basic updates

zeroheliumkit/fem/freefemer.py

@@ -338,6 +338,7 @@ def add_helium_curvature_edp(self, extract_cfg: ExtractConfig) -> str:
 
 
     def write_edpScript(self):
+        # TODO: split the logic for caseA (coupling constants only) and caseB (Greens function extraction) into separate functions for better readability and maintainability
         """
         Creates the main FreeFEM script based on the configuration and physical surfaces.
         """
@@ -517,6 +518,10 @@ def script_problem_definition(self, electrode_name: str) -> str:
         return code
 
 
+    def script_include_charge(self, coordinate: list | tuple):
+        pass
+
+
     def script_save_data(self, config: dict) -> str:
         """
         Generates a code block for extracting 2D slice data based on the provided configuration.

zeroheliumkit/helpers/resonator_calc.py

@@ -1,6 +1,6 @@
 import numpy as np
 
-from math import pi, sinh
+from math import pi, sinh, tanh
 from scipy.special import ellipk
 
 from tabulate import tabulate
@@ -193,7 +193,7 @@ def resonator_frequency(self,
                         "width, um": round(self.width/um, 2),
                         "gap, um": round(self.gap/um, 2),
                         "eps ": round(self.eps_substrate),
-                        "eps_eff": round(self.eps_eff, 2),
+                        "eps_eff": round(self.eps_eff2, 2),
                         "impedance, Ohm": round(self.Z, 2),
                         "L, nH/m": round(self.L * 1e9, 3),
                         "C, pF/m":round(self.C* 1e12, 3)
@@ -218,7 +218,7 @@ def resonator_length(self,
                         "width, um": round(self.width/um, 2),
                         "gap, um": round(self.gap/um, 2),
                         "eps ": round(self.eps_substrate),
-                        "eps_eff": round(self.eps_eff, 2),
+                        "eps_eff": round(self.eps_eff2, 2),
                         "impedance, Ohm": round(self.Z, 2),
                         "L, nH/m": round(self.L * 1e9, 3),
                         "C, pF/m":round(self.C* 1e12, 3)

zeroheliumkit/src/__init__.py

@@ -1,6 +1,6 @@
 from .anchors import Anchor, MultiAnchor, Skeletone, Layer
-from .core import Entity, Structure, GeomCollection
-from .supercore import SuperStructure, ContinuousLineBuilder, RoutingConfig, ObjsAlongConfig
+from .core import Entity, Structure
+from .supercore import SuperStructure, ContinuousLineBuilder, RoutingConfig, ObjsAlongConfig, GeomCollection
 
 from .geometries import (StraightLine, ArbitraryLine, Taper, Fillet,
                         MicroChannels, SpiralInductor, IDC,

zeroheliumkit/src/anchors.py

@@ -14,10 +14,13 @@
         Provides methods for creating and manipulating these paths.
     `Layer`: Represents a layer containing polygons with attributes such as name, color, and grid snapping.
 """
+from __future__ import annotations
 
 import copy
 import numpy as np
 import matplotlib.pyplot as plt
+
+from typing import Self
 from tabulate import tabulate
 from shapely import Point, MultiPoint, LineString, MultiLineString, Polygon, MultiPolygon, GeometryCollection
 from shapely import (affinity, unary_union,
@@ -1036,54 +1039,60 @@ def mirror(
 
 
     @snap_on_grid(attr="polygons")
-    def add(self, geom: Polygon | MultiPolygon) -> 'Layer':
+    def add(self, geom: Polygon | MultiPolygon | Layer) -> Self:
         """ 
         Adds a polygon or multipolygon to the layer.
 
         Args:
-            geom (Polygon | MultiPolygon): The polygon or multipolygon to add.
+            geom (Polygon | MultiPolygon | Layer): The polygon or multipolygon to add.
 
         Returns:
             Updated instance (self) of the class with the added polygon.
         """
+        if isinstance(geom, Layer):
+            geom = geom.polygons
         return unary_union([self.polygons, geom])
 
 
     @snap_on_grid(attr="polygons")
     def cut(self,
-            geom: Polygon | MultiPolygon,
-            loc: tuple[float, float]=None) -> 'Layer':
+            geom: Polygon | MultiPolygon | Layer,
+            loc: tuple[float, float]=None) -> Self:
         """ 
         Cuts the layer with a polygon or multipolygon.
 
         Args:
-            geom (Polygon | MultiPolygon): The polygon to be cut.
+            geom (Polygon | MultiPolygon | Layer): The polygon to be cut.
             loc (tuple[float, float], optional): The location where the polygon will be cut.
                 Defaults to None.
 
         Returns:
             Updated instance (self) of the class with the cut geometry.
         """
+        if isinstance(geom, Layer):
+            geom = geom.polygons
         cut_geom = affinity.translate(geom, xoff=loc[0], yoff=loc[1]) if loc else geom
         updated = self.polygons.difference(cut_geom)
         return updated
 
 
     @snap_on_grid(attr="polygons")
     def crop(self,
-             geom: Polygon | MultiPolygon,
-             loc: tuple[float, float] = None) -> 'Layer':
+             geom: Polygon | MultiPolygon | Layer,
+             loc: tuple[float, float] = None) -> Self:
         """ 
         Crops the layer with a polygon or multipolygon.
 
         Args:
-            geom (Polygon | MultiPolygon): The polygon to be used for cropping.
+            geom (Polygon | MultiPolygon | Layer): The polygon to be used for cropping.
             loc (tuple[float, float], optional): The location where the polygon will be applied.
                 Defaults to None.
 
         Returns:
             Updated instance (self) of the class with the cropped geometry.
         """
+        if isinstance(geom, Layer):
+            geom = geom.polygons
         crop_geom = affinity.translate(geom, xoff = loc[0], yoff = loc[1]) if loc else geom
         updated = self.polygons.intersection(crop_geom)
         if isinstance(updated, (Point, MultiPoint, LineString, MultiLineString)):

zeroheliumkit/src/core.py

@@ -13,8 +13,7 @@
 import matplotlib.pyplot as plt
 from warnings import warn
 
-from shapely import (Point, MultiPoint, LineString, MultiLineString,
-                     Polygon, MultiPolygon, GeometryCollection)
+from shapely import Point, LineString, Polygon, MultiPolygon
 
 from .plotting import interactive_widget_handler, listify_colors, ColorHandler
 from .importing import Exporter_DXF, Exporter_GDS, Exporter_Pickle
@@ -53,7 +52,7 @@ def __init__(self):
         self.layers = []
         self.skeletone = Skeletone()
         self.anchors = MultiAnchor()
-        self.colors = ColorHandler({})
+        # self.colors = ColorHandler({})
         self.errors = None
 
 
@@ -94,7 +93,7 @@ def add(self, layer: Layer):
             Updated instance (self) of the class with the new layer added.
         """
         self.layers.append(layer.name)
-        self.colors.add_color(layer.name, layer.color[0], layer.color[1])
+        # self.colors.add_color(layer.name, layer.color[0], layer.color[1])
         setattr(self, layer.name, layer)
         return self
 
@@ -112,7 +111,7 @@ def remove(self, lname: str):
         if lname in self.layers:
             self.layers.remove(lname)
             delattr(self, lname)
-            self.colors.remove_color(lname)
+            # self.colors.remove_color(lname)
         else:
             print(f"Layer '{lname}' not found in layers.")
 
@@ -134,7 +133,7 @@ def rename(self, old: str, new: str) -> None:
             self.__dict__[new] = self.__dict__.pop(old)
             self.layers[self.layers.index(old)] = new
             self.__dict__[new].name = new
-            self.colors.rename_color(old, new)
+            # self.colors.rename_color(old, new)
         else:
             print(f"Layer '{old}' not found in layers.")
 
@@ -153,7 +152,7 @@ def has_layer(self, name: str) -> bool:
         return name in self.layers
 
 
-    def cut(self, geom: Polygon | MultiPolygon, loc: tuple[float, float]=None):
+    def cut(self, geom: Polygon | MultiPolygon, loc: tuple[float, float]=None, ignore: list[str]=[]):
         """
         Cuts the specified polygon from polygons in all layers.
 
@@ -164,11 +163,12 @@ def cut(self, geom: Polygon | MultiPolygon, loc: tuple[float, float]=None):
             Updated instance (self) of the class with the specified polygon cut from all layers.
         """
         for lname in self.layers:
-            getattr(self, lname).cut(geom, loc)
+            if lname not in ignore:
+                getattr(self, lname).cut(geom, loc)
         return self
 
 
-    def crop(self, geom: Polygon | MultiPolygon, loc: tuple[float, float]=None):
+    def crop(self, geom: Polygon | MultiPolygon, loc: tuple[float, float]=None, ignore: list[str]=[]):
         """
         Crops polygons in all layers.
 
@@ -179,11 +179,12 @@ def crop(self, geom: Polygon | MultiPolygon, loc: tuple[float, float]=None):
             Updated instance (self) of the class with polygons in all layers cropped by the specified polygon.
         """
         for lname in self.layers:
-            getattr(self, lname).crop(geom, loc)
+            if lname not in ignore:
+                getattr(self, lname).crop(geom, loc)
         return self
 
 
-    def slice(self, slice_line: LineString | list[LineString]):
+    def slice(self, slice_line: LineString | list[LineString], ignore: list[str]=[]):
         """
         Slices polygons in a layer using a given line.
 
@@ -192,7 +193,8 @@ def slice(self, slice_line: LineString | list[LineString]):
             slice_line (LineString): The line used for slicing.
         """
         for lname in self.layers:
-            getattr(self, lname).slice(slice_line)
+            if lname not in ignore:
+                getattr(self, lname).slice(slice_line)
         return self
 
 
@@ -369,7 +371,7 @@ def export_pickle(self, filename: str) -> None:
         exp.save()
 
 
-    def export_gds(self, filename: str, layer_cfg: dict) -> None:
+    def export_gds(self, filename: str, layer_cfg: dict, cellname: str="toplevel") -> None:
         """
         Exports all layers as a GDS file.
 
@@ -379,7 +381,7 @@ def export_gds(self, filename: str, layer_cfg: dict) -> None:
                 See `gdspy docs <https://gdspy.readthedocs.io/en/stable/gettingstarted.html#layer-and-datatype>`_ for 'datatype' details.
         """
         zhkdict = self.export_dict(remove_holes=True)
-        exp = Exporter_GDS(filename, zhkdict, layer_cfg)
+        exp = Exporter_GDS(filename, zhkdict, layer_cfg, cellname)
         exp.save()
 
 
@@ -450,7 +452,7 @@ def quickplot(
         #plot layers
         plot_config = {k:v for k,v in plot_config.items() if k not in off}
         for lname, lcolor in plot_config.items():
-            if self.has_layer(lname):
+            if self.has_layer(lname) and (not getattr(self, lname).is_empty):
                 getattr(self, lname).color = lcolor
                 getattr(self, lname).plot(ax=ax, show_idx=show_idx, labels=labels, **kwargs)
 
@@ -514,15 +516,15 @@ def append(self,
                 Defaults to None.
         """
         s = structure.copy()
-        if move_s:
-            s.move(*move_s)
         if rotate_s:
             s.rotate(rotate_s, origin=(0,0))
+        if move_s:
+            s.move(*move_s)
         attr_list_device = self.layers
         attr_list_structure = s.layers
         self.layers = list(set(attr_list_device + attr_list_structure))
 
-        self.colors.colors = self.colors.colors | s.colors.colors
+        # self.colors.colors = self.colors.colors | s.colors.colors
 
         # snapping direction
         if direction_snap:
@@ -581,47 +583,3 @@ def return_mirrored(self, aroundaxis: str, **kwargs) -> 'Structure':
         """
         cc = self.copy()
         return cc.mirror(aroundaxis, **kwargs)
-
-
-class GeomCollection(Structure):
-    """
-    Represents a collection of geometries.
-    Class attributes are created by layers dictionary.
-
-    Args:
-        layers (dict): Dictionary containing the layers and corresponding polygons/skeletone/anchors/colors.
-    """
-    def __init__(self, layers: dict=None):
-        super().__init__()
-        if layers:
-            for items in layers.items():
-                match items:
-                    case ("skeletone", LineString()) | ("skeletone", MultiLineString()):
-                        self.skeletone.lines = items[1]
-                    case ("skeletone", Skeletone()):
-                        self.skeletone = items[1]
-                    case ("skeletone", GeometryCollection()):
-                        warn(message="imported skeletone contains GeometryCollection object. It will be ignored.")
-                    case ("anchors", MultiAnchor()):
-                        self.anchors = items[1]
-                    case ("anchors", MultiPoint()):
-                        for i, pt in enumerate(items[1].geoms):
-                            self.anchors.add(Anchor(pt, 0, "anchor" + str(i)))
-                    case ("colors", ColorHandler()):
-                        self.colors = items[1]
-                    case (str(), Polygon()) | (str(), MultiPolygon()):
-                        layer = Layer(name=items[0], polygons=items[1])
-                        self.layers.append(items[0])
-                        setattr(self, items[0], layer)
-                    case _:
-                        self.layers.append(items[0])
-                        setattr(self, *items)
-
-        if not hasattr(self, "anchors"):
-            self.anchors = MultiAnchor()
-
-        if not hasattr(self, "skeletone"):
-            self.skeletone = Skeletone()
-
-        if self.colors.is_empty:
-            self.colors.update_colors(self.layers)

zeroheliumkit/src/geometries.py

@@ -502,7 +502,7 @@ def __init__(self,
         # create polygons
         if layers:
             for k, width in layers.items():
-                polygon = self.skeletone.buffer(offset=width/2, cap_style='square', **kwargs)
+                polygon = self.skeletone.buffer(offset=width/2, cap_style=cap_style, **kwargs)
                 self.add(Layer(name=k, polygons=polygon))
 
         # create anchors

zeroheliumkit/src/importing.py

@@ -10,6 +10,7 @@
 from svgpathtools import parse_path, Line, CubicBezier, QuadraticBezier
 
 from .errors import *
+from .utils import to_geometry_list
 
 
 def sample_bezier(bezier, num_points=20):
@@ -36,13 +37,13 @@ class Exporter_GDS():
 
     __slots__ = "name", "zhk_layers", "gdsii", "layer_cfg"
 
-    def __init__(self, name: str, zhk_layers: dict, layer_cfg: dict) -> None:
+    def __init__(self, name: str, zhk_layers: dict, layer_cfg: dict, cellname: str="toplevel") -> None:
         self.name = name
         self.zhk_layers = zhk_layers
         self.layer_cfg = layer_cfg
-        self.preapre_gds()
+        self.preapre_gds(cellname)
 
-    def preapre_gds(self) -> None:
+    def preapre_gds(self, cellname: str="toplevel") -> None:
         """
         Prepare the GDSII library by creating a top-level cell and adding polygons.
 
@@ -51,12 +52,12 @@ def preapre_gds(self) -> None:
         - gdstk polygons use `layer` and `datatype` (same concepts).
         """
         self.gdsii = gdstk.Library()
-        cell = gdstk.Cell("toplevel")
+        cell = gdstk.Cell(cellname)
         self.gdsii.add(cell)
 
         for lname, l_property in self.layer_cfg.items():
             polygons = self.zhk_layers[lname].polygons
-            for poly in polygons.geoms:
+            for poly in to_geometry_list(polygons):
                 points = list(poly.exterior.coords)
 
                 # Optional: shapely exterior repeats the first point at the end.
@@ -179,7 +180,7 @@ def preapre_dxf(self) -> None:
         for i, lname in enumerate(self.layer_cfg):
             self.dxf.layers.add(lname, color = i + 1)
             polygons = self.zhk_layers[lname].polygons
-            for poly in polygons.geoms:
+            for poly in to_geometry_list(polygons):
                 points = list(poly.exterior.coords)
                 msp.add_lwpolyline(points, dxfattribs={"layer": lname,
                                                        "color": BYLAYER})