update

Author: MartinPdeS

FiberFusing/background.py

@@ -3,15 +3,14 @@
 
 from typing import Tuple, Optional
 from pydantic.dataclasses import dataclass
-from pydantic import ConfigDict
 import numpy as np
 
 from FiberFusing.coordinate_system import CoordinateSystem
 from FiberFusing.helper import OverlayStructureBaseClass
-from FiberFusing.utils import NameSpace
+from FiberFusing.utils import NameSpace, config_dict
+from FiberFusing
 
-
-@dataclass(config=ConfigDict(extra='forbid', kw_only=True))
+@dataclass(config=config_dict)
 class BackGround(OverlayStructureBaseClass):
     """
     Represents a background structure overlayed on a mesh, characterized by a circular shape.

FiberFusing/coordinate_system.py

@@ -4,11 +4,13 @@
 import numpy as np
 from typing import Tuple, Optional
 from pydantic.dataclasses import dataclass
-from pydantic import ConfigDict, field_validator
+from pydantic import field_validator
 from dataclasses import field
 
+from FiberFusing.utils import config_dict
 
-@dataclass(config=ConfigDict(extra='forbid', strict=True, kw_only=True, arbitrary_types_allowed=True, frozen=False))
+
+@dataclass(config=config_dict)
 class CoordinateSystem:
     """
     A 2D Cartesian coordinate system for fiber optics simulations.

FiberFusing/fiber/generic_fiber.py

@@ -6,12 +6,12 @@
 import pprint
 from copy import deepcopy
 import matplotlib.pyplot as plt
+from MPSPlots import helper
 
 from FiberFusing import Circle, CircleOpticalStructure
 from FiberFusing.geometries.point import Point
 from FiberFusing.coordinate_system import CoordinateSystem
 from FiberFusing.plottings import plot_polygon
-from FiberFusing.helper import _plot_helper
 from FiberFusing.graded_index import GradedIndex
 
 pp = pprint.PrettyPrinter(indent=4, sort_dicts=False, compact=True, width=1)
@@ -508,8 +508,8 @@ def overlay_structures_on_mesh(self, mesh: numpy.ndarray, coordinate_system: Coo
             coordinate_system=coordinate_system
         )
 
-    @_plot_helper
-    def plot(self, ax: plt.Axes = None) -> None:
+    @helper.pre_plot(nrows=1, ncols=1)
+    def plot(self, axes: plt.Axes = None) -> None:
         """
         Plot the fiber geometry representation including patch and raster-mesh.
 
@@ -519,7 +519,7 @@ def plot(self, ax: plt.Axes = None) -> None:
             Resolution for rasterizing structures. Default is 300.
         """
         for structure in self.fiber_structure:
-            plot_polygon(ax=ax, polygon=structure.polygon._shapely_object)
+            plot_polygon(ax=axes, polygon=structure.polygon._shapely_object)
 
     def get_structures_boundaries(self) -> numpy.ndarray:
         """
@@ -565,8 +565,8 @@ def boundaries(self):
         """
         return self.get_structure_max_min_boundaries()
 
-    @_plot_helper
-    def plot_raster(self, coordinate_system, ax: plt.Axes = None) -> None:
+    @helper.pre_plot(nrows=1, ncols=1)
+    def plot_raster(self, axes: plt.Axes, coordinate_system) -> None:
         """
         Render the rasterized representation of the geometry onto a given matplotlib axis.
 
@@ -582,7 +582,16 @@ def plot_raster(self, coordinate_system, ax: plt.Axes = None) -> None:
         None
         """
         mesh = self.get_raster_mesh(coordinate_system=coordinate_system)
-        ax.pcolormesh(coordinate_system.x_vector, coordinate_system.y_vector, mesh, cmap='Blues')
+        axes.pcolormesh(
+            coordinate_system.x_vector,
+            coordinate_system.y_vector,
+            mesh,
+            cmap='Blues'
+        )
+
+        axes.set(
+            title='Fiber structure',
+            xlabel=r'x-distance',
+            ylabel=r'y-distance'
+        )
 
-        ax.set(title='Fiber structure', xlabel=r'x-distance [m]', ylabel=r'y-distance [m]')
-        ax.ticklabel_format(axis='both', style='sci', scilimits=(-6, -6), useOffset=False)

FiberFusing/geometries/__init__.py

@@ -1,11 +1,3 @@
-from pydantic import ConfigDict
-
-config_dict = ConfigDict(
-    extra='forbid',
-    arbitrary_types_allowed=True,
-    kw_only=True
-)
-
 from .base_class import Alteration  # noqa: F401
 from .point import Point  # noqa: F401
 from .linestring import LineString  # noqa: F401

FiberFusing/geometries/linestring.py

@@ -9,9 +9,10 @@
 import shapely.geometry as geo
 
 from FiberFusing.geometries.base_class import Alteration
-from FiberFusing import geometries
+from FiberFusing.utils import config_dict
+import geometries
 
-@dataclass(config=geometries.config_dict)
+@dataclass(config=config_dict)
 class LineString(Alteration):
     coordinates: Optional[Tuple] = field(default=None, repr=False)
     instance: Optional[geo.LineString] = field(default=None, repr=False)

FiberFusing/geometries/point.py

@@ -7,11 +7,12 @@
 from pydantic.dataclasses import dataclass
 import shapely.geometry as geo
 import matplotlib.pyplot as plt
+from MPSPlots import helper
 
-from FiberFusing.helper import _plot_helper
 from FiberFusing import geometries
+from FiberFusing.utils import config_dict
 
-@dataclass(config=geometries.config_dict)
+@dataclass(config=config_dict)
 class Point(geometries.base_class.Alteration):
     position: Optional[Tuple[float, float]] = None
     instance: Optional[geo.Point] = None
@@ -106,8 +107,8 @@ def distance(self, other: Self) -> float:
         """
         return numpy.sqrt((self.x - other.x)**2 + (self.y - other.y)**2)
 
-    @_plot_helper
-    def plot(self, ax: plt.Axes = None, marker: str = 'x', size: int = 20, label: str = None) -> None:
+    @helper.pre_plot(nrows=1, ncols=1)
+    def plot(self, axes: plt.Axes, marker: str = 'x', size: int = 20, label: str = None) -> None:
         """
         Renders this point on the given axis, optionally with text.
 
@@ -122,4 +123,4 @@ def plot(self, ax: plt.Axes = None, marker: str = 'x', size: int = 20, label: st
         label : str
             The label for the point, if any.
         """
-        ax.scatter(self.x, self.y, label=label, marker=marker, s=size)
+        axes.scatter(self.x, self.y, label=label, marker=marker, s=size)

FiberFusing/geometries/polygon.py

@@ -8,10 +8,10 @@
 import matplotlib.pyplot as plt
 from shapely.ops import split
 from shapely import affinity
+from MPSPlots import helper
 
 from FiberFusing.coordinate_system import CoordinateSystem
 from FiberFusing.plottings import plot_polygon
-from FiberFusing.helper import _plot_helper
 from FiberFusing import geometries
 
 class Polygon(geometries.base_class.Alteration):
@@ -142,8 +142,8 @@ def _contain_points_with_holes(self, coordinates: np.ndarray, polygon: geo.Polyg
         # Points are inside if they are in the exterior but not in any hole
         return exterior_mask & ~hole_mask
 
-    @_plot_helper
-    def plot(self, ax: plt.Axes, **kwargs) -> None:
+    @helper.pre_plot(nrows=1, ncols=1)
+    def plot(self, axes: plt.Axes, **kwargs) -> None:
         """
         Plots the polygon on the given Matplotlib axis.
 
@@ -154,7 +154,7 @@ def plot(self, ax: plt.Axes, **kwargs) -> None:
         **kwargs
             Additional keyword arguments passed to the plotting function.
         """
-        plot_polygon(ax=ax, polygon=self._shapely_object, **kwargs)
+        plot_polygon(ax=axes, polygon=self._shapely_object, **kwargs)
 
     def rasterize(self, coordinate_system: CoordinateSystem) -> np.ndarray:
         """

FiberFusing/geometry.py

@@ -7,13 +7,15 @@
 from scipy.ndimage import gaussian_filter
 import FiberFusing
 import matplotlib.pyplot as plt
-from FiberFusing.coordinate_system import CoordinateSystem
-from mpl_toolkits.axes_grid1 import make_axes_locatable
 import matplotlib.colors as colors
-from MPSPlots.styles import mps
-from FiberFusing.helper import _plot_helper
-from pydantic import field_validator, ConfigDict
+from mpl_toolkits.axes_grid1 import make_axes_locatable
+from pydantic import field_validator
 from pydantic.dataclasses import dataclass
+from MPSPlots import helper
+
+
+from FiberFusing.coordinate_system import CoordinateSystem
+from FiberFusing.utils import config_dict
 
 class DomainAlignment(Enum):
     """Boundary positioning modes."""
@@ -25,7 +27,7 @@ class DomainAlignment(Enum):
     CENTERING = "centering"
 
 
-@dataclass(config=ConfigDict(extra='forbid', kw_only=True, arbitrary_types_allowed=True))
+@dataclass(config=config_dict)
 class Geometry():
     """
     Represents the refractive index (RI) geometric profile including background and fiber structures.
@@ -326,8 +328,8 @@ def generate_mesh(self) -> numpy.ndarray:
 
         return mesh
 
-    @_plot_helper
-    def plot_patch(self, ax: plt.Axes = None, show: bool = True) -> None:
+    @helper.pre_plot(nrows=1, ncols=1)
+    def plot_patch(self, axes: plt.Axes) -> None:
         """
         Render the patch representation of the geometry onto a given matplotlib axis.
 
@@ -347,16 +349,15 @@ def plot_patch(self, ax: plt.Axes = None, show: bool = True) -> None:
                 continue
 
             if isinstance(structure, FiberFusing.profile.Profile):
-                structure.plot(ax=ax, show=False, show_added=False, show_removed=False, show_centers=False, show_fibers=True)
+                structure.plot(axes=axes, show=False, show_added=False, show_removed=False, show_centers=False, show_fibers=True)
                 continue
 
-            structure.plot(ax=ax, show=False)
+            structure.plot(axes=axes, show=False)
 
-        ax.set(title='Fiber structure', xlabel=r'x-distance [m]', ylabel=r'y-distance [m]')
-        ax.ticklabel_format(axis='both', style='sci', scilimits=(-6, -6), useOffset=False)
+        axes.set(title='Fiber structure', xlabel=r'x-distance [m]', ylabel=r'y-distance [m]')
 
-    @_plot_helper
-    def plot_raster(self, ax: plt.Axes = None, gamma: float = 5) -> None:
+    @helper.pre_plot(nrows=1, ncols=1)
+    def plot_raster(self, axes: plt.Axes, gamma: float = 5) -> None:
         """
         Render the rasterized representation of the geometry onto a given matplotlib axis.
 
@@ -373,31 +374,27 @@ def plot_raster(self, ax: plt.Axes = None, gamma: float = 5) -> None:
         -------
         None
         """
-        image = ax.pcolormesh(
+        image = axes.pcolormesh(
             self.coordinate_system.x_vector,
             self.coordinate_system.y_vector,
             self.mesh,
             cmap='Blues',
             norm=colors.PowerNorm(gamma=gamma)
         )
 
-        divider = make_axes_locatable(ax)
+        divider = make_axes_locatable(axes)
         cax = divider.append_axes('right', size='5%', pad=0.05)
-        ax.get_figure().colorbar(image, cax=cax, orientation='vertical')
+        axes.get_figure().colorbar(image, cax=cax, orientation='vertical')
 
-        ax.set(title='Fiber structure', xlabel=r'x-distance [m]', ylabel=r'y-distance [m]')
-        ax.ticklabel_format(axis='both', style='sci', scilimits=(-6, -6), useOffset=False)
+        axes.set(title='Fiber structure', xlabel=r'x-distance [m]', ylabel=r'y-distance [m]')
 
-    def plot(self, show_patch: bool = True, show_mesh: bool = True, show: bool = True, gamma: float = 5) -> plt.Figure:
+    @helper.pre_plot(nrows=1, ncols=2, subplot_kw=dict(aspect='equal', xlabel='x-distance [m]', ylabel='y-distance [m]'))
+    def plot(self, axes, gamma: float = 5) -> plt.Figure:
         """
         Plot the different representations (patch and mesh) of the geometry.
 
         Parameters
         ----------
-        show_patch : bool, optional
-            Whether to display the patch representation of the geometry. Default is True.
-        show_mesh : bool, optional
-            Whether to display the mesh (rasterized) representation of the geometry. Default is True.
         show : bool, optional
             Whether to immediately show the plot. Default is True.
         gamma : float, optional
@@ -408,29 +405,10 @@ def plot(self, show_patch: bool = True, show_mesh: bool = True, show: bool = Tru
         plt.Figure
             The matplotlib figure encompassing all the axes used in the plot.
         """
-        n_ax = bool(show_patch) + bool(show_mesh)
-        unit_size = numpy.array([1, n_ax])
-
-        with plt.style.context(mps):
-            figure, axes = plt.subplots(
-                *unit_size,
-                figsize=5 * numpy.flip(unit_size),
-                sharex=True,
-                sharey=True,
-                subplot_kw=dict(aspect='equal', xlabel='x-distance [m]', ylabel='y-distance [m]'),
-            )
-
-        axes_iter = iter(axes.flatten())
-
-        if show_patch:
-            ax = next(axes_iter)
-            self.plot_patch(ax, show=False)
+        axes[0].sharex(axes[1])
+        axes[0].sharey(axes[1])
 
-        if show_mesh:
-            ax = next(axes_iter)
-            self.plot_raster(ax, show=False, gamma=gamma)
 
-        if show:
-            plt.show()
+        self.plot_patch(axes=axes[0], show=False)
 
-        return figure
+        self.plot_raster(axes=axes[1], show=False, gamma=gamma)

FiberFusing/helper.py

@@ -1,32 +1,4 @@
 import numpy
-from MPSPlots.styles import mps
-import matplotlib.pyplot as plt
-
-
-def _plot_helper(function):
-    def wrapper(self, ax: plt.Axes = None, show: bool = True, **kwargs):
-        if ax is None:
-            with plt.style.context(mps):
-                _, ax = plt.subplots(1, 1)
-                ax.set_aspect('equal')
-                ax.set(title='Fiber structure', xlabel=r'x-distance [m]', ylabel=r'y-distance [m]')
-                ax.ticklabel_format(axis='both', style='sci')  # , scilimits=(-6, -6), useOffset=False)
-
-        function(self, ax=ax, **kwargs)
-
-        _, labels = ax.get_legend_handles_labels()
-
-        # Only add a legend if there are labels
-        if labels:
-            ax.legend()
-
-        if show:
-            plt.show()
-
-        return ax
-
-    return wrapper
-
 
 class OverlayStructureBaseClass:
     def _overlay_structure_on_mesh_(self, structure_list: dict, mesh: numpy.ndarray, coordinate_system: object) -> numpy.ndarray:

FiberFusing/optical_structure.py

@@ -2,15 +2,17 @@
 from .geometries import Point, LineString, Polygon, EmptyPolygon  # noqa: F401
 from .shapes import Circle, Square, Ellipse  # noqa: F401
 from .background import BackGround  # noqa: F401
-from pydantic.dataclasses import dataclass
-from pydantic import ConfigDict
-from FiberFusing.graded_index import GradedIndex
 
-from typing import Optional, Tuple
+from pydantic.dataclasses import dataclass
+from typing import Tuple
 import numpy as np
 
 
-@dataclass(config=ConfigDict(extra='forbid', kw_only=True))
+from FiberFusing.graded_index import GradedIndex
+from FiberFusing.utils import config_dict
+
+
+@dataclass(config=config_dict)
 class CircleOpticalStructure:
     """
     Represents a circular optical structure.