def initializeDICOMDatabase(self):
# Create alias for convenience
slicer.dicomDatabase = slicer.app.dicomDatabase()
# Set the dicom pre-cache tags once all plugin classes have been initialized.
# Pre-caching tags is very important for fast DICOM loading because tags that are
# not pre-cached during DICOM import in bulk, will be cached during Examine step one-by-one
# (which takes magnitudes more time).
tagsToPrecache = list(slicer.dicomDatabase.tagsToPrecache)
for pluginClass in slicer.modules.dicomPlugins:
plugin = slicer.modules.dicomPlugins[pluginClass]()
tagsToPrecache += list(plugin.tags.values())
tagsToPrecache = sorted(set(tagsToPrecache)) # remove duplicates
slicer.dicomDatabase.tagsToPrecache = tagsToPrecache
# Try to initialize the database using the location stored in settings
if slicer.app.commandOptions().testingEnabled:
# For automatic tests (use a separate DICOM database for testing)
slicer.dicomDatabaseDirectorySettingsKey = 'DatabaseDirectoryTest_' + ctk.ctkDICOMDatabase(
).schemaVersion()
databaseDirectory = os.path.join(
slicer.app.temporaryPath, 'temp' + slicer.app.applicationName +
'DICOMDatabase_' + ctk.ctkDICOMDatabase().schemaVersion())
else:
# For production
slicer.dicomDatabaseDirectorySettingsKey = 'DatabaseDirectory_' + ctk.ctkDICOMDatabase(
).schemaVersion()
settings = qt.QSettings()
databaseDirectory = settings.value(
slicer.dicomDatabaseDirectorySettingsKey)
if not databaseDirectory:
documentsLocation = qt.QStandardPaths.DocumentsLocation
documents = qt.QStandardPaths.writableLocation(
documentsLocation)
databaseDirectory = os.path.join(
documents, slicer.app.applicationName + "DICOMDatabase")
settings.setValue(slicer.dicomDatabaseDirectorySettingsKey,
databaseDirectory)
# Attempt to open the database. If it fails then user will have to configure it using DICOM module.
databaseFileName = databaseDirectory + "/ctkDICOM.sql"
slicer.dicomDatabase.openDatabase(databaseFileName)
if slicer.dicomDatabase.isOpen:
# There is an existing database at the current location
if slicer.dicomDatabase.schemaVersionLoaded(
) != slicer.dicomDatabase.schemaVersion():
# Schema does not match, do not use it
slicer.dicomDatabase.closeDatabase()
def performPostModuleDiscoveryTasks(self):
"""Since dicom plugins are discovered while the application
is initialized, they may be found after the DICOM module
itself if initialized. This method is tied to a singleShot
that will be called once the event loop is read to start.
"""
if slicer.mrmlScene.GetTagByClassName(
"vtkMRMLScriptedModuleNode") != 'ScriptedModule':
slicer.mrmlScene.RegisterNodeClass(vtkMRMLScriptedModuleNode())
# initialize the dicom infrastructure
slicer.dicomDatabase = None
settings = qt.QSettings()
# the dicom database is a global object for slicer
if settings.contains('DatabaseDirectory'):
databaseDirectory = settings.value('DatabaseDirectory')
if databaseDirectory:
slicer.dicomDatabase = ctk.ctkDICOMDatabase()
slicer.dicomDatabase.openDatabase(
databaseDirectory + "/ctkDICOM.sql", "SLICER")
if not slicer.dicomDatabase.isOpen:
# can't open the database, so prompt the user later if they enter module
slicer.dicomDatabase = None
else:
self.startListener()
if slicer.dicomDatabase:
slicer.app.setDICOMDatabase(slicer.dicomDatabase)
# set the dicom pre-cache tags once all plugin classes have been initialized
DICOMLib.setDatabasePrecacheTags()
if not slicer.app.commandOptions().noMainWindow:
# add to the main app file menu
self.addMenu()
# add the settings options
self.settingsPanel = DICOMSettingsPanel()
slicer.app.settingsDialog().addPanel("DICOM", self.settingsPanel)
dataProbe = slicer.util.mainWindow().findChild(
"QWidget", "DataProbeCollapsibleWidget")
self.wasDataProbeVisible = dataProbe.isVisible()
layoutManager = slicer.app.layoutManager()
layoutManager.layoutChanged.connect(self.onLayoutChanged)
layout = ("<layout type=\"horizontal\">"
" <item>"
" <dicombrowser></dicombrowser>"
" </item>"
"</layout>")
layoutNode = slicer.app.layoutManager().layoutLogic(
).GetLayoutNode()
layoutNode.AddLayoutDescription(
slicer.vtkMRMLLayoutNode.SlicerLayoutDicomBrowserView, layout)
self.currentViewArrangement = layoutNode.GetViewArrangement()
self.previousViewArrangement = layoutNode.GetViewArrangement()
self.detailsPopup = None
self.viewWidget = None
self.browserSettingsWidget = None
self.setDetailsPopup(DICOMWidget.getSavedDICOMDetailsWidgetType()())
def createTemporaryDatabase(directory=None):
""" Open temporary DICOM database, return new database object
"""
# Specify temporary directory
if not directory or directory == '':
from time import gmtime, strftime
directory = strftime("%Y%m%d_%H%M%S_", gmtime()) + 'TempDICOMDatabase'
if os.path.isabs(directory):
tempDatabaseDir = directory
else:
tempDatabaseDir = slicer.app.temporaryPath + '/' + directory
logging.info('Switching to temporary DICOM database: ' + tempDatabaseDir)
if not os.access(tempDatabaseDir, os.F_OK):
qt.QDir().mkpath(tempDatabaseDir)
databaseFileName = tempDatabaseDir + "/ctkDICOM.sql"
dicomDatabase = ctk.ctkDICOMDatabase()
dicomDatabase.openDatabase(databaseFileName)
if dicomDatabase.isOpen:
if dicomDatabase.schemaVersionLoaded() != dicomDatabase.schemaVersion():
dicomDatabase.closeDatabase()
if dicomDatabase.isOpen:
return dicomDatabase
else:
return None
def performPostModuleDiscoveryTasks(self):
"""Since dicom plugins are discovered while the application
is initialized, they may be found after the DICOM module
itself if initialized. This method is tied to a singleShot
that will be called once the event loop is read to start.
"""
if slicer.mrmlScene.GetTagByClassName( "vtkMRMLScriptedModuleNode" ) != 'ScriptedModule':
slicer.mrmlScene.RegisterNodeClass(vtkMRMLScriptedModuleNode())
# initialize the dicom infrastructure
slicer.dicomDatabase = None
settings = qt.QSettings()
# the dicom database is a global object for slicer
if settings.contains('DatabaseDirectory'):
databaseDirectory = settings.value('DatabaseDirectory')
if databaseDirectory:
slicer.dicomDatabase = ctk.ctkDICOMDatabase()
slicer.dicomDatabase.openDatabase(databaseDirectory + "/ctkDICOM.sql", "SLICER")
if not slicer.dicomDatabase.isOpen:
# can't open the database, so prompt the user later if they enter module
slicer.dicomDatabase = None
else:
self.startListener()
if slicer.dicomDatabase:
slicer.app.setDICOMDatabase(slicer.dicomDatabase)
# set the dicom pre-cache tags once all plugin classes have been initialized
DICOMLib.setDatabasePrecacheTags()
if not slicer.app.commandOptions().noMainWindow:
# add to the main app file menu
self.addMenu()
# add the settings options
self.settingsPanel = DICOMSettingsPanel()
slicer.app.settingsDialog().addPanel("DICOM", self.settingsPanel)
def __init__(self, parent):
ScriptedLoadableModule.__init__(self, parent)
import string
self.parent.title = "DICOM"
self.parent.categories = ["", "Informatics"] # top level module
self.parent.contributors = ["Steve Pieper (Isomics)"]
self.parent.helpText = string.Template("""
The DICOM module integrates DICOM classes from CTK (based on DCMTK). See <a href=\"$a/Documentation/$b.$c/Modules/DICOM\">the documentaiton</a> for more information.
""").substitute({
'a': parent.slicerWikiUrl,
'b': slicer.app.majorVersion,
'c': slicer.app.minorVersion
})
self.parent.acknowledgementText = """
This work is supported by NA-MIC, NAC, BIRN, NCIGT, and the Slicer Community. See <a href=http://www.slicer.org>http://www.slicer.org</a> for details. Module implemented by Steve Pieper. Based on work from CommonTK (http://www.commontk.org).
"""
self.parent.icon = qt.QIcon(':Icons/Medium/SlicerLoadDICOM.png')
self.parent.dependencies = ["SubjectHierarchy"]
if slicer.mrmlScene.GetTagByClassName(
"vtkMRMLScriptedModuleNode") != 'ScriptedModule':
slicer.mrmlScene.RegisterNodeClass(vtkMRMLScriptedModuleNode())
# initialize the dicom infrastructure
slicer.dicomDatabase = None
settings = qt.QSettings()
# the dicom database is a global object for slicer
if settings.contains('DatabaseDirectory'):
databaseDirectory = settings.value('DatabaseDirectory')
if databaseDirectory:
slicer.dicomDatabase = ctk.ctkDICOMDatabase()
slicer.dicomDatabase.openDatabase(
databaseDirectory + "/ctkDICOM.sql", "SLICER")
if not slicer.dicomDatabase.isOpen:
# can't open the database, so prompt the user later if they enter module
slicer.dicomDatabase = None
else:
# the dicom listener is also global, but only started on app start if
# the user so chooses
if settings.contains('DICOM/RunListenerAtStart'):
if settings.value(
'DICOM/RunListenerAtStart') == 'true':
if not hasattr(slicer, 'dicomListener'):
try:
slicer.dicomListener = DICOMLib.DICOMListener(
slicer.dicomDatabase)
slicer.dicomListener.start()
except (UserWarning, OSError) as message:
logging.error(
'Problem trying to start DICOMListener:\n %s'
% message)
if slicer.dicomDatabase:
slicer.app.setDICOMDatabase(slicer.dicomDatabase)
# Trigger the menu to be added when application has started up
if not slicer.app.commandOptions().noMainWindow:
qt.QTimer.singleShot(0, self.addMenu)
# set the dicom pre-cache tags once all plugin classes have been initialized
qt.QTimer.singleShot(0, DICOMLib.setDatabasePrecacheTags)
def __init__(self, parent):
ScriptedLoadableModule.__init__(self, parent)
import string
self.parent.title = "DICOM"
self.parent.categories = ["", "Informatics"] # top level module
self.parent.contributors = ["Steve Pieper (Isomics)"]
self.parent.helpText = """
The DICOM module integrates DICOM classes from CTK (based on DCMTK).
"""
self.parent.helpText += self.getDefaultModuleDocumentationLink()
self.parent.acknowledgementText = """
This work is supported by NA-MIC, NAC, BIRN, NCIGT, and the Slicer Community. See <a href=http://www.slicer.org>http://www.slicer.org</a> for details. Module implemented by Steve Pieper. Based on work from CommonTK (http://www.commontk.org).
"""
self.parent.icon = qt.QIcon(':Icons/Medium/SlicerLoadDICOM.png')
self.parent.dependencies = ["SubjectHierarchy"]
if slicer.mrmlScene.GetTagByClassName(
"vtkMRMLScriptedModuleNode") != 'ScriptedModule':
slicer.mrmlScene.RegisterNodeClass(vtkMRMLScriptedModuleNode())
# initialize the dicom infrastructure
slicer.dicomDatabase = None
settings = qt.QSettings()
# the dicom database is a global object for slicer
if settings.contains('DatabaseDirectory'):
databaseDirectory = settings.value('DatabaseDirectory')
if databaseDirectory:
slicer.dicomDatabase = ctk.ctkDICOMDatabase()
slicer.dicomDatabase.openDatabase(
databaseDirectory + "/ctkDICOM.sql", "SLICER")
if not slicer.dicomDatabase.isOpen:
# can't open the database, so prompt the user later if they enter module
slicer.dicomDatabase = None
else:
# the dicom listener is also global, but only started on app start if
# the user so chooses
if settings.contains('DICOM/RunListenerAtStart'):
if settings.value(
'DICOM/RunListenerAtStart') == 'true':
if not hasattr(slicer, 'dicomListener'):
try:
slicer.dicomListener = DICOMLib.DICOMListener(
slicer.dicomDatabase)
slicer.dicomListener.start()
except (UserWarning, OSError) as message:
logging.error(
'Problem trying to start DICOMListener:\n %s'
% message)
if slicer.dicomDatabase:
slicer.app.setDICOMDatabase(slicer.dicomDatabase)
# Tasks to execute after the application has started up
slicer.app.connect("startupCompleted()",
self.performPostModuleDiscoveryTasks)
def __init__(self, parent):
ScriptedLoadableModule.__init__(self, parent)
import string
self.parent.title = "DICOM"
self.parent.categories = ["", "Informatics"] # top level module
self.parent.contributors = ["Steve Pieper (Isomics)"]
self.parent.helpText = """
The DICOM module integrates DICOM classes from CTK (based on DCMTK).
"""
self.parent.helpText += self.getDefaultModuleDocumentationLink()
self.parent.acknowledgementText = """
This work is supported by NA-MIC, NAC, BIRN, NCIGT, and the Slicer Community. See <a href=http://www.slicer.org>http://www.slicer.org</a> for details. Module implemented by Steve Pieper. Based on work from CommonTK (http://www.commontk.org).
"""
self.parent.icon = qt.QIcon(':Icons/Medium/SlicerLoadDICOM.png')
self.parent.dependencies = ["SubjectHierarchy"]
if slicer.mrmlScene.GetTagByClassName( "vtkMRMLScriptedModuleNode" ) != 'ScriptedModule':
slicer.mrmlScene.RegisterNodeClass(vtkMRMLScriptedModuleNode())
# initialize the dicom infrastructure
slicer.dicomDatabase = None
settings = qt.QSettings()
# the dicom database is a global object for slicer
if settings.contains('DatabaseDirectory'):
databaseDirectory = settings.value('DatabaseDirectory')
if databaseDirectory:
slicer.dicomDatabase = ctk.ctkDICOMDatabase()
slicer.dicomDatabase.openDatabase(databaseDirectory + "/ctkDICOM.sql", "SLICER")
if not slicer.dicomDatabase.isOpen:
# can't open the database, so prompt the user later if they enter module
slicer.dicomDatabase = None
else:
# the dicom listener is also global, but only started on app start if
# the user so chooses
if settings.contains('DICOM/RunListenerAtStart'):
if settings.value('DICOM/RunListenerAtStart') == 'true':
if not hasattr(slicer, 'dicomListener'):
try:
slicer.dicomListener = DICOMLib.DICOMListener(slicer.dicomDatabase)
slicer.dicomListener.start()
except (UserWarning,OSError) as message:
logging.error('Problem trying to start DICOMListener:\n %s' % message)
if slicer.dicomDatabase:
slicer.app.setDICOMDatabase(slicer.dicomDatabase)
# Trigger the menu to be added when application has started up
if not slicer.app.commandOptions().noMainWindow :
qt.QTimer.singleShot(0, self.addMenu)
# set the dicom pre-cache tags once all plugin classes have been initialized
qt.QTimer.singleShot(0, DICOMLib.setDatabasePrecacheTags)
def onDatabaseDirectoryChanged(self,databaseDirectory):
if not hasattr(slicer, 'dicomDatabase') or not slicer.dicomDatabase:
slicer.dicomDatabase = ctk.ctkDICOMDatabase()
setDatabasePrecacheTags(self.dicomBrowser)
databaseFilepath = databaseDirectory + "/ctkDICOM.sql"
messages = ""
if not os.path.exists(databaseDirectory):
try:
os.mkdir(databaseDirectory)
except OSError:
messages += "Directory does not exist and cannot be created. "
else:
if not os.access(databaseDirectory, os.W_OK):
messages += "Directory not writable. "
if not os.access(databaseDirectory, os.R_OK):
messages += "Directory not readable. "
if os.listdir(databaseDirectory) and not os.path.isfile(databaseFilepath):
# Prevent users from the error of trying to import a DICOM directory by selecting it as DICOM database path
messages += "Directory is not empty and not an existing DICOM database."
if messages != "":
slicer.util.warningDisplay('The database file path "%s" cannot be used. %s\n'
'Please pick a different database directory using the '
'LocalDatabase button in the DICOM Browser' % (databaseFilepath,messages),
windowTitle="DICOM")
else:
slicer.dicomDatabase.openDatabase(databaseDirectory + "/ctkDICOM.sql", "SLICER")
if not slicer.dicomDatabase.isOpen:
slicer.util.warningDisplay('The database file path "%s" cannot be opened.\n'
'Please pick a different database directory using the '
'LocalDatabase button in the DICOM Browser.' % databaseFilepath,
windowTitle="DICOM")
self.dicomDatabase = None
else:
if self.dicomBrowser:
if self.dicomBrowser.databaseDirectory != databaseDirectory:
self.dicomBrowser.databaseDirectory = databaseDirectory
else:
settings = qt.QSettings()
settings.setValue('DatabaseDirectory', databaseDirectory)
settings.sync()
if slicer.dicomDatabase:
slicer.app.setDICOMDatabase(slicer.dicomDatabase)
def onDatabaseDirectoryChanged(self,databaseDirectory):
if not hasattr(slicer, 'dicomDatabase') or not slicer.dicomDatabase:
slicer.dicomDatabase = ctk.ctkDICOMDatabase()
setDatabasePrecacheTags(self.dicomBrowser)
databaseFilepath = databaseDirectory + "/ctkDICOM.sql"
messages = ""
if not os.path.exists(databaseDirectory):
try:
os.mkdir(databaseDirectory)
except OSError:
messages += "Directory does not exist and cannot be created. "
else:
if not os.access(databaseDirectory, os.W_OK):
messages += "Directory not writable. "
if not os.access(databaseDirectory, os.R_OK):
messages += "Directory not readable. "
if os.listdir(databaseDirectory) and not os.path.isfile(databaseFilepath):
# Prevent users from the error of trying to import a DICOM directory by selecting it as DICOM database path
messages += "Directory is not empty and not an existing DICOM database."
if messages != "":
slicer.util.warningDisplay('The database file path "%s" cannot be used. %s\n'
'Please pick a different database directory using the '
'LocalDatabase button in the DICOM Browser' % (databaseFilepath,messages),
windowTitle="DICOM")
else:
slicer.dicomDatabase.openDatabase(databaseDirectory + "/ctkDICOM.sql", "SLICER")
if not slicer.dicomDatabase.isOpen:
slicer.util.warningDisplay('The database file path "%s" cannot be opened.\n'
'Please pick a different database directory using the '
'LocalDatabase button in the DICOM Browser.' % databaseFilepath,
windowTitle="DICOM")
self.dicomDatabase = None
else:
if self.dicomBrowser:
if self.dicomBrowser.databaseDirectory != databaseDirectory:
self.dicomBrowser.databaseDirectory = databaseDirectory
else:
settings = qt.QSettings()
settings.setValue('DatabaseDirectory', databaseDirectory)
settings.sync()
if slicer.dicomDatabase:
slicer.app.setDICOMDatabase(slicer.dicomDatabase)
def performPostModuleDiscoveryTasks(self):
"""Since dicom plugins are discovered while the application
is initialized, they may be found after the DICOM module
itself if initialized. This method is tied to a singleShot
that will be called once the event loop is read to start.
"""
if slicer.mrmlScene.GetTagByClassName(
"vtkMRMLScriptedModuleNode") != 'ScriptedModule':
slicer.mrmlScene.RegisterNodeClass(vtkMRMLScriptedModuleNode())
# initialize the dicom infrastructure
slicer.dicomDatabase = None
settings = qt.QSettings()
# the dicom database is a global object for slicer
if settings.contains('DatabaseDirectory'):
databaseDirectory = settings.value('DatabaseDirectory')
if databaseDirectory:
slicer.dicomDatabase = ctk.ctkDICOMDatabase()
slicer.dicomDatabase.openDatabase(
databaseDirectory + "/ctkDICOM.sql", "SLICER")
if not slicer.dicomDatabase.isOpen:
# can't open the database, so prompt the user later if they enter module
slicer.dicomDatabase = None
else:
self.startListener()
if slicer.dicomDatabase:
slicer.app.setDICOMDatabase(slicer.dicomDatabase)
# set the dicom pre-cache tags once all plugin classes have been initialized
DICOMLib.setDatabasePrecacheTags()
if not slicer.app.commandOptions().noMainWindow:
# add to the main app file menu
self.addMenu()
# add the settings options
self.settingsPanel = DICOMSettingsPanel()
slicer.app.settingsDialog().addPanel("DICOM", self.settingsPanel)