emerge 0.6.7__py3-none-any.whl → 0.6.9__py3-none-any.whl

emerge/_emerge/plot/pyvista/display.py

@@ -284,15 +284,16 @@ class PVDisplay(BaseDisplay):
         self._ruler.min_length = max(1e-3, min(self._mesh.edge_lengths))
         self._update_camera()
         self._add_aux_items()
+        # self._plot.renderer.enable_depth_peeling(20, 0.8)
+        # self._plot.enable_anti_aliasing(self.set.anti_aliassing)
         if self._do_animate:
             self._wire_close_events()
             self.add_text('Press Q to close!',color='red', position='upper_left')
             self._plot.show(auto_close=False, interactive_update=True, before_close_callback=self._close_callback)
             self._animate()
-            
-            
         else:
             self._plot.show()
+        
         self._reset()
     
     def set_mesh(self, mesh: Mesh3D):
@@ -315,7 +316,6 @@ class PVDisplay(BaseDisplay):
         """The private callback function that stops the animation.
         """
         self._stop = True
-        print('CLOSE!')
 
     def _animate(self) -> None:
         """Private function that starts the animation loop.
@@ -441,8 +441,20 @@ class PVDisplay(BaseDisplay):
         opacity = obj.opacity
         line_width = 0.5
         color = obj.color_rgb
+        metal = obj._metal
         style='surface'
         
+        # Default render settings
+        metallic = 0.05
+        roughness = 0.5
+        pbr = False
+        
+        if metal:
+            pbr = True
+            metallic = 0.8
+            roughness = 0.3
+        
+        # Default keyword arguments when plotting Mesh mode.
         if mesh is True:
             show_edges = True
             opacity = 0.7
@@ -450,13 +462,28 @@ class PVDisplay(BaseDisplay):
             style='wireframe'
             color=next(C_CYCLE)
         
-        kwargs = setdefault(kwargs, color=color, opacity=opacity, line_width=line_width, show_edges=show_edges, pickable=True, style=style)
+        # Defining the default keyword arguments for PyVista
+        kwargs = setdefault(kwargs, color=color, 
+                            opacity=opacity, 
+                            metallic=metallic, 
+                            pbr=pbr,
+                            roughness=roughness,
+                            line_width=line_width, 
+                            show_edges=show_edges, 
+                            pickable=True, 
+                            style=style)
         mesh_obj = self.mesh(obj)
         
         if mesh is True and volume_mesh is True:
             mesh_obj = mesh_obj.extract_all_edges()
-        
         actor = self._plot.add_mesh(mesh_obj, *args, **kwargs)
+        
+        # Push 3D Geometries back to avoid Z-fighting with 2D geometries.
+        if obj.dim==3:
+            mapper = actor.GetMapper()
+            mapper.SetResolveCoincidentTopology(1)
+            mapper.SetRelativeCoincidentTopologyPolygonOffsetParameters(1,1)
+        
         self._plot.add_mesh(self._volume_edges(_select(obj)), color='#000000', line_width=2, show_edges=True)
 
     def add_scatter(self, xs: np.ndarray, ys: np.ndarray, zs: np.ndarray):
@@ -567,6 +594,7 @@ class PVDisplay(BaseDisplay):
         grid = pv.StructuredGrid(x,y,z)
         field_flat = field.flatten(order='F')
 
+
         if scale=='log':
             T = lambda x: np.log10(np.abs(x))
         elif scale=='symlog':
@@ -582,25 +610,28 @@ class PVDisplay(BaseDisplay):
         self._ctr += 1
         grid[name] = static_field
 
+        grid_no_nan = grid.threshold(scalars=name)
+
+        # Determine color limits
         if clim is None:
-            fmin = np.min(static_field)
-            fmax = np.max(static_field)
+            fmin = np.nanmin(static_field)
+            fmax = np.nanmax(static_field)
             clim = (fmin, fmax)
-        
         if symmetrize:
-            lim = max(abs(clim[0]),abs(clim[1]))
+            lim = max(abs(clim[0]), abs(clim[1]))
             clim = (-lim, lim)
 
         kwargs = setdefault(kwargs, cmap=cmap, clim=clim, opacity=opacity, pickable=False, multi_colors=True)
-        actor = self._plot.add_mesh(grid, scalars=name, **kwargs)
+        actor = self._plot.add_mesh(grid_no_nan, scalars=name, **kwargs)
+
 
         if self._do_animate:
             def on_update(obj: _AnimObject, phi: complex):
-                field = obj.T(np.real(obj.field*phi))
-                obj.grid[name] = field
-            self._objs.append(_AnimObject(field_flat, T, grid, actor, on_update)) # type: ignore
-        
-        
+                field_anim = obj.T(np.real(obj.field * phi))
+                obj.grid[name] = field_anim
+            self._objs.append(_AnimObject(field_flat, T, grid_no_nan, actor, on_update))
+
+
     def add_title(self, title: str) -> None:
         """Adds a title
 
@@ -652,6 +683,11 @@ class PVDisplay(BaseDisplay):
         dx = dx.flatten().real
         dy = dy.flatten().real
         dz = dz.flatten().real
+        
+        ids = np.invert(np.isnan(dx))
+        
+        x, y, z, dx, dy, dz = x[ids], y[ids], z[ids], dx[ids], dy[ids], dz[ids]
+        
         dmin = _min_distance(x,y,z)
 
         dmax = np.max(_norm(dx,dy,dz))
@@ -667,8 +703,10 @@ class PVDisplay(BaseDisplay):
         kwargs = dict()
         if color is not None:
             kwargs['color'] = color
+            
         pl = self._plot.add_arrows(Coo, Vec, scalars=None, clim=None, cmap=None, **kwargs)
 
+        
     def add_contour(self,
                      X: np.ndarray,
                      Y: np.ndarray,

emerge/_emerge/plot/pyvista/display_settings.py

@@ -1,3 +1,4 @@
+from typing import Literal
 
 class PVDisplaySettings:
 
@@ -22,4 +23,6 @@ class PVDisplaySettings:
         self.background_bottom: str = "#c0d2e8"
         self.background_top: str = "#ffffff"
         self.grid_line_color: str = "#8e8e8e"
-        self.z_boost: float = 1e-6
+        self.z_boost: float = 0#1e-9
+        self.depth_peeling: bool = True
+        self.anti_aliassing: Literal["msaa","ssaa",'fxaa'] = "msaa"

emerge/_emerge/plot/simple_plots.py

@@ -406,21 +406,21 @@ and sparse frequency annotations (e.g., labeled by frequency).
     plt.tight_layout()
     plt.show()
 
-def plot_sp(f: np.ndarray, S: list[np.ndarray] | np.ndarray, 
-                      dblim=[-40, 5], 
-                    xunit="GHz", 
-                    levelindicator: int | float | None = None, 
-                    noise_floor=-150, 
-                    fill_areas: list[tuple] | None = None, 
-                    spec_area: list[tuple[float,...]] | None = None,
-                    unwrap_phase=False, 
-                    logx: bool = False,
-                    labels: list[str] | None = None,
-                    linestyles: list[str] | None = None,
-                    colorcycle: list[int] | None = None,
-                    filename: str | None = None,
-                    show_plot: bool = True,
-                    figdata: tuple | None = None) -> tuple[plt.Figure, plt.Axes, plt.Axes]:
+def plot_sp(f: np.ndarray | list[np.ndarray], S: list[np.ndarray] | np.ndarray, 
+            dblim=[-40, 5], 
+            xunit="GHz", 
+            levelindicator: int | float | None = None, 
+            noise_floor=-150, 
+            fill_areas: list[tuple] | None = None, 
+            spec_area: list[tuple[float,...]] | None = None,
+            unwrap_phase=False, 
+            logx: bool = False,
+            labels: list[str] | None = None,
+            linestyles: list[str] | None = None,
+            colorcycle: list[int] | None = None,
+            filename: str | None = None,
+            show_plot: bool = True,
+            figdata: tuple | None = None) -> tuple[plt.Figure, plt.Axes, plt.Axes]:
     """Plot S-parameters in dB and phase
 
     Args:
@@ -444,7 +444,12 @@ def plot_sp(f: np.ndarray, S: list[np.ndarray] | np.ndarray,
         Ss = [S]
     else:
         Ss = S
-
+        
+    if not isinstance(f, list):
+        fs = [f for _ in Ss]
+    else:
+        fs = f
+    
     if linestyles is None:
         linestyles = ['-' for _ in S]
 
@@ -452,7 +457,8 @@ def plot_sp(f: np.ndarray, S: list[np.ndarray] | np.ndarray,
         colorcycle = [i for i, S in enumerate(S)]
 
     unitdivider: dict[str, float] = {"MHz": 1e6, "GHz": 1e9, "kHz": 1e3}
-    fnew = f / unitdivider[xunit]
+    
+    fs = [f / unitdivider[xunit] for f in fs]
 
     if figdata is None:
         # Create two subplots: one for magnitude and one for phase
@@ -463,10 +469,10 @@ def plot_sp(f: np.ndarray, S: list[np.ndarray] | np.ndarray,
     minphase, maxphase = -180, 180
 
     maxy = 0
-    for s, ls, cid in zip(Ss, linestyles, colorcycle):
+    for f, s, ls, cid in zip(fs, Ss, linestyles, colorcycle):
         # Calculate and plot magnitude in dB
         SdB = 20 * np.log10(np.abs(s) + 10**(noise_floor/20) * np.random.rand(*s.shape) + 10**((noise_floor-30)/20))
-        ax_mag.plot(fnew, SdB, label="Magnitude (dB)", linestyle=ls, color=EMERGE_COLORS[cid % len(EMERGE_COLORS)])
+        ax_mag.plot(f, SdB, label="Magnitude (dB)", linestyle=ls, color=EMERGE_COLORS[cid % len(EMERGE_COLORS)])
         if np.max(SdB) > maxy:
             maxy = np.max(SdB)
         # Calculate and plot phase in degrees
@@ -475,12 +481,12 @@ def plot_sp(f: np.ndarray, S: list[np.ndarray] | np.ndarray,
             phase = np.unwrap(phase, period=360)
             minphase = min(np.min(phase), minphase)
             maxphase = max(np.max(phase), maxphase)
-        ax_phase.plot(fnew, phase, label="Phase (degrees)", linestyle=ls, color=EMERGE_COLORS[cid % len(EMERGE_COLORS)])
+        ax_phase.plot(f, phase, label="Phase (degrees)", linestyle=ls, color=EMERGE_COLORS[cid % len(EMERGE_COLORS)])
 
         # Annotate level indicators if specified
         if isinstance(levelindicator, (int, float)) and levelindicator is not None:
             lvl = levelindicator
-            fcross = hintersections(fnew, SdB, lvl)
+            fcross = hintersections(f, SdB, lvl)
             for fs in fcross:
                 ax_mag.annotate(
                     f"{str(fs)[:4]}{xunit}",
@@ -500,16 +506,18 @@ def plot_sp(f: np.ndarray, S: list[np.ndarray] | np.ndarray,
             f2 = fmax / unitdivider[xunit]
             ax_mag.fill_between([f1, f2], vmin,vmax, color='red', alpha=0.2)
     # Configure magnitude plot (ax_mag)
+    fmin = min([min(f) for f in fs])
+    fmax = max([max(f) for f in fs])
     ax_mag.set_ylabel("Magnitude (dB)")
     ax_mag.set_xlabel(f"Frequency ({xunit})")
-    ax_mag.axis([min(fnew), max(fnew), dblim[0], max(maxy*1.1,dblim[1])]) # type: ignore
+    ax_mag.axis([fmin, fmax, dblim[0], max(maxy*1.1,dblim[1])]) # type: ignore
     ax_mag.axhline(y=0, color="k", linewidth=1)
     ax_mag.xaxis.set_minor_locator(tck.AutoMinorLocator(2))
     ax_mag.yaxis.set_minor_locator(tck.AutoMinorLocator(2))
     # Configure phase plot (ax_phase)
     ax_phase.set_ylabel("Phase (degrees)")
     ax_phase.set_xlabel(f"Frequency ({xunit})")
-    ax_phase.axis([min(fnew), max(fnew), minphase, maxphase]) # type: ignore
+    ax_phase.axis([fmin, fmax, minphase, maxphase]) # type: ignore
     ax_phase.xaxis.set_minor_locator(tck.AutoMinorLocator(2))
     ax_phase.yaxis.set_minor_locator(tck.AutoMinorLocator(2))
     if logx:
@@ -533,7 +541,7 @@ def plot_ff(
     dB: bool = False,
     labels: Optional[List[str]] = None,
     xlabel: str = "Theta (rad)",
-    ylabel: str = "|E|",
+    ylabel: str = "",
     linestyles: Union[str, List[str]] = "-",
     linewidth: float = 2.0,
     markers: Optional[Union[str, List[Optional[str]]]] = None,
@@ -612,6 +620,8 @@ def plot_ff(
 def plot_ff_polar(
     theta: np.ndarray,
     E: Union[np.ndarray, Sequence[np.ndarray]],
+    dB: bool = False,
+    dBfloor: float = -30,
     labels: Optional[List[str]] = None,
     linestyles: Union[str, List[str]] = "-",
     linewidth: float = 2.0,
@@ -649,6 +659,8 @@ def plot_ff_polar(
         E_list = list(E)
     n_series = len(E_list)
 
+    if dB:
+        E_list = [20*np.log10(np.clip(np.abs(e), a_min=10**(dBfloor/20), a_max = 1e9)) for e in E_list]
     # Style broadcasting
     def _broadcast(param, default):
         if isinstance(param, list):
@@ -665,11 +677,15 @@ def plot_ff_polar(
     ax.set_theta_zero_location(zero_location) # type: ignore
     ax.set_theta_direction(-1 if clockwise else 1) # type: ignore
     ax.set_rlabel_position(rlabel_angle) # type: ignore
+    ymin = min([min(E) for E in E_list])
+    ymax = max([max(E) for E in E_list])
+    yrange = ymax-ymin
 
+    ax.set_ylim(ymin-0.05*yrange, ymax+0.05*yrange)
     for i, Ei in enumerate(E_list):
-        mag = np.abs(Ei)
+        
         ax.plot(
-            theta, mag,
+            theta, Ei,
             linestyle=linestyles[i],
             linewidth=linewidth,
             marker=markers[i],

emerge/_emerge/projects/_load_base.txt

@@ -17,8 +17,7 @@ with em.Simulation("myfile", load_file=True) as m:
     S11 = data.S(1,1)
     S21 = data.S(2,1)
     plt.plot_sp(f/1e9, [S11, S21])
-
-    m.set_mesh(m.data.mw.field[0].mesh)
+    
     m.display.add_object(m['box'])
     m.display.add_surf(*m.data.mw.field[0].cutplane(1*mm, z=5*mm).scalar('Ez','real'))
     m.display.show()

emerge/_emerge/selection.py

@@ -205,6 +205,10 @@ class Selection:
     def centers(self) -> list[tuple[float, float, float],]:
         return [gmsh.model.occ.get_center_of_mass(self.dim, tag) for tag in self.tags]
     
+    @property
+    def _metal(self) -> bool:
+        return False
+    
     @property
     def opacity(self) -> float:
         return 0.6

emerge/_emerge/simmodel.py

@@ -31,7 +31,7 @@ from typing import Literal, Generator, Any
 from loguru import logger
 import numpy as np
 import gmsh # type: ignore
-import joblib # type: ignore
+import cloudpickle
 import os
 import inspect
 from pathlib import Path
@@ -181,7 +181,10 @@ class Simulation:
 
             # Restier the Exit GMSH function on proper program abortion
             register(self._exit_gmsh)
-
+        else:
+            gmsh.finalize()
+            gmsh.initialize()
+            
         # Create a new GMSH model or load it
         if not self.load_file:
             gmsh.model.add(self.modelname)
@@ -245,13 +248,20 @@ class Simulation:
         vM, vm, vp = [float(x) for x in version.split('.')]
         cM, cm, cp = [float(x) for x in __version__.split('.')]
         if vM != cM:
-            raise VersionError(f"You are running a script designed for version {version} with a possibly incompatible version of EMerge {__version__}")
+            raise VersionError(f"You are running a script designed for version {version} with a possibly incompatible version of EMerge {__version__}. \n You can upgrade your version of emerge with: pip --upgrade emerge")
         if vm != cm:
-            raise VersionError(f"You are running a script designed for version {version} with a possibly incompatible version of EMerge {__version__}")
+            raise VersionError(f"You are running a script designed for version {version} with a possibly incompatible version of EMerge {__version__}. \n You can upgrade your version of emerge with: pip --upgrade emerge")
         if vp != cp:
-            logger.warning(f"You are running a script designed for version {version} with a possibly incompatible version of EMerge {__version__}")
+            logger.warning("You are running a script designed for a different version of EMerge.")
+            logger.warning(f"The script version: {version}")
+            logger.warning(f"EMerge version:     {__version__}")
+            logger.warning("Usually EMerge works without a problem but Errors may occur.")
+            logger.warning("You can upgrade your version of emerge with: pip --upgrade emerge")
             logger.warning("You may suppress this error by removing the call to .check_version().")
-            input('Press enter to proceed...')
+            logger.warning("Press Ctrl+C to abort.")
+            ans = input('Press enter to proceed or [Q] to quit:')
+            if ans.lower().strip()=='q':
+                quit()
 
     def save(self) -> None:
         """Saves the current model in the provided project directory."""
@@ -276,7 +286,8 @@ class Simulation:
         # Pack and save data
         dataset = dict(simdata=self.data, mesh=self.mesh)
         data_path = self.modelpath / 'simdata.emerge'
-        joblib.dump(dataset, str(data_path))
+        with open(str(data_path), "wb") as f_out:
+            cloudpickle.dump(dataset, f_out)
         logger.info(f"Saved simulation data to: {data_path}")
 
     def load(self) -> None:
@@ -297,7 +308,8 @@ class Simulation:
         #self.mesh.update([])
 
         # Load data
-        datapack = joblib.load(str(data_path))
+        with open(str(data_path), "rb") as f_in:
+            datapack= cloudpickle.load(f_in)
         self.data = datapack['simdata']
         self._set_mesh(datapack['mesh'])
         logger.info(f"Loaded simulation data from: {data_path}")
@@ -458,7 +470,7 @@ class Simulation:
 
             logger.info(f'Iterating: {params}')
             if len(dims_flat)==1:
-                yield (dims_flat[0][i_iter],)
+                yield dims_flat[0][i_iter]
             else:
                 yield (dim[i_iter] for dim in dims_flat) # type: ignore
         self.mw.cache_matrices = True

emerge/_emerge/solver.py

@@ -289,10 +289,14 @@ class Solver:
 
     def __init__(self):
         self.own_preconditioner: bool = False
+        self.initialized: bool = False
 
     def __str__(self) -> str:
         return f'{self.__class__.__name__}'
     
+    def initialize(self) -> None:
+        return None
+
     def duplicate(self) -> Solver:
         return self.__class__()
 
@@ -324,6 +328,9 @@ class EigSolver:
     def __init__(self):
         self.own_preconditioner: bool = False
 
+    def initialize(self) -> None:
+        return None
+
     def __str__(self) -> str:
         return f'{self.__class__.__name__}'
     
@@ -513,7 +520,19 @@ class SolverUMFPACK(Solver):
         super().__init__()
         self.A: np.ndarray = None
         self.b: np.ndarray = None
-        self.umfpack: um.UmfpackContext = um.UmfpackContext('zl')
+        
+        self.umfpack: um.UmfpackContext | None = None
+        
+        # SETTINGS
+        self._pivoting_threshold: float = 0.001
+
+        self.fact_symb: bool = False
+        self.initalized: bool = False
+
+    def initialize(self):
+        if self.initalized:
+            return
+        self.umfpack = um.UmfpackContext('zl')
         self.umfpack.control[um.UMFPACK_PRL] = 0 # ty: ignore
         self.umfpack.control[um.UMFPACK_IRSTEP] = 2 # ty: ignore
         self.umfpack.control[um.UMFPACK_STRATEGY] = um.UMFPACK_STRATEGY_SYMMETRIC # ty: ignore
@@ -522,21 +541,16 @@ class SolverUMFPACK(Solver):
         self.umfpack.control[um.UMFPACK_SYM_PIVOT_TOLERANCE] = 0.001 # ty: ignore
         self.umfpack.control[um.UMFPACK_BLOCK_SIZE] = 64 # ty: ignore
         self.umfpack.control[um.UMFPACK_FIXQ] = -1 # ty: ignore
-        
-        # SETTINGS
-        self._pivoting_threshold: float = 0.001
-
-        self.fact_symb: bool = False
-
+        self.initalized = True
     def reset(self) -> None:
         self.fact_symb = False
     
-    def set_options(self,
-                    pivoting_threshold: float | None = None) -> None:
-            if pivoting_threshold is not None:
-                self.umfpack.control[um.UMFPACK_PIVOT_TOLERANCE] = pivoting_threshold # ty: ignore
-                self.umfpack.control[um.UMFPACK_SYM_PIVOT_TOLERANCE] = pivoting_threshold # ty: ignore
-                self._pivoting_threshold = pivoting_threshold
+    def set_options(self, pivoting_threshold: float | None = None) -> None:
+        self.initialize()
+        if pivoting_threshold is not None:
+            self.umfpack.control[um.UMFPACK_PIVOT_TOLERANCE] = pivoting_threshold # ty: ignore
+            self.umfpack.control[um.UMFPACK_SYM_PIVOT_TOLERANCE] = pivoting_threshold # ty: ignore
+            self._pivoting_threshold = pivoting_threshold
 
     def duplicate(self) -> Solver:
         new_solver = self.__class__()
@@ -568,11 +582,17 @@ class SolverPardiso(Solver):
 
     def __init__(self):
         super().__init__()
-        self.solver: PardisoInterface = PardisoInterface()
+        self.solver: PardisoInterface | None = None
         self.fact_symb: bool = False
         self.A: np.ndarray = None
         self.b: np.ndarray = None
 
+    def initialize(self) -> None:
+        if self.initialized:
+            return
+        self.solver = PardisoInterface()
+        self.initialized = True
+        
     def solve(self, A, b, precon, reuse_factorization: bool = False, id: int = -1) -> tuple[np.ndarray, SolveReport]:
         logger.info(f'[ID={id}] Calling Pardiso Solver')
         if self.fact_symb is False:
@@ -594,11 +614,18 @@ class SolverPardiso(Solver):
 class CuDSSSolver(Solver):
     real_only = False
     def __init__(self):
-        self._cudss = CuDSSInterface()
+        super().__init__()
+        self._cudss: CuDSSInterface | None = None
         self.fact_symb: bool = False
         self.fact_numb: bool = False
+        
+    def initialize(self) -> None:
+        if self.initialized:
+            return
+        self._cudss = CuDSSInterface()
         self._cudss._PRES = 2
-
+        self.initialized = True
+        
     def reset(self) -> None:
         self.fact_symb = False
         self.fact_numb = False
@@ -1085,7 +1112,7 @@ class SolveRoutine:
             np.ndarray: The resultant solution.
         """
         solver: Solver = self._get_solver(A, b)
-
+        solver.initialize()
         NF = A.shape[0]
         NS = solve_ids.shape[0]
 
@@ -1178,7 +1205,7 @@ class SolveRoutine:
             SolveReport: The solution report
         """
         solver = self._get_eig_solver_bma(A, B, direct=direct)
-
+        solver.initialize()
         NF = A.shape[0]
         NS = solve_ids.shape[0]