwise distance matrix." << std::endl << std::endl;
std::cout << "[-v --verbose]: verbose output (recommended)." << std::endl << std::endl;
std::cout << "[--vista]: read/write vista (.v) files [default is nifti (.nii) and compact (.cmpct) files]." << std::endl << std::endl;
std::cout << "[-p --pthreads]: number of processing threads to run the program in parallel. Default: use all available processors." << std::endl << std::endl;
std::cout << std::endl;
std::cout << "* Usage example:" << std::endl << std::endl;
std::cout << " cpcc -t tree_lh.txt -I distBlocks/ -v" << std::endl << std::endl;
std::cout << std::endl;
std::cout << "* Outputs:" << std::endl << std::endl;
std::cout << " - Introduces the cpcc value in the #cpcc field of the tree file defined at option -t." << std::endl;
std::cout << std::endl;
exit(0);
}
if (variableMap.count("version")) {
std::cout << progName <<", version 2.0"<<std::endl;
exit(0);
}
if (variableMap.count("verbose")) {
std::cout << "verbose output"<<std::endl;
verbose=true;
}
if (variableMap.count("pthreads"))
{
if (threads==1)
{
std::cout <<"Using a single processor"<< std::endl;
}
else if(threads==0 || threads>=omp_get_max_threads())
{
threads = omp_get_max_threads();
std::cout <<"Using all available processors ("<< threads <<")." << std::endl;
}
else
{
std::cout <<"Using a maximum of "<< threads <<" processors "<< std::endl;
}
omp_set_num_threads( threads );
}
else
{
threads = omp_get_max_threads();
omp_set_num_threads( threads );
std::cout <<"Using all available processors ("<< threads <<")." << std::endl;
}
if (variableMap.count("tree")) {
if(!boost::filesystem::is_regular_file(boost::filesystem::path(treeFilename))) {
std::cerr << "ERROR: tree file \""<<treeFilename<<"\" is not a regular file"<<std::endl;
std::cerr << visibleOptions << std::endl;
exit(-1);
}
std::cout << "Input tree file: "<< treeFilename << std::endl;
} else {
std::cerr << "ERROR: no tree file stated"<<std::endl;
std::cerr << visibleOptions << std::endl;
exit(-1);
}
if (variableMap.count("inputf")) {
if(!boost::filesystem::is_directory(boost::filesystem::path(distMatrixFolder))) {
std::cerr << "ERROR: distance matrix folder \""<<distMatrixFolder<<"\" is not a directory"<<std::endl;
std::cerr << visibleOptions << std::endl;
exit(-1);
}
std::cout << "Distance matrix folder: "<< distMatrixFolder << std::endl;
} else {
std::cerr << "ERROR: no distance matrix folder stated"<<std::endl;
std::cerr << visibleOptions << std::endl;
exit(-1);
}
if ( variableMap.count( "vista" ) )
{
if( verbose )
{
std::cout << "Using vista format" << std::endl;
}
fileManagerFactory fmf;
fmf.setVista();
niftiMode = false;
}
else
{
if( verbose )
{
std::cout << "Using nifti format" << std::endl;
}
fileManagerFactory fmf;
fmf.setNifti();
niftiMode = true;
}
/////////////////////////////////////////////////////////////////
WHtree tree(treeFilename);
if (verbose)
{
std::cout<<tree.getReport()<<std::endl;
}
if( !tree.isLoaded() )
{
std::cerr << "Error while loading tree "<< std::endl;
exit(-1);
}
treeManager treeMngr(&tree, verbose);
treeMngr.setDistMatrixFolder(distMatrixFolder);
float cpcc(treeMngr.doCpcc());
tree.writeTree(treeFilename,niftiMode);
std::cout<<std::endl<<std::endl<<"CPCC: "<< cpcc <<std::endl<<std::endl;
/////////////////////////////////////////////////////////////////
// save and print total time
time_t programEndTime(time(NULL));
int totalTime( difftime(programEndTime,programStartTime) );
std::cout << "Program Finished, total time: " << totalTime/3600 <<"h "<< (totalTime%3600)/60 <<"' "<< ((totalTime%3600)%60) <<"\""<< std::endl;
// }
// catch(std::exception& e)
// {
// std::cout << e.what() << std::endl;
// return 1;
// }
return 0;
}
JobResult
PythonJob::exec()
{
// We assume m_scriptFile to be relative to m_workingPath.
QDir workingDir( m_workingPath );
if ( !workingDir.exists() ||
!workingDir.isReadable() )
{
return JobResult::error( tr( "Bad working directory path" ),
tr( "Working directory %1 for python job %2 is not readable." )
.arg( m_workingPath )
.arg( prettyName() ) );
}
QFileInfo scriptFI( workingDir.absoluteFilePath( m_scriptFile ) );
if ( !scriptFI.exists() ||
!scriptFI.isFile() ||
!scriptFI.isReadable() )
{
return JobResult::error( tr( "Bad main script file" ),
tr( "Main script file %1 for python job %2 is not readable." )
.arg( scriptFI.absoluteFilePath() )
.arg( prettyName() ) );
}
try
{
bp::dict scriptNamespace = helper()->createCleanNamespace();
bp::object calamaresModule = bp::import( "libcalamares" );
bp::dict calamaresNamespace = bp::extract< bp::dict >( calamaresModule.attr( "__dict__" ) );
calamaresNamespace[ "job" ] = CalamaresPython::PythonJobInterface( this );
calamaresNamespace[ "globalstorage" ] = CalamaresPython::GlobalStoragePythonWrapper(
JobQueue::instance()->globalStorage() );
bp::object execResult = bp::exec_file( scriptFI.absoluteFilePath().toLocal8Bit().data(),
scriptNamespace,
scriptNamespace );
bp::object entryPoint = scriptNamespace[ "run" ];
bp::object prettyNameFunc = scriptNamespace.get("pretty_name", bp::object());
cDebug() << "Job file" << scriptFI.absoluteFilePath();
if ( !prettyNameFunc.is_none() )
{
bp::extract< std::string > prettyNameResult( prettyNameFunc() );
if ( prettyNameResult.check() )
{
m_description = QString::fromStdString( prettyNameResult() ).trimmed();
}
if ( !m_description.isEmpty() )
{
cDebug() << "Job description from pretty_name" << prettyName() << "=" << m_description;
emit progress( 0 );
}
}
if ( m_description.isEmpty() )
{
bp::extract< std::string > entryPoint_doc_attr(entryPoint.attr( "__doc__" ) );
if ( entryPoint_doc_attr.check() )
{
m_description = QString::fromStdString( entryPoint_doc_attr() ).trimmed();
auto i_newline = m_description.indexOf('\n');
if ( i_newline > 0 )
m_description.truncate( i_newline );
cDebug() << "Job description from __doc__" << prettyName() << "=" << m_description;
emit progress( 0 );
}
}
bp::object runResult = entryPoint();
if ( runResult.is_none() )
{
return JobResult::ok();
}
else // Something happened in the Python job
{
bp::tuple resultTuple = bp::extract< bp::tuple >( runResult );
QString message = QString::fromStdString( bp::extract< std::string >( resultTuple[ 0 ] ) );
QString description = QString::fromStdString( bp::extract< std::string >( resultTuple[ 1 ] ) );
return JobResult::error( message, description );
}
}
catch ( bp::error_already_set )
{
QString msg;
if ( PyErr_Occurred() )
{
msg = helper()->handleLastError();
}
bp::handle_exception();
PyErr_Clear();
return JobResult::internalError(
tr( "Boost.Python error in job \"%1\"." ).arg( prettyName() ),
msg,
JobResult::PythonUncaughtException );
}
}
void ClientApp::OnContextCreated(CefRefPtr<CefBrowser> browser, CefRefPtr<CefFrame> frame, CefRefPtr<CefV8Context> context)
{
/**
N.B. this code is poor and needs tidying up
**/
CefRefPtr<CefCommandLine> commandLine = AppGetCommandLine();
#if defined(OS_WIN)
FilePath workingDir(commandLine->GetProgram().ToWString().c_str());
FilePath bootPath = workingDir.DirName().Append(L"webinosBoot.js");
#else
FilePath workingDir(commandLine->GetProgram());
FilePath bootPath = workingDir.DirName().Append("webinosBoot.js");
#endif
int64 bootDataSize;
if (file_util::GetFileSize(bootPath, &bootDataSize))
{
char* bootData = new char[bootDataSize+1];
file_util::ReadFile(bootPath, bootData, bootDataSize);
bootData[bootDataSize] = 0;
std::string widgetInterface;
webinos::WidgetConfig cfg;
if (cfg.LoadFromURL(frame->GetURL()))
{
std::string widgetArgs;
AppGetWidgetArgs(cfg.GetSessionId(),widgetArgs);
/*
We need to expose the w3c widget interface (http://www.w3.org/TR/widgets-apis/)
interface Widget {
readonly attribute DOMString author;
readonly attribute DOMString description;
readonly attribute DOMString name;
readonly attribute DOMString shortName;
readonly attribute DOMString version;
readonly attribute DOMString id;
readonly attribute DOMString authorEmail;
readonly attribute DOMString authorHref;
readonly attribute WidgetStorage preferences; <!-- TBD!
readonly attribute unsigned long height;
readonly attribute unsigned long width;
};
*/
std::stringstream wifStr(std::stringstream::in | std::stringstream::out);
wifStr << "\
// Widget interface\r\n\
window.widget = { \r\n\
author: \"" << cfg.author() << "\",\r\n\
description: \"" << cfg.description() << "\",\r\n\
name: \"" << cfg.name() << "\",\r\n\
shortName: \"" << cfg.shortName() << "\",\r\n\
version: \"" << cfg.version() << "\",\r\n\
id: \"" << cfg.id() << "\",\r\n\
authorEmail: \"" << cfg.authorEmail() << "\",\r\n\
authorHref: \"" << cfg.authorHref() << "\",\r\n\
preferences: {},\r\n\
bool hasRequiredProperties() const
{
return !project().empty() &&
!workingDir().empty();
}
