Source code for gen_gallery

#!/usr/bin/env python
"""
Generate the images and rst files for gallery of SfePy examples.

The following steps need to be made to regenerate the documentation with the
updated example files:

1. remove doc/examples/*::

   $ rm -rf doc/examples/*

2. generate the files:

   $ ./tools/gen_gallery.py

3. regenerate the documentation::

   $ python setup.py htmldocs
"""
import sys
sys.path.append('.')
import os
import tempfile
import glob
import re
import shutil
import subprocess
from itertools import chain
from argparse import ArgumentParser, RawDescriptionHelpFormatter

import numpy as nm
import matplotlib.image as image

import sfepy
from sfepy.base.base import (get_default, ordered_iteritems,
                             import_file, output, Struct)
from sfepy.base.ioutils import (ensure_path, locate_files, remove_files,
                                edit_filename)
from sfepy.scripts.resview import pv_plot, get_camera_position
import pyvista as pv

omits = [
    '__init__.py',
]

omit_images = [
    'band_gaps_conf.py',
    'dg_plot_1D.py',
    'example_dg_common.py',
    'homogenization_opt.py', # Is parameterized.
    'linear_elasticity_opt.py', # Is parameterized.
    'linear_homogenization_postproc.py',
    'linear_homogenization_up.py', # Used in linear_elastic_mM.py.
    'material_opt.py', # Very long calculation.
    'nonlinear_homogenization.py',
    'piezo_elasticity_micro.py', # Used in piezo_elasticity_macro.py.
    'quantum_common.py',
]

omit_dirs = [
    re.compile('.*output.*/').match,
]

custom = {
    'acoustics/vibro_acoustic3d.py': {
        '_Gamma0': {'view_2d': True, 'max_plots': 2},
        '_Omega1': {'camera': [45, 55, 0.8]},
        '_Omega2': {'camera': [45, 55, 0.8]},
    },
    'acoustics/acoustics3d.py': {
        '_Omega_1': {
            'camera': [75, 135, 1.4],
            'grid_vector1': [1.2, 0, 0],
        },
        '_Omega_2': {
            'camera': [75, 135, 1],
            'grid_vector1': [1.2, 0, 0],
        },
    },
    'acoustics/helmholtz_apartment.py': {
        '': {
            'fields': ['imag.E:wimag.E:f10%:p0', 'mat_id:p1'],
            'force_view_3d': True,
            'grid_vector1': [1.1, 0, 0],
            'camera_position': [-9.22684,-8.37688,10.7623,
                                1.51653,0.122742,-0.646791,
                                0.472758,0.432784,0.767593],
            'color_map': 'seismic',
        },
    },
    'diffusion/cube.py': {
        '': {'camera': [225, 55, 0.7]},
    },
    'diffusion/laplace_time_ebcs.py': {
        '': {'camera': [225, 55, 0.7]},
    },
    'diffusion/laplace_fluid_2d.py': {
        '': {'fields': ['phi:p0', 'phi:t50:p0']},
    },
    'diffusion/laplace_1d.py': {
        '': {
            'fields': ['t:wt:p0', 't:p0'],
            'force_view_3d': True,
            'camera_position': [0.243787,-1.51098,0.486608,
                                0.5,0,0,
                                0,0,1],
        },
    },
    'dg/advection_1D.py': {
        '': {
            'fields': ['p_modal0:r:wp_modal0:p0', '1:vw:p0',
                       'p_modal1:r:wp_modal1:p1', '1:vw:p1',
                       'p_modal2:r:wp_modal2:p2', '1:vw:p2'],
            'force_view_3d': True,
            'camera_position': [0.300893,-2.41044,0.408743,
                                0.4,0,0.55728,
                                0,0,1],
            'grid_vector2': [0, 0, 55],
            'max_plots': 1,
            'color_map': 'cool',
        },
    },
    'diffusion/laplace_coupling_lcbcs.py': {
        '': {
            'fields': ['u1:wu1:p0', 'u1:vw:p0',
                       'u2:wu2:p1', 'u2:vw:p1'],
            'force_view_3d': True,
        },
    },
    'diffusion/laplace_iga_interactive.py': {
        'command': 'python3 sfepy/examples/diffusion/laplace_iga_interactive.py -o output',
        'result': 'output/concentric_circles.vtk',
        'dim': 2,
        'sfepy-view-options': {
            '': {
            },
        },
    },
    'diffusion/laplace_refine_interactive.py': {
        'command': 'python3 sfepy/examples/diffusion/laplace_refine_interactive.py output',
        'result': 'output/hanging.vtk',
        'sfepy-view-options': {
            '': {
                'fields': ['u:wu', '1:vw'],
                'camera_position': [-1.27046,-1.02066,2.28476,
                                    -0.0525852,0.116151,0.00474463,
                                    0.169164,0.842974,0.510664],
            },
        },
    },
    'diffusion/laplace_shifted_periodic.py': {
        'command': 'python3 sfepy/examples/diffusion/laplace_shifted_periodic.py',
        'result': 'laplace_shifted_periodic.vtk',
        'sfepy-view-options': {
            '': {
                'fields': ['u:wu:f0.5', '1:vw'],
                'camera_position': [-1.42703,0.70237,1.33953,
                                    -0.0817071,-0.0547046,0.0280939,
                                    0.616241,-0.216582,0.757192],
            },
        },
    },
    'diffusion/poisson_iga.py': {
        '': {
            'fields': ['t:wt:p0', 't:vw:o0.4:p0'],
            'force_view_3d': True,
            'camera': [30, 60, 1.],
        },
    },
    'diffusion/poisson_parallel_interactive.py': {
        'command': 'python3 sfepy/examples/diffusion/poisson_parallel_interactive.py output-parallel -2 --shape=101,101',
        'result': 'output-parallel/sol.h5',
        'sfepy-view-options': {
            '': {
                'fields': ['u:wu', '1:vw'],
                'camera_position': [-1.00607,-1.49437,0.843106,
                                    0.0141441,-0.0501477,-0.0173962,
                                    0.309532,0.315757,0.896932],
            },
        },
    },
    'diffusion/poisson_parametric_study.py': {
        'command': 'sfepy-run sfepy/examples/diffusion/poisson_parametric_study.py',
        'result': 'output/r_omega1/circles_in_square_0_1_2_3_4_5_6.vtk',
        'dim': 2,
        'sfepy-view-options': {
            '': {
            },
        },
    },
    'diffusion/sinbc.py': {
        '_t': {
            'fields': ['t:wt:p0', '1:vw:p0'],
            'force_view_3d': True,
            'camera': [0, -45, 1.],
        },
        '_grad': {
            'fields': ['grad:g:f0.01:p0', '1:vw:p0'],
            'force_view_3d': True,
            'camera': [0, -45, 1.5],
        },
    },
    'diffusion/time_heat_equation_multi_material.py': {
        '': {
            'isosurfaces': 10,
            'outline': True,
            'camera': [-50, -230, 1],
        },
    },
    'diffusion/time_poisson_interactive.py': {
        'command': 'python3 sfepy/examples/diffusion/time_poisson_interactive.py -p',
        'image': 'time_poisson_interactive_probe_04.png',
        'result': 'domain.10.vtk',
        'sfepy-view-options': {
            '': {
            },
        },
    },
    'homogenization/linear_homogenization.py': {
        'command': 'sfepy-run sfepy/examples/homogenization/linear_homogenization.py',
        'result': 'output/corrs_le.vtk',
        'sfepy-view-options': {
            '': {
                'max_plots': 3,
                'camera_position': [-8.57147,2.10122,2.76537,
                                    0.37,2.04405,2.14477,
                                    0,0,1],
                'show_labels': False,
                'show_scalar_bars': False,
            }
        },
    },
    'homogenization/perfusion_micro.py': {
        'command': 'sfepy-run sfepy/examples/homogenization/perfusion_micro.py',
        'result': 'output/corrs_3d_2ch.vtk',
        'sfepy-view-options': {
            '_etaA_YM': {
                'camera_position': [-1.69531,-0.966016,2.3648,
                                    0.480252,0.486045,0.46669,
                                    0.51024,0.292658,0.808707],
            },
            '_etaB_YM': {
                'camera_position': [-1.69531,-0.966016,2.3648,
                                    0.480252,0.486045,0.46669,
                                    0.51024,0.292658,0.808707],
            },
            # '_gamma_A_1_YA': {
            #     'camera_position': [-0.96887,-2.21765,1.25047,
            #                         1,0.4,0.5,
            #                         0.107002,0.198813,0.974179],
            #     'grid_vector1': [1.2,0,0],
            # },
            # '_gamma_A_2_YA': {
            #     'camera_position': [-0.96887,-2.21765,1.25047,
            #                         1,0.4,0.5,
            #                         0.107002,0.198813,0.974179],
            #     'grid_vector1': [1.2,0,0],
            # },
            # '_gamma_A_3_YA': {
            #     'camera_position': [-0.96887,-2.21765,1.25047,
            #                         1,0.4,0.5,
            #                         0.107002,0.198813,0.974179],
            #     'grid_vector1': [1.2,0,0],
            # },
            # '_gamma_B_1_YB': {
            #     'camera_position': [-0.96887,-2.21765,1.25047,
            #                         1,0.4,0.5,
            #                         0.107002,0.198813,0.974179],
            #     'grid_vector1': [1.2,0,0],
            # },
            # '_gamma_B_2_YB': {
            #     'camera_position': [-0.96887,-2.21765,1.25047,
            #                         1,0.4,0.5,
            #                         0.107002,0.198813,0.974179],
            #     'grid_vector1': [1.2,0,0],
            # },
            # '_gamma_B_3_YB': {
            #     'camera_position': [-0.96887,-2.21765,1.25047,
            #                         1,0.4,0.5,
            #                         0.107002,0.198813,0.974179],
            #     'grid_vector1': [1.2,0,0],
            # },
            # '_gamma_m_YM': {
            #     'camera_position': [-1.69531,-0.966016,2.3648,
            #                         0.480252,0.486045,0.46669,
            #                         0.51024,0.292658,0.808707],
            # },
            '_gamma_p_YM': {
                'camera_position': [-1.69531,-0.966016,2.3648,
                                    0.480252,0.486045,0.46669,
                                    0.51024,0.292658,0.808707],
            },
            # '_oneA_YM': {
            #     'camera_position': [-1.69531,-0.966016,2.3648,
            #                         0.480252,0.486045,0.46669,
            #                         0.51024,0.292658,0.808707],
            # },
            # '_oneB_YM': {
            #     'camera_position': [-1.69531,-0.966016,2.3648,
            #                         0.480252,0.486045,0.46669,
            #                         0.51024,0.292658,0.808707],
            # },
            # '_piA_YA': {
            #     'max_plots': 2,
            #     'camera_position': [-2.02509,0.148141,3.9141,
            #                         0.913524,1.35355,0.462869,
            #                         0.714983,0.186315,0.673859],
            #     'grid_vector1': [1.2,0,0],
            # },
            # '_piB_YB': {
            #     'max_plots': 2,
            #     'camera_position': [-2.02509,0.148141,3.9141,
            #                         0.913524,1.35355,0.462869,
            #                         0.714983,0.186315,0.673859],
            #     'grid_vector1': [1.2,0,0],
            # },
        },
    },
    'homogenization/rs_correctors.py': {
        'command': 'python3 sfepy/examples/homogenization/rs_correctors.py -n',
        'result': 'corrs_elastic.vtk',
        'sfepy-view-options': {
            '': {
                'max_plots': 2,
                'camera_position': [1.16983,0.660181,7.63496,
                                    1.16983,0.660181,
                                    0,0,1,0],
            },
        },
    },
    'large_deformation/compare_elastic_materials.py': {
        'command': 'python3 sfepy/examples/large_deformation/compare_elastic_materials.py -n',
        'image': 'pressure_displacement.png',
        'sfepy-view-options': {
        },
    },
    'large_deformation/gen_yeoh_tl_up_interactive.py': {
        'command': 'python3 sfepy/examples/large_deformation/gen_yeoh_tl_up_interactive.py -pn',
        'image': 'gen_yeoh_tl_up_comparison.png',
        'result': 'domain.10.vtk',
        'sfepy-view-options': {
            '': {
                'fields': ['stress:wu:f1:p0', '1:vw:p0'],
                'camera_position': [-1.89068,-2.47529,0.674151,
                                    0.793688,0.209075,0.574171,
                                    0,0,1],
            }
        },
    },
    'large_deformation/hyperelastic_tl_up_interactive.py': {
        'command': 'python3 sfepy/examples/large_deformation/hyperelastic_tl_up_interactive.py -pn',
        'image': 'hyperelastic_tl_up_comparison.png',
        'result': 'domain.10.vtk',
        'sfepy-view-options': {
            '': {
                'fields': ['stress:wu:f1:p0', '1:vw:p0'],
                'camera_position': [-4.04955,-6.37091,3.78116,
                                    2.06774,-0.866196,1.16309,
                                    0.220544,0.208124,0.952914],
            }
        },
    },
    'linear_elasticity/dispersion_analysis.py': {
        'command_0': 'python3 sfepy/examples/linear_elasticity/dispersion_analysis.py meshes/2d/special/circle_in_square.mesh --log-std-waves --eigs-only --no-show',
        'command_1': 'python3 sfepy/scripts/plot_logs.py output/frequencies.txt -o output/frequencies.png -n',
        'image': 'output/frequencies.png',
        'sfepy-view-options': {
        },
    },
    'linear_elasticity/elastic_contact_planes.py': {
        '': {
            'fields': ['u:wu:p0', '1:vw:p0'],
            'camera': [225, 55, 0.7],
        },
    },
    'linear_elasticity/elastic_contact_sphere.py': {
        '': {
            'fields': ['u:wu:p0', '1:vw:p0'],
            'camera': [225, 55, 0.7],
        },
    },
    'linear_elasticity/elastic_shifted_periodic.py': {
        '': {'fields': ['von_mises_stress:r:wu:p0', '1:vw:p0']},
    },
    'linear_elasticity/elastodynamic.py': {
        '': {
            'fields': ['u:wu:f1e3:p0', '1:vw:p0',
                       'cauchy_strain:p1', 'cauchy_stress:p2'],
        },
    },
    'linear_elasticity/elastodynamic_identification.py': {
        'command_0': 'python3 sfepy/examples/linear_elasticity/elastodynamic_identification.py --output-dir=output/edi',
        'image_0': 'output/edi/res00004.png',
        'command_1': 'python3 sfepy/scripts/plot_logs.py output/edi/pars.txt -o output/edi/pars.png -n',
        'image_1': 'output/edi/pars.png',
        'sfepy-view-options': {
        },
    },
    'linear_elasticity/its2D_4.py': {
        'command_0': 'sfepy-run sfepy/examples/linear_elasticity/its2D_4.py',
        'command_1': 'sfepy-probe sfepy/examples/linear_elasticity/its2D_4.py its2D.h5',
        'image_0': 'its2D_0.png',
        'image_1': 'its2D_1.png',
        'result': 'its2D.h5',
        'dim': 2,
        'sfepy-view-options': {
            '': {
            },
        },
    },
    'linear_elasticity/its2D_5.py': {
        'command': 'sfepy-run sfepy/examples/linear_elasticity/its2D_5.py',
        'image_0': 'its2D_probe_line0.png',
        'image_1': 'its2D_probe_line1.png',
        'result': 'its2D.vtk',
        'dim': 2,
        'sfepy-view-options': {
            '': {
            },
        },
    },
    'linear_elasticity/its2D_interactive.py': {
        'command': 'python3 sfepy/examples/linear_elasticity/its2D_interactive.py -p',
        'image_0': 'its2D_interactive_probe_0.png',
        'image_1': 'its2D_interactive_probe_1.png',
        'result': 'its2D_interactive.vtk',
        'dim': 2,
        'sfepy-view-options': {
            '': {
            },
        },
    },
    'linear_elasticity/linear_elastic_iga.py': {
        '': {
            'fields': ['u:wu:p0', '1:vw:p0'],
            'camera': [-45, 55, 1],
        },
    },
    'linear_elasticity/linear_elastic_interactive.py': {
        'command': 'python3 sfepy/examples/linear_elasticity/linear_elastic_interactive.py',
        'result': 'linear_elasticity.vtk',
        'dim': 2,
        'sfepy-view-options': {
            '': {
                'fields': ['u:wu:p0', '1:vw:p0'],
            },
        },
    },
    'linear_elasticity/linear_elastic_probes.py': {
        'command': 'sfepy-run sfepy/examples/linear_elasticity/linear_elastic_probes.py',
        'image_0': 'cylinder_probe_line.png',
        'image_1': 'cylinder_probe_circle.png',
        'image_2': 'cylinder_probe_ray.png',
        'result': 'cylinder.vtk',
        'sfepy-view-options': {
            '': {
                'fields': ['cauchy_stress:wu:p0', '1:vw:p0'],
                'camera_position': [-0.0496419,-0.132205,0.0339214,
                                    0.0495001,0.00309172,-0.00112878,
                                    0.146854,0.145842,0.978348],
            },
        },
    },
    'linear_elasticity/linear_viscoelastic.py': {
        '': {'camera': [225, 75, 0.88]}
    },
    'linear_elasticity/modal_analysis.py': {
        'command': 'python3 sfepy/examples/linear_elasticity/modal_analysis.py  -s 31,31 -n 3',
        'result': 'eigenshapes.vtk',
        'sfepy-view-options': {
            '': {
                'fields': ['strain000:wu000:f10%:p0', '1:vw:p0',
                           'strain001:wu001:f10%:p1', '1:vw:p1',
                           'strain002:wu002:f10%:p2', '1:vw:p2'],
                'camera_position': [1.1,-0.1,5.41561,
                                    1.1,-0.1,
                                    0,0,1,0],
                'grid_vector1': [1.2,0,0],
            },
        },
    },
    'linear_elasticity/modal_analysis_declarative.py': {
        '': {
            'fields': ['u003:wu003:f30%:p0', '1:vw:p0'],
            'camera_position': [-2.30562,-2.2604,-0.325838,
                                -0.0714771,0.0374911,0.0287214,
                                -0.0245554,-0.129086,0.991329],
        },
    },
    'linear_elasticity/multi_node_lcbcs.py': {
        '': {
            'fields': ['u:wu:e'],
            'force_view_3d': True,
            'camera_position': [0.175,0.125,0.735014,
                                0.175,0.125,0,
                                0,1,0],
        },
    },
    'linear_elasticity/multi_point_constraints.py': {
        '': {
            'fields': ['u:wu:f1:p0', '1:vw:p0', 'u:gu:p0'],
            'force_view_3d': True,
            'camera_position': [0.0565,0.0434999,19.8951,
                                0.0565,0.0434999,0,
                                0,1,0],
        },
    },
    'linear_elasticity/seismic_load.py': {
        '': {
            'fields': ['cauchy_stress:wu:f10:p0', '1:vw:p0'],
        },
    },
    'linear_elasticity/shell10x_cantilever.py': {
        '': {
            'fields': ['u_disp:wu_disp:p0', '1:vw:p0',
                       'u_rot:p1', '1:vw:p1'],
            'camera': [-45, 75, 1],
            'grid_vector1': [1, 0, 0],
        },
    },
    'linear_elasticity/shell10x_cantilever_interactive.py': {
        'command': 'python3 sfepy/examples/linear_elasticity/shell10x_cantilever_interactive.py -t bend --plot --no-show output',
        'image': 'output/shell10x_cantilever_convergence_bent.png',
        'result': 'output/shell10x_cantilever.vtk',
        'sfepy-view-options': {
            '': {
                'fields': ['u_disp:wu_disp:p0', '1:vw:p0',
                           'u_rot:p1', '1:vw:p1'],
                'camera': [-45, 75, 1],
                'grid_vector1': [1, 0, 0],
            },
        },
    },
    'linear_elasticity/truss_bridge.py': {
        '': {
            'view_2d': True,
            'fields': ['u:wu:p0', '1:vw:p0', 'S:e:p1'],
            'grid_vector1': [0, 2, 0],
        },
    },
    'linear_elasticity/truss_bridge3d.py': {
        '_Solid': {
            'fields': ['u_solid:wu_solid:f1e3:p0'],
            'camera_position': [-5.912, -6.64883, 1.80888,
                                5.05199, 2.28013, -1.49468,
                                0, 0, 1],
        },
        '_Struct': {
            'fields': ['u_struct:wu_struct:f1e3:p0'],
            'camera_position': [-5.912, -6.64883, 1.80888,
                                5.05199, 2.28013, -1.49468,
                                0, 0, 1],
        },
    },
    'linear_elasticity/wedge_mesh.py': {
        'command': 'sfepy-run sfepy/examples/linear_elasticity/wedge_mesh.py',
        'result': 'beam_w14.vtk',
        'sfepy-view-options': {
            '': {
                'fields': ['u:wu:e:o0.5'],
                'camera_position': [0.927482,-0.574865,0.307926,
                                    0.372897,0.120369,-0.0347131,
                                    -0.326236,0.19556,0.924838],
            }
        },
    },
    'miscellaneous/live_plot.py': {
        'command_0': 'python3 sfepy/examples/miscellaneous/live_plot.py -o output',
        'command_1': 'python3 sfepy/scripts/plot_logs.py output/live_plot.txt -o output/live_plot.png -n',
        'image_1': 'output/live_plot.png',
        'command_2': 'python3 sfepy/scripts/plot_logs.py output/live_plot2.txt -o output/live_plot2.png -n',
        'image_2': 'output/live_plot2.png',
        'sfepy-view-options': {
        },
    },
    'miscellaneous/refine_evp.py': {
        'command': 'python3 sfepy/examples/miscellaneous/refine_evp.py --max-order=5 --max-refine=2 --fig-suffix=.png --no-show',
        'image': 'output/h-refinement-0-laplace-lagrange-primme-none-a.png',
        'sfepy-view-options': {
        },
    },
    'multi_physics/biot_parallel_interactive.py': {
        'command': 'python3 sfepy/examples/multi_physics/biot_parallel_interactive.py output-parallel',
        'result': 'output-parallel/sol.h5',
        'sfepy-view-options': {
            '': {
                'fields': ['u:t1000:p0', '1:vw:o0.1:p0', 'p:p1'],
                'camera_position': [-0.740809,-2.67483,2.43604,
                                    0.579298,-0.106475,0.0404841,
                                    0.183213,0.618527,0.764106],
                'grid_vector1': [1.2, 0, 0]
            },
        },
    },
    'multi_physics/piezo_elasticity.py': {
        '': {'fields': ['u:g:p0', 'cauchy_strain:p1',
                        'elastic_stress:p2', 'piezo_stress:p3'],
             'grid_vector1': [1.2, 0, 0],
             'max_plots': 4},
    },
    'multi_physics/piezo_elastodynamic.py': {
        '': {
            'fields': ['p:wu:f2000:p0', '1:vw:wu:f2000:p0'],
            'camera_position': [-0.0125588,-0.00559266,0.0117482,
                                0.00438669,0.00487109,0.00135715,
                                0.334487,0.333581,0.881387],
            'color_map': 'inferno',
        }
    },
    'multi_physics/thermal_electric.py': {
        'command': 'python3 sfepy/examples/multi_physics/thermal_electric.py',
        'result': 'sfepy/examples/multi_physics/output/circle_in_square.vtk',
        'dim': 2,
        'sfepy-view-options': {
            '.el': {
            },
            '.10': {
            },
        },
    },
    'multi_physics/thermo_elasticity_ess.py': {
        '': {
            'fields': ['T:wu:f1e3:p0', '1:vw:p0'],
            'camera': [-45, 75, 1],
        },
    },
    'multi_physics/thermo_elasticity.py': {
        '': {'camera': [225, 75, 0.9]}
    },
    'navier_stokes/stokes_slip_bc.py': {
        '': {
            'fields': ['u:g:f.25:p0', 'u:o.4:p0', 'p:p1'],
            'camera': [-45, 55, 1],
            'grid_vector1': [0, 1.2, 0]
        },
    },
    'phononic/band_gaps.py': {
        'command': 'sfepy-run sfepy/examples/phononic/band_gaps.py --phonon-band-gaps --phonon-plot -O plot_options={show=False,legend=True},fig_suffix=\'.png\'',
        'image': 'sfepy/examples/phononic/output/band_gaps/band_gaps.png',
        'result': 'sfepy/examples/phononic/output/band_gaps/evp.vtk',
        'sfepy-view-options': {
            '': {
                'camera_position': [1.8,-1.2,7.28269,
                                    1.8,-1.2,0,
                                    0,1,0],
                'grid_vector1': [1.2, 0, 0],
                'grid_vector2': [0, -1.2, 0],
                'max_plots': 4,
                'show_labels': False,
                'show_scalar_bars': False,
            },
        },
    },
    'phononic/band_gaps_rigid.py': {
        'command': 'sfepy-run sfepy/examples/phononic/band_gaps_rigid.py --phonon-band-gaps --phonon-plot -O plot_options={show=False,legend=True},fig_suffix=\'_rigid.png\'',
        'image': 'sfepy/examples/phononic/output/band_gaps_rigid/band_gaps_rigid.png',
        'result': 'sfepy/examples/phononic/output/band_gaps_rigid/evp.vtk',
        'sfepy-view-options': {
            '': {
                'fields': list(chain(
                    *[[f'u{ii:03d}:vs:o.4:p{ii}', f'u{ii:03d}:g:p{ii}']
                      for ii in range(12)]
                )),
                'camera_position': [1.8,-1.2,7.28269,
                                    1.8,-1.2,0,
                                    0,1,0],
                'grid_vector1': [1.2, 0, 0],
                'grid_vector2': [0, -1.2, 0],
                'max_plots': 4,
                'show_labels': False,
                'show_scalar_bars': False,
            },
        },
    },
    'quantum/boron.py': {
        '': {'fields': ['Psi000:p0', 'Psi001:p1', 'Psi002:p2', 'Psi003:p3'],
             'grid_vector1': [1.2, 0, 0],
             'max_plots': 4},
    },
    'quantum/hydrogen.py': {
        '': {'fields': ['Psi000:p0', 'Psi001:p1', 'Psi002:p2', 'Psi003:p3'],
             'grid_vector1': [1.2, 0, 0],
             'max_plots': 4},
    },
    'quantum/oscillator.py': {
        '': {'fields': ['Psi000:p0', 'Psi001:p1', 'Psi002:p2', 'Psi003:p3'],
             'grid_vector1': [1.2, 0, 0],
             'max_plots': 4},
    },
    'quantum/well.py': {
        '': {'fields': ['Psi000:p0', 'Psi001:p1', 'Psi002:p2', 'Psi003:p3'],
             'grid_vector1': [1.2, 0, 0],
             'max_plots': 4},
    },
}


[docs]def resview_plot(filename, filename_out, options): pv.set_plot_theme("document") plotter = pv.Plotter(off_screen=True) plotter = pv_plot([filename], options, plotter=plotter, use_cache=False) if options.axes_visibility: plotter.add_axes(**dict(options.axes_options)) if options.view_2d: plotter.view_xy() plotter.show(screenshot=filename_out, window_size=(800, 600)) else: if options.camera_position is not None: cpos = nm.array(options.camera_position) cpos = cpos.reshape((3, 3)) elif options.camera: zoom = options.camera[2] if len(options.camera) > 2 else 1. cpos = get_camera_position(plotter.bounds, options.camera[0], options.camera[1], zoom=zoom) else: cpos = None plotter.show(cpos=cpos, screenshot=filename_out, window_size=(800, 600))
[docs]def run_resview_plot(*args): """ A fix for the problem that calling :func:`resview_plot()` directly often terminates the program. """ from multiprocessing import Process process = Process(target=resview_plot, args=args) process.start() process.join()
def _omit(filename, omits, omit_dirs): omit = False base = os.path.basename(filename) if base in omits: omit = True for omit_dir in omit_dirs: if omit_dir(filename) is not None: omit = True break return omit
[docs]def ebase2fbase(ebase): return os.path.splitext(ebase)[0].replace(os.path.sep, '-')
def _make_fig_name(fig_base, fig_filename): return fig_base + '-' + os.path.basename(fig_filename) def _get_image_names(custom_options): for key, val in custom_options.items(): if key.startswith('image'): yield val def _get_fig_filenames(ebase, images_dir): fig_base = ebase2fbase(ebase) if ebase in custom: custom_options = custom.get(ebase) if 'sfepy-view-options' in custom_options: custom_view_options = custom_options['sfepy-view-options'] for fig_filename in _get_image_names(custom_options): yield os.path.join(images_dir, _make_fig_name(fig_base, fig_filename)) else: custom_view_options = custom_options if custom_view_options: suffixes = sorted(custom_view_options.keys()) for suffix in suffixes: yield os.path.join(images_dir, fig_base + suffix + '.png') else: yield os.path.join(images_dir, fig_base + '.png') def _get_fig_filename(ebase, images_dir, suffix): fig_base = ebase2fbase(ebase) return os.path.join(images_dir, fig_base + suffix + '.png') def _make_sphinx_path(path, relative=False): if relative: aux = path.replace(sfepy.data_dir, '') prefix = ('..' + os.path.sep) * aux.count(os.path.sep) sphinx_path = prefix[:-1] + aux else: sphinx_path = path.replace(sfepy.data_dir, '/..') return sphinx_path def _apply_commands(custom_options, ebase, images_dir): for key, val in custom_options.items(): if key.startswith('command'): cmd = custom_options[key] subprocess.run(cmd.split()).check_returncode() if key.startswith('image'): shutil.copy(val, os.path.join(images_dir, _make_fig_name(ebase2fbase(ebase), val)))
[docs]def apply_view_options(views, default): out = {} for kview, view in views.items(): ov = default.copy() for k, v in view.items(): if k == 'fields': fv = [k.split(':') for k in v] fv = [(k[0], ':'.join(k[1:])) for k in fv] setattr(ov, k, fv) else: setattr(ov, k, v) out[kview] = ov return out
[docs]def generate_images(images_dir, examples_dir, pattern='*.py'): """ Generate images from results of running examples found in `examples_dir` directory. The generated images are stored to `images_dir`, """ from sfepy.applications import solve_pde from sfepy.solvers.ts_solvers import StationarySolver prefix = output.prefix output_dir = tempfile.mkdtemp() trunk = os.path.join(output_dir, 'result') options = Struct(output_filename_trunk=trunk, output_format='vtk', save_ebc=False, save_ebc_nodes=False, save_regions=False, save_regions_as_groups=False, solve_not=False) view_options = Struct(step=0, fields=[], fields_map=[], outline=False, isosurfaces=0, show_edges=False, warp=None, factor=1., opacity=1., color_map='viridis', axes_options=[], axes_visibility=False, grid_vector1=None, grid_vector2=None, max_plots=3, show_labels=False, label_position=[-1, -1, 0, 0.2], scalar_bar_size=[0.15, 0.06], scalar_bar_position=[0.04, 0.92, 0, -1.5], show_scalar_bars=True, camera=[225, 75, 1], camera_position=None, view_2d=False, force_view_3d=False, show_step_time=False) ensure_path(images_dir + os.path.sep) for ex_filename in locate_files(pattern, examples_dir): if _omit(ex_filename, omits + omit_images, omit_dirs): continue output.level = 0 output.prefix = prefix ebase = ex_filename.replace(examples_dir, '')[1:] output('trying "%s"...' % ebase) _ebase = ebase.replace(os.path.sep, '/') custom_options = custom.get(_ebase) if custom_options and 'sfepy-view-options' in custom_options: try: _apply_commands(custom_options, ebase, images_dir) filename = custom_options.get('result') dim = custom_options.get('dim') custom_view_options = custom_options['sfepy-view-options'] except subprocess.CalledProcessError: filename = None output('***** failed! *****') else: custom_view_options = custom_options try: problem, state = solve_pde(ex_filename, options=options) try: tsolver = problem.get_solver() except ValueError: suffix = None else: if isinstance(tsolver, StationarySolver): suffix = None else: suffix = tsolver.ts.suffix % (tsolver.ts.n_step - 1) filename = problem.get_output_name(suffix=suffix) dim = problem.get_dim() except KeyboardInterrupt: raise except: filename = None output('***** failed! *****') if filename is not None: if custom_view_options is not None: views = apply_view_options(custom_view_options, view_options) else: views = {'': view_options.copy()} for suffix, kwargs in views.items(): if dim in (1, 2) and not kwargs.force_view_3d: kwargs.view_2d = True kwargs.scalar_bar_position = [0.04, 0.92, 1.7, 0] if kwargs.grid_vector1 is None: kwargs.grid_vector1 = [1.2, 0, 0] if kwargs.grid_vector2 is None: kwargs.grid_vector2 = [0, -1.2, 0] fig_filename = _get_fig_filename(ebase, images_dir, suffix) fname = edit_filename(filename, suffix=suffix) output('displaying results from "%s"' % fname) disp_name = fig_filename.replace(sfepy.data_dir, '') output('to "%s"...' % disp_name.lstrip(os.path.sep)) run_resview_plot(fname, fig_filename, kwargs) output('...done') remove_files(output_dir) output('...done')
[docs]def generate_thumbnails(thumbnails_dir, images_dir, scale=0.3): """ Generate thumbnails into `thumbnails_dir` corresponding to images in `images_dir`. """ ensure_path(thumbnails_dir + os.path.sep) output('generating thumbnails...') filenames = glob.glob(os.path.join(images_dir, '*.png')) for fig_filename in filenames: ebase = fig_filename.replace(sfepy.data_dir, '').lstrip(os.path.sep) output('"%s"' % ebase) base = os.path.basename(fig_filename) thumb_filename = os.path.join(thumbnails_dir, base) image.thumbnail(fig_filename, thumb_filename, scale=scale) output('...done')
_index = """\ .. _%s-index: %s %s .. toctree:: :maxdepth: 2 """ _image = '.. image:: %s' _include = """\ .. _%s: %s %s **Description** %s %s :download:`source code <%s>` .. literalinclude:: %s """
[docs]def generate_rst_files(rst_dir, examples_dir, images_dir, pattern='*.py'): """ Generate Sphinx rst files for examples in `examples_dir` with images in `images_dir` and put them into `rst_dir`. Returns ------- dir_map : dict The directory mapping of examples and corresponding rst files. """ ensure_path(rst_dir + os.path.sep) output('generating rst files...') dir_map = {} for ex_filename in locate_files(pattern, examples_dir): if _omit(ex_filename, omits, omit_dirs): continue ebase = ex_filename.replace(examples_dir, '')[1:] base_dir = os.path.dirname(ebase) rst_filename = ebase2fbase(ebase) + '.rst' dir_map.setdefault(base_dir, []).append((ex_filename, rst_filename)) for dirname, filenames in dir_map.items(): filenames = sorted(filenames, key=lambda a: a[1]) dir_map[dirname] = filenames # Main index. mfd = open(os.path.join(rst_dir, 'index.rst'), 'w') mfd.write(_index % ('examples', 'Examples', '=' * 8)) for dirname, filenames in ordered_iteritems(dir_map): # Subdirectory index. ifd = open(os.path.join(rst_dir, '%s-index.rst' % dirname), 'w') ifd.write(_index % (dirname + '-examples', dirname, '=' * len(dirname))) for ex_filename, rst_filename in filenames: full_rst_filename = os.path.join(rst_dir, rst_filename) output('"%s"' % rst_filename) ebase = ex_filename.replace(examples_dir, '')[1:] rst_base = os.path.splitext(rst_filename)[0] rst_ex_filename = _make_sphinx_path(ex_filename) try: docstring = get_default(import_file(ex_filename).__doc__, 'missing description!') except KeyboardInterrupt: raise except: output('***** failed! *****') docstring = 'example import failed!' ifd.write(' %s <%s>\n' % (os.path.basename(ebase), rst_base)) fig_include = '' for fig_filename in _get_fig_filenames(ebase, images_dir): rst_fig_filename = _make_sphinx_path(fig_filename) if os.path.exists(fig_filename): fig_include += _image % rst_fig_filename + '\n' else: output(' warning: figure "%s" not found' % fig_filename) # Example rst file. fd = open(full_rst_filename, 'w', encoding='utf-8') fd.write(_include % (rst_base, ebase, '=' * len(ebase), docstring, fig_include, rst_ex_filename, rst_ex_filename)) fd.close() ifd.close() mfd.write(' %s-index\n' % dirname) mfd.close() output('...done') return dir_map
_rst_empty_item = """\ - .. """ _rst_item = """\ %s - .. figure:: %s :target: %s :ref:`%s <%s>` """ _gallery_table = """\ .. list-table:: :align: center :class: gallery """ _gallery_head = """\ .. only:: html .. _gallery-index: Gallery ======= """ helps = { 'doc_dir': 'top level directory of gallery files', 'pattern': 'example files search pattern [default: %(default)s]', 'no_images': 'do not (re)generate images', 'no_thumbnails': 'do not (re)generate thumbnails', 'output_filename': 'output file name [default: %(default)s]', }
[docs]def main(): parser = ArgumentParser(description=__doc__, formatter_class=RawDescriptionHelpFormatter) parser.add_argument('--version', action='version', version='%(prog)s') parser.add_argument('-d', '--doc-dir', metavar='doc_dir', action='store', dest='doc_dir', default='doc', help=helps['doc_dir']) parser.add_argument('-p', '--pattern', metavar='pattern', action='store', dest='pattern', default='*.py', help=helps['pattern']) parser.add_argument('-n', '--no-images', action='store_false', dest='images', default=True, help=helps['no_images']) parser.add_argument('--no-thumbnails', action='store_false', dest='thumbnails', default=True, help=helps['no_thumbnails']) parser.add_argument('-o', '--output', metavar='output_filename', action='store', dest='output_filename', default='gallery.rst', help=helps['output_filename']) options = parser.parse_args() rst_dir = 'examples' doc_dir = os.path.realpath(options.doc_dir) examples_dir = os.path.realpath('sfepy/examples') full_rst_dir = os.path.join(doc_dir, rst_dir) images_dir = os.path.join(doc_dir, 'images/gallery') thumbnails_dir = os.path.join(images_dir, 'thumbnails') output_filename = os.path.join(full_rst_dir, options.output_filename) if options.images: generate_images(images_dir, examples_dir, pattern=options.pattern) if options.thumbnails: generate_thumbnails(thumbnails_dir, images_dir) dir_map = generate_rst_files(full_rst_dir, examples_dir, images_dir, pattern=options.pattern) generate_gallery(examples_dir, output_filename, doc_dir, rst_dir, thumbnails_dir, dir_map)
if __name__ == '__main__': main()