ENH: adding first draft for new reporting module (issue QIICR#74)

- Segment Editor and measurement table still needs to be added

Py/CMakeLists.txt

@@ -12,3 +12,8 @@ slicerMacroBuildScriptedModule(
   NAME SEGExporterSelfTest
   SCRIPTS SEGExporterSelfTest.py
   )
+
+slicerMacroBuildScriptedModule(
+  NAME Reporting
+  SCRIPTS Reporting.py
+  )

Py/Reporting.py

@@ -0,0 +1,201 @@
+import getpass
+
+from slicer.ScriptedLoadableModule import *
+
+from SlicerProstateUtils.mixins import *
+from SlicerProstateUtils.helpers import WatchBoxAttribute, DICOMBasedInformationWatchBox
+from SlicerProstateUtils.constants import DICOMTAGS
+
+class Reporting(ScriptedLoadableModule):
+  """Uses ScriptedLoadableModule base class, available at:
+  https://github.com/Slicer/Slicer/blob/master/Base/Python/slicer/ScriptedLoadableModule.py
+  """
+
+  def __init__(self, parent):
+    ScriptedLoadableModule.__init__(self, parent)
+    self.parent.title = "Reporting" # TODO make this more human readable by adding spaces
+    self.parent.categories = ["Examples"]
+    self.parent.dependencies = ["SlicerProstate"]
+    self.parent.contributors = ["Andrey Fedorov (SPL, BWH), Nicole Aucoin (SPL, BWH), "
+                                "Steve Pieper (Isomics), Christian Herz (SPL)"]
+    self.parent.helpText = """
+    This is an example of scripted loadable module bundled in an extension.
+    It performs a simple thresholding on the input volume and optionally captures a screenshot.
+    """
+    self.parent.acknowledgementText = """
+    This file was originally developed by Jean-Christophe Fillion-Robin, Kitware Inc.
+    and Steve Pieper, Isomics, Inc. and was partially funded by NIH grant 3P41RR013218-12S1.
+""" # replace with organization, grant and thanks.
+
+
+class ReportingWidget(ModuleWidgetMixin, ScriptedLoadableModuleWidget):
+  """Uses ScriptedLoadableModuleWidget base class, available at:
+  https://github.com/Slicer/Slicer/blob/master/Base/Python/slicer/ScriptedLoadableModule.py
+  """
+
+  def __init__(self, parent=None):
+    ScriptedLoadableModuleWidget.__init__(self, parent)
+
+  def cleanup(self):
+    pass
+
+  def setup(self):
+    ScriptedLoadableModuleWidget.setup(self)
+    self.setupWatchbox()
+    self.setupSelectionArea()
+    self.setupViewSettingsArea()
+    self.setupSegmentationsArea()
+    self.setupMeasurementsArea()
+    self.setupActionButtons()
+    self.setupConnections()
+    self.layout.addStretch(1)
+
+  def setupWatchbox(self):
+    self.watchBoxInformation = [
+      WatchBoxAttribute('StudyID', 'Study ID: ', DICOMTAGS.PATIENT_BIRTH_DATE),
+      WatchBoxAttribute('PatientName', 'Patient Name: ', DICOMTAGS.PATIENT_NAME),
+      WatchBoxAttribute('DOB', 'Date of Birth: ', DICOMTAGS.PATIENT_BIRTH_DATE),
+      WatchBoxAttribute('Reader', 'Reader Name: ', callback=getpass.getuser)]
+    self.watchBox = DICOMBasedInformationWatchBox(self.watchBoxInformation)
+    self.layout.addWidget(self.watchBox)
+
+  def setupSelectionArea(self):
+    self.imageVolumeSelector = self.createComboBox(nodeTypes=["vtkMRMLScalarVolumeNode", ""], showChildNodeTypes=False,
+                                                   selectNodeUponCreation=True, toolTip="Select image volume to annotate")
+    self.measurementReportSelector = self.createComboBox(nodeTypes=["vtkMRMLScriptedModuleNode", ""], showChildNodeTypes=False,
+                                                         selectNodeUponCreation=True, toolTip="Select measurement report")
+    self.layout.addWidget(self.createHLayout([qt.QLabel("Image volume to annotate"), self.imageVolumeSelector]))
+    self.layout.addWidget(self.createHLayout([qt.QLabel("Measurement report"), self.measurementReportSelector]))
+
+  def setupViewSettingsArea(self):
+    pass
+
+  def setupSegmentationsArea(self):
+    pass
+
+  def setupMeasurementsArea(self):
+    pass
+
+  def setupActionButtons(self):
+    self.saveReportButton = self.createButton("Save Report")
+    self.completeReportButton = self.createButton("Complete Report")
+    self.layout.addWidget(self.createHLayout([self.saveReportButton, self.completeReportButton]))
+
+  def setupConnections(self):
+
+    def setupSelectorConnections():
+      self.imageVolumeSelector.connect('currentNodeChanged(vtkMRMLNode*)', self.onImageVolumeSelectorChanged)
+
+    def setupButtonConnections():
+      self.saveReportButton.clicked.connect(self.onSaveReportButtonClicked)
+      self.completeReportButton.clicked.connect(self.onCompleteReportButtonClicked)
+
+    setupSelectorConnections()
+    setupButtonConnections()
+
+  def onImageVolumeSelectorChanged(self, node):
+    # TODO: save, cleanup open sessions
+    try:
+      dicomFileName = node.GetStorageNode().GetFileName()
+      self.watchBox.sourceFile = dicomFileName if os.path.exists(dicomFileName) else None
+    except AttributeError:
+      self.watchBox.sourceFile = None
+
+  def onSaveReportButtonClicked(self):
+    print "on save report button clicked"
+
+  def onCompleteReportButtonClicked(self):
+    print "on complete report button clicked"
+
+
+class ReportingLogic(ScriptedLoadableModuleLogic):
+  """This class should implement all the actual
+  computation done by your module.  The interface
+  should be such that other python code can import
+  this class and make use of the functionality without
+  requiring an instance of the Widget.
+  Uses ScriptedLoadableModuleLogic base class, available at:
+  https://github.com/Slicer/Slicer/blob/master/Base/Python/slicer/ScriptedLoadableModule.py
+  """
+
+  def hasImageData(self, volumeNode):
+    """This is an example logic method that
+    returns true if the passed in volume
+    node has valid image data
+    """
+    if not volumeNode:
+      logging.debug('hasImageData failed: no volume node')
+      return False
+    if volumeNode.GetImageData() is None:
+      logging.debug('hasImageData failed: no image data in volume node')
+      return False
+    return True
+
+  def isValidInputOutputData(self, inputVolumeNode, outputVolumeNode):
+    """Validates if the output is not the same as input
+    """
+    if not inputVolumeNode:
+      logging.debug('isValidInputOutputData failed: no input volume node defined')
+      return False
+    if not outputVolumeNode:
+      logging.debug('isValidInputOutputData failed: no output volume node defined')
+      return False
+    if inputVolumeNode.GetID()==outputVolumeNode.GetID():
+      logging.debug('isValidInputOutputData failed: input and output volume is the same. Create a new volume for output to avoid this error.')
+      return False
+    return True
+
+
+class ReportingTest(ScriptedLoadableModuleTest):
+  """
+  This is the test case for your scripted module.
+  Uses ScriptedLoadableModuleTest base class, available at:
+  https://github.com/Slicer/Slicer/blob/master/Base/Python/slicer/ScriptedLoadableModule.py
+  """
+
+  def setUp(self):
+    """ Do whatever is needed to reset the state - typically a scene clear will be enough.
+    """
+    slicer.mrmlScene.Clear(0)
+
+  def runTest(self):
+    """Run as few or as many tests as needed here.
+    """
+    self.setUp()
+    self.test_Reporting1()
+
+  def test_Reporting1(self):
+    """ Ideally you should have several levels of tests.  At the lowest level
+    tests should exercise the functionality of the logic with different inputs
+    (both valid and invalid).  At higher levels your tests should emulate the
+    way the user would interact with your code and confirm that it still works
+    the way you intended.
+    One of the most important features of the tests is that it should alert other
+    developers when their changes will have an impact on the behavior of your
+    module.  For example, if a developer removes a feature that you depend on,
+    your test should break so they know that the feature is needed.
+    """
+
+    self.delayDisplay("Starting the test")
+    #
+    # first, get some data
+    #
+    import urllib
+    downloads = (
+        ('http://slicer.kitware.com/midas3/download?items=5767', 'FA.nrrd', slicer.util.loadVolume),
+        )
+
+    for url,name,loader in downloads:
+      filePath = slicer.app.temporaryPath + '/' + name
+      if not os.path.exists(filePath) or os.stat(filePath).st_size == 0:
+        logging.info('Requesting download %s from %s...\n' % (name, url))
+        urllib.urlretrieve(url, filePath)
+      if loader:
+        logging.info('Loading %s...' % (name,))
+        loader(filePath)
+    self.delayDisplay('Finished with download and loading')
+
+    volumeNode = slicer.util.getNode(pattern="FA")
+    logic = ReportingLogic()
+    self.assertIsNotNone( logic.hasImageData(volumeNode) )
+    self.delayDisplay('Test passed!')