Tool Class Reference

List of all members.

Public Types
enum	ToolType {   NONE = 0, IR_FFT, IR_REFINE_TRANSLATE, IR_REFINE_GRID,   IR_MOSAIC_OVERRIDE, IR_ASSEMBLE, IR_STOS_BRUTE, IR_STOS_GRID,   IR_ADD_TRANSFORMS, IR_STOM, IR_STOS_OVERRIDE, SNAPSHOT,   IR_BLOB, IR_CLAHE, SMART_IMPORT = 20, IR_ASSEMBLE_TILED = 22,   INVALID_TOOL = 32767 }
Public Slots
void	Run (bool askUserInput=true, bool userRequest=true, bool runOnAllSlices=false)
void	SaveCustomArgs ()
bool	ExecuteSettingsDialog (QHash< QString, ToolFlag * > &flags, bool askUserInput=true, bool onlyOkButton=false)
void	Clean ()
Public Member Functions
	Tool (QXmlStreamReader &xml, ToolType type)
QString	GetToolName ()
QString	GetProcessName ()
QString	GetIconName ()
QString	GetDetails ()
QString	GetShortDetails ()
QString	GetFriendlyName ()
QString	GetSearchName ()
QString	GetSaveName ()
QString	InsertAliasId (const QString &addTo)
bool	GetRunPerImage ()
QStringList	GetFilterList (const QString &tag="")
bool	RunPerChannel ()
int	GetGroupType ()
QStringList	GetPossibleInputFiles (QList< VolumeIndex * > *slices, const QString &inputTag)
QHash< QString, QStringList >	GetAllPossibleInputFiles (QList< VolumeIndex * > *indices)
bool	FilenameMatchesSearch (const QString &filename)
void	SetIndices (QList< VolumeIndex * > *indices)
void	QueueOnly (bool queueOnly)
void	SetUpstreamInput (const QStringList &upstreams)
void	ClearUpstreamInput ()
void	SetAlias (ToolAlias *alias)
void	ClearAlias ()
ToolAlias *	GetAlias ()
Tool::ToolType	GetToolType ()
void	SaveCustomArgs (QXmlStreamWriter &xml, bool loadSettings=true)
void	LoadCustomArgs (QXmlStreamReader &xml, QHash< QString, ToolFlag * > *newFlags=NULL)
bool	RunOnSections ()
bool	NoOperation ()
bool	RunInTerminal ()
void	ToolCompletedSuccessfully (int timeTaken)
float	TotalRuntime ()
float	AverageRuntime ()
QHash< QString, ToolFlag * >	GetFlags ()
void	OverrideFlags (QHash< QString, ToolFlag * > *flags)
void	ClearOverride ()
bool	CanRunAfter (ToolAlias *before)
int	QueueProcess (const QString &prog, VolumeIndex *index)
int	NumThreads ()
int	SectionsRequired ()
bool	ChecksValid ()
QString	PrintValidChecks ()
Static Public Member Functions
static QString	GetToolName (Tool::ToolType type)
static QString	GetIconName (Tool::ToolType type)
static QString	GetDetails (Tool::ToolType type)
static bool	FileToComboBoxDetails (const QString &fileName, QString &properName, QIcon &icon)
static ToolAlias *	LoadNextTool (QXmlStreamReader &xml, int &separator, bool onlyOverride=false, QHash< QString, ToolFlag * > *newFlags=NULL)
static Tool *	GetTool (ToolType type)
static Tool *	GetOperable (int idx)
static QHash< int, Tool * > &	GetOperables ()
static int	ConvertToGroupId (const QString &groupStr)
Protected Attributes
QString	name
QString	processName
QString	icon
QString	description
QString	shortDescription
QString	friendlyName
QString	saveName
QString	searchName
QHash< QString, QStringList >	inputFilters
Tool::ToolType	type
QStringList	checkList
QStringList	invalidList
bool	singleRun
bool	runOnSections
bool	useSlicesAsInput
bool	runPerImage
bool	runPerChannel
int	runType
int	numThreads
int	sectionsRequired
int	groupId
float	totalTime
int	timesFinished
ToolAlias *	currentAlias
QHash< QString, ToolFlag * >	flags
QHash< QString, ToolFlag * > *	overrideFlags
bool	queueOnly
QList< VolumeIndex * > *	activeIndices
QStringList	upstreamArgs
Static Protected Attributes
static QHash< ToolType, Tool * >	toolList
static QHash< int, Tool * >	operableTools
Friends
class	Iris::IrisTests

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Constructor & Destructor Documentation

Tool::Tool	(	QXmlStreamReader &	xml,
		ToolType	type
	)

Tools are generated from Tool\ToolList.xml file. This file allows for easy addition of custom tools. The tools are the backbone of Iris, and make up a Pipeline. The list contains xml elements with sub lists of xml attributes. The marked attributes are required.

Required Elements:

• Tool - Each tool begins witha tool tag.
  • uid - A unique id for the tool.

• ProcessName - Command line name of the tool. In order for Iris to find your tool it must be in a location it can recognize. See UserPreferences::toolsInPath for more information.

• ProcessCheck - Runs the below command to verify that this process has it's run requirements fulfilled.

• Name - Name used to reference the tool in Iris.

• Save - Path to any output generated by the tool. Supports all custom symbols, Slice::ReplaceSymbols().
  • dir - Directory for save files. See VolumeIndex::XmlToTag() .

• Search - Search string for other tools' to use as input. Supports all custom symbols, Slice::ReplaceSymbols().
  • dir - Directory for search files. See VolumeIndex::XmlToTag() .

• Input - Valid input files for this tool. Wildcards are accepted.
  • tag - Allows for extra input types, in case more than one input is needed. Default value [<Empty>].
  • section - [true] Check section directory for input files. Default value [false].
  • slice - [true] Check slice directory for input files. Default value [false]
  • image - [true] Check the section and slice image directories for input files. Default value [false]
  • volume - [true] Check the section to section directory for input files. Default value [false]

Optional Elements:

• FunctionName - Name of a supported internal function name.

• NoOperation - Don't actually run the tool. Used solely to keep track of items.

• ShortDescription - Short name used .

• Description - Name used to reference the tool in Iris.

• Icon - Optional icon path. Path is local to the Iris executable.

• NumberOfThreads - Number of threads this tool requires. Set to -1 for all threads. Note, if the system does not have the requested number of threads this tool will not be able to run.

Optional Elements (Defult to false)

• RunPerImage - Run the tool once per image. See ir-clahe.

• RunPerChannel - Run the tool once per channel. See ir-assemble.

• RunOnSection - Tools can either be run once per section (true) or once per slice (false).

• SingleRun - Only run the tool once for all the sections and slices. The run will be performed on the last section.

• GroupType - The group type determines what menus this tool should be added to.

• Argument - Any additional number of arguments may be added See ToolFlag::LoadFromXml().

• Checkbox - Any additional number of checkboxes may be added See ToolFlag::LoadFromXml().

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

• C:/CRCNS/Development/code/iris/Tool.h
• C:/CRCNS/Development/code/iris/Tool.cpp