View source for Whole-Brain-Tractography-Wizard

=The Idea of a Wizard=
Make a simple set of steps that will guide the user through a complex process. An example of this is the simple wizard that takes the user from a DICOM or NRRD Diffusion Weighted Image to a Full brain tractography. There are 4 steps to this process:

<gallery>
Image:dicom2dti.png|[DICOM to DWI]
Image:dwi2dti.png|[DWI to DTI]
Image:dti2fibers.png|[DTI to Fibers]
Image:fibers.png|[Fibers]
</gallery>
In order to generate this wizard, we will use the For each step, we must:
* Obtain the input from the interface
* Validate the input
* Set up the parameters for the next step
* Provide the user with the appropriate information about errors in the processing and/or missing data

=API support for workflows=
In order to do this, we use CTK's support for workflows:
* [http://www.commontk.org/docs/html/classctkWorkflowStackedWidget.html ctkWorkflowStackedWidget]
* [http://www.commontk.org/docs/html/classctkWorkflowWidgetStep.html ctkWorkflowWidgetStep]

In which the idea is to derive a new class from ctkWorkflowWidgetStep for each step and then add them all to the workflow widget ctkWorkflowStackedWidget making the transition explicit

===Events of each workflow widget step (ctkWorkflowWidgetStep)===
* createUserInterface
* onEntry(comingFrom, transitionType)
* onExit(goingTo, transitionType)
* validate(validationSucceded, desiredBranchId)

==Obtaining the input from the Interface==

You can find the example at 
  Modules/Scripted/Scripts/DICOM2FullBrainTractography/DICOM2FullBrainTractographyLib/full_tractography_workflow.py

In this example there is a helper class that makes things easy for linear workflows: 
  WorkflowConfiguration

This class:
* Takes the widget for each step from a UI file generated by the designer
* Setups the widgets into a sequential workflow
* Obtain the data from the fields on the Qt window and put it into a python dictionary and passes it to the appropriate validation step
And requires
* Each step to be declared as the name of such file
* The fields from each step to be declared
*  The validation for each step to be implemented

====Declaring the Modules====
    step_widget_files = [
        'dicom2nrrd',
        'dwi2dti',
        'dti2fibers',
        'done',
    ]

====Declaring Each Module's Fields====
    step_widget_fields = {
        'dicom2nrrd':[
            ('DICOMRadioButton', 'checked'),
            ('NRRDDWIRadioButton', 'checked'),
            ('inputDicomDirectory', 'directory'),
            ('outputVolume', 'currentPath'),
            ('useBMatrixGradientDirections','checked'),
            ('inputNRRDVolume','currentPath'),
        ],
        'dwi2dti':[
            ('leastSquaresEstimation', 'checked'),
            ('weightedLeastSquaresEstimation', 'checked'),
            ('thresholdParameter', 'value'),
            ('removeIslands', 'checked'),
            ('applyMask', 'checked'),
        ],
        'dti2fibers':[
            ('seedSpacing','value'),
            ('stoppingFAValue','value'),
            ('minimumFAValueSeed','value'),
            ('stoppingTrackCurvature','value'),
        ],
        'done':[],
    }

====Validating Data for a Field====

  def validate_dicom2nrrd(self, step_object, data):
        if data[step_object.id()]['DICOMRadioButton']:
Running a CLI module from a python script
            self.dicomtonrrdconverter_parameter_node = slicer.cli.run(
                slicer.modules.dicomtonrrdconverter, self.dicomtonrrdconverter_parameter_node,
                data[step_object.id()],
                wait_for_completion = True)
Validating the result of a CLI module 
           if self.dicomtonrrdconverter_parameter_node.GetStatusString() == 'Completed':
                file_path = data[step_object.id()]['outputVolume']
                result_status, node = slicer.util.loadVolume(
                    file_path,
                    True
                )
            else:
                result_status = False
Setting data for the next module
            if result_status:
                self.dwi_node = node
                self.dwi_node_name = node.GetID()
Output errors if needed
        if not result_status:
            display_error("Error in DICOM to NRRD conversion, please see log")
        return result_status

==Details on Each Step's CallBack Implementation==
Entry Callback
    def onEntry(self, comingFrom, transitionType):
        comingFromId = "None"
        if comingFrom: comingFromId = comingFrom.id()
        super(GeneralizedStep, self).onEntry(comingFrom, transitionType)
        if hasattr(self, 'onEntryCallback'):
            self.onEntryCallback(self, comingFrom, transitionType)

Exit Callback
    def onExit(self, goingTo, transitionType):
        goingToId = "None"
        if goingTo: goingToId = goingTo.id()
        super(GeneralizedStep, self).onExit(goingTo, transitionType)
        if hasattr(self, 'onExitCallback'):
            self.onExitCallback(self, goingTo, transitionType)

Validation Callabck
    def validate(self, desiredBranchId):
        validationSuceeded = True
        if hasattr(self, 'validateCallback'):
            validationSuceeded = self.validateCallback(self, desiredBranchId)
        super(GeneralizedStep, self).validate(validationSuceeded, desiredBranchId)