1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 301 302 303 304 305 306 307 308 309 310 311 312 313 314 315 316 317 318 319 320 321 322 323 324 325 326 327 328 329 330 331 332 333 334 335 336 337 338 339 340 341 342 343 344 345 346 347 348 349 350 351 352 353 354 355 356 357 358 359 360 361 362 363 364 365 366 367 368 369 370 371 372 373 374 375 376 377 378 379 380 381 382 383 384 385 386 387 388 389 390 391 392 393 394 395 396 397 398 399 400 401 402 403 404 405 406 407 408 409 410 411 412 413 414 415 416 417 418 419 420 421 422 423 424 425 426 427 428 429 430 431 432 433 434 435 436 437 438 439 440 441 442 443 444 445 446 447 448 449 450 451 452 453 454 455 456 457 458 459 460 461 462 463 464 465 466 467 468 469 470 471 472 473 474 475 476 477 478 479 480 481 482 483 484 485 486 487 488 489 490 491 492 493 494 495 496 497 498 499 500 501 502 503 504 505 506 507 508 509 510 511 512 513 514 515 516 517 518 519 520 521 522 523 524 525 526 527 528 529 530 531 532 533 534 535 536 537 538 539 540 541 542 543 544 545 546 547 548 549 550 551 552 553 554 555 556 557 558 559 560 561 562 563 564 565 566 567 568 569 570 571 572 573 574 575 576 577 578 579 580 581 582 583 584 585 586 587 588 589 590 591 592 593 594 595 596 597 598 599 600 601 602 603 604 605 606 607 608 609 610 611 612 613 614 615 616 617 618 619 620 621 622 623 624 625 626 627 628 629 630 631 632 633 634 635 636 637 638 639 640 641 642 643 644 645 646 647 648 649 650 651 652 653 654 655 656 657 658 659 660
|
import itertools
from brian2.codegen.cpp_prefs import C99Check
from brian2.core.functions import DEFAULT_FUNCTIONS, Function
from brian2.core.variables import (
AuxiliaryVariable,
Constant,
Subexpression,
Variable,
get_dtype_str,
)
from brian2.devices.device import all_devices
from brian2.parsing.bast import brian_dtype_from_dtype
from brian2.parsing.rendering import NodeRenderer
from brian2.utils.stringtools import deindent, indent, word_substitute
from .base import CodeGenerator
__all__ = ["CythonCodeGenerator"]
# fmt: off
data_type_conversion_table = [
# canonical C++ Numpy
('float32', 'float', 'float32'),
('float64', 'double', 'float64'),
('int32', 'int32_t', 'int32'),
('int64', 'int64_t', 'int64'),
('bool', 'bool', 'bool'),
('uint8', 'char', 'uint8'),
('uint64', 'uint64_t', 'uint64'),
]
# fmt: on
cpp_dtype = {canonical: cpp for canonical, cpp, np in data_type_conversion_table}
numpy_dtype = {canonical: np for canonical, cpp, np in data_type_conversion_table}
def get_cpp_dtype(obj):
return cpp_dtype[get_dtype_str(obj)]
def get_numpy_dtype(obj):
return numpy_dtype[get_dtype_str(obj)]
class CythonNodeRenderer(NodeRenderer):
def render_NameConstant(self, node):
return {True: "1", False: "0"}.get(node.value, node.value)
def render_Name(self, node):
return {"True": "1", "False": "0"}.get(node.id, node.id)
def render_BinOp(self, node):
if node.op.__class__.__name__ == "Mod":
left = self.render_node(node.left)
right = self.render_node(node.right)
return f"((({left})%({right}))+({right}))%({right})"
else:
return super().render_BinOp(node)
class CythonCodeGenerator(CodeGenerator):
"""
Cython code generator
"""
class_name = "cython"
def __init__(self, *args, **kwds):
self.temporary_vars = set()
super().__init__(*args, **kwds)
def translate_expression(self, expr):
expr = word_substitute(expr, self.func_name_replacements)
return (
CythonNodeRenderer(auto_vectorise=self.auto_vectorise)
.render_expr(expr, self.variables)
.strip()
)
def translate_statement(self, statement):
var, op, expr, comment = (
statement.var,
statement.op,
statement.expr,
statement.comment,
)
if op == ":=": # make no distinction in Cython (declaration are done elsewhere)
op = "="
# For Cython we replace complex expressions involving boolean variables into a sequence of
# if/then expressions with simpler expressions. This is provided by the optimise_statements
# function.
if (
statement.used_boolean_variables is not None
and len(statement.used_boolean_variables)
# todo: improve dtype analysis so that this isn't necessary
and brian_dtype_from_dtype(statement.dtype) == "float"
):
used_boolvars = statement.used_boolean_variables
bool_simp = statement.boolean_simplified_expressions
codelines = []
firstline = True
# bool assigns is a sequence of (var, value) pairs giving the conditions under
# which the simplified expression simp_expr holds
for bool_assigns, simp_expr in bool_simp.items():
# generate a boolean expression like ``var1 and var2 and not var3``
atomics = []
for boolvar, boolval in bool_assigns:
if boolval:
atomics.append(boolvar)
else:
atomics.append(f"not {boolvar}")
# use if/else/elif correctly
if firstline:
line = f"if {' and '.join(atomics)}:"
else:
if len(used_boolvars) > 1:
line = f"elif {' and '.join(atomics)}:"
else:
line = "else:"
line += "\n "
line += f"{var} {op} {self.translate_expression(simp_expr)}"
codelines.append(line)
firstline = False
code = "\n".join(codelines)
else:
code = f"{var} {op} {self.translate_expression(expr)}"
if len(comment):
code += f" # {comment}"
return code
def translate_one_statement_sequence(self, statements, scalar=False):
# Note that we do not call this function from
# `translate_statement_sequence` (which has been overwritten)
# It is nevertheless implemented, so that it can be called explicitly
# (e.g. from the GSL code generation)
read, write, indices, conditional_write_vars = self.arrays_helper(statements)
lines = []
# index and read arrays (index arrays first)
lines += self.translate_to_read_arrays(read, indices)
# the actual code
lines += self.translate_to_statements(statements, conditional_write_vars)
# write arrays
lines += self.translate_to_write_arrays(write)
return lines
def translate_to_read_arrays(self, read, indices):
lines = []
for varname in itertools.chain(sorted(indices), sorted(read)):
var = self.variables[varname]
index = self.variable_indices[varname]
arrayname = self.get_array_name(var)
line = f"{varname} = {arrayname}[{index}]"
lines.append(line)
return lines
def translate_to_statements(self, statements, conditional_write_vars):
lines = []
for stmt in statements:
if stmt.op == ":=" and stmt.var not in self.variables:
self.temporary_vars.add((stmt.var, stmt.dtype))
line = self.translate_statement(stmt)
if stmt.var in conditional_write_vars:
condvar = conditional_write_vars[stmt.var]
lines.append(f"if {condvar}:")
lines.append(indent(line))
else:
lines.append(line)
return lines
def translate_to_write_arrays(self, write):
lines = []
for varname in sorted(write):
index_var = self.variable_indices[varname]
var = self.variables[varname]
line = (
f"{self.get_array_name(var, self.variables)}[{index_var}] = {varname}"
)
lines.append(line)
return lines
def translate_statement_sequence(self, sc_statements, ve_statements):
# This function is overwritten, since we do not want to completely
# separate the code generation for scalar and vector code
assert set(sc_statements.keys()) == set(ve_statements.keys())
sc_code = {}
ve_code = {}
for block_name in sc_statements:
sc_block = sc_statements[block_name]
ve_block = ve_statements[block_name]
(sc_read, sc_write, sc_indices, sc_cond_write) = self.arrays_helper(
sc_block
)
(ve_read, ve_write, ve_indices, ve_cond_write) = self.arrays_helper(
ve_block
)
# We want to read all scalar variables that are needed in the
# vector code already in the scalar code, if they are not written
for varname in set(ve_read):
var = self.variables[varname]
if var.scalar and varname not in ve_write:
sc_read.add(varname)
ve_read.remove(varname)
for code, stmts, read, write, indices, cond_write in [
(sc_code, sc_block, sc_read, sc_write, sc_indices, sc_cond_write),
(ve_code, ve_block, ve_read, ve_write, ve_indices, ve_cond_write),
]:
lines = []
# index and read arrays (index arrays first)
lines += self.translate_to_read_arrays(read, indices)
# the actual code
lines += self.translate_to_statements(stmts, cond_write)
# write arrays
lines += self.translate_to_write_arrays(write)
code[block_name] = "\n".join(lines)
kwds = self.determine_keywords()
return sc_code, ve_code, kwds
def _add_user_function(self, varname, var, added):
user_functions = []
load_namespace = []
support_code = []
impl = var.implementations[self.codeobj_class]
if (impl.name, var) in added:
return # nothing to do
else:
added.add((impl.name, var))
func_code = impl.get_code(self.owner)
# Implementation can be None if the function is already
# available in Cython (possibly under a different name)
if func_code is not None:
if isinstance(func_code, str):
# Function is provided as Cython code
# To make namespace variables available to functions, we
# create global variables and assign to them in the main
# code
user_functions.append((varname, var))
func_namespace = impl.get_namespace(self.owner) or {}
for ns_key, ns_value in func_namespace.items():
load_namespace.append(f"# namespace for function {varname}")
if hasattr(ns_value, "dtype"):
if ns_value.shape == ():
raise NotImplementedError(
"Directly replace scalar values in the function "
"instead of providing them via the namespace"
)
newlines = [
"global _namespace{var_name}",
"global _namespace_num{var_name}",
(
"cdef _numpy.ndarray[{cpp_dtype}, ndim=1, mode='c']"
" _buf_{var_name} = _namespace['{var_name}']"
),
(
"_namespace{var_name} = <{cpp_dtype} *>"
" _buf_{var_name}.data"
),
"_namespace_num{var_name} = len(_namespace['{var_name}'])",
]
support_code.append(
f"cdef {get_cpp_dtype(ns_value.dtype)} *_namespace{ns_key}"
)
else: # e.g. a function
newlines = ["_namespace{var_name} = namespace['{var_name}']"]
for line in newlines:
load_namespace.append(
line.format(
cpp_dtype=get_cpp_dtype(ns_value.dtype),
numpy_dtype=get_numpy_dtype(ns_value.dtype),
var_name=ns_key,
)
)
# Rename references to any dependencies if necessary
for dep_name, dep in impl.dependencies.items():
dep_impl = dep.implementations[self.codeobj_class]
dep_impl_name = dep_impl.name
if dep_impl_name is None:
dep_impl_name = dep.pyfunc.__name__
if dep_name != dep_impl_name:
func_code = word_substitute(
func_code, {dep_name: dep_impl_name}
)
support_code.append(deindent(func_code))
elif callable(func_code):
self.variables[varname] = func_code
line = f'{varname} = _namespace["{varname}"]'
load_namespace.append(line)
else:
raise TypeError(
"Provided function implementation for function "
f"'{varname}' is neither a string nor callable (is "
f"type {type(func_code)} instead)."
)
dep_support_code = []
dep_load_namespace = []
dep_user_functions = []
if impl.dependencies is not None:
for dep_name, dep in impl.dependencies.items():
if dep_name not in self.variables:
self.variables[dep_name] = dep
user_func = self._add_user_function(dep_name, dep, added)
if user_func is not None:
sc, ln, uf = user_func
dep_support_code.extend(sc)
dep_load_namespace.extend(ln)
dep_user_functions.extend(uf)
return (
support_code + dep_support_code,
dep_load_namespace + load_namespace,
dep_user_functions + user_functions,
)
def determine_keywords(self):
from brian2.devices.device import get_device
device = get_device()
# load variables from namespace
load_namespace = []
support_code = []
handled_pointers = set()
user_functions = []
added = set()
for varname, var in sorted(self.variables.items()):
if isinstance(var, Variable) and not isinstance(
var, (Subexpression, AuxiliaryVariable)
):
load_namespace.append(f'_var_{varname} = _namespace["_var_{varname}"]')
if isinstance(var, AuxiliaryVariable):
line = f"cdef {get_cpp_dtype(var.dtype)} {varname}"
load_namespace.append(line)
elif isinstance(var, Subexpression):
dtype = get_cpp_dtype(var.dtype)
line = f"cdef {dtype} {varname}"
load_namespace.append(line)
elif isinstance(var, Constant):
dtype_name = get_cpp_dtype(var.value)
line = f'cdef {dtype_name} {varname} = _namespace["{varname}"]'
load_namespace.append(line)
elif isinstance(var, Variable):
if var.dynamic:
pointer_name = self.get_array_name(var, False)
load_namespace.append(
f'{pointer_name} = _namespace["{pointer_name}"]'
)
# This is the "true" array name, not the restricted pointer.
array_name = device.get_array_name(var)
pointer_name = self.get_array_name(var)
if pointer_name in handled_pointers:
continue
if getattr(var, "ndim", 1) > 1:
continue # multidimensional (dynamic) arrays have to be treated differently
if get_dtype_str(var.dtype) == "bool":
newlines = [
(
"cdef _numpy.ndarray[char, ndim=1, mode='c', cast=True]"
" _buf_{array_name} = _namespace['{array_name}']"
),
(
"cdef {cpp_dtype} * {array_name} = <{cpp_dtype} *>"
" _buf_{array_name}.data"
),
]
else:
newlines = [
(
"cdef _numpy.ndarray[{cpp_dtype}, ndim=1, mode='c']"
" _buf_{array_name} = _namespace['{array_name}']"
),
(
"cdef {cpp_dtype} * {array_name} = <{cpp_dtype} *>"
" _buf_{array_name}.data"
),
]
if not var.scalar:
newlines += [
"cdef size_t _num{array_name} = len(_namespace['{array_name}'])"
]
if var.scalar and var.constant:
newlines += ['cdef {cpp_dtype} {varname} = _namespace["{varname}"]']
else:
newlines += ["cdef {cpp_dtype} {varname}"]
for line in newlines:
line = line.format(
cpp_dtype=get_cpp_dtype(var.dtype),
numpy_dtype=get_numpy_dtype(var.dtype),
pointer_name=pointer_name,
array_name=array_name,
varname=varname,
)
load_namespace.append(line)
handled_pointers.add(pointer_name)
elif isinstance(var, Function):
user_func = self._add_user_function(varname, var, added)
if user_func is not None:
sc, ln, uf = user_func
support_code.extend(sc)
load_namespace.extend(ln)
user_functions.extend(uf)
else:
# fallback to Python object
load_namespace.append(f'{varname} = _namespace["{varname}"]')
for varname, dtype in sorted(self.temporary_vars):
cpp_dtype = get_cpp_dtype(dtype)
line = f"cdef {cpp_dtype} {varname}"
load_namespace.append(line)
return {
"load_namespace": "\n".join(load_namespace),
"support_code_lines": support_code,
}
###############################################################################
# Implement functions
################################################################################
# Functions that exist under the same name in C++
for func in [
"sin",
"cos",
"tan",
"sinh",
"cosh",
"tanh",
"exp",
"log",
"log10",
"sqrt",
"ceil",
"floor",
"abs",
]:
DEFAULT_FUNCTIONS[func].implementations.add_implementation(
CythonCodeGenerator, code=None
)
DEFAULT_FUNCTIONS["expm1"].implementations.add_implementation(
CythonCodeGenerator, code=None, availability_check=C99Check("expm1")
)
DEFAULT_FUNCTIONS["log1p"].implementations.add_implementation(
CythonCodeGenerator, code=None, availability_check=C99Check("log1p")
)
# Functions that need a name translation
for func, func_cpp in [
("arcsin", "asin"),
("arccos", "acos"),
("arctan", "atan"),
("int", "int_"), # from stdint_compat.h
]:
DEFAULT_FUNCTIONS[func].implementations.add_implementation(
CythonCodeGenerator, code=None, name=func_cpp
)
exprel_code = """
cdef inline double _exprel(double x) nogil:
if fabs(x) < 1e-16:
return 1.0
elif x > 717: # near log(DBL_MAX)
return NPY_INFINITY
else:
return expm1(x) / x
"""
DEFAULT_FUNCTIONS["exprel"].implementations.add_implementation(
CythonCodeGenerator,
code=exprel_code,
name="_exprel",
availability_check=C99Check("exprel"),
)
_BUFFER_SIZE = 20000
rand_code = """
cdef double _rand(int _idx):
cdef double **buffer_pointer = <double**>_namespace_rand_buffer
cdef double *buffer = buffer_pointer[0]
cdef _numpy.ndarray _new_rand
if(_namespace_rand_buffer_index[0] == 0):
if buffer != NULL:
free(buffer)
_new_rand = _numpy.random.rand(_BUFFER_SIZE)
buffer = <double *>_numpy.PyArray_DATA(_new_rand)
PyArray_CLEARFLAGS(<_numpy.PyArrayObject*>_new_rand, _numpy.NPY_ARRAY_OWNDATA)
buffer_pointer[0] = buffer
cdef double val = buffer[_namespace_rand_buffer_index[0]]
_namespace_rand_buffer_index[0] += 1
if _namespace_rand_buffer_index[0] == _BUFFER_SIZE:
_namespace_rand_buffer_index[0] = 0
return val
""".replace(
"_BUFFER_SIZE", str(_BUFFER_SIZE)
)
randn_code = rand_code.replace("rand", "randn").replace("randnom", "random")
poisson_code = """
cdef double _loggam(double x):
cdef double x0, x2, xp, gl, gl0
cdef int32_t k, n
cdef double a[10]
a[:] = [8.333333333333333e-02, -2.777777777777778e-03,
7.936507936507937e-04, -5.952380952380952e-04,
8.417508417508418e-04, -1.917526917526918e-03,
6.410256410256410e-03, -2.955065359477124e-02,
1.796443723688307e-01, -1.39243221690590e+00]
x0 = x
n = 0
if (x == 1.0) or (x == 2.0):
return 0.0
elif x <= 7.0:
n = <int32_t>(7 - x)
x0 = x + n
x2 = 1.0 / (x0 * x0)
xp = 2 * M_PI
gl0 = a[9]
for k in range(8, -1, -1):
gl0 *= x2
gl0 += a[k]
gl = gl0 / x0 + 0.5 * log(xp) + (x0 - 0.5) * log(x0) - x0
if x <= 7.0:
for k in range(1, n+1):
gl -= log(x0 - 1.0)
x0 -= 1.0
return gl
cdef int32_t _poisson_mult(double lam, int _vectorisation_idx):
cdef int32_t X
cdef double prod, U, enlam
enlam = exp(-lam)
X = 0
prod = 1.0
while True:
U = _rand(_vectorisation_idx)
prod *= U
if (prod > enlam):
X += 1
else:
return X
cdef int32_t _poisson_ptrs(double lam, int _vectorisation_idx):
cdef int32_t k
cdef double U, V, slam, loglam, a, b, invalpha, vr, us
slam = sqrt(lam)
loglam = log(lam)
b = 0.931 + 2.53 * slam
a = -0.059 + 0.02483 * b
invalpha = 1.1239 + 1.1328 / (b - 3.4)
vr = 0.9277 - 3.6224 / (b - 2)
while True:
U = _rand(_vectorisation_idx) - 0.5
V = _rand(_vectorisation_idx)
us = 0.5 - abs(U)
k = <int32_t>floor((2 * a / us + b) * U + lam + 0.43)
if (us >= 0.07) and (V <= vr):
return k
if ((k < 0) or ((us < 0.013) and (V > us))):
continue
if ((log(V) + log(invalpha) - log(a / (us * us) + b)) <=
(-lam + k * loglam - _loggam(k + 1))):
return k
cdef int32_t _poisson(double lam, int32_t _idx):
if lam >= 10:
return _poisson_ptrs(lam, _idx)
elif lam == 0:
return 0
else:
return _poisson_mult(lam, _idx)
"""
device = all_devices["runtime"]
DEFAULT_FUNCTIONS["rand"].implementations.add_implementation(
CythonCodeGenerator,
code=rand_code,
name="_rand",
namespace={
"_rand_buffer": device.rand_buffer,
"_rand_buffer_index": device.rand_buffer_index,
},
)
DEFAULT_FUNCTIONS["randn"].implementations.add_implementation(
CythonCodeGenerator,
code=randn_code,
name="_randn",
namespace={
"_randn_buffer": device.randn_buffer,
"_randn_buffer_index": device.randn_buffer_index,
},
)
DEFAULT_FUNCTIONS["poisson"].implementations.add_implementation(
CythonCodeGenerator,
code=poisson_code,
name="_poisson",
dependencies={"_rand": DEFAULT_FUNCTIONS["rand"]},
)
sign_code = """
ctypedef fused _to_sign:
char
short
int
long
float
double
cdef int _sign(_to_sign x):
return (0 < x) - (x < 0)
"""
DEFAULT_FUNCTIONS["sign"].implementations.add_implementation(
CythonCodeGenerator, code=sign_code, name="_sign"
)
clip_code = """
ctypedef fused _to_clip:
char
short
int
long
float
double
cdef _to_clip _clip(_to_clip x, double low, double high):
if x < low:
return <_to_clip?>low
if x > high:
return <_to_clip?>high
return x
"""
DEFAULT_FUNCTIONS["clip"].implementations.add_implementation(
CythonCodeGenerator, code=clip_code, name="_clip"
)
timestep_code = """
cdef int64_t _timestep(double t, double dt):
return <int64_t>((t + 1e-3*dt)/dt)
"""
DEFAULT_FUNCTIONS["timestep"].implementations.add_implementation(
CythonCodeGenerator, code=timestep_code, name="_timestep"
)
|