def _initEditor(self):
"""Initialize the Volume Editor GUI."""
self.editor = VolumeEditor(self.layerstack, crosshair=False)
self.volumeEditorWidget = VolumeEditorWidget()
self.volumeEditorWidget.init(self.editor)
# The editor's layerstack is in charge of which layer movement buttons are enabled
model = self.editor.layerStack
self._viewerControlWidget.setupConnections(model)
self.editor._lastImageViewFocus = 0
def _initEditor(self):
"""Initialize the Volume Editor GUI."""
self.editor = VolumeEditor(self.layerstack, crosshair=False)
self.volumeEditorWidget = VolumeEditorWidget()
self.volumeEditorWidget.init(self.editor)
# The editor's layerstack is in charge of which layer movement buttons are enabled
model = self.editor.layerStack
model.canMoveSelectedUp.connect(self._viewerControlWidget.UpButton.setEnabled)
model.canMoveSelectedDown.connect(self._viewerControlWidget.DownButton.setEnabled)
model.canDeleteSelected.connect(self._viewerControlWidget.DeleteButton.setEnabled)
# Connect our layer movement buttons to the appropriate layerstack actions
self._viewerControlWidget.layerWidget.init(model)
self._viewerControlWidget.UpButton.clicked.connect(model.moveSelectedUp)
self._viewerControlWidget.DownButton.clicked.connect(model.moveSelectedDown)
self._viewerControlWidget.DeleteButton.clicked.connect(model.deleteSelected)
self.editor._lastImageViewFocus = 0
class ObjectExtractionGui(QWidget):
###########################################
### AppletGuiInterface Concrete Methods ###
###########################################
def centralWidget(self):
""" Return the widget that will be displayed in the main viewer area. """
return self.volumeEditorWidget
def appletDrawer(self):
return self._drawer
def menus(self):
return []
def viewerControlWidget(self):
return self._viewerControlWidget
def stopAndCleanUp(self):
pass
###########################################
###########################################
def __init__(self, topLevelOperatorView):
super(ObjectExtractionGui, self).__init__()
self.mainOperator = topLevelOperatorView
self.layerstack = LayerStackModel()
self._viewerControlWidget = None
self._initViewerControlUi()
self.editor = None
self._initEditor()
self._initAppletDrawerUi()
assert(self.appletDrawer() is not None)
self._initViewer()
def _onMetaChanged(self, slot):
if slot is self.mainOperator.BinaryImage:
if slot.meta.shape:
self.editor.dataShape = slot.meta.shape
if slot is self.mainOperator.RawImage:
if slot.meta.shape and not self.rawsrc:
self.rawsrc = LazyflowSource(self.mainOperator.RawImage)
layerraw = GrayscaleLayer(self.rawsrc)
layerraw.name = "Raw"
self.layerstack.append(layerraw)
def _onReady(self, slot):
if slot is self.mainOperator.RawImage:
if slot.meta.shape and not self.rawsrc:
self.rawsrc = LazyflowSource(self.mainOperator.RawImage)
layerraw = GrayscaleLayer(self.rawsrc)
layerraw.name = "Raw"
self.layerstack.append(layerraw)
def _initViewer(self):
mainOperator = self.mainOperator
# white foreground on transparent background
ct = [QColor(0, 0, 0, 0).rgba(),
QColor(255, 255, 255, 255).rgba()]
self.binaryimagesrc = LazyflowSource(mainOperator.BinaryImage)
self.binaryimagesrc.setObjectName("Binary LazyflowSrc")
layer = ColortableLayer(self.binaryimagesrc, ct)
layer.name = "Binary Image"
self.layerstack.append(layer)
ct = colortables.create_default_16bit()
self.objectssrc = LazyflowSource(mainOperator.LabelImage)
self.objectssrc.setObjectName("LabelImage LazyflowSrc")
ct[0] = QColor(0, 0, 0, 0).rgba() # make 0 transparent
layer = ColortableLayer(self.objectssrc, ct)
layer.name = "Label Image"
layer.visible = False
layer.opacity = 0.5
self.layerstack.append(layer)
self.centerimagesrc = LazyflowSource(mainOperator.ObjectCenterImage)
layer = RGBALayer(red=ConstantSource(255), alpha=self.centerimagesrc)
layer.name = "Object Centers"
layer.visible = False
self.layerstack.append(layer)
## raw data layer
self.rawsrc = None
self.rawsrc = LazyflowSource(self.mainOperator.RawImage)
self.rawsrc.setObjectName("Raw Lazyflow Src")
layerraw = GrayscaleLayer(self.rawsrc)
layerraw.name = "Raw"
self.layerstack.insert(len(self.layerstack), layerraw)
mainOperator.RawImage.notifyReady(self._onReady)
mainOperator.RawImage.notifyMetaChanged(self._onMetaChanged)
if mainOperator.BinaryImage.meta.shape:
self.editor.dataShape = mainOperator.BinaryImage.meta.shape
mainOperator.BinaryImage.notifyMetaChanged(self._onMetaChanged)
def _initEditor(self):
"""Initialize the Volume Editor GUI."""
self.editor = VolumeEditor(self.layerstack, crosshair=False)
self.volumeEditorWidget = VolumeEditorWidget()
self.volumeEditorWidget.init(self.editor)
# The editor's layerstack is in charge of which layer movement buttons are enabled
model = self.editor.layerStack
self._viewerControlWidget.setupConnections(model)
self.editor._lastImageViewFocus = 0
def _initAppletDrawerUi(self):
# Load the ui file (find it in our own directory)
localDir = os.path.split(__file__)[0]
self._drawer = uic.loadUi(localDir+"/drawer.ui")
self._drawer.selectFeaturesButton.pressed.connect(self._selectFeaturesButtonPressed)
def _initViewerControlUi(self):
self._viewerControlWidget = ViewerControls(self)
def _selectFeaturesButtonPressed(self):
featureDict = {}
slot = self.mainOperator.Features
if slot.ready():
selectedFeatures = self.mainOperator.Features([]).wait()
else:
selectedFeatures = None
try:
plugins = pluginManager.getPluginsOfCategory('ObjectFeatures')
except:
QMessageBox.warning(self,
'object features unavailable',
'Object features plugins failed. Perhaps Yapsy is not installed?',
QMessageBox.Ok)
return
imgshape = list(self.mainOperator.RawImage.meta.shape)
axistags = self.mainOperator.RawImage.meta.axistags
imgshape.pop(axistags.index('t'))
fakeimg = np.empty(imgshape, dtype=np.float32)
labelshape = list(self.mainOperator.BinaryImage.meta.shape)
axistags = self.mainOperator.BinaryImage.meta.axistags
labelshape.pop(axistags.index('t'))
labelshape.pop(axistags.index('c') - 1)
fakelabels = np.empty(labelshape, dtype=np.uint32)
for pluginInfo in plugins:
featureDict[pluginInfo.name] = pluginInfo.plugin_object.availableFeatures(fakeimg, fakelabels)
dlg = FeatureSelectionDialog(featureDict=featureDict,
selectedFeatures=selectedFeatures)
dlg.exec_()
if dlg.result() == QDialog.Accepted:
self.mainOperator.Features.setValue(dlg.selectedFeatures)
self._calculateFeatures()
def _calculateFeatures(self):
self.mainOperator.ObjectCenterImage.setDirty(SubRegion(self.mainOperator.ObjectCenterImage))
maxt = self.mainOperator.LabelImage.meta.shape[0]
progress = QProgressDialog("Calculating features...", "Cancel", 0, maxt)
progress.setWindowModality(Qt.ApplicationModal)
progress.setMinimumDuration(0)
progress.setValue(0)
# We will use notify_finished() to update the progress bar.
# However, the callback will be called from a non-gui thread,
# which cannot access gui elements directly. Therefore we use
# this callback object to send signals back to this thread.
class Callback(QObject):
ndone = 0
timestep_done = pyqtSignal(int)
all_finished = pyqtSignal()
def __call__(self, *args, **kwargs):
self.ndone += 1
self.timestep_done.emit(self.ndone)
if self.ndone == len(reqs):
self.all_finished.emit()
callback = Callback()
def updateProgress(progress, n):
progress.setValue(n)
callback.timestep_done.connect(partial(updateProgress, progress))
def finished():
self.mainOperator._opRegFeats.fixed = True
print 'Object Extraction: done.'
callback.all_finished.connect(finished)
self.mainOperator._opRegFeats.fixed = False
reqs = []
for t in range(maxt):
req = self.mainOperator.RegionFeatures([t])
req.submit()
reqs.append(req)
for i, req in enumerate(reqs):
req.notify_finished(callback)
# handle cancel button
def cancel():
for req in reqs:
req.cancel()
progress.canceled.connect(cancel)
class ObjectExtractionGui(QWidget):
###########################################
### AppletGuiInterface Concrete Methods ###
###########################################
def centralWidget(self):
""" Return the widget that will be displayed in the main viewer area. """
return self.volumeEditorWidget
def appletDrawer(self):
return self._drawer
def menus(self):
return []
def viewerControlWidget(self):
return self._viewerControlWidget
def stopAndCleanUp(self):
pass
###########################################
###########################################
def __init__(self, topLevelOperatorView):
super(ObjectExtractionGui, self).__init__()
self.mainOperator = topLevelOperatorView
self.layerstack = LayerStackModel()
self._viewerControlWidget = None
self._initViewerControlUi()
self.editor = None
self._initEditor()
self._initAppletDrawerUi()
assert(self.appletDrawer() is not None)
self._initViewer()
def _onMetaChanged(self, slot):
if slot is self.mainOperator.BinaryImage:
if slot.meta.shape:
self.editor.dataShape = slot.meta.shape
if slot is self.mainOperator.RawImage:
if slot.meta.shape and not self.rawsrc:
self.rawsrc = LazyflowSource(self.mainOperator.RawImage)
layerraw = GrayscaleLayer(self.rawsrc)
layerraw.name = "Raw"
self.layerstack.append(layerraw)
def _onReady(self, slot):
if slot is self.mainOperator.RawImage:
if slot.meta.shape and not self.rawsrc:
self.rawsrc = LazyflowSource(self.mainOperator.RawImage)
layerraw = GrayscaleLayer(self.rawsrc)
layerraw.name = "Raw"
self.layerstack.append(layerraw)
def _initViewer(self):
mainOperator = self.mainOperator
# white foreground on transparent background
ct = [QColor(0, 0, 0, 0).rgba(),
QColor(255, 255, 255, 255).rgba()]
self.binaryimagesrc = LazyflowSource(mainOperator.BinaryImage)
self.binaryimagesrc.setObjectName("Binary LazyflowSrc")
layer = ColortableLayer(self.binaryimagesrc, ct)
layer.name = "Binary Image"
self.layerstack.append(layer)
ct = colortables.create_default_16bit()
self.objectssrc = LazyflowSource(mainOperator.LabelImage)
self.objectssrc.setObjectName("LabelImage LazyflowSrc")
ct[0] = QColor(0, 0, 0, 0).rgba() # make 0 transparent
layer = ColortableLayer(self.objectssrc, ct)
layer.name = "Label Image"
layer.visible = False
layer.opacity = 0.5
self.layerstack.append(layer)
self.centerimagesrc = LazyflowSource(mainOperator.ObjectCenterImage)
layer = RGBALayer(red=ConstantSource(255), alpha=self.centerimagesrc)
layer.name = "Object Centers"
layer.visible = False
self.layerstack.append(layer)
## raw data layer
self.rawsrc = None
self.rawsrc = LazyflowSource(self.mainOperator.RawImage)
self.rawsrc.setObjectName("Raw Lazyflow Src")
layerraw = GrayscaleLayer(self.rawsrc)
layerraw.name = "Raw"
self.layerstack.insert(len(self.layerstack), layerraw)
mainOperator.RawImage.notifyReady(self._onReady)
mainOperator.RawImage.notifyMetaChanged(self._onMetaChanged)
if mainOperator.BinaryImage.meta.shape:
self.editor.dataShape = mainOperator.BinaryImage.meta.shape
mainOperator.BinaryImage.notifyMetaChanged(self._onMetaChanged)
def _initEditor(self):
"""Initialize the Volume Editor GUI."""
self.editor = VolumeEditor(self.layerstack, crosshair=False)
self.volumeEditorWidget = VolumeEditorWidget()
self.volumeEditorWidget.init(self.editor)
# The editor's layerstack is in charge of which layer movement buttons are enabled
model = self.editor.layerStack
model.canMoveSelectedUp.connect(self._viewerControlWidget.UpButton.setEnabled)
model.canMoveSelectedDown.connect(self._viewerControlWidget.DownButton.setEnabled)
model.canDeleteSelected.connect(self._viewerControlWidget.DeleteButton.setEnabled)
# Connect our layer movement buttons to the appropriate layerstack actions
self._viewerControlWidget.layerWidget.init(model)
self._viewerControlWidget.UpButton.clicked.connect(model.moveSelectedUp)
self._viewerControlWidget.DownButton.clicked.connect(model.moveSelectedDown)
self._viewerControlWidget.DeleteButton.clicked.connect(model.deleteSelected)
self.editor._lastImageViewFocus = 0
def _initAppletDrawerUi(self):
# Load the ui file (find it in our own directory)
localDir = os.path.split(__file__)[0]
self._drawer = uic.loadUi(localDir+"/drawer.ui")
self._drawer.calculateFeaturesButton.pressed.connect(self._calculateFeaturesButtonPressed)
def _initViewerControlUi(self):
p = os.path.split(__file__)[0]+'/'
if p == "/": p = "."+p
self._viewerControlWidget = uic.loadUi(p+"viewerControls.ui")
def _calculateFeaturesButtonPressed(self):
maxt = self.mainOperator.LabelImage.meta.shape[0]
progress = QProgressDialog("Calculating featuers...", "Stop", 0, maxt)
progress.setWindowModality(Qt.ApplicationModal)
progress.setMinimumDuration(0)
progress.setCancelButtonText(QString())
reqs = []
self.mainOperator._opRegFeats.fixed = False
for t in range(maxt):
reqs.append(self.mainOperator.RegionFeatures([t]))
reqs[-1].submit()
for i, req in enumerate(reqs):
progress.setValue(i)
if progress.wasCanceled():
req.cancel()
else:
req.wait()
self.mainOperator._opRegFeats.fixed = True
progress.setValue(maxt)
self.mainOperator.ObjectCenterImage.setDirty(SubRegion(self.mainOperator.ObjectCenterImage))
print 'Object Extraction: done.'