Python api.GrayscaleLayer类代码示例

 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 setupLayers(self):
        mainOperator = self.topLevelOperatorView
        layers = []

        if mainOperator.ObjectCenterImage.ready():
            self.centerimagesrc = LazyflowSource(mainOperator.ObjectCenterImage)
            redct = [0, QColor(255, 0, 0).rgba()]
            layer = ColortableLayer(self.centerimagesrc, redct)
            layer.name = "Object centers"
            layer.setToolTip("Object center positions, marked with a little red cross")
            layer.visible = False
            layers.append(layer)

        ct = colortables.create_default_16bit()
        if mainOperator.LabelImage.ready():
            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 = "Objects (connected components)"
            layer.setToolTip("Segmented objects, shown in different colors")
            layer.visible = False
            layer.opacity = 0.5
            layers.append(layer)

        # white foreground on transparent background, even for labeled images
        binct = [QColor(255, 255, 255, 255).rgba()]*65536
        binct[0] = 0
        if mainOperator.BinaryImage.ready():
            self.binaryimagesrc = LazyflowSource(mainOperator.BinaryImage)
            self.binaryimagesrc.setObjectName("Binary LazyflowSrc")
            layer = ColortableLayer(self.binaryimagesrc, binct)
            layer.name = "Binary image"
            layer.setToolTip("Segmented objects, binary mask")
            layers.append(layer)

        ## raw data layer
        self.rawsrc = None
        self.rawsrc = LazyflowSource(mainOperator.RawImage)
        self.rawsrc.setObjectName("Raw Lazyflow Src")
        layerraw = GrayscaleLayer(self.rawsrc)
        layerraw.name = "Raw data"
        layers.insert(len(layers), layerraw)

        mainOperator.RawImage.notifyReady(self._onReady)
        self.__cleanup_fns.append( partial( mainOperator.RawImage.unregisterReady, self._onReady ) )

        mainOperator.RawImage.notifyMetaChanged(self._onMetaChanged)
        self.__cleanup_fns.append( partial( mainOperator.RawImage.unregisterMetaChanged, self._onMetaChanged ) )

        if mainOperator.BinaryImage.meta.shape:
            self.editor.dataShape = mainOperator.BinaryImage.meta.shape

        mainOperator.BinaryImage.notifyMetaChanged(self._onMetaChanged)
        self.__cleanup_fns.append( partial( mainOperator.BinaryImage.unregisterMetaChanged, self._onMetaChanged ) )

        return layers

    def _onMetaChanged( self, slot ):
        if slot is self.mainOperator.LabelImage:
            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 _onMetaChanged(self, slot):
        #FiXME: why do we need that?
        if slot is self.topLevelOperatorView.BinaryImage:
            if slot.meta.shape:
                self.editor.dataShape = slot.meta.shape

        if slot is self.topLevelOperatorView.RawImage:
            if slot.meta.shape and not self.rawsrc:
                self.rawsrc = LazyflowSource(self.topLevelOperatorView.RawImage)
                layerraw = GrayscaleLayer(self.rawsrc)
                layerraw.name = "Raw data"
                self.layerstack.append(layerraw)

    def setupLayers(self):
        mainOperator = self.topLevelOperatorView
        layers = []

        if mainOperator.ObjectCenterImage.ready():
            self.centerimagesrc = LazyflowSource(mainOperator.ObjectCenterImage)
            #layer = RGBALayer(red=ConstantSource(255), alpha=self.centerimagesrc)
            redct = [0, QColor(255, 0, 0).rgba()]
            layer = ColortableLayer(self.centerimagesrc, redct)
            layer.name = "Object Centers"
            layer.visible = False
            layers.append(layer)

        ct = colortables.create_default_16bit()
        if mainOperator.LabelImage.ready():
            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
            layers.append(layer)

        # white foreground on transparent background
        binct = [QColor(0, 0, 0, 0).rgba(), QColor(255, 255, 255, 255).rgba()]
        if mainOperator.BinaryImage.ready():
            self.binaryimagesrc = LazyflowSource(mainOperator.BinaryImage)
            self.binaryimagesrc.setObjectName("Binary LazyflowSrc")
            layer = ColortableLayer(self.binaryimagesrc, binct)
            layer.name = "Binary Image"
            layers.append(layer)

        ## raw data layer
        self.rawsrc = None
        self.rawsrc = LazyflowSource(mainOperator.RawImage)
        self.rawsrc.setObjectName("Raw Lazyflow Src")
        layerraw = GrayscaleLayer(self.rawsrc)
        layerraw.name = "Raw"
        layers.insert(len(layers), 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)

        return layers

    def _onMetaChanged( self, slot ):
        if slot is self.mainOperator.LabelImage:
            if slot.meta.shape:                
                self.editor.dataShape = slot.meta.shape
                
#                maxt = slot.meta.shape[0] - 1
#                self._setRanges()
#                self._drawer.from_time.setValue(0)                
#                self._drawer.to_time.setValue(maxt)
            
        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 _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

 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

    def setupLayers( self ):        
        layers = []
                        
        self.ct[0] = QColor(0,0,0,0).rgba() # make 0 transparent        
        self.ct[255] = QColor(0,0,0,255).rgba() # make -1 black
        self.ct[-1] = QColor(0,0,0,255).rgba()
        self.trackingsrc = LazyflowSource( self.topLevelOperatorView.TrackImage )
        trackingLayer = ColortableLayer( self.trackingsrc, self.ct )
        trackingLayer.name = "Manual Tracking"
        trackingLayer.visible = True
        trackingLayer.opacity = 0.8

        def toggleTrackingVisibility():
            trackingLayer.visible = not trackingLayer.visible
            
        trackingLayer.shortcutRegistration = (
                "Layer Visibilities",
                "Toggle Manual Tracking Layer Visibility",
                QtGui.QShortcut( QtGui.QKeySequence("e"), self.viewerControlWidget(), toggleTrackingVisibility),
                trackingLayer )
        layers.append(trackingLayer)
        
        
        ct = colortables.create_random_16bit()
        ct[1] = QColor(230,0,0,150).rgba()
        ct[0] = QColor(0,0,0,0).rgba() # make 0 transparent
        self.untrackedsrc = LazyflowSource( self.topLevelOperatorView.UntrackedImage )
        untrackedLayer = ColortableLayer( self.untrackedsrc, ct )
        untrackedLayer.name = "Untracked Objects"
        untrackedLayer.visible = False
        untrackedLayer.opacity = 0.8
        layers.append(untrackedLayer)
        
        self.objectssrc = LazyflowSource( self.topLevelOperatorView.BinaryImage )
        ct = colortables.create_random_16bit()
        ct[0] = QColor(0,0,0,0).rgba() # make 0 transparent
        ct[1] = QColor(255,255,0,100).rgba() 
        objLayer = ColortableLayer( self.objectssrc, ct )
        objLayer.name = "Objects"
        objLayer.opacity = 0.8
        objLayer.visible = True
        
        def toggleObjectVisibility():
            objLayer.visible = not objLayer.visible
            
        objLayer.shortcutRegistration = (
                "Layer Visibilities",
                "Toggle Objects Layer Visibility",
                QtGui.QShortcut( QtGui.QKeySequence("r"), self.viewerControlWidget(), toggleObjectVisibility),
                objLayer )
        
        layers.append(objLayer)


        ## raw data layer
        self.rawsrc = None
        self.rawsrc = LazyflowSource( self.mainOperator.RawImage )
        rawLayer = GrayscaleLayer( self.rawsrc )
        rawLayer.name = "Raw"        
        layers.insert( len(layers), rawLayer )   
        
        
        if self.topLevelOperatorView.LabelImage.meta.shape:
            self.editor.dataShape = self.topLevelOperatorView.LabelImage.meta.shape    
        
        self.topLevelOperatorView.RawImage.notifyReady( self._onReady )
        self.topLevelOperatorView.RawImage.notifyMetaChanged( self._onMetaChanged )
        
        self._setDivisionsList()
        self._setActiveTrackList()
        
        return layers

 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 initGraph(self):
        shape = self.inputProvider.outputs["Output"].shape
        srcs    = []
        minMax = []
        
        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):
            if self._normalize_data:
                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)
            else:
                minMax.append(None)
            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], normalize=minMax[0])
            layer1.set_range(0,minMax[0])
            print "  - showing raw data as grayscale"
        elif nchannels==2:
            layer1 = RGBALayer(red  = srcs[0], normalizeR=minMax[0],
                               green = srcs[1], normalizeG=minMax[1])
            layer1.set_range(0, minMax[0])
            layer1.set_range(1, minMax[1])
            print "  - showing channel 1 as red, channel 2 as green"
        elif nchannels==3:
            layer1 = RGBALayer(red   = srcs[0], normalizeR=minMax[0],
                               green = srcs[1], normalizeG=minMax[1],
                               blue  = srcs[2], normalizeB=minMax[2])
            layer1.set_range(0, minMax[0])
            layer1.set_range(1, minMax[1])
            layer1.set_range(2, minMax[2])
            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)
 
        self.workflow = PixelClassificationLazyflow( self.g, self.featScalesList, self.inputProvider.outputs["Output"])

        self.initLabels()
        self.startClassification()
        self.dataReadyToView.emit()

    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 )
#.........这里部分代码省略.........

    def setupLayers( self ):        
        layers = []
                
        self.ct[0] = QColor(0,0,0,0).rgba() # make 0 transparent        
        self.ct[255] = QColor(0,0,0,255).rgba() # make -1 black
        self.ct[-1] = QColor(0,0,0,255).rgba()
        self.trackingsrc = LazyflowSource( self.topLevelOperatorView.TrackImage )
        trackingLayer = ColortableLayer( self.trackingsrc, self.ct )
        trackingLayer.name = "Manual Tracking"
        trackingLayer.visible = True
        trackingLayer.opacity = 0.8
        layers.append(trackingLayer)
        
        ct = colortables.create_random_16bit()
        ct[1] = QColor(230,0,0,150).rgba()
        ct[0] = QColor(0,0,0,0).rgba() # make 0 transparent
        self.untrackedsrc = LazyflowSource( self.topLevelOperatorView.UntrackedImage )
        untrackedLayer = ColortableLayer( self.untrackedsrc, ct )
        untrackedLayer.name = "Untracked Objects"
        untrackedLayer.visible = False
        untrackedLayer.opacity = 0.8
        layers.append(untrackedLayer)
        
        self.objectssrc = LazyflowSource( self.topLevelOperatorView.BinaryImage )
#        ct = colortables.create_default_8bit()
        ct = colortables.create_random_16bit()
        ct[0] = QColor(0,0,0,0).rgba() # make 0 transparent
        ct[1] = QColor(255,255,0,100).rgba() # make 0 transparent
        objLayer = ColortableLayer( self.objectssrc, ct )
        objLayer.name = "Objects"
        objLayer.opacity = 0.8
        objLayer.visible = True
        layers.append(objLayer)


        ## raw data layer
        self.rawsrc = None
        self.rawsrc = LazyflowSource( self.mainOperator.RawImage )
        rawLayer = GrayscaleLayer( self.rawsrc )
        rawLayer.name = "Raw"        
        layers.insert( len(layers), rawLayer )   
        
        
        if self.topLevelOperatorView.LabelImage.meta.shape:
            self.editor.dataShape = self.topLevelOperatorView.LabelImage.meta.shape    
            
#            maxt = self.topLevelOperatorView.LabelImage.meta.shape[0] - 1
#            maxx = self.topLevelOperatorView.LabelImage.meta.shape[1] - 1
#            maxy = self.topLevelOperatorView.LabelImage.meta.shape[2] - 1
#            maxz = self.topLevelOperatorView.LabelImage.meta.shape[3] - 1
#        
#            self._setRanges()
#            self._drawer.from_time.setValue(0)
#            self._drawer.to_time.setValue(maxt) 
#            self._drawer.from_x.setValue(0)
#            self._drawer.to_x.setValue(maxx)
#            self._drawer.from_y.setValue(0)
#            self._drawer.to_y.setValue(maxy)   
#            self._drawer.from_z.setValue(0)    
#            self._drawer.to_z.setValue(maxz)
        
        self.topLevelOperatorView.RawImage.notifyReady( self._onReady )
        self.topLevelOperatorView.RawImage.notifyMetaChanged( self._onMetaChanged )
        
        self._setDivisionsList()
        self._setActiveTrackList()
        
        return layers