from collections.abc import Iterable, Mapping
from numbers import Integral, Real
from pathlib import Path
import lxml.etree as ET
from typing import Optional
import h5py
import numpy as np
import openmc
import openmc.checkvalue as cv
from openmc.checkvalue import PathLike
from ._xml import clean_indentation, get_elem_tuple, reorder_attributes, get_text
from .mixin import IDManagerMixin
_BASES = ['xy', 'xz', 'yz']
_SVG_COLORS = {
'aliceblue': (240, 248, 255),
'antiquewhite': (250, 235, 215),
'aqua': (0, 255, 255),
'aquamarine': (127, 255, 212),
'azure': (240, 255, 255),
'beige': (245, 245, 220),
'bisque': (255, 228, 196),
'black': (0, 0, 0),
'blanchedalmond': (255, 235, 205),
'blue': (0, 0, 255),
'blueviolet': (138, 43, 226),
'brown': (165, 42, 42),
'burlywood': (222, 184, 135),
'cadetblue': (95, 158, 160),
'chartreuse': (127, 255, 0),
'chocolate': (210, 105, 30),
'coral': (255, 127, 80),
'cornflowerblue': (100, 149, 237),
'cornsilk': (255, 248, 220),
'crimson': (220, 20, 60),
'cyan': (0, 255, 255),
'darkblue': (0, 0, 139),
'darkcyan': (0, 139, 139),
'darkgoldenrod': (184, 134, 11),
'darkgray': (169, 169, 169),
'darkgreen': (0, 100, 0),
'darkgrey': (169, 169, 169),
'darkkhaki': (189, 183, 107),
'darkmagenta': (139, 0, 139),
'darkolivegreen': (85, 107, 47),
'darkorange': (255, 140, 0),
'darkorchid': (153, 50, 204),
'darkred': (139, 0, 0),
'darksalmon': (233, 150, 122),
'darkseagreen': (143, 188, 143),
'darkslateblue': (72, 61, 139),
'darkslategray': (47, 79, 79),
'darkslategrey': (47, 79, 79),
'darkturquoise': (0, 206, 209),
'darkviolet': (148, 0, 211),
'deeppink': (255, 20, 147),
'deepskyblue': (0, 191, 255),
'dimgray': (105, 105, 105),
'dimgrey': (105, 105, 105),
'dodgerblue': (30, 144, 255),
'firebrick': (178, 34, 34),
'floralwhite': (255, 250, 240),
'forestgreen': (34, 139, 34),
'fuchsia': (255, 0, 255),
'gainsboro': (220, 220, 220),
'ghostwhite': (248, 248, 255),
'gold': (255, 215, 0),
'goldenrod': (218, 165, 32),
'gray': (128, 128, 128),
'green': (0, 128, 0),
'greenyellow': (173, 255, 47),
'grey': (128, 128, 128),
'honeydew': (240, 255, 240),
'hotpink': (255, 105, 180),
'indianred': (205, 92, 92),
'indigo': (75, 0, 130),
'ivory': (255, 255, 240),
'khaki': (240, 230, 140),
'lavender': (230, 230, 250),
'lavenderblush': (255, 240, 245),
'lawngreen': (124, 252, 0),
'lemonchiffon': (255, 250, 205),
'lightblue': (173, 216, 230),
'lightcoral': (240, 128, 128),
'lightcyan': (224, 255, 255),
'lightgoldenrodyellow': (250, 250, 210),
'lightgray': (211, 211, 211),
'lightgreen': (144, 238, 144),
'lightgrey': (211, 211, 211),
'lightpink': (255, 182, 193),
'lightsalmon': (255, 160, 122),
'lightseagreen': (32, 178, 170),
'lightskyblue': (135, 206, 250),
'lightslategray': (119, 136, 153),
'lightslategrey': (119, 136, 153),
'lightsteelblue': (176, 196, 222),
'lightyellow': (255, 255, 224),
'lime': (0, 255, 0),
'limegreen': (50, 205, 50),
'linen': (250, 240, 230),
'magenta': (255, 0, 255),
'maroon': (128, 0, 0),
'mediumaquamarine': (102, 205, 170),
'mediumblue': (0, 0, 205),
'mediumorchid': (186, 85, 211),
'mediumpurple': (147, 112, 219),
'mediumseagreen': (60, 179, 113),
'mediumslateblue': (123, 104, 238),
'mediumspringgreen': (0, 250, 154),
'mediumturquoise': (72, 209, 204),
'mediumvioletred': (199, 21, 133),
'midnightblue': (25, 25, 112),
'mintcream': (245, 255, 250),
'mistyrose': (255, 228, 225),
'moccasin': (255, 228, 181),
'navajowhite': (255, 222, 173),
'navy': (0, 0, 128),
'oldlace': (253, 245, 230),
'olive': (128, 128, 0),
'olivedrab': (107, 142, 35),
'orange': (255, 165, 0),
'orangered': (255, 69, 0),
'orchid': (218, 112, 214),
'palegoldenrod': (238, 232, 170),
'palegreen': (152, 251, 152),
'paleturquoise': (175, 238, 238),
'palevioletred': (219, 112, 147),
'papayawhip': (255, 239, 213),
'peachpuff': (255, 218, 185),
'peru': (205, 133, 63),
'pink': (255, 192, 203),
'plum': (221, 160, 221),
'powderblue': (176, 224, 230),
'purple': (128, 0, 128),
'red': (255, 0, 0),
'rosybrown': (188, 143, 143),
'royalblue': (65, 105, 225),
'saddlebrown': (139, 69, 19),
'salmon': (250, 128, 114),
'sandybrown': (244, 164, 96),
'seagreen': (46, 139, 87),
'seashell': (255, 245, 238),
'sienna': (160, 82, 45),
'silver': (192, 192, 192),
'skyblue': (135, 206, 235),
'slateblue': (106, 90, 205),
'slategray': (112, 128, 144),
'slategrey': (112, 128, 144),
'snow': (255, 250, 250),
'springgreen': (0, 255, 127),
'steelblue': (70, 130, 180),
'tan': (210, 180, 140),
'teal': (0, 128, 128),
'thistle': (216, 191, 216),
'tomato': (255, 99, 71),
'turquoise': (64, 224, 208),
'violet': (238, 130, 238),
'wheat': (245, 222, 179),
'white': (255, 255, 255),
'whitesmoke': (245, 245, 245),
'yellow': (255, 255, 0),
'yellowgreen': (154, 205, 50)
}
def _get_plot_image(plot, cwd):
from IPython.display import Image
# Make sure .png file was created
stem = plot.filename if plot.filename is not None else f'plot_{plot.id}'
png_file = Path(cwd) / f'{stem}.png'
if not png_file.exists():
raise FileNotFoundError(
f"Could not find .png image for plot {plot.id}. Your version of "
"OpenMC may not be built against libpng.")
return Image(str(png_file))
[docs]def voxel_to_vtk(voxel_file: PathLike, output: PathLike = 'plot.vti'):
"""Converts a voxel HDF5 file to a VTK file
.. versionadded:: 0.14.0
Parameters
----------
voxel_file : path-like
Path of the input h5 to convert
output : path-like
Path of the output vti file produced
Returns
-------
Path
Path of the .vti file produced
"""
# imported vtk only if used as vtk is an option dependency
import vtk
_min_version = (2, 0)
# Read data from voxel file
with h5py.File(voxel_file, "r") as fh:
# check version
version = tuple(fh.attrs["version"])
if version < _min_version:
old_version = ".".join(map(str, version))
min_version = ".".join(map(str, _min_version))
err_msg = (
f"This voxel file's version is {old_version}. This function only "
f" supports voxel files with version {min_version} or higher. "
"Please generate a new voxel file using a newer version of OpenMC."
)
raise ValueError(err_msg)
dimension = fh.attrs["num_voxels"]
width = fh.attrs["voxel_width"]
lower_left = fh.attrs["lower_left"]
nx, ny, nz = dimension
grid = vtk.vtkImageData()
grid.SetDimensions(nx + 1, ny + 1, nz + 1)
grid.SetOrigin(*lower_left)
grid.SetSpacing(*width)
# transpose data from OpenMC ordering (zyx) to VTK ordering (xyz)
# and flatten to 1-D array
h5data = fh["data"][...]
data = vtk.vtkIntArray()
data.SetName("id")
# set the array using the h5data array
data.SetArray(h5data, h5data.size, True)
# add data to image grid
grid.GetCellData().AddArray(data)
writer = vtk.vtkXMLImageDataWriter()
if vtk.vtkVersion.GetVTKMajorVersion() > 5:
writer.SetInputData(grid)
else:
writer.SetInput(grid)
if not output.endswith(".vti"):
output += ".vti"
writer.SetFileName(str(output))
writer.Write()
return output
class PlotBase(IDManagerMixin):
"""
Parameters
----------
plot_id : int
Unique identifier for the plot
name : str
Name of the plot
Attributes
----------
id : int
Unique identifier
name : str
Name of the plot
pixels : Iterable of int
Number of pixels to use in each direction
filename : str
Path to write the plot to
color_by : {'cell', 'material'}
Indicate whether the plot should be colored by cell or by material
background : Iterable of int or str
Color of the background
mask_components : Iterable of openmc.Cell or openmc.Material or int
The cells or materials (or corresponding IDs) to mask
mask_background : Iterable of int or str
Color to apply to all cells/materials listed in mask_components
show_overlaps : bool
Indicate whether or not overlapping regions are shown
overlap_color : Iterable of int or str
Color to apply to overlapping regions
colors : dict
Dictionary indicating that certain cells/materials should be
displayed with a particular color. The keys can be of type
:class:`~openmc.Cell`, :class:`~openmc.Material`, or int (ID for a
cell/material).
level : int
Universe depth to plot at
"""
next_id = 1
used_ids = set()
def __init__(self, plot_id=None, name=''):
# Initialize Plot class attributes
self.id = plot_id
self.name = name
self._pixels = [400, 400]
self._filename = None
self._color_by = 'cell'
self._background = None
self._mask_components = None
self._mask_background = None
self._show_overlaps = False
self._overlap_color = None
self._colors = {}
self._level = None
@property
def name(self):
return self._name
@name.setter
def name(self, name):
cv.check_type('plot name', name, str)
self._name = name
@property
def pixels(self):
return self._pixels
@pixels.setter
def pixels(self, pixels):
cv.check_type('plot pixels', pixels, Iterable, Integral)
cv.check_length('plot pixels', pixels, 2, 3)
for dim in pixels:
cv.check_greater_than('plot pixels', dim, 0)
self._pixels = pixels
@property
def filename(self):
return self._filename
@filename.setter
def filename(self, filename):
cv.check_type('filename', filename, str)
self._filename = filename
@property
def color_by(self):
return self._color_by
@color_by.setter
def color_by(self, color_by):
cv.check_value('plot color_by', color_by, ['cell', 'material'])
self._color_by = color_by
@property
def background(self):
return self._background
@background.setter
def background(self, background):
self._check_color('plot background', background)
self._background = background
@property
def mask_components(self):
return self._mask_components
@mask_components.setter
def mask_components(self, mask_components):
cv.check_type('plot mask components', mask_components, Iterable,
(openmc.Cell, openmc.Material, Integral))
self._mask_components = mask_components
@property
def mask_background(self):
return self._mask_background
@mask_background.setter
def mask_background(self, mask_background):
self._check_color('plot mask background', mask_background)
self._mask_background = mask_background
@property
def show_overlaps(self):
return self._show_overlaps
@show_overlaps.setter
def show_overlaps(self, show_overlaps):
cv.check_type(f'Show overlaps flag for Plot ID="{self.id}"',
show_overlaps, bool)
self._show_overlaps = show_overlaps
@property
def overlap_color(self):
return self._overlap_color
@overlap_color.setter
def overlap_color(self, overlap_color):
self._check_color('plot overlap color', overlap_color)
self._overlap_color = overlap_color
@property
def colors(self):
return self._colors
@colors.setter
def colors(self, colors):
cv.check_type('plot colors', colors, Mapping)
for key, value in colors.items():
cv.check_type('plot color key', key,
(openmc.Cell, openmc.Material, Integral))
self._check_color('plot color value', value)
self._colors = colors
@property
def level(self):
return self._level
@level.setter
def level(self, plot_level):
cv.check_type('plot level', plot_level, Integral)
cv.check_greater_than('plot level', plot_level, 0, equality=True)
self._level = plot_level
@staticmethod
def _check_color(err_string, color):
cv.check_type(err_string, color, Iterable)
if isinstance(color, str):
if color.lower() not in _SVG_COLORS:
raise ValueError(f"'{color}' is not a valid color.")
else:
cv.check_length(err_string, color, 3)
for rgb in color:
cv.check_type(err_string, rgb, Real)
cv.check_greater_than('RGB component', rgb, 0, True)
cv.check_less_than('RGB component', rgb, 256)
# Helper function that returns the domain ID given either a
# Cell/Material object or the domain ID itself
@staticmethod
def _get_id(domain):
return domain if isinstance(domain, Integral) else domain.id
def colorize(self, geometry, seed=1):
"""Generate a color scheme for each domain in the plot.
This routine may be used to generate random, reproducible color schemes.
The colors generated are based upon cell/material IDs in the geometry.
Parameters
----------
geometry : openmc.Geometry
The geometry for which the plot is defined
seed : Integral
The random number seed used to generate the color scheme
"""
cv.check_type('geometry', geometry, openmc.Geometry)
cv.check_type('seed', seed, Integral)
cv.check_greater_than('seed', seed, 1, equality=True)
# Get collections of the domains which will be plotted
if self.color_by == 'material':
domains = geometry.get_all_materials().values()
else:
domains = geometry.get_all_cells().values()
# Set the seed for the random number generator
np.random.seed(seed)
# Generate random colors for each feature
for domain in domains:
self.colors[domain] = np.random.randint(0, 256, (3,))
def to_xml_element(self):
"""Save common plot attributes to XML element
Returns
-------
element : lxml.etree._Element
XML element containing plot data
"""
element = ET.Element("plot")
element.set("id", str(self._id))
if len(self._name) > 0:
element.set("name", str(self.name))
if self._filename is not None:
element.set("filename", self._filename)
element.set("color_by", self._color_by)
subelement = ET.SubElement(element, "pixels")
subelement.text = ' '.join(map(str, self._pixels))
if self._background is not None:
subelement = ET.SubElement(element, "background")
color = self._background
if isinstance(color, str):
color = _SVG_COLORS[color.lower()]
subelement.text = ' '.join(str(x) for x in color)
if self._mask_components is not None:
subelement = ET.SubElement(element, "mask")
subelement.set("components", ' '.join(
str(PlotBase._get_id(d)) for d in self._mask_components))
color = self._mask_background
if color is not None:
if isinstance(color, str):
color = _SVG_COLORS[color.lower()]
subelement.set("background", ' '.join(
str(x) for x in color))
if self._level is not None:
subelement = ET.SubElement(element, "level")
subelement.text = str(self._level)
return element
[docs]class Plot(PlotBase):
"""Definition of a finite region of space to be plotted.
OpenMC is capable of generating two-dimensional slice plots, or
three-dimensional voxel or projection plots. Colors that are used in plots can be given as
RGB tuples, e.g. (255, 255, 255) would be white, or by a string indicating a
valid `SVG color <https://www.w3.org/TR/SVG11/types.html#ColorKeywords>`_.
Parameters
----------
plot_id : int
Unique identifier for the plot
name : str
Name of the plot
Attributes
----------
id : int
Unique identifier
name : str
Name of the plot
pixels : Iterable of int
Number of pixels to use in each direction
filename : str
Path to write the plot to
color_by : {'cell', 'material'}
Indicate whether the plot should be colored by cell or by material
background : Iterable of int or str
Color of the background
mask_components : Iterable of openmc.Cell or openmc.Material or int
The cells or materials (or corresponding IDs) to mask
mask_background : Iterable of int or str
Color to apply to all cells/materials listed in mask_components
show_overlaps : bool
Indicate whether or not overlapping regions are shown
overlap_color : Iterable of int or str
Color to apply to overlapping regions
colors : dict
Dictionary indicating that certain cells/materials should be
displayed with a particular color. The keys can be of type
:class:`~openmc.Cell`, :class:`~openmc.Material`, or int (ID for a
cell/material).
level : int
Universe depth to plot at
width : Iterable of float
Width of the plot in each basis direction
origin : tuple or list of ndarray
Origin (center) of the plot
type : {'slice', 'voxel'}
The type of the plot
basis : {'xy', 'xz', 'yz'}
The basis directions for the plot
meshlines : dict
Dictionary defining type, id, linewidth and color of a mesh to be
plotted on top of a plot
"""
def __init__(self, plot_id=None, name=''):
super().__init__(plot_id, name)
self._width = [4.0, 4.0]
self._origin = [0., 0., 0.]
self._type = 'slice'
self._basis = 'xy'
self._meshlines = None
@property
def width(self):
return self._width
@width.setter
def width(self, width):
cv.check_type('plot width', width, Iterable, Real)
cv.check_length('plot width', width, 2, 3)
self._width = width
@property
def origin(self):
return self._origin
@origin.setter
def origin(self, origin):
cv.check_type('plot origin', origin, Iterable, Real)
cv.check_length('plot origin', origin, 3)
self._origin = origin
@property
def type(self):
return self._type
@type.setter
def type(self, plottype):
cv.check_value('plot type', plottype, ['slice', 'voxel'])
self._type = plottype
@property
def basis(self):
return self._basis
@basis.setter
def basis(self, basis):
cv.check_value('plot basis', basis, _BASES)
self._basis = basis
@property
def meshlines(self):
return self._meshlines
@meshlines.setter
def meshlines(self, meshlines):
cv.check_type('plot meshlines', meshlines, dict)
if 'type' not in meshlines:
msg = f'Unable to set the meshlines to "{meshlines}" which ' \
'does not have a "type" key'
raise ValueError(msg)
elif meshlines['type'] not in ['tally', 'entropy', 'ufs', 'cmfd']:
msg = 'Unable to set the meshlines with ' \
'type "{}"'.format(meshlines['type'])
raise ValueError(msg)
if 'id' in meshlines:
cv.check_type('plot meshlines id', meshlines['id'], Integral)
cv.check_greater_than('plot meshlines id', meshlines['id'], 0,
equality=True)
if 'linewidth' in meshlines:
cv.check_type('plot mesh linewidth',
meshlines['linewidth'], Integral)
cv.check_greater_than('plot mesh linewidth', meshlines['linewidth'],
0, equality=True)
if 'color' in meshlines:
self._check_color('plot meshlines color', meshlines['color'])
self._meshlines = meshlines
def __repr__(self):
string = 'Plot\n'
string += '{: <16}=\t{}\n'.format('\tID', self._id)
string += '{: <16}=\t{}\n'.format('\tName', self._name)
string += '{: <16}=\t{}\n'.format('\tFilename', self._filename)
string += '{: <16}=\t{}\n'.format('\tType', self._type)
string += '{: <16}=\t{}\n'.format('\tBasis', self._basis)
string += '{: <16}=\t{}\n'.format('\tWidth', self._width)
string += '{: <16}=\t{}\n'.format('\tOrigin', self._origin)
string += '{: <16}=\t{}\n'.format('\tPixels', self._pixels)
string += '{: <16}=\t{}\n'.format('\tColor by', self._color_by)
string += '{: <16}=\t{}\n'.format('\tBackground', self._background)
string += '{: <16}=\t{}\n'.format('\tMask components',
self._mask_components)
string += '{: <16}=\t{}\n'.format('\tMask background',
self._mask_background)
string += '{: <16}=\t{}\n'.format('\tOverlap Color',
self._overlap_color)
string += '{: <16}=\t{}\n'.format('\tColors', self._colors)
string += '{: <16}=\t{}\n'.format('\tLevel', self._level)
string += '{: <16}=\t{}\n'.format('\tMeshlines', self._meshlines)
return string
[docs] @classmethod
def from_geometry(cls, geometry, basis='xy', slice_coord=0.):
"""Return plot that encompasses a geometry.
Parameters
----------
geometry : openmc.Geometry
The geometry to base the plot off of
basis : {'xy', 'xz', 'yz'}
The basis directions for the plot
slice_coord : float
The level at which the slice plot should be plotted. For example, if
the basis is 'xy', this would indicate the z value used in the
origin.
"""
cv.check_type('geometry', geometry, openmc.Geometry)
cv.check_value('basis', basis, _BASES)
# Decide which axes to keep
if basis == 'xy':
pick_index = (0, 1)
slice_index = 2
elif basis == 'yz':
pick_index = (1, 2)
slice_index = 0
elif basis == 'xz':
pick_index = (0, 2)
slice_index = 1
# Get lower-left and upper-right coordinates for desired axes
lower_left, upper_right = geometry.bounding_box
lower_left = lower_left[np.array(pick_index)]
upper_right = upper_right[np.array(pick_index)]
if np.any(np.isinf((lower_left, upper_right))):
raise ValueError('The geometry does not appear to be bounded '
f'in the {basis} plane.')
plot = cls()
plot.origin = np.insert((lower_left + upper_right)/2,
slice_index, slice_coord)
plot.width = upper_right - lower_left
plot.basis = basis
return plot
[docs] def highlight_domains(self, geometry, domains, seed=1,
alpha=0.5, background='gray'):
"""Use alpha compositing to highlight one or more domains in the plot.
This routine generates a color scheme and applies alpha compositing to
make all domains except the highlighted ones appear partially
transparent.
Parameters
----------
geometry : openmc.Geometry
The geometry for which the plot is defined
domains : Iterable of openmc.Cell or openmc.Material
A collection of the domain IDs to highlight in the plot
seed : int
The random number seed used to generate the color scheme
alpha : float
The value between 0 and 1 to apply in alpha compositing
background : 3-tuple of int or str
The background color to apply in alpha compositing
"""
cv.check_type('domains', domains, Iterable,
(openmc.Cell, openmc.Material))
cv.check_type('alpha', alpha, Real)
cv.check_greater_than('alpha', alpha, 0., equality=True)
cv.check_less_than('alpha', alpha, 1., equality=True)
cv.check_type('background', background, Iterable)
# Get a background (R,G,B) tuple to apply in alpha compositing
if isinstance(background, str):
if background.lower() not in _SVG_COLORS:
raise ValueError(f"'{background}' is not a valid color.")
background = _SVG_COLORS[background.lower()]
# Generate a color scheme
self.colorize(geometry, seed)
# Apply alpha compositing to the colors for all domains
# other than those the user wishes to highlight
for domain, color in self.colors.items():
if domain not in domains:
if isinstance(color, str):
color = _SVG_COLORS[color.lower()]
r, g, b = color
r = int(((1-alpha) * background[0]) + (alpha * r))
g = int(((1-alpha) * background[1]) + (alpha * g))
b = int(((1-alpha) * background[2]) + (alpha * b))
self._colors[domain] = (r, g, b)
[docs] def to_xml_element(self):
"""Return XML representation of the slice/voxel plot
Returns
-------
element : lxml.etree._Element
XML element containing plot data
"""
element = super().to_xml_element()
element.set("type", self._type)
if self._type == 'slice':
element.set("basis", self._basis)
subelement = ET.SubElement(element, "origin")
subelement.text = ' '.join(map(str, self._origin))
subelement = ET.SubElement(element, "width")
subelement.text = ' '.join(map(str, self._width))
if self._colors:
for domain, color in sorted(self._colors.items(),
key=lambda x: PlotBase._get_id(x[0])):
subelement = ET.SubElement(element, "color")
subelement.set("id", str(PlotBase._get_id(domain)))
if isinstance(color, str):
color = _SVG_COLORS[color.lower()]
subelement.set("rgb", ' '.join(str(x) for x in color))
if self._show_overlaps:
subelement = ET.SubElement(element, "show_overlaps")
subelement.text = "true"
if self._overlap_color is not None:
color = self._overlap_color
if isinstance(color, str):
color = _SVG_COLORS[color.lower()]
subelement = ET.SubElement(element, "overlap_color")
subelement.text = ' '.join(str(x) for x in color)
if self._meshlines is not None:
subelement = ET.SubElement(element, "meshlines")
subelement.set("meshtype", self._meshlines['type'])
if 'id' in self._meshlines:
subelement.set("id", str(self._meshlines['id']))
if 'linewidth' in self._meshlines:
subelement.set("linewidth", str(self._meshlines['linewidth']))
if 'color' in self._meshlines:
subelement.set("color", ' '.join(map(
str, self._meshlines['color'])))
return element
[docs] @classmethod
def from_xml_element(cls, elem):
"""Generate plot object from an XML element
Parameters
----------
elem : lxml.etree._Element
XML element
Returns
-------
openmc.Plot
Plot object
"""
plot_id = int(elem.get("id"))
name = get_text(elem, 'name', '')
plot = cls(plot_id, name)
if "filename" in elem.keys():
plot.filename = elem.get("filename")
plot.color_by = elem.get("color_by")
plot.type = elem.get("type")
if plot.type == 'slice':
plot.basis = elem.get("basis")
plot.origin = get_elem_tuple(elem, "origin", float)
plot.width = get_elem_tuple(elem, "width", float)
plot.pixels = get_elem_tuple(elem, "pixels")
plot._background = get_elem_tuple(elem, "background")
# Set plot colors
colors = {}
for color_elem in elem.findall("color"):
uid = int(color_elem.get("id"))
colors[uid] = tuple([int(x)
for x in color_elem.get("rgb").split()])
plot.colors = colors
# Set masking information
mask_elem = elem.find("mask")
if mask_elem is not None:
plot.mask_components = [
int(x) for x in mask_elem.get("components").split()]
background = mask_elem.get("background")
if background is not None:
plot.mask_background = tuple(
[int(x) for x in background.split()])
# show overlaps
overlap_elem = elem.find("show_overlaps")
if overlap_elem is not None:
plot.show_overlaps = (overlap_elem.text in ('true', '1'))
overlap_color = get_elem_tuple(elem, "overlap_color")
if overlap_color is not None:
plot.overlap_color = overlap_color
# Set universe level
level = elem.find("level")
if level is not None:
plot.level = int(level.text)
# Set meshlines
mesh_elem = elem.find("meshlines")
if mesh_elem is not None:
meshlines = {'type': mesh_elem.get('meshtype')}
if 'id' in mesh_elem.keys():
meshlines['id'] = int(mesh_elem.get('id'))
if 'linewidth' in mesh_elem.keys():
meshlines['linewidth'] = int(mesh_elem.get('linewidth'))
if 'color' in mesh_elem.keys():
meshlines['color'] = tuple(
[int(x) for x in mesh_elem.get('color').split()]
)
plot.meshlines = meshlines
return plot
[docs] def to_ipython_image(self, openmc_exec='openmc', cwd='.'):
"""Render plot as an image
This method runs OpenMC in plotting mode to produce a .png file.
.. versionchanged:: 0.13.0
The *convert_exec* argument was removed since OpenMC now produces
.png images directly.
Parameters
----------
openmc_exec : str
Path to OpenMC executable
cwd : str, optional
Path to working directory to run in
Returns
-------
IPython.display.Image
Image generated
"""
# Create plots.xml
Plots([self]).export_to_xml(cwd)
# Run OpenMC in geometry plotting mode
openmc.plot_geometry(False, openmc_exec, cwd)
# Return produced image
return _get_plot_image(self, cwd)
[docs] def to_vtk(self, output: Optional[PathLike] = None,
openmc_exec: str = 'openmc', cwd: str = '.'):
"""Render plot as an voxel image
This method runs OpenMC in plotting mode to produce a .vti file.
.. versionadded:: 0.14.0
Parameters
----------
output : path-like
Path of the output .vti file produced
openmc_exec : str
Path to OpenMC executable
cwd : str, optional
Path to working directory to run in
Returns
-------
Path
Path of the .vti file produced
"""
if self.type != 'voxel':
raise ValueError('Generating a VTK file only works for voxel plots')
# Create plots.xml
Plots([self]).export_to_xml(cwd)
# Run OpenMC in geometry plotting mode and produces a h5 file
openmc.plot_geometry(False, openmc_exec, cwd)
stem = self.filename if self.filename is not None else f'plot_{self.id}'
h5_voxel_file = Path(cwd) / f'{stem}.h5'
if output is None:
output = h5_voxel_file.with_suffix('.vti')
return voxel_to_vtk(h5_voxel_file, output)
[docs]class ProjectionPlot(PlotBase):
"""Definition of a camera's view of OpenMC geometry
Colors are defined in the same manner as the Plot class, but with the addition
of a coloring parameter resembling a macroscopic cross section in units of inverse
centimeters. The volume rendering technique is used to color regions of the model.
An infinite cross section denotes a fully opaque region, and zero represents a
transparent region which will expose the color of the regions behind it.
The camera projection may either by orthographic or perspective. Perspective
projections are more similar to a pinhole camera, and orthographic projections
preserve parallel lines and distances.
.. versionadded:: 0.14.0
Parameters
----------
plot_id : int
Unique identifier for the plot
name : str
Name of the plot
Attributes
----------
horizontal_field_of_view : float
Field of view horizontally, in units of degrees, defaults to 70.
camera_position : tuple or list of ndarray
Position of the camera in 3D space. Defaults to (1, 0, 0).
look_at : tuple or list of ndarray
The center of the camera's image points to this place in 3D space.
Set to (0, 0, 0) by default.
up : tuple or list of ndarray
Which way is up for the camera. Must not be parallel to the
line between look_at and camera_position. Set to (0, 0, 1) by default.
orthographic_width : float
If set to a nonzero value, an orthographic projection is used.
All rays traced from the orthographic pixel array travel in the
same direction. The width of the starting array must be specified,
unlike with the default perspective projection. The height of the
array is deduced from the ratio of pixel dimensions for the image.
Defaults to zero, i.e. using perspective projection.
wireframe_thickness : int
Line thickness employed for drawing wireframes around cells or
material regions. Can be set to zero for no wireframes at all.
Defaults to one pixel.
wireframe_color : tuple of ints
RGB color of the wireframe lines. Defaults to black.
wireframe_domains : iterable of either Material or Cells
If provided, the wireframe is only drawn around these.
If color_by is by material, it must be a list of materials, else cells.
xs : dict
A mapping from cell/material IDs to floats. The floating point values
are macroscopic cross sections influencing the volume rendering opacity
of each geometric region. Zero corresponds to perfect transparency, and
infinity equivalent to opaque. These must be set by the user, but default
values can be obtained using the set_transparent method.
"""
def __init__(self, plot_id=None, name=''):
# Initialize Plot class attributes
super().__init__(plot_id, name)
self._horizontal_field_of_view = 70.0
self._camera_position = (1.0, 0.0, 0.0)
self._look_at = (0.0, 0.0, 0.0)
self._up = (0.0, 0.0, 1.0)
self._orthographic_width = 0.0
self._wireframe_thickness = 1
self._wireframe_color = _SVG_COLORS['black']
self._wireframe_domains = []
self._xs = {}
@property
def horizontal_field_of_view(self):
return self._horizontal_field_of_view
@horizontal_field_of_view.setter
def horizontal_field_of_view(self, horizontal_field_of_view):
cv.check_type('plot horizontal field of view', horizontal_field_of_view,
Real)
assert horizontal_field_of_view > 0.0
assert horizontal_field_of_view < 180.0
self._horizontal_field_of_view = horizontal_field_of_view
@property
def camera_position(self):
return self._camera_position
@camera_position.setter
def camera_position(self, camera_position):
cv.check_type('plot camera position', camera_position, Iterable, Real)
cv.check_length('plot camera position', camera_position, 3)
self._camera_position = camera_position
@property
def look_at(self):
return self._look_at
@look_at.setter
def look_at(self, look_at):
cv.check_type('plot look at', look_at, Iterable, Real)
cv.check_length('plot look at', look_at, 3)
self._look_at = look_at
@property
def up(self):
return self._up
@up.setter
def up(self, up):
cv.check_type('plot up', up, Iterable, Real)
cv.check_length('plot up', up, 3)
self._up = up
@property
def orthographic_width(self):
return self._orthographic_width
@orthographic_width.setter
def orthographic_width(self, orthographic_width):
cv.check_type('plot orthographic width', orthographic_width, Real)
assert orthographic_width >= 0.0
self._orthographic_width = orthographic_width
@property
def wireframe_thickness(self):
return self._wireframe_thickness
@wireframe_thickness.setter
def wireframe_thickness(self, wireframe_thickness):
cv.check_type('plot wireframe thickness',
wireframe_thickness, Integral)
assert wireframe_thickness >= 0
self._wireframe_thickness = wireframe_thickness
@property
def wireframe_color(self):
return self._wireframe_color
@wireframe_color.setter
def wireframe_color(self, wireframe_color):
self._check_color('plot wireframe color', wireframe_color)
self._wireframe_color = wireframe_color
@property
def wireframe_domains(self):
return self._wireframe_domains
@wireframe_domains.setter
def wireframe_domains(self, wireframe_domains):
for region in wireframe_domains:
if self._color_by == 'material':
if not isinstance(region, openmc.Material):
raise Exception('Must provide a list of materials for \
wireframe_region if color_by=Material')
else:
if not isinstance(region, openmc.Cell):
raise Exception('Must provide a list of cells for \
wireframe_region if color_by=cell')
self._wireframe_domains = wireframe_domains
@property
def xs(self):
return self._xs
@xs.setter
def xs(self, xs):
cv.check_type('plot xs', xs, Mapping)
for key, value in xs.items():
cv.check_type('plot xs key', key, (openmc.Cell, openmc.Material))
cv.check_type('plot xs value', value, Real)
assert value >= 0.0
self._xs = xs
[docs] def set_transparent(self, geometry):
"""Sets all volume rendering XS to zero for the model
Parameters
----------
geometry : openmc.Geometry
The geometry for which the plot is defined
"""
cv.check_type('geometry', geometry, openmc.Geometry)
# Get collections of the domains which will be plotted
if self.color_by == 'material':
domains = geometry.get_all_materials().values()
else:
domains = geometry.get_all_cells().values()
# Generate random colors for each feature
for domain in domains:
self.xs[domain] = 0.0
[docs] def to_xml_element(self):
"""Return XML representation of the projection plot
Returns
-------
element : lxml.etree._Element
XML element containing plot data
"""
element = super().to_xml_element()
element.set("type", "projection")
subelement = ET.SubElement(element, "camera_position")
subelement.text = ' '.join(map(str, self._camera_position))
subelement = ET.SubElement(element, "look_at")
subelement.text = ' '.join(map(str, self._look_at))
subelement = ET.SubElement(element, "wireframe_thickness")
subelement.text = str(self._wireframe_thickness)
subelement = ET.SubElement(element, "wireframe_color")
color = self._wireframe_color
if isinstance(color, str):
color = _SVG_COLORS[color.lower()]
subelement.text = ' '.join(str(x) for x in color)
if self._wireframe_domains:
id_list = [x.id for x in self._wireframe_domains]
subelement = ET.SubElement(element, "wireframe_ids")
subelement.text = ' '.join([str(x) for x in id_list])
# note that this differs from the slice plot colors
# in that "xs" must also be specified
if self._colors:
for domain, color in sorted(self._colors.items(),
key=lambda x: x[0].id):
subelement = ET.SubElement(element, "color")
subelement.set("id", str(domain.id))
if isinstance(color, str):
color = _SVG_COLORS[color.lower()]
subelement.set("rgb", ' '.join(str(x) for x in color))
subelement.set("xs", str(self._xs[domain]))
subelement = ET.SubElement(element, "horizontal_field_of_view")
subelement.text = str(self._horizontal_field_of_view)
# do not need to write if orthographic_width == 0.0
if self._orthographic_width > 0.0:
subelement = ET.SubElement(element, "orthographic_width")
subelement.text = str(self._orthographic_width)
return element
def __repr__(self):
string = 'Projection Plot\n'
string += '{: <16}=\t{}\n'.format('\tID', self._id)
string += '{: <16}=\t{}\n'.format('\tName', self._name)
string += '{: <16}=\t{}\n'.format('\tFilename', self._filename)
string += '{: <16}=\t{}\n'.format('\tHorizontal FOV',
self._horizontal_field_of_view)
string += '{: <16}=\t{}\n'.format('\tOrthographic width',
self._orthographic_width)
string += '{: <16}=\t{}\n'.format('\tWireframe thickness',
self._wireframe_thickness)
string += '{: <16}=\t{}\n'.format('\tWireframe color',
self._wireframe_color)
string += '{: <16}=\t{}\n'.format('\tWireframe domains',
self._wireframe_domains)
string += '{: <16}=\t{}\n'.format('\tCamera position',
self._camera_position)
string += '{: <16}=\t{}\n'.format('\tLook at', self._look_at)
string += '{: <16}=\t{}\n'.format('\tUp', self._up)
string += '{: <16}=\t{}\n'.format('\tPixels', self._pixels)
string += '{: <16}=\t{}\n'.format('\tColor by', self._color_by)
string += '{: <16}=\t{}\n'.format('\tBackground', self._background)
string += '{: <16}=\t{}\n'.format('\tColors', self._colors)
string += '{: <16}=\t{}\n'.format('\tTransparencies', self._xs)
string += '{: <16}=\t{}\n'.format('\tLevel', self._level)
return string
[docs] @classmethod
def from_xml_element(cls, elem):
"""Generate plot object from an XML element
Parameters
----------
elem : lxml.etree._Element
XML element
Returns
-------
openmc.ProjectionPlot
ProjectionPlot object
"""
plot_id = int(elem.get("id"))
plot = cls(plot_id)
if "filename" in elem.keys():
plot.filename = elem.get("filename")
plot.color_by = elem.get("color_by")
plot.type = "projection"
horizontal_fov = elem.find("horizontal_field_of_view")
if horizontal_fov is not None:
plot.horizontal_field_of_view = float(horizontal_fov.text)
tmp = elem.find("orthographic_width")
if tmp is not None:
plot.orthographic_width = float(tmp)
plot.pixels = get_elem_tuple(elem, "pixels")
plot.camera_position = get_elem_tuple(elem, "camera_position", float)
plot.look_at = get_elem_tuple(elem, "look_at", float)
# Attempt to get wireframe thickness. May not be present
wireframe_thickness = elem.get("wireframe_thickness")
if wireframe_thickness:
plot.wireframe_thickness = int(wireframe_thickness)
wireframe_color = elem.get("wireframe_color")
if wireframe_color:
plot.wireframe_color = [int(item) for item in wireframe_color]
# Set plot colors
colors = {}
xs = {}
for color_elem in elem.findall("color"):
uid = color_elem.get("id")
colors[uid] = get_elem_tuple(color_elem, "rgb")
xs[uid] = float(color_elem.get("xs"))
# Set masking information
mask_elem = elem.find("mask")
if mask_elem is not None:
mask_components = [int(x)
for x in mask_elem.get("components").split()]
# TODO: set mask components (needs geometry information)
background = mask_elem.get("background")
if background is not None:
plot.mask_background = tuple(
[int(x) for x in background.split()])
# Set universe level
level = elem.find("level")
if level is not None:
plot.level = int(level.text)
return plot
[docs]class Plots(cv.CheckedList):
"""Collection of Plots used for an OpenMC simulation.
This class corresponds directly to the plots.xml input file. It can be
thought of as a normal Python list where each member is inherits from
:class:`PlotBase`. It behaves like a list as the following example
demonstrates:
>>> xz_plot = openmc.Plot()
>>> big_plot = openmc.Plot()
>>> small_plot = openmc.Plot()
>>> p = openmc.Plots((xz_plot, big_plot))
>>> p.append(small_plot)
>>> small_plot = p.pop()
Parameters
----------
plots : Iterable of openmc.Plot or openmc.ProjectionPlot
plots to add to the collection
"""
def __init__(self, plots=None):
super().__init__((Plot, ProjectionPlot), 'plots collection')
self._plots_file = ET.Element("plots")
if plots is not None:
self += plots
[docs] def append(self, plot):
"""Append plot to collection
Parameters
----------
plot : openmc.Plot or openmc.ProjectionPlot
Plot to append
"""
super().append(plot)
[docs] def insert(self, index, plot):
"""Insert plot before index
Parameters
----------
index : int
Index in list
plot : openmc.Plot
Plot to insert
"""
super().insert(index, plot)
[docs] def colorize(self, geometry, seed=1):
"""Generate a consistent color scheme for each domain in each plot.
This routine may be used to generate random, reproducible color schemes.
The colors generated are based upon cell/material IDs in the geometry.
The color schemes will be consistent for all plots in "plots.xml".
Parameters
----------
geometry : openmc.Geometry
The geometry for which the plots are defined
seed : Integral
The random number seed used to generate the color scheme
"""
for plot in self:
plot.colorize(geometry, seed)
[docs] def highlight_domains(self, geometry, domains, seed=1,
alpha=0.5, background='gray'):
"""Use alpha compositing to highlight one or more domains in the plot.
This routine generates a color scheme and applies alpha compositing to
make all domains except the highlighted ones appear partially
transparent.
Parameters
----------
geometry : openmc.Geometry
The geometry for which the plot is defined
domains : Iterable of openmc.Cell or openmc.Material
A collection of the domain IDs to highlight in the plot
seed : int
The random number seed used to generate the color scheme
alpha : float
The value between 0 and 1 to apply in alpha compositing
background : 3-tuple of int or str
The background color to apply in alpha compositing
"""
for plot in self:
plot.highlight_domains(geometry, domains, seed, alpha, background)
def _create_plot_subelements(self):
for plot in self:
xml_element = plot.to_xml_element()
if len(plot.name) > 0:
self._plots_file.append(ET.Comment(plot.name))
self._plots_file.append(xml_element)
[docs] def to_xml_element(self):
"""Create a 'plots' element to be written to an XML file.
Returns
-------
element : lxml.etree._Element
XML element containing all plot elements
"""
# Reset xml element tree
self._plots_file.clear()
self._create_plot_subelements()
# Clean the indentation in the file to be user-readable
clean_indentation(self._plots_file)
# TODO: Remove when support is Python 3.8+
reorder_attributes(self._plots_file)
return self._plots_file
[docs] def export_to_xml(self, path='plots.xml'):
"""Export plot specifications to an XML file.
Parameters
----------
path : str
Path to file to write. Defaults to 'plots.xml'.
"""
# Check if path is a directory
p = Path(path)
if p.is_dir():
p /= 'plots.xml'
self.to_xml_element()
# Write the XML Tree to the plots.xml file
tree = ET.ElementTree(self._plots_file)
tree.write(str(p), xml_declaration=True, encoding='utf-8')
[docs] @classmethod
def from_xml_element(cls, elem):
"""Generate plots collection from XML file
Parameters
----------
elem : lxml.etree._Element
XML element
Returns
-------
openmc.Plots
Plots collection
"""
# Generate each plot
plots = cls()
for e in elem.findall('plot'):
plot_type = e.get('type')
if plot_type == 'projection':
plots.append(ProjectionPlot.from_xml_element(e))
else:
plots.append(Plot.from_xml_element(e))
return plots
[docs] @classmethod
def from_xml(cls, path='plots.xml'):
"""Generate plots collection from XML file
Parameters
----------
path : str, optional
Path to plots XML file
Returns
-------
openmc.Plots
Plots collection
"""
tree = ET.parse(path)
root = tree.getroot()
return cls.from_xml_element(root)