Python LazyflowSource.setObjectName方法代码示例

# 需要导入模块: from volumina.api import LazyflowSource [as 别名]
# 或者: from volumina.api.LazyflowSource import setObjectName [as 别名]
 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)

# 需要导入模块: from volumina.api import LazyflowSource [as 别名]
# 或者: from volumina.api.LazyflowSource import setObjectName [as 别名]
 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)

# 需要导入模块: from volumina.api import LazyflowSource [as 别名]
# 或者: from volumina.api.LazyflowSource import setObjectName [as 别名]
class ObjectExtractionGui(LayerViewerGui):

    def stopAndCleanUp(self):
        # Unsubscribe to all signals
        for fn in self.__cleanup_fns:
            fn()

        super(ObjectExtractionGui, self).stopAndCleanUp()

    def __init__(self, *args, **kwargs):
        self.__cleanup_fns = []
        self._lock = threading.Lock()
        super( ObjectExtractionGui, self ).__init__(*args, **kwargs)

    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):
        #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 _onReady(self, slot):
        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 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)
        if not ilastik_config.getboolean("ilastik", "debug"):
#.........这里部分代码省略.........

# 需要导入模块: from volumina.api import LazyflowSource [as 别名]
# 或者: from volumina.api.LazyflowSource import setObjectName [as 别名]
 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()

# 需要导入模块: from volumina.api import LazyflowSource [as 别名]
# 或者: from volumina.api.LazyflowSource import setObjectName [as 别名]
class ObjectExtractionGui(LayerViewerGui):

    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):
        #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"
                self.layerstack.append(layerraw)

    def _onReady(self, slot):
        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"
                self.layerstack.append(layerraw)


    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 _selectFeaturesButtonPressed(self):
        featureDict = {}
        mainOperator = self.topLevelOperatorView
        slot = mainOperator.Features
        if slot.ready():
            selectedFeatures = mainOperator.Features([]).wait()
        else:
            selectedFeatures = None

        plugins = pluginManager.getPluginsOfCategory('ObjectFeatures')

        imgshape = list(mainOperator.RawImage.meta.shape)
        axistags = mainOperator.RawImage.meta.axistags
        imgshape.pop(axistags.index('t'))
        fakeimg = np.empty(imgshape, dtype=np.float32)

        labelshape = list(mainOperator.BinaryImage.meta.shape)
        axistags = mainOperator.BinaryImage.meta.axistags
        labelshape.pop(axistags.index('t'))
        labelshape.pop(axistags.index('c') - 1)
#.........这里部分代码省略.........

# 需要导入模块: from volumina.api import LazyflowSource [as 别名]
# 或者: from volumina.api.LazyflowSource import setObjectName [as 别名]
    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()

# 需要导入模块: from volumina.api import LazyflowSource [as 别名]
# 或者: from volumina.api.LazyflowSource import setObjectName [as 别名]
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:
#.........这里部分代码省略.........

# 需要导入模块: from volumina.api import LazyflowSource [as 别名]
# 或者: from volumina.api.LazyflowSource import setObjectName [as 别名]
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)

#.........这里部分代码省略.........