def plot3Dsilx(nodeData):
from silx.gui.plot import StackView
saveType = nodeData[0]
plot = StackView()
plot.setColormap('viridis')
plot.setGraphTitle(nodeData[1] + ' ' + saveType)
plot.setLabels(nodeData[3])
savedColumns = nodeData[4]
for fname, props in savedColumns.items():
maps = read3D(saveType, fname, props)
# applied only to one (first) 3D map:
v = maps[0]
plot.setStack(v)
# plot.saveGraph('test.png')
plot.show() # end plot3Dsilx
class ArrayStackPlot(qt.QWidget):
"""
Widget for plotting a n-D array (n >= 3) as a stack of images.
Three axis arrays can be provided to calibrate the axes.
The signal array can have an arbitrary number of dimensions, the only
limitation being that the last 3 dimensions must have the same length as
the axes arrays.
Sliders are provided to select indices on the first (n - 3) dimensions of
the signal array, and the plot is updated to load the stack corresponding
to the selection.
"""
def __init__(self, parent=None):
"""
:param parent: Parent QWidget
"""
super(ArrayStackPlot, self).__init__(parent)
self.__signal = None
self.__signal_name = None
# the Z, Y, X axes apply to the last three dimensions of the signal
# (in that order)
self.__z_axis = None
self.__z_axis_name = None
self.__y_axis = None
self.__y_axis_name = None
self.__x_axis = None
self.__x_axis_name = None
self._stack_view = StackView(self)
self._hline = qt.QFrame(self)
self._hline.setFrameStyle(qt.QFrame.HLine)
self._hline.setFrameShadow(qt.QFrame.Sunken)
self._legend = qt.QLabel(self)
self._selector = NumpyAxesSelector(self)
self._selector.setNamedAxesSelectorVisibility(False)
self.__selector_is_connected = False
layout = qt.QVBoxLayout()
layout.addWidget(self._stack_view)
layout.addWidget(self._hline)
layout.addWidget(self._legend)
layout.addWidget(self._selector)
self.setLayout(layout)
def getStackView(self):
"""Returns the plot used for the display
:rtype: StackView
"""
return self._stack_view
def setStackData(self,
signal,
x_axis=None,
y_axis=None,
z_axis=None,
signal_name=None,
xlabel=None,
ylabel=None,
zlabel=None,
title=None):
"""
:param signal: n-D dataset, whose last 3 dimensions are used as the
3D stack values.
:param x_axis: 1-D dataset used as the image's x coordinates. If
provided, its lengths must be equal to the length of the last
dimension of ``signal``.
:param y_axis: 1-D dataset used as the image's y. If provided,
its lengths must be equal to the length of the 2nd to last
dimension of ``signal``.
:param z_axis: 1-D dataset used as the image's z. If provided,
its lengths must be equal to the length of the 3rd to last
dimension of ``signal``.
:param signal_name: Label used in the legend
:param xlabel: Label for X axis
:param ylabel: Label for Y axis
:param zlabel: Label for Z axis
:param title: Graph title
"""
if self.__selector_is_connected:
self._selector.selectionChanged.disconnect(self._updateStack)
self.__selector_is_connected = False
self.__signal = signal
self.__signal_name = signal_name or ""
self.__x_axis = x_axis
self.__x_axis_name = xlabel
self.__y_axis = y_axis
self.__y_axis_name = ylabel
self.__z_axis = z_axis
self.__z_axis_name = zlabel
self._selector.setData(signal)
self._selector.setAxisNames(["Y", "X", "Z"])
self._stack_view.setGraphTitle(title or "")
# by default, the z axis is the image position (dimension not plotted)
self._stack_view.getPlotWidget().getXAxis().setLabel(self.__x_axis_name
or "X")
self._stack_view.getPlotWidget().getYAxis().setLabel(self.__y_axis_name
or "Y")
self._updateStack()
ndims = len(signal.shape)
self._stack_view.setFirstStackDimension(ndims - 3)
# the legend label shows the selection slice producing the volume
# (only interesting for ndim > 3)
if ndims > 3:
self._selector.setVisible(True)
self._legend.setVisible(True)
self._hline.setVisible(True)
else:
self._selector.setVisible(False)
self._legend.setVisible(False)
self._hline.setVisible(False)
if not self.__selector_is_connected:
self._selector.selectionChanged.connect(self._updateStack)
self.__selector_is_connected = True
@staticmethod
def _get_origin_scale(axis):
"""Assuming axis is a regularly spaced 1D array,
return a tuple (origin, scale) where:
- origin = axis[0]
- scale = (axis[n-1] - axis[0]) / (n -1)
:param axis: 1D numpy array
:return: Tuple (axis[0], (axis[-1] - axis[0]) / (len(axis) - 1))
"""
return axis[0], (axis[-1] - axis[0]) / (len(axis) - 1)
def _updateStack(self):
"""Update displayed stack according to the current axes selector
data."""
stk = self._selector.selectedData()
x_axis = self.__x_axis
y_axis = self.__y_axis
z_axis = self.__z_axis
calibrations = []
for axis in [z_axis, y_axis, x_axis]:
if axis is None:
calibrations.append(NoCalibration())
elif len(axis) == 2:
calibrations.append(
LinearCalibration(y_intercept=axis[0], slope=axis[1]))
else:
calibrations.append(ArrayCalibration(axis))
legend = self.__signal_name + "["
for sl in self._selector.selection():
if sl == slice(None):
legend += ":, "
else:
legend += str(sl) + ", "
legend = legend[:-2] + "]"
self._legend.setText("Displayed data: " + legend)
self._stack_view.setStack(stk, calibrations=calibrations)
self._stack_view.setLabels(labels=[
self.__z_axis_name, self.__y_axis_name, self.__x_axis_name
])
def clear(self):
old = self._selector.blockSignals(True)
self._selector.clear()
self._selector.blockSignals(old)
self._stack_view.clear()
class ArrayStackPlot(qt.QWidget):
"""
Widget for plotting a n-D array (n >= 3) as a stack of images.
Three axis arrays can be provided to calibrate the axes.
The signal array can have an arbitrary number of dimensions, the only
limitation being that the last 3 dimensions must have the same length as
the axes arrays.
Sliders are provided to select indices on the first (n - 3) dimensions of
the signal array, and the plot is updated to load the stack corresponding
to the selection.
"""
def __init__(self, parent=None):
"""
:param parent: Parent QWidget
"""
super(ArrayStackPlot, self).__init__(parent)
self.__signal = None
self.__signal_name = None
# the Z, Y, X axes apply to the last three dimensions of the signal
# (in that order)
self.__z_axis = None
self.__z_axis_name = None
self.__y_axis = None
self.__y_axis_name = None
self.__x_axis = None
self.__x_axis_name = None
self._stack_view = StackView(self)
self._hline = qt.QFrame(self)
self._hline.setFrameStyle(qt.QFrame.HLine)
self._hline.setFrameShadow(qt.QFrame.Sunken)
self._legend = qt.QLabel(self)
self._selector = NumpyAxesSelector(self)
self._selector.setNamedAxesSelectorVisibility(False)
self.__selector_is_connected = False
layout = qt.QVBoxLayout()
layout.addWidget(self._stack_view)
layout.addWidget(self._hline)
layout.addWidget(self._legend)
layout.addWidget(self._selector)
self.setLayout(layout)
def getStackView(self):
"""Returns the plot used for the display
:rtype: StackView
"""
return self._stack_view
def setStackData(self, signal,
x_axis=None, y_axis=None, z_axis=None,
signal_name=None,
xlabel=None, ylabel=None, zlabel=None,
title=None):
"""
:param signal: n-D dataset, whose last 3 dimensions are used as the
3D stack values.
:param x_axis: 1-D dataset used as the image's x coordinates. If
provided, its lengths must be equal to the length of the last
dimension of ``signal``.
:param y_axis: 1-D dataset used as the image's y. If provided,
its lengths must be equal to the length of the 2nd to last
dimension of ``signal``.
:param z_axis: 1-D dataset used as the image's z. If provided,
its lengths must be equal to the length of the 3rd to last
dimension of ``signal``.
:param signal_name: Label used in the legend
:param xlabel: Label for X axis
:param ylabel: Label for Y axis
:param zlabel: Label for Z axis
:param title: Graph title
"""
if self.__selector_is_connected:
self._selector.selectionChanged.disconnect(self._updateStack)
self.__selector_is_connected = False
self.__signal = signal
self.__signal_name = signal_name or ""
self.__x_axis = x_axis
self.__x_axis_name = xlabel
self.__y_axis = y_axis
self.__y_axis_name = ylabel
self.__z_axis = z_axis
self.__z_axis_name = zlabel
self._selector.setData(signal)
self._selector.setAxisNames(["Y", "X", "Z"])
self._stack_view.setGraphTitle(title or "")
# by default, the z axis is the image position (dimension not plotted)
self._stack_view.getPlot().getXAxis().setLabel(self.__x_axis_name or "X")
self._stack_view.getPlot().getYAxis().setLabel(self.__y_axis_name or "Y")
self._updateStack()
ndims = len(signal.shape)
self._stack_view.setFirstStackDimension(ndims - 3)
# the legend label shows the selection slice producing the volume
# (only interesting for ndim > 3)
if ndims > 3:
self._selector.setVisible(True)
self._legend.setVisible(True)
self._hline.setVisible(True)
else:
self._selector.setVisible(False)
self._legend.setVisible(False)
self._hline.setVisible(False)
if not self.__selector_is_connected:
self._selector.selectionChanged.connect(self._updateStack)
self.__selector_is_connected = True
@staticmethod
def _get_origin_scale(axis):
"""Assuming axis is a regularly spaced 1D array,
return a tuple (origin, scale) where:
- origin = axis[0]
- scale = (axis[n-1] - axis[0]) / (n -1)
:param axis: 1D numpy array
:return: Tuple (axis[0], (axis[-1] - axis[0]) / (len(axis) - 1))
"""
return axis[0], (axis[-1] - axis[0]) / (len(axis) - 1)
def _updateStack(self):
"""Update displayed stack according to the current axes selector
data."""
stk = self._selector.selectedData()
x_axis = self.__x_axis
y_axis = self.__y_axis
z_axis = self.__z_axis
calibrations = []
for axis in [z_axis, y_axis, x_axis]:
if axis is None:
calibrations.append(NoCalibration())
elif len(axis) == 2:
calibrations.append(
LinearCalibration(y_intercept=axis[0],
slope=axis[1]))
else:
calibrations.append(ArrayCalibration(axis))
legend = self.__signal_name + "["
for sl in self._selector.selection():
if sl == slice(None):
legend += ":, "
else:
legend += str(sl) + ", "
legend = legend[:-2] + "]"
self._legend.setText("Displayed data: " + legend)
self._stack_view.setStack(stk, calibrations=calibrations)
self._stack_view.setLabels(
labels=[self.__z_axis_name,
self.__y_axis_name,
self.__x_axis_name])
def clear(self):
old = self._selector.blockSignals(True)
self._selector.clear()
self._selector.blockSignals(old)
self._stack_view.clear()