ImageView cleanups

- fixed auto-levelling when normalization options change
- added autoHistogramRange argument to setImage
This commit is contained in:
Luke Campagnola 2013-05-30 09:33:09 -04:00
parent ba56899a36
commit 59bbe0127e

View File

@ -90,14 +90,6 @@ class ImageView(QtGui.QWidget):
self.ignoreTimeLine = False 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()
if view is None: if view is None:
self.view = ViewBox() self.view = ViewBox()
else: else:
@ -106,13 +98,6 @@ class ImageView(QtGui.QWidget):
self.view.setAspectLocked(True) self.view.setAspectLocked(True)
self.view.invertY() 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')
if imageItem is None: if imageItem is None:
self.imageItem = ImageItem() self.imageItem = ImageItem()
else: else:
@ -133,7 +118,6 @@ class ImageView(QtGui.QWidget):
self.normRoi.setZValue(20) self.normRoi.setZValue(20)
self.view.addItem(self.normRoi) self.view.addItem(self.normRoi)
self.normRoi.hide() self.normRoi.hide()
#self.ui.roiPlot.hide()
self.roiCurve = self.ui.roiPlot.plot() self.roiCurve = self.ui.roiPlot.plot()
self.timeLine = InfiniteLine(0, movable=True) self.timeLine = InfiniteLine(0, movable=True)
self.timeLine.setPen(QtGui.QPen(QtGui.QColor(255, 255, 0, 200))) self.timeLine.setPen(QtGui.QPen(QtGui.QColor(255, 255, 0, 200)))
@ -147,13 +131,6 @@ class ImageView(QtGui.QWidget):
self.playRate = 0 self.playRate = 0
self.lastPlayTime = 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 = LinearRegionItem()
self.normRgn.setZValue(0) self.normRgn.setZValue(0)
self.ui.roiPlot.addItem(self.normRgn) self.ui.roiPlot.addItem(self.normRgn)
@ -168,7 +145,6 @@ class ImageView(QtGui.QWidget):
setattr(self, fn, getattr(self.ui.histogram, fn)) setattr(self, fn, getattr(self.ui.histogram, fn))
self.timeLine.sigPositionChanged.connect(self.timeLineChanged) self.timeLine.sigPositionChanged.connect(self.timeLineChanged)
#self.ui.gradientWidget.sigGradientChanged.connect(self.updateImage)
self.ui.roiBtn.clicked.connect(self.roiClicked) self.ui.roiBtn.clicked.connect(self.roiClicked)
self.roi.sigRegionChanged.connect(self.roiChanged) self.roi.sigRegionChanged.connect(self.roiChanged)
self.ui.normBtn.toggled.connect(self.normToggled) self.ui.normBtn.toggled.connect(self.normToggled)
@ -187,31 +163,32 @@ class ImageView(QtGui.QWidget):
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.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 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): 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. Set the image to be displayed in the widget.
============== ======================================================================= ================== =======================================================================
**Arguments:** **Arguments:**
*img* (numpy array) the image to be displayed. img (numpy array) the image to be displayed.
*xvals* (numpy array) 1D array of z-axis values corresponding to the third axis 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. 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. 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. autoLevels (bool) whether to update the white/black levels to fit the image.
*levels* (min, max); the white and black level values to use. levels (min, max); the white and black level values to use.
*axes* Dictionary indicating the interpretation for each axis. axes Dictionary indicating the interpretation for each axis.
This is only needed to override the default guess. Format is:: This is only needed to override the default guess. Format is::
{'t':0, 'x':1, 'y':2, 'c':3}; {'t':0, 'x':1, 'y':2, 'c':3};
*pos* Change the position of the displayed image pos Change the position of the displayed image
*scale* Change the scale of the displayed image scale Change the scale of the displayed image
*transform* Set the transform of the displayed image. This option overrides *pos* transform Set the transform of the displayed image. This option overrides *pos*
and *scale*. and *scale*.
============== ======================================================================= autoHistogramRange If True, the histogram y-range is automatically scaled to fit the
image data.
================== =======================================================================
""" """
prof = debug.Profiler('ImageView.setImage', disabled=True) prof = debug.Profiler('ImageView.setImage', disabled=True)
@ -231,9 +208,7 @@ class ImageView(QtGui.QWidget):
self.tVals = np.arange(img.shape[0]) self.tVals = np.arange(img.shape[0])
else: else:
self.tVals = np.arange(img.shape[0]) 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') prof.mark('1')
if axes is None: if axes is None:
@ -265,14 +240,12 @@ class ImageView(QtGui.QWidget):
prof.mark('3') prof.mark('3')
self.currentIndex = 0 self.currentIndex = 0
self.updateImage() self.updateImage(autoHistogramRange=autoHistogramRange)
if levels is None and autoLevels: if levels is None and autoLevels:
self.autoLevels() self.autoLevels()
if levels is not None: ## this does nothing since getProcessedImage sets these values again. if levels is not None: ## this does nothing since getProcessedImage sets these values again.
#self.levelMax = levels[1]
#self.levelMin = levels[0]
self.setLevels(*levels) self.setLevels(*levels)
if self.ui.roiBtn.isChecked(): if self.ui.roiBtn.isChecked():
@ -329,15 +302,9 @@ class ImageView(QtGui.QWidget):
if not self.playTimer.isActive(): if not self.playTimer.isActive():
self.playTimer.start(16) self.playTimer.start(16)
def autoLevels(self): def autoLevels(self):
"""Set the min/max levels automatically to match the image data.""" """Set the min/max intensity levels automatically to match the image data."""
#image = self.getProcessedImage()
self.setLevels(self.levelMin, self.levelMax) self.setLevels(self.levelMin, self.levelMax)
#self.ui.histogram.imageChanged(autoLevel=True)
def setLevels(self, min, max): def setLevels(self, min, max):
"""Set the min/max (bright and dark) levels.""" """Set the min/max (bright and dark) levels."""
@ -346,17 +313,16 @@ class ImageView(QtGui.QWidget):
def autoRange(self): def autoRange(self):
"""Auto scale and pan the view around the image.""" """Auto scale and pan the view around the image."""
image = self.getProcessedImage() image = self.getProcessedImage()
self.view.autoRange()
#self.ui.graphicsView.setRange(QtCore.QRectF(0, 0, image.shape[self.axes['x']], image.shape[self.axes['y']]), padding=0., lockAspect=True)
self.view.autoRange() ##setRange(self.imageItem.viewBoundingRect(), padding=0.)
def getProcessedImage(self): def getProcessedImage(self):
"""Returns the image data after it has been processed by any normalization options in use.""" """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: if self.imageDisp is None:
image = self.normalize(self.image) image = self.normalize(self.image)
self.imageDisp = image self.imageDisp = image
self.levelMin, self.levelMax = list(map(float, ImageView.quickMinMax(self.imageDisp))) self.levelMin, self.levelMax = list(map(float, ImageView.quickMinMax(self.imageDisp)))
self.ui.histogram.setHistogramRange(self.levelMin, self.levelMax)
return self.imageDisp return self.imageDisp
@ -365,7 +331,6 @@ class ImageView(QtGui.QWidget):
"""Closes the widget nicely, making sure to clear the graphics scene and release memory.""" """Closes the widget nicely, making sure to clear the graphics scene and release memory."""
self.ui.roiPlot.close() self.ui.roiPlot.close()
self.ui.graphicsView.close() self.ui.graphicsView.close()
#self.ui.gradientWidget.sigGradientChanged.disconnect(self.updateImage)
self.scene.clear() self.scene.clear()
del self.image del self.image
del self.imageDisp del self.imageDisp
@ -468,20 +433,12 @@ class ImageView(QtGui.QWidget):
def normRadioChanged(self): def normRadioChanged(self):
self.imageDisp = None self.imageDisp = None
self.updateImage() self.updateImage()
self.autoLevels()
self.roiChanged() self.roiChanged()
self.sigProcessingChanged.emit(self) self.sigProcessingChanged.emit(self)
def updateNorm(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(): if self.ui.normTimeRangeCheck.isChecked():
#print "show!" #print "show!"
self.normRgn.show() self.normRgn.show()
@ -497,6 +454,7 @@ class ImageView(QtGui.QWidget):
if not self.ui.normOffRadio.isChecked(): if not self.ui.normOffRadio.isChecked():
self.imageDisp = None self.imageDisp = None
self.updateImage() self.updateImage()
self.autoLevels()
self.roiChanged() self.roiChanged()
self.sigProcessingChanged.emit(self) self.sigProcessingChanged.emit(self)
@ -634,22 +592,19 @@ class ImageView(QtGui.QWidget):
#self.emit(QtCore.SIGNAL('timeChanged'), ind, time) #self.emit(QtCore.SIGNAL('timeChanged'), ind, time)
self.sigTimeChanged.emit(ind, time) self.sigTimeChanged.emit(ind, time)
def updateImage(self): def updateImage(self, autoHistogramRange=True):
## Redraw image on screen ## Redraw image on screen
if self.image is None: if self.image is None:
return return
image = self.getProcessedImage() image = self.getProcessedImage()
#print "update:", image.ndim, image.max(), image.min(), self.blackLevel(), self.whiteLevel()
if autoHistogramRange:
self.ui.histogram.setHistogramRange(self.levelMin, self.levelMax)
if self.axes['t'] is None: if self.axes['t'] is None:
#self.ui.timeSlider.hide()
self.imageItem.updateImage(image) self.imageItem.updateImage(image)
#self.ui.roiPlot.hide()
#self.ui.roiBtn.hide()
else: else:
#self.ui.roiBtn.show()
self.ui.roiPlot.show() self.ui.roiPlot.show()
#self.ui.timeSlider.show()
self.imageItem.updateImage(image[self.currentIndex]) self.imageItem.updateImage(image[self.currentIndex])
@ -657,38 +612,22 @@ class ImageView(QtGui.QWidget):
## Return the time and frame index indicated by a slider ## Return the time and frame index indicated by a slider
if self.image is None: if self.image is None:
return (0,0) return (0,0)
#v = slider.value()
#vmax = slider.maximum()
#f = float(v) / vmax
t = slider.value() t = slider.value()
#t = 0.0
#xv = self.image.xvals('Time')
xv = self.tVals xv = self.tVals
if xv is None: if xv is None:
ind = int(t) ind = int(t)
#ind = int(f * self.image.shape[0])
else: else:
if len(xv) < 2: if len(xv) < 2:
return (0,0) return (0,0)
totTime = xv[-1] + (xv[-1]-xv[-2]) totTime = xv[-1] + (xv[-1]-xv[-2])
#t = f * totTime
inds = np.argwhere(xv < t) inds = np.argwhere(xv < t)
if len(inds) < 1: if len(inds) < 1:
return (0,t) return (0,t)
ind = inds[-1,0] ind = inds[-1,0]
#print ind
return ind, t return ind, t
#def whiteLevel(self):
#return self.levelMin + (self.levelMax-self.levelMin) * self.ui.gradientWidget.tickValue(self.ticks[1])
##return self.levelMin + (self.levelMax-self.levelMin) * self.ui.whiteSlider.value() / self.ui.whiteSlider.maximum()
#def blackLevel(self):
#return self.levelMin + (self.levelMax-self.levelMin) * self.ui.gradientWidget.tickValue(self.ticks[0])
##return self.levelMin + ((self.levelMax-self.levelMin) / self.ui.blackSlider.maximum()) * self.ui.blackSlider.value()
def getView(self): def getView(self):
"""Return the ViewBox (or other compatible object) which displays the ImageItem""" """Return the ViewBox (or other compatible object) which displays the ImageItem"""
return self.view return self.view