Add GridRepetition: a SubPattern-like object which implements regular spatial arrays.

Also rework masque.file.gdsii to consolidate write() and
write_dose2dtype()
This commit is contained in:
jan 2019-03-31 20:57:10 -07:00
parent 539198435c
commit c50bd8e148
4 changed files with 492 additions and 132 deletions

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@ -27,6 +27,7 @@ from .error import PatternError
from .shapes import Shape
from .label import Label
from .subpattern import SubPattern
from .repetition import GridRepetition
from .pattern import Pattern

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@ -6,12 +6,12 @@ import gdsii.library
import gdsii.structure
import gdsii.elements
from typing import List, Any, Dict
from typing import List, Any, Dict, Tuple
import re
import numpy
from .utils import mangle_name, make_dose_table
from .. import Pattern, SubPattern, PatternError, Label
from .. import Pattern, SubPattern, GridRepetition, PatternError, Label, Shape
from ..shapes import Polygon
from ..utils import rotation_matrix_2d, get_bit, set_bit, vector2, is_scalar
@ -74,45 +74,13 @@ def write(patterns: Pattern or List[Pattern],
structure = gdsii.structure.Structure(name=encoded_name)
lib.append(structure)
# Add a Boundary element for each shape
for shape in pat.shapes:
layer, data_type = _mlayer2gds(shape.layer)
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, :]))
structure.append(gdsii.elements.Boundary(layer=layer,
data_type=data_type,
xy=xy_closed))
for label in pat.labels:
layer, text_type = _mlayer2gds(label.layer)
xy = numpy.round([label.offset]).astype(int)
structure.append(gdsii.elements.Text(layer=layer,
text_type=text_type,
xy=xy,
string=label.string.encode('ASCII')))
structure += _shapes_to_boundaries(pat.shapes)
# Add an SREF for each subpattern entry
# strans must be set for angle and mag to take effect
for subpat in pat.subpatterns:
sanitized_name = re.compile('[^A-Za-z0-9_\?\$]').sub('_', subpat.pattern.name)
encoded_name = sanitized_name.encode('ASCII')
if len(encoded_name) == 0:
raise PatternError('Zero-length name after sanitize+encode, originally "{}"'.format(subpat.pattern.name))
sref = gdsii.elements.SRef(struct_name=encoded_name,
xy=numpy.round([subpat.offset]).astype(int))
sref.strans = 0
sref.angle = subpat.rotation * 180 / numpy.pi
mirror_x, mirror_y = subpat.mirrored
if mirror_y and mirror_y:
sref.angle += 180
elif mirror_x:
sref.strans = set_bit(sref.strans, 15 - 0, True)
elif mirror_y:
sref.angle += 180
sref.strans = set_bit(sref.strans, 15 - 0, True)
sref.mag = subpat.scale
structure.append(sref)
structure += _labels_to_texts(pat.labels)
# Add an SREF / AREF for each subpattern entry
structure += _subpatterns_to_refs(pat.subpatterns)
with open(filename, mode='wb') as stream:
lib.save(stream)
@ -155,12 +123,31 @@ def write_dose2dtype(patterns: Pattern or List[Pattern],
:returns: A list of doses, providing a mapping between datatype (int, list index)
and dose (float, list entry).
"""
# Create library
lib = gdsii.library.Library(version=600,
name='masque-write_dose2dtype'.encode('ASCII'),
logical_unit=logical_units_per_unit,
physical_unit=meters_per_unit)
patterns, dose_vals = dose2dtype(patterns)
write(patterns, filename, meters_per_unit, logical_units_per_unit)
return dose_vals
def dose2dtype(patterns: Pattern or List[Pattern],
) -> Tuple[List[Pattern], List[float]]:
"""
For each shape in each pattern, set shape.layer to the tuple
(base_layer, datatype), where:
layer is chosen to be equal to the original shape.layer if it is an int,
or shape.layer[0] if it is a tuple
datatype is chosen arbitrarily, based on calcualted dose for each shape.
Shapes with equal calcualted dose will have the same datatype.
A list of doses is retured, providing a mapping between datatype
(list index) and dose (list entry).
Note that this function modifies the input Pattern(s).
:param patterns: A Pattern or list of patterns to write to file. Modified by this function.
:returns: (patterns, dose_list)
patterns: modified input patterns
dose_list: A list of doses, providing a mapping between datatype (int, list index)
and dose (float, list entry).
"""
if isinstance(patterns, Pattern):
patterns = [patterns]
@ -183,66 +170,36 @@ def write_dose2dtype(patterns: Pattern or List[Pattern],
if len(dose_vals) > 256:
raise PatternError('Too many dose values: {}, maximum 256 when using dtypes.'.format(len(dose_vals)))
dose_vals_list = list(dose_vals)
# Now create a structure for each row in sd_table (ie, each pattern + dose combination)
# and add in any Boundary and SREF elements
# 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:
pat = patterns_by_id[pat_id]
if pat_dose == 1:
new_pats[(pat_id, pat_dose)] = patterns_by_id[pat_id]
continue
pat = patterns_by_id[pat_id].deepcopy()
encoded_name = mangle_name(pat, pat_dose).encode('ASCII')
if len(encoded_name) == 0:
raise PatternError('Zero-length name after mangle+encode, originally "{}"'.format(pat.name))
structure = gdsii.structure.Structure(name=encoded_name)
lib.append(structure)
# Add a Boundary element for each shape
for shape in pat.shapes:
for polygon in shape.to_polygons():
data_type = dose_vals_list.index(polygon.dose * pat_dose)
xy_open = numpy.round(polygon.vertices + polygon.offset).astype(int)
xy_closed = numpy.vstack((xy_open, xy_open[0, :]))
if is_scalar(polygon.layer):
layer = polygon.layer
else:
layer = polygon.layer[0]
structure.append(gdsii.elements.Boundary(layer=layer,
data_type=data_type,
xy=xy_closed))
for label in pat.labels:
layer, text_type = _mlayer2gds(label.layer)
xy = numpy.round([label.offset]).astype(int)
structure.append(gdsii.elements.Text(layer=layer,
text_type=text_type,
xy=xy,
string=label.string.encode('ASCII')))
data_type = dose_vals_list.index(shape.dose * pat_dose)
if is_scalar(shape.layer):
layer = (shape.layer, data_type)
else:
layer = (shape.layer[0], data_type)
# Add an SREF for each subpattern entry
# strans must be set for angle and mag to take effect
new_pats[(pat_id, pat_dose)] = 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
encoded_name = mangle_name(subpat.pattern, dose_mult).encode('ASCII')
if len(encoded_name) == 0:
raise PatternError('Zero-length name after mangle+encode, originally "{}"'.format(subpat.pattern.name))
sref = gdsii.elements.SRef(struct_name=encoded_name,
xy=numpy.round([subpat.offset]).astype(int))
sref.strans = 0
sref.angle = subpat.rotation * 180 / numpy.pi
sref.mag = subpat.scale
mirror_x, mirror_y = subpat.mirrored
if mirror_y and mirror_y:
sref.angle += 180
elif mirror_x:
sref.strans = set_bit(sref.strans, 15 - 0, True)
elif mirror_y:
sref.angle += 180
sref.strans = set_bit(sref.strans, 15 - 0, True)
structure.append(sref)
subpat.pattern = new_pats[(id(subpat.pattern), dose_mult)]
with open(filename, mode='wb') as stream:
lib.save(stream)
return dose_vals_list
return patterns, list(dose_vals)
def read_dtype2dose(filename: str) -> (List[Pattern], Dict[str, Any]):
@ -285,34 +242,6 @@ def read(filename: str,
'logical_units_per_unit': lib.logical_unit,
}
def ref_element_to_subpat(element, offset: vector2) -> SubPattern:
# Helper function to create a SubPattern from an SREF or AREF. Sets subpat.pattern to None
# and sets the instance attribute .ref_name to the struct_name.
#
# BUG: "Absolute" means not affected by parent elements.
# That's not currently supported by masque at all, so need to either tag it and
# undo the parent transformations, or implement it in masque.
subpat = SubPattern(pattern=None, offset=offset)
subpat.ref_name = element.struct_name
if element.strans is not None:
if element.mag is not None:
subpat.scale = element.mag
# Bit 13 means absolute scale
if get_bit(element.strans, 15 - 13):
#subpat.offset *= subpat.scale
raise PatternError('Absolute scale is not implemented yet!')
if element.angle is not None:
subpat.rotation = element.angle * numpy.pi / 180
# Bit 14 means absolute rotation
if get_bit(element.strans, 15 - 14):
#subpat.offset = numpy.dot(rotation_matrix_2d(subpat.rotation), subpat.offset)
raise PatternError('Absolute rotation is not implemented yet!')
# Bit 0 means mirror x-axis
if get_bit(element.strans, 15 - 0):
subpat.mirror(axis=0)
return subpat
patterns = []
for structure in lib:
pat = Pattern(name=structure.name.decode('ASCII'))
@ -341,18 +270,10 @@ def read(filename: str,
pat.labels.append(label)
elif isinstance(element, gdsii.elements.SRef):
pat.subpatterns.append(ref_element_to_subpat(element, element.xy))
pat.subpatterns.append(_sref_to_subpat(element))
elif isinstance(element, gdsii.elements.ARef):
xy = numpy.array(element.xy)
origin = xy[0]
col_spacing = (xy[1] - origin) / element.cols
row_spacing = (xy[2] - origin) / element.rows
for c in range(element.cols):
for r in range(element.rows):
offset = origin + c * col_spacing + r * row_spacing
pat.subpatterns.append(ref_element_to_subpat(element, offset))
pat.subpatterns.append(_aref_to_gridrep(element))
patterns.append(pat)
@ -378,3 +299,149 @@ def _mlayer2gds(mlayer):
else:
data_type = 0
return layer, data_type
def _sref_to_subpat(element: gdsii.elements.SRef) -> SubPattern:
# Helper function to create a SubPattern from an SREF. Sets subpat.pattern to None
# and sets the instance attribute .ref_name to the struct_name.
#
# BUG: "Absolute" means not affected by parent elements.
# That's not currently supported by masque at all, so need to either tag it and
# undo the parent transformations, or implement it in masque.
subpat = SubPattern(pattern=None, offset=element.xy)
subpat.ref_name = element.struct_name
if element.strans is not None:
if element.mag is not None:
subpat.scale = element.mag
# Bit 13 means absolute scale
if get_bit(element.strans, 15 - 13):
#subpat.offset *= subpat.scale
raise PatternError('Absolute scale is not implemented yet!')
if element.angle is not None:
subpat.rotation = element.angle * numpy.pi / 180
# Bit 14 means absolute rotation
if get_bit(element.strans, 15 - 14):
#subpat.offset = numpy.dot(rotation_matrix_2d(subpat.rotation), subpat.offset)
raise PatternError('Absolute rotation is not implemented yet!')
# Bit 0 means mirror x-axis
if get_bit(element.strans, 15 - 0):
subpat.mirror(axis=0)
return subpat
def _aref_to_gridrep(element: gdsii.elements.ARef) -> GridRepetition:
# Helper function to create a GridRepetition from an AREF. Sets gridrep.pattern to None
# and sets the instance attribute .ref_name to the struct_name.
#
# BUG: "Absolute" means not affected by parent elements.
# That's not currently supported by masque at all, so need to either tag it and
# undo the parent transformations, or implement it in masque.i
rotation = 0
offset = numpy.array(element.xy[0])
scale = 1
mirror_signs = numpy.ones(2)
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 yet!')
if element.angle is not None:
rotation = element.angle * numpy.pi / 180
# Bit 14 means absolute rotation
if get_bit(element.strans, 15 - 14):
raise PatternError('Absolute rotation is not implemented yet!')
# Bit 0 means mirror x-axis
if get_bit(element.strans, 15 - 0):
mirror_signs[0] = -1
counts = [element.cols, element.rows]
vec_a0 = element.xy[1] - offset
vec_b0 = element.xy[2] - offset
a_vector = numpy.dot(rotation_matrix_2d(-rotation), vec_a0 / scale / counts[0]) * mirror_signs[0]
b_vector = numpy.dot(rotation_matrix_2d(-rotation), vec_b0 / scale / counts[1]) * mirror_signs[1]
gridrep = GridRepetition(pattern=None,
a_vector=a_vector,
b_vector=b_vector,
a_count=counts[0],
b_count=counts[1],
offset=offset,
rotation=rotation,
scale=scale,
mirrored=(mirror_signs == -1))
gridrep.ref_name = element.struct_name
return gridrep
def _subpatterns_to_refs(subpatterns: List[SubPattern or GridRepetition]
) -> List[gdsii.elements.ARef or gdsii.elements.SRef]:
# strans must be set for angle and mag to take effect
refs = []
for subpat in subpatterns:
sanitized_name = re.compile('[^A-Za-z0-9_\?\$]').sub('_', subpat.pattern.name)
encoded_name = sanitized_name.encode('ASCII')
if len(encoded_name) == 0:
raise PatternError('Zero-length name after sanitize+encode, originally "{}"'.format(subpat.pattern.name))
if isinstance(subpat, GridRepetition):
mirror_signs = (-1) ** numpy.array(subpat.mirrored)
xy = numpy.array(subpat.offset) + [
[0, 0],
numpy.dot(rotation_matrix_2d(subpat.rotation), subpat.a_vector * mirror_signs) * subpat.scale * subpat.a_count,
numpy.dot(rotation_matrix_2d(subpat.rotation), subpat.b_vector * mirror_signs) * subpat.scale * subpat.b_count,
]
ref = gdsii.elements.ARef(struct_name=encoded_name,
xy=numpy.round(xy).astype(int),
cols=subpat.a_count,
rows=subpat.b_count)
else:
ref = gdsii.elements.SRef(struct_name=encoded_name,
xy=numpy.round([subpat.offset]).astype(int))
ref.strans = 0
ref.angle = subpat.rotation * 180 / numpy.pi
mirror_x, mirror_y = subpat.mirrored
if mirror_y and mirror_y:
ref.angle += 180
elif mirror_x:
ref.strans = set_bit(ref.strans, 15 - 0, True)
elif mirror_y:
ref.angle += 180
ref.strans = set_bit(ref.strans, 15 - 0, True)
ref.mag = subpat.scale
refs.append(ref)
return refs
def _shapes_to_boundaries(shapes: List[Shape]
) -> List[gdsii.elements.Boundary]:
# Add a Boundary element for each shape
boundaries = []
for shape in shapes:
layer, data_type = _mlayer2gds(shape.layer)
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, :]))
boundaries.append(gdsii.elements.Boundary(layer=layer,
data_type=data_type,
xy=xy_closed))
return boundaries
def _labels_to_texts(labels: List[Label]) -> List[gdsii.elements.Text]:
texts = []
for label in labels:
layer, text_type = _mlayer2gds(label.layer)
xy = numpy.round([label.offset]).astype(int)
texts.append(gdsii.elements.Text(layer=layer,
text_type=text_type,
xy=xy,
string=label.string.encode('ASCII')))
return texts

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@ -12,6 +12,7 @@ import numpy
# .visualize imports matplotlib and matplotlib.collections
from .subpattern import SubPattern
from .repetition import GridRepetition
from .shapes import Shape, Polygon
from .label import Label
from .utils import rotation_matrix_2d, vector2
@ -34,7 +35,7 @@ class Pattern:
"""
shapes = None # type: List[Shape]
labels = None # type: List[Labels]
subpatterns = None # type: List[SubPattern]
subpatterns = None # type: List[SubPattern or GridRepetition]
name = None # type: str
def __init__(self,

291
masque/repetition.py Normal file
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@ -0,0 +1,291 @@
"""
Repetitions provides support for efficiently nesting multiple identical
instances of a Pattern in the same parent Pattern.
"""
from typing import Union, List
import copy
import numpy
from numpy import pi
from .error import PatternError
from .utils import is_scalar, rotation_matrix_2d, vector2
__author__ = 'Jan Petykiewicz'
# TODO need top-level comment about what order rotation/scale/offset/mirror/array are applied
class GridRepetition:
"""
GridRepetition provides support for efficiently embedding multiple copies of a Pattern
into another Pattern at regularly-spaced offsets.
"""
pattern = None # type: Pattern
_offset = (0.0, 0.0) # type: numpy.ndarray
_rotation = 0.0 # type: float
_dose = 1.0 # type: float
_scale = 1.0 # type: float
_mirrored = None # type: List[bool]
_a_vector = None # type: numpy.ndarray
_b_vector = None # type: numpy.ndarray
a_count = None # type: int
b_count = 1 # type: int
def __init__(self,
pattern: 'Pattern',
a_vector: numpy.ndarray,
a_count: int,
b_vector: numpy.ndarray = None,
b_count: int = 1,
offset: vector2 = (0.0, 0.0),
rotation: float = 0.0,
mirrored: List[bool] = None,
dose: float = 1.0,
scale: float = 1.0):
"""
:param a_vector: First lattice vector, of the form [x, y].
Specifies center-to-center spacing between adjacent elements.
:param a_count: Number of elements in the a_vector direction.
:param b_vector: Second lattice vector, of the form [x, y].
Specifies center-to-center spacing between adjacent elements.
Can be omitted when specifying a 1D array.
:param b_count: Number of elements in the b_vector direction.
Should be omitted if b_vector was omitted.
:raises: InvalidDataError if b_* inputs conflict with each other
or a_count < 1.
"""
if b_vector is None:
if b_count > 1:
raise PatternError('Repetition has b_count > 1 but no b_vector')
else:
b_vector = numpy.array([0.0, 0.0])
if a_count < 1:
raise InvalidDataError('Repetition has too-small a_count: '
'{}'.format(a_count))
if b_count < 1:
raise InvalidDataError('Repetition has too-small b_count: '
'{}'.format(b_count))
self.a_vector = a_vector
self.b_vector = b_vector
self.a_count = a_count
self.b_count = b_count
self.pattern = pattern
self.offset = offset
self.rotation = rotation
self.dose = dose
self.scale = scale
if mirrored is None:
mirrored = [False, False]
self.mirrored = mirrored
# offset property
@property
def offset(self) -> numpy.ndarray:
return self._offset
@offset.setter
def offset(self, val: vector2):
if not isinstance(val, numpy.ndarray):
val = numpy.array(val, dtype=float)
if val.size != 2:
raise PatternError('Offset must be convertible to size-2 ndarray')
self._offset = val.flatten()
# dose property
@property
def dose(self) -> float:
return self._dose
@dose.setter
def dose(self, val: float):
if not is_scalar(val):
raise PatternError('Dose must be a scalar')
if not val >= 0:
raise PatternError('Dose must be non-negative')
self._dose = val
# scale property
@property
def scale(self) -> float:
return self._scale
@scale.setter
def scale(self, val: float):
if not is_scalar(val):
raise PatternError('Scale must be a scalar')
if not val > 0:
raise PatternError('Scale must be positive')
self._scale = val
# Rotation property [ccw]
@property
def rotation(self) -> float:
return self._rotation
@rotation.setter
def rotation(self, val: float):
if not is_scalar(val):
raise PatternError('Rotation must be a scalar')
self._rotation = val % (2 * pi)
# Mirrored property
@property
def mirrored(self) -> List[bool]:
return self._mirrored
@mirrored.setter
def mirrored(self, val: List[bool]):
if is_scalar(val):
raise PatternError('Mirrored must be a 2-element list of booleans')
self._mirrored = val
# a_vector property
@property
def a_vector(self) -> numpy.ndarray:
return self._a_vector
@a_vector.setter
def a_vector(self, val: vector2):
if not isinstance(val, numpy.ndarray):
val = numpy.array(val, dtype=float)
if val.size != 2:
raise PatternError('a_vector must be convertible to size-2 ndarray')
self._a_vector = val.flatten()
# b_vector property
@property
def b_vector(self) -> numpy.ndarray:
return self._b_vector
@b_vector.setter
def b_vector(self, val: vector2):
if not isinstance(val, numpy.ndarray):
val = numpy.array(val, dtype=float)
if val.size != 2:
raise PatternError('b_vector must be convertible to size-2 ndarray')
self._b_vector = val.flatten()
def as_pattern(self) -> 'Pattern':
"""
Returns a copy of self.pattern which has been scaled, rotated, etc. according to this
SubPattern's properties.
:return: Copy of self.pattern that has been altered to reflect the SubPattern's properties.
"""
#xy = numpy.array(element.xy)
#origin = xy[0]
#col_spacing = (xy[1] - origin) / element.cols
#row_spacing = (xy[2] - origin) / element.rows
patterns = []
for a in range(self.a_count):
for b in range(self.b_count):
offset = a * self.a_vector + b * self.b_vector
newPat = self.pattern.deepcopy()
newPat.translate_elements(offset)
patterns.append(newPat)
combined = patterns[0]
for p in patterns[1:]:
combined.append(p)
combined.scale_by(self.scale)
[combined.mirror(ax) for ax, do in enumerate(self.mirrored) if do]
combined.rotate_around((0.0, 0.0), self.rotation)
combined.translate_elements(self.offset)
combined.scale_element_doses(self.dose)
return combined
def translate(self, offset: vector2) -> 'GridRepetition':
"""
Translate by the given offset
:param offset: Translate by this offset
:return: self
"""
self.offset += offset
return self
def rotate_around(self, pivot: vector2, rotation: float) -> 'GridRepetition':
"""
Rotate around a point
:param pivot: Point to rotate around
:param rotation: Angle to rotate by (counterclockwise, radians)
:return: self
"""
pivot = numpy.array(pivot, dtype=float)
self.translate(-pivot)
self.offset = numpy.dot(rotation_matrix_2d(rotation), self.offset)
self.rotate(rotation)
self.translate(+pivot)
return self
def rotate(self, rotation: float) -> 'GridRepetition':
"""
Rotate around (0, 0)
:param rotation: Angle to rotate by (counterclockwise, radians)
:return: self
"""
self.rotation += rotation
return self
def mirror(self, axis: int) -> 'GridRepetition':
"""
Mirror the subpattern across an axis.
:param axis: Axis to mirror across.
:return: self
"""
self.mirrored[axis] = not self.mirrored[axis]
return self
def get_bounds(self) -> numpy.ndarray or None:
"""
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.
:return: [[x_min, y_min], [x_max, y_max]] or None
"""
return self.as_pattern().get_bounds()
def scale_by(self, c: float) -> 'GridRepetition':
"""
Scale the subpattern by a factor
:param c: scaling factor
"""
self.scale *= c
return self
def copy(self) -> 'GridRepetition':
"""
Return a shallow copy of the repetition.
:return: copy.copy(self)
"""
return copy.copy(self)
def deepcopy(self) -> 'SubPattern':
"""
Return a deep copy of the repetition.
:return: copy.copy(self)
"""
return copy.deepcopy(self)