Display an image in an external viewer (Fiji by default) More...

#include <sitkImageViewer.h>

Collaboration diagram for itk::simple::ImageViewer:

Public Member Functions
void	Execute (const Image &image)
	Launch the viewing application to display the given image. More...

const std::string &	GetApplication () const
	Get the full path to the viewing application used in the command string. More...

const std::string &	GetCommand () const

virtual std::string	GetName () const

	ImageViewer ()

void	SetApplication (const std::string &app, const std::string &command="%a %f")
	Set the full path to the viewing application used in the command string. More...

void	SetCommand (const std::string &command)
	Set the command string used to launch the viewing application. More...

std::string	ToString () const
	Print ourself out to a string. More...


void	SetFileExtension (const std::string &ext)
	Set/Get file extension of the temporary image file (default='.nii') More...

const std::string &	GetFileExtension () const
	Set/Get file extension of the temporary image file (default='.nii') More...


void	SetTitle (const std::string &t)
	Set/Get Title string on the ImageJ window. More...

const std::string &	GetTitle () const
	Set/Get Title string on the ImageJ window. More...

Static Public Member Functions

static void	SetGlobalDefaultSearchPath (const std::vector< std::string > &path)
	Set/Get the search path used to find the viewing application. More...

static const std::vector< std::string > &	GetGlobalDefaultSearchPath ()
	Set/Get the search path used to find the viewing application. More...


static void	SetGlobalDefaultExecutableNames (const std::vector< std::string > &names)
	Set/Get name list used to find the viewing application. More...

static const std::vector< std::string > &	GetGlobalDefaultExecutableNames ()
	Set/Get name list used to find the viewing application. More...


static void	SetGlobalDefaultFileExtension (const std::string &ext)
	Set/Get the default file extension. More...

static const std::string &	GetGlobalDefaultFileExtension ()
	Set/Get the default file extension. More...


static void	SetGlobalDefaultApplication (const std::string &app)
	Set/Get the default application used in the command string. More...

static const std::string &	GetGlobalDefaultApplication ()
	Set/Get the default application used in the command string. More...


static void	SetGlobalDefaultDebug (const bool dbg)
	Set/Get Debug flag. More...

static bool	GetGlobalDefaultDebug ()
	Set/Get Debug flag. More...

static void	SetGlobalDefaultDebugOn ()
	Set/Get Debug flag. More...

static void	SetGlobalDefaultDebugOff ()
	Set/Get Debug flag. More...


static void	SetProcessDelay (const unsigned int delay)
	Set/Get Process delay, the wait time after launching the viewing application. More...

static unsigned int	GetProcessDelay ()
	Set/Get Process delay, the wait time after launching the viewing application. More...

Static Private Member Functions
static std::string	FindViewingApplication ()

static void	initializeDefaults ()

Private Attributes
std::string	m_Application

std::string	m_CustomCommand

std::string	m_FileExtension

std::string	m_Title

std::string	m_ViewCommand

Static Private Attributes
static bool	m_GlobalAreDefaultsInitialized

static std::string	m_GlobalDefaultApplication

static bool	m_GlobalDefaultDebug

static std::vector< std::string >	m_GlobalDefaultExecutableNames

static std::string	m_GlobalDefaultFileExtension

static std::vector< std::string >	m_GlobalDefaultSearchPath

static std::string	m_GlobalDefaultViewCommand

static unsigned int	m_GlobalProcessDelay

static int	m_GlobalViewerImageCount

Detailed Description

Display an image in an external viewer (Fiji by default)

The ImageViewer class displays an image with an external image display application. By default the class will search for a Fiji ( https://fiji.sc ) executable. The image is written out to a temporary file and then passed to the application.

When SimpleITK is first invoked the following environment variables are queried to set up the external viewer:

SITK_SHOW_EXTENSION: file format extension of the temporary image file. The default is '.mha', the MetaIO file format.

SITK_SHOW_COMMAND: The user can specify an application other than Fiji to view images.

These environment variables are only checked at SimpleITK's launch.

Definition at line 50 of file sitkImageViewer.h.

Constructor & Destructor Documentation

itk::simple::ImageViewer::ImageViewer ( )

Member Function Documentation

void itk::simple::ImageViewer::Execute ( const Image & image )

Launch the viewing application to display the given image.

static std::string itk::simple::ImageViewer::FindViewingApplication ( )

staticprivate

const std::string& itk::simple::ImageViewer::GetApplication ( ) const

Get the full path to the viewing application used in the command string.

const std::string& itk::simple::ImageViewer::GetCommand ( ) const

const std::string& itk::simple::ImageViewer::GetFileExtension ( ) const

Set/Get file extension of the temporary image file (default='.nii')

If the viewing application is Fiji, the default image format is MetaIO, '.mha'.

If the viewing application is ImageJ, the default image format is NifTi, '.nii'. This is because by default ImageJ does not come with the MetaIO plugin.

static const std::string& itk::simple::ImageViewer::GetGlobalDefaultApplication ( )

static

Set/Get the default application used in the command string.

static bool itk::simple::ImageViewer::GetGlobalDefaultDebug ( )

static

Set/Get Debug flag.

Turning on/off the Debug flag produces output showing the command string used to launch the viewing application.

static const std::vector<std::string>& itk::simple::ImageViewer::GetGlobalDefaultExecutableNames ( )

static

Set/Get name list used to find the viewing application.

static const std::string& itk::simple::ImageViewer::GetGlobalDefaultFileExtension ( )

static

Set/Get the default file extension.

The file extension determines the image file type used when writing out the temporary image file.

static const std::vector<std::string>& itk::simple::ImageViewer::GetGlobalDefaultSearchPath ( )

static

Set/Get the search path used to find the viewing application.

virtual std::string itk::simple::ImageViewer::GetName ( ) const

inlinevirtual

Return the user readable name of the class

Definition at line 57 of file sitkImageViewer.h.

static unsigned int itk::simple::ImageViewer::GetProcessDelay ( )

static

Set/Get Process delay, the wait time after launching the viewing application.

On Windows the delay is in seconds, default=1sec. On Mac/Linux the delay is in milli-seconds, default=500ms.

const std::string& itk::simple::ImageViewer::GetTitle ( ) const

Set/Get Title string on the ImageJ window.

static void itk::simple::ImageViewer::initializeDefaults ( )

staticprivate

void itk::simple::ImageViewer::SetApplication	(	const std::string &	app,
		const std::string &	command = `"%a %f"`
	)

Set the full path to the viewing application used in the command string.

The SetApplication method expects a full path name.

Using this method overrides the default application search.

By default, when this method is called, the command string is set to "%a %f" which simply means the application path followed by the temporary image file.

void itk::simple::ImageViewer::SetCommand ( const std::string & command )

Set the command string used to launch the viewing application.

This command string may include the following tokens:

'a' for the image viewing application (Fiji by default)
'f' for SimpleITK's temporary image file

For example, the default command string on Linux systems is:

%a -o %f

After token substitution it may become:

/opt/Fiji.app/ImageJ-linux64 -o /tmp/Temp-65535-0.mha

For another example, the default command string on Mac OS X is:

open -a %a -n --args -eval \'open(\"%f\"); rename(\"%t\"); \'

After token substitution the string may become:

open -a /Applications/Fiji.app -n --args -eval 'open("/tmp/TempFile-29696-0.mha"); rename("/tmp/TempFile-29696-0.mha");'

The string after '-eval' is an ImageJ macro the opens the file and sets the title of the window.

If the 'f' token is not found in the command string, the temporary file name is automatically appended to the command argument list.

Note: Using the ImageViewer::SetCommand method overrides the default command and/or the SITK_SHOW_COMMAND environment variable.

void itk::simple::ImageViewer::SetFileExtension ( const std::string & ext )

Set/Get file extension of the temporary image file (default='.nii')

If the viewing application is Fiji, the default image format is MetaIO, '.mha'.

If the viewing application is ImageJ, the default image format is NifTi, '.nii'. This is because by default ImageJ does not come with the MetaIO plugin.

static void itk::simple::ImageViewer::SetGlobalDefaultApplication ( const std::string & app )

static

Set/Get the default application used in the command string.

static void itk::simple::ImageViewer::SetGlobalDefaultDebug ( const bool dbg )

static

Set/Get Debug flag.

Turning on/off the Debug flag produces output showing the command string used to launch the viewing application.

static void itk::simple::ImageViewer::SetGlobalDefaultDebugOff ( )

static

Set/Get Debug flag.

Turning on/off the Debug flag produces output showing the command string used to launch the viewing application.

static void itk::simple::ImageViewer::SetGlobalDefaultDebugOn ( )

static

Set/Get Debug flag.

Turning on/off the Debug flag produces output showing the command string used to launch the viewing application.

static void itk::simple::ImageViewer::SetGlobalDefaultExecutableNames ( const std::vector< std::string > & names )

static

Set/Get name list used to find the viewing application.

static void itk::simple::ImageViewer::SetGlobalDefaultFileExtension ( const std::string & ext )

static

Set/Get the default file extension.

The file extension determines the image file type used when writing out the temporary image file.

static void itk::simple::ImageViewer::SetGlobalDefaultSearchPath ( const std::vector< std::string > & path )

static

Set/Get the search path used to find the viewing application.

static void itk::simple::ImageViewer::SetProcessDelay ( const unsigned int delay )

static

Set/Get Process delay, the wait time after launching the viewing application.

On Windows the delay is in seconds, default=1sec. On Mac/Linux the delay is in milli-seconds, default=500ms.

void itk::simple::ImageViewer::SetTitle ( const std::string & t )

Set/Get Title string on the ImageJ window.

std::string itk::simple::ImageViewer::ToString ( ) const

Print ourself out to a string.

Member Data Documentation

std::string itk::simple::ImageViewer::m_Application

private

Definition at line 221 of file sitkImageViewer.h.

std::string itk::simple::ImageViewer::m_CustomCommand

private

Definition at line 219 of file sitkImageViewer.h.

std::string itk::simple::ImageViewer::m_FileExtension

private

Definition at line 223 of file sitkImageViewer.h.

bool itk::simple::ImageViewer::m_GlobalAreDefaultsInitialized

staticprivate

Definition at line 204 of file sitkImageViewer.h.

std::string itk::simple::ImageViewer::m_GlobalDefaultApplication

staticprivate

Definition at line 213 of file sitkImageViewer.h.

bool itk::simple::ImageViewer::m_GlobalDefaultDebug

staticprivate

Definition at line 216 of file sitkImageViewer.h.

std::vector<std::string> itk::simple::ImageViewer::m_GlobalDefaultExecutableNames

staticprivate

Definition at line 208 of file sitkImageViewer.h.

std::string itk::simple::ImageViewer::m_GlobalDefaultFileExtension

staticprivate

Definition at line 212 of file sitkImageViewer.h.

std::vector<std::string> itk::simple::ImageViewer::m_GlobalDefaultSearchPath

staticprivate

Definition at line 207 of file sitkImageViewer.h.

std::string itk::simple::ImageViewer::m_GlobalDefaultViewCommand

staticprivate

Definition at line 211 of file sitkImageViewer.h.

unsigned int itk::simple::ImageViewer::m_GlobalProcessDelay

staticprivate

Definition at line 209 of file sitkImageViewer.h.

int itk::simple::ImageViewer::m_GlobalViewerImageCount

staticprivate

Definition at line 203 of file sitkImageViewer.h.

std::string itk::simple::ImageViewer::m_Title

private

Definition at line 225 of file sitkImageViewer.h.

std::string itk::simple::ImageViewer::m_ViewCommand

private

Definition at line 218 of file sitkImageViewer.h.

The documentation for this class was generated from the following file:

sitkImageViewer.h

Public Member Functions

Static Public Member Functions

Static Private Member Functions

Private Attributes

Static Private Attributes

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation