def __init__(self, topLevelOperatorView, additionalMonitoredSlots=[], centralWidgetOnly=False, crosshair=True):
"""
Constructor. **All** slots of the provided *topLevelOperatorView* will be monitored for changes.
Changes include slot resize events, and slot ready/unready status changes.
When a change is detected, the `setupLayers()` function is called, and the result is used to update the list of layers shown in the central widget.
:param topLevelOperatorView: The top-level operator for the applet this GUI belongs to.
:param additionalMonitoredSlots: Optional. Can be used to add additional slots to the set of viewable layers (all slots from the top-level operator are already monitored).
:param centralWidgetOnly: If True, provide only a central widget without drawer or viewer controls.
"""
super(LayerViewerGui, self).__init__()
self._stopped = False
self._initialized = False
self.threadRouter = ThreadRouter(self) # For using @threadRouted
self.topLevelOperatorView = topLevelOperatorView
observedSlots = []
for slot in topLevelOperatorView.inputs.values() + topLevelOperatorView.outputs.values():
if slot.level == 0 or slot.level == 1:
observedSlots.append(slot)
observedSlots += additionalMonitoredSlots
self._orphanOperators = [] # Operators that are owned by this GUI directly (not owned by the top-level operator)
self.observedSlots = []
for slot in observedSlots:
if slot.level == 0:
if not isinstance(slot.stype, ArrayLike):
# We don't support visualization of non-Array slots.
continue
# To be monitored and updated correctly by this GUI, slots must have level=1, but this slot is of level 0.
# Pass it through a trivial "up-leveling" operator so it will have level 1 for our purposes.
opPromoteInput = Op1ToMulti(graph=slot.operator.graph)
opPromoteInput.Input.connect(slot)
slot = opPromoteInput.Outputs
self._orphanOperators.append( opPromoteInput )
# Each slot should now be indexed as slot[layer_index]
assert slot.level == 1
self.observedSlots.append( slot )
slot.notifyInserted( bind(self._handleLayerInsertion) )
slot.notifyRemoved( bind(self._handleLayerRemoval) )
for i in range(len(slot)):
self._handleLayerInsertion(slot, i)
self.layerstack = LayerStackModel()
self._initCentralUic()
self._initEditor(crosshair=crosshair)
self.__viewerControlWidget = None
if not centralWidgetOnly:
self.initViewerControlUi() # Might be overridden in a subclass. Default implementation loads a standard layer widget.
#self._drawer = QWidget( self )
self.initAppletDrawerUi() # Default implementation loads a blank drawer from drawer.ui.
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()
class LayerViewerGui(QWidget):
"""
Implements an applet GUI whose central widget is a VolumeEditor
and whose layer controls simply contains a layer list widget.
Intended to be used as a subclass for applet GUI objects.
Provides: Central widget (viewer), View Menu, and Layer controls
Provides an EMPTY applet drawer widget. Subclasses should replace it with their own applet drawer.
"""
__metaclass__ = LayerViewerGuiMetaclass
###########################################
### AppletGuiInterface Concrete Methods ###
###########################################
def centralWidget( self ):
return self
def appletDrawer(self):
return self._drawer
def menus( self ):
return [self.menuView] # From the .ui file
def viewerControlWidget(self):
return self.__viewerControlWidget
def stopAndCleanUp(self):
self._stopped = True
# Remove all layers
self.layerstack.clear()
# Stop rendering
for scene in self.editor.imageScenes:
if scene._tileProvider:
scene._tileProvider.notifyThreadsToStop()
scene.joinRendering()
for op in self._orphanOperators:
op.cleanUp()
###########################################
###########################################
@traceLogged(traceLogger)
def __init__(self, topLevelOperatorView, additionalMonitoredSlots=[], centralWidgetOnly=False, crosshair=True):
"""
Constructor. **All** slots of the provided *topLevelOperatorView* will be monitored for changes.
Changes include slot resize events, and slot ready/unready status changes.
When a change is detected, the `setupLayers()` function is called, and the result is used to update the list of layers shown in the central widget.
:param topLevelOperatorView: The top-level operator for the applet this GUI belongs to.
:param additionalMonitoredSlots: Optional. Can be used to add additional slots to the set of viewable layers (all slots from the top-level operator are already monitored).
:param centralWidgetOnly: If True, provide only a central widget without drawer or viewer controls.
"""
super(LayerViewerGui, self).__init__()
self._stopped = False
self._initialized = False
self.threadRouter = ThreadRouter(self) # For using @threadRouted
self.topLevelOperatorView = topLevelOperatorView
observedSlots = []
for slot in topLevelOperatorView.inputs.values() + topLevelOperatorView.outputs.values():
if slot.level == 0 or slot.level == 1:
observedSlots.append(slot)
observedSlots += additionalMonitoredSlots
self._orphanOperators = [] # Operators that are owned by this GUI directly (not owned by the top-level operator)
self.observedSlots = []
for slot in observedSlots:
if slot.level == 0:
if not isinstance(slot.stype, ArrayLike):
# We don't support visualization of non-Array slots.
continue
# To be monitored and updated correctly by this GUI, slots must have level=1, but this slot is of level 0.
# Pass it through a trivial "up-leveling" operator so it will have level 1 for our purposes.
opPromoteInput = Op1ToMulti(graph=slot.operator.graph)
opPromoteInput.Input.connect(slot)
slot = opPromoteInput.Outputs
self._orphanOperators.append( opPromoteInput )
# Each slot should now be indexed as slot[layer_index]
assert slot.level == 1
self.observedSlots.append( slot )
slot.notifyInserted( bind(self._handleLayerInsertion) )
slot.notifyRemoved( bind(self._handleLayerRemoval) )
for i in range(len(slot)):
self._handleLayerInsertion(slot, i)
self.layerstack = LayerStackModel()
self._initCentralUic()
self._initEditor(crosshair=crosshair)
self.__viewerControlWidget = None
if not centralWidgetOnly:
self.initViewerControlUi() # Might be overridden in a subclass. Default implementation loads a standard layer widget.
#self._drawer = QWidget( self )
self.initAppletDrawerUi() # Default implementation loads a blank drawer from drawer.ui.
def _after_init(self):
self._initialized = True
self.updateAllLayers()
def setupLayers( self ):
"""
Create a list of layers to be displayed in the central widget.
Subclasses should override this method to create the list of layers that can be displayed.
For debug and development purposes, the base class implementation simply generates layers for all topLevelOperatorView slots.
"""
layers = []
for multiLayerSlot in self.observedSlots:
for j, slot in enumerate(multiLayerSlot):
if slot.ready() and slot.meta.axistags is not None:
layer = self.createStandardLayerFromSlot(slot)
# Name the layer after the slot name.
if isinstance( multiLayerSlot.getRealOperator(), Op1ToMulti ):
# We attached an 'upleveling' operator, so look upstream for the real slot.
layer.name = multiLayerSlot.getRealOperator().Input.partner.name
else:
layer.name = multiLayerSlot.name + " " + str(j)
#layers.append(layer)
return layers
@traceLogged(traceLogger)
def _handleLayerInsertion(self, slot, slotIndex):
"""
The multislot providing our layers has a new item.
Make room for it in the layer GUI and subscribe to updates.
"""
# When the slot is ready, we'll replace the blank layer with real data
slot[slotIndex].notifyReady( bind(self.updateAllLayers) )
slot[slotIndex].notifyUnready( bind(self.updateAllLayers) )
@traceLogged(traceLogger)
def _handleLayerRemoval(self, slot, slotIndex):
"""
An item is about to be removed from the multislot that is providing our layers.
Remove the layer from the GUI.
"""
self.updateAllLayers()
def generateAlphaModulatedLayersFromChannels(self, slot):
# TODO
assert False
@classmethod
def createStandardLayerFromSlot(cls, slot, lastChannelIsAlpha=False):
"""
Convenience function.
Generates a volumina layer using the given slot.
Chooses between grayscale or RGB depending on the number of channels in the slot.
* If *slot* has 1 channel, a GrayscaleLayer is created.
* If *slot* has 2 non-alpha channels, an RGBALayer is created with R and G channels.
* If *slot* has 3 non-alpha channels, an RGBALayer is created with R,G, and B channels.
* If *slot* has 4 channels, an RGBA layer is created
:param slot: The slot to generate a layer from
:param lastChannelIsAlpha: If True, the last channel in the slot is assumed to be an alpha channel.
If slot has 4 channels, this parameter has no effect.
"""
def getRange(meta):
if 'drange' in meta:
return meta.drange
if meta.dtype == numpy.uint8:
return (0, 255)
else:
# If we don't know the range of the data, create a layer that is auto-normalized.
# See volumina.pixelpipeline.datasources for details.
#
# Even in the case of integer data, which has more than 255 possible values,
# (like uint16), it seems reasonable to use this setting as default
return 'autoPercentiles'
# Examine channel dimension to determine Grayscale vs. RGB
shape = slot.meta.shape
normalize = getRange(slot.meta)
try:
channelAxisIndex = slot.meta.axistags.index('c')
#assert channelAxisIndex < len(slot.meta.axistags), \
# "slot %s has shape = %r, axistags = %r, but no channel dimension" \
# % (slot.name, slot.meta.shape, slot.meta.axistags)
numChannels = shape[channelAxisIndex]
except:
numChannels = 1
if numChannels == 4:
lastChannelIsAlpha = True
if lastChannelIsAlpha:
assert numChannels <= 4, "Can't display a standard layer with more than four channels (with alpha). Your image has {} channels.".format(numChannels)
else:
assert numChannels <= 3, "Can't display a standard layer with more than three channels (with no alpha). Your image has {} channels.".format(numChannels)
if numChannels == 1:
assert not lastChannelIsAlpha, "Can't have an alpha channel if there is no color channel"
source = LazyflowSource(slot)
normSource = NormalizingSource( source, bounds=normalize )
return GrayscaleLayer(normSource)
assert numChannels > 2 or (numChannels == 2 and not lastChannelIsAlpha), \
"Unhandled combination of channels. numChannels={}, lastChannelIsAlpha={}, axistags={}".format( numChannels, lastChannelIsAlpha, slot.meta.axistags )
redProvider = OpSingleChannelSelector(graph=slot.graph)
redProvider.Input.connect(slot)
redProvider.Index.setValue( 0 )
redSource = LazyflowSource( redProvider.Output )
redNormSource = NormalizingSource( redSource, bounds=normalize )
greenProvider = OpSingleChannelSelector(graph=slot.graph)
greenProvider.Input.connect(slot)
greenProvider.Index.setValue( 1 )
greenSource = LazyflowSource( greenProvider.Output )
greenNormSource = NormalizingSource( greenSource, bounds=normalize )
blueNormSource = None
if numChannels > 3 or (numChannels == 3 and not lastChannelIsAlpha):
blueProvider = OpSingleChannelSelector(graph=slot.graph)
blueProvider.Input.connect(slot)
blueProvider.Index.setValue( 2 )
blueSource = LazyflowSource( blueProvider.Output )
blueNormSource = NormalizingSource( blueSource, bounds=normalize )
alphaNormSource = None
if lastChannelIsAlpha:
alphaProvider = OpSingleChannelSelector(graph=slot.graph)
alphaProvider.Input.connect(slot)
alphaProvider.Index.setValue( numChannels-1 )
alphaSource = LazyflowSource( alphaProvider.Output )
alphaNormSource = NormalizingSource( alphaSource, bounds=normalize )
layer = RGBALayer( red=redNormSource, green=greenNormSource, blue=blueNormSource, alpha=alphaNormSource )
return layer
@traceLogged(traceLogger)
@threadRouted
def updateAllLayers(self):
if self._stopped or not self._initialized:
return
# Ask for the updated layer list (usually provided by the subclass)
newGuiLayers = self.setupLayers()
newNames = set(l.name for l in newGuiLayers)
if len(newNames) != len(newGuiLayers):
msg = "All layers must have unique names.\n"
msg += "You're attempting to use these layer names:\n"
msg += str( [l.name for l in newGuiLayers] )
raise RuntimeError(msg)
# If the datashape changed, tell the editor
# FIXME: This may not be necessary now that this gui doesn't handle the multi-image case...
newDataShape = self.determineDatashape()
if newDataShape is not None and self.editor.dataShape != newDataShape:
self.editor.dataShape = newDataShape
#if the image is 2D, do not show the HUD action (issue #190)
is2D = numpy.sum(numpy.asarray(newDataShape[1:4]) == 1) == 1
self.menuGui.actionToggleSelectedHud.setVisible(not is2D)
self.menuGui.actionToggleAllHuds.setVisible(not is2D)
# Find the xyz midpoint
midpos5d = [x/2 for x in newDataShape]
midpos3d = midpos5d[1:4]
# Start in the center of the volume
self.editor.posModel.slicingPos = midpos3d
self.editor.navCtrl.panSlicingViews( midpos3d, [0,1,2] )
# Old layers are deleted if
# (1) They are not in the new set or
# (2) Their data has changed
for index, oldLayer in reversed(list(enumerate(self.layerstack))):
if oldLayer.name not in newNames:
needDelete = True
else:
newLayer = filter(lambda l: l.name == oldLayer.name, newGuiLayers)[0]
needDelete = (newLayer.datasources != oldLayer.datasources)
if needDelete:
layer = self.layerstack[index]
if hasattr(layer, 'shortcutRegistration'):
obsoleteShortcut = layer.shortcutRegistration[2]
obsoleteShortcut.setEnabled(False)
ShortcutManager().unregister( obsoleteShortcut )
self.layerstack.selectRow(index)
self.layerstack.deleteSelected()
# Insert all layers that aren't already in the layerstack
# (Identified by the name attribute)
existingNames = set(l.name for l in self.layerstack)
for index, layer in enumerate(newGuiLayers):
if layer.name not in existingNames:
# Insert new
self.layerstack.insert( index, layer )
# If this layer has an associated shortcut, register it with the shortcut manager
if hasattr(layer, 'shortcutRegistration'):
ShortcutManager().register( *layer.shortcutRegistration )
else:
# Clean up the layer instance that the client just gave us.
# We don't want to use it.
if hasattr(layer, 'shortcutRegistration'):
shortcut = layer.shortcutRegistration[2]
shortcut.setEnabled(False)
# Move existing layer to the correct position
stackIndex = self.layerstack.findMatchingIndex(lambda l: l.name == layer.name)
self.layerstack.selectRow(stackIndex)
while stackIndex > index:
self.layerstack.moveSelectedUp()
stackIndex -= 1
while stackIndex < index:
self.layerstack.moveSelectedDown()
stackIndex += 1
@traceLogged(traceLogger)
def determineDatashape(self):
newDataShape = None
for provider in self.observedSlots:
for i, slot in enumerate(provider):
if newDataShape is None and slot.ready() and slot.meta.axistags is not None:
# Use an Op5ifyer adapter to transpose the shape for us.
op5 = Op5ifyer( graph=slot.graph )
op5.input.connect( slot )
newDataShape = op5.output.meta.shape
# We just needed the operator to determine the transposed shape.
# Disconnect it so it can be garbage collected.
op5.input.disconnect()
if newDataShape is not None:
# For now, this base class combines multi-channel images into a single layer,
# So, we want the volume editor to behave as though there is only one channel
newDataShape = newDataShape[:-1] + (1,)
return newDataShape
@traceLogged(traceLogger)
def initViewerControlUi(self):
"""
Load the viewer controls GUI, which appears below the applet bar.
In our case, the viewer control GUI consists mainly of a layer list.
Subclasses should override this if they provide their own viewer control widget.
"""
localDir = os.path.split(__file__)[0]
self.__viewerControlWidget = ViewerControls()
# The editor's layerstack is in charge of which layer movement buttons are enabled
model = self.editor.layerStack
if self.__viewerControlWidget is not None:
self.__viewerControlWidget.setupConnections(model)
@traceLogged(traceLogger)
def initAppletDrawerUi(self):
"""
By default, this base class provides a blank applet drawer.
Override this in a subclass to get a real applet drawer.
"""
# Load the ui file (find it in our own directory)
localDir = os.path.split(__file__)[0]
self._drawer = uic.loadUi(localDir+"/drawer.ui")
def getAppletDrawerUi(self):
return self._drawer
@traceLogged(traceLogger)
def _initCentralUic(self):
"""
Load the GUI from the ui file into this class and connect it with event handlers.
"""
# Load the ui file into this class (find it in our own directory)
localDir = os.path.split(__file__)[0]
uic.loadUi(localDir+"/centralWidget.ui", self)
# Menu is specified in a separate ui file with a dummy window
self.menuGui = uic.loadUi(localDir+"/menu.ui") # Save as member so it doesn't get picked up by GC
self.menuBar = self.menuGui.menuBar
self.menuView = self.menuGui.menuView
def toggleDebugPatches(show):
self.editor.showDebugPatches = show
def setCacheSize( cache_size ):
dlg = QDialog(self)
layout = QHBoxLayout()
layout.addWidget( QLabel("Cached Slices Per View:") )
cache_size = [self.editor.cacheSize]
def parseCacheSize( strSize ):
try:
cache_size[0] = int(strSize)
except:
pass
edit = QLineEdit( str(cache_size[0]), parent=dlg )
edit.textChanged.connect( parseCacheSize )
layout.addWidget( edit )
okButton = QPushButton( "OK", parent=dlg )
okButton.clicked.connect( dlg.accept )
layout.addWidget( okButton )
dlg.setLayout( layout )
dlg.setModal(True)
dlg.exec_()
self.editor.cacheSize = cache_size[0]
def enablePrefetching( enable ):
for scene in self.editor.imageScenes:
scene.setPrefetchingEnabled( enable )
def fitToScreen():
shape = self.editor.posModel.shape
for i, v in enumerate(self.editor.imageViews):
s = list(shape)
del s[i]
v.changeViewPort(v.scene().data2scene.mapRect(QRectF(0,0,*s)))
def fitImage():
if hasattr(self.editor, '_lastImageViewFocus'):
self.editor.imageViews[self.editor._lastImageViewFocus].fitImage()
def restoreImageToOriginalSize():
if hasattr(self.editor, '_lastImageViewFocus'):
self.editor.imageViews[self.editor._lastImageViewFocus].doScaleTo()
'''
def rubberBandZoom():
if hasattr(self.editor, '_lastImageViewFocus'):
if not self.editor.imageViews[self.editor._lastImageViewFocus]._isRubberBandZoom:
self.editor.imageViews[self.editor._lastImageViewFocus]._isRubberBandZoom = True
self.editor.imageViews[self.editor._lastImageViewFocus]._cursorBackup = self.editor.imageViews[self.editor._lastImageViewFocus].cursor()
self.editor.imageViews[self.editor._lastImageViewFocus].setCursor(Qt.CrossCursor)
else:
self.editor.imageViews[self.editor._lastImageViewFocus]._isRubberBandZoom = False
self.editor.imageViews[self.editor._lastImageViewFocus].setCursor(self.editor.imageViews[self.editor._lastImageViewFocus]._cursorBackup)
'''
def hideHud():
hide = not self.editor.imageViews[0]._hud.isVisible()
for i, v in enumerate(self.editor.imageViews):
v.setHudVisible(hide)
def toggleSelectedHud():
if hasattr(self.editor, '_lastImageViewFocus'):
self.editor.imageViews[self.editor._lastImageViewFocus].toggleHud()
def centerAllImages():
for i, v in enumerate(self.editor.imageViews):
v.centerImage()
def centerImage():
if hasattr(self.editor, '_lastImageViewFocus'):
self.editor.imageViews[self.editor._lastImageViewFocus].centerImage()
self.menuGui.actionOnly_for_current_view.setEnabled(True)
def resetAxes():
if hasattr(self.editor, '_lastImageViewFocus'):
self.editor.imageScenes[self.editor._lastImageViewFocus].resetAxes()
self.menuGui.actionOnly_for_current_view.setEnabled(True)
def resetAllAxes():
for i, s in enumerate(self.editor.imageScenes):
s.resetAxes()
self.menuGui.actionCenterAllImages.triggered.connect(centerAllImages)
self.menuGui.actionCenterImage.triggered.connect(centerImage)
self.menuGui.actionToggleAllHuds.triggered.connect(hideHud)
self.menuGui.actionResetAllAxes.triggered.connect(resetAllAxes)
self.menuGui.actionToggleSelectedHud.triggered.connect(toggleSelectedHud)
self.menuGui.actionResetAxes.triggered.connect(resetAxes)
self.menuGui.actionShowDebugPatches.toggled.connect(toggleDebugPatches)
self.menuGui.actionFitToScreen.triggered.connect(fitToScreen)
self.menuGui.actionFitImage.triggered.connect(fitImage)
self.menuGui.actionReset_zoom.triggered.connect(restoreImageToOriginalSize)
#FIXME: this needs bug fixing
#self.menuGui.actionRubberBandZoom.triggered.connect(rubberBandZoom)
self.menuGui.actionSetCacheSize.triggered.connect(setCacheSize)
self.menuGui.actionUsePrefetching.toggled.connect(enablePrefetching)
@traceLogged(traceLogger)
def _initEditor(self, crosshair):
"""
Initialize the Volume Editor GUI.
"""
self.editor = VolumeEditor(self.layerstack, crosshair=crosshair)
# Replace the editor's navigation interpreter with one that has extra functionality
self.clickReporter = ClickReportingInterpreter( self.editor.navInterpret, self.editor.posModel )
self.editor.setNavigationInterpreter( self.clickReporter )
self.clickReporter.rightClickReceived.connect( self._handleEditorRightClick )
self.clickReporter.leftClickReceived.connect( self._handleEditorLeftClick )
self.editor.newImageView2DFocus.connect(self._setIconToViewMenu)
self.editor.setInteractionMode( 'navigation' )
self.volumeEditorWidget.init(self.editor)
self.editor._lastImageViewFocus = 0
# Zoom at a 1-1 scale to avoid loading big datasets entirely...
for view in self.editor.imageViews:
view.doScaleTo(1)
@traceLogged(traceLogger)
def _setIconToViewMenu(self):
"""
In the "Only for Current View" menu item of the View menu,
show the user which axis is the current one by changing the menu item icon.
"""
self.menuGui.actionOnly_for_current_view.setIcon(QIcon(self.editor.imageViews[self.editor._lastImageViewFocus]._hud.axisLabel.pixmap()))
@traceLogged(traceLogger)
def _convertPositionToDataSpace(self, voluminaPosition):
taggedPosition = {k:p for k,p in zip('txyzc', voluminaPosition)}
# Find the first lazyflow layer in the stack
# We assume that all lazyflow layers have the same axistags
dataTags = None
for layer in self.layerstack:
for datasource in layer.datasources:
if isinstance( datasource, NormalizingSource ):
datasource = datasource._rawSource
if isinstance(datasource, LazyflowSource):
dataTags = datasource.dataSlot.meta.axistags
if dataTags is not None:
break
assert dataTags is not None, "Can't convert mouse click coordinates from volumina-5d: Could not find a lazyflow data source in any layer."
position = ()
for tag in dataTags:
position += (taggedPosition[tag.key],)
return position
def _handleEditorRightClick(self, position5d, globalWindowCoordinate):
dataPosition = self._convertPositionToDataSpace(position5d)
self.handleEditorRightClick(dataPosition, globalWindowCoordinate)
def _handleEditorLeftClick(self, position5d, globalWindowCoordinate):
dataPosition = self._convertPositionToDataSpace(position5d)
self.handleEditorLeftClick(dataPosition, globalWindowCoordinate)
def handleEditorRightClick(self, position5d, globalWindowCoordinate):
# Override me
pass
def handleEditorLeftClick(self, position5d, globalWindowCoordiante):
# Override me
pass
class LayerViewerGui(QWidget):
"""
Implements an applet GUI whose central widget is a VolumeEditor
and whose layer controls simply contains a layer list widget.
Intended to be used as a subclass for applet GUI objects.
Provides: Central widget (viewer), View Menu, and Layer controls
Provides an EMPTY applet drawer widget. Subclasses should replace it with their own applet drawer.
"""
__metaclass__ = LayerViewerGuiMetaclass
###########################################
### AppletGuiInterface Concrete Methods ###
###########################################
def centralWidget( self ):
return self
def appletDrawer(self):
return self._drawer
def menus( self ):
debug_mode = ilastik_config.getboolean("ilastik", "debug")
return [ self.volumeEditorWidget.getViewMenu(debug_mode) ]
def viewerControlWidget(self):
return self.__viewerControlWidget
def stopAndCleanUp(self):
self._stopped = True
# Remove all layers
self.layerstack.clear()
# Stop rendering
for scene in self.editor.imageScenes:
if scene._tileProvider:
scene._tileProvider.notifyThreadsToStop()
scene.joinRendering()
for op in self._orphanOperators:
op.cleanUp()
###########################################
###########################################
@traceLogged(traceLogger)
def __init__(self, topLevelOperatorView, additionalMonitoredSlots=[], centralWidgetOnly=False, crosshair=True):
"""
Constructor. **All** slots of the provided *topLevelOperatorView* will be monitored for changes.
Changes include slot resize events, and slot ready/unready status changes.
When a change is detected, the `setupLayers()` function is called, and the result is used to update the list of layers shown in the central widget.
:param topLevelOperatorView: The top-level operator for the applet this GUI belongs to.
:param additionalMonitoredSlots: Optional. Can be used to add additional slots to the set of viewable layers (all slots from the top-level operator are already monitored).
:param centralWidgetOnly: If True, provide only a central widget without drawer or viewer controls.
"""
super(LayerViewerGui, self).__init__()
self._stopped = False
self._initialized = False
self.threadRouter = ThreadRouter(self) # For using @threadRouted
self.topLevelOperatorView = topLevelOperatorView
observedSlots = []
for slot in topLevelOperatorView.inputs.values() + topLevelOperatorView.outputs.values():
if slot.level == 0 or slot.level == 1:
observedSlots.append(slot)
observedSlots += additionalMonitoredSlots
self._orphanOperators = [] # Operators that are owned by this GUI directly (not owned by the top-level operator)
self.observedSlots = []
for slot in observedSlots:
if slot.level == 0:
if not isinstance(slot.stype, ArrayLike):
# We don't support visualization of non-Array slots.
continue
# To be monitored and updated correctly by this GUI, slots must have level=1, but this slot is of level 0.
# Pass it through a trivial "up-leveling" operator so it will have level 1 for our purposes.
opPromoteInput = OpWrapSlot(parent=slot.getRealOperator().parent)
opPromoteInput.Input.connect(slot)
slot = opPromoteInput.Output
self._orphanOperators.append( opPromoteInput )
# Each slot should now be indexed as slot[layer_index]
assert slot.level == 1
self.observedSlots.append( slot )
slot.notifyInserted( bind(self._handleLayerInsertion) )
slot.notifyRemoved( bind(self._handleLayerRemoval) )
for i in range(len(slot)):
self._handleLayerInsertion(slot, i)
self.layerstack = LayerStackModel()
self._initCentralUic()
self._initEditor(crosshair=crosshair)
self.__viewerControlWidget = None
if not centralWidgetOnly:
self.initViewerControlUi() # Might be overridden in a subclass. Default implementation loads a standard layer widget.
#self._drawer = QWidget( self )
self.initAppletDrawerUi() # Default implementation loads a blank drawer from drawer.ui.
def _after_init(self):
self._initialized = True
self.updateAllLayers()
def setupLayers( self ):
"""
Create a list of layers to be displayed in the central widget.
Subclasses should override this method to create the list of layers that can be displayed.
For debug and development purposes, the base class implementation simply generates layers for all topLevelOperatorView slots.
"""
layers = []
for multiLayerSlot in self.observedSlots:
for j, slot in enumerate(multiLayerSlot):
if slot.ready() and slot.meta.axistags is not None:
layer = self.createStandardLayerFromSlot(slot)
# Name the layer after the slot name.
if isinstance( multiLayerSlot.getRealOperator(), OpWrapSlot ):
# We attached an 'upleveling' operator, so look upstream for the real slot.
layer.name = multiLayerSlot.getRealOperator().Input.partner.name
else:
layer.name = multiLayerSlot.name + " " + str(j)
layers.append(layer)
return layers
@traceLogged(traceLogger)
def _handleLayerInsertion(self, slot, slotIndex):
"""
The multislot providing our layers has a new item.
Make room for it in the layer GUI and subscribe to updates.
"""
# When the slot is ready, we'll replace the blank layer with real data
slot[slotIndex].notifyReady( bind(self.updateAllLayers) )
slot[slotIndex].notifyUnready( bind(self.updateAllLayers) )
@traceLogged(traceLogger)
def _handleLayerRemoval(self, slot, slotIndex):
"""
An item is about to be removed from the multislot that is providing our layers.
Remove the layer from the GUI.
"""
self.updateAllLayers(slot)
def generateAlphaModulatedLayersFromChannels(self, slot):
# TODO
assert False
@classmethod
def createStandardLayerFromSlot(cls, slot, lastChannelIsAlpha=False):
"""
Convenience function.
Generates a volumina layer using the given slot.
Chooses between grayscale or RGB depending on the number of channels in the slot.
* If *slot* has 1 channel or more than 4 channels, a GrayscaleLayer is created.
* If *slot* has 2 non-alpha channels, an RGBALayer is created with R and G channels.
* If *slot* has 3 non-alpha channels, an RGBALayer is created with R,G, and B channels.
* If *slot* has 4 channels, an RGBA layer is created
:param slot: The slot to generate a layer from
:param lastChannelIsAlpha: If True, the last channel in the slot is assumed to be an alpha channel.
If slot has 4 channels, this parameter has no effect.
"""
def getRange(meta):
if meta.drange is not None and meta.normalizeDisplay is False:
# do not normalize if the user provided a range and set normalization to False
return meta.drange
else:
# If we don't know the range of the data and normalization is allowed
# by the user, create a layer that is auto-normalized.
# See volumina.pixelpipeline.datasources for details.
#
# Even in the case of integer data, which has more than 255 possible values,
# (like uint16), it seems reasonable to use this setting as default
return None # means autoNormalize
shape = slot.meta.shape
try:
channelAxisIndex = slot.meta.axistags.index('c')
#assert channelAxisIndex < len(slot.meta.axistags), \
# "slot %s has shape = %r, axistags = %r, but no channel dimension" \
# % (slot.name, slot.meta.shape, slot.meta.axistags)
numChannels = shape[channelAxisIndex]
axisinfo = slot.meta.axistags["c"].description
except:
numChannels = 1
axisinfo = "" # == no info on channels given
rindex = None
bindex = None
gindex = None
aindex = None
if axisinfo == "" or axisinfo == "default":
# Examine channel dimension to determine Grayscale vs. RGB
if numChannels == 4:
lastChannelIsAlpha = True
if lastChannelIsAlpha:
assert numChannels <= 4, "Can't display a standard layer with more than four channels (with alpha). Your image has {} channels.".format(numChannels)
if numChannels == 1 or (numChannels > 4):
assert not lastChannelIsAlpha, "Can't have an alpha channel if there is no color channel"
source = LazyflowSource(slot)
layer = GrayscaleLayer(source)
layer.numberOfChannels = numChannels
normalize = getRange(slot.meta)
layer.set_normalize(0,normalize)
return layer
assert numChannels > 2 or (numChannels == 2 and not lastChannelIsAlpha), \
"Unhandled combination of channels. numChannels={}, lastChannelIsAlpha={}, axistags={}".format( numChannels, lastChannelIsAlpha, slot.meta.axistags )
rindex = 0
gindex = 1
if numChannels > 3 or (numChannels == 3 and not lastChannelIsAlpha):
bindex = 2
if lastChannelIsAlpha:
aindex = numChannels-1
elif axisinfo == "grayscale":
source = LazyflowSource(slot)
layer = GrayscaleLayer(source)
layer.numberOfChannels = numChannels
normalize = getRange(slot.meta)
layer.set_normalize(0,normalize)
return layer
elif axisinfo == "rgba":
rindex = 0
if numChannels>=2:
gindex = 1
if numChannels>=3:
bindex = 2
if numChannels>=4:
aindex = numChannels-1
else:
raise RuntimeError("unknown channel display mode")
redSource = None
if rindex is not None:
redProvider = OpSingleChannelSelector(parent=slot.getRealOperator().parent)
redProvider.Input.connect(slot)
redProvider.Index.setValue( rindex )
redSource = LazyflowSource( redProvider.Output )
greenSource = None
if gindex is not None:
greenProvider = OpSingleChannelSelector(parent=slot.getRealOperator().parent)
greenProvider.Input.connect(slot)
greenProvider.Index.setValue( gindex )
greenSource = LazyflowSource( greenProvider.Output )
blueSource = None
if bindex is not None:
blueProvider = OpSingleChannelSelector(parent=slot.getRealOperator().parent)
blueProvider.Input.connect(slot)
blueProvider.Index.setValue( bindex )
blueSource = LazyflowSource( blueProvider.Output )
alphaSource = None
if aindex is not None:
alphaProvider = OpSingleChannelSelector(parent=slot.getRealOperator().parent)
alphaProvider.Input.connect(slot)
alphaProvider.Index.setValue( aindex )
alphaSource = LazyflowSource( alphaProvider.Output )
layer = RGBALayer( red=redSource, green=greenSource, blue=blueSource, alpha=alphaSource)
normalize = getRange(slot.meta)
print "createLayer normalize", normalize
for i in xrange(4):
if [redSource,greenSource,blueSource,alphaSource][i]:
layer.set_normalize(i,normalize)
return layer
@traceLogged(traceLogger)
@threadRouted
def updateAllLayers(self, slot=None):
if self._stopped or not self._initialized:
return
if slot is not None and slot.ready() and slot.meta.axistags is None:
# Don't update in response to value slots.
return
# Ask for the updated layer list (usually provided by the subclass)
newGuiLayers = self.setupLayers()
newNames = set(l.name for l in newGuiLayers)
if len(newNames) != len(newGuiLayers):
msg = "All layers must have unique names.\n"
msg += "You're attempting to use these layer names:\n"
msg += str( [l.name for l in newGuiLayers] )
raise RuntimeError(msg)
# If the datashape changed, tell the editor
# FIXME: This may not be necessary now that this gui doesn't handle the multi-image case...
newDataShape = self.determineDatashape()
if newDataShape is not None and self.editor.dataShape != newDataShape:
self.editor.dataShape = newDataShape
# Find the xyz midpoint
midpos5d = [x/2 for x in newDataShape]
midpos3d = midpos5d[1:4]
# Start in the center of the volume
self.editor.posModel.slicingPos = midpos3d
self.editor.navCtrl.panSlicingViews( midpos3d, [0,1,2] )
# Old layers are deleted if
# (1) They are not in the new set or
# (2) Their data has changed
for index, oldLayer in reversed(list(enumerate(self.layerstack))):
if oldLayer.name not in newNames:
needDelete = True
else:
newLayer = filter(lambda l: l.name == oldLayer.name, newGuiLayers)[0]
needDelete = (newLayer.datasources != oldLayer.datasources)
if needDelete:
layer = self.layerstack[index]
if hasattr(layer, 'shortcutRegistration'):
obsoleteShortcut = layer.shortcutRegistration[2]
obsoleteShortcut.setEnabled(False)
ShortcutManager().unregister( obsoleteShortcut )
self.layerstack.selectRow(index)
self.layerstack.deleteSelected()
# Insert all layers that aren't already in the layerstack
# (Identified by the name attribute)
existingNames = set(l.name for l in self.layerstack)
for index, layer in enumerate(newGuiLayers):
if layer.name not in existingNames:
# Insert new
self.layerstack.insert( index, layer )
# If this layer has an associated shortcut, register it with the shortcut manager
if hasattr(layer, 'shortcutRegistration'):
ShortcutManager().register( *layer.shortcutRegistration )
else:
# Clean up the layer instance that the client just gave us.
# We don't want to use it.
if hasattr(layer, 'shortcutRegistration'):
shortcut = layer.shortcutRegistration[2]
shortcut.setEnabled(False)
# Move existing layer to the correct position
stackIndex = self.layerstack.findMatchingIndex(lambda l: l.name == layer.name)
self.layerstack.selectRow(stackIndex)
while stackIndex > index:
self.layerstack.moveSelectedUp()
stackIndex -= 1
while stackIndex < index:
self.layerstack.moveSelectedDown()
stackIndex += 1
@traceLogged(traceLogger)
def determineDatashape(self):
newDataShape = None
for provider in self.observedSlots:
for i, slot in enumerate(provider):
if newDataShape is None and slot.ready() and slot.meta.axistags is not None:
# Use an OpReorderAxes adapter to transpose the shape for us.
op5 = OpReorderAxes( parent=slot.getRealOperator().parent )
op5.Input.connect( slot )
newDataShape = op5.Output.meta.shape
# We just needed the operator to determine the transposed shape.
# Disconnect it so it can be garbage collected.
op5.Input.disconnect()
return newDataShape
@traceLogged(traceLogger)
def initViewerControlUi(self):
"""
Load the viewer controls GUI, which appears below the applet bar.
In our case, the viewer control GUI consists mainly of a layer list.
Subclasses should override this if they provide their own viewer control widget.
"""
localDir = os.path.split(__file__)[0]
self.__viewerControlWidget = ViewerControls()
# The editor's layerstack is in charge of which layer movement buttons are enabled
model = self.editor.layerStack
if self.__viewerControlWidget is not None:
self.__viewerControlWidget.setupConnections(model)
@traceLogged(traceLogger)
def initAppletDrawerUi(self):
"""
By default, this base class provides a blank applet drawer.
Override this in a subclass to get a real applet drawer.
"""
# Load the ui file (find it in our own directory)
localDir = os.path.split(__file__)[0]
self._drawer = uic.loadUi(localDir+"/drawer.ui")
def getAppletDrawerUi(self):
return self._drawer
@traceLogged(traceLogger)
def _initCentralUic(self):
"""
Load the GUI from the ui file into this class and connect it with event handlers.
"""
# Load the ui file into this class (find it in our own directory)
localDir = os.path.split(__file__)[0]
uic.loadUi(localDir+"/centralWidget.ui", self)
@traceLogged(traceLogger)
def _initEditor(self, crosshair):
"""
Initialize the Volume Editor GUI.
"""
self.editor = VolumeEditor(self.layerstack, crosshair=crosshair)
# Replace the editor's navigation interpreter with one that has extra functionality
self.clickReporter = ClickReportingInterpreter( self.editor.navInterpret, self.editor.posModel )
self.editor.setNavigationInterpreter( self.clickReporter )
self.clickReporter.rightClickReceived.connect( self._handleEditorRightClick )
self.clickReporter.leftClickReceived.connect( self._handleEditorLeftClick )
clickReporter2 = ClickReportingInterpreter( self.editor.brushingInterpreter, self.editor.posModel )
clickReporter2.rightClickReceived.connect( self._handleEditorRightClick )
self.editor.brushingInterpreter = clickReporter2
self.editor.setInteractionMode( 'navigation' )
self.volumeEditorWidget.init(self.editor)
self.editor._lastImageViewFocus = 0
# Zoom at a 1-1 scale to avoid loading big datasets entirely...
for view in self.editor.imageViews:
view.doScaleTo(1)
@traceLogged(traceLogger)
def _convertPositionToDataSpace(self, voluminaPosition):
taggedPosition = {k:p for k,p in zip('txyzc', voluminaPosition)}
# Find the first lazyflow layer in the stack
# We assume that all lazyflow layers have the same axistags
dataTags = None
for layer in self.layerstack:
for datasource in layer.datasources:
try: # not all datasources have the dataSlot property, find out by trying
dataTags = datasource.dataSlot.meta.axistags
if dataTags is not None:
break
except AttributeError:
pass
if(dataTags is None):
raise RuntimeError("Can't convert mouse click coordinates from volumina-5d: Could not find a lazyflow data source in any layer.")
position = ()
for tag in dataTags:
position += (taggedPosition[tag.key],)
return position
def _handleEditorRightClick(self, position5d, globalWindowCoordinate):
dataPosition = self._convertPositionToDataSpace(position5d)
self.handleEditorRightClick(dataPosition, globalWindowCoordinate)
def _handleEditorLeftClick(self, position5d, globalWindowCoordinate):
dataPosition = self._convertPositionToDataSpace(position5d)
self.handleEditorLeftClick(dataPosition, globalWindowCoordinate)
def handleEditorRightClick(self, position5d, globalWindowCoordinate):
# Override me
pass
def handleEditorLeftClick(self, position5d, globalWindowCoordiante):
# Override me
pass
class LayerViewerGui(with_metaclass(LayerViewerGuiMetaclass, QWidget)):
"""
Implements an applet GUI whose central widget is a VolumeEditor
and whose layer controls simply contains a layer list widget.
Intended to be used as a superclass for applet GUI objects.
Provides: Central widget (viewer), View Menu, and Layer controls
Provides an EMPTY applet drawer widget. Subclasses should replace it with their own applet drawer.
"""
###########################################
### AppletGuiInterface Concrete Methods ###
###########################################
def centralWidget(self):
return self
def appletDrawer(self):
return self._drawer
def menus(self):
debug_mode = ilastik_config.getboolean("ilastik", "debug")
return [self.volumeEditorWidget.getViewMenu(debug_mode)]
def viewerControlWidget(self):
return self.__viewerControlWidget
def stopAndCleanUp(self):
self._stopped = True
# Remove all layers
self.layerstack.clear()
# Unsubscribe to all signals
for fn in self.__cleanup_fns:
fn()
for op in self._orphanOperators:
op.cleanUp()
###########################################
###########################################
def __init__(self,
parentApplet,
topLevelOperatorView,
additionalMonitoredSlots=[],
centralWidgetOnly=False,
crosshair=True,
is_3d_widget_visible=False):
"""
Constructor. **All** slots of the provided *topLevelOperatorView* will be monitored for changes.
Changes include slot resize events, and slot ready/unready status changes.
When a change is detected, the `setupLayers()` function is called, and the result is used to update the list of layers shown in the central widget.
:param topLevelOperatorView: The top-level operator for the applet this GUI belongs to.
:param additionalMonitoredSlots: Optional. Can be used to add additional slots to the set of viewable layers (all slots from the top-level operator are already monitored).
:param centralWidgetOnly: If True, provide only a central widget without drawer or viewer controls.
"""
super(LayerViewerGui, self).__init__()
self._stopped = False
self._initialized = False
self.__cleanup_fns = []
self.threadRouter = ThreadRouter(self) # For using @threadRouted
self.topLevelOperatorView = topLevelOperatorView
observedSlots = []
for slot in list(topLevelOperatorView.inputs.values()) + list(
topLevelOperatorView.outputs.values()):
if slot.level == 0 or slot.level == 1:
observedSlots.append(slot)
observedSlots += additionalMonitoredSlots
self._orphanOperators = [
] # Operators that are owned by this GUI directly (not owned by the top-level operator)
self.observedSlots = []
for slot in observedSlots:
if slot.level == 0:
if not isinstance(slot.stype, ArrayLike):
# We don't support visualization of non-Array slots.
continue
# To be monitored and updated correctly by this GUI, slots must have level=1, but this slot is of level 0.
# Pass it through a trivial "up-leveling" operator so it will have level 1 for our purposes.
opPromoteInput = OpWrapSlot(
parent=slot.getRealOperator().parent)
opPromoteInput.Input.connect(slot)
slot = opPromoteInput.Output
self._orphanOperators.append(opPromoteInput)
# Each slot should now be indexed as slot[layer_index]
assert slot.level == 1
self.observedSlots.append(slot)
slot.notifyInserted(bind(self._handleLayerInsertion))
self.__cleanup_fns.append(
partial(slot.unregisterInserted,
bind(self._handleLayerInsertion)))
slot.notifyRemoved(bind(self._handleLayerRemoval))
self.__cleanup_fns.append(
partial(slot.unregisterRemoved,
bind(self._handleLayerRemoval)))
for i in range(len(slot)):
self._handleLayerInsertion(slot, i)
self.layerstack = LayerStackModel()
self.saved_layer_visibilities = None
self._initCentralUic()
self._initEditor(crosshair=crosshair,
is_3d_widget_visible=is_3d_widget_visible)
self.__viewerControlWidget = None
if not centralWidgetOnly:
self.initViewerControlUi(
) # Might be overridden in a subclass. Default implementation loads a standard layer widget.
#self._drawer = QWidget( self )
self.initAppletDrawerUi(
) # Default implementation loads a blank drawer from drawer.ui.
self._up_to_date = False
# By default, we start out disabled until we have at least one layer.
self.centralWidget().setEnabled(False)
def _after_init(self):
self._initialized = True
self.updateAllLayers()
def setNeedUpdate(self, slot=None):
self._need_update = True
if self.isVisible():
if slot.graph:
slot.graph.call_when_setup_finished(self.updateAllLayers)
else:
self.updateAllLayers()
def showEvent(self, event):
if self._need_update:
self.updateAllLayers()
super(LayerViewerGui, self).showEvent(event)
def setupLayers(self):
"""
Create a list of layers to be displayed in the central widget.
Subclasses should override this method to create the list of layers that can be displayed.
For debug and development purposes, the base class implementation simply generates layers for all topLevelOperatorView slots.
"""
layers = []
for multiLayerSlot in self.observedSlots:
for j, slot in enumerate(multiLayerSlot):
has_space = slot.meta.axistags and slot.meta.axistags.axisTypeCount(
vigra.AxisType.Space) > 2
if slot.ready() and has_space:
layer = self.createStandardLayerFromSlot(slot)
# Name the layer after the slot name.
if isinstance(multiLayerSlot.getRealOperator(),
OpWrapSlot):
# We attached an 'upleveling' operator, so look upstream for the real slot.
layer.name = multiLayerSlot.getRealOperator(
).Input.upstream_slot.name
else:
layer.name = multiLayerSlot.name + " " + str(j)
layers.append(layer)
return layers
def _handleLayerInsertion(self, slot, slotIndex):
"""
The multislot providing our layers has a new item.
Make room for it in the layer GUI and subscribe to updates.
"""
# When the slot is ready, we'll replace the blank layer with real data
slot[slotIndex].notifyReady(bind(self.setNeedUpdate))
slot[slotIndex].notifyUnready(bind(self.setNeedUpdate))
self.__cleanup_fns.append(
partial(slot[slotIndex].unregisterReady, bind(self.setNeedUpdate)))
self.__cleanup_fns.append(
partial(slot[slotIndex].unregisterUnready,
bind(self.setNeedUpdate)))
def _handleLayerRemoval(self, slot, slotIndex):
"""
An item is about to be removed from the multislot that is providing our layers.
Remove the layer from the GUI.
"""
self.setNeedUpdate(slot)
def generateAlphaModulatedLayersFromChannels(self, slot):
# TODO
assert False
@classmethod
def createStandardLayerFromSlot(cls, slot, lastChannelIsAlpha=False):
"""
Convenience function.
Generates a volumina layer using the given slot.
Will be either a GrayscaleLayer or RGBALayer, depending on the channel metadata.
:param slot: The slot to generate a layer from
:param lastChannelIsAlpha: If True, the last channel in the slot is assumed to be an alpha channel.
"""
numChannels = 1
display_mode = "default"
c_index = slot.meta.axistags.index('c')
if c_index < len(slot.meta.axistags):
numChannels = slot.meta.shape[c_index]
display_mode = slot.meta.display_mode
if display_mode == "" or display_mode == "default":
## Figure out whether the default should be rgba or grayscale
if lastChannelIsAlpha:
assert numChannels <= 4, \
"This function doesn't support alpha for slots with more than 4 channels. "\
"Your image has {} channels.".format(numChannels)
# Automatically select Grayscale or RGBA based on number of channels
if numChannels == 2 or numChannels == 3:
display_mode = "rgba"
elif slot.meta.dtype == numpy.uint64:
display_mode = "random-colortable"
else:
display_mode = "grayscale"
# Override RGBA --> Grayscale if there's only 1 channel.
if display_mode == "rgba" and numChannels == 1:
display_mode = "grayscale"
if display_mode == "grayscale":
assert not lastChannelIsAlpha, "Can't have an alpha channel if there is no color channel"
return cls._create_grayscale_layer_from_slot(slot, numChannels)
elif display_mode == "rgba":
assert numChannels > 2 or (numChannels == 2 and not lastChannelIsAlpha), \
"Unhandled combination of channels. numChannels={}, lastChannelIsAlpha={}, axistags={}"\
.format( numChannels, lastChannelIsAlpha, slot.meta.axistags )
return cls._create_rgba_layer_from_slot(slot, numChannels,
lastChannelIsAlpha)
elif display_mode == "random-colortable":
return cls._create_random_colortable_layer_from_slot(slot)
elif display_mode == "alpha-modulated":
return cls._create_alpha_modulated_layer_from_slot(slot)
elif display_mode == "binary-mask":
return cls._create_binary_mask_layer_from_slot(slot)
else:
raise RuntimeError("unknown channel display mode: " + display_mode)
@classmethod
def _create_grayscale_layer_from_slot(cls, slot, n_channels):
source = LazyflowSource(slot)
layer = GrayscaleLayer(source)
layer.numberOfChannels = n_channels
layer.set_range(0, slot.meta.drange)
normalize = cls._should_normalize_display(slot)
layer.set_normalize(0, normalize)
return layer
@classmethod
def _create_random_colortable_layer_from_slot(cls, slot, num_colors=256):
colortable = generateRandomColors(num_colors,
clamp={
'v': 1.0,
's': 0.5
},
zeroIsTransparent=True)
layer = ColortableLayer(LazyflowSource(slot), colortable)
layer.colortableIsRandom = True
return layer
@classmethod
def _create_alpha_modulated_layer_from_slot(cls, slot):
layer = AlphaModulatedLayer(LazyflowSource(slot),
tintColor=QColor(Qt.cyan),
range=(0.0, 1.0),
normalize=(0.0, 1.0))
return layer
@classmethod
def _create_binary_mask_layer_from_slot(cls, slot):
# 0: black, 1-255: transparent
# This works perfectly for uint8.
# For uint32, etc., values of 256,512, etc. will be appear 'off'.
# But why would you use uint32 for a binary mask anyway?
colortable = [QColor(0, 0, 0, 255).rgba()]
colortable += 255 * [QColor(0, 0, 0, 0).rgba()]
layer = ColortableLayer(LazyflowSource(slot), colortable)
return layer
@classmethod
def _create_rgba_layer_from_slot(cls, slot, numChannels,
lastChannelIsAlpha):
bindex = aindex = None
rindex, gindex = 0, 1
if numChannels > 3 or (numChannels == 3 and not lastChannelIsAlpha):
bindex = 2
if lastChannelIsAlpha:
aindex = numChannels - 1
if numChannels >= 2:
gindex = 1
if numChannels >= 3:
bindex = 2
if numChannels >= 4:
aindex = numChannels - 1
redSource = None
if rindex is not None:
redProvider = OpSingleChannelSelector(
parent=slot.getRealOperator().parent)
redProvider.Input.connect(slot)
redProvider.Index.setValue(rindex)
redSource = LazyflowSource(redProvider.Output)
redSource.additional_owned_ops.append(redProvider)
greenSource = None
if gindex is not None:
greenProvider = OpSingleChannelSelector(
parent=slot.getRealOperator().parent)
greenProvider.Input.connect(slot)
greenProvider.Index.setValue(gindex)
greenSource = LazyflowSource(greenProvider.Output)
greenSource.additional_owned_ops.append(greenProvider)
blueSource = None
if bindex is not None:
blueProvider = OpSingleChannelSelector(
parent=slot.getRealOperator().parent)
blueProvider.Input.connect(slot)
blueProvider.Index.setValue(bindex)
blueSource = LazyflowSource(blueProvider.Output)
blueSource.additional_owned_ops.append(blueProvider)
alphaSource = None
if aindex is not None:
alphaProvider = OpSingleChannelSelector(
parent=slot.getRealOperator().parent)
alphaProvider.Input.connect(slot)
alphaProvider.Index.setValue(aindex)
alphaSource = LazyflowSource(alphaProvider.Output)
alphaSource.additional_owned_ops.append(alphaProvider)
layer = RGBALayer(red=redSource,
green=greenSource,
blue=blueSource,
alpha=alphaSource)
normalize = cls._should_normalize_display(slot)
for i in range(4):
if [redSource, greenSource, blueSource, alphaSource][i]:
layer.set_range(i, slot.meta.drange)
layer.set_normalize(i, normalize)
return layer
def _get_numchannels(self, slot, n_channels):
pass
@classmethod
def _should_normalize_display(cls, slot):
if slot.meta.drange is not None and slot.meta.normalizeDisplay is False:
# do not normalize if the user provided a range and set normalization to False
return False
else:
# If we don't know the range of the data and normalization is allowed
# by the user, create a layer that is auto-normalized.
# See volumina.pixelpipeline.datasources for details.
#
# Even in the case of integer data, which has more than 255 possible values,
# (like uint16), it seems reasonable to use this setting as default
return None # means autoNormalize
@threadRouted
def updateAllLayers(self, slot=None):
if self._stopped or not self._initialized:
return
if slot is not None and slot.ready() and slot.meta.axistags is None:
# Don't update in response to value slots.
return
self._need_update = False
# Ask for the updated layer list (usually provided by the subclass)
newGuiLayers = self.setupLayers()
# The order of the initial layerstack has to be static, where the "Raw Input" layer is at the stacks last position
for i in range(len(newGuiLayers)):
if newGuiLayers[i].name == "Raw Input":
rlayer = newGuiLayers[i]
newGuiLayers.remove(rlayer)
newGuiLayers.append(rlayer)
break
for layer in newGuiLayers:
assert not [l for l in self.layerstack if l is layer], \
"You are attempting to re-use a layer ({}). " \
"Your setupOutputs() function may not re-use layer objects. " \
"The layerstack retains ownership of the layers you provide and " \
"may choose to clean and delete them without your knowledge.".format( layer.name )
newNames = set(l.name for l in newGuiLayers)
if len(newNames) != len(newGuiLayers):
msg = "All layers must have unique names.\n"
msg += "You're attempting to use these layer names:\n"
msg += str([l.name for l in newGuiLayers])
raise RuntimeError(msg)
# If the datashape changed, tell the editor
# FIXME: This may not be necessary now that this gui doesn't handle the multi-image case...
newDataShape = self.determineDatashape()
if newDataShape is not None and self.editor.dataShape != newDataShape:
self.editor.dataShape = newDataShape
# Find the xyz midpoint
midpos5d = [x // 2 for x in newDataShape]
# center viewer there
self.setViewerPos(midpos5d)
# Old layers are deleted if
# (1) They are not in the new set or
# (2) Their data has changed
for index, oldLayer in reversed(list(enumerate(self.layerstack))):
if oldLayer.name not in newNames:
needDelete = True
else:
newLayer = list(
filter(lambda l: l.name == oldLayer.name, newGuiLayers))[0]
needDelete = newLayer.isDifferentEnough(oldLayer)
if needDelete:
layer = self.layerstack[index]
if hasattr(layer, 'shortcutRegistration'):
action_info = layer.shortcutRegistration[1]
ShortcutManager().unregister(action_info)
self.layerstack.selectRow(index)
self.layerstack.deleteSelected()
# Insert all layers that aren't already in the layerstack
# (Identified by the name attribute)
existingNames = set(l.name for l in self.layerstack)
for index, layer in enumerate(newGuiLayers):
if layer.name not in existingNames:
# Insert new
self.layerstack.insert(index, layer)
# If this layer has an associated shortcut, register it with the shortcut manager
if hasattr(layer, 'shortcutRegistration'):
ShortcutManager().register(*layer.shortcutRegistration)
else:
# Clean up the layer instance that the client just gave us.
# We don't want to use it.
layer.clean_up()
# Move existing layer to the correct position
stackIndex = self.layerstack.findMatchingIndex(
lambda l: l.name == layer.name)
self.layerstack.selectRow(stackIndex)
while stackIndex > index:
self.layerstack.moveSelectedUp()
stackIndex -= 1
while stackIndex < index:
self.layerstack.moveSelectedDown()
stackIndex += 1
if len(self.layerstack) > 0:
self.centralWidget().setEnabled(True)
def determineDatashape(self):
newDataShape = None
for provider in self.observedSlots:
for i, slot in enumerate(provider):
if newDataShape is None:
newDataShape = self.getVoluminaShapeForSlot(slot)
return newDataShape
def getLayerByName(self, name):
matches = [l for l in list(self.layerstack) if l.name == name]
if not matches:
return None
if len(matches) == 1:
return matches[0]
assert False, "Found more than one matching layer with name {}".format(
name)
def toggle_show_raw(self, raw_layer_name="Raw Data"):
"""
Convenience function.
Hide all layers except for the raw data layer specified by the given layer name.
The next time this function is called, restore previous layer visibility states.
"""
if self.saved_layer_visibilities:
for layer in self.layerstack:
layer.visible = self.saved_layer_visibilities[layer.name]
self.saved_layer_visibilities = None
else:
self.saved_layer_visibilities = {
layer.name: layer.visible
for layer in self.layerstack
}
for layer in self.layerstack:
layer.visible = False
self.getLayerByName(raw_layer_name).visible = True
@threadRouted
def setViewerPos(self, pos, setTime=False, setChannel=False):
try:
pos5d = self.validatePos(pos, dims=5)
# set xyz position
pos3d = pos5d[1:4]
self.editor.posModel.slicingPos = pos3d
# set time and channel if requested
if setTime:
self.editor.posModel.time = pos5d[0]
if setChannel:
self.editor.posModel.channel = pos5d[4]
self.editor.navCtrl.panSlicingViews(pos3d, [0, 1, 2])
for i in range(3):
self.editor.navCtrl.changeSliceAbsolute(pos3d[i], i)
except Exception as e:
logger.warning("Failed to navigate to position (%s): %s" %
(pos, e))
return
def validatePos(self, pos, dims=5):
if not isinstance(pos, list):
raise Exception("Wrong data format")
if not len(pos) == dims:
raise Exception("Wrong data format")
ds = self.editor.dataShape
for i in range(dims):
try:
pos[i] = max(0, min(int(pos[i]), ds[i] - 1))
except:
pos[i] = 0
return pos
@classmethod
def getVoluminaShapeForSlot(self, slot):
shape = None
if slot.ready() and slot.meta.axistags is not None:
# Use an OpReorderAxes adapter to transpose the shape for us.
op5 = OpReorderAxes(parent=slot.getRealOperator().parent)
op5.Input.connect(slot)
op5.AxisOrder.setValue('txyzc')
shape = op5.Output.meta.shape
# We just needed the operator to determine the transposed shape.
# Disconnect it so it can be garbage collected.
op5.Input.disconnect()
op5.cleanUp()
return shape
def initViewerControlUi(self):
"""
Load the viewer controls GUI, which appears below the applet bar.
In our case, the viewer control GUI consists mainly of a layer list.
Subclasses should override this if they provide their own viewer control widget.
"""
localDir = os.path.split(__file__)[0]
self.__viewerControlWidget = ViewerControls()
# The editor's layerstack is in charge of which layer movement buttons are enabled
model = self.editor.layerStack
if self.__viewerControlWidget is not None:
self.__viewerControlWidget.setupConnections(model)
def initAppletDrawerUi(self):
"""
By default, this base class provides a blank applet drawer.
Override this in a subclass to get a real applet drawer.
"""
# Load the ui file (find it in our own directory)
localDir = os.path.split(__file__)[0]
self._drawer = uic.loadUi(localDir + "/drawer.ui")
def getAppletDrawerUi(self):
return self._drawer
def _initCentralUic(self):
"""
Load the GUI from the ui file into this class and connect it with event handlers.
"""
# Load the ui file into this class (find it in our own directory)
localDir = os.path.split(__file__)[0]
uic.loadUi(localDir + "/centralWidget.ui", self)
def _initEditor(self, crosshair, is_3d_widget_visible):
"""
Initialize the Volume Editor GUI.
"""
self.editor = VolumeEditor(self.layerstack,
parent=self,
crosshair=crosshair,
is_3d_widget_visible=is_3d_widget_visible)
# Replace the editor's navigation interpreter with one that has extra functionality
self.clickReporter = ClickReportingInterpreter(
self.editor.navInterpret, self.editor.posModel)
self.editor.setNavigationInterpreter(self.clickReporter)
self.clickReporter.rightClickReceived.connect(
self._handleEditorRightClick)
self.clickReporter.leftClickReceived.connect(
self._handleEditorLeftClick)
self.clickReporter.toolTipReceived.connect(self._handleEditorToolTip)
clickReporter2 = ClickReportingInterpreter(
self.editor.brushingInterpreter, self.editor.posModel)
clickReporter2.rightClickReceived.connect(self._handleEditorRightClick)
self.editor.brushingInterpreter = clickReporter2
self.editor.setInteractionMode('navigation')
self.volumeEditorWidget.init(self.editor)
self.editor._lastImageViewFocus = 0
# Zoom at a 1-1 scale to avoid loading big datasets entirely...
for view in self.editor.imageViews:
view.doScaleTo(1)
# Should we default to 2D?
prefer_2d = False
for multislot in self.observedSlots:
for slot in multislot:
if slot.ready() and slot.meta.prefer_2d:
prefer_2d = True
break
if prefer_2d:
# Default to Z (axis 2 in the editor)
self.volumeEditorWidget.quadview.ensureMaximized(2)
def _convertPositionToDataSpace(self, voluminaPosition):
taggedPosition = {k: p for k, p in zip('txyzc', voluminaPosition)}
# Find the first lazyflow layer in the stack
# We assume that all lazyflow layers have the same axistags
dataTags = None
for layer in self.layerstack:
for datasource in layer.datasources:
try: # not all datasources have the dataSlot property, find out by trying
dataTags = datasource.dataSlot.meta.axistags
if dataTags is not None:
break
except AttributeError:
pass
if (dataTags is None):
raise RuntimeError(
"Can't convert mouse click coordinates from volumina-5d: Could not find a lazyflow data source in any layer."
)
position = ()
for tag in dataTags:
position += (taggedPosition[tag.key], )
return position
def _handleEditorRightClick(self, position5d, globalWindowCoordinate):
if len(self.layerstack) > 0:
dataPosition = self._convertPositionToDataSpace(position5d)
self.handleEditorRightClick(dataPosition, globalWindowCoordinate)
def _handleEditorLeftClick(self, position5d, globalWindowCoordinate):
if len(self.layerstack) > 0:
dataPosition = self._convertPositionToDataSpace(position5d)
self.handleEditorLeftClick(dataPosition, globalWindowCoordinate)
def handleEditorRightClick(self, position5d, globalWindowCoordinate):
# Override me
pass
def handleEditorLeftClick(self, position5d, globalWindowCoordiante):
# Override me
pass
def _handleEditorToolTip(self, position5d, globalWindowCoordinate):
if len(self.layerstack) > 0:
dataPosition = self._convertPositionToDataSpace(position5d)
self.handleEditorToolTip(dataPosition, globalWindowCoordinate)
def handleEditorToolTip(self, position5d, globalWindowCoordinate):
# Override me
pass
def __init__(self,
parentApplet,
topLevelOperatorView,
additionalMonitoredSlots=[],
centralWidgetOnly=False,
crosshair=True,
is_3d_widget_visible=False):
"""
Constructor. **All** slots of the provided *topLevelOperatorView* will be monitored for changes.
Changes include slot resize events, and slot ready/unready status changes.
When a change is detected, the `setupLayers()` function is called, and the result is used to update the list of layers shown in the central widget.
:param topLevelOperatorView: The top-level operator for the applet this GUI belongs to.
:param additionalMonitoredSlots: Optional. Can be used to add additional slots to the set of viewable layers (all slots from the top-level operator are already monitored).
:param centralWidgetOnly: If True, provide only a central widget without drawer or viewer controls.
"""
super(LayerViewerGui, self).__init__()
self._stopped = False
self._initialized = False
self.__cleanup_fns = []
self.threadRouter = ThreadRouter(self) # For using @threadRouted
self.topLevelOperatorView = topLevelOperatorView
observedSlots = []
for slot in list(topLevelOperatorView.inputs.values()) + list(
topLevelOperatorView.outputs.values()):
if slot.level == 0 or slot.level == 1:
observedSlots.append(slot)
observedSlots += additionalMonitoredSlots
self._orphanOperators = [
] # Operators that are owned by this GUI directly (not owned by the top-level operator)
self.observedSlots = []
for slot in observedSlots:
if slot.level == 0:
if not isinstance(slot.stype, ArrayLike):
# We don't support visualization of non-Array slots.
continue
# To be monitored and updated correctly by this GUI, slots must have level=1, but this slot is of level 0.
# Pass it through a trivial "up-leveling" operator so it will have level 1 for our purposes.
opPromoteInput = OpWrapSlot(
parent=slot.getRealOperator().parent)
opPromoteInput.Input.connect(slot)
slot = opPromoteInput.Output
self._orphanOperators.append(opPromoteInput)
# Each slot should now be indexed as slot[layer_index]
assert slot.level == 1
self.observedSlots.append(slot)
slot.notifyInserted(bind(self._handleLayerInsertion))
self.__cleanup_fns.append(
partial(slot.unregisterInserted,
bind(self._handleLayerInsertion)))
slot.notifyRemoved(bind(self._handleLayerRemoval))
self.__cleanup_fns.append(
partial(slot.unregisterRemoved,
bind(self._handleLayerRemoval)))
for i in range(len(slot)):
self._handleLayerInsertion(slot, i)
self.layerstack = LayerStackModel()
self.saved_layer_visibilities = None
self._initCentralUic()
self._initEditor(crosshair=crosshair,
is_3d_widget_visible=is_3d_widget_visible)
self.__viewerControlWidget = None
if not centralWidgetOnly:
self.initViewerControlUi(
) # Might be overridden in a subclass. Default implementation loads a standard layer widget.
#self._drawer = QWidget( self )
self.initAppletDrawerUi(
) # Default implementation loads a blank drawer from drawer.ui.
self._up_to_date = False
# By default, we start out disabled until we have at least one layer.
self.centralWidget().setEnabled(False)
def __init__(self, topLevelOperator):
"""
Args:
observedSlots - A list of slots that we'll listen for changes on.
Each must be a multislot with level=1 or level=2.
The first index in the multislot is the image index.
"""
super(LayerViewerGui, self).__init__()
self.threadRouter = ThreadRouter(self) # For using @threadRouted
self.topLevelOperator = topLevelOperator
observedSlots = []
for slot in topLevelOperator.inputs.values(
) + topLevelOperator.outputs.values():
if slot.level == 1 or slot.level == 2:
observedSlots.append(slot)
self.observedSlots = []
for slot in observedSlots:
if slot.level == 1:
# The user gave us a slot that is indexed as slot[image]
# Wrap the operator so it has the right level. Indexed as: slot[image][0]
opPromoteInput = OperatorWrapper(Op1ToMulti,
graph=slot.operator.graph)
opPromoteInput.Input.connect(slot)
slot = opPromoteInput.Outputs
# Each slot should now be indexed as slot[image][sub_index]
assert slot.level == 2
self.observedSlots.append(slot)
self.layerstack = LayerStackModel()
self.initAppletDrawerUi(
) # Default implementation loads a blank drawer.
self.initCentralUic()
self.__viewerControlWidget = None
self.initViewerControlUi()
self.initEditor()
self.imageIndex = -1
self.lastUpdateImageIndex = -1
def handleDatasetInsertion(slot, imageIndex):
if self.imageIndex == -1 and self.areProvidersInSync():
self.setImageIndex(imageIndex)
for provider in self.observedSlots:
provider.notifyInserted(bind(handleDatasetInsertion))
def handleDatasetRemoval(slot, index, finalsize):
if finalsize == 0:
# Clear everything
self.setImageIndex(-1)
elif index == self.imageIndex:
# Our currently displayed image is being removed.
# Switch to the first image (unless that's the one being removed!)
newIndex = 0
if index == newIndex:
newIndex = 1
self.setImageIndex(newIndex)
for provider in self.observedSlots:
provider.notifyRemove(bind(handleDatasetRemoval))
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.'
def __init__(self, topLevelOperator):
"""
Args:
observedSlots - A list of slots that we'll listen for changes on.
Each must be a multislot with level=1 or level=2.
The first index in the multislot is the image index.
"""
super(LayerViewerGui, self).__init__()
self.threadRouter = ThreadRouter(self) # For using @threadRouted
self.topLevelOperator = topLevelOperator
observedSlots = []
for slot in topLevelOperator.inputs.values() + topLevelOperator.outputs.values():
if slot.level == 1 or slot.level == 2:
observedSlots.append(slot)
self.observedSlots = []
for slot in observedSlots:
if slot.level == 1:
# The user gave us a slot that is indexed as slot[image]
# Wrap the operator so it has the right level. Indexed as: slot[image][0]
opPromoteInput = OperatorWrapper( Op1ToMulti, graph=slot.operator.graph )
opPromoteInput.Input.connect(slot)
slot = opPromoteInput.Outputs
# Each slot should now be indexed as slot[image][sub_index]
assert slot.level == 2
self.observedSlots.append( slot )
self.layerstack = LayerStackModel()
self.initAppletDrawerUi() # Default implementation loads a blank drawer.
self.initCentralUic()
self.__viewerControlWidget = None
self.initViewerControlUi()
self.initEditor()
self.imageIndex = -1
self.lastUpdateImageIndex = -1
def handleDatasetInsertion(slot, imageIndex):
if self.imageIndex == -1 and self.areProvidersInSync():
self.setImageIndex( imageIndex )
for provider in self.observedSlots:
provider.notifyInserted( bind( handleDatasetInsertion ) )
def handleDatasetRemoval(slot, index, finalsize):
if finalsize == 0:
# Clear everything
self.setImageIndex(-1)
elif index == self.imageIndex:
# Our currently displayed image is being removed.
# Switch to the first image (unless that's the one being removed!)
newIndex = 0
if index == newIndex:
newIndex = 1
self.setImageIndex(newIndex)
for provider in self.observedSlots:
provider.notifyRemove( bind( handleDatasetRemoval ) )
class LayerViewerGui(QMainWindow):
"""
Implements an applet GUI whose central widget is a VolumeEditor
and whose layer controls simply contains a layer list widget.
Intended to be used as a subclass for applet GUI objects.
Provides: - Central widget (viewer)
- View Menu
- Layer controls
Does NOT provide an applet drawer widget.
"""
###########################################
### AppletGuiInterface Concrete Methods ###
###########################################
def centralWidget( self ):
return self
def appletDrawers(self):
return [('Viewer', QWidget())]
def menus( self ):
return [self.menuView] # From the .ui file
def viewerControlWidget(self):
return self.__viewerControlWidget
def setImageIndex(self, index):
self._setImageIndex(index)
def reset(self):
# Remove all layers
self.layerstack.clear()
###########################################
###########################################
def operatorForCurrentImage(self):
try:
return self.topLevelOperator[self.imageIndex]
except IndexError:
return None
@traceLogged(traceLogger)
def __init__(self, topLevelOperator):
"""
Args:
observedSlots - A list of slots that we'll listen for changes on.
Each must be a multislot with level=1 or level=2.
The first index in the multislot is the image index.
"""
super(LayerViewerGui, self).__init__()
self.threadRouter = ThreadRouter(self) # For using @threadRouted
self.topLevelOperator = topLevelOperator
observedSlots = []
for slot in topLevelOperator.inputs.values() + topLevelOperator.outputs.values():
if slot.level == 1 or slot.level == 2:
observedSlots.append(slot)
self.observedSlots = []
for slot in observedSlots:
if slot.level == 1:
# The user gave us a slot that is indexed as slot[image]
# Wrap the operator so it has the right level. Indexed as: slot[image][0]
opPromoteInput = OperatorWrapper( Op1ToMulti, graph=slot.operator.graph )
opPromoteInput.Input.connect(slot)
slot = opPromoteInput.Outputs
# Each slot should now be indexed as slot[image][sub_index]
assert slot.level == 2
self.observedSlots.append( slot )
self.layerstack = LayerStackModel()
self.initAppletDrawerUi() # Default implementation loads a blank drawer.
self.initCentralUic()
self.__viewerControlWidget = None
self.initViewerControlUi()
self.initEditor()
self.imageIndex = -1
self.lastUpdateImageIndex = -1
def handleDatasetInsertion(slot, imageIndex):
if self.imageIndex == -1 and self.areProvidersInSync():
self.setImageIndex( imageIndex )
for provider in self.observedSlots:
provider.notifyInserted( bind( handleDatasetInsertion ) )
def handleDatasetRemoval(slot, index, finalsize):
if finalsize == 0:
# Clear everything
self.setImageIndex(-1)
elif index == self.imageIndex:
# Our currently displayed image is being removed.
# Switch to the first image (unless that's the one being removed!)
newIndex = 0
if index == newIndex:
newIndex = 1
self.setImageIndex(newIndex)
for provider in self.observedSlots:
provider.notifyRemove( bind( handleDatasetRemoval ) )
def setupLayers( self, currentImageIndex ):
layers = []
for multiImageSlot in self.observedSlots:
if 0 <= currentImageIndex < len(multiImageSlot):
multiLayerSlot = multiImageSlot[currentImageIndex]
for j, slot in enumerate(multiLayerSlot):
if slot.ready():
layer = self.createStandardLayerFromSlot(slot)
layer.name = multiImageSlot.name + " " + str(j)
layers.append(layer)
return layers
@traceLogged(traceLogger)
def _setImageIndex(self, imageIndex):
if self.imageIndex != -1:
for provider in self.observedSlots:
# We're switching datasets. Unsubscribe from the old one's notifications.
provider[self.imageIndex].unregisterInserted( bind(self.handleLayerInsertion) )
provider[self.imageIndex].unregisterRemove( bind(self.handleLayerRemoval) )
self.imageIndex = imageIndex
# Don't repopulate the GUI if there isn't a current dataset. Stop now.
if imageIndex is -1:
self.layerstack.clear()
return
# Update the GUI for all layers in the current dataset
self.updateAllLayers()
# For layers that already exist, subscribe to ready notifications
for provider in self.observedSlots:
for slotIndex, slot in enumerate(provider):
slot.notifyReady( bind(self.updateAllLayers) )
slot.notifyUnready( bind(self.updateAllLayers) )
# Make sure we're notified if a layer is inserted in the future so we can subscribe to its ready notifications
for provider in self.observedSlots:
if self.imageIndex < len(provider):
provider[self.imageIndex].notifyInserted( bind(self.handleLayerInsertion) )
provider[self.imageIndex].notifyRemoved( bind(self.handleLayerRemoval) )
def handleLayerInsertion(self, slot, slotIndex):
"""
The multislot providing our layers has a new item.
Make room for it in the layer GUI and subscribe to updates.
"""
with Tracer(traceLogger):
# When the slot is ready, we'll replace the blank layer with real data
slot[slotIndex].notifyReady( bind(self.updateAllLayers) )
slot[slotIndex].notifyUnready( bind(self.updateAllLayers) )
def handleLayerRemoval(self, slot, slotIndex):
"""
An item is about to be removed from the multislot that is providing our layers.
Remove the layer from the GUI.
"""
with Tracer(traceLogger):
self.updateAllLayers()
def generateAlphaModulatedLayersFromChannels(self, slot):
# TODO
assert False
@traceLogged(traceLogger)
def createStandardLayerFromSlot(self, slot, lastChannelIsAlpha=False):
"""
Generate a volumina layer using the given slot.
Choose between grayscale or RGB depending on the number of channels.
"""
def getRange(meta):
if 'drange' in meta:
return meta.drange
if numpy.issubdtype(meta.dtype, numpy.integer):
# We assume that ints range up to their max possible value,
return (0, numpy.iinfo( meta.dtype ).max)
else:
# If we don't know the range of the data, create a layer that is auto-normalized.
# See volumina.pixelpipeline.datasources for details.
return 'autoPercentiles'
# Examine channel dimension to determine Grayscale vs. RGB
shape = slot.meta.shape
normalize = getRange(slot.meta)
try:
channelAxisIndex = slot.meta.axistags.index('c')
#assert channelAxisIndex < len(slot.meta.axistags), \
# "slot %s has shape = %r, axistags = %r, but no channel dimension" \
# % (slot.name, slot.meta.shape, slot.meta.axistags)
numChannels = shape[channelAxisIndex]
except:
numChannels = 1
if lastChannelIsAlpha:
assert numChannels <= 4, "Can't display a standard layer with more than four channels (with alpha). Your image has {} channels.".format(numChannels)
else:
assert numChannels <= 3, "Can't display a standard layer with more than three channels (with no alpha). Your image has {} channels.".format(numChannels)
if numChannels == 1:
assert not lastChannelIsAlpha, "Can't have an alpha channel if there is no color channel"
source = LazyflowSource(slot)
normSource = NormalizingSource( source, bounds=normalize )
return GrayscaleLayer(normSource)
assert numChannels > 2 or (numChannels == 2 and not lastChannelIsAlpha)
redProvider = OpSingleChannelSelector(graph=slot.graph)
redProvider.Input.connect(slot)
redProvider.Index.setValue( 0 )
redSource = LazyflowSource( redProvider.Output )
redNormSource = NormalizingSource( redSource, bounds=normalize )
greenProvider = OpSingleChannelSelector(graph=slot.graph)
greenProvider.Input.connect(slot)
greenProvider.Index.setValue( 1 )
greenSource = LazyflowSource( greenProvider.Output )
greenNormSource = NormalizingSource( greenSource, bounds=normalize )
blueNormSource = None
if numChannels > 3 or (numChannels == 3 and not lastChannelIsAlpha):
blueProvider = OpSingleChannelSelector(graph=slot.graph)
blueProvider.Input.connect(slot)
blueProvider.Index.setValue( 2 )
blueSource = LazyflowSource( blueProvider.Output )
blueNormSource = NormalizingSource( blueSource, bounds=normalize )
alphaNormSource = None
if lastChannelIsAlpha:
alphaProvider = OpSingleChannelSelector(graph=slot.graph)
alphaProvider.Input.connect(slot)
alphaProvider.Index.setValue( numChannels-1 )
alphaSource = LazyflowSource( alphaProvider.Output )
alphaNormSource = NormalizingSource( alphaSource, bounds=normalize )
layer = RGBALayer( red=redNormSource, green=greenNormSource, blue=blueNormSource, alpha=alphaNormSource )
return layer
@traceLogged(traceLogger)
def areProvidersInSync(self):
"""
When an image is appended to the workflow, not all slots are resized simultaneously.
We should avoid calling setupLayers() until all the slots have been resized with the new image.
"""
try:
numImages = len(self.observedSlots[0])
except IndexError: # observedSlots is empty
pass
inSync = True
for slot in self.observedSlots:
# Check each slot for out-of-sync status except:
# - slots that are optional and unconnected
# - slots that are not images (e.g. a classifier or other object)
if not (slot._optional and slot.partner is None):
if len(slot) == 0:
inSync = False
break
elif len(slot[0]) > 0 and slot[0][0].meta.axistags is not None:
inSync &= (len(slot) == numImages)
return inSync
@traceLogged(traceLogger)
@threadRouted
def updateAllLayers(self):
# Check to make sure all layers are in sync
# (During image insertions, outputs are resized one at a time.)
if not self.areProvidersInSync():
return
if self.imageIndex >= 0:
# Ask the subclass for the updated layer list
newGuiLayers = self.setupLayers(self.imageIndex)
else:
newGuiLayers = []
newNames = set(l.name for l in newGuiLayers)
if len(newNames) != len(newGuiLayers):
msg = "All layers must have unique names.\n"
msg += "You're attempting to use these layer names:\n"
msg += [l.name for l in newGuiLayers]
raise RuntimeError()
# Copy the old visibilities and opacities
if self.imageIndex != self.lastUpdateImageIndex:
existing = {l.name : l for l in self.layerstack}
for layer in newGuiLayers:
if layer.name in existing.keys():
layer.visible = existing[layer.name].visible
layer.opacity = existing[layer.name].opacity
# Clear all existing layers.
self.layerstack.clear()
self.lastUpdateImageIndex = self.imageIndex
# Zoom at a 1-1 scale to avoid loading big datasets entirely...
for view in self.editor.imageViews:
view.doScaleTo(1)
# If the datashape changed, tell the editor
newDataShape = self.determineDatashape()
if newDataShape is not None and self.editor.dataShape != newDataShape:
self.editor.dataShape = newDataShape
# Find the xyz midpoint
midpos5d = [x/2 for x in newDataShape]
midpos3d = midpos5d[1:4]
# Start in the center of the volume
self.editor.posModel.slicingPos = midpos3d
self.editor.navCtrl.panSlicingViews( midpos3d, [0,1,2] )
# If one of the xyz dimensions is 1, the data is 2d.
singletonDims = filter( lambda (i,dim): dim == 1, enumerate(newDataShape[1:4]) )
if len(singletonDims) == 1:
# Maximize the slicing view for this axis
axis = singletonDims[0][0]
self.volumeEditorWidget.quadview.ensureMaximized(axis)
# Old layers are deleted if
# (1) They are not in the new set or
# (2) Their data has changed
for index, oldLayer in reversed(list(enumerate(self.layerstack))):
if oldLayer.name not in newNames:
needDelete = True
else:
newLayer = filter(lambda l: l.name == oldLayer.name, newGuiLayers)[0]
needDelete = (newLayer.datasources != oldLayer.datasources)
if needDelete:
layer = self.layerstack[index]
if hasattr(layer, 'shortcutRegistration'):
obsoleteShortcut = layer.shortcutRegistration[2]
obsoleteShortcut.setEnabled(False)
ShortcutManager().unregister( obsoleteShortcut )
self.layerstack.selectRow(index)
self.layerstack.deleteSelected()
# Insert all layers that aren't already in the layerstack
# (Identified by the name attribute)
existingNames = set(l.name for l in self.layerstack)
for index, layer in enumerate(newGuiLayers):
if layer.name not in existingNames:
# Insert new
self.layerstack.insert( index, layer )
# If this layer has an associated shortcut, register it with the shortcut manager
if hasattr(layer, 'shortcutRegistration'):
ShortcutManager().register( *layer.shortcutRegistration )
else:
# Clean up the layer instance that the client just gave us.
# We don't want to use it.
if hasattr(layer, 'shortcutRegistration'):
shortcut = layer.shortcutRegistration[2]
shortcut.setEnabled(False)
# Move existing layer to the correct positon
stackIndex = self.layerstack.findMatchingIndex(lambda l: l.name == layer.name)
self.layerstack.selectRow(stackIndex)
while stackIndex > index:
self.layerstack.moveSelectedUp()
stackIndex -= 1
while stackIndex < index:
self.layerstack.moveSelectedDown()
stackIndex += 1
@traceLogged(traceLogger)
def determineDatashape(self):
if self.imageIndex < 0:
return None
newDataShape = None
for provider in self.observedSlots:
if self.imageIndex < len(provider):
for i, slot in enumerate(provider[self.imageIndex]):
if newDataShape is None and slot.ready() and slot.meta.axistags is not None:
# Use an Op5ifyer adapter to transpose the shape for us.
op5 = Op5ifyer( graph=slot.graph )
op5.input.connect( slot )
newDataShape = op5.output.meta.shape
# We just needed the operator to determine the transposed shape.
# Disconnect it so it can be garbage collected.
op5.input.disconnect()
if newDataShape is not None:
# For now, this base class combines multi-channel images into a single layer,
# So, we want the volume editor to behave as though there is only one channel
newDataShape = newDataShape[:-1] + (1,)
return newDataShape
@traceLogged(traceLogger)
def initViewerControlUi(self):
"""
Load the viewer controls GUI, which appears below the applet bar.
In our case, the viewer control GUI consists mainly of a layer list.
"""
localDir = os.path.split(__file__)[0]
self.__viewerControlWidget = uic.loadUi(localDir + "/viewerControls.ui")
@traceLogged(traceLogger)
def initAppletDrawerUi(self):
"""
By default, this base class provides a blank applet drawer.
Override this in a subclass to get a real applet drawer.
"""
# Load the ui file (find it in our own directory)
localDir = os.path.split(__file__)[0]
self._drawer = uic.loadUi(localDir+"/drawer.ui")
def getAppletDrawerUi(self):
return self._drawer
@traceLogged(traceLogger)
def initCentralUic(self):
"""
Load the GUI from the ui file into this class and connect it with event handlers.
"""
# Load the ui file into this class (find it in our own directory)
localDir = os.path.split(__file__)[0]
uic.loadUi(localDir+"/centralWidget.ui", self)
# Menu is specified in a separate ui file with a dummy window
self.menuGui = uic.loadUi(localDir+"/menu.ui") # Save as member so it doesn't get picked up by GC
self.menuBar = self.menuGui.menuBar
self.menuView = self.menuGui.menuView
def toggleDebugPatches(show):
self.editor.showDebugPatches = show
def setCacheSize( cache_size ):
dlg = QDialog(self)
layout = QHBoxLayout()
layout.addWidget( QLabel("Cached Slices Per View:") )
cache_size = [self.editor.cacheSize]
def parseCacheSize( strSize ):
try:
cache_size[0] = int(strSize)
except:
pass
edit = QLineEdit( str(cache_size[0]), parent=dlg )
edit.textChanged.connect( parseCacheSize )
layout.addWidget( edit )
okButton = QPushButton( "OK", parent=dlg )
okButton.clicked.connect( dlg.accept )
layout.addWidget( okButton )
dlg.setLayout( layout )
dlg.setModal(True)
dlg.exec_()
self.editor.cacheSize = cache_size[0]
def fitToScreen():
shape = self.editor.posModel.shape
for i, v in enumerate(self.editor.imageViews):
s = list(shape)
del s[i]
v.changeViewPort(v.scene().data2scene.mapRect(QRectF(0,0,*s)))
def fitImage():
if hasattr(self.editor, '_lastImageViewFocus'):
self.editor.imageViews[self.editor._lastImageViewFocus].fitImage()
def restoreImageToOriginalSize():
if hasattr(self.editor, '_lastImageViewFocus'):
self.editor.imageViews[self.editor._lastImageViewFocus].doScaleTo()
def rubberBandZoom():
if hasattr(self.editor, '_lastImageViewFocus'):
if not self.editor.imageViews[self.editor._lastImageViewFocus]._isRubberBandZoom:
self.editor.imageViews[self.editor._lastImageViewFocus]._isRubberBandZoom = True
self.editor.imageViews[self.editor._lastImageViewFocus]._cursorBackup = self.editor.imageViews[self.editor._lastImageViewFocus].cursor()
self.editor.imageViews[self.editor._lastImageViewFocus].setCursor(Qt.CrossCursor)
else:
self.editor.imageViews[self.editor._lastImageViewFocus]._isRubberBandZoom = False
self.editor.imageViews[self.editor._lastImageViewFocus].setCursor(self.editor.imageViews[self.editor._lastImageViewFocus]._cursorBackup)
def hideHud():
hide = not self.editor.imageViews[0]._hud.isVisible()
for i, v in enumerate(self.editor.imageViews):
v.setHudVisible(hide)
def toggleSelectedHud():
if hasattr(self.editor, '_lastImageViewFocus'):
self.editor.imageViews[self.editor._lastImageViewFocus].toggleHud()
def centerAllImages():
for i, v in enumerate(self.editor.imageViews):
v.centerImage()
def centerImage():
if hasattr(self.editor, '_lastImageViewFocus'):
self.editor.imageViews[self.editor._lastImageViewFocus].centerImage()
self.actionOnly_for_current_view.setEnabled(True)
self.menuGui.actionCenterAllImages.triggered.connect(centerAllImages)
self.menuGui.actionCenterImage.triggered.connect(centerImage)
self.menuGui.actionToggleAllHuds.triggered.connect(hideHud)
self.menuGui.actionToggleSelectedHud.triggered.connect(toggleSelectedHud)
self.menuGui.actionShowDebugPatches.toggled.connect(toggleDebugPatches)
self.menuGui.actionFitToScreen.triggered.connect(fitToScreen)
self.menuGui.actionFitImage.triggered.connect(fitImage)
self.menuGui.actionReset_zoom.triggered.connect(restoreImageToOriginalSize)
self.menuGui.actionRubberBandZoom.triggered.connect(rubberBandZoom)
self.menuGui.actionSetCacheSize.triggered.connect(setCacheSize)
@traceLogged(traceLogger)
def initEditor(self):
"""
Initialize the Volume Editor GUI.
"""
self.editor = VolumeEditor(self.layerstack)
# Replace the editor's navigation interpreter with one that has extra functionality
self.clickReporter = ClickReportingInterpreter( self.editor.navInterpret, self.editor.posModel )
self.editor.setNavigationInterpreter( self.clickReporter )
self.clickReporter.rightClickReceived.connect( self._handleEditorRightClick )
self.clickReporter.leftClickReceived.connect( self._handleEditorLeftClick )
self.editor.newImageView2DFocus.connect(self.setIconToViewMenu)
self.editor.setInteractionMode( 'navigation' )
self.volumeEditorWidget.init(self.editor)
# The editor's layerstack is in charge of which layer movement buttons are enabled
model = self.editor.layerStack
if self.__viewerControlWidget is not None:
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
@traceLogged(traceLogger)
def setIconToViewMenu(self):
"""
In the "Only for Current View" menu item of the View menu,
show the user which axis is the current one by changing the menu item icon.
"""
self.actionOnly_for_current_view.setIcon(QIcon(self.editor.imageViews[self.editor._lastImageViewFocus]._hud.axisLabel.pixmap()))
@traceLogged(traceLogger)
def _convertPositionToDataSpace(self, voluminaPosition):
taggedPosition = {k:p for k,p in zip('txyzc', voluminaPosition)}
# Find the first lazyflow layer in the stack
# We assume that all lazyflow layers have the same axistags
dataTags = None
for layer in self.layerstack:
for datasource in layer.datasources:
if isinstance( datasource, NormalizingSource ):
datasource = datasource._rawSource
if isinstance(datasource, LazyflowSource):
dataTags = datasource.dataSlot.meta.axistags
if dataTags is not None:
break
assert dataTags is not None, "Can't convert mouse click coordinates from volumina-5d: Could not find a lazyflow data source in any layer."
position = ()
for tag in dataTags:
position += (taggedPosition[tag.key],)
return position
def _handleEditorRightClick(self, position5d, globalWindowCoordinate):
dataPosition = self._convertPositionToDataSpace(position5d)
self.handleEditorRightClick(self.imageIndex, dataPosition, globalWindowCoordinate)
def _handleEditorLeftClick(self, position5d, globalWindowCoordinate):
dataPosition = self._convertPositionToDataSpace(position5d)
self.handleEditorLeftClick(self.imageIndex, dataPosition, globalWindowCoordinate)
def handleEditorRightClick(self, currentImageIndex, position5d, globalWindowCoordinate):
# Override me
pass
def handleEditorLeftClick(self, currentImageIndex, position5d, globalWindowCoordiante):
# Override me
pass
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 LayerViewerGui(with_metaclass(LayerViewerGuiMetaclass, QWidget)):
"""
Implements an applet GUI whose central widget is a VolumeEditor
and whose layer controls simply contains a layer list widget.
Intended to be used as a superclass for applet GUI objects.
Provides: Central widget (viewer), View Menu, and Layer controls
Provides an EMPTY applet drawer widget. Subclasses should replace it with their own applet drawer.
"""
###########################################
### AppletGuiInterface Concrete Methods ###
###########################################
def centralWidget( self ):
return self
def appletDrawer(self):
return self._drawer
def menus( self ):
debug_mode = ilastik_config.getboolean("ilastik", "debug")
return [ self.volumeEditorWidget.getViewMenu(debug_mode) ]
def viewerControlWidget(self):
return self.__viewerControlWidget
def stopAndCleanUp(self):
self._stopped = True
# Remove all layers
self.layerstack.clear()
# Unsubscribe to all signals
for fn in self.__cleanup_fns:
fn()
for op in self._orphanOperators:
op.cleanUp()
###########################################
###########################################
def __init__(self, parentApplet, topLevelOperatorView, additionalMonitoredSlots=[], centralWidgetOnly=False,
crosshair=True, is_3d_widget_visible=False):
"""
Constructor. **All** slots of the provided *topLevelOperatorView* will be monitored for changes.
Changes include slot resize events, and slot ready/unready status changes.
When a change is detected, the `setupLayers()` function is called, and the result is used to update the list of layers shown in the central widget.
:param topLevelOperatorView: The top-level operator for the applet this GUI belongs to.
:param additionalMonitoredSlots: Optional. Can be used to add additional slots to the set of viewable layers (all slots from the top-level operator are already monitored).
:param centralWidgetOnly: If True, provide only a central widget without drawer or viewer controls.
"""
super(LayerViewerGui, self).__init__()
self._stopped = False
self._initialized = False
self.__cleanup_fns = []
self.threadRouter = ThreadRouter(self) # For using @threadRouted
self.topLevelOperatorView = topLevelOperatorView
observedSlots = []
for slot in list(topLevelOperatorView.inputs.values()) + list(topLevelOperatorView.outputs.values()):
if slot.level == 0 or slot.level == 1:
observedSlots.append(slot)
observedSlots += additionalMonitoredSlots
self._orphanOperators = [] # Operators that are owned by this GUI directly (not owned by the top-level operator)
self.observedSlots = []
for slot in observedSlots:
if slot.level == 0:
if not isinstance(slot.stype, ArrayLike):
# We don't support visualization of non-Array slots.
continue
# To be monitored and updated correctly by this GUI, slots must have level=1, but this slot is of level 0.
# Pass it through a trivial "up-leveling" operator so it will have level 1 for our purposes.
opPromoteInput = OpWrapSlot(parent=slot.getRealOperator().parent)
opPromoteInput.Input.connect(slot)
slot = opPromoteInput.Output
self._orphanOperators.append( opPromoteInput )
# Each slot should now be indexed as slot[layer_index]
assert slot.level == 1
self.observedSlots.append( slot )
slot.notifyInserted( bind(self._handleLayerInsertion) )
self.__cleanup_fns.append( partial( slot.unregisterInserted, bind(self._handleLayerInsertion) ) )
slot.notifyRemoved( bind(self._handleLayerRemoval) )
self.__cleanup_fns.append( partial( slot.unregisterRemoved, bind(self._handleLayerRemoval) ) )
for i in range(len(slot)):
self._handleLayerInsertion(slot, i)
self.layerstack = LayerStackModel()
self.saved_layer_visibilities = None
self._initCentralUic()
self._initEditor(crosshair=crosshair, is_3d_widget_visible=is_3d_widget_visible)
self.__viewerControlWidget = None
if not centralWidgetOnly:
self.initViewerControlUi() # Might be overridden in a subclass. Default implementation loads a standard layer widget.
#self._drawer = QWidget( self )
self.initAppletDrawerUi() # Default implementation loads a blank drawer from drawer.ui.
self._up_to_date = False
# By default, we start out disabled until we have at least one layer.
self.centralWidget().setEnabled(False)
def _after_init(self):
self._initialized = True
self.updateAllLayers()
def setNeedUpdate(self, slot=None):
self._need_update = True
if self.isVisible():
if slot.graph:
slot.graph.call_when_setup_finished( self.updateAllLayers )
else:
self.updateAllLayers()
def showEvent(self, event):
if self._need_update:
self.updateAllLayers()
super( LayerViewerGui, self ).showEvent(event)
def setupLayers( self ):
"""
Create a list of layers to be displayed in the central widget.
Subclasses should override this method to create the list of layers that can be displayed.
For debug and development purposes, the base class implementation simply generates layers for all topLevelOperatorView slots.
"""
layers = []
for multiLayerSlot in self.observedSlots:
for j, slot in enumerate(multiLayerSlot):
has_space = slot.meta.axistags and slot.meta.axistags.axisTypeCount(vigra.AxisType.Space) > 2
if slot.ready() and has_space:
layer = self.createStandardLayerFromSlot(slot)
# Name the layer after the slot name.
if isinstance( multiLayerSlot.getRealOperator(), OpWrapSlot ):
# We attached an 'upleveling' operator, so look upstream for the real slot.
layer.name = multiLayerSlot.getRealOperator().Input.upstream_slot.name
else:
layer.name = multiLayerSlot.name + " " + str(j)
layers.append(layer)
return layers
def _handleLayerInsertion(self, slot, slotIndex):
"""
The multislot providing our layers has a new item.
Make room for it in the layer GUI and subscribe to updates.
"""
# When the slot is ready, we'll replace the blank layer with real data
slot[slotIndex].notifyReady( bind(self.setNeedUpdate) )
slot[slotIndex].notifyUnready( bind(self.setNeedUpdate) )
self.__cleanup_fns.append( partial( slot[slotIndex].unregisterReady, bind(self.setNeedUpdate) ) )
self.__cleanup_fns.append( partial( slot[slotIndex].unregisterUnready, bind(self.setNeedUpdate) ) )
def _handleLayerRemoval(self, slot, slotIndex):
"""
An item is about to be removed from the multislot that is providing our layers.
Remove the layer from the GUI.
"""
self.setNeedUpdate(slot)
def generateAlphaModulatedLayersFromChannels(self, slot):
# TODO
assert False
@classmethod
def createStandardLayerFromSlot(cls, slot, lastChannelIsAlpha=False, name=None, opacity=1.0, visible=True):
"""
Convenience function.
Generates a volumina layer using the given slot.
Will be either a GrayscaleLayer or RGBALayer, depending on the channel metadata.
:param slot: The slot to generate a layer from
:param lastChannelIsAlpha: If True, the last channel in the slot is assumed to be an alpha channel.
"""
numChannels = 1
display_mode = "default"
c_index = slot.meta.axistags.index('c')
if c_index < len(slot.meta.axistags):
numChannels = slot.meta.shape[c_index]
display_mode = slot.meta.display_mode
if display_mode == "" or display_mode == "default":
## Figure out whether the default should be rgba or grayscale
if lastChannelIsAlpha:
assert numChannels <= 4, \
"This function doesn't support alpha for slots with more than 4 channels. "\
"Your image has {} channels.".format(numChannels)
# Automatically select Grayscale or RGBA based on number of channels
if numChannels == 2 or numChannels == 3:
display_mode = "rgba"
elif slot.meta.dtype == numpy.uint64:
display_mode = "random-colortable"
else:
display_mode = "grayscale"
# Override RGBA --> Grayscale if there's only 1 channel.
if display_mode == "rgba" and numChannels == 1:
display_mode = "grayscale"
if display_mode == "grayscale":
assert not lastChannelIsAlpha, "Can't have an alpha channel if there is no color channel"
layer = cls._create_grayscale_layer_from_slot( slot, numChannels )
elif display_mode == "rgba":
assert numChannels > 2 or (numChannels == 2 and not lastChannelIsAlpha), \
"Unhandled combination of channels. numChannels={}, lastChannelIsAlpha={}, axistags={}"\
.format( numChannels, lastChannelIsAlpha, slot.meta.axistags )
layer = cls._create_rgba_layer_from_slot(slot, numChannels, lastChannelIsAlpha)
elif display_mode == "random-colortable":
layer = cls._create_random_colortable_layer_from_slot(slot)
elif display_mode == "alpha-modulated":
layer = cls._create_alpha_modulated_layer_from_slot(slot)
elif display_mode == "binary-mask":
layer = cls._create_binary_mask_layer_from_slot(slot)
else:
raise RuntimeError("unknown channel display mode: " + display_mode )
layer.name = name or slot.name
layer.visible = visible
layer.opacity = opacity
return layer
@classmethod
def _create_grayscale_layer_from_slot(cls, slot, n_channels):
#FIXME: move all of this stuff into the class constructor. Same for all
# _create_*layer_from_slot methods.
source = LazyflowSource(slot)
layer = GrayscaleLayer(source, window_leveling=True)
layer.numberOfChannels = n_channels
layer.set_range(0, slot.meta.drange)
normalize = cls._should_normalize_display(slot)
layer.set_normalize( 0, normalize )
return layer
@classmethod
def _create_random_colortable_layer_from_slot(cls, slot, num_colors=256):
colortable = generateRandomColors(num_colors, clamp={'v': 1.0, 's' : 0.5}, zeroIsTransparent=True)
layer = ColortableLayer(LazyflowSource(slot), colortable)
layer.colortableIsRandom = True
return layer
@classmethod
def _create_alpha_modulated_layer_from_slot(cls, slot):
layer = AlphaModulatedLayer( LazyflowSource(slot),
tintColor=QColor( Qt.cyan ),
range=(0.0, 1.0),
normalize=(0.0, 1.0) )
return layer
@classmethod
def _create_binary_mask_layer_from_slot(cls, slot):
# 0: black, 1-255: transparent
# This works perfectly for uint8.
# For uint32, etc., values of 256,512, etc. will be appear 'off'.
# But why would you use uint32 for a binary mask anyway?
colortable = [QColor(0,0,0,255).rgba()]
colortable += 255*[QColor(0,0,0,0).rgba()]
layer = ColortableLayer(LazyflowSource(slot), colortable)
return layer
@classmethod
def _create_rgba_layer_from_slot(cls, slot, numChannels, lastChannelIsAlpha):
bindex = aindex = None
rindex, gindex = 0,1
if numChannels > 3 or (numChannels == 3 and not lastChannelIsAlpha):
bindex = 2
if lastChannelIsAlpha:
aindex = numChannels-1
if numChannels>=2:
gindex = 1
if numChannels>=3:
bindex = 2
if numChannels>=4:
aindex = numChannels-1
redSource = None
if rindex is not None:
redProvider = OpSingleChannelSelector(parent=slot.getRealOperator().parent)
redProvider.Input.connect(slot)
redProvider.Index.setValue( rindex )
redSource = LazyflowSource( redProvider.Output )
redSource.additional_owned_ops.append( redProvider )
greenSource = None
if gindex is not None:
greenProvider = OpSingleChannelSelector(parent=slot.getRealOperator().parent)
greenProvider.Input.connect(slot)
greenProvider.Index.setValue( gindex )
greenSource = LazyflowSource( greenProvider.Output )
greenSource.additional_owned_ops.append( greenProvider )
blueSource = None
if bindex is not None:
blueProvider = OpSingleChannelSelector(parent=slot.getRealOperator().parent)
blueProvider.Input.connect(slot)
blueProvider.Index.setValue( bindex )
blueSource = LazyflowSource( blueProvider.Output )
blueSource.additional_owned_ops.append( blueProvider )
alphaSource = None
if aindex is not None:
alphaProvider = OpSingleChannelSelector(parent=slot.getRealOperator().parent)
alphaProvider.Input.connect(slot)
alphaProvider.Index.setValue( aindex )
alphaSource = LazyflowSource( alphaProvider.Output )
alphaSource.additional_owned_ops.append( alphaProvider )
layer = RGBALayer( red=redSource, green=greenSource, blue=blueSource, alpha=alphaSource)
normalize = cls._should_normalize_display(slot)
for i in range(4):
if [redSource,greenSource,blueSource,alphaSource][i]:
layer.set_range(i, slot.meta.drange)
layer.set_normalize(i, normalize)
return layer
def _get_numchannels(self, slot, n_channels):
pass
@classmethod
def _should_normalize_display(cls, slot):
if slot.meta.drange is not None and slot.meta.normalizeDisplay is False:
# do not normalize if the user provided a range and set normalization to False
return False
else:
# If we don't know the range of the data and normalization is allowed
# by the user, create a layer that is auto-normalized.
# See volumina.pixelpipeline.datasources for details.
#
# Even in the case of integer data, which has more than 255 possible values,
# (like uint16), it seems reasonable to use this setting as default
return None # means autoNormalize
@threadRouted
def updateAllLayers(self, slot=None):
if self._stopped or not self._initialized:
return
if slot is not None and slot.ready() and slot.meta.axistags is None:
# Don't update in response to value slots.
return
self._need_update = False
# Ask for the updated layer list (usually provided by the subclass)
newGuiLayers = self.setupLayers()
# The order of the initial layerstack has to be static, where the "Raw Input" layer is at the stacks last position
for i in range(len(newGuiLayers)):
if newGuiLayers[i].name == "Raw Input":
rlayer = newGuiLayers[i]
newGuiLayers.remove(rlayer)
newGuiLayers.append(rlayer)
break
for layer in newGuiLayers:
assert not [l for l in self.layerstack if l is layer], \
"You are attempting to re-use a layer ({}). " \
"Your setupOutputs() function may not re-use layer objects. " \
"The layerstack retains ownership of the layers you provide and " \
"may choose to clean and delete them without your knowledge.".format( layer.name )
newNames = set(l.name for l in newGuiLayers)
if len(newNames) != len(newGuiLayers):
msg = "All layers must have unique names.\n"
msg += "You're attempting to use these layer names:\n"
msg += str( [l.name for l in newGuiLayers] )
raise RuntimeError(msg)
# If the datashape changed, tell the editor
# FIXME: This may not be necessary now that this gui doesn't handle the multi-image case...
newDataShape = self.determineDatashape()
if newDataShape is not None and self.editor.dataShape != newDataShape:
self.editor.dataShape = newDataShape
# Find the xyz midpoint
midpos5d = [x//2 for x in newDataShape]
# center viewer there
self.setViewerPos(midpos5d)
# Old layers are deleted if
# (1) They are not in the new set or
# (2) Their data has changed
for index, oldLayer in reversed(list(enumerate(self.layerstack))):
if oldLayer.name not in newNames:
needDelete = True
else:
newLayer = list(filter(lambda l: l.name == oldLayer.name, newGuiLayers))[0]
needDelete = newLayer.isDifferentEnough(oldLayer)
if needDelete:
layer = self.layerstack[index]
if hasattr(layer, 'shortcutRegistration'):
action_info = layer.shortcutRegistration[1]
ShortcutManager().unregister( action_info )
self.layerstack.selectRow(index)
self.layerstack.deleteSelected()
# Insert all layers that aren't already in the layerstack
# (Identified by the name attribute)
existingNames = set(l.name for l in self.layerstack)
for index, layer in enumerate(newGuiLayers):
if layer.name not in existingNames:
# Insert new
self.layerstack.insert( index, layer )
# If this layer has an associated shortcut, register it with the shortcut manager
if hasattr(layer, 'shortcutRegistration'):
ShortcutManager().register( *layer.shortcutRegistration )
else:
# Clean up the layer instance that the client just gave us.
# We don't want to use it.
layer.clean_up()
# Move existing layer to the correct position
stackIndex = self.layerstack.findMatchingIndex(lambda l: l.name == layer.name)
self.layerstack.selectRow(stackIndex)
while stackIndex > index:
self.layerstack.moveSelectedUp()
stackIndex -= 1
while stackIndex < index:
self.layerstack.moveSelectedDown()
stackIndex += 1
if len(self.layerstack) > 0:
self.centralWidget().setEnabled( True )
def determineDatashape(self):
newDataShape = None
for provider in self.observedSlots:
for i, slot in enumerate(provider):
if newDataShape is None:
newDataShape = self.getVoluminaShapeForSlot(slot)
return newDataShape
def getLayerByName(self, name):
matches = [l for l in list(self.layerstack) if l.name == name]
if not matches:
return None
if len(matches) == 1:
return matches[0]
assert False, "Found more than one matching layer with name {}".format( name )
def toggle_show_raw(self, raw_layer_name="Raw Data"):
"""
Convenience function.
Hide all layers except for the raw data layer specified by the given layer name.
The next time this function is called, restore previous layer visibility states.
"""
if self.saved_layer_visibilities:
for layer in self.layerstack:
layer.visible = self.saved_layer_visibilities[layer.name]
self.saved_layer_visibilities = None
else:
self.saved_layer_visibilities = {layer.name : layer.visible for layer in self.layerstack}
for layer in self.layerstack:
layer.visible = False
self.getLayerByName(raw_layer_name).visible = True
@threadRouted
def setViewerPos(self, pos, setTime=False, setChannel=False):
try:
pos5d = self.validatePos(pos, dims=5)
# set xyz position
pos3d = pos5d[1:4]
self.editor.posModel.slicingPos = pos3d
# set time and channel if requested
if setTime:
self.editor.posModel.time = pos5d[0]
if setChannel:
self.editor.posModel.channel = pos5d[4]
self.editor.navCtrl.panSlicingViews( pos3d, [0,1,2] )
for i in range(3):
self.editor.navCtrl.changeSliceAbsolute(pos3d[i],i)
except Exception as e:
logger.warning("Failed to navigate to position (%s): %s" % (pos, e))
return
def validatePos(self, pos, dims=5):
if not isinstance(pos, list):
raise Exception("Wrong data format")
if not len(pos) == dims:
raise Exception("Wrong data format")
ds = self.editor.dataShape
for i in range(dims):
try:
pos[i] = max(0, min(int(pos[i]), ds[i]-1))
except:
pos[i] = 0
return pos
@classmethod
def getVoluminaShapeForSlot(self, slot):
shape = None
if slot.ready() and slot.meta.axistags is not None:
# Use an OpReorderAxes adapter to transpose the shape for us.
op5 = OpReorderAxes( parent=slot.getRealOperator().parent )
op5.Input.connect( slot )
op5.AxisOrder.setValue('txyzc')
shape = op5.Output.meta.shape
# We just needed the operator to determine the transposed shape.
# Disconnect it so it can be garbage collected.
op5.Input.disconnect()
op5.cleanUp()
return shape
def initViewerControlUi(self):
"""
Load the viewer controls GUI, which appears below the applet bar.
In our case, the viewer control GUI consists mainly of a layer list.
Subclasses should override this if they provide their own viewer control widget.
"""
localDir = os.path.split(__file__)[0]
self.__viewerControlWidget = ViewerControls()
# The editor's layerstack is in charge of which layer movement buttons are enabled
model = self.editor.layerStack
if self.__viewerControlWidget is not None:
self.__viewerControlWidget.setupConnections(model)
def initAppletDrawerUi(self):
"""
By default, this base class provides a blank applet drawer.
Override this in a subclass to get a real applet drawer.
"""
# Load the ui file (find it in our own directory)
localDir = os.path.split(__file__)[0]
self._drawer = uic.loadUi(localDir+"/drawer.ui")
def getAppletDrawerUi(self):
return self._drawer
def _initCentralUic(self):
"""
Load the GUI from the ui file into this class and connect it with event handlers.
"""
# Load the ui file into this class (find it in our own directory)
localDir = os.path.split(__file__)[0]
uic.loadUi(localDir+"/centralWidget.ui", self)
def _initEditor(self, crosshair, is_3d_widget_visible):
"""
Initialize the Volume Editor GUI.
"""
self.editor = VolumeEditor(self.layerstack, parent=self, crosshair=crosshair, is_3d_widget_visible=is_3d_widget_visible)
# Replace the editor's navigation interpreter with one that has extra functionality
self.clickReporter = ClickReportingInterpreter( self.editor.navInterpret, self.editor.posModel )
self.editor.setNavigationInterpreter( self.clickReporter )
self.clickReporter.rightClickReceived.connect( self._handleEditorRightClick )
self.clickReporter.leftClickReceived.connect( self._handleEditorLeftClick )
self.clickReporter.toolTipReceived.connect( self._handleEditorToolTip )
clickReporter2 = ClickReportingInterpreter( self.editor.brushingInterpreter, self.editor.posModel )
clickReporter2.rightClickReceived.connect( self._handleEditorRightClick )
self.editor.brushingInterpreter = clickReporter2
self.editor.setInteractionMode( 'navigation' )
self.volumeEditorWidget.init(self.editor)
self.editor._lastImageViewFocus = 0
# Zoom at a 1-1 scale to avoid loading big datasets entirely...
for view in self.editor.imageViews:
view.doScaleTo(1)
# Should we default to 2D?
prefer_2d = False
for multislot in self.observedSlots:
for slot in multislot:
if slot.ready() and slot.meta.prefer_2d:
prefer_2d = True
break
if prefer_2d:
# Default to Z (axis 2 in the editor)
self.volumeEditorWidget.quadview.ensureMaximized(2)
def _convertPositionToDataSpace(self, voluminaPosition):
taggedPosition = {k:p for k,p in zip('txyzc', voluminaPosition)}
# Find the first lazyflow layer in the stack
# We assume that all lazyflow layers have the same axistags
dataTags = None
for layer in self.layerstack:
for datasource in layer.datasources:
try: # not all datasources have the dataSlot property, find out by trying
dataTags = datasource.dataSlot.meta.axistags
if dataTags is not None:
break
except AttributeError:
pass
if(dataTags is None):
raise RuntimeError("Can't convert mouse click coordinates from volumina-5d: Could not find a lazyflow data source in any layer.")
position = ()
for tag in dataTags:
position += (taggedPosition[tag.key],)
return position
def _handleEditorRightClick(self, position5d, globalWindowCoordinate):
if len(self.layerstack) > 0:
dataPosition = self._convertPositionToDataSpace(position5d)
self.handleEditorRightClick(dataPosition, globalWindowCoordinate)
def _handleEditorLeftClick(self, position5d, globalWindowCoordinate):
if len(self.layerstack) > 0:
dataPosition = self._convertPositionToDataSpace(position5d)
self.handleEditorLeftClick(dataPosition, globalWindowCoordinate)
def handleEditorRightClick(self, position5d, globalWindowCoordinate):
# Override me
pass
def handleEditorLeftClick(self, position5d, globalWindowCoordiante):
# Override me
pass
def _handleEditorToolTip(self, position5d, globalWindowCoordinate):
if len(self.layerstack) > 0:
dataPosition = self._convertPositionToDataSpace(position5d)
self.handleEditorToolTip(dataPosition, globalWindowCoordinate)
def handleEditorToolTip(self, position5d, globalWindowCoordinate):
# Override me
pass
class LayerViewerGui(QWidget):
"""
Implements an applet GUI whose central widget is a VolumeEditor
and whose layer controls simply contains a layer list widget.
Intended to be used as a subclass for applet GUI objects.
Provides: Central widget (viewer), View Menu, and Layer controls
Provides an EMPTY applet drawer widget. Subclasses should replace it with their own applet drawer.
"""
__metaclass__ = LayerViewerGuiMetaclass
###########################################
### AppletGuiInterface Concrete Methods ###
###########################################
def centralWidget(self):
return self
def appletDrawer(self):
return self._drawer
def menus(self):
debug_mode = ilastik_config.getboolean("ilastik", "debug")
return [self.volumeEditorWidget.getViewMenu(debug_mode)]
def viewerControlWidget(self):
return self.__viewerControlWidget
def stopAndCleanUp(self):
self._stopped = True
# Remove all layers
self.layerstack.clear()
# Unsubscribe to all signals
for fn in self.__cleanup_fns:
fn()
# Stop rendering
for scene in self.editor.imageScenes:
if scene._tileProvider:
scene._tileProvider.notifyThreadsToStop()
scene.joinRendering()
for op in self._orphanOperators:
op.cleanUp()
###########################################
###########################################
def __init__(self,
topLevelOperatorView,
additionalMonitoredSlots=[],
centralWidgetOnly=False,
crosshair=True):
"""
Constructor. **All** slots of the provided *topLevelOperatorView* will be monitored for changes.
Changes include slot resize events, and slot ready/unready status changes.
When a change is detected, the `setupLayers()` function is called, and the result is used to update the list of layers shown in the central widget.
:param topLevelOperatorView: The top-level operator for the applet this GUI belongs to.
:param additionalMonitoredSlots: Optional. Can be used to add additional slots to the set of viewable layers (all slots from the top-level operator are already monitored).
:param centralWidgetOnly: If True, provide only a central widget without drawer or viewer controls.
"""
super(LayerViewerGui, self).__init__()
self._stopped = False
self._initialized = False
self.__cleanup_fns = []
self.threadRouter = ThreadRouter(self) # For using @threadRouted
self.topLevelOperatorView = topLevelOperatorView
observedSlots = []
for slot in topLevelOperatorView.inputs.values(
) + topLevelOperatorView.outputs.values():
if slot.level == 0 or slot.level == 1:
observedSlots.append(slot)
observedSlots += additionalMonitoredSlots
self._orphanOperators = [
] # Operators that are owned by this GUI directly (not owned by the top-level operator)
self.observedSlots = []
for slot in observedSlots:
if slot.level == 0:
if not isinstance(slot.stype, ArrayLike):
# We don't support visualization of non-Array slots.
continue
# To be monitored and updated correctly by this GUI, slots must have level=1, but this slot is of level 0.
# Pass it through a trivial "up-leveling" operator so it will have level 1 for our purposes.
opPromoteInput = OpWrapSlot(
parent=slot.getRealOperator().parent)
opPromoteInput.Input.connect(slot)
slot = opPromoteInput.Output
self._orphanOperators.append(opPromoteInput)
# Each slot should now be indexed as slot[layer_index]
assert slot.level == 1
self.observedSlots.append(slot)
slot.notifyInserted(bind(self._handleLayerInsertion))
self.__cleanup_fns.append(
partial(slot.unregisterInserted,
bind(self._handleLayerInsertion)))
slot.notifyRemoved(bind(self._handleLayerRemoval))
self.__cleanup_fns.append(
partial(slot.unregisterRemoved,
bind(self._handleLayerRemoval)))
for i in range(len(slot)):
self._handleLayerInsertion(slot, i)
self.layerstack = LayerStackModel()
self._initCentralUic()
self._initEditor(crosshair=crosshair)
self.__viewerControlWidget = None
if not centralWidgetOnly:
self.initViewerControlUi(
) # Might be overridden in a subclass. Default implementation loads a standard layer widget.
#self._drawer = QWidget( self )
self.initAppletDrawerUi(
) # Default implementation loads a blank drawer from drawer.ui.
def _after_init(self):
self._initialized = True
self.updateAllLayers()
def setupLayers(self):
"""
Create a list of layers to be displayed in the central widget.
Subclasses should override this method to create the list of layers that can be displayed.
For debug and development purposes, the base class implementation simply generates layers for all topLevelOperatorView slots.
"""
layers = []
for multiLayerSlot in self.observedSlots:
for j, slot in enumerate(multiLayerSlot):
if slot.ready() and slot.meta.axistags is not None:
layer = self.createStandardLayerFromSlot(slot)
# Name the layer after the slot name.
if isinstance(multiLayerSlot.getRealOperator(),
OpWrapSlot):
# We attached an 'upleveling' operator, so look upstream for the real slot.
layer.name = multiLayerSlot.getRealOperator(
).Input.partner.name
else:
layer.name = multiLayerSlot.name + " " + str(j)
layers.append(layer)
return layers
def _handleLayerInsertion(self, slot, slotIndex):
"""
The multislot providing our layers has a new item.
Make room for it in the layer GUI and subscribe to updates.
"""
# When the slot is ready, we'll replace the blank layer with real data
slot[slotIndex].notifyReady(bind(self.updateAllLayers))
slot[slotIndex].notifyUnready(bind(self.updateAllLayers))
self.__cleanup_fns.append(
partial(slot[slotIndex].unregisterReady,
bind(self.updateAllLayers)))
self.__cleanup_fns.append(
partial(slot[slotIndex].unregisterUnready,
bind(self.updateAllLayers)))
def _handleLayerRemoval(self, slot, slotIndex):
"""
An item is about to be removed from the multislot that is providing our layers.
Remove the layer from the GUI.
"""
self.updateAllLayers(slot)
def generateAlphaModulatedLayersFromChannels(self, slot):
# TODO
assert False
@classmethod
def createStandardLayerFromSlot(cls, slot, lastChannelIsAlpha=False):
"""
Convenience function.
Generates a volumina layer using the given slot.
Chooses between grayscale or RGB depending on the number of channels in the slot.
* If *slot* has 1 channel or more than 4 channels, a GrayscaleLayer is created.
* If *slot* has 2 non-alpha channels, an RGBALayer is created with R and G channels.
* If *slot* has 3 non-alpha channels, an RGBALayer is created with R,G, and B channels.
* If *slot* has 4 channels, an RGBA layer is created
:param slot: The slot to generate a layer from
:param lastChannelIsAlpha: If True, the last channel in the slot is assumed to be an alpha channel.
If slot has 4 channels, this parameter has no effect.
"""
def getRange(meta):
return meta.drange
def getNormalize(meta):
if meta.drange is not None and meta.normalizeDisplay is False:
# do not normalize if the user provided a range and set normalization to False
return False
else:
# If we don't know the range of the data and normalization is allowed
# by the user, create a layer that is auto-normalized.
# See volumina.pixelpipeline.datasources for details.
#
# Even in the case of integer data, which has more than 255 possible values,
# (like uint16), it seems reasonable to use this setting as default
return None # means autoNormalize
shape = slot.meta.shape
try:
channelAxisIndex = slot.meta.axistags.index('c')
#assert channelAxisIndex < len(slot.meta.axistags), \
# "slot %s has shape = %r, axistags = %r, but no channel dimension" \
# % (slot.name, slot.meta.shape, slot.meta.axistags)
numChannels = shape[channelAxisIndex]
axisinfo = slot.meta.axistags["c"].description
except:
numChannels = 1
axisinfo = "" # == no info on channels given
rindex = None
bindex = None
gindex = None
aindex = None
if axisinfo == "" or axisinfo == "default":
# Examine channel dimension to determine Grayscale vs. RGB
if numChannels == 4:
lastChannelIsAlpha = True
if lastChannelIsAlpha:
assert numChannels <= 4, "Can't display a standard layer with more than four channels (with alpha). Your image has {} channels.".format(
numChannels)
if numChannels == 1 or (numChannels > 4):
assert not lastChannelIsAlpha, "Can't have an alpha channel if there is no color channel"
source = LazyflowSource(slot)
layer = GrayscaleLayer(source)
layer.numberOfChannels = numChannels
normalize = getNormalize(slot.meta)
range = getRange(slot.meta)
layer.set_range(0, range)
layer.set_normalize(0, normalize)
return layer
assert numChannels > 2 or (numChannels == 2 and not lastChannelIsAlpha), \
"Unhandled combination of channels. numChannels={}, lastChannelIsAlpha={}, axistags={}".format( numChannels, lastChannelIsAlpha, slot.meta.axistags )
rindex = 0
gindex = 1
if numChannels > 3 or (numChannels == 3
and not lastChannelIsAlpha):
bindex = 2
if lastChannelIsAlpha:
aindex = numChannels - 1
elif axisinfo == "grayscale":
source = LazyflowSource(slot)
layer = GrayscaleLayer(source)
layer.numberOfChannels = numChannels
normalize = getNormalize(slot.meta)
range = getRange(slot.meta)
layer.set_range(0, range)
layer.set_normalize(0, normalize)
return layer
elif axisinfo == "rgba":
rindex = 0
if numChannels >= 2:
gindex = 1
if numChannels >= 3:
bindex = 2
if numChannels >= 4:
aindex = numChannels - 1
else:
raise RuntimeError("unknown channel display mode")
redSource = None
if rindex is not None:
redProvider = OpSingleChannelSelector(
parent=slot.getRealOperator().parent)
redProvider.Input.connect(slot)
redProvider.Index.setValue(rindex)
redSource = LazyflowSource(redProvider.Output)
redSource.additional_owned_ops.append(redProvider)
greenSource = None
if gindex is not None:
greenProvider = OpSingleChannelSelector(
parent=slot.getRealOperator().parent)
greenProvider.Input.connect(slot)
greenProvider.Index.setValue(gindex)
greenSource = LazyflowSource(greenProvider.Output)
greenSource.additional_owned_ops.append(greenProvider)
blueSource = None
if bindex is not None:
blueProvider = OpSingleChannelSelector(
parent=slot.getRealOperator().parent)
blueProvider.Input.connect(slot)
blueProvider.Index.setValue(bindex)
blueSource = LazyflowSource(blueProvider.Output)
blueSource.additional_owned_ops.append(blueProvider)
alphaSource = None
if aindex is not None:
alphaProvider = OpSingleChannelSelector(
parent=slot.getRealOperator().parent)
alphaProvider.Input.connect(slot)
alphaProvider.Index.setValue(aindex)
alphaSource = LazyflowSource(alphaProvider.Output)
alphaSource.additional_owned_ops.append(alphaProvider)
layer = RGBALayer(red=redSource,
green=greenSource,
blue=blueSource,
alpha=alphaSource)
normalize = getNormalize(slot.meta)
range = getRange(slot.meta)
for i in xrange(4):
if [redSource, greenSource, blueSource, alphaSource][i]:
layer.set_range(i, range)
layer.set_normalize(i, normalize)
return layer
@threadRouted
def updateAllLayers(self, slot=None):
if self._stopped or not self._initialized:
return
if slot is not None and slot.ready() and slot.meta.axistags is None:
# Don't update in response to value slots.
return
# Ask for the updated layer list (usually provided by the subclass)
newGuiLayers = self.setupLayers()
for layer in newGuiLayers:
assert not filter( lambda l: l is layer, self.layerstack ), \
"You are attempting to re-use a layer ({}). " \
"Your setupOutputs() function may not re-use layer objects. " \
"The layerstack retains ownership of the layers you provide and " \
"may choose to clean and delete them without your knowledge.".format( layer.name )
newNames = set(l.name for l in newGuiLayers)
if len(newNames) != len(newGuiLayers):
msg = "All layers must have unique names.\n"
msg += "You're attempting to use these layer names:\n"
msg += str([l.name for l in newGuiLayers])
raise RuntimeError(msg)
# If the datashape changed, tell the editor
# FIXME: This may not be necessary now that this gui doesn't handle the multi-image case...
newDataShape = self.determineDatashape()
if newDataShape is not None and self.editor.dataShape != newDataShape:
self.editor.dataShape = newDataShape
# Find the xyz midpoint
midpos5d = [x / 2 for x in newDataShape]
midpos3d = midpos5d[1:4]
# Start in the center of the volume
self.editor.posModel.slicingPos = midpos3d
self.editor.navCtrl.panSlicingViews(midpos3d, [0, 1, 2])
# Old layers are deleted if
# (1) They are not in the new set or
# (2) Their data has changed
for index, oldLayer in reversed(list(enumerate(self.layerstack))):
if oldLayer.name not in newNames:
needDelete = True
else:
newLayer = filter(lambda l: l.name == oldLayer.name,
newGuiLayers)[0]
needDelete = newLayer.isDifferentEnough(oldLayer)
if needDelete:
layer = self.layerstack[index]
if hasattr(layer, 'shortcutRegistration'):
obsoleteShortcut = layer.shortcutRegistration[2]
obsoleteShortcut.setEnabled(False)
ShortcutManager().unregister(obsoleteShortcut)
self.layerstack.selectRow(index)
self.layerstack.deleteSelected()
# Insert all layers that aren't already in the layerstack
# (Identified by the name attribute)
existingNames = set(l.name for l in self.layerstack)
for index, layer in enumerate(newGuiLayers):
if layer.name not in existingNames:
# Insert new
self.layerstack.insert(index, layer)
# If this layer has an associated shortcut, register it with the shortcut manager
if hasattr(layer, 'shortcutRegistration'):
ShortcutManager().register(*layer.shortcutRegistration)
else:
# Clean up the layer instance that the client just gave us.
# We don't want to use it.
if hasattr(layer, 'shortcutRegistration'):
shortcut = layer.shortcutRegistration[2]
shortcut.setEnabled(False)
layer.clean_up()
# Move existing layer to the correct position
stackIndex = self.layerstack.findMatchingIndex(
lambda l: l.name == layer.name)
self.layerstack.selectRow(stackIndex)
while stackIndex > index:
self.layerstack.moveSelectedUp()
stackIndex -= 1
while stackIndex < index:
self.layerstack.moveSelectedDown()
stackIndex += 1
def determineDatashape(self):
newDataShape = None
for provider in self.observedSlots:
for i, slot in enumerate(provider):
if newDataShape is None:
newDataShape = self.getVoluminaShapeForSlot(slot)
return newDataShape
@classmethod
def getVoluminaShapeForSlot(self, slot):
shape = None
if slot.ready() and slot.meta.axistags is not None:
# Use an OpReorderAxes adapter to transpose the shape for us.
op5 = OpReorderAxes(parent=slot.getRealOperator().parent)
op5.Input.connect(slot)
shape = op5.Output.meta.shape
# We just needed the operator to determine the transposed shape.
# Disconnect it so it can be garbage collected.
op5.Input.disconnect()
op5.cleanUp()
return shape
def initViewerControlUi(self):
"""
Load the viewer controls GUI, which appears below the applet bar.
In our case, the viewer control GUI consists mainly of a layer list.
Subclasses should override this if they provide their own viewer control widget.
"""
localDir = os.path.split(__file__)[0]
self.__viewerControlWidget = ViewerControls()
# The editor's layerstack is in charge of which layer movement buttons are enabled
model = self.editor.layerStack
if self.__viewerControlWidget is not None:
self.__viewerControlWidget.setupConnections(model)
def initAppletDrawerUi(self):
"""
By default, this base class provides a blank applet drawer.
Override this in a subclass to get a real applet drawer.
"""
# Load the ui file (find it in our own directory)
localDir = os.path.split(__file__)[0]
self._drawer = uic.loadUi(localDir + "/drawer.ui")
def getAppletDrawerUi(self):
return self._drawer
def _initCentralUic(self):
"""
Load the GUI from the ui file into this class and connect it with event handlers.
"""
# Load the ui file into this class (find it in our own directory)
localDir = os.path.split(__file__)[0]
uic.loadUi(localDir + "/centralWidget.ui", self)
def _initEditor(self, crosshair):
"""
Initialize the Volume Editor GUI.
"""
self.editor = VolumeEditor(self.layerstack, crosshair=crosshair)
# Replace the editor's navigation interpreter with one that has extra functionality
self.clickReporter = ClickReportingInterpreter(
self.editor.navInterpret, self.editor.posModel)
self.editor.setNavigationInterpreter(self.clickReporter)
self.clickReporter.rightClickReceived.connect(
self._handleEditorRightClick)
self.clickReporter.leftClickReceived.connect(
self._handleEditorLeftClick)
clickReporter2 = ClickReportingInterpreter(
self.editor.brushingInterpreter, self.editor.posModel)
clickReporter2.rightClickReceived.connect(self._handleEditorRightClick)
self.editor.brushingInterpreter = clickReporter2
self.editor.setInteractionMode('navigation')
self.volumeEditorWidget.init(self.editor)
self.editor._lastImageViewFocus = 0
# Zoom at a 1-1 scale to avoid loading big datasets entirely...
for view in self.editor.imageViews:
view.doScaleTo(1)
def _convertPositionToDataSpace(self, voluminaPosition):
taggedPosition = {k: p for k, p in zip('txyzc', voluminaPosition)}
# Find the first lazyflow layer in the stack
# We assume that all lazyflow layers have the same axistags
dataTags = None
for layer in self.layerstack:
for datasource in layer.datasources:
try: # not all datasources have the dataSlot property, find out by trying
dataTags = datasource.dataSlot.meta.axistags
if dataTags is not None:
break
except AttributeError:
pass
if (dataTags is None):
raise RuntimeError(
"Can't convert mouse click coordinates from volumina-5d: Could not find a lazyflow data source in any layer."
)
position = ()
for tag in dataTags:
position += (taggedPosition[tag.key], )
return position
def _handleEditorRightClick(self, position5d, globalWindowCoordinate):
dataPosition = self._convertPositionToDataSpace(position5d)
self.handleEditorRightClick(dataPosition, globalWindowCoordinate)
def _handleEditorLeftClick(self, position5d, globalWindowCoordinate):
dataPosition = self._convertPositionToDataSpace(position5d)
self.handleEditorLeftClick(dataPosition, globalWindowCoordinate)
def handleEditorRightClick(self, position5d, globalWindowCoordinate):
# Override me
pass
def handleEditorLeftClick(self, position5d, globalWindowCoordiante):
# Override me
pass
class Main(QMainWindow):
haveData = pyqtSignal()
dataReadyToView = pyqtSignal()
def __init__(self, argv):
QMainWindow.__init__(self)
#Normalize the data if true
self._normalize_data=True
if 'notnormalize' in sys.argv:
print sys.argv
self._normalize_data=False
sys.argv.remove('notnormalize')
self.opPredict = None
self.opTrain = None
self.opThreshold = None
self._colorTable16 = self._createDefault16ColorColorTable()
#self.g = Graph(7, 2048*1024**2*5)
self.g = Graph()
self.fixableOperators = []
self.featureDlg=None
#The old ilastik provided the following scale names:
#['Tiny', 'Small', 'Medium', 'Large', 'Huge', 'Megahuge', 'Gigahuge']
#The corresponding scales are:
self.featScalesList=[0.3, 0.7, 1, 1.6, 3.5, 5.0, 10.0]
self.initUic()
#if the filename was specified on command line, load it
if len(sys.argv) >= 2:
def loadFile():
self._openFile(sys.argv[1:])
QTimer.singleShot(0, loadFile)
def setIconToViewMenu(self):
self.actionOnly_for_current_view.setIcon(QIcon(self.editor.imageViews[self.editor._lastImageViewFocus]._hud.axisLabel.pixmap()))
def initUic(self):
p = os.path.split(__file__)[0]+'/'
if p == "/": p = "."+p
uic.loadUi(p+"MainWindow_cc.ui", self)
#connect the window and graph creation to the opening of the file
self.actionOpen.triggered.connect(self.openFile)
self.actionQuit.triggered.connect(qApp.quit)
def toggleDebugPatches(show):
self.editor.showDebugPatches = show
def fitToScreen():
shape = self.editor.posModel.shape
for i, v in enumerate(self.editor.imageViews):
s = list(copy.copy(shape))
del s[i]
v.changeViewPort(v.scene().data2scene.mapRect(QRectF(0,0,*s)))
def fitImage():
if hasattr(self.editor, '_lastImageViewFocus'):
self.editor.imageViews[self.editor._lastImageViewFocus].fitImage()
def restoreImageToOriginalSize():
if hasattr(self.editor, '_lastImageViewFocus'):
self.editor.imageViews[self.editor._lastImageViewFocus].doScaleTo()
def rubberBandZoom():
if hasattr(self.editor, '_lastImageViewFocus'):
if not self.editor.imageViews[self.editor._lastImageViewFocus]._isRubberBandZoom:
self.editor.imageViews[self.editor._lastImageViewFocus]._isRubberBandZoom = True
self.editor.imageViews[self.editor._lastImageViewFocus]._cursorBackup = self.editor.imageViews[self.editor._lastImageViewFocus].cursor()
self.editor.imageViews[self.editor._lastImageViewFocus].setCursor(Qt.CrossCursor)
else:
self.editor.imageViews[self.editor._lastImageViewFocus]._isRubberBandZoom = False
self.editor.imageViews[self.editor._lastImageViewFocus].setCursor(self.editor.imageViews[self.editor._lastImageViewFocus]._cursorBackup)
def hideHud():
if self.editor.imageViews[0]._hud.isVisible():
hide = False
else:
hide = True
for i, v in enumerate(self.editor.imageViews):
v.hideHud(hide)
def toggleSelectedHud():
if hasattr(self.editor, '_lastImageViewFocus'):
self.editor.imageViews[self.editor._lastImageViewFocus].toggleHud()
def centerAllImages():
for i, v in enumerate(self.editor.imageViews):
v.centerImage()
def centerImage():
if hasattr(self.editor, '_lastImageViewFocus'):
self.editor.imageViews[self.editor._lastImageViewFocus].centerImage()
self.actionOnly_for_current_view.setEnabled(True)
self.actionCenterAllImages.triggered.connect(centerAllImages)
self.actionCenterImage.triggered.connect(centerImage)
self.actionToggleAllHuds.triggered.connect(hideHud)
self.actionToggleSelectedHud.triggered.connect(toggleSelectedHud)
self.actionShowDebugPatches.toggled.connect(toggleDebugPatches)
self.actionFitToScreen.triggered.connect(fitToScreen)
self.actionFitImage.triggered.connect(fitImage)
self.actionReset_zoom.triggered.connect(restoreImageToOriginalSize)
self.actionRubberBandZoom.triggered.connect(rubberBandZoom)
self.haveData.connect(self.initGraph)
self.dataReadyToView.connect(self.initEditor)
self.layerstack = LayerStackModel()
model = LabelListModel()
self.labelListView.setModel(model)
self.labelListModel=model
self.labelListModel.rowsAboutToBeRemoved.connect(self.onLabelAboutToBeRemoved)
self.labelListModel.labelSelected.connect(self.switchLabel)
def onDataChanged(topLeft, bottomRight):
firstRow = topLeft.row()
lastRow = bottomRight.row()
firstCol = topLeft.column()
lastCol = bottomRight.column()
if lastCol == firstCol == 0:
assert(firstRow == lastRow) #only one data item changes at a time
#in this case, the actual data (for example color) has changed
self.switchColor(firstRow+1, self.labelListModel[firstRow].color)
self.editor.scheduleSlicesRedraw()
else:
#this column is used for the 'delete' buttons, we don't care
#about data changed here
pass
self.labelListModel.dataChanged.connect(onDataChanged)
self.AddLabelButton.clicked.connect(self.addLabel)
self.SelectFeaturesButton.clicked.connect(self.onFeatureButtonClicked)
self.StartClassificationButton.clicked.connect(self.startClassification)
self.StartClassificationButton.setEnabled(False)
self.checkInteractive.setEnabled(False)
self.checkInteractive.toggled.connect(self.toggleInteractive)
self.interactionComboBox.currentIndexChanged.connect(self.changeInteractionMode)
self.interactionComboBox.setEnabled(False)
self.AddThresholdButton.clicked.connect(self.addThresholdOperator)
self.AddThresholdButton.setEnabled(False)
self.CCButton.clicked.connect(self.addCCOperator)
self.CCButton.setEnabled(False)
self._initFeatureDlg()
def toggleInteractive(self, checked):
print "toggling interactive mode to '%r'" % checked
#Check if the number of labels in the layer stack is equals to the number of Painted labels
if checked==True:
labels =numpy.unique(numpy.asarray(self.opLabels.outputs["nonzeroValues"][:].allocate().wait()[0]))
nPaintedLabels=labels.shape[0]
nLabelsLayers = self.labelListModel.rowCount()
selectedFeatures = numpy.asarray(self.featureDlg.featureTableWidget.createSelectedFeaturesBoolMatrix())
if nPaintedLabels!=nLabelsLayers:
self.checkInteractive.setCheckState(0)
mexBox=QMessageBox()
mexBox.setText("Did you forget to paint some labels?")
mexBox.setInformativeText("Painted Labels %d \nNumber Active Labels Layers %d"%(nPaintedLabels,self.labelListModel.rowCount()))
mexBox.exec_()
return
if (selectedFeatures==0).all():
self.checkInteractive.setCheckState(0)
mexBox=QMessageBox()
mexBox.setText("The are no features selected ")
mexBox.exec_()
return
else:
self.g.stopGraph()
self.g.resumeGraph()
self.AddLabelButton.setEnabled(not checked)
self.SelectFeaturesButton.setEnabled(not checked)
for o in self.fixableOperators:
o.inputs["fixAtCurrent"].setValue(not checked)
self.labelListModel.allowRemove(not checked)
self.editor.scheduleSlicesRedraw()
def changeInteractionMode( self, index ):
modes = {0: "navigation", 1: "brushing"}
self.editor.setInteractionMode( modes[index] )
self.interactionComboBox.setCurrentIndex(index)
print "interaction mode switched to", modes[index]
def switchLabel(self, row):
print "switching to label=%r" % (self.labelListModel[row])
#+1 because first is transparent
#FIXME: shouldn't be just row+1 here
self.editor.brushingModel.setDrawnNumber(row+1)
self.editor.brushingModel.setBrushColor(self.labelListModel[row].color)
def switchColor(self, row, color):
print "label=%d changes color to %r" % (row, color)
self.labellayer.colorTable[row]=color.rgba()
self.editor.brushingModel.setBrushColor(color)
self.editor.scheduleSlicesRedraw()
def addLabel(self):
color = QColor(numpy.random.randint(0,255), numpy.random.randint(0,255), numpy.random.randint(0,255))
numLabels = len(self.labelListModel)
if numLabels < len(self._colorTable16):
color = self._colorTable16[numLabels]
self.labellayer.colorTable.append(color.rgba())
self.labelListModel.insertRow(self.labelListModel.rowCount(), Label("Label %d" % (self.labelListModel.rowCount() + 1), color))
nlabels = self.labelListModel.rowCount()
if self.opPredict is not None:
print "Label added, changing predictions"
#re-train the forest now that we have more labels
self.opPredict.inputs['LabelsCount'].setValue(nlabels)
self.addPredictionLayer(nlabels-1, self.labelListModel._labels[nlabels-1])
#make the new label selected
index = self.labelListModel.index(nlabels-1, 1)
self.labelListModel._selectionModel.select(index, QItemSelectionModel.ClearAndSelect)
#FIXME: this should watch for model changes
#drawing will be enabled when the first label is added
self.changeInteractionMode( 1 )
self.interactionComboBox.setEnabled(True)
def onLabelAboutToBeRemoved(self, parent, start, end):
#the user deleted a label, reshape prediction and remove the layer
#the interface only allows to remove one label at a time?
nout = start-end+1
ncurrent = self.labelListModel.rowCount()
print "removing", nout, "out of ", ncurrent
if self.opPredict is not None:
self.opPredict.inputs['LabelsCount'].setValue(ncurrent-nout)
for il in range(start, end+1):
labelvalue = self.labelListModel._labels[il]
self.removePredictionLayer(labelvalue)
self.opLabels.inputs["deleteLabel"].setValue(il+1)
self.editor.scheduleSlicesRedraw()
def startClassification(self):
if self.opTrain is None:
#initialize all classification operators
print "initializing classification..."
opMultiL = Op5ToMulti(self.g)
opMultiL.inputs["Input0"].connect(self.opLabels.outputs["Output"])
opMultiLblocks = Op5ToMulti(self.g)
opMultiLblocks.inputs["Input0"].connect(self.opLabels.outputs["nonzeroBlocks"])
self.opTrain = OpTrainRandomForestBlocked(self.g)
self.opTrain.inputs['Labels'].connect(opMultiL.outputs["Outputs"])
self.opTrain.inputs['Images'].connect(self.opFeatureCache.outputs["Output"])
self.opTrain.inputs["nonzeroLabelBlocks"].connect(opMultiLblocks.outputs["Outputs"])
self.opTrain.inputs['fixClassifier'].setValue(False)
opClassifierCache = OpArrayCache(self.g)
opClassifierCache.inputs["Input"].connect(self.opTrain.outputs['Classifier'])
################## Prediction
self.opPredict=OpPredictRandomForest(self.g)
nclasses = self.labelListModel.rowCount()
self.opPredict.inputs['LabelsCount'].setValue(nclasses)
self.opPredict.inputs['Classifier'].connect(opClassifierCache.outputs['Output'])
self.opPredict.inputs['Image'].connect(self.opPF.outputs["Output"])
pCache = OpSlicedBlockedArrayCache(self.g)
pCache.inputs["fixAtCurrent"].setValue(False)
pCache.inputs["innerBlockShape"].setValue(((1,256,256,1,2),(1,256,1,256,2),(1,1,256,256,2)))
pCache.inputs["outerBlockShape"].setValue(((1,256,256,4,2),(1,256,4,256,2),(1,4,256,256,2)))
pCache.inputs["Input"].connect(self.opPredict.outputs["PMaps"])
self.pCache = pCache
#add prediction results for all classes as separate channels
for icl in range(nclasses):
self.addPredictionLayer(icl, self.labelListModel._labels[icl])
self.StartClassificationButton.setEnabled(False)
self.checkInteractive.setEnabled(True)
self.AddThresholdButton.setEnabled(True)
def addPredictionLayer(self, icl, ref_label):
selector=OpSingleChannelSelector(self.g)
selector.inputs["Input"].connect(self.pCache.outputs['Output'])
selector.inputs["Index"].setValue(icl)
if self.checkInteractive.isChecked():
self.pCache.inputs["fixAtCurrent"].setValue(False)
else:
self.pCache.inputs["fixAtCurrent"].setValue(True)
predictsrc = LazyflowSource(selector.outputs["Output"][0])
def srcName(newName):
predictsrc.setObjectName("Prediction for %s" % ref_label.name)
srcName("")
predictLayer = AlphaModulatedLayer(predictsrc, tintColor=ref_label.color)
predictLayer.nameChanged.connect(srcName)
def setLayerColor(c):
print "as the color of label '%s' has changed, setting layer's '%s' tint color to %r" % (ref_label.name, predictLayer.name, c)
predictLayer.tintColor = c
ref_label.colorChanged.connect(setLayerColor)
def setLayerName(n):
newName = "Prediction for %s" % ref_label.name
print "as the name of label '%s' has changed, setting layer's '%s' name to '%s'" % (ref_label.name, predictLayer.name, newName)
predictLayer.name = newName
setLayerName(ref_label.name)
ref_label.nameChanged.connect(setLayerName)
predictLayer.ref_object = ref_label
#make sure that labels (index = 0) stay on top!
self.layerstack.insert(1, predictLayer )
self.fixableOperators.append(self.pCache)
def removePredictionLayer(self, ref_label):
for il, layer in enumerate(self.layerstack):
if layer.ref_object==ref_label:
print "found the prediction", layer.ref_object, ref_label
self.layerstack.removeRows(il, 1)
break
def addThresholdOperator(self):
if self.opThreshold is None:
self.opThreshold = OpThreshold(self.g)
self.opThreshold.inputs["Input"].connect(self.pCache.outputs["Output"])
#channel, value = ThresholdDlg(self.labelListModel._labels)
channel = 0
value = 0.5
ref_label = self.labelListModel._labels[channel]
self.opThreshold.inputs["Channel"].setValue(channel)
self.opThreshold.inputs["Threshold"].setValue(value)
threshsrc = LazyflowSource(self.opThreshold.outputs["Output"][0])
threshsrc.setObjectName("Threshold for %s" % ref_label.name)
transparent = QColor(0,0,0,0)
white = QColor(255,255,255)
colorTable = [transparent.rgba(), white.rgba()]
threshLayer = ColortableLayer(threshsrc, colorTable = colorTable )
threshLayer.name = "Threshold for %s" % ref_label.name
self.layerstack.insert(1, threshLayer)
self.CCButton.setEnabled(True)
def addCCOperator(self):
self.opCC = OpConnectedComponents(self.g)
self.opCC.inputs["Input"].connect(self.opThreshold.outputs["Output"])
#we shouldn't have to define these. But just in case...
self.opCC.inputs["Neighborhood"].setValue(6)
self.opCC.inputs["Background"].setValue(0)
ccsrc = LazyflowSource(self.opCC.outputs["Output"][0])
ccsrc.setObjectName("Connected Components")
ctb = colortables.create_default_16bit()
ctb.insert(0, QColor(0, 0, 0, 0).rgba()) # make background transparent
ccLayer = ColortableLayer(ccsrc, ctb)
ccLayer.name = "Connected Components"
self.layerstack.insert(1, ccLayer)
def openFile(self):
fileNames = QFileDialog.getOpenFileNames(self, "Open Image", os.path.abspath(__file__), "Numpy and h5 files (*.npy *.h5)")
if fileNames.count() == 0:
return
self._openFile(fileNames)
def _openFile(self, fileNames):
self.inputProvider = None
fName, fExt = os.path.splitext(str(fileNames[0]))
print "Opening Files %r" % fileNames
if fExt=='.npy':
fileName = fileNames[0]
if len(fileNames)>1:
print "WARNING: only the first file will be read, multiple file prediction not supported yet"
fName, fExt = os.path.splitext(str(fileName))
self.raw = numpy.load(str(fileName))
self.min, self.max = numpy.min(self.raw), numpy.max(self.raw)
self.inputProvider = OpArrayPiper(self.g)
self.raw = self.raw.view(vigra.VigraArray)
self.raw.axistags = vigra.AxisTags(
vigra.AxisInfo('t',vigra.AxisType.Time),
vigra.AxisInfo('x',vigra.AxisType.Space),
vigra.AxisInfo('y',vigra.AxisType.Space),
vigra.AxisInfo('z',vigra.AxisType.Space),
vigra.AxisInfo('c',vigra.AxisType.Channels))
self.inputProvider.inputs["Input"].setValue(self.raw)
elif fExt=='.h5':
readerNew=OpH5ReaderBigDataset(self.g)
readerNew.inputs["Filenames"].setValue(fileNames)
readerNew.inputs["hdf5Path"].setValue("volume/data")
readerCache = OpSlicedBlockedArrayCache(self.g)
readerCache.inputs["fixAtCurrent"].setValue(False)
readerCache.inputs["innerBlockShape"].setValue(((1,256,256,1,2),(1,256,1,256,2),(1,1,256,256,2)))
readerCache.inputs["outerBlockShape"].setValue(((1,256,256,4,2),(1,256,4,256,2),(1,4,256,256,2)))
readerCache.inputs["Input"].connect(readerNew.outputs["Output"])
self.inputProvider = OpArrayPiper(self.g)
self.inputProvider.inputs["Input"].connect(readerCache.outputs["Output"])
else:
raise RuntimeError("opening filenames=%r not supported yet" % fileNames)
self.haveData.emit()
def initGraph(self):
shape = self.inputProvider.outputs["Output"].shape
srcs = []
minMax = []
normalize = []
print "* Data has shape=%r" % (shape,)
#create a layer for each channel of the input:
slicer=OpMultiArraySlicer2(self.g)
slicer.inputs["Input"].connect(self.inputProvider.outputs["Output"])
slicer.inputs["AxisFlag"].setValue('c')
nchannels = shape[-1]
for ich in xrange(nchannels):
data=slicer.outputs['Slices'][ich][:].allocate().wait()
#find the minimum and maximum value for normalization
mm = (numpy.min(data), numpy.max(data))
print " - channel %d: min=%r, max=%r" % (ich, mm[0], mm[1])
minMax.append(mm)
if self._normalize_data:
normalize.append(mm)
else:
normalize.append((0,255))
layersrc = LazyflowSource(slicer.outputs['Slices'][ich], priority = 100)
layersrc.setObjectName("raw data channel=%d" % ich)
srcs.append(layersrc)
#FIXME: we shouldn't merge channels automatically, but for now it's prettier
layer1 = None
if nchannels == 1:
layer1 = GrayscaleLayer(srcs[0], range=minMax[0], normalize=normalize[0])
print " - showing raw data as grayscale"
elif nchannels==2:
layer1 = RGBALayer(red = srcs[0], normalizeR=normalize[0],
green = srcs[1], normalizeG=normalize[1], range=minMax[0:2]+[(0,255), (0,255)])
print " - showing channel 1 as red, channel 2 as green"
elif nchannels==3:
layer1 = RGBALayer(red = srcs[0], normalizeR=normalize[0],
green = srcs[1], normalizeG=normalize[1],
blue = srcs[2], normalizeB=normalize[2],
range = minMax[0:3])
print " - showing channel 1 as red, channel 2 as green, channel 3 as blue"
else:
print "only 1,2 or 3 channels supported so far"
return
print
layer1.name = "Input data"
layer1.ref_object = None
self.layerstack.append(layer1)
opImageList = Op5ToMulti(self.g)
opImageList.inputs["Input0"].connect(self.inputProvider.outputs["Output"])
#init the features operator
opPF = OpPixelFeaturesPresmoothed(self.g)
opPF.inputs["Input"].connect(opImageList.outputs["Outputs"])
opPF.inputs["Scales"].setValue(self.featScalesList)
self.opPF=opPF
#Caches the features
opFeatureCache = OpBlockedArrayCache(self.g)
opFeatureCache.inputs["innerBlockShape"].setValue((1,32,32,32,16))
opFeatureCache.inputs["outerBlockShape"].setValue((1,128,128,128,64))
opFeatureCache.inputs["Input"].connect(opPF.outputs["Output"])
opFeatureCache.inputs["fixAtCurrent"].setValue(False)
self.opFeatureCache=opFeatureCache
self.initLabels()
self.dataReadyToView.emit()
def initLabels(self):
#Add the layer to draw the labels, but don't add any labels
shape=self.inputProvider.outputs["Output"].shape
self.opLabels = OpBlockedSparseLabelArray(self.g)
self.opLabels.inputs["shape"].setValue(shape[:-1] + (1,))
self.opLabels.inputs["blockShape"].setValue((1, 32, 32, 32, 1))
self.opLabels.inputs["eraser"].setValue(100)
self.labelsrc = LazyflowSinkSource(self.opLabels, self.opLabels.outputs["Output"], self.opLabels.inputs["Input"])
self.labelsrc.setObjectName("labels")
transparent = QColor(0,0,0,0)
self.labellayer = ColortableLayer(self.labelsrc, colorTable = [transparent.rgba()] )
self.labellayer.name = "Labels"
self.labellayer.ref_object = None
self.layerstack.append(self.labellayer)
def initEditor(self):
shape=self.inputProvider.outputs["Output"].shape
self.editor = VolumeEditor(self.layerstack, labelsink=self.labelsrc)
self.editor.dataShape = shape
self.editor.newImageView2DFocus.connect(self.setIconToViewMenu)
#drawing will be enabled when the first label is added
self.editor.setInteractionMode( 'navigation' )
self.volumeEditorWidget.init(self.editor)
model = self.editor.layerStack
self.layerWidget.init(model)
self.UpButton.clicked.connect(model.moveSelectedUp)
model.canMoveSelectedUp.connect(self.UpButton.setEnabled)
self.DownButton.clicked.connect(model.moveSelectedDown)
model.canMoveSelectedDown.connect(self.DownButton.setEnabled)
self.DeleteButton.clicked.connect(model.deleteSelected)
model.canDeleteSelected.connect(self.DeleteButton.setEnabled)
self.opLabels.inputs["eraser"].setValue(self.editor.brushingModel.erasingNumber)
def _createDefault16ColorColorTable(self):
c = []
c.append(QColor(0, 0, 255))
c.append(QColor(255, 255, 0))
c.append(QColor(255, 0, 0))
c.append(QColor(0, 255, 0))
c.append(QColor(0, 255, 255))
c.append(QColor(255, 0, 255))
c.append(QColor(255, 105, 180)) #hot pink
c.append(QColor(102, 205, 170)) #dark aquamarine
c.append(QColor(165, 42, 42)) #brown
c.append(QColor(0, 0, 128)) #navy
c.append(QColor(255, 165, 0)) #orange
c.append(QColor(173, 255, 47)) #green-yellow
c.append(QColor(128,0, 128)) #purple
c.append(QColor(192, 192, 192)) #silver
c.append(QColor(240, 230, 140)) #khaki
c.append(QColor(69, 69, 69)) # dark grey
return c
def onFeatureButtonClicked(self):
self.featureDlg.show()
def onDlgAccepted():
self.StartClassificationButton.setEnabled(True)
self.featureDlg.accepted.connect(onDlgAccepted)
def _onFeaturesChosen(self):
selectedFeatures = self.featureDlg.featureTableWidget.createSelectedFeaturesBoolMatrix()
print "new feature set:", selectedFeatures
self.opPF.inputs['Matrix'].setValue(numpy.asarray(selectedFeatures))
def _initFeatureDlg(self):
dlg = self.featureDlg = FeatureDlg()
dlg.setWindowTitle("Features")
dlg.createFeatureTable({"Features": [FeatureEntry("Gaussian smoothing"), \
FeatureEntry("Laplacian of Gaussian"), \
FeatureEntry("Structure Tensor Eigenvalues"), \
FeatureEntry("Hessian of Gaussian EV"), \
FeatureEntry("Gaussian Gradient Magnitude"), \
FeatureEntry("Difference Of Gaussian")]}, \
self.featScalesList)
dlg.setImageToPreView(None)
m = [[1,0,0,0,0,0,0],[1,0,0,0,0,0,0],[0,0,0,0,0,0,0],[1,0,0,0,0,0,0],[1,0,0,0,0,0,0],[1,0,0,0,0,0,0]]
dlg.featureTableWidget.setSelectedFeatureBoolMatrix(m)
dlg.accepted.connect(self._onFeaturesChosen)
class LayerViewerGui(QMainWindow):
"""
Implements an applet GUI whose central widget is a VolumeEditor
and whose layer controls simply contains a layer list widget.
Intended to be used as a subclass for applet GUI objects.
Provides: - Central widget (viewer)
- View Menu
- Layer controls
Does NOT provide an applet drawer widget.
"""
###########################################
### AppletGuiInterface Concrete Methods ###
###########################################
def centralWidget(self):
return self
def appletDrawers(self):
return [('Viewer', QWidget())]
def menus(self):
return [self.menuView] # From the .ui file
def viewerControlWidget(self):
return self.__viewerControlWidget
def setImageIndex(self, index):
self._setImageIndex(index)
def reset(self):
# Remove all layers
self.layerstack.clear()
###########################################
###########################################
def operatorForCurrentImage(self):
try:
return self.topLevelOperator[self.imageIndex]
except IndexError:
return None
@traceLogged(traceLogger)
def __init__(self, topLevelOperator):
"""
Args:
observedSlots - A list of slots that we'll listen for changes on.
Each must be a multislot with level=1 or level=2.
The first index in the multislot is the image index.
"""
super(LayerViewerGui, self).__init__()
self.threadRouter = ThreadRouter(self) # For using @threadRouted
self.topLevelOperator = topLevelOperator
observedSlots = []
for slot in topLevelOperator.inputs.values(
) + topLevelOperator.outputs.values():
if slot.level == 1 or slot.level == 2:
observedSlots.append(slot)
self.observedSlots = []
for slot in observedSlots:
if slot.level == 1:
# The user gave us a slot that is indexed as slot[image]
# Wrap the operator so it has the right level. Indexed as: slot[image][0]
opPromoteInput = OperatorWrapper(Op1ToMulti,
graph=slot.operator.graph)
opPromoteInput.Input.connect(slot)
slot = opPromoteInput.Outputs
# Each slot should now be indexed as slot[image][sub_index]
assert slot.level == 2
self.observedSlots.append(slot)
self.layerstack = LayerStackModel()
self.initAppletDrawerUi(
) # Default implementation loads a blank drawer.
self.initCentralUic()
self.__viewerControlWidget = None
self.initViewerControlUi()
self.initEditor()
self.imageIndex = -1
self.lastUpdateImageIndex = -1
def handleDatasetInsertion(slot, imageIndex):
if self.imageIndex == -1 and self.areProvidersInSync():
self.setImageIndex(imageIndex)
for provider in self.observedSlots:
provider.notifyInserted(bind(handleDatasetInsertion))
def handleDatasetRemoval(slot, index, finalsize):
if finalsize == 0:
# Clear everything
self.setImageIndex(-1)
elif index == self.imageIndex:
# Our currently displayed image is being removed.
# Switch to the first image (unless that's the one being removed!)
newIndex = 0
if index == newIndex:
newIndex = 1
self.setImageIndex(newIndex)
for provider in self.observedSlots:
provider.notifyRemove(bind(handleDatasetRemoval))
def setupLayers(self, currentImageIndex):
layers = []
for multiImageSlot in self.observedSlots:
if 0 <= currentImageIndex < len(multiImageSlot):
multiLayerSlot = multiImageSlot[currentImageIndex]
for j, slot in enumerate(multiLayerSlot):
if slot.ready():
layer = self.createStandardLayerFromSlot(slot)
layer.name = multiImageSlot.name + " " + str(j)
layers.append(layer)
return layers
@traceLogged(traceLogger)
def _setImageIndex(self, imageIndex):
if self.imageIndex != -1:
for provider in self.observedSlots:
# We're switching datasets. Unsubscribe from the old one's notifications.
provider[self.imageIndex].unregisterInserted(
bind(self.handleLayerInsertion))
provider[self.imageIndex].unregisterRemove(
bind(self.handleLayerRemoval))
self.imageIndex = imageIndex
# Don't repopulate the GUI if there isn't a current dataset. Stop now.
if imageIndex is -1:
self.layerstack.clear()
return
# Update the GUI for all layers in the current dataset
self.updateAllLayers()
# For layers that already exist, subscribe to ready notifications
for provider in self.observedSlots:
for slotIndex, slot in enumerate(provider):
slot.notifyReady(bind(self.updateAllLayers))
slot.notifyUnready(bind(self.updateAllLayers))
# Make sure we're notified if a layer is inserted in the future so we can subscribe to its ready notifications
for provider in self.observedSlots:
if self.imageIndex < len(provider):
provider[self.imageIndex].notifyInserted(
bind(self.handleLayerInsertion))
provider[self.imageIndex].notifyRemoved(
bind(self.handleLayerRemoval))
def handleLayerInsertion(self, slot, slotIndex):
"""
The multislot providing our layers has a new item.
Make room for it in the layer GUI and subscribe to updates.
"""
with Tracer(traceLogger):
# When the slot is ready, we'll replace the blank layer with real data
slot[slotIndex].notifyReady(bind(self.updateAllLayers))
slot[slotIndex].notifyUnready(bind(self.updateAllLayers))
def handleLayerRemoval(self, slot, slotIndex):
"""
An item is about to be removed from the multislot that is providing our layers.
Remove the layer from the GUI.
"""
with Tracer(traceLogger):
self.updateAllLayers()
def generateAlphaModulatedLayersFromChannels(self, slot):
# TODO
assert False
@traceLogged(traceLogger)
def createStandardLayerFromSlot(self, slot, lastChannelIsAlpha=False):
"""
Generate a volumina layer using the given slot.
Choose between grayscale or RGB depending on the number of channels.
"""
def getRange(meta):
if 'drange' in meta:
return meta.drange
if numpy.issubdtype(meta.dtype, numpy.integer):
# We assume that ints range up to their max possible value,
return (0, numpy.iinfo(meta.dtype).max)
else:
# If we don't know the range of the data, create a layer that is auto-normalized.
# See volumina.pixelpipeline.datasources for details.
return 'autoPercentiles'
# Examine channel dimension to determine Grayscale vs. RGB
shape = slot.meta.shape
normalize = getRange(slot.meta)
try:
channelAxisIndex = slot.meta.axistags.index('c')
#assert channelAxisIndex < len(slot.meta.axistags), \
# "slot %s has shape = %r, axistags = %r, but no channel dimension" \
# % (slot.name, slot.meta.shape, slot.meta.axistags)
numChannels = shape[channelAxisIndex]
except:
numChannels = 1
if lastChannelIsAlpha:
assert numChannels <= 4, "Can't display a standard layer with more than four channels (with alpha). Your image has {} channels.".format(
numChannels)
else:
assert numChannels <= 3, "Can't display a standard layer with more than three channels (with no alpha). Your image has {} channels.".format(
numChannels)
if numChannels == 1:
assert not lastChannelIsAlpha, "Can't have an alpha channel if there is no color channel"
source = LazyflowSource(slot)
normSource = NormalizingSource(source, bounds=normalize)
return GrayscaleLayer(normSource)
assert numChannels > 2 or (numChannels == 2 and not lastChannelIsAlpha)
redProvider = OpSingleChannelSelector(graph=slot.graph)
redProvider.Input.connect(slot)
redProvider.Index.setValue(0)
redSource = LazyflowSource(redProvider.Output)
redNormSource = NormalizingSource(redSource, bounds=normalize)
greenProvider = OpSingleChannelSelector(graph=slot.graph)
greenProvider.Input.connect(slot)
greenProvider.Index.setValue(1)
greenSource = LazyflowSource(greenProvider.Output)
greenNormSource = NormalizingSource(greenSource, bounds=normalize)
blueNormSource = None
if numChannels > 3 or (numChannels == 3 and not lastChannelIsAlpha):
blueProvider = OpSingleChannelSelector(graph=slot.graph)
blueProvider.Input.connect(slot)
blueProvider.Index.setValue(2)
blueSource = LazyflowSource(blueProvider.Output)
blueNormSource = NormalizingSource(blueSource, bounds=normalize)
alphaNormSource = None
if lastChannelIsAlpha:
alphaProvider = OpSingleChannelSelector(graph=slot.graph)
alphaProvider.Input.connect(slot)
alphaProvider.Index.setValue(numChannels - 1)
alphaSource = LazyflowSource(alphaProvider.Output)
alphaNormSource = NormalizingSource(alphaSource, bounds=normalize)
layer = RGBALayer(red=redNormSource,
green=greenNormSource,
blue=blueNormSource,
alpha=alphaNormSource)
return layer
@traceLogged(traceLogger)
def areProvidersInSync(self):
"""
When an image is appended to the workflow, not all slots are resized simultaneously.
We should avoid calling setupLayers() until all the slots have been resized with the new image.
"""
try:
numImages = len(self.observedSlots[0])
except IndexError: # observedSlots is empty
pass
inSync = True
for slot in self.observedSlots:
# Check each slot for out-of-sync status except:
# - slots that are optional and unconnected
# - slots that are not images (e.g. a classifier or other object)
if not (slot._optional and slot.partner is None):
if len(slot) == 0:
inSync = False
break
elif len(slot[0]) > 0 and slot[0][0].meta.axistags is not None:
inSync &= (len(slot) == numImages)
return inSync
@traceLogged(traceLogger)
@threadRouted
def updateAllLayers(self):
# Check to make sure all layers are in sync
# (During image insertions, outputs are resized one at a time.)
if not self.areProvidersInSync():
return
if self.imageIndex >= 0:
# Ask the subclass for the updated layer list
newGuiLayers = self.setupLayers(self.imageIndex)
else:
newGuiLayers = []
newNames = set(l.name for l in newGuiLayers)
if len(newNames) != len(newGuiLayers):
msg = "All layers must have unique names.\n"
msg += "You're attempting to use these layer names:\n"
msg += [l.name for l in newGuiLayers]
raise RuntimeError()
# Copy the old visibilities and opacities
if self.imageIndex != self.lastUpdateImageIndex:
existing = {l.name: l for l in self.layerstack}
for layer in newGuiLayers:
if layer.name in existing.keys():
layer.visible = existing[layer.name].visible
layer.opacity = existing[layer.name].opacity
# Clear all existing layers.
self.layerstack.clear()
self.lastUpdateImageIndex = self.imageIndex
# Zoom at a 1-1 scale to avoid loading big datasets entirely...
for view in self.editor.imageViews:
view.doScaleTo(1)
# If the datashape changed, tell the editor
newDataShape = self.determineDatashape()
if newDataShape is not None and self.editor.dataShape != newDataShape:
self.editor.dataShape = newDataShape
# Find the xyz midpoint
midpos5d = [x / 2 for x in newDataShape]
midpos3d = midpos5d[1:4]
# Start in the center of the volume
self.editor.posModel.slicingPos = midpos3d
self.editor.navCtrl.panSlicingViews(midpos3d, [0, 1, 2])
# If one of the xyz dimensions is 1, the data is 2d.
singletonDims = filter(lambda (i, dim): dim == 1,
enumerate(newDataShape[1:4]))
if len(singletonDims) == 1:
# Maximize the slicing view for this axis
axis = singletonDims[0][0]
self.volumeEditorWidget.quadview.ensureMaximized(axis)
# Old layers are deleted if
# (1) They are not in the new set or
# (2) Their data has changed
for index, oldLayer in reversed(list(enumerate(self.layerstack))):
if oldLayer.name not in newNames:
needDelete = True
else:
newLayer = filter(lambda l: l.name == oldLayer.name,
newGuiLayers)[0]
needDelete = (newLayer.datasources != oldLayer.datasources)
if needDelete:
layer = self.layerstack[index]
if hasattr(layer, 'shortcutRegistration'):
obsoleteShortcut = layer.shortcutRegistration[2]
obsoleteShortcut.setEnabled(False)
ShortcutManager().unregister(obsoleteShortcut)
self.layerstack.selectRow(index)
self.layerstack.deleteSelected()
# Insert all layers that aren't already in the layerstack
# (Identified by the name attribute)
existingNames = set(l.name for l in self.layerstack)
for index, layer in enumerate(newGuiLayers):
if layer.name not in existingNames:
# Insert new
self.layerstack.insert(index, layer)
# If this layer has an associated shortcut, register it with the shortcut manager
if hasattr(layer, 'shortcutRegistration'):
ShortcutManager().register(*layer.shortcutRegistration)
else:
# Clean up the layer instance that the client just gave us.
# We don't want to use it.
if hasattr(layer, 'shortcutRegistration'):
shortcut = layer.shortcutRegistration[2]
shortcut.setEnabled(False)
# Move existing layer to the correct positon
stackIndex = self.layerstack.findMatchingIndex(
lambda l: l.name == layer.name)
self.layerstack.selectRow(stackIndex)
while stackIndex > index:
self.layerstack.moveSelectedUp()
stackIndex -= 1
while stackIndex < index:
self.layerstack.moveSelectedDown()
stackIndex += 1
@traceLogged(traceLogger)
def determineDatashape(self):
if self.imageIndex < 0:
return None
newDataShape = None
for provider in self.observedSlots:
if self.imageIndex < len(provider):
for i, slot in enumerate(provider[self.imageIndex]):
if newDataShape is None and slot.ready(
) and slot.meta.axistags is not None:
# Use an Op5ifyer adapter to transpose the shape for us.
op5 = Op5ifyer(graph=slot.graph)
op5.input.connect(slot)
newDataShape = op5.output.meta.shape
# We just needed the operator to determine the transposed shape.
# Disconnect it so it can be garbage collected.
op5.input.disconnect()
if newDataShape is not None:
# For now, this base class combines multi-channel images into a single layer,
# So, we want the volume editor to behave as though there is only one channel
newDataShape = newDataShape[:-1] + (1, )
return newDataShape
@traceLogged(traceLogger)
def initViewerControlUi(self):
"""
Load the viewer controls GUI, which appears below the applet bar.
In our case, the viewer control GUI consists mainly of a layer list.
"""
localDir = os.path.split(__file__)[0]
self.__viewerControlWidget = uic.loadUi(localDir +
"/viewerControls.ui")
@traceLogged(traceLogger)
def initAppletDrawerUi(self):
"""
By default, this base class provides a blank applet drawer.
Override this in a subclass to get a real applet drawer.
"""
# Load the ui file (find it in our own directory)
localDir = os.path.split(__file__)[0]
self._drawer = uic.loadUi(localDir + "/drawer.ui")
def getAppletDrawerUi(self):
return self._drawer
@traceLogged(traceLogger)
def initCentralUic(self):
"""
Load the GUI from the ui file into this class and connect it with event handlers.
"""
# Load the ui file into this class (find it in our own directory)
localDir = os.path.split(__file__)[0]
uic.loadUi(localDir + "/centralWidget.ui", self)
# Menu is specified in a separate ui file with a dummy window
self.menuGui = uic.loadUi(
localDir +
"/menu.ui") # Save as member so it doesn't get picked up by GC
self.menuBar = self.menuGui.menuBar
self.menuView = self.menuGui.menuView
def toggleDebugPatches(show):
self.editor.showDebugPatches = show
def setCacheSize(cache_size):
dlg = QDialog(self)
layout = QHBoxLayout()
layout.addWidget(QLabel("Cached Slices Per View:"))
cache_size = [self.editor.cacheSize]
def parseCacheSize(strSize):
try:
cache_size[0] = int(strSize)
except:
pass
edit = QLineEdit(str(cache_size[0]), parent=dlg)
edit.textChanged.connect(parseCacheSize)
layout.addWidget(edit)
okButton = QPushButton("OK", parent=dlg)
okButton.clicked.connect(dlg.accept)
layout.addWidget(okButton)
dlg.setLayout(layout)
dlg.setModal(True)
dlg.exec_()
self.editor.cacheSize = cache_size[0]
def fitToScreen():
shape = self.editor.posModel.shape
for i, v in enumerate(self.editor.imageViews):
s = list(shape)
del s[i]
v.changeViewPort(v.scene().data2scene.mapRect(QRectF(0, 0,
*s)))
def fitImage():
if hasattr(self.editor, '_lastImageViewFocus'):
self.editor.imageViews[
self.editor._lastImageViewFocus].fitImage()
def restoreImageToOriginalSize():
if hasattr(self.editor, '_lastImageViewFocus'):
self.editor.imageViews[
self.editor._lastImageViewFocus].doScaleTo()
def rubberBandZoom():
if hasattr(self.editor, '_lastImageViewFocus'):
if not self.editor.imageViews[
self.editor._lastImageViewFocus]._isRubberBandZoom:
self.editor.imageViews[
self.editor.
_lastImageViewFocus]._isRubberBandZoom = True
self.editor.imageViews[
self.editor.
_lastImageViewFocus]._cursorBackup = self.editor.imageViews[
self.editor._lastImageViewFocus].cursor()
self.editor.imageViews[
self.editor._lastImageViewFocus].setCursor(
Qt.CrossCursor)
else:
self.editor.imageViews[
self.editor.
_lastImageViewFocus]._isRubberBandZoom = False
self.editor.imageViews[
self.editor._lastImageViewFocus].setCursor(
self.editor.imageViews[
self.editor._lastImageViewFocus]._cursorBackup)
def hideHud():
hide = not self.editor.imageViews[0]._hud.isVisible()
for i, v in enumerate(self.editor.imageViews):
v.setHudVisible(hide)
def toggleSelectedHud():
if hasattr(self.editor, '_lastImageViewFocus'):
self.editor.imageViews[
self.editor._lastImageViewFocus].toggleHud()
def centerAllImages():
for i, v in enumerate(self.editor.imageViews):
v.centerImage()
def centerImage():
if hasattr(self.editor, '_lastImageViewFocus'):
self.editor.imageViews[
self.editor._lastImageViewFocus].centerImage()
self.actionOnly_for_current_view.setEnabled(True)
self.menuGui.actionCenterAllImages.triggered.connect(centerAllImages)
self.menuGui.actionCenterImage.triggered.connect(centerImage)
self.menuGui.actionToggleAllHuds.triggered.connect(hideHud)
self.menuGui.actionToggleSelectedHud.triggered.connect(
toggleSelectedHud)
self.menuGui.actionShowDebugPatches.toggled.connect(toggleDebugPatches)
self.menuGui.actionFitToScreen.triggered.connect(fitToScreen)
self.menuGui.actionFitImage.triggered.connect(fitImage)
self.menuGui.actionReset_zoom.triggered.connect(
restoreImageToOriginalSize)
self.menuGui.actionRubberBandZoom.triggered.connect(rubberBandZoom)
self.menuGui.actionSetCacheSize.triggered.connect(setCacheSize)
@traceLogged(traceLogger)
def initEditor(self):
"""
Initialize the Volume Editor GUI.
"""
self.editor = VolumeEditor(self.layerstack)
# Replace the editor's navigation interpreter with one that has extra functionality
self.clickReporter = ClickReportingInterpreter(
self.editor.navInterpret, self.editor.posModel)
self.editor.setNavigationInterpreter(self.clickReporter)
self.clickReporter.rightClickReceived.connect(
self._handleEditorRightClick)
self.clickReporter.leftClickReceived.connect(
self._handleEditorLeftClick)
self.editor.newImageView2DFocus.connect(self.setIconToViewMenu)
self.editor.setInteractionMode('navigation')
self.volumeEditorWidget.init(self.editor)
# The editor's layerstack is in charge of which layer movement buttons are enabled
model = self.editor.layerStack
if self.__viewerControlWidget is not None:
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
@traceLogged(traceLogger)
def setIconToViewMenu(self):
"""
In the "Only for Current View" menu item of the View menu,
show the user which axis is the current one by changing the menu item icon.
"""
self.actionOnly_for_current_view.setIcon(
QIcon(self.editor.imageViews[
self.editor._lastImageViewFocus]._hud.axisLabel.pixmap()))
@traceLogged(traceLogger)
def _convertPositionToDataSpace(self, voluminaPosition):
taggedPosition = {k: p for k, p in zip('txyzc', voluminaPosition)}
# Find the first lazyflow layer in the stack
# We assume that all lazyflow layers have the same axistags
dataTags = None
for layer in self.layerstack:
for datasource in layer.datasources:
if isinstance(datasource, NormalizingSource):
datasource = datasource._rawSource
if isinstance(datasource, LazyflowSource):
dataTags = datasource.dataSlot.meta.axistags
if dataTags is not None:
break
assert dataTags is not None, "Can't convert mouse click coordinates from volumina-5d: Could not find a lazyflow data source in any layer."
position = ()
for tag in dataTags:
position += (taggedPosition[tag.key], )
return position
def _handleEditorRightClick(self, position5d, globalWindowCoordinate):
dataPosition = self._convertPositionToDataSpace(position5d)
self.handleEditorRightClick(self.imageIndex, dataPosition,
globalWindowCoordinate)
def _handleEditorLeftClick(self, position5d, globalWindowCoordinate):
dataPosition = self._convertPositionToDataSpace(position5d)
self.handleEditorLeftClick(self.imageIndex, dataPosition,
globalWindowCoordinate)
def handleEditorRightClick(self, currentImageIndex, position5d,
globalWindowCoordinate):
# Override me
pass
def handleEditorLeftClick(self, currentImageIndex, position5d,
globalWindowCoordiante):
# Override me
pass
def initUic(self):
p = os.path.split(__file__)[0]+'/'
if p == "/": p = "."+p
uic.loadUi(p+"MainWindow_cc.ui", self)
#connect the window and graph creation to the opening of the file
self.actionOpen.triggered.connect(self.openFile)
self.actionQuit.triggered.connect(qApp.quit)
def toggleDebugPatches(show):
self.editor.showDebugPatches = show
def fitToScreen():
shape = self.editor.posModel.shape
for i, v in enumerate(self.editor.imageViews):
s = list(copy.copy(shape))
del s[i]
v.changeViewPort(v.scene().data2scene.mapRect(QRectF(0,0,*s)))
def fitImage():
if hasattr(self.editor, '_lastImageViewFocus'):
self.editor.imageViews[self.editor._lastImageViewFocus].fitImage()
def restoreImageToOriginalSize():
if hasattr(self.editor, '_lastImageViewFocus'):
self.editor.imageViews[self.editor._lastImageViewFocus].doScaleTo()
def rubberBandZoom():
if hasattr(self.editor, '_lastImageViewFocus'):
if not self.editor.imageViews[self.editor._lastImageViewFocus]._isRubberBandZoom:
self.editor.imageViews[self.editor._lastImageViewFocus]._isRubberBandZoom = True
self.editor.imageViews[self.editor._lastImageViewFocus]._cursorBackup = self.editor.imageViews[self.editor._lastImageViewFocus].cursor()
self.editor.imageViews[self.editor._lastImageViewFocus].setCursor(Qt.CrossCursor)
else:
self.editor.imageViews[self.editor._lastImageViewFocus]._isRubberBandZoom = False
self.editor.imageViews[self.editor._lastImageViewFocus].setCursor(self.editor.imageViews[self.editor._lastImageViewFocus]._cursorBackup)
def hideHud():
if self.editor.imageViews[0]._hud.isVisible():
hide = False
else:
hide = True
for i, v in enumerate(self.editor.imageViews):
v.hideHud(hide)
def toggleSelectedHud():
if hasattr(self.editor, '_lastImageViewFocus'):
self.editor.imageViews[self.editor._lastImageViewFocus].toggleHud()
def centerAllImages():
for i, v in enumerate(self.editor.imageViews):
v.centerImage()
def centerImage():
if hasattr(self.editor, '_lastImageViewFocus'):
self.editor.imageViews[self.editor._lastImageViewFocus].centerImage()
self.actionOnly_for_current_view.setEnabled(True)
self.actionCenterAllImages.triggered.connect(centerAllImages)
self.actionCenterImage.triggered.connect(centerImage)
self.actionToggleAllHuds.triggered.connect(hideHud)
self.actionToggleSelectedHud.triggered.connect(toggleSelectedHud)
self.actionShowDebugPatches.toggled.connect(toggleDebugPatches)
self.actionFitToScreen.triggered.connect(fitToScreen)
self.actionFitImage.triggered.connect(fitImage)
self.actionReset_zoom.triggered.connect(restoreImageToOriginalSize)
self.actionRubberBandZoom.triggered.connect(rubberBandZoom)
self.haveData.connect(self.initGraph)
self.dataReadyToView.connect(self.initEditor)
self.layerstack = LayerStackModel()
model = LabelListModel()
self.labelListView.setModel(model)
self.labelListModel=model
self.labelListModel.rowsAboutToBeRemoved.connect(self.onLabelAboutToBeRemoved)
self.labelListModel.labelSelected.connect(self.switchLabel)
def onDataChanged(topLeft, bottomRight):
firstRow = topLeft.row()
lastRow = bottomRight.row()
firstCol = topLeft.column()
lastCol = bottomRight.column()
if lastCol == firstCol == 0:
assert(firstRow == lastRow) #only one data item changes at a time
#in this case, the actual data (for example color) has changed
self.switchColor(firstRow+1, self.labelListModel[firstRow].color)
self.editor.scheduleSlicesRedraw()
else:
#this column is used for the 'delete' buttons, we don't care
#about data changed here
pass
self.labelListModel.dataChanged.connect(onDataChanged)
self.AddLabelButton.clicked.connect(self.addLabel)
self.SelectFeaturesButton.clicked.connect(self.onFeatureButtonClicked)
self.StartClassificationButton.clicked.connect(self.startClassification)
self.StartClassificationButton.setEnabled(False)
self.checkInteractive.setEnabled(False)
self.checkInteractive.toggled.connect(self.toggleInteractive)
self.interactionComboBox.currentIndexChanged.connect(self.changeInteractionMode)
self.interactionComboBox.setEnabled(False)
self.AddThresholdButton.clicked.connect(self.addThresholdOperator)
self.AddThresholdButton.setEnabled(False)
self.CCButton.clicked.connect(self.addCCOperator)
self.CCButton.setEnabled(False)
self._initFeatureDlg()
def __init__(self, topLevelOperator):
"""
Constructor. **All** slots of the provided *topLevelOperator* will be monitored for changes.
Changes include slot resize events, and slot ready/unready status changes.
When a change is detected, the `setupLayers()` function is called, and the result is used to update the list of layers shown in the central widget.
:param topLevelOperator: The top-level operator for the applet this GUI belongs to.
"""
super(LayerViewerGui, self).__init__()
self.threadRouter = ThreadRouter(self) # For using @threadRouted
self.topLevelOperator = topLevelOperator
observedSlots = []
for slot in topLevelOperator.inputs.values() + topLevelOperator.outputs.values():
if slot.level == 1 or slot.level == 2:
observedSlots.append(slot)
self.observedSlots = []
for slot in observedSlots:
if slot.level == 1:
# The user gave us a slot that is indexed as slot[image]
# Wrap the operator so it has the right level. Indexed as: slot[image][0]
opPromoteInput = OperatorWrapper( Op1ToMulti, graph=slot.operator.graph )
opPromoteInput.Input.connect(slot)
slot = opPromoteInput.Outputs
# Each slot should now be indexed as slot[image][sub_index]
assert slot.level == 2
self.observedSlots.append( slot )
self.layerstack = LayerStackModel()
self.initAppletDrawerUi() # Default implementation loads a blank drawer.
self._initCentralUic()
self.__viewerControlWidget = None
self.initViewerControlUi()
self._initEditor()
self.imageIndex = -1
self.lastUpdateImageIndex = -1
def handleDatasetInsertion(slot, imageIndex):
if self.imageIndex == -1 and self._areProvidersInSync():
self.setImageIndex( imageIndex )
for provider in self.observedSlots:
provider.notifyInserted( bind( handleDatasetInsertion ) )
def handleDatasetRemoval(slot, index, finalsize):
if finalsize == 0:
# Clear everything
self.setImageIndex(-1)
elif index == self.imageIndex:
# Our currently displayed image is being removed.
# Switch to the first image (unless that's the one being removed!)
newIndex = 0
if index == newIndex:
newIndex = 1
self.setImageIndex(newIndex)
for provider in self.observedSlots:
provider.notifyRemove( bind( handleDatasetRemoval ) )
