646 lines
23 KiB
Python
646 lines
23 KiB
Python
# -*- coding: utf-8 -*-
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"""
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ImageView.py - Widget for basic image dispay and analysis
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Copyright 2010 Luke Campagnola
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Distributed under MIT/X11 license. See license.txt for more infomation.
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Widget used for displaying 2D or 3D data. Features:
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- float or int (including 16-bit int) image display via ImageItem
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- zoom/pan via GraphicsView
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- black/white level controls
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- time slider for 3D data sets
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- ROI plotting
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- Image normalization through a variety of methods
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"""
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from pyqtgraph.Qt import QtCore, QtGui, USE_PYSIDE
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if USE_PYSIDE:
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from .ImageViewTemplate_pyside import *
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else:
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from .ImageViewTemplate_pyqt import *
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from pyqtgraph.graphicsItems.ImageItem import *
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from pyqtgraph.graphicsItems.ROI import *
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from pyqtgraph.graphicsItems.LinearRegionItem import *
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from pyqtgraph.graphicsItems.InfiniteLine import *
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from pyqtgraph.graphicsItems.ViewBox import *
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#from widgets import ROI
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import sys
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#from numpy import ndarray
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import pyqtgraph.ptime as ptime
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import numpy as np
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import pyqtgraph.debug as debug
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from pyqtgraph.SignalProxy import SignalProxy
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#try:
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#import pyqtgraph.metaarray as metaarray
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#HAVE_METAARRAY = True
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#except:
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#HAVE_METAARRAY = False
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class PlotROI(ROI):
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def __init__(self, size):
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ROI.__init__(self, pos=[0,0], size=size) #, scaleSnap=True, translateSnap=True)
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self.addScaleHandle([1, 1], [0, 0])
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self.addRotateHandle([0, 0], [0.5, 0.5])
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class ImageView(QtGui.QWidget):
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"""
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Widget used for display and analysis of image data.
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Implements many features:
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* Displays 2D and 3D image data. For 3D data, a z-axis
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slider is displayed allowing the user to select which frame is displayed.
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* Displays histogram of image data with movable region defining the dark/light levels
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* Editable gradient provides a color lookup table
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* Frame slider may also be moved using left/right arrow keys as well as pgup, pgdn, home, and end.
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* Basic analysis features including:
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* ROI and embedded plot for measuring image values across frames
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* Image normalization / background subtraction
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Basic Usage::
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imv = pg.ImageView()
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imv.show()
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imv.setImage(data)
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"""
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sigTimeChanged = QtCore.Signal(object, object)
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sigProcessingChanged = QtCore.Signal(object)
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def __init__(self, parent=None, name="ImageView", view=None, imageItem=None, *args):
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"""
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By default, this class creates an :class:`ImageItem <pyqtgraph.ImageItem>` to display image data
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and a :class:`ViewBox <pyqtgraph.ViewBox>` to contain the ImageItem. Custom items may be given instead
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by specifying the *view* and/or *imageItem* arguments.
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"""
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QtGui.QWidget.__init__(self, parent, *args)
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self.levelMax = 4096
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self.levelMin = 0
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self.name = name
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self.image = None
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self.axes = {}
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self.imageDisp = None
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self.ui = Ui_Form()
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self.ui.setupUi(self)
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self.scene = self.ui.graphicsView.scene()
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self.ignoreTimeLine = False
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if view is None:
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self.view = ViewBox()
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else:
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self.view = view
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self.ui.graphicsView.setCentralItem(self.view)
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self.view.setAspectLocked(True)
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self.view.invertY()
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if imageItem is None:
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self.imageItem = ImageItem()
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else:
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self.imageItem = imageItem
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self.view.addItem(self.imageItem)
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self.currentIndex = 0
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self.ui.histogram.setImageItem(self.imageItem)
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self.ui.normGroup.hide()
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self.roi = PlotROI(10)
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self.roi.setZValue(20)
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self.view.addItem(self.roi)
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self.roi.hide()
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self.normRoi = PlotROI(10)
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self.normRoi.setPen(QtGui.QPen(QtGui.QColor(255,255,0)))
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self.normRoi.setZValue(20)
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self.view.addItem(self.normRoi)
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self.normRoi.hide()
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self.roiCurve = self.ui.roiPlot.plot()
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self.timeLine = InfiniteLine(0, movable=True)
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self.timeLine.setPen(QtGui.QPen(QtGui.QColor(255, 255, 0, 200)))
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self.timeLine.setZValue(1)
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self.ui.roiPlot.addItem(self.timeLine)
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self.ui.splitter.setSizes([self.height()-35, 35])
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self.ui.roiPlot.hideAxis('left')
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self.keysPressed = {}
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self.playTimer = QtCore.QTimer()
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self.playRate = 0
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self.lastPlayTime = 0
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self.normRgn = LinearRegionItem()
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self.normRgn.setZValue(0)
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self.ui.roiPlot.addItem(self.normRgn)
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self.normRgn.hide()
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## wrap functions from view box
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for fn in ['addItem', 'removeItem']:
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setattr(self, fn, getattr(self.view, fn))
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## wrap functions from histogram
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for fn in ['setHistogramRange', 'autoHistogramRange', 'getLookupTable', 'getLevels']:
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setattr(self, fn, getattr(self.ui.histogram, fn))
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self.timeLine.sigPositionChanged.connect(self.timeLineChanged)
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self.ui.roiBtn.clicked.connect(self.roiClicked)
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self.roi.sigRegionChanged.connect(self.roiChanged)
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self.ui.normBtn.toggled.connect(self.normToggled)
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self.ui.normDivideRadio.clicked.connect(self.normRadioChanged)
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self.ui.normSubtractRadio.clicked.connect(self.normRadioChanged)
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self.ui.normOffRadio.clicked.connect(self.normRadioChanged)
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self.ui.normROICheck.clicked.connect(self.updateNorm)
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self.ui.normFrameCheck.clicked.connect(self.updateNorm)
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self.ui.normTimeRangeCheck.clicked.connect(self.updateNorm)
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self.playTimer.timeout.connect(self.timeout)
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self.normProxy = SignalProxy(self.normRgn.sigRegionChanged, slot=self.updateNorm)
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self.normRoi.sigRegionChangeFinished.connect(self.updateNorm)
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self.ui.roiPlot.registerPlot(self.name + '_ROI')
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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]
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self.roiClicked() ## initialize roi plot to correct shape / visibility
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def setImage(self, img, autoRange=True, autoLevels=True, levels=None, axes=None, xvals=None, pos=None, scale=None, transform=None, autoHistogramRange=True):
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"""
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Set the image to be displayed in the widget.
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================== =======================================================================
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**Arguments:**
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img (numpy array) the image to be displayed.
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xvals (numpy array) 1D array of z-axis values corresponding to the third axis
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in a 3D image. For video, this array should contain the time of each frame.
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autoRange (bool) whether to scale/pan the view to fit the image.
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autoLevels (bool) whether to update the white/black levels to fit the image.
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levels (min, max); the white and black level values to use.
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axes Dictionary indicating the interpretation for each axis.
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This is only needed to override the default guess. Format is::
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{'t':0, 'x':1, 'y':2, 'c':3};
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pos Change the position of the displayed image
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scale Change the scale of the displayed image
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transform Set the transform of the displayed image. This option overrides *pos*
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and *scale*.
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autoHistogramRange If True, the histogram y-range is automatically scaled to fit the
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image data.
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================== =======================================================================
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"""
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prof = debug.Profiler('ImageView.setImage', disabled=True)
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if hasattr(img, 'implements') and img.implements('MetaArray'):
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img = img.asarray()
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if not isinstance(img, np.ndarray):
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raise Exception("Image must be specified as ndarray.")
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self.image = img
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if xvals is not None:
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self.tVals = xvals
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elif hasattr(img, 'xvals'):
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try:
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self.tVals = img.xvals(0)
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except:
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self.tVals = np.arange(img.shape[0])
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else:
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self.tVals = np.arange(img.shape[0])
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prof.mark('1')
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if axes is None:
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if img.ndim == 2:
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self.axes = {'t': None, 'x': 0, 'y': 1, 'c': None}
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elif img.ndim == 3:
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if img.shape[2] <= 4:
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self.axes = {'t': None, 'x': 0, 'y': 1, 'c': 2}
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else:
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self.axes = {'t': 0, 'x': 1, 'y': 2, 'c': None}
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elif img.ndim == 4:
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self.axes = {'t': 0, 'x': 1, 'y': 2, 'c': 3}
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else:
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raise Exception("Can not interpret image with dimensions %s" % (str(img.shape)))
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elif isinstance(axes, dict):
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self.axes = axes.copy()
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elif isinstance(axes, list) or isinstance(axes, tuple):
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self.axes = {}
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for i in range(len(axes)):
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self.axes[axes[i]] = i
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else:
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raise Exception("Can not interpret axis specification %s. Must be like {'t': 2, 'x': 0, 'y': 1} or ('t', 'x', 'y', 'c')" % (str(axes)))
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for x in ['t', 'x', 'y', 'c']:
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self.axes[x] = self.axes.get(x, None)
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prof.mark('2')
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self.imageDisp = None
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prof.mark('3')
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self.currentIndex = 0
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self.updateImage(autoHistogramRange=autoHistogramRange)
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if levels is None and autoLevels:
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self.autoLevels()
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if levels is not None: ## this does nothing since getProcessedImage sets these values again.
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self.setLevels(*levels)
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if self.ui.roiBtn.isChecked():
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self.roiChanged()
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prof.mark('4')
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if self.axes['t'] is not None:
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#self.ui.roiPlot.show()
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self.ui.roiPlot.setXRange(self.tVals.min(), self.tVals.max())
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self.timeLine.setValue(0)
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#self.ui.roiPlot.setMouseEnabled(False, False)
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if len(self.tVals) > 1:
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start = self.tVals.min()
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stop = self.tVals.max() + abs(self.tVals[-1] - self.tVals[0]) * 0.02
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elif len(self.tVals) == 1:
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start = self.tVals[0] - 0.5
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stop = self.tVals[0] + 0.5
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else:
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start = 0
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stop = 1
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for s in [self.timeLine, self.normRgn]:
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s.setBounds([start, stop])
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#else:
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#self.ui.roiPlot.hide()
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prof.mark('5')
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self.imageItem.resetTransform()
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if scale is not None:
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self.imageItem.scale(*scale)
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if pos is not None:
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self.imageItem.setPos(*pos)
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if transform is not None:
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self.imageItem.setTransform(transform)
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prof.mark('6')
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if autoRange:
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self.autoRange()
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self.roiClicked()
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prof.mark('7')
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prof.finish()
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def play(self, rate):
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"""Begin automatically stepping frames forward at the given rate (in fps).
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This can also be accessed by pressing the spacebar."""
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#print "play:", rate
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self.playRate = rate
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if rate == 0:
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self.playTimer.stop()
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return
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self.lastPlayTime = ptime.time()
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if not self.playTimer.isActive():
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self.playTimer.start(16)
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def autoLevels(self):
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"""Set the min/max intensity levels automatically to match the image data."""
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self.setLevels(self.levelMin, self.levelMax)
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def setLevels(self, min, max):
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"""Set the min/max (bright and dark) levels."""
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self.ui.histogram.setLevels(min, max)
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def autoRange(self):
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"""Auto scale and pan the view around the image."""
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image = self.getProcessedImage()
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self.view.autoRange()
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def getProcessedImage(self):
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"""Returns the image data after it has been processed by any normalization options in use.
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This method also sets the attributes self.levelMin and self.levelMax
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to indicate the range of data in the image."""
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if self.imageDisp is None:
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image = self.normalize(self.image)
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self.imageDisp = image
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self.levelMin, self.levelMax = list(map(float, ImageView.quickMinMax(self.imageDisp)))
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return self.imageDisp
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def close(self):
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"""Closes the widget nicely, making sure to clear the graphics scene and release memory."""
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self.ui.roiPlot.close()
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self.ui.graphicsView.close()
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self.scene.clear()
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del self.image
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del self.imageDisp
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self.setParent(None)
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def keyPressEvent(self, ev):
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#print ev.key()
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if ev.key() == QtCore.Qt.Key_Space:
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if self.playRate == 0:
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fps = (self.getProcessedImage().shape[0]-1) / (self.tVals[-1] - self.tVals[0])
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self.play(fps)
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#print fps
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else:
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self.play(0)
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ev.accept()
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elif ev.key() == QtCore.Qt.Key_Home:
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self.setCurrentIndex(0)
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self.play(0)
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ev.accept()
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elif ev.key() == QtCore.Qt.Key_End:
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self.setCurrentIndex(self.getProcessedImage().shape[0]-1)
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self.play(0)
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ev.accept()
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elif ev.key() in self.noRepeatKeys:
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ev.accept()
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if ev.isAutoRepeat():
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return
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self.keysPressed[ev.key()] = 1
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self.evalKeyState()
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else:
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QtGui.QWidget.keyPressEvent(self, ev)
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def keyReleaseEvent(self, ev):
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if ev.key() in [QtCore.Qt.Key_Space, QtCore.Qt.Key_Home, QtCore.Qt.Key_End]:
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ev.accept()
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elif ev.key() in self.noRepeatKeys:
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ev.accept()
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if ev.isAutoRepeat():
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return
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try:
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del self.keysPressed[ev.key()]
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except:
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self.keysPressed = {}
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self.evalKeyState()
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else:
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QtGui.QWidget.keyReleaseEvent(self, ev)
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def evalKeyState(self):
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if len(self.keysPressed) == 1:
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key = list(self.keysPressed.keys())[0]
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if key == QtCore.Qt.Key_Right:
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self.play(20)
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self.jumpFrames(1)
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self.lastPlayTime = ptime.time() + 0.2 ## 2ms wait before start
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## This happens *after* jumpFrames, since it might take longer than 2ms
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elif key == QtCore.Qt.Key_Left:
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self.play(-20)
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self.jumpFrames(-1)
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self.lastPlayTime = ptime.time() + 0.2
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elif key == QtCore.Qt.Key_Up:
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self.play(-100)
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elif key == QtCore.Qt.Key_Down:
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self.play(100)
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elif key == QtCore.Qt.Key_PageUp:
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self.play(-1000)
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elif key == QtCore.Qt.Key_PageDown:
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self.play(1000)
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else:
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self.play(0)
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def timeout(self):
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now = ptime.time()
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dt = now - self.lastPlayTime
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if dt < 0:
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return
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n = int(self.playRate * dt)
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#print n, dt
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if n != 0:
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#print n, dt, self.lastPlayTime
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self.lastPlayTime += (float(n)/self.playRate)
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if self.currentIndex+n > self.image.shape[0]:
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self.play(0)
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self.jumpFrames(n)
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def setCurrentIndex(self, ind):
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"""Set the currently displayed frame index."""
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self.currentIndex = np.clip(ind, 0, self.getProcessedImage().shape[0]-1)
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self.updateImage()
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self.ignoreTimeLine = True
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self.timeLine.setValue(self.tVals[self.currentIndex])
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self.ignoreTimeLine = False
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def jumpFrames(self, n):
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"""Move video frame ahead n frames (may be negative)"""
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if self.axes['t'] is not None:
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self.setCurrentIndex(self.currentIndex + n)
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def normRadioChanged(self):
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self.imageDisp = None
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self.updateImage()
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self.autoLevels()
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self.roiChanged()
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self.sigProcessingChanged.emit(self)
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def updateNorm(self):
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if self.ui.normTimeRangeCheck.isChecked():
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#print "show!"
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self.normRgn.show()
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else:
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self.normRgn.hide()
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if self.ui.normROICheck.isChecked():
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#print "show!"
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self.normRoi.show()
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else:
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self.normRoi.hide()
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if not self.ui.normOffRadio.isChecked():
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self.imageDisp = None
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self.updateImage()
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self.autoLevels()
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self.roiChanged()
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self.sigProcessingChanged.emit(self)
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def normToggled(self, b):
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self.ui.normGroup.setVisible(b)
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self.normRoi.setVisible(b and self.ui.normROICheck.isChecked())
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self.normRgn.setVisible(b and self.ui.normTimeRangeCheck.isChecked())
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def hasTimeAxis(self):
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return 't' in self.axes and self.axes['t'] is not None
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def roiClicked(self):
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showRoiPlot = False
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if self.ui.roiBtn.isChecked():
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showRoiPlot = True
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self.roi.show()
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#self.ui.roiPlot.show()
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self.ui.roiPlot.setMouseEnabled(True, True)
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self.ui.splitter.setSizes([self.height()*0.6, self.height()*0.4])
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self.roiCurve.show()
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self.roiChanged()
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self.ui.roiPlot.showAxis('left')
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else:
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self.roi.hide()
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self.ui.roiPlot.setMouseEnabled(False, False)
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self.roiCurve.hide()
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self.ui.roiPlot.hideAxis('left')
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if self.hasTimeAxis():
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showRoiPlot = True
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mn = self.tVals.min()
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mx = self.tVals.max()
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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)
|
|
|
|
#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, 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)
|
|
if self.axes['t'] is None:
|
|
self.imageItem.updateImage(image)
|
|
else:
|
|
self.ui.roiPlot.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)
|
|
|
|
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
|