Matching standard layout

dataExplorer/dataExplorer.py

@@ -1,318 +0,0 @@
-import os
-import unittest
-import vtk, qt, ctk, slicer
-from slicer.ScriptedLoadableModule import *
-import logging
-import slicerNetwork
-import json
-import loadPatient
-
-#
-# dataExplorer
-#
-
-class dataExplorer(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 = "dataExplorer" # TODO make this more human readable by adding spaces
-    self.parent.categories = ["EMBRACE"]
-    self.parent.dependencies = []
-    self.parent.contributors = ["Andrej Studen (University of Ljubljana)"] # replace with "Firstname Lastname (Organization)"
-    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.helpText += self.getDefaultModuleDocumentationLink()
-    self.parent.acknowledgementText = """
-This extension developed within Medical Physics research programe of ARRS
-""" # replace with organization, grant and thanks.
-
-#
-# dataExplorerWidget
-#
-
-class dataExplorerWidget(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)
-    self.loadPatientLogic=loadPatient.loadPatientLogic(self)
-    # Instantiate and connect widgets ...
-
-    #
-    # Parameters Area
-    #
-    basePath=os.path.join(os.path.expanduser('~'),'.EMBRACE')
-    #'D:\\Sw\\src\\EMBRACE'
-    netConfig=os.path.join(basePath,'onko-nix.json')
-    self.sNet=slicerNetwork.labkeyURIHandler()
-    self.sNet.parseConfig(netConfig)
-    self.sNet.initRemote()
-
-    self.loadPatientLogic.setURIHandler(self.sNet)
-    self.project="EMBRACE/Studija"
-    self.dataset="ImagingVisitsManaged"
-
-
-    datasetCollapsibleButton = ctk.ctkCollapsibleButton()
-    datasetCollapsibleButton.text = "Dataset"
-    self.layout.addWidget(datasetCollapsibleButton)
-    # Layout within the dummy collapsible button
-    datasetFormLayout = qt.QFormLayout(datasetCollapsibleButton)
-
-    self.datasetButton=qt.QPushButton("Load")
-    self.datasetButton.connect('clicked(bool)',self.onDatasetLoadButtonClicked)
-    datasetFormLayout.addRow("Data:",self.datasetButton)
-
-    self.patientId=qt.QLineEdit("LJU004")
-    datasetFormLayout.addRow("Patient ID:",self.patientId)
-
-    loadCTButton=qt.QPushButton("CT")
-    loadCTButton.clicked.connect(self.onLoadCTButtonClicked)
-    datasetFormLayout.addRow("Load:",loadCTButton)
-
-    loadCTRSButton=qt.QPushButton("CT-RS")
-    loadCTRSButton.clicked.connect(self.onLoadCTRSButtonClicked)
-    datasetFormLayout.addRow("Load:",loadCTRSButton)
-
-    loadDMRButton=qt.QPushButton("DMR")
-    loadDMRButton.clicked.connect(self.onLoadDMRButtonClicked)
-    datasetFormLayout.addRow("Load:",loadDMRButton)
-
-
-
-    dataCollapsibleButton = ctk.ctkCollapsibleButton()
-    dataCollapsibleButton.text = "Data"
-    self.layout.addWidget(dataCollapsibleButton)
-    # Layout within the dummy collapsible button
-    dataFormLayout = qt.QVBoxLayout(dataCollapsibleButton)
-
-    self.data=qt.QTableWidget(3,3)
-    dataFormLayout.addWidget(self.data)
-
-    patientsCollapsibleButton = ctk.ctkCollapsibleButton()
-    patientsCollapsibleButton.text = "Patients"
-    self.layout.addWidget(patientsCollapsibleButton)
-    # Layout within the dummy collapsible button
-    self.patientsFormLayout = qt.QVBoxLayout(patientsCollapsibleButton)
-    self.signalMapper=qt.QSignalMapper()
-    self.signalMapper.connect(self.signalMapper, qt.SIGNAL("mapped(const QString &)"), self.onPatientButtonClicked)
-
-
-  def cleanup(self):
-    pass
-
-
-
-  def onDatasetLoadButtonClicked(self):
-
-      ds=self.sNet.loadDataset(self.project,self.dataset)
-      #loaded a JSON object -> convert to suitable display
-      columns=ds['columnModel']
-      self.data.setColumnCount(len(columns))
-      self.data.setRowCount(len(ds['rows']))
-      columnNames=[f['header'] for f in columns]
-      self.data.setHorizontalHeaderLabels(columnNames)
-      columnID=[f['dataIndex'] for f in columns]
-      insertRowID=0
-      for row in ds['rows']:
-          insertColumnID=0
-          for c in columnID:
-              item=qt.QTableWidgetItem(str(row[c]))
-              self.data.setItem(insertRowID,insertColumnID,item)
-              insertColumnID+=1
-          insertRowID+=1
-
-      #clear patient list
-      while self.patientsFormLayout.count():
-           child=self.patientsFormLayout.takeAt(0)
-           if child.widget():
-               self.signalMapper.removeMapping(child.widget())
-               child.widget().deleteLater()
-
-      #populate patient list
-      patientList=[f['EMBRACE_ID'] for f in ds['rows']]
-      #remove duplicates
-      patientSet=set(patientList)
-      for p in patientSet:
-           patientButton=qt.QPushButton(p)
-           patientButton.connect(patientButton, qt.SIGNAL("clicked()"),
-                self.signalMapper, qt.SLOT("map()"))
-           self.patientsFormLayout.addWidget(patientButton)
-           self.signalMapper.setMapping(patientButton,p)
-
-  def onPatientButtonClicked(self, label):
-      print "onPatientButtonClicked() for {}".format(label)
-      self.loadPatientLogic.load(label)
-
-  def onLoadCTButtonClicked(self):
-      self.CT=self.loadPatientLogic.loadCT(self.patientId.text)
-      self.CT[0]['node'].SetName(self.patientId.text+"_CT")
-
-  def onLoadCTRSButtonClicked(self):
-      self.CTRS=self.loadPatientLogic.loadCTRS(self.patientId.text)
-
-  def onLoadDMRButtonClicked(self):
-      self.DMR=self.loadPatientLogic.loadDMR(self.patientId.text)
-      self.DMR[0]['node'].SetName(self.patientId.text+"_DMR")
-
-#
-# dataExplorerLogic
-#
-
-class dataExplorerLogic(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
-
-  def takeScreenshot(self,name,description,type=-1):
-    # show the message even if not taking a screen shot
-    slicer.util.delayDisplay('Take screenshot: '+description+'.\nResult is available in the Annotations module.', 3000)
-
-    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
-    qimage = ctk.ctkWidgetsUtils.grabWidget(widget)
-    imageData = vtk.vtkImageData()
-    slicer.qMRMLUtils().qImageToVtkImageData(qimage,imageData)
-
-    annotationLogic = slicer.modules.annotations.logic()
-    annotationLogic.CreateSnapShot(name, description, type, 1, imageData)
-
-  def run(self, inputVolume, outputVolume, imageThreshold, enableScreenshots=0):
-    """
-    Run the actual algorithm
-    """
-
-    if not self.isValidInputOutputData(inputVolume, outputVolume):
-      slicer.util.errorDisplay('Input volume is the same as output volume. Choose a different output volume.')
-      return False
-
-    logging.info('Processing started')
-
-    # Compute the thresholded output volume using the Threshold Scalar Volume CLI module
-    cliParams = {'InputVolume': inputVolume.GetID(), 'OutputVolume': outputVolume.GetID(), 'ThresholdValue' : imageThreshold, 'ThresholdType' : 'Above'}
-    cliNode = slicer.cli.run(slicer.modules.thresholdscalarvolume, None, cliParams, wait_for_completion=True)
-
-    # Capture screenshot
-    if enableScreenshots:
-      self.takeScreenshot('dataExplorerTest-Start','MyScreenshot',-1)
-
-    logging.info('Processing completed')
-
-    return True
-
-
-class dataExplorerTest(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_dataExplorer1()
-
-  def test_dataExplorer1(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 = dataExplorerLogic()
-    self.assertIsNotNone( logic.hasImageData(volumeNode) )
-    self.delayDisplay('Test passed!')

dataExplorer/loadPatient.py → slicerModules/loadPatient.py

@@ -22,8 +22,6 @@ class loadPatientLogic(slicer.ScriptedLoadableModule.ScriptedLoadableModuleLogic
     def __init__(self,parent):
        slicer.ScriptedLoadableModule.ScriptedLoadableModuleLogic.__init__(self, parent)
 
-       #self.plugin=slicer.modules.dicomPlugins['DicomRtImportExportPlugin']()
-       #self.volumePlugin=slicer.modules.dicomPlugins['DICOMScalarVolumePlugin']()
        self.dicomLoader=loadDicom.loadDicomLogic(self)
        self.dicomImporter=importDicom.importDicomLogic(self)
        self.dicomImporter.local=self.local