def __init__(self, parent, tileview, featuredlg=None, *args, **kw):
super(AtContrastWidget, self).__init__(parent)
self.tileview = tileview
self.featuredlg = featuredlg
self.parent = parent
self.colors = None
vbox = QtWidgets.QVBoxLayout(self)
self.enhancer = AtEnhancerWidget(self)
vbox.addWidget(self.enhancer)
vbox.setContentsMargins(0, 0, 0, 0)
self.enhancer.sliderReleased.connect(self.enhanceContrast)
def __init__(self, parent, viewer, *args, **kw):
super(ChannelBar, self).__init__(parent, *args, **kw)
self._images = None
self._contours = None
self._channel_count = 0
self.viewer = viewer
vbox = QtWidgets.QVBoxLayout(self)
self.gbox = QtWidgets.QGridLayout()
cbox = QtWidgets.QVBoxLayout()
self.enhancer = AtEnhancerWidget(self)
self.enhancer.valuesUpdated.connect(self.updateImage)
cbox.addWidget(self.enhancer)
vbox.addLayout(self.gbox)
vbox.addLayout(cbox)
vbox.setContentsMargins(3, 3, 3, 3)
self.gbox.setContentsMargins(0, 0, 0, 0)
cbox.setContentsMargins(0, 0, 0, 0)
def __init__(self, parent, tileview, featuredlg=None, *args, **kw):
super(AtContrastWidget, self).__init__(parent)
self.tileview = tileview
self.featuredlg = featuredlg
self.parent = parent
self.colors = None
vbox = QtWidgets.QVBoxLayout(self)
self.enhancer= AtEnhancerWidget(self)
vbox.addWidget(self.enhancer)
vbox.setContentsMargins(0, 0, 0, 0)
self.enhancer.sliderReleased.connect(self.enhanceContrast)
class AtContrastWidget(QtWidgets.QWidget):
def __init__(self, parent, tileview, featuredlg=None, *args, **kw):
super(AtContrastWidget, self).__init__(parent)
self.tileview = tileview
self.featuredlg = featuredlg
self.parent = parent
self.colors = None
vbox = QtWidgets.QVBoxLayout(self)
self.enhancer= AtEnhancerWidget(self)
vbox.addWidget(self.enhancer)
vbox.setContentsMargins(0, 0, 0, 0)
self.enhancer.sliderReleased.connect(self.enhanceContrast)
def setChannelNames(self, channels, colors):
self.colors = colors
self.enhancer.clear()
for channel in channels:
self.enhancer.addChannel(cn.display(channel), no_auto_button=True)
def enhanceContrast(self):
try:
QApplication.setOverrideCursor(QCursor(Qt.WaitCursor))
i = self.enhancer.currentChannelIndex()
color = QtGui.QColor(self.colors[i])
lut = self.enhancer.lut_from_color(i, color, 256)
for item in self.tileview.items:
item.enhancePixmap(i, lut)
finally:
QApplication.restoreOverrideCursor()
class AtContrastWidget(QtWidgets.QWidget):
def __init__(self, parent, tileview, featuredlg=None, *args, **kw):
super(AtContrastWidget, self).__init__(parent)
self.tileview = tileview
self.featuredlg = featuredlg
self.parent = parent
self.colors = None
vbox = QtWidgets.QVBoxLayout(self)
self.enhancer = AtEnhancerWidget(self)
vbox.addWidget(self.enhancer)
vbox.setContentsMargins(0, 0, 0, 0)
self.enhancer.sliderReleased.connect(self.enhanceContrast)
def setChannelNames(self, channels, colors):
self.colors = colors
self.enhancer.clear()
for channel in channels:
self.enhancer.addChannel(cn.display(channel), no_auto_button=True)
def enhanceContrast(self):
try:
QApplication.setOverrideCursor(QCursor(Qt.WaitCursor))
i = self.enhancer.currentChannelIndex()
color = QtGui.QColor(self.colors[i])
lut = self.enhancer.lut_from_color(i, color, 256)
for item in self.tileview.items:
item.enhancePixmap(i, lut)
finally:
QApplication.restoreOverrideCursor()
def __init__(self, parent, viewer, *args, **kw):
super(ChannelBar, self).__init__(parent, *args, **kw)
self._images = None
self._contours = None
self._channel_count = 0
self.viewer = viewer
vbox = QtWidgets.QVBoxLayout(self)
self.gbox = QtWidgets.QGridLayout()
cbox = QtWidgets.QVBoxLayout()
self.enhancer = AtEnhancerWidget(self)
self.enhancer.valuesUpdated.connect(self.updateImage)
cbox.addWidget(self.enhancer)
vbox.addLayout(self.gbox)
vbox.addLayout(cbox)
vbox.setContentsMargins(3, 3, 3, 3)
self.gbox.setContentsMargins(0, 0, 0, 0)
cbox.setContentsMargins(0, 0, 0, 0)
class AtContrastWidget(QtWidgets.QWidget):
def __init__(self, parent, view, featuredlg=None, *args, **kw):
super(AtContrastWidget, self).__init__(parent)
self.view = view
self.featuredlg = featuredlg
self.parent = parent
vbox = QtWidgets.QVBoxLayout(self)
vbox.setContentsMargins(2, 2, 2, 2)
self.enhancer = AtEnhancerWidget(self)
vbox.addWidget(self.enhancer)
self.enhancer.sliderReleased.connect(self.enhanceContrast)
def setChannelNames(self, channels, colors):
self.enhancer.clear()
for channel, color in zip(channels, colors):
self.enhancer.addChannel(cn.display(channel), color,
no_auto_button=True)
def updateView(self, index=None):
channels = self.enhancer.channelFlags()
for item in self.view.items:
item.setActiveChannels(channels)
item.toggleOutline(self.view.vflags & ViewFlags.Outline)
self.enhanceContrast(index)
def enhanceContrast(self, index=None):
if index is None:
index = self.enhancer.currentChannelIndex()
try:
QApplication.setOverrideCursor(QCursor(Qt.WaitCursor))
lut = self.enhancer.lut_from_channel(index, 256)
for item in self.view.items:
item.enhancePixmap(index, lut)
finally:
QApplication.restoreOverrideCursor()
class ChannelBar(QtWidgets.QWidget):
"""ChannelBar is a layer between the import dialog and the viewer widget.
It modifies the image drawn in the viewer i.e. it turns on/off the channels,
enhances the contrast and sets the color table of the image."""
newPixmap = QtCore.pyqtSignal(QtGui.QPixmap)
newContourImage = QtCore.pyqtSignal(QtGui.QPixmap, "PyQt_PyObject")
def __init__(self, parent, viewer, *args, **kw):
super(ChannelBar, self).__init__(parent, *args, **kw)
self._images = None
self._contours = None
self._channel_count = 0
self.viewer = viewer
vbox = QtWidgets.QVBoxLayout(self)
self.gbox = QtWidgets.QGridLayout()
cbox = QtWidgets.QVBoxLayout()
self.enhancer = AtEnhancerWidget(self)
self.enhancer.valuesUpdated.connect(self.updateImage)
cbox.addWidget(self.enhancer)
vbox.addLayout(self.gbox)
vbox.addLayout(cbox)
vbox.setContentsMargins(3, 3, 3, 3)
self.gbox.setContentsMargins(0, 0, 0, 0)
cbox.setContentsMargins(0, 0, 0, 0)
def addChannels(self, n):
self.clear()
self._channel_count = n
if n > 1:
colors = lambda i: ColorButton.colors[i % len(ColorButton.colors)]
else:
colors = lambda i: ColorButton.white
for i in xrange(n):
cb = QtWidgets.QCheckBox("Channel %d" % (i + 1))
cb.setCheckState(QtCore.Qt.Checked)
cb.stateChanged.connect(self.updateImage)
cbtn = ColorButton(colors(i))
cbtn.colorChanged.connect(self.updateImage)
self.gbox.addWidget(cb, i, 0)
self.gbox.addWidget(cbtn, i, 1)
self.enhancer.addChannel(cb.text())
def setColor(self, name, color):
chnames = self.allChannels()
try:
i = chnames.index(name)
except ValueError:
warnings.warn("can not set color for channel %s" % name)
else:
cb = self.widgetAt(i, 1)
cb.setColor(QtGui.QColor(color))
def activateChannels(self, channels):
for i in xrange(self._channel_count):
cb = self.widgetAt(i, 0)
if cb.text() in channels:
cb.setCheckState(QtCore.Qt.Checked)
else:
cb.setCheckState(QtCore.Qt.Unchecked)
def widgetAt(self, row, column):
return self.gbox.itemAtPosition(row, column).widget()
def clear(self):
self.enhancer.clear()
for i in range(self.gbox.count()):
item = self.gbox.takeAt(0)
item.widget().close()
def channelNames(self):
cnames = list()
for i in self.checkedChannels():
cnames.append(self.widgetAt(i, 0).text())
return cnames
def colors(self):
colors = dict()
for i in xrange(self._channel_count):
colors[self.widgetAt(i, 0).text()] = \
self.widgetAt(i, 1).currentColor().name()
return colors
def checkedChannels(self):
channels = OrderedDict()
for i in xrange(self._channel_count):
cb = self.widgetAt(i, 0)
if cb.isChecked():
channels[i] = cb.text()
return channels
def allChannels(self):
return [
self.widgetAt(i, 0).text() for i in xrange(self._channel_count)
]
def updateImage(self, dummy=None):
if self._images is None:
raise RuntimeError("No images set!")
images = list()
contours = dict()
ccolor = AtConfig().contours_complementary_color
for i, n in self.checkedChannels().iteritems():
# converting the gray image to the color defined in the button
color = self.widgetAt(i, 1).currentColor()
image = self._images[i]
lut = self.enhancer.lut_from_color(i, color, 256)
image.setColorTable(lut)
images.append(image)
if self._contours is not None:
if ccolor:
color = AtPainter.complementaryColor(color)
contours[color] = self._contours[n]
pixmap = AtPainter.blend(images)
# sometimes qt segfaults when drawing polygons
if AtConfig().draw_contours_in_pixmap:
pixmap = AtPainter.drawContours(pixmap, contours)
self.newContourImage.emit(pixmap, None)
else:
self.newContourImage.emit(pixmap, contours)
def setImages(self, images, image_props=None):
self._images = images
if image_props is not None:
self.enhancer.setImageProps(image_props)
self.updateImage()
def setContours(self, contours_dict):
cnts = defaultdict(list)
for contours in contours_dict.itervalues():
# operate only on checked channels here, since there
# no contours available for unchecked channels
for cname in self.checkedChannels().itervalues():
polygon = QtGui.QPolygonF(
[QPointF(*c) for c in contours[cname]])
cnts[cname].append(polygon)
self._contours = cnts
self.updateImage()
def clearContours(self):
self._contours = None
def drawRectangles(self, centers, gsize, isize):
hsize = int(math.floor(gsize / 2.0))
# left, top, width, height
centers = np.array([(x - hsize, y - hsize) for x, y in centers])
centers[:, 0] = np.clip(centers[:, 0], 0, isize[1] - gsize)
centers[:, 1] = np.clip(centers[:, 1], 0, isize[0] - gsize)
rects = tuple([(x, y, gsize, gsize) for x, y in centers])
self.viewer.drawRects(rects)
def contourImage(self, images, contours_dict):
"""Combines setImage and setContours but updates viewer only once."""
self._images = images
self.setContours(contours_dict)
class ChannelBar(QtWidgets.QWidget):
"""ChannelBar is a layer between the import dialog and the viewer widget.
It modifies the image drawn in the viewer i.e. it turns on/off the channels,
enhances the contrast and sets the color table of the image."""
newPixmap = QtCore.pyqtSignal(QtGui.QPixmap)
newContourImage = QtCore.pyqtSignal(QtGui.QPixmap, "PyQt_PyObject")
def __init__(self, parent, viewer, *args, **kw):
super(ChannelBar, self).__init__(parent, *args, **kw)
self._images = None
self._contours = None
self._channel_count = 0
self.viewer = viewer
vbox = QtWidgets.QVBoxLayout(self)
self.gbox = QtWidgets.QGridLayout()
cbox = QtWidgets.QVBoxLayout()
self.enhancer = AtEnhancerWidget(self)
self.enhancer.valuesUpdated.connect(self.updateImage)
cbox.addWidget(self.enhancer)
vbox.addLayout(self.gbox)
vbox.addLayout(cbox)
vbox.setContentsMargins(3, 3, 3, 3)
self.gbox.setContentsMargins(0, 0, 0, 0)
cbox.setContentsMargins(0, 0, 0, 0)
def addChannels(self, n):
self.clear()
self._channel_count = n
if n > 1:
colors = lambda i: ColorButton.colors[i % len(ColorButton.colors)]
else:
colors = lambda i: ColorButton.white
for i in xrange(n):
cb = QtWidgets.QCheckBox("Channel %d" %(i+1))
cb.setCheckState(QtCore.Qt.Checked)
cb.stateChanged.connect(self.updateImage)
cbtn = ColorButton(colors(i))
cbtn.colorChanged.connect(self.updateImage)
self.gbox.addWidget(cb, i, 0)
self.gbox.addWidget(cbtn, i, 1)
self.enhancer.addChannel(cb.text())
def setColor(self, name, color):
chnames = self.allChannels()
try:
i = chnames.index(name)
except ValueError:
warnings.warn("can not set color for channel %s" %name)
else:
cb = self.widgetAt(i, 1)
cb.setColor(QtGui.QColor(color))
def activateChannels(self, channels):
for i in xrange(self._channel_count):
cb = self.widgetAt(i, 0)
if cb.text() in channels:
cb.setCheckState(QtCore.Qt.Checked)
else:
cb.setCheckState(QtCore.Qt.Unchecked)
def widgetAt(self, row, column):
return self.gbox.itemAtPosition(row, column).widget()
def clear(self):
self.enhancer.clear()
for i in range(self.gbox.count()):
item = self.gbox.takeAt(0)
item.widget().close()
def channelNames(self):
cnames = list()
for i in self.checkedChannels():
cnames.append(self.widgetAt(i, 0).text())
return cnames
def colors(self):
colors = dict()
for i in xrange(self._channel_count):
colors[self.widgetAt(i, 0).text()] = \
self.widgetAt(i, 1).currentColor().name()
return colors
def checkedChannels(self):
channels = OrderedDict()
for i in xrange(self._channel_count):
cb = self.widgetAt(i, 0)
if cb.isChecked():
channels[i] = cb.text()
return channels
def allChannels(self):
return [self.widgetAt(i, 0).text() for i in xrange(self._channel_count)]
def updateImage(self, dummy=None):
if self._images is None:
raise RuntimeError("No images set!")
images = list()
contours = dict()
ccolor = AtConfig().contours_complementary_color
for i, n in self.checkedChannels().iteritems():
# converting the gray image to the color defined in the button
color = self.widgetAt(i, 1).currentColor()
image = self._images[i]
lut = self.enhancer.lut_from_color(i, color, 256)
image.setColorTable(lut)
images.append(image)
if self._contours is not None:
if ccolor:
color = AtPainter.complementaryColor(color)
contours[color] = self._contours[n]
pixmap = AtPainter.blend(images)
# sometimes qt segfaults when drawing polygons
if AtConfig().draw_contours_in_pixmap:
pixmap = AtPainter.drawContours(pixmap, contours)
self.newContourImage.emit(pixmap, None)
else:
self.newContourImage.emit(pixmap, contours)
def setImages(self, images, image_props=None):
self._images = images
if image_props is not None:
self.enhancer.setImageProps(image_props)
self.updateImage()
def setContours(self, contours_dict):
cnts = defaultdict(list)
for contours in contours_dict.itervalues():
# operate only on checked channels here, since there
# no contours available for unchecked channels
for cname in self.checkedChannels().itervalues():
polygon = QtGui.QPolygonF(
[QPointF(*c) for c in contours[cname]])
cnts[cname].append(polygon)
self._contours = cnts
self.updateImage()
def clearContours(self):
self._contours = None
def drawRectangles(self, centers, gsize, isize):
hsize = int(math.floor(gsize/2.0))
# left, top, width, height
centers = np.array([(x-hsize, y-hsize) for x, y in centers])
centers [:, 0] = np.clip(centers[:, 0], 0, isize[1]-gsize)
centers [:, 1] = np.clip(centers[:, 1], 0, isize[0]-gsize)
rects = tuple([(x, y, gsize, gsize) for x, y in centers])
self.viewer.drawRects(rects)
def contourImage(self, images, contours_dict):
"""Combines setImage and setContours but updates viewer only once."""
self._images = images
self.setContours(contours_dict)