How to load an entire entire dicom directory using the widget button on a python code?

Rahul_Banerjee · June 6, 2018, 1:42pm

I could only load individual files using the default slicelet code given on the website and the documentation, would like help as I want to upload an entire dicom directory.

lassoan · June 6, 2018, 8:41pm

You can use DICOMLib.DICOMUtils.LoadDICOMFilesToDatabase See complete example here:

github.com

Slicer/Slicer/blob/5ec342768faff961fd3b236935dfe95d7198b117/Applications/SlicerApp/Testing/Python/SubjectHierarchyGenericSelfTest.py#L165-L184


try:
  # Open test database and empty it
  with DICOMUtils.TemporaryDICOMDatabase(self.dicomDatabaseDir) as db:
    self.assertTrue( db.isOpen )
    self.assertEqual( slicer.dicomDatabase, db)


    # Download, unzip, import, and load data. Verify loaded nodes.
    loadedNodes = {'vtkMRMLScalarVolumeNode':1}
    with DICOMUtils.LoadDICOMFilesToDatabase( \
        self.dicomZipFileUrl, self.dicomZipFilePath, \
        self.dicomDataDir, self.expectedNumOfFilesInDicomDataDir, \
        {}, loadedNodes) as success:
      self.assertTrue(success)


  self.assertEqual( len( slicer.util.getNodes('vtkMRMLSubjectHierarchyNode*') ), 1 )


except Exception, e:
  import traceback
  traceback.print_exc()
  self.delayDisplay('Test caused exception!\n' + str(e),self.delayMs*2)

See also this post: Imported dicom files do not show in the dicomDatabase

Rahul_Banerjee · June 7, 2018, 5:40am

How do I get the following segment to load dicom database, instead of the individual files it is loading at present?

loadDataButton = qt.QPushButton(“Load Data”)
hlayout.addWidget(loadDataButton)
loadDataButton.connect(‘clicked()’, slicer.util.openAddVolumeDialog)

Entire Code:

def onModuleSelected(modulename):
  global tabWidget
  scrollArea = qt.QScrollArea(tabWidget)
  scrollArea.setWidget(getattr(slicer.modules, modulename.lower()).widgetRepresentation())
  scrollArea.setHorizontalScrollBarPolicy(qt.Qt.ScrollBarAlwaysOff)
  scrollArea.setWidgetResizable(True)
  tabWidget.addTab(scrollArea, modulename)



import qt
import __main__try:
 



mainWidget = qt.QWidget()
mainWidget.objectName = "qSlicerAppMainWindow"
vlayout = qt.QVBoxLayout()
mainWidget.setLayout(vlayout)


# splitter between "layout" and "bottom frame"
#splitter = qt.QSplitter()
#splitter.orientation = qt.Qt.Vertical
#vlayout = qt.QVBoxLayout()
#vlayout.addWidget(splitter)

# layout
layoutManager = slicer.qMRMLLayoutWidget()
layoutManager.setMRMLScene(slicer.mrmlScene)
layoutManager.setLayout(slicer.vtkMRMLLayoutNode.SlicerLayoutOneUp3DView)
vlayout.addWidget(layoutManager)

# Bottom frame: including control buttons and tab widget
bottomFrame = qt.QFrame()
bottomVlayout = qt.QVBoxLayout()
bottomFrame.setLayout(bottomVlayout)
vlayout.addWidget(bottomFrame)

# Horizontal layout: Load Data, Save Data, Module Selector
hlayout = qt.QHBoxLayout()
bottomVlayout.addLayout(hlayout)

loadDataButton = qt.QPushButton("Load Data")
#loadDataButton = Button(root, text="Load Data", command=browsefunc)
#loadDataButton.pack()
hlayout.addWidget(loadDataButton)
#loadDataButton.connect('clicked()', browsefunc)
loadDataButton.connect('clicked()', slicer.util.openAddVolumeDialog)
#loadDataButton.connect('clicked()', slicer.util.loadVolume('/path/of/*'))
#loadDataButton.connect('clicked()',DICOMUtils.LoadDICOMFilesToDatabase)


saveDataButton = qt.QPushButton("Save Data")
hlayout.addWidget(saveDataButton)
saveDataButton.connect('clicked()', slicer.util.openSaveDataDialog)

moduleSelector = slicer.qSlicerModuleSelectorToolBar()
moduleSelector.setModuleManager(slicer.app.moduleManager())
hlayout.addWidget(moduleSelector)
#moduleSelector.connect('moduleSelected(QString)', onModuleSelected)



# Tab widget
tabWidget = qt.QTabWidget()
bottomVlayout.addWidget(tabWidget)

# Connections
moduleSelector.connect('moduleSelected(QString)', onModuleSelected)

# Initialize
modules = ["volumes", "models", "labelstatistics"]
for module in modules:
  onModuleSelected(module)

#tabWidget.show()
mainWidget.show()
#__main__.tabWidget = tabWidget # Keep track of the widget to avoid its premature destruction


__main__.mainWidget = mainWidget # Keep track of the widget to avoid its premature destruction

Rahul_Banerjee · June 7, 2018, 5:41am

How do I get the following segment to load dicom database, instead of the individual files it is loading at present?

loadDataButton = qt.QPushButton(“Load Data”)
hlayout.addWidget(loadDataButton)
loadDataButton.connect(‘clicked()’, slicer.util.openAddVolumeDialog)

Entire Code:

def onModuleSelected(modulename):

global tabWidget

scrollArea = qt.QScrollArea(tabWidget)

scrollArea.setWidget(getattr(slicer.modules, modulename.lower()).widgetRepresentation())

scrollArea.setHorizontalScrollBarPolicy(qt.Qt.ScrollBarAlwaysOff)

scrollArea.setWidgetResizable(True)

tabWidget.addTab(scrollArea, modulename)

import qt

import __main__try:

mainWidget = qt.QWidget()

mainWidget.objectName = “qSlicerAppMainWindow”

vlayout = qt.QVBoxLayout()

mainWidget.setLayout(vlayout)

# splitter between “layout” and “bottom frame”
#splitter = qt.QSplitter()

#splitter.orientation = qt.Qt.Vertical

#vlayout = qt.QVBoxLayout()

#vlayout.addWidget(splitter)

# layout
layoutManager = slicer.qMRMLLayoutWidget()

layoutManager.setMRMLScene(slicer.mrmlScene)

layoutManager.setLayout(slicer.vtkMRMLLayoutNode.SlicerLayoutOneUp3DView)

vlayout.addWidget(layoutManager)

# Bottom frame: including control buttons and tab widget
bottomFrame = qt.QFrame()

bottomVlayout = qt.QVBoxLayout()

bottomFrame.setLayout(bottomVlayout)

vlayout.addWidget(bottomFrame)

# Horizontal layout: Load Data, Save Data, Module Selector
hlayout = qt.QHBoxLayout()

bottomVlayout.addLayout(hlayout)

loadDataButton = qt.QPushButton(“Load Data”)

#loadDataButton = Button(root, text=“Load Data”, command=browsefunc)

#loadDataButton.pack()

hlayout.addWidget(loadDataButton)

#loadDataButton.connect(‘clicked()’, browsefunc)

loadDataButton.connect(‘clicked()’, slicer.util.openAddVolumeDialog)

#loadDataButton.connect(‘clicked()’, slicer.util.loadVolume(’/path/of/*’))

#loadDataButton.connect(‘clicked()’,DICOMUtils.LoadDICOMFilesToDatabase)

saveDataButton = qt.QPushButton(“Save Data”)

hlayout.addWidget(saveDataButton)

saveDataButton.connect(‘clicked()’, slicer.util.openSaveDataDialog)

moduleSelector = slicer.qSlicerModuleSelectorToolBar()

moduleSelector.setModuleManager(slicer.app.moduleManager())

hlayout.addWidget(moduleSelector)

#moduleSelector.connect(‘moduleSelected(QString)’, onModuleSelected)

# Tab widget
tabWidget = qt.QTabWidget()

bottomVlayout.addWidget(tabWidget)

# Connections
moduleSelector.connect(‘moduleSelected(QString)’, onModuleSelected)

# Initialize
modules = [“volumes”, “models”, “labelstatistics”]

for module in modules:

onModuleSelected(module)

#tabWidget.show()

mainWidget.show()

#**main**.tabWidget = tabWidget # Keep track of the widget to avoid its premature destruction

**main**.mainWidget = mainWidget # Keep track of the widget to avoid its premature destruction

lassoan · June 7, 2018, 2:29pm

Please provide more information. It is not obvious what you would like to do, what do you expect your current code should do, and what happens instead.

The forum is good for discussion but not well suited for code review. If you upload your code to github and send a link to it then there is a better chance that somebody can look at it and give you feeback.

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How to load an entire entire dicom directory using the widget button on a python code?

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