def onDatabaseDirectoryChanged(self,databaseDirectory):
if not hasattr(slicer, 'dicomDatabase') or not slicer.dicomDatabase:
slicer.dicomDatabase = ctk.ctkDICOMDatabase()
DICOM.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 messages != "":
self.messageBox('The database file path "%s" cannot be used. %s\nPlease pick a different database directory using the LocalDatabase button in the DICOM Browser.' % (databaseFilepath,messages))
else:
slicer.dicomDatabase.openDatabase(databaseDirectory + "/ctkDICOM.sql", "SLICER")
if not slicer.dicomDatabase.isOpen:
self.messageBox('The database file path "%s" cannot be opened.\nPlease pick a different database directory using the LocalDatabase button in the DICOM Browser.' % databaseFilepath)
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()
self.setDatabasePrecacheTags()
databaseFilepath = databaseDirectory + "/ctkDICOM.sql"
messages = ""
if not os.path.exists(databaseDirectory):
messages += "Directory does not exist. "
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 messages != "":
self.messageBox(
'The database file path "%s" cannot be used. %s\nPlease pick a different database directory using the LocalDatabase button in the DICOM Browser.'
% (databaseFilepath, messages))
else:
slicer.dicomDatabase.openDatabase(
databaseDirectory + "/ctkDICOM.sql", "SLICER")
if not slicer.dicomDatabase.isOpen:
self.messageBox(
'The database file path "%s" cannot be opened.\nPlease pick a different database directory using the LocalDatabase button in the DICOM Browser.'
% databaseFilepath)
self.dicomDatabase = None
else:
if self.dicomApp:
if self.dicomApp.databaseDirectory != databaseDirectory:
self.dicomApp.databaseDirectory = databaseDirectory
else:
settings = qt.QSettings()
settings.setValue('DatabaseDirectory', databaseDirectory)
settings.sync()
if slicer.dicomDatabase:
slicer.app.setDICOMDatabase(slicer.dicomDatabase)
def __init__(self, parent):
parent.title = "DICOM"
parent.category = "Work in Progress"
parent.contributor = "Steve Pieper"
parent.helpText = """
The DICOM module is a place to experiment a bit with dicom classes from CTK (based on DCMTK). It is a 'tent' because it is meant to be suitable for explorers, but may not be robust enough for civilized people.
Warning: all data directories are temporary and data may be gone next time you look!
"""
parent.acknowledgementText = """
This work is supported by NA-MIC, NAC, BIRN, NCIGT, and the Slicer Community. See <a>http://www.slicer.org</a> for details. Module implemented by Steve Pieper. Based on work from CommonTK (http://www.commontk.org).
"""
self.parent = parent
if slicer.mrmlScene.GetTagByClassName( "vtkMRMLScriptedModuleNode" ) != 'ScriptedModule':
slicer.mrmlScene.RegisterNodeClass(vtkMRMLScriptedModuleNode())
# initialize the dicom infrastructure
settings = qt.QSettings()
# the dicom listener is also global, but only started on app start if
# the user so chooses
if settings.contains('DICOM/RunListenerAtStart'):
if bool(settings.value('DICOM/RunListenerAtStart')):
# the dicom database is a global object for slicer
databaseDirectory = settings.value('DatabaseDirectory')
if databaseDirectory:
slicer.dicomDatabase = ctk.ctkDICOMDatabase()
slicer.dicomDatabase.openDatabase(databaseDirectory + "/ctkDICOM.sql", "SLICER")
if not hasattr(slicer, 'dicomListener'):
try:
slicer.dicomListener = DICOMLib.DICOMListener(slicer.dicomDatabase)
except UserWarning as message:
# TODO: how to put this into the error log?
print ('Problem trying to start DICOMListener:\n %s' % message)
slicer.dicomListener.start()
def onDatabaseDirectoryChanged(self, databaseDirectory):
if not hasattr(slicer, 'dicomDatabase') or not slicer.dicomDatabase:
slicer.dicomDatabase = ctk.ctkDICOMDatabase()
self.setDatabasePrecacheTags()
databaseFilepath = databaseDirectory + "/ctkDICOM.sql"
if not (os.access(databaseDirectory, os.W_OK)
and os.access(databaseDirectory, os.R_OK)):
self.messageBox('The database file path "%s" cannot be opened.' %
databaseFilepath)
else:
slicer.dicomDatabase.openDatabase(
databaseDirectory + "/ctkDICOM.sql", "SLICER")
if not slicer.dicomDatabase.isOpen:
self.messageBox(
'The database file path "%s" cannot be opened.' %
databaseFilepath)
self.dicomDatabase = None
else:
if self.dicomApp:
if self.dicomApp.databaseDirectory != databaseDirectory:
self.dicomApp.databaseDirectory = databaseDirectory
else:
settings = qt.QSettings()
settings.setValue('DatabaseDirectory', databaseDirectory)
settings.sync()
if slicer.dicomDatabase:
slicer.app.setDICOMDatabase(slicer.dicomDatabase)
def __init__(self, parent):
import string
parent.title = "DICOM"
parent.categories = ["", "Informatics"] # top level module
parent.contributors = ["Steve Pieper (Isomics)"]
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
})
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).
"""
parent.icon = qt.QIcon(':Icons/Medium/SlicerLoadDICOM.png')
self.parent = parent
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:
# TODO: how to put this into the error log?
print(
'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, DICOM.setDatabasePrecacheTags)
def onDatabaseDirectoryChanged(self,databaseDirectory):
if not hasattr(slicer, 'dicomDatabase'):
slicer.dicomDatabase = ctk.ctkDICOMDatabase()
databaseFilepath = databaseDirectory + "/ctkDICOM.sql"
if not (os.access(databaseDirectory, os.W_OK) and os.access(databaseDirectory, os.R_OK)):
self.messageBox('The database file path "%s" cannot be opened.' % databaseFilepath)
return
slicer.dicomDatabase.openDatabase(databaseDirectory + "/ctkDICOM.sql", "SLICER")
if not slicer.dicomDatabase.isOpen:
self.messageBox('The database file path "%s" cannot be opened.' % databaseFilepath)
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:
# TODO: how to put this into the error log?
print ('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, DICOM.setDatabasePrecacheTags)
def onDatabaseDirectoryChanged(self, databaseDirectory):
if not hasattr(slicer, 'dicomDatabase'):
slicer.dicomDatabase = ctk.ctkDICOMDatabase()
databaseFilepath = databaseDirectory + "/ctkDICOM.sql"
if not (os.access(databaseDirectory, os.W_OK)
and os.access(databaseDirectory, os.R_OK)):
self.messageBox('The database file path "%s" cannot be opened.' %
databaseFilepath)
return
slicer.dicomDatabase.openDatabase(databaseDirectory + "/ctkDICOM.sql",
"SLICER")
if not slicer.dicomDatabase.isOpen:
self.messageBox('The database file path "%s" cannot be opened.' %
databaseFilepath)
def __init__(self, parent):
import string
parent.title = "DICOM"
parent.categories = ["", "Informatics"] # top level module
parent.contributors = ["Steve Pieper (Isomics)"]
parent.helpText = string.Template(
"""
The DICOM module integrates DICOM classes from CTK (based on DCMTK). See <a href=\"$a/Documentation/$b.$c/Modules/DICOM\">$a/Documentation/$b.$c/Modules/DICOM</a> for more information.
"""
).substitute({"a": parent.slicerWikiUrl, "b": slicer.app.majorVersion, "c": slicer.app.minorVersion})
parent.acknowledgementText = """
This work is supported by NA-MIC, NAC, BIRN, NCIGT, and the Slicer Community. See <a>http://www.slicer.org</a> for details. Module implemented by Steve Pieper. Based on work from CommonTK (http://www.commontk.org).
"""
parent.icon = qt.QIcon(":Icons/Medium/SlicerLoadDICOM.png")
self.parent = parent
if slicer.mrmlScene.GetTagByClassName("vtkMRMLScriptedModuleNode") != "ScriptedModule":
slicer.mrmlScene.RegisterNodeClass(vtkMRMLScriptedModuleNode())
# initialize the dicom infrastructure
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")
# the dicom listener is also global, but only started on app start if
# the user so chooses
if settings.contains("DICOM/RunListenerAtStart"):
if bool(settings.value("DICOM/RunListenerAtStart")):
if not hasattr(slicer, "dicomListener"):
try:
slicer.dicomListener = DICOMLib.DICOMListener(slicer.dicomDatabase)
slicer.dicomListener.start()
except (UserWarning, OSError) as message:
# TODO: how to put this into the error log?
print("Problem trying to start DICOMListener:\n %s" % message)
else:
slicer.dicomDatabase = None
# Trigger the menu to be added when application has started up
if not slicer.app.commandOptions().noMainWindow:
qt.QTimer.singleShot(0, self.addMenu)
def __init__(self, parent=None):
self.testingServer = None
self.dicomDatabase = ctk.ctkDICOMDatabase()
# TODO: are these wrapped so we can avoid magic numbers?
self.dicomModelUIDRole = 32
self.dicomModelTypeRole = self.dicomModelUIDRole + 1
self.dicomModelTypes = ('Root', 'Patient', 'Study', 'Series', 'Image')
if not parent:
self.parent = slicer.qMRMLWidget()
self.parent.setLayout(qt.QVBoxLayout())
self.parent.setMRMLScene(slicer.mrmlScene)
self.layout = self.parent.layout()
self.setup()
self.parent.show()
else:
self.parent = parent
self.layout = parent.layout()
def onDatabaseDirectoryChanged(self,databaseDirectory):
if not hasattr(slicer, 'dicomDatabase') or not slicer.dicomDatabase:
slicer.dicomDatabase = ctk.ctkDICOMDatabase()
self.setDatabasePrecacheTags()
databaseFilepath = databaseDirectory + "/ctkDICOM.sql"
if not (os.access(databaseDirectory, os.W_OK) and os.access(databaseDirectory, os.R_OK)):
self.messageBox('The database file path "%s" cannot be opened.' % databaseFilepath)
return
slicer.dicomDatabase.openDatabase(databaseDirectory + "/ctkDICOM.sql", "SLICER")
if not slicer.dicomDatabase.isOpen:
self.messageBox('The database file path "%s" cannot be opened.' % databaseFilepath)
self.dicomDatabase = None
return
if self.dicomApp:
if self.dicomApp.databaseDirectory != databaseDirectory:
self.dicomApp.databaseDirectory = databaseDirectory
else:
settings = qt.QSettings()
settings.setValue('DatabaseDirectory', databaseDirectory)
settings.sync()
def __init__(self, parent):
parent.title = "DICOM"
parent.category = "" # top level module
parent.contributor = "Steve Pieper"
parent.helpText = """
The DICOM module is a place to experiment a bit with dicom classes from CTK (based on DCMTK). It is a 'tent' because it is meant to be suitable for explorers, but may not be robust enough for civilized people.
Warning: all data directories are temporary and data may be gone next time you look!
"""
parent.acknowledgementText = """
This work is supported by NA-MIC, NAC, BIRN, NCIGT, and the Slicer Community. See <a>http://www.slicer.org</a> for details. Module implemented by Steve Pieper. Based on work from CommonTK (http://www.commontk.org).
"""
self.parent = parent
if slicer.mrmlScene.GetTagByClassName(
"vtkMRMLScriptedModuleNode") != 'ScriptedModule':
slicer.mrmlScene.RegisterNodeClass(vtkMRMLScriptedModuleNode())
# initialize the dicom infrastructure
settings = qt.QSettings()
# the dicom database is a global object for slicer
databaseDirectory = settings.value('DatabaseDirectory')
if databaseDirectory:
slicer.dicomDatabase = ctk.ctkDICOMDatabase()
slicer.dicomDatabase.openDatabase(
databaseDirectory + "/ctkDICOM.sql", "SLICER")
# the dicom listener is also global, but only started on app start if
# the user so chooses
if settings.contains('DICOM/RunListenerAtStart'):
if bool(settings.value('DICOM/RunListenerAtStart')):
if not hasattr(slicer, 'dicomListener'):
try:
slicer.dicomListener = DICOMLib.DICOMListener(
slicer.dicomDatabase)
except UserWarning as message:
# TODO: how to put this into the error log?
print(
'Problem trying to start DICOMListener:\n %s' %
message)
slicer.dicomListener.start()
def test_RoundTrip(self):
"""
Test fiducial round trip to and from AIM XML file on disk
"""
print("ctest, please don't truncate my output: CTEST_FULL_OUTPUT")
# enter the module
mainWindow = slicer.util.mainWindow()
mainWindow.moduleSelector().selectModule('Reporting')
# l = slicer.modulelogic.vtkSlicerReportingModuleLogic()
l = slicer.modules.reporting.logic()
l.GUIHiddenOff()
# testDataPath = os.path.normpath(os.path.join(os.path.realpath(__file__), "..", "..", "Prototype/TestData/DICOM.CT/")
print("Reporting round trip test, current working directory = " +
os.getcwd())
testDataPath = os.path.join(os.getcwd(),
"../../Testing/Temporary/DICOM.CT")
# testDataPath = "/projects/birn/nicole/Slicer4/Reporting/Prototype/TestData/DICOM.CT"
print("test data path = " + testDataPath)
# set up a new DICOM database
print("Creating a dicomDatabase!")
ddb = ctk.ctkDICOMDatabase()
if not ddb:
print("ERROR: failed to create a new dicom database!")
return
dbpath = slicer.app.slicerHome + '/Testing/Temporary/TestingDCMDB/ctkDICOM.sql'
print('database path set to ' + dbpath)
if not os.path.exists(os.path.dirname(dbpath)):
print('Creating dir ' + os.path.dirname(dbpath))
os.makedirs(os.path.dirname(dbpath))
ddb.openDatabase(dbpath, "ReportingTesting")
if not ddb.isOpen:
print("ERROR: failed to open a new dicom database at path " +
dbpath)
return
retval = ddb.initializeDatabase()
if not retval:
print("ERROR: failed to init database")
return
l.InitializeDICOMDatabase(dbpath)
testFileNames = []
for n in [487, 488, 489]:
filename = os.path.join(testDataPath,
"instance_" + str(n) + ".dcm")
print("Adding file " + filename)
testFileNames.append(filename)
# check to see if the test data is already in it
patients = ddb.patients()
if len(patients) == 0:
# add the files
for filename in testFileNames:
print("Inserting file " + filename)
retval = ddb.insert(filename)
patients = ddb.patients()
if len(patients) == 0:
print("ERROR: unable to add test files to database!")
print(str(testFileNames))
return
# get the UID for the series
study = ddb.studiesForPatient(patients[0])
series = ddb.seriesForStudy(study[0])
seriesUID = series[0]
# seriesUID = "1.2.392.200103.20080913.113635.2.2009.6.22.21.43.10.23432.1"
# seriesUID = "2.16.840.1.114362.1.759508.1251415878280.192"
# seriesUID = "1.3.12.2.1107.5.1.4.53031.30000011032906120157800000219"
print("For test, using the AIM sample volume with series UID of " +
seriesUID)
fileList = ddb.filesForSeries(seriesUID)
print("fileList = " + str(fileList))
if not fileList:
print("ERROR: sample series with id " + seriesUID +
" not found in database!")
return
# add a parameter node
parameterNode = slicer.vtkMRMLScriptedModuleNode()
parameterNode.SetModuleName('Reporting')
slicer.mrmlScene.AddNode(parameterNode)
# set it to be the active parameter node
l.SetActiveParameterNodeID(parameterNode.GetID())
#
# create a new report, make it the report in the parameter node, set up hierarchy
#
reportNode = slicer.mrmlScene.CreateNodeByClass(
"vtkMRMLReportingReportNode")
reportNode.SetReferenceCount(reportNode.GetReferenceCount() - 1)
# set the color id
colorID = 'vtkMRMLColorTableNodeFileGenericAnatomyColors.txt'
reportNode.SetColorNodeID(colorID)
reportNode.SetDICOMDatabaseFileName(dbpath)
slicer.mrmlScene.AddNode(reportNode)
parameterNode.SetParameter("reportID", reportNode.GetID())
print(
"Init hierarchy for report node, set parameter node to report id of "
+ reportNode.GetID())
l.InitializeHierarchyForReport(reportNode)
#
# get some sample data from the database
#
volId = 1
volumeNode = None
volName = 'AIM volume ' + str(volId)
print("Dicom data base = " + ddb)
slicer.dicomDatabase = ddb
scalarVolumePlugin = slicer.modules.dicomPlugins[
'DICOMScalarVolumePlugin']()
scalarVolumeLoadables = scalarVolumePlugin.examine([filelist])
volumeNode = scalarVolumePlugin.load(scalarVolumeLoadables[0])
volumeNode.SetName(volName)
# print "volumeNode = ",volumeNode
print("Initialize Hierarchy For Volume with id " + volumeNode.GetID())
l.InitializeHierarchyForVolume(volumeNode)
print("---Now active mark up is " + l.GetActiveMarkupHierarchyID())
print("adding a fiducial")
#
# define a fiducial
#
fidNode = slicer.vtkMRMLAnnotationFiducialNode()
fidName = "AIM Round Trip Test Fiducial"
fidNode.SetName(fidName)
fidNode.SetSelected(1)
fidNode.SetVisible(1)
fidNode.SetLocked(0)
print("Calling set fid coords")
startCoords = [15.8, 70.8, -126.7]
fidNode.SetFiducialCoordinates(startCoords[0], startCoords[1],
startCoords[2])
print("Starting fiducial coordinates: " + str(startCoords))
# point it to the volume
fidNode.SetAttribute("AssociatedNodeID", volumeNode.GetID())
fidNode.SetScene(slicer.mrmlScene)
print("Adding text disp node")
fidNode.CreateAnnotationTextDisplayNode()
print("Adding point display node")
fidNode.CreateAnnotationPointDisplayNode()
print("add node:")
# slicer.mrmlScene.DebugOn()
# l.DebugOn()
slicer.mrmlScene.AddNode(fidNode)
print("getting slice uid")
uid = l.GetSliceUIDFromMarkUp(fidNode)
print("fidNode uid = " + uid)
#
# create a label volume
#
volumesLogic = slicer.modules.volumes.logic()
labelNode = volumesLogic.CreateLabelVolume(slicer.mrmlScene,
volumeNode, "Segmentation")
labelDisplayNode = labelNode.GetDisplayNode()
labelDisplayNode.SetAndObserveColorNodeID(
'vtkMRMLColorTableNodeFileGenericAnatomyColors.txt')
l.AddNodeToReport(labelNode)
# initialize image content
labelImage = labelNode.GetImageData()
extent = labelImage.GetExtent()
pixelCounter = 0
for k in range(extent[5]):
for j in range(extent[3]):
for i in range(extent[1]):
if pixelCounter in initializedSegmentationVoxels:
labelImage.SetScalarComponentFromFloat(i, j, k, 0, 1)
else:
labelImage.SetScalarComponentFromFloat(i, j, k, 0, 0)
pixelCounter = pixelCounter + 1
# test save to mrml
# slicer.mrmlScene.SetURL('/spl/tmp/nicole/Testing/aim/RoundTripTest.mrml')
# slicer.mrmlScene.Commit()
#
# output AIM XML
#
dirName = slicer.app.slicerHome + '/Testing/Temporary/'
reportNode.SetStorageDirectoryName(dirName)
print("Saving report to " + dirName)
retval = l.SaveReportToAIM(reportNode)
if (retval != 0):
print("ERROR: unable to save report to aim file " + dirName +
", retval=" + retval)
else:
print("Saved report to " + dirName)
self.assertEqual(retval, 0)
print("\n\n\nReloading aim file...")
#
# now clear the scene so can read in
#
# TBD: this causes a crash
# slicer.mrmlScene.Clear(0)
#
# load in the aim file
#
newReport = slicer.mrmlScene.CreateNodeByClass(
"vtkMRMLReportingReportNode")
newReport.SetReferenceCount(newReport.GetReferenceCount() - 1)
# set the default color map
newReport.SetColorNodeID(colorID)
newReport.SetDICOMDatabaseFileName(dbpath)
slicer.mrmlScene.AddNode(newReport)
parameterNode.SetParameter("reportID", newReport.GetID())
Helper.LoadAIMFile(newReport.GetID(), aimFileName)
# check the fiducial
endCoords = [0, 0, 0]
col = slicer.mrmlScene.GetNodesByClass("vtkMRMLAnnotationFiducialNode")
col.SetReferenceCount(col.GetReferenceCount() - 1)
# if the scene is not cleared, we should have 2 fiducials
nFiducials = col.GetNumberOfItems()
if nFiducials != 2:
print("Failed to read fiducial form the saved report!")
self.assertTrue(False)
f = col.GetItemAsObject(1)
f.GetFiducialCoordinates(endCoords)
print("Start Coords = " + str(startCoords[0]) + "," +
str(startCoords[1]) + "," + str(startCoords[2]))
print("End Coords = " + str(endCoords))
xdiff = endCoords[0] - startCoords[0]
ydiff = endCoords[1] - startCoords[1]
zdiff = endCoords[2] - startCoords[2]
diffTotal = xdiff + ydiff + zdiff
print(
"Difference between coordinates after loaded the aim file and value from before stored the aim file: "
+ str(xdiff) + "," + str(ydiff) + "," + str(zdiff) +
". Total difference = " + str(diffTotal))
if diffTotal > 0.1:
print("Fiducial coordinates error exceeds the allowed bounds")
self.assertTrue(False)
# check the label node
sceneVolumes = slicer.mrmlScene.GetNodesByClass(
"vtkMRMLScalarVolumeNode")
sceneVolumes.SetReferenceCount(sceneVolumes.GetReferenceCount() - 1)
sceneLabels = []
for i in range(sceneVolumes.GetNumberOfItems()):
vol = sceneVolumes.GetItemAsObject(i)
if vol.GetLabelMap():
sceneLabels.append(vol)
if len(sceneLabels) != 2:
print(
"Scene does not have two label nodes after reloading from AIM!"
)
self.assertTrue(False)
newLabelNode = sceneLabels[1]
newLabelImage = newLabelNode.GetImageData()
extent = newLabelImage.GetExtent()
pixelCounter = 0
for k in range(extent[5]):
for j in range(extent[3]):
for i in range(extent[1]):
pixel = newLabelImage.GetScalarComponentAsFloat(i, j, k, 0)
if ((pixelCounter in initializedSegmentationVoxels)
and pixel != 1) or (not (
pixelCounter in initializedSegmentationVoxels)
and pixel != 0):
print("Segmentation content not recovered correctly!")
print("Pixel counter " + str(pixelCounter) +
" is set to " + str(pixel))
self.assertTrue(False)
pixelCounter = pixelCounter + 1
self.assertTrue(True)
def test_RoundTrip(self):
"""
Test fiducial round trip to and from AIM XML file on disk
"""
print("ctest, please don't truncate my output: CTEST_FULL_OUTPUT")
# enter the module
mainWindow = slicer.util.mainWindow()
mainWindow.moduleSelector().selectModule('Reporting')
# l = slicer.modulelogic.vtkSlicerReportingModuleLogic()
l = slicer.modules.reporting.logic()
l.GUIHiddenOff()
# testDataPath = os.path.normpath(os.path.join(os.path.realpath(__file__), "..", "..", "Prototype/TestData/DICOM.CT/")
print("Reporting round trip test, current working directory = "+os.getcwd())
testDataPath = os.path.join(os.getcwd(),"../../Testing/Temporary/DICOM.CT")
# testDataPath = "/projects/birn/nicole/Slicer4/Reporting/Prototype/TestData/DICOM.CT"
print("test data path = "+testDataPath)
# set up a new DICOM database
print("Creating a dicomDatabase!")
ddb = ctk.ctkDICOMDatabase()
if not ddb:
print("ERROR: failed to create a new dicom database!")
return
dbpath = slicer.app.slicerHome + '/Testing/Temporary/TestingDCMDB/ctkDICOM.sql'
print('database path set to '+dbpath)
if not os.path.exists(os.path.dirname(dbpath)):
print('Creating dir '+os.path.dirname(dbpath))
os.makedirs(os.path.dirname(dbpath))
ddb.openDatabase(dbpath,"ReportingTesting")
if not ddb.isOpen:
print("ERROR: failed to open a new dicom database at path "+dbpath)
return
retval = ddb.initializeDatabase()
if not retval:
print("ERROR: failed to init database")
return
l.InitializeDICOMDatabase(dbpath)
testFileNames = []
for n in [487, 488, 489]:
filename = os.path.join(testDataPath, "instance_" + str(n) + ".dcm")
print("Adding file "+filename)
testFileNames.append(filename)
# check to see if the test data is already in it
patients = ddb.patients()
if len(patients) == 0:
# add the files
for filename in testFileNames:
print("Inserting file "+filename)
retval = ddb.insert(filename)
patients = ddb.patients()
if len(patients) == 0:
print("ERROR: unable to add test files to database!")
print(str(testFileNames))
return
# get the UID for the series
study = ddb.studiesForPatient(patients[0])
series = ddb.seriesForStudy(study[0])
seriesUID = series[0]
# seriesUID = "1.2.392.200103.20080913.113635.2.2009.6.22.21.43.10.23432.1"
# seriesUID = "2.16.840.1.114362.1.759508.1251415878280.192"
# seriesUID = "1.3.12.2.1107.5.1.4.53031.30000011032906120157800000219"
print("For test, using the AIM sample volume with series UID of "+seriesUID)
fileList = ddb.filesForSeries(seriesUID)
print("fileList = "+str(fileList))
if not fileList:
print("ERROR: sample series with id "+seriesUID+" not found in database!")
return
# add a parameter node
parameterNode = slicer.vtkMRMLScriptedModuleNode()
parameterNode.SetModuleName('Reporting')
slicer.mrmlScene.AddNode(parameterNode)
# set it to be the active parameter node
l.SetActiveParameterNodeID(parameterNode.GetID())
#
# create a new report, make it the report in the parameter node, set up hierarchy
#
reportNode = slicer.mrmlScene.CreateNodeByClass("vtkMRMLReportingReportNode")
reportNode.SetReferenceCount(reportNode.GetReferenceCount() - 1)
# set the color id
colorID = 'vtkMRMLColorTableNodeFileGenericAnatomyColors.txt'
reportNode.SetColorNodeID(colorID)
reportNode.SetDICOMDatabaseFileName(dbpath)
slicer.mrmlScene.AddNode(reportNode)
parameterNode.SetParameter("reportID", reportNode.GetID())
#
# get some sample data from the database
#
volId = 1
volumeNode = None
volName = 'AIM volume '+str(volId)
# print("Dicom data base = "+ddb)
slicer.dicomDatabase = ddb
scalarVolumePlugin = slicer.modules.dicomPlugins['DICOMScalarVolumePlugin']()
scalarVolumeLoadables = scalarVolumePlugin.examine([fileList])
volumeNode = scalarVolumePlugin.load(scalarVolumeLoadables[0])
volumeNode.SetName(volName)
# print "volumeNode = ",volumeNode
print("Adding to Report: Volume with id "+volumeNode.GetID())
l.AddVolumeToReport(volumeNode)
# set it on the report
reportNode.SetVolumeNodeID(volumeNode.GetID())
print("adding a fiducial")
#
# define a fiducial
#
fidNode = slicer.vtkMRMLAnnotationFiducialNode()
fidName = "AIM Round Trip Test Fiducial"
fidNode.SetName(fidName)
fidNode.SetSelected(1)
fidNode.SetDisplayVisibility(1)
fidNode.SetLocked(0)
print("Calling set fid coords")
startCoords = [15.8, 70.8, -126.7]
fidNode.SetFiducialCoordinates(startCoords[0],startCoords[1],startCoords[2])
print("Starting fiducial coordinates: "+str(startCoords))
# point it to the volume
fidNode.SetAttribute("AssociatedNodeID", volumeNode.GetID())
# point it to the report
fidNode.SetAttribute("ReportingReportNodeID", reportNode.GetID())
fidNode.SetScene(slicer.mrmlScene)
print("Adding text disp node")
fidNode.CreateAnnotationTextDisplayNode()
print("Adding point display node")
fidNode.CreateAnnotationPointDisplayNode()
print("add node:")
# slicer.mrmlScene.DebugOn()
# l.DebugOn()
slicer.mrmlScene.AddNode(fidNode)
print("getting slice uid")
uid = l.GetSliceUIDFromMarkUp(fidNode)
print("fidNode uid = "+uid)
#
# create a label volume
#
volumesLogic = slicer.modules.volumes.logic()
labelNode = volumesLogic.CreateAndAddLabelVolume(slicer.mrmlScene, volumeNode, "Segmentation")
labelDisplayNode = labelNode.GetDisplayNode()
labelDisplayNode.SetAndObserveColorNodeID('vtkMRMLColorTableNodeFileGenericAnatomyColors.txt')
l.AddNodeToReport(labelNode)
# initialize image content
labelImage = labelNode.GetImageData()
extent = labelImage.GetExtent()
pixelCounter = 0
for k in range(extent[5]):
for j in range(extent[3]):
for i in range(extent[1]):
if pixelCounter in initializedSegmentationVoxels:
labelImage.SetScalarComponentFromFloat(i,j,k,0,1)
else:
labelImage.SetScalarComponentFromFloat(i,j,k,0,0)
pixelCounter = pixelCounter + 1
# test save to mrml
# slicer.mrmlScene.SetURL('/spl/tmp/nicole/Testing/aim/RoundTripTest.mrml')
# slicer.mrmlScene.Commit()
#
# output AIM XML
#
dirName = slicer.app.slicerHome + '/Testing/Temporary/'
reportNode.SetStorageDirectoryName(dirName)
print("Saving report to "+dirName)
retval = l.SaveReportToAIM(reportNode)
if (retval != 0):
print("ERROR: unable to save report to aim file "+dirName+", retval="+retval)
else:
print("Saved report to "+dirName+" in file "+reportNode.GetAIMFileName())
self.assertEqual(retval, 0)
print("\n\n\nReloading aim file"+reportNode.GetAIMFileName())
#
# now clear the scene so can read in
#
# TBD: this causes a crash
# slicer.mrmlScene.Clear(0)
#
# load in the aim file
#
newReport = slicer.mrmlScene.CreateNodeByClass("vtkMRMLReportingReportNode")
newReport.SetReferenceCount(newReport.GetReferenceCount()-1)
# set the default color map
newReport.SetColorNodeID(colorID)
newReport.SetDICOMDatabaseFileName(dbpath)
slicer.mrmlScene.AddNode(newReport)
parameterNode.SetParameter("reportID", newReport.GetID())
Helper.LoadAIMFile(newReport.GetID(),reportNode.GetAIMFileName())
# check the fiducial
endCoords = [0,0,0]
col = slicer.mrmlScene.GetNodesByClass("vtkMRMLAnnotationFiducialNode")
col.SetReferenceCount(col.GetReferenceCount() - 1)
# if the scene is not cleared, we should have 2 fiducials
nFiducials = col.GetNumberOfItems()
if nFiducials != 2:
print("Failed to read a fiducial from the saved report! Expect 2 in the non cleared scene, have " + str(nFiducials))
self.assertTrue(False)
f = col.GetItemAsObject(1)
f.GetFiducialCoordinates(endCoords)
print("Start Coords = "+str(startCoords[0])+","+str(startCoords[1])+","+str(startCoords[2]))
print("End Coords = "+str(endCoords))
xdiff = endCoords[0] - startCoords[0]
ydiff = endCoords[1] - startCoords[1]
zdiff = endCoords[2] - startCoords[2]
diffTotal = xdiff + ydiff + zdiff
print("Difference between coordinates after loaded the aim file and value from before stored the aim file: "+str(xdiff)+","+str(ydiff)+","+str(zdiff)+". Total difference = "+str(diffTotal))
if diffTotal > 0.1:
print("Fiducial coordinates error exceeds the allowed bounds")
self.assertTrue(False)
# check the label node
sceneVolumes = slicer.mrmlScene.GetNodesByClass("vtkMRMLScalarVolumeNode")
sceneVolumes.SetReferenceCount(sceneVolumes.GetReferenceCount() - 1)
sceneLabels = []
for i in range(sceneVolumes.GetNumberOfItems()):
vol = sceneVolumes.GetItemAsObject(i)
if vol.GetLabelMap():
sceneLabels.append(vol)
if len(sceneLabels) != 2:
print("Scene does not have two label nodes after reloading from AIM!")
self.assertTrue(False)
newLabelNode = sceneLabels[1]
newLabelImage = newLabelNode.GetImageData()
extent = newLabelImage.GetExtent()
pixelCounter = 0
for k in range(extent[5]):
for j in range(extent[3]):
for i in range(extent[1]):
pixel = newLabelImage.GetScalarComponentAsFloat(i,j,k,0)
if ((pixelCounter in initializedSegmentationVoxels) and pixel != 1) or (not(pixelCounter in initializedSegmentationVoxels) and pixel != 0):
print("Segmentation content not recovered correctly!")
print("Pixel counter "+str(pixelCounter)+" is set to "+str(pixel))
self.assertTrue(False)
pixelCounter = pixelCounter + 1
self.assertTrue(True)
