class SliceableGraphicsView(GraphicsView, SlicingView):
sigToggleHorizontalSlice = Signal(bool)
sigToggleVerticalSlice = Signal(bool)
sigToggleDepthSlice = Signal(bool)
sigMakePrimary = Signal(object, object)
sigCrosshairMoved = Signal()
SUPPORTED_NDIM = 2
def __init__(self, slice_direction, parent=None, xlink=None, ylink=None):
super(SliceableGraphicsView, self).__init__(parent=parent)
self.slice_direction = slice_direction
self.setContentsMargins(0, 0, 0, 0)
# Add axes
self.view = SliceableAxes(slice_direction)
self.view.axes["left"]["item"].setZValue(10)
self.view.axes["top"]["item"].setZValue(10)
self.setCentralItem(self.view)
for sig in [
'sigToggleVerticalSlice', 'sigToggleHorizontalSlice',
'sigToggleDepthSlice', 'sigMakePrimary'
]:
if hasattr(self.view, sig):
getattr(self.view, sig).connect(getattr(self, sig))
# Add imageitem
self.image_item = ImageItem(axisOrder='row-major')
self.image_item.setOpts()
self.view.addItem(self.image_item)
# add crosshair
self.crosshair = BetterCrosshairROI((0, 0),
parent=self.view,
resizable=False)
self.crosshair.sigMoved.connect(self.sigCrosshairMoved)
self.view.getViewBox().addItem(self.crosshair)
# find top-level parent NDImageView
while not isinstance(parent, NDImageView):
parent = parent.parent()
# Initialize lut, levels
self.image_item.setLevels(parent.levels, update=True)
self.image_item.setLookupTable(parent.lut, update=True)
# Link axes
if ylink:
self.view.vb.setYLink(ylink)
if xlink:
self.view.vb.setXLink(xlink)
def setData(self, data):
# Constrain squareness when units match
is_square = data.dims[-2].split('(')[-1] == data.dims[-1].split(
'(')[-1]
self.view.vb.setAspectLocked(is_square)
xvals = data.coords[data.dims[-1]]
yvals = data.coords[data.dims[-2]]
xmin = float(xvals.min())
xmax = float(xvals.max())
ymin = float(yvals.min())
ymax = float(yvals.max())
# Position the image according to coords
shape = data.shape
a = [(0, shape[-2]), (shape[-1], shape[-2]), (shape[-1], 0), (0, 0)]
# b = [(ymin, xmax), (ymax, xmax), (ymax, xmin), (ymin, xmin)]
if self.slice_direction in ['horizontal', 'depth']:
b = [(xmin, ymin), (xmax, ymin), (xmax, ymax), (xmin, ymax)]
elif self.slice_direction == 'vertical':
b = [(xmax, ymax), (xmin, ymax), (xmin, ymin), (xmax, ymin)]
quad1 = QPolygonF()
quad2 = QPolygonF()
for p, q in zip(a, b):
quad1.append(QPointF(*p))
quad2.append(QPointF(*q))
transform = QTransform()
QTransform.quadToQuad(quad1, quad2, transform)
# Bind coords from the xarray to the timeline axis
# super(SliceableGraphicsView, self).setImage(img, autoRange, autoLevels, levels, axes, np.asarray(img.coords[img.dims[0]]), pos, scale, transform, autoHistogramRange, levelMode)
self.image_item.setImage(np.asarray(data), autoLevels=False)
self.image_item.setTransform(transform)
# Label the image axes
self.view.setLabel('left', data.dims[-2])
self.view.setLabel('bottom', data.dims[-1])
def resetCrosshair(self):
transform = self.image_item.viewTransform()
new_pos = transform.map(self.image_item.boundingRect().center())
self.crosshair.setPos(new_pos)
# self.crosshair.sigMoved.emit(new_pos)
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
]
ax_swap = [image.dims[ax_index] for ax_index in axorder]
image = image.transpose(*ax_swap)
# Select time index
if self.axes['t'] is not None:
self.ui.roiPlot.show()
image = image[self.currentIndex]
self.imageItem.updateImage(np.asarray(image))
def updateCrosshair(self, x, y):
self.crosshair.setPos(x, y)
def quickMinMax(self, data):
"""
Estimate the min/max values of *data* by subsampling. MODIFIED TO USE THE 99TH PERCENTILE instead of max.
"""
if data is None:
return 0, 0
sl = slice(None, None, max(1, int(data.size // 1e6)))
data = np.asarray(data[sl])
levels = (np.nanmin(data),
np.nanpercentile(
np.where(data < np.nanmax(data), data, np.nanmin(data)),
99))
return [levels]
class SliceableGraphicsView(GraphicsView):
sigToggleHorizontalSlice = Signal(bool)
sigToggleVerticalSlice = Signal(bool)
sigMakePrimary = Signal(object, object)
def __init__(self):
super(SliceableGraphicsView, self).__init__()
self.setContentsMargins(0, 0, 0, 0)
# Add axes
self.view = SliceableAxes()
self.view.axes["left"]["item"].setZValue(10)
self.view.axes["top"]["item"].setZValue(10)
self.setCentralItem(self.view)
self.view.sigToggleVerticalSlice.connect(self.sigToggleVerticalSlice)
self.view.sigToggleHorizontalSlice.connect(self.sigToggleHorizontalSlice)
self.view.sigMakePrimary.connect(self.sigMakePrimary)
# Add imageitem
self.image_item = ImageItem()
self.view.addItem(self.image_item)
# add crosshair
self.crosshair = BetterCrosshairROI((0, 0), parent=self.view, resizable=False)
self.view.getViewBox().addItem(self.crosshair)
def setData(self, data):
xvals = data.coords[data.dims[-1]]
yvals = data.coords[data.dims[-2]]
xmin = float(xvals.min())
xmax = float(xvals.max())
ymin = float(yvals.min())
ymax = float(yvals.max())
# Position the image according to coords
shape = data.shape
a = [(0, shape[-1]), (shape[-2] - 1, shape[-1]), (shape[-2] - 1, 1), (0, 1)]
# b = [(ymin, xmax), (ymax, xmax), (ymax, xmin), (ymin, xmin)]
b = [(xmax, ymin), (xmax, ymax), (xmin, ymax), (xmin, ymin)]
quad1 = QPolygonF()
quad2 = QPolygonF()
for p, q in zip(a, b):
quad1.append(QPointF(*p))
quad2.append(QPointF(*q))
transform = QTransform()
QTransform.quadToQuad(quad1, quad2, transform)
# Bind coords from the xarray to the timeline axis
# super(SliceableGraphicsView, self).setImage(img, autoRange, autoLevels, levels, axes, np.asarray(img.coords[img.dims[0]]), pos, scale, transform, autoHistogramRange, levelMode)
self.image_item.setImage(np.asarray(data), autoLevels=False)
self.image_item.setTransform(transform)
# Label the image axes
self.view.setLabel('left', data.dims[-2])
self.view.setLabel('bottom', data.dims[-1])
def resetCrosshair(self):
transform = self.image_item.viewTransform()
new_pos = transform.map(self.image_item.boundingRect().center())
self.crosshair.setPos(new_pos)
self.crosshair.sigMoved.emit(new_pos)
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]
ax_swap = [image.dims[ax_index] for ax_index in axorder]
image = image.transpose(*ax_swap)
# Select time index
if self.axes['t'] is not None:
self.ui.roiPlot.show()
image = image[self.currentIndex]
self.imageItem.updateImage(np.asarray(image))
def quickMinMax(self, data):
"""
Estimate the min/max values of *data* by subsampling. MODIFIED TO USE THE 99TH PERCENTILE instead of max.
"""
if data is None:
return 0, 0
sl = slice(None, None, max(1, int(data.size // 1e6)))
data = np.asarray(data[sl])
levels = (np.nanmin(data), np.nanpercentile(np.where(data < np.nanmax(data), data, np.nanmin(data)), 99))
return [levels]
