def createUI(self):
self.ui = Ui_DialogVolumeManualSkeletonization()
self.ui.setupUi(self)
self.connect(self.ui.horizontalSliderStartingDensity,QtCore.SIGNAL("valueChanged(int)"),self.startingDensityChanged)
self.connect(self.ui.pushButtonStart,QtCore.SIGNAL("pressed ()"),self.startSkeletonization)
self.connect(self.ui.pushButtonClose, QtCore.SIGNAL("pressed ()"), self.endSkeletonization)
self.connect(self.ui.pushButtonClear, QtCore.SIGNAL("pressed ()"), self.clearSkeleton)
self.connect(self.app, QtCore.SIGNAL("keyReleased(QKeyEvent)"), self.keyReleased)
self.connect(self.app, QtCore.SIGNAL("keyPressed(QKeyEvent)"), self.keyPressed)
class CAlphaInteractiveLoopBuilder(VolumeManualSkeletonizationForm):
def __init__(self, main, chain, parent=None):
QtGui.QWidget.__init__(self, parent)
self.app = main
self.chain = chain
self.app.themes.addDefaultRGB("InteractiveLoopBuilder:StartingPoint",
0, 0, 255, 150)
self.app.themes.addDefaultRGB("InteractiveLoopBuilder:EndingPoint", 0,
255, 0, 150)
self.app.themes.addDefaultRGB("InteractiveLoopBuilder:Sketch", 0, 128,
0, 255)
self.started = False
self.sketchStarted = False
self.viewer = self.app.viewers['volume']
self.skeletonViewer = self.app.viewers["skeleton"]
self.calphaViewer = self.app.viewers["calpha"]
self.connect(self.viewer, QtCore.SIGNAL("modelLoaded()"),
self.modelLoaded)
self.connect(self.viewer, QtCore.SIGNAL("modelChanged()"),
self.modelChanged)
self.connect(self.viewer, QtCore.SIGNAL("modelUnloaded()"),
self.modelUnloaded)
self.isSkeletonClicked = False
self.createUI()
self.oldSkeletonViewerMouseMoveEnabledRay = self.skeletonViewer.mouseMoveEnabledRay
self.connect(
self.skeletonViewer,
QtCore.SIGNAL(
"mouseClickRay(PyQt_PyObject, float, PyQt_PyObject, QMouseEvent)"
), self.processClickRay)
self.connect(
self.skeletonViewer,
QtCore.SIGNAL(
"mouseOverRay(PyQt_PyObject, float, PyQt_PyObject, QMouseEvent)"
), self.processMouseOverRay)
self.connect(self.skeletonViewer, QtCore.SIGNAL("modelChanged()"),
self.skeletonChanged)
maxDensity = self.viewer.renderer.getMaxDensity()
minDensity = self.viewer.renderer.getMinDensity()
self.ui.horizontalSliderStartingDensity.setMinimum(
int(minDensity * 100))
self.ui.horizontalSliderStartingDensity.setMaximum(
int(maxDensity * 100))
defaultDensity = (int(minDensity * 100) + int(maxDensity * 100.0)) / 2
self.ui.horizontalSliderStartingDensity.setValue(defaultDensity)
self.startIndex = 0
self.endIndex = 0
self.startSkeletonization()
def __del__(self):
self.engine.finishLoopBuilding()
self.skeletonViewer.unloadData()
self.endSkeletonization()
def endSkeletonization(self):
self.startEndSkeletonization(False)
def createUI(self):
self.ui = Ui_DialogVolumeManualSkeletonization()
self.ui.setupUi(self)
self.connect(self.ui.horizontalSliderStartingDensity,
QtCore.SIGNAL("valueChanged(int)"),
self.startingDensityChanged)
self.connect(self.ui.pushButtonStart, QtCore.SIGNAL("pressed ()"),
self.startSkeletonization)
self.connect(self.ui.pushButtonClose, QtCore.SIGNAL("pressed ()"),
self.endSkeletonization)
self.connect(self.ui.pushButtonClear, QtCore.SIGNAL("pressed ()"),
self.clearSkeleton)
self.connect(self.app, QtCore.SIGNAL("keyReleased(QKeyEvent)"),
self.keyReleased)
self.connect(self.app, QtCore.SIGNAL("keyPressed(QKeyEvent)"),
self.keyPressed)
def initializeEngine(self, medialnessScoringFunction):
self.engine = InteractiveLoopBuilderEngine(self.volume, self.mesh,
self.calphaViewer.renderer,
self.getStartingDensity(),
self.getStepCount(),
self.getCurveRadius(),
self.getMinCurveLength(),
medialnessScoringFunction)
self.engine.setTranslation(self.viewer.renderer.getOriginX(),
self.viewer.renderer.getOriginY(),
self.viewer.renderer.getOriginZ())
self.engine.setScaling(self.viewer.renderer.getSpacingX(),
self.viewer.renderer.getSpacingY(),
self.viewer.renderer.getSpacingZ())
def modelLoaded(self):
pass
def skeletonChanged(self):
self.calphaViewer.emitModelChanged()
def processClickRay(self, rayWorld, rayWidth, eyeWorld, event):
ray = self.viewer.worldVectorToObjectCoordinates(rayWorld)
eye = self.viewer.worldToObjectCoordinates(eyeWorld)
divisor = float(self.getMedialness()) + float(self.getSmoothness())
medialnessRatio = float(self.getMedialness()) / divisor
smoothnessRatio = float(self.getSmoothness()) / divisor
sketchPriority = float(self.getSketchPriority())
if (self.started):
if ((event.modifiers() & QtCore.Qt.CTRL)
and (event.modifiers() & QtCore.Qt.ALT)):
self.engine.selectRootRay(ray[0], ray[1], ray[2], eye[0],
eye[1], eye[2], rayWidth,
medialnessRatio, smoothnessRatio)
elif (event.modifiers() & QtCore.Qt.CTRL):
self.engine.selectEndSeed(medialnessRatio, smoothnessRatio)
self.engine.selectStartSeedRay(ray[0], ray[1], ray[2], eye[0],
eye[1], eye[2], rayWidth,
medialnessRatio,
smoothnessRatio)
self.skeletonViewer.emitModelChanged()
elif (event.modifiers() & QtCore.Qt.ALT):
self.engine.selectEndSeed(medialnessRatio, smoothnessRatio)
self.skeletonViewer.emitModelChanged()
def setLoopAtoms(self, startIndex, endIndex):
self.engine.clearAtomList()
self.engine.clearCurrentPath()
for i in range(startIndex, endIndex + 1):
if (i in self.chain.residueRange()):
atom = self.chain[i].getAtom('CA')
if (not atom):
raw = PDBAtom(self.chain.getPdbID(),
self.chain.getChainID(), i, 'CA')
raw.setPosition(Vector3DFloat(0, 0, 0))
atom = self.calphaViewer.renderer.addAtom(raw)
atom.setVisible(False)
print atom
self.chain[i].addAtomObject(atom)
self.chain[i].setCAlphaColorToDefault()
bondBefore = None
bondAfter = None
if i - 1 in self.chain.residueRange():
prevCAlpha = self.chain[i - 1].getAtom('CA')
if prevCAlpha:
print "adding a bond before"
bondBefore = PDBBond()
bondBefore.setAtom0Ix(prevCAlpha.getHashKey())
bondBefore.setAtom1Ix(atom.getHashKey())
if i + 1 in self.chain.residueRange():
nextCAlpha = self.chain[i + 1].getAtom('CA')
if nextCAlpha:
print "adding a bond after"
bondAfter = PDBBond()
bondAfter.setAtom0Ix(nextCAlpha.getHashKey())
bondAfter.setAtom1Ix(atom.getHashKey())
if bondBefore:
self.calphaViewer.renderer.addBond(bondBefore)
if bondAfter:
self.calphaViewer.renderer.addBond(bondAfter)
self.engine.addAtom(atom.getHashKey())
if not self.calphaViewer.loaded:
self.calphaViewer.loaded = True
self.calphaViewer.emitModelLoaded()
else:
self.calphaViewer.emitModelChanged()
def drawOverlay(self):
if self.started:
manualColors = [
self.app.themes.getColor(
"InteractiveLoopBuilder:StartingPoint"),
self.app.themes.getColor("InteractiveLoopBuilder:EndingPoint"),
self.app.themes.getColor("InteractiveLoopBuilder:Sketch")
]
for i in range(3):
glPushAttrib(GL_LIGHTING_BIT)
self.skeletonViewer.setMaterials(manualColors[i])
self.engine.draw(i)
glPopAttrib()
class VolumeManualSkeletonizationForm(BaseDockWidget):
MedialnessScoringFunctionBinary, MedialnessScoringFunctionGlobalRank, MedialnessScoringFunctionLocalRank = range(3)
def __init__(self, main, viewer, parent=None):
BaseDockWidget.__init__(self,
main,
"&Interactive Skeletonization",
"Perform interactive skeletonization",
"perform_VolumeManualSkeletonization",
"actions-volume-skeletonization-manual",
"actions-volume-skeletonization",
QtCore.Qt.LeftDockWidgetArea | QtCore.Qt.RightDockWidgetArea | QtCore.Qt.BottomDockWidgetArea,
QtCore.Qt.BottomDockWidgetArea,
parent)
self.app = main
self.app.themes.addDefaultRGB("InteractiveSkeletonizer:StartingPoint", 0, 0, 255, 255)
self.app.themes.addDefaultRGB("InteractiveSkeletonizer:EndingPoint", 0, 255, 0, 255)
self.app.themes.addDefaultRGB("InteractiveSkeletonizer:Sketch", 0, 128, 0, 255)
self.app.themes.addDefaultRGB("InteractiveSkeletonizer:UnconfirmedCurve", 255, 255, 0, 255)
self.app.themes.addDefaultRGB("InteractiveSkeletonizer:RemovableCurve", 100, 255, 100, 255)
self.started = False
self.sketchStarted = False
self.viewer = viewer
self.connect(self.viewer, QtCore.SIGNAL("modelLoaded()"), self.modelLoaded)
self.connect(self.viewer, QtCore.SIGNAL("modelChanged()"), self.modelChanged)
self.connect(self.viewer, QtCore.SIGNAL("modelUnloaded()"), self.modelUnloaded)
self.isSkeletonClicked = False;
self.createUI()
self.createActions()
def createUI(self):
self.ui = Ui_DialogVolumeManualSkeletonization()
self.ui.setupUi(self)
self.connect(self.ui.horizontalSliderStartingDensity,QtCore.SIGNAL("valueChanged(int)"),self.startingDensityChanged)
self.connect(self.ui.pushButtonStart,QtCore.SIGNAL("pressed ()"),self.startSkeletonization)
self.connect(self.ui.pushButtonClose, QtCore.SIGNAL("pressed ()"), self.endSkeletonization)
self.connect(self.ui.pushButtonClear, QtCore.SIGNAL("pressed ()"), self.clearSkeleton)
self.connect(self.app, QtCore.SIGNAL("keyReleased(QKeyEvent)"), self.keyReleased)
self.connect(self.app, QtCore.SIGNAL("keyPressed(QKeyEvent)"), self.keyPressed)
def createActions(self):
self.skeletonizeAct = self.displayAct
self.skeletonizeAct.setEnabled(False)
def showWidget(self, show):
BaseDockWidget.showWidget(self, show)
if(not show):
self.setSkeletonViewerProperties(False)
self.ui.pushButtonStart.setEnabled(True)
self.ui.pushButtonClose.setEnabled(False)
def startSkeletonization(self):
self.startEndSkeletonization(True)
def endSkeletonization(self):
self.startEndSkeletonization(False)
self.dock.close()
def initializeEngine(self, medialnessScoringFunction):
self.engine = InteractiveSkeletonEngine(self.volume, self.mesh, self.getStartingDensity(), self.getStepCount(), self.getCurveRadius(), self.getMinCurveLength(), medialnessScoringFunction)
def startEndSkeletonization(self, start):
if(start):
self.volume = self.viewer.renderer.getVolume()
if self.skeletonViewer.loaded:
self.skeletonViewer.unloadData()
self.mesh = self.skeletonViewer.renderer.getMesh()
self.skeletonViewer.setScale(self.viewer.renderer.getSpacingX(), self.viewer.renderer.getSpacingY(), self.viewer.renderer.getSpacingZ())
self.skeletonViewer.setLocation(self.viewer.renderer.getOriginX(), self.viewer.renderer.getOriginY(), self.viewer.renderer.getOriginZ())
if self.ui.radioButtonBinary.isChecked():
medialnessScoringFunction = self.MedialnessScoringFunctionBinary
elif self.ui.radioButtonGlobalRank.isChecked():
medialnessScoringFunction = self.MedialnessScoringFunctionGlobalRank
else :
medialnessScoringFunction = self.MedialnessScoringFunctionLocalRank
self.initializeEngine(medialnessScoringFunction)
self.engine.setIsoValue(self.viewer.renderer.getSurfaceValue())
self.connect(self.app.viewers["skeleton"], QtCore.SIGNAL("elementSelected (int, int, int, int, int, int, QMouseEvent)"), self.skeletonClicked)
self.connect(self.app.mainCamera, QtCore.SIGNAL("cameraChanged()"), self.processCameraChanged)
self.connect(self.app.viewers["skeleton"], QtCore.SIGNAL("thicknessChanged(int)"), self.thicknessChanged)
self.connect(self.app.viewers["skeleton"], QtCore.SIGNAL("modelDrawing()"), self.drawOverlay)
self.engine.setLineThickness(self.skeletonViewer.lineThickness)
self.setSkeletonViewerProperties(True)
self.skeletonViewer.loaded = True
self.ui.pushButtonStart.setEnabled(False)
self.ui.pushButtonClose.setEnabled(True)
self.skeletonViewer.emitModelLoaded()
else:
self.disconnect(self.app.viewers["skeleton"], QtCore.SIGNAL("elementSelected (int, int, int, int, int, int, QMouseEvent)"), self.skeletonClicked)
self.disconnect(self.app.mainCamera, QtCore.SIGNAL("cameraChanged()"), self.processCameraChanged)
self.disconnect(self.app.viewers["skeleton"], QtCore.SIGNAL("thicknessChanged(int)"), self.thicknessChanged)
self.disconnect(self.app.viewers["skeleton"], QtCore.SIGNAL("modelDrawing()"), self.drawOverlay)
self.engine.finalizeSkeleton()
del self.engine
self.setSkeletonViewerProperties(False)
self.ui.pushButtonStart.setEnabled(True)
self.ui.pushButtonClose.setEnabled(False)
self.started = start
self.skeletonViewer.emitModelChanged()
def startingDensityChanged(self, newLevel):
self.ui.labelStartingDensityDisplay.setNum(newLevel/100.0)
def getStartingDensity(self):
return self.ui.horizontalSliderStartingDensity.value()/100.0
def getMedialness(self):
return self.ui.horizontalSliderMedialness.value()
def getSmoothness(self):
return self.ui.horizontalSliderSmoothness.value()
def getSketchPriority(self):
return self.ui.horizontalSliderSketchPriority.value()
def getStepCount(self):
return self.ui.horizontalSliderStepCount.value()
def getCurveRadius(self):
return self.ui.spinBoxCurveRadius.value()
def getMinCurveLength(self):
return self.ui.spinBoxMinCurve.value()
def setSkeletonViewerProperties(self, opening):
if(opening):
#self.oldSkeletonViewerSelectEnabled = self.skeletonViewer.selectEnabled
#self.oldSkeletonViewerMouseMoveEnabled = self.skeletonViewer.mouseMoveEnabled
self.oldSkeletonViewerMouseMoveEnabledRay = self.skeletonViewer.mouseMoveEnabledRay
self.skeletonViewer.setViewerAutonomy(False);
if self.skeletonViewer.loaded:
self.skeletonViewer.unloadData()
self.skeletonViewer.setSelectEnabled(True)
self.skeletonViewer.setMouseMoveEnabledRay(True)
color = self.app.themes.getColor("Volume:Model:0")
color.setAlpha(150)
self.viewer.setModelColor(color)
#self.skeletonViewer.setMouseMoveEnabled(True)
else:
self.skeletonViewer.setViewerAutonomy(True);
#self.skeletonViewer.setSelectEnabled(self.oldSkeletonViewerSelectEnabled)
self.skeletonViewer.setMouseMoveEnabledRay(self.oldSkeletonViewerMouseMoveEnabledRay)
#self.skeletonViewer.setMouseMoveEnabled(self.oldSkeletonViewerMouseMoveEnabled)
def filterMouseHits(self, mouseHits):
hits = list()
for hit_record in mouseHits:
minDepth, maxDepth, names = hit_record
names = list(names)
if(names[0] == self.skeletonViewer.sceneIndex):
names.pop(0)
for i in range(2-len(names)):
names.append(-1)
hits.append(names)
return hits
def processClickRay(self, rayWorld, rayWidth, eyeWorld, event):
ray = self.viewer.worldVectorToObjectCoordinates(rayWorld)
eye = self.viewer.worldToObjectCoordinates(eyeWorld)
divisor = float(self.getMedialness()) + float(self.getSmoothness());
medialnessRatio = float(self.getMedialness()) / divisor;
smoothnessRatio = float(self.getSmoothness()) / divisor;
sketchPriority = float(self.getSketchPriority());
if(self.started):
if((event.modifiers() & QtCore.Qt.CTRL) and (event.modifiers() & QtCore.Qt.ALT)):
self.engine.selectRootRay(ray[0], ray[1], ray[2], eye[0], eye[1], eye[2], rayWidth, medialnessRatio, smoothnessRatio)
elif(event.modifiers() & QtCore.Qt.CTRL):
self.engine.selectEndSeed(medialnessRatio, smoothnessRatio)
self.engine.selectStartSeedRay(ray[0], ray[1], ray[2], eye[0], eye[1], eye[2], rayWidth, medialnessRatio, smoothnessRatio)
self.skeletonViewer.emitModelChanged()
elif (event.modifiers() & QtCore.Qt.ALT):
self.engine.selectEndSeed(medialnessRatio, smoothnessRatio)
self.skeletonViewer.emitModelChanged()
def processMouseOverRay(self, rayWorld, rayWidth, eyeWorld, event):
ray = self.viewer.worldVectorToObjectCoordinates(rayWorld)
eye = self.viewer.worldToObjectCoordinates(eyeWorld)
if(self.started and event.modifiers() & QtCore.Qt.CTRL ):
self.engine.browseStartSeedRay(ray[0], ray[1], ray[2], eye[0], eye[1], eye[2], rayWidth)
self.engine.analyzePathRay(ray[0], ray[1], ray[2], eye[0], eye[1], eye[2], rayWidth)
self.skeletonViewer.emitModelChanged()
elif(self.started and event.modifiers() & QtCore.Qt.ALT ):
self.engine.analyzePathRay(ray[0], ray[1], ray[2], eye[0], eye[1], eye[2], rayWidth)
self.skeletonViewer.emitModelChanged()
elif(self.started and event.modifiers() & QtCore.Qt.SHIFT):
self.engine.setSketch2D(self.app.mainCamera.width(), self.app.mainCamera.height(), event.x(), event.y())
self.engine.setSketchRay(ray[0], ray[1], ray[2], eye[0], eye[1], eye[2], rayWidth)
self.skeletonViewer.emitModelChanged()
def processCameraChanged(self):
if(self.engine.clearSketch2D()) :
self.skeletonViewer.emitModelChanged()
def modelLoaded(self):
self.skeletonViewer = self.app.viewers["skeleton"];
#self.oldSkeletonViewerSelectEnabled = self.skeletonViewer.selectEnabled
#self.oldSkeletonViewerMouseMoveEnabled = self.skeletonViewer.mouseMoveEnabled
self.oldSkeletonViewerMouseMoveEnabledRay = self.skeletonViewer.mouseMoveEnabledRay
#self.connect(self.app.mainCamera, QtCore.SIGNAL("mouseMovedRAW(PyQt_PyObject, QMouseEvent)"), self.processMouseOverMultiple)
#self.connect(self.app.mainCamera, QtCore.SIGNAL("mouseClickedRAW(PyQt_PyObject, QMouseEvent)"), self.processClickMultiple)
#self.connect(self.skeletonViewer, QtCore.SIGNAL("elementSelected (int, int, int, int, int, int, QMouseEvent)"), self.processClick)
#self.connect(self.skeletonViewer, QtCore.SIGNAL("elementMouseOver (int, int, int, int, int, int, QMouseEvent)"), self.processMouseOver)
self.connect(self.skeletonViewer, QtCore.SIGNAL("mouseClickRay(PyQt_PyObject, float, PyQt_PyObject, QMouseEvent)"), self.processClickRay)
self.connect(self.skeletonViewer, QtCore.SIGNAL("mouseOverRay(PyQt_PyObject, float, PyQt_PyObject, QMouseEvent)"), self.processMouseOverRay)
self.skeletonizeAct.setEnabled(True)
self.showWidget(False)
maxDensity = self.viewer.renderer.getMaxDensity()
minDensity = self.viewer.renderer.getMinDensity()
self.ui.horizontalSliderStartingDensity.setMinimum(int(minDensity*100))
self.ui.horizontalSliderStartingDensity.setMaximum(int(maxDensity*100))
defaultDensity = (int(minDensity*100) + int(maxDensity*100.0)) / 2
self.ui.horizontalSliderStartingDensity.setValue(defaultDensity)
if(self.started):
self.engine.setIsoValue(self.viewer.renderer.getSurfaceValue())
def modelUnloaded(self):
self.skeletonizeAct.setEnabled(False)
self.showWidget(False)
def modelChanged(self):
if(self.started):
self.engine.setIsoValue(self.viewer.renderer.getSurfaceValue())
self.skeletonViewer.emitModelChanged()
def clearSkeleton(self):
self.engine.clearSkeleton()
self.skeletonViewer.emitModelChanged()
def skeletonClicked(self, hit0, hit1, hit2, hit3, hit4, hit5, event):
self.engine.addSelectionPoint(hit0, hit1)
self.skeletonViewer.emitModelChanged()
def keyPressed(self, event):
if self.started:
if(event.key() == QtCore.Qt.Key_Control):
self.engine.startEndPolyLineMode(True)
self.skeletonViewer.emitModelChanged()
elif(event.key() == QtCore.Qt.Key_Alt):
self.engine.startEndSingleRootMode(True)
self.skeletonViewer.emitModelChanged()
def keyReleased(self, event):
if self.started:
divisor = float(self.getMedialness()) + float(self.getSmoothness());
medialnessRatio = float(self.getMedialness()) / divisor;
smoothnessRatio = float(self.getSmoothness()) / divisor;
sketchPriority = float(self.getSketchPriority());
if(event.key() == QtCore.Qt.Key_Control):
self.engine.startEndPolyLineMode(False)
self.skeletonViewer.emitModelChanged()
elif(event.key() == QtCore.Qt.Key_Alt):
self.engine.startEndSingleRootMode(False)
self.skeletonViewer.emitModelChanged()
elif(event.key() == QtCore.Qt.Key_Escape):
self.engine.clearCurrentPath();
self.skeletonViewer.emitModelChanged()
elif(event.key() == QtCore.Qt.Key_Shift):
self.engine.endSketchRay(medialnessRatio, smoothnessRatio, 1.0, sketchPriority)
self.skeletonViewer.emitModelChanged()
elif(event.key() == QtCore.Qt.Key_Plus):
self.engine.selectEndSeed(medialnessRatio, smoothnessRatio)
self.skeletonViewer.emitModelChanged()
elif(event.key() == QtCore.Qt.Key_Delete):
self.engine.deleteSelection();
self.skeletonViewer.emitModelChanged()
def thicknessChanged(self, value):
self.engine.setLineThickness(value)
def drawOverlay(self):
if self.started:
manualColors = [self.app.themes.getColor("InteractiveSkeletonizer:StartingPoint"),
self.app.themes.getColor("InteractiveSkeletonizer:EndingPoint"),
self.app.themes.getColor("InteractiveSkeletonizer:Sketch"),
self.app.themes.getColor("InteractiveSkeletonizer:UnconfirmedCurve"),
self.app.themes.getColor("InteractiveSkeletonizer:RemovableCurve")]
for i in range(5):
glPushAttrib(GL_LIGHTING_BIT)
self.skeletonViewer.setMaterials(manualColors[i])
self.engine.draw(i)
glPopAttrib()