def __init__(self, parent=None):
self.moduleName = 'Workflow'
self._layouts = []
self.maximumNumberOfInput = 3
self._CurrentViewID = 1
self._CurrentViewNodes = {}
for i in range(1, self.maximumNumberOfInput + 1):
subDictionnary = {
'Background': '',
'Foreground': '',
'Label': '',
}
self._CurrentViewNodes['Input%i' % i] = subDictionnary
if not parent:
self.parent = slicer.qMRMLWidget()
self.parent.setLayout(qt.QVBoxLayout())
self.parent.setMRMLScene(slicer.mrmlScene)
else:
self.parent = parent
self.layout = self.parent.layout()
if not parent:
self.setup()
self.parent.show()
self._setupLayouts()
def setupEditorWidget(self): editorWidgetParent = slicer.qMRMLWidget() editorWidgetParent.setLayout(qt.QVBoxLayout()) editorWidgetParent.setMRMLScene(slicer.mrmlScene) self.editorWidget = EditorWidget(parent=editorWidgetParent) self.editorWidget.setup() self.segmentationGroupBoxLayout.addWidget(self.editorWidget.parent)
def __init__(self, parent = None):
if not parent:
self.parent = slicer.qMRMLWidget()
self.parent.setLayout(qt.QVBoxLayout())
self.parent.setMRMLScene(slicer.mrmlScene)
else:
self.parent = parent
self.layout = self.parent.layout()
if not parent:
self.setup()
self.parent.show()
jsonFiles = glob(SimpleFilters.JSON_DIR+"*.json")
jsonFiles.sort(cmp=lambda x,y: cmp(os.path.basename(x), os.path.basename(y)))
self.jsonFilters = []
for fname in jsonFiles:
try:
fp = file(fname, "r")
j = json.load(fp,object_pairs_hook=OrderedDict)
if j["name"] in dir(sitk):
self.jsonFilters.append(j)
else:
import sys
sys.stderr.write("Unknown SimpleITK class \"{0}\".\n".format(j["name"]))
except Exception as e:
import sys
sys.stderr.write("Error while reading \"{0}\". Exception: {1}\n".format(fname, e))
self.filterParameters = None
self.logic = None
def __init__(self, parent = None):
if not parent:
self.parent = slicer.qMRMLWidget()
self.parent.setLayout(qt.QVBoxLayout())
self.parent.setMRMLScene(slicer.mrmlScene)
else:
self.parent = parent
self.layout = self.parent.layout()
if not parent:
self.setup()
self.parent.show()
self.fileDialog = None
# Initialize Data Nodes List
self.inputDataNodes = []
# use OrderedDict for class-specific dictionary of function calls
# map feature class to list of features
self.featureClassKeys = collections.OrderedDict()
self.featureClassKeys["Node Information"] = ["Node"]
self.featureClassKeys["First-Order Statistics"] = ["Voxel Count", "Gray Levels", "Energy", "Entropy" , "Minimum Intensity", "Maximum Intensity", "Mean Intensity", "Median Intensity", "Range", "Mean Deviation", "Root Mean Square", "Standard Deviation", "Skewness", "Kurtosis", "Variance", "Uniformity"]
self.featureClassKeys["Morphology and Shape"] = ["Volume mm^3", "Volume cc", "Surface Area mm^2", "Surface:Volume Ratio", "Compactness 1", "Compactness 2", "Maximum 3D Diameter", "Spherical Disproportion", "Sphericity"]
self.featureClassKeys["Texture: GLCM"] = ["Autocorrelation", "Cluster Prominence", "Cluster Shade", "Cluster Tendency", "Contrast", "Correlation", "Difference Entropy", "Dissimilarity", "Energy (GLCM)", "Entropy(GLCM)", "Homogeneity 1", "Homogeneity 2", "IMC1", "IDMN", "IDN", "Inverse Variance", "Maximum Probability", "Sum Average", "Sum Entropy", "Sum Variance", "Variance (GLCM)"] #IMC2 missing
self.featureClassKeys["Texture: GLRL"] = ["SRE", "LRE", "GLN", "RLN", "RP", "LGLRE", "HGLRE", "SRLGLE", "SRHGLE", "LRLGLE", "LRHGLE"]
self.featureClassKeys["Geometrical Measures"] = ["Extruded Surface Area", "Extruded Volume", "Extruded Surface:Volume Ratio"]
self.featureClassKeys["Renyi Dimensions"] = ["Box-Counting Dimension", "Information Dimension", "Correlation Dimension"]
# used to map feature class to a list of auto-generated feature checkbox widgets
self.featureWidgets = collections.OrderedDict()
for key in self.featureClassKeys.keys():
self.featureWidgets[key] = list()
def __init__(self, parent = None):
if not parent:
self.parent = slicer.qMRMLWidget()
self.parent.setLayout(qt.QVBoxLayout())
self.parent.setMRMLScene(slicer.mrmlScene)
else:
self.parent = parent
self.layout = self.parent.layout()
if not parent:
self.setup()
self.parent.show()
pathToJSON = os.path.dirname(os.path.realpath(__file__)) + '/Resources/json/'
# need to hit reload to get correct file
print("pathToJSON: ",pathToJSON)
print(__file__)
jsonFiles = glob(pathToJSON+"*.json")
self.jsonFilters = []
for fname in jsonFiles:
try:
fp = file(fname, "r")
j = json.load(fp,object_pairs_hook=OrderedDict)
self.jsonFilters.append(j)
except:
print "Error while reading $1", fname
self.filterParameters = None
def __init__(self, parent=None):
if not parent:
self.parent = slicer.qMRMLWidget()
self.parent.setLayout(qt.QVBoxLayout())
self.parent.setMRMLScene(slicer.mrmlScene)
else:
self.parent = parent
self.layout = self.parent.layout()
# this flag is 1 if there is an update in progress
self.__updating = 1
# the pointer to the logic
self.__logic = None
if not parent:
self.setup()
self.__inputVolumeNodeSelector.setMRMLScene(slicer.mrmlScene)
self.__seedFiducialsNodeSelector.setMRMLScene(slicer.mrmlScene)
self.__vesselnessVolumeNodeSelector.setMRMLScene(slicer.mrmlScene)
self.__outputVolumeNodeSelector.setMRMLScene(slicer.mrmlScene)
self.__outputModelNodeSelector.setMRMLScene(slicer.mrmlScene)
self.__stopperFiducialsNodeSelector.setMRMLScene(slicer.mrmlScene)
# after setup, be ready for events
self.__updating = 0
self.parent.show()
# register default slots
self.parent.connect('mrmlSceneChanged(vtkMRMLScene*)',
self.onMRMLSceneChanged)
def __init__(self, parent = None, rootDir = None, MODULE = None):
"""
Init function.
@param parent: The parent qt.QWidget of the settings file.
@type parent: qt.QWidget
@param rootDir: The root directory where to store the settings file.
@type rootDir: str
@param MODULE: The XNAT Slicer module.
@type MODULE: XNATSlicerWidget
"""
if not parent:
self.parent = slicer.qMRMLWidget()
else:
self.parent = parent
self.Events = MokaUtils.Events(self.EVENT_TYPES)
self.MODULE = MODULE
self.filepath = os.path.join(rootDir, self.FILE_PREFIX + self.FILE_SUFFIX)
#--------------------
# OS specific database settings
#--------------------
self.dbFormat = qt.QSettings.IniFormat
self.__resetDatabase()
self.defaultHosts = {'Central': 'https://central.xnat.org',
'CNDA': 'https://cnda.wustl.edu'}
self.setup()
self.currErrorMessage = ""
slicer.app.processEvents()
def __init__(self,
parent=None,
embedded=False,
suppliedEffects=[],
showVolumesFrame=True):
self.observerTags = []
# set attributes from ctor parameters
self.embedded = embedded
self.suppliedEffects = suppliedEffects
self.showVolumesFrame = showVolumesFrame
# TODO: figure out why module/class hierarchy is different
# between developer builds ans packages
try:
# for developer build...
self.editUtil = EditorLib.EditUtil.EditUtil()
except AttributeError:
# for release package...
self.editUtil = EditorLib.EditUtil()
#->> check to make sure it works with a supplied parent
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()
#self.setup()
if self.embedded:
self.setup()
def __init__(self, parent = None):
self.moduleName = 'Workflow'
self._layouts = []
self.maximumNumberOfInput = 3
self._CurrentViewID = 1
self._CurrentViewNodes = {}
for i in range(1, self.maximumNumberOfInput + 1):
subDictionnary = {
'Background' : '',
'Foreground' : '',
'Label' : '',
}
self._CurrentViewNodes['Input%i' %i] = subDictionnary
if not parent:
self.parent = slicer.qMRMLWidget()
self.parent.setLayout(qt.QVBoxLayout())
self.parent.setMRMLScene(slicer.mrmlScene)
else:
self.parent = parent
self.layout = self.parent.layout()
if not parent:
self.setup()
self.parent.show()
self._setupLayouts()
def __init__(self, parent=None, test=False):
logFile = os.path.join(os.environ['TMPDIR'], "DerivedImageQAWidget" + '.log')
logging.basicConfig(filename=logFile,
level=logging.DEBUG,
format='%(module)s.%(funcName)s - %(levelname)s: %(message)s')
self.logging = logging.getLogger(__name__)
self.images = ('t2_average', 't1_average') # T1 is second so that reviewers see it as background for regions
self.regions = ('labels_tissue',
'caudate_left', 'caudate_right',
'accumben_left', 'accumben_right',
'putamen_left', 'putamen_right',
'globus_left', 'globus_right',
'thalamus_left', 'thalamus_right',
'hippocampus_left', 'hippocampus_right')
self.currentSession = None
self.imageQAWidget = None
self.navigationWidget = None
self.followUpDialog = None
self.notes = None
# Handle the UI display with/without Slicer
if parent is None and not test:
self.parent = slicer.qMRMLWidget()
self.parent.setLayout(qt.QVBoxLayout())
self.parent.setMRMLScene(slicer.mrmlScene)
self.layout = self.parent.layout()
self.logic = DerivedImageQALogic(self)
self.setup()
self.parent.show()
elif not test:
self.parent = parent
self.layout = self.parent.layout()
self.logic = DerivedImageQALogic(self, test=test)
elif test:
self.logic = DerivedImageQALogic(self, test=test)
def __init__(self, parent=None):
VTKObservationMixin.__init__(self)
self.editUtil = EditUtil() # Kept for backward compatibility
# mrml volume node instances
self.master = None
self.masterWhenMergeWasSet = None
# Editor color LUT
self.colorNodeID = None
# string
self.createMergeOptions = ""
self.mergeVolumePostfix = "-label"
# slicer helper class
self.volumesLogic = slicer.modules.volumes.logic()
# widgets that are dynamically created on demand
# pseudo signals
# - python callable that gets True or False
self.selectCommand = None
if not parent:
self.parent = slicer.qMRMLWidget()
self.parent.setLayout(qt.QVBoxLayout())
self.parent.setMRMLScene(slicer.mrmlScene)
self.create()
self.parent.show()
else:
self.parent = parent
self.create()
def createUserInterface(self):
""" This step is mostly empty. A volume rendering threshold is added to be useful.
"""
self.__layout = self.__parent.createUserInterface()
self.__threshRange = slicer.qMRMLRangeWidget()
self.__threshRange.decimals = 0
self.__threshRange.singleStep = 1
self.__threshRange.connect('valuesChanged(double,double)',
self.onThresholdChanged)
qt.QTimer.singleShot(0, self.killButton)
ThreshGroupBox = qt.QGroupBox()
ThreshGroupBox.setTitle('3D Visualization Intensity Threshold')
ThreshGroupBoxLayout = qt.QFormLayout(ThreshGroupBox)
ThreshGroupBoxLayout.addRow(self.__threshRange)
self.__layout.addRow(ThreshGroupBox)
editorWidgetParent = slicer.qMRMLWidget()
editorWidgetParent.setLayout(qt.QVBoxLayout())
editorWidgetParent.setMRMLScene(slicer.mrmlScene)
self.__editorWidget = EditorWidget(parent=editorWidgetParent)
self.__editorWidget.setup()
self.__layout.addRow(editorWidgetParent)
self.hideUnwantedEditorUIElements()
RestartGroupBox = qt.QGroupBox()
RestartGroupBox.setTitle('Restart')
RestartGroupBoxLayout = qt.QFormLayout(RestartGroupBox)
self.__RestartButton = qt.QPushButton('Return to Step 1')
RestartGroupBoxLayout.addRow(self.__RestartButton)
self.__RemoveCroppedSubtractionMap = qt.QCheckBox()
self.__RemoveCroppedSubtractionMap.checked = True
self.__RemoveCroppedSubtractionMap.setToolTip(
"Delete the cropped version of your subtaction map.")
RestartGroupBoxLayout.addRow("Delete cropped subtraction map: ",
self.__RemoveCroppedSubtractionMap)
self.__RemoveFullSubtracitonMap = qt.QCheckBox()
self.__RemoveFullSubtracitonMap.checked = True
self.__RemoveFullSubtracitonMap.setToolTip(
"Delete the full version of your subtaction map.")
RestartGroupBoxLayout.addRow("Delete full subtraction map: ",
self.__RemoveFullSubtracitonMap)
self.__RemoveROI = qt.QCheckBox()
self.__RemoveROI.checked = False
self.__RemoveROI.setToolTip(
"Delete the ROI resulting from your subtaction map.")
RestartGroupBoxLayout.addRow("Delete ROI: ", self.__RemoveROI)
# self.__RestartButton.setEnabled(0)
self.__RestartButton.connect('clicked()', self.Restart)
self.__RestartActivated = True
self.__layout.addRow(RestartGroupBox)
def __init__(self, parent=None):
self.testingServer = None
self.dicomBrowser = None
# options for browser
self.browserPersistent = False
# 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')
# state management for compressing events
# - each time an update is requested, start the singleShot timer
# - if the update is requested before the timeout, the call to timer.start() resets it
# - the actual update only happens when the the full time elapses since the last request
self.updateRecentActivityTimer = qt.QTimer()
self.updateRecentActivityTimer.singleShot = True
self.updateRecentActivityTimer.interval = 500
self.updateRecentActivityTimer.connect('timeout()', self.onUpateRecentActivityRequestTimeout)
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()
globals()['d'] = self
def __init__(self, parent=None):
if not parent:
self.parent = slicer.qMRMLWidget()
self.parent.setLayout(qt.QVBoxLayout())
else:
self.parent = parent
self.layout = self.parent.layout()
# this flag is 1 if there is an update in progress
self.__updating = 1
self.__mvNode = None
self.extractFrame = False
# chart view node
self.__cvn = None
# data node
#slicer.mrmlScene.AddNode(slicer.vtkMRMLDoubleArrayNode())
# chart node
self.__cn = slicer.vtkMRMLChartNode()
self.__cn.SetScene(slicer.mrmlScene)
slicer.mrmlScene.AddNode(self.__cn)
# image play setup
self.timer = qt.QTimer()
self.timer.setInterval(50)
self.timer.connect('timeout()', self.goToNext)
def __init__(self, parent=None, showVolumesFrame=True):
self.observerTags = []
self.shortcuts = []
self.toolsBox = None
# set attributes from ctor parameters
self.showVolumesFrame = showVolumesFrame
# TODO: figure out why module/class hierarchy is different
# between developer builds ans packages
try:
# for developer build...
self.editUtil = EditorLib.EditUtil.EditUtil()
except AttributeError:
# for release package...
self.editUtil = EditorLib.EditUtil()
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 __init__( self, parent=None ):
if not parent:
self.parent = slicer.qMRMLWidget()
self.parent.setLayout( qt.QVBoxLayout() )
else:
self.parent = parent
self.layout = self.parent.layout()
# this flag is 1 if there is an update in progress
self.__updating = 1
self.__mvNode = None
self.extractFrame = False
# chart view node
self.__cvn = None
# data node
#slicer.mrmlScene.AddNode(slicer.vtkMRMLDoubleArrayNode())
# chart node
self.__cn = slicer.vtkMRMLChartNode()
self.__cn.SetScene(slicer.mrmlScene)
slicer.mrmlScene.AddNode(self.__cn)
# image play setup
self.timer = qt.QTimer()
self.timer.setInterval(50)
self.timer.connect('timeout()', self.goToNext)
def __init__(self, parent=None):
VTKObservationMixin.__init__(self)
self.editUtil = EditUtil() # Kept for backward compatibility
# mrml volume node instances
self.master = None
self.masterWhenMergeWasSet = None
# Editor color LUT
self.colorNodeID = None
# string
self.createMergeOptions = ""
self.mergeVolumePostfix = "-label"
# slicer helper class
self.volumesLogic = slicer.modules.volumes.logic()
# widgets that are dynamically created on demand
# pseudo signals
# - python callable that gets True or False
self.selectCommand = None
if not parent:
self.parent = slicer.qMRMLWidget()
self.parent.setLayout(qt.QVBoxLayout())
self.parent.setMRMLScene(slicer.mrmlScene)
self.create()
self.parent.show()
else:
self.parent = parent
self.create()
def __init__(self, parent=None):
if not parent:
self.parent = slicer.qMRMLWidget()
self.parent.setLayout(qt.QVBoxLayout())
self.parent.setMRMLScene(slicer.mrmlScene)
else:
self.parent = parent
self.layout = self.parent.layout()
# this flag is 1 if there is an update in progress
self.__updating = 1
# the pointer to the logic and the mrmlManager
self.__mrmlManager = None
self.__logic = None
if not parent:
self.setup()
# after setup, be ready for events
self.__updating = 0
self.parent.show()
if slicer.mrmlScene.GetTagByClassName(
"vtkMRMLScriptedModuleNode") != 'ScriptedModule':
slicer.mrmlScene.RegisterNodeClass(vtkMRMLScriptedModuleNode())
def __init__(self, parent=None):
self.testingServer = None
# state management for compressing events
# - each time an update is requested, start the singleShot timer
# - if the update is requested before the timeout, the call to timer.start() resets it
# - the actual update only happens when the the full time elapses since the last request
self.updateRecentActivityTimer = qt.QTimer()
self.updateRecentActivityTimer.singleShot = True
self.updateRecentActivityTimer.interval = 500
self.updateRecentActivityTimer.connect(
'timeout()', self.onUpateRecentActivityRequestTimeout)
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()
globals()['d'] = self
def __init__(self, parent=None):
self.testingServer = None
# let the popup window manage data loading
self.useDetailsPopup = True
# hide the search box
self.hideSearch = True
# options for browser
self.browserPersistent = False
# 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()
globals()['d'] = self
def __init__(self, parent=None):
self.testingServer = None
# let the popup window manage data loading
self.useDetailsPopup = True
# hide the search box
self.hideSearch = True
# options for browser
self.browserPersistent = False
# 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()
globals()['d'] = self
def __init__(self, parent=None):
self.testingServer = None
self.dicomApp = None
# hide the search box
self.hideSearch = True
# options for browser
self.browserPersistent = False
# 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')
# state management for compressing events
self.resumeModelRequested = False
self.updateRecentActivityRequested = False
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()
globals()['d'] = self
def __init__(self, parent=None, configFile=None):
self.util = QAUtil()
if configFile is None:
configFile = os.path.join(os.path.dirname(slicer.modules.qualityassurance.path),
"qualityassurance.cfg.EXAMPLE")
else:
print "This is the config file:", configFile
self.util.CONFIG_FILE = configFile
self.logger = self.util.getLogger()
for name in self.util.findModules():
print name
exec "self.{module} = QAModule(self.logger, '{module}')".format(module=name) in globals(), locals()
if parent is None:
self.logger.debug("Parent is None")
self.parent = slicer.qMRMLWidget()
self.parent.setLayout(qt.QVBoxLayout())
self.parent.setMRMLScene(slicer.mrmlScene)
self.layout = self.parent.layout()
self.setup()
# self.createModuleButtons(self.parent)
self.parent.show()
else:
self.logger.debug("Parent is: %s" % type(parent))
self.parent = parent
self.layout = self.parent.layout()
def __init__(self, parent=None):
if not parent:
self.parent = slicer.qMRMLWidget()
self.parent.setLayout(qt.QVBoxLayout())
self.parent.setMRMLScene(slicer.mrmlScene)
else:
self.parent = parent
self.layout = self.parent.layout()
# this flag is 1 if there is an update in progress
self.__updating = 1
# the pointer to the logic
self.__logic = None
if not parent:
self.setup()
self.__inputVolumeNodeSelector.setMRMLScene(slicer.mrmlScene)
self.__seedFiducialsNodeSelector.setMRMLScene(slicer.mrmlScene)
self.__outputVolumeNodeSelector.setMRMLScene(slicer.mrmlScene)
self.__previewVolumeNodeSelector.setMRMLScene(slicer.mrmlScene)
# after setup, be ready for events
self.__updating = 0
self.parent.show()
# register default slots
self.parent.connect("mrmlSceneChanged(vtkMRMLScene*)", self.onMRMLSceneChanged)
def __init__(self,
parent=None,
parameterNode=None,
parameter=None,
colorNode=None,
selectCommand=None):
self.colorNode = colorNode
self.parameterNode = parameterNode
self.parameter = parameter
self.selectCommand = selectCommand
self.recents = []
self.label = None
if not parent:
self.parent = slicer.qMRMLWidget()
self.parent.setObjectName('EditMRMLWidget')
self.parent.setLayout(qt.QVBoxLayout())
self.parent.setMRMLScene(slicer.mrmlScene)
self.create()
p = qt.QCursor().pos()
self.parent.setGeometry(p.x(), p.y(), 300, 700)
self.parent.show()
self.parent.raise_()
else:
self.parent = parent
self.create()
def __init__(self, parent=None, showVolumesFrame=True):
self.observerTags = []
self.shortcuts = []
self.toolsBox = None
# set attributes from ctor parameters
self.showVolumesFrame = showVolumesFrame
# TODO: figure out why module/class hierarchy is different
# between developer builds ans packages
try:
# for developer build...
self.editUtil = EditorLib.EditUtil.EditUtil()
except AttributeError:
# for release package...
self.editUtil = EditorLib.EditUtil()
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 __init__(self, parent=None):
self.testingServer = None
self.dicomApp = None
# hide the search box
self.hideSearch = True
# options for browser
self.browserPersistent = False
# 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')
# state management for compressing events
self.resumeModelRequested = False
self.updateRecentActivityRequested = False
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()
globals()['d'] = self
def __init__(self, parent = None):
if not parent:
self.parent = slicer.qMRMLWidget()
self.parent.setLayout(qt.QVBoxLayout())
self.parent.setMRMLScene(slicer.mrmlScene)
else:
self.parent = parent
self.layout = self.parent.layout()
if not parent:
self.setup()
self.parent.show()
self.fileDialog = None
# Initialize Data Nodes List
self.inputDataNodes = []
# use OrderedDict for class-specific dictionary of function calls
# map feature class to list of features
self.featureClassKeys = collections.OrderedDict()
self.featureClassKeys["Node Information"] = ["Node"]
self.featureClassKeys["First-Order Statistics"] = ["Voxel Count", "Gray Levels", "Energy", "Entropy" , "Minimum Intensity", "Maximum Intensity", "Mean Intensity", "Median Intensity", "Range", "Mean Deviation", "Root Mean Square", "Standard Deviation", "Skewness", "Kurtosis", "Variance", "Uniformity"]
self.featureClassKeys["Morphology and Shape"] = ["Volume mm^3", "Volume cc", "Surface Area mm^2", "Surface:Volume Ratio", "Compactness 1", "Compactness 2", "Maximum 3D Diameter", "Spherical Disproportion", "Sphericity"]
self.featureClassKeys["Texture: GLCM"] = ["Autocorrelation", "Cluster Prominence", "Cluster Shade", "Cluster Tendency", "Contrast", "Correlation", "Difference Entropy", "Dissimilarity", "Energy (GLCM)", "Entropy(GLCM)", "Homogeneity 1", "Homogeneity 2", "IMC1", "IDMN", "IDN", "Inverse Variance", "Maximum Probability", "Sum Average", "Sum Entropy", "Sum Variance", "Variance (GLCM)"] #IMC2 missing
self.featureClassKeys["Texture: GLRL"] = ["SRE", "LRE", "GLN", "RLN", "RP", "LGLRE", "HGLRE", "SRLGLE", "SRHGLE", "LRLGLE", "LRHGLE"]
self.featureClassKeys["Geometrical Measures"] = ["Extruded Surface Area", "Extruded Volume", "Extruded Surface:Volume Ratio"]
self.featureClassKeys["Renyi Dimensions"] = ["Box-Counting Dimension", "Information Dimension", "Correlation Dimension"]
# used to map feature class to a list of auto-generated feature checkbox widgets
self.featureWidgets = collections.OrderedDict()
for key in self.featureClassKeys.keys():
self.featureWidgets[key] = list()
def __init__(self, parent = None):
#def __init__(self, parent):
#ScriptedLoadableModuleWidget.setup(self)
self.tnode = None
self.strHostname = None
self.times0 = 0
self.chooseCell = False
self.connectTag = False
self.registTag = False
self.receiveCurrentNode = None
if not parent:
self.parent = slicer.qMRMLWidget()
self.parent.setLayout(qt.QVBoxLayout())
self.parent.setMRMLScene(slicer.mrmlScene)
else:
self.parent = parent
self.layout = self.parent.layout()
if not parent:
self.setup()
self.parent.show()
self.logic = SmartTemplateLogic(None)
self.generateTag = False
def __init__(self, parent=None):
if not parent:
self.parent = slicer.qMRMLWidget()
self.parent.setLayout(qt.QVBoxLayout())
self.parent.setMRMLScene(slicer.mrmlScene)
else:
self.parent = parent
self.layout = self.parent.layout()
self.transformNode = None
self.transformNodeObserverTag = None
self.transformObserverTag = None
self.transform = None
self.acquireButtonFlag = False
self.collectSignal = False
self.pointerPosition = np.zeros(3)
self.pointsCounts = 0
self.recordedpoint = np.zeros(3)
self.statusTimer = qt.QTimer()
self.statusTimer.setInterval(100)
self.statusTimer.connect('timeout()', self.changeTrackerStatus)
if not parent:
self.setup()
self.parent.show()
def __init__(self, parent=None, embedded=False, suppliedEffects=[], showVolumesFrame=True):
self.observerTags = []
# set attributes from ctor parameters
self.embedded = embedded
self.suppliedEffects = suppliedEffects
self.showVolumesFrame = showVolumesFrame
# TODO: figure out why module/class hierarchy is different
# between developer builds ans packages
try:
# for developer build...
self.editUtil = EditorLib.EditUtil.EditUtil()
except AttributeError:
# for release package...
self.editUtil = EditorLib.EditUtil()
#->> check to make sure it works with a supplied parent
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()
#self.setup()
if self.embedded:
self.setup()
def __init__(self, parent = None):
if not parent:
self.parent = slicer.qMRMLWidget()
self.parent.setLayout(qt.QVBoxLayout())
self.parent.setMRMLScene(slicer.mrmlScene)
else:
self.parent = parent
self.layout = self.parent.layout()
if not parent:
self.setup()
self.markersFiducialsNodeSelector.setMRMLScene(slicer.mrmlScene)
self.targetFiducialNodeSelector.setMRMLScene(slicer.mrmlScene)
self.entryFiducialNodeSelector.setMRMLScene(slicer.mrmlScene)
self.parent.show()
def __init__(self, parent=None):
self.testingServer = None
self.dicomBrowser = None
# options for browser
self.browserPersistent = False
# 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')
# state management for compressing events
# - each time an update is requested, start the singleShot timer
# - if the update is requested before the timeout, the call to timer.start() resets it
# - the actual update only happens when the the full time elapses since the last request
self.updateRecentActivityTimer = qt.QTimer()
self.updateRecentActivityTimer.singleShot = True
self.updateRecentActivityTimer.interval = 500
self.updateRecentActivityTimer.connect(
'timeout()', self.onUpateRecentActivityRequestTimeout)
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()
globals()['d'] = self
def __init__( self, parent=None ):
if not parent:
self.parent = slicer.qMRMLWidget()
self.parent.setLayout( qt.QVBoxLayout() )
self.parent.setMRMLScene( slicer.mrmlScene )
else:
self.parent = parent
self.layout = self.parent.layout()
# this flag is 1 if there is an update in progress
self.__updating = 1
# the pointer to the logic and the mrmlManager
self.__mrmlManager = None
self.__logic = None
if not parent:
self.setup()
# after setup, be ready for events
self.__updating = 0
self.parent.show()
if slicer.mrmlScene.GetTagByClassName( "vtkMRMLScriptedModuleNode" ) != 'ScriptedModule':
slicer.mrmlScene.RegisterNodeClass(vtkMRMLScriptedModuleNode())
def __init__(self, parent=None):
if not parent:
self.parent = slicer.qMRMLWidget()
self.parent.setLayout(qt.QVBoxLayout())
self.parent.setMRMLScene(slicer.mrmlScene)
else:
self.parent = parent
self.layout = self.parent.layout()
if not parent:
self.setup()
self.parent.show()
# Module Variables
self.timer = qt.QTimer()
self.timer.setInterval(20)
self.timer.connect('timeout()', self.doSomething)
self.fiducialMatrixStatus = False
self.outsideSign = 0
self.needleInsertionStarted = False
self.dataBufferIsEmpty = True
self.trajectoryRawData = [ 0, 0, 0]
self.minimumDistanceBetweenSeperatePoints = 2
#self.n = 48
#self.p = numpy.zeros((self.n,3))
# 10 mm offset for template widt
self.templateWidth = -10
def __init__(self, parent=None, rootDir=None, MODULE=None):
"""
Init function.
@param parent: The parent qt.QWidget of the settings file.
@type parent: qt.QWidget
@param rootDir: The root directory where to store the settings file.
@type rootDir: str
@param MODULE: The XNAT Slicer module.
@type MODULE: XNATSlicerWidget
"""
if not parent:
self.parent = slicer.qMRMLWidget()
else:
self.parent = parent
self.Events = MokaUtils.Events(self.EVENT_TYPES)
self.MODULE = MODULE
self.filepath = os.path.join(rootDir,
self.FILE_PREFIX + self.FILE_SUFFIX)
#--------------------
# OS specific database settings
#--------------------
self.dbFormat = qt.QSettings.IniFormat
self.__resetDatabase()
self.defaultHosts = {
'Central': 'https://central.xnat.org',
'CNDA': 'https://cnda.wustl.edu'
}
self.setup()
self.currErrorMessage = ""
slicer.app.processEvents()
def __init__(self, parent = None):
if not parent:
self.parent = slicer.qMRMLWidget()
self.parent.setLayout(qt.QVBoxLayout())
self.parent.setMRMLScene(slicer.mrmlScene)
else:
self.parent = parent
self.layout = self.parent.layout()
if not parent:
self.setup()
self.parent.show()
self.logic = ViewpointLogic()
self.sliderTranslationDefaultMm = 0
self.sliderTranslationMinMm = -200
self.sliderTranslationMaxMm = 200
self.sliderViewAngleDefaultDeg = 30
self.cameraViewAngleMinDeg = 5.0 # maximum magnification
self.cameraViewAngleMaxDeg = 150.0 # minimum magnification
self.sliderParallelScaleDefaultDeg = 1
self.cameraParallelScaleMinDeg = 0.001 # maximum magnification
self.cameraParallelScaleMaxDeg = 1000.0 # minimum magnification
self.sliderSingleStepValue = 1
self.sliderPageStepValue = 10
self.enableViewpointButtonState = 0
self.enableViewpointButtonTextState0 = "Enable Viewpoint Mode"
self.enableViewpointButtonTextState1 = "Disable Viewpoint Mode"
def __init__(self, parent=None):
if not parent:
self.parent = slicer.qMRMLWidget()
self.parent.setLayout(qt.QVBoxLayout())
self.parent.setMRMLScene(slicer.mrmlScene)
else:
self.parent = parent
self.logic = VolumeMaskerLogic()
def __init__(self, parent=None):
if not parent:
self.parent = slicer.qMRMLWidget()
self.parent.setLayout(qt.QVBoxLayout())
else:
self.parent = parent
self.layout = self.parent.layout()
if not parent:
self.setup()
self.parent.show()
self.inputsFilled = False
def __init__(self, parent = None):
if not parent:
self.parent = slicer.qMRMLWidget()
self.parent.setLayout(qt.QVBoxLayout())
self.parent.setMRMLScene(slicer.mrmlScene)
else:
self.parent = parent
self.layout = self.parent.layout()
if not parent:
self.setup()
self.parent.show()
def __init__(self, parent=None):
if not parent:
self.parent = slicer.qMRMLWidget()
self.parent.setLayout(qt.QVBoxLayout())
self.parent.setMRMLScene(slicer.mrmlScene)
else:
self.parent = parent
self.layout = self.parent.layout()
if not parent:
self.setup()
self.parent.show()
def __init__(self, parent = None):
self.developerMode = False # change this to true to get reload and test
if not parent:
self.parent = slicer.qMRMLWidget()
self.parent.setLayout(qt.QVBoxLayout())
self.parent.setMRMLScene(slicer.mrmlScene)
else:
self.parent = parent
self.layout = self.parent.layout()
if not parent:
self.setup()
self.parent.show()
def __init__(self, parent=None, rootDir=None, browser = None):
if not parent:
self.parent = slicer.qMRMLWidget()
else:
self.parent = parent
self.browser = browser
self.filepath = os.path.join(rootDir, 'XNATSettings.ini')
self.database = qt.QSettings(self.filepath, qt.QSettings.IniFormat)
self.defaultHosts = {'Central': 'https://central.xnat.org',
'CNDA': 'https://cnda.wustl.edu'}
self.setup()
self.currErrorMessage = ""
def __init__(self, parent = None):
"""Widget constructor (existing module)"""
if not parent:
self.parent = slicer.qMRMLWidget()
self.parent.setLayout(qt.QVBoxLayout())
self.parent.setMRMLScene(slicer.mrmlScene)
else:
self.parent = parent
self.layout = self.parent.layout()
if not parent:
self.setup()
self.parent.show()
def __init__(self, parent = None):
self.developerMode = False # change this to true to get reload and test
if not parent:
self.parent = slicer.qMRMLWidget()
self.parent.setLayout(qt.QVBoxLayout())
self.parent.setMRMLScene(slicer.mrmlScene)
else:
self.parent = parent
self.layout = self.parent.layout()
if not parent:
self.setup()
self.parent.show()
def __init__(self, parent=None):
"""Widget constructor (existing module)"""
if not parent:
self.parent = slicer.qMRMLWidget()
self.parent.setLayout(qt.QVBoxLayout())
self.parent.setMRMLScene(slicer.mrmlScene)
else:
self.parent = parent
self.layout = self.parent.layout()
if not parent:
self.setup()
self.parent.show()
def __init__(self, parent=None):
""" It seems to be that Slicer creates an instance of this class with a
qMRMLWidget parent. If for some reason it doesn't, this __init__ will.
"""
if not parent:
self.parent = slicer.qMRMLWidget()
self.parent.setLayout(qt.QVBoxLayout())
self.parent.setMRMLScene(slicer.mrmlScene)
else:
self.parent = parent
self.layout = self.parent.layout()
def __init__(self, parent=None):
if not parent:
self.parent = slicer.qMRMLWidget()
self.parent.setLayout(qt.QVBoxLayout())
self.parent.setMRMLScene(slicer.mrmlScene)
else:
self.parent = parent
# self.parent = slicer.modules.cropvolume.widgetRepresentation()
self.layout = self.parent.layout()
if not parent:
self.setup()
self.parent.show()
def __init__(self, parent = None):
self.moduleName = 'Workflow'
self._ViewNodeIDs = { 'Active' : None, 'Secondary' : None, 'Label' : None}
if not parent:
self.parent = slicer.qMRMLWidget()
self.parent.setLayout(qt.QVBoxLayout())
self.parent.setMRMLScene(slicer.mrmlScene)
else:
self.parent = parent
self.layout = self.parent.layout()
if not parent:
self.setup()
self.parent.show()
def __init__(self, parent = None):
if not parent:
self.parent = slicer.qMRMLWidget()
self.parent.setLayout(qt.QVBoxLayout())
self.parent.setMRMLScene(slicer.mrmlScene)
else:
self.parent = parent
self.layout = self.parent.layout()
if not parent:
self.setup()
self.parent.show()
self.logic = InBoreWorkspaceCheckerLogic()
self.tag = 0
def __init__(self, moduleName, parentWidget=None):
"""Widget constructor (existing module)"""
# EventsTrigger.__init__(self)
if not parentWidget:
self.parent = slicer.qMRMLWidget()
self.parent.setLayout(qt.QVBoxLayout())
self.parent.setMRMLScene(slicer.mrmlScene)
else:
self.parent = parentWidget
self.__moduleName__ = moduleName
self.layout = self.parent.layout()
self.logic = PreProcessingLogic(moduleName)
def __init__(self, parent=None):
if not parent:
self.parent = slicer.qMRMLWidget()
self.parent.setLayout(qt.QVBoxLayout())
self.parent.setMRMLScene(slicer.mrmlScene)
else:
self.parent = parent
self.layout = self.parent.layout()
self.lastCommandId = 0
self.timeoutCounter = 0
if not parent:
self.setup()
self.parent.show()
def __init__( self, parent=None ):
""" It seems to be that Slicer creates an instance of this class with a
qMRMLWidget parent. My understanding of parenthood when it comes to modules
is currently limited -- I'll update this when I know more.
"""
if not parent:
self.parent = slicer.qMRMLWidget()
self.parent.setLayout( qt.QVBoxLayout() )
self.parent.setMRMLScene( slicer.mrmlScene )
else:
self.parent = parent
self.layout = self.parent.layout()
def __init__( self, parent=None ): """ It seems to be that Slicer creates an instance of this class with a qMRMLWidget parent. If for some reason it doesn't, this __init__ will. """ if not parent: self.parent = slicer.qMRMLWidget() self.parent.setLayout( qt.QVBoxLayout() ) self.parent.setMRMLScene( slicer.mrmlScene ) else: self.parent = parent self.layout = self.parent.layout()
def __init__(self, parent=None):
if not parent:
self.parent = slicer.qMRMLWidget()
self.parent.setLayout(
qt.QVBoxLayout()) # dispone los elementos de manera vertical
self.parent.setMRMLScene(
slicer.mrmlScene) # Asocia la escena mrml al widget
else:
self.parent = parent
self.layout = self.parent.layout()
if not parent:
self.setup()
self.parent.show()
def __init__( self, parent=None ):
if not parent:
self.parent = slicer.qMRMLWidget()
self.parent.setLayout( qt.QVBoxLayout() )
self.parent.setMRMLScene( slicer.mrmlScene )
else:
self.parent = parent
self.logic = WebGLExportLogic()
self.__httpd = None
self.__port = 3456
self.__p = None
if not parent:
self.setup()
self.parent.show()
def __init__(self, parent = None):
if not parent:
self.parent = slicer.qMRMLWidget()
self.parent.setLayout(qt.QVBoxLayout())
self.parent.setMRMLScene(slicer.mrmlScene)
else:
self.parent = parent
self.layout = self.parent.layout()
if not parent:
self.setup()
self.parent.show()
self.moduleName = 'SlicerTestRecentFilesTests'
self.tester = SlicerTestRecentFilesTestsTest()
def __init__(self, parent=None):
self.observerTags = []
self.logic = SampleDataLogic(self.logMessage)
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 __init__(self, parent=None):
if not parent:
self.parent = slicer.qMRMLWidget()
self.parent.setLayout(qt.QVBoxLayout())
self.parent.setMRMLScene(slicer.mrmlScene)
else:
self.parent = parent
self.distanceTable = list()
self.outputNode = None
if not parent:
self.setup()
self.vtkSelector.setMRMLScene(slicer.mrmlScene)
self.outputSelector.setMRMLScene(slicer.mrmlScene)
self.parent.show()
