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make klamath the default gdsii reader/writer, and install it automatically

python-gdsii code is now under masque.file.python_gdsii
lethe/LATEST
jan 1 year ago
parent
commit
e2fdd5a347
  1. 5
      README.md
  2. 519
      masque/file/gdsii.py
  3. 660
      masque/file/klamath.py
  4. 553
      masque/file/python_gdsii.py
  5. 2
      setup.py

5
README.md

@ -15,9 +15,8 @@ E-beam doses, and the ability to output to multiple formats.
Requirements:
* python >= 3.7 (written and tested with 3.8)
* numpy
* klamath (used for `gdsii` i/o and library management)
* matplotlib (optional, used for `visualization` functions and `text`)
* python-gdsii (optional, used for `gdsii` i/o)
* klamath (optional, used for `gdsii` i/o and library management)
* ezdxf (optional, used for `dxf` i/o)
* fatamorgana (optional, used for `oasis` i/o)
* svgwrite (optional, used for `svg` output)
@ -26,7 +25,7 @@ Requirements:
Install with pip:
```bash
pip3 install 'masque[visualization,gdsii,oasis,dxf,svg,text,klamath]'
pip3 install 'masque[visualization,oasis,dxf,svg,text]'
```
Alternatively, install from git

519
masque/file/gdsii.py

@ -1,5 +1,5 @@
"""
GDSII file format readers and writers
GDSII file format readers and writers using the `klamath` library.
Note that GDSII references follow the same convention as `masque`,
with this order of operations:
@ -16,11 +16,13 @@ Notes:
* PLEX is not supported
* ELFLAGS are not supported
* GDS does not support library- or structure-level annotations
* Creation/modification/access times are set to 1900-01-01 for reproducibility.
"""
from typing import List, Any, Dict, Tuple, Callable, Union, Iterable, Optional
from typing import Sequence
from typing import Sequence, BinaryIO
import re
import io
import mmap
import copy
import base64
import struct
@ -29,23 +31,20 @@ import pathlib
import gzip
import numpy # type: ignore
# python-gdsii
import gdsii.library
import gdsii.structure
import gdsii.elements
import klamath
from klamath import records
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
from ..repetition import Grid
from ..utils import get_bit, set_bit, layer_t, normalize_mirror, annotations_t
from ..utils import layer_t, normalize_mirror, annotations_t
from ..library import Library
logger = logging.getLogger(__name__)
path_cap_map = {
None: Path.Cap.Flush,
0: Path.Cap.Flush,
1: Path.Cap.Circle,
2: Path.Cap.Square,
@ -53,19 +52,23 @@ path_cap_map = {
}
def build(patterns: Union[Pattern, Sequence[Pattern]],
def write(patterns: Union[Pattern, Sequence[Pattern]],
stream: BinaryIO,
meters_per_unit: float,
logical_units_per_unit: float = 1,
library_name: str = 'masque-gdsii-write',
library_name: str = 'masque-klamath',
*,
modify_originals: bool = False,
disambiguate_func: Callable[[Iterable[Pattern]], None] = None,
) -> gdsii.library.Library:
) -> None:
"""
Convert a `Pattern` or list of patterns to a GDSII stream, by first calling
`.polygonize()` to change the shapes into polygons, and then writing patterns
as GDSII structures, polygons as boundary elements, and subpatterns as structure
references (sref).
Convert a `Pattern` or list of patterns to a GDSII stream, and then mapping data as follows:
Pattern -> GDSII structure
SubPattern -> GDSII SREF or AREF
Path -> GSDII path
Shape (other than path) -> GDSII boundary/ies
Label -> GDSII text
annnotations -> properties, where possible
For each shape,
layer is chosen to be equal to `shape.layer` if it is an int,
@ -87,7 +90,7 @@ def build(patterns: Union[Pattern, Sequence[Pattern]],
"logical" unit which is different from the "database" unit, for display purposes.
Default `1`.
library_name: Library name written into the GDSII file.
Default 'masque-gdsii-write'.
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.
Default `False`.
@ -95,9 +98,6 @@ def build(patterns: Union[Pattern, Sequence[Pattern]],
to make their names valid and unique. Default is `disambiguate_pattern_names`, which
attempts to adhere to the GDSII standard as well as possible.
WARNING: No additional error checking is performed on the results.
Returns:
`gdsii.library.Library`
"""
if isinstance(patterns, Pattern):
patterns = [patterns]
@ -112,10 +112,10 @@ def build(patterns: Union[Pattern, Sequence[Pattern]],
patterns = [p.wrap_repeated_shapes() for p in patterns]
# Create library
lib = gdsii.library.Library(version=600,
name=library_name.encode('ASCII'),
logical_unit=logical_units_per_unit,
physical_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}
@ -127,49 +127,30 @@ def build(patterns: Union[Pattern, Sequence[Pattern]],
# 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'))
lib.append(structure)
structure += _shapes_to_elements(pat.shapes)
structure += _labels_to_texts(pat.labels)
structure += _subpatterns_to_refs(pat.subpatterns)
elements: List[klamath.elements.Element] = []
elements += _shapes_to_elements(pat.shapes)
elements += _labels_to_texts(pat.labels)
elements += _subpatterns_to_refs(pat.subpatterns)
return lib
klamath.library.write_struct(stream, name=pat.name.encode('ASCII'), elements=elements)
records.ENDLIB.write(stream, None)
def write(patterns: Union[Pattern, Sequence[Pattern]],
stream: io.BufferedIOBase,
*args,
**kwargs):
"""
Write a `Pattern` or list of patterns to a GDSII file.
See `masque.file.gdsii.build()` for details.
Args:
patterns: A Pattern or list of patterns to write to file.
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.save(stream)
return
def writefile(patterns: Union[Sequence[Pattern], 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
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':
@ -178,8 +159,7 @@ def writefile(patterns: Union[Sequence[Pattern], Pattern],
open_func = open
with io.BufferedWriter(open_func(path, mode='wb')) as stream:
results = write(patterns, stream, *args, **kwargs)
return results
write(patterns, stream, *args, **kwargs)
def readfile(filename: Union[str, pathlib.Path],
@ -187,14 +167,14 @@ def readfile(filename: Union[str, pathlib.Path],
**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):
@ -207,8 +187,8 @@ def readfile(filename: Union[str, pathlib.Path],
return results
def read(stream: io.BufferedIOBase,
clean_vertices: bool = True,
def read(stream: BinaryIO,
raw_mode: bool = True,
) -> Tuple[Dict[str, Pattern], Dict[str, Any]]:
"""
Read a gdsii file and translate it into a dict of Pattern objects. GDSII structures are
@ -223,61 +203,83 @@ def read(stream: io.BufferedIOBase,
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`.
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
"""
lib = gdsii.library.Library.load(stream)
library_info = {'name': lib.name.decode('ASCII'),
'meters_per_unit': lib.physical_unit,
'logical_units_per_unit': lib.logical_unit,
}
raw_mode = True # Whether to construct shapes in raw mode (less error checking)
library_info = _read_header(stream)
patterns = []
for structure in lib:
pat = Pattern(name=structure.name.decode('ASCII'))
for element in structure:
# Switch based on element type:
if isinstance(element, gdsii.elements.Boundary):
poly = _boundary_to_polygon(element, raw_mode)
pat.shapes.append(poly)
if isinstance(element, gdsii.elements.Path):
path = _gpath_to_mpath(element, raw_mode)
pat.shapes.append(path)
elif isinstance(element, gdsii.elements.Text):
label = Label(offset=element.xy.astype(float),
layer=(element.layer, element.text_type),
string=element.string.decode('ASCII'))
pat.labels.append(label)
elif isinstance(element, (gdsii.elements.SRef, gdsii.elements.ARef)):
pat.subpatterns.append(_ref_to_subpat(element))
if clean_vertices:
clean_pattern_vertices(pat)
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)
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].decode('ASCII')]
sp.pattern = patterns_dict[sp.identifier[0]]
del sp.identifier
return patterns_dict, library_info
def _read_header(stream: BinaryIO) -> Dict[str, Any]:
"""
Read the file header and create the library_info dict.
"""
header = klamath.library.FileHeader.read(stream)
library_info = {'name': header.name.decode('ASCII'),
'meters_per_unit': header.meters_per_db_unit,
'logical_units_per_unit': header.user_units_per_db_unit,
}
return library_info
def read_elements(stream: BinaryIO,
name: str,
raw_mode: bool = True,
) -> Pattern:
"""
Read elements from a GDS structure and build a Pattern from them.
Args:
stream: Seekable stream, positioned at a record boundary.
Will be read until an ENDSTR record is consumed.
name: Name of the resulting Pattern
raw_mode: If True, bypass per-shape data validation. Default True.
Returns:
A pattern containing the elements that were read.
"""
pat = Pattern(name)
elements = klamath.library.read_elements(stream)
for element in elements:
if isinstance(element, klamath.elements.Boundary):
poly = _boundary_to_polygon(element, raw_mode)
pat.shapes.append(poly)
elif isinstance(element, klamath.elements.Path):
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))
pat.labels.append(label)
elif isinstance(element, klamath.elements.Reference):
pat.subpatterns.append(_ref_to_subpat(element))
return pat
def _mlayer2gds(mlayer: layer_t) -> Tuple[int, int]:
""" Helper to turn a layer tuple-or-int into a layer and datatype"""
if isinstance(mlayer, int):
@ -294,93 +296,63 @@ def _mlayer2gds(mlayer: layer_t) -> Tuple[int, int]:
return layer, data_type
def _ref_to_subpat(element: Union[gdsii.elements.SRef,
gdsii.elements.ARef]
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,).
NOTE: "Absolute" means not affected by parent elements.
That's not currently supported by masque at all (and not planned).
"""
rotation = 0.0
offset = numpy.array(element.xy[0], dtype=float)
scale = 1.0
mirror_across_x = False
xy = ref.xy.astype(float)
offset = xy[0]
repetition = None
if element.strans is not None:
if element.mag is not None:
scale = element.mag
# Bit 13 means absolute scale
if get_bit(element.strans, 15 - 13):
raise PatternError('Absolute scale is not implemented in masque!')
if element.angle is not None:
rotation = numpy.deg2rad(element.angle)
# Bit 14 means absolute rotation
if get_bit(element.strans, 15 - 14):
raise PatternError('Absolute rotation is not implemented in masque!')
# Bit 0 means mirror x-axis
if get_bit(element.strans, 15 - 0):
mirror_across_x = True
if isinstance(element, gdsii.elements.ARef):
a_count = element.cols
b_count = element.rows
a_vector = (element.xy[1] - offset) / a_count
b_vector = (element.xy[2] - offset) / b_count
if ref.colrow is not None:
a_count, b_count = ref.colrow
a_vector = (xy[1] - offset) / a_count
b_vector = (xy[2] - offset) / b_count
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=rotation,
scale=scale,
mirrored=(mirror_across_x, False),
annotations=_properties_to_annotations(element.properties),
rotation=numpy.deg2rad(ref.angle_deg),
scale=ref.mag,
mirrored=(ref.invert_y, False),
annotations=_properties_to_annotations(ref.properties),
repetition=repetition)
subpat.identifier = (element.struct_name,)
subpat.identifier = (ref.struct_name.decode('ASCII'),)
return subpat
def _gpath_to_mpath(element: gdsii.elements.Path, raw_mode: bool) -> Path:
if element.path_type in path_cap_map:
cap = path_cap_map[element.path_type]
def _gpath_to_mpath(gpath: klamath.library.Path, raw_mode: bool) -> Path:
if gpath.path_type in path_cap_map:
cap = path_cap_map[gpath.path_type]
else:
raise PatternError(f'Unrecognized path type: {element.path_type}')
args = {'vertices': element.xy.astype(float),
'layer': (element.layer, element.data_type),
'width': element.width if element.width is not None else 0.0,
'cap': cap,
'offset': numpy.zeros(2),
'annotations': _properties_to_annotations(element.properties),
'raw': raw_mode,
}
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,
)
if cap == Path.Cap.SquareCustom:
args['cap_extensions'] = numpy.zeros(2)
if element.bgn_extn is not None:
args['cap_extensions'][0] = element.bgn_extn
if element.end_extn is not None:
args['cap_extensions'][1] = element.end_extn
return Path(**args)
mpath.cap_extensions = gpath.extension
return mpath
def _boundary_to_polygon(element: gdsii.elements.Boundary, raw_mode: bool) -> Polygon:
args = {'vertices': element.xy[:-1].astype(float),
'layer': (element.layer, element.data_type),
'offset': numpy.zeros(2),
'annotations': _properties_to_annotations(element.properties),
'raw': raw_mode,
}
return Polygon(**args)
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,
)
def _subpatterns_to_refs(subpatterns: List[SubPattern]
) -> List[Union[gdsii.elements.ARef, gdsii.elements.SRef]]:
) -> List[klamath.library.Reference]:
refs = []
for subpat in subpatterns:
if subpat.pattern is None:
@ -390,47 +362,52 @@ def _subpatterns_to_refs(subpatterns: List[SubPattern]
# Note: GDS mirrors first and rotates second
mirror_across_x, extra_angle = normalize_mirror(subpat.mirrored)
rep = subpat.repetition
angle_deg = numpy.rad2deg(subpat.rotation + extra_angle) % 360
properties = _annotations_to_properties(subpat.annotations, 512)
new_refs: List[Union[gdsii.elements.SRef, gdsii.elements.ARef]]
ref: Union[gdsii.elements.SRef, gdsii.elements.ARef]
if isinstance(rep, Grid):
xy = numpy.array(subpat.offset) + [
[0, 0],
rep.a_vector * rep.a_count,
rep.b_vector * rep.b_count,
]
ref = gdsii.elements.ARef(struct_name=encoded_name,
xy=numpy.round(xy).astype(int),
cols=numpy.round(rep.a_count).astype(int),
rows=numpy.round(rep.b_count).astype(int))
new_refs = [ref]
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)
refs.append(aref)
elif rep is None:
ref = gdsii.elements.SRef(struct_name=encoded_name,
xy=numpy.round([subpat.offset]).astype(int))
new_refs = [ref]
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)
refs.append(ref)
else:
new_refs = [gdsii.elements.SRef(struct_name=encoded_name,
xy=numpy.round([subpat.offset + dd]).astype(int))
for dd in rep.displacements]
for ref in new_refs:
ref.angle = numpy.rad2deg(subpat.rotation + extra_angle) % 360
# strans must be non-None for angle and mag to take effect
ref.strans = set_bit(0, 15 - 0, mirror_across_x)
ref.mag = subpat.scale
ref.properties = _annotations_to_properties(subpat.annotations, 512)
refs += new_refs
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]
refs += new_srefs
return refs
def _properties_to_annotations(properties: List[Tuple[int, bytes]]) -> annotations_t:
return {str(k): [v.decode()] for k, v in properties}
def _properties_to_annotations(properties: Dict[int, bytes]) -> annotations_t:
return {str(k): [v.decode()] for k, v in properties.items()}
def _annotations_to_properties(annotations: annotations_t, max_len: int = 126) -> List[Tuple[int, bytes]]:
def _annotations_to_properties(annotations: annotations_t, max_len: int = 126) -> Dict[int, bytes]:
cum_len = 0
props = []
props = {}
for key, vals in annotations.items():
try:
i = int(key)
@ -446,14 +423,14 @@ def _annotations_to_properties(annotations: annotations_t, max_len: int = 126) -
cum_len += numpy.ceil(len(b) / 2) * 2 + 2
if cum_len > max_len:
raise PatternError(f'Sum of annotation data will be longer than {max_len} bytes! Generated bytes were {b!r}')
props.append((i, b))
props[i] = b
return props
def _shapes_to_elements(shapes: List[Shape],
polygonize_paths: bool = False
) -> List[Union[gdsii.elements.Boundary, gdsii.elements.Path]]:
elements: List[Union[gdsii.elements.Boundary, gdsii.elements.Path]] = []
) -> List[klamath.elements.Element]:
elements: List[klamath.elements.Element] = []
# Add a Boundary element for each shape, and Path elements if necessary
for shape in shapes:
layer, data_type = _mlayer2gds(shape.layer)
@ -462,36 +439,55 @@ def _shapes_to_elements(shapes: List[Shape],
xy = numpy.round(shape.vertices + shape.offset).astype(int)
width = numpy.round(shape.width).astype(int)
path_type = next(k for k, v in path_cap_map.items() if v == shape.cap) # reverse lookup
path = gdsii.elements.Path(layer=layer,
data_type=data_type,
xy=xy)
path.path_type = path_type
path.width = width
path.properties = properties
extension: Tuple[int, int]
if shape.cap == Path.Cap.SquareCustom and shape.cap_extensions is not None:
extension = tuple(shape.cap_extensions) # type: ignore
else:
extension = (0, 0)
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_open = numpy.round(polygon.vertices + polygon.offset).astype(int)
xy_closed = numpy.vstack((xy_open, xy_open[0, :]))
boundary = klamath.elements.Boundary(layer=(layer, data_type),
xy=xy_closed,
properties=properties)
elements.append(boundary)
else:
for polygon in shape.to_polygons():
xy_open = numpy.round(polygon.vertices + polygon.offset).astype(int)
xy_closed = numpy.vstack((xy_open, xy_open[0, :]))
boundary = gdsii.elements.Boundary(layer=layer,
data_type=data_type,
xy=xy_closed)
boundary.properties = properties
boundary = klamath.elements.Boundary(layer=(layer, data_type),
xy=xy_closed,
properties=properties)
elements.append(boundary)
return elements
def _labels_to_texts(labels: List[Label]) -> List[gdsii.elements.Text]:
def _labels_to_texts(labels: List[Label]) -> List[klamath.elements.Text]:
texts = []
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 = gdsii.elements.Text(layer=layer,
text_type=text_type,
xy=xy,
string=label.string.encode('ASCII'))
text.properties = properties
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
@ -551,3 +547,112 @@ def disambiguate_pattern_names(patterns: Sequence[Pattern],
pat.name = suffixed_name
used_names.append(suffixed_name)
def load_library(stream: BinaryIO,
tag: str,
is_secondary: Optional[Callable[[str], bool]] = None,
*,
full_load: bool = False,
) -> Tuple[Library, Dict[str, Any]]:
"""
Scan a GDSII stream to determine what structures are present, and create
a library from them. This enables deferred reading of structures
on an as-needed basis.
All structures are loaded as secondary
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.
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.
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):
return False
assert(is_secondary is not None)
stream.seek(0)
lib = Library()
if full_load:
# 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))
return lib, library_info
# Normal approach (scan and defer load)
library_info = _read_header(stream)
structs = klamath.library.scan_structs(stream)
for name_bytes, pos in structs.items():
name = name_bytes.decode('ASCII')
def mkstruct(pos: int = pos, name: str = name) -> Pattern:
stream.seek(pos)
return read_elements(stream, name, raw_mode=True)
lib.set_value(name, tag, mkstruct, secondary=is_secondary(name))
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,
) -> Tuple[Library, Dict[str, Any]]:
"""
Wrapper for `load_library()` that takes a filename or path instead of a stream.
Will automatically decompress the file if it is gzipped.
NOTE that any streams/mmaps opened will remain open until ALL of the
`PatternGenerator` objects in the library are garbage collected.
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
and reopened as an `io.BytesIO` stream.
full_load: If `True`, immediately loads all data. See `load_library`.
Returns:
Library object, allowing for deferred load of structures.
Additional library info (dict, same format as from `read`).
"""
path = pathlib.Path(filename)
if is_gzipped(path):
if mmap:
logger.info('Asked to mmap a gzipped file, reading into memory instead...')
base_stream = gzip.open(path, mode='rb')
stream = io.BytesIO(base_stream.read())
else:
base_stream = gzip.open(path, mode='rb')
stream = io.BufferedReader(base_stream)
else:
base_stream = open(path, mode='rb')
if mmap:
stream = mmap.mmap(base_stream.fileno(), 0, access=mmap.ACCESS_READ)
else:
stream = io.BufferedReader(base_stream)
return load_library(stream, tag, is_secondary)

660
masque/file/klamath.py

@ -1,658 +1,2 @@
"""
GDSII file format readers and writers using the `klamath` 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
* Creation/modification/access times are set to 1900-01-01 for reproducibility.
"""
from typing import List, Any, Dict, Tuple, Callable, Union, Iterable, Optional
from typing import Sequence, BinaryIO
import re
import io
import mmap
import copy
import base64
import struct
import logging
import pathlib
import gzip
import numpy # type: ignore
import klamath
from klamath import records
from .utils import is_gzipped
from .. import Pattern, SubPattern, PatternError, Label, Shape
from ..shapes import Polygon, Path
from ..repetition import Grid
from ..utils import layer_t, normalize_mirror, annotations_t
from ..library import Library
logger = logging.getLogger(__name__)
path_cap_map = {
0: Path.Cap.Flush,
1: Path.Cap.Circle,
2: Path.Cap.Square,
4: Path.Cap.SquareCustom,
}
def write(patterns: Union[Pattern, Sequence[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,
) -> None:
"""
Convert a `Pattern` or list of patterns to a GDSII stream, and then mapping data as follows:
Pattern -> GDSII structure
SubPattern -> GDSII SREF or AREF
Path -> GSDII path
Shape (other than path) -> GDSII boundary/ies
Label -> GDSII text
annnotations -> properties, where possible
For each shape,
layer is chosen to be equal to `shape.layer` if it is an int,
or `shape.layer[0]` if it is a tuple
datatype is chosen to be `shape.layer[1]` if available,
otherwise `0`
It is often a good idea to run `pattern.subpatternize()` prior to calling this function,
especially if calling `.polygonize()` will result in very many vertices.
If you want pattern polygonized with non-default arguments, just call `pattern.polygonize()`
prior to calling this function.
Args:
patterns: A Pattern or list of patterns to convert.
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
"logical" unit which is different from the "database" unit, for display purposes.
Default `1`.
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.
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.
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
if not modify_originals:
patterns = [p.deepunlock() for p in copy.deepcopy(patterns)]
patterns = [p.wrap_repeated_shapes() for p in patterns]
# 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.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():
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)
records.ENDLIB.write(stream, None)
def writefile(patterns: Union[Sequence[Pattern], Pattern],
filename: Union[str, pathlib.Path],
*args,
**kwargs,
) -> None:
"""
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
filename: Filename to save to.
*args: passed to `write()`
**kwargs: passed to `write()`
"""
path = pathlib.Path(filename)
if path.suffix == '.gz':
open_func: Callable = gzip.open
else:
open_func = open
with io.BufferedWriter(open_func(path, mode='wb')) as stream:
write(patterns, stream, *args, **kwargs)
def readfile(filename: Union[str, pathlib.Path],
*args,
**kwargs,
) -> Tuple[Dict[str, Pattern], 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()`
"""
path = pathlib.Path(filename)
if is_gzipped(path):
open_func: Callable = gzip.open
else:
open_func = open
with io.BufferedReader(open_func(path, mode='rb')) as stream:
results = read(stream, *args, **kwargs)
return results
def read(stream: BinaryIO,
raw_mode: bool = True,
) -> Tuple[Dict[str, Pattern], Dict[str, Any]]:
"""
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 SubPattern 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(stream)
patterns = []
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)
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
def _read_header(stream: BinaryIO) -> Dict[str, Any]:
"""
Read the file header and create the library_info dict.
"""
header = klamath.library.FileHeader.read(stream)
library_info = {'name': header.name.decode('ASCII'),
'meters_per_unit': header.meters_per_db_unit,
'logical_units_per_unit': header.user_units_per_db_unit,
}
return library_info
def read_elements(stream: BinaryIO,
name: str,
raw_mode: bool = True,
) -> Pattern:
"""
Read elements from a GDS structure and build a Pattern from them.
Args:
stream: Seekable stream, positioned at a record boundary.
Will be read until an ENDSTR record is consumed.
name: Name of the resulting Pattern
raw_mode: If True, bypass per-shape data validation. Default True.
Returns:
A pattern containing the elements that were read.
"""
pat = Pattern(name)
elements = klamath.library.read_elements(stream)
for element in elements:
if isinstance(element, klamath.elements.Boundary):
poly = _boundary_to_polygon(element, raw_mode)
pat.shapes.append(poly)
elif isinstance(element, klamath.elements.Path):
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))
pat.labels.append(label)
elif isinstance(element, klamath.elements.Reference):
pat.subpatterns.append(_ref_to_subpat(element))
return pat
def _mlayer2gds(mlayer: layer_t) -> Tuple[int, int]:
""" Helper to turn a layer tuple-or-int into a layer and datatype"""
if isinstance(mlayer, int):
layer = mlayer
data_type = 0
elif isinstance(mlayer, tuple):
layer = mlayer[0]
if len(mlayer) > 1:
data_type = mlayer[1]
else:
data_type = 0
else:
raise PatternError(f'Invalid layer for gdsii: {mlayer}. Note that gdsii layers cannot be strings.')
return layer, data_type
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,).
"""
xy = ref.xy.astype(float)
offset = xy[0]
repetition = None
if ref.colrow is not None:
a_count, b_count = ref.colrow
a_vector = (xy[1] - offset) / a_count
b_vector = (xy[2] - offset) / b_count
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'),)
return subpat
def _gpath_to_mpath(gpath: klamath.library.Path, raw_mode: bool) -> Path:
if gpath.path_type in path_cap_map:
cap = path_cap_map[gpath.path_type]
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,
)
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,
)
def _subpatterns_to_refs(subpatterns: List[SubPattern]
) -> List[klamath.library.Reference]:
refs = []
for subpat in subpatterns:
if subpat.pattern is None:
continue
encoded_name = subpat.pattern.name.encode('ASCII')
# Note: GDS mirrors first and rotates second
mirror_across_x, extra_angle = normalize_mirror(subpat.mirrored)
rep = subpat.repetition
angle_deg = numpy.rad2deg(subpat.rotation + extra_angle) % 360
properties = _annotations_to_properties(subpat.annotations, 512)
if isinstance(rep, Grid):
xy = numpy.array(subpat.offset) + [
[0, 0],
rep.a_vector * rep.a_count,
rep.b_vector * rep.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)
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)
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]
refs += new_srefs
return refs
def _properties_to_annotations(properties: Dict[int, bytes]) -> annotations_t:
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]:
cum_len = 0
props = {}
for key, vals in annotations.items():
try:
i = int(key)
except ValueError:
raise PatternError(f'Annotation key {key} is not convertable to an integer')
if not (0 < i < 126):
raise PatternError(f'Annotation key {key} converts to {i} (must be in the range [1,125])')
val_strings = ' '.join(str(val) for val in vals)
b = val_strings.encode()
if len(b) > 126:
raise PatternError(f'Annotation value {b!r} is longer than 126 characters!')
cum_len += numpy.ceil(len(b) / 2) * 2 + 2
if cum_len > max_len:
raise PatternError(f'Sum of annotation data will be longer than {max_len} bytes! Generated bytes were {b!r}')
props[i] = b
return props
def _shapes_to_elements(shapes: List[Shape],
polygonize_paths: bool = False
) -> List[klamath.elements.Element]:
elements: List[klamath.elements.Element] = []
# Add a Boundary element for each shape, and Path elements if necessary
for shape in shapes:
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)
path_type = next(k for k, v in path_cap_map.items() if v == shape.cap) # reverse lookup
extension: Tuple[int, int]
if shape.cap == Path.Cap.SquareCustom and shape.cap_extensions is not None:
extension = tuple(shape.cap_extensions) # type: ignore
else:
extension = (0, 0)
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_open = numpy.round(polygon.vertices + polygon.offset).astype(int)
xy_closed = numpy.vstack((xy_open, xy_open[0, :]))
boundary = klamath.elements.Boundary(layer=(layer, data_type),
xy=xy_closed,
properties=properties)
elements.append(boundary)
else:
for polygon in shape.to_polygons():
xy_open = numpy.round(polygon.vertices + polygon.offset).astype(int)
xy_closed = numpy.vstack((xy_open, xy_open[0, :]))
boundary = klamath.elements.Boundary(layer=(layer, data_type),
xy=xy_closed,
properties=properties)
elements.append(boundary)
return elements
def _labels_to_texts(labels: List[Label]) -> List[klamath.elements.Text]:
texts = []
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)
texts.append(text)
return texts
def disambiguate_pattern_names(patterns: Sequence[Pattern],
max_name_length: int = 32,
suffix_length: int = 6,
dup_warn_filter: Optional[Callable[[str], bool]] = None,
):
"""
Args:
patterns: List of patterns 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):