def _set3DScaleAndOrigin(self, calibrations):
"""Set scale and origin for all 3 axes, to be used when plotting
an image.
See setStack for parameter documentation
"""
if calibrations is None:
self.calibrations3D = (calibration.NoCalibration(),
calibration.NoCalibration(),
calibration.NoCalibration())
else:
self.calibrations3D = []
for i, calib in enumerate(calibrations):
if hasattr(calib, "__len__") and len(calib) == 2:
calib = calibration.LinearCalibration(calib[0], calib[1])
elif calib is None:
calib = calibration.NoCalibration()
elif not isinstance(calib, calibration.AbstractCalibration):
raise TypeError("calibration must be a 2-tuple, None or" +
" an instance of an AbstractCalibration " +
"subclass")
elif not calib.is_affine():
_logger.warning(
"Calibration for dimension %d is not linear, "
"it will be ignored for scaling the graph axes.",
i)
self.calibrations3D.append(calib)
def getCalibrations(self, order='array'):
"""Returns currently used calibrations for each axis
Returned calibrations might differ from the ones that were set as
non-linear calibrations used for image axes are temporarily ignored.
:param str order:
'array' to sort calibrations as data array (dim0, dim1, dim2),
'axes' to sort calibrations as currently selected x, y and z axes.
:return: Calibrations ordered depending on order
:rtype: List[~silx.math.calibration.AbstractCalibration]
"""
assert order in ('array', 'axes')
calibs = []
# filter out non-linear calibration for graph axes
for index, calib in enumerate(self.calibrations3D):
if index != self._perspective and not calib.is_affine():
calib = calibration.NoCalibration()
calibs.append(calib)
if order == 'axes': # Move 'z' axis to the end
xy_dims = [d for d in (0, 1, 2) if d != self._perspective]
calibs = [calibs[max(xy_dims)],
calibs[min(xy_dims)],
calibs[self._perspective]]
return tuple(calibs)
def _set3DScaleAndOrigin(self, calibrations):
"""Set scale and origin for all 3 axes, to be used when plotting
an image.
See setStack for parameter documentation
"""
if calibrations is None:
self.calibrations3D = (calibration.NoCalibration(),
calibration.NoCalibration(),
calibration.NoCalibration())
else:
self.calibrations3D = []
for calib in calibrations:
if hasattr(calib, "__len__") and len(calib) == 2:
calib = calibration.LinearCalibration(calib[0], calib[1])
elif calib is None:
calib = calibration.NoCalibration()
elif not isinstance(calib, calibration.AbstractCalibration):
raise TypeError("calibration must be a 2-tuple, None or" +
" an instance of an AbstractCalibration " +
"subclass")
self.calibrations3D.append(calib)
def __init__(self, parent=None, resetzoom=True, backend=None,
autoScale=False, logScale=False, grid=False,
colormap=True, aspectRatio=True, yinverted=True,
copy=True, save=True, print_=True, control=False,
position=None, mask=True):
qt.QMainWindow.__init__(self, parent)
if parent is not None:
# behave as a widget
self.setWindowFlags(qt.Qt.Widget)
else:
self.setWindowTitle('StackView')
self._stack = None
"""Loaded stack, as a 3D array, a 3D dataset or a list of 2D arrays."""
self.__transposed_view = None
"""View on :attr:`_stack` with the axes sorted, to have
the orthogonal dimension first"""
self._perspective = 0
"""Orthogonal dimension (depth) in :attr:`_stack`"""
self.__imageLegend = '__StackView__image' + str(id(self))
self.__autoscaleCmap = False
"""Flag to disable/enable colormap auto-scaling
based on the min/max values of the entire 3D volume"""
self.__dimensionsLabels = ["Dimension 0", "Dimension 1",
"Dimension 2"]
"""These labels are displayed on the X and Y axes.
:meth:`setLabels` updates this attribute."""
self._first_stack_dimension = 0
"""Used for dimension labels and combobox"""
self._titleCallback = self._defaultTitleCallback
"""Function returning the plot title based on the frame index.
It can be set to a custom function using :meth:`setTitleCallback`"""
self.calibrations3D = (calibration.NoCalibration(),
calibration.NoCalibration(),
calibration.NoCalibration())
central_widget = qt.QWidget(self)
self._plot = PlotWindow(parent=central_widget, backend=backend,
resetzoom=resetzoom, autoScale=autoScale,
logScale=logScale, grid=grid,
curveStyle=False, colormap=colormap,
aspectRatio=aspectRatio, yInverted=yinverted,
copy=copy, save=save, print_=print_,
control=control, position=position,
roi=False, mask=mask)
self._plot.getIntensityHistogramAction().setVisible(True)
self.sigInteractiveModeChanged = self._plot.sigInteractiveModeChanged
self.sigActiveImageChanged = self._plot.sigActiveImageChanged
self.sigPlotSignal = self._plot.sigPlotSignal
if silx.config.DEFAULT_PLOT_IMAGE_Y_AXIS_ORIENTATION == 'downward':
self._plot.getYAxis().setInverted(True)
self._addColorBarAction()
self._plot.profile = Profile3DToolBar(parent=self._plot,
stackview=self)
self._plot.addToolBar(self._plot.profile)
self._plot.getXAxis().setLabel('Columns')
self._plot.getYAxis().setLabel('Rows')
self._plot.sigPlotSignal.connect(self._plotCallback)
self.__planeSelection = PlanesWidget(self._plot)
self.__planeSelection.sigPlaneSelectionChanged.connect(self.setPerspective)
self._browser_label = qt.QLabel("Image index (Dim0):")
self._browser = HorizontalSliderWithBrowser(central_widget)
self._browser.setRange(0, 0)
self._browser.valueChanged[int].connect(self.__updateFrameNumber)
self._browser.setEnabled(False)
layout = qt.QGridLayout()
layout.setContentsMargins(0, 0, 0, 0)
layout.addWidget(self._plot, 0, 0, 1, 3)
layout.addWidget(self.__planeSelection, 1, 0)
layout.addWidget(self._browser_label, 1, 1)
layout.addWidget(self._browser, 1, 2)
central_widget.setLayout(layout)
self.setCentralWidget(central_widget)
# clear profile lines when the perspective changes (plane browsed changed)
self.__planeSelection.sigPlaneSelectionChanged.connect(
self._plot.profile.getProfilePlot().clear)
self.__planeSelection.sigPlaneSelectionChanged.connect(
self._plot.profile.clearProfile)
