StackView
: Plot a stack of images¶
QWidget displaying a 3D volume as a stack of 2D images.
The StackView
class implements this widget.
Basic usage of StackView
is through the following methods:
StackView.getColormap()
,StackView.setColormap()
to update the default colormap to use and update the currently displayed image.StackView.setStack()
to update the displayed image.
The StackView
uses PlotWindow
and also
exposes a subset of the silx.gui.plot.Plot
API for further control
(plot title, axes labels, …).
The StackViewMainWindow
class implements a widget that adds a status
bar displaying the 3D index and the value under the mouse cursor.
Example:
import numpy
import sys
from silx.gui import qt
from silx.gui.plot.StackView import StackViewMainWindow
app = qt.QApplication(sys.argv[1:])
# synthetic data, stack of 100 images of size 200x300
mystack = numpy.fromfunction(
lambda i, j, k: numpy.sin(i/15.) + numpy.cos(j/4.) + 2 * numpy.sin(k/6.),
(100, 200, 300)
)
sv = StackViewMainWindow()
sv.setColormap("jet", autoscale=True)
sv.setStack(mystack)
sv.setLabels(["1st dim (0-99)", "2nd dim (0-199)",
"3rd dim (0-299)"])
sv.show()
app.exec_()
StackView
class¶
-
class
StackView
(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)[source]¶ Stack view widget, to display and browse through stack of images.
The profile tool can be switched to “3D” mode, to compute the profile on each image of the stack (not only the active image currently displayed) and display the result as a slice.
- Parameters
parent (QWidget) – the Qt parent, or None
backend (str or
BackendBase.BackendBase
) – The backend to use for the plot (default: matplotlib). SeePlotWidget
for the list of supported backend.resetzoom (bool) – Toggle visibility of reset zoom action.
autoScale (bool) – Toggle visibility of axes autoscale actions.
logScale (bool) – Toggle visibility of axes log scale actions.
grid (bool) – Toggle visibility of grid mode action.
colormap (bool) – Toggle visibility of colormap action.
aspectRatio (bool) – Toggle visibility of aspect ratio button.
yInverted (bool) – Toggle visibility of Y axis direction button.
copy (bool) – Toggle visibility of copy action.
save (bool) – Toggle visibility of save action.
print (bool) – Toggle visibility of print action.
control (bool) – True to display an Options button with a sub-menu to show legends, toggle crosshair and pan with arrows. (Default: False)
position – True to display widget with (x, y) mouse position (Default: False). It also supports a list of (name, funct(x, y)->value) to customize the displayed values. See
silx.gui.plot.PlotTools.PositionInfo
.mask (bool) – Toggle visibilty of mask action.
-
valueChanged
¶ Signals that the data value under the cursor has changed.
It provides: row, column, data value.
-
sigPlaneSelectionChanged
¶ Signal emitted when there is a change is perspective/displayed axes.
It provides the perspective as an integer, with the following meaning:
0: axis Y is the 2nd dimension, axis X is the 3rd dimension
1: axis Y is the 1st dimension, axis X is the 3rd dimension
2: axis Y is the 1st dimension, axis X is the 2nd dimension
-
sigStackChanged
¶ Signal emitted when the stack is changed. This happens when a new volume is loaded, or when the current volume is transposed (change in perspective).
The signal provides the size (number of pixels) of the stack. This will be 0 if the stack is cleared, else it will be a positive integer.
-
sigFrameChanged
¶ Signal emitter when the frame number has changed.
This signal provides the current frame number.
-
getPerspective
()[source]¶ Returns the index of the dimension the stack is browsed with
Possible values are: 0, 1, or 2.
- Return type
int
-
setPerspective
(perspective)[source]¶ Set the index of the dimension the stack is browsed with:
slice plane Dim1-Dim2: perspective 0
slice plane Dim0-Dim2: perspective 1
slice plane Dim0-Dim1: perspective 2
- Parameters
perspective (int) – Orthogonal dimension number (0, 1, or 2)
-
getCalibrations
(order='array')[source]¶ 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.
- Parameters
order (str) – ‘array’ to sort calibrations as data array (dim0, dim1, dim2), ‘axes’ to sort calibrations as currently selected x, y and z axes.
- Returns
Calibrations ordered depending on order
- Return type
List[AbstractCalibration]
-
setStack
(stack, perspective=None, reset=True, calibrations=None)[source]¶ Set the 3D stack.
The perspective parameter is used to define which dimension of the 3D array is to be used as frame index. The lowest remaining dimension number is the row index of the displayed image (Y axis), and the highest remaining dimension is the column index (X axis).
- Parameters
stack (3D numpy.ndarray, or 3D h5py.Dataset, or list/tuple of 2D numpy arrays, or None.) – 3D stack, or None to clear plot.
perspective (int) – Dimension for the frame index: 0, 1 or 2. Use
None
to keep the current perspective (default).reset (bool) – Whether to reset zoom or not.
calibrations – Sequence of 3 calibration objects for each axis. These objects can be a subclass of
AbstractCalibration
, or 2-tuples (a, b) where a is the y-intercept and b is the slope of a linear calibration (\(x \mapsto a + b x\))
-
getStack
(copy=True, returnNumpyArray=False)[source]¶ Get the original stack, as a 3D array or dataset.
The output has the form: [data, params] where params is a dictionary containing display parameters.
- Parameters
copy (bool) – If True (default), then the object is copied and returned as a numpy array. Else, a reference to original data is returned, if possible. If the original data is not a numpy array and parameter returnNumpyArray is True, a copy will be made anyway.
returnNumpyArray (bool) – If True, the returned object is guaranteed to be a numpy array.
- Returns
3D stack and parameters.
- Return type
(numpy.ndarray, dict)
-
getCurrentView
(copy=True, returnNumpyArray=False)[source]¶ Get the stack, as it is currently displayed.
The first index of the returned stack is always the frame index. If the perspective has been changed in the widget since the data was first loaded, this will be reflected in the order of the dimensions of the returned object.
The output has the form: [data, params] where params is a dictionary containing display parameters.
- Parameters
copy (bool) – If True (default), then the object is copied and returned as a numpy array. Else, a reference to original data is returned, if possible. If the original data is not a numpy array and parameter returnNumpyArray is True, a copy will be made anyway.
returnNumpyArray (bool) – If True, the returned object is guaranteed to be a numpy array.
- Returns
3D stack and parameters.
- Return type
(numpy.ndarray, dict)
-
setFrameNumber
(number)[source]¶ Set the frame selection to a specific value
- Parameters
number (int) – Number of the frame
-
getFrameNumber
()[source]¶ Set the frame selection to a specific value
- Returns
Index of currently displayed frame
- Return type
int
-
setFirstStackDimension
(first_stack_dimension)[source]¶ When viewing the last 3 dimensions of an n-D array (n>3), you can use this method to change the text in the combobox.
For instance, for a 7-D array, first stack dim is 4, so the default “Dim1-Dim2” text should be replaced with “Dim5-Dim6” (dimensions numbers are 0-based).
- Parameters
first_stack_dim (int) – First stack dimension (n-3) when viewing the last 3 dimensions of an n-D array.
-
setTitleCallback
(callback)[source]¶ Set a user defined function to generate the plot title based on the image/frame index.
The callback function must accept an integer as a its first positional parameter and must not require any other mandatory parameter. It must return a string.
To switch back the default behavior, you can pass
None
:mystackview.setTitleCallback(None)
To have no title, pass a function that returns an empty string:
mystackview.setTitleCallback(lambda idx: "")
- Parameters
callback – Callback function generating the stack title based on the frame number.
-
setLabels
(labels=None)[source]¶ Set the labels to be displayed on the plot axes.
You must provide a sequence of 3 strings, corresponding to the 3 dimensions of the original data volume. The proper label will automatically be selected for each plot axis when the volume is rotated (when different axes are selected as the X and Y axes).
- Parameters
labels (List[str]) – 3 labels corresponding to the 3 dimensions of the data volumes.
-
getLabels
()[source]¶ Return dimension labels displayed on the plot axes
- Returns
List of three strings corresponding to the 3 dimensions of the stack: (name_dim0, name_dim1, name_dim2)
-
getColormap
()[source]¶ Get the current colormap description.
- Returns
A description of the current colormap. See
setColormap()
for details.- Return type
dict
-
setColormap
(colormap=None, normalization=None, autoscale=None, vmin=None, vmax=None, colors=None)[source]¶ Set the colormap and update active image.
Parameters that are not provided are taken from the current colormap.
The colormap parameter can also be a dict with the following keys:
name: string. The colormap to use: ‘gray’, ‘reversed gray’, ‘temperature’, ‘red’, ‘green’, ‘blue’.
normalization: string. The mapping to use for the colormap: either ‘linear’ or ‘log’.
autoscale: bool. Whether to use autoscale (True) or range provided by keys ‘vmin’ and ‘vmax’ (False).
vmin: float. The minimum value of the range to use if ‘autoscale’ is False.
vmax: float. The maximum value of the range to use if ‘autoscale’ is False.
- colors: optional. Nx3 or Nx4 array of float in [0, 1] or uint8.
List of RGB or RGBA colors to use (only if name is None)
- Parameters
colormap (dict or str.) – Name of the colormap in ‘gray’, ‘reversed gray’, ‘temperature’, ‘red’, ‘green’, ‘blue’. Or a :class`.Colormap` object.
normalization (str) – Colormap mapping: ‘linear’ or ‘log’.
autoscale (bool) – Whether to use autoscale or [vmin, vmax] range. Default value of autoscale is False. This option is not compatible with h5py datasets.
vmin (float) – The minimum value of the range to use if ‘autoscale’ is False.
vmax (float) – The maximum value of the range to use if ‘autoscale’ is False.
colors (numpy.ndarray) – Only used if name is None. Custom colormap colors as Nx3 or Nx4 RGB or RGBA arrays
-
getPlotWidget
()[source]¶ Return the
PlotWidget
.This gives access to advanced plot configuration options. Be warned that modifying the plot can cause issues, and some changes you make to the plot could be overwritten by the
StackView
widget’s internal methods and callbacks.- Returns
instance of
PlotWidget
used in widget
-
setOptionVisible
(isVisible)[source]¶ Set the visibility of the browsing options.
- Parameters
isVisible (bool) – True to have the options visible, else False
-
setGraphTitle
(title='')[source]¶ Set the plot main title.
- Parameters
title (str) – Main title of the plot (default: ‘’)
-
setGraphXLabel
(label=None)[source]¶ Set the plot horizontal axis label.
- Parameters
label (str) – The horizontal axis label
-
getGraphYLabel
(axis='left')[source]¶ Return the current vertical axis label as a str.
- Parameters
axis (str) – The Y axis for which to get the label (left or right)
-
setGraphYLabel
(label=None, axis='left')[source]¶ Set the vertical axis label on the plot.
- Parameters
label (str) – The Y axis label
axis (str) – The Y axis for which to set the label (left or right)
StackViewMainWindow
class¶
-
class
StackViewMainWindow
(parent=None)[source]¶ Bases:
silx.gui.plot.StackView.StackView
This class is a
StackView
with a menu, an additional toolbar to set the plot limits, and a status bar to display the value and 3D index of the data samples hovered by the mouse cursor.- Parameters
parent (QWidget) – Parent widget, or None
-
setStack
(stack, *args, **kwargs)[source]¶ Set the displayed stack.
See
StackView.setStack()
for details.