feature: add new method inspect to SolverFIT3D to interactively show the imported solids and beam path in the simulation domain - Feature/solver inspect geometry (#43)

* fix: bug related to an empty path, was preventing cadquery STL export

* style: apply RUFFs suggestions + add logo with private function

* refact: include stl_colors in prepare stl dicts, now it will always contain colors as values and not material names. Private functions now start with _

* style: modify materials and colors dictionaries

* feature: allow logger to be saved from any class, by passing the material folder + forward the logger to solver if wake object is passed to constructor

* feature: add method `inspect()` to interactively show all the solids imported, with the materials and colors from dicts + the beam and integration path if wake object is passed, that can be toggled via checkboxes. Other minor changes to follow Ruff suggestions

* fix: apply codeQL findings + fix test failing

* feature: add progress bar to STL importing when grid is large >5M cells

* fix: solve some visualization errors + homogenize parameters `offscreen`-->`off_screen`

* feature: add `solver.inspect()` to notebook 002

* test: reorganize test, now all 3D interactive plotting routines are in `test_008`

* test: solve deprecation warnings and off_screen/on_screen test passing in test_008

* style: change default stainless steel material to `silver`

* tests: use vtk-osmesa to run the 3D plotting offscreen

* tests: update interactive plots, now not skipped thanks to vtk-osmesa + ignore HTML outputs

Author: elenafuengar

.github/workflows/manual_tests_CPU.yml

@@ -28,6 +28,8 @@ jobs:
     - name: pip install
       run:  |
         pip install wakis['notebook']
+        pip uninstall vtk -y
+        pip install --extra-index-url https://wheels.vtk.org vtk-osmesa
 
     - name: Print versions
       run: conda list

.github/workflows/nightly_tests_CPU.yml

@@ -28,7 +28,8 @@ jobs:
     - name: pip install
       run:  |
         pip install wakis['notebook']
-
+        pip uninstall vtk -y
+        pip install --extra-index-url https://wheels.vtk.org vtk-osmesa
     - name: Print versions
       run: conda list
     - name: Checkout wakis

.github/workflows/pull_request_CPU.yml

@@ -32,6 +32,8 @@ jobs:
         run: |
           cd wakis
           pip install .['notebook']
+          pip uninstall vtk -y
+          pip install --extra-index-url https://wheels.vtk.org vtk-osmesa
 
       - name: Print installed packages
         run: conda list

.gitignore

@@ -7,6 +7,7 @@ FDTD_*
 ECT_*
 */img*
 *.png
+*.html
 *.gif
 *.old*
 *.svg

notebooks/002_Wakefield_simulation.ipynb

@@ -1,20 +1,24 @@
-import os, sys
-import numpy as np
+import os
+import sys
 import pyvista as pv
 import matplotlib.pyplot as plt
 from scipy.constants import c
 
 sys.path.append('../wakis')
-                
+
 from wakis import SolverFIT3D
-from wakis import GridFIT3D 
+from wakis import GridFIT3D
 from wakis.sources import PlaneWave
 
-import pytest 
+import pytest
 
-flag_interactive = False # Set to true to run PyVista tests
+# Turn False when running local
+flag_offscreen = True
 
 class TestPlanewave:
+
+    img_folder = 'tests/003_img/'
+
     def test_simulation(self):
         print("\n---------- Initializing simulation ------------------")
         # Number of mesh cells
@@ -23,7 +27,7 @@ def test_simulation(self):
         Nz = 120
 
         # Embedded boundaries
-        stl_file = 'tests/stl/003_sphere.stl' 
+        stl_file = 'tests/stl/003_sphere.stl'
         surf = pv.read(stl_file)
 
         stl_solids = {'Sphere': stl_file}
@@ -44,90 +48,75 @@ def test_simulation(self):
         xmax, ymax, zmax = (xmax+padx), (ymax+pady), (zmax+padz)
 
         global grid
-        grid = GridFIT3D(xmin, xmax, ymin, ymax, zmin, zmax, Nx, Ny, Nz, 
-                stl_solids=stl_solids, 
+        grid = GridFIT3D(xmin, xmax, ymin, ymax, zmin, zmax, Nx, Ny, Nz,
+                stl_solids=stl_solids,
                 stl_rotate=stl_rotate,
                 stl_scale=stl_scale,
                 stl_materials=stl_materials)
 
-        # Boundary conditions and 
+        # Boundary conditions and
         bc_low=['periodic', 'periodic', 'pec']
         bc_high=['periodic', 'periodic', 'pml']
-        
+
+        # -------------- Output folder ---------------------
+        if not os.path.exists(self.img_folder):
+            os.mkdir(self.img_folder)
+
         # simulation
         global solver
         solver = SolverFIT3D(grid, use_stl=True, bc_low=bc_low, bc_high=bc_high)
-        
+
         # source
         f = 15/((solver.z.max()-solver.z.min())/c)
-        source = PlaneWave(xs=slice(1, Nx-1), ys=slice(1,Ny-1), zs=1, 
+        source = PlaneWave(xs=slice(1, Nx-1), ys=slice(1,Ny-1), zs=1,
                            f=f, beta=1.0)
-        
+
         Nt = int(1.0*(solver.z.max()-solver.z.min())/c/solver.dt)
         solver.emsolve(Nt, source)
 
-    def test_plot2D(self):
+    def test_plot1D(self):
         global solver
-        solver.plot2D('Ex', plane='ZY', pos=0.5, cmap='rainbow', 
-                    add_patch='Sphere', patch_alpha=0.3, 
-                    off_screen=False)
-        if not flag_interactive:
-            plt.close()
-            
-    def test_plot2D_offscreen(self):
+        solver.plot1D('Ex', line='z', pos=[0.7, 0.6, 0.5, 0.4, 0.3, 0.2],
+                    xscale='linear', yscale='linear',
+                    off_screen=flag_offscreen, n=solver.Nt,
+                    colors=['#5ccfe6', '#fdb6d0', '#ffae57', '#bae67e', '#ffd580', '#a2aabc'],
+                    title=self.img_folder+'1Dplot_Ex')
+
+    def test_plot2D(self):
         global solver
-        solver.plot2D('Hy', plane='ZY', pos=0.5, cmap='bwr', 
+        solver.plot2D('Hy', plane='ZY', pos=0.5, cmap='bwr',
                     add_patch='Sphere', patch_alpha=0.1, interpolation='spline36',
-                    off_screen=True, n=solver.Nt, title='003_2Dplot_Hy') 
-        if not flag_interactive:
-            os.remove(f'003_2Dplot_Hy_{str(solver.Nt).zfill(6)}.png')
-    
-    @pytest.mark.skipif(not flag_interactive, reason="Requires interactive plotting")
+                    off_screen=flag_offscreen, n=solver.Nt,
+                    title=self.img_folder+'2Dplot_Hy')
+
+    @pytest.mark.skipif(flag_offscreen, reason="Requires interactive plotting")
     def test_plot3D_interactive(self):
         global solver
         solver.plot3D(field='E', component='x', cmap='jet',
             add_stl='Sphere', stl_opacity=0.1, stl_colors='white',
             clip_interactive=True, clip_normal='-y',
-            off_screen=False)  
-        
-    @pytest.mark.skipif(not flag_interactive, reason="Requires Xserver connection for plotting")     
+            off_screen=False)
+
     def test_plot3D_offscreen(self):
         global solver
         solver.plot3D(field='H', component='y', cmap='bwr',
                       add_stl='Sphere', stl_opacity=0.1, stl_colors='white',
-                      clip_box=True, clip_bounds=None, 
-                      off_screen=True, title='003_3Dplot_Hy')
-        if not flag_interactive:
-            os.remove('003_3Dplot_Hy.png')
-    
-    @pytest.mark.skipif(not flag_interactive, reason="Requires interactive plotting")
+                      clip_box=True, clip_bounds=None,
+                      off_screen=flag_offscreen, title=self.img_folder+'3Dplot_Hy')
+
+    @pytest.mark.skipif(flag_offscreen, reason="Requires interactive plotting")
     def test_plot3DonSTL_interactive(self):
         global solver
-        solver.plot3DonSTL('Ex', cmap='jet', 
+        solver.plot3DonSTL('Ex', cmap='jet',
                            stl_with_field='Sphere', field_opacity=1.,
                            stl_transparent='Sphere', stl_opacity=0.3, stl_colors='white',
                            clip_interactive=True, clip_normal='-y',
                            off_screen=False, zoom=1.0)
-        
-    @pytest.mark.skipif(not flag_interactive, reason="Requires Xserver connection for plotting")
+
     def test_plot3DonSTL_offscreen(self):
         global solver
-        solver.plot3DonSTL('Ex', cmap='jet', 
+        solver.plot3DonSTL('Ex', cmap='jet',
                            stl_with_field='Sphere', field_opacity=1.,
                            stl_transparent=None, stl_opacity=0., stl_colors=None,
-                           off_screen=True, zoom=1.0, title='003_3DplotOnSTL_Hy')
-        if not flag_interactive:
-            os.remove('003_3DplotOnSTL_Hy.png')
-        
-
-    @pytest.mark.skipif(not flag_interactive, reason="Requires interactive plotting")
-    def test_grid_inspect(self):
-        global grid
-        grid.inspect(add_stl=None, stl_opacity=0.5, stl_colors=None, 
-                     anti_aliasing='ssa')
-
-    @pytest.mark.skipif(not flag_interactive, reason="Requires interactive plotting")
-    def test_grid_plot_solids(self):
-        global grid
-        grid.plot_solids(bounding_box=False, opacity=1.0, specular=0.5,
-                         anti_aliasing=None)
+                           off_screen=flag_offscreen, zoom=1.0,
+                           title=self.img_folder+'3DplotOnSTL_Hy')

tests/test_003_planewave_sphere.py

@@ -86,19 +86,19 @@ class TestMPILossyCavity:
                     -6.04105997e+01 ,-3.06532160e+01 ,-1.17749936e+01 ,-3.12574866e+00,
                     -7.35339521e-01 ,-1.13085658e-01 , 7.18247535e-01 , 8.73829036e-02])
 
-    gridLogs = {'use_mesh_refinement': False, 'Nx': 60, 'Ny': 60, 'Nz': 140, 'dx': 0.00866666634877522, 
-                'dy': 0.00866666634877522, 'dz': 0.005714285799435207, 
-                'xmin': -0.25999999046325684, 'xmax': 0.25999999046325684, 
-                'ymin': -0.25999999046325684, 'ymax': 0.25999999046325684, 
-                'zmin': -0.25, 'zmax': 0.550000011920929, 
+    gridLogs = {'use_mesh_refinement': False, 'Nx': 60, 'Ny': 60, 'Nz': 140, 'dx': 0.00866666634877522,
+                'dy': 0.00866666634877522, 'dz': 0.005714285799435207,
+                'xmin': -0.25999999046325684, 'xmax': 0.25999999046325684,
+                'ymin': -0.25999999046325684, 'ymax': 0.25999999046325684,
+                'zmin': -0.25, 'zmax': 0.550000011920929,
                 'stl_solids': {'cavity': 'tests/stl/007_vacuum_cavity.stl', 'shell': 'tests/stl/007_lossymetal_shell.stl'},
-                'stl_materials': {'cavity': 'vacuum', 'shell': [30, 1.0, 30]}, 
+                'stl_materials': {'cavity': 'vacuum', 'shell': [30, 1.0, 30]},
                 'gridInitializationTime': 0}
-    
+
     solverLogs = {'use_gpu': False, 'use_mpi': False, 'background': 'pec',
-                'bc_low': ['pec', 'pec', 'pec'], 'bc_high': ['pec', 'pec', 'pec'], 
+                'bc_low': ['pec', 'pec', 'pec'], 'bc_high': ['pec', 'pec', 'pec'],
                 'dt': 6.970326728398966e-12, 'solverInitializationTime': 0}
-    
+
     wakeSolverLogs = {'ti': 2.8516132094735135e-09, 'q': 1e-09, 'sigmaz': 0.1, 'beta': 1.0,
                        'xsource': 0.0, 'ysource': 0.0, 'xtest': 0.0, 'ytest': 0.0, 'chargedist': None,
                        'skip_cells': 10, 'results_folder': 'tests/007_results/', 'wakelength': 10.0, 'simulationTime': 0}
@@ -252,29 +252,6 @@ def test_mpi_plot1D(self):
                 xscale='linear', yscale='linear',
                 off_screen=True, title=self.img_folder+'Ez1d', n=3000)
 
-    @pytest.mark.skipif(not flag_plot_3D, reason="Requires interactive plotting")
-    def test_mpi_plot3D(self):
-        # Plot Abs Electric field on domain
-        # disabled when mpi = True
-        global solver
-        solver.plot3D('E', component='Abs',
-                cmap='rainbow', clim=[0, 500],
-                add_stl=['cavity', 'shell'], stl_opacity=0.1,
-                clip_interactive=True, clip_normal='-y')
-
-    @pytest.mark.skipif(not flag_plot_3D, reason="Requires interactive plotting")
-    def test_mpi_plot3DonSTL(self):
-        # Plot Abs Electric field on STL solid `cavity`
-        # disabled when mpi = True
-        global solver
-        solver.plot3DonSTL('E', component='Abs',
-                        cmap='rainbow', clim=[0, 500],
-                        stl_with_field='cavity', field_opacity=1.0,
-                        stl_transparent='shell', stl_opacity=0.1, stl_colors='white',
-                        clip_plane=True, clip_normal='-y', clip_origin=[0,0,0],
-                        off_screen=False, zoom=1.2, title=self.img_folder+'Ez3d')
-
-
     def test_mpi_wakefield(self):
         # Reset fields
         global solver
@@ -343,7 +320,7 @@ def test_long_impedance(self):
             assert np.allclose(np.real(wake.Z)[::20], np.real(self.Z), rtol=0.1), "Real Impedance samples failed"
             assert np.allclose(np.imag(wake.Z)[::20], np.imag(self.Z), rtol=0.1), "Imag Impedance samples failed"
             assert np.cumsum(np.abs(wake.Z))[-1] == pytest.approx(250910.51090497518, 0.1), "Abs Impedance cumsum failed"
-    
+
     def test_log_file(self):
         # Helper function to compare nested dicts with float tolerance
         def assert_dict_allclose(d1, d2, rtol=1e-6, atol=1e-12, path=""):
@@ -379,7 +356,7 @@ def assert_dict_allclose(d1, d2, rtol=1e-6, atol=1e-12, path=""):
 
         global solver
         # Exclude timing info from comparison as they can vary between runs
-        solver.logger.grid["gridInitializationTime"] = 0 
+        solver.logger.grid["gridInitializationTime"] = 0
         solver.logger.solver["solverInitializationTime"] = 0
         solver.logger.wakeSolver["simulationTime"] = 0
         self.solverLogs['use_mpi'] = use_mpi