This library provides system-related classes, such as command line parsing, memory allocation, threading, synchronization, and timing. More...

Collaboration diagram for cmtkSystem Library:

Classes
class	cmtk::CannotBeCopied
	Base class to prevent copying of derived classes. More...
class	cmtk::CommandLine
	Command line argument parser. More...
class	cmtk::CommandLineTypeTraitsBase< T >
class	cmtk::CommandLineTypeTraits< T >
	Template for traits to handle command line arguments of different types. More...
class	cmtk::CommandLineTypeTraits< const char * >
	Inherit generic template members. More...
class	cmtk::CommandLineTypeTraits< std::string >
	Inherit generic template members. More...
class	cmtk::CommandLineTypeTraits< std::vector< std::string > >
	Inherit generic template members. More...
class	cmtk::CommandLineTypeTraits< int >
	Inherit generic template members. More...
class	cmtk::CommandLineTypeTraits< unsigned int >
	Inherit generic template members. More...
class	cmtk::CommandLineTypeTraits< short >
	Inherit generic template members. More...
class	cmtk::CommandLineTypeTraits< unsigned short >
	Inherit generic template members. More...
class	cmtk::CommandLineTypeTraits< signed char >
	Inherit generic template members. More...
class	cmtk::CommandLineTypeTraits< unsigned char >
class	cmtk::CommandLineTypeTraits< float >
	Inherit generic template members. More...
class	cmtk::CommandLineTypeTraits< double >
	Inherit generic template members. More...
class	cmtk::CommandLineTypeTraits< bool >
	Inherit generic template members. More...
class	cmtk::CompressedStream
	Stream with on-the-fly decompression. More...
class	cmtk::ConditionVariable
	Condition variable for thread synchronization. More...
class	cmtk::Console
	Standard error output console for library. More...
class	cmtk::Exception
	Exception class. More...
class	cmtk::ExitException
	Program exit exception class. More...
class	cmtk::LockingPtr< T >
	Class for mutually exclusive access to objects. More...
class	cmtk::MountPoints
	Directory translation. More...
class	cmtk::MutexLock
	Generic mutex lock. More...
class	cmtk::Progress
	Generic class for progress indication. More...
class	cmtk::SafeCounter
	Thread-safe counter. More...
class	cmtk::SmartConstPointer< T >
	Smart pointer with reference counting. More...
class	cmtk::SmartPointer< T >
	Smart pointer with reference counting. More...
class	cmtk::StackBacktrace
	Class for printing stack backtrace in the event of a crash. More...
class	cmtk::TestFunctionMap
	Map from test name to test function. More...
class	cmtk::ThreadParameterArray< TClass, TParam >
	Array of thread parameters. More...
class	cmtk::ThreadParameters< T >
	Base class for thread parameter blocks. More...
class	cmtk::ThreadPool
	Class that provides a pool of continuously running threads that can be used for reducing overhead in SMP computations. More...
class	cmtk::ThreadPool::ThreadPoolArg
	Thread function arguments: identify pool and index of thread in it. More...
class	cmtk::ThreadSemaphore
	Semaphore for thread synchronization. More...
Namespaces
namespace	cmtk::FileUtils
	Utility functions for file and directory access.
namespace	cmtk::Memory
	Memory-related helper functions.
namespace	cmtk
namespace	cmtk::Threads
	Thread-related utility functions and global configuration variables.
namespace	cmtk::Timers
	Namespace that contains functions and variables for CPU time measurements.
Defines
#define	CMTK_MAX_THREADS 256
	Maximum number of threads supported.
Typedefs
typedef SmartPointer< Self >	cmtk::ThreadPool::SmartPtr
	Smart pointer.
typedef void(*	cmtk::ThreadPool::TaskFunction )(void *const args, const size_t taskIdx, const size_t taskCnt, const size_t threadIdx, const size_t threadCont)
	Task function: this is the interface for the functions called by the pooled threads to do the actual work.
typedef int	cmtk::ThreadIDType
	Dummy definition for non-threading builds.
typedef CMTK_THREAD_RETURN_TYPE(*	cmtk::ThreadFunction )(CMTK_THREAD_ARG_TYPE)
	Type of thread function.
Functions
	cmtk::CannotBeCopied::~CannotBeCopied ()
	Default destructor.
	cmtk::CannotBeCopied::CannotBeCopied (const CannotBeCopied &)
	Undefined copy constructor.
CannotBeCopied &	cmtk::CannotBeCopied::operator= (const CannotBeCopied &)
	Undefined assignment operator.
Console &	cmtk::operator<< (Console &console, CommandLine::Exception e)
	Output of command line exception.
template<>
std::vector< std::string >	cmtk::CommandLine::Item::Convert< std::vector< std::string > > (const char *str)
	Convert string to vector.
static std::string	cmtk::CommandLineTypeTraitsBase::ValueToStringMinimal (const T *value)
	Convert a value of this type to string with minimal added markup (for XML output).
static std::string	cmtk::CommandLineTypeTraits< const char * >::ValueToString (const char const value)
	Convert a value of this type to string.
static std::string	cmtk::CommandLineTypeTraits< const char * >::ValueToStringMinimal (const char const value)
	Convert a value of this type to string with minimal added markup (for XML output).
static std::string	cmtk::CommandLineTypeTraits< std::vector< std::string > >::ValueToString (const std::vector< std::string > *value)
	Convert a value of this type to string.
static std::string	cmtk::CommandLineTypeTraits< std::vector< std::string > >::ValueToStringMinimal (const std::vector< std::string > *value)
	Convert a value of this type to string with minimal added markup (for XML output).
const char *	cmtk::cmtkWhitespaceWriteMiniXML (mxml_node_t *, int where)
int	cmtk::FileUtils::RecursiveMkPrefixDir (const char *filename, const int permissions=0755)
	Recursively create all directories on a full filename's prefix.
char *	cmtk::FileUtils::GetAbsolutePath (char absPath, const char relPath)
	Make an absolute path name from a (possibly) relative path.
int	cmtk::StrCmp (const char s1, const char s2)
	Safe string comparison.
void	cmtk::StrReplace (char &s1, const char s2)
	Replace a string.
void	cmtk::StrFree (char *const s)
	Safe deallocation of strings.
int	cmtk::StrPrefixCmp (const char s, const char prefix)
	Compare string prefix.
const char *	cmtk::StrDir (const char *path)
	Extract directory component from a complete filesystem path.
const char *	cmtk::StrFName (const char *path)
	Extract filename component from a complete filesystem path.
std::string	cmtk::StrReplace (const std::string &str, const std::map< std::string, std::string > &rules, const bool multiple=false)
	Replace string components.
	cmtk::ThreadPool::ThreadPool (const size_t nThreads=0)
	Constructor: create a pool of nThreads running threads.
	cmtk::ThreadPool::~ThreadPool ()
	Destructor: stop all running threads.
size_t	cmtk::ThreadPool::GetNumberOfThreads () const
	Return number of threads in the pool.
template<class TParam >
void	cmtk::ThreadPool::Run (TaskFunction taskFunction, std::vector< TParam > &taskParameters, const size_t numberOfTasksOverride=0)
	Run actual worker functions through running threads.
void	cmtk::ThreadPool::ThreadFunction (const size_t threadIdx)
	This function is run as a thread.
static Self &	cmtk::ThreadPool::GetGlobalThreadPool ()
	Get reference to global thread pool.
void	cmtk::ThreadPool::StartThreads ()
	Start threads for this pool.
void	cmtk::ThreadPool::EndThreads ()
	End threads for this pool.
	cmtk::CommandLine::CommandLine (const int properties=PROPS_NOXML)
	Constructor using const inputs.
	cmtk::CommandLine::~CommandLine ()
	Destructor: spit out a warning if there are unused extra arguments on the command line.
void	cmtk::CommandLine::SetDefaultInfo ()
	Set default values for meta information.
KeyActionGroupType::SmartPtr &	cmtk::CommandLine::BeginGroup (const char name, const char description)
	Begin parameter group.
void	cmtk::CommandLine::EndGroup ()
	End last parameter group.
bool	cmtk::CommandLine::Parse (const int argc, const char *argv[]) throw ( ExitException, Self::Exception )
	Parse command line.
void	cmtk::CommandLine::PrintHelp () const
	Print help text.
void	cmtk::CommandLine::PrintWiki () const
	Print help text.
template<class T >
T	cmtk::CommandLine::Item::Convert (const char *str)
	Convert function.
mxml_node_t *	cmtk::CommandLine::AddProgramInfoXML (mxml_node_t const parent, const ProgramProperties key, const char name) const
	Add program info item to XML tree.
void	cmtk::CommandLine::WriteXML () const
	Write XML self description according to Slice3 execution model.
	cmtk::CompressedStream::CompressedStream (const char *filename)
	Create stream from filename.
	cmtk::CompressedStream::~CompressedStream ()
	Dispose stream object.
bool	cmtk::CompressedStream::Open (const char *filename)
	Open new stream from filename.
void	cmtk::CompressedStream::Close ()
	Close current file stream.
bool	cmtk::CompressedStream::OpenDecompressionPipe (const char filename, const char suffix, const char command, const char compressedSuffix)
	Open decompressing pipe.
static std::string	cmtk::CompressedStream::GetBaseName (const std::string &path)
	Return base name of a path without compression suffix.
static int	cmtk::CompressedStream::Stat (const char path, struct stat const buf=NULL)
	Do stat() on compressed file.
	cmtk::CompressedStream::File::File (const char *filename)
	Open new stream from filename.
virtual void	cmtk::CompressedStream::File::Close ()
	Close current file stream.
virtual void	cmtk::CompressedStream::File::Rewind ()
	Reset read pointer to beginning of stream.
virtual int	cmtk::CompressedStream::File::Seek (const long int offset, int whence)
	Set filepointer.
virtual size_t	cmtk::CompressedStream::File::Read (void *data, size_t size, size_t count)
	Read block of data.
virtual bool	cmtk::CompressedStream::File::Get (char &c)
	Read a single character from the stream.
virtual int	cmtk::CompressedStream::File::Tell () const
	Return number of bytes read from stream.
virtual bool	cmtk::CompressedStream::File::Feof () const
	Return 1 if and only if end of file reached.
	cmtk::CompressedStream::Pipe::Pipe (const char filename, const char command)
	Open new pipe from filename.
virtual void	cmtk::CompressedStream::Pipe::Close ()
	Close current file stream.
virtual void	cmtk::CompressedStream::Pipe::Rewind ()
	Reset read pointer to beginning of stream.
virtual size_t	cmtk::CompressedStream::Pipe::Read (void *data, size_t size, size_t count)
	Read block of data.
virtual bool	cmtk::CompressedStream::Pipe::Get (char &c)
	Read a single character from the stream.
virtual int	cmtk::CompressedStream::Pipe::Tell () const
	Return number of bytes read from stream.
virtual bool	cmtk::CompressedStream::Pipe::Feof () const
	Return 1 if and only if end of file reached.
	cmtk::CompressedStream::Zlib::Zlib (const char *filename)
	Open new stream from filename.
virtual void	cmtk::CompressedStream::Zlib::Close ()
	Close current file stream.
virtual void	cmtk::CompressedStream::Zlib::Rewind ()
	Reset read pointer to beginning of stream.
virtual int	cmtk::CompressedStream::Zlib::Seek (const long int offset, int whence)
	Set filepointer.
virtual size_t	cmtk::CompressedStream::Zlib::Read (void *data, size_t size, size_t count)
	Read block of data.
virtual bool	cmtk::CompressedStream::Zlib::Get (char &c)
	Read a single character from the stream.
virtual int	cmtk::CompressedStream::Zlib::Tell () const
	Return number of bytes read from stream.
virtual bool	cmtk::CompressedStream::Zlib::Feof () const
	Return 1 if and only if end of file reached.
size_t	cmtk::Console::GetLineWidth () const
	Get terminal line width, if possible.
Console &	cmtk::Console::FormatText (const std::string &text, const size_t margin=0, const size_t width=0, const int firstLine=0)
	Format text with line breaks etc.
void	cmtk::Console::printf (const char *format,...)
	Formatted output.
void	cmtk::Console::Indent (size_t level=0)
	Perform indentation.
static const char *	cmtk::MountPoints::Translate (const char *path)
	Perform directory substitutions.
static void	cmtk::Progress::Begin (const double start, const double end, const double increment, const std::string &taskName=std::string(""))
	Set total number of steps to complete.
virtual void	cmtk::Progress::BeginVirtual (const double start, const double end, const double increment, const std::string &taskName=std::string(""))
	Set total number of steps to complete.
void	cmtk::Progress::SetProgressCurrent (const double progress)
	Set number of tasks completed.
static ResultEnum	cmtk::Progress::SetProgress (const double progress)
	Set number of tasks completed.
static void	cmtk::Progress::Done ()
	Done with progress indicator.
virtual void	cmtk::Progress::DoneVirtual ()
	Clean up progress output.
double	cmtk::Progress::Range::GetFractionComplete (const double nestedFraction=0) const
	Get complete fraction for this range.
double	cmtk::Progress::GetFractionComplete () const
	Compute current completion fraction from range stack.
const std::string	cmtk::Progress::GetCurrentTaskName () const
	Return the name of the current task (at the lowest level of nested ranges).
	cmtk::ProgressConsole::ProgressConsole (const std::string &programName=std::string(""))
	Default constructor: connect to progress indicator.
virtual	cmtk::ProgressConsole::~ProgressConsole ()
	Destructor: finish things up.
virtual ResultEnum	cmtk::ProgressConsole::UpdateProgress ()
	Output progress to console.
virtual void	cmtk::ProgressConsole::BeginVirtual (const double start, const double end, const double increment, const std::string &taskName)
	Begin a new level of progress reporting.
	cmtk::StackBacktrace::StackBacktrace ()
	Constructor: register signal handler.
static void	cmtk::StackBacktrace::PrintBacktrace (const int levels=0)
	Print current stack backtrace.
void	cmtk::ThreadParameterArray::RunInParallelAsynchronous (ThreadFunction threadCall)
	Run thread function in parallel without joining.
void	cmtk::ThreadParameterArray::JoinAsynchronousThreads ()
	Collect (join) threads previously started by RunInParallelAsynchronous.
void	cmtk::ThreadParameterArray::CancelAsynchronousThreads ()
	Cancel (terminate) threads previously started by RunInParallelAsynchronous.
void	cmtk::ThreadParameterArray::RunInParallelFIFO (ThreadFunction threadCall, const size_t numberOfThreadsTotal, const size_t firstThreadIdx=0)
	Run thread functions using a static FIFO scheduler.
int	cmtk::Threads::GetNumberOfThreads ()
	Number of threads to run in parallel.
bool	cmtk::Threads::Available ()
	Check whether this system supports threads.
int	cmtk::Threads::SetNumberOfThreads (const int numberOfThreads=0, const bool force=false)
	Set the number of threads to run in parallel.
int	cmtk::Threads::GetMaxThreads ()
	Return number of threads allowed per process on this system.
int	cmtk::Threads::GetNumberOfProcessors ()
	Return number of processors currently online.
void	cmtk::Threads::RunThreads (ThreadFunction threadCall, const unsigned numberOfThreads, void *const parameters, const size_t parameterSize)
	Specialized but more hands-on thread scheduling function.
void	cmtk::Threads::CheckEnvironment ()
	Check environment variables that control thread creation.
Variables
Console	cmtk::StdErr (std::cerr)
	Standard error output for the library.
Console	cmtk::StdOut (std::cout)
	Standard output for the library.
const char *const	cmtk::CMTK_MOUNTPOINTSVAR = "CMTK_MOUNTPOINTS"
	Name of the shell variable defining the directory translation.
const char *const	cmtk::IGS_MOUNTPOINTSVAR = "IGS_MOUNTPOINTS"
	Legacy environment variable.
static char	cmtk::StrBuffer [PATH_MAX]
size_t	cmtk::ThreadPool::ThreadPoolArg::m_Index
	Index of thread in pool.
ThreadSemaphore	cmtk::ThreadPool::m_TaskWaitingSemaphore
	Semaphore to signal running threads when tasks are waiting.
ThreadSemaphore	cmtk::ThreadPool::m_ThreadWaitingSemaphore
	Semaphore that threads use to signal when tasks they are ready for the next task.
size_t	cmtk::ThreadPool::m_NumberOfTasks
	Total number of tasks to execute.
size_t	cmtk::ThreadPool::m_NextTaskIndex
	Index of next available task.
MutexLock	cmtk::ThreadPool::m_NextTaskIndexLock
	Lock to ensure exclusive access to the task index counter.
TaskFunction	cmtk::ThreadPool::m_TaskFunction
	The current task function.
std::vector< void * >	cmtk::ThreadPool::m_TaskParameters
	Task function parameter pointers.
std::vector< Self::ThreadPoolArg >	cmtk::ThreadPool::m_ThreadArgs
	Thread function parameters.
size_t	cmtk::ThreadPool::m_NumberOfThreads
	Number of running threads.
bool	cmtk::ThreadPool::m_ThreadsRunning
	Flag whether threads for this pool are running.
bool	cmtk::ThreadPool::m_ContinueThreads
	Flag whether threads should continue or terminate.
static const ArchiveLookupEntry	cmtk::CompressedStream::ArchiveLookup []
	The suffix-to-archiver assignment table.
static char	cmtk::MountPoints::Buffer [PATH_MAX]
	Static buffer holding paths after pattern substitution.
static Self *	cmtk::Progress::ProgressInstance = 0
	Instance of a derived class that handles GUI interaction etc.
static Self	cmtk::SmartConstPointer::Null
	Null object.
static Self	cmtk::SmartPointer::Null
	Null object.
static int	cmtk::StackBacktrace::ExitCode = 1
	Exit code.
int	cmtk::Threads::NumberOfThreads = 0
	(Maximum) number of threads to run in parallel.

Detailed Description

This library provides system-related classes, such as command line parsing, memory allocation, threading, synchronization, and timing.

Define Documentation

#define CMTK_MAX_THREADS 256

Maximum number of threads supported.

This value determines the size of the statically allocated array of thread IDs. If you need more than 256 parallel threads (default), you may use -DCMTK_MAX_THREADS=

as a preprocessor switch when compiling this library.

Definition at line 81 of file cmtkThreadSystemTypes.h.

Referenced by cmtk::Threads::GetMaxThreads(), cmtk::Threads::GetNumberOfProcessors(), and cmtk::Threads::RunThreads().

Typedef Documentation

typedef SmartPointer<Self> cmtk::ThreadPool::SmartPtr [inherited]

Smart pointer.

Definition at line 114 of file cmtkThreadPool.h.

typedef void(* cmtk::ThreadPool::TaskFunction)(void *const args,const size_t taskIdx,const size_t taskCnt,const size_t threadIdx,const size_t threadCont) [inherited]

Task function: this is the interface for the functions called by the pooled threads to do the actual work.

The task function receives five parameters: a) a pointer to its parameter black, b) the index of the task, c) the number of tasks, d) the index of the thread within the pool that is calling the task, and e) the number of threads in the pool. Whereas the function should use b) and c) to determine what portion of work it needs to do, d) and e) must be used to determine, for example, what local memory should be used, if temporary storage has been allocated for each thread. Because the number of tasks typically exceeds the number of threads, this is more efficient than allocating temporary storage for each task.

Definition at line 124 of file cmtkThreadPool.h.

typedef CMTK_THREAD_RETURN_TYPE(* cmtk::ThreadFunction)(CMTK_THREAD_ARG_TYPE)

Type of thread function.

Definition at line 72 of file cmtkThreadSystemTypes.h.

typedef int cmtk::ThreadIDType

Dummy definition for non-threading builds.

Definition at line 65 of file cmtkThreadSystemTypes.h.

Function Documentation

mxml_node_t * cmtk::CommandLine::AddProgramInfoXML	(	mxml_node_t *const	parent,
		const ProgramProperties	key,
		const char *	name
	)		const `[private, inherited]`

Add program info item to XML tree.

Parameters:

parent	Parent node for new entry in XML tree.
key	Key code for program property.
name	Name of XML tag for this property.

Definition at line 47 of file cmtkCommandLineXML.cxx.

References NULL.

bool cmtk::Threads::Available ( )

Check whether this system supports threads.

Definition at line 93 of file cmtkThreads.cxx.

void cmtk::Progress::Begin	(	const double	start,
		const double	end,
		const double	increment,
		const std::string &	taskName = `std::string("")`
	)		`[static, inherited]`

Set total number of steps to complete.

Definition at line 47 of file cmtkProgress.cxx.

Referenced by cmtk::ReformatVolume::PlainReformat(), cmtk::VoxelRegistration::Register(), cmtk::ImagePairRegistration::Register(), and cmtk::ImageSymmetryPlaneCommandLineBase::Run().

CommandLine::KeyActionGroupType::SmartPtr & cmtk::CommandLine::BeginGroup	(	const char *	name,
		const char *	description
	)		`[inherited]`

Begin parameter group.

Definition at line 84 of file cmtkCommandLine.cxx.

void cmtk::Progress::BeginVirtual	(	const double	start,
		const double	end,
		const double	increment,
		const std::string &	taskName = `std::string("")`
	)		`[protected, virtual, inherited]`

Set total number of steps to complete.

Reimplemented in cmtk::QtProgress, and cmtk::ProgressConsole.

Definition at line 56 of file cmtkProgress.cxx.

void cmtk::ProgressConsole::BeginVirtual	(	const double	start,
		const double	end,
		const double	increment,
		const std::string &	taskName
	)		`[protected, virtual, inherited]`

Begin a new level of progress reporting.

Reimplemented from cmtk::Progress.

Definition at line 102 of file cmtkProgressConsole.cxx.

References cmtk::Timers::GetTimeProcess().

template<class TClass , class TParam >

void cmtk::ThreadParameterArray< TClass, TParam >::CancelAsynchronousThreads ( ) [inherited]

Cancel (terminate) threads previously started by RunInParallelAsynchronous.

Definition at line 126 of file cmtkThreadParameterArray.txx.

References cmtk::Threads::GetNumberOfThreads(), NULL, and cmtk::StdErr.

cmtk::CannotBeCopied::CannotBeCopied ( const CannotBeCopied & ) [private, inherited]

Undefined copy constructor.

void cmtk::Threads::CheckEnvironment ( )

Check environment variables that control thread creation.

Definition at line 284 of file cmtkThreads.cxx.

References cmtk::Threads::SetNumberOfThreads().

Referenced by cmtk::Threads::GetNumberOfThreads().

void cmtk::CompressedStream::Close ( ) [inherited]

Close current file stream.

Definition at line 139 of file cmtkCompressedStream.cxx.

References cmtk::CompressedStream::m_Reader, and NULL.

Referenced by cmtk::CompressedStream::Open(), cmtk::VolumeFromFile::ReadNifti(), and cmtk::CompressedStream::~CompressedStream().

void cmtk::CompressedStream::File::Close ( ) [virtual, inherited]

Close current file stream.

Implements cmtk::CompressedStream::ReaderBase.

Definition at line 56 of file cmtkCompressedStreamFile.cxx.

void cmtk::CompressedStream::Pipe::Close ( ) [virtual, inherited]

Close current file stream.

Implements cmtk::CompressedStream::ReaderBase.

Definition at line 95 of file cmtkCompressedStreamPipe.cxx.

void cmtk::CompressedStream::Zlib::Close ( ) [virtual, inherited]

Close current file stream.

Implements cmtk::CompressedStream::ReaderBase.

Definition at line 54 of file cmtkCompressedStreamZlib.cxx.

const char* cmtk::cmtkWhitespaceWriteMiniXML	(	mxml_node_t *	,
		int	where
	)

Definition at line 60 of file cmtkCommandLineXML.cxx.

References NULL.

Referenced by cmtk::CommandLine::WriteXML().

cmtk::CommandLine::CommandLine ( const int properties = PROPS_NOXML ) [inherited]

Constructor using const inputs.

Definition at line 48 of file cmtkCommandLine.cxx.

References cmtk::CommandLine::BeginGroup(), cmtk::CommandLine::m_Properties, and cmtk::CommandLine::SetDefaultInfo().

template<>

std::vector<std::string> cmtk::CommandLine::Item::Convert< std::vector< std::string > > ( const char * str ) [inline]

Convert string to vector.

Definition at line 139 of file cmtkCommandLineConvert.txx.

cmtk::CompressedStream::CompressedStream ( const char * filename ) [inherited]

Create stream from filename.

Definition at line 79 of file cmtkCompressedStream.cxx.

References cmtk::CompressedStream::Open().

const char * cmtk::CommandLine::Item::Convert< const char * > ( const char * str ) [inline, protected, inherited]

Convert function.

Convert string to string.

Convert string to signed char.

Convert string to unsigned char.

Convert string to char.

Convert string to unsigned long.

Convert string to unsigned int.

Convert string to int.

Convert string to long int.

Convert string to double.

Convert string to float.

Convert string to bool.

Definition at line 41 of file cmtkCommandLineConvert.txx.

void cmtk::Progress::Done ( ) [static, inherited]

Done with progress indicator.

Definition at line 85 of file cmtkProgress.cxx.

Referenced by cmtk::VoxelRegistration::Register(), cmtk::ImagePairRegistration::Register(), and cmtk::ImageSymmetryPlaneCommandLineBase::Run().

void cmtk::Progress::DoneVirtual ( ) [protected, virtual, inherited]

Clean up progress output.

This member function can be overriden by derived classes.

Reimplemented in cmtk::QtProgress.

Definition at line 92 of file cmtkProgress.cxx.

void cmtk::CommandLine::EndGroup ( ) [inherited]

End last parameter group.

Definition at line 93 of file cmtkCommandLine.cxx.

void cmtk::ThreadPool::EndThreads ( ) [private, inherited]

End threads for this pool.

Definition at line 129 of file cmtkThreadPool.cxx.

References cmtk::ThreadPool::m_ContinueThreads, cmtk::ThreadPool::m_NumberOfThreads, cmtk::ThreadPool::m_TaskWaitingSemaphore, cmtk::ThreadPool::m_ThreadsRunning, NULL, and cmtk::ThreadSemaphore::Post().

Referenced by cmtk::ThreadPool::~ThreadPool().

bool cmtk::CompressedStream::Zlib::Feof ( ) const [virtual, inherited]

Return 1 if and only if end of file reached.

Implements cmtk::CompressedStream::ReaderBase.

Definition at line 101 of file cmtkCompressedStreamZlib.cxx.

bool cmtk::CompressedStream::File::Feof ( ) const [virtual, inherited]

Return 1 if and only if end of file reached.

Implements cmtk::CompressedStream::ReaderBase.

Definition at line 103 of file cmtkCompressedStreamFile.cxx.

bool cmtk::CompressedStream::Pipe::Feof ( ) const [virtual, inherited]

Return 1 if and only if end of file reached.

Implements cmtk::CompressedStream::ReaderBase.

Definition at line 140 of file cmtkCompressedStreamPipe.cxx.

cmtk::CompressedStream::File::File ( const char * filename ) [inherited]

Open new stream from filename.

Definition at line 46 of file cmtkCompressedStreamFile.cxx.

References CMTK_FILE_MODE.

Console & cmtk::Console::FormatText	(	const std::string &	text,
		const size_t	margin = `0`,
		const size_t	width = `0`,
		const int	firstLine = `0`
	)		`[inherited]`

Format text with line breaks etc.

Parameters:

text	The text to format with line breaks.
margin	Left margin: this many space characters are printed at the beginning of each line.
firstLine	Relative indent of first line, i.e., firstLine = -margin means no indentation of first line.

Definition at line 73 of file cmtkConsole.cxx.

Referenced by cmtk::CommandLine::KeyToActionSingle::PrintHelp(), cmtk::CommandLine::KeyToActionEnum::PrintHelp(), and cmtk::CommandLine::PrintHelp().

bool cmtk::CompressedStream::Zlib::Get ( char & c ) [virtual, inherited]

Read a single character from the stream.

Implements cmtk::CompressedStream::ReaderBase.

Definition at line 81 of file cmtkCompressedStreamZlib.cxx.

bool cmtk::CompressedStream::File::Get ( char & c ) [virtual, inherited]

Read a single character from the stream.

Implements cmtk::CompressedStream::ReaderBase.

Definition at line 83 of file cmtkCompressedStreamFile.cxx.

bool cmtk::CompressedStream::Pipe::Get ( char & c ) [virtual, inherited]

Read a single character from the stream.

Implements cmtk::CompressedStream::ReaderBase.

Definition at line 120 of file cmtkCompressedStreamPipe.cxx.

char * cmtk::FileUtils::GetAbsolutePath	(	char *	absPath,
		const char *	relPath
	)

Make an absolute path name from a (possibly) relative path.

Definition at line 105 of file cmtkFileUtils.cxx.

Referenced by cmtk::XformIO::Write(), and cmtk::VolumeIO::Write().

std::string cmtk::CompressedStream::GetBaseName ( const std::string & path ) [static, inherited]

Return base name of a path without compression suffix.

Definition at line 191 of file cmtkCompressedStream.cxx.

References cmtk::CompressedStream::ArchiveLookup, and cmtk::CompressedStream::ArchiveLookupEntry::suffix.

Referenced by cmtk::ImagePairAffineRegistrationCommandLine::OutputResultList(), cmtk::AffineRegistrationCommandLine::OutputResultList(), and cmtk::CompressedStream::Stat().

const std::string cmtk::Progress::GetCurrentTaskName ( ) const [protected, inherited]

Return the name of the current task (at the lowest level of nested ranges).

Definition at line 117 of file cmtkProgress.cxx.

Referenced by cmtk::ProgressConsole::UpdateProgress().

double cmtk::Progress::Range::GetFractionComplete ( const double nestedFraction = 0 ) const [inherited]

Get complete fraction for this range.

Parameters:

nestedFraction For nexted ranges, this is the fraction achieved in he next level down.

Definition at line 99 of file cmtkProgress.cxx.

double cmtk::Progress::GetFractionComplete ( ) const [protected, inherited]

Compute current completion fraction from range stack.

Definition at line 105 of file cmtkProgress.cxx.

Referenced by cmtk::ProgressConsole::UpdateProgress().

ThreadPool & cmtk::ThreadPool::GetGlobalThreadPool ( ) [static, inherited]

Get reference to global thread pool.

This is shared by all functions in the process and allows re-use of the same "physical" threads for all types of computations. The thread pool itself is a local static instance within this function, thus making sure it is initialized properly (see Effective C++, 3rd, Item 4).

Definition at line 188 of file cmtkThreadPool.cxx.

Referenced by cmtk::CongealingFunctional< TXform >::Evaluate(), cmtk::EntropyMinimizationIntensityCorrectionFunctionalBase::UpdateOutputImage(), and cmtk::CongealingFunctional< TXform >::UpdateStandardDeviationByPixel().

size_t cmtk::Console::GetLineWidth ( ) const [inherited]

Get terminal line width, if possible.

Definition at line 61 of file cmtkConsole.cxx.

Referenced by cmtk::CommandLine::KeyToActionSingle::PrintHelp(), cmtk::CommandLine::KeyToActionEnum::PrintHelp(), and cmtk::CommandLine::PrintHelp().

int cmtk::Threads::GetMaxThreads ( )

Return number of threads allowed per process on this system.

Definition at line 146 of file cmtkThreads.cxx.

References CMTK_MAX_THREADS.

Referenced by cmtk::Threads::GetNumberOfThreads(), and cmtk::Threads::SetNumberOfThreads().

int cmtk::Threads::GetNumberOfProcessors ( )

Return number of processors currently online.

Definition at line 171 of file cmtkThreads.cxx.

References CMTK_MAX_THREADS, and NULL.

Referenced by cmtk::Threads::GetNumberOfThreads(), cmtk::ImagePairNonrigidRegistrationCommandLine::OutputWarp(), cmtk::ElasticRegistrationCommandLine::OutputWarp(), and cmtk::Threads::SetNumberOfThreads().

size_t cmtk::ThreadPool::GetNumberOfThreads ( ) const [inline, inherited]

Return number of threads in the pool.

Definition at line 142 of file cmtkThreadPool.h.

Referenced by cmtk::UniformDistanceMap< TDistanceDataType >::ComputeEDT(), cmtk::EntropyMinimizationIntensityCorrectionFunctional< NOrderAdd, NOrderMul >::EntropyMinimizationIntensityCorrectionFunctional(), cmtk::SplineWarpMultiChannelRegistrationFunctional< TMetricFunctional >::Evaluate(), cmtk::SplineWarpCongealingFunctional::Evaluate(), cmtk::SplineWarpMultiChannelRegistrationFunctional< TMetricFunctional >::EvaluateWithGradient(), cmtk::SplineWarpXform::GetJacobianConstraint(), cmtk::SplineWarpXform::GetJacobianFoldingConstraint(), cmtk::GroupwiseRegistrationFunctionalXformTemplate< SplineWarpXform >::InterpolateImage(), cmtk::GroupwiseRegistrationFunctionalXformTemplate< AffineXform >::InterpolateImage(), cmtk::ParallelElasticFunctional< VM >::ParallelElasticFunctional(), cmtk::UniformVolume::Resample(), cmtk::ThreadPool::ThreadPool(), cmtk::EntropyMinimizationIntensityCorrectionFunctional< NOrderAdd, NOrderMul >::UpdateBiasFieldAdd(), cmtk::EntropyMinimizationIntensityCorrectionFunctional< NOrderAdd, NOrderMul >::UpdateBiasFieldMul(), cmtk::EntropyMinimizationIntensityCorrectionFunctional< NOrderAdd, NOrderMul >::UpdateBiasFields(), and cmtk::EntropyMinimizationIntensityCorrectionFunctionalBase::UpdateOutputImage().

int cmtk::Threads::GetNumberOfThreads ( )

Number of threads to run in parallel.

Definition at line 77 of file cmtkThreads.cxx.

References cmtk::Threads::CheckEnvironment(), cmtk::Threads::GetMaxThreads(), cmtk::Threads::GetNumberOfProcessors(), and cmtk::Threads::NumberOfThreads.

Referenced by cmtk::ThreadParameterArray< TClass, TParam >::CancelAsynchronousThreads(), cmtk::SplineWarpGroupwiseRegistrationRMIFunctional::EvaluateWithGradient(), cmtk::SplineWarpCongealingFunctional::EvaluateWithGradient(), cmtk::ReformatVolume::GetTransformedReference(), cmtk::ReformatVolume::GetTransformedReferenceJacobianAvg(), cmtk::GroupwiseRegistrationFunctionalXformTemplate< TXform >::GroupwiseRegistrationFunctionalXformTemplate(), cmtk::ThreadParameterArray< TClass, TParam >::JoinAsynchronousThreads(), cmtk::ThreadPool::Run(), cmtk::ThreadParameterArray< TClass, TParam >::RunInParallel(), cmtk::ThreadParameterArray< TClass, TParam >::RunInParallelAsynchronous(), cmtk::ThreadParameterArray< TClass, TParam >::RunInParallelFIFO(), cmtk::Threads::RunThreads(), and cmtk::FilterVolume::StudholmeFilter().

void cmtk::Console::Indent ( size_t level = 0 ) [private, inherited]

Perform indentation.

Definition at line 147 of file cmtkConsole.cxx.

template<class TClass , class TParam >

void cmtk::ThreadParameterArray< TClass, TParam >::JoinAsynchronousThreads ( ) [inherited]

Collect (join) threads previously started by RunInParallelAsynchronous.

Definition at line 96 of file cmtkThreadParameterArray.txx.

References cmtk::Threads::GetNumberOfThreads(), and cmtk::StdErr.

bool cmtk::CompressedStream::Open ( const char * filename ) [inherited]

Open new stream from filename.

Definition at line 92 of file cmtkCompressedStream.cxx.

References cmtk::CompressedStream::ArchiveLookup, cmtk::CompressedStream::Close(), cmtk::CompressedStream::IsValid(), cmtk::CompressedStream::m_Compressed, cmtk::CompressedStream::m_Reader, NULL, cmtk::CompressedStream::OpenDecompressionPipe(), cmtk::CompressedStream::Stat(), cmtk::StdErr, and cmtk::CompressedStream::ArchiveLookupEntry::suffix.

Referenced by cmtk::CompressedStream::CompressedStream().

bool cmtk::CompressedStream::OpenDecompressionPipe	(	const char *	filename,
		const char *	suffix,
		const char *	command,
		const char *	compressedSuffix
	)		`[private, inherited]`

Open decompressing pipe.

A suffix is appended to the desired filename, unless the name has has already been given this suffix. Afterwards, a pipe through a user-defined command is opened.

Parameters:

filename	The name of the file to read through the pipe.
suffix	Actual suffix of the file to be read through the pipe.
command	The command to pipe the file through. This should be the name of a program that reads the file with the given name (referenced by "%s" in the command string) and writes its output to stdout.
compressedSuffix	The file suffix corresponding to input files for the given pipe command, e.g. ".gz" for gzip.

Definition at line 150 of file cmtkCompressedStream.cxx.

Referenced by cmtk::CompressedStream::Open().

Console & cmtk::operator<<	(	Console &	console,
		CommandLine::Exception	e
	)

Output of command line exception.

Definition at line 401 of file cmtkCommandLine.cxx.

References cmtk::CommandLine::Exception::Index, and cmtk::CommandLine::Exception::Message.

CannotBeCopied& cmtk::CannotBeCopied::operator= ( const CannotBeCopied & ) [private, inherited]

Undefined assignment operator.

bool cmtk::CommandLine::Parse	(	const int	argc,
		const char *	argv[]
	)		throw ( ExitException, Self::Exception ) `[inherited]`

Parse command line.

Definition at line 99 of file cmtkCommandLine.cxx.

Referenced by cmtk::AffineRegistrationCommandLine::AffineRegistrationCommandLine(), cmtk::ElasticRegistrationCommandLine::ElasticRegistrationCommandLine(), cmtk::ImagePairAffineRegistrationCommandLine::ImagePairAffineRegistrationCommandLine(), and cmtk::ImagePairNonrigidRegistrationCommandLine::ImagePairNonrigidRegistrationCommandLine().

cmtk::CompressedStream::Pipe::Pipe	(	const char *	filename,
		const char *	command
	)		`[inherited]`

Open new pipe from filename.

Definition at line 50 of file cmtkCompressedStreamPipe.cxx.

References CMTK_FILE_MODE, and cmtk::StdErr.

void cmtk::StackBacktrace::PrintBacktrace ( const int levels = 0 ) [static, inherited]

Print current stack backtrace.

Parameters:

levels Maximum number of levels to display (default: 0 = no limit).

Definition at line 67 of file cmtkStackBacktrace.cxx.

Referenced by cmtkStackBacktraceSignalHandler().

void cmtk::Console::printf	(	const char *	format,
			...
	)		`[inherited]`

Formatted output.

Definition at line 125 of file cmtkConsole.cxx.

Referenced by cmtk::VolumeFromStudy::AssembleVolume(), cmtk::VolumeFromSlices::CheckImage(), cmtk::CreateEntropyMinimizationIntensityCorrectionFunctional(), cmtk::CreateEntropyMinimizationIntensityCorrectionFunctionalDevice(), cmtk::BestDirectionOptimizer::Optimize(), cmtk::ImageSymmetryPlaneCommandLineBase::ParseCommandLine(), cmtk::ScalarImage::Print(), cmtk::Matrix4x4< Types::Coordinate >::Print(), cmtk::DataGrid::Print(), cmtk::AffineXform::Print(), cmtk::VolumeIO::Read(), cmtk::TypedStreamStudylist::Read(), cmtk::ResourceFile::Read(), cmtk::PGM::Read(), cmtk::DICOM::Read(), cmtk::ScalarImageIO::ReadAnalyze(), cmtk::VolumeFromFile::ReadAnalyzeHdr(), cmtk::VolumeIO::ReadGrid(), cmtk::VolumeFromFile::ReadNifti(), cmtk::ImageSymmetryPlaneCommandLineBase::Run(), cmtk::ThreadPool::StartThreads(), cmtk::ProgressConsole::UpdateProgress(), cmtk::SplineWarpMultiChannelRegistrationFunctional< TMetricFunctional >::UpdateTransformationFixedControlPoints(), cmtk::ResourceFile::Write(), cmtk::ScalarImageIO::WriteAnalyze(), and cmtk::VolumeFromFile::WriteAnalyzeHdr().

void cmtk::CommandLine::PrintHelp ( ) const [inherited]

Print help text.

Definition at line 220 of file cmtkCommandLine.cxx.

References cmtk::Console::FormatText(), cmtk::Console::GetLineWidth(), and cmtk::StdErr.

void cmtk::CommandLine::PrintWiki ( ) const [inherited]

Print help text.

Definition at line 326 of file cmtkCommandLine.cxx.

References cmtk::StdOut.

cmtk::ProgressConsole::ProgressConsole ( const std::string & programName = std::string("") ) [inherited]

Default constructor: connect to progress indicator.

Definition at line 47 of file cmtkProgressConsole.cxx.

References cmtk::ProgressConsole::m_InsideSlicer3, cmtk::ProgressConsole::m_ProgramName, and NULL.

size_t cmtk::CompressedStream::Zlib::Read	(	void *	data,
		size_t	size,
		size_t	count
	)		`[virtual, inherited]`

Read block of data.

Implements cmtk::CompressedStream::ReaderBase.

Definition at line 73 of file cmtkCompressedStreamZlib.cxx.

size_t cmtk::CompressedStream::File::Read	(	void *	data,
		size_t	size,
		size_t	count
	)		`[virtual, inherited]`

Read block of data.

Implements cmtk::CompressedStream::ReaderBase.

Definition at line 75 of file cmtkCompressedStreamFile.cxx.

size_t cmtk::CompressedStream::Pipe::Read	(	void *	data,
		size_t	size,
		size_t	count
	)		`[virtual, inherited]`

Read block of data.

Implements cmtk::CompressedStream::ReaderBase.

Definition at line 112 of file cmtkCompressedStreamPipe.cxx.

int cmtk::FileUtils::RecursiveMkPrefixDir	(	const char *	filename,
		const int	permissions = `0755`
	)

Recursively create all directories on a full filename's prefix.

Returns:: Zero if operation was successful, mkdir() error code otherwise.

Definition at line 80 of file cmtkFileUtils.cxx.

Referenced by cmtk::TypedStream::Open(), cmtk::FileUtils::RecursiveMkDir(), and cmtk::VolumeIO::Write().

void cmtk::CompressedStream::Zlib::Rewind ( ) [virtual, inherited]

Reset read pointer to beginning of stream.

Reimplemented from cmtk::CompressedStream::ReaderBase.

Definition at line 60 of file cmtkCompressedStreamZlib.cxx.

void cmtk::CompressedStream::File::Rewind ( ) [virtual, inherited]

Reset read pointer to beginning of stream.

Reimplemented from cmtk::CompressedStream::ReaderBase.

Definition at line 62 of file cmtkCompressedStreamFile.cxx.

void cmtk::CompressedStream::Pipe::Rewind ( ) [virtual, inherited]

Reset read pointer to beginning of stream.

Reimplemented from cmtk::CompressedStream::ReaderBase.

Definition at line 105 of file cmtkCompressedStreamPipe.cxx.

References cmtk::StdErr.

template<class TParam >

void cmtk::ThreadPool::Run	(	TaskFunction	taskFunction,
		std::vector< TParam > &	taskParameters,
		const size_t	numberOfTasksOverride = `0`
	)		`[inherited]`

Run actual worker functions through running threads.

Parameters:

taskFunction	Pointer to task function.
taskParameters	Vector of task parameter blocks, one per task.
numberOfTasksOverride	This can be used to run a smaller number of tasks than taskParameters.size(), which is useful to allow re-use of larger, allocated vector.

Definition at line 42 of file cmtkThreadPool.txx.

References cmtk::Threads::GetNumberOfThreads(), and cmtk::StdErr.

Referenced by cmtk::UniformDistanceMap< TDistanceDataType >::ComputeEDT(), cmtk::SplineWarpMultiChannelRegistrationFunctional< TMetricFunctional >::Evaluate(), cmtk::SplineWarpCongealingFunctional::Evaluate(), cmtk::GroupwiseRegistrationRMIFunctional< TXform >::Evaluate(), cmtk::CongealingFunctional< TXform >::Evaluate(), cmtk::SplineWarpMultiChannelRegistrationFunctional< TMetricFunctional >::EvaluateWithGradient(), cmtk::ParallelElasticFunctional< VM >::EvaluateWithGradient(), cmtk::SplineWarpXform::GetJacobianConstraint(), cmtk::SplineWarpXform::GetJacobianFoldingConstraint(), cmtk::GroupwiseRegistrationFunctionalXformTemplate< SplineWarpXform >::InterpolateImage(), cmtk::GroupwiseRegistrationFunctionalXformTemplate< AffineXform >::InterpolateImage(), cmtk::GroupwiseRegistrationFunctionalXformTemplate< TXform >::InterpolateImage(), cmtk::UniformVolume::Resample(), cmtk::EntropyMinimizationIntensityCorrectionFunctional< NOrderAdd, NOrderMul >::UpdateBiasFieldAdd(), cmtk::EntropyMinimizationIntensityCorrectionFunctional< NOrderAdd, NOrderMul >::UpdateBiasFieldMul(), cmtk::EntropyMinimizationIntensityCorrectionFunctional< NOrderAdd, NOrderMul >::UpdateBiasFields(), cmtk::EntropyMinimizationIntensityCorrectionFunctionalBase::UpdateOutputImage(), and cmtk::CongealingFunctional< TXform >::UpdateStandardDeviationByPixel().

template<class TClass , class TParam >

void cmtk::ThreadParameterArray< TClass, TParam >::RunInParallelAsynchronous ( ThreadFunction threadCall ) [inherited]

Run thread function in parallel without joining.

Definition at line 45 of file cmtkThreadParameterArray.txx.

References cmtk::Threads::GetNumberOfThreads(), NULL, and cmtk::StdErr.

template<class TClass , class TParam >

void cmtk::ThreadParameterArray< TClass, TParam >::RunInParallelFIFO	(	ThreadFunction	threadCall,
		const size_t	numberOfThreadsTotal,
		const size_t	firstThreadIdx = `0`
	)		`[inherited]`

Run thread functions using a static FIFO scheduler.

Definition at line 158 of file cmtkThreadParameterArray.txx.

References cmtk::Threads::GetNumberOfThreads(), and NULL.

Referenced by cmtk::SplineWarpGroupwiseRegistrationRMIFunctional::EvaluateWithGradient().

void cmtk::Threads::RunThreads	(	ThreadFunction	threadCall,
		const unsigned	numberOfThreads,
		void *const	parameters,
		const size_t	parameterSize
	)

Specialized but more hands-on thread scheduling function.

Parameters:

threadCall	Thread function to be called.
numberOfThreads	Number of parallel threads. This parameter must not exceed the number of threads set using and returned by SetNumberOfThreads.
parameters	Pointer to an array of parameter blocks for all parallel threads.
parameterSize	Size in bytes of each thread parameter block in the array pointed to by the previous parameter.

Definition at line 193 of file cmtkThreads.cxx.

References CMTK_MAX_THREADS, cmtk::Threads::GetNumberOfThreads(), and NULL.

Referenced by cmtk::ReformatVolume::GetTransformedReference(), cmtk::ReformatVolume::GetTransformedReferenceJacobianAvg(), cmtk::ThreadParameterArray< TClass, TParam >::RunInParallel(), and cmtk::Threads::RunThreads().

int cmtk::CompressedStream::Zlib::Seek	(	const long int	offset,
		int	whence
	)		`[virtual, inherited]`

Set filepointer.

If the object represents a pipe with on-the-fly decompression, only the set mode "SEEK_CUR" is supported and will be simulated by successive reading of 8kB data blocks from the pipe.

Parameters:

offset	Offset the file pointer is set to, depending on the value of whence.
whence	File pointer set mode as defined for fseek.

Reimplemented from cmtk::CompressedStream::ReaderBase.

Definition at line 67 of file cmtkCompressedStreamZlib.cxx.

int cmtk::CompressedStream::File::Seek	(	const long int	offset,
		int	whence
	)		`[virtual, inherited]`

Set filepointer.

If the object represents a pipe with on-the-fly decompression, only the set mode "SEEK_CUR" is supported and will be simulated by successive reading of 8kB data blocks from the pipe.

Parameters:

offset	Offset the file pointer is set to, depending on the value of whence.
whence	File pointer set mode as defined for fseek.

Reimplemented from cmtk::CompressedStream::ReaderBase.

Definition at line 69 of file cmtkCompressedStreamFile.cxx.

void cmtk::CommandLine::SetDefaultInfo ( ) [private, inherited]

Set default values for meta information.

Definition at line 72 of file cmtkCommandLine.cxx.

References cmtk::CommandLine::m_ProgramInfo, cmtk::CommandLine::PRG_ACKNL, cmtk::CommandLine::PRG_CATEG, cmtk::CommandLine::PRG_CNTRB, cmtk::CommandLine::PRG_DOCUM, cmtk::CommandLine::PRG_LCNSE, and cmtk::CommandLine::PRG_VERSN.

Referenced by cmtk::CommandLine::CommandLine().

int cmtk::Threads::SetNumberOfThreads	(	const int	numberOfThreads = `0`,
		const bool	force = `false`
	)

Set the number of threads to run in parallel.

If the given parameter is less than or equal to zero, the number of threads is set to equal the number of currently available CPUs. This also applies when this function is called without any parameter.

Parameters:

numberOfThreads	Number of parallel threads to run. This is a maximum value. Particular tasks may execute with less parallel threads than this value.
force	If this flag is off (default), then the number of parallel threads is limited by the number of available CPUs on the current host. If the flag is true, the limitation is not entirely lifted, but the number of threads is limited by the maximum number of threads that can be created by a process on the current operating system.

Returns:: The actual number of threads that the library was set to.

Definition at line 122 of file cmtkThreads.cxx.

References cmtk::Threads::GetMaxThreads(), cmtk::Threads::GetNumberOfProcessors(), and cmtk::Threads::NumberOfThreads.

Referenced by cmtk::Threads::CheckEnvironment().

Progress::ResultEnum cmtk::Progress::SetProgress ( const double progress ) [static, inherited]

Set number of tasks completed.

Definition at line 73 of file cmtkProgress.cxx.

Referenced by cmtk::ReformatVolume::GetTransformedReferenceGrey(), cmtk::ReformatVolume::GetTransformedReferenceJacobianAvgThread(), cmtk::ReformatVolume::GetTransformedReferenceLabel(), cmtk::ReformatVolume::PlainReformat(), cmtk::VoxelRegistration::Register(), cmtk::ImagePairRegistration::Register(), and cmtk::ImageSymmetryPlaneCommandLineBase::Run().

void cmtk::Progress::SetProgressCurrent ( const double progress ) [inherited]

Set number of tasks completed.

Definition at line 62 of file cmtkProgress.cxx.

cmtk::StackBacktrace::StackBacktrace ( ) [inherited]

Constructor: register signal handler.

Definition at line 50 of file cmtkStackBacktrace.cxx.

References cmtkStackBacktraceSignalHandler(), and NULL.

void cmtk::ThreadPool::StartThreads ( ) [private, inherited]

Start threads for this pool.

Definition at line 65 of file cmtkThreadPool.cxx.

References cmtkThreadPoolThreadFunction(), cmtk::ThreadPool::m_NumberOfThreads, cmtk::ThreadPool::m_ThreadArgs, cmtk::ThreadPool::m_ThreadsRunning, NULL, cmtk::Console::printf(), and cmtk::StdErr.

int cmtk::CompressedStream::Stat	(	const char *	path,
		struct stat *const	buf = `NULL`
	)		`[static, inherited]`

Do stat() on compressed file.

Returns:: -1 if the file does not exist; 0 if the file exists under the given name; 1 if the file exists with an additional suffix corresponding to one of the supported compression schemes, e.g., ".gz"; 2 if the file exists with both its plain name AND at least one compressed suffix. The last case indicates a potential consistency problem because it is not clear, which file should be read.

Definition at line 210 of file cmtkCompressedStream.cxx.

References cmtk::CompressedStream::ArchiveLookup, cmtk::CompressedStream::GetBaseName(), and cmtk::CompressedStream::ArchiveLookupEntry::suffix.

Referenced by cmtk::CompressedStream::Open().

int cmtk::StrCmp	(	const char *	s1,
		const char *	s2
	)

Safe string comparison.

This function is a wrapper for the standard library's "strcmp" function. This wrapper is safe in that it accepts any combination of NULL and non-NULL pointers to both arguments.

Returns:: 0 if the strings pointed to by "s1" and "s2" are equal, a value greater than zero if s1 is greater than s2, and a value smaller than zero if s1 is smaller than s2. NULL pointers are considered smaller than any other string except the NULL pointer itself.

Definition at line 51 of file cmtkStrUtility.cxx.

References NULL.

Referenced by cmtk::TypedStreamStudylist::Read().

const char * cmtk::StrDir ( const char * path )

Extract directory component from a complete filesystem path.

Parameters:

path	A complete filesystem path.

Returns:: A pointer to a buffer containing the directory component of 'path' as a null-terminated string. This is a static buffer that is only guaranteed to remain unchanged until the next call to one of the functions in the library.

Definition at line 88 of file cmtkStrUtility.cxx.

References cmtk::StrBuffer.

const char * cmtk::StrFName ( const char * path )

Extract filename component from a complete filesystem path.

Parameters:

path	A complete filesystem path.

Returns:: A pointer to a buffer containing the filename component of 'path' as a null-terminated string. This is a static buffer that is only guaranteed to remain unchanged until the next call to one of the functions in the library.

Definition at line 108 of file cmtkStrUtility.cxx.

References cmtk::StrBuffer.

void cmtk::StrFree ( char *const s )

Safe deallocation of strings.

The memory pointed to by "s" is freed if "s" is non-NULL. Otherwise, nothing is done.

Definition at line 75 of file cmtkStrUtility.cxx.

Referenced by cmtk::StrReplace().

int cmtk::StrPrefixCmp	(	const char *	s,
		const char *	prefix
	)

Compare string prefix.

This function tests whether a given string contains another string as its intial character sequence.

Parameters:

s	The string.
prefix	The initial sequence to be tested.

Returns:: A non-zero value is returned if and only if the string 's' starts with the string 'prefix'.

Definition at line 80 of file cmtkStrUtility.cxx.

std::string cmtk::StrReplace	(	const std::string &	str,
		const std::map< std::string, std::string > &	rules,
		const bool	multiple = `false`
	)

Replace string components.

Todo:: This is highly unsafe, since we're not checking for infinite loops and the likes. We should really work on this sometimes... or be REALLY carefull.

Definition at line 124 of file cmtkStrUtility.cxx.

void cmtk::StrReplace	(	char *&	s1,
		const char *	s2
	)

Replace a string.

The null-terminated string "s2" is duplicated and replaces the string "s1". If "s1" is non-NULL when this function is called, the memory pointed to by it is freed first. If "s2" is NULL, "s1" is set to NULL, too.

Definition at line 66 of file cmtkStrUtility.cxx.

References NULL, and cmtk::StrFree().

int cmtk::CompressedStream::Zlib::Tell ( ) const [virtual, inherited]

Return number of bytes read from stream.

Implements cmtk::CompressedStream::ReaderBase.

Definition at line 95 of file cmtkCompressedStreamZlib.cxx.

int cmtk::CompressedStream::File::Tell ( ) const [virtual, inherited]

Return number of bytes read from stream.

Implements cmtk::CompressedStream::ReaderBase.

Definition at line 97 of file cmtkCompressedStreamFile.cxx.

int cmtk::CompressedStream::Pipe::Tell ( ) const [virtual, inherited]

Return number of bytes read from stream.

Implements cmtk::CompressedStream::ReaderBase.

Definition at line 134 of file cmtkCompressedStreamPipe.cxx.

void cmtk::ThreadPool::ThreadFunction ( const size_t threadIdx ) [inherited]

This function is run as a thread.

Parameters:

threadIdx Index of the actual thread in the pool.

Definition at line 157 of file cmtkThreadPool.cxx.

References cmtk::MutexLock::Lock(), cmtk::ThreadPool::m_ContinueThreads, cmtk::ThreadPool::m_NextTaskIndex, cmtk::ThreadPool::m_NextTaskIndexLock, cmtk::ThreadPool::m_NumberOfTasks, cmtk::ThreadPool::m_NumberOfThreads, cmtk::ThreadPool::m_TaskFunction, cmtk::ThreadPool::m_TaskParameters, cmtk::ThreadPool::m_TaskWaitingSemaphore, cmtk::ThreadPool::m_ThreadWaitingSemaphore, cmtk::ThreadSemaphore::Post(), cmtk::MutexLock::Unlock(), and cmtk::ThreadSemaphore::Wait().

cmtk::ThreadPool::ThreadPool ( const size_t nThreads = 0 ) [inherited]

Constructor: create a pool of nThreads running threads.

Parameters:

nThreads Number of threads to create for this pool. By default, the number of threads created is the current number of available threads, i.e., typically the number of CPUs minus the number of currently running threads, if any.

Definition at line 43 of file cmtkThreadPool.cxx.

References cmtk::ThreadPool::GetNumberOfThreads(), cmtk::ThreadPool::m_NumberOfThreads, and cmtk::ThreadPool::m_ThreadArgs.

const char * cmtk::MountPoints::Translate ( const char * path ) [static, inherited]

Perform directory substitutions.

Parameters:

path	The original path before substitions.

Returns:: A pointer to a static buffer holding the path after all substitions have been done. The buffer is guaranteed to remain unchanged until and only until the next time Translate() is called.

See also:: CMTK_MOUNTPOINTSVAR

Definition at line 49 of file cmtkMountPoints.cxx.

References cmtk::CMTK_MOUNTPOINTSVAR, cmtk::IGS_MOUNTPOINTSVAR, and NULL.

Referenced by cmtk::AffineRegistrationCommandLine::AffineRegistrationCommandLine(), and cmtk::ImagePairAffineRegistrationCommandLine::ImagePairAffineRegistrationCommandLine().

Progress::ResultEnum cmtk::ProgressConsole::UpdateProgress ( ) [virtual, inherited]

Output progress to console.

Implements cmtk::Progress.

Definition at line 75 of file cmtkProgressConsole.cxx.

References cmtk::Progress::GetCurrentTaskName(), cmtk::Progress::GetFractionComplete(), cmtk::ProgressConsole::m_InsideSlicer3, cmtk::Progress::OK, cmtk::Console::printf(), and cmtk::StdErr.

static std::string cmtk::CommandLineTypeTraits< std::vector< std::string > >::ValueToString ( const std::vector< std::string > * value ) [inline, static, inherited]

Convert a value of this type to string.

Reimplemented from cmtk::CommandLineTypeTraitsBase< std::vector< std::string > >.

Definition at line 135 of file cmtkCommandLineTypeTraits.h.

static std::string cmtk::CommandLineTypeTraits< const char * >::ValueToString ( const char *const * value ) [inline, static, inherited]

Convert a value of this type to string.

Reimplemented from cmtk::CommandLineTypeTraitsBase< const char * >.

Definition at line 91 of file cmtkCommandLineTypeTraits.h.

static std::string cmtk::CommandLineTypeTraits< std::vector< std::string > >::ValueToStringMinimal ( const std::vector< std::string > * value ) [inline, static, inherited]

Convert a value of this type to string with minimal added markup (for XML output).

Reimplemented from cmtk::CommandLineTypeTraitsBase< std::vector< std::string > >.

Definition at line 144 of file cmtkCommandLineTypeTraits.h.

static std::string cmtk::CommandLineTypeTraits< const char * >::ValueToStringMinimal ( const char *const * value ) [inline, static, inherited]

Convert a value of this type to string with minimal added markup (for XML output).

Reimplemented from cmtk::CommandLineTypeTraitsBase< const char * >.

Definition at line 101 of file cmtkCommandLineTypeTraits.h.

template<class T>

static std::string cmtk::CommandLineTypeTraitsBase< T >::ValueToStringMinimal ( const T * value ) [inline, static, inherited]

Convert a value of this type to string with minimal added markup (for XML output).

Reimplemented in cmtk::CommandLineTypeTraits< const char * >, and cmtk::CommandLineTypeTraits< std::vector< std::string > >.

Definition at line 56 of file cmtkCommandLineTypeTraits.h.

void cmtk::CommandLine::WriteXML ( ) const [inherited]

Write XML self description according to Slice3 execution model.

See also:

Definition at line 78 of file cmtkCommandLineXML.cxx.

References cmtk::cmtkWhitespaceWriteMiniXML().

cmtk::CompressedStream::Zlib::Zlib ( const char * filename ) [inherited]

Open new stream from filename.

Definition at line 44 of file cmtkCompressedStreamZlib.cxx.

References CMTK_FILE_MODE.

cmtk::CannotBeCopied::~CannotBeCopied ( ) [inline, protected, inherited]

Default destructor.

Definition at line 55 of file cmtkCannotBeCopied.h.

cmtk::CommandLine::~CommandLine ( ) [inherited]

Destructor: spit out a warning if there are unused extra arguments on the command line.

Definition at line 58 of file cmtkCommandLine.cxx.

References cmtk::CommandLine::ArgC, cmtk::CommandLine::ArgV, cmtk::CommandLine::Index, and cmtk::StdErr.

cmtk::CompressedStream::~CompressedStream ( ) [inherited]

Dispose stream object.

Definition at line 86 of file cmtkCompressedStream.cxx.

References cmtk::CompressedStream::Close().

cmtk::ProgressConsole::~ProgressConsole ( ) [virtual, inherited]

Destructor: finish things up.

Definition at line 62 of file cmtkProgressConsole.cxx.

References cmtk::Timers::GetTimeProcess(), cmtk::ProgressConsole::m_InsideSlicer3, cmtk::ProgressConsole::m_ProgramName, and cmtk::ProgressConsole::m_TimeAtStart.

cmtk::ThreadPool::~ThreadPool ( ) [inherited]

Destructor: stop all running threads.

Definition at line 122 of file cmtkThreadPool.cxx.

References cmtk::ThreadPool::EndThreads().

Variable Documentation

const CompressedStream::ArchiveLookupEntry cmtk::CompressedStream::ArchiveLookup [static, private, inherited]

Initial value:

 {








  {".Z",    "gunzip -c %s"},
  {".gz",   "gzip -cd %s"},
  {".bz",   "bzip -Q -cd %s"},
  {".bz2",  "bzip2 -cd %s"},
  {".lzma", "lzma -cd %s"},
  {".xz",   "xz -cd %s"},

  { NULL,   NULL} 
}

The suffix-to-archiver assignment table.

Definition at line 197 of file cmtkCompressedStream.h.

Referenced by cmtk::CompressedStream::GetBaseName(), cmtk::CompressedStream::Open(), and cmtk::CompressedStream::Stat().

char cmtk::MountPoints::Buffer [static, private, inherited]

Static buffer holding paths after pattern substitution.

Definition at line 89 of file cmtkMountPoints.h.

const char* const cmtk::CMTK_MOUNTPOINTSVAR = "CMTK_MOUNTPOINTS"

Name of the shell variable defining the directory translation.

This variable can be set to contain a list of substitution rules. Every ruls has the form "target=source", where all appearances of "source" are to be replaced by "target" in all filesystem paths. Several of these rules may be concatenated by "," -- an example is "j:=/cdrom,k:=/home". This results in all paths relative to "/cdrom" being relative to "j:" after substituion. The same holds for "k:" and "/home". This example could be used to read data on a PC mounting Unix filesystems to network drives. Conversely, the Unix box would define "/cdrom=j:,/home=k:" in order to be able to read data written by this PC.