Source code for openmc.plots

from collections.abc import Iterable, Mapping
from numbers import Integral, Real
from pathlib import Path
from typing import Optional

import h5py
import lxml.etree as ET
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
    png_filename = plot.filename if plot.filename is not None else f'plot_{plot.id}'

    # Add file extension if not already present. The C++ code added it
    # automatically if it wasn't present.
    if Path(png_filename).suffix != ".png":
        png_filename += ".png"

    png_file = Path(cwd) / png_filename
    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 rng = np.random.RandomState(seed) # Generate random colors for each feature for domain in domains: self.colors[domain] = rng.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 = f"Unable to set the meshlines with type \"{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) h5_voxel_filename = self.filename if self.filename is not None else f'plot_{self.id}' # Add file extension if not already present if Path(h5_voxel_filename).suffix != ".h5": h5_voxel_filename += ".h5" h5_voxel_file = Path(cwd) / h5_voxel_filename 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 """ parser = ET.XMLParser(huge_tree=True) tree = ET.parse(path, parser=parser) root = tree.getroot() return cls.from_xml_element(root)