WIP: make libraries and names first-class!

examples/nested_poly_test.py

@@ -0,0 +1,28 @@
+import numpy
+from pyclipper import (
+    Pyclipper, PT_CLIP, PT_SUBJECT, CT_UNION, CT_INTERSECTION, PFT_NONZERO,
+    scale_to_clipper, scale_from_clipper,
+    )
+p = Pyclipper()
+p.AddPaths([
+  [(-10, -10), (-10, 10), (-9, 10), (-9, -10)],
+  [(-10, 10), (10, 10), (10, 9), (-10, 9)],
+  [(10, 10), (10, -10), (9, -10), (9, 10)],
+  [(10, -10), (-10, -10), (-10, -9), (10, -9)],
+  ], PT_SUBJECT, closed=True)
+p.Execute2?
+p.Execute?
+p.Execute(PT_UNION, PT_NONZERO, PT_NONZERO)
+p.Execute(CT_UNION, PT_NONZERO, PT_NONZERO)
+p.Execute(CT_UNION, PFT_NONZERO, PFT_NONZERO)
+p = Pyclipper()
+p.AddPaths([
+  [(-10, -10), (-10, 10), (-9, 10), (-9, -10)],
+  [(-10, 10), (10, 10), (10, 9), (-10, 9)],
+  [(10, 10), (10, -10), (9, -10), (9, 10)],
+  [(10, -10), (-10, -10), (-10, -9), (10, -9)],
+  ], PT_SUBJECT, closed=True)
+r = p.Execute2(CT_UNION, PFT_NONZERO, PFT_NONZERO)
+r
+r.Childs
+%history -f nested_poly_test.py

examples/pcgen.py

@@ -0,0 +1,298 @@
+"""
+Routines for creating normalized 2D lattices and common photonic crystal
+ cavity designs.
+"""
+
+from typing import Sequence, Tuple
+
+import numpy        # type: ignore
+
+
+def triangular_lattice(dims: Tuple[int, int],
+                       asymmetric: bool = False,
+                       origin: str = 'center',
+                       ) -> numpy.ndarray:
+    """
+    Return an ndarray of `[[x0, y0], [x1, y1], ...]` denoting lattice sites for
+     a triangular lattice in 2D.
+
+    Args:
+        dims: Number of lattice sites in the [x, y] directions.
+        asymmetric: If true, each row will contain the same number of
+            x-coord lattice sites. If false, every other row will be
+            one site shorter (to make the structure symmetric).
+        origin: If 'corner', the least-(x,y) lattice site is placed at (0, 0)
+            If 'center', the center of the lattice (not necessarily a
+            lattice site) is placed at (0, 0).
+
+    Returns:
+        `[[x0, y0], [x1, 1], ...]` denoting lattice sites.
+    """
+    sx, sy = numpy.meshgrid(numpy.arange(dims[0], dtype=float),
+                            numpy.arange(dims[1], dtype=float), indexing='ij')
+
+    sx[sy % 2 == 1] += 0.5
+    sy *= numpy.sqrt(3) / 2
+
+    if not asymmetric:
+        which = sx != sx.max()
+        sx = sx[which]
+        sy = sy[which]
+
+    xy = numpy.column_stack((sx.flat, sy.flat))
+
+    if origin == 'center':
+        xy -= (xy.max(axis=0) - xy.min(axis=0)) / 2
+    elif origin == 'corner':
+        pass
+    else:
+        raise Exception(f'Invalid value for `origin`: {origin}')
+
+    return xy[xy[:, 0].argsort(), :]
+
+
+def square_lattice(dims: Tuple[int, int]) -> numpy.ndarray:
+    """
+    Return an ndarray of `[[x0, y0], [x1, y1], ...]` denoting lattice sites for
+     a square lattice in 2D. The lattice will be centered around (0, 0).
+
+    Args:
+        dims: Number of lattice sites in the [x, y] directions.
+
+    Returns:
+        `[[x0, y0], [x1, 1], ...]` denoting lattice sites.
+    """
+    xs, ys = numpy.meshgrid(range(dims[0]), range(dims[1]), 'xy')
+    xs -= dims[0]/2
+    ys -= dims[1]/2
+    xy = numpy.vstack((xs.flatten(), ys.flatten())).T
+    return xy[xy[:, 0].argsort(), ]
+
+
+# ### Photonic crystal functions ###
+
+
+def nanobeam_holes(a_defect: float,
+                   num_defect_holes: int,
+                   num_mirror_holes: int
+                   ) -> numpy.ndarray:
+    """
+    Returns a list of `[[x0, r0], [x1, r1], ...]` of nanobeam hole positions and radii.
+     Creates a region in which the lattice constant and radius are progressively
+     (linearly) altered over num_defect_holes holes until they reach the value
+     specified by a_defect, then symmetrically returned to a lattice constant and
+     radius of 1, which is repeated num_mirror_holes times on each side.
+
+    Args:
+        a_defect: Minimum lattice constant for the defect, as a fraction of the
+            mirror lattice constant (ie., for no defect, a_defect = 1).
+        num_defect_holes: How many holes form the defect (per-side)
+        num_mirror_holes: How many holes form the mirror (per-side)
+
+    Returns:
+        Ndarray `[[x0, r0], [x1, r1], ...]` of nanobeam hole positions and radii.
+    """
+    a_values = numpy.linspace(a_defect, 1, num_defect_holes, endpoint=False)
+    xs = a_values.cumsum() - (a_values[0] / 2)  # Later mirroring makes center distance 2x as long
+    mirror_xs = numpy.arange(1, num_mirror_holes + 1, dtype=float) + xs[-1]
+    mirror_rs = numpy.ones_like(mirror_xs)
+    return numpy.vstack((numpy.hstack((-mirror_xs[::-1], -xs[::-1], xs, mirror_xs)),
+                         numpy.hstack((mirror_rs[::-1], a_values[::-1], a_values, mirror_rs)))).T
+
+
+def waveguide(length: int, num_mirror: int) -> numpy.ndarray:
+    """
+    Line defect waveguide in a triangular lattice.
+
+    Args:
+        length: waveguide length (number of holes in x direction)
+        num_mirror: Mirror length (number of holes per side; total size is
+            `2 * n + 1` holes.
+
+    Returns:
+        `[[x0, y0], [x1, y1], ...]` for all the holes
+    """
+    p = triangular_lattice([length, 2 * num_mirror + 1])
+    p_wg = p[p[:, 1] != 0, :]
+    return p_wg
+
+
+def wgbend(num_mirror: int) -> numpy.ndarray:
+    """
+    Line defect waveguide bend in a triangular lattice.
+
+    Args:
+        num_mirror: Mirror length (number of holes per side; total size is
+            approximately `2 * n + 1`
+
+    Returns:
+        `[[x0, y0], [x1, y1], ...]` for all the holes
+    """
+    p = triangular_lattice([2 * num_mirror, 2 * num_mirror + 1])
+    left_horiz = (p[:, 1] == 0) & (p[:, 0] <= 0)
+    p = p[~left_horiz, :]
+
+    right_diag = numpy.isclose(p[:, 1], p[:, 0] * numpy.sqrt(3)) & (p[:, 0] >= 0)
+    p = p[~right_diag, :]
+    return p
+
+
+def y_splitter(num_mirror: int) -> numpy.ndarray:
+    """
+    Line defect waveguide y-splitter in a triangular lattice.
+
+    Args:
+        num_mirror: Mirror length (number of holes per side; total size is
+            approximately `2 * n + 1` holes.
+
+    Returns:
+        `[[x0, y0], [x1, y1], ...]` for all the holes
+    """
+    p = triangular_lattice([2 * num_mirror, 2 * num_mirror + 1])
+    left_horiz = (p[:, 1] == 0) & (p[:, 0] <= 0)
+    p = p[~left_horiz, :]
+
+    right_diag_up = numpy.isclose(p[:, 1], p[:, 0] * numpy.sqrt(3)) & (p[:, 0] >= 0)
+    p = p[~right_diag_up, :]
+
+    right_diag_dn = numpy.isclose(p[:, 1], -p[:, 0] * numpy.sqrt(3)) & (p[:, 0] >= 0)
+    p = p[~right_diag_dn, :]
+    return p
+
+
+def ln_defect(mirror_dims: Tuple[int, int],
+              defect_length: int,
+              ) -> numpy.ndarray:
+    """
+    N-hole defect in a triangular lattice.
+
+    Args:
+        mirror_dims: [x, y] mirror lengths (number of holes). Total number of holes
+            is 2 * n + 1 in each direction.
+        defect_length: Length of defect. Should be an odd number.
+
+    Returns:
+        `[[x0, y0], [x1, y1], ...]` for all the holes
+    """
+    if defect_length % 2 != 1:
+        raise Exception('defect_length must be odd!')
+    p = triangular_lattice([2 * d + 1 for d in mirror_dims])
+    half_length = numpy.floor(defect_length / 2)
+    hole_nums = numpy.arange(-half_length, half_length + 1)
+    holes_to_keep = numpy.in1d(p[:, 0], hole_nums, invert=True)
+    return p[numpy.logical_or(holes_to_keep, p[:, 1] != 0), ]
+
+
+def ln_shift_defect(mirror_dims: Tuple[int, int],
+                    defect_length: int,
+                    shifts_a: Sequence[float] = (0.15, 0, 0.075),
+                    shifts_r: Sequence[float] = (1, 1, 1)
+                    ) -> numpy.ndarray:
+    """
+    N-hole defect with shifted holes (intended to give the mode a gaussian profile
+     in real- and k-space so as to improve both Q and confinement). Holes along the
+     defect line are shifted and altered according to the shifts_* parameters.
+
+    Args:
+        mirror_dims: [x, y] mirror lengths (number of holes). Total number of holes
+            is `2 * n + 1` in each direction.
+        defect_length: Length of defect. Should be an odd number.
+        shifts_a: Percentage of a to shift (1st, 2nd, 3rd,...) holes along the defect line
+        shifts_r: Factor to multiply the radius by. Should match length of shifts_a
+
+    Returns:
+        `[[x0, y0, r0], [x1, y1, r1], ...]` for all the holes
+    """
+    if not hasattr(shifts_a, "__len__") and shifts_a is not None:
+        shifts_a = [shifts_a]
+    if not hasattr(shifts_r, "__len__") and shifts_r is not None:
+        shifts_r = [shifts_r]
+
+    xy = ln_defect(mirror_dims, defect_length)
+
+    # Add column for radius
+    xyr = numpy.hstack((xy, numpy.ones((xy.shape[0], 1))))
+
+    # Shift holes
+    # Expand shifts as necessary
+    n_shifted = max(len(shifts_a), len(shifts_r))
+
+    tmp_a = numpy.array(shifts_a)
+    shifts_a = numpy.ones((n_shifted, ))
+    shifts_a[:len(tmp_a)] = tmp_a
+
+    tmp_r = numpy.array(shifts_r)
+    shifts_r = numpy.ones((n_shifted, ))
+    shifts_r[:len(tmp_r)] = tmp_r
+
+    x_removed = numpy.floor(defect_length / 2)
+
+    for ind in range(n_shifted):
+        for sign in (-1, 1):
+            x_val = sign * (x_removed + ind + 1)
+            which = numpy.logical_and(xyr[:, 0] == x_val, xyr[:, 1] == 0)
+            xyr[which, ] = (x_val + numpy.sign(x_val) * shifts_a[ind], 0, shifts_r[ind])
+
+    return xyr
+
+
+def r6_defect(mirror_dims: Tuple[int, int]) -> numpy.ndarray:
+    """
+    R6 defect in a triangular lattice.
+
+    Args:
+        mirror_dims: [x, y] mirror lengths (number of holes). Total number of holes
+            is 2 * n + 1 in each direction.
+
+    Returns:
+        `[[x0, y0], [x1, y1], ...]` specifying hole centers.
+    """
+    xy = triangular_lattice([2 * d + 1 for d in mirror_dims])
+
+    rem_holes_plus = numpy.array([[1, 0],
+                                  [0.5, +numpy.sqrt(3)/2],
+                                  [0.5, -numpy.sqrt(3)/2]])
+    rem_holes = numpy.vstack((rem_holes_plus, -rem_holes_plus))
+
+    for rem_xy in rem_holes:
+        xy = xy[(xy != rem_xy).any(axis=1), ]
+
+    return xy
+
+
+def l3_shift_perturbed_defect(
+    mirror_dims: Tuple[int, int],
+    perturbed_radius: float = 1.1,
+    shifts_a: Sequence[float] = (),
+    shifts_r: Sequence[float] = ()
+    ) -> numpy.ndarray:
+    """
+    3-hole defect with perturbed hole sizes intended to form an upwards-directed
+     beam. Can also include shifted holes along the defect line, intended
+     to give the mode a more gaussian profile to improve Q.
+
+    Args:
+        mirror_dims: [x, y] mirror lengths (number of holes). Total number of holes
+            is 2 * n + 1 in each direction.
+        perturbed_radius: Amount to perturb the radius of the holes used for beam-forming
+        shifts_a: Percentage of a to shift (1st, 2nd, 3rd,...) holes along the defect line
+        shifts_r: Factor to multiply the radius by. Should match length of shifts_a
+
+    Returns:
+        `[[x0, y0, r0], [x1, y1, r1], ...]` for all the holes
+    """
+    xyr = ln_shift_defect(mirror_dims, 3, shifts_a, shifts_r)
+
+    abs_x, abs_y = (numpy.fabs(xyr[:, i]) for i in (0, 1))
+
+    # Sorted unique xs and ys
+    # Ignore row y=0 because it might have shifted holes
+    xs = numpy.unique(abs_x[abs_x != 0])
+    ys = numpy.unique(abs_y)
+
+    # which holes should be perturbed? (xs[[3, 7]], ys[1]) and (xs[[2, 6]], ys[2])
+    perturbed_holes = ((xs[a], ys[b]) for a, b in ((3, 1), (7, 1), (2, 2), (6, 2)))
+    for row in xyr:
+        if numpy.fabs(row) in perturbed_holes:
+            row[2] = perturbed_radius
+    return xyr

examples/phc.py

@@ -0,0 +1,178 @@
+from typing import Tuple, Sequence
+
+import numpy        # type: ignore
+from numpy import pi
+
+from masque import layer_t, Pattern, SubPattern, Label
+from masque.shapes import Polygon, Circle
+from masque.builder import Device, Port
+from masque.library import Library, DeviceLibrary
+from masque.file.klamath import writefile
+
+import pcgen
+
+
+HOLE_SCALE: float = 1000
+''' Radius for the 'hole' cell. Should be significantly bigger than
+    1 (minimum database unit) in order to have enough precision to
+    reasonably represent a polygonized circle (for GDS)
+'''
+
+def hole(layer: layer_t,
+         radius: float = HOLE_SCALE * 0.35,
+         ) -> Pattern:
+    """
+    Generate a pattern containing a single circular hole.
+
+    Args:
+        layer: Layer to draw the circle on.
+        radius: Circle radius.
+
+    Returns:
+        Pattern, named `'hole'`
+    """
+    pat = Pattern('hole', shapes=[
+        Circle(radius=radius, offset=(0, 0), layer=layer, dose=1.0)
+        ])
+    return pat
+
+
+def perturbed_l3(lattice_constant: float,
+                 hole: Pattern,
+                 trench_dose: float = 1.0,
+                 trench_layer: layer_t = (1, 0),
+                 shifts_a: Sequence[float] = (0.15, 0, 0.075),
+                 shifts_r: Sequence[float] = (1.0, 1.0, 1.0),
+                 xy_size: Tuple[int, int] = (10, 10),
+                 perturbed_radius: float = 1.1,
+                 trench_width: float = 1200,
+                 ) -> Device:
+    """
+    Generate a `Device` representing a perturbed L3 cavity.
+
+    Args:
+        lattice_constant: Distance between nearest neighbor holes
+        hole: `Pattern` object containing a single hole
+        trench_dose: Dose for the trenches. Default 1.0. (Hole dose is 1.0.)
+        trench_layer: Layer for the trenches, default `(1, 0)`.
+        shifts_a: passed to `pcgen.l3_shift`; specifies lattice constant
+            (1 - multiplicative factor) for shifting holes adjacent to
+            the defect (same row). Default `(0.15, 0, 0.075)` for first,
+            second, third holes.
+        shifts_r: passed to `pcgen.l3_shift`; specifies radius for perturbing
+            holes adjacent to the defect (same row). Default 1.0 for all holes.
+            Provided sequence should have same length as `shifts_a`.
+        xy_size: `(x, y)` number of mirror periods in each direction; total size is
+                `2 * n + 1` holes in each direction. Default (10, 10).
+        perturbed_radius: radius of holes perturbed to form an upwards-driected beam
+                (multiplicative factor). Default 1.1.
+        trench width: Width of the undercut trenches. Default 1200.
+
+    Returns:
+        `Device` object representing the L3 design.
+    """
+    xyr = pcgen.l3_shift_perturbed_defect(mirror_dims=xy_size,
+                                          perturbed_radius=perturbed_radius,
+                                          shifts_a=shifts_a,
+                                          shifts_r=shifts_r)
+
+    pat = Pattern(f'L3p-a{lattice_constant:g}rp{perturbed_radius:g}')
+    pat.subpatterns += [SubPattern(hole, offset=(lattice_constant * x,
+                                                 lattice_constant * y), scale=r * lattice_constant / HOLE_SCALE)
+                        for x, y, r in xyr]
+
+    min_xy, max_xy = pat.get_bounds()
+    trench_dx = max_xy[0] - min_xy[0]
+
+    pat.shapes += [
+        Polygon.rect(ymin=max_xy[1], xmin=min_xy[0], lx=trench_dx, ly=trench_width,
+                     layer=trench_layer, dose=trench_dose),
+        Polygon.rect(ymax=min_xy[1], xmin=min_xy[0], lx=trench_dx, ly=trench_width,
+                     layer=trench_layer, dose=trench_dose),
+        ]
+
+    ports = {
+        'input': Port((-lattice_constant * xy_size[0], 0), rotation=0, ptype=1),
+        'output': Port((lattice_constant * xy_size[0], 0), rotation=pi, ptype=1),
+        }
+
+    return Device(pat, ports)
+
+
+def waveguide(lattice_constant: float,
+              hole: Pattern,
+              length: int,
+              mirror_periods: int,
+              ) -> Device:
+    xy = pcgen.waveguide(length=length + 2, num_mirror=mirror_periods)
+
+    pat = Pattern(f'_wg-a{lattice_constant:g}l{length}')
+    pat.subpatterns += [SubPattern(hole, offset=(lattice_constant * x,
+                                                 lattice_constant * y), scale=lattice_constant / HOLE_SCALE)
+                        for x, y in xy]
+
+    ports = {
+        'left': Port((-lattice_constant * length / 2, 0), rotation=0, ptype=1),
+        'right': Port((lattice_constant * length / 2, 0), rotation=pi, ptype=1),
+        }
+    return Device(pat, ports)
+
+
+def bend(lattice_constant: float,
+         hole: Pattern,
+         mirror_periods: int,
+         ) -> Device:
+    xy = pcgen.wgbend(num_mirror=mirror_periods)
+
+    pat_half = Pattern(f'_wgbend_half-a{lattice_constant:g}l{mirror_periods}')
+    pat_half.subpatterns += [SubPattern(hole, offset=(lattice_constant * x,
+                                                      lattice_constant * y), scale=lattice_constant / HOLE_SCALE)
+                             for x, y in xy]
+
+    pat = Pattern(f'_wgbend-a{lattice_constant:g}l{mirror_periods}')
+    pat.addsp(pat_half, offset=(0, 0), rotation=0, mirrored=(False, False))
+    pat.addsp(pat_half, offset=(0, 0), rotation=-2 * pi / 3, mirrored=(True, False))
+
+
+    ports = {
+        'left': Port((-lattice_constant * mirror_periods, 0), rotation=0, ptype=1),
+        'right': Port((lattice_constant * mirror_periods / 2,
+                       lattice_constant * mirror_periods * numpy.sqrt(3) / 2), rotation=pi * 4 / 3, ptype=1),
+        }
+    return Device(pat, ports)
+
+
+def label_ports(device: Device, layer: layer_t = (3, 0)) -> Device:
+    for name, port in device.ports.items():
+        angle_deg = numpy.rad2deg(port.rotation)
+        device.pattern.labels += [
+            Label(string=f'{name} (angle {angle_deg:g})', layer=layer, offset=port.offset)
+            ]
+    return device
+
+
+def main():
+    hole_layer = (1, 2)
+    a = 512
+    hole_pat = hole(layer=hole_layer)
+    wg0 = label_ports(waveguide(lattice_constant=a, hole=hole_pat, length=10, mirror_periods=5))
+    wg1 = label_ports(waveguide(lattice_constant=a, hole=hole_pat, length=5, mirror_periods=5))
+    bend0 = label_ports(bend(lattice_constant=a, hole=hole_pat, mirror_periods=5))
+    l3cav = label_ports(perturbed_l3(lattice_constant=a, hole=hole_pat, xy_size=(4, 10)))
+
+    dev = Device(name='my_bend', ports={})
+    dev.place(wg0, offset=(0, 0), port_map={'left': 'in', 'right': 'signal'})
+    dev.plug(wg0, {'signal': 'left'})
+    dev.plug(bend0, {'signal': 'left'})
+    dev.plug(wg1, {'signal': 'left'})
+    dev.plug(bend0, {'signal': 'right'})
+    dev.plug(wg0, {'signal': 'left'})
+    dev.plug(l3cav, {'signal': 'input'})
+    dev.plug(wg0, {'signal': 'left'})
+
+    writefile(dev.pattern, 'phc.gds', 1e-9, 1e-3)
+    dev.pattern.visualize()
+
+
+if __name__ == '__main__':
+    main()

masque/__init__.py

@@ -24,17 +24,17 @@
     metaclass is used to auto-generate slots based on superclass type annotations.
  - File I/O submodules are imported by `masque.file` to avoid creating hard dependencies on
     external file-format reader/writers
- - Pattern locking/unlocking is quite slow for large hierarchies.
 
 """
 
-from .error import PatternError, PatternLockedError
+from .error import PatternError
 from .shapes import Shape
 from .label import Label
 from .subpattern import SubPattern
 from .pattern import Pattern
 from .utils import layer_t, annotations_t
-from .library import Library, DeviceLibrary
+from .library import Library, PatternGenerator
+from .builder import DeviceLibrary, LibDeviceLibrary, Device, Port
 
 
 __author__ = 'Jan Petykiewicz'

masque/builder/__init__.py

@@ -1,3 +1,4 @@
 from .devices import Port, Device
 from .utils import ell
 from .tools import Tool
+from .device_library import DeviceLibrary, LibDeviceLibrary

masque/builder/device_library.py

@@ -79,16 +79,6 @@ class DeviceLibrary:
     def __repr__(self) -> str:
         return '<DeviceLibrary with keys ' + repr(list(self.generators.keys())) + '>'
 
-    def set_const(self, const: Device) -> None:
-        """
-        Convenience function to avoid having to manually wrap
-         already-generated Device objects into callables.
-
-        Args:
-            const: Pre-generated device object
-        """
-        self.generators[const.pattern.name] = lambda: const
-
     def add(
             self: D,
             other: D,
@@ -175,7 +165,6 @@ class DeviceLibrary:
         def build_dev() -> Device:
             dev = fn()
             dev.pattern = dev2pat(dev)
-            dev.pattern.rename(prefix + name)
             return dev
 
         self[prefix + name] = build_dev
@@ -200,8 +189,8 @@ class DeviceLibrary:
 
         def build_wrapped_dev() -> Device:
             old_dev = self[old_name]
-            wrapper = Pattern(name=name)
-            wrapper.addsp(old_dev.pattern)
+            wrapper = Pattern()
+            wrapper.addsp(old_name)
             return Device(wrapper, old_dev.ports)
 
         self[name] = build_wrapped_dev

masque/builder/devices.py

@@ -125,7 +125,7 @@ class Device(Copyable, Mirrorable):
     - `Device(pattern, ports={'A': port_a, 'C': port_c})` uses an existing
         pattern and defines some ports.
 
-    - `Device(name='my_dev_name', ports=None)` makes a new empty pattern with
+    - `Device(ports=None)` makes a new empty pattern with
         default ports ('A' and 'B', in opposite directions, at (0, 0)).
 
     - `my_device.build('my_layout')` makes a new pattern and instantiates
@@ -182,7 +182,6 @@ class Device(Copyable, Mirrorable):
             ports: Optional[Dict[str, Port]] = None,
             *,
             tools: Union[None, Tool, Dict[Optional[str], Tool]] = None,
-            name: Optional[str] = None,
             ) -> None:
         """
         If `ports` is `None`, two default ports ('A' and 'B') are created.
@@ -190,14 +189,7 @@ class Device(Copyable, Mirrorable):
           (attached devices will be placed to the left) and 'B' has rotation
           pi (attached devices will be placed to the right).
         """
-        if pattern is not None:
-            if name is not None:
-                raise DeviceError('Only one of `pattern` and `name` may be specified')
-            self.pattern = pattern
-        else:
-            if name is None:
-                raise DeviceError('Must specify either `pattern` or `name`')
-            self.pattern = Pattern(name=name)
+        self.pattern = pattern or Pattern()
 
         if ports is None:
             self.ports = {
@@ -336,25 +328,22 @@ class Device(Copyable, Mirrorable):
 
         return self
 
-    def build(self, name: str) -> 'Device':
+    def build(self) -> 'Device':
         """
         Begin building a new device around an instance of the current device
           (rather than modifying the current device).
 
-        Args:
-            name: A name for the new device
-
         Returns:
             The new `Device` object.
         """
-        pat = Pattern(name)
+        # TODO lib: this needs a name for self, rather than for the built thing
+        pat = Pattern()
         pat.addsp(self.pattern)
         new = Device(pat, ports=self.ports, tools=self.tools)
         return new
 
     def as_interface(
             self,
-            name: str,
             in_prefix: str = 'in_',
             out_prefix: str = '',
             port_map: Optional[Union[Dict[str, str], Sequence[str]]] = None
@@ -380,7 +369,6 @@ class Device(Copyable, Mirrorable):
           current device.
 
         Args:
-            name: Name for the new device
             in_prefix: Prepended to port names for newly-created ports with
                 reversed directions compared to the current device.
             out_prefix: Prepended to port names for ports which are directly
@@ -424,12 +412,13 @@ class Device(Copyable, Mirrorable):
         if duplicates:
             raise DeviceError(f'Duplicate keys after prefixing, try a different prefix: {duplicates}')
 
-        new = Device(name=name, ports={**ports_in, **ports_out}, tools=self.tools)
+        new = Device(ports={**ports_in, **ports_out}, tools=self.tools)
         return new
 
     def plug(
             self: D,
-            other: O,
+            library: Mapping[str, 'Device'],
+            name: str,
             map_in: Dict[str, str],
             map_out: Optional[Dict[str, Optional[str]]] = None,
             *,
@@ -438,27 +427,29 @@ class Device(Copyable, Mirrorable):
             set_rotation: Optional[bool] = None,
             ) -> D:
         """
-        Instantiate the device `other` into the current device, connecting
+        Instantiate a device `library[name]` into the current device, connecting
           the ports specified by `map_in` and renaming the unconnected
           ports specified by `map_out`.
 
         Examples:
         =========
-        - `my_device.plug(subdevice, {'A': 'C', 'B': 'B'}, map_out={'D': 'myport'})`
-            instantiates `subdevice` into `my_device`, plugging ports 'A' and 'B'
+        - `my_device.plug(lib, 'subdevice', {'A': 'C', 'B': 'B'}, map_out={'D': 'myport'})`
+            instantiates `lib['subdevice']` into `my_device`, plugging ports 'A' and 'B'
             of `my_device` into ports 'C' and 'B' of `subdevice`. The connected ports
             are removed and any unconnected ports from `subdevice` are added to
             `my_device`. Port 'D' of `subdevice` (unconnected) is renamed to 'myport'.
 
-        - `my_device.plug(wire, {'myport': 'A'})` places port 'A' of `wire` at 'myport'
-            of `my_device`. If `wire` has only two ports (e.g. 'A' and 'B'), no `map_out`,
-            argument is provided, and the `inherit_name` argument is not explicitly
-            set to `False`, the unconnected port of `wire` is automatically renamed to
-            'myport'. This allows easy extension of existing ports without changing
-            their names or having to provide `map_out` each time `plug` is called.
+        - `my_device.plug(lib, 'wire', {'myport': 'A'})` places port 'A' of `lib['wire']`
+            at 'myport' of `my_device`.
+            If `'wire'` has only two ports (e.g. 'A' and 'B'), no `map_out` argument is
+            provided, and the `inherit_name` argument is not explicitly set to `False`,
+            the unconnected port of `wire` is automatically renamed to 'myport'. This
+            allows easy extension of existing ports without changing their names or
+            having to provide `map_out` each time `plug` is called.
 
         Args:
-            other: A device to instantiate into the current device.
+            library: A `DeviceLibrary` containing the device to be instatiated.
+            name: The name of the device to be instantiated (from `library`).
             map_in: Dict of `{'self_port': 'other_port'}` mappings, specifying
                 port connections between the two devices.
             map_out: Dict of `{'old_name': 'new_name'}` mappings, specifying
@@ -513,13 +504,14 @@ class Device(Copyable, Mirrorable):
             del self.ports[ki]
             map_out[vi] = None
 
-        self.place(other, offset=translation, rotation=rotation, pivot=pivot,
+        self.place(library, name, offset=translation, rotation=rotation, pivot=pivot,
                    mirrored=mirrored, port_map=map_out, skip_port_check=True)
         return self
 
     def place(
             self: D,
-            other: O,
+            library: Mapping[str, 'Device'],
+            name: str,
             *,
             offset: ArrayLike = (0, 0),
             rotation: float = 0,
@@ -529,7 +521,7 @@ class Device(Copyable, Mirrorable):
             skip_port_check: bool = False,
             ) -> D:
         """
-        Instantiate the device `other` into the current device, adding its
+        Instantiate the device `library[name]` into the current device, adding its
           ports to those of the current device (but not connecting any ports).
 
         Mirroring is applied before rotation; translation (`offset`) is applied last.
@@ -543,16 +535,17 @@ class Device(Copyable, Mirrorable):
             rather than the port name on the original `pad` device.
 
         Args:
-            other: A device to instantiate into the current device.
-            offset: Offset at which to place `other`. Default (0, 0).
-            rotation: Rotation applied to `other` before placement. Default 0.
+            library: A `DeviceLibrary` containing the device to be instatiated.
+            name: The name of the device to be instantiated (from `library`).
+            offset: Offset at which to place the instance. Default (0, 0).
+            rotation: Rotation applied to the instance before placement. Default 0.
             pivot: Rotation is applied around this pivot point (default (0, 0)).
                 Rotation is applied prior to translation (`offset`).
-            mirrored: Whether `other` should be mirrored across the x and y axes.
+            mirrored: Whether theinstance should be mirrored across the x and y axes.
                 Mirroring is applied before translation and rotation.
             port_map: Dict of `{'old_name': 'new_name'}` mappings, specifying
-                new names for ports in `other`. New names can be `None`, which will
-                delete those ports.
+                new names for ports in the instantiated device. New names can be
+                `None`, which will delete those ports.
             skip_port_check: Can be used to skip the internal call to `check_ports`,
                 in case it has already been performed elsewhere.
 
@@ -561,7 +554,7 @@ class Device(Copyable, Mirrorable):
 
         Raises:
             `DeviceError` if any ports specified in `map_in` or `map_out` do not
-                exist in `self.ports` or `other_names`.
+                exist in `self.ports` or `library[name].ports`.
             `DeviceError` if there are any duplicate names after `map_in` and `map_out`
                 are applied.
         """
@@ -572,6 +565,8 @@ class Device(Copyable, Mirrorable):
         if port_map is None:
             port_map = {}
 
+        other = library[name]
+
         if not skip_port_check:
             self.check_ports(other.ports.keys(), map_in=None, map_out=port_map)
 
@@ -589,7 +584,7 @@ class Device(Copyable, Mirrorable):
             p.translate(offset)
             self.ports[name] = p
 
-        sp = SubPattern(other.pattern, mirrored=mirrored)
+        sp = SubPattern(name, mirrored=mirrored)   #TODO figure out how this should work?!
         sp.rotate_around(pivot, rotation)
         sp.translate(offset)
         self.pattern.subpatterns.append(sp)
@@ -748,19 +743,6 @@ class Device(Copyable, Mirrorable):
         self._dead = True
         return self
 
-    def rename(self: D, name: str) -> D:
-        """
-        Renames the pattern and returns the device
-
-        Args:
-            name: The new name
-
-        Returns:
-            self
-        """
-        self.pattern.name = name
-        return self
-
     def __repr__(self) -> str:
         s = f'<Device {self.pattern} ['
         for name, port in self.ports.items():
@@ -831,7 +813,7 @@ class Device(Copyable, Mirrorable):
 
         return self.path(portspec, ccw, length, tool_port_names=tool_port_names, **kwargs)
 
-    def busL(
+    def mpath(
             self: D,
             portspec: Union[str, Sequence[str]],
             ccw: Optional[bool],
@@ -839,7 +821,6 @@ class Device(Copyable, Mirrorable):
             spacing: Optional[Union[float, ArrayLike]] = None,
             set_rotation: Optional[float] = None,
             tool_port_names: Sequence[str] = ('A', 'B'),
-            container_name: str = '_busL',
             force_container: bool = False,
             **kwargs,
             ) -> D:
@@ -873,7 +854,7 @@ class Device(Copyable, Mirrorable):
             port_name = tuple(portspec)[0]
             return self.path(port_name, ccw, extensions[port_name], tool_port_names=tool_port_names)
         else:
-            dev = Device(name='', ports=ports, tools=self.tools).as_interface(container_name)
+            dev = Device(name='', ports=ports, tools=self.tools).as_interface()
             for name, length in extensions.items():
                 dev.path(name, ccw, length, tool_port_names=tool_port_names)
             return self.plug(dev, {sp: 'in_' + sp for sp in ports.keys()})       # TODO safe to use 'in_'?

masque/error.py

@@ -11,13 +11,6 @@ class PatternError(MasqueError):
     """
     pass
 
-class PatternLockedError(PatternError):
-    """
-    Exception raised when trying to modify a locked pattern
-    """
-    def __init__(self):
-        PatternError.__init__(self, 'Tried to modify a locked Pattern, subpattern, or shape')
-
 
 class LibraryError(MasqueError):
     """

masque/file/dxf.py

@@ -1,7 +1,7 @@
 """
 DXF file format readers and writers
 """
-from typing import List, Any, Dict, Tuple, Callable, Union, Sequence, Iterable
+from typing import List, Any, Dict, Tuple, Callable, Union, Sequence, Iterable, Mapping
 import re
 import io
 import base64
@@ -10,7 +10,7 @@ import logging
 import pathlib
 import gzip
 
-import numpy        # type: ignore
+import numpy
 import ezdxf        # type: ignore
 
 from .. import Pattern, SubPattern, PatternError, Label, Shape
@@ -29,12 +29,13 @@ DEFAULT_LAYER = 'DEFAULT'
 
 
 def write(
-        pattern: Pattern,
+        top_name: str,
+        library: Mapping[str, Pattern],
         stream: io.TextIOBase,
         *,
         modify_originals: bool = False,
         dxf_version='AC1024',
-        disambiguate_func: Callable[[Iterable[Pattern]], None] = None,
+        disambiguate_func: Callable[[Iterable[str]], List[str]] = None,
         ) -> None:
     """
     Write a `Pattern` to a DXF file, by first calling `.polygonize()` to change the shapes
@@ -60,10 +61,12 @@ def write(
      array with rotated instances must be manhattan _after_ having a compensating rotation applied.
 
     Args:
-        patterns: A Pattern or list of patterns to write to the stream.
+        top_name: Name of the top-level pattern to write.
+        library: A {name: Pattern} mapping of patterns. Only `top_name` and patterns referenced
+            by it are written.
         stream: Stream object to write to.
         modify_original: If `True`, the original pattern is modified as part of the writing
-            process. Otherwise, a copy is made and `deepunlock()`-ed.
+            process. Otherwise, a copy is made.
             Default `False`.
         disambiguate_func: Function which takes a list of patterns and alters them
             to make their names valid and unique. Default is `disambiguate_pattern_names`.
@@ -75,11 +78,14 @@ def write(
     assert(disambiguate_func is not None)
 
     if not modify_originals:
-        pattern = pattern.deepcopy().deepunlock()
+        library = library.deepcopy()
 
-    # Get a dict of id(pattern) -> pattern
-    patterns_by_id = pattern.referenced_patterns_by_id()
-    disambiguate_func(patterns_by_id.values())
+    pattern = library[top_name]
+
+    old_names = list(library.keys())
+    new_names = disambiguate_func(old_names)
+    renamed_lib = {new_name: library[old_name]
+                   for old_name, new_name in zip(old_names, new_names)}
 
     # Create library
     lib = ezdxf.new(dxf_version, setup=True)
@@ -89,9 +95,9 @@ def write(
     _subpatterns_to_refs(msp, pattern.subpatterns)
 
     # Now create a block for each referenced pattern, and add in any shapes
-    for pat in patterns_by_id.values():
+    for name, pat in renamed_lib.items():
         assert(pat is not None)
-        block = lib.blocks.new(name=pat.name)
+        block = lib.blocks.new(name=name)
 
         _shapes_to_elements(block, pat.shapes)
         _labels_to_texts(block, pat.labels)
@@ -101,7 +107,8 @@ def write(
 
 
 def writefile(
-        pattern: Pattern,
+        top_name: str,
+        library: Mapping[str, Pattern],
         filename: Union[str, pathlib.Path],
         *args,
         **kwargs,
@@ -112,7 +119,9 @@ def writefile(
     Will automatically compress the file if it has a .gz suffix.
 
     Args:
-        pattern: `Pattern` to save
+        top_name: Name of the top-level pattern to write.
+        library: A {name: Pattern} mapping of patterns. Only `top_name` and patterns referenced
+            by it are written.
         filename: Filename to save to.
         *args: passed to `dxf.write`
         **kwargs: passed to `dxf.write`
@@ -124,7 +133,7 @@ def writefile(
         open_func = open
 
     with open_func(path, mode='wt') as stream:
-        write(pattern, stream, *args, **kwargs)
+        write(top_name, library, stream, *args, **kwargs)
 
 
 def readfile(
@@ -156,7 +165,7 @@ def readfile(
 def read(
         stream: io.TextIOBase,
         clean_vertices: bool = True,
-        ) -> Tuple[Pattern, Dict[str, Any]]:
+        ) -> Tuple[Dict[str, Pattern], Dict[str, Any]]:
     """
     Read a dxf file and translate it into a dict of `Pattern` objects. DXF `Block`s are
      translated into `Pattern` objects; `LWPolyline`s are translated into polygons, and `Insert`s
@@ -176,26 +185,20 @@ def read(
     lib = ezdxf.read(stream)
     msp = lib.modelspace()
 
-    pat = _read_block(msp, clean_vertices)
-    patterns = [pat] + [_read_block(bb, clean_vertices) for bb in lib.blocks if bb.name != '*Model_Space']
-
-    # Create a dict of {pattern.name: pattern, ...}, then fix up all subpattern.pattern entries
-    #  according to the subpattern.identifier (which is deleted after use).
-    patterns_dict = dict(((p.name, p) for p in patterns))
-    for p in patterns_dict.values():
-        for sp in p.subpatterns:
-            sp.pattern = patterns_dict[sp.identifier[0]]
-            del sp.identifier
+    npat = _read_block(msp, clean_vertices)
+    patterns_dict = dict([npat]
+        + [_read_block(bb, clean_vertices) for bb in lib.blocks if bb.name != '*Model_Space'])
 
     library_info = {
         'layers': [ll.dxfattribs() for ll in lib.layers]
         }
 
-    return pat, library_info
+    return patterns_dict, library_info
 
 
-def _read_block(block, clean_vertices: bool) -> Pattern:
-    pat = Pattern(block.name)
+def _read_block(block, clean_vertices: bool) -> Tuple[str, Pattern]:
+    name = block.name
+    pat = Pattern()
     for element in block:
         eltype = element.dxftype()
         if eltype in ('POLYLINE', 'LWPOLYLINE'):
@@ -258,12 +261,12 @@ def _read_block(block, clean_vertices: bool) -> Pattern:
             offset = numpy.array(attr.get('insert', (0, 0, 0)))[:2]
 
             args = {
+                'target': (attr.get('name', None),),
                 'offset': offset,
                 'scale': scale,
                 'mirrored': mirrored,
                 'rotation': rotation,
                 'pattern': None,
-                'identifier': (attr.get('name', None),),
                 }
 
             if 'column_count' in attr:
@@ -274,7 +277,7 @@ def _read_block(block, clean_vertices: bool) -> Pattern:
             pat.subpatterns.append(SubPattern(**args))
         else:
             logger.warning(f'Ignoring DXF element {element.dxftype()} (not implemented).')
-    return pat
+    return name, pat
 
 
 def _subpatterns_to_refs(
@@ -282,9 +285,9 @@ def _subpatterns_to_refs(
         subpatterns: List[SubPattern],
         ) -> None:
     for subpat in subpatterns:
-        if subpat.pattern is None:
+        if subpat.target is None:
             continue
-        encoded_name = subpat.pattern.name
+        encoded_name = subpat.target
 
         rotation = (subpat.rotation * 180 / numpy.pi) % 360
         attribs = {
@@ -360,18 +363,24 @@ def _mlayer2dxf(layer: layer_t) -> str:
 
 
 def disambiguate_pattern_names(
-        patterns: Iterable[Pattern],
+        names: Iterable[str],
         max_name_length: int = 32,
         suffix_length: int = 6,
-        dup_warn_filter: Callable[[str], bool] = None,      # If returns False, don't warn about this name
-        ) -> None:
-    used_names = []
-    for pat in patterns:
-        sanitized_name = re.compile(r'[^A-Za-z0-9_\?\$]').sub('_', pat.name)
+        ) -> List[str]:
+    """
+    Args:
+        names: List of pattern names to disambiguate
+        max_name_length: Names longer than this will be truncated
+        suffix_length: Names which get truncated are truncated by this many extra characters. This is to
+            leave room for a suffix if one is necessary.
+    """
+    new_names = []
+    for name in names:
+        sanitized_name = re.compile(r'[^A-Za-z0-9_\?\$]').sub('_', name)
 
         i = 0
         suffixed_name = sanitized_name
-        while suffixed_name in used_names or suffixed_name == '':
+        while suffixed_name in new_names or suffixed_name == '':
             suffix = base64.b64encode(struct.pack('>Q', i), b'$?').decode('ASCII')
 
             suffixed_name = sanitized_name + '$' + suffix[:-1].lstrip('A')
@@ -380,17 +389,16 @@ def disambiguate_pattern_names(
         if sanitized_name == '':
             logger.warning(f'Empty pattern name saved as "{suffixed_name}"')
         elif suffixed_name != sanitized_name:
-            if dup_warn_filter is None or dup_warn_filter(pat.name):
-                logger.warning(f'Pattern name "{pat.name}" ({sanitized_name}) appears multiple times;\n'
+            if dup_warn_filter is None or dup_warn_filter(name):
+                logger.warning(f'Pattern name "{name}" ({sanitized_name}) appears multiple times;\n'
                                + f' renaming to "{suffixed_name}"')
 
         if len(suffixed_name) == 0:
             # Should never happen since zero-length names are replaced
-            raise PatternError(f'Zero-length name after sanitize,\n originally "{pat.name}"')
+            raise PatternError(f'Zero-length name after sanitize,\n originally "{name}"')
         if len(suffixed_name) > max_name_length:
             raise PatternError(f'Pattern name "{suffixed_name!r}" length > {max_name_length} after encode,\n'
-                               + f' originally "{pat.name}"')
-
-        pat.name = suffixed_name
-        used_names.append(suffixed_name)
+                               + f' originally "{name}"')
 
+        new_names.append(suffixed_name)
+    return new_names

masque/file/gdsii.py

@@ -53,18 +53,22 @@ path_cap_map = {
     }
 
 
+def rint_cast(val: ArrayLike) -> NDArray[numpy.int32]:
+    return numpy.rint(val, dtype=numpy.int32, casting='unsafe')
+
+
 def write(
-        patterns: Union[Pattern, Sequence[Pattern]],
+        library: Mapping[str, Pattern],
         stream: BinaryIO,
         meters_per_unit: float,
         logical_units_per_unit: float = 1,
         library_name: str = 'masque-klamath',
         *,
         modify_originals: bool = False,
-        disambiguate_func: Callable[[Iterable[Pattern]], None] = None,
+        disambiguate_func: Callable[[Iterable[str]], List[str]] = None,
         ) -> None:
     """
-    Convert a `Pattern` or list of patterns to a GDSII stream,  and then mapping data as follows:
+    Convert a library to a GDSII stream, mapping data as follows:
          Pattern -> GDSII structure
          SubPattern -> GDSII SREF or AREF
          Path -> GSDII path
@@ -85,7 +89,7 @@ def write(
      prior to calling this function.
 
     Args:
-        patterns: A Pattern or list of patterns to convert.
+        library: A {name: Pattern} mapping of patterns to write.
         meters_per_unit: Written into the GDSII file, meters per (database) length unit.
             All distances are assumed to be an integer multiple of this unit, and are stored as such.
         logical_units_per_unit: Written into the GDSII file. Allows the GDSII to specify a
@@ -94,52 +98,48 @@ def write(
         library_name: Library name written into the GDSII file.
             Default 'masque-klamath'.
         modify_originals: If `True`, the original pattern is modified as part of the writing
-            process. Otherwise, a copy is made and `deepunlock()`-ed.
+            process. Otherwise, a copy is made.
             Default `False`.
-        disambiguate_func: Function which takes a list of patterns and alters them
-            to make their names valid and unique. Default is `disambiguate_pattern_names`, which
-            attempts to adhere to the GDSII standard as well as possible.
+        disambiguate_func: Function which takes a list of pattern names and returns a list of names
+            altered to be valid and unique. Default is `disambiguate_pattern_names`, which
+            attempts to adhere to the GDSII standard reasonably well.
             WARNING: No additional error checking is performed on the results.
     """
-    if isinstance(patterns, Pattern):
-        patterns = [patterns]
-
     if disambiguate_func is None:
-        disambiguate_func = disambiguate_pattern_names          # type: ignore
-    assert(disambiguate_func is not None)       # placate mypy
+        disambiguate_func = disambiguate_pattern_names
 
     if not modify_originals:
-        patterns = [p.deepunlock() for p in copy.deepcopy(patterns)]
+        library = copy.deepcopy(library)
 
-    patterns = [p.wrap_repeated_shapes() for p in patterns]
+    for p in library.values():
+        library.add(p.wrap_repeated_shapes())
+
+    old_names = list(library.keys())
+    new_names = disambiguate_func(old_names)
+    renamed_lib = {new_name: library[old_name]
+                   for old_name, new_name in zip(old_names, new_names)}
 
     # Create library
-    header = klamath.library.FileHeader(name=library_name.encode('ASCII'),
-                                        user_units_per_db_unit=logical_units_per_unit,
-                                        meters_per_db_unit=meters_per_unit)
+    header = klamath.library.FileHeader(
+        name=library_name.encode('ASCII'),
+        user_units_per_db_unit=logical_units_per_unit,
+        meters_per_db_unit=meters_per_unit,
+        )
     header.write(stream)
 
-    # Get a dict of id(pattern) -> pattern
-    patterns_by_id = {id(pattern): pattern for pattern in patterns}
-    for pattern in patterns:
-        for i, p in pattern.referenced_patterns_by_id().items():
-            patterns_by_id[i] = p
-
-    disambiguate_func(patterns_by_id.values())
-
     # Now create a structure for each pattern, and add in any Boundary and SREF elements
-    for pat in patterns_by_id.values():
+    for name, pat in renamed_lib.items():
         elements: List[klamath.elements.Element] = []
         elements += _shapes_to_elements(pat.shapes)
         elements += _labels_to_texts(pat.labels)
         elements += _subpatterns_to_refs(pat.subpatterns)
 
-        klamath.library.write_struct(stream, name=pat.name.encode('ASCII'), elements=elements)
+        klamath.library.write_struct(stream, name=name.encode('ASCII'), elements=elements)
     records.ENDLIB.write(stream, None)
 
 
 def writefile(
-        patterns: Union[Sequence[Pattern], Pattern],
+        library: Mapping[str, Pattern],
         filename: Union[str, pathlib.Path],
         *args,
         **kwargs,
@@ -150,7 +150,7 @@ def writefile(
     Will automatically compress the file if it has a .gz suffix.
 
     Args:
-        patterns: `Pattern` or list of patterns to save
+        library: {name: Pattern} pairs to save.
         filename: Filename to save to.
         *args: passed to `write()`
         **kwargs: passed to `write()`
@@ -216,22 +216,14 @@ def read(
     """
     library_info = _read_header(stream)
 
-    patterns = []
+    patterns_dict = {}
     found_struct = records.BGNSTR.skip_past(stream)
     while found_struct:
         name = records.STRNAME.skip_and_read(stream)
-        pat = read_elements(stream, name=name.decode('ASCII'), raw_mode=raw_mode)
-        patterns.append(pat)
+        pat = read_elements(stream, raw_mode=raw_mode)
+        patterns_dict[name.decode('ASCII')] = pat
         found_struct = records.BGNSTR.skip_past(stream)
 
-    # Create a dict of {pattern.name: pattern, ...}, then fix up all subpattern.pattern entries
-    #  according to the subpattern.identifier (which is deleted after use).
-    patterns_dict = dict(((p.name, p) for p in patterns))
-    for p in patterns_dict.values():
-        for sp in p.subpatterns:
-            sp.pattern = patterns_dict[sp.identifier[0]]
-            del sp.identifier
-
     return patterns_dict, library_info
 
 
@@ -250,7 +242,6 @@ def _read_header(stream: BinaryIO) -> Dict[str, Any]:
 
 def read_elements(
         stream: BinaryIO,
-        name: str,
         raw_mode: bool = True,
         ) -> Pattern:
     """
@@ -265,7 +256,7 @@ def read_elements(
     Returns:
         A pattern containing the elements that were read.
     """
-    pat = Pattern(name)
+    pat = Pattern()
 
     elements = klamath.library.read_elements(stream)
     for element in elements:
@@ -276,10 +267,12 @@ def read_elements(
             path = _gpath_to_mpath(element, raw_mode)
             pat.shapes.append(path)
         elif isinstance(element, klamath.elements.Text):
-            label = Label(offset=element.xy.astype(float),
-                          layer=element.layer,
-                          string=element.string.decode('ASCII'),
-                          annotations=_properties_to_annotations(element.properties))
+            label = Label(
+                offset=element.xy.astype(float),
+                layer=element.layer,
+                string=element.string.decode('ASCII'),
+                annotations=_properties_to_annotations(element.properties),
+                )
             pat.labels.append(label)
         elif isinstance(element, klamath.elements.Reference):
             pat.subpatterns.append(_ref_to_subpat(element))
@@ -304,8 +297,7 @@ def _mlayer2gds(mlayer: layer_t) -> Tuple[int, int]:
 
 def _ref_to_subpat(ref: klamath.library.Reference) -> SubPattern:
     """
-    Helper function to create a SubPattern from an SREF or AREF. Sets subpat.pattern to None
-     and sets the instance .identifier to (struct_name,).
+    Helper function to create a SubPattern from an SREF or AREF. Sets subpat.target to struct_name.
     """
     xy = ref.xy.astype(float)
     offset = xy[0]
@@ -317,14 +309,15 @@ def _ref_to_subpat(ref: klamath.library.Reference) -> SubPattern:
         repetition = Grid(a_vector=a_vector, b_vector=b_vector,
                           a_count=a_count, b_count=b_count)
 
-    subpat = SubPattern(pattern=None,
-                        offset=offset,
-                        rotation=numpy.deg2rad(ref.angle_deg),
-                        scale=ref.mag,
-                        mirrored=(ref.invert_y, False),
-                        annotations=_properties_to_annotations(ref.properties),
-                        repetition=repetition)
-    subpat.identifier = (ref.struct_name.decode('ASCII'),)
+    subpat = SubPattern(
+        pattern=ref.struct_name.decode('ASCII'),
+        offset=offset,
+        rotation=numpy.deg2rad(ref.angle_deg),
+        scale=ref.mag,
+        mirrored=(ref.invert_y, False),
+        annotations=_properties_to_annotations(ref.properties),
+        repetition=repetition,
+        )
     return subpat
 
 
@@ -334,34 +327,36 @@ def _gpath_to_mpath(gpath: klamath.library.Path, raw_mode: bool) -> Path:
     else:
         raise PatternError(f'Unrecognized path type: {gpath.path_type}')
 
-    mpath = Path(vertices=gpath.xy.astype(float),
-                 layer=gpath.layer,
-                 width=gpath.width,
-                 cap=cap,
-                 offset=numpy.zeros(2),
-                 annotations=_properties_to_annotations(gpath.properties),
-                 raw=raw_mode,
-                 )
+    mpath = Path(
+        vertices=gpath.xy.astype(float),
+        layer=gpath.layer,
+        width=gpath.width,
+        cap=cap,
+        offset=numpy.zeros(2),
+        annotations=_properties_to_annotations(gpath.properties),
+        raw=raw_mode,
+        )
     if cap == Path.Cap.SquareCustom:
         mpath.cap_extensions = gpath.extension
     return mpath
 
 
 def _boundary_to_polygon(boundary: klamath.library.Boundary, raw_mode: bool) -> Polygon:
-    return Polygon(vertices=boundary.xy[:-1].astype(float),
-                   layer=boundary.layer,
-                   offset=numpy.zeros(2),
-                   annotations=_properties_to_annotations(boundary.properties),
-                   raw=raw_mode,
-                   )
+    return Polygon(
+        vertices=boundary.xy[:-1].astype(float),
+        layer=boundary.layer,
+        offset=numpy.zeros(2),
+        annotations=_properties_to_annotations(boundary.properties),
+        raw=raw_mode,
+        )
 
 
 def _subpatterns_to_refs(subpatterns: List[SubPattern]) -> List[klamath.library.Reference]:
     refs = []
     for subpat in subpatterns:
-        if subpat.pattern is None:
+        if subpat.target is None:
             continue
-        encoded_name = subpat.pattern.name.encode('ASCII')
+        encoded_name = subpat.target.encode('ASCII')
 
         # Note: GDS mirrors first and rotates second
         mirror_across_x, extra_angle = normalize_mirror(subpat.mirrored)
@@ -377,32 +372,39 @@ def _subpatterns_to_refs(subpatterns: List[SubPattern]) -> List[klamath.library.
                 rep.a_vector * rep.a_count,
                 b_vector * b_count,
                 ]
-            aref = klamath.library.Reference(struct_name=encoded_name,
-                                             xy=numpy.round(xy).astype(int),
-                                             colrow=(numpy.round(rep.a_count), numpy.round(rep.b_count)),
-                                             angle_deg=angle_deg,
-                                             invert_y=mirror_across_x,
-                                             mag=subpat.scale,
-                                             properties=properties)
+            aref = klamath.library.Reference(
+                struct_name=encoded_name,
+                xy=rint_cast(xy),
+                colrow=(numpy.rint(rep.a_count), numpy.rint(rep.b_count)),
+                angle_deg=angle_deg,
+                invert_y=mirror_across_x,
+                mag=subpat.scale,
+                properties=properties,
+                )
             refs.append(aref)
         elif rep is None:
-            ref = klamath.library.Reference(struct_name=encoded_name,
-                                            xy=numpy.round([subpat.offset]).astype(int),
-                                            colrow=None,
-                                            angle_deg=angle_deg,
-                                            invert_y=mirror_across_x,
-                                            mag=subpat.scale,
-                                            properties=properties)
+            ref = klamath.library.Reference(
+                struct_name=encoded_name,
+                xy=rint_cast([subpat.offset]),
+                colrow=None,
+                angle_deg=angle_deg,
+                invert_y=mirror_across_x,
+                mag=subpat.scale,
+                properties=properties,
+                )
             refs.append(ref)
         else:
-            new_srefs = [klamath.library.Reference(struct_name=encoded_name,
-                                                   xy=numpy.round([subpat.offset + dd]).astype(int),
-                                                   colrow=None,
-                                                   angle_deg=angle_deg,
-                                                   invert_y=mirror_across_x,
-                                                   mag=subpat.scale,
-                                                   properties=properties)
-                         for dd in rep.displacements]
+            new_srefs = [
+                klamath.library.Reference(
+                    struct_name=encoded_name,
+                    xy=rint_cast([subpat.offset + dd]),
+                    colrow=None,
+                    angle_deg=angle_deg,
+                    invert_y=mirror_across_x,
+                    mag=subpat.scale,
+                    properties=properties,
+                    )
+                for dd in rep.displacements]
             refs += new_srefs
     return refs
 
@@ -443,8 +445,8 @@ def _shapes_to_elements(
         layer, data_type = _mlayer2gds(shape.layer)
         properties = _annotations_to_properties(shape.annotations, 128)
         if isinstance(shape, Path) and not polygonize_paths:
-            xy = numpy.round(shape.vertices + shape.offset).astype(int)
-            width = numpy.round(shape.width).astype(int)
+            xy = rint_cast(shape.vertices + shape.offset)
+            width = rint_cast(shape.width)
             path_type = next(k for k, v in path_cap_map.items() if v == shape.cap)    # reverse lookup
 
             extension: Tuple[int, int]
@@ -453,30 +455,36 @@ def _shapes_to_elements(
             else:
                 extension = (0, 0)
 
-            path = klamath.elements.Path(layer=(layer, data_type),
-                                         xy=xy,
-                                         path_type=path_type,
-                                         width=width,
-                                         extension=extension,
-                                         properties=properties)
+            path = klamath.elements.Path(
+                layer=(layer, data_type),
+                xy=xy,
+                path_type=path_type,
+                width=width,
+                extension=extension,
+                properties=properties,
+                )
             elements.append(path)
         elif isinstance(shape, Polygon):
             polygon = shape
             xy_closed = numpy.empty((polygon.vertices.shape[0] + 1, 2), dtype=numpy.int32)
             numpy.rint(polygon.vertices + polygon.offset, out=xy_closed[:-1], casting='unsafe')
             xy_closed[-1] = xy_closed[0]
-            boundary = klamath.elements.Boundary(layer=(layer, data_type),
-                                                 xy=xy_closed,
-                                                 properties=properties)
+            boundary = klamath.elements.Boundary(
+                layer=(layer, data_type),
+                xy=xy_closed,
+                properties=properties,
+                )
             elements.append(boundary)
         else:
             for polygon in shape.to_polygons():
                 xy_closed = numpy.empty((polygon.vertices.shape[0] + 1, 2), dtype=numpy.int32)
                 numpy.rint(polygon.vertices + polygon.offset, out=xy_closed[:-1], casting='unsafe')
                 xy_closed[-1] = xy_closed[0]
-                boundary = klamath.elements.Boundary(layer=(layer, data_type),
-                                                     xy=xy_closed,
-                                                     properties=properties)
+                boundary = klamath.elements.Boundary(
+                    layer=(layer, data_type),
+                    xy=xy_closed,
+                    properties=properties,
+                    )
                 elements.append(boundary)
     return elements
 
@@ -486,46 +494,44 @@ def _labels_to_texts(labels: List[Label]) -> List[klamath.elements.Text]:
     for label in labels:
         properties = _annotations_to_properties(label.annotations, 128)
         layer, text_type = _mlayer2gds(label.layer)
-        xy = numpy.round([label.offset]).astype(int)
-        text = klamath.elements.Text(layer=(layer, text_type),
-                                     xy=xy,
-                                     string=label.string.encode('ASCII'),
-                                     properties=properties,
-                                     presentation=0,  # TODO maybe set some of these?
-                                     angle_deg=0,
-                                     invert_y=False,
-                                     width=0,
-                                     path_type=0,
-                                     mag=1)
+        xy = rint_cast([label.offset])
+        text = klamath.elements.Text(
+            layer=(layer, text_type),
+            xy=xy,
+            string=label.string.encode('ASCII'),
+            properties=properties,
+            presentation=0,  # TODO maybe set some of these?
+            angle_deg=0,
+            invert_y=False,
+            width=0,
+            path_type=0,
+            mag=1,
+            )
         texts.append(text)
     return texts
 
 
 def disambiguate_pattern_names(
-        patterns: Sequence[Pattern],
+        names: Iterable[str],
         max_name_length: int = 32,
         suffix_length: int = 6,
-        dup_warn_filter: Optional[Callable[[str], bool]] = None,
-        ) -> None:
+        ) -> List[str]:
     """
     Args:
-        patterns: List of patterns to disambiguate
+        names: List of pattern names to disambiguate
         max_name_length: Names longer than this will be truncated
         suffix_length: Names which get truncated are truncated by this many extra characters. This is to
             leave room for a suffix if one is necessary.
-        dup_warn_filter: (optional) Function for suppressing warnings about cell names changing. Receives
-            the cell name and returns `False` if the warning should be suppressed and `True` if it should
-            be displayed. Default displays all warnings.
     """
-    used_names = []
-    for pat in set(patterns):
+    new_names = []
+    for name in names:
         # Shorten names which already exceed max-length
-        if len(pat.name) > max_name_length:
-            shortened_name = pat.name[:max_name_length - suffix_length]
-            logger.warning(f'Pattern name "{pat.name}" is too long ({len(pat.name)}/{max_name_length} chars),\n'
+        if len(name) > max_name_length:
+            shortened_name = name[:max_name_length - suffix_length]
+            logger.warning(f'Pattern name "{name}" is too long ({len(name)}/{max_name_length} chars),\n'
                            + f' shortening to "{shortened_name}" before generating suffix')
         else:
-            shortened_name = pat.name
+            shortened_name = name
 
         # Remove invalid characters
         sanitized_name = re.compile(r'[^A-Za-z0-9_\?\$]').sub('_', shortened_name)
@@ -533,7 +539,7 @@ def disambiguate_pattern_names(
         # Add a suffix that makes the name unique
         i = 0
         suffixed_name = sanitized_name
-        while suffixed_name in used_names or suffixed_name == '':
+        while suffixed_name in new_names or suffixed_name == '':
             suffix = base64.b64encode(struct.pack('>Q', i), b'$?').decode('ASCII')
 
             suffixed_name = sanitized_name + '$' + suffix[:-1].lstrip('A')
@@ -542,27 +548,25 @@ def disambiguate_pattern_names(
         if sanitized_name == '':
             logger.warning(f'Empty pattern name saved as "{suffixed_name}"')
         elif suffixed_name != sanitized_name:
-            if dup_warn_filter is None or dup_warn_filter(pat.name):
-                logger.warning(f'Pattern name "{pat.name}" ({sanitized_name}) appears multiple times;\n'
+            if dup_warn_filter is None or dup_warn_filter(name):
+                logger.warning(f'Pattern name "{name}" ({sanitized_name}) appears multiple times;\n'
                                + f' renaming to "{suffixed_name}"')
 
         # Encode into a byte-string and perform some final checks
         encoded_name = suffixed_name.encode('ASCII')
         if len(encoded_name) == 0:
             # Should never happen since zero-length names are replaced
-            raise PatternError(f'Zero-length name after sanitize+encode,\n originally "{pat.name}"')
+            raise PatternError(f'Zero-length name after sanitize+encode,\n originally "{name}"')
         if len(encoded_name) > max_name_length:
             raise PatternError(f'Pattern name "{encoded_name!r}" length > {max_name_length} after encode,\n'
-                               + f' originally "{pat.name}"')
+                               + f' originally "{name}"')
 
-        pat.name = suffixed_name
-        used_names.append(suffixed_name)
+        new_names.append(suffixed_name)
+    return new_names
 
 
 def load_library(
         stream: BinaryIO,
-        tag: str,
-        is_secondary: Optional[Callable[[str], bool]] = None,
         *,
         full_load: bool = False,
         ) -> Tuple[Library, Dict[str, Any]]:
@@ -574,28 +578,17 @@ def load_library(
 
     Args:
         stream: Seekable stream. Position 0 should be the start of the file.
-                The caller should leave the stream open while the library
-                is still in use, since the library will need to access it
-                in order to read the structure contents.
-        tag: Unique identifier that will be used to identify this data source
-        is_secondary: Function which takes a structure name and returns
-                      True if the structure should only be used as a subcell
-                      and not appear in the main Library interface.
-                      Default always returns False.
+            The caller should leave the stream open while the library
+            is still in use, since the library will need to access it
+            in order to read the structure contents.
         full_load: If True, force all structures to be read immediately rather
-                   than as-needed. Since data is read sequentially from the file,
-                   this will be faster than using the resulting library's
-                   `precache` method.
+            than as-needed. Since data is read sequentially from the file, this
+            will be faster than using the resulting library's `precache` method.
 
     Returns:
         Library object, allowing for deferred load of structures.
         Additional library info (dict, same format as from `read`).
     """
-    if is_secondary is None:
-        def is_secondary(k: str) -> bool:
-            return False
-    assert(is_secondary is not None)
-
     stream.seek(0)
     lib = Library()
 
@@ -603,7 +596,7 @@ def load_library(
         # Full load approach (immediately load everything)
         patterns, library_info = read(stream)
         for name, pattern in patterns.items():
-            lib.set_const(name, tag, pattern, secondary=is_secondary(name))
+            lib[name] = lambda: pattern
         return lib, library_info
 
     # Normal approach (scan and defer load)
@@ -613,19 +606,17 @@ def load_library(
     for name_bytes, pos in structs.items():
         name = name_bytes.decode('ASCII')
 
-        def mkstruct(pos: int = pos, name: str = name) -> Pattern:
+        def mkstruct(pos: int = pos) -> Pattern:
             stream.seek(pos)
-            return read_elements(stream, name, raw_mode=True)
+            return read_elements(stream, raw_mode=True)
 
-        lib.set_value(name, tag, mkstruct, secondary=is_secondary(name))
+        lib[name] = mkstruct
 
     return lib, library_info
 
 
 def load_libraryfile(
         filename: Union[str, pathlib.Path],
-        tag: str,
-        is_secondary: Optional[Callable[[str], bool]] = None,
         *,
         use_mmap: bool = True,
         full_load: bool = False,
@@ -640,8 +631,6 @@ def load_libraryfile(
 
     Args:
         path: filename or path to read from
-        tag: Unique identifier for library, see `load_library`
-        is_secondary: Function specifying subcess, see `load_library`
         use_mmap: If `True`, will attempt to memory-map the file instead
                   of buffering. In the case of gzipped files, the file
                   is decompressed into a python `bytes` object in memory
@@ -667,4 +656,4 @@ def load_libraryfile(
             stream = mmap.mmap(base_stream.fileno(), 0, access=mmap.ACCESS_READ)
         else:
             stream = io.BufferedReader(base_stream)
-    return load_library(stream, tag, is_secondary)
+    return load_library(stream, full_load=full_load)

masque/file/oasis.py

@@ -11,7 +11,7 @@ Note that OASIS references follow the same convention as `masque`,
   Scaling, rotation, and mirroring apply to individual instances, not grid
    vectors or offsets.
 """
-from typing import List, Any, Dict, Tuple, Callable, Union, Sequence, Iterable, Optional
+from typing import List, Any, Dict, Tuple, Callable, Union, Sequence, Iterable, Mapping, Optional
 import re
 import io
 import copy
@@ -22,11 +22,12 @@ import pathlib
 import gzip
 
 import numpy
+from numpy.typing import ArrayLike, NDArray
 import fatamorgana
 import fatamorgana.records as fatrec
 from fatamorgana.basic import PathExtensionScheme, AString, NString, PropStringReference
 
-from .utils import clean_pattern_vertices, is_gzipped
+from .utils import is_gzipped
 from .. import Pattern, SubPattern, PatternError, Label, Shape
 from ..shapes import Polygon, Path, Circle
 from ..repetition import Grid, Arbitrary, Repetition
@@ -47,19 +48,22 @@ path_cap_map = {
 
 #TODO implement more shape types?
 
+def rint_cast(val: ArrayLike) -> NDArray[numpy.int64]:
+    return numpy.rint(val, dtype=numpy.int64, casting='unsafe')
+
+
 def build(
-        patterns: Union[Pattern, Sequence[Pattern]],
+        library: Mapping[str, Pattern],           # NOTE: Pattern here should be treated as immutable!
         units_per_micron: int,
         layer_map: Optional[Dict[str, Union[int, Tuple[int, int]]]] = None,
         *,
-        modify_originals: bool = False,
-        disambiguate_func: Optional[Callable[[Iterable[Pattern]], None]] = None,
+        disambiguate_func: Optional[Callable[[Iterable[str]], List[str]]] = None,
         annotations: Optional[annotations_t] = None,
         ) -> fatamorgana.OasisLayout:
     """
-    Convert a `Pattern` or list of patterns to an OASIS stream, writing patterns
-     as OASIS cells, subpatterns as Placement records, and other shapes and labels
-     mapped to equivalent record types (Polygon, Path, Circle, Text).
+    Convert a collection of {name: Pattern} pairs to an OASIS stream, writing patterns
+     as OASIS cells, subpatterns as Placement records, and mapping other shapes and labels
+     to equivalent record types (Polygon, Path, Circle, Text).
      Other shape types may be converted to polygons if no equivalent
      record type exists (or is not implemented here yet).
 
@@ -75,7 +79,7 @@ def build(
      prior to calling this function.
 
     Args:
-        patterns: A Pattern or list of patterns to convert.
+        library: A {name: Pattern} mapping of patterns to write.
         units_per_micron: Written into the OASIS file, number of grid steps per micrometer.
             All distances are assumed to be an integer multiple of the grid step, and are stored as such.
         layer_map: Dictionary which translates layer names into layer numbers. If this argument is
@@ -86,11 +90,8 @@ def build(
             into numbers, omit this argument, and manually generate the required
             `fatamorgana.records.LayerName` entries.
             Default is an empty dict (no names provided).
-        modify_originals: If `True`, the original pattern is modified as part of the writing
-            process. Otherwise, a copy is made and `deepunlock()`-ed.
-            Default `False`.
-        disambiguate_func: Function which takes a list of patterns and alters them
-            to make their names valid and unique. Default is `disambiguate_pattern_names`.
+        disambiguate_func: Function which takes a list of pattern names and returns a list of names
+            altered to be valid and unique. Default is `disambiguate_pattern_names`.
         annotations: dictionary of key-value pairs which are saved as library-level properties
 
     Returns:
@@ -108,9 +109,6 @@ def build(
     if annotations is None:
         annotations = {}
 
-    if not modify_originals:
-        patterns = [p.deepunlock() for p in copy.deepcopy(patterns)]
-
     # Create library
     lib = fatamorgana.OasisLayout(unit=units_per_micron, validation=None)
     lib.properties = annotations_to_properties(annotations)
@@ -119,10 +117,12 @@ def build(
         for name, layer_num in layer_map.items():
             layer, data_type = _mlayer2oas(layer_num)
             lib.layers += [
-                fatrec.LayerName(nstring=name,
-                                 layer_interval=(layer, layer),
-                                 type_interval=(data_type, data_type),
-                                 is_textlayer=tt)
+                fatrec.LayerName(
+                    nstring=name,
+                    layer_interval=(layer, layer),
+                    type_interval=(data_type, data_type),
+                    is_textlayer=tt,
+                    )
                 for tt in (True, False)]
 
         def layer2oas(mlayer: layer_t) -> Tuple[int, int]:
@@ -132,17 +132,14 @@ def build(
     else:
         layer2oas = _mlayer2oas
 
-    # Get a dict of id(pattern) -> pattern
-    patterns_by_id = {id(pattern): pattern for pattern in patterns}
-    for pattern in patterns:
-        for i, p in pattern.referenced_patterns_by_id().items():
-            patterns_by_id[i] = p
-
-    disambiguate_func(patterns_by_id.values())
+    old_names = list(library.keys())
+    new_names = disambiguate_func(old_names)
+    renamed_lib = {new_name: library[old_name]
+                   for old_name, new_name in zip(old_names, new_names)}
 
     # Now create a structure for each pattern
-    for pat in patterns_by_id.values():
-        structure = fatamorgana.Cell(name=pat.name)
+    for name, pat in renamed_lib.items():
+        structure = fatamorgana.Cell(name=name)
         lib.cells.append(structure)
 
         structure.properties += annotations_to_properties(pat.annotations)
@@ -229,7 +226,6 @@ def readfile(
 
 def read(
         stream: io.BufferedIOBase,
-        clean_vertices: bool = True,
         ) -> Tuple[Dict[str, Pattern], Dict[str, Any]]:
     """
     Read a OASIS file and translate it into a dict of Pattern objects. OASIS cells are
@@ -243,9 +239,6 @@ def read(
 
     Args:
         stream: Stream to read from.
-        clean_vertices: If `True`, remove any redundant vertices when loading polygons.
-            The cleaning process removes any polygons with zero area or <3 vertices.
-            Default `True`.
 
     Returns:
         - Dict of `pattern_name`:`Pattern`s generated from OASIS cells
@@ -264,14 +257,14 @@ def read(
         layer_map[str(layer_name.nstring)] = layer_name
     library_info['layer_map'] = layer_map
 
-    patterns = []
+    patterns_dict = {}
     for cell in lib.cells:
         if isinstance(cell.name, int):
             cell_name = lib.cellnames[cell.name].nstring.string
         else:
             cell_name = cell.name.string
 
-        pat = Pattern(name=cell_name)
+        pat = Pattern()
         for element in cell.geometry:
             if isinstance(element, fatrec.XElement):
                 logger.warning('Skipping XElement record')
@@ -453,19 +446,7 @@ def read(
         for placement in cell.placements:
             pat.subpatterns.append(_placement_to_subpat(placement, lib))
 
-        if clean_vertices:
-            clean_pattern_vertices(pat)
-        patterns.append(pat)
-
-    # Create a dict of {pattern.name: pattern, ...}, then fix up all subpattern.pattern entries
-    #  according to the subpattern.identifier (which is deleted after use).
-    patterns_dict = dict(((p.name, p) for p in patterns))
-    for p in patterns_dict.values():
-        for sp in p.subpatterns:
-            ident = sp.identifier[0]
-            name = ident if isinstance(ident, str) else lib.cellnames[ident].nstring.string
-            sp.pattern = patterns_dict[name]
-            del sp.identifier
+        patterns_dict[name] = pat
 
     return patterns_dict, library_info
 
@@ -489,8 +470,7 @@ def _mlayer2oas(mlayer: layer_t) -> Tuple[int, int]:
 
 def _placement_to_subpat(placement: fatrec.Placement, lib: fatamorgana.OasisLayout) -> SubPattern:
     """
-    Helper function to create a SubPattern from a placment. Sets subpat.pattern to None
-     and sets the instance .identifier to (struct_name,).
+    Helper function to create a SubPattern from a placment. Sets subpat.target to the placemen name.
     """
     assert(not isinstance(placement.repetition, fatamorgana.ReuseRepetition))
     xy = numpy.array((placement.x, placement.y))
@@ -502,14 +482,15 @@ def _placement_to_subpat(placement: fatrec.Placement, lib: fatamorgana.OasisLayo
         rotation = 0
     else:
         rotation = numpy.deg2rad(float(placement.angle))
-    subpat = SubPattern(offset=xy,
-                        pattern=None,
-                        mirrored=(placement.flip, False),
-                        rotation=rotation,
-                        scale=float(mag),
-                        identifier=(name,),
-                        repetition=repetition_fata2masq(placement.repetition),
-                        annotations=annotations)
+    subpat = SubPattern(
+        target=name,
+        offset=xy,
+        mirrored=(placement.flip, False),
+        rotation=rotation,
+        scale=float(mag),
+        repetition=repetition_fata2masq(placement.repetition),
+        annotations=annotations,
+        )
     return subpat
 
 
@@ -518,17 +499,17 @@ def _subpatterns_to_placements(
         ) -> List[fatrec.Placement]:
     refs = []
     for subpat in subpatterns:
-        if subpat.pattern is None:
+        if subpat.target is None:
             continue
 
         # Note: OASIS mirrors first and rotates second
         mirror_across_x, extra_angle = normalize_mirror(subpat.mirrored)
         frep, rep_offset = repetition_masq2fata(subpat.repetition)
 
-        offset = numpy.round(subpat.offset + rep_offset).astype(int)
+        offset = rint_cast(subpat.offset + rep_offset)
         angle = numpy.rad2deg(subpat.rotation + extra_angle) % 360
         ref = fatrec.Placement(
-            name=subpat.pattern.name,
+            name=subpat.target,
             flip=mirror_across_x,
             angle=angle,
             magnification=subpat.scale,
@@ -552,46 +533,51 @@ def _shapes_to_elements(
         repetition, rep_offset = repetition_masq2fata(shape.repetition)
         properties = annotations_to_properties(shape.annotations)
         if isinstance(shape, Circle):
-            offset = numpy.round(shape.offset + rep_offset).astype(int)
-            radius = numpy.round(shape.radius).astype(int)
-            circle = fatrec.Circle(layer=layer,
-                                   datatype=datatype,
-                                   radius=radius,
-                                   x=offset[0],
-                                   y=offset[1],
-                                   properties=properties,
-                                   repetition=repetition)
+            offset = rint_cast(shape.offset + rep_offset)
+            radius = rint_cast(shape.radius)
+            circle = fatrec.Circle(
+                layer=layer,
+                datatype=datatype,
+                radius=radius,
+                x=offset[0],
+                y=offset[1],
+                properties=properties,
+                repetition=repetition,
+                )
             elements.append(circle)
         elif isinstance(shape, Path):
-            xy = numpy.round(shape.offset + shape.vertices[0] + rep_offset).astype(int)
-            deltas = numpy.round(numpy.diff(shape.vertices, axis=0)).astype(int)
-            half_width = numpy.round(shape.width / 2).astype(int)
+            xy = rint_cast(shape.offset + shape.vertices[0] + rep_offset)
+            deltas = rint_cast(numpy.diff(shape.vertices, axis=0))
+            half_width = rint_cast(shape.width / 2)
             path_type = next(k for k, v in path_cap_map.items() if v == shape.cap)    # reverse lookup
             extension_start = (path_type, shape.cap_extensions[0] if shape.cap_extensions is not None else None)
             extension_end = (path_type, shape.cap_extensions[1] if shape.cap_extensions is not None else None)
-            path = fatrec.Path(layer=layer,
-                               datatype=datatype,
-                               point_list=deltas,
-                               half_width=half_width,
-                               x=xy[0],
-                               y=xy[1],
-                               extension_start=extension_start,       # TODO implement multiple cap types?
-                               extension_end=extension_end,
-                               properties=properties,
-                               repetition=repetition,
-                               )
+            path = fatrec.Path(
+                layer=layer,
+                datatype=datatype,
+                point_list=deltas,
+                half_width=half_width,
+                x=xy[0],
+                y=xy[1],
+                extension_start=extension_start,       # TODO implement multiple cap types?
+                extension_end=extension_end,
+                properties=properties,
+                repetition=repetition,
+                )
             elements.append(path)
         else:
             for polygon in shape.to_polygons():
-                xy = numpy.round(polygon.offset + polygon.vertices[0] + rep_offset).astype(int)
-                points = numpy.round(numpy.diff(polygon.vertices, axis=0)).astype(int)
-                elements.append(fatrec.Polygon(layer=layer,
-                                               datatype=datatype,
-                                               x=xy[0],
-                                               y=xy[1],
-                                               point_list=points,
-                                               properties=properties,
-                                               repetition=repetition))
+                xy = rint_cast(polygon.offset + polygon.vertices[0] + rep_offset)
+                points = rint_cast(numpy.diff(polygon.vertices, axis=0))
+                elements.append(fatrec.Polygon(
+                    layer=layer,
+                    datatype=datatype,
+                    x=xy[0],
+                    y=xy[1],
+                    point_list=points,
+                    properties=properties,
+                    repetition=repetition,
+                    ))
     return elements
 
 
@@ -603,29 +589,31 @@ def _labels_to_texts(
     for label in labels:
         layer, datatype = layer2oas(label.layer)
         repetition, rep_offset = repetition_masq2fata(label.repetition)
-        xy = numpy.round(label.offset + rep_offset).astype(int)
+        xy = rint_cast(label.offset + rep_offset)
         properties = annotations_to_properties(label.annotations)
-        texts.append(fatrec.Text(layer=layer,
-                                 datatype=datatype,
-                                 x=xy[0],
-                                 y=xy[1],
-                                 string=label.string,
-                                 properties=properties,
-                                 repetition=repetition))
+        texts.append(fatrec.Text(
+            layer=layer,
+            datatype=datatype,
+            x=xy[0],
+            y=xy[1],
+            string=label.string,
+            properties=properties,
+            repetition=repetition,
+            ))
     return texts
 
 
 def disambiguate_pattern_names(
-        patterns,
+        names: Iterable[str],
         dup_warn_filter: Callable[[str], bool] = None,      # If returns False, don't warn about this name
-        ) -> None:
-    used_names = []
-    for pat in patterns:
-        sanitized_name = re.compile(r'[^A-Za-z0-9_\?\$]').sub('_', pat.name)
+        ) -> List[str]:
+    new_names = []
+    for name in names:
+        sanitized_name = re.compile(r'[^A-Za-z0-9_\?\$]').sub('_', name)
 
         i = 0
         suffixed_name = sanitized_name
-        while suffixed_name in used_names or suffixed_name == '':
+        while suffixed_name in new_names or suffixed_name == '':
             suffix = base64.b64encode(struct.pack('>Q', i), b'$?').decode('ASCII')
 
             suffixed_name = sanitized_name + '$' + suffix[:-1].lstrip('A')
@@ -634,16 +622,16 @@ def disambiguate_pattern_names(
         if sanitized_name == '':
             logger.warning(f'Empty pattern name saved as "{suffixed_name}"')
         elif suffixed_name != sanitized_name:
-            if dup_warn_filter is None or dup_warn_filter(pat.name):
-                logger.warning(f'Pattern name "{pat.name}" ({sanitized_name}) appears multiple times;\n'
+            if dup_warn_filter is None or dup_warn_filter(name):
+                logger.warning(f'Pattern name "{name}" ({sanitized_name}) appears multiple times;\n'
                                + f' renaming to "{suffixed_name}"')
 
         if len(suffixed_name) == 0:
             # Should never happen since zero-length names are replaced
-            raise PatternError(f'Zero-length name after sanitize+encode,\n originally "{pat.name}"')
+            raise PatternError(f'Zero-length name after sanitize+encode,\n originally "{name}"')
 
-        pat.name = suffixed_name
-        used_names.append(suffixed_name)
+        new_names.append(suffixed_name)
+    return new_names
 
 
 def repetition_fata2masq(

masque/file/python_gdsii.py

@@ -18,7 +18,7 @@ Notes:
  * GDS does not support library- or structure-level annotations
 """
 from typing import List, Any, Dict, Tuple, Callable, Union, Iterable, Optional
-from typing import Sequence
+from typing import Sequence, Mapping
 import re
 import io
 import copy
@@ -59,13 +59,13 @@ def rint_cast(val: ArrayLike) -> NDArray[numpy.int32]:
 
 
 def build(
-        patterns: Union[Pattern, Sequence[Pattern]],
+        library: Mapping[str, Pattern],
         meters_per_unit: float,
         logical_units_per_unit: float = 1,
         library_name: str = 'masque-gdsii-write',
         *,
         modify_originals: bool = False,
-        disambiguate_func: Callable[[Iterable[Pattern]], None] = None,
+        disambiguate_func: Callable[[Iterable[str]], List[str]] = None,
         ) -> gdsii.library.Library:
     """
     Convert a `Pattern` or list of patterns to a GDSII stream, by first calling
@@ -86,7 +86,7 @@ def build(
      prior to calling this function.
 
     Args:
-        patterns: A Pattern or list of patterns to convert.
+        library: A {name: Pattern} mapping of patterns to write.
         meters_per_unit: Written into the GDSII file, meters per (database) length unit.
             All distances are assumed to be an integer multiple of this unit, and are stored as such.
         logical_units_per_unit: Written into the GDSII file. Allows the GDSII to specify a
@@ -95,27 +95,29 @@ def build(
         library_name: Library name written into the GDSII file.
             Default 'masque-gdsii-write'.
         modify_originals: If `True`, the original pattern is modified as part of the writing
-            process. Otherwise, a copy is made and `deepunlock()`-ed.
+            process. Otherwise, a copy is made.
             Default `False`.
-        disambiguate_func: Function which takes a list of patterns and alters them
-            to make their names valid and unique. Default is `disambiguate_pattern_names`, which
-            attempts to adhere to the GDSII standard as well as possible.
+        disambiguate_func: Function which takes a list of pattern names and returns a list of names
+            altered to be valid and unique. Default is `disambiguate_pattern_names`, which
+            attempts to adhere to the GDSII standard reasonably well.
             WARNING: No additional error checking is performed on the results.
 
     Returns:
         `gdsii.library.Library`
     """
-    if isinstance(patterns, Pattern):
-        patterns = [patterns]
-
     if disambiguate_func is None:
-        disambiguate_func = disambiguate_pattern_names          # type: ignore
-    assert(disambiguate_func is not None)       # placate mypy
+        disambiguate_func = disambiguate_pattern_names
 
     if not modify_originals:
-        patterns = [p.deepunlock() for p in copy.deepcopy(patterns)]
+        library = copy.deepcopy(library)
 
-    patterns = [p.wrap_repeated_shapes() for p in patterns]
+    for p in library.values():
+        library.add(p.wrap_repeated_shapes())
+
+    old_names = list(library.keys())
+    new_names = disambiguate_func(old_names)
+    renamed_lib = {new_name: library[old_name]
+                   for old_name, new_name in zip(old_names, new_names)}
 
     # Create library
     lib = gdsii.library.Library(version=600,
@@ -123,17 +125,9 @@ def build(
                                 logical_unit=logical_units_per_unit,
                                 physical_unit=meters_per_unit)
 
-    # Get a dict of id(pattern) -> pattern
-    patterns_by_id = {id(pattern): pattern for pattern in patterns}
-    for pattern in patterns:
-        for i, p in pattern.referenced_patterns_by_id().items():
-            patterns_by_id[i] = p
-
-    disambiguate_func(patterns_by_id.values())
-
     # Now create a structure for each pattern, and add in any Boundary and SREF elements
-    for pat in patterns_by_id.values():
-        structure = gdsii.structure.Structure(name=pat.name.encode('ASCII'))
+    for name, pat in renamed_lib.items():
+        structure = gdsii.structure.Structure(name=name.encode('ASCII'))
         lib.append(structure)
 
         structure += _shapes_to_elements(pat.shapes)
@@ -144,7 +138,7 @@ def build(
 
 
 def write(
-        patterns: Union[Pattern, Sequence[Pattern]],
+        library: Mapping[str, Pattern],
         stream: io.BufferedIOBase,
         *args,
         **kwargs,
@@ -154,31 +148,31 @@ def write(
     See `masque.file.gdsii.build()` for details.
 
     Args:
-        patterns: A Pattern or list of patterns to write to file.
+        library: A {name: Pattern} mapping of patterns to write.
         stream: Stream to write to.
         *args: passed to `masque.file.gdsii.build()`
         **kwargs: passed to `masque.file.gdsii.build()`
     """
-    lib = build(patterns, *args, **kwargs)
+    lib = build(library, *args, **kwargs)
     lib.save(stream)
     return
 
 def writefile(
-        patterns: Union[Sequence[Pattern], Pattern],
+        library: Mapping[str, Pattern],
         filename: Union[str, pathlib.Path],
         *args,
         **kwargs,
         ) -> None:
     """
-    Wrapper for `masque.file.gdsii.write()` that takes a filename or path instead of a stream.
+    Wrapper for `write()` that takes a filename or path instead of a stream.
 
     Will automatically compress the file if it has a .gz suffix.
 
     Args:
-        patterns: `Pattern` or list of patterns to save
+        library: {name: Pattern} pairs to save.
         filename: Filename to save to.
-        *args: passed to `masque.file.gdsii.write`
-        **kwargs: passed to `masque.file.gdsii.write`
+        *args: passed to `write()`
+        **kwargs: passed to `write()`
     """
     path = pathlib.Path(filename)
     if path.suffix == '.gz':
@@ -196,14 +190,14 @@ def readfile(
         **kwargs,
         ) -> Tuple[Dict[str, Pattern], Dict[str, Any]]:
     """
-    Wrapper for `masque.file.gdsii.read()` that takes a filename or path instead of a stream.
+    Wrapper for `read()` that takes a filename or path instead of a stream.
 
     Will automatically decompress gzipped files.
 
     Args:
         filename: Filename to save to.
-        *args: passed to `masque.file.gdsii.read`
-        **kwargs: passed to `masque.file.gdsii.read`
+        *args: passed to `read()`
+        **kwargs: passed to `read()`
     """
     path = pathlib.Path(filename)
     if is_gzipped(path):
@@ -251,9 +245,10 @@ def read(
 
     raw_mode = True     # Whether to construct shapes in raw mode (less error checking)
 
-    patterns = []
+    patterns_dict = {}
     for structure in lib:
-        pat = Pattern(name=structure.name.decode('ASCII'))
+        pat = Pattern()
+        name=structure.name.decode('ASCII')
         for element in structure:
             # Switch based on element type:
             if isinstance(element, gdsii.elements.Boundary):
@@ -275,15 +270,7 @@ def read(
 
         if clean_vertices:
             clean_pattern_vertices(pat)
-        patterns.append(pat)
-
-    # Create a dict of {pattern.name: pattern, ...}, then fix up all subpattern.pattern entries
-    #  according to the subpattern.identifier (which is deleted after use).
-    patterns_dict = dict(((p.name, p) for p in patterns))
-    for p in patterns_dict.values():
-        for sp in p.subpatterns:
-            sp.pattern = patterns_dict[sp.identifier[0].decode('ASCII')]
-            del sp.identifier
+        patterns_dict[name] = pat
 
     return patterns_dict, library_info
 
@@ -309,8 +296,7 @@ def _ref_to_subpat(
                        gdsii.elements.ARef]
         ) -> SubPattern:
     """
-    Helper function to create a SubPattern from an SREF or AREF. Sets subpat.pattern to None
-     and sets the instance .identifier to (struct_name,).
+    Helper function to create a SubPattern from an SREF or AREF. Sets subpat.target to struct_name.
 
     NOTE: "Absolute" means not affected by parent elements.
            That's not currently supported by masque at all (and not planned).
@@ -351,7 +337,6 @@ def _ref_to_subpat(
                         mirrored=(mirror_across_x, False),
                         annotations=_properties_to_annotations(element.properties),
                         repetition=repetition)
-    subpat.identifier = (element.struct_name,)
     return subpat
 
 
@@ -395,9 +380,9 @@ def _subpatterns_to_refs(
         ) -> List[Union[gdsii.elements.ARef, gdsii.elements.SRef]]:
     refs = []
     for subpat in subpatterns:
-        if subpat.pattern is None:
+        if subpat.target is None:
             continue
-        encoded_name = subpat.pattern.name.encode('ASCII')
+        encoded_name = subpat.target.encode('ASCII')
 
         # Note: GDS mirrors first and rotates second
         mirror_across_x, extra_angle = normalize_mirror(subpat.mirrored)
@@ -523,14 +508,14 @@ def _labels_to_texts(labels: List[Label]) -> List[gdsii.elements.Text]:
 
 
 def disambiguate_pattern_names(
-        patterns: Sequence[Pattern],
+        names: Iterable[str],
         max_name_length: int = 32,
         suffix_length: int = 6,
         dup_warn_filter: Optional[Callable[[str], bool]] = None,
-        ) -> None:
+        ) -> List[str]:
     """
     Args:
-        patterns: List of patterns to disambiguate
+        names: List of pattern names to disambiguate
         max_name_length: Names longer than this will be truncated
         suffix_length: Names which get truncated are truncated by this many extra characters. This is to
             leave room for a suffix if one is necessary.
@@ -538,15 +523,15 @@ def disambiguate_pattern_names(
             the cell name and returns `False` if the warning should be suppressed and `True` if it should
             be displayed. Default displays all warnings.
     """
-    used_names = []
-    for pat in set(patterns):
+    new_names = []
+    for name in names:
         # Shorten names which already exceed max-length
-        if len(pat.name) > max_name_length:
-            shortened_name = pat.name[:max_name_length - suffix_length]
-            logger.warning(f'Pattern name "{pat.name}" is too long ({len(pat.name)}/{max_name_length} chars),\n'
+        if len(name) > max_name_length:
+            shortened_name = name[:max_name_length - suffix_length]
+            logger.warning(f'Pattern name "{name}" is too long ({len(name)}/{max_name_length} chars),\n'
                            + f' shortening to "{shortened_name}" before generating suffix')
         else:
-            shortened_name = pat.name
+            shortened_name = name
 
         # Remove invalid characters
         sanitized_name = re.compile(r'[^A-Za-z0-9_\?\$]').sub('_', shortened_name)
@@ -554,7 +539,7 @@ def disambiguate_pattern_names(
         # Add a suffix that makes the name unique
         i = 0
         suffixed_name = sanitized_name
-        while suffixed_name in used_names or suffixed_name == '':
+        while suffixed_name in new_names or suffixed_name == '':
             suffix = base64.b64encode(struct.pack('>Q', i), b'$?').decode('ASCII')
 
             suffixed_name = sanitized_name + '$' + suffix[:-1].lstrip('A')
@@ -563,18 +548,19 @@ def disambiguate_pattern_names(
         if sanitized_name == '':
             logger.warning(f'Empty pattern name saved as "{suffixed_name}"')
         elif suffixed_name != sanitized_name:
-            if dup_warn_filter is None or dup_warn_filter(pat.name):
-                logger.warning(f'Pattern name "{pat.name}" ({sanitized_name}) appears multiple times;\n'
+            if dup_warn_filter is None or dup_warn_filter(name):
+                logger.warning(f'Pattern name "{name}" ({sanitized_name}) appears multiple times;\n'
                                + f' renaming to "{suffixed_name}"')
 
         # Encode into a byte-string and perform some final checks
         encoded_name = suffixed_name.encode('ASCII')
         if len(encoded_name) == 0:
             # Should never happen since zero-length names are replaced
-            raise PatternError(f'Zero-length name after sanitize+encode,\n originally "{pat.name}"')
+            raise PatternError(f'Zero-length name after sanitize+encode,\n originally "{name}"')
         if len(encoded_name) > max_name_length:
             raise PatternError(f'Pattern name "{encoded_name!r}" length > {max_name_length} after encode,\n'
-                               + f' originally "{pat.name}"')
+                               + f' originally "{name}"')
+
+        new_names.append(suffixed_name)
+    return new_names
 
-        pat.name = suffixed_name
-        used_names.append(suffixed_name)

masque/file/svg.py

@@ -1,7 +1,7 @@
 """
 SVG file format readers and writers
 """
-from typing import Dict, Optional
+from typing import Dict, Optional, Mapping
 import warnings
 
 import numpy
@@ -13,7 +13,8 @@ from .. import Pattern
 
 
 def writefile(
-        pattern: Pattern,
+        library: Mapping[str, Pattern],
+        top: str,
         filename: str,
         custom_attributes: bool = False,
         ) -> None:
@@ -41,11 +42,12 @@ def writefile(
         custom_attributes: Whether to write non-standard `pattern_layer` and
             `pattern_dose` attributes to the SVG elements.
     """
+    pattern = library[top]
 
     # Polygonize pattern
     pattern.polygonize()
 
-    bounds = pattern.get_bounds()
+    bounds = pattern.get_bounds(library=library)
     if bounds is None:
         bounds_min, bounds_max = numpy.array([[-1, -1], [1, 1]])
         warnings.warn('Pattern had no bounds (empty?); setting arbitrary viewbox')
@@ -59,15 +61,10 @@ def writefile(
     svg = svgwrite.Drawing(filename, profile='full', viewBox=viewbox_string,
                            debug=(not custom_attributes))
 
-    # Get a dict of id(pattern) -> pattern
-    patterns_by_id = {**(pattern.referenced_patterns_by_id()), id(pattern): pattern}        # type: Dict[int, Optional[Pattern]]
-
     # Now create a group for each row in sd_table (ie, each pattern + dose combination)
     #  and add in any Boundary and Use elements
-    for pat in patterns_by_id.values():
-        if pat is None:
-            continue
-        svg_group = svg.g(id=mangle_name(pat), fill='blue', stroke='red')
+    for name, pat in library.items():
+        svg_group = svg.g(id=mangle_name(name), fill='blue', stroke='red')
 
         for shape in pat.shapes:
             for polygon in shape.to_polygons():
@@ -81,20 +78,24 @@ def writefile(
                 svg_group.add(path)
 
         for subpat in pat.subpatterns:
-            if subpat.pattern is None:
+            if subpat.target is None:
                 continue
             transform = f'scale({subpat.scale:g}) rotate({subpat.rotation:g}) translate({subpat.offset[0]:g},{subpat.offset[1]:g})'
-            use = svg.use(href='#' + mangle_name(subpat.pattern), transform=transform)
+            use = svg.use(href='#' + mangle_name(subpat.target), transform=transform)
             if custom_attributes:
                 use['pattern_dose'] = subpat.dose
             svg_group.add(use)
 
         svg.defs.add(svg_group)
-    svg.add(svg.use(href='#' + mangle_name(pattern)))
+    svg.add(svg.use(href='#' + mangle_name(top)))
     svg.save()
 
 
-def writefile_inverted(pattern: Pattern, filename: str):
+def writefile_inverted(
+        library: Mapping[str, Pattern],
+        top: str,
+        filename: str,
+        ) -> None:
     """
     Write an inverted Pattern to an SVG file, by first calling `.polygonize()` and
      `.flatten()` on it to change the shapes into polygons, then drawing a bounding
@@ -110,10 +111,12 @@ def writefile_inverted(pattern: Pattern, filename: str):
         pattern: Pattern to write to file. Modified by this function.
         filename: Filename to write to.
     """
+    pattern = library[top]
+
     # Polygonize and flatten pattern
     pattern.polygonize().flatten()
 
-    bounds = pattern.get_bounds()
+    bounds = pattern.get_bounds(library=library)
     if bounds is None:
         bounds_min, bounds_max = numpy.array([[-1, -1], [1, 1]])
         warnings.warn('Pattern had no bounds (empty?); setting arbitrary viewbox')

masque/file/utils.py

@@ -1,7 +1,7 @@
 """
 Helper functions for file reading and writing
 """
-from typing import Set, Tuple, List
+from typing import Set, Tuple, List, Iterable, Mapping
 import re
 import copy
 import pathlib
@@ -10,19 +10,22 @@ from .. import Pattern, PatternError
 from ..shapes import Polygon, Path
 
 
-def mangle_name(pattern: Pattern, dose_multiplier: float = 1.0) -> str:
+def mangle_name(name: str, dose_multiplier: float = 1.0) -> str:
     """
-    Create a name using `pattern.name`, `id(pattern)`, and the dose multiplier.
+    Create a new name using `name` and the `dose_multiplier`.
 
     Args:
-        pattern: Pattern whose name we want to mangle.
+        name: Name we want to mangle.
         dose_multiplier: Dose multiplier to mangle with.
 
     Returns:
         Mangled name.
     """
+    if dose_multiplier == 1:
+        full_name = name
+    else:
+        full_name = f'{name}_dm{dose_multiplier}'
     expression = re.compile(r'[^A-Za-z0-9_\?\$]')
-    full_name = '{}_{}_{}'.format(pattern.name, dose_multiplier, id(pattern))
     sanitized_name = expression.sub('_', full_name)
     return sanitized_name
 
@@ -51,25 +54,30 @@ def clean_pattern_vertices(pat: Pattern) -> Pattern:
     return pat
 
 
-def make_dose_table(patterns: List[Pattern], dose_multiplier: float = 1.0) -> Set[Tuple[int, float]]:
+def make_dose_table(
+        top_names: Iterable[str],
+        library: Mapping[str, Pattern],
+        dose_multiplier: float = 1.0,
+        ) -> Set[Tuple[int, float]]:
     """
-    Create a set containing `(id(pat), written_dose)` for each pattern (including subpatterns)
+    Create a set containing `(name, written_dose)` for each pattern (including subpatterns)
 
     Args:
+        top_names: Names of all topcells
         pattern: Source Patterns.
         dose_multiplier: Multiplier for all written_dose entries.
 
     Returns:
-        `{(id(subpat.pattern), written_dose), ...}`
+        `{(name, written_dose), ...}`
     """
-    dose_table = {(id(pattern), dose_multiplier) for pattern in patterns}
-    for pattern in patterns:
+    dose_table = {(top_name, dose_multiplier) for top_name in top_names}
+    for name, pattern in library.items():
         for subpat in pattern.subpatterns:
-            if subpat.pattern is None:
+            if subpat.target is None:
                 continue
-            subpat_dose_entry = (id(subpat.pattern), subpat.dose * dose_multiplier)
+            subpat_dose_entry = (subpat.target, subpat.dose * dose_multiplier)
             if subpat_dose_entry not in dose_table:
-                subpat_dose_table = make_dose_table([subpat.pattern], subpat.dose * dose_multiplier)
+                subpat_dose_table = make_dose_table(subpat.target, library, subpat.dose * dose_multiplier)
                 dose_table = dose_table.union(subpat_dose_table)
     return dose_table
 
@@ -96,7 +104,7 @@ def dtype2dose(pattern: Pattern) -> Pattern:
 
 
 def dose2dtype(
-        patterns: List[Pattern],
+        library: List[Pattern],
         ) -> Tuple[List[Pattern], List[float]]:
     """
      For each shape in each pattern, set shape.layer to the tuple
@@ -119,21 +127,16 @@ def dose2dtype(
             dose_list: A list of doses, providing a mapping between datatype (int, list index)
                        and dose (float, list entry).
     """
-    # Get a dict of id(pattern) -> pattern
-    patterns_by_id = {id(pattern): pattern for pattern in patterns}
-    for pattern in patterns:
-        for i, p in pattern.referenced_patterns_by_id().items():
-            patterns_by_id[i] = p
-
+    logger.warning('TODO: dose2dtype() needs to be tested!')
     # Get a table of (id(pat), written_dose) for each pattern and subpattern
-    sd_table = make_dose_table(patterns)
+    sd_table = make_dose_table(library.find_topcells(), library)
 
     # Figure out all the unique doses necessary to write this pattern
     #  This means going through each row in sd_table and adding the dose values needed to write
     #  that subpattern at that dose level
     dose_vals = set()
-    for pat_id, pat_dose in sd_table:
-        pat = patterns_by_id[pat_id]
+    for name, pat_dose in sd_table:
+        pat = library[name]
         for shape in pat.shapes:
             dose_vals.add(shape.dose * pat_dose)
 
@@ -144,21 +147,22 @@ def dose2dtype(
 
     # Create a new pattern for each non-1-dose entry in the dose table
     #   and update the shapes to reflect their new dose
-    new_pats = {}  # (id, dose) -> new_pattern mapping
-    for pat_id, pat_dose in sd_table:
+    new_names = {}  # {(old name, dose): new name} mapping
+    new_lib = {}  # {new_name: new_pattern} mapping
+    for name, pat_dose in sd_table:
+        mangled_name = mangle_name(name, pat_dose)
+        new_names[(name, pat_dose)] = mangled_name
+
+        old_pat = library[name]
+
         if pat_dose == 1:
-            new_pats[(pat_id, pat_dose)] = patterns_by_id[pat_id]
+            new_lib[mangled_name] = old_pat
             continue
 
-        old_pat = patterns_by_id[pat_id]
-        pat = old_pat.copy()  # keep old subpatterns
-        pat.shapes = copy.deepcopy(old_pat.shapes)
-        pat.labels = copy.deepcopy(old_pat.labels)
+        pat = old_pat.deepcopy()
 
-        encoded_name = mangle_name(pat, pat_dose)
         if len(encoded_name) == 0:
-            raise PatternError('Zero-length name after mangle+encode, originally "{}"'.format(pat.name))
-        pat.name = encoded_name
+            raise PatternError('Zero-length name after mangle+encode, originally "{name}"'.format(pat.name))
 
         for shape in pat.shapes:
             data_type = dose_vals_list.index(shape.dose * pat_dose)
@@ -169,15 +173,9 @@ def dose2dtype(
             else:
                 raise PatternError(f'Invalid layer for gdsii: {shape.layer}')
 
-        new_pats[(pat_id, pat_dose)] = pat
+        new_lib[mangled_name] = pat
 
-    # Go back through all the dose-specific patterns and fix up their subpattern entries
-    for (pat_id, pat_dose), pat in new_pats.items():
-        for subpat in pat.subpatterns:
-            dose_mult = subpat.dose * pat_dose
-            subpat.pattern = new_pats[(id(subpat.pattern), dose_mult)]
-
-    return patterns, dose_vals_list
+    return new_lib, dose_vals_list
 
 
 def is_gzipped(path: pathlib.Path) -> bool:

masque/label.py

@@ -6,14 +6,14 @@ from numpy.typing import ArrayLike, NDArray
 
 from .repetition import Repetition
 from .utils import rotation_matrix_2d, layer_t, AutoSlots, annotations_t
-from .traits import PositionableImpl, LayerableImpl, Copyable, Pivotable, LockableImpl, RepeatableImpl
+from .traits import PositionableImpl, LayerableImpl, Copyable, Pivotable, RepeatableImpl
 from .traits import AnnotatableImpl
 
 
 L = TypeVar('L', bound='Label')
 
 
-class Label(PositionableImpl, LayerableImpl, LockableImpl, RepeatableImpl, AnnotatableImpl,
+class Label(PositionableImpl, LayerableImpl, RepeatableImpl, AnnotatableImpl,
             Pivotable, Copyable, metaclass=AutoSlots):
     """
     A text annotation with a position and layer (but no size; it is not drawn)
@@ -49,32 +49,28 @@ class Label(PositionableImpl, LayerableImpl, LockableImpl, RepeatableImpl, Annot
             layer: layer_t = 0,
             repetition: Optional[Repetition] = None,
             annotations: Optional[annotations_t] = None,
-            locked: bool = False,
             identifier: Tuple = (),
             ) -> None:
-        LockableImpl.unlock(self)
         self.identifier = identifier
         self.string = string
         self.offset = numpy.array(offset, dtype=float, copy=True)
         self.layer = layer
         self.repetition = repetition
         self.annotations = annotations if annotations is not None else {}
-        self.set_locked(locked)
 
     def __copy__(self: L) -> L:
-        return type(self)(string=self.string,
-                          offset=self.offset.copy(),
-                          layer=self.layer,
-                          repetition=self.repetition,
-                          locked=self.locked,
-                          identifier=self.identifier)
+        return type(self)(
+            string=self.string,
+            offset=self.offset.copy(),
+            layer=self.layer,
+            repetition=self.repetition,
+            identifier=self.identifier,
+            )
 
     def __deepcopy__(self: L, memo: Dict = None) -> L:
         memo = {} if memo is None else memo
         new = copy.copy(self)
-        LockableImpl.unlock(new)
         new._offset = self._offset.copy()
-        new.set_locked(self.locked)
         return new
 
     def rotate_around(self: L, pivot: ArrayLike, rotation: float) -> L:
@@ -106,17 +102,3 @@ class Label(PositionableImpl, LayerableImpl, LockableImpl, RepeatableImpl, Annot
             Bounds [[xmin, xmax], [ymin, ymax]]
         """
         return numpy.array([self.offset, self.offset])
-
-    def lock(self: L) -> L:
-        PositionableImpl._lock(self)
-        LockableImpl.lock(self)
-        return self
-
-    def unlock(self: L) -> L:
-        LockableImpl.unlock(self)
-        PositionableImpl._unlock(self)
-        return self
-
-    def __repr__(self) -> str:
-        locked = ' L' if self.locked else ''
-        return f'<Label "{self.string}" l{self.layer} o{self.offset}{locked}>'

masque/library.py

@@ -0,0 +1,594 @@
+"""
+Library class for managing unique name->pattern mappings and
+ deferred loading or creation.
+"""
+from typing import List, Dict, Callable, TypeVar, Type, TYPE_CHECKING
+from typing import Any, Tuple, Union, Iterator, Mapping, MutableMapping, Set, Optional, Sequence
+import logging
+import copy
+import base64
+import struct
+import re
+from pprint import pformat
+from collections import defaultdict
+
+import numpy
+from numpy.typing import ArrayLike, NDArray, NDArray
+
+from .error import LibraryError, PatternError
+from .utils import rotation_matrix_2d, normalize_mirror
+from .shapes import Shape, Polygon
+from .label import Label
+
+if TYPE_CHECKING:
+    from .pattern import Pattern
+
+
+logger = logging.getLogger(__name__)
+
+
+visitor_function_t = Callable[['Pattern', Tuple['Pattern'], Dict, NDArray[numpy.float64]], 'Pattern']
+L = TypeVar('L', bound='Library')
+
+
+class Library:
+    """
+    This class is usually used to create a library of Patterns by mapping names to
+     functions which generate or load the relevant `Pattern` object as-needed.
+
+    The cache can be disabled by setting the `enable_cache` attribute to `False`.
+    """
+    dict: Dict[str, Callable[[], Pattern]]
+    cache: Dict[str, 'Pattern']
+    enable_cache: bool = True
+
+    def __init__(self) -> None:
+        self.dict = {}
+        self.cache = {}
+
+    def __setitem__(self, key: str, value: Callable[[], Pattern]) -> None:
+        self.dict[key] = value
+        if key in self.cache:
+            del self.cache[key]
+
+    def __delitem__(self, key: str) -> None:
+        del self.dict[key]
+        if key in self.cache:
+            del self.cache[key]
+
+    def __getitem__(self, key: str) -> 'Pattern':
+        logger.debug(f'loading {key}')
+        if self.enable_cache and key in self.cache:
+            logger.debug(f'found {key} in cache')
+            return self.cache[key]
+
+        func = self.dict[key]
+        pat = func()
+        self.cache[key] = pat
+        return pat
+
+    def __iter__(self) -> Iterator[str]:
+        return iter(self.keys())
+
+    def __contains__(self, key: str) -> bool:
+        return key in self.dict
+
+    def keys(self) -> Iterator[str]:
+        return iter(self.dict.keys())
+
+    def values(self) -> Iterator['Pattern']:
+        return iter(self[key] for key in self.keys())
+
+    def items(self) -> Iterator[Tuple[str, 'Pattern']]:
+        return iter((key, self[key]) for key in self.keys())
+
+    def __repr__(self) -> str:
+        return '<Library with keys ' + repr(list(self.dict.keys())) + '>'
+
+    def precache(self: L) -> L:
+        """
+        Force all patterns into the cache
+
+        Returns:
+            self
+        """
+        for key in self.dict:
+            _ = self.dict.__getitem__(key)
+        return self
+
+    def add(
+            self: L,
+            other: L,
+            use_ours: Callable[[str], bool] = lambda name: False,
+            use_theirs: Callable[[str], bool] = lambda name: False,
+            ) -> L:
+        """
+        Add keys from another library into this one.
+
+        Args:
+            other: The library to insert keys from
+            use_ours: Decision function for name conflicts, called with cell name.
+                Should return `True` if the value from `self` should be used.
+            use_theirs: Decision function for name conflicts. Same format as `use_ours`.
+                Should return `True` if the value from `other` should be used.
+                `use_ours` takes priority over `use_theirs`.
+        Returns:
+            self
+        """
+        duplicates = set(self.keys()) & set(other.keys())
+        keep_ours = set(name for name in duplicates if use_ours(name))
+        keep_theirs = set(name for name in duplicates - keep_ours if use_theirs(name))
+        conflicts = duplicates - keep_ours - keep_theirs
+
+        if conflicts:
+            raise LibraryError('Unresolved duplicate keys encountered in library merge: ' + pformat(conflicts))
+
+        for key in set(other.keys()) - keep_ours:
+            self.dict[key] = other.dict[key]
+            if key in other.cache:
+                self.cache[key] = other.cache[key]
+
+        return self
+
+    def clear_cache(self: L) -> L:
+        """
+        Clear the cache of this library.
+        This is usually used before modifying or deleting cells, e.g. when merging
+          with another library.
+
+        Returns:
+            self
+        """
+        self.cache.clear()
+        return self
+
+    def referenced_patterns(
+            self,
+            tops: Union[str, Sequence[str]],
+            skip: Optional[Set[Optional[str]]] = None,
+            ) -> Set[Optional[str]]:
+        """
+        Get the set of all pattern names referenced by `top`. Recursively traverses into any subpatterns.
+
+        Args:
+            top: Name of the top pattern(s) to check.
+            skip: Memo, set patterns which have already been traversed.
+
+        Returns:
+            Set of all referenced pattern names
+        """
+        if skip is None:
+            skip = set([None])
+
+        if isinstance(tops, str):
+            tops = (tops,)
+
+        # Get referenced patterns for all tops
+        targets = set()
+        for top in set(tops):
+            targets |= self[top].referenced_patterns()
+
+        # Perform recursive lookups, but only once for each name
+        for target in targets - skip:
+            assert(target is not None)
+            self.referenced_patterns(target, skip)
+            skip.add(target)
+
+        return targets
+
+    def subtree(
+            self: L,
+            tops: Union[str, Sequence[str]],
+            ) -> L:
+        """
+         Return a new `Library`, containing only the specified patterns and the patterns they
+        reference (recursively).
+
+        Args:
+            tops: Name(s) of patterns to keep
+
+        Returns:
+            A `Library` containing only `tops` and the patterns they reference.
+        """
+        keep: Set[str] = self.referenced_patterns(tops) - set((None,))      # type: ignore
+
+        new = type(self)()
+        for key in keep:
+            new.dict[key] = self.dict[key]
+            if key in self.cache:
+                new.cache[key] = self.cache[key]
+
+        return new
+
+    def dfs(
+            self: L,
+            top: str,
+            visit_before: visitor_function_t = None,
+            visit_after: visitor_function_t = None,
+            transform: Union[ArrayLike, bool, None] = False,
+            memo: Optional[Dict] = None,
+            hierarchy: Tuple[str, ...] = (),
+            ) -> L:
+        """
+        Convenience function.
+        Performs a depth-first traversal of a pattern and its subpatterns.
+        At each pattern in the tree, the following sequence is called:
+            ```
+            current_pattern = visit_before(current_pattern, **vist_args)
+            for sp in current_pattern.subpatterns]
+                self.dfs(sp.target, visit_before, visit_after, updated_transform,
+                         memo, (current_pattern,) + hierarchy)
+            current_pattern = visit_after(current_pattern, **visit_args)
+            ```
+          where `visit_args` are
+            `hierarchy`:  (top_pattern, L1_pattern, L2_pattern, ..., parent_pattern)
+                          tuple of all parent-and-higher patterns
+            `transform`:  numpy.ndarray containing cumulative
+                          [x_offset, y_offset, rotation (rad), mirror_x (0 or 1)]
+                          for the instance being visited
+            `memo`:  Arbitrary dict (not altered except by `visit_before()` and `visit_after()`)
+
+        Args:
+            top: Name of the pattern to start at (root node of the tree).
+            visit_before: Function to call before traversing subpatterns.
+                Should accept a `Pattern` and `**visit_args`, and return the (possibly modified)
+                pattern. Default `None` (not called).
+            visit_after: Function to call after traversing subpatterns.
+                Should accept a `Pattern` and `**visit_args`, and return the (possibly modified)
+                pattern. Default `None` (not called).
+            transform: Initial value for `visit_args['transform']`.
+                Can be `False`, in which case the transform is not calculated.
+                `True` or `None` is interpreted as `[0, 0, 0, 0]`.
+            memo: Arbitrary dict for use by `visit_*()` functions. Default `None` (empty dict).
+            hierarchy: Tuple of patterns specifying the hierarchy above the current pattern.
+                Appended to the start of the generated `visit_args['hierarchy']`.
+                Default is an empty tuple.
+
+        Returns:
+            self
+        """
+        if memo is None:
+            memo = {}
+
+        if transform is None or transform is True:
+            transform = numpy.zeros(4)
+        elif transform is not False:
+            transform = numpy.array(transform)
+
+        if top in hierarchy:
+            raise PatternError('.dfs() called on pattern with circular reference')
+
+        pat = self[top]
+        if visit_before is not None:
+            pat = visit_before(pat, hierarchy=hierarchy, memo=memo, transform=transform)        # type: ignore
+
+        for subpattern in pat.subpatterns:
+            if transform is not False:
+                sign = numpy.ones(2)
+                if transform[3]:
+                    sign[1] = -1
+                xy = numpy.dot(rotation_matrix_2d(transform[2]), subpattern.offset * sign)
+                mirror_x, angle = normalize_mirror(subpattern.mirrored)
+                angle += subpattern.rotation
+                sp_transform = transform + (xy[0], xy[1], angle, mirror_x)
+                sp_transform[3] %= 2
+            else:
+                sp_transform = False
+
+            if subpattern.target is None:
+                continue
+
+            self.dfs(
+                top=subpattern.target,
+                visit_before=visit_before,
+                visit_after=visit_after,
+                transform=sp_transform,
+                memo=memo,
+                hierarchy=hierarchy + (top,),
+                )
+
+        if visit_after is not None:
+            pat = visit_after(pat, hierarchy=hierarchy, memo=memo, transform=transform)         # type: ignore
+
+        self[top] = lambda: pat
+        return self
+
+    def polygonize(
+            self: L,
+            poly_num_points: Optional[int] = None,
+            poly_max_arclen: Optional[float] = None,
+            ) -> L:
+        """
+        Calls `.polygonize(...)` on each pattern in this library.
+        Arguments are passed on to `shape.to_polygons(...)`.
+
+        Args:
+            poly_num_points: Number of points to use for each polygon. Can be overridden by
+                `poly_max_arclen` if that results in more points. Optional, defaults to shapes'
+                internal defaults.
+            poly_max_arclen: Maximum arclength which can be approximated by a single line
+             segment. Optional, defaults to shapes' internal defaults.
+
+        Returns:
+            self
+        """
+        for pat in self.values():
+            pat.polygonize(poly_num_points, poly_max_arclen)
+        return self
+
+    def manhattanize(
+            self: L,
+            grid_x: ArrayLike,
+            grid_y: ArrayLike,
+            ) -> L:
+        """
+        Calls `.manhattanize(grid_x, grid_y)` on each pattern in this library.
+
+        Args:
+            grid_x: List of allowed x-coordinates for the Manhattanized polygon edges.
+            grid_y: List of allowed y-coordinates for the Manhattanized polygon edges.
+
+        Returns:
+            self
+        """
+        for pat in self.values():
+            pat.manhattanize(grid_x, grid_y)
+        return self
+
+    def subpatternize(
+            self: L,
+            norm_value: int = int(1e6),
+            exclude_types: Tuple[Type] = (Polygon,),
+            label2name: Optional[Callable[[Tuple], str]] = None,
+            threshold: int = 2,
+            ) -> L:
+        """
+        Iterates through all `Pattern`s. Within each `Pattern`, it iterates
+         over all shapes, calling `.normalized_form(norm_value)` on them to retrieve a scale-,
+         offset-, dose-, and rotation-independent form. Each shape whose normalized form appears
+         more than once is removed and re-added using subpattern objects referencing a newly-created
+         `Pattern` containing only the normalized form of the shape.
+
+        Note:
+            The default norm_value was chosen to give a reasonable precision when using
+            integer values for coordinates.
+
+        Args:
+            norm_value: Passed to `shape.normalized_form(norm_value)`. Default `1e6` (see function
+                note)
+            exclude_types: Shape types passed in this argument are always left untouched, for
+                speed or convenience. Default: `(shapes.Polygon,)`
+            label2name: Given a label tuple as returned by `shape.normalized_form(...)`, pick
+                a name for the generated pattern. Default `self.get_name('_shape')`.
+            threshold: Only replace shapes with subpatterns if there will be at least this many
+                instances.
+
+        Returns:
+            self
+        """
+        # This currently simplifies globally (same shape in different patterns is
+        # merged into the same subpattern target.
+
+        if exclude_types is None:
+            exclude_types = ()
+
+        if label2name is None:
+            label2name = lambda label: self.get_name('_shape')
+
+
+        shape_counts: MutableMapping[Tuple, int] = defaultdict(int)
+        shape_funcs = {}
+
+        ### First pass ###
+        #  Using the label tuple from `.normalized_form()` as a key, check how many of each shape
+        # are present and store the shape function for each one
+        for pat in tuple(self.values()):
+            for i, shape in enumerate(pat.shapes):
+                if not any(isinstance(shape, t) for t in exclude_types):
+                    label, _values, func = shape.normalized_form(norm_value)
+                    shape_funcs[label] = func
+                    shape_counts[label] += 1
+
+        shape_pats = {}
+        for label, count in shape_counts.items():
+            if count < threshold:
+                continue
+
+            shape_func = shape_funcs[label]
+            shape_pat = Pattern(shapes=[shape_func()])
+            shape_pats[label] = shape_pat
+
+        ### Second pass ###
+        for pat in tuple(self.values()):
+            #  Store `[(index_in_shapes, values_from_normalized_form), ...]` for all shapes which
+            # are to be replaced.
+            # The `values` are `(offset, scale, rotation, dose)`.
+
+            shape_table: MutableMapping[Tuple, List] = defaultdict(list)
+            for i, shape in enumerate(pat.shapes):
+                if any(isinstance(shape, t) for t in exclude_types):
+                    continue
+
+                label, values, _func = shape.normalized_form(norm_value)
+
+                if label not in shape_pats:
+                    continue
+
+                shape_table[label].append((i, values))
+
+            #  For repeated shapes, create a `Pattern` holding a normalized shape object,
+            # and add `pat.subpatterns` entries for each occurrence in pat. Also, note down that
+            # we should delete the `pat.shapes` entries for which we made SubPatterns.
+            shapes_to_remove = []
+            for label in shape_table:
+                target = label2name(label)
+                for i, values in shape_table[label]:
+                    offset, scale, rotation, mirror_x, dose = values
+                    pat.addsp(target=target, offset=offset, scale=scale,
+                              rotation=rotation, dose=dose, mirrored=(mirror_x, False))
+                    shapes_to_remove.append(i)
+
+            # Remove any shapes for which we have created subpatterns.
+            for i in sorted(shapes_to_remove, reverse=True):
+                del pat.shapes[i]
+
+        for ll, pp in shape_pats.items():
+            self[label2name(ll)] = lambda: pp
+
+        return self
+
+    def wrap_repeated_shapes(
+            self: L,
+            name_func: Optional[Callable[['Pattern', Union[Shape, Label]], str]] = None,
+            ) -> L:
+        """
+        Wraps all shapes and labels with a non-`None` `repetition` attribute
+          into a `SubPattern`/`Pattern` combination, and applies the `repetition`
+          to each `SubPattern` instead of its contained shape.
+
+        Args:
+            name_func: Function f(this_pattern, shape) which generates a name for the
+                        wrapping pattern. Default is `self.get_name('_rep')`.
+
+        Returns:
+            self
+        """
+        if name_func is None:
+            name_func = lambda _pat, _shape: self.get_name('_rep')
+
+        for pat in tuple(self.values()):
+            new_shapes = []
+            for shape in pat.shapes:
+                if shape.repetition is None:
+                    new_shapes.append(shape)
+                    continue
+
+                name = name_func(pat, shape)
+                self[name] = lambda: Pattern(shapes=[shape])
+                pat.addsp(name, repetition=shape.repetition)
+                shape.repetition = None
+            pat.shapes = new_shapes
+
+            new_labels = []
+            for label in pat.labels:
+                if label.repetition is None:
+                    new_labels.append(label)
+                    continue
+                name = name_func(pat, label)
+                self[name] = lambda: Pattern(labels=[label])
+                pat.addsp(name, repetition=label.repetition)
+                label.repetition = None
+            pat.labels = new_labels
+
+        return self
+
+    def flatten(
+            self: L,
+            tops: Union[str, Sequence[str]],
+            ) -> Dict[str, Pattern]:
+        """
+        Removes all subpatterns and adds equivalent shapes.
+        Also flattens all subpatterns.
+
+        Args:
+            tops: The pattern(s) to flattern.
+
+        Returns:
+            {name: flat_pattern} mapping for all flattened patterns.
+        """
+        if isinstance(tops, str):
+            tops = (tops,)
+
+        flattened: Dict[str, Optional[Pattern]] = {}
+
+        def flatten_single(name) -> None:
+            flattened[name] = None
+            pat = self[name].deepcopy()
+
+            for subpat in pat.subpatterns:
+                target = subpat.target
+                if target is None:
+                    continue
+
+                if target not in flattened:
+                    flatten_single(target)
+                if flattened[target] is None:
+                    raise PatternError(f'Circular reference in {name} to {target}')
+
+                p = subpat.as_pattern(pattern=flattened[target])
+                pat.append(p)
+
+            pat.subpatterns.clear()
+            flattened[name] = pat
+
+        for top in tops:
+            flatten_single(top)
+
+        assert(None not in flattened.values())
+        return flattened    # type: ignore
+
+    def get_name(
+            self,
+            name: str = '__',
+            sanitize: bool = True,
+            max_length: int = 32,
+            quiet: bool = False,
+            ) -> str:
+        """
+        Find a unique name for the pattern.
+
+        This function may be overridden in a subclass or monkey-patched to fit the caller's requirements.
+
+        Args:
+            name: Preferred name for the pattern. Default '__'.
+            sanitize: Allows only alphanumeric charaters and _?$. Replaces invalid characters with underscores.
+            max_length: Names longer than this will be truncated.
+            quiet: If `True`, suppress log messages.
+
+        Returns:
+            Unique name for this library.
+        """
+        if sanitize:
+            # Remove invalid characters
+            sanitized_name = re.compile(r'[^A-Za-z0-9_\?\$]').sub('_', name)
+        else:
+            sanitized_name = name
+
+        ii = 0
+        suffixed_name = sanitized_name
+        while suffixed_name in self or suffixed_name == '':
+            suffix = base64.b64encode(struct.pack('>Q', ii), b'$?').decode('ASCII')
+
+            suffixed_name = sanitized_name + '$' + suffix[:-1].lstrip('A')
+            ii += 1
+
+        if len(suffixed_name) > max_length:
+            if name == '':
+                raise LibraryError(f'No valid pattern names remaining within the specified {max_length=}')
+
+            cropped_name = self.get_name(sanitized_name[:-1], sanitize=sanitize, max_length=max_length, quiet=True)
+        else:
+            cropped_name = suffixed_name
+
+        if not quiet:
+            logger.info(f'Requested name "{name}" changed to "{cropped_name}"')
+
+        return cropped_name
+
+    def find_toplevel(self) -> List[str]:
+        """
+        Return the list of all patterns that are not referenced by any other pattern in the library.
+
+        Returns:
+            A list of pattern names in which no pattern is referenced by any other pattern.
+        """
+        names = set(self.keys())
+        not_toplevel: Set[Optional[str]] = set()
+        for name in names:
+            not_toplevel |= set(sp.target for sp in self[name].subpatterns)
+
+        toplevel = list(names - not_toplevel)
+        return toplevel
+
+    def __deepcopy__(self, memo: Dict = None) -> 'Library':
+        raise LibraryError('Libraries cannot be deepcopied (deepcopy doesn\'t descend into closures)')

masque/library/__init__.py

@@ -1,2 +0,0 @@
-from .library import Library, PatternGenerator
-from .device_library import DeviceLibrary, LibDeviceLibrary

masque/library/library.py

@@ -1,355 +0,0 @@
-"""
-Library class for managing unique name->pattern mappings and
- deferred loading or creation.
-"""
-from typing import Dict, Callable, TypeVar, TYPE_CHECKING
-from typing import Any, Tuple, Union, Iterator
-import logging
-from pprint import pformat
-from dataclasses import dataclass
-import copy
-
-from ..error import LibraryError
-
-if TYPE_CHECKING:
-    from ..pattern import Pattern
-
-
-logger = logging.getLogger(__name__)
-
-
-@dataclass
-class PatternGenerator:
-    __slots__ = ('tag', 'gen')
-    tag: str
-    """ Unique identifier for the source """
-
-    gen: Callable[[], 'Pattern']
-    """ Function which generates a pattern when called """
-
-
-L = TypeVar('L', bound='Library')
-
-
-class Library:
-    """
-    This class is usually used to create a library of Patterns by mapping names to
-     functions which generate or load the relevant `Pattern` object as-needed.
-
-    Generated/loaded patterns can have "symbolic" references, where a SubPattern
-     object `sp` has a `None`-valued `sp.pattern` attribute, in which case the
-     Library expects `sp.identifier[0]` to contain a string which specifies the
-     referenced pattern's name.
-
-    Patterns can either be "primary" (default) or "secondary". Both get the
-     same deferred-load behavior, but "secondary" patterns may have conflicting
-     names and are not accessible through basic []-indexing. They are only used
-     to fill symbolic references in cases where there is no "primary" pattern
-     available, and only if both the referencing and referenced pattern-generators'
-     `tag` values match (i.e., only if they came from the same source).
-
-    Primary patterns can be turned into secondary patterns with the `demote`
-     method, `promote` performs the reverse (secondary -> primary) operation.
-
-    The `set_const` and `set_value` methods provide an easy way to transparently
-      construct PatternGenerator objects and directly set create "secondary"
-      patterns.
-
-    The cache can be disabled by setting the `enable_cache` attribute to `False`.
-    """
-    primary: Dict[str, PatternGenerator]
-    secondary: Dict[Tuple[str, str], PatternGenerator]
-    cache: Dict[Union[str, Tuple[str, str]], 'Pattern']
-    enable_cache: bool = True
-
-    def __init__(self) -> None:
-        self.primary = {}
-        self.secondary = {}
-        self.cache = {}
-
-    def __setitem__(self, key: str, value: PatternGenerator) -> None:
-        self.primary[key] = value
-        if key in self.cache:
-            logger.warning(f'Replaced library item "{key}" & existing cache entry.'
-                           ' Previously-generated Pattern will *not* be updated!')
-            del self.cache[key]
-
-    def __delitem__(self, key: str) -> None:
-        if isinstance(key, str):
-            del self.primary[key]
-        elif isinstance(key, tuple):
-            del self.secondary[key]
-
-        if key in self.cache:
-            logger.warning(f'Deleting library item "{key}" & existing cache entry.'
-                           ' Previously-generated Pattern may remain in the wild!')
-            del self.cache[key]
-
-    def __getitem__(self, key: str) -> 'Pattern':
-        return self.get_primary(key)
-
-    def __iter__(self) -> Iterator[str]:
-        return iter(self.keys())
-
-    def __contains__(self, key: str) -> bool:
-        return key in self.primary
-
-    def get_primary(self, key: str) -> 'Pattern':
-        if self.enable_cache and key in self.cache:
-            logger.debug(f'found {key} in cache')
-            return self.cache[key]
-
-        logger.debug(f'loading {key}')
-        pg = self.primary[key]
-        pat = pg.gen()
-        self.resolve_subpatterns(pat, pg.tag)
-        self.cache[key] = pat
-        return pat
-
-    def get_secondary(self, key: str, tag: str) -> 'Pattern':
-        logger.debug(f'get_secondary({key}, {tag})')
-        key2 = (key, tag)
-        if self.enable_cache and key2 in self.cache:
-            return self.cache[key2]
-
-        pg = self.secondary[key2]
-        pat = pg.gen()
-        self.resolve_subpatterns(pat, pg.tag)
-        self.cache[key2] = pat
-        return pat
-
-    def set_secondary(self, key: str, tag: str, value: PatternGenerator) -> None:
-        self.secondary[(key, tag)] = value
-        if (key, tag) in self.cache:
-            logger.warning(f'Replaced library item "{key}" & existing cache entry.'
-                           ' Previously-generated Pattern will *not* be updated!')
-            del self.cache[(key, tag)]
-
-    def resolve_subpatterns(self, pat: 'Pattern', tag: str) -> 'Pattern':
-        logger.debug(f'Resolving subpatterns in {pat.name}')
-        for sp in pat.subpatterns:
-            if sp.pattern is not None:
-                continue
-
-            key = sp.identifier[0]
-            if key in self.primary:
-                sp.pattern = self.get_primary(key)
-                continue
-
-            if (key, tag) in self.secondary:
-                sp.pattern = self.get_secondary(key, tag)
-                continue
-
-            raise LibraryError(f'Broken reference to {key} (tag {tag})')
-        return pat
-
-    def keys(self) -> Iterator[str]:
-        return iter(self.primary.keys())
-
-    def values(self) -> Iterator['Pattern']:
-        return iter(self[key] for key in self.keys())
-
-    def items(self) -> Iterator[Tuple[str, 'Pattern']]:
-        return iter((key, self[key]) for key in self.keys())
-
-    def __repr__(self) -> str:
-        return '<Library with keys ' + repr(list(self.primary.keys())) + '>'
-
-    def set_const(
-            self,
-            key: str,
-            tag: Any,
-            const: 'Pattern',
-            secondary: bool = False,
-            ) -> None:
-        """
-        Convenience function to avoid having to manually wrap
-         constant values into callables.
-
-        Args:
-            key: Lookup key, usually the cell/pattern name
-            tag: Unique tag for the source, used to disambiguate secondary patterns
-            const: Pattern object to return
-            secondary: If True, this pattern is not accessible for normal lookup, and is
-                        only used as a sub-component of other patterns if no non-secondary
-                        equivalent is available.
-        """
-        pg = PatternGenerator(tag=tag, gen=lambda: const)
-        if secondary:
-            self.secondary[(key, tag)] = pg
-        else:
-            self.primary[key] = pg
-
-    def set_value(
-            self,
-            key: str,
-            tag: str,
-            value: Callable[[], 'Pattern'],
-            secondary: bool = False,
-            ) -> None:
-        """
-        Convenience function to automatically build a PatternGenerator.
-
-        Args:
-            key: Lookup key, usually the cell/pattern name
-            tag: Unique tag for the source, used to disambiguate secondary patterns
-            value: Callable which takes no arguments and generates the `Pattern` object
-            secondary: If True, this pattern is not accessible for normal lookup, and is
-                        only used as a sub-component of other patterns if no non-secondary
-                        equivalent is available.
-        """
-        pg = PatternGenerator(tag=tag, gen=value)
-        if secondary:
-            self.secondary[(key, tag)] = pg
-        else:
-            self.primary[key] = pg
-
-    def precache(self: L) -> L:
-        """
-        Force all patterns into the cache
-
-        Returns:
-            self
-        """
-        for key in self.primary:
-            _ = self.get_primary(key)
-        for key2 in self.secondary:
-            _ = self.get_secondary(*key2)
-        return self
-
-    def add(
-            self: L,
-            other: L,
-            use_ours: Callable[[Union[str, Tuple[str, str]]], bool] = lambda name: False,
-            use_theirs: Callable[[Union[str, Tuple[str, str]]], bool] = lambda name: False,
-            ) -> L:
-        """
-        Add keys from another library into this one.
-
-        Args:
-            other: The library to insert keys from
-            use_ours: Decision function for name conflicts.
-                May be called with cell names and (name, tag) tuples for primary or
-                secondary cells, respectively.
-                Should return `True` if the value from `self` should be used.
-            use_theirs: Decision function for name conflicts. Same format as `use_ours`.
-                Should return `True` if the value from `other` should be used.
-                `use_ours` takes priority over `use_theirs`.
-        Returns:
-            self
-        """
-        duplicates1 = set(self.primary.keys()) & set(other.primary.keys())
-        duplicates2 = set(self.secondary.keys()) & set(other.secondary.keys())
-        keep_ours1 = set(name for name in duplicates1 if use_ours(name))
-        keep_ours2 = set(name for name in duplicates2 if use_ours(name))
-        keep_theirs1 = set(name for name in duplicates1 - keep_ours1 if use_theirs(name))
-        keep_theirs2 = set(name for name in duplicates2 - keep_ours2 if use_theirs(name))
-        conflicts1 = duplicates1 - keep_ours1 - keep_theirs1
-        conflicts2 = duplicates2 - keep_ours2 - keep_theirs2
-
-        if conflicts1:
-            raise LibraryError('Unresolved duplicate keys encountered in library merge: ' + pformat(conflicts1))
-
-        if conflicts2:
-            raise LibraryError('Unresolved duplicate secondary keys encountered in library merge: ' + pformat(conflicts2))
-
-        for key1 in set(other.primary.keys()) - keep_ours1:
-            self[key1] = other.primary[key1]
-            if key1 in other.cache:
-                self.cache[key1] = other.cache[key1]
-
-        for key2 in set(other.secondary.keys()) - keep_ours2:
-            self.set_secondary(*key2, other.secondary[key2])
-            if key2 in other.cache:
-                self.cache[key2] = other.cache[key2]
-
-        return self
-
-    def demote(self, key: str) -> None:
-        """
-        Turn a primary pattern into a secondary one.
-        It will no longer be accessible through [] indexing and will only be used to
-          when referenced by other patterns from the same source, and only if no primary
-          pattern with the same name exists.
-
-        Args:
-            key: Lookup key, usually the cell/pattern name
-        """
-        pg = self.primary[key]
-        key2 = (key, pg.tag)
-        self.secondary[key2] = pg
-        if key in self.cache:
-            self.cache[key2] = self.cache[key]
-        del self[key]
-
-    def promote(self, key: str, tag: str) -> None:
-        """
-        Turn a secondary pattern into a primary one.
-        It will become accessible through [] indexing and will be used to satisfy any
-          reference to a pattern with its key, regardless of tag.
-
-        Args:
-            key: Lookup key, usually the cell/pattern name
-            tag: Unique tag for identifying the pattern's source, used to disambiguate
-                    secondary patterns
-        """
-        if key in self.primary:
-            raise LibraryError(f'Promoting ({key}, {tag}), but {key} already exists in primary!')
-
-        key2 = (key, tag)
-        pg = self.secondary[key2]
-        self.primary[key] = pg
-        if key2 in self.cache:
-            self.cache[key] = self.cache[key2]
-        del self.secondary[key2]
-        del self.cache[key2]
-
-    def copy(self, preserve_cache: bool = False) -> 'Library':
-        """
-        Create a copy of this `Library`.
-
-        A shallow copy is made of the contained dicts.
-        Note that you should probably clear the cache (with `clear_cache()`) after copying.
-
-        Returns:
-            A copy of self
-        """
-        new = Library()
-        new.primary.update(self.primary)
-        new.secondary.update(self.secondary)
-        new.cache.update(self.cache)
-        return new
-
-    def clear_cache(self: L) -> L:
-        """
-        Clear the cache of this library.
-        This is usually used before modifying or deleting cells, e.g. when merging
-          with another library.
-
-        Returns:
-            self
-        """
-        self.cache = {}
-        return self
-
-
-r"""
-    #   Add a filter for names which aren't added
-
-  - Registration:
-    - scanned files (tag=filename, gen_fn[stream, {name: pos}])
-    - generator functions (tag='fn?', gen_fn[params])
-    - merge decision function (based on tag and cell name, can be "neither") ??? neither=keep both, load using same tag!
-  - Load process:
-    - file:
-        - read single cell
-        - check subpat identifiers, and load stuff recursively based on those. If not present, load from same file??
-    - function:
-        - generate cell
-        - traverse and check if we should load any subcells from elsewhere. replace if so.
-            * should fn generate subcells at all, or register those separately and have us control flow? maybe ask us and generate itself if not present?
-
-  - Scan all GDS files, save name -> (file, position). Keep the streams handy.
-  - Merge all names. This requires subcell merge because we don't know hierarchy.
-      - possibly include a "neither" option during merge, to deal with subcells. Means: just use parent's file.
-"""

masque/pattern.py

@@ -3,9 +3,8 @@
 """
 
 from typing import List, Callable, Tuple, Dict, Union, Set, Sequence, Optional, Type, overload, cast
-from typing import MutableMapping, Iterable, TypeVar, Any
+from typing import Mapping, MutableMapping, Iterable, TypeVar, Any
 import copy
-import pickle
 from itertools import chain
 from collections import defaultdict
 
@@ -18,23 +17,20 @@ from .subpattern import SubPattern
 from .shapes import Shape, Polygon
 from .label import Label
 from .utils import rotation_matrix_2d, normalize_mirror, AutoSlots, annotations_t
-from .error import PatternError, PatternLockedError
-from .traits import LockableImpl, AnnotatableImpl, Scalable, Mirrorable
+from .error import PatternError
+from .traits import AnnotatableImpl, Scalable, Mirrorable
 from .traits import Rotatable, Positionable
 
 
-visitor_function_t = Callable[['Pattern', Tuple['Pattern'], Dict, NDArray[numpy.float64]], 'Pattern']
-
-
 P = TypeVar('P', bound='Pattern')
 
 
-class Pattern(LockableImpl, AnnotatableImpl, Mirrorable, metaclass=AutoSlots):
+class Pattern(AnnotatableImpl, Mirrorable, metaclass=AutoSlots):
     """
     2D layout consisting of some set of shapes, labels, and references to other Pattern objects
      (via SubPattern). Shapes are assumed to inherit from masque.shapes.Shape or provide equivalent functions.
     """
-    __slots__ = ('shapes', 'labels', 'subpatterns', 'name')
+    __slots__ = ('shapes', 'labels', 'subpatterns')
 
     shapes: List[Shape]
     """ List of all shapes in this Pattern.
@@ -50,18 +46,13 @@ class Pattern(LockableImpl, AnnotatableImpl, Mirrorable, metaclass=AutoSlots):
       (i.e. multiple instances of the same object).
     """
 
-    name: str
-    """ A name for this pattern """
-
     def __init__(
             self,
-            name: str = '',
             *,
             shapes: Sequence[Shape] = (),
             labels: Sequence[Label] = (),
             subpatterns: Sequence[SubPattern] = (),
             annotations: Optional[annotations_t] = None,
-            locked: bool = False,
             ) -> None:
         """
         Basic init; arguments get assigned to member variables.
@@ -71,10 +62,7 @@ class Pattern(LockableImpl, AnnotatableImpl, Mirrorable, metaclass=AutoSlots):
             shapes: Initial shapes in the Pattern
             labels: Initial labels in the Pattern
             subpatterns: Initial subpatterns in the Pattern
-            name: An identifier for the Pattern
-            locked: Whether to lock the pattern after construction
         """
-        LockableImpl.unlock(self)
         if isinstance(shapes, list):
             self.shapes = shapes
         else:
@@ -91,41 +79,25 @@ class Pattern(LockableImpl, AnnotatableImpl, Mirrorable, metaclass=AutoSlots):
             self.subpatterns = list(subpatterns)
 
         self.annotations = annotations if annotations is not None else {}
-        self.name = name
-        self.set_locked(locked)
 
     def __copy__(self, memo: Dict = None) -> 'Pattern':
-        return Pattern(name=self.name,
-                       shapes=copy.deepcopy(self.shapes),
-                       labels=copy.deepcopy(self.labels),
-                       subpatterns=[copy.copy(sp) for sp in self.subpatterns],
-                       annotations=copy.deepcopy(self.annotations),
-                       locked=self.locked)
+        return Pattern(
+            shapes=copy.deepcopy(self.shapes),
+            labels=copy.deepcopy(self.labels),
+            subpatterns=[copy.copy(sp) for sp in self.subpatterns],
+            annotations=copy.deepcopy(self.annotations),
+            )
 
     def __deepcopy__(self, memo: Dict = None) -> 'Pattern':
         memo = {} if memo is None else memo
         new = Pattern(
-            name=self.name,
             shapes=copy.deepcopy(self.shapes, memo),
             labels=copy.deepcopy(self.labels, memo),
             subpatterns=copy.deepcopy(self.subpatterns, memo),
             annotations=copy.deepcopy(self.annotations, memo),
-            locked=self.locked)
+            )
         return new
 
-    def rename(self: P, name: str) -> P:
-        """
-        Chainable function for renaming the pattern.
-
-        Args:
-            name: The new name
-
-        Returns:
-            self
-        """
-        self.name = name
-        return self
-
     def append(self: P, other_pattern: P) -> P:
         """
         Appends all shapes, labels and subpatterns from other_pattern to self's shapes,
@@ -144,10 +116,9 @@ class Pattern(LockableImpl, AnnotatableImpl, Mirrorable, metaclass=AutoSlots):
 
     def subset(
             self,
-            shapes_func: Callable[[Shape], bool] = None,
-            labels_func: Callable[[Label], bool] = None,
-            subpatterns_func: Callable[[SubPattern], bool] = None,
-            recursive: bool = False,
+            shapes: Callable[[Shape], bool] = None,
+            labels: Callable[[Label], bool] = None,
+            subpatterns: Callable[[SubPattern], bool] = None,
             ) -> 'Pattern':
         """
         Returns a Pattern containing only the entities (e.g. shapes) for which the
@@ -155,169 +126,24 @@ class Pattern(LockableImpl, AnnotatableImpl, Mirrorable, metaclass=AutoSlots):
         Self is _not_ altered, but shapes, labels, and subpatterns are _not_ copied.
 
         Args:
-            shapes_func: Given a shape, returns a boolean denoting whether the shape is a member
+            shapes: Given a shape, returns a boolean denoting whether the shape is a member
                 of the subset. Default always returns False.
-            labels_func: Given a label, returns a boolean denoting whether the label is a member
+            labels: Given a label, returns a boolean denoting whether the label is a member
                 of the subset. Default always returns False.
-            subpatterns_func: Given a subpattern, returns a boolean denoting if it is a member
+            subpatterns: Given a subpattern, returns a boolean denoting if it is a member
                 of the subset. Default always returns False.
-            recursive: If True, also calls .subset() recursively on patterns referenced by this
-                pattern.
 
         Returns:
             A Pattern containing all the shapes and subpatterns for which the parameter
                 functions return True
         """
-        def do_subset(src: Optional['Pattern']) -> Optional['Pattern']:
-            if src is None:
-                return None
-            pat = Pattern(name=src.name)
-            if shapes_func is not None:
-                pat.shapes = [s for s in src.shapes if shapes_func(s)]
-            if labels_func is not None:
-                pat.labels = [s for s in src.labels if labels_func(s)]
-            if subpatterns_func is not None:
-                pat.subpatterns = [s for s in src.subpatterns if subpatterns_func(s)]
-            return pat
-
-        if recursive:
-            pat = self.apply(do_subset)
-        else:
-            pat = do_subset(self)
-
-        assert(pat is not None)
-        return pat
-
-    def apply(
-            self,
-            func: Callable[[Optional['Pattern']], Optional['Pattern']],
-            memo: Optional[Dict[int, Optional['Pattern']]] = None,
-            ) -> Optional['Pattern']:
-        """
-        Recursively apply func() to this pattern and any pattern it references.
-        func() is expected to take and return a Pattern.
-        func() is first applied to the pattern as a whole, then any referenced patterns.
-        It is only applied to any given pattern once, regardless of how many times it is
-            referenced.
-
-        Args:
-            func: Function which accepts a Pattern, and returns a pattern.
-            memo: Dictionary used to avoid re-running on multiply-referenced patterns.
-                Stores `{id(pattern): func(pattern)}` for patterns which have already been processed.
-                Default `None` (no already-processed patterns).
-
-        Returns:
-            The result of applying func() to this pattern and all subpatterns.
-
-        Raises:
-            PatternError if called on a pattern containing a circular reference.
-        """
-        if memo is None:
-            memo = {}
-
-        pat_id = id(self)
-        if pat_id not in memo:
-            memo[pat_id] = None
-            pat = func(self)
-            if pat is not None:
-                for subpat in pat.subpatterns:
-                    if subpat.pattern is None:
-                        subpat.pattern = func(None)
-                    else:
-                        subpat.pattern = subpat.pattern.apply(func, memo)
-            memo[pat_id] = pat
-        elif memo[pat_id] is None:
-            raise PatternError('.apply() called on pattern with circular reference')
-        else:
-            pat = memo[pat_id]
-        return pat
-
-    def dfs(
-            self: P,
-            visit_before: visitor_function_t = None,
-            visit_after: visitor_function_t = None,
-            transform: Union[ArrayLike, bool, None] = False,
-            memo: Optional[Dict] = None,
-            hierarchy: Tuple[P, ...] = (),
-            ) -> P:
-        """
-        Convenience function.
-        Performs a depth-first traversal of this pattern and its subpatterns.
-        At each pattern in the tree, the following sequence is called:
-            ```
-            current_pattern = visit_before(current_pattern, **vist_args)
-            for sp in current_pattern.subpatterns]
-                sp.pattern = sp.pattern.df(visit_before, visit_after, updated_transform,
-                                           memo, (current_pattern,) + hierarchy)
-            current_pattern = visit_after(current_pattern, **visit_args)
-            ```
-          where `visit_args` are
-            `hierarchy`:  (top_pattern, L1_pattern, L2_pattern, ..., parent_pattern)
-                          tuple of all parent-and-higher patterns
-            `transform`:  numpy.ndarray containing cumulative
-                          [x_offset, y_offset, rotation (rad), mirror_x (0 or 1)]
-                          for the instance being visited
-            `memo`:  Arbitrary dict (not altered except by visit_*())
-
-        Args:
-            visit_before: Function to call before traversing subpatterns.
-                Should accept a `Pattern` and `**visit_args`, and return the (possibly modified)
-                pattern. Default `None` (not called).
-            visit_after: Function to call after traversing subpatterns.
-                Should accept a Pattern and **visit_args, and return the (possibly modified)
-                pattern. Default `None` (not called).
-            transform: Initial value for `visit_args['transform']`.
-                Can be `False`, in which case the transform is not calculated.
-                `True` or `None` is interpreted as `[0, 0, 0, 0]`.
-            memo: Arbitrary dict for use by `visit_*()` functions. Default `None` (empty dict).
-            hierarchy: Tuple of patterns specifying the hierarchy above the current pattern.
-                Appended to the start of the generated `visit_args['hierarchy']`.
-                Default is an empty tuple.
-
-        Returns:
-            The result, including `visit_before(self, ...)` and `visit_after(self, ...)`.
-            Note that `self` may also be altered!
-        """
-        if memo is None:
-            memo = {}
-
-        if transform is None or transform is True:
-            transform = numpy.zeros(4)
-        elif transform is not False:
-            transform = numpy.array(transform)
-
-        if self in hierarchy:
-            raise PatternError('.dfs() called on pattern with circular reference')
-
-        pat = self
-        if visit_before is not None:
-            pat = visit_before(pat, hierarchy=hierarchy, memo=memo, transform=transform)        # type: ignore
-
-        for subpattern in self.subpatterns:
-            if transform is not False:
-                sign = numpy.ones(2)
-                if transform[3]:
-                    sign[1] = -1
-                xy = numpy.dot(rotation_matrix_2d(transform[2]), subpattern.offset * sign)
-                mirror_x, angle = normalize_mirror(subpattern.mirrored)
-                angle += subpattern.rotation
-                sp_transform = transform + (xy[0], xy[1], angle, mirror_x)
-                sp_transform[3] %= 2
-            else:
-                sp_transform = False
-
-            if subpattern.pattern is not None:
-                result = subpattern.pattern.dfs(visit_before=visit_before,
-                                                visit_after=visit_after,
-                                                transform=sp_transform,
-                                                memo=memo,
-                                                hierarchy=hierarchy + (self,))
-                if result is not subpattern.pattern:
-                    # skip assignment to avoid PatternLockedError unless modified
-                    subpattern.pattern = result
-
-        if visit_after is not None:
-            pat = visit_after(pat, hierarchy=hierarchy, memo=memo, transform=transform)         # type: ignore
+        pat = Pattern()
+        if shapes is not None:
+            pat.shapes = [s for s in self.shapes if shapes(s)]
+        if labels is not None:
+            pat.labels = [s for s in self.labels if labels(s)]
+        if subpatterns is not None:
+            pat.subpatterns = [s for s in self.subpatterns if subpatterns(s)]
         return pat
 
     def polygonize(
@@ -326,8 +152,7 @@ class Pattern(LockableImpl, AnnotatableImpl, Mirrorable, metaclass=AutoSlots):
             poly_max_arclen: Optional[float] = None,
             ) -> P:
         """
-        Calls `.to_polygons(...)` on all the shapes in this Pattern and any referenced patterns,
-         replacing them with the returned polygons.
+        Calls `.to_polygons(...)` on all the shapes in this Pattern, replacing them with the returned polygons.
         Arguments are passed directly to `shape.to_polygons(...)`.
 
         Args:
@@ -341,12 +166,9 @@ class Pattern(LockableImpl, AnnotatableImpl, Mirrorable, metaclass=AutoSlots):
             self
         """
         old_shapes = self.shapes
-        self.shapes = list(chain.from_iterable(
-            (shape.to_polygons(poly_num_points, poly_max_arclen)
-             for shape in old_shapes)))
-        for subpat in self.subpatterns:
-            if subpat.pattern is not None:
-                subpat.pattern.polygonize(poly_num_points, poly_max_arclen)
+        self.shapes = list(chain.from_iterable((
+            shape.to_polygons(poly_num_points, poly_max_arclen)
+            for shape in old_shapes)))
         return self
 
     def manhattanize(
@@ -355,7 +177,7 @@ class Pattern(LockableImpl, AnnotatableImpl, Mirrorable, metaclass=AutoSlots):
             grid_y: ArrayLike,
             ) -> P:
         """
-        Calls `.polygonize()` and `.flatten()` on the pattern, then calls `.manhattanize()` on all the
+        Calls `.polygonize()` on the pattern, then calls `.manhattanize()` on all the
          resulting shapes, replacing them with the returned Manhattan polygons.
 
         Args:
@@ -366,84 +188,13 @@ class Pattern(LockableImpl, AnnotatableImpl, Mirrorable, metaclass=AutoSlots):
             self
         """
 
-        self.polygonize().flatten()
+        self.polygonize()
         old_shapes = self.shapes
         self.shapes = list(chain.from_iterable(
             (shape.manhattanize(grid_x, grid_y) for shape in old_shapes)))
         return self
 
-    def subpatternize(
-            self: P,
-            recursive: bool = True,
-            norm_value: int = int(1e6),
-            exclude_types: Tuple[Type] = (Polygon,)
-            ) -> P:
-        """
-        Iterates through this `Pattern` and all referenced `Pattern`s. Within each `Pattern`, it iterates
-         over all shapes, calling `.normalized_form(norm_value)` on them to retrieve a scale-,
-         offset-, dose-, and rotation-independent form. Each shape whose normalized form appears
-         more than once is removed and re-added using subpattern objects referencing a newly-created
-         `Pattern` containing only the normalized form of the shape.
-
-        Note:
-            The default norm_value was chosen to give a reasonable precision when converting
-            to GDSII, which uses integer values for pixel coordinates.
-
-        Args:
-            recursive: Whether to call recursively on self's subpatterns. Default `True`.
-            norm_value: Passed to `shape.normalized_form(norm_value)`. Default `1e6` (see function
-                note about GDSII)
-            exclude_types: Shape types passed in this argument are always left untouched, for
-                speed or convenience. Default: `(shapes.Polygon,)`
-
-        Returns:
-            self
-        """
-
-        if exclude_types is None:
-            exclude_types = ()
-
-        if recursive:
-            for subpat in self.subpatterns:
-                if subpat.pattern is None:
-                    continue
-                subpat.pattern.subpatternize(recursive=True,
-                                             norm_value=norm_value,
-                                             exclude_types=exclude_types)
-
-        # Create a dict which uses the label tuple from `.normalized_form()` as a key, and which
-        #  stores `(function_to_create_normalized_shape, [(index_in_shapes, values), ...])`, where
-        #  values are the `(offset, scale, rotation, dose)` values as calculated by `.normalized_form()`
-        shape_table: MutableMapping[Tuple, List] = defaultdict(lambda: [None, list()])
-        for i, shape in enumerate(self.shapes):
-            if not any((isinstance(shape, t) for t in exclude_types)):
-                label, values, func = shape.normalized_form(norm_value)
-                shape_table[label][0] = func
-                shape_table[label][1].append((i, values))
-
-        # Iterate over the normalized shapes in the table. If any normalized shape occurs more than
-        #  once, create a `Pattern` holding a normalized shape object, and add `self.subpatterns`
-        #  entries for each occurrence in self. Also, note down that we should delete the
-        #  `self.shapes` entries for which we made SubPatterns.
-        shapes_to_remove = []
-        for label in shape_table:
-            if len(shape_table[label][1]) > 1:
-                shape = shape_table[label][0]()
-                pat = Pattern(shapes=[shape])
-
-                for i, values in shape_table[label][1]:
-                    (offset, scale, rotation, mirror_x, dose) = values
-                    self.addsp(pattern=pat, offset=offset, scale=scale,
-                               rotation=rotation, dose=dose, mirrored=(mirror_x, False))
-                    shapes_to_remove.append(i)
-
-        # Remove any shapes for which we have created subpatterns.
-        for i in sorted(shapes_to_remove, reverse=True):
-            del self.shapes[i]
-
-        return self
-
-    def as_polygons(self) -> List[NDArray[numpy.float64]]:
+    def as_polygons(self, library: Mapping[str, Pattern]) -> List[NDArray[numpy.float64]]:
         """
         Represents the pattern as a list of polygons.
 
@@ -454,95 +205,22 @@ class Pattern(LockableImpl, AnnotatableImpl, Mirrorable, metaclass=AutoSlots):
             A list of `(Ni, 2)` `numpy.ndarray`s specifying vertices of the polygons. Each ndarray
              is of the form `[[x0, y0], [x1, y1],...]`.
         """
-        pat = self.deepcopy().deepunlock().polygonize().flatten()
+        pat = self.deepcopy().polygonize().flatten(library=library)
         return [shape.vertices + shape.offset for shape in pat.shapes]      # type: ignore      # mypy can't figure out that shapes are all Polygons now
 
-    @overload
-    def referenced_patterns_by_id(self) -> Dict[int, 'Pattern']:
-        pass
-
-    @overload
-    def referenced_patterns_by_id(self, include_none: bool) -> Dict[int, Optional['Pattern']]:
-        pass
-
-    def referenced_patterns_by_id(
-            self,
-            include_none: bool = False,
-            recursive: bool = True,
-            ) -> Union[Dict[int, Optional['Pattern']],
-                       Dict[int, 'Pattern']]:
-
+    def referenced_patterns(self) -> Set[Optional[str]]:
         """
-        Create a dictionary with `{id(pat): pat}` for all Pattern objects referenced by this
-         Pattern (by default, operates recursively on all referenced Patterns as well).
-
-        Args:
-            include_none: If `True`, references to `None` will be included. Default `False`.
-            recursive: If `True`, operates recursively on all referenced patterns. Default `True`.
+        Get all pattern namers referenced by this pattern. Non-recursive.
 
         Returns:
-            Dictionary with `{id(pat): pat}` for all referenced Pattern objects
+            A set of all pattern names referenced by this pattern.
         """
-        ids: Dict[int, Optional['Pattern']] = {}
-        for subpat in self.subpatterns:
-            pat = subpat.pattern
-            if id(pat) in ids:
-                continue
-            if include_none or pat is not None:
-                ids[id(pat)] = pat
-            if recursive and pat is not None:
-                ids.update(pat.referenced_patterns_by_id())
-        return ids
+        return set(sp.target for sp in self.subpatterns)
 
-    def referenced_patterns_by_name(
+    def get_bounds(
             self,
-            **kwargs: Any,
-            ) -> List[Tuple[Optional[str], Optional['Pattern']]]:
-        """
-        Create a list of `(pat.name, pat)` tuples for all Pattern objects referenced by this
-         Pattern (operates recursively on all referenced Patterns as well).
-
-        Note that names are not necessarily unique, so a list of tuples is returned
-         rather than a dict.
-
-        Args:
-            **kwargs: passed to `referenced_patterns_by_id()`.
-
-        Returns:
-            List of `(pat.name, pat)` tuples for all referenced Pattern objects
-        """
-        pats_by_id = self.referenced_patterns_by_id(**kwargs)
-        pat_list: List[Tuple[Optional[str], Optional['Pattern']]]
-        pat_list = [(p.name if p is not None else None, p) for p in pats_by_id.values()]
-        return pat_list
-
-    def subpatterns_by_id(
-            self,
-            include_none: bool = False,
-            recursive: bool = True,
-            ) -> Dict[int, List[SubPattern]]:
-        """
-        Create a dictionary which maps `{id(referenced_pattern): [subpattern0, ...]}`
-         for all SubPattern objects referenced by this Pattern (by default, operates
-         recursively on all referenced Patterns as well).
-
-        Args:
-            include_none: If `True`, references to `None` will be included. Default `False`.
-            recursive: If `True`, operates recursively on all referenced patterns. Default `True`.
-
-        Returns:
-            Dictionary mapping each pattern id to a list of subpattern objects referencing the pattern.
-        """
-        ids: Dict[int, List[SubPattern]] = defaultdict(list)
-        for subpat in self.subpatterns:
-            pat = subpat.pattern
-            if include_none or pat is not None:
-                ids[id(pat)].append(subpat)
-            if recursive and pat is not None:
-                ids.update(pat.subpatterns_by_id(include_none=include_none))
-        return dict(ids)
-
-    def get_bounds(self) -> Union[NDArray[numpy.float64], None]:
+            library: Optional[Mapping[str, 'Pattern']] = None,
+            ) -> Optional[NDArray[numpy.float64]]:
         """
         Return a `numpy.ndarray` containing `[[x_min, y_min], [x_max, y_max]]`, corresponding to the
          extent of the Pattern's contents in each dimension.
@@ -557,119 +235,42 @@ class Pattern(LockableImpl, AnnotatableImpl, Mirrorable, metaclass=AutoSlots):
         min_bounds = numpy.array((+inf, +inf))
         max_bounds = numpy.array((-inf, -inf))
 
-        for entry in chain(self.shapes, self.subpatterns, self.labels):
+        for entry in chain(self.shapes, self.labels):
             bounds = entry.get_bounds()
             if bounds is None:
                 continue
             min_bounds = numpy.minimum(min_bounds, bounds[0, :])
             max_bounds = numpy.maximum(max_bounds, bounds[1, :])
+
+        if self.subpatterns and (library is None):
+            raise PatternError('Must provide a library to get_bounds() to resolve subpatterns')
+
+        for entry in self.subpatterns:
+            bounds = entry.get_bounds(library=library)
+            if bounds is None:
+                continue
+            min_bounds = numpy.minimum(min_bounds, bounds[0, :])
+            max_bounds = numpy.maximum(max_bounds, bounds[1, :])
+
         if (max_bounds < min_bounds).any():
             return None
         else:
             return numpy.vstack((min_bounds, max_bounds))
 
-    def get_bounds_nonempty(self) -> NDArray[numpy.float64]:
+    def get_bounds_nonempty(
+            self,
+            library: Optional[Mapping[str, 'Pattern']] = None,
+            ) -> NDArray[numpy.float64]:
         """
         Convenience wrapper for `get_bounds()` which asserts that the Pattern as non-None bounds.
 
         Returns:
             `[[x_min, y_min], [x_max, y_max]]`
         """
-        bounds = self.get_bounds()
+        bounds = self.get_bounds(library)
         assert(bounds is not None)
         return bounds
 
-    def flatten(self: P) -> P:
-        """
-        Removes all subpatterns and adds equivalent shapes.
-        Also flattens all subpatterns.
-        Modifies patterns in-place.
-
-        Shape/label identifiers are changed to represent their original position in the
-         pattern hierarchy:
-         `(L1_sp_index (int), L2_sp_index (int), ..., sh_index (int), *original_shape_identifier)`
-         where the original shape can be accessed as e.g.
-            `self.subpatterns[L1_sp_index].pattern.subpatterns[L2_sp_index].shapes[L1_sh_index]`
-
-        Returns:
-            self
-        """
-        def flatten_single(pat: P, flattened: Set[P]) -> P:
-            # Update identifiers so each shape has a unique one
-            for ss, shape in enumerate(pat.shapes):
-                shape.identifier = (ss,) + shape.identifier
-            for ll, label in enumerate(pat.labels):
-                label.identifier = (ll,) + label.identifier
-
-            for pp, subpat in enumerate(pat.subpatterns):
-                if subpat.pattern is None:
-                    continue
-
-                if subpat.pattern not in flattened:
-                    flatten_single(subpat.pattern, flattened)
-                    flattened.add(subpat.pattern)
-
-                p = subpat.as_pattern()
-                for item in chain(p.shapes, p.labels):
-                    item.identifier = (pp,) + item.identifier
-                pat.append(p)
-
-            pat.subpatterns = []
-            return pat
-
-        flatten_single(self, set())
-        return self
-
-    def wrap_repeated_shapes(
-            self: P,
-            name_func: Callable[['Pattern', Union[Shape, Label]], str] = lambda p, s: '_repetition',
-            recursive: bool = True,
-            ) -> P:
-        """
-        Wraps all shapes and labels with a non-`None` `repetition` attribute
-          into a `SubPattern`/`Pattern` combination, and applies the `repetition`
-          to each `SubPattern` instead of its contained shape.
-
-        Args:
-            name_func: Function f(this_pattern, shape) which generates a name for the
-                        wrapping pattern. Default always returns '_repetition'.
-            recursive: If `True`, this function is also applied to all referenced patterns
-                        recursively. Default `True`.
-
-        Returns:
-            self
-        """
-        def do_wrap(pat: Optional[Pattern]) -> Optional[Pattern]:
-            if pat is None:
-                return pat
-
-            new_shapes = []
-            for shape in pat.shapes:
-                if shape.repetition is None:
-                    new_shapes.append(shape)
-                    continue
-                pat.addsp(Pattern(name_func(pat, shape), shapes=[shape]), repetition=shape.repetition)
-                shape.repetition = None
-            pat.shapes = new_shapes
-
-            new_labels = []
-            for label in pat.labels:
-                if label.repetition is None:
-                    new_labels.append(label)
-                    continue
-                pat.addsp(Pattern(name_func(pat, label), labels=[label]), repetition=label.repetition)
-                label.repetition = None
-            pat.labels = new_labels
-
-            return pat
-
-        if recursive:
-            self.apply(do_wrap)
-        else:
-            do_wrap(self)
-
-        return self
-
     def translate_elements(self: P, offset: ArrayLike) -> P:
         """
         Translates all shapes, label, and subpatterns by the given offset.
@@ -872,98 +473,51 @@ class Pattern(LockableImpl, AnnotatableImpl, Mirrorable, metaclass=AutoSlots):
         self.subpatterns.append(SubPattern(*args, **kwargs))
         return self
 
-    def lock(self: P) -> P:
+    def flatten(
+            self: P,
+            library: Mapping[str, P],
+            ) -> 'Pattern':
         """
-        Lock the pattern, raising an exception if it is modified.
-        Also see `deeplock()`.
-
-        Returns:
-            self
-        """
-        if not self.locked:
-            self.shapes = tuple(self.shapes)
-            self.labels = tuple(self.labels)
-            self.subpatterns = tuple(self.subpatterns)
-            LockableImpl.lock(self)
-        return self
-
-    def unlock(self: P) -> P:
-        """
-        Unlock the pattern
-
-        Returns:
-            self
-        """
-        if self.locked:
-            LockableImpl.unlock(self)
-            self.shapes = list(self.shapes)
-            self.labels = list(self.labels)
-            self.subpatterns = list(self.subpatterns)
-        return self
-
-    def deeplock(self: P) -> P:
-        """
-        Recursively lock the pattern, all referenced shapes, subpatterns, and labels.
-
-        Returns:
-            self
-        """
-        self.lock()
-        for ss in chain(self.shapes, self.labels):
-            ss.lock()       # type: ignore      # mypy struggles with multiple inheritance :(
-        for sp in self.subpatterns:
-            sp.deeplock()
-        return self
-
-    def deepunlock(self: P) -> P:
-        """
-        Recursively unlock the pattern, all referenced shapes, subpatterns, and labels.
-
-        This is dangerous unless you have just performed a deepcopy, since anything
-          you change will be changed everywhere it is referenced!
-
-        Return:
-            self
-        """
-        self.unlock()
-        for ss in chain(self.shapes, self.labels):
-            ss.unlock()       # type: ignore      # mypy struggles with multiple inheritance :(
-        for sp in self.subpatterns:
-            sp.deepunlock()
-        return self
-
-    @staticmethod
-    def load(filename: str) -> 'Pattern':
-        """
-        Load a Pattern from a file using pickle
+        Removes all subpatterns (recursively) and adds equivalent shapes.
+        Alters the current pattern in-place
 
         Args:
-            filename: Filename to load from
-
-        Returns:
-            Loaded Pattern
-        """
-        with open(filename, 'rb') as f:
-            pattern = pickle.load(f)
-
-        return pattern
-
-    def save(self, filename: str) -> 'Pattern':
-        """
-        Save the Pattern to a file using pickle
-
-        Args:
-            filename: Filename to save to
+            library: Source for referenced patterns.
 
         Returns:
             self
         """
-        with open(filename, 'wb') as f:
-            pickle.dump(self, f, protocol=pickle.HIGHEST_PROTOCOL)
+        flattened: Dict[Optional[str], Optional[P]] = {}
+
+        def flatten_single(name: Optional[str]) -> None:
+            if name is None:
+                pat = self
+            else:
+                pat = library[name].deepcopy()
+                flattened[name] = None
+
+            for subpat in pat.subpatterns:
+                target = subpat.target
+                if target is None:
+                    continue
+
+                if target not in flattened:
+                    flatten_single(target)
+                if flattened[target] is None:
+                    raise PatternError(f'Circular reference in {name} to {target}')
+
+                p = subpat.as_pattern(pattern=flattened[target])
+                pat.append(p)
+
+            pat.subpatterns.clear()
+            flattened[name] = pat
+
+        flatten_single(None)
         return self
 
     def visualize(
-            self,
+            self: P,
+            library: Optional[Mapping[str, P]] = None,
             offset: ArrayLike = (0., 0.),
             line_color: str = 'k',
             fill_color: str = 'none',
@@ -987,6 +541,9 @@ class Pattern(LockableImpl, AnnotatableImpl, Mirrorable, metaclass=AutoSlots):
         from matplotlib import pyplot       # type: ignore
         import matplotlib.collections       # type: ignore
 
+        if self.subpatterns and library is None:
+            raise PatternError('Must provide a library when visualizing a pattern with subpatterns')
+
         offset = numpy.array(offset, dtype=float)
 
         if not overdraw:
@@ -1001,50 +558,27 @@ class Pattern(LockableImpl, AnnotatableImpl, Mirrorable, metaclass=AutoSlots):
         for shape in self.shapes:
             polygons += [offset + s.offset + s.vertices for s in shape.to_polygons()]
 
-        mpl_poly_collection = matplotlib.collections.PolyCollection(polygons,
-                                                                    facecolors=fill_color,
-                                                                    edgecolors=line_color)
+        mpl_poly_collection = matplotlib.collections.PolyCollection(
+            polygons,
+            facecolors=fill_color,
+            edgecolors=line_color,
+            )
         axes.add_collection(mpl_poly_collection)
         pyplot.axis('equal')
 
         for subpat in self.subpatterns:
-            subpat.as_pattern().visualize(offset=offset, overdraw=True,
-                                          line_color=line_color, fill_color=fill_color)
+            subpat.as_pattern(library=library).visualize(
+                library=library,
+                offset=offset,
+                overdraw=True,
+                line_color=line_color,
+                fill_color=fill_color,
+                )
 
         if not overdraw:
             pyplot.xlabel('x')
             pyplot.ylabel('y')
             pyplot.show()
 
-    @staticmethod
-    def find_toplevel(patterns: Iterable['Pattern']) -> List['Pattern']:
-        """
-        Given a list of Pattern objects, return those that are not referenced by
-         any other pattern.
-
-        Args:
-            patterns: A list of patterns to filter.
-
-        Returns:
-            A filtered list in which no pattern is referenced by any other pattern.
-        """
-        def get_children(pat: Pattern, memo: Set) -> Set:
-            children = set(sp.pattern for sp in pat.subpatterns if sp.pattern is not None)
-            new_children = children - memo
-            memo |= new_children
-
-            for child_pat in new_children:
-                memo |= get_children(child_pat, memo)
-            return memo
-
-        patterns = set(patterns)
-        not_toplevel: Set['Pattern'] = set()
-        for pattern in patterns:
-            not_toplevel |= get_children(pattern, not_toplevel)
-
-        toplevel = list(patterns - not_toplevel)
-        return toplevel
-
     def __repr__(self) -> str:
-        locked = ' L' if self.locked else ''
-        return (f'<Pattern "{self.name}": sh{len(self.shapes)} sp{len(self.subpatterns)} la{len(self.labels)}{locked}>')
+        return (f'<Pattern: sh{len(self.shapes)} sp{len(self.subpatterns)} la{len(self.labels)}>')

masque/repetition.py

@@ -12,7 +12,7 @@ from numpy.typing import ArrayLike, NDArray
 
 from .error import PatternError
 from .utils import rotation_matrix_2d, AutoSlots
-from .traits import LockableImpl, Copyable, Scalable, Rotatable, Mirrorable
+from .traits import Copyable, Scalable, Rotatable, Mirrorable
 
 
 class Repetition(Copyable, Rotatable, Mirrorable, Scalable, metaclass=ABCMeta):
@@ -30,7 +30,7 @@ class Repetition(Copyable, Rotatable, Mirrorable, Scalable, metaclass=ABCMeta):
         pass
 
 
-class Grid(LockableImpl, Repetition, metaclass=AutoSlots):
+class Grid(Repetition, metaclass=AutoSlots):
     """
     `Grid` describes a 2D grid formed by two basis vectors and two 'counts' (sizes).
 
@@ -67,7 +67,6 @@ class Grid(LockableImpl, Repetition, metaclass=AutoSlots):
             a_count: int,
             b_vector: Optional[ArrayLike] = None,
             b_count: Optional[int] = 1,
-            locked: bool = False,
             ) -> None:
         """
         Args:
@@ -79,7 +78,6 @@ class Grid(LockableImpl, Repetition, metaclass=AutoSlots):
                 Can be omitted when specifying a 1D array.
             b_count: Number of elements in the `b_vector` direction.
                 Should be omitted if `b_vector` was omitted.
-            locked: Whether the `Grid` is locked after initialization.
 
         Raises:
             PatternError if `b_*` inputs conflict with each other
@@ -99,12 +97,10 @@ class Grid(LockableImpl, Repetition, metaclass=AutoSlots):
         if b_count < 1:
             raise PatternError(f'Repetition has too-small b_count: {b_count}')
 
-        object.__setattr__(self, 'locked', False)
         self.a_vector = a_vector        # type: ignore     # setter handles type conversion
         self.b_vector = b_vector        # type: ignore     # setter handles type conversion
         self.a_count = a_count
         self.b_count = b_count
-        self.locked = locked
 
     @classmethod
     def aligned(
@@ -129,18 +125,17 @@ class Grid(LockableImpl, Repetition, metaclass=AutoSlots):
         return cls(a_vector=(x, 0), b_vector=(0, y), a_count=x_count, b_count=y_count)
 
     def __copy__(self) -> 'Grid':
-        new = Grid(a_vector=self.a_vector.copy(),
-                   b_vector=copy.copy(self.b_vector),
-                   a_count=self.a_count,
-                   b_count=self.b_count,
-                   locked=self.locked)
+        new = Grid(
+            a_vector=self.a_vector.copy(),
+            b_vector=copy.copy(self.b_vector),
+            a_count=self.a_count,
+            b_count=self.b_count,
+            )
         return new
 
     def __deepcopy__(self, memo: Dict = None) -> 'Grid':
         memo = {} if memo is None else memo
         new = copy.copy(self)
-        LocakbleImpl.unlock(new)
-        new.locked = self.locked
         return new
 
     # a_vector property
@@ -264,36 +259,9 @@ class Grid(LockableImpl, Repetition, metaclass=AutoSlots):
             self.b_vector *= c
         return self
 
-    def lock(self) -> 'Grid':
-        """
-        Lock the `Grid`, disallowing changes.
-
-        Returns:
-            self
-        """
-        self.a_vector.flags.writeable = False
-        if self.b_vector is not None:
-            self.b_vector.flags.writeable = False
-        LockableImpl.lock(self)
-        return self
-
-    def unlock(self) -> 'Grid':
-        """
-        Unlock the `Grid`
-
-        Returns:
-            self
-        """
-        self.a_vector.flags.writeable = True
-        if self.b_vector is not None:
-            self.b_vector.flags.writeable = True
-        LockableImpl.unlock(self)
-        return self
-
     def __repr__(self) -> str:
-        locked = ' L' if self.locked else ''
         bv = f', {self.b_vector}' if self.b_vector is not None else ''
-        return (f'<Grid {self.a_count}x{self.b_count} ({self.a_vector}{bv}){locked}>')
+        return (f'<Grid {self.a_count}x{self.b_count} ({self.a_vector}{bv})>')
 
     def __eq__(self, other: Any) -> bool:
         if not isinstance(other, type(self)):
@@ -308,12 +276,10 @@ class Grid(LockableImpl, Repetition, metaclass=AutoSlots):
             return False
         if any(self.b_vector[ii] != other.b_vector[ii] for ii in range(2)):
             return False
-        if self.locked != other.locked:
-            return False
         return True
 
 
-class Arbitrary(LockableImpl, Repetition, metaclass=AutoSlots):
+class Arbitrary(Repetition, metaclass=AutoSlots):
     """
     `Arbitrary` is a simple list of (absolute) displacements for instances.
 
@@ -342,48 +308,19 @@ class Arbitrary(LockableImpl, Repetition, metaclass=AutoSlots):
     def __init__(
             self,
             displacements: ArrayLike,
-            locked: bool = False,
             ) -> None:
         """
         Args:
             displacements: List of vectors (Nx2 ndarray) specifying displacements.
-            locked: Whether the object is locked after initialization.
         """
-        object.__setattr__(self, 'locked', False)
         self.displacements = displacements
-        self.locked = locked
-
-    def lock(self) -> 'Arbitrary':
-        """
-        Lock the object, disallowing changes.
-
-        Returns:
-            self
-        """
-        self._displacements.flags.writeable = False
-        LockableImpl.lock(self)
-        return self
-
-    def unlock(self) -> 'Arbitrary':
-        """
-        Unlock the object
-
-        Returns:
-            self
-        """
-        self._displacements.flags.writeable = True
-        LockableImpl.unlock(self)
-        return self
 
     def __repr__(self) -> str:
-        locked = ' L' if self.locked else ''
-        return (f'<Arbitrary {len(self.displacements)}pts {locked}>')
+        return (f'<Arbitrary {len(self.displacements)}pts >')
 
     def __eq__(self, other: Any) -> bool:
         if not isinstance(other, type(self)):
             return False
-        if self.locked != other.locked:
-            return False
         return numpy.array_equal(self.displacements, other.displacements)
 
     def rotate(self, rotation: float) -> 'Arbitrary':

masque/shapes/arc.py

@@ -10,7 +10,6 @@ from . import Shape, Polygon, normalized_shape_tuple, DEFAULT_POLY_NUM_POINTS
 from .. import PatternError
 from ..repetition import Repetition
 from ..utils import is_scalar, layer_t, AutoSlots, annotations_t
-from ..traits import LockableImpl
 
 
 class Arc(Shape, metaclass=AutoSlots):
@@ -166,10 +165,8 @@ class Arc(Shape, metaclass=AutoSlots):
             dose: float = 1.0,
             repetition: Optional[Repetition] = None,
             annotations: Optional[annotations_t] = None,
-            locked: bool = False,
             raw: bool = False,
             ) -> None:
-        LockableImpl.unlock(self)
         self.identifier = ()
         if raw:
             assert(isinstance(radii, numpy.ndarray))
@@ -197,17 +194,14 @@ class Arc(Shape, metaclass=AutoSlots):
         self.poly_num_points = poly_num_points
         self.poly_max_arclen = poly_max_arclen
         [self.mirror(a) for a, do in enumerate(mirrored) if do]
-        self.set_locked(locked)
 
     def __deepcopy__(self, memo: Dict = None) -> 'Arc':
         memo = {} if memo is None else memo
         new = copy.copy(self)
-        Shape.unlock(new)
         new._offset = self._offset.copy()
         new._radii = self._radii.copy()
         new._angles = self._angles.copy()
         new._annotations = copy.deepcopy(self._annotations)
-        new.set_locked(self.locked)
         return new
 
     def to_polygons(
@@ -429,21 +423,8 @@ class Arc(Shape, metaclass=AutoSlots):
             a.append((a0, a1))
         return numpy.array(a)
 
-    def lock(self) -> 'Arc':
-        self.radii.flags.writeable = False
-        self.angles.flags.writeable = False
-        Shape.lock(self)
-        return self
-
-    def unlock(self) -> 'Arc':
-        Shape.unlock(self)
-        self.radii.flags.writeable = True
-        self.angles.flags.writeable = True
-        return self
-
     def __repr__(self) -> str:
         angles = f' a°{numpy.rad2deg(self.angles)}'
         rotation = f' r°{numpy.rad2deg(self.rotation):g}' if self.rotation != 0 else ''
         dose = f' d{self.dose:g}' if self.dose != 1 else ''
-        locked = ' L' if self.locked else ''
-        return f'<Arc l{self.layer} o{self.offset} r{self.radii}{angles} w{self.width:g}{rotation}{dose}{locked}>'
+        return f'<Arc l{self.layer} o{self.offset} r{self.radii}{angles} w{self.width:g}{rotation}{dose}>'

masque/shapes/circle.py

@@ -9,7 +9,6 @@ from . import Shape, Polygon, normalized_shape_tuple, DEFAULT_POLY_NUM_POINTS
 from .. import PatternError
 from ..repetition import Repetition
 from ..utils import is_scalar, layer_t, AutoSlots, annotations_t
-from ..traits import LockableImpl
 
 
 class Circle(Shape, metaclass=AutoSlots):
@@ -54,10 +53,8 @@ class Circle(Shape, metaclass=AutoSlots):
             dose: float = 1.0,
             repetition: Optional[Repetition] = None,
             annotations: Optional[annotations_t] = None,
-            locked: bool = False,
             raw: bool = False,
             ) -> None:
-        LockableImpl.unlock(self)
         self.identifier = ()
         if raw:
             assert(isinstance(offset, numpy.ndarray))
@@ -76,15 +73,12 @@ class Circle(Shape, metaclass=AutoSlots):
             self.dose = dose
         self.poly_num_points = poly_num_points
         self.poly_max_arclen = poly_max_arclen
-        self.set_locked(locked)
 
     def __deepcopy__(self, memo: Dict = None) -> 'Circle':
         memo = {} if memo is None else memo
         new = copy.copy(self)
-        Shape.unlock(new)
         new._offset = self._offset.copy()
         new._annotations = copy.deepcopy(self._annotations)
-        new.set_locked(self.locked)
         return new
 
     def to_polygons(
@@ -138,5 +132,4 @@ class Circle(Shape, metaclass=AutoSlots):
 
     def __repr__(self) -> str:
         dose = f' d{self.dose:g}' if self.dose != 1 else ''
-        locked = ' L' if self.locked else ''
-        return f'<Circle l{self.layer} o{self.offset} r{self.radius:g}{dose}{locked}>'
+        return f'<Circle l{self.layer} o{self.offset} r{self.radius:g}{dose}>'

masque/shapes/ellipse.py

@@ -10,7 +10,6 @@ from . import Shape, Polygon, normalized_shape_tuple, DEFAULT_POLY_NUM_POINTS
 from .. import PatternError
 from ..repetition import Repetition
 from ..utils import is_scalar, rotation_matrix_2d, layer_t, AutoSlots, annotations_t
-from ..traits import LockableImpl
 
 
 class Ellipse(Shape, metaclass=AutoSlots):
@@ -101,10 +100,8 @@ class Ellipse(Shape, metaclass=AutoSlots):
             dose: float = 1.0,
             repetition: Optional[Repetition] = None,
             annotations: Optional[annotations_t] = None,
-            locked: bool = False,
             raw: bool = False,
             ) -> None:
-        LockableImpl.unlock(self)
         self.identifier = ()
         if raw:
             assert(isinstance(radii, numpy.ndarray))
@@ -127,16 +124,13 @@ class Ellipse(Shape, metaclass=AutoSlots):
         [self.mirror(a) for a, do in enumerate(mirrored) if do]
         self.poly_num_points = poly_num_points
         self.poly_max_arclen = poly_max_arclen
-        self.set_locked(locked)
 
     def __deepcopy__(self, memo: Dict = None) -> 'Ellipse':
         memo = {} if memo is None else memo
         new = copy.copy(self)
-        Shape.unlock(new)
         new._offset = self._offset.copy()
         new._radii = self._radii.copy()
         new._annotations = copy.deepcopy(self._annotations)
-        new.set_locked(self.locked)
         return new
 
     def to_polygons(
@@ -209,18 +203,7 @@ class Ellipse(Shape, metaclass=AutoSlots):
                 (self.offset, scale / norm_value, angle, False, self.dose),
                 lambda: Ellipse(radii=radii * norm_value, layer=self.layer))
 
-    def lock(self) -> 'Ellipse':
-        self.radii.flags.writeable = False
-        Shape.lock(self)
-        return self
-
-    def unlock(self) -> 'Ellipse':
-        Shape.unlock(self)
-        self.radii.flags.writeable = True
-        return self
-
     def __repr__(self) -> str:
         rotation = f' r{self.rotation*180/pi:g}' if self.rotation != 0 else ''
         dose = f' d{self.dose:g}' if self.dose != 1 else ''
-        locked = ' L' if self.locked else ''
-        return f'<Ellipse l{self.layer} o{self.offset} r{self.radii}{rotation}{dose}{locked}>'
+        return f'<Ellipse l{self.layer} o{self.offset} r{self.radii}{rotation}{dose}>'

masque/shapes/path.py

@@ -11,7 +11,6 @@ from .. import PatternError
 from ..repetition import Repetition
 from ..utils import is_scalar, rotation_matrix_2d, layer_t, AutoSlots
 from ..utils import remove_colinear_vertices, remove_duplicate_vertices, annotations_t
-from ..traits import LockableImpl
 
 
 class PathCap(Enum):
@@ -155,10 +154,8 @@ class Path(Shape, metaclass=AutoSlots):
             dose: float = 1.0,
             repetition: Optional[Repetition] = None,
             annotations: Optional[annotations_t] = None,
-            locked: bool = False,
             raw: bool = False,
             ) -> None:
-        LockableImpl.unlock(self)
         self._cap_extensions = None     # Since .cap setter might access it
 
         self.identifier = ()
@@ -187,18 +184,15 @@ class Path(Shape, metaclass=AutoSlots):
             self.cap_extensions = cap_extensions
         self.rotate(rotation)
         [self.mirror(a) for a, do in enumerate(mirrored) if do]
-        self.set_locked(locked)
 
     def __deepcopy__(self, memo: Dict = None) -> 'Path':
         memo = {} if memo is None else memo
         new = copy.copy(self)
-        Shape.unlock(new)
         new._offset = self._offset.copy()
         new._vertices = self._vertices.copy()
         new._cap = copy.deepcopy(self._cap, memo)
         new._cap_extensions = copy.deepcopy(self._cap_extensions, memo)
         new._annotations = copy.deepcopy(self._annotations)
-        new.set_locked(self.locked)
         return new
 
     @staticmethod
@@ -424,22 +418,7 @@ class Path(Shape, metaclass=AutoSlots):
             extensions = numpy.zeros(2)
         return extensions
 
-    def lock(self) -> 'Path':
-        self.vertices.flags.writeable = False
-        if self.cap_extensions is not None:
-            self.cap_extensions.flags.writeable = False
-        Shape.lock(self)
-        return self
-
-    def unlock(self) -> 'Path':
-        Shape.unlock(self)
-        self.vertices.flags.writeable = True
-        if self.cap_extensions is not None:
-            self.cap_extensions.flags.writeable = True
-        return self
-
     def __repr__(self) -> str:
         centroid = self.offset + self.vertices.mean(axis=0)
         dose = f' d{self.dose:g}' if self.dose != 1 else ''
-        locked = ' L' if self.locked else ''
-        return f'<Path l{self.layer} centroid {centroid} v{len(self.vertices)} w{self.width} c{self.cap}{dose}{locked}>'
+        return f'<Path l{self.layer} centroid {centroid} v{len(self.vertices)} w{self.width} c{self.cap}{dose}>'

masque/shapes/polygon.py

@@ -10,7 +10,6 @@ from .. import PatternError
 from ..repetition import Repetition
 from ..utils import is_scalar, rotation_matrix_2d, layer_t, AutoSlots
 from ..utils import remove_colinear_vertices, remove_duplicate_vertices, annotations_t
-from ..traits import LockableImpl
 
 
 class Polygon(Shape, metaclass=AutoSlots):
@@ -83,10 +82,8 @@ class Polygon(Shape, metaclass=AutoSlots):
             dose: float = 1.0,
             repetition: Optional[Repetition] = None,
             annotations: Optional[annotations_t] = None,
-            locked: bool = False,
             raw: bool = False,
             ) -> None:
-        LockableImpl.unlock(self)
         self.identifier = ()
         if raw:
             assert(isinstance(vertices, numpy.ndarray))
@@ -106,16 +103,13 @@ class Polygon(Shape, metaclass=AutoSlots):
             self.dose = dose
         self.rotate(rotation)
         [self.mirror(a) for a, do in enumerate(mirrored) if do]
-        self.set_locked(locked)
 
     def __deepcopy__(self, memo: Optional[Dict] = None) -> 'Polygon':
         memo = {} if memo is None else memo
         new = copy.copy(self)
-        Shape.unlock(new)
         new._offset = self._offset.copy()
         new._vertices = self._vertices.copy()
         new._annotations = copy.deepcopy(self._annotations)
-        new.set_locked(self.locked)
         return new
 
     @staticmethod
@@ -430,18 +424,7 @@ class Polygon(Shape, metaclass=AutoSlots):
         self.vertices = remove_colinear_vertices(self.vertices, closed_path=True)
         return self
 
-    def lock(self) -> 'Polygon':
-        self.vertices.flags.writeable = False
-        Shape.lock(self)
-        return self
-
-    def unlock(self) -> 'Polygon':
-        Shape.unlock(self)
-        self.vertices.flags.writeable = True
-        return self
-
     def __repr__(self) -> str:
         centroid = self.offset + self.vertices.mean(axis=0)
         dose = f' d{self.dose:g}' if self.dose != 1 else ''
-        locked = ' L' if self.locked else ''
-        return f'<Polygon l{self.layer} centroid {centroid} v{len(self.vertices)}{dose}{locked}>'
+        return f'<Polygon l{self.layer} centroid {centroid} v{len(self.vertices)}{dose}>'

masque/shapes/shape.py

@@ -4,10 +4,11 @@ from abc import ABCMeta, abstractmethod
 import numpy
 from numpy.typing import NDArray, ArrayLike
 
-from ..traits import (PositionableImpl, LayerableImpl, DoseableImpl,
-                      Rotatable, Mirrorable, Copyable, Scalable,
-                      PivotableImpl, LockableImpl, RepeatableImpl,
-                      AnnotatableImpl)
+from ..traits import (
+    PositionableImpl, LayerableImpl, DoseableImpl,
+    Rotatable, Mirrorable, Copyable, Scalable,
+    PivotableImpl, RepeatableImpl, AnnotatableImpl,
+    )
 
 if TYPE_CHECKING:
     from . import Polygon
@@ -27,7 +28,7 @@ T = TypeVar('T', bound='Shape')
 
 
 class Shape(PositionableImpl, LayerableImpl, DoseableImpl, Rotatable, Mirrorable, Copyable, Scalable,
-            PivotableImpl, RepeatableImpl, LockableImpl, AnnotatableImpl, metaclass=ABCMeta):
+            PivotableImpl, RepeatableImpl, AnnotatableImpl, metaclass=ABCMeta):
     """
     Abstract class specifying functions common to all shapes.
     """
@@ -303,13 +304,3 @@ class Shape(PositionableImpl, LayerableImpl, DoseableImpl, Rotatable, Mirrorable
                     dose=self.dose))
 
         return manhattan_polygons
-
-    def lock(self: T) -> T:
-        PositionableImpl._lock(self)
-        LockableImpl.lock(self)
-        return self
-
-    def unlock(self: T) -> T:
-        LockableImpl.unlock(self)
-        PositionableImpl._unlock(self)
-        return self

masque/shapes/text.py

@@ -11,7 +11,6 @@ from ..repetition import Repetition
 from ..traits import RotatableImpl
 from ..utils import is_scalar, get_bit, normalize_mirror, layer_t, AutoSlots
 from ..utils import annotations_t
-from ..traits import LockableImpl
 
 # Loaded on use:
 # from freetype import Face
@@ -74,10 +73,8 @@ class Text(RotatableImpl, Shape, metaclass=AutoSlots):
             dose: float = 1.0,
             repetition: Optional[Repetition] = None,
             annotations: Optional[annotations_t] = None,
-            locked: bool = False,
             raw: bool = False,
             ) -> None:
-        LockableImpl.unlock(self)
         self.identifier = ()
         if raw:
             assert(isinstance(offset, numpy.ndarray))
@@ -102,16 +99,13 @@ class Text(RotatableImpl, Shape, metaclass=AutoSlots):
             self.repetition = repetition
             self.annotations = annotations if annotations is not None else {}
         self.font_path = font_path
-        self.set_locked(locked)
 
     def __deepcopy__(self, memo: Dict = None) -> 'Text':
         memo = {} if memo is None else memo
         new = copy.copy(self)
-        Shape.unlock(new)
         new._offset = self._offset.copy()
         new._mirrored = copy.deepcopy(self._mirrored, memo)
         new._annotations = copy.deepcopy(self._annotations)
-        new.set_locked(self.locked)
         return new
 
     def to_polygons(
@@ -259,19 +253,8 @@ def get_char_as_polygons(
 
     return polygons, advance
 
-    def lock(self) -> 'Text':
-        self.mirrored.flags.writeable = False
-        Shape.lock(self)
-        return self
-
-    def unlock(self) -> 'Text':
-        Shape.unlock(self)
-        self.mirrored.flags.writeable = True
-        return self
-
     def __repr__(self) -> str:
         rotation = f' r°{self.rotation*180/pi:g}' if self.rotation != 0 else ''
         dose = f' d{self.dose:g}' if self.dose != 1 else ''
-        locked = ' L' if self.locked else ''
         mirrored = ' m{:d}{:d}'.format(*self.mirrored) if self.mirrored.any() else ''
-        return f'<TextShape "{self.string}" l{self.layer} o{self.offset} h{self.height:g}{rotation}{mirrored}{dose}{locked}>'
+        return f'<TextShape "{self.string}" l{self.layer} o{self.offset} h{self.height:g}{rotation}{mirrored}{dose}>'

masque/subpattern.py

@@ -4,7 +4,7 @@
 """
 #TODO more top-level documentation
 
-from typing import Dict, Tuple, Optional, Sequence, TYPE_CHECKING, Any, TypeVar
+from typing import Dict, Tuple, Optional, Sequence, Mapping, TYPE_CHECKING, Any, TypeVar
 import copy
 
 import numpy
@@ -14,9 +14,10 @@ from numpy.typing import NDArray, ArrayLike
 from .error import PatternError
 from .utils import is_scalar, AutoSlots, annotations_t
 from .repetition import Repetition
-from .traits import (PositionableImpl, DoseableImpl, RotatableImpl, ScalableImpl,
-                     Mirrorable, PivotableImpl, Copyable, LockableImpl, RepeatableImpl,
-                     AnnotatableImpl)
+from .traits import (
+    PositionableImpl, DoseableImpl, RotatableImpl, ScalableImpl,
+    Mirrorable, PivotableImpl, Copyable, RepeatableImpl, AnnotatableImpl,
+    )
 
 
 if TYPE_CHECKING:
@@ -27,19 +28,16 @@ S = TypeVar('S', bound='SubPattern')
 
 
 class SubPattern(PositionableImpl, DoseableImpl, RotatableImpl, ScalableImpl, Mirrorable,
-                 PivotableImpl, Copyable, RepeatableImpl, LockableImpl, AnnotatableImpl,
+                 PivotableImpl, Copyable, RepeatableImpl, AnnotatableImpl,
                  metaclass=AutoSlots):
     """
     SubPattern provides basic support for nesting Pattern objects within each other, by adding
      offset, rotation, scaling, and associated methods.
     """
-    __slots__ = ('_pattern',
-                 '_mirrored',
-                 'identifier',
-                 )
+    __slots__ = ('_target', '_mirrored', 'identifier')
 
-    _pattern: Optional['Pattern']
-    """ The `Pattern` being instanced """
+    _target: Optional[str]
+    """ The name of the `Pattern` being instanced """
 
     _mirrored: NDArray[numpy.bool_]
     """ Whether to mirror the instance across the x and/or y axes. """
@@ -49,7 +47,7 @@ class SubPattern(PositionableImpl, DoseableImpl, RotatableImpl, ScalableImpl, Mi
 
     def __init__(
             self,
-            pattern: Optional['Pattern'],
+            target: Optional[str],
             *,
             offset: ArrayLike = (0.0, 0.0),
             rotation: float = 0.0,
@@ -58,24 +56,21 @@ class SubPattern(PositionableImpl, DoseableImpl, RotatableImpl, ScalableImpl, Mi
             scale: float = 1.0,
             repetition: Optional[Repetition] = None,
             annotations: Optional[annotations_t] = None,
-            locked: bool = False,
             identifier: Tuple[Any, ...] = (),
             ) -> None:
         """
         Args:
-            pattern: Pattern to reference.
+            target: Name of the Pattern to reference.
             offset: (x, y) offset applied to the referenced pattern. Not affected by rotation etc.
             rotation: Rotation (radians, counterclockwise) relative to the referenced pattern's (0, 0).
             mirrored: Whether to mirror the referenced pattern across its x and y axes.
             dose: Scaling factor applied to the dose.
             scale: Scaling factor applied to the pattern's geometry.
-            repetition: TODO
-            locked: Whether the `SubPattern` is locked after initialization.
+            repetition: `Repetition` object, default `None`
             identifier: Arbitrary tuple, used internally by some `masque` functions.
         """
-        LockableImpl.unlock(self)
         self.identifier = identifier
-        self.pattern = pattern
+        self.target = target
         self.offset = offset
         self.rotation = rotation
         self.dose = dose
@@ -85,41 +80,37 @@ class SubPattern(PositionableImpl, DoseableImpl, RotatableImpl, ScalableImpl, Mi
         self.mirrored = mirrored
         self.repetition = repetition
         self.annotations = annotations if annotations is not None else {}
-        self.set_locked(locked)
 
     def __copy__(self) -> 'SubPattern':
-        new = SubPattern(pattern=self.pattern,
-                         offset=self.offset.copy(),
-                         rotation=self.rotation,
-                         dose=self.dose,
-                         scale=self.scale,
-                         mirrored=self.mirrored.copy(),
-                         repetition=copy.deepcopy(self.repetition),
-                         annotations=copy.deepcopy(self.annotations),
-                         locked=self.locked)
+        new = SubPattern(
+            target=self.target,
+            offset=self.offset.copy(),
+            rotation=self.rotation,
+            dose=self.dose,
+            scale=self.scale,
+            mirrored=self.mirrored.copy(),
+            repetition=copy.deepcopy(self.repetition),
+            annotations=copy.deepcopy(self.annotations),
+            )
         return new
 
     def __deepcopy__(self, memo: Dict = None) -> 'SubPattern':
         memo = {} if memo is None else memo
         new = copy.copy(self)
-        LockableImpl.unlock(new)
-        new.pattern = copy.deepcopy(self.pattern, memo)
         new.repetition = copy.deepcopy(self.repetition, memo)
         new.annotations = copy.deepcopy(self.annotations, memo)
-        new.set_locked(self.locked)
         return new
 
-    # pattern property
+    # target property
     @property
-    def pattern(self) -> Optional['Pattern']:
-        return self._pattern
+    def target(self) -> Optional[str]:
+        return self._target
 
-    @pattern.setter
-    def pattern(self, val: Optional['Pattern']) -> None:
-        from .pattern import Pattern
-        if val is not None and not isinstance(val, Pattern):
-            raise PatternError(f'Provided pattern {val} is not a Pattern object or None!')
-        self._pattern = val
+    @target.setter
+    def target(self, val: Optional[str]) -> None:
+        if val is not None and not isinstance(val, str):
+            raise PatternError(f'Provided target {val} is not a str or None!')
+        self._target = val
 
     # Mirrored property
     @property
@@ -132,14 +123,31 @@ class SubPattern(PositionableImpl, DoseableImpl, RotatableImpl, ScalableImpl, Mi
             raise PatternError('Mirrored must be a 2-element list of booleans')
         self._mirrored = numpy.array(val, dtype=bool, copy=True)
 
-    def as_pattern(self) -> 'Pattern':
+    def as_pattern(
+            self,
+            *,
+            pattern: Optional[Pattern] = None,
+            library: Optional[Mapping[str, Pattern]] = None,
+            ) -> 'Pattern':
         """
+        Args:
+            pattern: Pattern object to transform
+            library: A str->Pattern mapping, used instead of `pattern`. Must contain
+                `self.target`.
+
         Returns:
-            A copy of self.pattern which has been scaled, rotated, etc. according to this
-             `SubPattern`'s properties.
+            A copy of the referenced Pattern which has been scaled, rotated, etc.
+             according to this `SubPattern`'s properties.
         """
-        assert(self.pattern is not None)
-        pattern = self.pattern.deepcopy().deepunlock()
+        if pattern is None:
+            if library is None:
+                raise PatternError('as_pattern() must be given a pattern or library.')
+
+            assert(self.target is not None)
+            pattern = library[self.target]
+
+        pattern = pattern.deepcopy()
+
         if self.scale != 1:
             pattern.scale_by(self.scale)
         if numpy.any(self.mirrored):
@@ -152,7 +160,7 @@ class SubPattern(PositionableImpl, DoseableImpl, RotatableImpl, ScalableImpl, Mi
             pattern.scale_element_doses(self.dose)
 
         if self.repetition is not None:
-            combined = type(pattern)(name='__repetition__')
+            combined = type(pattern)()
             for dd in self.repetition.displacements:
                 temp_pat = pattern.deepcopy()
                 temp_pat.translate_elements(dd)
@@ -174,75 +182,33 @@ class SubPattern(PositionableImpl, DoseableImpl, RotatableImpl, ScalableImpl, Mi
             self.repetition.mirror(axis)
         return self
 
-    def get_bounds(self) -> Optional[NDArray[numpy.float64]]:
+    def get_bounds(
+            self,
+            *,
+            pattern: Optional[Pattern] = None,
+            library: Optional[Mapping[str, Pattern]] = None,
+            ) -> Optional[NDArray[numpy.float64]]:
         """
         Return a `numpy.ndarray` containing `[[x_min, y_min], [x_max, y_max]]`, corresponding to the
          extent of the `SubPattern` in each dimension.
         Returns `None` if the contained `Pattern` is empty.
 
+        Args:
+            library: Name-to-Pattern mapping for resul
+
         Returns:
             `[[x_min, y_min], [x_max, y_max]]` or `None`
         """
-        if self.pattern is None:
+        if pattern is None and library is None:
+            raise PatternError('as_pattern() must be given a pattern or library.')
+        if pattern is None and self.target is None:
             return None
-        return self.as_pattern().get_bounds()
-
-    def lock(self: S) -> S:
-        """
-        Lock the SubPattern, disallowing changes
-
-        Returns:
-            self
-        """
-        self.mirrored.flags.writeable = False
-        PositionableImpl._lock(self)
-        LockableImpl.lock(self)
-        return self
-
-    def unlock(self: S) -> S:
-        """
-        Unlock the SubPattern
-
-        Returns:
-            self
-        """
-        LockableImpl.unlock(self)
-        PositionableImpl._unlock(self)
-        self.mirrored.flags.writeable = True
-        return self
-
-    def deeplock(self: S) -> S:
-        """
-        Recursively lock the SubPattern and its contained pattern
-
-        Returns:
-            self
-        """
-        assert(self.pattern is not None)
-        self.lock()
-        self.pattern.deeplock()
-        return self
-
-    def deepunlock(self: S) -> S:
-        """
-        Recursively unlock the SubPattern and its contained pattern
-
-        This is dangerous unless you have just performed a deepcopy, since
-        the subpattern and its components may be used in more than one once!
-
-        Returns:
-            self
-        """
-        assert(self.pattern is not None)
-        self.unlock()
-        self.pattern.deepunlock()
-        return self
+        return self.as_pattern(pattern=pattern, library=library).get_bounds()
 
     def __repr__(self) -> str:
-        name = self.pattern.name if self.pattern is not None else None
+        name = f'"{self.target}"' if self.target is not None else None
         rotation = f' r{self.rotation*180/pi:g}' if self.rotation != 0 else ''
         scale = f' d{self.scale:g}' if self.scale != 1 else ''
         mirrored = ' m{:d}{:d}'.format(*self.mirrored) if self.mirrored.any() else ''
         dose = f' d{self.dose:g}' if self.dose != 1 else ''
-        locked = ' L' if self.locked else ''
-        return f'<SubPattern "{name}" at {self.offset}{rotation}{scale}{mirrored}{dose}{locked}>'
+        return f'<SubPattern {name} at {self.offset}{rotation}{scale}{mirrored}{dose}>'

masque/traits/__init__.py

@@ -9,5 +9,4 @@ from .repeatable import Repeatable, RepeatableImpl
 from .scalable import Scalable, ScalableImpl
 from .mirrorable import Mirrorable
 from .copyable import Copyable
-from .lockable import Lockable, LockableImpl
 from .annotatable import Annotatable, AnnotatableImpl

masque/traits/annotatable.py

@@ -44,9 +44,6 @@ class AnnotatableImpl(Annotatable, metaclass=ABCMeta):
     @property
     def annotations(self) -> annotations_t:
         return self._annotations
-#        # TODO: Find a way to make sure the subclass implements Lockable without dealing with diamond inheritance or this extra hasattr
-#        if hasattr(self, 'is_locked') and self.is_locked():
-#            return MappingProxyType(self._annotations)
 
     @annotations.setter
     def annotations(self, annotations: annotations_t):

masque/traits/positionable.py

@@ -120,23 +120,3 @@ class PositionableImpl(Positionable, metaclass=ABCMeta):
     def translate(self: I, offset: ArrayLike) -> I:
         self._offset += offset   # type: ignore         # NDArray += ArrayLike should be fine??
         return self
-
-    def _lock(self: I) -> I:
-        """
-        Lock the entity, disallowing further changes
-
-        Returns:
-            self
-        """
-        self._offset.flags.writeable = False
-        return self
-
-    def _unlock(self: I) -> I:
-        """
-        Unlock the entity
-
-        Returns:
-            self
-        """
-        self._offset.flags.writeable = True
-        return self

masque/utils/__init__.py

@@ -5,6 +5,7 @@ from .types import layer_t, annotations_t
 
 from .array import is_scalar
 from .autoslots import AutoSlots
+from .deferreddict import DeferredDict
 
 from .bitwise import get_bit, set_bit
 from .vertices import (

masque/utils/pack2d.py

@@ -1,7 +1,7 @@
 """
 2D bin-packing
 """
-from typing import Tuple, List, Set, Sequence, Callable
+from typing import Tuple, List, Set, Sequence, Callable, Mapping
 
 import numpy
 from numpy.typing import NDArray, ArrayLike
@@ -11,16 +11,18 @@ from ..pattern import Pattern
 from ..subpattern import SubPattern
 
 
-def pack_patterns(patterns: Sequence[Pattern],
-                  regions: numpy.ndarray,
-                  spacing: Tuple[float, float],
-                  presort: bool = True,
-                  allow_rejects: bool = True,
-                  packer: Callable = maxrects_bssf,
-                  ) -> Tuple[Pattern, List[Pattern]]:
+def pack_patterns(
+        library: Mapping[str, Pattern],
+        patterns: Sequence[str],
+        regions: numpy.ndarray,
+        spacing: Tuple[float, float],
+        presort: bool = True,
+        allow_rejects: bool = True,
+        packer: Callable = maxrects_bssf,
+        ) -> Tuple[Pattern, List[str]]:
     half_spacing = numpy.array(spacing) / 2
 
-    bounds = [pp.get_bounds() for pp in patterns]
+    bounds = [library[pp].get_bounds() for pp in patterns]
     sizes = [bb[1] - bb[0] + spacing if bb is not None else spacing for bb in bounds]
     offsets = [half_spacing - bb[0] if bb is not None else (0, 0) for bb in bounds]