Exemple #1
0
    def __init__(self, image=None, fillHistogram=True):
        """
        If *image* (ImageItem) is provided, then the control will be automatically linked to the image and changes to the control will be immediately reflected in the image's appearance.
        By default, the histogram is rendered with a fill. For performance, set *fillHistogram* = False.
        """
        GraphicsWidget.__init__(self)
        self.lut = None
        self.imageItem = lambda: None  # fake a dead weakref

        self.layout = QtWidgets.QGraphicsGridLayout()
        self.setLayout(self.layout)
        self.layout.setContentsMargins(1, 1, 1, 1)
        self.layout.setSpacing(0)
        self.vb = ViewBox(parent=self)
        self.vb.setMaximumWidth(152)
        self.vb.setMinimumWidth(45)
        self.vb.setMouseEnabled(x=False, y=True)
        self.gradient = GradientEditorItem()
        self.gradient.setOrientation('right')
        self.gradient.loadPreset('grey')
        self.region = LinearRegionItem([0, 1], LinearRegionItem.Horizontal)
        self.region.setZValue(1000)
        self.vb.addItem(self.region)
        self.axis = AxisItem('left',
                             linkView=self.vb,
                             maxTickLength=-10,
                             parent=self)
        self.layout.addItem(self.axis, 0, 0)
        self.layout.addItem(self.vb, 0, 1)
        self.layout.addItem(self.gradient, 0, 2)
        self.range = None
        self.gradient.setFlag(self.gradient.ItemStacksBehindParent)
        self.vb.setFlag(self.gradient.ItemStacksBehindParent)

        #self.grid = GridItem()
        #self.vb.addItem(self.grid)

        self.gradient.sigGradientChanged.connect(self.gradientChanged)
        self.region.sigRegionChanged.connect(self.regionChanging)
        self.region.sigRegionChangeFinished.connect(self.regionChanged)
        self.vb.sigRangeChanged.connect(self.viewRangeChanged)
        self.plot = PlotDataItem()
        self.plot.rotate(90)
        self.fillHistogram(fillHistogram)

        self.vb.addItem(self.plot)
        self.autoHistogramRange()

        if image is not None:
            self.setImageItem(image)
Exemple #2
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    def __init__(self, image=None, fillHistogram=True):
        """
        If *image* (ImageItem) is provided, then the control will be automatically linked to the image and changes to the control will be immediately reflected in the image's appearance.
        By default, the histogram is rendered with a fill. For performance, set *fillHistogram* = False.
        """
        GraphicsWidget.__init__(self)
        self.lut = None
        self.imageItem = lambda: None  # fake a dead weakref

        self.layout = QtWidgets.QGraphicsGridLayout()
        self.setLayout(self.layout)
        self.layout.setContentsMargins(1,1,1,1)
        self.layout.setSpacing(0)
        self.vb = ViewBox(parent=self)
        self.vb.setMaximumWidth(152)
        self.vb.setMinimumWidth(45)
        self.vb.setMouseEnabled(x=False, y=True)
        self.gradient = GradientEditorItem()
        self.gradient.setOrientation('right')
        self.gradient.loadPreset('grey')
        self.region = LinearRegionItem([0, 1], LinearRegionItem.Horizontal)
        self.region.setZValue(1000)
        self.vb.addItem(self.region)
        self.axis = AxisItem('left', linkView=self.vb, maxTickLength=-10, parent=self)
        self.layout.addItem(self.axis, 0, 0)
        self.layout.addItem(self.vb, 0, 1)
        self.layout.addItem(self.gradient, 0, 2)
        self.range = None
        self.gradient.setFlag(self.gradient.ItemStacksBehindParent)
        self.vb.setFlag(self.gradient.ItemStacksBehindParent)

        #self.grid = GridItem()
        #self.vb.addItem(self.grid)

        self.gradient.sigGradientChanged.connect(self.gradientChanged)
        self.region.sigRegionChanged.connect(self.regionChanging)
        self.region.sigRegionChangeFinished.connect(self.regionChanged)
        self.vb.sigRangeChanged.connect(self.viewRangeChanged)
        self.plot = PlotDataItem()
        self.plot.rotate(90)
        self.fillHistogram(fillHistogram)

        self.vb.addItem(self.plot)
        self.autoHistogramRange()

        if image is not None:
            self.setImageItem(image)
Exemple #3
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    def __init__(self, image=None, fillHistogram=True):
        """
        If *image* (ImageItem) is provided, then the control will be automatically linked to the image and changes to the control will be immediately reflected in the image's appearance.
        By default, the histogram is rendered with a fill. For performance, set *fillHistogram* = False.
        """
        GraphicsWidget.__init__(self)
        self.lut = None
        self.imageItem = None
        self.first_image = True
        self.percentageLevel = False

        self.layout = QtGui.QGraphicsGridLayout()
        self.setLayout(self.layout)
        self.layout.setContentsMargins(1, 1, 1, 1)
        self.layout.setSpacing(0)
        self.vb = ViewBox()
        self.vb.setMaximumHeight(30)
        self.vb.setMinimumHeight(45)
        self.vb.setMouseEnabled(x=True, y=False)
        self.gradient = GradientEditorItem()
        self.gradient.setOrientation("top")
        self.gradient.loadPreset("grey")
        self.region = LinearRegionItem([0, 1], LinearRegionItem.Vertical)
        self.region.setZValue(1000)
        self.vb.addItem(self.region)
        self.layout.addItem(self.vb, 1, 0)
        self.layout.addItem(self.gradient, 0, 0)
        self.range = None
        self.gradient.setFlag(self.gradient.ItemStacksBehindParent)
        self.vb.setFlag(self.gradient.ItemStacksBehindParent)

        # self.grid = GridItem()
        # self.vb.addItem(self.grid)

        self.gradient.sigGradientChanged.connect(self.gradientChanged)
        self.region.sigRegionChanged.connect(self.regionChanging)
        self.region.sigRegionChangeFinished.connect(self.regionChanged)
        self.vb.sigRangeChanged.connect(self.viewRangeChanged)
        self.plot = PlotDataItem()
        self.fillHistogram(fillHistogram)

        self.vb.addItem(self.plot)
        self.autoHistogramRange()

        if image is not None:
            self.setImageItem(image)
Exemple #4
0
class TimeSeriesView(QtGui.QWidget):
    """
    Widget used for display and analysis of image data.
    Implements many features:
    
    * Displays 2D and 3D image data. For 3D data, a z-axis
      slider is displayed allowing the user to select which frame is displayed.
    * Displays histogram of image data with movable region defining the dark/light levels
    * Editable gradient provides a color lookup table 
    * Frame slider may also be moved using left/right arrow keys as well as pgup, pgdn, home, and end.
    * Basic analysis features including:
    
        * ROI and embedded plot for measuring image values across frames
        * Image normalization / background subtraction 
    
    Basic Usage::
    
        imv = pg.ImageView()
        imv.show()
        imv.setImage(data)
        
    **Keyboard interaction**
    
    * left/right arrows step forward/backward 1 frame when pressed,
      seek at 20fps when held.
    * up/down arrows seek at 100fps
    * pgup/pgdn seek at 1000fps
    * home/end seek immediately to the first/last frame
    * space begins playing frames. If time values (in seconds) are given 
      for each frame, then playback is in realtime.
    """
    sigTimeChanged = QtCore.Signal(object, object)
    sigProcessingChanged = QtCore.Signal(object)

    def __init__(self,
                 parent=None,
                 name="ImageView",
                 view=None,
                 imageItem=None,
                 *args):
        """
        By default, this class creates an :class:`ImageItem <pyqtgraph.ImageItem>` to display image data
        and a :class:`ViewBox <pyqtgraph.ViewBox>` to contain the ImageItem. 
        
        ============= =========================================================
        **Arguments** 
        parent        (QWidget) Specifies the parent widget to which
                      this ImageView will belong. If None, then the ImageView
                      is created with no parent.
        name          (str) The name used to register both the internal ViewBox
                      and the PlotItem used to display ROI data. See the *name*
                      argument to :func:`ViewBox.__init__() 
                      <pyqtgraph.ViewBox.__init__>`.
        view          (ViewBox or PlotItem) If specified, this will be used
                      as the display area that contains the displayed image. 
                      Any :class:`ViewBox <pyqtgraph.ViewBox>`, 
                      :class:`PlotItem <pyqtgraph.PlotItem>`, or other 
                      compatible object is acceptable.
        imageItem     (ImageItem) If specified, this object will be used to
                      display the image. Must be an instance of ImageItem
                      or other compatible object.
        ============= =========================================================
        
        Note: to display axis ticks inside the ImageView, instantiate it 
        with a PlotItem instance as its view::
                
            pg.ImageView(view=pg.PlotItem())
        """
        QtGui.QWidget.__init__(self, parent, *args)
        self.levelMax = 4096
        self.levelMin = 0
        self.name = name
        self.image = None
        self.axes = {}
        self.imageDisp = None
        self.ui = Ui_Form()
        self.ui.setupUi(self)
        self.scene = self.ui.graphicsView.scene()

        self.ignoreTimeLine = False

        if view is None:
            self.view = ViewBox()
        else:
            self.view = view
        self.ui.graphicsView.setCentralItem(self.view)
        self.view.setAspectLocked(True)
        self.view.invertY()

        if imageItem is None:
            self.imageItem = ImageItem()
        else:
            self.imageItem = imageItem
        self.view.addItem(self.imageItem)
        self.currentIndex = 0

        self.ui.histogram.setImageItem(self.imageItem)

        self.menu = None

        self.ui.normGroup.hide()

        self.roi = PlotROI(10)
        self.roi.setZValue(20)
        self.view.addItem(self.roi)
        self.roi.hide()
        self.normRoi = PlotROI(10)
        self.normRoi.setPen('y')
        self.normRoi.setZValue(20)
        self.view.addItem(self.normRoi)
        self.normRoi.hide()
        self.roiCurve = self.ui.roiPlot.plot()
        self.timeLine = InfiniteLine(0, movable=True)
        self.timeLine.setPen((255, 255, 0, 200))
        self.timeLine.setZValue(1)
        self.ui.roiPlot.addItem(self.timeLine)
        self.ui.splitter.setSizes([self.height() - 35, 35])
        self.ui.roiPlot.hideAxis('left')

        self.keysPressed = {}
        self.playTimer = QtCore.QTimer()
        self.playRate = 0
        self.lastPlayTime = 0

        self.normRgn = LinearRegionItem()
        self.normRgn.setZValue(0)
        self.ui.roiPlot.addItem(self.normRgn)
        self.normRgn.hide()

        ## wrap functions from view box
        for fn in ['addItem', 'removeItem']:
            setattr(self, fn, getattr(self.view, fn))

        ## wrap functions from histogram
        for fn in [
                'setHistogramRange', 'autoHistogramRange', 'getLookupTable',
                'getLevels'
        ]:
            setattr(self, fn, getattr(self.ui.histogram, fn))

        self.timeLine.sigPositionChanged.connect(self.timeLineChanged)
        self.ui.roiBtn.clicked.connect(self.roiClicked)
        self.roi.sigRegionChanged.connect(self.roiChanged)
        #self.ui.normBtn.toggled.connect(self.normToggled)
        self.ui.menuBtn.clicked.connect(self.menuClicked)
        self.ui.normDivideRadio.clicked.connect(self.normRadioChanged)
        self.ui.normSubtractRadio.clicked.connect(self.normRadioChanged)
        self.ui.normOffRadio.clicked.connect(self.normRadioChanged)
        self.ui.normROICheck.clicked.connect(self.updateNorm)
        self.ui.normFrameCheck.clicked.connect(self.updateNorm)
        self.ui.normTimeRangeCheck.clicked.connect(self.updateNorm)
        self.playTimer.timeout.connect(self.timeout)

        self.normProxy = SignalProxy(self.normRgn.sigRegionChanged,
                                     slot=self.updateNorm)
        self.normRoi.sigRegionChangeFinished.connect(self.updateNorm)

        self.ui.roiPlot.registerPlot(self.name + '_ROI')
        self.view.register(self.name)

        self.noRepeatKeys = [
            QtCore.Qt.Key_Right, QtCore.Qt.Key_Left, QtCore.Qt.Key_Up,
            QtCore.Qt.Key_Down, QtCore.Qt.Key_PageUp, QtCore.Qt.Key_PageDown
        ]

        self.roiClicked()  ## initialize roi plot to correct shape / visibility

    def setImage(self,
                 img,
                 autoRange=True,
                 autoLevels=True,
                 levels=None,
                 axes=None,
                 xvals=None,
                 pos=None,
                 scale=None,
                 transform=None,
                 autoHistogramRange=True):
        """
        Set the image to be displayed in the widget.
        
        ================== ===========================================================================
        **Arguments:**
        img                (numpy array) the image to be displayed. See :func:`ImageItem.setImage` and
                           *notes* below.
        xvals              (numpy array) 1D array of z-axis values corresponding to the third axis
                           in a 3D image. For video, this array should contain the time of each frame.
        autoRange          (bool) whether to scale/pan the view to fit the image.
        autoLevels         (bool) whether to update the white/black levels to fit the image.
        levels             (min, max); the white and black level values to use.
        axes               Dictionary indicating the interpretation for each axis.
                           This is only needed to override the default guess. Format is::
                       
                               {'t':0, 'x':1, 'y':2, 'c':3};
        
        pos                Change the position of the displayed image
        scale              Change the scale of the displayed image
        transform          Set the transform of the displayed image. This option overrides *pos*
                           and *scale*.
        autoHistogramRange If True, the histogram y-range is automatically scaled to fit the
                           image data.
        ================== ===========================================================================

        **Notes:**        
        
        For backward compatibility, image data is assumed to be in column-major order (column, row).
        However, most image data is stored in row-major order (row, column) and will need to be
        transposed before calling setImage()::
        
            imageview.setImage(imagedata.T)
            
        This requirement can be changed by the ``imageAxisOrder``
        :ref:`global configuration option <apiref_config>`.
        
        """
        profiler = debug.Profiler()

        if hasattr(img, 'implements') and img.implements('MetaArray'):
            img = img.asarray()

        if not isinstance(img, np.ndarray):
            required = ['dtype', 'max', 'min', 'ndim', 'shape', 'size']
            if not all([hasattr(img, attr) for attr in required]):
                raise TypeError(
                    "Image must be NumPy array or any object "
                    "that provides compatible attributes/methods:\n"
                    "  %s" % str(required))

        self.image = img
        self.imageDisp = None

        profiler()

        if axes is None:
            x, y = (0, 1) if self.imageItem.axisOrder == 'col-major' else (1,
                                                                           0)

            if img.ndim == 2:
                self.axes = {'t': None, 'x': x, 'y': y, 'c': None}
            elif img.ndim == 3:
                # Ambiguous case; make a guess
                if img.shape[2] <= 4:
                    self.axes = {'t': None, 'x': x, 'y': y, 'c': 2}
                else:
                    self.axes = {'t': 0, 'x': x + 1, 'y': y + 1, 'c': None}
            elif img.ndim == 4:
                # Even more ambiguous; just assume the default
                self.axes = {'t': 0, 'x': x + 1, 'y': y + 1, 'c': 3}
            else:
                raise Exception("Can not interpret image with dimensions %s" %
                                (str(img.shape)))
        elif isinstance(axes, dict):
            self.axes = axes.copy()
        elif isinstance(axes, list) or isinstance(axes, tuple):
            self.axes = {}
            for i in range(len(axes)):
                self.axes[axes[i]] = i
        else:
            raise Exception(
                "Can not interpret axis specification %s. Must be like {'t': 2, 'x': 0, 'y': 1} or ('t', 'x', 'y', 'c')"
                % (str(axes)))

        for x in ['t', 'x', 'y', 'c']:
            self.axes[x] = self.axes.get(x, None)
        axes = self.axes

        if xvals is not None:
            self.tVals = xvals
        elif axes['t'] is not None:
            if hasattr(img, 'xvals'):
                try:
                    self.tVals = img.xvals(axes['t'])
                except:
                    self.tVals = np.arange(img.shape[axes['t']])
            else:
                self.tVals = np.arange(img.shape[axes['t']])

        profiler()

        self.currentIndex = 0
        self.updateImage(autoHistogramRange=autoHistogramRange)
        if levels is None and autoLevels:
            self.autoLevels()
        if levels is not None:  ## this does nothing since getProcessedImage sets these values again.
            self.setLevels(*levels)

        if self.ui.roiBtn.isChecked():
            self.roiChanged()

        profiler()

        if self.axes['t'] is not None:
            #self.ui.roiPlot.show()
            self.ui.roiPlot.setXRange(self.tVals.min(), self.tVals.max())
            self.timeLine.setValue(0)
            #self.ui.roiPlot.setMouseEnabled(False, False)
            if len(self.tVals) > 1:
                start = self.tVals.min()
                stop = self.tVals.max() + abs(self.tVals[-1] -
                                              self.tVals[0]) * 0.02
            elif len(self.tVals) == 1:
                start = self.tVals[0] - 0.5
                stop = self.tVals[0] + 0.5
            else:
                start = 0
                stop = 1
            for s in [self.timeLine, self.normRgn]:
                s.setBounds([start, stop])
        #else:
        #self.ui.roiPlot.hide()
        profiler()

        self.imageItem.resetTransform()
        if scale is not None:
            self.imageItem.scale(*scale)
        if pos is not None:
            self.imageItem.setPos(*pos)
        if transform is not None:
            self.imageItem.setTransform(transform)

        profiler()

        if autoRange:
            self.autoRange()
        self.roiClicked()

        profiler()

    def clear(self):
        self.image = None
        self.imageItem.clear()

    def play(self, rate):
        """Begin automatically stepping frames forward at the given rate (in fps).
        This can also be accessed by pressing the spacebar."""
        #print "play:", rate
        self.playRate = rate
        if rate == 0:
            self.playTimer.stop()
            return

        self.lastPlayTime = ptime.time()
        if not self.playTimer.isActive():
            self.playTimer.start(16)

    def autoLevels(self):
        """Set the min/max intensity levels automatically to match the image data."""
        self.setLevels(self.levelMin, self.levelMax)

    def setLevels(self, min, max):
        """Set the min/max (bright and dark) levels."""
        self.ui.histogram.setLevels(min, max)

    def autoRange(self):
        """Auto scale and pan the view around the image such that the image fills the view."""
        image = self.getProcessedImage()
        self.view.autoRange()

    def getProcessedImage(self):
        """Returns the image data after it has been processed by any normalization options in use.
        This method also sets the attributes self.levelMin and self.levelMax 
        to indicate the range of data in the image."""
        if self.imageDisp is None:
            image = self.normalize(self.image)
            self.imageDisp = image
            self.levelMin, self.levelMax = list(
                map(float, self.quickMinMax(self.imageDisp)))

        return self.imageDisp

    def close(self):
        """Closes the widget nicely, making sure to clear the graphics scene and release memory."""
        self.ui.roiPlot.close()
        self.ui.graphicsView.close()
        self.scene.clear()
        del self.image
        del self.imageDisp
        super(ImageView, self).close()
        self.setParent(None)

    def keyPressEvent(self, ev):
        #print ev.key()
        if ev.key() == QtCore.Qt.Key_Space:
            if self.playRate == 0:
                fps = (self.getProcessedImage().shape[0] -
                       1) / (self.tVals[-1] - self.tVals[0])
                self.play(fps)
                #print fps
            else:
                self.play(0)
            ev.accept()
        elif ev.key() == QtCore.Qt.Key_Home:
            self.setCurrentIndex(0)
            self.play(0)
            ev.accept()
        elif ev.key() == QtCore.Qt.Key_End:
            self.setCurrentIndex(self.getProcessedImage().shape[0] - 1)
            self.play(0)
            ev.accept()
        elif ev.key() in self.noRepeatKeys:
            ev.accept()
            if ev.isAutoRepeat():
                return
            self.keysPressed[ev.key()] = 1
            self.evalKeyState()
        else:
            QtGui.QWidget.keyPressEvent(self, ev)

    def keyReleaseEvent(self, ev):
        if ev.key() in [
                QtCore.Qt.Key_Space, QtCore.Qt.Key_Home, QtCore.Qt.Key_End
        ]:
            ev.accept()
        elif ev.key() in self.noRepeatKeys:
            ev.accept()
            if ev.isAutoRepeat():
                return
            try:
                del self.keysPressed[ev.key()]
            except:
                self.keysPressed = {}
            self.evalKeyState()
        else:
            QtGui.QWidget.keyReleaseEvent(self, ev)

    def evalKeyState(self):
        if len(self.keysPressed) == 1:
            key = list(self.keysPressed.keys())[0]
            if key == QtCore.Qt.Key_Right:
                self.play(20)
                self.jumpFrames(1)
                self.lastPlayTime = ptime.time(
                ) + 0.2  ## 2ms wait before start
                ## This happens *after* jumpFrames, since it might take longer than 2ms
            elif key == QtCore.Qt.Key_Left:
                self.play(-20)
                self.jumpFrames(-1)
                self.lastPlayTime = ptime.time() + 0.2
            elif key == QtCore.Qt.Key_Up:
                self.play(-100)
            elif key == QtCore.Qt.Key_Down:
                self.play(100)
            elif key == QtCore.Qt.Key_PageUp:
                self.play(-1000)
            elif key == QtCore.Qt.Key_PageDown:
                self.play(1000)
        else:
            self.play(0)

    def timeout(self):
        now = ptime.time()
        dt = now - self.lastPlayTime
        if dt < 0:
            return
        n = int(self.playRate * dt)
        if n != 0:
            self.lastPlayTime += (float(n) / self.playRate)
            if self.currentIndex + n > self.image.shape[0]:
                self.play(0)
            self.jumpFrames(n)

    def setCurrentIndex(self, ind):
        """Set the currently displayed frame index."""
        self.currentIndex = np.clip(
            ind, 0,
            self.getProcessedImage().shape[self.axes['t']] - 1)
        self.updateImage()
        self.ignoreTimeLine = True
        self.timeLine.setValue(self.tVals[self.currentIndex])
        self.ignoreTimeLine = False

    def jumpFrames(self, n):
        """Move video frame ahead n frames (may be negative)"""
        if self.axes['t'] is not None:
            self.setCurrentIndex(self.currentIndex + n)

    def normRadioChanged(self):
        self.imageDisp = None
        self.updateImage()
        self.autoLevels()
        self.roiChanged()
        self.sigProcessingChanged.emit(self)

    def updateNorm(self):
        if self.ui.normTimeRangeCheck.isChecked():
            self.normRgn.show()
        else:
            self.normRgn.hide()

        if self.ui.normROICheck.isChecked():
            self.normRoi.show()
        else:
            self.normRoi.hide()

        if not self.ui.normOffRadio.isChecked():
            self.imageDisp = None
            self.updateImage()
            self.autoLevels()
            self.roiChanged()
            self.sigProcessingChanged.emit(self)

    def normToggled(self, b):
        self.ui.normGroup.setVisible(b)
        self.normRoi.setVisible(b and self.ui.normROICheck.isChecked())
        self.normRgn.setVisible(b and self.ui.normTimeRangeCheck.isChecked())

    def hasTimeAxis(self):
        return 't' in self.axes and self.axes['t'] is not None

    def roiClicked(self):
        showRoiPlot = False
        if self.ui.roiBtn.isChecked():
            showRoiPlot = True
            self.roi.show()
            #self.ui.roiPlot.show()
            self.ui.roiPlot.setMouseEnabled(True, True)
            self.ui.splitter.setSizes(
                [self.height() * 0.6, self.height() * 0.4])
            self.roiCurve.show()
            self.roiChanged()
            self.ui.roiPlot.showAxis('left')
        else:
            self.roi.hide()
            self.ui.roiPlot.setMouseEnabled(False, False)
            self.roiCurve.hide()
            self.ui.roiPlot.hideAxis('left')

        if self.hasTimeAxis():
            showRoiPlot = True
            mn = self.tVals.min()
            mx = self.tVals.max()
            self.ui.roiPlot.setXRange(mn, mx, padding=0.01)
            self.timeLine.show()
            self.timeLine.setBounds([mn, mx])
            self.ui.roiPlot.show()
            if not self.ui.roiBtn.isChecked():
                self.ui.splitter.setSizes([self.height() - 35, 35])
        else:
            self.timeLine.hide()
            #self.ui.roiPlot.hide()

        self.ui.roiPlot.setVisible(showRoiPlot)

    def roiChanged(self):
        if self.image is None:
            return

        image = self.getProcessedImage()
        if image.ndim == 2:
            axes = (0, 1)
        elif image.ndim == 3:
            axes = (1, 2)
        else:
            return

        data, coords = self.roi.getArrayRegion(image.view(np.ndarray),
                                               self.imageItem,
                                               axes,
                                               returnMappedCoords=True)
        if data is not None:
            while data.ndim > 1:
                data = data.mean(axis=1)
            if image.ndim == 3:
                self.roiCurve.setData(y=data, x=self.tVals)
            else:
                while coords.ndim > 2:
                    coords = coords[:, :, 0]
                coords = coords - coords[:, 0, np.newaxis]
                xvals = (coords**2).sum(axis=0)**0.5
                self.roiCurve.setData(y=data, x=xvals)

    def quickMinMax(self, data):
        """
        Estimate the min/max values of *data* by subsampling.
        """
        while data.size > 1e6:
            ax = np.argmax(data.shape)
            sl = [slice(None)] * data.ndim
            sl[ax] = slice(None, None, 2)
            data = data[sl]
        return nanmin(data), nanmax(data)

    def normalize(self, image):
        """
        Process *image* using the normalization options configured in the
        control panel.
        
        This can be repurposed to process any data through the same filter.
        """
        if self.ui.normOffRadio.isChecked():
            return image

        div = self.ui.normDivideRadio.isChecked()
        norm = image.view(np.ndarray).copy()
        #if div:
        #norm = ones(image.shape)
        #else:
        #norm = zeros(image.shape)
        if div:
            norm = norm.astype(np.float32)

        if self.ui.normTimeRangeCheck.isChecked() and image.ndim == 3:
            (sind, start) = self.timeIndex(self.normRgn.lines[0])
            (eind, end) = self.timeIndex(self.normRgn.lines[1])
            #print start, end, sind, eind
            n = image[sind:eind + 1].mean(axis=0)
            n.shape = (1, ) + n.shape
            if div:
                norm /= n
            else:
                norm -= n

        if self.ui.normFrameCheck.isChecked() and image.ndim == 3:
            n = image.mean(axis=1).mean(axis=1)
            n.shape = n.shape + (1, 1)
            if div:
                norm /= n
            else:
                norm -= n

        if self.ui.normROICheck.isChecked() and image.ndim == 3:
            n = self.normRoi.getArrayRegion(norm, self.imageItem,
                                            (1, 2)).mean(axis=1).mean(axis=1)
            n = n[:, np.newaxis, np.newaxis]
            #print start, end, sind, eind
            if div:
                norm /= n
            else:
                norm -= n

        return norm

    def timeLineChanged(self):
        #(ind, time) = self.timeIndex(self.ui.timeSlider)
        if self.ignoreTimeLine:
            return
        self.play(0)
        (ind, time) = self.timeIndex(self.timeLine)
        if ind != self.currentIndex:
            self.currentIndex = ind
            self.updateImage()
        #self.timeLine.setPos(time)
        #self.emit(QtCore.SIGNAL('timeChanged'), ind, time)
        self.sigTimeChanged.emit(ind, time)

    def updateImage(self, autoHistogramRange=True):
        ## Redraw image on screen
        if self.image is None:
            return

        image = self.getProcessedImage()

        if autoHistogramRange:
            self.ui.histogram.setHistogramRange(self.levelMin, self.levelMax)

        # Transpose image into order expected by ImageItem
        if self.imageItem.axisOrder == 'col-major':
            axorder = ['t', 'x', 'y', 'c']
        else:
            axorder = ['t', 'y', 'x', 'c']
        axorder = [
            self.axes[ax] for ax in axorder if self.axes[ax] is not None
        ]
        image = image.transpose(axorder)

        # Select time index
        if self.axes['t'] is not None:
            self.ui.roiPlot.show()
            image = image[self.currentIndex]

        self.imageItem.updateImage(image)

    def timeIndex(self, slider):
        ## Return the time and frame index indicated by a slider
        if self.image is None:
            return (0, 0)

        t = slider.value()

        xv = self.tVals
        if xv is None:
            ind = int(t)
        else:
            if len(xv) < 2:
                return (0, 0)
            totTime = xv[-1] + (xv[-1] - xv[-2])
            inds = np.argwhere(xv < t)
            if len(inds) < 1:
                return (0, t)
            ind = inds[-1, 0]
        return ind, t

    def getView(self):
        """Return the ViewBox (or other compatible object) which displays the ImageItem"""
        return self.view

    def getImageItem(self):
        """Return the ImageItem for this ImageView."""
        return self.imageItem

    def getRoiPlot(self):
        """Return the ROI PlotWidget for this ImageView"""
        return self.ui.roiPlot

    def getHistogramWidget(self):
        """Return the HistogramLUTWidget for this ImageView"""
        return self.ui.histogram

    def export(self, fileName):
        """
        Export data from the ImageView to a file, or to a stack of files if
        the data is 3D. Saving an image stack will result in index numbers
        being added to the file name. Images are saved as they would appear
        onscreen, with levels and lookup table applied.
        """
        img = self.getProcessedImage()
        if self.hasTimeAxis():
            base, ext = os.path.splitext(fileName)
            fmt = "%%s%%0%dd%%s" % int(np.log10(img.shape[0]) + 1)
            for i in range(img.shape[0]):
                self.imageItem.setImage(img[i], autoLevels=False)
                self.imageItem.save(fmt % (base, i, ext))
            self.updateImage()
        else:
            self.imageItem.save(fileName)

    def exportClicked(self):
        fileName = QtGui.QFileDialog.getSaveFileName()
        if fileName == '':
            return
        self.export(fileName)

    def buildMenu(self):
        self.menu = QtGui.QMenu()
        self.normAction = QtGui.QAction("Normalization", self.menu)
        self.normAction.setCheckable(True)
        self.normAction.toggled.connect(self.normToggled)
        self.menu.addAction(self.normAction)
        self.exportAction = QtGui.QAction("Export", self.menu)
        self.exportAction.triggered.connect(self.exportClicked)
        self.menu.addAction(self.exportAction)

    def menuClicked(self):
        if self.menu is None:
            self.buildMenu()
        self.menu.popup(QtGui.QCursor.pos())

    def setColorMap(self, colormap):
        """Set the color map. 

        ============= =========================================================
        **Arguments**
        colormap      (A ColorMap() instance) The ColorMap to use for coloring 
                      images.
        ============= =========================================================
        """
        self.ui.histogram.gradient.setColorMap(colormap)

    @addGradientListToDocstring()
    def setPredefinedGradient(self, name):
        """Set one of the gradients defined in :class:`GradientEditorItem <pyqtgraph.graphicsItems.GradientEditorItem>`.
        Currently available gradients are:   
        """
        self.ui.histogram.gradient.loadPreset(name)
Exemple #5
0
    def __init__(self,
                 parent=None,
                 name="ImageView",
                 view=None,
                 imageItem=None,
                 *args):
        """
        By default, this class creates an :class:`ImageItem <pyqtgraph.ImageItem>` to display image data
        and a :class:`ViewBox <pyqtgraph.ViewBox>` to contain the ImageItem. 
        
        ============= =========================================================
        **Arguments** 
        parent        (QWidget) Specifies the parent widget to which
                      this ImageView will belong. If None, then the ImageView
                      is created with no parent.
        name          (str) The name used to register both the internal ViewBox
                      and the PlotItem used to display ROI data. See the *name*
                      argument to :func:`ViewBox.__init__() 
                      <pyqtgraph.ViewBox.__init__>`.
        view          (ViewBox or PlotItem) If specified, this will be used
                      as the display area that contains the displayed image. 
                      Any :class:`ViewBox <pyqtgraph.ViewBox>`, 
                      :class:`PlotItem <pyqtgraph.PlotItem>`, or other 
                      compatible object is acceptable.
        imageItem     (ImageItem) If specified, this object will be used to
                      display the image. Must be an instance of ImageItem
                      or other compatible object.
        ============= =========================================================
        
        Note: to display axis ticks inside the ImageView, instantiate it 
        with a PlotItem instance as its view::
                
            pg.ImageView(view=pg.PlotItem())
        """
        QtGui.QWidget.__init__(self, parent, *args)
        self.levelMax = 4096
        self.levelMin = 0
        self.name = name
        self.image = None
        self.axes = {}
        self.imageDisp = None
        self.ui = Ui_Form()
        self.ui.setupUi(self)
        self.scene = self.ui.graphicsView.scene()

        self.ignoreTimeLine = False

        if view is None:
            self.view = ViewBox()
        else:
            self.view = view
        self.ui.graphicsView.setCentralItem(self.view)
        self.view.setAspectLocked(True)
        self.view.invertY()

        if imageItem is None:
            self.imageItem = ImageItem()
        else:
            self.imageItem = imageItem
        self.view.addItem(self.imageItem)
        self.currentIndex = 0

        self.ui.histogram.setImageItem(self.imageItem)

        self.menu = None

        self.ui.normGroup.hide()

        self.roi = PlotROI(10)
        self.roi.setZValue(20)
        self.view.addItem(self.roi)
        self.roi.hide()
        self.normRoi = PlotROI(10)
        self.normRoi.setPen('y')
        self.normRoi.setZValue(20)
        self.view.addItem(self.normRoi)
        self.normRoi.hide()
        self.roiCurve = self.ui.roiPlot.plot()
        self.timeLine = InfiniteLine(0, movable=True)
        self.timeLine.setPen((255, 255, 0, 200))
        self.timeLine.setZValue(1)
        self.ui.roiPlot.addItem(self.timeLine)
        self.ui.splitter.setSizes([self.height() - 35, 35])
        self.ui.roiPlot.hideAxis('left')

        self.keysPressed = {}
        self.playTimer = QtCore.QTimer()
        self.playRate = 0
        self.lastPlayTime = 0

        self.normRgn = LinearRegionItem()
        self.normRgn.setZValue(0)
        self.ui.roiPlot.addItem(self.normRgn)
        self.normRgn.hide()

        ## wrap functions from view box
        for fn in ['addItem', 'removeItem']:
            setattr(self, fn, getattr(self.view, fn))

        ## wrap functions from histogram
        for fn in [
                'setHistogramRange', 'autoHistogramRange', 'getLookupTable',
                'getLevels'
        ]:
            setattr(self, fn, getattr(self.ui.histogram, fn))

        self.timeLine.sigPositionChanged.connect(self.timeLineChanged)
        self.ui.roiBtn.clicked.connect(self.roiClicked)
        self.roi.sigRegionChanged.connect(self.roiChanged)
        #self.ui.normBtn.toggled.connect(self.normToggled)
        self.ui.menuBtn.clicked.connect(self.menuClicked)
        self.ui.normDivideRadio.clicked.connect(self.normRadioChanged)
        self.ui.normSubtractRadio.clicked.connect(self.normRadioChanged)
        self.ui.normOffRadio.clicked.connect(self.normRadioChanged)
        self.ui.normROICheck.clicked.connect(self.updateNorm)
        self.ui.normFrameCheck.clicked.connect(self.updateNorm)
        self.ui.normTimeRangeCheck.clicked.connect(self.updateNorm)
        self.playTimer.timeout.connect(self.timeout)

        self.normProxy = SignalProxy(self.normRgn.sigRegionChanged,
                                     slot=self.updateNorm)
        self.normRoi.sigRegionChangeFinished.connect(self.updateNorm)

        self.ui.roiPlot.registerPlot(self.name + '_ROI')
        self.view.register(self.name)

        self.noRepeatKeys = [
            QtCore.Qt.Key_Right, QtCore.Qt.Key_Left, QtCore.Qt.Key_Up,
            QtCore.Qt.Key_Down, QtCore.Qt.Key_PageUp, QtCore.Qt.Key_PageDown
        ]

        self.roiClicked()  ## initialize roi plot to correct shape / visibility
class HistogramLUTItem(GraphicsWidget):
    """
    This is a graphicsWidget which provides controls for adjusting the display of an image.
    Includes:

    - Image histogram 
    - Movable region over histogram to select black/white levels
    - Gradient editor to define color lookup table for single-channel images
    """

    sigLookupTableChanged = QtCore.Signal(object)
    sigLevelsChanged = QtCore.Signal(object)
    sigLevelChangeFinished = QtCore.Signal(object)

    def __init__(self, image=None, fillHistogram=False, orientation='horizontal', autoLevel=None):
        """
        If *image* (ImageItem) is provided, then the control will be automatically linked to the image and changes to the control will be immediately reflected in the image's appearance.
        By default, the histogram is rendered with a fill. For performance, set *fillHistogram* = False.
        """
        GraphicsWidget.__init__(self)
        self.lut = None
        self.imageItem = None
        self.first_image = True
        self.percentageLevel = False
        self.orientation = orientation
        self.autoLevel = autoLevel

        self.layout = QtWidgets.QGraphicsGridLayout()
        self.setLayout(self.layout)
        self.layout.setContentsMargins(1, 1, 1, 1)
        self.layout.setSpacing(0)

        self.vb = ViewBox()

        self.gradient = GradientEditorItem()
        self.gradient.loadPreset('grey')

        if orientation == 'horizontal':
            self.vb.setMouseEnabled(x=True, y=False)
            self.vb.setMaximumHeight(30)
            self.vb.setMinimumHeight(45)
            self.gradient.setOrientation('top')
            self.region = LogarithmRegionItem([0, 1], LinearRegionItem.Vertical)
            self.layout.addItem(self.vb, 1, 0)
            self.layout.addItem(self.gradient, 0, 0)
            self.gradient.setFlag(self.gradient.ItemStacksBehindParent)
            self.vb.setFlag(self.gradient.ItemStacksBehindParent)
        elif orientation == 'vertical':
            self.vb.setMouseEnabled(x=False, y=True)
            self.vb.setMaximumWidth(30)
            self.vb.setMinimumWidth(45)
            self.gradient.setOrientation('right')
            self.region = LogarithmRegionItem([0, 1], LinearRegionItem.Horizontal)
            self.layout.addItem(self.vb, 0, 0)
            self.layout.addItem(self.gradient, 0, 1)

        self.gradient.setFlag(self.gradient.ItemStacksBehindParent)
        self.vb.setFlag(self.gradient.ItemStacksBehindParent)
        self.region.setZValue(1000)
        self.vb.addItem(self.region)
        self.vb.setMenuEnabled(False)

        # self.grid = GridItem()
        # self.vb.addItem(self.grid)

        self.gradient.sigGradientChanged.connect(self.gradientChanged)
        self.region.sigRegionChanged.connect(self.regionChanging)
        self.region.sigRegionChangeFinished.connect(self.regionChanged)

        self.vb.sigRangeChanged.connect(self.viewRangeChanged)
        self.plot = PlotDataItem()
        self.vb.autoRange()
        self.fillHistogram(fillHistogram)
        self.plot.setPen(pg.mkPen(color=(50, 150, 50), size=3))

        self.vb.addItem(self.plot)
        self.autoHistogramRange()

        if image is not None:
            self.setImageItem(image)
            # self.setSizePolicy(QtWidgets.QSizePolicy.Preferred, QtWidgets.QSizePolicy.Expanding)

        self.vb.mouseClickEvent = self.empty_function
        self.vb.mouseDragEvent = self.empty_function
        self.vb.mouseDoubleClickEvent = self.empty_function
        self.vb.wheelEvent = self.empty_function

    def fillHistogram(self, fill=True, level=0.0, color=(100, 100, 200)):
        if fill:
            self.plot.setFillLevel(level)
            self.plot.setFillBrush(color)
        else:
            self.plot.setFillLevel(None)

            # def sizeHint(self, *args):
            # return QtCore.QSizeF(115, 200)

    def paint(self, p, *args):
        pen = self.region.lines[0].pen
        rgn = self.getLevels()
        if self.orientation == 'horizontal':
            p1 = self.vb.mapFromViewToItem(self, Point(rgn[0], self.vb.viewRect().center().y()))
            p2 = self.vb.mapFromViewToItem(self, Point(rgn[1], self.vb.viewRect().center().y()))
            gradRect = self.gradient.mapRectToParent(self.gradient.gradRect.rect())
            for pen in [fn.mkPen('k', width=3), pen]:
                p.setPen(pen)
                p.drawLine(p1, gradRect.bottomLeft())
                p.drawLine(p2, gradRect.bottomRight())
                p.drawLine(gradRect.bottomLeft(), gradRect.topLeft())
                p.drawLine(gradRect.bottomRight(), gradRect.topRight())

        elif self.orientation == 'vertical':
            p1 = self.vb.mapFromViewToItem(self, Point(self.vb.viewRect().center().x(), rgn[0]))
            p2 = self.vb.mapFromViewToItem(self, Point(self.vb.viewRect().center().x(), rgn[1]))
            gradRect = self.gradient.mapRectToParent(self.gradient.gradRect.rect())
            for pen in [fn.mkPen('k', width=3), pen]:
                p.setPen(pen)
                p.drawLine(p1, gradRect.bottomLeft())
                p.drawLine(p2, gradRect.topLeft())
                p.drawLine(gradRect.topLeft(), gradRect.topRight())
                p.drawLine(gradRect.bottomLeft(), gradRect.bottomRight())

    def setHistogramRange(self, mn, mx, padding=0.1):
        """Set the Y range on the histogram plot. This disables auto-scaling."""
        self.vb.enableAutoRange(self.vb.YAxis, False)
        if self.orientation == 'horizontal':
            self.vb.setXRange(mn, mx, padding)
        elif self.orientation == 'vertical':
            self.vb.setYrange(mn, mx, padding)
            # mn -= d*padding
            # mx += d*padding
            # self.range = [mn,mx]
            # self.updateRange()
            # self.vb.setMouseEnabled(False, True)
            # self.region.setBounds([mn,mx])

    def autoHistogramRange(self):
        """Enable auto-scaling on the histogram plot."""
        self.vb.enableAutoRange(self.vb.XAxis, True)
        self.vb.enableAutoRange(self.vb.YAxis, True)
        # self.range = None
        # self.updateRange()
        # self.vb.setMouseEnabled(False, False)

        # def updateRange(self):
        # self.vb.autoRange()
        # if self.range is not None:
        # self.vb.setYRange(*self.range)
        # vr = self.vb.viewRect()

        # self.region.setBounds([vr.top(), vr.bottom()])

    def setImageItem(self, img):
        self.imageItem = img
        img.sigImageChanged.connect(self.imageChanged)
        img.setLookupTable(self.getLookupTable)  ## send function pointer, not the result
        # self.gradientChanged()
        self.regionChanged()
        self.imageChanged()
        # self.vb.autoRange()

    def gradientChanged(self):
        if self.imageItem is not None:
            if self.gradient.isLookupTrivial():
                self.imageItem.setLookupTable(None)  # lambda x: x.astype(np.uint8))
            else:
                self.imageItem.setLookupTable(self.getLookupTable)  ## send function pointer, not the result

        self.lut = None
        # if self.imageItem is not None:
        # self.imageItem.setLookupTable(self.gradient.getLookupTable(512))
        self.sigLookupTableChanged.emit(self)

    def getLookupTable(self, img=None, n=None, alpha=None):
        if n is None:
            if img.dtype == np.uint8:
                n = 256
            else:
                n = 512
        if self.lut is None:
            self.lut = self.gradient.getLookupTable(n, alpha=alpha)
        return self.lut

    def regionChanged(self):
        self.sigLevelChangeFinished.emit(self)

    def regionChanging(self):
        if self.imageItem is not None:
            self.imageItem.setLevels(np.exp(self.region.getRegion()))
        self.sigLevelsChanged.emit(self)
        self.update()

    def imageChanged(self, autoRange=False):
        hist_x, hist_y = list(self.imageItem.getHistogram(bins=3000))

        if hist_x is None:
            return

        hist_x, hist_y = np.array(hist_x), np.array(hist_y)

        hist_x = hist_x[np.where(hist_y>0)]
        hist_y = hist_y[np.where(hist_y>0)]

        self.hist_x = hist_x
        self.hist_y = hist_y

        hist_y_log = np.log(hist_y[1:])
        hist_x_log = np.log(hist_x[1:])

        if self.orientation == 'horizontal':
            self.plot.setData(hist_x_log, hist_y_log)
        elif self.orientation == 'vertical':
            self.plot.setData(hist_y_log, hist_x_log)

    def getLevels(self):
        return self.region.getRegion()

    def getExpLevels(self):
        rgn = self.getLevels()
        return np.exp(rgn[0]), np.exp(rgn[1])

    def setLevels(self, mn, mx):
        self.region.setRegion([mn, mx])
        if self.imageItem is not None:
            self.imageItem.setLevels(np.exp(self.region.getRegion()))

    def empty_function(self, *args):
        pass
    def __init__(self, image=None, fillHistogram=False, orientation='horizontal', autoLevel=None):
        """
        If *image* (ImageItem) is provided, then the control will be automatically linked to the image and changes to the control will be immediately reflected in the image's appearance.
        By default, the histogram is rendered with a fill. For performance, set *fillHistogram* = False.
        """
        GraphicsWidget.__init__(self)
        self.lut = None
        self.imageItem = None
        self.first_image = True
        self.percentageLevel = False
        self.orientation = orientation
        self.autoLevel = autoLevel

        self.layout = QtWidgets.QGraphicsGridLayout()
        self.setLayout(self.layout)
        self.layout.setContentsMargins(1, 1, 1, 1)
        self.layout.setSpacing(0)

        self.vb = ViewBox()

        self.gradient = GradientEditorItem()
        self.gradient.loadPreset('grey')

        if orientation == 'horizontal':
            self.vb.setMouseEnabled(x=True, y=False)
            self.vb.setMaximumHeight(30)
            self.vb.setMinimumHeight(45)
            self.gradient.setOrientation('top')
            self.region = LogarithmRegionItem([0, 1], LinearRegionItem.Vertical)
            self.layout.addItem(self.vb, 1, 0)
            self.layout.addItem(self.gradient, 0, 0)
            self.gradient.setFlag(self.gradient.ItemStacksBehindParent)
            self.vb.setFlag(self.gradient.ItemStacksBehindParent)
        elif orientation == 'vertical':
            self.vb.setMouseEnabled(x=False, y=True)
            self.vb.setMaximumWidth(30)
            self.vb.setMinimumWidth(45)
            self.gradient.setOrientation('right')
            self.region = LogarithmRegionItem([0, 1], LinearRegionItem.Horizontal)
            self.layout.addItem(self.vb, 0, 0)
            self.layout.addItem(self.gradient, 0, 1)

        self.gradient.setFlag(self.gradient.ItemStacksBehindParent)
        self.vb.setFlag(self.gradient.ItemStacksBehindParent)
        self.region.setZValue(1000)
        self.vb.addItem(self.region)
        self.vb.setMenuEnabled(False)

        # self.grid = GridItem()
        # self.vb.addItem(self.grid)

        self.gradient.sigGradientChanged.connect(self.gradientChanged)
        self.region.sigRegionChanged.connect(self.regionChanging)
        self.region.sigRegionChangeFinished.connect(self.regionChanged)

        self.vb.sigRangeChanged.connect(self.viewRangeChanged)
        self.plot = PlotDataItem()
        self.vb.autoRange()
        self.fillHistogram(fillHistogram)
        self.plot.setPen(pg.mkPen(color=(50, 150, 50), size=3))

        self.vb.addItem(self.plot)
        self.autoHistogramRange()

        if image is not None:
            self.setImageItem(image)
            # self.setSizePolicy(QtWidgets.QSizePolicy.Preferred, QtWidgets.QSizePolicy.Expanding)

        self.vb.mouseClickEvent = self.empty_function
        self.vb.mouseDragEvent = self.empty_function
        self.vb.mouseDoubleClickEvent = self.empty_function
        self.vb.wheelEvent = self.empty_function
Exemple #8
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class ImageView(QtGui.QWidget):
    """
    Widget used for display and analysis of image data.
    Implements many features:
    
    * Displays 2D and 3D image data. For 3D data, a z-axis
      slider is displayed allowing the user to select which frame is displayed.
    * Displays histogram of image data with movable region defining the dark/light levels
    * Editable gradient provides a color lookup table 
    * Frame slider may also be moved using left/right arrow keys as well as pgup, pgdn, home, and end.
    * Basic analysis features including:
    
        * ROI and embedded plot for measuring image values across frames
        * Image normalization / background subtraction 
    
    Basic Usage::
    
        imv = pg.ImageView()
        imv.show()
        imv.setImage(data)
    """
    sigTimeChanged = QtCore.Signal(object, object)
    sigProcessingChanged = QtCore.Signal(object)
    
    def __init__(self, parent=None, name="ImageView", *args):
        QtGui.QWidget.__init__(self, parent, *args)
        self.levelMax = 4096
        self.levelMin = 0
        self.name = name
        self.image = None
        self.axes = {}
        self.imageDisp = None
        self.ui = Ui_Form()
        self.ui.setupUi(self)
        self.scene = self.ui.graphicsView.scene()
        
        self.ignoreTimeLine = False
        
        #if 'linux' in sys.platform.lower():   ## Stupid GL bug in linux.
        #    self.ui.graphicsView.setViewport(QtGui.QWidget())
        
        #self.ui.graphicsView.enableMouse(True)
        #self.ui.graphicsView.autoPixelRange = False
        #self.ui.graphicsView.setAspectLocked(True)
        #self.ui.graphicsView.invertY()
        #self.ui.graphicsView.enableMouse()
        self.view = ViewBox()
        self.ui.graphicsView.setCentralItem(self.view)
        self.view.setAspectLocked(True)
        self.view.invertY()
        
        #self.ticks = [t[0] for t in self.ui.gradientWidget.listTicks()]
        #self.ticks[0].colorChangeAllowed = False
        #self.ticks[1].colorChangeAllowed = False
        #self.ui.gradientWidget.allowAdd = False
        #self.ui.gradientWidget.setTickColor(self.ticks[1], QtGui.QColor(255,255,255))
        #self.ui.gradientWidget.setOrientation('right')
        
        self.imageItem = ImageItem()
        self.view.addItem(self.imageItem)
        self.currentIndex = 0
        
        self.ui.histogram.setImageItem(self.imageItem)
        
        self.ui.normGroup.hide()

        self.roi = PlotROI(10)
        self.roi.setZValue(20)
        self.view.addItem(self.roi)
        self.roi.hide()
        self.normRoi = PlotROI(10)
        self.normRoi.setPen(QtGui.QPen(QtGui.QColor(255,255,0)))
        self.normRoi.setZValue(20)
        self.view.addItem(self.normRoi)
        self.normRoi.hide()
        #self.ui.roiPlot.hide()
        self.roiCurve = self.ui.roiPlot.plot()
        self.timeLine = InfiniteLine(0, movable=True)
        self.timeLine.setPen(QtGui.QPen(QtGui.QColor(255, 255, 0, 200)))
        self.timeLine.setZValue(1)
        self.ui.roiPlot.addItem(self.timeLine)
        self.ui.splitter.setSizes([self.height()-35, 35])
        self.ui.roiPlot.hideAxis('left')
        
        self.keysPressed = {}
        self.playTimer = QtCore.QTimer()
        self.playRate = 0
        self.lastPlayTime = 0
        
        #self.normLines = []
        #for i in [0,1]:
            #l = InfiniteLine(self.ui.roiPlot, 0)
            #l.setPen(QtGui.QPen(QtGui.QColor(0, 100, 200, 200)))
            #self.ui.roiPlot.addItem(l)
            #self.normLines.append(l)
            #l.hide()
        self.normRgn = LinearRegionItem()
        self.normRgn.setZValue(0)
        self.ui.roiPlot.addItem(self.normRgn)
        self.normRgn.hide()
            
        ## wrap functions from view box
        for fn in ['addItem', 'removeItem']:
            setattr(self, fn, getattr(self.view, fn))

        ## wrap functions from histogram
        for fn in ['setHistogramRange', 'autoHistogramRange', 'getLookupTable', 'getLevels']:
            setattr(self, fn, getattr(self.ui.histogram, fn))

        self.timeLine.sigPositionChanged.connect(self.timeLineChanged)
        #self.ui.gradientWidget.sigGradientChanged.connect(self.updateImage)
        self.ui.roiBtn.clicked.connect(self.roiClicked)
        self.roi.sigRegionChanged.connect(self.roiChanged)
        self.ui.normBtn.toggled.connect(self.normToggled)
        self.ui.normDivideRadio.clicked.connect(self.normRadioChanged)
        self.ui.normSubtractRadio.clicked.connect(self.normRadioChanged)
        self.ui.normOffRadio.clicked.connect(self.normRadioChanged)
        self.ui.normROICheck.clicked.connect(self.updateNorm)
        self.ui.normFrameCheck.clicked.connect(self.updateNorm)
        self.ui.normTimeRangeCheck.clicked.connect(self.updateNorm)
        self.playTimer.timeout.connect(self.timeout)
        
        self.normProxy = SignalProxy(self.normRgn.sigRegionChanged, slot=self.updateNorm)
        self.normRoi.sigRegionChangeFinished.connect(self.updateNorm)
        
        self.ui.roiPlot.registerPlot(self.name + '_ROI')
        
        self.noRepeatKeys = [QtCore.Qt.Key_Right, QtCore.Qt.Key_Left, QtCore.Qt.Key_Up, QtCore.Qt.Key_Down, QtCore.Qt.Key_PageUp, QtCore.Qt.Key_PageDown]
        
        
        self.roiClicked() ## initialize roi plot to correct shape / visibility

    def setImage(self, img, autoRange=True, autoLevels=True, levels=None, axes=None, xvals=None, pos=None, scale=None):
        """
        Set the image to be displayed in the widget.
        
        ============== =======================================================================
        **Arguments:**
        *img*          (numpy array) the image to be displayed.
        *xvals*        (numpy array) 1D array of z-axis values corresponding to the third axis
                       in a 3D image. For video, this array should contain the time of each frame.
        *autoRange*    (bool) whether to scale/pan the view to fit the image.
        *autoLevels*   (bool) whether to update the white/black levels to fit the image.
        *levels*       (min, max); the white and black level values to use.
        *axes*         Dictionary indicating the interpretation for each axis.
                       This is only needed to override the default guess. Format is::
                       
                           {'t':0, 'x':1, 'y':2, 'c':3}; 
        ============== =======================================================================
        """
        prof = debug.Profiler('ImageView.setImage', disabled=True)
        
        if not isinstance(img, np.ndarray):
            raise Exception("Image must be specified as ndarray.")
        self.image = img
        
        if xvals is not None:
            self.tVals = xvals
        elif hasattr(img, 'xvals'):
            try:
                self.tVals = img.xvals(0)
            except:
                self.tVals = np.arange(img.shape[0])
        else:
            self.tVals = np.arange(img.shape[0])
        #self.ui.timeSlider.setValue(0)
        #self.ui.normStartSlider.setValue(0)
        #self.ui.timeSlider.setMaximum(img.shape[0]-1)
        prof.mark('1')
        
        if axes is None:
            if img.ndim == 2:
                self.axes = {'t': None, 'x': 0, 'y': 1, 'c': None}
            elif img.ndim == 3:
                if img.shape[2] <= 4:
                    self.axes = {'t': None, 'x': 0, 'y': 1, 'c': 2}
                else:
                    self.axes = {'t': 0, 'x': 1, 'y': 2, 'c': None}
            elif img.ndim == 4:
                self.axes = {'t': 0, 'x': 1, 'y': 2, 'c': 3}
            else:
                raise Exception("Can not interpret image with dimensions %s" % (str(img.shape)))
        elif isinstance(axes, dict):
            self.axes = axes.copy()
        elif isinstance(axes, list) or isinstance(axes, tuple):
            self.axes = {}
            for i in range(len(axes)):
                self.axes[axes[i]] = i
        else:
            raise Exception("Can not interpret axis specification %s. Must be like {'t': 2, 'x': 0, 'y': 1} or ('t', 'x', 'y', 'c')" % (str(axes)))
            
        for x in ['t', 'x', 'y', 'c']:
            self.axes[x] = self.axes.get(x, None)
        prof.mark('2')
            
        self.imageDisp = None
        
        
        prof.mark('3')
            
        self.currentIndex = 0
        self.updateImage()
        if levels is None and autoLevels:
            self.autoLevels()
        if levels is not None:  ## this does nothing since getProcessedImage sets these values again.
            self.levelMax = levels[1]
            self.levelMin = levels[0]
            
        if self.ui.roiBtn.isChecked():
            self.roiChanged()
        prof.mark('4')
            
            
        if self.axes['t'] is not None:
            #self.ui.roiPlot.show()
            self.ui.roiPlot.setXRange(self.tVals.min(), self.tVals.max())
            self.timeLine.setValue(0)
            #self.ui.roiPlot.setMouseEnabled(False, False)
            if len(self.tVals) > 1:
                start = self.tVals.min()
                stop = self.tVals.max() + abs(self.tVals[-1] - self.tVals[0]) * 0.02
            elif len(self.tVals) == 1:
                start = self.tVals[0] - 0.5
                stop = self.tVals[0] + 0.5
            else:
                start = 0
                stop = 1
            for s in [self.timeLine, self.normRgn]:
                s.setBounds([start, stop])
        #else:
            #self.ui.roiPlot.hide()
        prof.mark('5')
            
        self.imageItem.resetTransform()
        if scale is not None:
            self.imageItem.scale(*scale)
        if pos is not None:
            self.imageItem.setPos(*pos)
        prof.mark('6')
            
        if autoRange:
            self.autoRange()
        self.roiClicked()
        prof.mark('7')
        prof.finish()

        
    def play(self, rate):
        """Begin automatically stepping frames forward at the given rate (in fps).
        This can also be accessed by pressing the spacebar."""
        #print "play:", rate
        self.playRate = rate
        if rate == 0:
            self.playTimer.stop()
            return
            
        self.lastPlayTime = ptime.time()
        if not self.playTimer.isActive():
            self.playTimer.start(16)
            
        

    def autoLevels(self):
        """Set the min/max levels automatically to match the image data."""
        #image = self.getProcessedImage()
        self.setLevels(self.levelMin, self.levelMax)
        
        #self.ui.histogram.imageChanged(autoLevel=True)
            

    def setLevels(self, min, max):
        """Set the min/max (bright and dark) levels."""
        self.ui.histogram.setLevels(min, max)

    def autoRange(self):
        """Auto scale and pan the view around the image."""
        image = self.getProcessedImage()
        
        #self.ui.graphicsView.setRange(QtCore.QRectF(0, 0, image.shape[self.axes['x']], image.shape[self.axes['y']]), padding=0., lockAspect=True)        
        self.view.setRange(self.imageItem.boundingRect(), padding=0.)
        
    def getProcessedImage(self):
        """Returns the image data after it has been processed by any normalization options in use."""
        if self.imageDisp is None:
            image = self.normalize(self.image)
            self.imageDisp = image
            self.levelMin, self.levelMax = map(float, ImageView.quickMinMax(self.imageDisp))
            self.ui.histogram.setHistogramRange(self.levelMin, self.levelMax)
            
        return self.imageDisp
        
        
    def close(self):
        """Closes the widget nicely, making sure to clear the graphics scene and release memory."""
        self.ui.roiPlot.close()
        self.ui.graphicsView.close()
        #self.ui.gradientWidget.sigGradientChanged.disconnect(self.updateImage)
        self.scene.clear()
        del self.image
        del self.imageDisp
        self.setParent(None)
        
    def keyPressEvent(self, ev):
        #print ev.key()
        if ev.key() == QtCore.Qt.Key_Space:
            if self.playRate == 0:
                fps = (self.getProcessedImage().shape[0]-1) / (self.tVals[-1] - self.tVals[0])
                self.play(fps)
                #print fps
            else:
                self.play(0)
            ev.accept()
        elif ev.key() == QtCore.Qt.Key_Home:
            self.setCurrentIndex(0)
            self.play(0)
            ev.accept()
        elif ev.key() == QtCore.Qt.Key_End:
            self.setCurrentIndex(self.getProcessedImage().shape[0]-1)
            self.play(0)
            ev.accept()
        elif ev.key() in self.noRepeatKeys:
            ev.accept()
            if ev.isAutoRepeat():
                return
            self.keysPressed[ev.key()] = 1
            self.evalKeyState()
        else:
            QtGui.QWidget.keyPressEvent(self, ev)

    def keyReleaseEvent(self, ev):
        if ev.key() in [QtCore.Qt.Key_Space, QtCore.Qt.Key_Home, QtCore.Qt.Key_End]:
            ev.accept()
        elif ev.key() in self.noRepeatKeys:
            ev.accept()
            if ev.isAutoRepeat():
                return
            try:
                del self.keysPressed[ev.key()]
            except:
                self.keysPressed = {}
            self.evalKeyState()
        else:
            QtGui.QWidget.keyReleaseEvent(self, ev)
        
        
    def evalKeyState(self):
        if len(self.keysPressed) == 1:
            key = self.keysPressed.keys()[0]
            if key == QtCore.Qt.Key_Right:
                self.play(20)
                self.jumpFrames(1)
                self.lastPlayTime = ptime.time() + 0.2  ## 2ms wait before start
                                                        ## This happens *after* jumpFrames, since it might take longer than 2ms
            elif key == QtCore.Qt.Key_Left:
                self.play(-20)
                self.jumpFrames(-1)
                self.lastPlayTime = ptime.time() + 0.2
            elif key == QtCore.Qt.Key_Up:
                self.play(-100)
            elif key == QtCore.Qt.Key_Down:
                self.play(100)
            elif key == QtCore.Qt.Key_PageUp:
                self.play(-1000)
            elif key == QtCore.Qt.Key_PageDown:
                self.play(1000)
        else:
            self.play(0)
        
        
    def timeout(self):
        now = ptime.time()
        dt = now - self.lastPlayTime
        if dt < 0:
            return
        n = int(self.playRate * dt)
        #print n, dt
        if n != 0:
            #print n, dt, self.lastPlayTime
            self.lastPlayTime += (float(n)/self.playRate)
            if self.currentIndex+n > self.image.shape[0]:
                self.play(0)
            self.jumpFrames(n)
        
    def setCurrentIndex(self, ind):
        """Set the currently displayed frame index."""
        self.currentIndex = np.clip(ind, 0, self.getProcessedImage().shape[0]-1)
        self.updateImage()
        self.ignoreTimeLine = True
        self.timeLine.setValue(self.tVals[self.currentIndex])
        self.ignoreTimeLine = False

    def jumpFrames(self, n):
        """Move video frame ahead n frames (may be negative)"""
        if self.axes['t'] is not None:
            self.setCurrentIndex(self.currentIndex + n)

    def normRadioChanged(self):
        self.imageDisp = None
        self.updateImage()
        self.roiChanged()
        self.sigProcessingChanged.emit(self)
        
    
    def updateNorm(self):
        #for l, sl in zip(self.normLines, [self.ui.normStartSlider, self.ui.normStopSlider]):
            #if self.ui.normTimeRangeCheck.isChecked():
                #l.show()
            #else:
                #l.hide()
            
            #i, t = self.timeIndex(sl)
            #l.setPos(t)
        
        if self.ui.normTimeRangeCheck.isChecked():
            #print "show!"
            self.normRgn.show()
        else:
            self.normRgn.hide()
        
        if self.ui.normROICheck.isChecked():
            #print "show!"
            self.normRoi.show()
        else:
            self.normRoi.hide()
        
        if not self.ui.normOffRadio.isChecked():
            self.imageDisp = None
            self.updateImage()
            self.roiChanged()
            self.sigProcessingChanged.emit(self)

    def normToggled(self, b):
        self.ui.normGroup.setVisible(b)
        self.normRoi.setVisible(b and self.ui.normROICheck.isChecked())
        self.normRgn.setVisible(b and self.ui.normTimeRangeCheck.isChecked())

    def hasTimeAxis(self):
        return 't' in self.axes and self.axes['t'] is not None

    def roiClicked(self):
        showRoiPlot = False
        if self.ui.roiBtn.isChecked():
            showRoiPlot = True
            self.roi.show()
            #self.ui.roiPlot.show()
            self.ui.roiPlot.setMouseEnabled(True, True)
            self.ui.splitter.setSizes([self.height()*0.6, self.height()*0.4])
            self.roiCurve.show()
            self.roiChanged()
            self.ui.roiPlot.showAxis('left')
        else:
            self.roi.hide()
            self.ui.roiPlot.setMouseEnabled(False, False)
            self.roiCurve.hide()
            self.ui.roiPlot.hideAxis('left')
            
        if self.hasTimeAxis():
            showRoiPlot = True
            mn = self.tVals.min()
            mx = self.tVals.max()
            self.ui.roiPlot.setXRange(mn, mx, padding=0.01)
            self.timeLine.show()
            self.timeLine.setBounds([mn, mx])
            self.ui.roiPlot.show()
            if not self.ui.roiBtn.isChecked():
                self.ui.splitter.setSizes([self.height()-35, 35])
        else:
            self.timeLine.hide()
            #self.ui.roiPlot.hide()
            
        self.ui.roiPlot.setVisible(showRoiPlot)

    def roiChanged(self):
        if self.image is None:
            return
            
        image = self.getProcessedImage()
        if image.ndim == 2:
            axes = (0, 1)
        elif image.ndim == 3:
            axes = (1, 2)
        else:
            return
        data = self.roi.getArrayRegion(image.view(np.ndarray), self.imageItem, axes)
        if data is not None:
            while data.ndim > 1:
                data = data.mean(axis=1)
            if image.ndim == 3:
                self.roiCurve.setData(y=data, x=self.tVals)
            else:
                self.roiCurve.setData(y=data, x=range(len(data)))
                
            #self.ui.roiPlot.replot()


    @staticmethod
    def quickMinMax(data):
        while data.size > 1e6:
            ax = np.argmax(data.shape)
            sl = [slice(None)] * data.ndim
            sl[ax] = slice(None, None, 2)
            data = data[sl]
        return data.min(), data.max()

    def normalize(self, image):
        
        if self.ui.normOffRadio.isChecked():
            return image
            
        div = self.ui.normDivideRadio.isChecked()
        norm = image.view(np.ndarray).copy()
        #if div:
            #norm = ones(image.shape)
        #else:
            #norm = zeros(image.shape)
        if div:
            norm = norm.astype(np.float32)
            
        if self.ui.normTimeRangeCheck.isChecked() and image.ndim == 3:
            (sind, start) = self.timeIndex(self.normRgn.lines[0])
            (eind, end) = self.timeIndex(self.normRgn.lines[1])
            #print start, end, sind, eind
            n = image[sind:eind+1].mean(axis=0)
            n.shape = (1,) + n.shape
            if div:
                norm /= n
            else:
                norm -= n
                
        if self.ui.normFrameCheck.isChecked() and image.ndim == 3:
            n = image.mean(axis=1).mean(axis=1)
            n.shape = n.shape + (1, 1)
            if div:
                norm /= n
            else:
                norm -= n
            
        if self.ui.normROICheck.isChecked() and image.ndim == 3:
            n = self.normRoi.getArrayRegion(norm, self.imageItem, (1, 2)).mean(axis=1).mean(axis=1)
            n = n[:,np.newaxis,np.newaxis]
            #print start, end, sind, eind
            if div:
                norm /= n
            else:
                norm -= n
                
        return norm
        
    def timeLineChanged(self):
        #(ind, time) = self.timeIndex(self.ui.timeSlider)
        if self.ignoreTimeLine:
            return
        self.play(0)
        (ind, time) = self.timeIndex(self.timeLine)
        if ind != self.currentIndex:
            self.currentIndex = ind
            self.updateImage()
        #self.timeLine.setPos(time)
        #self.emit(QtCore.SIGNAL('timeChanged'), ind, time)
        self.sigTimeChanged.emit(ind, time)

    def updateImage(self):
        ## Redraw image on screen
        if self.image is None:
            return
            
        image = self.getProcessedImage()
        #print "update:", image.ndim, image.max(), image.min(), self.blackLevel(), self.whiteLevel()
        if self.axes['t'] is None:
            #self.ui.timeSlider.hide()
            self.imageItem.updateImage(image)
            #self.ui.roiPlot.hide()
            #self.ui.roiBtn.hide()
        else:
            #self.ui.roiBtn.show()
            self.ui.roiPlot.show()
            #self.ui.timeSlider.show()
            self.imageItem.updateImage(image[self.currentIndex])
            
            
    def timeIndex(self, slider):
        ## Return the time and frame index indicated by a slider
        if self.image is None:
            return (0,0)
        #v = slider.value()
        #vmax = slider.maximum()
        #f = float(v) / vmax
        
        t = slider.value()
        
        #t = 0.0
        #xv = self.image.xvals('Time') 
        xv = self.tVals
        if xv is None:
            ind = int(t)
            #ind = int(f * self.image.shape[0])
        else:
            if len(xv) < 2:
                return (0,0)
            totTime = xv[-1] + (xv[-1]-xv[-2])
            #t = f * totTime
            inds = np.argwhere(xv < t)
            if len(inds) < 1:
                return (0,t)
            ind = inds[-1,0]
        #print ind
        return ind, t
Exemple #9
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    def __init__(self, parent=None, name="ImageView", *args):
        QtGui.QWidget.__init__(self, parent, *args)
        self.levelMax = 4096
        self.levelMin = 0
        self.name = name
        self.image = None
        self.axes = {}
        self.imageDisp = None
        self.ui = Ui_Form()
        self.ui.setupUi(self)
        self.scene = self.ui.graphicsView.scene()
        
        self.ignoreTimeLine = False
        
        #if 'linux' in sys.platform.lower():   ## Stupid GL bug in linux.
        #    self.ui.graphicsView.setViewport(QtGui.QWidget())
        
        #self.ui.graphicsView.enableMouse(True)
        #self.ui.graphicsView.autoPixelRange = False
        #self.ui.graphicsView.setAspectLocked(True)
        #self.ui.graphicsView.invertY()
        #self.ui.graphicsView.enableMouse()
        self.view = ViewBox()
        self.ui.graphicsView.setCentralItem(self.view)
        self.view.setAspectLocked(True)
        self.view.invertY()
        
        #self.ticks = [t[0] for t in self.ui.gradientWidget.listTicks()]
        #self.ticks[0].colorChangeAllowed = False
        #self.ticks[1].colorChangeAllowed = False
        #self.ui.gradientWidget.allowAdd = False
        #self.ui.gradientWidget.setTickColor(self.ticks[1], QtGui.QColor(255,255,255))
        #self.ui.gradientWidget.setOrientation('right')
        
        self.imageItem = ImageItem()
        self.view.addItem(self.imageItem)
        self.currentIndex = 0
        
        self.ui.histogram.setImageItem(self.imageItem)
        
        self.ui.normGroup.hide()

        self.roi = PlotROI(10)
        self.roi.setZValue(20)
        self.view.addItem(self.roi)
        self.roi.hide()
        self.normRoi = PlotROI(10)
        self.normRoi.setPen(QtGui.QPen(QtGui.QColor(255,255,0)))
        self.normRoi.setZValue(20)
        self.view.addItem(self.normRoi)
        self.normRoi.hide()
        #self.ui.roiPlot.hide()
        self.roiCurve = self.ui.roiPlot.plot()
        self.timeLine = InfiniteLine(0, movable=True)
        self.timeLine.setPen(QtGui.QPen(QtGui.QColor(255, 255, 0, 200)))
        self.timeLine.setZValue(1)
        self.ui.roiPlot.addItem(self.timeLine)
        self.ui.splitter.setSizes([self.height()-35, 35])
        self.ui.roiPlot.hideAxis('left')
        
        self.keysPressed = {}
        self.playTimer = QtCore.QTimer()
        self.playRate = 0
        self.lastPlayTime = 0
        
        #self.normLines = []
        #for i in [0,1]:
            #l = InfiniteLine(self.ui.roiPlot, 0)
            #l.setPen(QtGui.QPen(QtGui.QColor(0, 100, 200, 200)))
            #self.ui.roiPlot.addItem(l)
            #self.normLines.append(l)
            #l.hide()
        self.normRgn = LinearRegionItem()
        self.normRgn.setZValue(0)
        self.ui.roiPlot.addItem(self.normRgn)
        self.normRgn.hide()
            
        ## wrap functions from view box
        for fn in ['addItem', 'removeItem']:
            setattr(self, fn, getattr(self.view, fn))

        ## wrap functions from histogram
        for fn in ['setHistogramRange', 'autoHistogramRange', 'getLookupTable', 'getLevels']:
            setattr(self, fn, getattr(self.ui.histogram, fn))

        self.timeLine.sigPositionChanged.connect(self.timeLineChanged)
        #self.ui.gradientWidget.sigGradientChanged.connect(self.updateImage)
        self.ui.roiBtn.clicked.connect(self.roiClicked)
        self.roi.sigRegionChanged.connect(self.roiChanged)
        self.ui.normBtn.toggled.connect(self.normToggled)
        self.ui.normDivideRadio.clicked.connect(self.normRadioChanged)
        self.ui.normSubtractRadio.clicked.connect(self.normRadioChanged)
        self.ui.normOffRadio.clicked.connect(self.normRadioChanged)
        self.ui.normROICheck.clicked.connect(self.updateNorm)
        self.ui.normFrameCheck.clicked.connect(self.updateNorm)
        self.ui.normTimeRangeCheck.clicked.connect(self.updateNorm)
        self.playTimer.timeout.connect(self.timeout)
        
        self.normProxy = SignalProxy(self.normRgn.sigRegionChanged, slot=self.updateNorm)
        self.normRoi.sigRegionChangeFinished.connect(self.updateNorm)
        
        self.ui.roiPlot.registerPlot(self.name + '_ROI')
        
        self.noRepeatKeys = [QtCore.Qt.Key_Right, QtCore.Qt.Key_Left, QtCore.Qt.Key_Up, QtCore.Qt.Key_Down, QtCore.Qt.Key_PageUp, QtCore.Qt.Key_PageDown]
        
        
        self.roiClicked() ## initialize roi plot to correct shape / visibility
Exemple #10
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    def __init__(self, parent=None, name="ImageView", view=None, imageItem=None, *args):
        """
        By default, this class creates an :class:`ImageItem <pyqtgraph.ImageItem>` to display image data
        and a :class:`ViewBox <pyqtgraph.ViewBox>` to contain the ImageItem. Custom items may be given instead 
        by specifying the *view* and/or *imageItem* arguments.
        """
        QtGui.QWidget.__init__(self, parent, *args)
        self.levelMax = 4096
        self.levelMin = 0
        self.name = name
        self.image = None
        self.axes = {}
        self.imageDisp = None
        self.ui = Ui_Form()
        self.ui.setupUi(self)
        self.scene = self.ui.graphicsView.scene()
        
        self.ignoreTimeLine = False
        
        if view is None:
            self.view = ViewBox()
        else:
            self.view = view
        self.ui.graphicsView.setCentralItem(self.view)
        self.view.setAspectLocked(True)
        self.view.invertY()
        
        if imageItem is None:
            self.imageItem = ImageItem()
        else:
            self.imageItem = imageItem
        self.view.addItem(self.imageItem)
        self.currentIndex = 0
        
        self.ui.histogram.setImageItem(self.imageItem)
        
        self.ui.normGroup.hide()

        self.roi = PlotROI(10)
        self.roi.setZValue(20)
        self.view.addItem(self.roi)
        self.roi.hide()
        self.normRoi = PlotROI(10)
        self.normRoi.setPen(QtGui.QPen(QtGui.QColor(255,255,0)))
        self.normRoi.setZValue(20)
        self.view.addItem(self.normRoi)
        self.normRoi.hide()
        self.roiCurve = self.ui.roiPlot.plot()
        self.timeLine = InfiniteLine(0, movable=True)
        self.timeLine.setPen(QtGui.QPen(QtGui.QColor(255, 255, 0, 200)))
        self.timeLine.setZValue(1)
        self.ui.roiPlot.addItem(self.timeLine)
        self.ui.splitter.setSizes([self.height()-35, 35])
        self.ui.roiPlot.hideAxis('left')
        
        self.keysPressed = {}
        self.playTimer = QtCore.QTimer()
        self.playRate = 0
        self.lastPlayTime = 0
        
        self.normRgn = LinearRegionItem()
        self.normRgn.setZValue(0)
        self.ui.roiPlot.addItem(self.normRgn)
        self.normRgn.hide()
            
        ## wrap functions from view box
        for fn in ['addItem', 'removeItem']:
            setattr(self, fn, getattr(self.view, fn))

        ## wrap functions from histogram
        for fn in ['setHistogramRange', 'autoHistogramRange', 'getLookupTable', 'getLevels']:
            setattr(self, fn, getattr(self.ui.histogram, fn))

        self.timeLine.sigPositionChanged.connect(self.timeLineChanged)
        self.ui.roiBtn.clicked.connect(self.roiClicked)
        self.roi.sigRegionChanged.connect(self.roiChanged)
        self.ui.normBtn.toggled.connect(self.normToggled)
        self.ui.normDivideRadio.clicked.connect(self.normRadioChanged)
        self.ui.normSubtractRadio.clicked.connect(self.normRadioChanged)
        self.ui.normOffRadio.clicked.connect(self.normRadioChanged)
        self.ui.normROICheck.clicked.connect(self.updateNorm)
        self.ui.normFrameCheck.clicked.connect(self.updateNorm)
        self.ui.normTimeRangeCheck.clicked.connect(self.updateNorm)
        self.playTimer.timeout.connect(self.timeout)
        
        self.normProxy = SignalProxy(self.normRgn.sigRegionChanged, slot=self.updateNorm)
        self.normRoi.sigRegionChangeFinished.connect(self.updateNorm)
        
        self.ui.roiPlot.registerPlot(self.name + '_ROI')
        
        self.noRepeatKeys = [QtCore.Qt.Key_Right, QtCore.Qt.Key_Left, QtCore.Qt.Key_Up, QtCore.Qt.Key_Down, QtCore.Qt.Key_PageUp, QtCore.Qt.Key_PageDown]
        
        self.roiClicked() ## initialize roi plot to correct shape / visibility
Exemple #11
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class HistogramLUTItem(GraphicsWidget):
    """
    This is a graphicsWidget which provides controls for adjusting the display of an image.
    Includes:

    - Image histogram
    - Movable region over histogram to select black/white levels
    - Gradient editor to define color lookup table for single-channel images
    """

    sigLookupTableChanged = QtCore.Signal(object)
    sigLevelsChanged = QtCore.Signal(object)
    sigLevelChangeFinished = QtCore.Signal(object)

    def __init__(self, image=None, fillHistogram=True):
        """
        If *image* (ImageItem) is provided, then the control will be automatically linked to the image and changes to the control will be immediately reflected in the image's appearance.
        By default, the histogram is rendered with a fill. For performance, set *fillHistogram* = False.
        """
        GraphicsWidget.__init__(self)
        self.lut = None
        self.imageItem = lambda: None  # fake a dead weakref

        self.layout = QtWidgets.QGraphicsGridLayout()
        self.setLayout(self.layout)
        self.layout.setContentsMargins(1, 1, 1, 1)
        self.layout.setSpacing(0)
        self.vb = ViewBox(parent=self)
        self.vb.setMaximumWidth(152)
        self.vb.setMinimumWidth(45)
        self.vb.setMouseEnabled(x=False, y=True)
        self.gradient = GradientEditorItem()
        self.gradient.setOrientation('right')
        self.gradient.loadPreset('grey')
        self.region = LinearRegionItem([0, 1], LinearRegionItem.Horizontal)
        self.region.setZValue(1000)
        self.vb.addItem(self.region)
        self.axis = AxisItem('left',
                             linkView=self.vb,
                             maxTickLength=-10,
                             parent=self)
        self.layout.addItem(self.axis, 0, 0)
        self.layout.addItem(self.vb, 0, 1)
        self.layout.addItem(self.gradient, 0, 2)
        self.range = None
        self.gradient.setFlag(self.gradient.ItemStacksBehindParent)
        self.vb.setFlag(self.gradient.ItemStacksBehindParent)

        #self.grid = GridItem()
        #self.vb.addItem(self.grid)

        self.gradient.sigGradientChanged.connect(self.gradientChanged)
        self.region.sigRegionChanged.connect(self.regionChanging)
        self.region.sigRegionChangeFinished.connect(self.regionChanged)
        self.vb.sigRangeChanged.connect(self.viewRangeChanged)
        self.plot = PlotDataItem()
        self.plot.rotate(90)
        self.fillHistogram(fillHistogram)

        self.vb.addItem(self.plot)
        self.autoHistogramRange()

        if image is not None:
            self.setImageItem(image)
        #self.setSizePolicy(QtWidgets.QSizePolicy.Preferred, QtWidgets.QSizePolicy.Expanding)

    def fillHistogram(self, fill=True, level=0.0, color=(100, 100, 200)):
        if fill:
            self.plot.setFillLevel(level)
            self.plot.setFillBrush(color)
        else:
            self.plot.setFillLevel(None)

    #def sizeHint(self, *args):
    #return QtCore.QSizeF(115, 200)

    def paint(self, p, *args):
        pen = self.region.lines[0].pen
        rgn = self.getLevels()
        p1 = self.vb.mapFromViewToItem(
            self, Point(self.vb.viewRect().center().x(), rgn[0]))
        p2 = self.vb.mapFromViewToItem(
            self, Point(self.vb.viewRect().center().x(), rgn[1]))
        gradRect = self.gradient.mapRectToParent(self.gradient.gradRect.rect())
        for pen in [fn.mkPen('k', width=3), pen]:
            p.setPen(pen)
            p.drawLine(p1, gradRect.bottomLeft())
            p.drawLine(p2, gradRect.topLeft())
            p.drawLine(gradRect.topLeft(), gradRect.topRight())
            p.drawLine(gradRect.bottomLeft(), gradRect.bottomRight())
        #p.drawRect(self.boundingRect())

    def setHistogramRange(self, mn, mx, padding=0.1):
        """Set the Y range on the histogram plot. This disables auto-scaling."""
        self.vb.enableAutoRange(self.vb.YAxis, False)
        self.vb.setYRange(mn, mx, padding)

        #d = mx-mn
        #mn -= d*padding
        #mx += d*padding
        #self.range = [mn,mx]
        #self.updateRange()
        #self.vb.setMouseEnabled(False, True)
        #self.region.setBounds([mn,mx])

    def autoHistogramRange(self):
        """Enable auto-scaling on the histogram plot."""
        self.vb.enableAutoRange(self.vb.XYAxes)
        #self.range = None
        #self.updateRange()
        #self.vb.setMouseEnabled(False, False)

    #def updateRange(self):
    #self.vb.autoRange()
    #if self.range is not None:
    #self.vb.setYRange(*self.range)
    #vr = self.vb.viewRect()

    #self.region.setBounds([vr.top(), vr.bottom()])

    def setImageItem(self, img):
        """Set an ImageItem to have its levels and LUT automatically controlled
        by this HistogramLUTItem.
        """
        self.imageItem = weakref.ref(img)
        img.sigImageChanged.connect(self.imageChanged)
        img.setLookupTable(
            self.getLookupTable)  ## send function pointer, not the result
        #self.gradientChanged()
        self.regionChanged()
        self.imageChanged(autoLevel=True)
        #self.vb.autoRange()

    def viewRangeChanged(self):
        self.update()

    def gradientChanged(self):
        if self.imageItem() is not None:
            if self.gradient.isLookupTrivial():
                self.imageItem().setLookupTable(
                    None)  #lambda x: x.astype(np.uint8))
            else:
                self.imageItem().setLookupTable(
                    self.getLookupTable
                )  ## send function pointer, not the result

        self.lut = None
        #if self.imageItem is not None:
        #self.imageItem.setLookupTable(self.gradient.getLookupTable(512))
        self.sigLookupTableChanged.emit(self)

    def getLookupTable(self, img=None, n=None, alpha=None):
        """Return a lookup table from the color gradient defined by this
        HistogramLUTItem.
        """
        if n is None:
            if img.dtype == np.uint8:
                n = 256
            else:
                n = 512
        if self.lut is None:
            self.lut = self.gradient.getLookupTable(n, alpha=alpha)
        return self.lut

    def regionChanged(self):
        #if self.imageItem is not None:
        #self.imageItem.setLevels(self.region.getRegion())
        self.sigLevelChangeFinished.emit(self)
        #self.update()

    def regionChanging(self):
        if self.imageItem() is not None:
            self.imageItem().setLevels(self.region.getRegion())
        self.sigLevelsChanged.emit(self)
        self.update()

    def imageChanged(self, autoLevel=False, autoRange=False):
        profiler = debug.Profiler()
        img = self.imageItem().image
        if img is None:
            histRange = None
        else:
            histRange = (np.nanmin(img), np.nanmax(img))

        h = self.imageItem().getHistogram(range=histRange)
        profiler('get histogram')
        if h[0] is None:
            return
        self.plot.setData(*h)
        profiler('set plot')
        if autoLevel:
            mn = h[0][0]
            mx = h[0][-1]
            self.region.setRegion([mn, mx])
            profiler('set region')

    def getLevels(self):
        """Return the min and max levels.
        """
        return self.region.getRegion()

    def setLevels(self, mn, mx):
        """Set the min and max levels.
        """
        self.region.setRegion([mn, mx])
Exemple #12
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class HorHistogramLUTItem(GraphicsWidget):
    """
    This is a graphicsWidget which provides controls for adjusting the display of an image.
    Includes:

    - Image histogram 
    - Movable region over histogram to select black/white levels
    - Gradient editor to define color lookup table for single-channel images
    """

    sigLookupTableChanged = QtCore.pyqtSignal(object)
    sigLevelsChanged = QtCore.pyqtSignal(object)
    sigLevelChangeFinished = QtCore.pyqtSignal(object)

    def __init__(self, image=None, fillHistogram=False, orientation='horizontal'):
        """
        If *image* (ImageItem) is provided, then the control will be automatically linked to the image and changes to the control will be immediately reflected in the image's appearance.
        By default, the histogram is rendered with a fill. For performance, set *fillHistogram* = False.
        """
        GraphicsWidget.__init__(self)
        self.lut = None
        self.imageItem = None
        self.first_image = True
        self.percentageLevel = False
        self.orientation = orientation
        self.range = None

        self.layout = QtGui.QGraphicsGridLayout()
        self.setLayout(self.layout)
        self.layout.setContentsMargins(1, 1, 1, 1)
        self.layout.setSpacing(0)

        self.vb = ViewBox()

        self.gradient = GradientEditorItem()
        self.gradient.loadPreset('grey')

        if orientation == 'horizontal':
            self.vb.setMouseEnabled(x=True, y=False)
            self.vb.setMaximumHeight(30)
            self.vb.setMinimumHeight(45)
            self.gradient.setOrientation('top')
            self.region = LogarithmRegionItem([0, 1], LinearRegionItem.Vertical)
            self.layout.addItem(self.vb, 1, 0)
            self.layout.addItem(self.gradient, 0, 0)
            self.gradient.setFlag(self.gradient.ItemStacksBehindParent)
            self.vb.setFlag(self.gradient.ItemStacksBehindParent)
        elif orientation == 'vertical':
            self.vb.setMouseEnabled(x=False, y=True)
            self.vb.setMaximumWidth(30)
            self.vb.setMinimumWidth(45)
            self.gradient.setOrientation('right')
            self.region = LogarithmRegionItem([0, 1], LinearRegionItem.Horizontal)
            self.layout.addItem(self.vb, 0, 0)
            self.layout.addItem(self.gradient, 0, 1)

        self.gradient.setFlag(self.gradient.ItemStacksBehindParent)
        self.vb.setFlag(self.gradient.ItemStacksBehindParent)
        self.region.setZValue(1000)
        self.vb.addItem(self.region)
        self.vb.setMenuEnabled(False)


        #self.grid = GridItem()
        #self.vb.addItem(self.grid)

        self.gradient.sigGradientChanged.connect(self.gradientChanged)
        self.region.sigRegionChanged.connect(self.regionChanging)
        self.region.sigRegionChangeFinished.connect(self.regionChanged)

        self.vb.sigRangeChanged.connect(self.viewRangeChanged)
        self.plot = PlotDataItem()
        if self.orientation == 'horizontal':
            self.plot.setLogMode(yMode=True, xMode=False)
        elif self.orientation == 'vertical':
            self.plot.setLogMode(yMode=False, xMode=True)
            self.vb.invertX(True)
        self.vb.autoRange()
        self.fillHistogram(fillHistogram)
        self.plot.setPen(pg.mkPen(color=(50, 150, 50), size=3))

        self.vb.addItem(self.plot)
        self.autoHistogramRange()

        if image is not None:
            self.setImageItem(image)
            #self.setSizePolicy(QtGui.QSizePolicy.Preferred, QtGui.QSizePolicy.Expanding)

        self.vb.mouseClickEvent = self.empty_function
        self.vb.mouseDragEvent = self.empty_function
        self.vb.mouseDoubleClickEvent = self.empty_function
        self.vb.wheelEvent = self.empty_function

    def fillHistogram(self, fill=True, level=0.0, color=(100, 100, 200)):
        if fill:
            self.plot.setFillLevel(level)
            self.plot.setFillBrush(color)
        else:
            self.plot.setFillLevel(None)

            #def sizeHint(self, *args):
            #return QtCore.QSizeF(115, 200)

    def paint(self, p, *args):
        pen = self.region.lines[0].pen
        rgn = self.getLevels()
        if self.orientation == 'horizontal':
            p1 = self.vb.mapFromViewToItem(self, Point(rgn[0], self.vb.viewRect().center().y()))
            p2 = self.vb.mapFromViewToItem(self, Point(rgn[1], self.vb.viewRect().center().y()))
            gradRect = self.gradient.mapRectToParent(self.gradient.gradRect.rect())
            for pen in [fn.mkPen('k', width=3), pen]:
                p.setPen(pen)
                p.drawLine(p1, gradRect.bottomLeft())
                p.drawLine(p2, gradRect.bottomRight())
                p.drawLine(gradRect.bottomLeft(), gradRect.topLeft())
                p.drawLine(gradRect.bottomRight(), gradRect.topRight())

        elif self.orientation == 'vertical':
            p1 = self.vb.mapFromViewToItem(self, Point(self.vb.viewRect().center().x(), rgn[0]))
            p2 = self.vb.mapFromViewToItem(self, Point(self.vb.viewRect().center().x(), rgn[1]))
            gradRect = self.gradient.mapRectToParent(self.gradient.gradRect.rect())
            for pen in [fn.mkPen('k', width=3), pen]:
                p.setPen(pen)
                p.drawLine(p1, gradRect.bottomLeft())
                p.drawLine(p2, gradRect.topLeft())
                p.drawLine(gradRect.topLeft(), gradRect.topRight())
                p.drawLine(gradRect.bottomLeft(), gradRect.bottomRight())


    def setHistogramRange(self, mn, mx, padding=0.1):
        """Set the Y range on the histogram plot. This disables auto-scaling."""
        self.vb.enableAutoRange(self.vb.YAxis, False)
        if self.orientation == 'horizontal':
            self.vb.setXRange(mn, mx, padding)
        elif self.orientation == 'vertical':
            self.vb.setYrange(mn, mx, padding)
            #mn -= d*padding
            #mx += d*padding
            #self.range = [mn,mx]
            #self.updateRange()
            #self.vb.setMouseEnabled(False, True)
            #self.region.setBounds([mn,mx])

    def autoHistogramRange(self):
        """Enable auto-scaling on the histogram plot."""
        self.vb.enableAutoRange(self.vb.XAxis, True)
        self.vb.enableAutoRange(self.vb.YAxis, True)
        #self.range = None
        #self.updateRange()
        #self.vb.setMouseEnabled(False, False)

        #def updateRange(self):
        #self.vb.autoRange()
        #if self.range is not None:
        #self.vb.setYRange(*self.range)
        #vr = self.vb.viewRect()

        #self.region.setBounds([vr.top(), vr.bottom()])

    def setImageItem(self, img):
        self.imageItem = img
        img.sigImageChanged.connect(self.imageChanged)
        img.setLookupTable(self.getLookupTable)  ## send function pointer, not the result
        #self.gradientChanged()
        self.regionChanged()
        self.imageChanged()
        #self.vb.autoRange()

    def viewRangeChanged(self):
        self.update()

    def gradientChanged(self):
        if self.imageItem is not None:
            if self.gradient.isLookupTrivial():
                self.imageItem.setLookupTable(None)  #lambda x: x.astype(np.uint8))
            else:
                self.imageItem.setLookupTable(self.getLookupTable)  ## send function pointer, not the result

        self.lut = None
        #if self.imageItem is not None:
        #self.imageItem.setLookupTable(self.gradient.getLookupTable(512))
        self.sigLookupTableChanged.emit(self)

    def getLookupTable(self, img=None, n=None, alpha=None):
        if n is None:
            if img.dtype == np.uint8:
                n = 256
            else:
                n = 512
        if self.lut is None:
            self.lut = self.gradient.getLookupTable(n, alpha=alpha)
        return self.lut

    def regionChanged(self):
        #if self.imageItem is not None:
        #self.imageItem.setLevels(self.region.getRegion())
        self.sigLevelChangeFinished.emit(self)
        #self.update()

    def regionChanging(self):
        if self.imageItem is not None:
            self.imageItem.setLevels(np.exp(self.region.getRegion()))
        self.sigLevelsChanged.emit(self)
        self.update()

    def imageChanged(self, autoRange=False):
        prof = debug.Profiler('HistogramLUTItem.imageChanged', disabled=True)
        h = list(self.imageItem.getHistogram(bins=1000))

        prof.mark('get histogram')
        if h[0] is None:
            return

        h[1][1:] = np.log(h[1][1:])
        h[0][1:] = np.log(h[0][1:])

        h[0][0] = 0
        h[1][0] = h[1][1]
        if self.orientation == 'horizontal':
            self.plot.setData(h[0], h[1])
        elif self.orientation == 'vertical':
            self.plot.setData(h[1], h[0])

        self.hist_x_range = np.max(h[0]) - np.min(h[0])
        # if self.percentageLevel:
        # if self.first_image:
        #         self.region.setRegion([h[0, 0], h[0, -1]])
        #         self.old_hist_x_range = self.hist_x_range
        #         self.first_image = False
        #     else:
        #         region_fraction = np.array(self.region.getRegion()) / self.old_hist_x_range
        #         self.region.setRegion(region_fraction * self.hist_x_range)
        #         self.old_hist_x_range = self.hist_x_range
        #
        #         #self.vb.setRange(yRange=[0, 1.2 * np.max(h[1])])

    def getLevels(self):
        return self.region.getRegion()

    def setLevels(self, mn, mx):
        self.region.setRegion([mn, mx])

    def empty_function(self, *args):
        pass
Exemple #13
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    def __init__(self, image=None, fillHistogram=False, orientation='horizontal'):
        """
        If *image* (ImageItem) is provided, then the control will be automatically linked to the image and changes to the control will be immediately reflected in the image's appearance.
        By default, the histogram is rendered with a fill. For performance, set *fillHistogram* = False.
        """
        GraphicsWidget.__init__(self)
        self.lut = None
        self.imageItem = None
        self.first_image = True
        self.percentageLevel = False
        self.orientation = orientation
        self.range = None

        self.layout = QtGui.QGraphicsGridLayout()
        self.setLayout(self.layout)
        self.layout.setContentsMargins(1, 1, 1, 1)
        self.layout.setSpacing(0)

        self.vb = ViewBox()

        self.gradient = GradientEditorItem()
        self.gradient.loadPreset('grey')

        if orientation == 'horizontal':
            self.vb.setMouseEnabled(x=True, y=False)
            self.vb.setMaximumHeight(30)
            self.vb.setMinimumHeight(45)
            self.gradient.setOrientation('top')
            self.region = LogarithmRegionItem([0, 1], LinearRegionItem.Vertical)
            self.layout.addItem(self.vb, 1, 0)
            self.layout.addItem(self.gradient, 0, 0)
            self.gradient.setFlag(self.gradient.ItemStacksBehindParent)
            self.vb.setFlag(self.gradient.ItemStacksBehindParent)
        elif orientation == 'vertical':
            self.vb.setMouseEnabled(x=False, y=True)
            self.vb.setMaximumWidth(30)
            self.vb.setMinimumWidth(45)
            self.gradient.setOrientation('right')
            self.region = LogarithmRegionItem([0, 1], LinearRegionItem.Horizontal)
            self.layout.addItem(self.vb, 0, 0)
            self.layout.addItem(self.gradient, 0, 1)

        self.gradient.setFlag(self.gradient.ItemStacksBehindParent)
        self.vb.setFlag(self.gradient.ItemStacksBehindParent)
        self.region.setZValue(1000)
        self.vb.addItem(self.region)
        self.vb.setMenuEnabled(False)


        #self.grid = GridItem()
        #self.vb.addItem(self.grid)

        self.gradient.sigGradientChanged.connect(self.gradientChanged)
        self.region.sigRegionChanged.connect(self.regionChanging)
        self.region.sigRegionChangeFinished.connect(self.regionChanged)

        self.vb.sigRangeChanged.connect(self.viewRangeChanged)
        self.plot = PlotDataItem()
        if self.orientation == 'horizontal':
            self.plot.setLogMode(yMode=True, xMode=False)
        elif self.orientation == 'vertical':
            self.plot.setLogMode(yMode=False, xMode=True)
            self.vb.invertX(True)
        self.vb.autoRange()
        self.fillHistogram(fillHistogram)
        self.plot.setPen(pg.mkPen(color=(50, 150, 50), size=3))

        self.vb.addItem(self.plot)
        self.autoHistogramRange()

        if image is not None:
            self.setImageItem(image)
            #self.setSizePolicy(QtGui.QSizePolicy.Preferred, QtGui.QSizePolicy.Expanding)

        self.vb.mouseClickEvent = self.empty_function
        self.vb.mouseDragEvent = self.empty_function
        self.vb.mouseDoubleClickEvent = self.empty_function
        self.vb.wheelEvent = self.empty_function
Exemple #14
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    def __init__(self,
                 parent=None,
                 name=None,
                 view=None,
                 plotItem=None,
                 *args):
        """
        By default, this class creates an :class:`ImageItem <pyqtgraph.ImageItem>` to display image data
        and a :class:`ViewBox <pyqtgraph.ViewBox>` to contain the ImageItem. 
        
        ============= =========================================================
        **Arguments** 
        parent        (QWidget) Specifies the parent widget to which
                      this ImageView will belong. If None, then the ImageView
                      is created with no parent.
        name          (str) The name used to register both the internal ViewBox
                      and the PlotItem used to display ROI data. See the *name*
                      argument to :func:`ViewBox.__init__() 
                      <pyqtgraph.ViewBox.__init__>`.
        view          (ViewBox or PlotItem) If specified, this will be used
                      as the display area that contains the displayed image. 
                      Any :class:`ViewBox <pyqtgraph.ViewBox>`, 
                      :class:`PlotItem <pyqtgraph.PlotItem>`, or other 
                      compatible object is acceptable.
        imageItem     (ImageItem) If specified, this object will be used to
                      display the image. Must be an instance of ImageItem
                      or other compatible object.
        ============= =========================================================
        
        Note: to display axis ticks inside the ImageView, instantiate it 
        with a PlotItem instance as its view::
                
            pg.ImageView(view=pg.PlotItem())
        """
        QtGui.QWidget.__init__(self, parent, *args)
        self.currentRowSelectedinTable = None
        self.markerRadius = 15  #circle radius marking single points/rois
        self.clicked = []
        self.image_Designation = None
        self.levelMax = 4096
        self.levelMin = 0
        self.name = name
        self.image = None
        self.axes = {}
        self.imageDisp = None
        self.ui = Ui_FormPlotROI()  #pyqtgraph.imageview.ImageViewTemplate_pyqt
        self.ui.setupUi(self)
        self.scene = self.ui.plotwidget.scene()
        if view is None:
            self.view = ViewBox()
        else:
            self.view = view

        self.ui.plotwidget.setCentralItem(self.view)

        if plotItem is None:
            self.plotItem = PlotItem()
        else:
            self.plotItem = PlotItem

        self.plotview = self.view.addItem(self.plotItem)

        self.plotItem.updatePlot(np.random.normal(size=100))
Exemple #15
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class ROIplotView(QtGui.QWidget):
    """
    Widget used for display and analysis of image data.
    Implements many features:
    
    * Displays 2D and 3D image data. For 3D data, a z-axis
      slider is displayed allowing the user to select which frame is displayed.
    * Displays histogram of image data with movable region defining the dark/light levels
    * Editable gradient provides a color lookup table 
    * Frame slider may also be moved using left/right arrow keys as well as pgup, pgdn, home, and end.
    * Basic analysis features including:
    
        * ROI and embedded plot for measuring image values across frames
        * Image normalization / background subtraction 
    
    Basic Usage::
    
        imv = pg.ImageView()
        imv.show()
        imv.setImage(data)
        
    **Keyboard interaction**
    
    * left/right arrows step forward/backward 1 frame when pressed,
      seek at 20fps when held.
    * up/down arrows seek at 100fps
    * pgup/pgdn seek at 1000fps
    * home/end seek immediately to the first/last frame
    * space begins playing frames. If time values (in seconds) are given 
      for each frame, then playback is in realtime.
    """
    sigTimeChanged = QtCore.Signal(object, object)
    sigProcessingChanged = QtCore.Signal(object)
    changePlot = QtCore.pyqtSignal(object)

    def __init__(self,
                 parent=None,
                 name=None,
                 view=None,
                 plotItem=None,
                 *args):
        """
        By default, this class creates an :class:`ImageItem <pyqtgraph.ImageItem>` to display image data
        and a :class:`ViewBox <pyqtgraph.ViewBox>` to contain the ImageItem. 
        
        ============= =========================================================
        **Arguments** 
        parent        (QWidget) Specifies the parent widget to which
                      this ImageView will belong. If None, then the ImageView
                      is created with no parent.
        name          (str) The name used to register both the internal ViewBox
                      and the PlotItem used to display ROI data. See the *name*
                      argument to :func:`ViewBox.__init__() 
                      <pyqtgraph.ViewBox.__init__>`.
        view          (ViewBox or PlotItem) If specified, this will be used
                      as the display area that contains the displayed image. 
                      Any :class:`ViewBox <pyqtgraph.ViewBox>`, 
                      :class:`PlotItem <pyqtgraph.PlotItem>`, or other 
                      compatible object is acceptable.
        imageItem     (ImageItem) If specified, this object will be used to
                      display the image. Must be an instance of ImageItem
                      or other compatible object.
        ============= =========================================================
        
        Note: to display axis ticks inside the ImageView, instantiate it 
        with a PlotItem instance as its view::
                
            pg.ImageView(view=pg.PlotItem())
        """
        QtGui.QWidget.__init__(self, parent, *args)
        self.currentRowSelectedinTable = None
        self.markerRadius = 15  #circle radius marking single points/rois
        self.clicked = []
        self.image_Designation = None
        self.levelMax = 4096
        self.levelMin = 0
        self.name = name
        self.image = None
        self.axes = {}
        self.imageDisp = None
        self.ui = Ui_FormPlotROI()  #pyqtgraph.imageview.ImageViewTemplate_pyqt
        self.ui.setupUi(self)
        self.scene = self.ui.plotwidget.scene()
        if view is None:
            self.view = ViewBox()
        else:
            self.view = view

        self.ui.plotwidget.setCentralItem(self.view)

        if plotItem is None:
            self.plotItem = PlotItem()
        else:
            self.plotItem = PlotItem

        self.plotview = self.view.addItem(self.plotItem)

        self.plotItem.updatePlot(np.random.normal(size=100))
Exemple #16
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    def __init__(self,
                 parent=None,
                 name="ImageView",
                 view=None,
                 imageItem=None,
                 *args):
        """
        By default, this class creates an :class:`ImageItem <pyqtgraph.ImageItem>` to display image data
        and a :class:`ViewBox <pyqtgraph.ViewBox>` to contain the ImageItem. Custom items may be given instead 
        by specifying the *view* and/or *imageItem* arguments.
        """
        QtGui.QWidget.__init__(self, parent, *args)
        self.levelMax = 4096
        self.levelMin = 0
        self.name = name
        self.image = None
        self.axes = {}
        self.imageDisp = None
        self.ui = Ui_Form()
        self.ui.setupUi(self)
        self.scene = self.ui.graphicsView.scene()

        self.ignoreTimeLine = False

        if view is None:
            self.view = ViewBox()
        else:
            self.view = view
        self.ui.graphicsView.setCentralItem(self.view)
        self.view.setAspectLocked(True)
        self.view.invertY()

        if imageItem is None:
            self.imageItem = ImageItem()
        else:
            self.imageItem = imageItem
        self.view.addItem(self.imageItem)
        self.currentIndex = 0

        self.ui.histogram.setImageItem(self.imageItem)

        self.ui.normGroup.hide()

        self.roi = PlotROI(10)
        self.roi.setZValue(20)
        self.view.addItem(self.roi)
        self.roi.hide()
        self.normRoi = PlotROI(10)
        self.normRoi.setPen(QtGui.QPen(QtGui.QColor(255, 255, 0)))
        self.normRoi.setZValue(20)
        self.view.addItem(self.normRoi)
        self.normRoi.hide()
        self.roiCurve = self.ui.roiPlot.plot()
        self.timeLine = InfiniteLine(0, movable=True)
        self.timeLine.setPen(QtGui.QPen(QtGui.QColor(255, 255, 0, 200)))
        self.timeLine.setZValue(1)
        self.ui.roiPlot.addItem(self.timeLine)
        self.ui.splitter.setSizes([self.height() - 35, 35])
        self.ui.roiPlot.hideAxis('left')

        self.keysPressed = {}
        self.playTimer = QtCore.QTimer()
        self.playRate = 0
        self.lastPlayTime = 0

        self.normRgn = LinearRegionItem()
        self.normRgn.setZValue(0)
        self.ui.roiPlot.addItem(self.normRgn)
        self.normRgn.hide()

        ## wrap functions from view box
        for fn in ['addItem', 'removeItem']:
            setattr(self, fn, getattr(self.view, fn))

        ## wrap functions from histogram
        for fn in [
                'setHistogramRange', 'autoHistogramRange', 'getLookupTable',
                'getLevels'
        ]:
            setattr(self, fn, getattr(self.ui.histogram, fn))

        self.timeLine.sigPositionChanged.connect(self.timeLineChanged)
        self.ui.roiBtn.clicked.connect(self.roiClicked)
        self.roi.sigRegionChanged.connect(self.roiChanged)
        self.ui.normBtn.toggled.connect(self.normToggled)
        self.ui.normDivideRadio.clicked.connect(self.normRadioChanged)
        self.ui.normSubtractRadio.clicked.connect(self.normRadioChanged)
        self.ui.normOffRadio.clicked.connect(self.normRadioChanged)
        self.ui.normROICheck.clicked.connect(self.updateNorm)
        self.ui.normFrameCheck.clicked.connect(self.updateNorm)
        self.ui.normTimeRangeCheck.clicked.connect(self.updateNorm)
        self.playTimer.timeout.connect(self.timeout)

        self.normProxy = SignalProxy(self.normRgn.sigRegionChanged,
                                     slot=self.updateNorm)
        self.normRoi.sigRegionChangeFinished.connect(self.updateNorm)

        self.ui.roiPlot.registerPlot(self.name + '_ROI')

        self.noRepeatKeys = [
            QtCore.Qt.Key_Right, QtCore.Qt.Key_Left, QtCore.Qt.Key_Up,
            QtCore.Qt.Key_Down, QtCore.Qt.Key_PageUp, QtCore.Qt.Key_PageDown
        ]

        self.roiClicked()  ## initialize roi plot to correct shape / visibility
Exemple #17
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class HistogramLUTItem(GraphicsWidget):
    """
    This is a graphicsWidget which provides controls for adjusting the display of an image.
    Includes:

    - Image histogram
    - Movable region over histogram to select black/white levels
    - Gradient editor to define color lookup table for single-channel images
    """

    sigLookupTableChanged = QtCore.Signal(object)
    sigLevelsChanged = QtCore.Signal(object)
    sigLevelChangeFinished = QtCore.Signal(object)

    def __init__(self, image=None, fillHistogram=True):
        """
        If *image* (ImageItem) is provided, then the control will be automatically linked to the image and changes to the control will be immediately reflected in the image's appearance.
        By default, the histogram is rendered with a fill. For performance, set *fillHistogram* = False.
        """
        GraphicsWidget.__init__(self)
        self.lut = None
        self.imageItem = lambda: None  # fake a dead weakref

        self.layout = QtWidgets.QGraphicsGridLayout()
        self.setLayout(self.layout)
        self.layout.setContentsMargins(1,1,1,1)
        self.layout.setSpacing(0)
        self.vb = ViewBox(parent=self)
        self.vb.setMaximumWidth(152)
        self.vb.setMinimumWidth(45)
        self.vb.setMouseEnabled(x=False, y=True)
        self.gradient = GradientEditorItem()
        self.gradient.setOrientation('right')
        self.gradient.loadPreset('grey')
        self.region = LinearRegionItem([0, 1], LinearRegionItem.Horizontal)
        self.region.setZValue(1000)
        self.vb.addItem(self.region)
        self.axis = AxisItem('left', linkView=self.vb, maxTickLength=-10, parent=self)
        self.layout.addItem(self.axis, 0, 0)
        self.layout.addItem(self.vb, 0, 1)
        self.layout.addItem(self.gradient, 0, 2)
        self.range = None
        self.gradient.setFlag(self.gradient.ItemStacksBehindParent)
        self.vb.setFlag(self.gradient.ItemStacksBehindParent)

        #self.grid = GridItem()
        #self.vb.addItem(self.grid)

        self.gradient.sigGradientChanged.connect(self.gradientChanged)
        self.region.sigRegionChanged.connect(self.regionChanging)
        self.region.sigRegionChangeFinished.connect(self.regionChanged)
        self.vb.sigRangeChanged.connect(self.viewRangeChanged)
        self.plot = PlotDataItem()
        self.plot.rotate(90)
        self.fillHistogram(fillHistogram)

        self.vb.addItem(self.plot)
        self.autoHistogramRange()

        if image is not None:
            self.setImageItem(image)
        #self.setSizePolicy(QtWidgets.QSizePolicy.Preferred, QtWidgets.QSizePolicy.Expanding)

    def fillHistogram(self, fill=True, level=0.0, color=(100, 100, 200)):
        if fill:
            self.plot.setFillLevel(level)
            self.plot.setFillBrush(color)
        else:
            self.plot.setFillLevel(None)

    #def sizeHint(self, *args):
        #return QtCore.QSizeF(115, 200)

    def paint(self, p, *args):
        pen = self.region.lines[0].pen
        rgn = self.getLevels()
        p1 = self.vb.mapFromViewToItem(self, Point(self.vb.viewRect().center().x(), rgn[0]))
        p2 = self.vb.mapFromViewToItem(self, Point(self.vb.viewRect().center().x(), rgn[1]))
        gradRect = self.gradient.mapRectToParent(self.gradient.gradRect.rect())
        for pen in [fn.mkPen('k', width=3), pen]:
            p.setPen(pen)
            p.drawLine(p1, gradRect.bottomLeft())
            p.drawLine(p2, gradRect.topLeft())
            p.drawLine(gradRect.topLeft(), gradRect.topRight())
            p.drawLine(gradRect.bottomLeft(), gradRect.bottomRight())
        #p.drawRect(self.boundingRect())


    def setHistogramRange(self, mn, mx, padding=0.1):
        """Set the Y range on the histogram plot. This disables auto-scaling."""
        self.vb.enableAutoRange(self.vb.YAxis, False)
        self.vb.setYRange(mn, mx, padding)

        #d = mx-mn
        #mn -= d*padding
        #mx += d*padding
        #self.range = [mn,mx]
        #self.updateRange()
        #self.vb.setMouseEnabled(False, True)
        #self.region.setBounds([mn,mx])

    def autoHistogramRange(self):
        """Enable auto-scaling on the histogram plot."""
        self.vb.enableAutoRange(self.vb.XYAxes)
        #self.range = None
        #self.updateRange()
        #self.vb.setMouseEnabled(False, False)

    #def updateRange(self):
        #self.vb.autoRange()
        #if self.range is not None:
            #self.vb.setYRange(*self.range)
        #vr = self.vb.viewRect()

        #self.region.setBounds([vr.top(), vr.bottom()])

    def setImageItem(self, img):
        """Set an ImageItem to have its levels and LUT automatically controlled
        by this HistogramLUTItem.
        """
        self.imageItem = weakref.ref(img)
        img.sigImageChanged.connect(self.imageChanged)
        img.setLookupTable(self.getLookupTable)  ## send function pointer, not the result
        #self.gradientChanged()
        self.regionChanged()
        self.imageChanged(autoLevel=True)
        #self.vb.autoRange()

    def viewRangeChanged(self):
        self.update()

    def gradientChanged(self):
        if self.imageItem() is not None:
            if self.gradient.isLookupTrivial():
                self.imageItem().setLookupTable(None) #lambda x: x.astype(np.uint8))
            else:
                self.imageItem().setLookupTable(self.getLookupTable)  ## send function pointer, not the result

        self.lut = None
        #if self.imageItem is not None:
            #self.imageItem.setLookupTable(self.gradient.getLookupTable(512))
        self.sigLookupTableChanged.emit(self)

    def getLookupTable(self, img=None, n=None, alpha=None):
        """Return a lookup table from the color gradient defined by this
        HistogramLUTItem.
        """
        if n is None:
            if img.dtype == np.uint8:
                n = 256
            else:
                n = 512
        if self.lut is None:
            self.lut = self.gradient.getLookupTable(n, alpha=alpha)
        return self.lut

    def regionChanged(self):
        #if self.imageItem is not None:
            #self.imageItem.setLevels(self.region.getRegion())
        self.sigLevelChangeFinished.emit(self)
        #self.update()

    def regionChanging(self):
        if self.imageItem() is not None:
            self.imageItem().setLevels(self.region.getRegion())
        self.sigLevelsChanged.emit(self)
        self.update()

    def imageChanged(self, autoLevel=False, autoRange=False):
        profiler = debug.Profiler()
        img = self.imageItem().image
        if img is None:
            histRange = None
        else:
            histRange = (np.nanmin(img), np.nanmax(img))

        h = self.imageItem().getHistogram(range=histRange)
        profiler('get histogram')
        if h[0] is None:
            return
        self.plot.setData(*h)
        profiler('set plot')
        if autoLevel:
            mn = h[0][0]
            mx = h[0][-1]
            self.region.setRegion([mn, mx])
            profiler('set region')

    def getLevels(self):
        """Return the min and max levels.
        """
        return self.region.getRegion()

    def setLevels(self, mn, mx):
        """Set the min and max levels.
        """
        self.region.setRegion([mn, mx])
Exemple #18
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    def __init__(self, parent=None, name="ImageView", *args):
        QtGui.QWidget.__init__(self, parent, *args)
        self.levelMax = 4096
        self.levelMin = 0
        self.name = name
        self.image = None
        self.axes = {}
        self.imageDisp = None
        self.ui = Ui_Form()
        self.ui.setupUi(self)
        self.scene = self.ui.graphicsView.scene()

        self.ignoreTimeLine = False

        #if 'linux' in sys.platform.lower():   ## Stupid GL bug in linux.
        #    self.ui.graphicsView.setViewport(QtGui.QWidget())

        #self.ui.graphicsView.enableMouse(True)
        #self.ui.graphicsView.autoPixelRange = False
        #self.ui.graphicsView.setAspectLocked(True)
        #self.ui.graphicsView.invertY()
        #self.ui.graphicsView.enableMouse()
        self.view = ViewBox()
        self.ui.graphicsView.setCentralItem(self.view)
        self.view.setAspectLocked(True)
        self.view.invertY()

        #self.ticks = [t[0] for t in self.ui.gradientWidget.listTicks()]
        #self.ticks[0].colorChangeAllowed = False
        #self.ticks[1].colorChangeAllowed = False
        #self.ui.gradientWidget.allowAdd = False
        #self.ui.gradientWidget.setTickColor(self.ticks[1], QtGui.QColor(255,255,255))
        #self.ui.gradientWidget.setOrientation('right')

        self.imageItem = ImageItem()
        self.view.addItem(self.imageItem)
        self.currentIndex = 0

        self.ui.histogram.setImageItem(self.imageItem)

        self.ui.normGroup.hide()

        self.roi = PlotROI(10)
        self.roi.setZValue(20)
        self.view.addItem(self.roi)
        self.roi.hide()
        self.normRoi = PlotROI(10)
        self.normRoi.setPen(QtGui.QPen(QtGui.QColor(255, 255, 0)))
        self.normRoi.setZValue(20)
        self.view.addItem(self.normRoi)
        self.normRoi.hide()
        #self.ui.roiPlot.hide()
        self.roiCurve = self.ui.roiPlot.plot()
        self.timeLine = InfiniteLine(0, movable=True)
        self.timeLine.setPen(QtGui.QPen(QtGui.QColor(255, 255, 0, 200)))
        self.timeLine.setZValue(1)
        self.ui.roiPlot.addItem(self.timeLine)
        self.ui.splitter.setSizes([self.height() - 35, 35])
        self.ui.roiPlot.hideAxis('left')

        self.keysPressed = {}
        self.playTimer = QtCore.QTimer()
        self.playRate = 0
        self.lastPlayTime = 0

        #self.normLines = []
        #for i in [0,1]:
        #l = InfiniteLine(self.ui.roiPlot, 0)
        #l.setPen(QtGui.QPen(QtGui.QColor(0, 100, 200, 200)))
        #self.ui.roiPlot.addItem(l)
        #self.normLines.append(l)
        #l.hide()
        self.normRgn = LinearRegionItem()
        self.normRgn.setZValue(0)
        self.ui.roiPlot.addItem(self.normRgn)
        self.normRgn.hide()

        ## wrap functions from view box
        for fn in ['addItem', 'removeItem']:
            setattr(self, fn, getattr(self.view, fn))

        ## wrap functions from histogram
        for fn in [
                'setHistogramRange', 'autoHistogramRange', 'getLookupTable',
                'getLevels'
        ]:
            setattr(self, fn, getattr(self.ui.histogram, fn))

        self.timeLine.sigPositionChanged.connect(self.timeLineChanged)
        #self.ui.gradientWidget.sigGradientChanged.connect(self.updateImage)
        self.ui.roiBtn.clicked.connect(self.roiClicked)
        self.roi.sigRegionChanged.connect(self.roiChanged)
        self.ui.normBtn.toggled.connect(self.normToggled)
        self.ui.normDivideRadio.clicked.connect(self.normRadioChanged)
        self.ui.normSubtractRadio.clicked.connect(self.normRadioChanged)
        self.ui.normOffRadio.clicked.connect(self.normRadioChanged)
        self.ui.normROICheck.clicked.connect(self.updateNorm)
        self.ui.normFrameCheck.clicked.connect(self.updateNorm)
        self.ui.normTimeRangeCheck.clicked.connect(self.updateNorm)
        self.playTimer.timeout.connect(self.timeout)

        self.normProxy = SignalProxy(self.normRgn.sigRegionChanged,
                                     slot=self.updateNorm)
        self.normRoi.sigRegionChangeFinished.connect(self.updateNorm)

        self.ui.roiPlot.registerPlot(self.name + '_ROI')

        self.noRepeatKeys = [
            QtCore.Qt.Key_Right, QtCore.Qt.Key_Left, QtCore.Qt.Key_Up,
            QtCore.Qt.Key_Down, QtCore.Qt.Key_PageUp, QtCore.Qt.Key_PageDown
        ]

        self.roiClicked()  ## initialize roi plot to correct shape / visibility
Exemple #19
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class ImageView(QtGui.QWidget):
    """
    Widget used for display and analysis of image data.
    Implements many features:
    
    * Displays 2D and 3D image data. For 3D data, a z-axis
      slider is displayed allowing the user to select which frame is displayed.
    * Displays histogram of image data with movable region defining the dark/light levels
    * Editable gradient provides a color lookup table 
    * Frame slider may also be moved using left/right arrow keys as well as pgup, pgdn, home, and end.
    * Basic analysis features including:
    
        * ROI and embedded plot for measuring image values across frames
        * Image normalization / background subtraction 
    
    Basic Usage::
    
        imv = pg.ImageView()
        imv.show()
        imv.setImage(data)
    """
    sigTimeChanged = QtCore.Signal(object, object)
    sigProcessingChanged = QtCore.Signal(object)

    def __init__(self, parent=None, name="ImageView", *args):
        QtGui.QWidget.__init__(self, parent, *args)
        self.levelMax = 4096
        self.levelMin = 0
        self.name = name
        self.image = None
        self.axes = {}
        self.imageDisp = None
        self.ui = Ui_Form()
        self.ui.setupUi(self)
        self.scene = self.ui.graphicsView.scene()

        self.ignoreTimeLine = False

        #if 'linux' in sys.platform.lower():   ## Stupid GL bug in linux.
        #    self.ui.graphicsView.setViewport(QtGui.QWidget())

        #self.ui.graphicsView.enableMouse(True)
        #self.ui.graphicsView.autoPixelRange = False
        #self.ui.graphicsView.setAspectLocked(True)
        #self.ui.graphicsView.invertY()
        #self.ui.graphicsView.enableMouse()
        self.view = ViewBox()
        self.ui.graphicsView.setCentralItem(self.view)
        self.view.setAspectLocked(True)
        self.view.invertY()

        #self.ticks = [t[0] for t in self.ui.gradientWidget.listTicks()]
        #self.ticks[0].colorChangeAllowed = False
        #self.ticks[1].colorChangeAllowed = False
        #self.ui.gradientWidget.allowAdd = False
        #self.ui.gradientWidget.setTickColor(self.ticks[1], QtGui.QColor(255,255,255))
        #self.ui.gradientWidget.setOrientation('right')

        self.imageItem = ImageItem()
        self.view.addItem(self.imageItem)
        self.currentIndex = 0

        self.ui.histogram.setImageItem(self.imageItem)

        self.ui.normGroup.hide()

        self.roi = PlotROI(10)
        self.roi.setZValue(20)
        self.view.addItem(self.roi)
        self.roi.hide()
        self.normRoi = PlotROI(10)
        self.normRoi.setPen(QtGui.QPen(QtGui.QColor(255, 255, 0)))
        self.normRoi.setZValue(20)
        self.view.addItem(self.normRoi)
        self.normRoi.hide()
        #self.ui.roiPlot.hide()
        self.roiCurve = self.ui.roiPlot.plot()
        self.timeLine = InfiniteLine(0, movable=True)
        self.timeLine.setPen(QtGui.QPen(QtGui.QColor(255, 255, 0, 200)))
        self.timeLine.setZValue(1)
        self.ui.roiPlot.addItem(self.timeLine)
        self.ui.splitter.setSizes([self.height() - 35, 35])
        self.ui.roiPlot.hideAxis('left')

        self.keysPressed = {}
        self.playTimer = QtCore.QTimer()
        self.playRate = 0
        self.lastPlayTime = 0

        #self.normLines = []
        #for i in [0,1]:
        #l = InfiniteLine(self.ui.roiPlot, 0)
        #l.setPen(QtGui.QPen(QtGui.QColor(0, 100, 200, 200)))
        #self.ui.roiPlot.addItem(l)
        #self.normLines.append(l)
        #l.hide()
        self.normRgn = LinearRegionItem()
        self.normRgn.setZValue(0)
        self.ui.roiPlot.addItem(self.normRgn)
        self.normRgn.hide()

        ## wrap functions from view box
        for fn in ['addItem', 'removeItem']:
            setattr(self, fn, getattr(self.view, fn))

        ## wrap functions from histogram
        for fn in [
                'setHistogramRange', 'autoHistogramRange', 'getLookupTable',
                'getLevels'
        ]:
            setattr(self, fn, getattr(self.ui.histogram, fn))

        self.timeLine.sigPositionChanged.connect(self.timeLineChanged)
        #self.ui.gradientWidget.sigGradientChanged.connect(self.updateImage)
        self.ui.roiBtn.clicked.connect(self.roiClicked)
        self.roi.sigRegionChanged.connect(self.roiChanged)
        self.ui.normBtn.toggled.connect(self.normToggled)
        self.ui.normDivideRadio.clicked.connect(self.normRadioChanged)
        self.ui.normSubtractRadio.clicked.connect(self.normRadioChanged)
        self.ui.normOffRadio.clicked.connect(self.normRadioChanged)
        self.ui.normROICheck.clicked.connect(self.updateNorm)
        self.ui.normFrameCheck.clicked.connect(self.updateNorm)
        self.ui.normTimeRangeCheck.clicked.connect(self.updateNorm)
        self.playTimer.timeout.connect(self.timeout)

        self.normProxy = SignalProxy(self.normRgn.sigRegionChanged,
                                     slot=self.updateNorm)
        self.normRoi.sigRegionChangeFinished.connect(self.updateNorm)

        self.ui.roiPlot.registerPlot(self.name + '_ROI')

        self.noRepeatKeys = [
            QtCore.Qt.Key_Right, QtCore.Qt.Key_Left, QtCore.Qt.Key_Up,
            QtCore.Qt.Key_Down, QtCore.Qt.Key_PageUp, QtCore.Qt.Key_PageDown
        ]

        self.roiClicked()  ## initialize roi plot to correct shape / visibility

    def setImage(self,
                 img,
                 autoRange=True,
                 autoLevels=True,
                 levels=None,
                 axes=None,
                 xvals=None,
                 pos=None,
                 scale=None):
        """
        Set the image to be displayed in the widget.
        
        ============== =======================================================================
        **Arguments:**
        *img*          (numpy array) the image to be displayed.
        *xvals*        (numpy array) 1D array of z-axis values corresponding to the third axis
                       in a 3D image. For video, this array should contain the time of each frame.
        *autoRange*    (bool) whether to scale/pan the view to fit the image.
        *autoLevels*   (bool) whether to update the white/black levels to fit the image.
        *levels*       (min, max); the white and black level values to use.
        *axes*         Dictionary indicating the interpretation for each axis.
                       This is only needed to override the default guess. Format is::
                       
                           {'t':0, 'x':1, 'y':2, 'c':3}; 
        ============== =======================================================================
        """
        prof = debug.Profiler('ImageView.setImage', disabled=True)

        if not isinstance(img, np.ndarray):
            raise Exception("Image must be specified as ndarray.")
        self.image = img

        if xvals is not None:
            self.tVals = xvals
        elif hasattr(img, 'xvals'):
            try:
                self.tVals = img.xvals(0)
            except:
                self.tVals = np.arange(img.shape[0])
        else:
            self.tVals = np.arange(img.shape[0])
        #self.ui.timeSlider.setValue(0)
        #self.ui.normStartSlider.setValue(0)
        #self.ui.timeSlider.setMaximum(img.shape[0]-1)
        prof.mark('1')

        if axes is None:
            if img.ndim == 2:
                self.axes = {'t': None, 'x': 0, 'y': 1, 'c': None}
            elif img.ndim == 3:
                if img.shape[2] <= 4:
                    self.axes = {'t': None, 'x': 0, 'y': 1, 'c': 2}
                else:
                    self.axes = {'t': 0, 'x': 1, 'y': 2, 'c': None}
            elif img.ndim == 4:
                self.axes = {'t': 0, 'x': 1, 'y': 2, 'c': 3}
            else:
                raise Exception("Can not interpret image with dimensions %s" %
                                (str(img.shape)))
        elif isinstance(axes, dict):
            self.axes = axes.copy()
        elif isinstance(axes, list) or isinstance(axes, tuple):
            self.axes = {}
            for i in range(len(axes)):
                self.axes[axes[i]] = i
        else:
            raise Exception(
                "Can not interpret axis specification %s. Must be like {'t': 2, 'x': 0, 'y': 1} or ('t', 'x', 'y', 'c')"
                % (str(axes)))

        for x in ['t', 'x', 'y', 'c']:
            self.axes[x] = self.axes.get(x, None)
        prof.mark('2')

        self.imageDisp = None

        prof.mark('3')

        self.currentIndex = 0
        self.updateImage()
        if levels is None and autoLevels:
            self.autoLevels()
        if levels is not None:  ## this does nothing since getProcessedImage sets these values again.
            self.levelMax = levels[1]
            self.levelMin = levels[0]

        if self.ui.roiBtn.isChecked():
            self.roiChanged()
        prof.mark('4')

        if self.axes['t'] is not None:
            #self.ui.roiPlot.show()
            self.ui.roiPlot.setXRange(self.tVals.min(), self.tVals.max())
            self.timeLine.setValue(0)
            #self.ui.roiPlot.setMouseEnabled(False, False)
            if len(self.tVals) > 1:
                start = self.tVals.min()
                stop = self.tVals.max() + abs(self.tVals[-1] -
                                              self.tVals[0]) * 0.02
            elif len(self.tVals) == 1:
                start = self.tVals[0] - 0.5
                stop = self.tVals[0] + 0.5
            else:
                start = 0
                stop = 1
            for s in [self.timeLine, self.normRgn]:
                s.setBounds([start, stop])
        #else:
        #self.ui.roiPlot.hide()
        prof.mark('5')

        self.imageItem.resetTransform()
        if scale is not None:
            self.imageItem.scale(*scale)
        if pos is not None:
            self.imageItem.setPos(*pos)
        prof.mark('6')

        if autoRange:
            self.autoRange()
        self.roiClicked()
        prof.mark('7')
        prof.finish()

    def play(self, rate):
        """Begin automatically stepping frames forward at the given rate (in fps).
        This can also be accessed by pressing the spacebar."""
        #print "play:", rate
        self.playRate = rate
        if rate == 0:
            self.playTimer.stop()
            return

        self.lastPlayTime = ptime.time()
        if not self.playTimer.isActive():
            self.playTimer.start(16)

    def autoLevels(self):
        """Set the min/max levels automatically to match the image data."""
        #image = self.getProcessedImage()
        self.setLevels(self.levelMin, self.levelMax)

        #self.ui.histogram.imageChanged(autoLevel=True)

    def setLevels(self, min, max):
        """Set the min/max (bright and dark) levels."""
        self.ui.histogram.setLevels(min, max)

    def autoRange(self):
        """Auto scale and pan the view around the image."""
        image = self.getProcessedImage()

        #self.ui.graphicsView.setRange(QtCore.QRectF(0, 0, image.shape[self.axes['x']], image.shape[self.axes['y']]), padding=0., lockAspect=True)
        self.view.setRange(self.imageItem.boundingRect(), padding=0.)

    def getProcessedImage(self):
        """Returns the image data after it has been processed by any normalization options in use."""
        if self.imageDisp is None:
            image = self.normalize(self.image)
            self.imageDisp = image
            self.levelMin, self.levelMax = map(
                float, ImageView.quickMinMax(self.imageDisp))
            self.ui.histogram.setHistogramRange(self.levelMin, self.levelMax)

        return self.imageDisp

    def close(self):
        """Closes the widget nicely, making sure to clear the graphics scene and release memory."""
        self.ui.roiPlot.close()
        self.ui.graphicsView.close()
        #self.ui.gradientWidget.sigGradientChanged.disconnect(self.updateImage)
        self.scene.clear()
        del self.image
        del self.imageDisp
        self.setParent(None)

    def keyPressEvent(self, ev):
        #print ev.key()
        if ev.key() == QtCore.Qt.Key_Space:
            if self.playRate == 0:
                fps = (self.getProcessedImage().shape[0] -
                       1) / (self.tVals[-1] - self.tVals[0])
                self.play(fps)
                #print fps
            else:
                self.play(0)
            ev.accept()
        elif ev.key() == QtCore.Qt.Key_Home:
            self.setCurrentIndex(0)
            self.play(0)
            ev.accept()
        elif ev.key() == QtCore.Qt.Key_End:
            self.setCurrentIndex(self.getProcessedImage().shape[0] - 1)
            self.play(0)
            ev.accept()
        elif ev.key() in self.noRepeatKeys:
            ev.accept()
            if ev.isAutoRepeat():
                return
            self.keysPressed[ev.key()] = 1
            self.evalKeyState()
        else:
            QtGui.QWidget.keyPressEvent(self, ev)

    def keyReleaseEvent(self, ev):
        if ev.key() in [
                QtCore.Qt.Key_Space, QtCore.Qt.Key_Home, QtCore.Qt.Key_End
        ]:
            ev.accept()
        elif ev.key() in self.noRepeatKeys:
            ev.accept()
            if ev.isAutoRepeat():
                return
            try:
                del self.keysPressed[ev.key()]
            except:
                self.keysPressed = {}
            self.evalKeyState()
        else:
            QtGui.QWidget.keyReleaseEvent(self, ev)

    def evalKeyState(self):
        if len(self.keysPressed) == 1:
            key = self.keysPressed.keys()[0]
            if key == QtCore.Qt.Key_Right:
                self.play(20)
                self.jumpFrames(1)
                self.lastPlayTime = ptime.time(
                ) + 0.2  ## 2ms wait before start
                ## This happens *after* jumpFrames, since it might take longer than 2ms
            elif key == QtCore.Qt.Key_Left:
                self.play(-20)
                self.jumpFrames(-1)
                self.lastPlayTime = ptime.time() + 0.2
            elif key == QtCore.Qt.Key_Up:
                self.play(-100)
            elif key == QtCore.Qt.Key_Down:
                self.play(100)
            elif key == QtCore.Qt.Key_PageUp:
                self.play(-1000)
            elif key == QtCore.Qt.Key_PageDown:
                self.play(1000)
        else:
            self.play(0)

    def timeout(self):
        now = ptime.time()
        dt = now - self.lastPlayTime
        if dt < 0:
            return
        n = int(self.playRate * dt)
        #print n, dt
        if n != 0:
            #print n, dt, self.lastPlayTime
            self.lastPlayTime += (float(n) / self.playRate)
            if self.currentIndex + n > self.image.shape[0]:
                self.play(0)
            self.jumpFrames(n)

    def setCurrentIndex(self, ind):
        """Set the currently displayed frame index."""
        self.currentIndex = np.clip(ind, 0,
                                    self.getProcessedImage().shape[0] - 1)
        self.updateImage()
        self.ignoreTimeLine = True
        self.timeLine.setValue(self.tVals[self.currentIndex])
        self.ignoreTimeLine = False

    def jumpFrames(self, n):
        """Move video frame ahead n frames (may be negative)"""
        if self.axes['t'] is not None:
            self.setCurrentIndex(self.currentIndex + n)

    def normRadioChanged(self):
        self.imageDisp = None
        self.updateImage()
        self.roiChanged()
        self.sigProcessingChanged.emit(self)

    def updateNorm(self):
        #for l, sl in zip(self.normLines, [self.ui.normStartSlider, self.ui.normStopSlider]):
        #if self.ui.normTimeRangeCheck.isChecked():
        #l.show()
        #else:
        #l.hide()

        #i, t = self.timeIndex(sl)
        #l.setPos(t)

        if self.ui.normTimeRangeCheck.isChecked():
            #print "show!"
            self.normRgn.show()
        else:
            self.normRgn.hide()

        if self.ui.normROICheck.isChecked():
            #print "show!"
            self.normRoi.show()
        else:
            self.normRoi.hide()

        if not self.ui.normOffRadio.isChecked():
            self.imageDisp = None
            self.updateImage()
            self.roiChanged()
            self.sigProcessingChanged.emit(self)

    def normToggled(self, b):
        self.ui.normGroup.setVisible(b)
        self.normRoi.setVisible(b and self.ui.normROICheck.isChecked())
        self.normRgn.setVisible(b and self.ui.normTimeRangeCheck.isChecked())

    def hasTimeAxis(self):
        return 't' in self.axes and self.axes['t'] is not None

    def roiClicked(self):
        showRoiPlot = False
        if self.ui.roiBtn.isChecked():
            showRoiPlot = True
            self.roi.show()
            #self.ui.roiPlot.show()
            self.ui.roiPlot.setMouseEnabled(True, True)
            self.ui.splitter.setSizes(
                [self.height() * 0.6, self.height() * 0.4])
            self.roiCurve.show()
            self.roiChanged()
            self.ui.roiPlot.showAxis('left')
        else:
            self.roi.hide()
            self.ui.roiPlot.setMouseEnabled(False, False)
            self.roiCurve.hide()
            self.ui.roiPlot.hideAxis('left')

        if self.hasTimeAxis():
            showRoiPlot = True
            mn = self.tVals.min()
            mx = self.tVals.max()
            self.ui.roiPlot.setXRange(mn, mx, padding=0.01)
            self.timeLine.show()
            self.timeLine.setBounds([mn, mx])
            self.ui.roiPlot.show()
            if not self.ui.roiBtn.isChecked():
                self.ui.splitter.setSizes([self.height() - 35, 35])
        else:
            self.timeLine.hide()
            #self.ui.roiPlot.hide()

        self.ui.roiPlot.setVisible(showRoiPlot)

    def roiChanged(self):
        if self.image is None:
            return

        image = self.getProcessedImage()
        if image.ndim == 2:
            axes = (0, 1)
        elif image.ndim == 3:
            axes = (1, 2)
        else:
            return
        data = self.roi.getArrayRegion(image.view(np.ndarray), self.imageItem,
                                       axes)
        if data is not None:
            while data.ndim > 1:
                data = data.mean(axis=1)
            if image.ndim == 3:
                self.roiCurve.setData(y=data, x=self.tVals)
            else:
                self.roiCurve.setData(y=data, x=range(len(data)))

            #self.ui.roiPlot.replot()

    @staticmethod
    def quickMinMax(data):
        while data.size > 1e6:
            ax = np.argmax(data.shape)
            sl = [slice(None)] * data.ndim
            sl[ax] = slice(None, None, 2)
            data = data[sl]
        return data.min(), data.max()

    def normalize(self, image):

        if self.ui.normOffRadio.isChecked():
            return image

        div = self.ui.normDivideRadio.isChecked()
        norm = image.view(np.ndarray).copy()
        #if div:
        #norm = ones(image.shape)
        #else:
        #norm = zeros(image.shape)
        if div:
            norm = norm.astype(np.float32)

        if self.ui.normTimeRangeCheck.isChecked() and image.ndim == 3:
            (sind, start) = self.timeIndex(self.normRgn.lines[0])
            (eind, end) = self.timeIndex(self.normRgn.lines[1])
            #print start, end, sind, eind
            n = image[sind:eind + 1].mean(axis=0)
            n.shape = (1, ) + n.shape
            if div:
                norm /= n
            else:
                norm -= n

        if self.ui.normFrameCheck.isChecked() and image.ndim == 3:
            n = image.mean(axis=1).mean(axis=1)
            n.shape = n.shape + (1, 1)
            if div:
                norm /= n
            else:
                norm -= n

        if self.ui.normROICheck.isChecked() and image.ndim == 3:
            n = self.normRoi.getArrayRegion(norm, self.imageItem,
                                            (1, 2)).mean(axis=1).mean(axis=1)
            n = n[:, np.newaxis, np.newaxis]
            #print start, end, sind, eind
            if div:
                norm /= n
            else:
                norm -= n

        return norm

    def timeLineChanged(self):
        #(ind, time) = self.timeIndex(self.ui.timeSlider)
        if self.ignoreTimeLine:
            return
        self.play(0)
        (ind, time) = self.timeIndex(self.timeLine)
        if ind != self.currentIndex:
            self.currentIndex = ind
            self.updateImage()
        #self.timeLine.setPos(time)
        #self.emit(QtCore.SIGNAL('timeChanged'), ind, time)
        self.sigTimeChanged.emit(ind, time)

    def updateImage(self):
        ## Redraw image on screen
        if self.image is None:
            return

        image = self.getProcessedImage()
        #print "update:", image.ndim, image.max(), image.min(), self.blackLevel(), self.whiteLevel()
        if self.axes['t'] is None:
            #self.ui.timeSlider.hide()
            self.imageItem.updateImage(image)
            #self.ui.roiPlot.hide()
            #self.ui.roiBtn.hide()
        else:
            #self.ui.roiBtn.show()
            self.ui.roiPlot.show()
            #self.ui.timeSlider.show()
            self.imageItem.updateImage(image[self.currentIndex])

    def timeIndex(self, slider):
        ## Return the time and frame index indicated by a slider
        if self.image is None:
            return (0, 0)
        #v = slider.value()
        #vmax = slider.maximum()
        #f = float(v) / vmax

        t = slider.value()

        #t = 0.0
        #xv = self.image.xvals('Time')
        xv = self.tVals
        if xv is None:
            ind = int(t)
            #ind = int(f * self.image.shape[0])
        else:
            if len(xv) < 2:
                return (0, 0)
            totTime = xv[-1] + (xv[-1] - xv[-2])
            #t = f * totTime
            inds = np.argwhere(xv < t)
            if len(inds) < 1:
                return (0, t)
            ind = inds[-1, 0]
        #print ind
        return ind, t
    def __init__(self, parent=None, name="ImageView", view=None, imageItem=None, *args):
        """
        By default, this class creates an :class:`ImageItem <pyqtgraph.ImageItem>` to display image data
        and a :class:`ViewBox <pyqtgraph.ViewBox>` to contain the ImageItem. 
        
        ============= =========================================================
        **Arguments** 
        parent        (QWidget) Specifies the parent widget to which
                      this ImageView will belong. If None, then the ImageView
                      is created with no parent.
        name          (str) The name used to register both the internal ViewBox
                      and the PlotItem used to display ROI data. See the *name*
                      argument to :func:`ViewBox.__init__() 
                      <pyqtgraph.ViewBox.__init__>`.
        view          (ViewBox or PlotItem) If specified, this will be used
                      as the display area that contains the displayed image. 
                      Any :class:`ViewBox <pyqtgraph.ViewBox>`, 
                      :class:`PlotItem <pyqtgraph.PlotItem>`, or other 
                      compatible object is acceptable.
        imageItem     (ImageItem) If specified, this object will be used to
                      display the image. Must be an instance of ImageItem
                      or other compatible object.
        ============= =========================================================
        
        Note: to display axis ticks inside the ImageView, instantiate it 
        with a PlotItem instance as its view::
                
            pg.ImageView(view=pg.PlotItem())
        """
        QtGui.QWidget.__init__(self, parent, *args)
        self.markerRadius = 50 #circle radius marking single points/rois
        self.clicked = []
        self.image_Designation = None
        self.levelMax = 4096
        self.levelMin = 0
        self.name = name
        self.image = None
        self.axes = {}
        self.imageDisp = None
        self.ui = Ui_Form() #pyqtgraph.imageview.ImageViewTemplate_pyqt
        self.ui.setupUi(self)
        self.scene = self.ui.graphicsView.scene()
        
        self.ignoreTimeLine = False
        self.ignoreZLine = False
        
        if view is None:
            self.view = ViewBox()
        else:
            self.view = view
        
        self.ui.graphicsView.setCentralItem(self.view)
        self.view.setAspectLocked(True)
        self.view.invertY()
        
        if imageItem is None:
            self.imageItem = ImageItem()
        else:
            self.imageItem = imageItem
        self.imageview = self.view.addItem(self.imageItem)
        self.currentTime = 0
        self.currentLayer = 0 #layer in z axis
        
        #relay x y coordinates within image
        self.view.scene().sigMouseMoved.connect(self.mouseMoved)
        self.view.scene().sigMouseClicked.connect(self.mouseClicked)
        #self.view.scene().mouseReleaseEvent(self.releaseEvent)
        #self.view.scene().mouseReleaseEvent(self.mouseReleased)
        #pdb.set_trace()
        #generate roi list
        self.croi = [] #holdes x,y,z points for roi
        self.ccroi = [] #hold pg roi for croi
        self.aroi = {} #place to store all rois, each roi is passed as dictionary with each index = currentLayer
        self.aaroi = [] #place to store pg of arois in self.currentLayer
        self.button1 = 'off'
        
        self.ui.histogram.setImageItem(self.imageItem)
        
        self.menu = None
        
        self.ui.normGroup.hide()

        self.roi = PlotROI(10)
        self.roi.setZValue(20)
        self.view.addItem(self.roi)
        self.roi.hide()
        self.normRoi = PlotROI(10)
        self.normRoi.setPen('y')
        self.normRoi.setZValue(20)
        self.view.addItem(self.normRoi)
        self.normRoi.hide()
        self.roiCurve = self.ui.roiPlot.plot()
        
        
        self.timeLine = InfiniteLine(0, movable=True)
        self.timeLine.setPen((255, 255, 0, 200))
        #self.timeLine.setPen((255, 255, 200, 0))
        self.timeLine.setZValue(1)
        self.ui.roiPlot.addItem(self.timeLine)
        self.ui.splitter.setSizes([self.height()-35, 35])
        self.ui.roiPlot.hideAxis('left')
        
        
        
        self.ui.splitter.setSizes([self.height(), 10])
        self.ui.zPlot.plot()
        self.zLine = InfiniteLine(0, movable=True, angle = 0)
        #self.zLine.setBounds([0, 42])
        self.zLine.setPen((255, 255, 0, 200))
        self.zLine.setZValue(self.currentLayer )
        self.ui.ztext.setText(str(self.currentLayer))
        
        self.ui.zPlot.addItem(self.zLine)
        self.ui.zPlot.hideAxis('bottom')
        
        
        
        self.keysPressed = {}
        self.playTimer = QtCore.QTimer()
        self.playRate = 0
        self.lastPlayTime = 0
        
        self.normRgn = LinearRegionItem()
        self.normRgn.setZValue(0)
        self.ui.roiPlot.addItem(self.normRgn)
        self.normRgn.hide()
            
        ## wrap functions from view box
        for fn in ['addItem', 'removeItem']:
            setattr(self, fn, getattr(self.view, fn))

        ## wrap functions from histogram
        for fn in ['setHistogramRange', 'autoHistogramRange', 'getLookupTable', 'getLevels']:
            setattr(self, fn, getattr(self.ui.histogram, fn))

        self.timeLine.sigPositionChanged.connect(self.timeLineChanged)
        self.zLine.sigPositionChanged.connect(self.zLineChanged)
        self.ui.roiBtn.clicked.connect(self.roiClicked)
        self.roi.sigRegionChanged.connect(self.roiChanged)
        #self.ui.normBtn.toggled.connect(self.normToggled)
        self.ui.menuBtn.clicked.connect(self.menuClicked)
        self.ui.normDivideRadio.clicked.connect(self.normRadioChanged)
        self.ui.normSubtractRadio.clicked.connect(self.normRadioChanged)
        self.ui.normOffRadio.clicked.connect(self.normRadioChanged)
        self.ui.normROICheck.clicked.connect(self.updateNorm)
        self.ui.normFrameCheck.clicked.connect(self.updateNorm)
        self.ui.normTimeRangeCheck.clicked.connect(self.updateNorm)
        #radio button for navigation and roi selection
        self.ui.navRadio.clicked.connect(self.NavigationStatus)
        self.ui.radioSinglePoint.clicked.connect(self.radioSinglePoint)
        self.ui.radioAreaROI.clicked.connect(self.radioAreaROI)
        self.ui.radioPolygon.clicked.connect(self.radioPolygon)
        self.ui.radioEdit.clicked.connect(self.radioEdit)
        
        self.playTimer.timeout.connect(self.timeout)
        
        self.normProxy = SignalProxy(self.normRgn.sigRegionChanged, slot=self.updateNorm)
        self.normRoi.sigRegionChangeFinished.connect(self.updateNorm)
        
        self.ui.roiPlot.registerPlot(self.name + '_ROI')
        self.view.register(self.name)
        
        self.noRepeatKeys = [QtCore.Qt.Key_Right, QtCore.Qt.Key_Left, QtCore.Qt.Key_Up, QtCore.Qt.Key_Down, QtCore.Qt.Key_PageUp, QtCore.Qt.Key_PageDown]
        
        self.roiClicked() ## initialize roi plot to correct shape / visibility