def open(self, username="", password=""):
"""Open the MorphoSource page and fill in or capture the url
"""
if username != "":
self.setLogin(username, password)
webWidget = slicer.qSlicerWebWidget()
slicerGeometry = slicer.util.mainWindow().geometry
webWidget.size = qt.QSize(slicerGeometry.width(),
slicerGeometry.height())
webWidget.pos = qt.QPoint(slicerGeometry.x() + 256,
slicerGeometry.y() + 128)
webWidget.url = "https://www.morphosource.org/LoginReg/form"
webWidget.show()
self.webWidget = webWidget
# TODO: need to expose loadFinished signal from QWebEngine via qSlicerWebWidget
# so that we will know when to send this (current 2 second delay is a hack
# that may not always work).
onFinishLoading = lambda: self.onFinishLoading(username, password)
connected = self.webWidget.connect('loadFinished(bool)',
onFinishLoading)
if not connected:
qt.QTimer.singleShot(
3000, lambda: self.onFinishLoading(username, password))
return self.webWidget
def onSiteButtonClicked(self, site): webWidget = slicer.qSlicerWebWidget() slicerGeometry = slicer.util.mainWindow().geometry webWidget.size = qt.QSize(1536,1024) webWidget.pos = qt.QPoint(slicerGeometry.x() + 256, slicerGeometry.y() + 128) webWidget.url = site["url"] webWidget.show() self.webWidgets.append(webWidget)
def createWebWidget():
webWidget = slicer.qSlicerWebWidget()
slicerGeometry = slicer.util.mainWindow().geometry
webWidget.size = qt.QSize(slicerGeometry.width(),
slicerGeometry.height())
webWidget.pos = qt.QPoint(slicerGeometry.x() + 256,
slicerGeometry.y() + 128)
webWidget.url = "http://localhost:8000"
webWidget.show()
return webWidget
def launchCovictory(self, url): lm = slicer.app.layoutManager() lm.setLayout(slicer.vtkMRMLLayoutNode.SlicerLayoutConventionalWidescreenView) lm.setLayout(slicer.vtkMRMLLayoutNode.SlicerLayoutConventionalView) splitter = lm.threeDWidget(0).parent() self.webWidget = slicer.qSlicerWebWidget() self.webWidget.url = url splitter = lm.threeDWidget(0).parent() splitter.insertWidget(0, self.webWidget) lm.threeDWidget(0).hide() sizes = [int(splitter.height*.67), 0, int(splitter.height*.33)] splitter.setSizes(sizes)
def onOpenSpecimenPage(self):
selection = self.resultsTable.selectionModel().selectedRows()
row = selection[0].row()
specimen_id = self.result_dataframe.iloc[row].specimen_id
url = base_specimen_page_url + '/' + specimen_id
specimen_page = slicer.qSlicerWebWidget()
geometry = slicer.util.mainWindow().geometry
geometry.setLeft(geometry.left() + 50)
geometry.setTop(geometry.top() + 50)
geometry.setWidth(1080)
geometry.setHeight(990)
specimen_page.setGeometry(geometry)
specimen_page.url = url
specimen_page.show()
self.specimen_pages.append(specimen_page)
def parallelCoordinatesPureD3(self):
"""Use parallel axes to explore parameter space
See: http://syntagmatic.github.io/parallel-coordinates/
Note also experimented with vtk version, but it has fewer features
and performance is not any better in practice.
https://vtk.org/Wiki/VTK/Examples/Python/Infovis/ParallelCoordinatesExtraction
"""
self.volumeStatistics()
fa = self.arrays['dtd_covariance_FA']
indices = numpy.where(fa != 0)
samples = {}
for key in self.arrays.keys():
samples[key] = self.arrays[key][indices]
dataToPlot = []
for index in range(len(samples['dtd_covariance_FA'])):
indexData = {}
for key in self.arrays.keys():
scalarLabel = key[len('dtd_covariance_'):]
indexData[scalarLabel] = samples[key][index]
dataToPlot.append(indexData)
dataToPlotString = json.dumps(dataToPlot)
modulePath = os.path.dirname(slicer.modules.multimapper.path)
resourceFilePath = os.path.join(modulePath, "Resources",
"parallel-template.html")
html = open(resourceFilePath).read().replace("%%dataToPlot%%",
dataToPlotString)
self.webWidget = slicer.qSlicerWebWidget()
self.webWidget.size = qt.QSize(1024, 512)
self.webWidget.setHtml(html)
self.webWidget.show()
open('/tmp/data.html', 'w').write(html)
def test_WebEngine1(self):
""" Testing WebEngine
"""
self.delayDisplay("Starting the test")
webWidget = slicer.qSlicerWebWidget()
webWidget.size = qt.QSize(1024, 512)
webWidget.webView().url = qt.QUrl("")
webWidget.show()
self.delayDisplay('Showing widget')
webWidget.evalJS("""
const paragraph = document.createElement('p');
paragraph.innerText = 'Hello from Slicer!';
document.body.appendChild(paragraph);
""")
self.delayDisplay('Slicer should be saying hello!')
#
# Test javascript evaluation + use of "evalResult()" signal
#
webWidget.connect("evalResult(QString,QString)", self.onEvalResult)
self.delayDisplay('Slicer setting a javascript value')
webWidget.evalJS("const valueFromSlicer = 42;")
webWidget.evalJS("valueFromSlicer;")
iteration = 0
while not self.gotResponse and iteration < 3:
# Specify an explicit delay to ensure async execution by the
# webengine has completed.
self.delayDisplay('Waiting for response...', msec=500)
iteration += 1
webWidget.disconnect("evalResult(QString,QString)", self.onEvalResult)
if not self.gotResponse:
raise RuntimeError("Never got response from evalJS")
if not self.gotCorrectResponse:
raise AssertionError("Did not get back expected result!")
#
# Test python evaluation from javascript
#
self.delayDisplay('Call a python method')
slicer.app.settings().setValue("WebEngine/AllowPythonExecution",
ctk.ctkMessageBox.AcceptRole)
webWidget.evalJS(r"""
let pythonCode = "dialog = qt.QInputDialog(slicer.util.mainWindow())\n";
pythonCode += "dialog.setLabelText('hello')\n";
pythonCode += "dialog.open()\n";
pythonCode += "qt.QTimer.singleShot(1000, dialog.close)\n";
window.slicerPython.evalPython(pythonCode);
""")
self.delayDisplay('Test access to python via js', msec=500)
if hasattr(slicer.modules, 'slicerPythonValueFromJS'):
del slicer.modules.slicerPythonValueFromJS
webWidget.evalJS("""
window.slicerPython.evalPython("slicer.modules.slicerPythonValueFromJS = 42");
""")
iteration = 0
while iteration < 3 and not hasattr(slicer.modules,
'slicerPythonValueFromJS'):
# Specify an explicit delay to ensure async execution by the
# webengine has completed.
self.delayDisplay('Waiting for python value from JS...', msec=500)
iteration += 1
if iteration >= 3:
raise RuntimeError("Couldn't get python value back from JS")
self.delayDisplay('Value of %d received via javascipt' %
slicer.modules.slicerPythonValueFromJS)
del slicer.modules.slicerPythonValueFromJS
self.delayDisplay('Test passed!')
def test_WebEngine1(self):
""" Testing WebEngine
"""
self.delayDisplay("Starting the test")
webWidget = slicer.qSlicerWebWidget()
webWidget.size = qt.QSize(1024,512)
webWidget.webView().url = qt.QUrl("")
webWidget.show()
self.delayDisplay('Showing widget')
webWidget.evalJS("""
const paragraph = document.createElement('p');
paragraph.innerText = 'Hello from Slicer!';
document.body.appendChild(paragraph);
""")
self.delayDisplay('Slicer should be saying hello!')
#
# Test javascript evaluation + use of "evalResult()" signal
#
webWidget.connect("evalResult(QString,QString)", self.onEvalResult)
self.delayDisplay('Slicer setting a javascript value')
webWidget.evalJS("const valueFromSlicer = 42;")
webWidget.evalJS("valueFromSlicer;");
iteration = 0
while not self.gotResponse and iteration < 3:
# Specify an explicit delay to ensure async execution by the
# webengine has completed.
self.delayDisplay('Waiting for response...', msec=500)
iteration += 1
webWidget.disconnect("evalResult(QString,QString)", self.onEvalResult)
if not self.gotResponse:
raise RuntimeError("Never got response from evalJS")
if not self.gotCorrectResponse:
raise AssertionError("Did not get back expected result!")
#
# Test python evaluation from javascript
#
self.delayDisplay('Call a python method')
slicer.app.settings().setValue("WebEngine/AllowPythonExecution", ctk.ctkMessageBox.AcceptRole)
webWidget.evalJS(r"""
let pythonCode = "dialog = qt.QInputDialog(slicer.util.mainWindow())\n";
pythonCode += "dialog.setLabelText('hello')\n";
pythonCode += "dialog.open()\n";
pythonCode += "qt.QTimer.singleShot(1000, dialog.close)\n";
window.slicerPython.evalPython(pythonCode);
""")
self.delayDisplay('Test access to python via js', msec=500)
if hasattr(slicer.modules, 'slicerPythonValueFromJS'):
del slicer.modules.slicerPythonValueFromJS
webWidget.evalJS("""
window.slicerPython.evalPython("slicer.modules.slicerPythonValueFromJS = 42");
""")
iteration = 0
while iteration < 3 and not hasattr(slicer.modules, 'slicerPythonValueFromJS'):
# Specify an explicit delay to ensure async execution by the
# webengine has completed.
self.delayDisplay('Waiting for python value from JS...', msec=500)
iteration += 1
if iteration >= 3:
raise RuntimeError("Couldn't get python value back from JS")
self.delayDisplay('Value of %d received via javascipt' % slicer.modules.slicerPythonValueFromJS)
del slicer.modules.slicerPythonValueFromJS
self.delayDisplay('Test passed!')
def parallelCoordinatesParCoords_RandomSample(self, sampleSize=1000):
"""Use parallel axes to explore parameter space
See: http://syntagmatic.github.io/parallel-coordinates/
https://github.com/BigFatDog/parcoords-es
Note also experimented with vtk version, but it has fewer features
and performance is not any better in practice.
https://vtk.org/Wiki/VTK/Examples/Python/Infovis/ParallelCoordinatesExtraction
"""
self.volumeStatistics()
fa = self.arrays['dtd_covariance_FA']
indices = numpy.where(fa != 0)
ijkCoordinates = numpy.transpose(indices)
ijkToRAS = vtk.vtkMatrix4x4()
slicer.util.getNode('dtd_covariance_FA').GetIJKToRASMatrix(ijkToRAS)
rasCoordinates = []
samples = {}
for key in self.arrays.keys():
samples[key] = self.arrays[key][indices]
dataToPlot = []
randomSample = random.sample(range(len(samples['dtd_covariance_FA'])),
sampleSize)
sampleIndex = 0
for index in randomSample:
indexData = {}
for key in self.arrays.keys():
scalarLabel = key[len('dtd_covariance_'):]
indexData[scalarLabel] = samples[key][index]
dataToPlot.append(indexData)
ijk = [*numpy.flip(numpy.transpose(indices)[index]), 1]
rasCoordinates.append(ijkToRAS.MultiplyPoint(ijk))
sampleIndex += 1
dataToPlotString = json.dumps(dataToPlot)
rasCoordinatesString = json.dumps(rasCoordinates)
modulePath = os.path.dirname(slicer.modules.multimapper.path)
resourceFilePath = os.path.join(modulePath, "Resources",
"ParCoords-template.html")
html = open(resourceFilePath).read()
html = html.replace("%%dataToPlot%%", dataToPlotString)
html = html.replace("%%rasCoordinates%%", rasCoordinatesString)
self.webWidget = slicer.qSlicerWebWidget()
self.webWidget.size = qt.QSize(1024, 768)
self.webWidget.setHtml(html)
self.webWidget.show()
def crosshairCallback(observer, eventID):
crosshairNode = slicer.mrmlScene.GetFirstNodeByClass(
'vtkMRMLCrosshairNode')
ras = [
0,
] * 3
crosshairNode.GetCursorPositionRAS(ras)
print(ras)
# TODO: update selector ranges based on QTI statistics
crosshairNode = slicer.mrmlScene.GetFirstNodeByClass(
'vtkMRMLCrosshairNode')
event = vtk.vtkCommand.ModifiedEvent
id_ = crosshairNode.AddObserver(event, crosshairCallback)
self.observerObjectIDPairs.append((crosshairNode, id_))
# save for debugging
open('/tmp/data.html', 'w').write(html)
def parallelCoordinatesSegmentation(self,
segmentationNode=None,
labelmapNode=None):
"""
Like parallelCoordinatesParCoords_RandomSample below, but
parcoords plot created from segmentation
"""
self.volumeStatistics()
if not segmentationNode:
try:
segmentationNode = slicer.util.getNode('Segmentation')
except slicer.util.MRMLNodeNotFoundException:
pass
if not segmentationNode:
print("need a segmentation")
slicer.util.selectModule("SegmentEditor")
return
if not labelmapNode:
try:
labelmapNode = slicer.util.getNode('Segmentation-labelmap')
except slicer.util.MRMLNodeNotFoundException:
labelmapNode = slicer.mrmlScene.AddNewNodeByClass(
'vtkMRMLLabelMapVolumeNode')
labelmapNode.SetName("Segmentation-labelmap")
segmentIDs = vtk.vtkStringArray()
segmentationNode.GetSegmentation().GetSegmentIDs(segmentIDs)
slicer.modules.segmentations.logic().ExportSegmentsToLabelmapNode(
segmentationNode, segmentIDs, labelmapNode,
self.nodes['dtd_covariance_FA'])
labelArray = slicer.util.arrayFromVolume(labelmapNode)
# list of non-zero segments in the labelmap
segmentIndices = list(numpy.unique(labelArray))[1:]
# data colors to match the segmentation colors to pass to js
segmentation = segmentationNode.GetSegmentation()
dataColors = [[0, 0, 0]]
for colorNumber in range(len(segmentIndices)):
dataColor = segmentation.GetNthSegment(colorNumber).GetColor()
dataColors.append(dataColor)
# make individual sample lines for parallel coordinates
ijkToRAS = vtk.vtkMatrix4x4()
labelmapNode.GetIJKToRASMatrix(ijkToRAS)
rasCoordinates = []
dataToPlot = []
for segmentIndex in segmentIndices:
# one data sample from each array per labeled voxel
coordinates = numpy.transpose(
numpy.where(labelArray == segmentIndex))
self._coordinates = coordinates
samples = {}
for key in self.arrays.keys():
samples[key] = []
for coordinate in coordinates:
self._array = self.arrays[key]
samples[key].append(self.arrays[key][coordinate[0]][
coordinate[1]][coordinate[2]])
for coordinateNumber in range(len(coordinates)):
indexData = {}
indexData['segmentIndex'] = int(segmentIndex)
for key in self.arrays.keys():
scalarLabel = key[len('dtd_covariance_'):]
indexData[scalarLabel] = samples[key][coordinateNumber]
dataToPlot.append(indexData)
ijkw = [*numpy.flip(coordinates)[coordinateNumber], 1]
ijkw = [*numpy.flip(coordinates)[coordinateNumber], 1]
rasCoordinate = ijkToRAS.MultiplyPoint(ijkw)
rasCoordinates.append(rasCoordinate)
dataColorsString = json.dumps(dataColors)
dataToPlotString = json.dumps(dataToPlot)
rasCoordinatesString = json.dumps(rasCoordinates)
modulePath = os.path.dirname(slicer.modules.multimapper.path)
resourceFilePath = os.path.join(modulePath, "Resources",
"ParCoords-SEG-template.html")
html = open(resourceFilePath).read()
html = html.replace("%%dataColors%%", dataColorsString)
html = html.replace("%%dataToPlot%%", dataToPlotString)
html = html.replace("%%rasCoordinates%%", rasCoordinatesString)
self.webWidget = slicer.qSlicerWebWidget()
self.webWidget.size = qt.QSize(1024, 768)
self.webWidget.setHtml(html)
self.webWidget.show()
def crosshairCallback(observer, eventID):
crosshairNode = slicer.mrmlScene.GetFirstNodeByClass(
'vtkMRMLCrosshairNode')
ras = [
0,
] * 3
crosshairNode.GetCursorPositionRAS(ras)
print(ras)
# TODO: update selector ranges based on QTI statistics
crosshairNode = slicer.mrmlScene.GetFirstNodeByClass(
'vtkMRMLCrosshairNode')
event = vtk.vtkCommand.ModifiedEvent
id_ = crosshairNode.AddObserver(event, crosshairCallback)
self.observerObjectIDPairs.append((crosshairNode, id_))
# save for debugging
open('/tmp/data.html', 'w').write(html)
def openQtLocalConnection(self):
self.webWidget = slicer.qSlicerWebWidget()
self.webWidget.url = f'http://localhost:{self.logic.port}'
self.webWidget.show()
