# /*##########################################################################
#
# Copyright (c) 2018-2023 European Synchrotron Radiation Facility
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
# in the Software without restriction, including without limitation the rights
# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
# copies of the Software, and to permit persons to whom the Software is
# furnished to do so, subject to the following conditions:
#
# The above copyright notice and this permission notice shall be included in
# all copies or substantial portions of the Software.
#
# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
# THE SOFTWARE.
#
# ###########################################################################*/
"""This module adds convenient functions to use plot3d widgets from the console.
"""
__authors__ = ["T. Vincent"]
__license__ = "MIT"
__date__ = "24/04/2018"
from collections import abc
import logging
import numpy
from ..gui import qt
from ..gui.plot3d.SceneWindow import SceneWindow
from ..gui.plot3d.ScalarFieldView import ScalarFieldView
from ..gui.plot3d import SFViewParamTree
from ..gui.colors import Colormap
from ..gui.colors import rgba
_logger = logging.getLogger(__name__)
[docs]
def contour3d(
scalars,
contours=1,
copy=True,
color=None,
colormap="viridis",
vmin=None,
vmax=None,
opacity=1.0,
):
"""
Plot isosurfaces of a 3D scalar field in a :class:`~silx.gui.plot3d.ScalarFieldView.ScalarFieldView` widget.
How to use:
>>> from silx import sx
Provided data, a 3D scalar field as a numpy array of float32:
>>> plot3d_window = sx.contour3d(data)
Alternatively you can provide the level of the isosurfaces:
>>> plot3d_window = sx.contour3d(data, contours=[0.2, 0.4])
This function provides a subset of `mayavi.mlab.contour3d
<http://docs.enthought.com/mayavi/mayavi/auto/mlab_helper_functions.html#contour3d>`_
arguments.
:param scalars: The 3D scalar field to visualize
:type scalars: numpy.ndarray of float32 with 3 dimensions
:param contours:
Either the number of isosurfaces to draw (as an int) or
the isosurface level (as a float) or a list of isosurface levels
(as a list of float)
:type contours: Union[int, float, List[float]]
:param bool copy:
True (default) to make a copy of scalars.
False to avoid this copy (do not modify provided data afterwards)
:param color:
Color.s to use for isosurfaces.
Either a single color or a list of colors (one for each isosurface).
A color can be defined by its name (as a str) or
as RGB(A) as float or uint8.
:param str colormap:
If color is not provided, this colormap is used
for coloring isosurfaces.
:param vmin: Minimum value of the colormap
:type vmin: Union[float, None]
:param vmax: Maximum value of the colormap
:type vmax: Union[float, None]
:param float opacity:
Transparency of the isosurfaces as a float in [0., 1.]
:return: The widget used to visualize the data
:rtype: ~silx.gui.plot3d.ScalarFieldView.ScalarFieldView
"""
# Prepare isolevel values
if isinstance(contours, int):
# Compute contours number of isovalues
mean = numpy.mean(scalars)
std = numpy.std(scalars)
start = mean - std * ((contours - 1) // 2)
contours = [start + std * index for index in range(contours)]
elif isinstance(contours, float):
contours = [contours]
assert isinstance(contours, abc.Iterable)
# Prepare colors
if color is not None:
if isinstance(color, str) or isinstance(color[0], (int, float)):
# Single color provided, use it for all isosurfaces
colors = [rgba(color)] * len(contours)
else:
# As many colors as contours
colors = [rgba(c) for c in color]
# convert colors from float to uint8
colors = (numpy.array(colors) * 255).astype(numpy.uint8)
else: # Use colormap
colormap = Colormap(name=colormap, vmin=vmin, vmax=vmax)
colors = colormap.applyToData(contours)
assert len(colors) == len(contours)
# Prepare and apply opacity
assert isinstance(opacity, float)
opacity = min(max(0.0, opacity), 1.0) # Clip opacity
colors[:, -1] = (colors[:, -1] * opacity).astype(numpy.uint8)
# Prepare widget
scalarField = ScalarFieldView()
scalarField.setBackgroundColor((0.9, 0.9, 0.9))
scalarField.setForegroundColor((0.1, 0.1, 0.1))
scalarField.setData(scalars, copy=copy)
# Create a parameter tree for the scalar field view
treeView = SFViewParamTree.TreeView(scalarField)
treeView.setSfView(scalarField) # Attach the parameter tree to the view
# Add the parameter tree to the main window in a dock widget
dock = qt.QDockWidget(scalarField)
dock.setWindowTitle("Parameters")
dock.setWidget(treeView)
scalarField.addDockWidget(qt.Qt.RightDockWidgetArea, dock)
for level, color in zip(contours, colors):
scalarField.addIsosurface(level, color)
scalarField.show()
return scalarField
_POINTS3D_MODE_CONVERSION = {
"2dcircle": "o",
"2dcross": "x",
"2ddash": "_",
"2ddiamond": "d",
"2dsquare": "s",
"point": ",",
}
[docs]
def points3d(
x,
y,
z=None,
values=0.0,
copy=True,
colormap="viridis",
vmin=None,
vmax=None,
mode=None,
):
"""
Plot a 3D scatter plot in a :class:`~silx.gui.plot3d.SceneWindow.SceneWindow` widget.
How to use:
>>> from silx import sx
Provided x, y, z, values, 4 numpy array of float32:
>>> plot3d_window = sx.points3d(x, y, z)
>>> plot3d_window = sx.points3d(x, y, z, values)
This function provides a subset of `mayavi.mlab.points3d
<http://docs.enthought.com/mayavi/mayavi/auto/mlab_helper_functions.html#points3d>`_
arguments.
:param numpy.ndarray x: X coordinates of the points
:param numpy.ndarray y: Y coordinates of the points
:param numpy.ndarray z: Z coordinates of the points (optional)
:param numpy.ndarray values: Values at each point (optional)
:param bool copy:
True (default) to make a copy of scalars.
False to avoid this copy (do not modify provided data afterwards)
:param str colormap:
Colormap to use for coding points as colors.
:param vmin: Minimum value of the colormap
:type vmin: Union[float, None]
:param vmax: Maximum value of the colormap
:type vmax: Union[float, None]
:param str mode: The type of marker to use
- Circle: 'o', '2dcircle'
- Diamond: 'd', '2ddiamond'
- Square: 's', '2dsquare'
- Plus: '+'
- Cross: 'x', '2dcross'
- Star: '*'
- Vertical line: '|'
- Horizontal line: '_', '2ddash'
- Point: '.'
- Pixel: ','
:return: The widget used to visualize the data
:rtype: ~silx.gui.plot3d.SceneWindow.SceneWindow
"""
# Prepare widget
window = SceneWindow()
sceneWidget = window.getSceneWidget()
sceneWidget.setBackgroundColor((0.9, 0.9, 0.9))
sceneWidget.setForegroundColor((0.5, 0.5, 0.5))
sceneWidget.setTextColor((0.1, 0.1, 0.1))
mode = _POINTS3D_MODE_CONVERSION.get(mode, mode)
if z is None: # 2D scatter plot
scatter = sceneWidget.add2DScatter(x, y, values, copy=copy)
else: # 3D scatter plot
scatter = sceneWidget.add3DScatter(x, y, z, values, copy=copy)
colormap = Colormap(name=colormap, vmin=vmin, vmax=vmax)
scatter.setColormap(colormap)
if mode is not None:
scatter.setSymbol(mode)
window.show()
return window
