gplugins 1.3.4__tar.gz → 1.3.6__tar.gz

{gplugins-1.3.4 → gplugins-1.3.6}/PKG-INFO

@@ -1,14 +1,14 @@
 Metadata-Version: 2.4
 Name: gplugins
-Version: 1.3.4
+Version: 1.3.6
 Summary: gdsfactory plugins
 Keywords: python
 Author-email: gdsfactory <contact@gdsfactory.com>
 Requires-Python: >=3.11
 Description-Content-Type: text/markdown
-Classifier: Programming Language :: Python :: 3.10
 Classifier: Programming Language :: Python :: 3.11
 Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
 Classifier: Operating System :: OS Independent
 License-File: LICENSE
 Requires-Dist: gdsfactory>=9.3.5
@@ -29,6 +29,7 @@ Requires-Dist: matplotlib ; extra == "docs"
 Requires-Dist: jupyter-book~=1.0 ; extra == "docs"
 Requires-Dist: pyvista[all]<=0.43.8 ; extra == "docs"
 Requires-Dist: bokeh ; extra == "docs"
+Requires-Dist: scikit-learn ; extra == "docs"
 Requires-Dist: femwell~=0.1.11 ; extra == "femwell"
 Requires-Dist: meshwell~=1.0.7 ; extra == "femwell"
 Requires-Dist: jinja2 ; extra == "gfviz"
@@ -58,20 +59,11 @@ Requires-Dist: jaxlib>=0.4.26 ; extra == "meow"
 Requires-Dist: flax>=0.8.2 ; extra == "meow"
 Requires-Dist: meow-sim>=0.13,<0.14 ; extra == "meow"
 Requires-Dist: tidy3d>=2.8.2,<2.9 ; extra == "meow"
-Requires-Dist: jax>=0.4.26 ; extra == "sax"
-Requires-Dist: jaxlib>=0.4.26 ; extra == "sax"
-Requires-Dist: flax>=0.8.2 ; extra == "sax"
 Requires-Dist: sax>=0.13.1,<0.15.0 ; extra == "sax"
-Requires-Dist: scikit-learn ; extra == "sax"
-Requires-Dist: pyvis<=0.3.1 ; extra == "sax"
-Requires-Dist: ray ; extra == "sax"
 Requires-Dist: bokeh ; extra == "schematic"
 Requires-Dist: ipywidgets ; extra == "schematic"
 Requires-Dist: natsort ; extra == "schematic"
 Requires-Dist: tidy3d>=2.8.2,<2.9 ; extra == "tidy3d"
-Requires-Dist: meshio ; extra == "tidy3d"
-Requires-Dist: numpy ; extra == "tidy3d"
-Requires-Dist: meshwell~=1.0.7 ; extra == "tidy3d"
 Requires-Dist: gdstk ; extra == "tidy3d"
 Requires-Dist: vlsir ; extra == "vlsir"
 Requires-Dist: vlsirtools ; extra == "vlsir"
@@ -90,7 +82,7 @@ Provides-Extra: schematic
 Provides-Extra: tidy3d
 Provides-Extra: vlsir
 
-# gplugins 1.3.4
+# gplugins 1.3.6
 
 [![docs](https://github.com/gdsfactory/gplugins/actions/workflows/pages.yml/badge.svg)](https://gdsfactory.github.io/gplugins/)
 [![PyPI](https://img.shields.io/pypi/v/gplugins)](https://pypi.org/project/gplugins/)

{gplugins-1.3.4 → gplugins-1.3.6}/README.md

@@ -1,4 +1,4 @@
-# gplugins 1.3.4
+# gplugins 1.3.6
 
 [![docs](https://github.com/gdsfactory/gplugins/actions/workflows/pages.yml/badge.svg)](https://gdsfactory.github.io/gplugins/)
 [![PyPI](https://img.shields.io/pypi/v/gplugins)](https://pypi.org/project/gplugins/)

{gplugins-1.3.4 → gplugins-1.3.6}/gplugins/__init__.py

@@ -1,6 +1,6 @@
 """gplugins - gdsfactory plugins."""
 
-__version__ = "1.3.4"
+__version__ = "1.3.6"
 
 import pathlib
 

{gplugins-1.3.4 → gplugins-1.3.6}/gplugins/common/base_models/component.py

@@ -2,6 +2,7 @@ from functools import cached_property
 from hashlib import md5
 from typing import TypeAlias
 
+import shapely
 import gdsfactory as gf
 import numpy as np
 from gdsfactory.component import Component
@@ -15,13 +16,77 @@ from pydantic import (
 )
 from shapely import MultiPolygon, Polygon
 
-from gplugins.gmsh.parse_gds import cleanup_component
 
 from ..types import AnyShapelyPolygon, GFComponent
 
+from gdsfactory.pdk import get_layer_stack, get_layer, get_layer_name
+
 Coordinate: TypeAlias = tuple[float, float]
 
 
+def round_coordinates(geom, ndigits=4):
+    """Round coordinates to n_digits to eliminate floating point errors."""
+
+    def _round_coords(x, y, z=None):
+        x = round(x, ndigits)
+        y = round(y, ndigits)
+
+        if z is not None:
+            z = round(x, ndigits)
+
+        return [c for c in (x, y, z) if c is not None]
+
+    return shapely.ops.transform(_round_coords, geom)
+
+
+def fuse_polygons(component, layer, round_tol=4, simplify_tol=1e-4, offset_tol=None):
+    """Take all polygons from a layer, and returns a single (Multi)Polygon shapely object."""
+    layer_region = layer.get_shapes(component)
+
+    # Convert polygons to shapely
+    # TODO: do all polygon processing in KLayout at the gplugins level for speed
+    shapely_polygons = []
+    for klayout_polygon in layer_region.each_merged():
+        exterior_points = [
+            (point.x / 1000, point.y / 1000)
+            for point in klayout_polygon.each_point_hull()
+        ]
+        interior_points = []
+        for hole_index in range(klayout_polygon.holes()):
+            holes_points = [
+                (point.x / 1000, point.y / 1000)
+                for point in klayout_polygon.each_point_hole(hole_index)
+            ]
+            interior_points.append(holes_points)
+
+        shapely_polygons.append(
+            round_coordinates(
+                shapely.geometry.Polygon(shell=exterior_points, holes=interior_points),
+                round_tol,
+            )
+        )
+
+    return shapely.ops.unary_union(shapely_polygons).simplify(
+        simplify_tol, preserve_topology=False
+    )
+
+
+def cleanup_component(component, layer_stack, round_tol=2, simplify_tol=1e-2):
+    """Process component polygons before meshing."""
+    layer_stack_dict = layer_stack.to_dict()
+
+    return {
+        layername: fuse_polygons(
+            component,
+            layer["layer"],
+            round_tol=round_tol,
+            simplify_tol=simplify_tol,
+        )
+        for layername, layer in layer_stack_dict.items()
+        if layer["layer"] is not None
+    }
+
+
 def move_polar_rad_copy(
     pos: Coordinate, angle: float, length: float
 ) -> NDArray[np.float64]:
@@ -223,13 +288,19 @@ class LayeredComponentBase(BaseModel):
         )
 
     def get_port_layers(self, port: gf.Port) -> tuple[str, ...]:
-        # FIXME: extract actual layer
-        # this needs to be a list of all layers and derived layers that are
-        # associated with the port layer enum
-        return ("core",)
-        return tuple(
-            k for k, v in self.layer_stack.layers.items() if port.layer in v.layer
-        )
+        layer_name = get_layer_name(port.layer)
+
+        derived_layers = []
+        for l_name, level in self.layer_stack.layers.items():
+            if layer_name in str(level.layer):
+                derived_layers.append(l_name)
+
+        return derived_layers
+
+        # return ("core",)
+        # return tuple(
+        #     k for k, v in self.layer_stack.layers.items() if port.layer in v.layer
+        # )
 
     def get_layer_bbox(
         self, layername: str

{gplugins-1.3.4 → gplugins-1.3.6}/gplugins/gmeep/get_meep_geometry.py

@@ -3,9 +3,13 @@ from __future__ import annotations
 import gdsfactory as gf
 import meep as mp
 import numpy as np
-from gdsfactory.pdk import get_layer_stack
+from kfactory import LayerEnum
+from typing import cast
+import shapely
+from gdsfactory.pdk import get_layer_stack, get_layer, get_layer_name
 from gdsfactory.technology import LayerStack
-from gdsfactory.typings import ComponentSpec, CrossSectionSpec
+from gdsfactory.technology import DerivedLayer, LayerStack, LayerViews, LogicalLayer
+from gdsfactory.typings import ComponentSpec, CrossSectionSpec, LayerSpecs
 
 from gplugins.common.utils.parse_layer_stack import order_layer_stack
 from gplugins.gmeep.get_material import get_material
@@ -18,6 +22,7 @@ def get_meep_geometry_from_component(
     wavelength: float = 1.55,
     is_3d: bool = False,
     dispersive: bool = False,
+    exclude_layers: LayerSpecs | None = None,
     **kwargs,
 ) -> list[mp.GeometricObject]:
     """Returns Meep geometry from a gdsfactory component.
@@ -32,6 +37,9 @@ def get_meep_geometry_from_component(
         kwargs: settings.
     """
     component = gf.get_component(component=component, **kwargs)
+    polygons_per_layer = component.get_polygons_points(merge=True)
+
+
     layer_stack = layer_stack or get_layer_stack()
 
     layer_to_thickness = layer_stack.get_layer_to_thickness()
@@ -41,24 +49,40 @@ def get_meep_geometry_from_component(
     component_with_booleans = layer_stack.get_component_with_derived_layers(component)
 
     geometry = []
+    exclude_layers = exclude_layers or []
     layer_to_polygons = component_with_booleans.get_polygons_points()
 
-    ordered_layer_stack_keys = order_layer_stack(layer_stack)[::-1]
+    # ordered_layer_stack_keys = order_layer_stack(layer_stack)[::-1]
+
+    for level in layer_stack.layers.values():
+        layer = level.layer
+
+        if isinstance(layer, LogicalLayer):
+            assert isinstance(layer.layer, tuple | LayerEnum)
+            layer_tuple = cast(tuple[int, int], tuple(layer.layer))
+        elif isinstance(layer, DerivedLayer):
+            assert level.derived_layer is not None
+            assert isinstance(level.derived_layer.layer, tuple | LayerEnum)
+            layer_tuple = cast(tuple[int, int], tuple(level.derived_layer.layer))
+        else:
+            raise ValueError(f"Layer {layer!r} is not a DerivedLayer or LogicalLayer")
 
-    for layername in ordered_layer_stack_keys:
-        layer = layer_stack.layers[layername].layer
+        layer_index = int(get_layer(layer_tuple))
 
-        if layer not in layer_to_polygons:
+        if layer_index in exclude_layers:
             continue
-        polygons = layer_to_polygons[layer]
-        print(f"layer: {layer}, polygons: {polygons}")
 
-        if layer in layer_to_thickness and layer in layer_to_material:
-            height = layer_to_thickness[layer] if is_3d else mp.inf
-            zmin_um = layer_to_zmin[layer] if is_3d else 0
-            # center = mp.Vector3(0, 0, (zmin_um + height) / 2)
+        if layer_index not in polygons_per_layer:
+            continue
 
+        zmin = level.zmin
+        zmin_um = layer_to_zmin[layer] if is_3d else 0
+        if zmin is not None:
+            has_polygons = True
+            polygons = polygons_per_layer[layer_index]
+            height = level.thickness
             for polygon in polygons:
+                p = shapely.geometry.Polygon(polygon)
                 vertices = [mp.Vector3(p[0], p[1], zmin_um) for p in polygon]
                 material_name = layer_to_material[layer]
 
@@ -80,6 +104,7 @@ def get_meep_geometry_from_component(
                             # center=center
                         )
                     )
+
     return geometry
 
 
@@ -163,7 +188,7 @@ if __name__ == "__main__":
 
     import gplugins.gmeep as gm
 
-    c = gf.components.taper_strip_to_ridge_trenches()
+    c = gf.components.straight()
     sp = gm.write_sparameters_meep(
         c, run=False, ymargin_top=3, ymargin_bot=3, is_3d=True
     )

{gplugins-1.3.4 → gplugins-1.3.6}/gplugins/gmeep/get_simulation.py

@@ -170,12 +170,8 @@ def get_simulation(
         else component
     )
 
-    component_extended.show()
-    # component_extended.flatten()
-
-    # geometry_center = [component_extended.x, component_extended.y]
-    # geometry_center = [0, 0]
-    # print(geometry_center)
+    component_extended = component_extended.copy()
+    component_extended.flatten()
 
     layers_thickness = [
         layer_to_thickness[layer]

{gplugins-1.3.4 → gplugins-1.3.6}/gplugins/gmeep/meep_adjoint_optimization.py

@@ -5,7 +5,6 @@ from types import LambdaType
 from typing import Any
 
 import gdsfactory as gf
-import nlopt
 import numpy as np
 from gdsfactory import Component
 from gdsfactory.technology import LayerStack
@@ -190,7 +189,7 @@ def run_meep_adjoint_optimizer(
     cost_function: LambdaType,
     update_variable: np.ndarray,
     maximize_cost_function: bool = True,
-    algorithm: int = nlopt.LD_MMA,
+    algorithm_name: str = "LD_MMA",
     lower_bound: Any = 0,
     upper_bound: Any = 1,
     maxeval: int = 10,
@@ -205,7 +204,7 @@ def run_meep_adjoint_optimizer(
         cost_function: cost function to optimize.
         update_variable: variable to update the optimization with.
         maximize_cost_function: if True, maximize the cost function, else minimize it.
-        algorithm: nlopt algorithm to use (default: nlopt.LD_MMA).
+        algorithm_name: nlopt algorithm to use (default: nlopt.LD_MMA).
         lower_bound: lower bound for the optimization.
         upper_bound: upper bound for the optimization.
         maxeval: maximum number of evaluations.
@@ -219,6 +218,9 @@ def run_meep_adjoint_optimizer(
         threshold_offset_from_max: threshold offset from max eps value.
         layer: layer to apply to the optimized component.
     """
+    import nlopt
+
+    algorithm = getattr(nlopt, algorithm_name)
     solver = nlopt.opt(algorithm, number_of_params)
     solver.set_lower_bounds(lower_bound)
     solver.set_upper_bounds(upper_bound)

{gplugins-1.3.4 → gplugins-1.3.6}/gplugins/gmeep/write_sparameters_meep.py

@@ -19,7 +19,7 @@ from gdsfactory.component import Component
 from gdsfactory.pdk import get_layer_stack
 from gdsfactory.serialization import clean_value_json
 from gdsfactory.technology import LayerStack
-from gdsfactory.typings import ComponentSpec, PathType, Port, PortSymmetries
+from gdsfactory.typings import ComponentSpec, PathType, Port, PortSymmetries, LayerSpec
 from tqdm.auto import tqdm
 
 from gplugins.common.utils import port_symmetries
@@ -151,6 +151,7 @@ def write_sparameters_meep(
     plot_args: dict | None = None,
     only_return_filepath_sim_settings=False,
     verbosity: int = 0,
+    padding_layers: tuple[LayerSpec, ...] = ("PADDING",),
     **settings,
 ) -> dict[str, np.ndarray]:
     r"""Returns Sparameters and writes them to npz filepath.
@@ -340,6 +341,7 @@ def write_sparameters_meep(
 
     component = gf.add_padding_container(
         component,
+        layers=padding_layers,
         default=0,
         top=ymargin_top,
         bottom=ymargin_bot,

{gplugins-1.3.4 → gplugins-1.3.6}/pyproject.toml

@@ -7,9 +7,9 @@ requires = ["flit_core >=3.2,<4"]
 [project]
 authors = [{name = "gdsfactory", email = "contact@gdsfactory.com"}]
 classifiers = [
-  "Programming Language :: Python :: 3.10",
   "Programming Language :: Python :: 3.11",
   "Programming Language :: Python :: 3.12",
+  "Programming Language :: Python :: 3.13",
   "Operating System :: OS Independent"
 ]
 dependencies = [
@@ -25,7 +25,7 @@ license = {file = "LICENSE"}
 name = "gplugins"
 readme = "README.md"
 requires-python = ">=3.11"
-version = "1.3.4"
+version = "1.3.6"
 
 [project.optional-dependencies]
 dev = [
@@ -36,7 +36,7 @@ dev = [
   "pyswarms"
 ]
 devsim = ["devsim", "pyvista<=0.43.8", "tidy3d>=2.8.2,<2.9"]
-docs = ["jupytext", "matplotlib", "jupyter-book~=1.0", "pyvista[all]<=0.43.8", "bokeh"]
+docs = ["jupytext", "matplotlib", "jupyter-book~=1.0", "pyvista[all]<=0.43.8", "bokeh", "scikit-learn"]
 femwell = ["femwell~=0.1.11", "meshwell~=1.0.7"]
 gfviz = ["jinja2", "fastapi", "shapely", "natsort"]
 gmsh = [
@@ -61,16 +61,13 @@ meow = [
   "tidy3d>=2.8.2,<2.9"
 ]
 sax = [
-  "jax>=0.4.26",
-  "jaxlib>=0.4.26",
-  "flax>=0.8.2",
-  "sax>=0.13.1,<0.15.0",
-  "scikit-learn",
-  "pyvis<=0.3.1",
-  "ray"
+  "sax>=0.13.1,<0.15.0"
 ]
 schematic = ["bokeh", "ipywidgets", "natsort"]
-tidy3d = ["tidy3d>=2.8.2,<2.9", "meshio", "numpy", "meshwell~=1.0.7", "gdstk"]
+tidy3d = [
+  "tidy3d>=2.8.2,<2.9",
+  "gdstk"
+]
 vlsir = ["vlsir", "vlsirtools"]
 
 [tool.codespell]
@@ -192,7 +189,7 @@ message_template = "Bump to {new_version}"
 tag_template = "v{new_version}"
 
 [tool.tbump.version]
-current = "1.3.4"
+current = "1.3.6"
 regex = '''
   (?P<major>\d+)
   \.