SlicerLabkeyExtension/labkeySlicerPythonExtension/labkeySlicerPythonExtension.py

import os
import unittest
from __main__ import vtk, qt, ctk, slicer
from slicer.ScriptedLoadableModule import *


#
# labkeySlicerPythonExtension
#

class labkeySlicerPythonExtension(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 = "labkeySlicerPythonExtension" # TODO make this more human readable by adding spaces
    self.parent.categories = ["Examples"]
    self.parent.dependencies = []
    self.parent.contributors = ["Andrej Studen (UL/FMF)"] # replace with "Firstname Lastname (Organization)"
    self.parent.helpText = """
    Labkey interface to slicer
    """
    self.parent.acknowledgementText = """
    Developed within the medical physics research programme of the Slovenian research agency.
    """ # replace with organization, grant and thanks.

#
# labkeySlicerPythonExtensionWidget
#

class labkeySlicerPythonExtensionWidget(ScriptedLoadableModuleWidget):
  """Uses ScriptedLoadableModuleWidget base class, available at:
  https://github.com/Slicer/Slicer/blob/master/Base/Python/slicer/ScriptedLoadableModule.py
  """

  def setup(self):
    ScriptedLoadableModuleWidget.setup(self)
    # Instantiate and connect widgets ...
    self.logic=labkeySlicerPythonExtensionLogic(self)
    #
    # Parameters Area
    #
    connectionCollapsibleButton = ctk.ctkCollapsibleButton()
    connectionCollapsibleButton.text = "Connection"
    self.layout.addWidget(connectionCollapsibleButton)

    connectionFormLayout = qt.QFormLayout(connectionCollapsibleButton)

    self.serverURL=qt.QLineEdit("https://merlin.fmf.uni-lj.si")

    connectionFormLayout.addRow("Server: ", self.serverURL)

    self.userCertButton=qt.QPushButton("Load")
    self.userCertButton.toolTip="Load user certificate (crt)"
    self.userCertButton.connect('clicked(bool)',self.onUserCertButtonClicked)

    connectionFormLayout.addRow("User certificate:",self.userCertButton)

    self.privateKeyButton=qt.QPushButton("Load")
    self.privateKeyButton.toolTip="Load private key"
    self.privateKeyButton.connect('clicked(bool)',self.onPrivateKeyButtonClicked)

    connectionFormLayout.addRow("Private key:",self.privateKeyButton)

    self.caCertButton=qt.QPushButton("Load")
    self.caCertButton.toolTip="Load CA certificate (crt)"
    self.caCertButton.connect('clicked(bool)',self.onCaCertButtonClicked)

    connectionFormLayout.addRow("CA certificate:",self.caCertButton)

    self.connectButton=qt.QPushButton("Connect")
    self.connectButton.toolTip="Connect to the server"
    self.connectButton.connect('clicked(bool)',self.onConnectButtonClicked)

    connectionFormLayout.addRow("Connection:",self.connectButton)

    parametersCollapsibleButton = ctk.ctkCollapsibleButton()
    parametersCollapsibleButton.text = "Parameters"
    self.layout.addWidget(parametersCollapsibleButton)

    # Layout within the dummy collapsible button
    parametersFormLayout = qt.QFormLayout(parametersCollapsibleButton)

    #
    # input volume selector
    #
    self.inputSelector = slicer.qMRMLNodeComboBox()
    self.inputSelector.nodeTypes = ( ("vtkMRMLScalarVolumeNode"), "" )
    self.inputSelector.addAttribute( "vtkMRMLScalarVolumeNode", "LabelMap", 0 )
    self.inputSelector.selectNodeUponCreation = True
    self.inputSelector.addEnabled = False
    self.inputSelector.removeEnabled = False
    self.inputSelector.noneEnabled = False
    self.inputSelector.showHidden = False
    self.inputSelector.showChildNodeTypes = False
    self.inputSelector.setMRMLScene( slicer.mrmlScene )
    self.inputSelector.setToolTip( "Pick the input to the algorithm." )
    parametersFormLayout.addRow("Input Volume: ", self.inputSelector)

    #
    # output volume selector
    #
    self.outputSelector = slicer.qMRMLNodeComboBox()
    self.outputSelector.nodeTypes = ( ("vtkMRMLScalarVolumeNode"), "" )
    self.outputSelector.addAttribute( "vtkMRMLScalarVolumeNode", "LabelMap", 0 )
    self.outputSelector.selectNodeUponCreation = False
    self.outputSelector.addEnabled = True
    self.outputSelector.removeEnabled = True
    self.outputSelector.noneEnabled = False
    self.outputSelector.showHidden = False
    self.outputSelector.showChildNodeTypes = False
    self.outputSelector.setMRMLScene( slicer.mrmlScene )
    self.outputSelector.setToolTip( "Pick the output to the algorithm." )
    parametersFormLayout.addRow("Output Volume: ", self.outputSelector)

    #
    # check box to trigger taking screen shots for later use in tutorials
    #
    self.enableScreenshotsFlagCheckBox = qt.QCheckBox()
    self.enableScreenshotsFlagCheckBox.checked = 0
    self.enableScreenshotsFlagCheckBox.setToolTip("If checked, take screen shots for tutorials. Use Save Data to write them to disk.")
    parametersFormLayout.addRow("Enable Screenshots", self.enableScreenshotsFlagCheckBox)

    #
    # scale factor for screen shots
    #
    self.screenshotScaleFactorSliderWidget = ctk.ctkSliderWidget()
    self.screenshotScaleFactorSliderWidget.singleStep = 1.0
    self.screenshotScaleFactorSliderWidget.minimum = 1.0
    self.screenshotScaleFactorSliderWidget.maximum = 50.0
    self.screenshotScaleFactorSliderWidget.value = 1.0
    self.screenshotScaleFactorSliderWidget.setToolTip("Set scale factor for the screen shots.")
    parametersFormLayout.addRow("Screenshot scale factor", self.screenshotScaleFactorSliderWidget)

    #
    # Apply Button
    #
    self.applyButton = qt.QPushButton("Apply")
    self.applyButton.toolTip = "Run the algorithm."
    self.applyButton.enabled = False
    parametersFormLayout.addRow(self.applyButton)

    # connections
    self.applyButton.connect('clicked(bool)', self.onApplyButton)
    self.inputSelector.connect("currentNodeChanged(vtkMRMLNode*)", self.onSelect)
    self.outputSelector.connect("currentNodeChanged(vtkMRMLNode*)", self.onSelect)

    # Add vertical spacer
    self.layout.addStretch(1)

  def cleanup(self):
    pass

  def onSelect(self):
    self.applyButton.enabled = self.inputSelector.currentNode() and self.outputSelector.currentNode()

  def onApplyButton(self):
    #logic = labkeySlicerPythonExtensionLogic()
    #enableScreenshotsFlag = self.enableScreenshotsFlagCheckBox.checked
    #screenshotScaleFactor = int(self.screenshotScaleFactorSliderWidget.value)
    print("Run the algorithm")
    #logic.run(self.inputSelector.currentNode(), self.outputSelector.currentNode(), enableScreenshotsFlag,screenshotScaleFactor)

  def onUserCertButtonClicked(self):
     startDir=os.environ['HOME']+"/temp"
     filename=qt.QFileDialog.getOpenFileName(None,'Open user certificate',
           startDir, '*.crt')
     #pwd=qt.QInputDialog.getText(None,'Certificate password',
     # 'Enter certificate password',qt.QLineEdit.Password)
     if not(filename) :
         print "No file selected"
         return

     f=qt.QFile(filename)
     if not (f.open(qt.QIODevice.ReadOnly)) :
         print "Could not open file"
         return

     certList=qt.QSslCertificate.fromPath(filename)
     if len(certList) < 1:
         print "Troubles parsing {0}".format(filename)
         return

     self.logic.cert=qt.QSslCertificate(f)
     print "cert.isNull()={0}".format(self.logic.cert.isNull())
     self.userCertButton.setText(filename)

  def onPrivateKeyButtonClicked(self):
      startDir=os.environ['HOME']+"/temp"
      filename=qt.QFileDialog.getOpenFileName(None,'Open private key',
            startDir, '*.key')
      if not (filename) :
          print "No file selected"
          return

      f=qt.QFile(filename)
      if not (f.open(qt.QIODevice.ReadOnly)) :
          print "Could not open file"
          return
      pwd=qt.QInputDialog.getText(None,'Private key password',
      'Enter key password',qt.QLineEdit.Password)

      self.logic.key=qt.QSslKey(f,qt.QSsl.Rsa,qt.QSsl.Pem,qt.QSsl.PrivateKey,str(pwd))
      self.privateKeyButton.setText(filename)

  def onCaCertButtonClicked(self):
      startDir=os.environ['HOME']+"/temp"
      filename=qt.QFileDialog.getOpenFileName(None,'Open authority certificate',
               startDir, '*.crt')
      if not(filename) :
         print "No file selected"
         return

      f=qt.QFile(filename)

      if not (f.open(qt.QIODevice.ReadOnly)) :
          print "Could not open file"
          return

      certList=qt.QSslCertificate.fromPath(filename)

      if len(certList) < 1:
          print "Troubles parsing {0}".format(filename)
          return
      self.logic.caCert=qt.QSslCertificate(f)#certList[0]
      self.caCertButton.setText(filename)

  def onConnectButtonClicked(self):
      uname=str(self.logic.cert.subjectInfo("emailAddress"))
      uname=qt.QInputDialog.getText(None,
        "Labkey credentials","Enter username",qt.QLineEdit.Normal,uname)

      pwd=qt.QInputDialog.getText(None,
        "Labkey credentials","Enter password",qt.QLineEdit.Password)

      self.logic.connectRemote(str(self.serverURL.text),uname,pwd)




#
# labkeySlicerPythonExtensionLogic
#

class labkeySlicerPythonExtensionLogic(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 __init__(self,parent):
      ScriptedLoadableModuleLogic.__init__(self, parent)
      self.qnam=qt.QNetworkAccessManager()

  def connectRemote(self,serverURL,uname,pwd):
     request=qt.QNetworkRequest()
     request.setUrl(qt.QUrl(serverURL));
     request.setHeader(qt.QNetworkRequest.ContentTypeHeader,
        "application/x-www-form-urlencoded")

     data="email="+uname+"&password="+pwd;

     #setup the transfer
     sConfig=qt.QSslConfiguration()

     #user certificate
     sConfig.setLocalCertificate(self.cert)
     sConfig.setPrivateKey(self.key)

     #ca certificate
     caList=[self.caCert]
     sConfig.setCaCertificates(caList)

     request.setSslConfiguration(sConfig)

     #post

     r=self.qnam.post(request,data)
     connect(qnam, qt.QNetworkAccessManager.finished, self, replyFinished);

  def replyFinished(self,res):
      print "Reply finished"


  def hasImageData(self,volumeNode):
    """This is a dummy logic method that
    returns true if the passed in volume
    node has valid image data
    """
    if not volumeNode:
      print('no volume node')
      return False
    if volumeNode.GetImageData() == None:
      print('no image data')
      return False
    return True

  def takeScreenshot(self,name,description,type=-1):
    # show the message even if not taking a screen shot
    self.delayDisplay(description)

    if self.enableScreenshots == 0:
      return

    lm = slicer.app.layoutManager()
    # switch on the type to get the requested window
    widget = 0
    if type == slicer.qMRMLScreenShotDialog.FullLayout:
      # full layout
      widget = lm.viewport()
    elif type == slicer.qMRMLScreenShotDialog.ThreeD:
      # just the 3D window
      widget = lm.threeDWidget(0).threeDView()
    elif type == slicer.qMRMLScreenShotDialog.Red:
      # red slice window
      widget = lm.sliceWidget("Red")
    elif type == slicer.qMRMLScreenShotDialog.Yellow:
      # yellow slice window
      widget = lm.sliceWidget("Yellow")
    elif type == slicer.qMRMLScreenShotDialog.Green:
      # green slice window
      widget = lm.sliceWidget("Green")
    else:
      # default to using the full window
      widget = slicer.util.mainWindow()
      # reset the type so that the node is set correctly
      type = slicer.qMRMLScreenShotDialog.FullLayout

    # grab and convert to vtk image data
    qpixMap = qt.QPixmap().grabWidget(widget)
    qimage = qpixMap.toImage()
    imageData = vtk.vtkImageData()
    slicer.qMRMLUtils().qImageToVtkImageData(qimage,imageData)

    annotationLogic = slicer.modules.annotations.logic()
    annotationLogic.CreateSnapShot(name, description, type, self.screenshotScaleFactor, imageData)

  def run(self,inputVolume,outputVolume,enableScreenshots=0,screenshotScaleFactor=1):
    """
    Run the actual algorithm
    """

    self.delayDisplay('Running the aglorithm')

    self.enableScreenshots = enableScreenshots
    self.screenshotScaleFactor = screenshotScaleFactor

    self.takeScreenshot('labkeySlicerPythonExtension-Start','Start',-1)

    return True


class labkeySlicerPythonExtensionTest(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_labkeySlicerPythonExtension1()

  def test_labkeySlicerPythonExtension1(self):
    """ Ideally you should have several levels of tests.  At the lowest level
    tests sould 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:
        print('Requesting download %s from %s...\n' % (name, url))
        urllib.urlretrieve(url, filePath)
      if loader:
        print('Loading %s...\n' % (name,))
        loader(filePath)
    self.delayDisplay('Finished with download and loading\n')

    volumeNode = slicer.util.getNode(pattern="FA")
    logic = labkeySlicerPythonExtensionLogic()
    self.assertTrue( logic.hasImageData(volumeNode) )
    self.delayDisplay('Test passed!')