[gdsii_arrow] fix rep_valid

breaking change, but properties are seldom used by anyone afaik

masque/file/gdsii.py

@@ -21,6 +21,7 @@ Notes:
 """
 from typing import IO, cast, Any
 from collections.abc import Iterable, Mapping, Callable
+from types import MappingProxyType
 import io
 import mmap
 import logging
@@ -52,6 +53,8 @@ path_cap_map = {
     4: Path.Cap.SquareCustom,
     }
 
+RO_EMPTY_DICT: Mapping[int, bytes] = MappingProxyType({})
+
 
 def rint_cast(val: ArrayLike) -> NDArray[numpy.int32]:
     return numpy.rint(val).astype(numpy.int32)
@@ -399,11 +402,15 @@ def _mrefs_to_grefs(refs: dict[str | None, list[Ref]]) -> list[klamath.library.R
     return grefs
 
 
-def _properties_to_annotations(properties: dict[int, bytes]) -> annotations_t:
+def _properties_to_annotations(properties: Mapping[int, bytes]) -> annotations_t:
+    if not properties:
+        return None
     return {str(k): [v.decode()] for k, v in properties.items()}
 
 
-def _annotations_to_properties(annotations: annotations_t, max_len: int = 126) -> dict[int, bytes]:
+def _annotations_to_properties(annotations: annotations_t, max_len: int = 126) -> Mapping[int, bytes]:
+    if annotations is None:
+        return RO_EMPTY_DICT
     cum_len = 0
     props = {}
     for key, vals in annotations.items():

masque/file/gdsii_arrow.py

@@ -0,0 +1,452 @@
+"""
+GDSII file format readers and writers using the `TODO` library.
+
+Note that GDSII references follow the same convention as `masque`,
+  with this order of operations:
+   1. Mirroring
+   2. Rotation
+   3. Scaling
+   4. Offset and array expansion (no mirroring/rotation/scaling applied to offsets)
+
+  Scaling, rotation, and mirroring apply to individual instances, not grid
+   vectors or offsets.
+
+Notes:
+ * absolute positioning is not supported
+ * PLEX is not supported
+ * ELFLAGS are not supported
+ * GDS does not support library- or structure-level annotations
+ * GDS creation/modification/access times are set to 1900-01-01 for reproducibility.
+ * Gzip modification time is set to 0 (start of current epoch, usually 1970-01-01)
+
+ TODO writing
+ TODO warn on boxes, nodes
+"""
+from typing import IO, cast, Any
+from collections.abc import Iterable, Mapping, Callable
+import io
+import mmap
+import logging
+import pathlib
+import gzip
+import string
+from pprint import pformat
+
+import numpy
+from numpy.typing import ArrayLike, NDArray
+from numpy.testing import assert_equal
+import pyarrow
+from pyarrow.cffi import ffi
+
+from .utils import is_gzipped, tmpfile
+from .. import Pattern, Ref, PatternError, LibraryError, Label, Shape
+from ..shapes import Polygon, Path, PolyCollection
+from ..repetition import Grid
+from ..utils import layer_t, annotations_t
+from ..library import LazyLibrary, Library, ILibrary, ILibraryView
+
+
+logger = logging.getLogger(__name__)
+
+clib = ffi.dlopen('/home/jan/projects/klamath-rs/target/release/libklamath_rs_ext.so')
+ffi.cdef('void read_path(char* path, struct ArrowArray* array, struct ArrowSchema* schema);')
+
+
+path_cap_map = {
+    0: Path.Cap.Flush,
+    1: Path.Cap.Circle,
+    2: Path.Cap.Square,
+    4: Path.Cap.SquareCustom,
+    }
+
+
+def rint_cast(val: ArrayLike) -> NDArray[numpy.int32]:
+    return numpy.rint(val).astype(numpy.int32)
+
+
+def _read_to_arrow(
+        filename: str | pathlib.Path,
+        *args,
+        **kwargs,
+        ) -> pyarrow.Array:
+    path = pathlib.Path(filename)
+    path.resolve()
+    ptr_array = ffi.new('struct ArrowArray[]', 1)
+    ptr_schema = ffi.new('struct ArrowSchema[]', 1)
+    clib.read_path(str(path).encode(), ptr_array, ptr_schema)
+
+    iptr_schema = int(ffi.cast('uintptr_t', ptr_schema))
+    iptr_array = int(ffi.cast('uintptr_t', ptr_array))
+    arrow_arr = pyarrow.Array._import_from_c(iptr_array, iptr_schema)
+
+    return arrow_arr
+
+
+def readfile(
+        filename: str | pathlib.Path,
+        *args,
+        **kwargs,
+        ) -> tuple[Library, dict[str, Any]]:
+    """
+    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 `read()`
+        **kwargs: passed to `read()`
+    """
+    arrow_arr = _read_to_arrow(filename)
+    assert len(arrow_arr) == 1
+
+    results = read_arrow(arrow_arr[0])
+
+    return results
+
+
+def read_arrow(
+        libarr: pyarrow.Array,
+        raw_mode: bool = True,
+        ) -> tuple[Library, dict[str, Any]]:
+    """
+    # TODO check GDSII file for cycles!
+    Read a gdsii file and translate it into a dict of Pattern objects. GDSII structures are
+     translated into Pattern objects; boundaries are translated into polygons, and srefs and arefs
+     are translated into Ref objects.
+
+    Additional library info is returned in a dict, containing:
+      'name': name of the library
+      'meters_per_unit': number of meters per database unit (all values are in database units)
+      'logical_units_per_unit': number of "logical" units displayed by layout tools (typically microns)
+                                per database unit
+
+    Args:
+        stream: Stream to read from.
+        raw_mode: If True, constructs shapes in raw mode, bypassing most data validation, Default True.
+
+    Returns:
+        - dict of pattern_name:Patterns generated from GDSII structures
+        - dict of GDSII library info
+    """
+    library_info = _read_header(libarr)
+
+    layer_names_np = libarr['layers'].values.to_numpy().view('i2').reshape((-1, 2))
+    layer_tups = [tuple(pair) for pair in layer_names_np]
+
+    cell_ids = libarr['cells'].values.field('id').to_numpy()
+    cell_names = libarr['cell_names'].as_py()
+
+    def get_geom(libarr: pyarrow.Array, geom_type: str) -> dict[str, Any]:
+        el = libarr['cells'].values.field(geom_type)
+        elem = dict(
+            offsets = el.offsets.to_numpy(),
+            xy_arr = el.values.field('xy').values.to_numpy().reshape((-1, 2)),
+            xy_off = el.values.field('xy').offsets.to_numpy() // 2,
+            layer_inds = el.values.field('layer').to_numpy(),
+            prop_off = el.values.field('properties').offsets.to_numpy(),
+            prop_key = el.values.field('properties').values.field('key').to_numpy(),
+            prop_val = el.values.field('properties').values.field('value').to_pylist(),
+            )
+        return elem
+
+    rf = libarr['cells'].values.field('refs')
+    refs = dict(
+        offsets = rf.offsets.to_numpy(),
+        targets = rf.values.field('target').to_numpy(),
+        xy = rf.values.field('xy').to_numpy().view('i4').reshape((-1, 2)),
+        invert_y = rf.values.field('invert_y').fill_null(False).to_numpy(zero_copy_only=False),
+        angle_rad = numpy.rad2deg(rf.values.field('angle_deg').fill_null(0).to_numpy()),
+        scale = rf.values.field('mag').fill_null(1).to_numpy(),
+        rep_valid = rf.values.field('repetition').is_valid().to_numpy(zero_copy_only=False),
+        rep_xy0 = rf.values.field('repetition').field('xy0').fill_null(0).to_numpy().view('i4').reshape((-1, 2)),
+        rep_xy1 = rf.values.field('repetition').field('xy1').fill_null(0).to_numpy().view('i4').reshape((-1, 2)),
+        rep_counts = rf.values.field('repetition').field('counts').fill_null(0).to_numpy().view('i2').reshape((-1, 2)),
+        prop_off = rf.values.field('properties').offsets.to_numpy(),
+        prop_key = rf.values.field('properties').values.field('key').to_numpy(),
+        prop_val = rf.values.field('properties').values.field('value').to_pylist(),
+        )
+
+    txt = libarr['cells'].values.field('texts')
+    texts = dict(
+        offsets = txt.offsets.to_numpy(),
+        layer_inds = txt.values.field('layer').to_numpy(),
+        xy = txt.values.field('xy').to_numpy().view('i4').reshape((-1, 2)),
+        string = txt.values.field('string').to_pylist(),
+        prop_off = txt.values.field('properties').offsets.to_numpy(),
+        prop_key = txt.values.field('properties').values.field('key').to_numpy(),
+        prop_val = txt.values.field('properties').values.field('value').to_pylist(),
+        )
+
+    elements = dict(
+        boundaries = get_geom(libarr, 'boundaries'),
+        paths = get_geom(libarr, 'paths'),
+        boxes = get_geom(libarr, 'boxes'),
+        nodes = get_geom(libarr, 'nodes'),
+        texts = texts,
+        refs = refs,
+        )
+
+    paths = libarr['cells'].values.field('paths')
+    elements['paths'].update(dict(
+        width = paths.values.field('width').fill_null(0).to_numpy(),
+        path_type = paths.values.field('path_type').fill_null(0).to_numpy(),
+        extensions = numpy.stack((
+            paths.values.field('extension_start').fill_null(0).to_numpy(),
+            paths.values.field('extension_end').fill_null(0).to_numpy(),
+            ), axis=-1),
+        ))
+
+    global_args = dict(
+        cell_names = cell_names,
+        layer_tups = layer_tups,
+        raw_mode = raw_mode,
+        )
+
+    mlib = Library()
+    for cc in range(len(libarr['cells'])):
+        name = cell_names[cell_ids[cc]]
+        pat = Pattern()
+        _boundaries_to_polygons(pat, global_args, elements['boundaries'], cc)
+        _gpaths_to_mpaths(pat, global_args, elements['paths'], cc)
+        _grefs_to_mrefs(pat, global_args, elements['refs'], cc)
+        _texts_to_labels(pat, global_args, elements['texts'], cc)
+        mlib[name] = pat
+
+    return mlib, library_info
+
+
+def _read_header(libarr: pyarrow.Array) -> dict[str, Any]:
+    """
+    Read the file header and create the library_info dict.
+    """
+    library_info = dict(
+        name = libarr['lib_name'],
+        meters_per_unit = libarr['meters_per_db_unit'],
+        logical_units_per_unit = libarr['user_units_per_db_unit'],
+        )
+    return library_info
+
+
+def _grefs_to_mrefs(
+        pat: Pattern,
+        global_args: dict[str, Any],
+        elem: dict[str, Any],
+        cc: int,
+        ) -> None:
+    cell_names = global_args['cell_names']
+    elem_off = elem['offsets']      # which elements belong to each cell
+    xy = elem['xy']
+    prop_key = elem['prop_key']
+    prop_val = elem['prop_val']
+    targets = elem['targets']
+
+    elem_count = elem_off[cc + 1] - elem_off[cc]
+    elem_slc = slice(elem_off[cc], elem_off[cc] + elem_count + 1)   # +1 to capture ending location for last elem
+    prop_offs = elem['prop_off'][elem_slc]  # which props belong to each element
+    elem_invert_y = elem['invert_y'][elem_slc][:elem_count]
+    elem_angle_rad = elem['angle_rad'][elem_slc][:elem_count]
+    elem_scale = elem['scale'][elem_slc][:elem_count]
+    elem_rep_xy0 = elem['rep_xy0'][elem_slc][:elem_count]
+    elem_rep_xy1 = elem['rep_xy1'][elem_slc][:elem_count]
+    elem_rep_counts = elem['rep_counts'][elem_slc][:elem_count]
+    rep_valid = elem['rep_valid'][elem_slc][:elem_count]
+
+
+    for ee in range(elem_count):
+        target = cell_names[targets[ee]]
+        offset = xy[ee]
+        mirr = elem_invert_y[ee]
+        rot = elem_angle_rad[ee]
+        mag = elem_scale[ee]
+
+        rep: None | Grid = None
+        if rep_valid[ee]:
+            a_vector = elem_rep_xy0[ee]
+            b_vector = elem_rep_xy1[ee]
+            a_count, b_count = elem_rep_counts[ee]
+            rep = Grid(a_vector=a_vector, b_vector=b_vector, a_count=a_count, b_count=b_count)
+
+        annotations: None | dict[str, list[int | float | str]] = None
+        prop_ii, prop_ff = prop_offs[ee], prop_offs[ee + 1]
+        if prop_ii < prop_ff:
+            annotations = {str(prop_key[off]): [prop_val[off]] for off in range(prop_ii, prop_ff)}
+
+        ref = Ref(offset=offset, mirrored=mirr, rotation=rot, scale=mag, repetition=rep, annotations=annotations)
+        pat.refs[target].append(ref)
+
+
+def _texts_to_labels(
+        pat: Pattern,
+        global_args: dict[str, Any],
+        elem: dict[str, Any],
+        cc: int,
+        ) -> None:
+    elem_off = elem['offsets']      # which elements belong to each cell
+    xy = elem['xy']
+    layer_tups = global_args['layer_tups']
+    layer_inds = elem['layer_inds']
+    prop_key = elem['prop_key']
+    prop_val = elem['prop_val']
+
+    elem_count = elem_off[cc + 1] - elem_off[cc]
+    elem_slc = slice(elem_off[cc], elem_off[cc] + elem_count + 1)   # +1 to capture ending location for last elem
+    prop_offs = elem['prop_off'][elem_slc]  # which props belong to each element
+    elem_layer_inds = layer_inds[elem_slc][:elem_count]
+    elem_strings = elem['string'][elem_slc][:elem_count]
+
+    for ee in range(elem_count):
+        layer = layer_tups[elem_layer_inds[ee]]
+        offset = xy[ee]
+        string = elem_strings[ee]
+
+        annotations: None | dict[str, list[int | float | str]] = None
+        prop_ii, prop_ff = prop_offs[ee], prop_offs[ee + 1]
+        if prop_ii < prop_ff:
+            annotations = {str(prop_key[off]): [prop_val[off]] for off in range(prop_ii, prop_ff)}
+
+        mlabel = Label(string=string, offset=offset, annotations=annotations)
+        pat.labels[layer].append(mlabel)
+
+
+def _gpaths_to_mpaths(
+        pat: Pattern,
+        global_args: dict[str, Any],
+        elem: dict[str, Any],
+        cc: int,
+        ) -> None:
+    elem_off = elem['offsets']      # which elements belong to each cell
+    xy_val = elem['xy_arr']
+    layer_tups = global_args['layer_tups']
+    layer_inds = elem['layer_inds']
+    prop_key = elem['prop_key']
+    prop_val = elem['prop_val']
+
+    elem_count = elem_off[cc + 1] - elem_off[cc]
+    elem_slc = slice(elem_off[cc], elem_off[cc] + elem_count + 1)   # +1 to capture ending location for last elem
+    xy_offs = elem['xy_off'][elem_slc]      # which xy coords belong to each element
+    prop_offs = elem['prop_off'][elem_slc]  # which props belong to each element
+    elem_layer_inds = layer_inds[elem_slc][:elem_count]
+    elem_widths = elem['width'][elem_slc][:elem_count]
+    elem_path_types = elem['path_type'][elem_slc][:elem_count]
+    elem_extensions = elem['extensions'][elem_slc][:elem_count]
+
+    zeros = numpy.zeros((elem_count, 2))
+    raw_mode = global_args['raw_mode']
+    for ee in range(elem_count):
+        layer = layer_tups[elem_layer_inds[ee]]
+        vertices = xy_val[xy_offs[ee]:xy_offs[ee + 1]]
+        width = elem_widths[ee]
+        cap_int = elem_path_types[ee]
+        cap = path_cap_map[cap_int]
+        if cap_int == 4:
+            cap_extensions = elem_extensions[ee]
+        else:
+            cap_extensions = None
+
+        annotations: None | dict[str, list[int | float | str]] = None
+        prop_ii, prop_ff = prop_offs[ee], prop_offs[ee + 1]
+        if prop_ii < prop_ff:
+            annotations = {str(prop_key[off]): [prop_val[off]] for off in range(prop_ii, prop_ff)}
+
+        path = Path(vertices=vertices, offset=zeros[ee], annotations=annotations, raw=raw_mode,
+            width=width, cap=cap,cap_extensions=cap_extensions)
+        pat.shapes[layer].append(path)
+
+
+def _boundaries_to_polygons(
+        pat: Pattern,
+        global_args: dict[str, Any],
+        elem: dict[str, Any],
+        cc: int,
+        ) -> None:
+    elem_off = elem['offsets']      # which elements belong to each cell
+    xy_val = elem['xy_arr']
+    layer_inds = elem['layer_inds']
+    layer_tups = global_args['layer_tups']
+    prop_key = elem['prop_key']
+    prop_val = elem['prop_val']
+
+    elem_count = elem_off[cc + 1] - elem_off[cc]
+    elem_slc = slice(elem_off[cc], elem_off[cc] + elem_count + 1)   # +1 to capture ending location for last elem
+    xy_offs = elem['xy_off'][elem_slc]      # which xy coords belong to each element
+    xy_counts = xy_offs[1:] - xy_offs[:-1]
+    prop_offs = elem['prop_off'][elem_slc]  # which props belong to each element
+    prop_counts = prop_offs[1:] - prop_offs[:-1]
+    elem_layer_inds = layer_inds[elem_slc][:elem_count]
+
+    order = numpy.argsort(elem_layer_inds, stable=True)
+    unilayer_inds, unilayer_first, unilayer_count = numpy.unique(elem_layer_inds, return_index=True, return_counts=True)
+
+    zeros = numpy.zeros((elem_count, 2))
+    raw_mode = global_args['raw_mode']
+    for layer_ind, ff, cc in zip(unilayer_inds, unilayer_first, unilayer_count, strict=True):
+        ee_inds = order[ff:ff + cc]
+        layer = layer_tups[layer_ind]
+        propless_mask = prop_counts[ee_inds] == 0
+
+        poly_count_on_layer = propless_mask.sum()
+        if poly_count_on_layer == 1:
+            propless_mask[:] = 0        # Never make a 1-element collection
+        elif poly_count_on_layer > 1:
+            propless_vert_counts = xy_counts[ee_inds[propless_mask]] - 1        # -1 to drop closing point
+            vertex_lists = numpy.empty((propless_vert_counts.sum(), 2), dtype=numpy.float64)
+            vertex_offsets = numpy.cumsum(numpy.concatenate([[0], propless_vert_counts]))
+
+            for ii, ee in enumerate(ee_inds[propless_mask]):
+                vo = vertex_offsets[ii]
+                vertex_lists[vo:vo + propless_vert_counts[ii]] = xy_val[xy_offs[ee]:xy_offs[ee + 1] - 1]
+
+            polys = PolyCollection(vertex_lists=vertex_lists, vertex_offsets=vertex_offsets, offset=zeros[ee])
+            pat.shapes[layer].append(polys)
+
+        # Handle single polygons
+        for ee in ee_inds[~propless_mask]:
+            layer = layer_tups[elem_layer_inds[ee]]
+            vertices = xy_val[xy_offs[ee]:xy_offs[ee + 1] - 1]    # -1 to drop closing point
+
+            annotations: None | dict[str, list[int | float | str]] = None
+            prop_ii, prop_ff = prop_offs[ee], prop_offs[ee + 1]
+            if prop_ii < prop_ff:
+                annotations = {str(prop_key[off]): prop_val[off] for off in range(prop_ii, prop_ff)}
+
+            poly = Polygon(vertices=vertices, offset=zeros[ee], annotations=annotations, raw=raw_mode)
+            pat.shapes[layer].append(poly)
+
+
+#def _properties_to_annotations(properties: pyarrow.Array) -> annotations_t:
+#    return {prop['key'].as_py(): prop['value'].as_py() for prop in properties}
+
+
+def check_valid_names(
+        names: Iterable[str],
+        max_length: int = 32,
+        ) -> None:
+    """
+    Check all provided names to see if they're valid GDSII cell names.
+
+    Args:
+        names: Collection of names to check
+        max_length: Max allowed length
+
+    """
+    allowed_chars = set(string.ascii_letters + string.digits + '_?$')
+
+    bad_chars = [
+        name for name in names
+        if not set(name).issubset(allowed_chars)
+        ]
+
+    bad_lengths = [
+        name for name in names
+        if len(name) > max_length
+        ]
+
+    if bad_chars:
+        logger.error('Names contain invalid characters:\n' + pformat(bad_chars))
+
+    if bad_lengths:
+        logger.error(f'Names too long (>{max_length}:\n' + pformat(bad_chars))
+
+    if bad_chars or bad_lengths:
+        raise LibraryError('Library contains invalid names, see log above')

masque/file/oasis.py

@@ -671,6 +671,8 @@ def repetition_masq2fata(
 
 def annotations_to_properties(annotations: annotations_t) -> list[fatrec.Property]:
     #TODO determine is_standard based on key?
+    if annotations is None:
+        return []
     properties = []
     for key, values in annotations.items():
         vals = [AString(v) if isinstance(v, str) else v

masque/pattern.py

@@ -332,7 +332,7 @@ class Pattern(PortList, AnnotatableImpl, Mirrorable):
             ))
 
         self.ports = dict(sorted(self.ports.items()))
-        self.annotations = dict(sorted(self.annotations.items()))
+        self.annotations = dict(sorted(self.annotations.items())) if self.annotations is not None else None
 
         return self
 
@@ -354,10 +354,13 @@ class Pattern(PortList, AnnotatableImpl, Mirrorable):
         for layer, lseq in other_pattern.labels.items():
             self.labels[layer].extend(lseq)
 
-        annotation_conflicts = set(self.annotations.keys()) & set(other_pattern.annotations.keys())
-        if annotation_conflicts:
-            raise PatternError(f'Annotation keys overlap: {annotation_conflicts}')
-        self.annotations.update(other_pattern.annotations)
+        if other_pattern.annotations is not None:
+            if self.annotations is None:
+                self.annotations = {}
+            annotation_conflicts = set(self.annotations.keys()) & set(other_pattern.annotations.keys())
+            if annotation_conflicts:
+                raise PatternError(f'Annotation keys overlap: {annotation_conflicts}')
+            self.annotations.update(other_pattern.annotations)
 
         port_conflicts = set(self.ports.keys()) & set(other_pattern.ports.keys())
         if port_conflicts:
@@ -415,7 +418,7 @@ class Pattern(PortList, AnnotatableImpl, Mirrorable):
         elif default_keep:
             pat.refs = copy.copy(self.refs)
 
-        if annotations is not None:
+        if annotations is not None and self.annotations is not None:
             pat.annotations = {k: v for k, v in self.annotations.items() if annotations(k, v)}
         elif default_keep:
             pat.annotations = copy.copy(self.annotations)

masque/shapes/__init__.py

@@ -10,6 +10,7 @@ from .shape import (
     )
 
 from .polygon import Polygon as Polygon
+from .poly_collection import PolyCollection as PolyCollection
 from .circle import Circle as Circle
 from .ellipse import Ellipse as Ellipse
 from .arc import Arc as Arc

masque/shapes/arc.py

@@ -157,7 +157,7 @@ class Arc(Shape):
             offset: ArrayLike = (0.0, 0.0),
             rotation: float = 0,
             repetition: Repetition | None = None,
-            annotations: annotations_t | None = None,
+            annotations: annotations_t = None,
             raw: bool = False,
             ) -> None:
         if raw:
@@ -170,7 +170,7 @@ class Arc(Shape):
             self._offset = offset
             self._rotation = rotation
             self._repetition = repetition
-            self._annotations = annotations if annotations is not None else {}
+            self._annotations = annotations
         else:
             self.radii = radii
             self.angles = angles
@@ -178,7 +178,7 @@ class Arc(Shape):
             self.offset = offset
             self.rotation = rotation
             self.repetition = repetition
-            self.annotations = annotations if annotations is not None else {}
+            self.annotations = annotations
 
     def __deepcopy__(self, memo: dict | None = None) -> 'Arc':
         memo = {} if memo is None else memo

masque/shapes/circle.py

@@ -48,7 +48,7 @@ class Circle(Shape):
             *,
             offset: ArrayLike = (0.0, 0.0),
             repetition: Repetition | None = None,
-            annotations: annotations_t | None = None,
+            annotations: annotations_t = None,
             raw: bool = False,
             ) -> None:
         if raw:
@@ -56,12 +56,12 @@ class Circle(Shape):
             self._radius = radius
             self._offset = offset
             self._repetition = repetition
-            self._annotations = annotations if annotations is not None else {}
+            self._annotations = annotations
         else:
             self.radius = radius
             self.offset = offset
             self.repetition = repetition
-            self.annotations = annotations if annotations is not None else {}
+            self.annotations = annotations
 
     def __deepcopy__(self, memo: dict | None = None) -> 'Circle':
         memo = {} if memo is None else memo

masque/shapes/ellipse.py

@@ -93,7 +93,7 @@ class Ellipse(Shape):
             offset: ArrayLike = (0.0, 0.0),
             rotation: float = 0,
             repetition: Repetition | None = None,
-            annotations: annotations_t | None = None,
+            annotations: annotations_t = None,
             raw: bool = False,
             ) -> None:
         if raw:
@@ -103,13 +103,13 @@ class Ellipse(Shape):
             self._offset = offset
             self._rotation = rotation
             self._repetition = repetition
-            self._annotations = annotations if annotations is not None else {}
+            self._annotations = annotations
         else:
             self.radii = radii
             self.offset = offset
             self.rotation = rotation
             self.repetition = repetition
-            self.annotations = annotations if annotations is not None else {}
+            self.annotations = annotations
 
     def __deepcopy__(self, memo: dict | None = None) -> Self:
         memo = {} if memo is None else memo

masque/shapes/path.py

@@ -170,7 +170,7 @@ class Path(Shape):
             offset: ArrayLike = (0.0, 0.0),
             rotation: float = 0,
             repetition: Repetition | None = None,
-            annotations: annotations_t | None = None,
+            annotations: annotations_t = None,
             raw: bool = False,
             ) -> None:
         self._cap_extensions = None     # Since .cap setter might access it
@@ -182,7 +182,7 @@ class Path(Shape):
             self._vertices = vertices
             self._offset = offset
             self._repetition = repetition
-            self._annotations = annotations if annotations is not None else {}
+            self._annotations = annotations
             self._width = width
             self._cap = cap
             self._cap_extensions = cap_extensions
@@ -190,7 +190,7 @@ class Path(Shape):
             self.vertices = vertices
             self.offset = offset
             self.repetition = repetition
-            self.annotations = annotations if annotations is not None else {}
+            self.annotations = annotations
             self.width = width
             self.cap = cap
             self.cap_extensions = cap_extensions

masque/shapes/poly_collection.py

@@ -0,0 +1,207 @@
+from typing import Any, cast, Self
+from collections.abc import Iterator
+import copy
+import functools
+from itertools import chain
+
+import numpy
+from numpy import pi
+from numpy.typing import NDArray, ArrayLike
+
+from . import Shape, normalized_shape_tuple
+from .polygon import Polygon
+from ..repetition import Repetition
+from ..utils import rotation_matrix_2d, annotations_lt, annotations_eq, rep2key, annotations_t
+
+
+@functools.total_ordering
+class PolyCollection(Shape):
+    """
+    A collection of polygons, consisting of concatenated vertex arrays (N_m x 2 ndarray) which specify
+       implicitly-closed boundaries, and an array of offets specifying the first vertex of each
+       successive polygon.
+
+    A `normalized_form(...)` is available, but is untested and probably fairly slow.
+    """
+    __slots__ = (
+        '_vertex_lists',
+        '_vertex_offsets',
+        # Inherited
+        '_offset', '_repetition', '_annotations',
+        )
+
+    _vertex_lists: NDArray[numpy.float64]
+    """ 2D NDArray ((N+M+...) x 2)  of vertices `[[xa0, ya0], [xa1, ya1], ..., [xb0, yb0], [xb1, yb1], ... ]` """
+
+    _vertex_offsets: NDArray[numpy.intp]
+    """ 1D NDArray specifying the starting offset for each polygon """
+
+    @property
+    def vertex_lists(self) -> Any:        # mypy#3004   NDArray[numpy.float64]:
+        """
+        Vertices of the polygons, ((N+M+...) x 2). Use with `vertex_offsets`.
+        """
+        return self._vertex_lists
+
+    @property
+    def vertex_offsets(self) -> Any:        # mypy#3004   NDArray[numpy.intp]:
+        """
+        Starting offset (in `vertex_lists`) for each polygon
+        """
+        return self._vertex_offsets
+
+    @property
+    def vertex_slices(self) -> Iterator[slice]:
+        """
+        Iterator which provides slices which index vertex_lists
+        """
+        for ii, ff in zip(
+                self._vertex_offsets,
+                chain(self._vertex_offsets, (self._vertex_lists.shape[0],)),
+                strict=True,
+                ):
+            yield slice(ii, ff)
+
+    @property
+    def polygon_vertices(self) -> Iterator[NDArray[numpy.float64]]:
+        for slc in self.vertex_slices:
+            yield self._vertex_lists[slc]
+
+    def __init__(
+            self,
+            vertex_lists: ArrayLike,
+            vertex_offsets: ArrayLike,
+            *,
+            offset: ArrayLike = (0.0, 0.0),
+            rotation: float = 0.0,
+            repetition: Repetition | None = None,
+            annotations: annotations_t = None,
+            raw: bool = False,
+            ) -> None:
+        if raw:
+            assert isinstance(vertex_lists, numpy.ndarray)
+            assert isinstance(vertex_offsets, numpy.ndarray)
+            assert isinstance(offset, numpy.ndarray)
+            self._vertex_lists = vertex_lists
+            self._vertex_offsets = vertex_offsets
+            self._offset = offset
+            self._repetition = repetition
+            self._annotations = annotations
+        else:
+            self._vertex_lists = numpy.asarray(vertex_lists, dtype=float)
+            self._vertex_offsets = numpy.asarray(vertex_offsets, dtype=numpy.intp)
+            self.offset = offset
+            self.repetition = repetition
+            self.annotations = annotations
+        if rotation:
+            self.rotate(rotation)
+
+    def __deepcopy__(self, memo: dict | None = None) -> Self:
+        memo = {} if memo is None else memo
+        new = copy.copy(self)
+        new._offset = self._offset.copy()
+        new._vertex_lists = self._vertex_lists.copy()
+        new._vertex_offsets = self._vertex_offsets.copy()
+        new._annotations = copy.deepcopy(self._annotations)
+        return new
+
+    def __eq__(self, other: Any) -> bool:
+        return (
+            type(self) is type(other)
+            and numpy.array_equal(self.offset, other.offset)
+            and numpy.array_equal(self._vertex_lists, other._vertex_lists)
+            and numpy.array_equal(self._vertex_offsets, other._vertex_offsets)
+            and self.repetition == other.repetition
+            and annotations_eq(self.annotations, other.annotations)
+            )
+
+    def __lt__(self, other: Shape) -> bool:
+        if type(self) is not type(other):
+            if repr(type(self)) != repr(type(other)):
+                return repr(type(self)) < repr(type(other))
+            return id(type(self)) < id(type(other))
+
+        other = cast('PolyCollection', other)
+
+        for vv, oo in zip(self.polygon_vertices, other.polygon_vertices, strict=False):
+            if not numpy.array_equal(vv, oo):
+                min_len = min(vv.shape[0], oo.shape[0])
+                eq_mask = vv[:min_len] != oo[:min_len]
+                eq_lt = vv[:min_len] < oo[:min_len]
+                eq_lt_masked = eq_lt[eq_mask]
+                if eq_lt_masked.size > 0:
+                    return eq_lt_masked.flat[0]
+                return vv.shape[0] < oo.shape[0]
+        if len(self.vertex_lists) != len(other.vertex_lists):
+            return len(self.vertex_lists) < len(other.vertex_lists)
+        if not numpy.array_equal(self.offset, other.offset):
+            return tuple(self.offset) < tuple(other.offset)
+        if self.repetition != other.repetition:
+            return rep2key(self.repetition) < rep2key(other.repetition)
+        return annotations_lt(self.annotations, other.annotations)
+
+    def to_polygons(
+            self,
+            num_vertices: int | None = None,      # unused  # noqa: ARG002
+            max_arclen: float | None = None,      # unused  # noqa: ARG002
+            ) -> list['Polygon']:
+        return [Polygon(
+            vertices = vv,
+            offset = self.offset,
+            repetition = copy.deepcopy(self.repetition),
+            annotations = copy.deepcopy(self.annotations),
+            ) for vv in self.polygon_vertices]
+
+    def get_bounds_single(self) -> NDArray[numpy.float64]:         # TODO note shape get_bounds doesn't include repetition
+        return numpy.vstack((self.offset + numpy.min(self._vertex_lists, axis=0),
+                             self.offset + numpy.max(self._vertex_lists, axis=0)))
+
+    def rotate(self, theta: float) -> Self:
+        if theta != 0:
+            rot = rotation_matrix_2d(theta)
+            self._vertex_lists = numpy.einsum('ij,kj->ki', rot, self._vertex_lists)
+        return self
+
+    def mirror(self, axis: int = 0) -> Self:
+        self._vertex_lists[:, axis - 1] *= -1
+        return self
+
+    def scale_by(self, c: float) -> Self:
+        self._vertex_lists *= c
+        return self
+
+    def normalized_form(self, norm_value: float) -> normalized_shape_tuple:
+        # Note: this function is going to be pretty slow for many-vertexed polygons, relative to
+        #   other shapes
+        meanv = self._vertex_lists.mean(axis=0)
+        zeroed_vertices = self._vertex_lists - [meanv]
+        offset = meanv + self.offset
+
+        scale = zeroed_vertices.std()
+        normed_vertices = zeroed_vertices / scale
+
+        _, _, vertex_axis = numpy.linalg.svd(zeroed_vertices)
+        rotation = numpy.arctan2(vertex_axis[0][1], vertex_axis[0][0]) % (2 * pi)
+        rotated_vertices = numpy.einsum('ij,kj->ki', rotation_matrix_2d(-rotation), normed_vertices)
+
+        # TODO consider how to reorder vertices for polycollection
+        ## Reorder the vertices so that the one with lowest x, then y, comes first.
+        #x_min = rotated_vertices[:, 0].argmin()
+        #if not is_scalar(x_min):
+        #    y_min = rotated_vertices[x_min, 1].argmin()
+        #    x_min = cast('Sequence', x_min)[y_min]
+        #reordered_vertices = numpy.roll(rotated_vertices, -x_min, axis=0)
+
+        # TODO: normalize mirroring?
+
+        return ((type(self), rotated_vertices.data.tobytes() + self._vertex_offsets.tobytes()),
+                (offset, scale / norm_value, rotation, False),
+                lambda: PolyCollection(
+                    vertex_lists=rotated_vertices * norm_value,
+                    vertex_offsets=self._vertex_offsets,
+                    ),
+                )
+
+    def __repr__(self) -> str:
+        centroid = self.offset + self.vertex_lists.mean(axis=0)
+        return f'<PolyCollection centroid {centroid} p{len(self.vertex_offsets)}>'

masque/shapes/polygon.py

@@ -92,7 +92,7 @@ class Polygon(Shape):
             offset: ArrayLike = (0.0, 0.0),
             rotation: float = 0.0,
             repetition: Repetition | None = None,
-            annotations: annotations_t | None = None,
+            annotations: annotations_t = None,
             raw: bool = False,
             ) -> None:
         if raw:
@@ -101,13 +101,14 @@ class Polygon(Shape):
             self._vertices = vertices
             self._offset = offset
             self._repetition = repetition
-            self._annotations = annotations if annotations is not None else {}
+            self._annotations = annotations
         else:
             self.vertices = vertices
             self.offset = offset
             self.repetition = repetition
-            self.annotations = annotations if annotations is not None else {}
-        self.rotate(rotation)
+            self.annotations = annotations
+        if rotation:
+            self.rotate(rotation)
 
     def __deepcopy__(self, memo: dict | None = None) -> 'Polygon':
         memo = {} if memo is None else memo

masque/shapes/text.py

@@ -71,7 +71,7 @@ class Text(RotatableImpl, Shape):
             offset: ArrayLike = (0.0, 0.0),
             rotation: float = 0.0,
             repetition: Repetition | None = None,
-            annotations: annotations_t | None = None,
+            annotations: annotations_t = None,
             raw: bool = False,
             ) -> None:
         if raw:
@@ -81,14 +81,14 @@ class Text(RotatableImpl, Shape):
             self._height = height
             self._rotation = rotation
             self._repetition = repetition
-            self._annotations = annotations if annotations is not None else {}
+            self._annotations = annotations
         else:
             self.offset = offset
             self.string = string
             self.height = height
             self.rotation = rotation
             self.repetition = repetition
-            self.annotations = annotations if annotations is not None else {}
+            self.annotations = annotations
         self.font_path = font_path
 
     def __deepcopy__(self, memo: dict | None = None) -> Self:

masque/traits/annotatable.py

@@ -45,6 +45,6 @@ class AnnotatableImpl(Annotatable, metaclass=ABCMeta):
 
     @annotations.setter
     def annotations(self, annotations: annotations_t) -> None:
-        if not isinstance(annotations, dict):
-            raise MasqueError(f'annotations expected dict, got {type(annotations)}')
+        if not isinstance(annotations, dict) and annotations is not None:
+            raise MasqueError(f'annotations expected dict or None, got {type(annotations)}')
         self._annotations = annotations

masque/utils/curves.py

@@ -5,7 +5,7 @@ from numpy import pi
 try:
     from numpy import trapezoid
 except ImportError:
-    from numpy import trapz as trapezoid
+    from numpy import trapz as trapezoid        # type:ignore
 
 
 def bezier(

masque/utils/types.py

@@ -5,7 +5,7 @@ from typing import Protocol
 
 
 layer_t = int | tuple[int, int] | str
-annotations_t = dict[str, list[int | float | str]]
+annotations_t = dict[str, list[int | float | str]] | None
 
 
 class SupportsBool(Protocol):