Source code for pyqtgraph.imageview.ImageView

# -*- coding: utf-8 -*-
"""
ImageView.py -  Widget for basic image dispay and analysis
Copyright 2010  Luke Campagnola
Distributed under MIT/X11 license. See license.txt for more infomation.

Widget used for displaying 2D or 3D data. Features:
  - float or int (including 16-bit int) image display via ImageItem
  - zoom/pan via GraphicsView
  - black/white level controls
  - time slider for 3D data sets
  - ROI plotting
  - Image normalization through a variety of methods
"""
import os
import numpy as np

from ..Qt import QtCore, QtGui, USE_PYSIDE
if USE_PYSIDE:
    from .ImageViewTemplate_pyside import *
else:
    from .ImageViewTemplate_pyqt import *
    
from ..graphicsItems.ImageItem import *
from ..graphicsItems.ROI import *
from ..graphicsItems.LinearRegionItem import *
from ..graphicsItems.InfiniteLine import *
from ..graphicsItems.ViewBox import *
from ..graphicsItems.GradientEditorItem import addGradientListToDocstring
from .. import ptime as ptime
from .. import debug as debug
from ..SignalProxy import SignalProxy
from .. import getConfigOption

try:
    from bottleneck import nanmin, nanmax
except ImportError:
    from numpy import nanmin, nanmax


class PlotROI(ROI):
    def __init__(self, size):
        ROI.__init__(self, pos=[0,0], size=size) #, scaleSnap=True, translateSnap=True)
        self.addScaleHandle([1, 1], [0, 0])
        self.addRotateHandle([0, 0], [0.5, 0.5])


[docs]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) **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)
[docs] 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
[docs] 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()
[docs] 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)
[docs] def autoLevels(self): """Set the min/max intensity levels automatically to match the image data.""" self.setLevels(self.levelMin, self.levelMax)
[docs] def setLevels(self, min, max): """Set the min/max (bright and dark) levels.""" self.ui.histogram.setLevels(min, max)
[docs] 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()
[docs] 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
[docs] 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)
[docs] 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
[docs] 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)
[docs] 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)
[docs] 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
[docs] def getView(self): """Return the ViewBox (or other compatible object) which displays the ImageItem""" return self.view
[docs] def getImageItem(self): """Return the ImageItem for this ImageView.""" return self.imageItem
[docs] def getRoiPlot(self): """Return the ROI PlotWidget for this ImageView""" return self.ui.roiPlot
[docs] def getHistogramWidget(self): """Return the HistogramLUTWidget for this ImageView""" return self.ui.histogram
[docs] 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())
[docs] 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()
[docs] 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)