class MeshPlot(GraphicsObject):
def __init__(self, *args, positions: np.array=None, data: np.array=None, colormap: str=None, **kwargs):
super().__init__(*args, **kwargs)
# Initialize data structures
self.positions = positions
self.data = data
self.rgb_data: Union[None, np.array] = None
self.polygons: List[QtCore.QPolygonF] = []
self.xmin, self.xmax = 0, 0
self.ymin, self.ymax = 0, 0
if positions is not None and data is not None:
self.calc_lims()
elif not (positions is None and data is None):
raise ValueError("Either positions and data must both be given, or neither.")
# Initialize menus
self.menu = None
self.gradientSelectorMenu = None
# Create LUT item
self._LUTitem = HistogramLUTItem()
self._LUTitem.sigLookupTableChanged.connect(self.changedColorScale)
self._LUTitem.sigLevelChangeFinished.connect(self.updateRGBData)
if colormap is not None:
self.changeColorScale(name=colormap)
else:
self.changeColorScale(name=DEFAULT_CMAP)
# And update color and polygon data
if self.data is not None:
self.updateRGBData()
self.calculate_polygons()
# Attach a signal handler on parent changed
self._parent = None
###
# Function related to plot data
def setData(self, positions, data):
self.positions = positions
self.data = data
# Calculate data size
self.calc_lims()
# Update plot
self.updateRGBData()
self.calculate_polygons()
# Update histogram and autorange
hist, bins = np.histogram(self.data, "auto")
newBins = np.ndarray(bins.size+1)
newHist = np.ndarray(hist.size+2)
newBins[0] = bins[0]
newBins[-1] = bins[-1]
newBins[1:-1] = (bins[:-1] + bins[1:])/2
newHist[[0,-1]] = 0
newHist[1:-1] = hist
self._LUTitem.plot.setData(newBins, newHist)
self._LUTitem.setLevels(newBins[0], newBins[-1])
self._LUTitem.plot.getViewBox().itemBoundsChanged(self._LUTitem.plot)
# Force viewport update
self.getViewBox().itemBoundsChanged(self)
self.update()
###
# Functions relating to the size of the image
def calc_lims(self):
if not self.positions:
self.xmin, self.xmax = 0, 0
self.ymin, self.ymax = 0, 0
return
self.xmin, self.ymin = self.positions[0]
self.xmax, self.ymax = self.positions[0]
for x, y in islice(self.positions, 1, None):
self.xmin, self.xmax = min(self.xmin, x), max(self.xmax, x)
self.ymin, self.ymax = min(self.ymin, y), max(self.ymax, y)
logger.debug("Calculated limits (%f, %f) - (%f, %f)", self.xmin, self.ymin,
self.xmax, self.ymax)
def width(self):
return self.xmax - self.xmin
def height(self):
return self.ymax - self.ymin
def boundingRect(self):
tl = QtCore.QPointF(self.xmin, self.ymin)
br = QtCore.QPointF(self.xmax, self.ymax)
return QtCore.QRectF(tl, br)
###
# Functions relating to the colorscale
def setLevels(self, levels, update=True):
"""
Hook setLevels to update histogram when the levels are changed in
the image
"""
super().setLevels(levels, update)
self._LUTitem.setLevels(*self.levels)
def changeColorScale(self, name=None):
if name is None:
raise ValueError("Name of color map must be given")
logger.debug("Changed color scale to %s.", name)
self._LUTitem.gradient.setColorMap(COLORMAPS[name])
def getHistogramLUTItem(self):
return self._LUTitem
@property
def histogram(self):
return self.getHistogramLUTItem()
def changedColorScale(self):
logger.debug("Changed color scale")
self.updateRGBData()
def updateRGBData(self):
minr, maxr = self._LUTitem.getLevels()
logger.debug("Recoloring to changed levels: (%f, %f)", minr, maxr)
if self.data is not None:
scaled = (self.data - minr)/(maxr - minr)
logger.debug("Calculating new colors")
self.rgb_data = self._LUTitem.gradient.colorMap().map(scaled, mode="qcolor")
logger.debug("Done")
self.update()
###
# Functions relating to drawing
def calculate_polygons(self):
"""
Calculate the polygons to be drawn by the mesh plot
"""
raise NotImplementedError()
def paint(self, p, _options, _widget):
logger.debug("Starting paint")
visible = self.parentItem().boundingRect()
if self.polygons is not None and self.polygons:
p.setPen(mkPen(None))
for poly in self.polygons: #pylint: disable=not-an-iterable
if not poly[1].boundingRect().intersects(visible):
continue
p.setBrush(self.rgb_data[poly[0]])
p.drawPolygon(poly[1])
logger.debug("Done painting")
else:
logger.debug("No polygons to draw")
def parentChanged(self):
super().parentChanged()
# Add the histogram to the parent
view_box = self.getViewBox()
if isinstance(view_box, ExtendedPlotWindow):
logger.debug("Adding _LUTitem to parent %r.", view_box)
view_box.addItem(self._LUTitem)
self._parent = view_box
elif view_box is None:
if getattr(self, "_parent", None) is not None:
self._parent.removeItem(self._LUTitem)
self._parent = None
elif isinstance(view_box, CustomViewBox):
# This second call always seems to occur... Ignore it, since we've added
# ourselves to the plot window.
pass
else:
raise NotImplementedError("parentChanged is not implemented for anything "
"other than ExtendedPlotWindows at this time. "
f"Got {type(view_box)}.")
class CustomImageViewer(GraphicsLayoutWidget):
@property
def view_box(self):
return self.image_plot.vb
def __init__(self, parent=None, **kwargs):
setConfigOptions(imageAxisOrder='row-major')
super(CustomImageViewer, self).__init__(parent)
self._scale = (1., 1.)
self._center = (0, 0)
self.__init_ui__()
def __init_ui__(self):
self.setWindowTitle('Image Viewer')
self.image_plot = self.addPlot()
self.image_plot.vb.setAspectLocked()
self.image_plot.vb.invertY()
self.image_item = ImageItem()
self.image_plot.addItem(self.image_item)
self.hist = HistogramLUTItem()
self.hist.setImageItem(self.image_item)
self.addItem(self.hist)
def set_data(self, data, change_limits: bool = True, reset_axes: bool = False):
if data is None:
return
self.image_item.setImage(data, change_limits)
if change_limits:
self.hist.setLevels(data.min(), data.max())
if reset_axes:
self.image_item.resetTransform()
self.set_default_range()
def set_default_range(self):
axes = self.get_axes()
self.image_plot.setRange(xRange=axes[0], yRange=axes[1])
def set_auto_range(self):
self.image_plot.autoRange()
def set_levels(self, levels=None):
if levels:
self.hist.setLevels(levels[0], levels[1])
else:
self.hist.setLevels(self.image_item.image.min(),
self.image_item.image.max())
def get_levels(self):
return self.hist.getLevels()
def set_center(self, center: tuple, pixel_units: bool = True):
if not pixel_units:
scale = self.get_scale()
center = (center[0] / scale[0], center[1] / scale[1])
if self._center != (0, 0) or self._scale != (1., 1.):
self.image_item.resetTransform()
self.image_item.scale(*self._scale)
self.image_item.translate(- center[0], - center[1])
self._center = center
self.set_default_range()
def set_scale(self, scale: float or tuple):
if isinstance(scale, float) or isinstance(scale, int):
scale = (scale, scale)
if self._center != (0, 0) or self._scale != (1., 1.):
self.image_item.resetTransform()
self.image_item.scale(*scale)
if self._center != (0, 0):
self.image_item.translate(- self._center[0], - self._center[1])
self._scale = scale
self.set_default_range()
def get_scale(self):
# scale property is occupied by Qt superclass.
return self._scale
def get_center(self):
return self._center
def set_x_axis(self, x_min, x_max):
self._set_axis(x_min, x_max, 0)
self.set_default_range()
def set_y_axis(self, y_min, y_max):
self._set_axis(y_min, y_max, 1)
self.set_default_range()
def _set_axis(self, min_: float, max_: float, axis_ind: int):
shape = self.image_item.image.shape
scale = np.array(self._scale)
scale[axis_ind] = (max_ - min_) / shape[axis_ind]
center = np.array(self._center)
center[axis_ind] = - min_ / scale[axis_ind]
if self._center != (0, 0) or self._scale != (1., 1.):
self.image_item.resetTransform()
self.image_item.scale(scale[0], scale[1])
self.image_item.translate(- center[0], - center[1])
self._scale = tuple(scale)
self._center = tuple(center)
def get_axes(self):
shape = np.array(self.image_item.image.shape)
scale = np.array(self._scale)
min_ = - np.array(self._center) * scale
max_ = min_ + shape * scale
return (min_[0], max_[0]), (min_[1], max_[1])
class CustomImageViewer(GraphicsLayoutWidget):
@property
def view_box(self):
return self.image_plot.vb
def __init__(self,
parent=None,
*,
hist_range: tuple = None,
sigma_factor: float = 3,
**kwargs):
setConfigOptions(imageAxisOrder='row-major')
super(CustomImageViewer, self).__init__(parent)
self._raw_data = None
self._use_clahe: bool = True
self._scale = (1., 1.)
self._center = (0, 0)
self._hist_range = hist_range
self._sigma_factor = sigma_factor
self._init_ui(**kwargs)
def _init_ui(self, **kwargs):
self.setWindowTitle('Image Viewer')
self.image_plot = self.addPlot(**kwargs)
self.image_plot.vb.setAspectLocked()
self.image_plot.vb.invertY()
self.image_item = ImageItem()
self.image_plot.addItem(self.image_item)
self.image_plot.setMenuEnabled(False)
self.hist = HistogramLUTItem()
self.hist.setImageItem(self.image_item)
self.addItem(self.hist)
self.hist.vb.menu = CustomViewBoxMenu(self.hist.vb)
self.hist.vb.menu.sigSigmaChanged.connect(self.set_sigma_factor)
self.hist.vb.menu.sigRangeAsDefault.connect(self.set_limit_as_default)
self.hist.vb.menu.sigUseClahe.connect(self.enable_clahe)
def set_data(self, data, *, reset_axes: bool = False):
self._raw_data = data
if data is None:
return
if self._use_clahe:
data = standard_contrast_correction(data)
self.image_item.setImage(data)
self.set_levels()
if reset_axes:
self.image_item.resetTransform()
self.set_default_range()
def hist_params(self) -> dict:
return dict(sigma_factor=self._sigma_factor,
hist_range=self._hist_range)
def clear_image(self):
self.set_data(np.zeros((1, 1)))
def set_default_range(self):
if self.image_item.image is None:
return
# self.set_auto_range()
axes = self.get_axes()
self.image_plot.setRange(xRange=axes[1], yRange=axes[0])
@pyqtSlot(bool)
def enable_clahe(self, enable: bool):
self._use_clahe = enable
self.set_data(self._raw_data)
def set_auto_range(self):
self.image_plot.autoRange()
def set_levels(self):
img = self.image_item.image
if img is None:
return
if self._sigma_factor and self._sigma_factor > 0:
m, s = img.flatten().mean(
), img.flatten().std() * self._sigma_factor
self.hist.setLevels(max(m - s, img.min()), min(m + s, img.max()))
elif self._hist_range:
self.hist.setLevels(*self._hist_range)
else:
self.hist.setLevels(self.image_item.image.min(),
self.image_item.image.max())
@pyqtSlot(float)
def set_sigma_factor(self, sigma_factor: float):
self._sigma_factor = sigma_factor
self.set_levels()
@pyqtSlot()
def set_limit_as_default(self):
self._hist_range = self.hist.getLevels()
self._sigma_factor = None
self.set_levels()
def get_levels(self):
return self.hist.getLevels()
def set_center(self, center: tuple, pixel_units: bool = True):
if not pixel_units:
scale = self.get_scale()
center = (center[0] / scale[0], center[1] / scale[1])
if self._center != (0, 0) or self._scale != (1., 1.):
self.image_item.resetTransform()
self.image_item.scale(*self._scale)
self.image_item.translate(-center[0], -center[1])
self._center = center
self.set_default_range()
def set_scale(self, scale: float or tuple):
if isinstance(scale, float) or isinstance(scale, int):
scale = (scale, scale)
if self._center != (0, 0) or self._scale != (1., 1.):
self.image_item.resetTransform()
self.image_item.scale(*scale)
if self._center != (0, 0):
self.image_item.translate(-self._center[0], -self._center[1])
self._scale = scale
self.set_default_range()
def get_scale(self) -> tuple:
# scale property is occupied by Qt superclass.
return self._scale
def get_center(self) -> tuple:
return self._center
def set_x_axis(self, x_min, x_max):
self._set_axis(x_min, x_max, 0)
self.set_default_range()
def set_y_axis(self, y_min, y_max):
self._set_axis(y_min, y_max, 1)
self.set_default_range()
def _set_axis(self, min_: float, max_: float, axis_ind: int):
shape = self.image_item.image.shape
scale = np.array(self._scale)
scale[axis_ind] = (max_ - min_) / shape[axis_ind]
center = np.array(self._center)
center[axis_ind] = -min_ / scale[axis_ind]
if self._center != (0, 0) or self._scale != (1., 1.):
self.image_item.resetTransform()
self.image_item.scale(scale[0], scale[1])
self.image_item.translate(-center[0], -center[1])
self._scale = tuple(scale)
self._center = tuple(center)
def get_axes(self):
shape = np.array(self.image_item.image.shape)
scale = np.array(self._scale)
min_ = -np.array((self._center[1], self._center[0])) * scale
max_ = min_ + shape * scale
return (min_[0], max_[0]), (min_[1], max_[1])
