The interface for the DICOM plugin for milxQt. More...

#include <milxQtDICOMPlugin.h>

Inheritance diagram for milxQtDICOMPlugin:

Public Types
typedef itk::GDCMImageIO	ImageIOType

typedef itk::MetaDataDictionary	DictionaryType

typedef itk::MetaDataObject< std::string >	MetaDataStringType

Public Slots
virtual void	loadExtension ()
	Load the extension. [Implement this in your plugin].

virtual void	update ()
	Update the plugin. [Implement this in your plugin]. More...

virtual void	preStartTasks ()
	Tasks to complete before running or starting the thread. [Implement this].

virtual void	postStartTasks ()
	Tasks to complete after running or starting the thread. [Implement this].

void	viewTags ()
	View DICOM tags of image series in the manager. More...

void	openSeries ()
	Open DICOM image series. More...

void	openStructureSet ()
	Open DICOM RT image series. More...

void	convert ()
	Convert a DICOM series (or a path to a number of series) to Nifti (*.nii.gz) images. More...

void	anonymize ()

void	showRSFileDialog ()

void	showInputFileDialog ()

void	showRTInputFileDialog ()

void	showOutputFileDialog ()

void	showRTOutputFileDialog ()

void	showInputFileDialogAnonymize ()

void	showOutputFileDialogAnonymize ()

void	affectValues ()
	Function called when the wizard for anonymization is validated It will verify that everything is in order and set a boolean value to true if yes.

bool	anonymizeDicomImage (const std::string &input, const QString &subject_output_folder, const QString &rel_dir, unsigned int index_subject, unsigned int index_dicom, bool &isFirst)
	Function used to anonymize a single dicom image. More...

void	makeFilename (const QString &path, ImageIOType::Pointer gdcmImageIO, unsigned int index, std::string &filename, unsigned int index_subject)
	Small helper to make filename from dicom tags. More...

void	removeForbiddenChar (std::string &str, char *charsToRemove)

void	writeLog (QString &filename, std::string &output)

void	getTagValue (ImageIOType::Pointer gdcmImageIO, const std::string &tag, std::string &tag_value)
	Retrieve tag value fromt he gdcmImageIO object. More...

virtual void	loadExtension ()

virtual void	update ()

virtual void	preStartTasks ()

virtual void	postStartTasks ()

void	convert ()

void	anonymize ()

virtual void	loadExtension ()

virtual void	update ()

virtual void	preStartTasks ()

virtual void	postStartTasks ()

void	convert ()

void	anonymize ()

void	showInputFileDialog ()

void	showOutputFileDialog ()

Public Slots inherited from milxQtPluginInterface
virtual void	loadExtension ()=0
	Load the extension. [Implement this in your plugin].

virtual void	update ()=0
	Update the plugin. [Implement this in your plugin]. More...

virtual void	preStartTasks ()=0
	Tasks to complete before running or starting the thread. [Implement this].

virtual void	postStartTasks ()=0
	Tasks to complete after running or starting the thread. [Implement this].

Public Member Functions
	milxQtDICOMPlugin (QObject *theParent=0)
	Default destructor. More...

virtual QString	name ()
	Get the Name of the plugin. [Implement this in your plugin].

virtual bool	hasOpenSupport ()
	Does the plugin support opening files? [Implement this in your plugin].

virtual QString	openFileSupport ()
	Get the file support string for opening (extension wildcard list). [Implement this in your plugin].

virtual QStringList	openExtensions ()
	Get a list of supported file format extensions. [Implement this in your plugin].

virtual bool	hasSaveSupport ()
	Does the plugin support opening files? [Implement this in your plugin].

virtual QString	saveFileSupport ()
	Get the file support string for saving (extension wildcard list). [Implement this in your plugin].

virtual QStringList	saveExtensions ()
	Get a list of supported file format extensions. [Implement this in your plugin].

virtual bool	hasCollectionSupport ()
	Does the plugin support collections (PolyData collection etc.). [Implement this in your plugin].

virtual void	SetInputCollection (vtkPolyDataCollection *collection, QStringList &filenames)
	Pass a collection to internal plugin class. [Implement this in your plugin].

virtual void	open (QString filename)
	Open the file using the plugin. [Implement this in your plugin].

virtual void	save (QString filename)
	Save the result as a file using the plugin. [Implement this in your plugin].

virtual milxQtRenderWindow *	genericResult ()
	Get the generic result, which is a milxQtRenderWindow. The result can then be displayed in milxQtMain etc. [Implement this in your plugin].

virtual milxQtModel *	modelResult ()
	Get the model result. The result can then be displayed in milxQtMain etc. [Implement this in your plugin].

virtual milxQtImage *	imageResult ()
	Get the image result. The result can then be displayed in milxQtMain etc.[Implement this in your plugin].

virtual QDockWidget *	dockWidget ()
	Return the dock widget (if one is provided by plugin). [Implement this in your plugin].

virtual Qt::DockWidgetArea	dockDefaultArea ()
	Return the default dock widget area (if one is provided by plugin). [Implement this in your plugin].

virtual bool	isPluginWindow (QWidget *window)
	Is the window provided a plugin generated window? In this case a milxQtShapeModel window. [Implement this in your plugin].

	milxQtDICOMPlugin (QObject *theParent=0)

virtual QString	name ()
	Get the Name of the plugin. [Implement this in your plugin].

virtual bool	hasOpenSupport ()
	Does the plugin support opening files? [Implement this in your plugin].

virtual QString	openFileSupport ()
	Get the file support string for opening (extension wildcard list). [Implement this in your plugin].

virtual QStringList	openExtensions ()
	Get a list of supported file format extensions. [Implement this in your plugin].

virtual bool	hasSaveSupport ()
	Does the plugin support opening files? [Implement this in your plugin].

virtual QString	saveFileSupport ()
	Get the file support string for saving (extension wildcard list). [Implement this in your plugin].

virtual QStringList	saveExtensions ()
	Get a list of supported file format extensions. [Implement this in your plugin].

virtual bool	hasCollectionSupport ()
	Does the plugin support collections (PolyData collection etc.). [Implement this in your plugin].

virtual void	SetInputCollection (vtkPolyDataCollection *collection, QStringList &filenames)
	Pass a collection to internal plugin class. [Implement this in your plugin].

virtual void	open (QString filename)
	Open the file using the plugin. [Implement this in your plugin].

virtual void	save (QString filename)
	Save the result as a file using the plugin. [Implement this in your plugin].

virtual milxQtRenderWindow *	genericResult ()
	Get the generic result, which is a milxQtRenderWindow. The result can then be displayed in milxQtMain etc. [Implement this in your plugin].

virtual milxQtModel *	modelResult ()
	Get the model result. The result can then be displayed in milxQtMain etc. [Implement this in your plugin].

virtual milxQtImage *	imageResult ()
	Get the image result. The result can then be displayed in milxQtMain etc.[Implement this in your plugin].

virtual QDockWidget *	dockWidget ()
	Return the dock widget (if one is provided by plugin). [Implement this in your plugin].

virtual Qt::DockWidgetArea	dockDefaultArea ()
	Return the default dock widget area (if one is provided by plugin). [Implement this in your plugin].

virtual bool	isPluginWindow (QWidget *window)
	Is the window provided a plugin generated window? In this case a milxQtShapeModel window. [Implement this in your plugin].

	milxQtDICOMPlugin (QObject *theParent=0)

virtual QString	name ()
	Get the Name of the plugin. [Implement this in your plugin].

virtual bool	hasOpenSupport ()
	Does the plugin support opening files? [Implement this in your plugin].

virtual QString	openFileSupport ()
	Get the file support string for opening (extension wildcard list). [Implement this in your plugin].

virtual QStringList	openExtensions ()
	Get a list of supported file format extensions. [Implement this in your plugin].

virtual bool	hasSaveSupport ()
	Does the plugin support opening files? [Implement this in your plugin].

virtual QString	saveFileSupport ()
	Get the file support string for saving (extension wildcard list). [Implement this in your plugin].

virtual QStringList	saveExtensions ()
	Get a list of supported file format extensions. [Implement this in your plugin].

virtual bool	hasCollectionSupport ()
	Does the plugin support collections (PolyData collection etc.). [Implement this in your plugin].

virtual void	SetInputCollection (vtkPolyDataCollection *collection, QStringList &filenames)
	Pass a collection to internal plugin class. [Implement this in your plugin].

virtual void	open (QString filename)
	Open the file using the plugin. [Implement this in your plugin].

virtual void	save (QString filename)
	Save the result as a file using the plugin. [Implement this in your plugin].

virtual milxQtRenderWindow *	genericResult ()
	Get the generic result, which is a milxQtRenderWindow. The result can then be displayed in milxQtMain etc. [Implement this in your plugin].

virtual milxQtModel *	modelResult ()
	Get the model result. The result can then be displayed in milxQtMain etc. [Implement this in your plugin].

virtual milxQtImage *	imageResult ()
	Get the image result. The result can then be displayed in milxQtMain etc.[Implement this in your plugin].

virtual QDockWidget *	dockWidget ()
	Return the dock widget (if one is provided by plugin). [Implement this in your plugin].

virtual Qt::DockWidgetArea	dockDefaultArea ()
	Return the default dock widget area (if one is provided by plugin). [Implement this in your plugin].

virtual bool	isPluginWindow (QWidget *window)
	Is the window provided a plugin generated window? In this case a milxQtShapeModel window. [Implement this in your plugin].

Public Member Functions inherited from milxQtPluginInterface
	milxQtPluginInterface (QObject *theParent=0)
	Default destructor.

void	setFileName (const QString filename)
	Set the Name of the data. [Don't Reimplement this]. More...

void	setConsole (milxQtConsole *con)
	Set console to be used by plugins for output. More...

bool	isThreaded ()
	Is the plugin threaded? [Don't Reimplement this].

bool	isDockable ()
	Is the plugin a dock window? [Don't Reimplement this].

bool	isConsole ()
	Is the plugin a console dock window? If so, it will be added to the console dock window. [Don't Reimplement this].

bool	isExtension ()
	Is the plugin an extension? [Don't Reimplement this].

QList< QAction * >	addToFileMenu ()
	Actions to add to the file or context menu. [Don't Reimplement this].

QList< QMenu * >	addToMenuBar ()
	Menus to add to the menu bar. [Don't Reimplement this].

Protected Member Functions
void	createActions ()

void	createMenu ()

void	createWizard ()

void	createRTWizard ()

void	createConnections ()

void	createWizardAnonymise ()

void	createActions ()

void	createMenu ()

void	createConnections ()

void	createActions ()

void	createMenu ()

void	createWizard ()

void	createConnections ()

Static Protected Member Functions
static void	trim (std::string &str)

template<class TImage >
static void	resetImage (typename itk::SmartPointer< TImage > imageSlice)

template<class TImage , class TSliceType >
static void	mergeImages (typename itk::SmartPointer< TSliceType > tempSlice, typename itk::SmartPointer< TImage > finalImage, int iRequiredSlice)

Protected Attributes
QPointer< milxQtMain >	MainWindow

QMenu *	menuDICOM
	DICOM menu.

QAction *	actionOpenSeries
	open series action

QAction *	actionTags
	open series action

QAction *	actionConvertStructure
	convert RT action

QAction *	actionConvert
	convert action

QAction *	actionAnonymize
	Anonymize action.

QWizard	wizard

QWizard	wizardRT

QWizard	wizardAnonymize

QString	inputDirectoryname

QLineEdit *	txtInputName

QString	outputDirectoryname

QLineEdit *	txtOutputName

QString	inputRTDirectoryname

QLineEdit *	txtRTInputName

QString	outputRTDirectoryname

QLineEdit *	txtRTOutputName

QString	rsFilename

QLineEdit *	txtRSName

QString	inputAnonymizeDirectoryname

QLineEdit *	txtInputAnonymizeName

QString	outputAnonymizeDirectoryname

QLineEdit *	txtOutputAnonymizeName

QString	outputPrefix

QLineEdit *	txtOutputPrefix

int	outputInitID

QLineEdit *	txtOutputInitID

QCheckBox *	checkboxPreserveFolderArc

QCheckBox *	checkboxPatientName

QCheckBox *	checkboxPatientID

QCheckBox *	checkboxSeriesDate

QCheckBox *	checkboxSeriesTime

QCheckBox *	checkboxStudyID

QCheckBox *	checkboxStudyDesc

QCheckBox *	checkboxSeriesNumber

QCheckBox *	checkboxSequenceName

QCheckBox *	checkboxProtocolName

QCheckBox *	checkboxSeriesDescription

QCheckBox *	anonPatientInfo

QCheckBox *	anonPhysician

QCheckBox *	anonOperator

QCheckBox *	anonScanDate

milxQtImage *	image

QPointer< milxQtManager >	manager
	Manager widget.

QPointer< QDockWidget >	dock
	Dock widget.

bool	valid

Protected Attributes inherited from milxQtPluginInterface
QString	pluginName

QString	dataName

bool	threaded
	Threaded plugin?

bool	dockable
	Dockable plugin?

bool	consoleWindow
	console window?

bool	extension
	Extension rather than a plugin?

QMutex	mutex

QList< QAction * >	fileMenuEntries

QList< QMenu * >	menuToAdd

milxQtConsole *	console
	console for logging

Additional Inherited Members
Signals inherited from milxQtPluginInterface
void	resultAvailable (milxQtRenderWindow *)
	Send signal that Resultant render window is available for showing.

void	resultAvailable (milxQtModel *)
	Send signal that Resultant model is available for showing.

void	resultAvailable (milxQtImage *)
	Send signal that Resultant image is available for showing.

void	resultAvailable (vtkPolyDataCollection *, QStringList &)
	Send signal that Resultant collection is available for showing.

void	working (int value)
	Send signal that computation is in progress. Value carries the progress,.

void	done (int value)
	Send signal that computation is done. Value carries the progress,.

Detailed Description

The interface for the DICOM plugin for milxQt.

Author

Definition at line 54 of file milxQtDICOMPlugin.h.

Constructor & Destructor Documentation

◆ milxQtDICOMPlugin()

milxQtDICOMPlugin::milxQtDICOMPlugin ( QObject * theParent = 0 )

Default destructor.

Up cast parent to milxQtMain

Definition at line 39 of file milxQtDICOMPlugin.cpp.

Member Function Documentation

◆ anonymize

void milxQtDICOMPlugin::anonymize ( )

slot

Open each series and save

Loop over all the subjects

Retrieve the dicom series

If there are dicom series for the subject Create the subject's output folder

Create the subject's output folder

Loop over the dicom series

Loop over the dicom files and anonymize them

Need to retrieve path relative to subject (in case keep folder architecture)

Anonymize

Definition at line 611 of file milxQtDICOMPlugin.cpp.

◆ anonymizeDicomImage

milxQtDICOMPlugin::anonymizeDicomImage	(	const std::string &	input,
		const QString &	subject_output_folder,
		const QString &	rel_dir,
		unsigned int	index_subject,
		unsigned int	index_dicom,
		bool &	isFirst
	)

slot

Function used to anonymize a single dicom image.

Parameters

input	the input image
subject_output_folder	the output folder for the subject
rel_dir	the relative path from the of the subject and the initial dicom
index_subject	the subject id
index_dicom	the id of the current dicom
isFirst	is it the first dicom anonymize for the subject?

Returns: true if successfully anonymized

Create the anonymization string - This is the folder of the subject

Create 2 readers –> need two in case of T2 maps

TODO: Again this should be retrieved from the DICOM

First the image need to be read with a random type to able to read the dicom tags

and checkthe image type for saving later one

Write the mapping of the subject's real name to his identifier

Here retrieve real name

And write

If it is a T2 map need change image type / and re-read (unfortunate)

This should be read from the function rather than dicom tags but works as well

List of DICOM tags to strip

Create output directory

Write some debug on the type of images

Change dicom header and re-write file

Definition at line 1232 of file milxQtDICOMPlugin.cpp.

◆ convert

void milxQtDICOMPlugin::convert ( )

slot

Convert a DICOM series (or a path to a number of series) to Nifti (*.nii.gz) images.

The function assumes either the path provided in the wizard is a path containing a DICOM series or that the path provided contains a number of directories each having a DICOM series.

Open each series and save See milxQtFile::openImageSeries() for more relevant code Get UIDs and filenames

Check if input path is a directory of series or just a series

Open each image

Create the subject's output folder

Todo:: handle 4D images here properly

Definition at line 404 of file milxQtDICOMPlugin.cpp.

◆ createWizardAnonymise()

void milxQtDICOMPlugin::createWizardAnonymise ( )

protected

Intro

Page for intput directory (existence will be checked at the end)

Page for output directory (existence will be checked at the end)

Page for choosing prefix (eg. anon)

Page for choosing initial ID (will then increment per subject)

Page for choosing options for anonymization / filenames / folder arch

Definition at line 1034 of file milxQtDICOMPlugin.cpp.

◆ getTagValue

milxQtDICOMPlugin::getTagValue	(	ImageIOType::Pointer	gdcmImageIO,
		const std::string &	tag,
		std::string &	tag_value
	)

slot

Retrieve tag value fromt he gdcmImageIO object.

Parameters

gdcmImageIO	the dicom object
tag	the dicom tag
tag_value	the tag value

Definition at line 1623 of file milxQtDICOMPlugin.cpp.

◆ makeFilename

milxQtDICOMPlugin::makeFilename	(	const QString &	path,
		ImageIOType::Pointer	gdcmImageIO,
		unsigned int	index,
		std::string &	filename,
		unsigned int	index_subject
	)

slot

Small helper to make filename from dicom tags.

Small helper to remove unwanted characters under windows.

Parameters

path	output directory
gdcmImageIO	the dicom object
index	the dicom index
index	the dicom index
filename	reference to the filename
std	string to strip
charsToRemove	unwanted characters

Definition at line 1492 of file milxQtDICOMPlugin.cpp.

◆ openSeries

milxQtDICOMPlugin::openSeries ( )

slot

Open DICOM image series.

If filenames list is empty ask for them

Get UIDs

Update case list in manager

< Case Browser

Definition at line 283 of file milxQtDICOMPlugin.cpp.

◆ openStructureSet

milxQtDICOMPlugin::openStructureSet ( )

slot

Open DICOM RT image series.

Get UIDs and filenames

Export Structures

Definition at line 356 of file milxQtDICOMPlugin.cpp.

◆ showRSFileDialog

void milxQtDICOMPlugin::showRSFileDialog ( )

slot

<

Todo:: Check and validate extensions support at Open in Main class

Definition at line 742 of file milxQtDICOMPlugin.cpp.

◆ update

milxQtDICOMPlugin::update ( )

inlinevirtualslot

Update the plugin. [Implement this in your plugin].

This generic call is called after plugin is loaded and is designed to be used to update the plugin internals such as manager displays etc.

Definition at line 192 of file milxQtDICOMPlugin.h.

◆ viewTags

milxQtDICOMPlugin::viewTags ( )

slot

View DICOM tags of image series in the manager.

If filenames list is empty ask for them

Get UIDs

Check if input path is a directory of series or just a series

Update case list in manager

< Case Browser

Definition at line 188 of file milxQtDICOMPlugin.cpp.

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

plugin/dicom/milxQtDICOMPlugin.h
plugin/dicom/milxQtDICOMPlugin.cpp

Public Types

Public Slots

Public Member Functions

Protected Member Functions

Static Protected Member Functions

Protected Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ milxQtDICOMPlugin()

Member Function Documentation

◆ anonymize

◆ anonymizeDicomImage

◆ convert

◆ createWizardAnonymise()

◆ getTagValue

◆ makeFilename

◆ openSeries

◆ openStructureSet

◆ showRSFileDialog

◆ update

◆ viewTags