Source code for flowws_analysis.Plato

import json

import flowws
from flowws import Argument as Arg
import numpy as np
import plato, plato.draw as draw


    'rounding_radius': 'radius',

    'additive_rendering': 'additive_rendering',
    'ambient_occlusion': 'ssao',
    'fast_antialiasing': 'fxaa',
    'transparency': 'translucency',

[docs]@flowws.add_stage_arguments class Plato(flowws.Stage): """Render shapes via :std:doc:`plato<plato:index>`. This module uses the `position`, `orientation`, `type`, `color`, and `type_shapes.json` quantities found in the scope, if provided, to produce a scene of plato shapes. The `type_shapes.json` value should provide a string of a json-encoded list containing one *shape description* object (described below) for each type. These will be converted into plato primitives in conjunction with the `type` and other arrays. Shape description objects are JSON objects with the following keys: - type: one of "ConvexPolyhedron", "Disk", "Mesh", "Polygon", "Sphere" - rounding_radius (only if type is "ConvexPolyhedron" or "Polygon"): rounding radius of a rounded shape, or 0 for perfectly faceted shapes - vertices (only if type is "ConvexPolyhedron", "Mesh", or "Polygon"): coordinates in the shape's reference frame for its vertices; 2D for polygon and 3D for other shapes - indices (only if type is "Mesh"): Array of triangle indices associated with the given set of vertices """ ARGS = [ Arg('outline', '-o', float, 0, help='High-quality outline for spheres and polyhedra'), Arg('cartoon_outline', None, float, 0, help='Cartoon-like outline mode for all shapes'), Arg('color_scale', None, float, 1, valid_values=flowws.Range(0, 10, True), help='Factor to scale color RGB intensities by'), Arg('draw_scale', '-s', float, 1, help='Scale to multiply particle size by'), Arg('display_box', '-b', bool, True, help='Display the system box'), Arg('transparency', None, bool, False, help='Enable special translucent particle rendering'), Arg('additive_rendering', None, bool, False, help='Use additive rendering for shapes'), Arg('fast_antialiasing', None, bool, False, help='Use Fast Approximate Antialiasing (FXAA)'), Arg('ambient_occlusion', None, bool, False, help='Use Screen Space Ambient Occlusion (SSAO)'), Arg('disable_rounding', None, bool, False, help='Disable spheropolyhedra and spheropolygons'), Arg('disable_selection', None, bool, False, help='Don\'t allow selection of particles for this scene'), ] def run(self, scope, storage): """Generate a scene of plato primitives.""" scene_kwargs = {} positions = np.asarray(scope['position']) N = len(positions) if 'type' in scope: types = np.asarray(scope['type']) else: types = np.repeat(0, N) unique_types = list(sorted(set(types))) if 'type_shapes.json' in scope: type_shapes = json.loads(scope['type_shapes.json']) else: type_shapes = [] if 'dimensions' in scope: dimensions = scope['dimensions'] try: dimensions = dimensions[0] except TypeError: pass elif type_shapes and any(shape['type'].lower() in ('disk', 'polygon') for shape in type_shapes): dimensions = 2 elif np.allclose(positions[:, 2], 0): dimensions = 2 else: dimensions = 3 orientations = np.atleast_2d(scope.get('orientation', [])) if len(orientations) < N: orientations = np.tile([[1, 0, 0, 0.]], (N, 1)) if 'color' not in scope or len(scope['color']) < N: colors = np.empty((N, 4), dtype=np.float32) colors[:, :3] = plato.cmap.cubeellipse_intensity( types.astype(np.float32), h=1.2, s=-0.25, lam=.45) colors[:, 3] = 1 else: colors = scope['color'] colors[:, :3] *= self.arguments['color_scale'] diameters = np.atleast_1d(scope.get('diameter', 1)) if len(diameters) < N: diameters = np.repeat(1, N) diameters = diameters*self.arguments['draw_scale'] if self.arguments.get('disable_rounding', False): for description in type_shapes: if 'rounding_radius' in description: description['rounding_radius'] = 0 while len(type_shapes) < len(unique_types): if dimensions == 2: type_shapes.append(dict(type='Disk')) else: type_shapes.append(dict(type='Sphere')) primitives = list(scope.get('plato_primitives', [])) primitive_indices = [[]]*len(primitives) for (t, description) in zip(unique_types, type_shapes): filt = np.where(types == t)[0] prim_type = description['type'].lower() is_2d = prim_type in ('disk', 'polygon') prim_class = PRIM_NAME_MAP[prim_type] if prim_type == 'convexpolyhedron' and description.get('rounding_radius', 0): prim_class = draw.ConvexSpheropolyhedra elif prim_type == 'polygon' and description.get('rounding_radius', 0): prim_class = draw.Spheropolygons kwargs = dict(description) kwargs.pop('type') for key in list(kwargs): new_key = TYPE_SHAPE_KWARG_MAP.get(key, key) kwargs[new_key] = kwargs.pop(key) prim = prim_class(**kwargs) if is_2d: prim.positions = positions[filt, :2] else: prim.positions = positions[filt] prim.orientations = orientations[filt]*np.sqrt(self.arguments['draw_scale']) prim.colors = colors[filt] prim.diameters = diameters[filt] prim.outline = self.arguments['outline'] primitive_indices.append(filt) primitives.append(prim) if 'box' in scope and self.arguments['display_box']: prim = draw.Box.from_box(scope['box']) prim.width = min(scope['box'][:dimensions])*5e-3 prim.color = (0, 0, 0, 1) primitive_indices.append([]) primitives.append(prim) scene_kwargs['size'] = 1.05*np.array(scope['box'][:2]) # use default size of 800px wide scene_kwargs['pixel_scale'] = 800/scene_kwargs['size'][0] self.scene = draw.Scene(primitives, **scene_kwargs) if dimensions == 2: self.scene.enable('pan') for (argument_name, feature_name) in SCENE_FEATURE_REMAP.items(): if self.arguments[argument_name]: self.scene.enable(feature_name) if self.arguments['cartoon_outline']: self.scene.enable('outlines', self.arguments['cartoon_outline']) scope['primitive_indices'] = primitive_indices scope.setdefault('visuals', []).append(self) scope.setdefault('visual_link_rotation', []).append(self) if not self.arguments['disable_selection']: scope['selection_visual_target'] = self def draw_plato(self): return self.scene